---
_id: '7103'
abstract:
- lang: eng
text: Origin and functions of intermittent transitions among sleep stages, including
short awakenings and arousals, constitute a challenge to the current homeostatic
framework for sleep regulation, focusing on factors modulating sleep over large
time scales. Here we propose that the complex micro-architecture characterizing
the sleep-wake cycle results from an underlying non-equilibrium critical dynamics,
bridging collective behaviors across spatio-temporal scales. We investigate θ
and δ wave dynamics in control rats and in rats with lesions of sleep-promoting
neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and
δ rhythms exhibit a complex temporal organization, with long-range power-law correlations
and a robust duality of power law (θ-bursts, active phase) and exponential-like
(δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium
systems self-organizing at criticality. Crucially, such temporal organization
relates to anti-correlated coupling between θ- and δ-bursts, and is independent
of the dominant physiologic state and lesions, a solid indication of a basic principle
in sleep dynamics.
article_number: e1007268
article_processing_charge: No
article_type: original
author:
- first_name: Jilin W. J. L.
full_name: Wang, Jilin W. J. L.
last_name: Wang
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Xiyun
full_name: Zhang, Xiyun
last_name: Zhang
- first_name: Christelle
full_name: Anaclet, Christelle
last_name: Anaclet
- first_name: Plamen Ch.
full_name: Ivanov, Plamen Ch.
last_name: Ivanov
citation:
ama: Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. Non-equilibrium critical
dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and
wake micro-architecture. PLoS Computational Biology. 2019;15(11). doi:10.1371/journal.pcbi.1007268
apa: Wang, J. W. J. L., Lombardi, F., Zhang, X., Anaclet, C., & Ivanov, P. C.
(2019). Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental
characteristic of sleep and wake micro-architecture. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007268
chicago: Wang, Jilin W. J. L., Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet,
and Plamen Ch. Ivanov. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ
Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLoS
Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007268.
ieee: J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “Non-equilibrium
critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of
sleep and wake micro-architecture,” PLoS Computational Biology, vol. 15,
no. 11. Public Library of Science, 2019.
ista: Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. 2019. Non-equilibrium
critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of
sleep and wake micro-architecture. PLoS Computational Biology. 15(11), e1007268.
mla: Wang, Jilin W. J. L., et al. “Non-Equilibrium Critical Dynamics of Bursts in
θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.”
PLoS Computational Biology, vol. 15, no. 11, e1007268, Public Library of
Science, 2019, doi:10.1371/journal.pcbi.1007268.
short: J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational
Biology 15 (2019).
date_created: 2019-11-25T08:20:47Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2025-04-14T07:44:06Z
day: '01'
ddc:
- '570'
- '000'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1007268
ec_funded: 1
external_id:
isi:
- '000500976100014'
pmid:
- '31725712'
file:
- access_level: open_access
checksum: 2a096a9c6dcc6eaa94077b2603bc6c12
content_type: application/pdf
creator: dernst
date_created: 2019-11-25T08:24:01Z
date_updated: 2020-07-14T12:47:49Z
file_id: '7104'
file_name: 2019_PLOSComBio_Wang.pdf
file_size: 3982516
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '11'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '11'
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: PLoS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental
characteristic of sleep and wake micro-architecture
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2019'
...
---
_id: '7105'
abstract:
- lang: eng
text: Cell migration is hypothesized to involve a cycle of behaviours beginning
with leading edge extension. However, recent evidence suggests that the leading
edge may be dispensable for migration, raising the question of what actually controls
cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages
to bridge the different temporal scales of the behaviours controlling motility.
This approach reveals that edge fluctuations during random motility are not persistent
and are weakly correlated with motion. In contrast, flow of the actin network
behind the leading edge is highly persistent. Quantification of actin flow structure
during migration reveals a stable organization and asymmetry in the cell-wide
flowfield that strongly correlates with cell directionality. This organization
is regulated by a gradient of actin network compression and destruction, which
is controlled by myosin contraction and cofilin-mediated disassembly. It is this
stable actin-flow polarity, which integrates rapid fluctuations of the leading
edge, that controls inherent cellular persistence.
article_processing_charge: No
article_type: original
author:
- first_name: Lawrence
full_name: Yolland, Lawrence
last_name: Yolland
- first_name: Mubarik
full_name: Burki, Mubarik
last_name: Burki
- first_name: Stefania
full_name: Marcotti, Stefania
last_name: Marcotti
- first_name: Andrei
full_name: Luchici, Andrei
last_name: Luchici
- first_name: Fiona N.
full_name: Kenny, Fiona N.
last_name: Kenny
- first_name: John Robert
full_name: Davis, John Robert
last_name: Davis
- first_name: Eduardo
full_name: Serna-Morales, Eduardo
last_name: Serna-Morales
- first_name: Jan
full_name: Müller, Jan
id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D
last_name: Müller
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Andrew
full_name: Davidson, Andrew
last_name: Davidson
- first_name: Will
full_name: Wood, Will
last_name: Wood
- first_name: Linus J.
full_name: Schumacher, Linus J.
last_name: Schumacher
- first_name: Robert G.
full_name: Endres, Robert G.
last_name: Endres
- first_name: Mark
full_name: Miodownik, Mark
last_name: Miodownik
- first_name: Brian M.
full_name: Stramer, Brian M.
last_name: Stramer
citation:
ama: Yolland L, Burki M, Marcotti S, et al. Persistent and polarized global actin
flow is essential for directionality during cell migration. Nature Cell Biology.
2019;21(11):1370-1381. doi:10.1038/s41556-019-0411-5
apa: Yolland, L., Burki, M., Marcotti, S., Luchici, A., Kenny, F. N., Davis, J.
R., … Stramer, B. M. (2019). Persistent and polarized global actin flow is essential
for directionality during cell migration. Nature Cell Biology. Springer
Nature. https://doi.org/10.1038/s41556-019-0411-5
chicago: Yolland, Lawrence, Mubarik Burki, Stefania Marcotti, Andrei Luchici, Fiona
N. Kenny, John Robert Davis, Eduardo Serna-Morales, et al. “Persistent and Polarized
Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature
Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0411-5.
ieee: L. Yolland et al., “Persistent and polarized global actin flow is essential
for directionality during cell migration,” Nature Cell Biology, vol. 21,
no. 11. Springer Nature, pp. 1370–1381, 2019.
ista: Yolland L, Burki M, Marcotti S, Luchici A, Kenny FN, Davis JR, Serna-Morales
E, Müller J, Sixt MK, Davidson A, Wood W, Schumacher LJ, Endres RG, Miodownik
M, Stramer BM. 2019. Persistent and polarized global actin flow is essential for
directionality during cell migration. Nature Cell Biology. 21(11), 1370–1381.
mla: Yolland, Lawrence, et al. “Persistent and Polarized Global Actin Flow Is Essential
for Directionality during Cell Migration.” Nature Cell Biology, vol. 21,
no. 11, Springer Nature, 2019, pp. 1370–81, doi:10.1038/s41556-019-0411-5.
short: L. Yolland, M. Burki, S. Marcotti, A. Luchici, F.N. Kenny, J.R. Davis, E.
Serna-Morales, J. Müller, M.K. Sixt, A. Davidson, W. Wood, L.J. Schumacher, R.G.
Endres, M. Miodownik, B.M. Stramer, Nature Cell Biology 21 (2019) 1370–1381.
date_created: 2019-11-25T08:55:00Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-09-06T11:08:52Z
day: '01'
department:
- _id: MiSi
doi: 10.1038/s41556-019-0411-5
external_id:
isi:
- '000495888300009'
pmid:
- '31685997'
intvolume: ' 21'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891
month: '11'
oa: 1
oa_version: Submitted Version
page: 1370-1381
pmid: 1
publication: Nature Cell Biology
publication_identifier:
eissn:
- 1476-4679
issn:
- 1465-7392
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Persistent and polarized global actin flow is essential for directionality
during cell migration
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 21
year: '2019'
...
---
_id: '7106'
abstract:
- lang: eng
text: PIN-FORMED (PIN) transporters mediate directional, intercellular movement
of the phytohormone auxin in land plants. To elucidate the evolutionary origins
of this developmentally crucial mechanism, we analysed the single PIN homologue
of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized
auxin exporter in land plants and heterologous models. While its role in algae
remains unclear, PIN-driven auxin export is probably an ancient and conserved
trait within streptophytes.
article_processing_charge: No
article_type: original
author:
- first_name: Roman
full_name: Skokan, Roman
last_name: Skokan
- first_name: Eva
full_name: Medvecká, Eva
last_name: Medvecká
- first_name: Tom
full_name: Viaene, Tom
last_name: Viaene
- first_name: Stanislav
full_name: Vosolsobě, Stanislav
last_name: Vosolsobě
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Karel
full_name: Müller, Karel
last_name: Müller
- first_name: Petr
full_name: Skůpa, Petr
last_name: Skůpa
- first_name: Michal
full_name: Karady, Michal
last_name: Karady
- first_name: Yuzhou
full_name: Zhang, Yuzhou
last_name: Zhang
- first_name: Dorina P.
full_name: Janacek, Dorina P.
last_name: Janacek
- first_name: Ulrich Z.
full_name: Hammes, Ulrich Z.
last_name: Hammes
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Skokan R, Medvecká E, Viaene T, et al. PIN-driven auxin transport emerged early
in streptophyte evolution. Nature Plants. 2019;5(11):1114-1119. doi:10.1038/s41477-019-0542-5
apa: Skokan, R., Medvecká, E., Viaene, T., Vosolsobě, S., Zwiewka, M., Müller, K.,
… Friml, J. (2019). PIN-driven auxin transport emerged early in streptophyte evolution.
Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0542-5
chicago: Skokan, Roman, Eva Medvecká, Tom Viaene, Stanislav Vosolsobě, Marta Zwiewka,
Karel Müller, Petr Skůpa, et al. “PIN-Driven Auxin Transport Emerged Early in
Streptophyte Evolution.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0542-5.
ieee: R. Skokan et al., “PIN-driven auxin transport emerged early in streptophyte
evolution,” Nature Plants, vol. 5, no. 11. Springer Nature, pp. 1114–1119,
2019.
ista: Skokan R, Medvecká E, Viaene T, Vosolsobě S, Zwiewka M, Müller K, Skůpa P,
Karady M, Zhang Y, Janacek DP, Hammes UZ, Ljung K, Nodzyński T, Petrášek J, Friml
J. 2019. PIN-driven auxin transport emerged early in streptophyte evolution. Nature
Plants. 5(11), 1114–1119.
mla: Skokan, Roman, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte
Evolution.” Nature Plants, vol. 5, no. 11, Springer Nature, 2019, pp. 1114–19,
doi:10.1038/s41477-019-0542-5.
short: R. Skokan, E. Medvecká, T. Viaene, S. Vosolsobě, M. Zwiewka, K. Müller, P.
Skůpa, M. Karady, Y. Zhang, D.P. Janacek, U.Z. Hammes, K. Ljung, T. Nodzyński,
J. Petrášek, J. Friml, Nature Plants 5 (2019) 1114–1119.
date_created: 2019-11-25T09:08:04Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2025-04-14T07:45:04Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41477-019-0542-5
ec_funded: 1
external_id:
isi:
- '000496526100010'
pmid:
- '31712756'
file:
- access_level: open_access
checksum: 94e0426856aad9a9bd0135d5436efbf1
content_type: application/pdf
creator: dernst
date_created: 2020-10-14T08:54:49Z
date_updated: 2020-10-14T08:54:49Z
file_id: '8660'
file_name: 2019_NaturePlants_Skokan_accepted.pdf
file_size: 1980851
relation: main_file
success: 1
file_date_updated: 2020-10-14T08:54:49Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 1114-1119
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Nature Plants
publication_identifier:
issn:
- 2055-0278
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: PIN-driven auxin transport emerged early in streptophyte evolution
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 5
year: '2019'
...
---
_id: '7108'
abstract:
- lang: eng
text: We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial
complex is shellable is NP-hard, hence NP-complete. This resolves a question raised,
e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d
≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable
is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible
pure d-dimensional complexes. Another simple corollary of our result is that it
is NP-hard to decide whether a given poset is CL-shellable.
article_number: '21'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Xavier
full_name: Goaoc, Xavier
last_name: Goaoc
- first_name: Pavel
full_name: Patak, Pavel
id: B593B804-1035-11EA-B4F1-947645A5BB83
last_name: Patak
- first_name: Zuzana
full_name: Patakova, Zuzana
id: 48B57058-F248-11E8-B48F-1D18A9856A87
last_name: Patakova
orcid: 0000-0002-3975-1683
- first_name: Martin
full_name: Tancer, Martin
last_name: Tancer
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete.
Journal of the ACM. 2019;66(3). doi:10.1145/3314024
apa: Goaoc, X., Patak, P., Patakova, Z., Tancer, M., & Wagner, U. (2019). Shellability
is NP-complete. Journal of the ACM. ACM. https://doi.org/10.1145/3314024
chicago: Goaoc, Xavier, Pavel Patak, Zuzana Patakova, Martin Tancer, and Uli Wagner.
“Shellability Is NP-Complete.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3314024.
ieee: X. Goaoc, P. Patak, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is
NP-complete,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.
ista: Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. 2019. Shellability is NP-complete.
Journal of the ACM. 66(3), 21.
mla: Goaoc, Xavier, et al. “Shellability Is NP-Complete.” Journal of the ACM,
vol. 66, no. 3, 21, ACM, 2019, doi:10.1145/3314024.
short: X. Goaoc, P. Patak, Z. Patakova, M. Tancer, U. Wagner, Journal of the ACM
66 (2019).
date_created: 2019-11-26T10:13:59Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2025-06-04T07:49:03Z
day: '01'
department:
- _id: UlWa
doi: 10.1145/3314024
external_id:
arxiv:
- '1711.08436'
isi:
- '000495406300007'
intvolume: ' 66'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.08436
month: '06'
oa: 1
oa_version: Preprint
publication: Journal of the ACM
publication_identifier:
issn:
- 0004-5411
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '184'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Shellability is NP-complete
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2019'
...
---
_id: '7109'
abstract:
- lang: eng
text: We show how to construct temporal testers for the logic MITL, a prominent
linear-time logic for real-time systems. A temporal tester is a transducer that
inputs a signal holding the Boolean value of atomic propositions and outputs the
truth value of a formula along time. Here we consider testers over continuous-time
Boolean signals that use clock variables to enforce duration constraints, as in
timed automata. We first rewrite the MITL formula into a “simple” formula using
a limited set of temporal modalities. We then build testers for these specific
modalities and show how to compose testers for simple formulae into complex ones.
Temporal testers can be turned into acceptors, yielding a compositional translation
from MITL to timed automata. This construction is much simpler than previously
known and remains asymptotically optimal. It supports both past and future operators
and can easily be extended.
article_number: '19'
article_processing_charge: No
article_type: original
author:
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Ničković, Dejan
last_name: Ničković
- first_name: Amir
full_name: Pnueli, Amir
last_name: Pnueli
citation:
ama: Ferrere T, Maler O, Ničković D, Pnueli A. From real-time logic to timed automata.
Journal of the ACM. 2019;66(3). doi:10.1145/3286976
apa: Ferrere, T., Maler, O., Ničković, D., & Pnueli, A. (2019). From real-time
logic to timed automata. Journal of the ACM. ACM. https://doi.org/10.1145/3286976
chicago: Ferrere, Thomas, Oded Maler, Dejan Ničković, and Amir Pnueli. “From Real-Time
Logic to Timed Automata.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3286976.
ieee: T. Ferrere, O. Maler, D. Ničković, and A. Pnueli, “From real-time logic to
timed automata,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.
ista: Ferrere T, Maler O, Ničković D, Pnueli A. 2019. From real-time logic to timed
automata. Journal of the ACM. 66(3), 19.
mla: Ferrere, Thomas, et al. “From Real-Time Logic to Timed Automata.” Journal
of the ACM, vol. 66, no. 3, 19, ACM, 2019, doi:10.1145/3286976.
short: T. Ferrere, O. Maler, D. Ničković, A. Pnueli, Journal of the ACM 66 (2019).
date_created: 2019-11-26T10:22:32Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2025-04-15T06:26:06Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/3286976
external_id:
isi:
- '000495406300005'
intvolume: ' 66'
isi: 1
issue: '3'
language:
- iso: eng
month: '05'
oa_version: None
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: Journal of the ACM
publication_identifier:
issn:
- 0004-5411
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: From real-time logic to timed automata
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 66
year: '2019'
...
---
_id: '7122'
abstract:
- lang: eng
text: Data-rich applications in machine-learning and control have motivated an intense
research on large-scale optimization. Novel algorithms have been proposed and
shown to have optimal convergence rates in terms of iteration counts. However,
their practical performance is severely degraded by the cost of exchanging high-dimensional
gradient vectors between computing nodes. Several gradient compression heuristics
have recently been proposed to reduce communications, but few theoretical results
exist that quantify how they impact algorithm convergence. This paper establishes
and strengthens the convergence guarantees for gradient descent under a family
of gradient compression techniques. For convex optimization problems, we derive
admissible step sizes and quantify both the number of iterations and the number
of bits that need to be exchanged to reach a target accuracy. Finally, we validate
the performance of different gradient compression techniques in simulations. The
numerical results highlight the properties of different gradient compression algorithms
and confirm that fast convergence with limited information exchange is possible.
article_number: '8619625'
article_processing_charge: No
author:
- first_name: Sarit
full_name: Khirirat, Sarit
last_name: Khirirat
- first_name: Mikael
full_name: Johansson, Mikael
last_name: Johansson
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Khirirat S, Johansson M, Alistarh D-A. Gradient compression for communication-limited
convex optimization. In: 2018 IEEE Conference on Decision and Control.
IEEE; 2019. doi:10.1109/cdc.2018.8619625'
apa: 'Khirirat, S., Johansson, M., & Alistarh, D.-A. (2019). Gradient compression
for communication-limited convex optimization. In 2018 IEEE Conference on Decision
and Control. Miami Beach, FL, United States: IEEE. https://doi.org/10.1109/cdc.2018.8619625'
chicago: Khirirat, Sarit, Mikael Johansson, and Dan-Adrian Alistarh. “Gradient Compression
for Communication-Limited Convex Optimization.” In 2018 IEEE Conference on
Decision and Control. IEEE, 2019. https://doi.org/10.1109/cdc.2018.8619625.
ieee: S. Khirirat, M. Johansson, and D.-A. Alistarh, “Gradient compression for communication-limited
convex optimization,” in 2018 IEEE Conference on Decision and Control,
Miami Beach, FL, United States, 2019.
ista: 'Khirirat S, Johansson M, Alistarh D-A. 2019. Gradient compression for communication-limited
convex optimization. 2018 IEEE Conference on Decision and Control. CDC: Conference
on Decision and Control, 8619625.'
mla: Khirirat, Sarit, et al. “Gradient Compression for Communication-Limited Convex
Optimization.” 2018 IEEE Conference on Decision and Control, 8619625, IEEE,
2019, doi:10.1109/cdc.2018.8619625.
short: S. Khirirat, M. Johansson, D.-A. Alistarh, in:, 2018 IEEE Conference on Decision
and Control, IEEE, 2019.
conference:
end_date: 2018-12-19
location: Miami Beach, FL, United States
name: 'CDC: Conference on Decision and Control'
start_date: 2018-12-17
date_created: 2019-11-26T15:07:49Z
date_published: 2019-01-21T00:00:00Z
date_updated: 2023-09-06T11:14:55Z
day: '21'
department:
- _id: DaAl
doi: 10.1109/cdc.2018.8619625
external_id:
isi:
- '000458114800023'
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
publication: 2018 IEEE Conference on Decision and Control
publication_identifier:
isbn:
- '9781538613955'
issn:
- 0743-1546
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gradient compression for communication-limited convex optimization
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7128'
abstract:
- lang: eng
text: Loss of functional cardiomyocytes is a major determinant of heart failure
after myocardial infarction. Previous high throughput screening studies have identified
a few microRNAs (miRNAs) that can induce cardiomyocyte proliferation and stimulate
cardiac regeneration in mice. Here, we show that all of the most effective of
these miRNAs activate nuclear localization of the master transcriptional cofactor
Yes-associated protein (YAP) and induce expression of YAP-responsive genes. In
particular, miR-199a-3p directly targets two mRNAs coding for proteins impinging
on the Hippo pathway, the upstream YAP inhibitory kinase TAOK1, and the E3 ubiquitin
ligase β-TrCP, which leads to YAP degradation. Several of the pro-proliferative
miRNAs (including miR-199a-3p) also inhibit filamentous actin depolymerization
by targeting Cofilin2, a process that by itself activates YAP nuclear translocation.
Thus, activation of YAP and modulation of the actin cytoskeleton are major components
of the pro-proliferative action of miR-199a-3p and other miRNAs that induce cardiomyocyte
proliferation.
article_processing_charge: Yes
article_type: original
author:
- first_name: Consuelo
full_name: Torrini, Consuelo
last_name: Torrini
- 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: Ellen
full_name: Dirkx, Ellen
last_name: Dirkx
- first_name: Luca
full_name: Braga, Luca
last_name: Braga
- first_name: Hashim
full_name: Ali, Hashim
last_name: Ali
- first_name: Giulia
full_name: Prosdocimo, Giulia
last_name: Prosdocimo
- first_name: Maria Ines
full_name: Gutierrez, Maria Ines
last_name: Gutierrez
- first_name: Chiara
full_name: Collesi, Chiara
last_name: Collesi
- first_name: Danilo
full_name: Licastro, Danilo
last_name: Licastro
- first_name: Lorena
full_name: Zentilin, Lorena
last_name: Zentilin
- first_name: Miguel
full_name: Mano, Miguel
last_name: Mano
- first_name: Serena
full_name: Zacchigna, Serena
last_name: Zacchigna
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Matteo
full_name: Marsili, Matteo
last_name: Marsili
- first_name: Areejit
full_name: Samal, Areejit
last_name: Samal
- first_name: Mauro
full_name: Giacca, Mauro
last_name: Giacca
citation:
ama: Torrini C, Cubero RJ, Dirkx E, et al. Common regulatory pathways mediate activity
of microRNAs inducing cardiomyocyte proliferation. Cell Reports. 2019;27(9):2759-2771.e5.
doi:10.1016/j.celrep.2019.05.005
apa: Torrini, C., Cubero, R. J., Dirkx, E., Braga, L., Ali, H., Prosdocimo, G.,
… Giacca, M. (2019). Common regulatory pathways mediate activity of microRNAs
inducing cardiomyocyte proliferation. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2019.05.005
chicago: Torrini, Consuelo, Ryan J Cubero, Ellen Dirkx, Luca Braga, Hashim Ali,
Giulia Prosdocimo, Maria Ines Gutierrez, et al. “Common Regulatory Pathways Mediate
Activity of MicroRNAs Inducing Cardiomyocyte Proliferation.” Cell Reports.
Elsevier, 2019. https://doi.org/10.1016/j.celrep.2019.05.005.
ieee: C. Torrini et al., “Common regulatory pathways mediate activity of
microRNAs inducing cardiomyocyte proliferation,” Cell Reports, vol. 27,
no. 9. Elsevier, p. 2759–2771.e5, 2019.
ista: Torrini C, Cubero RJ, Dirkx E, Braga L, Ali H, Prosdocimo G, Gutierrez MI,
Collesi C, Licastro D, Zentilin L, Mano M, Zacchigna S, Vendruscolo M, Marsili
M, Samal A, Giacca M. 2019. Common regulatory pathways mediate activity of microRNAs
inducing cardiomyocyte proliferation. Cell Reports. 27(9), 2759–2771.e5.
mla: Torrini, Consuelo, et al. “Common Regulatory Pathways Mediate Activity of MicroRNAs
Inducing Cardiomyocyte Proliferation.” Cell Reports, vol. 27, no. 9, Elsevier,
2019, p. 2759–2771.e5, doi:10.1016/j.celrep.2019.05.005.
short: C. Torrini, R.J. Cubero, E. Dirkx, L. Braga, H. Ali, G. Prosdocimo, M.I.
Gutierrez, C. Collesi, D. Licastro, L. Zentilin, M. Mano, S. Zacchigna, M. Vendruscolo,
M. Marsili, A. Samal, M. Giacca, Cell Reports 27 (2019) 2759–2771.e5.
date_created: 2019-11-26T22:30:07Z
date_published: 2019-05-28T00:00:00Z
date_updated: 2021-01-12T08:11:56Z
day: '28'
ddc:
- '576'
doi: 10.1016/j.celrep.2019.05.005
extern: '1'
external_id:
pmid:
- '31141697'
file:
- access_level: open_access
checksum: c5d855d07263bfec718673385d0ea2d7
content_type: application/pdf
creator: rcubero
date_created: 2019-11-26T22:30:43Z
date_updated: 2020-07-14T12:47:50Z
file_id: '7129'
file_name: torrini_cellreports_2019.pdf
file_size: 4650750
relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
intvolume: ' 27'
issue: '9'
keyword:
- cardiomyocyte
- cell cycle
- Cofilin2
- cytoskeleton
- Hippo
- microRNA
- regeneration
- YAP
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 2759-2771.e5
pmid: 1
publication: Cell Reports
publication_identifier:
issn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte
proliferation
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2019'
...
---
_id: '7130'
abstract:
- lang: eng
text: "We show that statistical criticality, i.e. the occurrence of power law frequency
distributions, arises in samples that are maximally informative about the underlying
generating process. In order to reach this conclusion, we first identify the frequency
with which different outcomes occur in a sample, as the variable carrying useful
information on the generative process. The entropy of the frequency, that we call
relevance, provides an upper bound to the number of informative bits. This differs
from the entropy of the data, that we take as a measure of resolution. Samples
that maximise relevance at a given resolution—that we call maximally informative
samples—exhibit statistical criticality. In particular, Zipf's law arises at the
optimal trade-off between resolution (i.e. compression) and relevance. As a byproduct,
we derive a bound of the maximal number of parameters that can be estimated from
a dataset, in the absence of prior knowledge on the generative model.\r\n\r\nFurthermore,
we relate criticality to the statistical properties of the representation of the
data generating process. We show that, as a consequence of the concentration property
of the asymptotic equipartition property, representations that are maximally informative
about the data generating process are characterised by an exponential distribution
of energy levels. This arises from a principle of minimal entropy, that is conjugate
of the maximum entropy principle in statistical mechanics. This explains why statistical
criticality requires no parameter fine tuning in maximally informative samples."
acknowledgement: We acknowledge interesting discussions with M Abbott, E Aurell, J
Barbier, R Monasson, T Mora, I Nemenman, N Tishby and R Zecchina. This research
was supported by the Kavli Foundation and the Centre of Excellence scheme of the
Research Council of Norway (Centre for Neural Computation) (RJC and YR), by the
Basic Science Research Program through the National Research Foundation of Korea
(NRF), funded by the Ministry of Education (2016R1D1A1B03932264) (JJ), and, in part,
by the ICTP through the OEA-AC-98 (JS).
article_number: '063402'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- 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: Junghyo
full_name: Jo, Junghyo
last_name: Jo
- first_name: Matteo
full_name: Marsili, Matteo
last_name: Marsili
- first_name: Yasser
full_name: Roudi, Yasser
last_name: Roudi
- first_name: Juyong
full_name: Song, Juyong
last_name: Song
citation:
ama: 'Cubero RJ, Jo J, Marsili M, Roudi Y, Song J. Statistical criticality arises
in most informative representations. Journal of Statistical Mechanics: Theory
and Experiment. 2019;2019(6). doi:10.1088/1742-5468/ab16c8'
apa: 'Cubero, R. J., Jo, J., Marsili, M., Roudi, Y., & Song, J. (2019). Statistical
criticality arises in most informative representations. Journal of Statistical
Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/ab16c8'
chicago: 'Cubero, Ryan J, Junghyo Jo, Matteo Marsili, Yasser Roudi, and Juyong Song.
“Statistical Criticality Arises in Most Informative Representations.” Journal
of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2019. https://doi.org/10.1088/1742-5468/ab16c8.'
ieee: 'R. J. Cubero, J. Jo, M. Marsili, Y. Roudi, and J. Song, “Statistical criticality
arises in most informative representations,” Journal of Statistical Mechanics:
Theory and Experiment, vol. 2019, no. 6. IOP Publishing, 2019.'
ista: 'Cubero RJ, Jo J, Marsili M, Roudi Y, Song J. 2019. Statistical criticality
arises in most informative representations. Journal of Statistical Mechanics:
Theory and Experiment. 2019(6), 063402.'
mla: 'Cubero, Ryan J., et al. “Statistical Criticality Arises in Most Informative
Representations.” Journal of Statistical Mechanics: Theory and Experiment,
vol. 2019, no. 6, 063402, IOP Publishing, 2019, doi:10.1088/1742-5468/ab16c8.'
short: 'R.J. Cubero, J. Jo, M. Marsili, Y. Roudi, J. Song, Journal of Statistical
Mechanics: Theory and Experiment 2019 (2019).'
date_created: 2019-11-26T22:36:09Z
date_published: 2019-06-17T00:00:00Z
date_updated: 2021-01-12T08:11:57Z
day: '17'
doi: 10.1088/1742-5468/ab16c8
extern: '1'
external_id:
arxiv:
- '1808.00249'
intvolume: ' 2019'
issue: '6'
keyword:
- optimization under uncertainty
- source coding
- large deviation
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.00249
month: '06'
oa: 1
oa_version: Preprint
publication: 'Journal of Statistical Mechanics: Theory and Experiment'
publication_identifier:
issn:
- 1742-5468
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
status: public
title: Statistical criticality arises in most informative representations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2019
year: '2019'
...
---
_id: '7136'
abstract:
- lang: eng
text: "It is well established that the notion of min-entropy fails to satisfy the
\\emph{chain rule} of the form H(X,Y)=H(X|Y)+H(Y), known for Shannon Entropy.
Such a property would help to analyze how min-entropy is split among smaller blocks.
Problems of this kind arise for example when constructing extractors and dispersers.\r\nWe
show that any sequence of variables exhibits a very strong strong block-source
structure (conditional distributions of blocks are nearly flat) when we \\emph{spoil
few correlated bits}. This implies, conditioned on the spoiled bits, that \\emph{splitting-recombination
properties} hold. In particular, we have many nice properties that min-entropy
doesn't obey in general, for example strong chain rules, \"information can't hurt\"
inequalities, equivalences of average and worst-case conditional entropy definitions
and others. Quantitatively, for any sequence X1,…,Xt of random variables over
an alphabet X we prove that, when conditioned on m=t⋅O(loglog|X|+loglog(1/ϵ)+logt)
bits of auxiliary information, all conditional distributions of the form Xi|X2019 IEEE International Symposium on Information Theory. IEEE; 2019. doi:10.1109/isit.2019.8849240'
apa: 'Skórski, M. (2019). Strong chain rules for min-entropy under few bits spoiled.
In 2019 IEEE International Symposium on Information Theory. Paris, France:
IEEE. https://doi.org/10.1109/isit.2019.8849240'
chicago: Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.”
In 2019 IEEE International Symposium on Information Theory. IEEE, 2019.
https://doi.org/10.1109/isit.2019.8849240.
ieee: M. Skórski, “Strong chain rules for min-entropy under few bits spoiled,” in
2019 IEEE International Symposium on Information Theory, Paris, France,
2019.
ista: 'Skórski M. 2019. Strong chain rules for min-entropy under few bits spoiled.
2019 IEEE International Symposium on Information Theory. ISIT: International Symposium
on Information Theory, 8849240.'
mla: Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.”
2019 IEEE International Symposium on Information Theory, 8849240, IEEE,
2019, doi:10.1109/isit.2019.8849240.
short: M. Skórski, in:, 2019 IEEE International Symposium on Information Theory,
IEEE, 2019.
conference:
end_date: 2019-07-12
location: Paris, France
name: 'ISIT: International Symposium on Information Theory'
start_date: 2019-07-07
date_created: 2019-11-28T10:19:21Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-09-06T11:15:41Z
day: '01'
department:
- _id: KrPi
doi: 10.1109/isit.2019.8849240
external_id:
arxiv:
- '1702.08476'
isi:
- '000489100301043'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.08476
month: '07'
oa: 1
oa_version: Preprint
publication: 2019 IEEE International Symposium on Information Theory
publication_identifier:
isbn:
- '9781538692912'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strong chain rules for min-entropy under few bits spoiled
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7143'
abstract:
- lang: eng
text: Roots grow downwards parallel to the gravity vector, to anchor a plant in
soil and acquire water and nutrients, using a gravitropic mechanism dependent
on the asymmetric distribution of the phytohormone auxin. Recently, Chang et al.
demonstrate that asymmetric distribution of another phytohormone, cytokinin, directs
root growth towards higher water content.
article_processing_charge: No
article_type: original
author:
- first_name: Scott A
full_name: Sinclair, Scott A
id: 2D99FE6A-F248-11E8-B48F-1D18A9856A87
last_name: Sinclair
orcid: 0000-0002-4566-0593
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Sinclair SA, Friml J. Defying gravity: a plant’s quest for moisture. Cell
Research. 2019;29:965-966. doi:10.1038/s41422-019-0254-4'
apa: 'Sinclair, S. A., & Friml, J. (2019). Defying gravity: a plant’s quest
for moisture. Cell Research. Springer Nature. https://doi.org/10.1038/s41422-019-0254-4'
chicago: 'Sinclair, Scott A, and Jiří Friml. “Defying Gravity: A Plant’s Quest for
Moisture.” Cell Research. Springer Nature, 2019. https://doi.org/10.1038/s41422-019-0254-4.'
ieee: 'S. A. Sinclair and J. Friml, “Defying gravity: a plant’s quest for moisture,”
Cell Research, vol. 29. Springer Nature, pp. 965–966, 2019.'
ista: 'Sinclair SA, Friml J. 2019. Defying gravity: a plant’s quest for moisture.
Cell Research. 29, 965–966.'
mla: 'Sinclair, Scott A., and Jiří Friml. “Defying Gravity: A Plant’s Quest for
Moisture.” Cell Research, vol. 29, Springer Nature, 2019, pp. 965–66, doi:10.1038/s41422-019-0254-4.'
short: S.A. Sinclair, J. Friml, Cell Research 29 (2019) 965–966.
date_created: 2019-12-02T12:30:48Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-09-06T11:20:58Z
day: '01'
department:
- _id: JiFr
doi: 10.1038/s41422-019-0254-4
external_id:
isi:
- '000500749600001'
pmid:
- '31745287'
intvolume: ' 29'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41422-019-0254-4
month: '12'
oa: 1
oa_version: Published Version
page: 965-966
pmid: 1
publication: Cell Research
publication_identifier:
eissn:
- 1748-7838
issn:
- 1001-0602
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Defying gravity: a plant''s quest for moisture'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 29
year: '2019'
...
---
_id: '7145'
abstract:
- lang: eng
text: End-to-end correlated bound states are investigated in superconductor-semiconductor
hybrid nanowires at zero magnetic field. Peaks in subgap conductance are independently
identified from each wire end, and a cross-correlation function is computed that
counts end-to-end coincidences, averaging over thousands of subgap features. Strong
correlations in a short, 300-nm device are reduced by a factor of 4 in a long,
900-nm device. In addition, subgap conductance distributions are investigated,
and correlations between the left and right distributions are identified based
on their mutual information.
article_number: '205412'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: G. L. R.
full_name: Anselmetti, G. L. R.
last_name: Anselmetti
- first_name: E. A.
full_name: Martinez, E. A.
last_name: Martinez
- first_name: G. C.
full_name: Ménard, G. C.
last_name: Ménard
- first_name: D.
full_name: Puglia, D.
last_name: Puglia
- first_name: F. K.
full_name: Malinowski, F. K.
last_name: Malinowski
- first_name: J. S.
full_name: Lee, J. S.
last_name: Lee
- first_name: S.
full_name: Choi, S.
last_name: Choi
- first_name: M.
full_name: Pendharkar, M.
last_name: Pendharkar
- first_name: C. J.
full_name: Palmstrøm, C. J.
last_name: Palmstrøm
- first_name: C. M.
full_name: Marcus, C. M.
last_name: Marcus
- first_name: L.
full_name: Casparis, L.
last_name: Casparis
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Anselmetti GLR, Martinez EA, Ménard GC, et al. End-to-end correlated subgap
states in hybrid nanowires. Physical Review B. 2019;100(20). doi:10.1103/physrevb.100.205412
apa: Anselmetti, G. L. R., Martinez, E. A., Ménard, G. C., Puglia, D., Malinowski,
F. K., Lee, J. S., … Higginbotham, A. P. (2019). End-to-end correlated subgap
states in hybrid nanowires. Physical Review B. American Physical Society.
https://doi.org/10.1103/physrevb.100.205412
chicago: Anselmetti, G. L. R., E. A. Martinez, G. C. Ménard, D. Puglia, F. K. Malinowski,
J. S. Lee, S. Choi, et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.”
Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.205412.
ieee: G. L. R. Anselmetti et al., “End-to-end correlated subgap states in
hybrid nanowires,” Physical Review B, vol. 100, no. 20. American Physical
Society, 2019.
ista: Anselmetti GLR, Martinez EA, Ménard GC, Puglia D, Malinowski FK, Lee JS, Choi
S, Pendharkar M, Palmstrøm CJ, Marcus CM, Casparis L, Higginbotham AP. 2019. End-to-end
correlated subgap states in hybrid nanowires. Physical Review B. 100(20), 205412.
mla: Anselmetti, G. L. R., et al. “End-to-End Correlated Subgap States in Hybrid
Nanowires.” Physical Review B, vol. 100, no. 20, 205412, American Physical
Society, 2019, doi:10.1103/physrevb.100.205412.
short: G.L.R. Anselmetti, E.A. Martinez, G.C. Ménard, D. Puglia, F.K. Malinowski,
J.S. Lee, S. Choi, M. Pendharkar, C.J. Palmstrøm, C.M. Marcus, L. Casparis, A.P.
Higginbotham, Physical Review B 100 (2019).
date_created: 2019-12-04T16:02:25Z
date_published: 2019-11-15T00:00:00Z
date_updated: 2024-02-28T13:13:51Z
day: '15'
department:
- _id: AnHi
doi: 10.1103/physrevb.100.205412
external_id:
arxiv:
- '1908.05549'
isi:
- '000495967500006'
intvolume: ' 100'
isi: 1
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1908.05549
month: '11'
oa: 1
oa_version: Preprint
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: End-to-end correlated subgap states in hybrid nanowires
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2019'
...
---
_id: '7146'
abstract:
- lang: eng
text: Prevailing models of sex-chromosome evolution were largely inspired by the
stable and highly differentiated XY pairs of model organisms, such as those of
mammals and flies. Recent work has uncovered an incredible diversity of sex-determining
systems, bringing some of the assumptions of these traditional models into question.
One particular question that has arisen is what drives some sex chromosomes to
be maintained over millions of years and differentiate fully, while others are
replaced by new sex-determining chromosomes before differentiation has occurred.
Here, I review recent data on the variability of sex-determining genes and sex
chromosomes in different non-model vertebrates and invertebrates, and discuss
some theoretical models that have been put forward to account for this diversity.
article_processing_charge: No
article_type: original
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Molecular and evolutionary dynamics of animal sex-chromosome turnover.
Nature Ecology & Evolution. 2019;3(12):1632-1641. doi:10.1038/s41559-019-1050-8
apa: Vicoso, B. (2019). Molecular and evolutionary dynamics of animal sex-chromosome
turnover. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-019-1050-8
chicago: Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome
Turnover.” Nature Ecology & Evolution. Springer Nature, 2019. https://doi.org/10.1038/s41559-019-1050-8.
ieee: B. Vicoso, “Molecular and evolutionary dynamics of animal sex-chromosome turnover,”
Nature Ecology & Evolution, vol. 3, no. 12. Springer Nature, pp. 1632–1641,
2019.
ista: Vicoso B. 2019. Molecular and evolutionary dynamics of animal sex-chromosome
turnover. Nature Ecology & Evolution. 3(12), 1632–1641.
mla: Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome
Turnover.” Nature Ecology & Evolution, vol. 3, no. 12, Springer Nature,
2019, pp. 1632–41, doi:10.1038/s41559-019-1050-8.
short: B. Vicoso, Nature Ecology & Evolution 3 (2019) 1632–1641.
date_created: 2019-12-04T16:05:25Z
date_published: 2019-11-25T00:00:00Z
date_updated: 2025-04-14T07:41:21Z
day: '25'
department:
- _id: BeVi
doi: 10.1038/s41559-019-1050-8
ec_funded: 1
external_id:
isi:
- '000500728800009'
intvolume: ' 3'
isi: 1
issue: '12'
language:
- iso: eng
month: '11'
oa_version: None
page: 1632-1641
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Nature Ecology & Evolution
publication_identifier:
issn:
- 2397-334X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular and evolutionary dynamics of animal sex-chromosome turnover
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 3
year: '2019'
...
---
_id: '7150'
abstract:
- lang: eng
text: "In this work, we use algebraic methods for studying distance computation
and subgraph detection tasks in the congested clique model. Specifically, we adapt
parallel matrix multiplication implementations to the congested clique, obtaining
an O(n1−2/ω) round matrix multiplication algorithm, where ω<2.3728639 is the exponent
of matrix multiplication. In conjunction with known techniques from centralised
algorithmics, this gives significant improvements over previous best upper bounds
in the congested clique model. The highlight results include:\r\n\r\n1. triangle
and 4-cycle counting in O(n0.158) rounds, improving upon the O(n1/3) algorithm
of Dolev et al. [DISC 2012],\r\n2. a (1+o(1))-approximation of all-pairs shortest
paths in O(n0.158) rounds, improving upon the O~(n1/2)-round (2+o(1))-approximation
algorithm given by Nanongkai [STOC 2014], and\r\n 3. computing the girth in O(n0.158)
rounds, which is the first non-trivial solution in this model.\r\n \r\nIn addition,
we present a novel constant-round combinatorial algorithm for detecting 4-cycles."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Keren
full_name: Censor-Hillel, Keren
last_name: Censor-Hillel
- first_name: Petteri
full_name: Kaski, Petteri
last_name: Kaski
- first_name: Janne
full_name: Korhonen, Janne
id: C5402D42-15BC-11E9-A202-CA2BE6697425
last_name: Korhonen
- first_name: Christoph
full_name: Lenzen, Christoph
last_name: Lenzen
- first_name: Ami
full_name: Paz, Ami
last_name: Paz
- first_name: Jukka
full_name: Suomela, Jukka
last_name: Suomela
citation:
ama: Censor-Hillel K, Kaski P, Korhonen J, Lenzen C, Paz A, Suomela J. Algebraic
methods in the congested clique. Distributed Computing. 2019;32(6):461-478.
doi:10.1007/s00446-016-0270-2
apa: Censor-Hillel, K., Kaski, P., Korhonen, J., Lenzen, C., Paz, A., & Suomela,
J. (2019). Algebraic methods in the congested clique. Distributed Computing.
Springer Nature. https://doi.org/10.1007/s00446-016-0270-2
chicago: Censor-Hillel, Keren, Petteri Kaski, Janne Korhonen, Christoph Lenzen,
Ami Paz, and Jukka Suomela. “Algebraic Methods in the Congested Clique.” Distributed
Computing. Springer Nature, 2019. https://doi.org/10.1007/s00446-016-0270-2.
ieee: K. Censor-Hillel, P. Kaski, J. Korhonen, C. Lenzen, A. Paz, and J. Suomela,
“Algebraic methods in the congested clique,” Distributed Computing, vol.
32, no. 6. Springer Nature, pp. 461–478, 2019.
ista: Censor-Hillel K, Kaski P, Korhonen J, Lenzen C, Paz A, Suomela J. 2019. Algebraic
methods in the congested clique. Distributed Computing. 32(6), 461–478.
mla: Censor-Hillel, Keren, et al. “Algebraic Methods in the Congested Clique.” Distributed
Computing, vol. 32, no. 6, Springer Nature, 2019, pp. 461–78, doi:10.1007/s00446-016-0270-2.
short: K. Censor-Hillel, P. Kaski, J. Korhonen, C. Lenzen, A. Paz, J. Suomela, Distributed
Computing 32 (2019) 461–478.
date_created: 2019-12-05T09:49:49Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2021-01-12T08:12:05Z
day: '01'
doi: 10.1007/s00446-016-0270-2
extern: '1'
external_id:
arxiv:
- '1503.04963'
intvolume: ' 32'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1503.04963
month: '12'
oa: 1
oa_version: Preprint
page: 461-478
publication: Distributed Computing
publication_identifier:
issn:
- 0178-2770
- 1432-0452
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Algebraic methods in the congested clique
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2019'
...
---
_id: '7154'
article_processing_charge: No
author:
- first_name: Ruslan
full_name: Guseinov, Ruslan
id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87
last_name: Guseinov
orcid: 0000-0001-9819-5077
citation:
ama: Guseinov R. Supplementary data for “Programming temporal morphing of self-actuated
shells.” 2019. doi:10.15479/AT:ISTA:7154
apa: Guseinov, R. (2019). Supplementary data for “Programming temporal morphing
of self-actuated shells.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7154
chicago: Guseinov, Ruslan. “Supplementary Data for ‘Programming Temporal Morphing
of Self-Actuated Shells.’” Institute of Science and Technology Austria, 2019.
https://doi.org/10.15479/AT:ISTA:7154.
ieee: R. Guseinov, “Supplementary data for ‘Programming temporal morphing of self-actuated
shells.’” Institute of Science and Technology Austria, 2019.
ista: Guseinov R. 2019. Supplementary data for ‘Programming temporal morphing of
self-actuated shells’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7154.
mla: Guseinov, Ruslan. Supplementary Data for “Programming Temporal Morphing
of Self-Actuated Shells.” Institute of Science and Technology Austria, 2019,
doi:10.15479/AT:ISTA:7154.
short: R. Guseinov, (2019).
contributor:
- first_name: Ruslan
id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87
last_name: Guseinov
orcid: 0000-0001-9819-5077
- first_name: Connor
last_name: McMahan
- first_name: Jesus
id: 2DC83906-F248-11E8-B48F-1D18A9856A87
last_name: Perez Rodriguez
- first_name: Chiara
last_name: Daraio
- first_name: Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
date_created: 2019-12-09T07:52:46Z
date_published: 2019-12-06T00:00:00Z
date_updated: 2025-06-12T06:58:31Z
day: '06'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.15479/AT:ISTA:7154
ec_funded: 1
file:
- access_level: open_access
checksum: 155133e6e188e85b3c0676a5e70b9341
content_type: application/x-zip-compressed
creator: dernst
date_created: 2019-12-09T07:52:17Z
date_updated: 2020-07-14T12:47:50Z
file_id: '7155'
file_name: temporal_morphing_supp_data.zip
file_size: 65307107
relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8433'
relation: used_in_publication
status: deleted
- id: '7262'
relation: used_in_publication
status: public
status: public
title: Supplementary data for "Programming temporal morphing of self-actuated shells"
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7165'
abstract:
- lang: eng
text: Cell division, movement and differentiation contribute to pattern formation
in developing tissues. This is the case in the vertebrate neural tube, in which
neurons differentiate in a characteristic pattern from a highly dynamic proliferating
pseudostratified epithelium. To investigate how progenitor proliferation and differentiation
affect cell arrangement and growth of the neural tube, we used experimental measurements
to develop a mechanical model of the apical surface of the neuroepithelium that
incorporates the effect of interkinetic nuclear movement and spatially varying
rates of neuronal differentiation. Simulations predict that tissue growth and
the shape of lineage-related clones of cells differ with the rate of differentiation.
Growth is isotropic in regions of high differentiation, but dorsoventrally biased
in regions of low differentiation. This is consistent with experimental observations.
The absence of directional signalling in the simulations indicates that global
mechanical constraints are sufficient to explain the observed differences in anisotropy.
This provides insight into how the tissue growth rate affects cell dynamics and
growth anisotropy and opens up possibilities to study the coupling between mechanics,
pattern formation and growth in the neural tube.
article_number: dev176297
article_processing_charge: No
article_type: original
author:
- first_name: Pilar
full_name: Guerrero, Pilar
last_name: Guerrero
- first_name: Ruben
full_name: Perez-Carrasco, Ruben
last_name: Perez-Carrasco
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: David
full_name: Page, David
last_name: Page
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
- first_name: Karen M.
full_name: Page, Karen M.
last_name: Page
citation:
ama: Guerrero P, Perez-Carrasco R, Zagórski MP, et al. Neuronal differentiation
influences progenitor arrangement in the vertebrate neuroepithelium. Development.
2019;146(23). doi:10.1242/dev.176297
apa: Guerrero, P., Perez-Carrasco, R., Zagórski, M. P., Page, D., Kicheva, A., Briscoe,
J., & Page, K. M. (2019). Neuronal differentiation influences progenitor arrangement
in the vertebrate neuroepithelium. Development. The Company of Biologists.
https://doi.org/10.1242/dev.176297
chicago: Guerrero, Pilar, Ruben Perez-Carrasco, Marcin P Zagórski, David Page, Anna
Kicheva, James Briscoe, and Karen M. Page. “Neuronal Differentiation Influences
Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development.
The Company of Biologists, 2019. https://doi.org/10.1242/dev.176297.
ieee: P. Guerrero et al., “Neuronal differentiation influences progenitor
arrangement in the vertebrate neuroepithelium,” Development, vol. 146,
no. 23. The Company of Biologists, 2019.
ista: Guerrero P, Perez-Carrasco R, Zagórski MP, Page D, Kicheva A, Briscoe J, Page
KM. 2019. Neuronal differentiation influences progenitor arrangement in the vertebrate
neuroepithelium. Development. 146(23), dev176297.
mla: Guerrero, Pilar, et al. “Neuronal Differentiation Influences Progenitor Arrangement
in the Vertebrate Neuroepithelium.” Development, vol. 146, no. 23, dev176297,
The Company of Biologists, 2019, doi:10.1242/dev.176297.
short: P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe,
K.M. Page, Development 146 (2019).
corr_author: '1'
date_created: 2019-12-10T14:39:50Z
date_published: 2019-12-04T00:00:00Z
date_updated: 2025-04-14T07:27:30Z
day: '04'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1242/dev.176297
ec_funded: 1
external_id:
isi:
- '000507575700004'
pmid:
- '31784457'
file:
- access_level: open_access
checksum: b6533c37dc8fbd803ffeca216e0a8b8a
content_type: application/pdf
creator: dernst
date_created: 2019-12-13T07:34:06Z
date_updated: 2020-07-14T12:47:50Z
file_id: '7177'
file_name: 2019_Development_Guerrero.pdf
file_size: 7797881
relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
intvolume: ' 146'
isi: 1
issue: '23'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
publication: Development
publication_identifier:
eissn:
- 1477-9129
issn:
- 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neuronal differentiation influences progenitor arrangement in the vertebrate
neuroepithelium
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 146
year: '2019'
...
---
_id: '7171'
abstract:
- lang: ger
text: "Wissen Sie, was sich hinter künstlicher Intelligenz und maschinellem Lernen
verbirgt? \r\nDieses Sachbuch erklärt Ihnen leicht verständlich und ohne komplizierte
Formeln die grundlegenden Methoden und Vorgehensweisen des maschinellen Lernens.
Mathematisches Vorwissen ist dafür nicht nötig. Kurzweilig und informativ illustriert
Lisa, die Protagonistin des Buches, diese anhand von Alltagssituationen. \r\nEin
Buch für alle, die in Diskussionen über Chancen und Risiken der aktuellen Entwicklung
der künstlichen Intelligenz und des maschinellen Lernens mit Faktenwissen punkten
möchten. Auch für Schülerinnen und Schüler geeignet!"
article_processing_charge: No
citation:
ama: 'Kersting K, Lampert C, Rothkopf C, eds. Wie Maschinen Lernen: Künstliche
Intelligenz Verständlich Erklärt. 1st ed. Wiesbaden: Springer Nature; 2019.
doi:10.1007/978-3-658-26763-6'
apa: 'Kersting, K., Lampert, C., & Rothkopf, C. (Eds.). (2019). Wie Maschinen
Lernen: Künstliche Intelligenz Verständlich Erklärt (1st ed.). Wiesbaden:
Springer Nature. https://doi.org/10.1007/978-3-658-26763-6'
chicago: 'Kersting, Kristian, Christoph Lampert, and Constantin Rothkopf, eds. Wie
Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed. Wiesbaden:
Springer Nature, 2019. https://doi.org/10.1007/978-3-658-26763-6.'
ieee: 'K. Kersting, C. Lampert, and C. Rothkopf, Eds., Wie Maschinen Lernen:
Künstliche Intelligenz Verständlich Erklärt, 1st ed. Wiesbaden: Springer Nature,
2019.'
ista: 'Kersting K, Lampert C, Rothkopf C eds. 2019. Wie Maschinen Lernen: Künstliche
Intelligenz Verständlich Erklärt 1st ed., Wiesbaden: Springer Nature, XIV, 245p.'
mla: 'Kersting, Kristian, et al., editors. Wie Maschinen Lernen: Künstliche Intelligenz
Verständlich Erklärt. 1st ed., Springer Nature, 2019, doi:10.1007/978-3-658-26763-6.'
short: 'K. Kersting, C. Lampert, C. Rothkopf, eds., Wie Maschinen Lernen: Künstliche
Intelligenz Verständlich Erklärt, 1st ed., Springer Nature, Wiesbaden, 2019.'
date_created: 2019-12-11T14:15:56Z
date_published: 2019-10-30T00:00:00Z
date_updated: 2021-12-22T14:40:58Z
day: '30'
department:
- _id: ChLa
doi: 10.1007/978-3-658-26763-6
edition: '1'
editor:
- first_name: Kristian
full_name: Kersting, Kristian
last_name: Kersting
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Constantin
full_name: Rothkopf, Constantin
last_name: Rothkopf
language:
- iso: ger
month: '10'
oa_version: None
page: XIV, 245
place: Wiesbaden
publication_identifier:
eisbn:
- 978-3-658-26763-6
isbn:
- 978-3-658-26762-9
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/book-release-how-machines-learn/
status: public
title: 'Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt'
type: book_editor
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2019'
...
---
_id: '7181'
abstract:
- lang: eng
text: Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary
predictions1,2, but the complexity of aligning large datasets requires the use
of approximate solutions3, including the progressive algorithm4. Progressive MSA
methods start by aligning the most similar sequences and subsequently incorporate
the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy
declines substantially as the number of sequences is scaled up5. We introduce
a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard
workstation and substantially improves accuracy on datasets larger than 10,000
sequences. Our regressive algorithm works the other way around to the progressive
algorithm and begins by aligning the most dissimilar sequences. It uses an efficient
divide-and-conquer strategy to run third-party alignment methods in linear time,
regardless of their original complexity. Our approach will enable analyses of
extremely large genomic datasets such as the recently announced Earth BioGenome
Project, which comprises 1.5 million eukaryotic genomes6.
article_processing_charge: No
article_type: original
author:
- first_name: Edgar
full_name: Garriga, Edgar
last_name: Garriga
- first_name: Paolo
full_name: Di Tommaso, Paolo
last_name: Di Tommaso
- first_name: Cedrik
full_name: Magis, Cedrik
last_name: Magis
- first_name: Ionas
full_name: Erb, Ionas
last_name: Erb
- first_name: Leila
full_name: Mansouri, Leila
last_name: Mansouri
- first_name: Athanasios
full_name: Baltzis, Athanasios
last_name: Baltzis
- first_name: Hafid
full_name: Laayouni, Hafid
last_name: Laayouni
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Evan
full_name: Floden, Evan
last_name: Floden
- first_name: Cedric
full_name: Notredame, Cedric
last_name: Notredame
citation:
ama: Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments
with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470.
doi:10.1038/s41587-019-0333-6
apa: Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A.,
… Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf
regressive method. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-019-0333-6
chicago: Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri,
Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric
Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive
Method.” Nature Biotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41587-019-0333-6.
ieee: E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf
regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature,
pp. 1466–1470, 2019.
ista: Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H,
Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments
with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470.
mla: Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf
Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature,
2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6.
short: E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H.
Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019)
1466–1470.
date_created: 2019-12-15T23:00:43Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2025-07-10T11:54:19Z
day: '01'
department:
- _id: FyKo
doi: 10.1038/s41587-019-0333-6
ec_funded: 1
external_id:
isi:
- '000500748900021'
pmid:
- '31792410'
intvolume: ' 37'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/
month: '12'
oa: 1
oa_version: Submitted Version
page: 1466-1470
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13059'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Large multiple sequence alignments with a root-to-leaf regressive method
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2019'
...
---
_id: '7190'
abstract:
- lang: eng
text: We investigate the ground-state energy of a one-dimensional Fermi gas with
two bosonic impurities. We consider spinless fermions with no fermion-fermion
interactions. The fermion-impurity and impurity-impurity interactions are modeled
with Dirac delta functions. First, we study the case where impurity and fermion
have equal masses, and the impurity-impurity two-body interaction is identical
to the fermion-impurity interaction, such that the system is solvable with the
Bethe ansatz. For attractive interactions, we find that the energy of the impurity-impurity
subsystem is below the energy of the bound state that exists without the Fermi
gas. We interpret this as a manifestation of attractive boson-boson interactions
induced by the fermionic medium, and refer to the impurity-impurity subsystem
as an in-medium bound state. For repulsive interactions, we find no in-medium
bound states. Second, we construct an effective model to describe these interactions,
and compare its predictions to the exact solution. We use this effective model
to study nonintegrable systems with unequal masses and/or potentials. We discuss
parameter regimes for which impurity-impurity attraction induced by the Fermi
gas can lead to the formation of in-medium bound states made of bosons that repel
each other in the absence of the Fermi gas.
article_number: '033177'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: D.
full_name: Huber, D.
last_name: Huber
- first_name: H.-W.
full_name: Hammer, H.-W.
last_name: Hammer
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Huber D, Hammer H-W, Volosniev A. In-medium bound states of two bosonic impurities
in a one-dimensional Fermi gas. Physical Review Research. 2019;1(3). doi:10.1103/physrevresearch.1.033177
apa: Huber, D., Hammer, H.-W., & Volosniev, A. (2019). In-medium bound states
of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research.
American Physical Society. https://doi.org/10.1103/physrevresearch.1.033177
chicago: Huber, D., H.-W. Hammer, and Artem Volosniev. “In-Medium Bound States of
Two Bosonic Impurities in a One-Dimensional Fermi Gas.” Physical Review Research.
American Physical Society, 2019. https://doi.org/10.1103/physrevresearch.1.033177.
ieee: D. Huber, H.-W. Hammer, and A. Volosniev, “In-medium bound states of two bosonic
impurities in a one-dimensional Fermi gas,” Physical Review Research, vol.
1, no. 3. American Physical Society, 2019.
ista: Huber D, Hammer H-W, Volosniev A. 2019. In-medium bound states of two bosonic
impurities in a one-dimensional Fermi gas. Physical Review Research. 1(3), 033177.
mla: Huber, D., et al. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional
Fermi Gas.” Physical Review Research, vol. 1, no. 3, 033177, American Physical
Society, 2019, doi:10.1103/physrevresearch.1.033177.
short: D. Huber, H.-W. Hammer, A. Volosniev, Physical Review Research 1 (2019).
corr_author: '1'
date_created: 2019-12-17T13:03:41Z
date_published: 2019-12-16T00:00:00Z
date_updated: 2025-04-14T07:44:06Z
day: '16'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/physrevresearch.1.033177
ec_funded: 1
external_id:
arxiv:
- '1908.02483'
file:
- access_level: open_access
checksum: 382eb67e62a77052a23887332d363f96
content_type: application/pdf
creator: dernst
date_created: 2019-12-18T07:13:14Z
date_updated: 2020-07-14T12:47:52Z
file_id: '7193'
file_name: 2019_PhysRevResearch_Huber.pdf
file_size: 1370022
relation: main_file
file_date_updated: 2020-07-14T12:47:52Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '3'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: In-medium bound states of two bosonic impurities in a one-dimensional Fermi
gas
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2019'
...
---
_id: '72'
abstract:
- lang: eng
text: We consider the totally asymmetric simple exclusion process (TASEP) with non-random
initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle
initially at the origin. For ρ<λ, there is a shock and the second class particle
moves with speed 1−λ−ρ. For large time t, we show that the position of the second
class particle fluctuates on a t1/3 scale and determine its limiting law. We also
obtain the limiting distribution of the number of steps made by the second class
particle until time t.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Patrick
full_name: Ferrari, Patrick
last_name: Ferrari
- first_name: Promit
full_name: Ghosal, Promit
last_name: Ghosal
- first_name: Peter
full_name: Nejjar, Peter
id: 4BF426E2-F248-11E8-B48F-1D18A9856A87
last_name: Nejjar
citation:
ama: Ferrari P, Ghosal P, Nejjar P. Limit law of a second class particle in TASEP
with non-random initial condition. Annales de l’institut Henri Poincare (B)
Probability and Statistics. 2019;55(3):1203-1225. doi:10.1214/18-AIHP916
apa: Ferrari, P., Ghosal, P., & Nejjar, P. (2019). Limit law of a second class
particle in TASEP with non-random initial condition. Annales de l’institut
Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics.
https://doi.org/10.1214/18-AIHP916
chicago: Ferrari, Patrick, Promit Ghosal, and Peter Nejjar. “Limit Law of a Second
Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut
Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics,
2019. https://doi.org/10.1214/18-AIHP916.
ieee: P. Ferrari, P. Ghosal, and P. Nejjar, “Limit law of a second class particle
in TASEP with non-random initial condition,” Annales de l’institut Henri Poincare
(B) Probability and Statistics, vol. 55, no. 3. Institute of Mathematical
Statistics, pp. 1203–1225, 2019.
ista: Ferrari P, Ghosal P, Nejjar P. 2019. Limit law of a second class particle
in TASEP with non-random initial condition. Annales de l’institut Henri Poincare
(B) Probability and Statistics. 55(3), 1203–1225.
mla: Ferrari, Patrick, et al. “Limit Law of a Second Class Particle in TASEP with
Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability
and Statistics, vol. 55, no. 3, Institute of Mathematical Statistics, 2019,
pp. 1203–25, doi:10.1214/18-AIHP916.
short: P. Ferrari, P. Ghosal, P. Nejjar, Annales de l’institut Henri Poincare (B)
Probability and Statistics 55 (2019) 1203–1225.
date_created: 2018-12-11T11:44:29Z
date_published: 2019-09-25T00:00:00Z
date_updated: 2025-04-14T07:27:49Z
day: '25'
department:
- _id: LaEr
- _id: JaMa
doi: 10.1214/18-AIHP916
ec_funded: 1
external_id:
arxiv:
- '1710.02323'
isi:
- '000487763200001'
intvolume: ' 55'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1710.02323
month: '09'
oa: 1
oa_version: Preprint
page: 1203-1225
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Annales de l'institut Henri Poincare (B) Probability and Statistics
publication_identifier:
issn:
- 0246-0203
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Limit law of a second class particle in TASEP with non-random initial condition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2019'
...
---
_id: '7200'
abstract:
- lang: eng
text: Recent scanning tunneling microscopy experiments in NbN thin disordered superconducting
films found an emergent inhomogeneity at the scale of tens of nanometers. This
inhomogeneity is mirrored by an apparent dimensional crossover in the paraconductivity
measured in transport above the superconducting critical temperature Tc. This
behavior was interpreted in terms of an anomalous diffusion of fluctuating Cooper
pairs that display a quasiconfinement (i.e., a slowing down of their diffusive
dynamics) on length scales shorter than the inhomogeneity identified by tunneling
experiments. Here, we assume this anomalous diffusive behavior of fluctuating
Cooper pairs and calculate the effect of these fluctuations on the electron density
of states above Tc. We find that the density of states is substantially suppressed
up to temperatures well above Tc. This behavior, which is closely reminiscent
of a pseudogap, only arises from the anomalous diffusion of fluctuating Cooper
pairs in the absence of stable preformed pairs, setting the stage for an intermediate
behavior between the two common paradigms in the superconducting-insulator transition,
namely, the localization of Cooper pairs (the so-called bosonic scenario) and
the breaking of Cooper pairs into unpaired electrons due to strong disorder (the
so-called fermionic scenario).
article_number: '174518'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Pietro
full_name: Brighi, Pietro
id: 4115AF5C-F248-11E8-B48F-1D18A9856A87
last_name: Brighi
orcid: 0000-0002-7969-2729
- first_name: Marco
full_name: Grilli, Marco
last_name: Grilli
- first_name: Brigitte
full_name: Leridon, Brigitte
last_name: Leridon
- first_name: Sergio
full_name: Caprara, Sergio
last_name: Caprara
citation:
ama: Brighi P, Grilli M, Leridon B, Caprara S. Effect of anomalous diffusion of
fluctuating Cooper pairs on the density of states of superconducting NbN thin
films. Physical Review B. 2019;100(17). doi:10.1103/PhysRevB.100.174518
apa: Brighi, P., Grilli, M., Leridon, B., & Caprara, S. (2019). Effect of anomalous
diffusion of fluctuating Cooper pairs on the density of states of superconducting
NbN thin films. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.100.174518
chicago: Brighi, Pietro, Marco Grilli, Brigitte Leridon, and Sergio Caprara. “Effect
of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of
Superconducting NbN Thin Films.” Physical Review B. American Physical Society,
2019. https://doi.org/10.1103/PhysRevB.100.174518.
ieee: P. Brighi, M. Grilli, B. Leridon, and S. Caprara, “Effect of anomalous diffusion
of fluctuating Cooper pairs on the density of states of superconducting NbN thin
films,” Physical Review B, vol. 100, no. 17. American Physical Society,
2019.
ista: Brighi P, Grilli M, Leridon B, Caprara S. 2019. Effect of anomalous diffusion
of fluctuating Cooper pairs on the density of states of superconducting NbN thin
films. Physical Review B. 100(17), 174518.
mla: Brighi, Pietro, et al. “Effect of Anomalous Diffusion of Fluctuating Cooper
Pairs on the Density of States of Superconducting NbN Thin Films.” Physical
Review B, vol. 100, no. 17, 174518, American Physical Society, 2019, doi:10.1103/PhysRevB.100.174518.
short: P. Brighi, M. Grilli, B. Leridon, S. Caprara, Physical Review B 100 (2019).
date_created: 2019-12-22T23:00:41Z
date_published: 2019-11-25T00:00:00Z
date_updated: 2024-02-28T13:14:08Z
day: '25'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.100.174518
external_id:
arxiv:
- '1907.13579'
isi:
- '000498845700006'
intvolume: ' 100'
isi: 1
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.13579
month: '11'
oa: 1
oa_version: Preprint
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: Effect of anomalous diffusion of fluctuating Cooper pairs on the density of
states of superconducting NbN thin films
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2019'
...