---
_id: '7767'
abstract:
- lang: eng
text: We present a model of soft active particles that leads to a rich array of
collective behavior found also in dense biological swarms of bacteria and other
unicellular organisms. Our model uses only local interactions, such as Vicsek-type
nearest-neighbor alignment, short-range repulsion, and a local boundary term.
Changing the relative strength of these interactions leads to migrating swarms,
rotating swarms, and jammed swarms, as well as swarms that exhibit run-and-tumble
motion, alternating between migration and either rotating or jammed states. Interestingly,
although a migrating swarm moves slower than an individual particle, the diffusion
constant can be up to three orders of magnitude larger, suggesting that collective
motion can be highly advantageous, for example, when searching for food.
article_number: '032706'
article_processing_charge: No
article_type: original
author:
- first_name: Ruben
full_name: van Drongelen, Ruben
last_name: van Drongelen
- first_name: Anshuman
full_name: Pal, Anshuman
last_name: Pal
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
citation:
ama: van Drongelen R, Pal A, Goodrich CP, Idema T. Collective dynamics of soft active
particles. Physical Review E. 2015;91(3). doi:10.1103/physreve.91.032706
apa: van Drongelen, R., Pal, A., Goodrich, C. P., & Idema, T. (2015). Collective
dynamics of soft active particles. Physical Review E. American Physical
Society. https://doi.org/10.1103/physreve.91.032706
chicago: Drongelen, Ruben van, Anshuman Pal, Carl Peter Goodrich, and Timon Idema.
“Collective Dynamics of Soft Active Particles.” Physical Review E. American
Physical Society, 2015. https://doi.org/10.1103/physreve.91.032706.
ieee: R. van Drongelen, A. Pal, C. P. Goodrich, and T. Idema, “Collective dynamics
of soft active particles,” Physical Review E, vol. 91, no. 3. American
Physical Society, 2015.
ista: van Drongelen R, Pal A, Goodrich CP, Idema T. 2015. Collective dynamics of
soft active particles. Physical Review E. 91(3), 032706.
mla: van Drongelen, Ruben, et al. “Collective Dynamics of Soft Active Particles.”
Physical Review E, vol. 91, no. 3, 032706, American Physical Society, 2015,
doi:10.1103/physreve.91.032706.
short: R. van Drongelen, A. Pal, C.P. Goodrich, T. Idema, Physical Review E 91 (2015).
date_created: 2020-04-30T11:41:38Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2021-01-12T08:15:24Z
day: '01'
doi: 10.1103/physreve.91.032706
extern: '1'
intvolume: ' 91'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Collective dynamics of soft active particles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2015'
...
---
_id: '7766'
abstract:
- lang: eng
text: We study the vibrational properties near a free surface of disordered spring
networks derived from jammed sphere packings. In bulk systems, without surfaces,
it is well understood that such systems have a plateau in the density of vibrational
modes extending down to a frequency scale ω*. This frequency is controlled by
ΔZ = 〈Z〉 − 2d, the difference between the average coordination of the spheres
and twice the spatial dimension, d, of the system, which vanishes at the jamming
transition. In the presence of a free surface we find that there is a density
of disordered vibrational modes associated with the surface that extends far below
ω*. The total number of these low-frequency surface modes is controlled by ΔZ,
and the profile of their decay into the bulk has two characteristic length scales,
which diverge as ΔZ−1/2 and ΔZ−1 as the jamming transition is approached.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel M.
full_name: Sussman, Daniel M.
last_name: Sussman
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Sussman DM, Goodrich CP, Liu AJ, Nagel SR. Disordered surface vibrations in
jammed sphere packings. Soft Matter. 2015;11(14):2745-2751. doi:10.1039/c4sm02905d
apa: Sussman, D. M., Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). Disordered
surface vibrations in jammed sphere packings. Soft Matter. Royal Society
of Chemistry. https://doi.org/10.1039/c4sm02905d
chicago: Sussman, Daniel M., Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel.
“Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter.
Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4sm02905d.
ieee: D. M. Sussman, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Disordered surface
vibrations in jammed sphere packings,” Soft Matter, vol. 11, no. 14. Royal
Society of Chemistry, pp. 2745–2751, 2015.
ista: Sussman DM, Goodrich CP, Liu AJ, Nagel SR. 2015. Disordered surface vibrations
in jammed sphere packings. Soft Matter. 11(14), 2745–2751.
mla: Sussman, Daniel M., et al. “Disordered Surface Vibrations in Jammed Sphere
Packings.” Soft Matter, vol. 11, no. 14, Royal Society of Chemistry, 2015,
pp. 2745–51, doi:10.1039/c4sm02905d.
short: D.M. Sussman, C.P. Goodrich, A.J. Liu, S.R. Nagel, Soft Matter 11 (2015)
2745–2751.
date_created: 2020-04-30T11:41:23Z
date_published: 2015-02-15T00:00:00Z
date_updated: 2021-01-12T08:15:23Z
day: '15'
doi: 10.1039/c4sm02905d
extern: '1'
intvolume: ' 11'
issue: '14'
language:
- iso: eng
month: '02'
oa_version: None
page: 2745-2751
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: Disordered surface vibrations in jammed sphere packings
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '777'
abstract:
- lang: eng
text: 'In many applications, the data is of rich structure that can be represented
by a hypergraph, where the data items are represented by vertices and the associations
among items are represented by hyperedges. Equivalently, we are given an input
bipartite graph with two types of vertices: items, and associations (which we
refer to as topics). We consider the problem of partitioning the set of items
into a given number of components such that the maximum number of topics covered
by a component is minimized. This is a clustering problem with various applications,
e.g. partitioning of a set of information objects such as documents, images, and
videos, and load balancing in the context of modern computation platforms.Inthis
paper, we focus on the streaming computation model for this problem, in which
items arrive online one at a time and each item must be assigned irrevocably to
a component at its arrival time. Motivated by scalability requirements, we focus
on the class of streaming computation algorithms with memory limited to be at
most linear in the number of components. We show that a greedy assignment strategy
is able to recover a hidden co-clustering of items under a natural set of recovery
conditions. We also report results of an extensive empirical evaluation, which
demonstrate that this greedy strategy yields superior performance when compared
with alternative approaches.'
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: Jennifer
full_name: Iglesias, Jennifer
last_name: Iglesias
- first_name: Milan
full_name: Vojnović, Milan
last_name: Vojnović
citation:
ama: 'Alistarh D-A, Iglesias J, Vojnović M. Streaming min-max hypergraph partitioning.
In: Vol 2015-January. Neural Information Processing Systems; 2015:1900-1908.'
apa: 'Alistarh, D.-A., Iglesias, J., & Vojnović, M. (2015). Streaming min-max
hypergraph partitioning (Vol. 2015–January, pp. 1900–1908). Presented at the NIPS:
Neural Information Processing Systems, Neural Information Processing Systems.'
chicago: Alistarh, Dan-Adrian, Jennifer Iglesias, and Milan Vojnović. “Streaming
Min-Max Hypergraph Partitioning,” 2015–January:1900–1908. Neural Information Processing
Systems, 2015.
ieee: 'D.-A. Alistarh, J. Iglesias, and M. Vojnović, “Streaming min-max hypergraph
partitioning,” presented at the NIPS: Neural Information Processing Systems, 2015,
vol. 2015–January, pp. 1900–1908.'
ista: 'Alistarh D-A, Iglesias J, Vojnović M. 2015. Streaming min-max hypergraph
partitioning. NIPS: Neural Information Processing Systems vol. 2015–January, 1900–1908.'
mla: Alistarh, Dan-Adrian, et al. Streaming Min-Max Hypergraph Partitioning.
Vol. 2015–January, Neural Information Processing Systems, 2015, pp. 1900–08.
short: D.-A. Alistarh, J. Iglesias, M. Vojnović, in:, Neural Information Processing
Systems, 2015, pp. 1900–1908.
conference:
name: 'NIPS: Neural Information Processing Systems'
date_created: 2018-12-11T11:48:27Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:17:09Z
day: '01'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://papers.nips.cc/paper/5897-streaming-min-max-hypergraph-partitioning
month: '01'
oa_version: None
page: 1900 - 1908
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '6879'
status: public
title: Streaming min-max hypergraph partitioning
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-January
year: '2015'
...
---
_id: '778'
abstract:
- lang: eng
text: Several Hybrid Transactional Memory (HyTM) schemes have recently been proposed
to complement the fast, but best-effort nature of Hardware Transactional Memory
(HTM) with a slow, reliable software backup. However, the costs of providing concurrency
between hardware and software transactions in HyTM are still not well understood.
In this paper, we propose a general model for HyTM implementations, which captures
the ability of hardware transactions to buffer memory accesses. The model allows
us to formally quantify and analyze the amount of overhead (instrumentation) caused
by the potential presence of software transactions.We prove that (1) it is impossible
to build a strictly serializable HyTM implementation that has both uninstrumented
reads and writes, even for very weak progress guarantees, and (2) the instrumentation
cost incurred by a hardware transaction in any progressive opaque HyTM is linear
in the size of the transaction’s data set.We further describe two implementations
which exhibit optimal instrumentation costs for two different progress conditions.
In sum, this paper proposes the first formal HyTM model and captures for the first
time the trade-off between the degree of hardware-software TM concurrency and
the amount of instrumentation overhead.
acknowledgement: P. Kuznetsov-The author is supported by the Agence Nationale de la
Recherche, ANR-14-CE35-0010-01, project DISCMAT. N. Shavit-Support is gratfeully
acknowledgedfrom the National Science Foundation under grants CCF-1217921, CCF-1201926,
and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and
the Oracle and Intel corporations.
alternative_title:
- LNCS
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: Justin
full_name: Kopinsky, Justin
last_name: Kopinsky
- first_name: Petr
full_name: Kuznetsov, Petr
last_name: Kuznetsov
- first_name: Srivatsan
full_name: Ravi, Srivatsan
last_name: Ravi
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. Inherent limitations
of hybrid transactional memory. In: Vol 9363. Springer; 2015:185-199. doi:10.1007/978-3-662-48653-5_13'
apa: 'Alistarh, D.-A., Kopinsky, J., Kuznetsov, P., Ravi, S., & Shavit, N. (2015).
Inherent limitations of hybrid transactional memory (Vol. 9363, pp. 185–199).
Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-662-48653-5_13'
chicago: Alistarh, Dan-Adrian, Justin Kopinsky, Petr Kuznetsov, Srivatsan Ravi,
and Nir Shavit. “Inherent Limitations of Hybrid Transactional Memory,” 9363:185–99.
Springer, 2015. https://doi.org/10.1007/978-3-662-48653-5_13.
ieee: 'D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, and N. Shavit, “Inherent
limitations of hybrid transactional memory,” presented at the DISC: Distributed
Computing, 2015, vol. 9363, pp. 185–199.'
ista: 'Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. 2015. Inherent limitations
of hybrid transactional memory. DISC: Distributed Computing, LNCS, vol. 9363,
185–199.'
mla: Alistarh, Dan-Adrian, et al. Inherent Limitations of Hybrid Transactional
Memory. Vol. 9363, Springer, 2015, pp. 185–99, doi:10.1007/978-3-662-48653-5_13.
short: D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, N. Shavit, in:, Springer,
2015, pp. 185–199.
conference:
name: 'DISC: Distributed Computing'
date_created: 2018-12-11T11:48:27Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:17:35Z
day: '01'
doi: 10.1007/978-3-662-48653-5_13
extern: '1'
external_id:
arxiv:
- '1405.5689'
intvolume: ' 9363'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1405.5689
month: '01'
oa: 1
oa_version: None
page: 185 - 199
publication_status: published
publisher: Springer
publist_id: '6880'
quality_controlled: '1'
status: public
title: Inherent limitations of hybrid transactional memory
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9363
year: '2015'
...
---
_id: '7779'
abstract:
- lang: eng
text: "The fact that a disordered material is not constrained in its properties
in\r\nthe same way as a crystal presents significant and yet largely untapped\r\npotential
for novel material design. However, unlike their crystalline\r\ncounterparts,
disordered solids are not well understood. One of the primary\r\nobstacles is
the lack of a theoretical framework for thinking about disorder\r\nand its relation
to mechanical properties. To this end, we study an idealized\r\nsystem of frictionless
athermal soft spheres that, when compressed, undergoes a\r\njamming phase transition
with diverging length scales and clean power-law\r\nsignatures. This critical
point is the cornerstone of a much larger \"jamming\r\nscenario\" that has the
potential to provide the essential theoretical\r\nfoundation necessary for a unified
understanding of the mechanics of disordered\r\nsolids. We begin by showing that
jammed sphere packings have a valid linear\r\nregime despite the presence of \"contact
nonlinearities.\" We then investigate\r\nthe critical nature of the transition,
focusing on diverging length scales and\r\nfinite-size effects. Next, we argue
that jamming plays the same role for\r\ndisordered solids as the perfect crystal
plays for crystalline solids. Not only\r\ncan it be considered an idealized starting
point for understanding disordered\r\nmaterials, but it can even influence systems
that have a relatively high amount\r\nof crystalline order. The behavior of solids
can thus be thought of as existing\r\non a spectrum, with the perfect crystal
and the jamming transition at opposing\r\nends. Finally, we introduce a new principle
wherein the contribution of an\r\nindividual bond to one global property is independent
of its contribution to\r\nanother. This principle allows the different global
responses of a disordered\r\nsystem to be manipulated independently and provides
a great deal of flexibility\r\nin designing materials with unique, textured and
tunable properties."
article_processing_charge: No
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
citation:
ama: 'Goodrich CP. Unearthing the anticrystal: Criticality in the linear response
of disordered solids. arXiv:151008820. 2015.'
apa: 'Goodrich, C. P. (2015). Unearthing the anticrystal: Criticality in the linear
response of disordered solids. arXiv:1510.08820.'
chicago: 'Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the
Linear Response of Disordered Solids.” ArXiv:1510.08820, 2015.'
ieee: 'C. P. Goodrich, “Unearthing the anticrystal: Criticality in the linear response
of disordered solids,” arXiv:1510.08820. 2015.'
ista: 'Goodrich CP. 2015. Unearthing the anticrystal: Criticality in the linear
response of disordered solids. arXiv:1510.08820, .'
mla: 'Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear
Response of Disordered Solids.” ArXiv:1510.08820, 2015.'
short: C.P. Goodrich, ArXiv:1510.08820 (2015).
date_created: 2020-04-30T12:16:18Z
date_published: 2015-10-29T00:00:00Z
date_updated: 2021-01-12T08:15:28Z
day: '29'
extern: '1'
external_id:
arxiv:
- '1510.08820'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1510.08820
month: '10'
oa: 1
oa_version: Preprint
page: '242'
publication: arXiv:1510.08820
publication_status: published
status: public
title: 'Unearthing the anticrystal: Criticality in the linear response of disordered
solids'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '779'
abstract:
- lang: eng
text: 'The concurrent memory reclamation problem is that of devising a way for a
deallocating thread to verify that no other concurrent threads hold references
to a memory block being deallocated. To date, in the absence of automatic garbage
collection, there is no satisfactory solution to this problem; existing tracking
methods like hazard pointers, reference counters, or epoch-based techniques like
RCU, are either prohibitively expensive or require significant programming expertise,
to the extent that implementing them efficiently can be worthy of a publication.
None of the existing techniques are automatic or even semi-automated. In this
paper, we take a new approach to concurrent memory reclamation: instead of manually
tracking access to memory locations as done in techniques like hazard pointers,
or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm,
called ThreadScan, leverages operating system signaling to automatically detect
which memory locations are being accessed by concurrent threads. Initial empirical
evidence shows that ThreadScan scales surprisingly well and requires negligible
programming effort beyond the standard use of Malloc and Free.'
acknowledgement: Support is gratefully acknowledged from the National Science Foundation
under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy
under grant ER26116/DE-SC0008923, and the Oracle corporation. In particular, we
would like to thank Dave Dice, Alex Kogan, and Mark Moir from the Oracle Scalable
Synchronization Research Group for very useful feedback on earlier drafts of this
paper.
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: Alexander
full_name: Matveev, Alexander
last_name: Matveev
- first_name: William
full_name: Leiserson, William
last_name: Leiserson
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Matveev A, Leiserson W, Shavit N. ThreadScan: Automatic and
scalable memory reclamation. In: Vol 2015-June. ACM; 2015:123-132. doi:10.1145/2755573.2755600'
apa: 'Alistarh, D.-A., Matveev, A., Leiserson, W., & Shavit, N. (2015). ThreadScan:
Automatic and scalable memory reclamation (Vol. 2015–June, pp. 123–132). Presented
at the SPAA: Symposium on Parallelism in Algorithms and Architectures, ACM. https://doi.org/10.1145/2755573.2755600'
chicago: 'Alistarh, Dan-Adrian, Alexander Matveev, William Leiserson, and Nir Shavit.
“ThreadScan: Automatic and Scalable Memory Reclamation,” 2015–June:123–32. ACM,
2015. https://doi.org/10.1145/2755573.2755600.'
ieee: 'D.-A. Alistarh, A. Matveev, W. Leiserson, and N. Shavit, “ThreadScan: Automatic
and scalable memory reclamation,” presented at the SPAA: Symposium on Parallelism
in Algorithms and Architectures, 2015, vol. 2015–June, pp. 123–132.'
ista: 'Alistarh D-A, Matveev A, Leiserson W, Shavit N. 2015. ThreadScan: Automatic
and scalable memory reclamation. SPAA: Symposium on Parallelism in Algorithms
and Architectures vol. 2015–June, 123–132.'
mla: 'Alistarh, Dan-Adrian, et al. ThreadScan: Automatic and Scalable Memory
Reclamation. Vol. 2015–June, ACM, 2015, pp. 123–32, doi:10.1145/2755573.2755600.'
short: D.-A. Alistarh, A. Matveev, W. Leiserson, N. Shavit, in:, ACM, 2015, pp.
123–132.
conference:
name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures'
date_created: 2018-12-11T11:48:27Z
date_published: 2015-06-13T00:00:00Z
date_updated: 2023-02-23T12:35:42Z
day: '13'
doi: 10.1145/2755573.2755600
extern: '1'
language:
- iso: eng
month: '06'
oa_version: None
page: 123 - 132
publication_status: published
publisher: ACM
publist_id: '6876'
related_material:
record:
- id: '6001'
relation: later_version
status: public
status: public
title: 'ThreadScan: Automatic and scalable memory reclamation'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-June
year: '2015'
...
---
_id: '780'
abstract:
- lang: eng
text: 'Population protocols are networks of finite-state agents, interacting randomly,
and updating their states using simple rules. Despite their extreme simplicity,
these systems have been shown to cooperatively perform complex computational tasks,
such as simulating register machines to compute standard arithmetic functions.
The election of a unique leader agent is a key requirement in such computational
constructions. Yet, the fastest currently known population protocol for electing
a leader only has linear convergence time, and it has recently been shown that
no population protocol using a constant number of states per node may overcome
this linear bound. In this paper, we give the first population protocol for leader
election with polylogarithmic convergence time, using polylogarithmic memory states
per node. The protocol structure is quite simple: each node has an associated
value, and is either a leader (still in contention) or a minion (following some
leader). A leader keeps incrementing its value and “defeats” other leaders in
one-to-one interactions, and will drop from contention and become a minion if
it meets a leader with higher value. Importantly, a leader also drops out if it
meets a minion with higher absolute value. While these rules are quite simple,
the proof that this algorithm achieves polylogarithmic convergence time is non-trivial.
In particular, the argument combines careful use of concentration inequalities
with anti-concentration bounds, showing that the leaders’ values become spread
apart as the execution progresses, which in turn implies that straggling leaders
get quickly eliminated. We complement our analysis with empirical results, showing
that our protocol converges extremely fast, even for large network sizes.'
acknowledgement: Support is gratefully acknowledged from the National Science Foundation
under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy
under grant ER26116/DE-SC0008923, and the Oracle and Intel corporations.”
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
citation:
ama: 'Alistarh D-A, Gelashvili R. Polylogarithmic-time leader election in population
protocols. In: Vol 9135. Springer; 2015:479-491. doi:10.1007/978-3-662-47666-6_38'
apa: 'Alistarh, D.-A., & Gelashvili, R. (2015). Polylogarithmic-time leader
election in population protocols (Vol. 9135, pp. 479–491). Presented at the ICALP:
International Colloquium on Automota, Languages and Programming, Springer. https://doi.org/10.1007/978-3-662-47666-6_38'
chicago: Alistarh, Dan-Adrian, and Rati Gelashvili. “Polylogarithmic-Time Leader
Election in Population Protocols,” 9135:479–91. Springer, 2015. https://doi.org/10.1007/978-3-662-47666-6_38.
ieee: 'D.-A. Alistarh and R. Gelashvili, “Polylogarithmic-time leader election in
population protocols,” presented at the ICALP: International Colloquium on Automota,
Languages and Programming, 2015, vol. 9135, pp. 479–491.'
ista: 'Alistarh D-A, Gelashvili R. 2015. Polylogarithmic-time leader election in
population protocols. ICALP: International Colloquium on Automota, Languages and
Programming vol. 9135, 479–491.'
mla: Alistarh, Dan-Adrian, and Rati Gelashvili. Polylogarithmic-Time Leader Election
in Population Protocols. Vol. 9135, Springer, 2015, pp. 479–91, doi:10.1007/978-3-662-47666-6_38.
short: D.-A. Alistarh, R. Gelashvili, in:, Springer, 2015, pp. 479–491.
conference:
name: 'ICALP: International Colloquium on Automota, Languages and Programming'
date_created: 2018-12-11T11:48:28Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:18:11Z
day: '01'
doi: 10.1007/978-3-662-47666-6_38
extern: '1'
external_id:
arxiv:
- '1502.05745'
intvolume: ' 9135'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1502.05745
month: '01'
oa: 1
oa_version: Preprint
page: 479 - 491
publication_status: published
publisher: Springer
publist_id: '6877'
status: public
title: Polylogarithmic-time leader election in population protocols
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9135
year: '2015'
...
---
_id: '781'
abstract:
- lang: eng
text: 'Population protocols, roughly defined as systems consisting of large numbers
of simple identical agents, interacting at random and updating their state following
simple rules, are an important research topic at the intersection of distributed
computing and biology. One of the fundamental tasks that a population protocol
may solve is majority: each node starts in one of two states; the goal is for
all nodes to reach a correct consensus on which of the two states was initially
the majority. Despite considerable research effort, known protocols for this problem
are either exact but slow (taking linear parallel time to converge), or fast but
approximate (with non-zero probability of error). In this paper, we show that
this trade-off between preciasion and speed is not inherent. We present a new
protocol called Average and Conquer (AVC) that solves majority ex-actly in expected
parallel convergence time O(log n/(sε) + log n log s), where n is the number of
nodes, εn is the initial node advantage of the majority state, and s = Ω(log n
log log n) is the number of states the protocol employs. This shows that the majority
problem can be solved exactly in time poly-logarithmic in n, provided that the
memory per node is s = Ω(1/ε + lognlog1/ε). On the negative side, we establish
a lower bound of Ω(1/ε) on the expected paraallel convergence time for the case
of four memory states per node, and a lower bound of Ω(logn) parallel time for
protocols using any number of memory states per node.per node, and a lower bound
of (log n) parallel time for protocols using any number of memory states per node.'
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: Milan
full_name: Vojnović, Milan
last_name: Vojnović
citation:
ama: 'Alistarh D-A, Gelashvili R, Vojnović M. Fast and exact majority in population
protocols. In: Vol 2015-July. ACM; 2015:47-56. doi:10.1145/2767386.2767429'
apa: 'Alistarh, D.-A., Gelashvili, R., & Vojnović, M. (2015). Fast and exact
majority in population protocols (Vol. 2015–July, pp. 47–56). Presented at the
PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767429'
chicago: Alistarh, Dan-Adrian, Rati Gelashvili, and Milan Vojnović. “Fast and Exact
Majority in Population Protocols,” 2015–July:47–56. ACM, 2015. https://doi.org/10.1145/2767386.2767429.
ieee: 'D.-A. Alistarh, R. Gelashvili, and M. Vojnović, “Fast and exact majority
in population protocols,” presented at the PODC: Principles of Distributed Computing,
2015, vol. 2015–July, pp. 47–56.'
ista: 'Alistarh D-A, Gelashvili R, Vojnović M. 2015. Fast and exact majority in
population protocols. PODC: Principles of Distributed Computing vol. 2015–July,
47–56.'
mla: Alistarh, Dan-Adrian, et al. Fast and Exact Majority in Population Protocols.
Vol. 2015–July, ACM, 2015, pp. 47–56, doi:10.1145/2767386.2767429.
short: D.-A. Alistarh, R. Gelashvili, M. Vojnović, in:, ACM, 2015, pp. 47–56.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:28Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2023-02-23T13:18:35Z
day: '21'
doi: 10.1145/2767386.2767429
extern: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 47 - 56
publication_status: published
publisher: ACM
publist_id: '6873'
status: public
title: Fast and exact majority in population protocols
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-July
year: '2015'
...
---
_id: '782'
abstract:
- lang: eng
text: 'In this work, we consider the following random process, mo- Tivated by the
analysis of lock-free concurrent algorithms under high memory contention. In each
round, a new scheduling step is allocated to one of n threads, according to a
distribution p = (p1; p2; : : : ; pn), where thread i is scheduled with probability
pi. When some thread first reaches a set threshold of executed steps, it registers
a win, completing its current operation, and resets its step count to 1. At the
same time, threads whose step count was close to the threshold also get reset
because of the win, but to 0 steps, being penalized for almost winning. We are
interested in two questions: how often does some thread complete an operation
(system latency), and how often does a specific thread complete an operation (individual
latency)? We provide asymptotically tight bounds for the system and individual
latency of this general concurrency pattern, for arbitrary scheduling distributions
p. Surprisingly, a sim- ple characterization exists: in expectation, the system
will complete a new operation every Θ(1/p 2) steps, while thread i will complete
a new operation every Θ(1/2=p i ) steps. The proof is interesting in its own right,
as it requires a careful analysis of how the higher norms of the vector p inuence
the thread step counts and latencies in this random process. Our result offers
a simple connection between the scheduling distribution and the average performance
of concurrent algorithms, which has several applications.'
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: Thomas
full_name: Sauerwald, Thomas
last_name: Sauerwald
- first_name: Milan
full_name: Vojnović, Milan
last_name: Vojnović
citation:
ama: 'Alistarh D-A, Sauerwald T, Vojnović M. Lock-Free algorithms under stochastic
schedulers. In: Vol 2015-July. ACM; 2015:251-260. doi:10.1145/2767386.2767430'
apa: 'Alistarh, D.-A., Sauerwald, T., & Vojnović, M. (2015). Lock-Free algorithms
under stochastic schedulers (Vol. 2015–July, pp. 251–260). Presented at the PODC:
Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767430'
chicago: Alistarh, Dan-Adrian, Thomas Sauerwald, and Milan Vojnović. “Lock-Free
Algorithms under Stochastic Schedulers,” 2015–July:251–60. ACM, 2015. https://doi.org/10.1145/2767386.2767430.
ieee: 'D.-A. Alistarh, T. Sauerwald, and M. Vojnović, “Lock-Free algorithms under
stochastic schedulers,” presented at the PODC: Principles of Distributed Computing,
2015, vol. 2015–July, pp. 251–260.'
ista: 'Alistarh D-A, Sauerwald T, Vojnović M. 2015. Lock-Free algorithms under stochastic
schedulers. PODC: Principles of Distributed Computing vol. 2015–July, 251–260.'
mla: Alistarh, Dan-Adrian, et al. Lock-Free Algorithms under Stochastic Schedulers.
Vol. 2015–July, ACM, 2015, pp. 251–60, doi:10.1145/2767386.2767430.
short: D.-A. Alistarh, T. Sauerwald, M. Vojnović, in:, ACM, 2015, pp. 251–260.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:28Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2023-02-23T13:18:50Z
day: '21'
doi: 10.1145/2767386.2767430
extern: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 251 - 260
publication_status: published
publisher: ACM
publist_id: '6874'
status: public
title: Lock-Free algorithms under stochastic schedulers
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-July
year: '2015'
...
---
_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.
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: 2021-01-12T08:16:33Z
day: '01'
department:
- _id: CaHe
doi: 10.1093/glycob/cwv059
external_id:
pmid:
- '26306635'
intvolume: ' 25'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
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: '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: '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'
...
---
_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: No
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: 2021-01-12T08:19:24Z
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
month: '10'
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '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.
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: 2021-01-12T08:19:33Z
day: '01'
doi: 10.1093/molbev/msu318
extern: '1'
intvolume: ' 32'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
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: '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
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: '928'
abstract:
- lang: eng
text: The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis,
thus a robust spatial control of cytoskeletal positioning is essential. In this
report, we demonstrate that actomyosin contractility and planar cell polarity
(PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition
actomyosin rings, which play an essential role for cell elongation. Intriguingly,
rings always form at the cells′ anterior edge before migrating towards the center
as contractility increases, reflecting a novel dynamical property of the cortex.
Our drug and genetic manipulations uncover a tug-of-war between contractility,
which localizes cortical flows toward the equator and PCP, which tries to reposition
them. We develop a simple model of the physical forces underlying this tug-of-war,
which quantitatively reproduces our results. We thus propose a quantitative framework
for dissecting the relative contribution of contractility and PCP to the self-assembly
and repositioning of cytoskeletal structures, which should be applicable to other
morphogenetic events.
article_number: e09206
author:
- first_name: Ivonne
full_name: Sehring, Ivonne
last_name: Sehring
- first_name: Pierre
full_name: Recho, Pierre
last_name: Recho
- first_name: Elsa
full_name: Denker, Elsa
last_name: Denker
- first_name: Matthew
full_name: Kourakis, Matthew
last_name: Kourakis
- first_name: Birthe
full_name: Mathiesen, Birthe
last_name: Mathiesen
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Bo
full_name: Dong, Bo
last_name: Dong
- first_name: Di
full_name: Jiang, Di
last_name: Jiang
citation:
ama: Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin
rings by contractility and planar cell polarity. eLife. 2015;4. doi:10.7554/eLife.09206
apa: Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E.
B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility
and planar cell polarity. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.09206
chicago: Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen,
Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin
Rings by Contractility and Planar Cell Polarity.” ELife. eLife Sciences
Publications, 2015. https://doi.org/10.7554/eLife.09206.
ieee: I. Sehring et al., “Assembly and positioning of actomyosin rings by
contractility and planar cell polarity,” eLife, vol. 4. eLife Sciences
Publications, 2015.
ista: Sehring I, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo EB, Dong B,
Jiang D. 2015. Assembly and positioning of actomyosin rings by contractility and
planar cell polarity. eLife. 4, e09206.
mla: Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility
and Planar Cell Polarity.” ELife, vol. 4, e09206, eLife Sciences Publications,
2015, doi:10.7554/eLife.09206.
short: I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo,
B. Dong, D. Jiang, ELife 4 (2015).
date_created: 2018-12-11T11:49:15Z
date_published: 2015-10-21T00:00:00Z
date_updated: 2021-01-12T08:21:58Z
day: '21'
ddc:
- '539'
- '570'
doi: 10.7554/eLife.09206
extern: '1'
file:
- access_level: open_access
checksum: 1e4024b3161adcae4a53a0b3dc8a946e
content_type: application/pdf
creator: dernst
date_created: 2018-12-20T15:50:56Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5769'
file_name: 2015_eLife_Sehring.pdf
file_size: 7202224
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6512'
quality_controlled: '1'
status: public
title: Assembly and positioning of actomyosin rings by contractility and planar cell
polarity
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: 4
year: '2015'
...
---
_id: '9575'
abstract:
- lang: eng
text: We give several results showing that different discrete structures typically
gain certain spanning substructures (in particular, Hamilton cycles) after a modest
random perturbation. First, we prove that adding linearly many random edges to
a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence
of a perfect matching or a loose Hamilton cycle. The proof involves an interesting
application of Szemerédi's Regularity Lemma, which might be independently useful.
We next prove that digraphs with certain strong expansion properties are pancyclic,
and use this to show that adding a linear number of random edges typically makes
a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent)
number of random edges in a tournament typically ensures the existence of multiple
edge-disjoint Hamilton cycles. All our results are tight.
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Krivelevich, Michael
last_name: Krivelevich
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed
digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 2015;49:181-187.
doi:10.1016/j.endm.2015.06.027
apa: Krivelevich, M., Kwan, M. A., & Sudakov, B. (2015). Cycles and matchings
in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete
Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2015.06.027
chicago: Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and
Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes
in Discrete Mathematics. Elsevier, 2015. https://doi.org/10.1016/j.endm.2015.06.027.
ieee: M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly
perturbed digraphs and hypergraphs,” Electronic Notes in Discrete Mathematics,
vol. 49. Elsevier, pp. 181–187, 2015.
ista: Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly
perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics.
49, 181–187.
mla: Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs
and Hypergraphs.” Electronic Notes in Discrete Mathematics, vol. 49, Elsevier,
2015, pp. 181–87, doi:10.1016/j.endm.2015.06.027.
short: M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics
49 (2015) 181–187.
date_created: 2021-06-21T06:40:34Z
date_published: 2015-11-01T00:00:00Z
date_updated: 2023-02-23T14:01:28Z
day: '01'
doi: 10.1016/j.endm.2015.06.027
extern: '1'
external_id:
arxiv:
- '1501.04816'
intvolume: ' 49'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1501.04816
month: '11'
oa: 1
oa_version: Preprint
page: 181-187
publication: Electronic Notes in Discrete Mathematics
publication_identifier:
issn:
- 1571-0653
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cycles and matchings in randomly perturbed digraphs and hypergraphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 49
year: '2015'
...
---
_id: '9673'
abstract:
- lang: eng
text: Current strategies of computational crystal plasticity that focus on individual
atoms or dislocations are impractical for real-scale, large-strain problems even
with today’s computing power. Dislocation-density based approaches are a way forward
but a critical issue to address is a realistic description of the interactions
between dislocations. In this paper, a new scheme for computational dynamics of
dislocation-density functions is proposed, which takes full consideration of the
mutual elastic interactions between dislocations based on the Hirth–Lothe formulation.
Other features considered include (i) the continuity nature of the movements of
dislocation densities, (ii) forest hardening, (iii) generation according to high
spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation
by the finite-volume method, which is well suited for flow problems with high
gradients, is discussed. Numerical examples performed for a single-crystal aluminum
model show typical strength anisotropy behavior comparable to experimental observations.
Furthermore, a detailed case study on small-scale crystal plasticity successfully
captures a number of key experimental features, including power-law relation between
strength and size, low dislocation storage and jerky deformation.
article_processing_charge: No
article_type: original
author:
- first_name: H.S.
full_name: Leung, H.S.
last_name: Leung
- first_name: P.S.S.
full_name: Leung, P.S.S.
last_name: Leung
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: A.H.W.
full_name: Ngan, A.H.W.
last_name: Ngan
citation:
ama: Leung HS, Leung PSS, Cheng B, Ngan AHW. A new dislocation-density-function
dynamics scheme for computational crystal plasticity by explicit consideration
of dislocation elastic interactions. International Journal of Plasticity.
2015;67:1-25. doi:10.1016/j.ijplas.2014.09.009
apa: Leung, H. S., Leung, P. S. S., Cheng, B., & Ngan, A. H. W. (2015). A new
dislocation-density-function dynamics scheme for computational crystal plasticity
by explicit consideration of dislocation elastic interactions. International
Journal of Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2014.09.009
chicago: Leung, H.S., P.S.S. Leung, Bingqing Cheng, and A.H.W. Ngan. “A New Dislocation-Density-Function
Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration
of Dislocation Elastic Interactions.” International Journal of Plasticity.
Elsevier, 2015. https://doi.org/10.1016/j.ijplas.2014.09.009.
ieee: H. S. Leung, P. S. S. Leung, B. Cheng, and A. H. W. Ngan, “A new dislocation-density-function
dynamics scheme for computational crystal plasticity by explicit consideration
of dislocation elastic interactions,” International Journal of Plasticity,
vol. 67. Elsevier, pp. 1–25, 2015.
ista: Leung HS, Leung PSS, Cheng B, Ngan AHW. 2015. A new dislocation-density-function
dynamics scheme for computational crystal plasticity by explicit consideration
of dislocation elastic interactions. International Journal of Plasticity. 67,
1–25.
mla: Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for
Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic
Interactions.” International Journal of Plasticity, vol. 67, Elsevier,
2015, pp. 1–25, doi:10.1016/j.ijplas.2014.09.009.
short: H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of
Plasticity 67 (2015) 1–25.
date_created: 2021-07-15T14:09:32Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-02-23T14:04:28Z
day: '01'
doi: 10.1016/j.ijplas.2014.09.009
extern: '1'
intvolume: ' 67'
language:
- iso: eng
month: '04'
oa_version: None
page: 1-25
publication: International Journal of Plasticity
publication_identifier:
issn:
- 0749-6419
publication_status: published
publisher: Elsevier
scopus_import: '1'
status: public
title: A new dislocation-density-function dynamics scheme for computational crystal
plasticity by explicit consideration of dislocation elastic interactions
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 67
year: '2015'
...
---
_id: '9688'
abstract:
- lang: eng
text: The properties of the interface between solid and melt are key to solidification
and melting, as the interfacial free energy introduces a kinetic barrier to phase
transitions. This makes solidification happen below the melting temperature, in
out-of-equilibrium conditions at which the interfacial free energy is ill defined.
Here we draw a connection between the atomistic description of a diffuse solid-liquid
interface and its thermodynamic characterization. This framework resolves the
ambiguities in defining the solid-liquid interfacial free energy above and below
the melting temperature. In addition, we introduce a simulation protocol that
allows solid-liquid interfaces to be reversibly created and destroyed at conditions
relevant for experiments. We directly evaluate the value of the interfacial free
energy away from the melting point for a simple but realistic atomic potential,
and find a more complex temperature dependence than the constant positive slope
that has been generally assumed based on phenomenological considerations and that
has been used to interpret experiments. This methodology could be easily extended
to the study of other phase transitions, from condensation to precipitation. Our
analysis can help reconcile the textbook picture of classical nucleation theory
with the growing body of atomistic studies and mesoscale models of solidification.
article_number: '180102'
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Gareth A.
full_name: Tribello, Gareth A.
last_name: Tribello
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Tribello GA, Ceriotti M. Solid-liquid interfacial free energy out
of equilibrium. Physical Review B - Condensed Matter and Materials Physics.
2015;92(18). doi:10.1103/physrevb.92.180102
apa: Cheng, B., Tribello, G. A., & Ceriotti, M. (2015). Solid-liquid interfacial
free energy out of equilibrium. Physical Review B - Condensed Matter and Materials
Physics. American Physical Society. https://doi.org/10.1103/physrevb.92.180102
chicago: Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “Solid-Liquid
Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed
Matter and Materials Physics. American Physical Society, 2015. https://doi.org/10.1103/physrevb.92.180102.
ieee: B. Cheng, G. A. Tribello, and M. Ceriotti, “Solid-liquid interfacial free
energy out of equilibrium,” Physical Review B - Condensed Matter and Materials
Physics, vol. 92, no. 18. American Physical Society, 2015.
ista: Cheng B, Tribello GA, Ceriotti M. 2015. Solid-liquid interfacial free energy
out of equilibrium. Physical Review B - Condensed Matter and Materials Physics.
92(18), 180102.
mla: Cheng, Bingqing, et al. “Solid-Liquid Interfacial Free Energy out of Equilibrium.”
Physical Review B - Condensed Matter and Materials Physics, vol. 92, no.
18, 180102, American Physical Society, 2015, doi:10.1103/physrevb.92.180102.
short: B. Cheng, G.A. Tribello, M. Ceriotti, Physical Review B - Condensed Matter
and Materials Physics 92 (2015).
date_created: 2021-07-19T10:07:22Z
date_published: 2015-11-01T00:00:00Z
date_updated: 2021-08-09T12:38:49Z
day: '01'
doi: 10.1103/physrevb.92.180102
extern: '1'
external_id:
arxiv:
- '1511.08668'
intvolume: ' 92'
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.08668
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review B - Condensed Matter and Materials Physics
publication_identifier:
eissn:
- 1550-235X
issn:
- 1098-0121
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Solid-liquid interfacial free energy out of equilibrium
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 92
year: '2015'
...
---
_id: '9711'
article_processing_charge: No
author:
- first_name: Guillaume
full_name: Chevereau, Guillaume
id: 424D78A0-F248-11E8-B48F-1D18A9856A87
last_name: Chevereau
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Tugce
full_name: Batur, Tugce
last_name: Batur
- first_name: Aysegul
full_name: Guvenek, Aysegul
last_name: Guvenek
- first_name: Dilay Hazal
full_name: Ayhan, Dilay Hazal
last_name: Ayhan
- first_name: Erdal
full_name: Toprak, Erdal
last_name: Toprak
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Chevereau G, Lukacisinova M, Batur T, et al. Excel file containing the raw
data for all figures. 2015. doi:10.1371/journal.pbio.1002299.s001
apa: Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak,
E., & Bollenbach, M. T. (2015). Excel file containing the raw data for all
figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299.s001
chicago: Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek,
Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Excel File Containing
the Raw Data for All Figures.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s001.
ieee: G. Chevereau et al., “Excel file containing the raw data for all figures.”
Public Library of Science, 2015.
ista: Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach
MT. 2015. Excel file containing the raw data for all figures, Public Library of
Science, 10.1371/journal.pbio.1002299.s001.
mla: Chevereau, Guillaume, et al. Excel File Containing the Raw Data for All
Figures. Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.s001.
short: G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak,
M.T. Bollenbach, (2015).
date_created: 2021-07-23T11:53:50Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2023-02-23T10:07:02Z
day: '18'
department:
- _id: ToBo
doi: 10.1371/journal.pbio.1002299.s001
month: '11'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1619'
relation: used_in_publication
status: public
status: public
title: Excel file containing the raw data for all figures
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '1855'
abstract:
- lang: eng
text: 'Summary: Declining populations of bee pollinators are a cause of concern,
with major repercussions for biodiversity loss and food security. RNA viruses
associated with honeybees represent a potential threat to other insect pollinators,
but the extent of this threat is poorly understood. This study aims to attain
a detailed understanding of the current and ongoing risk of emerging infectious
disease (EID) transmission between managed and wild pollinator species across
a wide range of RNA viruses. Within a structured large-scale national survey across
26 independent sites, we quantify the prevalence and pathogen loads of multiple
RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee
(Bombus spp.) populations. We then construct models that compare virus prevalence
between wild and managed pollinators. Multiple RNA viruses associated with honeybees
are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees
is a significant predictor of virus prevalence in bumblebees, but we remain cautious
in speculating over the principle direction of pathogen transmission. We demonstrate
species-specific differences in prevalence, indicating significant variation in
disease susceptibility or tolerance. Pathogen loads within individual bumblebees
may be high and in the case of at least one RNA virus, prevalence is higher in
wild bumblebees than in managed honeybee populations. Our findings indicate widespread
transmission of RNA viruses between managed and wild bee pollinators, pointing
to an interconnected network of potential disease pressures within and among pollinator
species. In the context of the biodiversity crisis, our study emphasizes the importance
of targeting a wide range of pathogens and defining host associations when considering
potential drivers of population decline.'
acknowledgement: We thank J.R. de Miranda, L. De Smet and D. de Graaf for supplying
qRT-PCR and MLPA positive controls, respectively, in the form of plasmids. This
work was supported by the Insect Pollinators Initiative (IPI grants BB/1000100/1
and BB/I000151/1). The IPI is funded jointly by the Biotechnology and Biological
Sciences Research Council, the Department for Environment, Food and Rural Affairs,
the Natural Environment Research Council, The Scottish Government and The Wellcome
Trust, under the Living with Environmental Change Partnership.
article_processing_charge: No
article_type: original
author:
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Jesicca
full_name: Caspar, Jesicca
last_name: Caspar
- first_name: Panagiotis
full_name: Theodorou, Panagiotis
last_name: Theodorou
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
citation:
ama: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. A sting in the
spit: Widespread cross-infection of multiple RNA viruses across wild and managed
bees. Journal of Animal Ecology. 2015;84(3):615-624. doi:10.1111/1365-2656.12345'
apa: 'Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton,
R. (2015). A sting in the spit: Widespread cross-infection of multiple RNA viruses
across wild and managed bees. Journal of Animal Ecology. Wiley. https://doi.org/10.1111/1365-2656.12345'
chicago: 'Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark
Brown, and Robert Paxton. “A Sting in the Spit: Widespread Cross-Infection of
Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology.
Wiley, 2015. https://doi.org/10.1111/1365-2656.12345.'
ieee: 'D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “A
sting in the spit: Widespread cross-infection of multiple RNA viruses across wild
and managed bees,” Journal of Animal Ecology, vol. 84, no. 3. Wiley, pp.
615–624, 2015.'
ista: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2015. A sting
in the spit: Widespread cross-infection of multiple RNA viruses across wild and
managed bees. Journal of Animal Ecology. 84(3), 615–624.'
mla: 'Mcmahon, Dino, et al. “A Sting in the Spit: Widespread Cross-Infection of
Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology,
vol. 84, no. 3, Wiley, 2015, pp. 615–24, doi:10.1111/1365-2656.12345.'
short: D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, Journal
of Animal Ecology 84 (2015) 615–624.
date_created: 2018-12-11T11:54:23Z
date_published: 2015-03-03T00:00:00Z
date_updated: 2023-02-23T14:06:09Z
day: '03'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1111/1365-2656.12345
external_id:
pmid:
- '25646973'
file:
- access_level: open_access
checksum: 542a0b9b07e78050a81b35f26f0b82da
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:29Z
date_updated: 2020-07-14T12:45:19Z
file_id: '5350'
file_name: IST-2016-460-v1+1_McMahon_et_al-2015-Journal_of_Animal_Ecology.pdf
file_size: 1823045
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 84'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 615 - 624
pmid: 1
publication: Journal of Animal Ecology
publication_status: published
publisher: Wiley
publist_id: '5245'
pubrep_id: '460'
quality_controlled: '1'
related_material:
record:
- id: '9720'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'A sting in the spit: Widespread cross-infection of multiple RNA viruses across
wild and managed bees'
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: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 84
year: '2015'
...
---
_id: '1830'
abstract:
- lang: eng
text: To prevent epidemics, insect societies have evolved collective disease defences
that are highly effective at curing exposed individuals and limiting disease transmission
to healthy group members. Grooming is an important sanitary behaviour—either performed
towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious
agents from the body surface of exposed individuals, but at the risk of disease
contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal
pathogen Metarhizium as a model system to study how pathogen presence affects
self-grooming and allogrooming between exposed and healthy individuals. We develop
an epidemiological SIS model to explore how experimentally observed grooming patterns
affect disease spread within the colony, thereby providing a direct link between
the expression and direction of sanitary behaviours, and their effects on colony-level
epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously
decreasing allogrooming. This behavioural modulation seems universally adaptive
and is predicted to contain disease spread in a great variety of host–pathogen
systems. In contrast, allogrooming directed towards pathogen-exposed individuals
might both increase and decrease disease risk. Our model reveals that the effect
of allogrooming depends on the balance between pathogen infectiousness and efficiency
of social host defences, which are likely to vary across host–pathogen systems.
acknowledgement: We thank Meghan L. Vyleta for the genetical fungal strain characterization
and Eva Sixt for ant drawings, Matthias Konrad for discussion and Christopher D.
Pull, Barbara Casillas-Peréz, Sebastian Novak, as well as three anonymous reviewers
and the theme issue editors Peter Kappeler and Charlie Nunn for valuable comments
on the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Fabian
full_name: Theis, Fabian
last_name: Theis
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Carsten
full_name: Marr, Carsten
last_name: Marr
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Theis F, Ugelvig LV, Marr C, Cremer S. Opposing effects of allogrooming on
disease transmission in ant societies. Philosophical Transactions of the Royal
Society of London Series B, Biological Sciences. 2015;370(1669). doi:10.1098/rstb.2014.0108
apa: Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Opposing effects
of allogrooming on disease transmission in ant societies. Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences. Royal Society,
The. https://doi.org/10.1098/rstb.2014.0108
chicago: Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Opposing
Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society, The, 2015. https://doi.org/10.1098/rstb.2014.0108.
ieee: F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Opposing effects of allogrooming
on disease transmission in ant societies,” Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669.
Royal Society, The, 2015.
ista: Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Opposing effects of allogrooming
on disease transmission in ant societies. Philosophical Transactions of the Royal
Society of London. Series B, Biological Sciences. 370(1669).
mla: Theis, Fabian, et al. “Opposing Effects of Allogrooming on Disease Transmission
in Ant Societies.” Philosophical Transactions of the Royal Society of London.
Series B, Biological Sciences, vol. 370, no. 1669, Royal Society, The, 2015,
doi:10.1098/rstb.2014.0108.
short: F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, Philosophical Transactions of
the Royal Society of London. Series B, Biological Sciences 370 (2015).
date_created: 2018-12-11T11:54:15Z
date_published: 2015-05-26T00:00:00Z
date_updated: 2023-02-23T14:06:12Z
day: '26'
department:
- _id: SyCr
doi: 10.1098/rstb.2014.0108
ec_funded: 1
external_id:
pmid:
- '25870394'
intvolume: ' 370'
issue: '1669'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410374/
month: '05'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
- _id: 25DDF0F0-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '302004'
name: 'Pathogen Detectors Collective disease defence and pathogen detection abilities
in ant societies: a chemo-neuro-immunological approach'
- _id: 25E0E184-B435-11E9-9278-68D0E5697425
name: Antnet
- _id: 25E24DB2-B435-11E9-9278-68D0E5697425
name: Fellowship of Wissenschaftskolleg zu Berlin
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: Royal Society, The
publist_id: '5273'
quality_controlled: '1'
related_material:
record:
- id: '9721'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Opposing effects of allogrooming on disease transmission in ant societies
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 370
year: '2015'
...
---
_id: '9721'
abstract:
- lang: eng
text: To prevent epidemics, insect societies have evolved collective disease defences
that are highly effective at curing exposed individuals and limiting disease transmission
to healthy group members. Grooming is an important sanitary behaviour—either performed
towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious
agents from the body surface of exposed individuals, but at the risk of disease
contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal
pathogen Metarhizium as a model system to study how pathogen presence affects
self-grooming and allogrooming between exposed and healthy individuals. We develop
an epidemiological SIS model to explore how experimentally observed grooming patterns
affect disease spread within the colony, thereby providing a direct link between
the expression and direction of sanitary behaviours, and their effects on colony-level
epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously
decreasing allogrooming. This behavioural modulation seems universally adaptive
and is predicted to contain disease spread in a great variety of host–pathogen
systems. In contrast, allogrooming directed towards pathogen-exposed individuals
might both increase and decrease disease risk. Our model reveals that the effect
of allogrooming depends on the balance between pathogen infectiousness and efficiency
of social host defences, which are likely to vary across host–pathogen systems.
article_processing_charge: No
author:
- first_name: Fabian
full_name: Theis, Fabian
last_name: Theis
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Carsten
full_name: Marr, Carsten
last_name: Marr
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Theis F, Ugelvig LV, Marr C, Cremer S. Data from: Opposing effects of allogrooming
on disease transmission in ant societies. 2015. doi:10.5061/dryad.dj2bf'
apa: 'Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Data from: Opposing
effects of allogrooming on disease transmission in ant societies. Dryad. https://doi.org/10.5061/dryad.dj2bf'
chicago: 'Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Data
from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.”
Dryad, 2015. https://doi.org/10.5061/dryad.dj2bf.'
ieee: 'F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Data from: Opposing effects
of allogrooming on disease transmission in ant societies.” Dryad, 2015.'
ista: 'Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Data from: Opposing effects
of allogrooming on disease transmission in ant societies, Dryad, 10.5061/dryad.dj2bf.'
mla: 'Theis, Fabian, et al. Data from: Opposing Effects of Allogrooming on Disease
Transmission in Ant Societies. Dryad, 2015, doi:10.5061/dryad.dj2bf.'
short: F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, (2015).
date_created: 2021-07-26T09:38:36Z
date_published: 2015-12-29T00:00:00Z
date_updated: 2023-02-23T10:16:22Z
day: '29'
department:
- _id: SyCr
doi: 10.5061/dryad.dj2bf
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.dj2bf
month: '12'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1830'
relation: used_in_publication
status: public
status: public
title: 'Data from: Opposing effects of allogrooming on disease transmission in ant
societies'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9718'
article_processing_charge: No
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Avraham E.
full_name: Mayo, Avraham E.
last_name: Mayo
- first_name: Tsvi
full_name: Tlusty, Tsvi
last_name: Tlusty
- first_name: Uri
full_name: Alon, Uri
last_name: Alon
citation:
ama: Friedlander T, Mayo AE, Tlusty T, Alon U. Supporting information text. 2015.
doi:10.1371/journal.pcbi.1004055.s001
apa: Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Supporting
information text. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s001
chicago: Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Supporting
Information Text.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s001.
ieee: T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information
text.” Public Library of Science, 2015.
ista: Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text,
Public Library of Science, 10.1371/journal.pcbi.1004055.s001.
mla: Friedlander, Tamar, et al. Supporting Information Text. Public Library
of Science, 2015, doi:10.1371/journal.pcbi.1004055.s001.
short: T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).
date_created: 2021-07-26T08:35:23Z
date_published: 2015-03-23T00:00:00Z
date_updated: 2023-02-23T10:16:13Z
day: '23'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1004055.s001
month: '03'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1827'
relation: used_in_publication
status: public
status: public
title: Supporting information text
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '1793'
abstract:
- lang: eng
text: We present a software platform for reconstructing and analyzing the growth
of a plant root system from a time-series of 3D voxelized shapes. It aligns the
shapes with each other, constructs a geometric graph representation together with
the function that records the time of growth, and organizes the branches into
a hierarchy that reflects the order of creation. The software includes the automatic
computation of structural and dynamic traits for each root in the system enabling
the quantification of growth on fine-scale. These are important advances in plant
phenotyping with applications to the study of genetic and environmental influences
on growth.
article_number: e0127657
author:
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
- first_name: Christopher
full_name: Topp, Christopher
last_name: Topp
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Symonova O, Topp C, Edelsbrunner H. DynamicRoots: A software platform for
the reconstruction and analysis of growing plant roots. PLoS One. 2015;10(6).
doi:10.1371/journal.pone.0127657'
apa: 'Symonova, O., Topp, C., & Edelsbrunner, H. (2015). DynamicRoots: A software
platform for the reconstruction and analysis of growing plant roots. PLoS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0127657'
chicago: 'Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “DynamicRoots:
A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.”
PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.'
ieee: 'O. Symonova, C. Topp, and H. Edelsbrunner, “DynamicRoots: A software platform
for the reconstruction and analysis of growing plant roots,” PLoS One,
vol. 10, no. 6. Public Library of Science, 2015.'
ista: 'Symonova O, Topp C, Edelsbrunner H. 2015. DynamicRoots: A software platform
for the reconstruction and analysis of growing plant roots. PLoS One. 10(6), e0127657.'
mla: 'Symonova, Olga, et al. “DynamicRoots: A Software Platform for the Reconstruction
and Analysis of Growing Plant Roots.” PLoS One, vol. 10, no. 6, e0127657,
Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.'
short: O. Symonova, C. Topp, H. Edelsbrunner, PLoS One 10 (2015).
date_created: 2018-12-11T11:54:02Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-02-23T14:06:33Z
day: '01'
ddc:
- '000'
department:
- _id: MaJö
- _id: HeEd
doi: 10.1371/journal.pone.0127657
file:
- access_level: open_access
checksum: d20f26461ca575276ad3ed9ce4bfc787
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:30Z
date_updated: 2020-07-14T12:45:16Z
file_id: '5150'
file_name: IST-2016-454-v1+1_journal.pone.0127657.pdf
file_size: 1850825
relation: main_file
file_date_updated: 2020-07-14T12:45:16Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5318'
pubrep_id: '454'
quality_controlled: '1'
related_material:
record:
- id: '9737'
relation: research_data
status: public
scopus_import: 1
status: public
title: 'DynamicRoots: A software platform for the reconstruction and analysis of growing
plant roots'
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: 10
year: '2015'
...
---
_id: '9737'
article_processing_charge: No
author:
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
- first_name: Christopher
full_name: Topp, Christopher
last_name: Topp
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Symonova O, Topp C, Edelsbrunner H. Root traits computed by DynamicRoots for
the maize root shown in fig 2. 2015. doi:10.1371/journal.pone.0127657.s001
apa: Symonova, O., Topp, C., & Edelsbrunner, H. (2015). Root traits computed
by DynamicRoots for the maize root shown in fig 2. Public Library of Science.
https://doi.org/10.1371/journal.pone.0127657.s001
chicago: Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “Root Traits
Computed by DynamicRoots for the Maize Root Shown in Fig 2.” Public Library of
Science, 2015. https://doi.org/10.1371/journal.pone.0127657.s001.
ieee: O. Symonova, C. Topp, and H. Edelsbrunner, “Root traits computed by DynamicRoots
for the maize root shown in fig 2.” Public Library of Science, 2015.
ista: Symonova O, Topp C, Edelsbrunner H. 2015. Root traits computed by DynamicRoots
for the maize root shown in fig 2, Public Library of Science, 10.1371/journal.pone.0127657.s001.
mla: Symonova, Olga, et al. Root Traits Computed by DynamicRoots for the Maize
Root Shown in Fig 2. Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.s001.
short: O. Symonova, C. Topp, H. Edelsbrunner, (2015).
date_created: 2021-07-28T06:20:13Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-02-23T10:14:42Z
day: '01'
department:
- _id: MaJö
- _id: HeEd
doi: 10.1371/journal.pone.0127657.s001
month: '06'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1793'
relation: used_in_publication
status: public
status: public
title: Root traits computed by DynamicRoots for the maize root shown in fig 2
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '1827'
abstract:
- lang: eng
text: Bow-tie or hourglass structure is a common architectural feature found in
many biological systems. A bow-tie in a multi-layered structure occurs when intermediate
layers have much fewer components than the input and output layers. Examples include
metabolism where a handful of building blocks mediate between multiple input nutrients
and multiple output biomass components, and signaling networks where information
from numerous receptor types passes through a small set of signaling pathways
to regulate multiple output genes. Little is known, however, about how bow-tie
architectures evolve. Here, we address the evolution of bow-tie architectures
using simulations of multi-layered systems evolving to fulfill a given input-output
goal. We find that bow-ties spontaneously evolve when the information in the evolutionary
goal can be compressed. Mathematically speaking, bow-ties evolve when the rank
of the input-output matrix describing the evolutionary goal is deficient. The
maximal compression possible (the rank of the goal) determines the size of the
narrowest part of the network—that is the bow-tie. A further requirement is that
a process is active to reduce the number of links in the network, such as product-rule
mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations.
This offers a mechanism to understand a common architectural principle of biological
systems, and a way to quantitate the effective rank of the goals under which they
evolved.
article_processing_charge: No
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Avraham
full_name: Mayo, Avraham
last_name: Mayo
- first_name: Tsvi
full_name: Tlusty, Tsvi
last_name: Tlusty
- first_name: Uri
full_name: Alon, Uri
last_name: Alon
citation:
ama: Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures
in biology. PLoS Computational Biology. 2015;11(3). doi:10.1371/journal.pcbi.1004055
apa: Friedlander, T., Mayo, A., Tlusty, T., & Alon, U. (2015). Evolution of
bow-tie architectures in biology. PLoS Computational Biology. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1004055
chicago: Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution
of Bow-Tie Architectures in Biology.” PLoS Computational Biology. Public
Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.
ieee: T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures
in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library
of Science, 2015.
ista: Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures
in biology. PLoS Computational Biology. 11(3).
mla: Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.”
PLoS Computational Biology, vol. 11, no. 3, Public Library of Science,
2015, doi:10.1371/journal.pcbi.1004055.
short: T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11
(2015).
date_created: 2018-12-11T11:54:14Z
date_published: 2015-03-23T00:00:00Z
date_updated: 2023-02-23T14:07:51Z
day: '23'
ddc:
- '576'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1004055
ec_funded: 1
file:
- access_level: open_access
checksum: b8aa66f450ff8de393014b87ec7d2efb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:39Z
date_updated: 2020-07-14T12:45:17Z
file_id: '5161'
file_name: IST-2016-452-v1+1_journal.pcbi.1004055.pdf
file_size: 1811647
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5278'
pubrep_id: '452'
quality_controlled: '1'
related_material:
record:
- id: '9718'
relation: research_data
status: public
- id: '9773'
relation: research_data
status: public
scopus_import: 1
status: public
title: Evolution of bow-tie architectures in biology
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '1809'
abstract:
- lang: eng
text: 'Background: Indirect genetic effects (IGEs) occur when genes expressed in
one individual alter the expression of traits in social partners. Previous studies
focused on the evolutionary consequences and evolutionary dynamics of IGEs, using
equilibrium solutions to predict phenotypes in subsequent generations. However,
whether or not such steady states may be reached may depend on the dynamics of
interactions themselves. Results: In our study, we focus on the dynamics of social
interactions and indirect genetic effects and investigate how they modify phenotypes
over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics;
rather we consider within-individual phenotypic changes, also referred to as phenotypic
plasticity. We analyse iterative interactions, when individuals interact in a
series of discontinuous events, and investigate the stability of steady state
solutions and the dependence on model parameters, such as population size, strength,
and the nature of interactions. We show that for interactions where a feedback
loop occurs, the possible parameter space of interaction strength is fairly limited,
affecting the evolutionary consequences of IGEs. We discuss the implications of
our results for current IGE model predictions and their limitations.'
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of
social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects
and the dynamics of social interactions. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0126907
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic
Effects and the Dynamics of Social Interactions.” PLoS One. Public Library
of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.
ieee: B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics
of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science,
2015.
ista: Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics
of social interactions. PLoS One. 10(5).
mla: Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social
Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015,
doi:10.1371/journal.pone.0126907.
short: B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).
date_created: 2018-12-11T11:54:07Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T14:07:48Z
day: '18'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0126907
file:
- access_level: open_access
checksum: d3a4a58ef4bd3b3e2f32b7fd7af4a743
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:07Z
date_updated: 2020-07-14T12:45:17Z
file_id: '4730'
file_name: IST-2016-453-v1+1_journal.pone.0126907.pdf
file_size: 2748982
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5299'
pubrep_id: '453'
quality_controlled: '1'
related_material:
record:
- id: '9715'
relation: research_data
status: public
- id: '9772'
relation: research_data
status: public
scopus_import: 1
status: public
title: Indirect genetic effects and the dynamics of social interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2015'
...
---
_id: '9772'
article_processing_charge: No
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Novak S, Hager R. Description of the agent based simulations.
2015. doi:10.1371/journal.pone.0126907.s003
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Description of the agent
based simulations. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s003
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of
the Agent Based Simulations.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s003.
ieee: B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.”
Public Library of Science, 2015.
ista: Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations,
Public Library of Science, 10.1371/journal.pone.0126907.s003.
mla: Trubenova, Barbora, et al. Description of the Agent Based Simulations.
Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003.
short: B. Trubenova, S. Novak, R. Hager, (2015).
date_created: 2021-08-05T12:55:20Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T10:15:25Z
day: '18'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0126907.s003
month: '05'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1809'
relation: used_in_publication
status: public
status: public
title: Description of the agent based simulations
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9773'
article_processing_charge: No
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Avraham E.
full_name: Mayo, Avraham E.
last_name: Mayo
- first_name: Tsvi
full_name: Tlusty, Tsvi
last_name: Tlusty
- first_name: Uri
full_name: Alon, Uri
last_name: Alon
citation:
ama: Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015.
doi:10.1371/journal.pcbi.1004055.s002
apa: Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Evolutionary
simulation code. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s002
chicago: Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary
Simulation Code.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s002.
ieee: T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation
code.” Public Library of Science, 2015.
ista: Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code,
Public Library of Science, 10.1371/journal.pcbi.1004055.s002.
mla: Friedlander, Tamar, et al. Evolutionary Simulation Code. Public Library
of Science, 2015, doi:10.1371/journal.pcbi.1004055.s002.
short: T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).
date_created: 2021-08-05T12:58:07Z
date_published: 2015-03-23T00:00:00Z
date_updated: 2023-02-23T10:16:13Z
day: '23'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1004055.s002
month: '03'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1827'
relation: used_in_publication
status: public
status: public
title: Evolutionary simulation code
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '981'
abstract:
- lang: eng
text: The tunability of topological surface states and controllable opening of the
Dirac gap are of fundamental and practical interest in the field of topological
materials. In the newly discovered topological crystalline insulators (TCIs),
theory predicts that the Dirac node is protected by a crystalline symmetry and
that the surface state electrons can acquire a mass if this symmetry is broken.
Recent studies have detected signatures of a spontaneously generated Dirac gap
in TCIs; however, the mechanism of mass formation remains elusive. In this work,
we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x
Sn x Se for a wide range of alloy compositions spanning the topological and non-topological
regimes. The STM topographies reveal a symmetry-breaking distortion on the surface,
which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous
to the long sought-after Higgs mechanism in particle physics. Interestingly, the
measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude
of the distortion remains nearly constant. Our data and calculations reveal that
the penetration depth of Dirac surface states controls the magnitude of the Dirac
mass. At the limit of the critical composition, the penetration depth is predicted
to go to infinity, resulting in zero mass, consistent with our measurements. Finally,
we discover the existence of surface states in the non-topological regime, which
have the characteristics of gapped, double-branched Dirac fermions and could be
exploited in realizing superconductivity in these materials.
acknowledgement: We thank R. Buczko, C. Chamon, J. C. Seamus Davis, M. El-Batanouny,
A. Mesaros, Y. Ran and A. Soumyanarayanan for useful conversations and G. McMahon
for help with EDS measurements. V.M. gratefully acknowledges funding from the US
Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880
for the support of I.Z., Y.O., W.Z. and D.W. for this project. Work at Massachusetts
Institute of Technology is supported by US Department of Energy, Office of Basic
Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526
(L.F.), and NSF-DMR-1104498 (M.S.). H.L. acknowledges the Singapore National Research
Foundation for support under NRF Award No. NRF-NRFF2013-03. Y.O. was partly supported
by JSPS KAKENHI Grant Numbers 26707016 and 00707656. The work at Northeastern University
is supported by the US Department of Energy grant number DE-FG02-07ER46352, and
benefited from Northeastern University’s Advanced Scientific Computation Center
(ASCC), theory support at the Advanced Light Source, Berkeley and the allocation
of supercomputer time at the NERSC through DOE grant number DE-AC02-05CH11231. Work
at Princeton University is supported by the US National Science Foundation Grant,
NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project
number NSC-102-2119-M-002-004.
author:
- first_name: Ilija
full_name: Zeljkovic, Ilija
last_name: Zeljkovic
- first_name: Yoshinori
full_name: Okada, Yoshinori
last_name: Okada
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Raman
full_name: Sankar, Raman
last_name: Sankar
- first_name: Daniel
full_name: Walkup, Daniel
last_name: Walkup
- first_name: Wenwen
full_name: Zhou, Wenwen
last_name: Zhou
- first_name: Junwei
full_name: Liu, Junwei
last_name: Liu
- first_name: Guoqing
full_name: Chang, Guoqing
last_name: Chang
- first_name: Yungjui
full_name: Wang, Yungjui
last_name: Wang
- first_name: Md
full_name: Hasan, Md Z
last_name: Hasan
- first_name: Fangcheng
full_name: Chou, Fangcheng
last_name: Chou
- first_name: Hsin
full_name: Lin, Hsin
last_name: Lin
- first_name: Arun
full_name: Bansil, Arun
last_name: Bansil
- first_name: Liang
full_name: Fu, Liang
last_name: Fu
- first_name: Vidya
full_name: Madhavan, Vidya
last_name: Madhavan
citation:
ama: Zeljkovic I, Okada Y, Serbyn M, et al. Dirac mass generation from crystal symmetry
breaking on the surfaces of topological crystalline insulators. Nature Materials.
2015;14(3):318-324. doi:10.1038/nmat4215
apa: Zeljkovic, I., Okada, Y., Serbyn, M., Sankar, R., Walkup, D., Zhou, W., … Madhavan,
V. (2015). Dirac mass generation from crystal symmetry breaking on the surfaces
of topological crystalline insulators. Nature Materials. Nature Publishing
Group. https://doi.org/10.1038/nmat4215
chicago: Zeljkovic, Ilija, Yoshinori Okada, Maksym Serbyn, Raman Sankar, Daniel
Walkup, Wenwen Zhou, Junwei Liu, et al. “Dirac Mass Generation from Crystal Symmetry
Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials.
Nature Publishing Group, 2015. https://doi.org/10.1038/nmat4215.
ieee: I. Zeljkovic et al., “Dirac mass generation from crystal symmetry breaking
on the surfaces of topological crystalline insulators,” Nature Materials,
vol. 14, no. 3. Nature Publishing Group, pp. 318–324, 2015.
ista: Zeljkovic I, Okada Y, Serbyn M, Sankar R, Walkup D, Zhou W, Liu J, Chang G,
Wang Y, Hasan M, Chou F, Lin H, Bansil A, Fu L, Madhavan V. 2015. Dirac mass generation
from crystal symmetry breaking on the surfaces of topological crystalline insulators.
Nature Materials. 14(3), 318–324.
mla: Zeljkovic, Ilija, et al. “Dirac Mass Generation from Crystal Symmetry Breaking
on the Surfaces of Topological Crystalline Insulators.” Nature Materials,
vol. 14, no. 3, Nature Publishing Group, 2015, pp. 318–24, doi:10.1038/nmat4215.
short: I. Zeljkovic, Y. Okada, M. Serbyn, R. Sankar, D. Walkup, W. Zhou, J. Liu,
G. Chang, Y. Wang, M. Hasan, F. Chou, H. Lin, A. Bansil, L. Fu, V. Madhavan, Nature
Materials 14 (2015) 318–324.
date_created: 2018-12-11T11:49:31Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2021-01-12T08:22:24Z
day: '01'
doi: 10.1038/nmat4215
extern: 1
intvolume: ' 14'
issue: '3'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.4906
month: '03'
oa: 1
page: 318 - 324
publication: Nature Materials
publication_status: published
publisher: Nature Publishing Group
publist_id: '6419'
quality_controlled: 0
status: public
title: Dirac mass generation from crystal symmetry breaking on the surfaces of topological
crystalline insulators
type: journal_article
volume: 14
year: '2015'
...
---
_id: '982'
abstract:
- lang: eng
text: We propose a new approach to probing ergodicity and its breakdown in one-dimensional
quantum manybody systems based on their response to a local perturbation. We study
the distribution of matrix elements of a local operator between the system's eigenstates,
finding a qualitatively different behavior in the manybody localized (MBL) and
ergodic phases. To characterize how strongly a local perturbation modifies the
eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the
disorder-averaged ratio of a typical matrix element of a local operator V to energy
level spacing δ this parameter is reminiscent of the Thouless conductance in the
single-particle localization. We show that the parameter g(L) decreases with system
size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization
transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate
our approach by studying the many-body localization transition and resolving the
many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using
exact diagonalization and time-evolving block-decimation methods. Our criterion
for the MBL transition gives insights into microscopic details of transition.
Its direct physical consequences, in particular, logarithmically slow transport
at the transition and extensive entanglement entropy of the eigenstates, are consistent
with recent renormalization-group predictions.
acknowledgement: We acknowledge helpful discussions with Sid Parameswaran, Andrew
Potter, Antonello Scardicchio, Romain Vasseur, and especially with Ehud Altman and
David Huse. We would like to thank Miles Stoudenmire for the assistance with ITensor
library. Research at Perimeter Institute is supported by the Government of Canada
through Industry Canada and by the Province of Ontario through the Ministry of Economic
Development & Innovation. This research was supported by Gordon and Betty Moore
Foundation EPiQS Initiative through Grant No. GBMF4307 (M. S.), Sloan Foundation,
NSERC, and Early Researcher Award of Ontario (D. A.). This work made use of the
facilities of N8 HPC Centre of Excellence, provided and funded by the N8 consortium
and EPSRC (Grant No. EP/K000225/1). The Centre is coordinated by the Universities
of Leeds and Manchester.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
citation:
ama: Serbyn M, Papić Z, Abanin D. Criterion for many-body localization-delocalization
phase transition. Physical Review X. 2015;5(4). doi:10.1103/PhysRevX.5.041047
apa: Serbyn, M., Papić, Z., & Abanin, D. (2015). Criterion for many-body localization-delocalization
phase transition. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.5.041047
chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Criterion for Many-Body
Localization-Delocalization Phase Transition.” Physical Review X. American
Physical Society, 2015. https://doi.org/10.1103/PhysRevX.5.041047.
ieee: M. Serbyn, Z. Papić, and D. Abanin, “Criterion for many-body localization-delocalization
phase transition,” Physical Review X, vol. 5, no. 4. American Physical
Society, 2015.
ista: Serbyn M, Papić Z, Abanin D. 2015. Criterion for many-body localization-delocalization
phase transition. Physical Review X. 5(4).
mla: Serbyn, Maksym, et al. “Criterion for Many-Body Localization-Delocalization
Phase Transition.” Physical Review X, vol. 5, no. 4, American Physical
Society, 2015, doi:10.1103/PhysRevX.5.041047.
short: M. Serbyn, Z. Papić, D. Abanin, Physical Review X 5 (2015).
date_created: 2018-12-11T11:49:32Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T08:22:25Z
day: '01'
doi: 10.1103/PhysRevX.5.041047
extern: 1
intvolume: ' 5'
issue: '4'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.01635
month: '01'
oa: 1
publication: Physical Review X
publication_status: published
publisher: American Physical Society
publist_id: '6418'
quality_controlled: 0
status: public
title: Criterion for many-body localization-delocalization phase transition
type: journal_article
volume: 5
year: '2015'
...
---
_id: '99'
abstract:
- lang: eng
text: Quasiparticle excitations can compromise the performance of superconducting
devices, causing high-frequency dissipation, decoherence in Josephson qubits,
and braiding errors in proposed Majorana-based topological quantum computers.
Quasiparticle dynamics have been studied in detail in metallic superconductors
but remain relatively unexplored in semiconductor-superconductor structures, which
are now being intensely pursued in the context of topological superconductivity.
To this end, we use a system comprising a gate-confined semiconductor nanowire
with an epitaxially grown superconductor layer, yielding an isolated, proximitized
nanowire segment. We identify bound states in the semiconductor by means of bias
spectroscopy, determine the characteristic temperatures and magnetic fields for
quasiparticle excitations, and extract a parity lifetime (poisoning time) of the
bound state in the semiconductor exceeding 10 ms.
acknowledgement: Research support by Microsoft Project Q, the Danish National Research
Foundation, the Lundbeck Foundation, the Carlsberg Foundation, and the European
Commission. A.P.H. acknowledges support from the US Department of Energy, C.M.M.
acknowledges support from the Villum Foundation.
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: S M
full_name: Albrecht, S M
last_name: Albrecht
- first_name: Gediminas
full_name: Kiršanskas, Gediminas
last_name: Kiršanskas
- first_name: W
full_name: Chang, W
last_name: Chang
- first_name: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
- first_name: Peter
full_name: Krogstrup, Peter
last_name: Krogstrup
- first_name: Thomas
full_name: Jespersen, Thomas
last_name: Jespersen
- first_name: Jesper
full_name: Nygård, Jesper
last_name: Nygård
- first_name: Karsten
full_name: Flensberg, Karsten
last_name: Flensberg
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
citation:
ama: Higginbotham AP, Albrecht SM, Kiršanskas G, et al. Parity lifetime of bound
states in a proximitized semiconductor nanowire. Nature Physics. 2015;11(12):1017-1021.
doi:10.1038/nphys3461
apa: Higginbotham, A. P., Albrecht, S. M., Kiršanskas, G., Chang, W., Kuemmeth,
F., Krogstrup, P., … Marcus, C. (2015). Parity lifetime of bound states in a proximitized
semiconductor nanowire. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3461
chicago: Higginbotham, Andrew P, S M Albrecht, Gediminas Kiršanskas, W Chang, Ferdinand
Kuemmeth, Peter Krogstrup, Thomas Jespersen, Jesper Nygård, Karsten Flensberg,
and Charles Marcus. “Parity Lifetime of Bound States in a Proximitized Semiconductor
Nanowire.” Nature Physics. Nature Publishing Group, 2015. https://doi.org/10.1038/nphys3461.
ieee: A. P. Higginbotham et al., “Parity lifetime of bound states in a proximitized
semiconductor nanowire,” Nature Physics, vol. 11, no. 12. Nature Publishing
Group, pp. 1017–1021, 2015.
ista: Higginbotham AP, Albrecht SM, Kiršanskas G, Chang W, Kuemmeth F, Krogstrup
P, Jespersen T, Nygård J, Flensberg K, Marcus C. 2015. Parity lifetime of bound
states in a proximitized semiconductor nanowire. Nature Physics. 11(12), 1017–1021.
mla: Higginbotham, Andrew P., et al. “Parity Lifetime of Bound States in a Proximitized
Semiconductor Nanowire.” Nature Physics, vol. 11, no. 12, Nature Publishing
Group, 2015, pp. 1017–21, doi:10.1038/nphys3461.
short: A.P. Higginbotham, S.M. Albrecht, G. Kiršanskas, W. Chang, F. Kuemmeth, P.
Krogstrup, T. Jespersen, J. Nygård, K. Flensberg, C. Marcus, Nature Physics 11
(2015) 1017–1021.
date_created: 2018-12-11T11:44:37Z
date_published: 2015-09-14T00:00:00Z
date_updated: 2021-01-12T08:22:28Z
day: '14'
doi: 10.1038/nphys3461
extern: '1'
external_id:
arxiv:
- '1501.05155'
intvolume: ' 11'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1501.05155
month: '09'
oa: 1
oa_version: Preprint
page: 1017 - 1021
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '7955'
quality_controlled: '1'
status: public
title: Parity lifetime of bound states in a proximitized semiconductor nanowire
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
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: '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: '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'
...
---
_id: '929'
abstract:
- lang: eng
text: 'An essential question of morphogenesis is how patterns arise without preexisting
positional information, as inspired by Turing. In the past few years, cytoskeletal
flows in the cell cortex have been identified as a key mechanism of molecular
patterning at the subcellular level. Theoretical and in vitro studies have suggested
that biological polymers such as actomyosin gels have the property to self-organize,
but the applicability of this concept in an in vivo setting remains unclear. Here,
we report that the regular spacing pattern of supracellular actin rings in the
Drosophila tracheal tubule is governed by a self-organizing principle. We propose
a simple biophysical model where pattern formation arises from the interplay of
myosin contractility and actin turnover. We validate the hypotheses of the model
using photobleaching experiments and report that the formation of actin rings
is contractility dependent. Moreover, genetic and pharmacological perturbations
of the physical properties of the actomyosin gel modify the spacing of the pattern,
as the model predicted. In addition, our model posited a role of cortical friction
in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion
of apical extracellular matrix caused strikingly dynamic movements of actin rings,
mirroring our model prediction of a transition from steady to chaotic actin patterns
at low cortical friction. Our results therefore demonstrate quantitatively that
a hydrodynamical instability of the actin cortex can trigger regular pattern formation
and drive morphogenesis in an in vivo setting. '
acknowledgement: We thank H. Oda, R. E. Ward, K. Saigo, T. Nishimura, D. Pinheiro,
Y. Bellaiche, the Bloomington Stock Center, Drosophila Genetic Resource Center (Kyoto),
and the Developmental Studies Hybridoma Bank for generously providing antibodies
and fly stocks; A. Hayashi for sharing phalloidin staining samples; Y. H. Zhang
for plasmid and protocol for CBP preparation; and T. Kondo and J. Prost for suggestions
and discussion. This work was supported by the Taishan Scholar Program of Shandong
and the Fundamental Research Funds for the Central Universities in China (3005000-841412019)
(to B.D.) and a Grant-in-Aid for Scientific Research on Innovative Areas from Ministry
of Education, Culture, Sports, Science and Technology of Japan (to S.H.). E.H. acknowledges
support from the Young Researcher Prize of the Bettencourt-Schueller Foundation.
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Bo
full_name: Dong, Bo
last_name: Dong
- first_name: Pierre
full_name: Recho, Pierre
last_name: Recho
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
- first_name: Shigeo
full_name: Hayashi, Shigeo
last_name: Hayashi
citation:
ama: Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. Cortical instability drives
periodic supracellular actin pattern formation in epithelial tubes. PNAS.
2015;112(28):8620-8625. doi:10.1073/pnas.1504762112
apa: Hannezo, E. B., Dong, B., Recho, P., Joanny, J., & Hayashi, S. (2015).
Cortical instability drives periodic supracellular actin pattern formation in
epithelial tubes. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1504762112
chicago: Hannezo, Edouard B, Bo Dong, Pierre Recho, Jean Joanny, and Shigeo Hayashi.
“Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in
Epithelial Tubes.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1504762112.
ieee: E. B. Hannezo, B. Dong, P. Recho, J. Joanny, and S. Hayashi, “Cortical instability
drives periodic supracellular actin pattern formation in epithelial tubes,” PNAS,
vol. 112, no. 28. National Academy of Sciences, pp. 8620–8625, 2015.
ista: Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. 2015. Cortical instability
drives periodic supracellular actin pattern formation in epithelial tubes. PNAS.
112(28), 8620–8625.
mla: Hannezo, Edouard B., et al. “Cortical Instability Drives Periodic Supracellular
Actin Pattern Formation in Epithelial Tubes.” PNAS, vol. 112, no. 28, National
Academy of Sciences, 2015, pp. 8620–25, doi:10.1073/pnas.1504762112.
short: E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625.
date_created: 2018-12-11T11:49:15Z
date_published: 2015-07-14T00:00:00Z
date_updated: 2021-01-12T08:21:59Z
day: '14'
doi: 10.1073/pnas.1504762112
extern: '1'
intvolume: ' 112'
issue: '28'
language:
- iso: eng
month: '07'
oa_version: None
page: 8620 - 8625
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6513'
status: public
title: Cortical instability drives periodic supracellular actin pattern formation
in epithelial tubes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '933'
abstract:
- lang: eng
text: Although collective cell motion plays an important role, for example during
wound healing, embryogenesis, or cancer progression, the fundamental rules governing
this motion are still not well understood, in particular at high cell density.
We study here the motion of human bronchial epithelial cells within a monolayer,
over long times. We observe that, as the monolayer ages, the cells slow down monotonously,
while the velocity correlation length first increases as the cells slow down but
eventually decreases at the slowest motions. By comparing experiments, analytic
model, and detailed particle-based simulations, we shed light on this biological
amorphous solidification process, demonstrating that the observed dynamics can
be explained as a consequence of the combined maturation and strengthening of
cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface
density due to proliferation is only secondary in this process. This analysis
is confirmed with two other cell types. The very general relations between the
mean cell velocity and velocity correlation lengths, which apply for aggregates
of self-propelled particles, as well as motile cells, can possibly be used to
discriminate between various parameter changes in vivo, from noninvasive microscopy
data.
author:
- first_name: Simón
full_name: García, Simón
last_name: García
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jens
full_name: Elgeti, Jens
last_name: Elgeti
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
- first_name: Pascal
full_name: Silberzan, Pascal
last_name: Silberzan
- first_name: Nir
full_name: Gov, Nir
last_name: Gov
citation:
ama: García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active
jamming during collective cellular motion in a monolayer. PNAS. 2015;112(50):15314-15319.
doi:10.1073/pnas.1510973112
apa: García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., & Gov,
N. (2015). Physics of active jamming during collective cellular motion in a monolayer.
PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510973112
chicago: García, Simón, Edouard B Hannezo, Jens Elgeti, Jean Joanny, Pascal Silberzan,
and Nir Gov. “Physics of Active Jamming during Collective Cellular Motion in a
Monolayer.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510973112.
ieee: S. García, E. B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, and N. Gov,
“Physics of active jamming during collective cellular motion in a monolayer,”
PNAS, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319,
2015.
ista: García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. 2015. Physics
of active jamming during collective cellular motion in a monolayer. PNAS. 112(50),
15314–15319.
mla: García, Simón, et al. “Physics of Active Jamming during Collective Cellular
Motion in a Monolayer.” PNAS, vol. 112, no. 50, National Academy of Sciences,
2015, pp. 15314–19, doi:10.1073/pnas.1510973112.
short: S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS
112 (2015) 15314–15319.
date_created: 2018-12-11T11:49:16Z
date_published: 2015-12-15T00:00:00Z
date_updated: 2021-01-12T08:22:01Z
day: '15'
doi: 10.1073/pnas.1510973112
extern: '1'
external_id:
pmid:
- '26627719'
intvolume: ' 112'
issue: '50'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pnas.org/content/pnas/112/50/15314.full.pdf
month: '12'
oa: 1
oa_version: None
page: 15314 - 15319
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6511'
quality_controlled: '1'
status: public
title: Physics of active jamming during collective cellular motion in a monolayer
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '9532'
abstract:
- lang: eng
text: Genomic imprinting, an inherently epigenetic phenomenon defined by parent
of origin-dependent gene expression, is observed in mammals and flowering plants.
Genome-scale surveys of imprinted expression and the underlying differential epigenetic
marks have led to the discovery of hundreds of imprinted plant genes and confirmed
DNA and histone methylation as key regulators of plant imprinting. However, the
biological roles of the vast majority of imprinted plant genes are unknown, and
the evolutionary forces shaping plant imprinting remain rather opaque. Here, we
review the mechanisms of plant genomic imprinting and discuss theories of imprinting
evolution and biological significance in light of recent findings.
article_processing_charge: No
article_type: review
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in
plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115
apa: Rodrigues, J. A., & Zilberman, D. (2015). Evolution and function of genomic
imprinting in plants. Genes and Development. Cold Spring Harbor Laboratory
Press. https://doi.org/10.1101/gad.269902.115
chicago: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of
Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor
Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115.
ieee: J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting
in plants,” Genes and Development, vol. 29, no. 24. Cold Spring Harbor
Laboratory Press, pp. 2517–2531, 2015.
ista: Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting
in plants. Genes and Development. 29(24), 2517–2531.
mla: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic
Imprinting in Plants.” Genes and Development, vol. 29, no. 24, Cold Spring
Harbor Laboratory Press, 2015, pp. 2517–2531, doi:10.1101/gad.269902.115.
short: J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.
date_created: 2021-06-08T09:56:24Z
date_published: 2015-12-15T00:00:00Z
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title: Evolution and function of genomic imprinting in plants
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