---
_id: '783'
abstract:
- lang: eng
text: 'The problem of electing a leader from among n contenders is one of the fundamental
questions in distributed computing. In its simplest formulation, the task is as
follows: given n processors, all participants must eventually return a win or
lose indication, such that a single contender may win. Despite a considerable
amount of work on leader election, the following question is still open: can we
elect a leader in an asynchronous fault-prone system faster than just running
a Θ(log n)-time tournament, against a strong adaptive adversary? In this paper,
we answer this question in the affirmative, improving on a decades-old upper bound.
We introduce two new algorithmic ideas to reduce the time complexity of electing
a leader to O(log∗ n), using O(n2) point-to-point messages. A non-trivial application
of our algorithm is a new upper bound for the tight renaming problem, assigning
n items to the n participants in expected O(log2 n) time and O(n2) messages. We
complement our results with lower bound of Ω(n2) messages for solving these two
problems, closing the question of their message complexity.'
acknowledgement: "Support is gratefully acknowledged from the National Science Foundation
under grants CCF-1217921, CCF-1301926,\r\nand IIS-1447786, the Department of
\ Energy under grant\r\nER26116/DE-SC0008923, and the Oracle and Intel corporations.\r\nThe
authors would like to thank Prof. Nir Shavit for ad-\r\nvice and encouragement
during this work, and the anonymous reviewers for their very useful suggestions."
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Adrian
full_name: Vladu, Adrian
last_name: Vladu
citation:
ama: 'Alistarh D-A, Gelashvili R, Vladu A. How to elect a leader faster than a tournament.
In: Vol 2015-July. ACM; 2015:365-374. doi:10.1145/2767386.2767420'
apa: 'Alistarh, D.-A., Gelashvili, R., & Vladu, A. (2015). How to elect a leader
faster than a tournament (Vol. 2015–July, pp. 365–374). Presented at the PODC:
Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767420'
chicago: Alistarh, Dan-Adrian, Rati Gelashvili, and Adrian Vladu. “How to Elect
a Leader Faster than a Tournament,” 2015–July:365–74. ACM, 2015. https://doi.org/10.1145/2767386.2767420.
ieee: 'D.-A. Alistarh, R. Gelashvili, and A. Vladu, “How to elect a leader faster
than a tournament,” presented at the PODC: Principles of Distributed Computing,
2015, vol. 2015–July, pp. 365–374.'
ista: 'Alistarh D-A, Gelashvili R, Vladu A. 2015. How to elect a leader faster than
a tournament. PODC: Principles of Distributed Computing vol. 2015–July, 365–374.'
mla: Alistarh, Dan-Adrian, et al. How to Elect a Leader Faster than a Tournament.
Vol. 2015–July, ACM, 2015, pp. 365–74, doi:10.1145/2767386.2767420.
short: D.-A. Alistarh, R. Gelashvili, A. Vladu, in:, ACM, 2015, pp. 365–374.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:28Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2023-02-23T13:18:55Z
day: '21'
doi: 10.1145/2767386.2767420
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1411.1001
month: '07'
oa: 1
oa_version: None
page: 365 - 374
publication_status: published
publisher: ACM
publist_id: '6875'
status: public
title: How to elect a leader faster than a tournament
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-July
year: '2015'
...
---
_id: '784'
abstract:
- lang: eng
text: We demonstrate an optical switch design that can scale up to a thousand ports
with high per-port bandwidth (25 Gbps+) and low switching latency (40 ns). Our
design uses a broadcast and select architecture, based on a passive star coupler
and fast tunable transceivers. In addition we employ time division multiplexing
to achieve very low switching latency. Our demo shows the feasibility of the switch
data plane using a small testbed, comprising two transmitters and a receiver,
connected through a star coupler.
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Hitesh
full_name: Ballani, Hitesh
last_name: Ballani
- first_name: Paolo
full_name: Costa, Paolo
last_name: Costa
- first_name: Adam
full_name: Funnell, Adam
last_name: Funnell
- first_name: Joshua
full_name: Benjamin, Joshua
last_name: Benjamin
- first_name: Philip
full_name: Watts, Philip
last_name: Watts
- first_name: Benn
full_name: Thomsen, Benn
last_name: Thomsen
citation:
ama: 'Alistarh D-A, Ballani H, Costa P, et al. A high-radix, low-latency optical
switch for data centers. In: ACM; 2015:367-368. doi:10.1145/2785956.2790035'
apa: 'Alistarh, D.-A., Ballani, H., Costa, P., Funnell, A., Benjamin, J., Watts,
P., & Thomsen, B. (2015). A high-radix, low-latency optical switch for data
centers (pp. 367–368). Presented at the SIGCOMM: Special Interest Group on Data
Communication, London, United Kindgdom: ACM. https://doi.org/10.1145/2785956.2790035'
chicago: Alistarh, Dan-Adrian, Hitesh Ballani, Paolo Costa, Adam Funnell, Joshua
Benjamin, Philip Watts, and Benn Thomsen. “A High-Radix, Low-Latency Optical Switch
for Data Centers,” 367–68. ACM, 2015. https://doi.org/10.1145/2785956.2790035.
ieee: 'D.-A. Alistarh et al., “A high-radix, low-latency optical switch for
data centers,” presented at the SIGCOMM: Special Interest Group on Data Communication,
London, United Kindgdom, 2015, pp. 367–368.'
ista: 'Alistarh D-A, Ballani H, Costa P, Funnell A, Benjamin J, Watts P, Thomsen
B. 2015. A high-radix, low-latency optical switch for data centers. SIGCOMM: Special
Interest Group on Data Communication, 367–368.'
mla: Alistarh, Dan-Adrian, et al. A High-Radix, Low-Latency Optical Switch for
Data Centers. ACM, 2015, pp. 367–68, doi:10.1145/2785956.2790035.
short: D.-A. Alistarh, H. Ballani, P. Costa, A. Funnell, J. Benjamin, P. Watts,
B. Thomsen, in:, ACM, 2015, pp. 367–368.
conference:
end_date: 2015-08-21
location: London, United Kindgdom
name: 'SIGCOMM: Special Interest Group on Data Communication'
start_date: 2015-08-17
date_created: 2018-12-11T11:48:29Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:18:57Z
day: '01'
doi: 10.1145/2785956.2790035
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 367 - 368
publication_identifier:
isbn:
- 978-1-4503-3542-3
publication_status: published
publisher: ACM
publist_id: '6872'
quality_controlled: '1'
status: public
title: A high-radix, low-latency optical switch for data centers
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '802'
abstract:
- lang: eng
text: Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at
the plasma membrane of various eukaryotes with the important exception of mammals.
In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man)
linked at position 2 of the inositol. However, several pathogenic fungi additionally
synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at
this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC
core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC,
which is the most abundant GIPC synthesized by this fungus. In this study, we
identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate
its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted
deletion of the gene encoding GntA in A. fumigatus resulted in complete absence
of zwitterionic GIPC; a phenotype that could be reverted by episomal expression
of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was
substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces
cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore
shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid
product resistant to saponification and to digestion by phosphatidylinositol-phospholipase
C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation
of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis.
article_processing_charge: No
author:
- first_name: Jakob
full_name: Engel, Jakob
last_name: Engel
- first_name: Philipp S
full_name: Schmalhorst, Philipp S
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Anke
full_name: Kruger, Anke
last_name: Kruger
- first_name: Christina
full_name: Muller, Christina
last_name: Muller
- first_name: Falk
full_name: Buettner, Falk
last_name: Buettner
- first_name: Françoise
full_name: Routier, Françoise
last_name: Routier
citation:
ama: Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. Characterization
of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic
glycoinositolphosphoceramide biosynthesis. Glycobiology. 2015;25(12):1423-1430.
doi:10.1093/glycob/cwv059
apa: Engel, J., Schmalhorst, P. S., Kruger, A., Muller, C., Buettner, F., &
Routier, F. (2015). Characterization of an N-acetylglucosaminyltransferase involved
in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis.
Glycobiology. Oxford University Press. https://doi.org/10.1093/glycob/cwv059
chicago: Engel, Jakob, Philipp S Schmalhorst, Anke Kruger, Christina Muller, Falk
Buettner, and Françoise Routier. “Characterization of an N-Acetylglucosaminyltransferase
Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.”
Glycobiology. Oxford University Press, 2015. https://doi.org/10.1093/glycob/cwv059.
ieee: J. Engel, P. S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, and F. Routier,
“Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis,” Glycobiology,
vol. 25, no. 12. Oxford University Press, pp. 1423–1430, 2015.
ista: Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. 2015.
Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology.
25(12), 1423–1430.
mla: Engel, Jakob, et al. “Characterization of an N-Acetylglucosaminyltransferase
Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.”
Glycobiology, vol. 25, no. 12, Oxford University Press, 2015, pp. 1423–30,
doi:10.1093/glycob/cwv059.
short: J. Engel, P.S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, F. Routier,
Glycobiology 25 (2015) 1423–1430.
date_created: 2018-12-11T11:48:35Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2025-09-23T08:14:24Z
day: '01'
department:
- _id: CaHe
doi: 10.1093/glycob/cwv059
external_id:
isi:
- '000368443700010'
pmid:
- '26306635'
intvolume: ' 25'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 1423 - 1430
pmid: 1
publication: Glycobiology
publication_status: published
publisher: Oxford University Press
publist_id: '6851'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 25
year: '2015'
...
---
_id: '814'
abstract:
- lang: eng
text: Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages.
First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein
lattice at the plasma membrane of the infected cell, inducing budding and release
of an immature particle. Second, Gag is cleaved by the viral protease, leading
to internal rearrangement of the virus into the mature, infectious form. Immature
and mature HIV-1 particles are heterogeneous in size and morphology, preventing
high-resolution analysis of their protein arrangement in situ by conventional
structural biology methods. Here we apply cryo-electron tomography and sub-tomogram
averaging methods to resolve the structure of the capsid lattice within intact
immature HIV-1 particles at subnanometre resolution, allowing unambiguous positioning
of all α-helices. The resulting model reveals tertiary and quaternary structural
interactions that mediate HIV-1 assembly. Strikingly, these interactions differ
from those predicted by the current model based on in vitro-assembled arrays of
Gag-derived proteins from Mason-Pfizer monkey virus. To validate this difference,
we solve the structure of the capsid lattice within intact immature Mason-Pfizer
monkey virus particles. Comparison with the immature HIV-1 structure reveals that
retroviral capsid proteins, while having conserved tertiary structures, adopt
different quaternary arrangements during virus assembly. The approach demonstrated
here should be applicable to determine structures of other proteins at subnanometre
resolution within heterogeneous environments.
acknowledgement: This study was supported by Deutsche Forschungsgemeinschaft grants
BR 3635/2-1 to J.A.G.B., KR 906/7-1 to H.-G.K. and by Grant Agency of the Czech
Republic 14-15326S to M.R. The Briggs laboratory acknowledges financial support
from the European Molecular Biology Laboratory and from the Chica und Heinz Schaller
Stiftung. We thank B. Glass, M. Anders and S. Mattei for preparation of samples,
and R. Hadravova, K. H. Bui, F. Thommen, M. Schorb, S. Dodonova, S. Glatt, P. Ulbrich
and T. Bharat for technical support and/or discussion. This study was technically
supported by the European Molecular Biology Laboratory IT services unit.
author:
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Wim
full_name: Hagen, Wim J
last_name: Hagen
- first_name: Michaela
full_name: Rumlová, Michaela
last_name: Rumlová
- first_name: Tomáš
full_name: Ruml, Tomáš
last_name: Ruml
- first_name: B
full_name: Müller B
last_name: Müller
- first_name: Hans
full_name: Kraüsslich, Hans Georg
last_name: Kraüsslich
- first_name: John
full_name: Briggs, John A
last_name: Briggs
citation:
ama: Schur FK, Hagen W, Rumlová M, et al. Structure of the immature HIV-1 capsid
in intact virus particles at 8.8 Å resolution. Nature. 2015;517(7535):505-508.
doi:10.1038/nature13838
apa: Schur, F. K., Hagen, W., Rumlová, M., Ruml, T., Müller, B., Kraüsslich, H.,
& Briggs, J. (2015). Structure of the immature HIV-1 capsid in intact virus
particles at 8.8 Å resolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13838
chicago: Schur, Florian KM, Wim Hagen, Michaela Rumlová, Tomáš Ruml, B Müller, Hans
Kraüsslich, and John Briggs. “Structure of the Immature HIV-1 Capsid in Intact
Virus Particles at 8.8 Å Resolution.” Nature. Nature Publishing Group,
2015. https://doi.org/10.1038/nature13838.
ieee: F. K. Schur et al., “Structure of the immature HIV-1 capsid in intact
virus particles at 8.8 Å resolution,” Nature, vol. 517, no. 7535. Nature
Publishing Group, pp. 505–508, 2015.
ista: Schur FK, Hagen W, Rumlová M, Ruml T, Müller B, Kraüsslich H, Briggs J. 2015.
Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution.
Nature. 517(7535), 505–508.
mla: Schur, Florian KM, et al. “Structure of the Immature HIV-1 Capsid in Intact
Virus Particles at 8.8 Å Resolution.” Nature, vol. 517, no. 7535, Nature
Publishing Group, 2015, pp. 505–08, doi:10.1038/nature13838.
short: F.K. Schur, W. Hagen, M. Rumlová, T. Ruml, B. Müller, H. Kraüsslich, J. Briggs,
Nature 517 (2015) 505–508.
date_created: 2018-12-11T11:48:39Z
date_published: 2015-01-22T00:00:00Z
date_updated: 2021-01-12T08:17:08Z
day: '22'
doi: 10.1038/nature13838
extern: 1
intvolume: ' 517'
issue: '7535'
month: '01'
page: 505 - 508
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6836'
quality_controlled: 0
status: public
title: Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution
type: journal_article
volume: 517
year: '2015'
...
---
_id: '815'
abstract:
- lang: eng
text: "The polyprotein Gag is the primary structural component of retroviruses.
Gag consists of independently folded domains connected by flexible linkers. Interactions
between the conserved capsid (CA) domains of Gag mediate formation of hexameric
protein lattices that drive assembly of immature virus particles. Proteolytic
cleavage of Gag by the viral protease (PR) is required for maturation of retroviruses
from an immature form into an infectious form. Within the assembled Gag lattices
of HIV-1 and Mason- Pfizer monkey virus (M-PMV), the C-terminal domain of CA adopts
similar quaternary arrangements, while the N-terminal domain of CA is packed in
very different manners. Here, we have used cryo-electron tomography and subtomogram
averaging to study in vitro-assembled, immature virus-like Rous sarcoma virus
(RSV) Gag particles and have determined the structure of CA and the surrounding
regions to a resolution of ~8 Å. We found that the C-terminal domain of RSV CA
is arranged similarly to HIV-1 and M-PMV, whereas the N-terminal domain of CA
adopts a novel arrangement in which the upstream p10 domain folds back into the
CA lattice. In this position the cleavage site between CA and p10 appears to be
inaccessible to PR. Below CA, an extended density is consistent with the presence
of a six-helix bundle formed by the spacer-peptide region. We have also assessed
the affect of lattice assembly on proteolytic processing by exogenous PR. The
cleavage between p10 and CA is indeed inhibited in the assembled lattice, a finding
consistent with structural regulation of proteolytic maturation.\r\n"
author:
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Robert
full_name: Dick, Robert
last_name: Dick
- first_name: Wim
full_name: Hagen, Wim
last_name: Hagen
- first_name: Volker
full_name: Vogt, Volker
last_name: Vogt
- first_name: John
full_name: Briggs, John
last_name: Briggs
citation:
ama: Schur FK, Dick R, Hagen W, Vogt V, Briggs J. The structure of immature virus
like Rous sarcoma virus gag particles reveals a structural role for the p10 domain
in assembly. Journal of Virology. 2015;89(20):10294-10302. doi:10.1128/JVI.01502-15
apa: Schur, F. K., Dick, R., Hagen, W., Vogt, V., & Briggs, J. (2015). The structure
of immature virus like Rous sarcoma virus gag particles reveals a structural role
for the p10 domain in assembly. Journal of Virology. ASM. https://doi.org/10.1128/JVI.01502-15
chicago: Schur, Florian KM, Robert Dick, Wim Hagen, Volker Vogt, and John Briggs.
“The Structure of Immature Virus like Rous Sarcoma Virus Gag Particles Reveals
a Structural Role for the P10 Domain in Assembly.” Journal of Virology.
ASM, 2015. https://doi.org/10.1128/JVI.01502-15.
ieee: F. K. Schur, R. Dick, W. Hagen, V. Vogt, and J. Briggs, “The structure of
immature virus like Rous sarcoma virus gag particles reveals a structural role
for the p10 domain in assembly,” Journal of Virology, vol. 89, no. 20.
ASM, pp. 10294–10302, 2015.
ista: Schur FK, Dick R, Hagen W, Vogt V, Briggs J. 2015. The structure of immature
virus like Rous sarcoma virus gag particles reveals a structural role for the
p10 domain in assembly. Journal of Virology. 89(20), 10294–10302.
mla: Schur, Florian KM, et al. “The Structure of Immature Virus like Rous Sarcoma
Virus Gag Particles Reveals a Structural Role for the P10 Domain in Assembly.”
Journal of Virology, vol. 89, no. 20, ASM, 2015, pp. 10294–302, doi:10.1128/JVI.01502-15.
short: F.K. Schur, R. Dick, W. Hagen, V. Vogt, J. Briggs, Journal of Virology 89
(2015) 10294–10302.
date_created: 2018-12-11T11:48:39Z
date_published: 2015-09-22T00:00:00Z
date_updated: 2021-01-12T08:17:09Z
day: '22'
doi: 10.1128/JVI.01502-15
extern: '1'
external_id:
pmid:
- '26223638'
intvolume: ' 89'
issue: '20'
language:
- iso: eng
month: '09'
oa_version: None
page: 10294 - 10302
pmid: 1
publication: Journal of Virology
publication_status: published
publisher: ASM
publist_id: '6837'
quality_controlled: '1'
status: public
title: The structure of immature virus like Rous sarcoma virus gag particles reveals
a structural role for the p10 domain in assembly
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2015'
...
---
_id: '8242'
article_number: AB101
article_processing_charge: No
article_type: original
author:
- first_name: Lukas
full_name: Einhorn, Lukas
last_name: Einhorn
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: Martina
full_name: Muhr, Martina
last_name: Muhr
- first_name: Alexandra
full_name: Schoos, Alexandra
last_name: Schoos
- first_name: Kumiko
full_name: Oida, Kumiko
last_name: Oida
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
- first_name: Lucia
full_name: Panakova, Lucia
last_name: Panakova
- first_name: Krisztina
full_name: Manzano-Szalai, Krisztina
last_name: Manzano-Szalai
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: Einhorn L, Singer J, Muhr M, et al. Generation of recombinant FcεRIα of dog,
cat and horse for component-resolved allergy diagnosis in veterinary patients.
Journal of Allergy and Clinical Immunology. 2015;135(2). doi:10.1016/j.jaci.2014.12.1263
apa: Einhorn, L., Singer, J., Muhr, M., Schoos, A., Oida, K., Singer, J., … Jensen-Jarolim,
E. (2015). Generation of recombinant FcεRIα of dog, cat and horse for component-resolved
allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology.
Elsevier. https://doi.org/10.1016/j.jaci.2014.12.1263
chicago: Einhorn, Lukas, Judit Singer, Martina Muhr, Alexandra Schoos, Kumiko Oida,
Josef Singer, Lucia Panakova, Krisztina Manzano-Szalai, and Erika Jensen-Jarolim.
“Generation of Recombinant FcεRIα of Dog, Cat and Horse for Component-Resolved
Allergy Diagnosis in Veterinary Patients.” Journal of Allergy and Clinical
Immunology. Elsevier, 2015. https://doi.org/10.1016/j.jaci.2014.12.1263.
ieee: L. Einhorn et al., “Generation of recombinant FcεRIα of dog, cat and
horse for component-resolved allergy diagnosis in veterinary patients,” Journal
of Allergy and Clinical Immunology, vol. 135, no. 2. Elsevier, 2015.
ista: Einhorn L, Singer J, Muhr M, Schoos A, Oida K, Singer J, Panakova L, Manzano-Szalai
K, Jensen-Jarolim E. 2015. Generation of recombinant FcεRIα of dog, cat and horse
for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy
and Clinical Immunology. 135(2), AB101.
mla: Einhorn, Lukas, et al. “Generation of Recombinant FcεRIα of Dog, Cat and Horse
for Component-Resolved Allergy Diagnosis in Veterinary Patients.” Journal of
Allergy and Clinical Immunology, vol. 135, no. 2, AB101, Elsevier, 2015, doi:10.1016/j.jaci.2014.12.1263.
short: L. Einhorn, J. Singer, M. Muhr, A. Schoos, K. Oida, J. Singer, L. Panakova,
K. Manzano-Szalai, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology
135 (2015).
date_created: 2020-08-10T11:54:09Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T08:17:42Z
day: '01'
doi: 10.1016/j.jaci.2014.12.1263
extern: '1'
intvolume: ' 135'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
publication: Journal of Allergy and Clinical Immunology
publication_identifier:
issn:
- 0091-6749
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Generation of recombinant FcεRIα of dog, cat and horse for component-resolved
allergy diagnosis in veterinary patients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2015'
...
---
_id: '832'
abstract:
- lang: eng
text: Plants maintain capacity to form new organs such as leaves, flowers, lateral
shoots and roots throughout their postembryonic lifetime. Lateral roots (LRs)
originate from a few pericycle cells that acquire attributes of founder cells
(FCs), undergo series of anticlinal divisions, and give rise to a few short initial
cells. After initiation, coordinated cell division and differentiation occur,
giving rise to lateral root primordia (LRP). Primordia continue to grow, emerge
through the cortex and epidermal layers of the primary root, and finally a new
apical meristem is established taking over the responsibility for growth of mature
lateral roots [for detailed description of the individual stages of lateral root
organogenesis see Malamy and Benfey (1997)]. To examine this highly dynamic developmental
process and to investigate a role of various hormonal, genetic and environmental
factors in the regulation of lateral root organogenesis, the real time imaging
based analyses represent extremely powerful tools (Laskowski et al., 2008; De
Smet et al., 2012; Marhavy et al., 2013 and 2014). Herein, we describe a protocol
for real time lateral root primordia (LRP) analysis, which enables the monitoring
of an onset of the specific gene expression and subcellular protein localization
during primordia organogenesis, as well as the evaluation of the impact of genetic
and environmental perturbations on LRP organogenesis.
acknowledgement: "European Research Council with a Starting Independent Research grant:
ERC-2007-Stg-207362-HCPO, Czech Science Foundation: GA13-39982S\nWe thank Matyas
Fendrych for critical reading and comments. The protocol was developed based on
previously published work of De Rybel et al. (2010) and Laskowski et al. (2008). "
author:
- first_name: Peter
full_name: Peter Marhavy
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Marhavý P, Benková E. Real time analysis of lateral root organogenesis in arabidopsis.
Bio-protocol. 2015;5(8). doi:10.21769/BioProtoc.1446
apa: Marhavý, P., & Benková, E. (2015). Real time analysis of lateral root organogenesis
in arabidopsis. Bio-Protocol. Bio-protocol LLC. https://doi.org/10.21769/BioProtoc.1446
chicago: Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis
in Arabidopsis.” Bio-Protocol. Bio-protocol LLC, 2015. https://doi.org/10.21769/BioProtoc.1446.
ieee: P. Marhavý and E. Benková, “Real time analysis of lateral root organogenesis
in arabidopsis,” Bio-protocol, vol. 5, no. 8. Bio-protocol LLC, 2015.
ista: Marhavý P, Benková E. 2015. Real time analysis of lateral root organogenesis
in arabidopsis. Bio-protocol. 5(8).
mla: Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis
in Arabidopsis.” Bio-Protocol, vol. 5, no. 8, Bio-protocol LLC, 2015, doi:10.21769/BioProtoc.1446.
short: P. Marhavý, E. Benková, Bio-Protocol 5 (2015).
date_created: 2018-12-11T11:48:44Z
date_published: 2015-04-20T00:00:00Z
date_updated: 2021-01-12T08:18:07Z
day: '20'
doi: 10.21769/BioProtoc.1446
extern: 1
intvolume: ' 5'
issue: '8'
month: '04'
publication: Bio-protocol
publication_status: published
publisher: Bio-protocol LLC
publist_id: '6816'
quality_controlled: 0
status: public
title: Real time analysis of lateral root organogenesis in arabidopsis
type: journal_article
volume: 5
year: '2015'
...
---
OA_place: publisher
OA_type: gold
_id: '8456'
abstract:
- lang: eng
text: The large majority of three-dimensional structures of biological macromolecules
have been determined by X-ray diffraction of crystalline samples. High-resolution
structure determination crucially depends on the homogeneity of the protein crystal.
Overall ‘rocking’ motion of molecules in the crystal is expected to influence
diffraction quality, and such motion may therefore affect the process of solving
crystal structures. Yet, so far overall molecular motion has not directly been
observed in protein crystals, and the timescale of such dynamics remains unclear.
Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics
simulations to directly characterize the rigid-body motion of a protein in different
crystal forms. For ubiquitin crystals investigated in this study we determine
the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude
of rocking varies from one crystal form to another and is correlated with the
resolution obtainable in X-ray diffraction experiments.
article_number: '8361'
article_processing_charge: Yes
article_type: original
author:
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Yi
full_name: Xue, Yi
last_name: Xue
- first_name: Nicolas
full_name: Coquelle, Nicolas
last_name: Coquelle
- first_name: Jens D.
full_name: Haller, Jens D.
last_name: Haller
- first_name: Tairan
full_name: Yuwen, Tairan
last_name: Yuwen
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Oleg
full_name: Mikhailovskii, Oleg
last_name: Mikhailovskii
- first_name: Dieter
full_name: Willbold, Dieter
last_name: Willbold
- first_name: Jacques-Philippe
full_name: Colletier, Jacques-Philippe
last_name: Colletier
- first_name: Nikolai R.
full_name: Skrynnikov, Nikolai R.
last_name: Skrynnikov
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Ma P, Xue Y, Coquelle N, et al. Observing the overall rocking motion of a protein
in a crystal. Nature Communications. 2015;6. doi:10.1038/ncomms9361
apa: Ma, P., Xue, Y., Coquelle, N., Haller, J. D., Yuwen, T., Ayala, I., … Schanda,
P. (2015). Observing the overall rocking motion of a protein in a crystal. Nature
Communications. Springer Nature. https://doi.org/10.1038/ncomms9361
chicago: Ma, Peixiang, Yi Xue, Nicolas Coquelle, Jens D. Haller, Tairan Yuwen, Isabel
Ayala, Oleg Mikhailovskii, et al. “Observing the Overall Rocking Motion of a Protein
in a Crystal.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms9361.
ieee: P. Ma et al., “Observing the overall rocking motion of a protein in
a crystal,” Nature Communications, vol. 6. Springer Nature, 2015.
ista: Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold
D, Colletier J-P, Skrynnikov NR, Schanda P. 2015. Observing the overall rocking
motion of a protein in a crystal. Nature Communications. 6, 8361.
mla: Ma, Peixiang, et al. “Observing the Overall Rocking Motion of a Protein in
a Crystal.” Nature Communications, vol. 6, 8361, Springer Nature, 2015,
doi:10.1038/ncomms9361.
short: P. Ma, Y. Xue, N. Coquelle, J.D. Haller, T. Yuwen, I. Ayala, O. Mikhailovskii,
D. Willbold, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications
6 (2015).
date_created: 2020-09-18T10:07:36Z
date_published: 2015-10-05T00:00:00Z
date_updated: 2025-01-22T14:39:22Z
day: '05'
doi: 10.1038/ncomms9361
extern: '1'
intvolume: ' 6'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/ncomms9361
month: '10'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Observing the overall rocking motion of a protein in a crystal
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '8457'
abstract:
- lang: eng
text: We review recent advances in methodologies to study microseconds‐to‐milliseconds
exchange processes in biological molecules using magic‐angle spinning solid‐state
nuclear magnetic resonance (MAS ssNMR) spectroscopy. The particularities of MAS
ssNMR, as compared to solution‐state NMR, are elucidated using numerical simulations
and experimental data. These simulations reveal the potential of MAS NMR to provide
detailed insight into short‐lived conformations of biological molecules. Recent
studies of conformational exchange dynamics in microcrystalline ubiquitin are
discussed.
article_processing_charge: No
article_type: original
author:
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Ma P, Schanda P. Conformational exchange processes in biological systems:
Detection by solid-state NMR. eMagRes. 2015;4(3):699-708. doi:10.1002/9780470034590.emrstm1418'
apa: 'Ma, P., & Schanda, P. (2015). Conformational exchange processes in biological
systems: Detection by solid-state NMR. EMagRes. Wiley. https://doi.org/10.1002/9780470034590.emrstm1418'
chicago: 'Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in
Biological Systems: Detection by Solid-State NMR.” EMagRes. Wiley, 2015.
https://doi.org/10.1002/9780470034590.emrstm1418.'
ieee: 'P. Ma and P. Schanda, “Conformational exchange processes in biological systems:
Detection by solid-state NMR,” eMagRes, vol. 4, no. 3. Wiley, pp. 699–708,
2015.'
ista: 'Ma P, Schanda P. 2015. Conformational exchange processes in biological systems:
Detection by solid-state NMR. eMagRes. 4(3), 699–708.'
mla: 'Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological
Systems: Detection by Solid-State NMR.” EMagRes, vol. 4, no. 3, Wiley,
2015, pp. 699–708, doi:10.1002/9780470034590.emrstm1418.'
short: P. Ma, P. Schanda, EMagRes 4 (2015) 699–708.
date_created: 2020-09-18T10:07:45Z
date_published: 2015-09-10T00:00:00Z
date_updated: 2021-01-12T08:19:24Z
day: '10'
doi: 10.1002/9780470034590.emrstm1418
extern: '1'
intvolume: ' 4'
issue: '3'
language:
- iso: eng
month: '09'
oa_version: None
page: 699-708
publication: eMagRes
publication_identifier:
isbn:
- '9780470034590'
- '9780470058213'
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: 'Conformational exchange processes in biological systems: Detection by solid-state
NMR'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2015'
...
---
_id: '848'
abstract:
- lang: eng
text: The nature of factors governing the tempo and mode of protein evolution is
a fundamental issue in evolutionary biology. Specifically, whether or not interactions
between different sites, or epistasis, are important in directing the course of
evolution became one of the central questions. Several recent reports have scrutinized
patterns of long-term protein evolution claiming them to be compatible only with
an epistatic fitness landscape. However, these claims have not yet been substantiated
with a formal model of protein evolution. Here, we formulate a simple covarion-like
model of protein evolution focusing on the rate at which the fitness impact of
amino acids at a site changes with time. We then apply the model to the data on
convergent and divergent protein evolution to test whether or not the incorporation
of epistatic interactions is necessary to explain the data. We find that convergent
evolution cannot be explained without the incorporation of epistasis and the rate
at which an amino acid state switches from being acceptable at a site to being
deleterious is faster than the rate of amino acid substitution. Specifically,
for proteins that have persisted in modern prokaryotic organisms since the last
universal common ancestor for one amino acid substitution approximately ten amino
acid states switch from being accessible to being deleterious, or vice versa.
Thus, molecular evolution can only be perceived in the context of rapid turnover
of which amino acids are available for evolution.
article_processing_charge: No
author:
- first_name: Dinara
full_name: Usmanova, Dinara
last_name: Usmanova
- first_name: Luca
full_name: Ferretti, Luca
last_name: Ferretti
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Peter
full_name: Vlasov, Peter
last_name: Vlasov
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. A model of
substitution trajectories in sequence space and long-term protein evolution. Molecular
Biology and Evolution. 2015;32(2):542-554. doi:10.1093/molbev/msu318
apa: Usmanova, D., Ferretti, L., Povolotskaya, I., Vlasov, P., & Kondrashov,
F. (2015). A model of substitution trajectories in sequence space and long-term
protein evolution. Molecular Biology and Evolution. Oxford University Press.
https://doi.org/10.1093/molbev/msu318
chicago: Usmanova, Dinara, Luca Ferretti, Inna Povolotskaya, Peter Vlasov, and Fyodor
Kondrashov. “A Model of Substitution Trajectories in Sequence Space and Long-Term
Protein Evolution.” Molecular Biology and Evolution. Oxford University
Press, 2015. https://doi.org/10.1093/molbev/msu318.
ieee: D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A
model of substitution trajectories in sequence space and long-term protein evolution,”
Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press,
pp. 542–554, 2015.
ista: Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. 2015. A model
of substitution trajectories in sequence space and long-term protein evolution.
Molecular Biology and Evolution. 32(2), 542–554.
mla: Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence
Space and Long-Term Protein Evolution.” Molecular Biology and Evolution,
vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:10.1093/molbev/msu318.
short: D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular
Biology and Evolution 32 (2015) 542–554.
date_created: 2018-12-11T11:48:49Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2025-09-22T14:32:37Z
day: '01'
doi: 10.1093/molbev/msu318
extern: '1'
external_id:
isi:
- '000350050700020'
intvolume: ' 32'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 542 - 554
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6804'
quality_controlled: '1'
status: public
title: A model of substitution trajectories in sequence space and long-term protein
evolution
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 32
year: '2015'
...
---
_id: '8495'
abstract:
- lang: eng
text: 'In this note, we consider the dynamics associated to a perturbation of an
integrable Hamiltonian system in action-angle coordinates in any number of degrees
of freedom and we prove the following result of ``micro-diffusion'''': under generic
assumptions on $ h$ and $ f$, there exists an orbit of the system for which the
drift of its action variables is at least of order $ \sqrt {\varepsilon }$, after
a time of order $ \sqrt {\varepsilon }^{-1}$. The assumptions, which are essentially
minimal, are that there exists a resonant point for $ h$ and that the corresponding
averaged perturbation is non-constant. The conclusions, although very weak when
compared to usual instability phenomena, are also essentially optimal within this
setting.'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Abed
full_name: Bounemoura, Abed
last_name: Bounemoura
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Bounemoura A, Kaloshin V. A note on micro-instability for Hamiltonian systems
close to integrable. Proceedings of the American Mathematical Society.
2015;144(4):1553-1560. doi:10.1090/proc/12796
apa: Bounemoura, A., & Kaloshin, V. (2015). A note on micro-instability for
Hamiltonian systems close to integrable. Proceedings of the American Mathematical
Society. American Mathematical Society. https://doi.org/10.1090/proc/12796
chicago: Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for
Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical
Society. American Mathematical Society, 2015. https://doi.org/10.1090/proc/12796.
ieee: A. Bounemoura and V. Kaloshin, “A note on micro-instability for Hamiltonian
systems close to integrable,” Proceedings of the American Mathematical Society,
vol. 144, no. 4. American Mathematical Society, pp. 1553–1560, 2015.
ista: Bounemoura A, Kaloshin V. 2015. A note on micro-instability for Hamiltonian
systems close to integrable. Proceedings of the American Mathematical Society.
144(4), 1553–1560.
mla: Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian
Systems Close to Integrable.” Proceedings of the American Mathematical Society,
vol. 144, no. 4, American Mathematical Society, 2015, pp. 1553–60, doi:10.1090/proc/12796.
short: A. Bounemoura, V. Kaloshin, Proceedings of the American Mathematical Society
144 (2015) 1553–1560.
date_created: 2020-09-18T10:46:14Z
date_published: 2015-12-21T00:00:00Z
date_updated: 2021-01-12T08:19:40Z
day: '21'
doi: 10.1090/proc/12796
extern: '1'
intvolume: ' 144'
issue: '4'
language:
- iso: eng
month: '12'
oa_version: None
page: 1553-1560
publication: Proceedings of the American Mathematical Society
publication_identifier:
issn:
- 0002-9939
- 1088-6826
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
status: public
title: A note on micro-instability for Hamiltonian systems close to integrable
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 144
year: '2015'
...
---
_id: '8498'
abstract:
- lang: eng
text: "In the present note we announce a proof of a strong form of Arnold diffusion
for smooth convex Hamiltonian systems. Let ${\\mathbb T}^2$ be a 2-dimensional
torus and B2 be the unit ball around the origin in ${\\mathbb R}^2$ . Fix ρ >
0. Our main result says that for a 'generic' time-periodic perturbation of an
integrable system of two degrees of freedom $H_0(p)+\\varepsilon H_1(\\theta,p,t),\\quad
\\ \\theta\\in {\\mathbb T}^2,\\ p\\in B^2,\\ t\\in {\\mathbb T}={\\mathbb R}/{\\mathbb
Z}$ , with a strictly convex H0, there exists a ρ-dense orbit (θε, pε, t)(t) in
${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ , namely, a ρ-neighborhood of
the orbit contains ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ .\r\n\r\nOur
proof is a combination of geometric and variational methods. The fundamental elements
of the construction are the usage of crumpled normally hyperbolic invariant cylinders
from [9], flower and simple normally hyperbolic invariant manifolds from [36]
as well as their kissing property at a strong double resonance. This allows us
to build a 'connected' net of three-dimensional normally hyperbolic invariant
manifolds. To construct diffusing orbits along this net we employ a version of
the Mather variational method [41] equipped with weak KAM theory [28], proposed
by Bernard in [7]."
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: K
full_name: Zhang, K
last_name: Zhang
citation:
ama: Kaloshin V, Zhang K. Arnold diffusion for smooth convex systems of two and
a half degrees of freedom. Nonlinearity. 2015;28(8):2699-2720. doi:10.1088/0951-7715/28/8/2699
apa: Kaloshin, V., & Zhang, K. (2015). Arnold diffusion for smooth convex systems
of two and a half degrees of freedom. Nonlinearity. IOP Publishing. https://doi.org/10.1088/0951-7715/28/8/2699
chicago: Kaloshin, Vadim, and K Zhang. “Arnold Diffusion for Smooth Convex Systems
of Two and a Half Degrees of Freedom.” Nonlinearity. IOP Publishing, 2015.
https://doi.org/10.1088/0951-7715/28/8/2699.
ieee: V. Kaloshin and K. Zhang, “Arnold diffusion for smooth convex systems of two
and a half degrees of freedom,” Nonlinearity, vol. 28, no. 8. IOP Publishing,
pp. 2699–2720, 2015.
ista: Kaloshin V, Zhang K. 2015. Arnold diffusion for smooth convex systems of two
and a half degrees of freedom. Nonlinearity. 28(8), 2699–2720.
mla: Kaloshin, Vadim, and K. Zhang. “Arnold Diffusion for Smooth Convex Systems
of Two and a Half Degrees of Freedom.” Nonlinearity, vol. 28, no. 8, IOP
Publishing, 2015, pp. 2699–720, doi:10.1088/0951-7715/28/8/2699.
short: V. Kaloshin, K. Zhang, Nonlinearity 28 (2015) 2699–2720.
date_created: 2020-09-18T10:46:43Z
date_published: 2015-06-30T00:00:00Z
date_updated: 2021-01-12T08:19:41Z
day: '30'
doi: 10.1088/0951-7715/28/8/2699
extern: '1'
intvolume: ' 28'
issue: '8'
keyword:
- Mathematical Physics
- General Physics and Astronomy
- Applied Mathematics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '06'
oa_version: None
page: 2699-2720
publication: Nonlinearity
publication_identifier:
issn:
- 0951-7715
- 1361-6544
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
status: public
title: Arnold diffusion for smooth convex systems of two and a half degrees of freedom
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2015'
...
---
_id: '8499'
abstract:
- lang: eng
text: "We consider the cubic defocusing nonlinear Schrödinger equation in the two
dimensional torus. Fix s>1. Recently Colliander, Keel, Staffilani, Tao and Takaoka
proved the existence of solutions with s-Sobolev norm growing in time.\r\n\r\nWe
establish the existence of solutions with polynomial time estimates. More exactly,
there is c>0 such that for any K≫1 we find a solution u and a time T such that
∥u(T)∥Hs≥K∥u(0)∥Hs. Moreover, the time T satisfies the polynomial bound 0Journal of the European Mathematical Society. 2015;17(1):71-149.
doi:10.4171/jems/499
apa: Guardia, M., & Kaloshin, V. (2015). Growth of Sobolev norms in the cubic
defocusing nonlinear Schrödinger equation. Journal of the European Mathematical
Society. European Mathematical Society Publishing House. https://doi.org/10.4171/jems/499
chicago: Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic
Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical
Society. European Mathematical Society Publishing House, 2015. https://doi.org/10.4171/jems/499.
ieee: M. Guardia and V. Kaloshin, “Growth of Sobolev norms in the cubic defocusing
nonlinear Schrödinger equation,” Journal of the European Mathematical Society,
vol. 17, no. 1. European Mathematical Society Publishing House, pp. 71–149, 2015.
ista: Guardia M, Kaloshin V. 2015. Growth of Sobolev norms in the cubic defocusing
nonlinear Schrödinger equation. Journal of the European Mathematical Society.
17(1), 71–149.
mla: Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic
Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical
Society, vol. 17, no. 1, European Mathematical Society Publishing House, 2015,
pp. 71–149, doi:10.4171/jems/499.
short: M. Guardia, V. Kaloshin, Journal of the European Mathematical Society 17
(2015) 71–149.
date_created: 2020-09-18T10:46:50Z
date_published: 2015-02-05T00:00:00Z
date_updated: 2021-01-12T08:19:41Z
day: '05'
doi: 10.4171/jems/499
extern: '1'
intvolume: ' 17'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 71-149
publication: Journal of the European Mathematical Society
publication_identifier:
issn:
- 1435-9855
publication_status: published
publisher: European Mathematical Society Publishing House
quality_controlled: '1'
status: public
title: Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2015'
...
---
_id: '866'
abstract:
- lang: eng
text: Proteases play important roles in many biologic processes and are key mediators
of cancer, inflammation, and thrombosis. However, comprehensive and quantitative
techniques to define the substrate specificity profile of proteases are lacking.
The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand
factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage
display library based on a 73-amino acid fragment of VWF was constructed, and
the ADAMTS13-dependent change in library complexity was evaluated over reaction
time points, using high-throughput sequencing. Reaction rate constants (kcat/KM)
were calculated for nearly every possible single amino acid substitution within
this fragment. This massively parallel enzyme kinetics analysis detailed the specificity
of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues
while defining exosite binding domains. These data provided empirical evidence
for the propensity for epistasis within VWF and showed strong correlation to conservation
across orthologs, highlighting evolutionary selective pressures for VWF.
acknowledgement: |
We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist.
author:
- first_name: Colin
full_name: Kretz, Colin A
last_name: Kretz
- first_name: Manhong
full_name: Dai, Manhong
last_name: Dai
- first_name: Onuralp
full_name: Soylemez, Onuralp
last_name: Soylemez
- first_name: Andrew
full_name: Yee, Andrew
last_name: Yee
- first_name: Karl
full_name: Desch, Karl C
last_name: Desch
- first_name: David
full_name: Siemieniak, David R
last_name: Siemieniak
- first_name: Kärt
full_name: Tomberg, Kärt
last_name: Tomberg
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Fan
full_name: Meng, Fan
last_name: Meng
- first_name: David
full_name: Ginsburg, David B
last_name: Ginsburg
citation:
ama: Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals
the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS.
2015;112(30):9328-9333. doi:10.1073/pnas.1511328112
apa: Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg,
D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition
landscape of the metalloprotease ADAMTS13. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1511328112
chicago: Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David
Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively
Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease
ADAMTS13.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511328112.
ieee: C. Kretz et al., “Massively parallel enzyme kinetics reveals the substrate
recognition landscape of the metalloprotease ADAMTS13,” PNAS, vol. 112,
no. 30. National Academy of Sciences, pp. 9328–9333, 2015.
ista: Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov
F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate
recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333.
mla: Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate
Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS, vol. 112,
no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:10.1073/pnas.1511328112.
short: C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg,
F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333.
date_created: 2018-12-11T11:48:55Z
date_published: 2015-07-28T00:00:00Z
date_updated: 2021-01-12T08:20:26Z
day: '28'
doi: 10.1073/pnas.1511328112
extern: 1
intvolume: ' 112'
issue: '30'
month: '07'
page: 9328 - 9333
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6783'
quality_controlled: 0
status: public
title: Massively parallel enzyme kinetics reveals the substrate recognition landscape
of the metalloprotease ADAMTS13
type: journal_article
volume: 112
year: '2015'
...
---
_id: '886'
abstract:
- lang: eng
text: The factors that determine the tempo and mode of protein evolution continue
to be a central question in molecular evolution. Traditionally, studies of protein
evolution focused on the rates of amino acid substitutions. More recently, with
the availability of sequence data and advanced experimental techniques, the focus
of attention has shifted toward the study of evolutionary trajectories and the
overall layout of protein fitness landscapes. In this review we describe the effect
of epistasis on the topology of evolutionary pathways that are likely to be found
in fitness landscapes and develop a simple theory to connect the number of maladapted
genotypes to the topology of fitness landscapes with epistatic interactions. Finally,
we review recent studies that have probed the extent of epistatic interactions
and have begun to chart the fitness landscapes in protein sequence space.
acknowledgement: 'This work has been supported by a grant from the HHMI International
Early Career Scientist Program (#55007424), the Spanish Ministry of Economy and
Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP program, two grants
from the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo
Ochoa 2013–2017 (#Sev-2012-0208) and BES-2013-064004 funded by the European Regional
Development Fund (ERDF), the European Union, and the European Research Council under
grant agreement no 335980_EinME.'
author:
- first_name: Dmitry
full_name: Kondrashov, Dmitry A
last_name: Kondrashov
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov D, Kondrashov F. Topological features of rugged fitness landscapes
in sequence space. Trends in Genetics. 2015;31(1):24-33. doi:10.1016/j.tig.2014.09.009
apa: Kondrashov, D., & Kondrashov, F. (2015). Topological features of rugged
fitness landscapes in sequence space. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2014.09.009
chicago: Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged
Fitness Landscapes in Sequence Space.” Trends in Genetics. Elsevier, 2015.
https://doi.org/10.1016/j.tig.2014.09.009.
ieee: D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes
in sequence space,” Trends in Genetics, vol. 31, no. 1. Elsevier, pp. 24–33,
2015.
ista: Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes
in sequence space. Trends in Genetics. 31(1), 24–33.
mla: Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged
Fitness Landscapes in Sequence Space.” Trends in Genetics, vol. 31, no.
1, Elsevier, 2015, pp. 24–33, doi:10.1016/j.tig.2014.09.009.
short: D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33.
date_created: 2018-12-11T11:49:01Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:16Z
day: '01'
doi: 10.1016/j.tig.2014.09.009
extern: 1
intvolume: ' 31'
issue: '1'
month: '01'
page: 24 - 33
publication: Trends in Genetics
publication_status: published
publisher: Elsevier
publist_id: '6764'
quality_controlled: 0
status: public
title: Topological features of rugged fitness landscapes in sequence space
type: journal_article
volume: 31
year: '2015'
...
---
_id: '9017'
abstract:
- lang: eng
text: MCM2 is a subunit of the replicative helicase machinery shown to interact
with histones H3 and H4 during the replication process through its N-terminal
domain. During replication, this interaction has been proposed to assist disassembly
and assembly of nucleosomes on DNA. However, how this interaction participates
in crosstalk with histone chaperones at the replication fork remains to be elucidated.
Here, we solved the crystal structure of the ternary complex between the histone-binding
domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4
assemble as a tetramer in the crystal structure, but MCM2 interacts only with
a single molecule of H3-H4. The latter interaction exploits binding surfaces that
contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome
core particle. Upon binding of the ternary complex with the histone chaperone
ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously
with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis
of the quaternary complex together with structural modeling support that ASF1
and MCM2 could form a chaperoning module for histones H3 and H4 protecting them
from promiscuous interactions. This suggests an additional function for MCM2 outside
its helicase function as a proper histone chaperone connected to the replication
pathway.
article_processing_charge: No
article_type: original
author:
- first_name: Nicolas
full_name: Richet, Nicolas
last_name: Richet
- first_name: Danni
full_name: Liu, Danni
last_name: Liu
- first_name: Pierre
full_name: Legrand, Pierre
last_name: Legrand
- first_name: Christophe
full_name: Velours, Christophe
last_name: Velours
- first_name: Armelle
full_name: Corpet, Armelle
last_name: Corpet
- first_name: Albane
full_name: Gaubert, Albane
last_name: Gaubert
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Gwenaelle
full_name: Moal-Raisin, Gwenaelle
last_name: Moal-Raisin
- first_name: Raphael
full_name: Guerois, Raphael
last_name: Guerois
- first_name: Christel
full_name: Compper, Christel
last_name: Compper
- first_name: Arthur
full_name: Besle, Arthur
last_name: Besle
- first_name: Berengère
full_name: Guichard, Berengère
last_name: Guichard
- first_name: Genevieve
full_name: Almouzni, Genevieve
last_name: Almouzni
- first_name: Françoise
full_name: Ochsenbein, Françoise
last_name: Ochsenbein
citation:
ama: Richet N, Liu D, Legrand P, et al. Structural insight into how the human helicase
subunit MCM2 may act as a histone chaperone together with ASF1 at the replication
fork. Nucleic Acids Research. 2015;43(3):1905-1917. doi:10.1093/nar/gkv021
apa: Richet, N., Liu, D., Legrand, P., Velours, C., Corpet, A., Gaubert, A., … Ochsenbein,
F. (2015). Structural insight into how the human helicase subunit MCM2 may act
as a histone chaperone together with ASF1 at the replication fork. Nucleic
Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv021
chicago: Richet, Nicolas, Danni Liu, Pierre Legrand, Christophe Velours, Armelle
Corpet, Albane Gaubert, May M Bakail, et al. “Structural Insight into How the
Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1
at the Replication Fork.” Nucleic Acids Research. Oxford University Press,
2015. https://doi.org/10.1093/nar/gkv021.
ieee: N. Richet et al., “Structural insight into how the human helicase subunit
MCM2 may act as a histone chaperone together with ASF1 at the replication fork,”
Nucleic Acids Research, vol. 43, no. 3. Oxford University Press, pp. 1905–1917,
2015.
ista: Richet N, Liu D, Legrand P, Velours C, Corpet A, Gaubert A, Bakail MM, Moal-Raisin
G, Guerois R, Compper C, Besle A, Guichard B, Almouzni G, Ochsenbein F. 2015.
Structural insight into how the human helicase subunit MCM2 may act as a histone
chaperone together with ASF1 at the replication fork. Nucleic Acids Research.
43(3), 1905–1917.
mla: Richet, Nicolas, et al. “Structural Insight into How the Human Helicase Subunit
MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.”
Nucleic Acids Research, vol. 43, no. 3, Oxford University Press, 2015,
pp. 1905–17, doi:10.1093/nar/gkv021.
short: N. Richet, D. Liu, P. Legrand, C. Velours, A. Corpet, A. Gaubert, M.M. Bakail,
G. Moal-Raisin, R. Guerois, C. Compper, A. Besle, B. Guichard, G. Almouzni, F.
Ochsenbein, Nucleic Acids Research 43 (2015) 1905–1917.
date_created: 2021-01-19T11:01:01Z
date_published: 2015-02-18T00:00:00Z
date_updated: 2023-02-23T13:46:50Z
day: '18'
doi: 10.1093/nar/gkv021
extern: '1'
external_id:
pmid:
- '25618846'
intvolume: ' 43'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: Published Version
page: 1905-1917
pmid: 1
publication: Nucleic Acids Research
publication_identifier:
issn:
- 1362-4962
- 0305-1048
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Structural insight into how the human helicase subunit MCM2 may act as a histone
chaperone together with ASF1 at the replication fork
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2015'
...
---
_id: '9057'
abstract:
- lang: eng
text: Motility is a basic feature of living microorganisms, and how it works is
often determined by environmental cues. Recent efforts have focused on developing
artificial systems that can mimic microorganisms, in particular their self-propulsion.
We report on the design and characterization of synthetic self-propelled particles
that migrate upstream, known as positive rheotaxis. This phenomenon results from
a purely physical mechanism involving the interplay between the polarity of the
particles and their alignment by a viscous torque. We show quantitative agreement
between experimental data and a simple model of an overdamped Brownian pendulum.
The model notably predicts the existence of a stagnation point in a diverging
flow. We take advantage of this property to demonstrate that our active particles
can sense and predictably organize in an imposed flow. Our colloidal system represents
an important step toward the realization of biomimetic microsystems with the ability
to sense and respond to environmental changes.
article_number: e1400214
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Stefano
full_name: Sacanna, Stefano
last_name: Sacanna
- first_name: Anaïs
full_name: Abramian, Anaïs
last_name: Abramian
- first_name: Jérémie
full_name: Barral, Jérémie
last_name: Barral
- first_name: Kasey
full_name: Hanson, Kasey
last_name: Hanson
- first_name: Alexander Y.
full_name: Grosberg, Alexander Y.
last_name: Grosberg
- first_name: David J.
full_name: Pine, David J.
last_name: Pine
- first_name: Paul M.
full_name: Chaikin, Paul M.
last_name: Chaikin
citation:
ama: Palacci JA, Sacanna S, Abramian A, et al. Artificial rheotaxis. Science
Advances. 2015;1(4). doi:10.1126/sciadv.1400214
apa: Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg,
A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. Science Advances.
American Association for the Advancement of Science . https://doi.org/10.1126/sciadv.1400214
chicago: Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey
Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial
Rheotaxis.” Science Advances. American Association for the Advancement
of Science , 2015. https://doi.org/10.1126/sciadv.1400214.
ieee: J. A. Palacci et al., “Artificial rheotaxis,” Science Advances,
vol. 1, no. 4. American Association for the Advancement of Science , 2015.
ista: Palacci JA, Sacanna S, Abramian A, Barral J, Hanson K, Grosberg AY, Pine DJ,
Chaikin PM. 2015. Artificial rheotaxis. Science Advances. 1(4), e1400214.
mla: Palacci, Jérémie A., et al. “Artificial Rheotaxis.” Science Advances,
vol. 1, no. 4, e1400214, American Association for the Advancement of Science ,
2015, doi:10.1126/sciadv.1400214.
short: J.A. Palacci, S. Sacanna, A. Abramian, J. Barral, K. Hanson, A.Y. Grosberg,
D.J. Pine, P.M. Chaikin, Science Advances 1 (2015).
date_created: 2021-02-02T13:15:02Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2023-02-23T13:47:52Z
day: '01'
ddc:
- '530'
doi: 10.1126/sciadv.1400214
extern: '1'
external_id:
arxiv:
- '1505.05111'
pmid:
- '26601175'
file:
- access_level: open_access
checksum: b97d62433581875c1b85210c5f6ae370
content_type: application/pdf
creator: cziletti
date_created: 2021-02-02T13:22:19Z
date_updated: 2021-02-02T13:22:19Z
file_id: '9058'
file_name: 2015_ScienceAdvances_Palacci.pdf
file_size: 2416780
relation: main_file
success: 1
file_date_updated: 2021-02-02T13:22:19Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: 'American Association for the Advancement of Science '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Artificial rheotaxis
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 1
year: '2015'
...
---
_id: '906'
abstract:
- lang: eng
text: The origin and evolution of novel biochemical functions remains one of the
key questions in molecular evolution. We study recently emerged methacrylate reductase
function that is thought to have emerged in the last century and reported in Geobacter
sulfurreducens strain AM-1. We report the sequence and study the evolution of
the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme
cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal
peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex
mechanism of biogenesis for chromoproteids of the methacrylate redox system. The
homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres
are also organized into an operon and their phylogenetic distribution suggested
that these two genes tend to be horizontally transferred together. Specifically,
the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any
of the homologs found in other Geobacter genomes. The acquisition of methacrylate
reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene
transfer event. However, the new function of the products of mrd and mcc may have
evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1.
acknowledgement: 'Funding: The work has been supported by a grant of the HHMI International
Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness
(EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish
Ministry of Economy and Competitiveness, "Centro de Excelencia Severo Ochoa 2013–2017
(Sev-2012-0208)" and (BFU2012-31329), the European Union and the European Research
Council under grant agreement 335980_EinME. The funders had no role in study design,
data collection and analysis, decision to publish, or preparation of the manuscript.Our
author Dr., Prof. Akimenko Vasilii K. (1942–2013) passed away during work on the
article. Prof. Akimenko was a leading biochemist in IBPM RAS and active researcher
until last days. A number of his work remains unfinished. We mourn premature care
of Prof. Akimenko Vasilii. We thank Heinz Himmelbauer and the CRG Genomic Unit for
the sequencing.'
author:
- first_name: Oksana
full_name: Arkhipova, Oksana V
last_name: Arkhipova
- first_name: Margarita
full_name: Meer, Margarita V
last_name: Meer
- first_name: Galina
full_name: Mikoulinskaia, Galina V
last_name: Mikoulinskaia
- first_name: Marina
full_name: Zakharova, Marina V
last_name: Zakharova
- first_name: Alexander
full_name: Galushko, Alexander S
last_name: Galushko
- first_name: Vasilii
full_name: Akimenko, Vasilii K
last_name: Akimenko
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Arkhipova O, Meer M, Mikoulinskaia G, et al. Recent origin of the methacrylate
redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer.
PLoS One. 2015;10(5). doi:10.1371/journal.pone.0125888
apa: Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko,
V., & Kondrashov, F. (2015). Recent origin of the methacrylate redox system
in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0125888
chicago: Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova,
Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of
the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal
Gene Transfer.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0125888.
ieee: O. Arkhipova et al., “Recent origin of the methacrylate redox system
in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One,
vol. 10, no. 5. Public Library of Science, 2015.
ista: Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V,
Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter
sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5).
mla: Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in
Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One,
vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888.
short: O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko,
F. Kondrashov, PLoS One 10 (2015).
date_created: 2018-12-11T11:49:08Z
date_published: 2015-05-11T00:00:00Z
date_updated: 2021-01-12T08:21:48Z
day: '11'
doi: 10.1371/journal.pone.0125888
extern: 1
intvolume: ' 10'
issue: '5'
month: '05'
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '6742'
quality_controlled: 0
status: public
title: Recent origin of the methacrylate redox system in Geobacter sulfurreducens
AM-1 through horizontal gene transfer
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
volume: 10
year: '2015'
...
---
_id: '9141'
abstract:
- lang: eng
text: The breaking of internal tides is believed to provide a large part of the
power needed to mix the abyssal ocean and sustain the meridional overturning circulation.
Both the fraction of internal tide energy that is dissipated locally and the resulting
vertical mixing distribution are crucial for the ocean state, but remain poorly
quantified. Here we present a first worldwide estimate of mixing due to internal
tides generated at small‐scale abyssal hills. Our estimate is based on linear
wave theory, a nonlinear parameterization for wave breaking and uses quasi‐global
small‐scale abyssal hill bathymetry, stratification, and tidal data. We show that
a large fraction of abyssal‐hill generated internal tide energy is locally dissipated
over mid‐ocean ridges in the Southern Hemisphere. Significant dissipation occurs
above ridge crests, and, upon rescaling by the local stratification, follows a
monotonic exponential decay with height off the bottom, with a nonuniform decay
scale. We however show that a substantial part of the dissipation occurs over
the smoother flanks of mid‐ocean ridges, and exhibits a middepth maximum due to
the interplay of wave amplitude with stratification. We link the three‐dimensional
map of dissipation to abyssal hills characteristics, ocean stratification, and
tidal forcing, and discuss its potential implementation in time‐evolving parameterizations
for global climate models. Current tidal parameterizations only account for waves
generated at large‐scale satellite‐resolved bathymetry. Our results suggest that
the presence of small‐scale, mostly unresolved abyssal hills could significantly
enhance the spatial inhomogeneity of tidal mixing, particularly above mid‐ocean
ridges in the Southern Hemisphere.
article_processing_charge: No
article_type: original
author:
- first_name: Adrien
full_name: Lefauve, Adrien
last_name: Lefauve
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Angélique
full_name: Melet, Angélique
last_name: Melet
citation:
ama: 'Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation
over abyssal hills. Journal of Geophysical Research: Oceans. 2015;120(7):4760-4777.
doi:10.1002/2014jc010598'
apa: 'Lefauve, A., Muller, C. J., & Melet, A. (2015). A three-dimensional map
of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans.
American Geophysical Union. https://doi.org/10.1002/2014jc010598'
chicago: 'Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional
Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research:
Oceans. American Geophysical Union, 2015. https://doi.org/10.1002/2014jc010598.'
ieee: 'A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal
dissipation over abyssal hills,” Journal of Geophysical Research: Oceans,
vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015.'
ista: 'Lefauve A, Muller CJ, Melet A. 2015. A three-dimensional map of tidal dissipation
over abyssal hills. Journal of Geophysical Research: Oceans. 120(7), 4760–4777.'
mla: 'Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over
Abyssal Hills.” Journal of Geophysical Research: Oceans, vol. 120, no.
7, American Geophysical Union, 2015, pp. 4760–77, doi:10.1002/2014jc010598.'
short: 'A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans
120 (2015) 4760–4777.'
date_created: 2021-02-15T14:21:49Z
date_published: 2015-06-08T00:00:00Z
date_updated: 2022-01-24T13:45:41Z
day: '08'
doi: 10.1002/2014jc010598
extern: '1'
intvolume: ' 120'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/2014JC010598
month: '06'
oa: 1
oa_version: Published Version
page: 4760-4777
publication: 'Journal of Geophysical Research: Oceans'
publication_identifier:
issn:
- 2169-9275
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
status: public
title: A three-dimensional map of tidal dissipation over abyssal hills
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 120
year: '2015'
...
---
_id: '924'
abstract:
- lang: eng
text: This paper presents a numerical study of a Capillary Pumped Loop evaporator.
A two-dimensional unsteady mathematical model of a flat evaporator is developed
to simulate heat and mass transfer in unsaturated porous wick with phase change.
The liquid-vapor phase change inside the porous wick is described by Langmuir's
law. The governing equations are solved by the Finite Element Method. The results
are presented then for a sintered nickel wick and methanol as a working fluid.
The heat flux required to the transition from the all-liquid wick to the vapor-liquid
wick is calculated. The dynamic and thermodynamic behavior of the working fluid
in the capillary structure are discussed in this paper.
acknowledgement: The work presented in this paper is supported by Alstom Transport,
site de Tarbes (Contract number is 11099).
article_processing_charge: No
author:
- first_name: Riadh
full_name: Boubaker, Riadh
last_name: Boubaker
- first_name: Vincent
full_name: Platel, Vincent
last_name: Platel
- first_name: Alexis
full_name: Bergès, Alexis
last_name: Bergès
- first_name: Mathieu
full_name: Bancelin, Mathieu
last_name: Bancelin
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. Dynamic model of heat
and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied
Thermal Engineering. 2015;76:1-8. doi:10.1016/j.applthermaleng.2014.10.009
apa: Boubaker, R., Platel, V., Bergès, A., Bancelin, M., & Hannezo, E. B. (2015).
Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary
pumped loop. Applied Thermal Engineering. Elsevier. https://doi.org/10.1016/j.applthermaleng.2014.10.009
chicago: Boubaker, Riadh, Vincent Platel, Alexis Bergès, Mathieu Bancelin, and Edouard
B Hannezo. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick
of Capillary Pumped Loop.” Applied Thermal Engineering. Elsevier, 2015.
https://doi.org/10.1016/j.applthermaleng.2014.10.009.
ieee: R. Boubaker, V. Platel, A. Bergès, M. Bancelin, and E. B. Hannezo, “Dynamic
model of heat and mass transfer in an unsaturated porous wick of capillary pumped
loop,” Applied Thermal Engineering, vol. 76. Elsevier, pp. 1–8, 2015.
ista: Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. 2015. Dynamic model
of heat and mass transfer in an unsaturated porous wick of capillary pumped loop.
Applied Thermal Engineering. 76, 1–8.
mla: Boubaker, Riadh, et al. “Dynamic Model of Heat and Mass Transfer in an Unsaturated
Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering, vol.
76, Elsevier, 2015, pp. 1–8, doi:10.1016/j.applthermaleng.2014.10.009.
short: R. Boubaker, V. Platel, A. Bergès, M. Bancelin, E.B. Hannezo, Applied Thermal
Engineering 76 (2015) 1–8.
date_created: 2018-12-11T11:49:13Z
date_published: 2015-02-05T00:00:00Z
date_updated: 2021-01-12T08:21:56Z
day: '05'
doi: 10.1016/j.applthermaleng.2014.10.009
extern: '1'
intvolume: ' 76'
language:
- iso: eng
month: '02'
oa_version: None
page: 1 - 8
publication: Applied Thermal Engineering
publication_status: published
publisher: Elsevier
publist_id: '6514'
status: public
title: Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary
pumped loop
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 76
year: '2015'
...