---
_id: '764'
abstract:
- lang: eng
text: Set agreement is a fundamental problem in distributed computing in which processes
collectively choose a small subset of values from a larger set of proposals. The
impossibility of fault-tolerant set agreement in asynchronous networks is one
of the seminal results in distributed computing. In synchronous networks, too,
the complexity of set agreement has been a significant research challenge that
has now been resolved. Real systems, however, are neither purely synchronous nor
purely asynchronous. Rather, they tend to alternate between periods of synchrony
and periods of asynchrony. Nothing specific is known about the complexity of set
agreement in such a "partially synchronous" setting. In this paper,
we address this challenge, presenting the first (asymptotically) tight bound on
the complexity of set agreement in such systems. We introduce a novel technique
for simulating, in a fault-prone asynchronous shared memory, executions of an
asynchronous and failure-prone message-passing system in which some fragments
appear synchronous to some processes. We use this simulation technique to derive
a lower bound on the round complexity of set agreement in a partially synchronous
system by a reduction from asynchronous wait-free set agreement. Specifically,
we show that every set agreement protocol requires at least $\lfloor\frac t k
\rfloor + 2$ synchronous rounds to decide. We present an (asymptotically) matching
algorithm that relies on a distributed asynchrony detection mechanism to decide
as soon as possible during periods of synchrony. From these two results, we derive
the size of the minimal window of synchrony needed to solve set agreement. By
relating synchronous, asynchronous and partially synchronous environments, our
simulation technique is of independent interest. In particular, it allows us to
obtain a new lower bound on the complexity of early deciding k-set agreement complementary
to that of Gafni et al. (in SIAM J. Comput. 40(1):63-78, 2011), and to re-derive
the combinatorial topology lower bound of Guerraoui et al. (in Theor. Comput.
Sci. 410(6-7):570-580, 2009) in an algorithmic way.
acknowledgement: "We would like to thank Hagit Attiya, Keren Censor-Hillel, and
the anonymous\r\nreviewers for their feedback on drafts of this paper.\r\nPart
of the work was performed as C. Travers was a Post-Doctoral Fellow at the Technion,
Haifa,\r\nsupported by the “Sam & Cecilia Neaman” Fellowship. Part of the work was
performed as S. Gilbert was\r\na Post-Doctoral Fellow at the Swiss Federal Institute
of Technology, Lausanne, Switzerland."
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: Seth
full_name: Gilbert, Seth
last_name: Gilbert
- first_name: Rachid
full_name: Guerraoui, Rachid
last_name: Guerraoui
- first_name: Corentin
full_name: Travers, Corentin
last_name: Travers
citation:
ama: 'Alistarh D-A, Gilbert S, Guerraoui R, Travers C. Of choices, failures and
asynchrony: the many faces of set agreement. Algorithmica (New York). 2012;62(1-2):595-629.
doi:10.1007/s00453-011-9581-7'
apa: 'Alistarh, D.-A., Gilbert, S., Guerraoui, R., & Travers, C. (2012). Of
choices, failures and asynchrony: the many faces of set agreement. Algorithmica
(New York). Springer. https://doi.org/10.1007/s00453-011-9581-7'
chicago: 'Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers.
“Of Choices, Failures and Asynchrony: The Many Faces of Set Agreement.” Algorithmica
(New York). Springer, 2012. https://doi.org/10.1007/s00453-011-9581-7.'
ieee: 'D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “Of choices, failures
and asynchrony: the many faces of set agreement,” Algorithmica (New York),
vol. 62, no. 1–2. Springer, pp. 595–629, 2012.'
ista: 'Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2012. Of choices, failures
and asynchrony: the many faces of set agreement. Algorithmica (New York). 62(1–2),
595–629.'
mla: 'Alistarh, Dan-Adrian, et al. “Of Choices, Failures and Asynchrony: The Many
Faces of Set Agreement.” Algorithmica (New York), vol. 62, no. 1–2, Springer,
2012, pp. 595–629, doi:10.1007/s00453-011-9581-7.'
short: D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, Algorithmica (New York)
62 (2012) 595–629.
date_created: 2018-12-11T11:48:23Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2023-02-23T13:13:02Z
day: '01'
doi: 10.1007/s00453-011-9581-7
extern: '1'
intvolume: ' 62'
issue: 1-2
language:
- iso: eng
month: '02'
oa_version: None
page: 595 - 629
publication: Algorithmica (New York)
publication_status: published
publisher: Springer
publist_id: '6894'
status: public
title: 'Of choices, failures and asynchrony: the many faces of set agreement'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 62
year: '2012'
...
---
_id: '766'
abstract:
- lang: eng
text: 'Asynchronous task allocation is a fundamental problem in distributed computing
in which p asynchronous processes must execute a set of m tasks. Also known as
write-all or do-all, this problem been studied extensively, both independently
and as a key building block for various distributed algorithms. In this paper,
we break new ground on this classic problem: we introduce the To-Do Tree concurrent
data structure, which improves on the best known randomized and deterministic
upper bounds. In the presence of an adaptive adversary, the randomized To-Do Tree
algorithm has O(m + p log p log2 m) work complexity. We then show that there exists
a deterministic variant of the To-Do Tree algorithm with work complexity O(m +
p log5 m log2 max(m, p)). For all values of m and p, our algorithms are within
log factors of the Ω(m + p log p) lower bound for this problem. The key technical
ingredient in our results is a new approach for analyzing concurrent executions
against a strong adaptive scheduler. This technique allows us to handle the complex
dependencies between the processes'' coin flips and their scheduling, and to tightly
bound the work needed to perform subsets of the tasks.'
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: Michael
full_name: Bender, Michael
last_name: Bender
- first_name: Seth
full_name: Gilbert, Seth
last_name: Gilbert
- first_name: Rachid
full_name: Guerraoui, Rachid
last_name: Guerraoui
citation:
ama: 'Alistarh D-A, Bender M, Gilbert S, Guerraoui R. How to allocate tasks asynchronously.
In: IEEE; 2012:331-340. doi:10.1109/FOCS.2012.41'
apa: 'Alistarh, D.-A., Bender, M., Gilbert, S., & Guerraoui, R. (2012). How
to allocate tasks asynchronously (pp. 331–340). Presented at the FOCS: Foundations
of Computer Science, IEEE. https://doi.org/10.1109/FOCS.2012.41'
chicago: Alistarh, Dan-Adrian, Michael Bender, Seth Gilbert, and Rachid Guerraoui.
“How to Allocate Tasks Asynchronously,” 331–40. IEEE, 2012. https://doi.org/10.1109/FOCS.2012.41.
ieee: 'D.-A. Alistarh, M. Bender, S. Gilbert, and R. Guerraoui, “How to allocate
tasks asynchronously,” presented at the FOCS: Foundations of Computer Science,
2012, pp. 331–340.'
ista: 'Alistarh D-A, Bender M, Gilbert S, Guerraoui R. 2012. How to allocate tasks
asynchronously. FOCS: Foundations of Computer Science, 331–340.'
mla: Alistarh, Dan-Adrian, et al. How to Allocate Tasks Asynchronously. IEEE,
2012, pp. 331–40, doi:10.1109/FOCS.2012.41.
short: D.-A. Alistarh, M. Bender, S. Gilbert, R. Guerraoui, in:, IEEE, 2012, pp.
331–340.
conference:
name: 'FOCS: Foundations of Computer Science'
date_created: 2018-12-11T11:48:23Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2023-02-23T13:13:27Z
day: '01'
doi: 10.1109/FOCS.2012.41
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 331 - 340
publication_status: published
publisher: IEEE
publist_id: '6890'
status: public
title: How to allocate tasks asynchronously
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '767'
abstract:
- lang: eng
text: Synchronous distributed algorithms are easier to design and prove correct
than algorithms that tolerate asynchrony. Yet, in the real world, networks experience
asynchrony and other timing anomalies. In this paper, we address the question
of how to efficiently transform an algorithm that relies on synchronous timing
into an algorithm that tolerates asynchronous executions. We introduce a transformation
technique from synchronous algorithms to indulgent algorithms (Guerraoui, in PODC,
pp. 289-297, 2000), which induces only a constant overhead in terms of time complexity
in well-behaved executions. Our technique is based on a new abstraction we call
an asynchrony detector, which the participating processes implement collectively.
The resulting transformation works for the class of colorless distributed tasks,
including consensus and set agreement. Interestingly, we also show that our technique
is relevant for colored tasks, by applying it to the renaming problem, to obtain
the first indulgent renaming algorithm.
acknowledgement: "Dan Alistarh was supported by the NCCR MICS Project. Corentin Travers
had additional support from INRIA team REGAL and ANR project SPREADS.\r\nThe authors
would like to thank Hagit Attiya and Nikola Kneževi\r\n ́\r\nc for their feed-\r\nback
on previous drafts of this paper, and the anonymous reviewers for their useful comments."
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: Seth
full_name: Gilbert, Seth
last_name: Gilbert
- first_name: Rachid
full_name: Guerraoui, Rachid
last_name: Guerraoui
- first_name: Corentin
full_name: Travers, Corentin
last_name: Travers
citation:
ama: Alistarh D-A, Gilbert S, Guerraoui R, Travers C. Generating Fast Indulgent
Algorithms. Theory of Computing Systems. 2012;51(4):404-424. doi:10.1007/s00224-012-9407-2
apa: Alistarh, D.-A., Gilbert, S., Guerraoui, R., & Travers, C. (2012). Generating
Fast Indulgent Algorithms. Theory of Computing Systems. Elsevier. https://doi.org/10.1007/s00224-012-9407-2
chicago: Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers.
“Generating Fast Indulgent Algorithms.” Theory of Computing Systems. Elsevier,
2012. https://doi.org/10.1007/s00224-012-9407-2.
ieee: D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “Generating Fast
Indulgent Algorithms,” Theory of Computing Systems, vol. 51, no. 4. Elsevier,
pp. 404–424, 2012.
ista: Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2012. Generating Fast Indulgent
Algorithms. Theory of Computing Systems. 51(4), 404–424.
mla: Alistarh, Dan-Adrian, et al. “Generating Fast Indulgent Algorithms.” Theory
of Computing Systems, vol. 51, no. 4, Elsevier, 2012, pp. 404–24, doi:10.1007/s00224-012-9407-2.
short: D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, Theory of Computing
Systems 51 (2012) 404–424.
date_created: 2018-12-11T11:48:23Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2023-02-23T13:13:40Z
day: '01'
doi: 10.1007/s00224-012-9407-2
extern: '1'
intvolume: ' 51'
issue: '4'
language:
- iso: eng
month: '01'
oa_version: None
page: 404 - 424
publication: Theory of Computing Systems
publication_status: published
publisher: Elsevier
publist_id: '6891'
status: public
title: Generating Fast Indulgent Algorithms
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2012'
...
---
_id: '7748'
abstract:
- lang: eng
text: Female mate choice acts as an important evolutionary force, yet the influence
of the environment on both its expression and the selective pressures acting upon
it remains unknown. We found consistent heritable differences between females
in their choice of mate based on ornament size during a 25‐year study of a population
of collared flycatchers. However, the fitness consequences of mate choice were
dependent on environmental conditions experienced whilst breeding. Females breeding
with highly ornamented males experienced high relative fitness during dry summer
conditions, but low relative fitness during wetter years. Our results imply that
sexual selection within a population can be highly variable and dependent upon
the prevailing weather conditions experienced by individuals.
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: G.
full_name: Sander van Doorn, G.
last_name: Sander van Doorn
- first_name: Lars
full_name: Gustafsson, Lars
last_name: Gustafsson
- first_name: Anna
full_name: Qvarnström, Anna
last_name: Qvarnström
citation:
ama: Robinson MR, Sander van Doorn G, Gustafsson L, Qvarnström A. Environment-dependent
selection on mate choice in a natural population of birds. Ecology Letters.
2012;15(6):611-618. doi:10.1111/j.1461-0248.2012.01780.x
apa: Robinson, M. R., Sander van Doorn, G., Gustafsson, L., & Qvarnström, A.
(2012). Environment-dependent selection on mate choice in a natural population
of birds. Ecology Letters. Wiley. https://doi.org/10.1111/j.1461-0248.2012.01780.x
chicago: Robinson, Matthew Richard, G. Sander van Doorn, Lars Gustafsson, and Anna
Qvarnström. “Environment-Dependent Selection on Mate Choice in a Natural Population
of Birds.” Ecology Letters. Wiley, 2012. https://doi.org/10.1111/j.1461-0248.2012.01780.x.
ieee: M. R. Robinson, G. Sander van Doorn, L. Gustafsson, and A. Qvarnström, “Environment-dependent
selection on mate choice in a natural population of birds,” Ecology Letters,
vol. 15, no. 6. Wiley, pp. 611–618, 2012.
ista: Robinson MR, Sander van Doorn G, Gustafsson L, Qvarnström A. 2012. Environment-dependent
selection on mate choice in a natural population of birds. Ecology Letters. 15(6),
611–618.
mla: Robinson, Matthew Richard, et al. “Environment-Dependent Selection on Mate
Choice in a Natural Population of Birds.” Ecology Letters, vol. 15, no.
6, Wiley, 2012, pp. 611–18, doi:10.1111/j.1461-0248.2012.01780.x.
short: M.R. Robinson, G. Sander van Doorn, L. Gustafsson, A. Qvarnström, Ecology
Letters 15 (2012) 611–618.
date_created: 2020-04-30T11:01:07Z
date_published: 2012-06-01T00:00:00Z
date_updated: 2021-01-12T08:15:15Z
day: '01'
doi: 10.1111/j.1461-0248.2012.01780.x
extern: '1'
intvolume: ' 15'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 611-618
publication: Ecology Letters
publication_identifier:
issn:
- 1461-023X
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Environment-dependent selection on mate choice in a natural population of birds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2012'
...
---
_id: '7749'
abstract:
- lang: eng
text: Although studies on laboratory species and natural populations of vertebrates
have shown reproduction to impair later performance, little is known of the age‐specific
associations between reproduction and survival, and how such findings apply to
the ageing of large, long‐lived species. Herein we develop a framework to examine
population‐level patterns of reproduction and survival across lifespan in long‐lived
organisms, and decompose those changes into individual‐level effects, and the
effects of age‐specific trade‐offs between fitness components. We apply this to
an extensive longitudinal dataset on female semi‐captive Asian timber elephants
(Elephas maximus) and report the first evidence of age‐specific fitness declines
that are driven by age‐specific associations between fitness components in a long‐lived
mammal. Associations between reproduction and survival are positive in early life,
but negative in later life with up to 71% of later‐life survival declines associated
with investing in the production of offspring within this population of this critically
endangered species.
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Khyne U
full_name: Mar, Khyne U
last_name: Mar
- first_name: Virpi
full_name: Lummaa, Virpi
last_name: Lummaa
citation:
ama: Robinson MR, Mar KU, Lummaa V. Senescence and age-specific trade-offs between
reproduction and survival in female Asian elephants. Ecology Letters. 2012;15(3):260-266.
doi:10.1111/j.1461-0248.2011.01735.x
apa: Robinson, M. R., Mar, K. U., & Lummaa, V. (2012). Senescence and age-specific
trade-offs between reproduction and survival in female Asian elephants. Ecology
Letters. Wiley. https://doi.org/10.1111/j.1461-0248.2011.01735.x
chicago: Robinson, Matthew Richard, Khyne U Mar, and Virpi Lummaa. “Senescence and
Age-Specific Trade-Offs between Reproduction and Survival in Female Asian Elephants.”
Ecology Letters. Wiley, 2012. https://doi.org/10.1111/j.1461-0248.2011.01735.x.
ieee: M. R. Robinson, K. U. Mar, and V. Lummaa, “Senescence and age-specific trade-offs
between reproduction and survival in female Asian elephants,” Ecology Letters,
vol. 15, no. 3. Wiley, pp. 260–266, 2012.
ista: Robinson MR, Mar KU, Lummaa V. 2012. Senescence and age-specific trade-offs
between reproduction and survival in female Asian elephants. Ecology Letters.
15(3), 260–266.
mla: Robinson, Matthew Richard, et al. “Senescence and Age-Specific Trade-Offs between
Reproduction and Survival in Female Asian Elephants.” Ecology Letters,
vol. 15, no. 3, Wiley, 2012, pp. 260–66, doi:10.1111/j.1461-0248.2011.01735.x.
short: M.R. Robinson, K.U. Mar, V. Lummaa, Ecology Letters 15 (2012) 260–266.
date_created: 2020-04-30T11:01:26Z
date_published: 2012-03-01T00:00:00Z
date_updated: 2021-01-12T08:15:16Z
day: '01'
doi: 10.1111/j.1461-0248.2011.01735.x
extern: '1'
intvolume: ' 15'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 260-266
publication: Ecology Letters
publication_identifier:
issn:
- 1461-023X
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Senescence and age-specific trade-offs between reproduction and survival in
female Asian elephants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2012'
...
---
_id: '7776'
abstract:
- lang: eng
text: We present an analysis of finite-size effects in jammed packings of N soft,
frictionless spheres at zero temperature. There is a 1/N correction to the discrete
jump in the contact number at the transition so that jammed packings exist only
above isostaticity. As a result, the canonical power-law scalings of the contact
number and elastic moduli break down at low pressure. These quantities exhibit
scaling collapse with a nontrivial scaling function, demonstrating that the jamming
transition can be considered a phase transition. Scaling is achieved as a function
of N in both two and three dimensions, indicating an upper critical dimension
of 2.
article_number: '095704'
article_processing_charge: No
article_type: original
author:
- 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: Goodrich CP, Liu AJ, Nagel SR. Finite-size scaling at the jamming transition.
Physical Review Letters. 2012;109(9). doi:10.1103/physrevlett.109.095704
apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2012). Finite-size scaling
at the jamming transition. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/physrevlett.109.095704
chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Finite-Size
Scaling at the Jamming Transition.” Physical Review Letters. American Physical
Society, 2012. https://doi.org/10.1103/physrevlett.109.095704.
ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Finite-size scaling at the jamming
transition,” Physical Review Letters, vol. 109, no. 9. American Physical
Society, 2012.
ista: Goodrich CP, Liu AJ, Nagel SR. 2012. Finite-size scaling at the jamming transition.
Physical Review Letters. 109(9), 095704.
mla: Goodrich, Carl Peter, et al. “Finite-Size Scaling at the Jamming Transition.”
Physical Review Letters, vol. 109, no. 9, 095704, American Physical Society,
2012, doi:10.1103/physrevlett.109.095704.
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 109 (2012).
date_created: 2020-04-30T11:44:12Z
date_published: 2012-08-27T00:00:00Z
date_updated: 2021-01-12T08:15:27Z
day: '27'
doi: 10.1103/physrevlett.109.095704
extern: '1'
intvolume: ' 109'
issue: '9'
language:
- iso: eng
month: '08'
oa_version: None
publication: Physical Review Letters
publication_identifier:
issn:
- 0031-9007
- 1079-7114
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Finite-size scaling at the jamming transition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 109
year: '2012'
...
---
_id: '801'
abstract:
- lang: eng
text: Fungal cell walls frequently contain a polymer of mannose and galactose called
galactomannan. In the pathogenic filamentous fungus Aspergillus fumigatus, this
polysaccharide is made of a linear mannan backbone with side chains of galactofuran
and is anchored to the plasma membrane via a glycosylphosphatidylinositol or is
covalently linked to the cell wall. To date, the biosynthesis and significance
of this polysaccharide are unknown. The present data demonstrate that deletion
of the Golgi UDP-galactofuranose transporter GlfB or the GDP-mannose transporter
GmtA leads to the absence of galactofuran or galactomannan, respectively. This
indicates that the biosynthesis of galactomannan probably occurs in the lumen
of the Golgi apparatus and thus contrasts with the biosynthesis of other fungal
cell wall polysaccharides studied to date that takes place at the plasma membrane.
Transglycosylation of galactomannan from the membrane to the cell wall is hypothesized
because both the cell wall-bound and membrane-bound polysaccharide forms are affected
in the generated mutants. Considering the severe growth defect of the A. fumigatus
GmtA-deficient mutant, proving this paradigm might provide new targets for antifungal
therapy.
acknowledgement: This work was supported by the Deutsche Forschungsgemeinschaft.
article_processing_charge: No
article_type: original
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: Françoise
full_name: Routier, Françoise
last_name: Routier
citation:
ama: Engel J, Schmalhorst PS, Routier F. Biosynthesis of the fungal cell wall polysaccharide
galactomannan requires intraluminal GDP-mannose. Journal of Biological Chemistry.
2012;287(53):44418-44424. doi:10.1074/jbc.M112.398321
apa: Engel, J., Schmalhorst, P. S., & Routier, F. (2012). Biosynthesis of the
fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose.
Journal of Biological Chemistry. American Society for Biochemistry and
Molecular Biology. https://doi.org/10.1074/jbc.M112.398321
chicago: Engel, Jakob, Philipp S Schmalhorst, and Françoise Routier. “Biosynthesis
of the Fungal Cell Wall Polysaccharide Galactomannan Requires Intraluminal GDP-Mannose.”
Journal of Biological Chemistry. American Society for Biochemistry and
Molecular Biology, 2012. https://doi.org/10.1074/jbc.M112.398321.
ieee: J. Engel, P. S. Schmalhorst, and F. Routier, “Biosynthesis of the fungal cell
wall polysaccharide galactomannan requires intraluminal GDP-mannose,” Journal
of Biological Chemistry, vol. 287, no. 53. American Society for Biochemistry
and Molecular Biology, pp. 44418–44424, 2012.
ista: Engel J, Schmalhorst PS, Routier F. 2012. Biosynthesis of the fungal cell
wall polysaccharide galactomannan requires intraluminal GDP-mannose. Journal of
Biological Chemistry. 287(53), 44418–44424.
mla: Engel, Jakob, et al. “Biosynthesis of the Fungal Cell Wall Polysaccharide Galactomannan
Requires Intraluminal GDP-Mannose.” Journal of Biological Chemistry, vol.
287, no. 53, American Society for Biochemistry and Molecular Biology, 2012, pp.
44418–24, doi:10.1074/jbc.M112.398321.
short: J. Engel, P.S. Schmalhorst, F. Routier, Journal of Biological Chemistry 287
(2012) 44418–44424.
date_created: 2018-12-11T11:48:34Z
date_published: 2012-12-28T00:00:00Z
date_updated: 2022-03-21T07:57:14Z
day: '28'
doi: 10.1074/jbc.M112.398321
extern: '1'
external_id:
pmid:
- '23139423'
intvolume: ' 287'
issue: '53'
language:
- iso: eng
month: '12'
oa_version: None
page: 44418 - 44424
pmid: 1
publication: Journal of Biological Chemistry
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '6852'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Biosynthesis of the fungal cell wall polysaccharide galactomannan requires
intraluminal GDP-mannose
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 287
year: '2012'
...
---
_id: '8024'
abstract:
- lang: eng
text: In dynamical models of cortical networks, the recurrent connectivity can amplify
the input given to the network in two distinct ways. One is induced by the presence
of near-critical eigenvalues in the connectivity matrix W, producing large but
slow activity fluctuations along the corresponding eigenvectors (dynamical slowing).
The other relies on W not being normal, which allows the network activity to make
large but fast excursions along specific directions. Here we investigate the trade-off
between non-normal amplification and dynamical slowing in the spontaneous activity
of large random neuronal networks composed of excitatory and inhibitory neurons.
We use a Schur decomposition of W to separate the two amplification mechanisms.
Assuming linear stochastic dynamics, we derive an exact expression for the expected
amount of purely non-normal amplification. We find that amplification is very
limited if dynamical slowing must be kept weak. We conclude that, to achieve strong
transient amplification with little slowing, the connectivity must be structured.
We show that unidirectional connections between neurons of the same type together
with reciprocal connections between neurons of different types, allow for amplification
already in the fast dynamical regime. Finally, our results also shed light on
the differences between balanced networks in which inhibition exactly cancels
excitation and those where inhibition dominates.
article_number: '011909'
article_processing_charge: No
article_type: original
author:
- first_name: Guillaume
full_name: Hennequin, Guillaume
last_name: Hennequin
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Wulfram
full_name: Gerstner, Wulfram
last_name: Gerstner
citation:
ama: Hennequin G, Vogels TP, Gerstner W. Non-normal amplification in random balanced
neuronal networks. Physical Review E. 2012;86(1). doi:10.1103/physreve.86.011909
apa: Hennequin, G., Vogels, T. P., & Gerstner, W. (2012). Non-normal amplification
in random balanced neuronal networks. Physical Review E. American Physical
Society. https://doi.org/10.1103/physreve.86.011909
chicago: Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Non-Normal Amplification
in Random Balanced Neuronal Networks.” Physical Review E. American Physical
Society, 2012. https://doi.org/10.1103/physreve.86.011909.
ieee: G. Hennequin, T. P. Vogels, and W. Gerstner, “Non-normal amplification in
random balanced neuronal networks,” Physical Review E, vol. 86, no. 1.
American Physical Society, 2012.
ista: Hennequin G, Vogels TP, Gerstner W. 2012. Non-normal amplification in random
balanced neuronal networks. Physical Review E. 86(1), 011909.
mla: Hennequin, Guillaume, et al. “Non-Normal Amplification in Random Balanced Neuronal
Networks.” Physical Review E, vol. 86, no. 1, 011909, American Physical
Society, 2012, doi:10.1103/physreve.86.011909.
short: G. Hennequin, T.P. Vogels, W. Gerstner, Physical Review E 86 (2012).
date_created: 2020-06-25T13:09:06Z
date_published: 2012-06-11T00:00:00Z
date_updated: 2021-01-12T08:16:35Z
day: '11'
doi: 10.1103/physreve.86.011909
extern: '1'
external_id:
pmid:
- '23005454'
intvolume: ' 86'
issue: '1'
language:
- iso: eng
month: '06'
oa_version: None
pmid: 1
publication: Physical Review E
publication_identifier:
eisbn:
- 1550-2376
issn:
- 1539-3755
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Non-normal amplification in random balanced neuronal networks
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 86
year: '2012'
...
---
_id: '808'
abstract:
- lang: eng
text: Using correlated live-cell imaging and electron tomography we found that actin
branch junctions in protruding and treadmilling lamellipodia are not concentrated
at the front as previously supposed, but link actin filament subsets in which
there is a continuum of distances from a junction to the filament plus ends, for
up to at least 1 mm. When branch sites were observed closely spaced on the same
filament their separation was commonly a multiple of the actin helical repeat
of 36 nm. Image averaging of branch junctions in the tomograms yielded a model
for the in vivo branch at 2.9 nm resolution, which was comparable with that derived
for the in vitro actin- Arp2/3 complex. Lamellipodium initiation was monitored
in an intracellular wound-healing model and was found to involve branching from
the sides of actin filaments oriented parallel to the plasmalemma. Many filament
plus ends, presumably capped, terminated behind the lamellipodium tip and localized
on the dorsal and ventral surfaces of the actin network. These findings reveal
how branching events initiate and maintain a network of actin filaments of variable
length, and provide the first structural model of the branch junction in vivo.
A possible role of filament capping in generating the lamellipodium leaflet is
discussed and a mathematical model of protrusion is also presented.
acknowledgement: This work was supported by the Austrian Science Fund [projects FWF
I516-B09 and FWF P21292-B09 to J.V.S.]; the Vienna Science and Technology Fund [WWTF-grant
numbers MA 09-004 to J.V.S. and C.S], ZIT - The Technology Agency of the City of
Vienna [VSOE, CMCN to J.V.S. and G.P.R.]; the Deutsche Forschungsgemeinschaft [grant
number RO 2414/1-2 to K.R.]; the Daiko research foundation [grant number 9134 to
A.N.]; and a Grant-in-Aid for Scientific Research [S, grant number 20227008 to Y.M.]
and a Grant-in-Aid for Young Scientists [B, grant number 22770145 to A.N.] (B) from
The Ministry of Education, Culture, Sports, Science and Technology of the Japanese
Government. Deposited in PMC for immediate release. We thank Tibor Kulcsar for assistance
with graphics.
article_processing_charge: No
author:
- first_name: Marlene
full_name: Vinzenz, Marlene
last_name: Vinzenz
- first_name: Maria
full_name: Nemethova, Maria
id: 34E27F1C-F248-11E8-B48F-1D18A9856A87
last_name: Nemethova
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Jan
full_name: Mueller, Jan
last_name: Mueller
- first_name: Akihiro
full_name: Narita, Akihiro
last_name: Narita
- first_name: Edit
full_name: Urban, Edit
last_name: Urban
- first_name: Christoph
full_name: Winkler, Christoph
last_name: Winkler
- first_name: Christian
full_name: Schmeiser, Christian
last_name: Schmeiser
- first_name: Stefan
full_name: Koestler, Stefan
last_name: Koestler
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- first_name: Guenter
full_name: Resch, Guenter
last_name: Resch
- first_name: Yuichiro
full_name: Maéda, Yuichiro
last_name: Maéda
- first_name: John
full_name: Small, John
last_name: Small
citation:
ama: Vinzenz M, Nemethova M, Schur FK, et al. Actin branching in the initiation
and maintenance of lamellipodia. Journal of Cell Science. 2012;125(11):2775-2785.
doi:10.1242/jcs.107623
apa: Vinzenz, M., Nemethova, M., Schur, F. K., Mueller, J., Narita, A., Urban, E.,
… Small, J. (2012). Actin branching in the initiation and maintenance of lamellipodia.
Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.107623
chicago: Vinzenz, Marlene, Maria Nemethova, Florian KM Schur, Jan Mueller, Akihiro
Narita, Edit Urban, Christoph Winkler, et al. “Actin Branching in the Initiation
and Maintenance of Lamellipodia.” Journal of Cell Science. Company of Biologists,
2012. https://doi.org/10.1242/jcs.107623.
ieee: M. Vinzenz et al., “Actin branching in the initiation and maintenance
of lamellipodia,” Journal of Cell Science, vol. 125, no. 11. Company of
Biologists, pp. 2775–2785, 2012.
ista: Vinzenz M, Nemethova M, Schur FK, Mueller J, Narita A, Urban E, Winkler C,
Schmeiser C, Koestler S, Rottner K, Resch G, Maéda Y, Small J. 2012. Actin branching
in the initiation and maintenance of lamellipodia. Journal of Cell Science. 125(11),
2775–2785.
mla: Vinzenz, Marlene, et al. “Actin Branching in the Initiation and Maintenance
of Lamellipodia.” Journal of Cell Science, vol. 125, no. 11, Company of
Biologists, 2012, pp. 2775–85, doi:10.1242/jcs.107623.
short: M. Vinzenz, M. Nemethova, F.K. Schur, J. Mueller, A. Narita, E. Urban, C.
Winkler, C. Schmeiser, S. Koestler, K. Rottner, G. Resch, Y. Maéda, J. Small,
Journal of Cell Science 125 (2012) 2775–2785.
date_created: 2018-12-11T11:48:37Z
date_published: 2012-06-01T00:00:00Z
date_updated: 2025-09-30T08:23:31Z
day: '01'
ddc:
- '570'
doi: 10.1242/jcs.107623
extern: '1'
external_id:
isi:
- '000306705000022'
file:
- access_level: open_access
checksum: 2f59e15cc3a85bb500a9887cef2aab67
content_type: application/pdf
creator: kschuh
date_created: 2019-02-12T08:54:51Z
date_updated: 2020-07-14T12:48:09Z
file_id: '5956'
file_name: 2012_Biologists_Vinzenz.pdf
file_size: 3326073
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
intvolume: ' 125'
isi: 1
issue: '11'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '06'
oa: 1
oa_version: None
page: 2775 - 2785
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '6842'
quality_controlled: '1'
status: public
title: Actin branching in the initiation and maintenance of lamellipodia
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 125
year: '2012'
...
---
_id: '8246'
abstract:
- lang: eng
text: The Staphylococcus aureus cell wall stress stimulon (CWSS) is activated by
cell envelope-targeting antibiotics or depletion of essential cell wall biosynthesis
enzymes. The functionally uncharacterized S. aureus LytR-CpsA-Psr (LCP) proteins,
MsrR, SA0908 and SA2103, all belong to the CWSS. Although not essential, deletion
of all three LCP proteins severely impairs cell division. We show here that VraSR-dependent
CWSS expression was up to 250-fold higher in single, double and triple LCP mutants
than in wild type S. aureus in the absence of external stress. The LCP triple
mutant was virtually depleted of wall teichoic acids (WTA), which could be restored
to different degrees by any of the single LCP proteins. Subinhibitory concentrations
of tunicamycin, which inhibits the first WTA synthesis enzyme TarO (TagO), could
partially complement the severe growth defect of the LCP triple mutant. Both of
the latter findings support a role for S. aureus LCP proteins in late WTA synthesis,
as in Bacillus subtilis where LCP proteins were recently proposed to transfer
WTA from lipid carriers to the cell wall peptidoglycan. Intrinsic activation of
the CWSS upon LCP deletion and the fact that LCP proteins were essential for WTA-loading
of the cell wall, highlight their important role(s) in S. aureus cell envelope
biogenesis.
article_processing_charge: No
article_type: original
author:
- first_name: Vanina
full_name: Dengler, Vanina
last_name: Dengler
- first_name: Patricia Stutzmann
full_name: Meier, Patricia Stutzmann
last_name: Meier
- first_name: Ronald
full_name: Heusser, Ronald
last_name: Heusser
- first_name: Peter
full_name: Kupferschmied, Peter
last_name: Kupferschmied
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: Sarah
full_name: Friebe, Sarah
last_name: Friebe
- first_name: Sibylle Burger
full_name: Staufer, Sibylle Burger
last_name: Staufer
- first_name: Paul A.
full_name: Majcherczyk, Paul A.
last_name: Majcherczyk
- first_name: Philippe
full_name: Moreillon, Philippe
last_name: Moreillon
- first_name: Brigitte
full_name: Berger-Bächi, Brigitte
last_name: Berger-Bächi
- first_name: Nadine
full_name: McCallum, Nadine
last_name: McCallum
citation:
ama: Dengler V, Meier PS, Heusser R, et al. Deletion of hypothetical wall teichoic
acid ligases in Staphylococcus aureus activates the cell wall stress response.
FEMS Microbiology Letters. 2012;333(2):109-120. doi:10.1111/j.1574-6968.2012.02603.x
apa: Dengler, V., Meier, P. S., Heusser, R., Kupferschmied, P., Singer, J., Friebe,
S., … McCallum, N. (2012). Deletion of hypothetical wall teichoic acid ligases
in Staphylococcus aureus activates the cell wall stress response. FEMS Microbiology
Letters. Oxford University Press. https://doi.org/10.1111/j.1574-6968.2012.02603.x
chicago: Dengler, Vanina, Patricia Stutzmann Meier, Ronald Heusser, Peter Kupferschmied,
Judit Singer, Sarah Friebe, Sibylle Burger Staufer, et al. “Deletion of Hypothetical
Wall Teichoic Acid Ligases in Staphylococcus Aureus Activates the Cell Wall Stress
Response.” FEMS Microbiology Letters. Oxford University Press, 2012. https://doi.org/10.1111/j.1574-6968.2012.02603.x.
ieee: V. Dengler et al., “Deletion of hypothetical wall teichoic acid ligases
in Staphylococcus aureus activates the cell wall stress response,” FEMS Microbiology
Letters, vol. 333, no. 2. Oxford University Press, pp. 109–120, 2012.
ista: Dengler V, Meier PS, Heusser R, Kupferschmied P, Singer J, Friebe S, Staufer
SB, Majcherczyk PA, Moreillon P, Berger-Bächi B, McCallum N. 2012. Deletion of
hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the
cell wall stress response. FEMS Microbiology Letters. 333(2), 109–120.
mla: Dengler, Vanina, et al. “Deletion of Hypothetical Wall Teichoic Acid Ligases
in Staphylococcus Aureus Activates the Cell Wall Stress Response.” FEMS Microbiology
Letters, vol. 333, no. 2, Oxford University Press, 2012, pp. 109–20, doi:10.1111/j.1574-6968.2012.02603.x.
short: V. Dengler, P.S. Meier, R. Heusser, P. Kupferschmied, J. Singer, S. Friebe,
S.B. Staufer, P.A. Majcherczyk, P. Moreillon, B. Berger-Bächi, N. McCallum, FEMS
Microbiology Letters 333 (2012) 109–120.
date_created: 2020-08-10T11:54:47Z
date_published: 2012-08-01T00:00:00Z
date_updated: 2021-01-12T08:17:43Z
day: '01'
doi: 10.1111/j.1574-6968.2012.02603.x
extern: '1'
external_id:
pmid:
- '22640011'
intvolume: ' 333'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
page: 109-120
pmid: 1
publication: FEMS Microbiology Letters
publication_identifier:
issn:
- 0378-1097
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus
activates the cell wall stress response
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 333
year: '2012'
...
---
_id: '826'
abstract:
- lang: eng
text: Plants exhibit a unique developmental flexibility to ever-changing environmental
conditions. To achieve their profound adaptability, plants are able to maintain
permanent stem cell populations and form new organs during the entire plant life
cycle. Signaling substances, called plant hormones, such as auxin, cytokinin,
abscisic acid, brassinosteroid, ethylene, gibberellin, jasmonic acid, and strigolactone,
govern and coordinate these developmental processes. Physiological and genetic
studies have dissected the molecular components of signal perception and transduction
of the individual hormonal pathways. However, over recent years it has become
evident that hormones do not act only in a linear pathway. Hormonal pathways are
interconnected by a complex network of interactions and feedback circuits that
determines the final outcome of the individual hormone actions. This raises questions
about the molecular mechanisms underlying hormonal cross talk and about how these
hormonal networks are established, maintained, and modulated throughout plant
development.
acknowledgement: We would like to thank Annick Bleys for help in preparing the manuscript.
This work was supported by the European Research Council with a Starting Independent
Research grant (ERC-2007-Stg-207362-HCPO) and the project CZ.1.07/2.3.00/20.0043
(to the Central European Institute of Technology, CEITEC) to E.B. M.V. is a postdoctoral
fellow of the Research Foundation Flanders. We apologize that, because of space
restrictions, the scientific contributions of only a limited number of original
articles could be cited and discussed.
author:
- first_name: Marleen
full_name: Vanstraelen, Marleen
last_name: Vanstraelen
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Vanstraelen M, Benková E. Hormonal interactions in the regulation of plant
development. Annual Review of Cell and Developmental Biology. 2012;28:463-487.
doi:10.1146/annurev-cellbio-101011-155741
apa: Vanstraelen, M., & Benková, E. (2012). Hormonal interactions in the regulation
of plant development. Annual Review of Cell and Developmental Biology.
Annual Reviews. https://doi.org/10.1146/annurev-cellbio-101011-155741
chicago: Vanstraelen, Marleen, and Eva Benková. “Hormonal Interactions in the Regulation
of Plant Development.” Annual Review of Cell and Developmental Biology.
Annual Reviews, 2012. https://doi.org/10.1146/annurev-cellbio-101011-155741.
ieee: M. Vanstraelen and E. Benková, “Hormonal interactions in the regulation of
plant development,” Annual Review of Cell and Developmental Biology, vol.
28. Annual Reviews, pp. 463–487, 2012.
ista: Vanstraelen M, Benková E. 2012. Hormonal interactions in the regulation of
plant development. Annual Review of Cell and Developmental Biology. 28, 463–487.
mla: Vanstraelen, Marleen, and Eva Benková. “Hormonal Interactions in the Regulation
of Plant Development.” Annual Review of Cell and Developmental Biology,
vol. 28, Annual Reviews, 2012, pp. 463–87, doi:10.1146/annurev-cellbio-101011-155741.
short: M. Vanstraelen, E. Benková, Annual Review of Cell and Developmental Biology
28 (2012) 463–487.
date_created: 2018-12-11T11:48:43Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2021-01-12T08:17:46Z
day: '01'
doi: 10.1146/annurev-cellbio-101011-155741
extern: 1
intvolume: ' 28'
month: '11'
page: 463 - 487
publication: Annual Review of Cell and Developmental Biology
publication_status: published
publisher: Annual Reviews
publist_id: '6822'
quality_controlled: 0
status: public
title: Hormonal interactions in the regulation of plant development
type: journal_article
volume: 28
year: '2012'
...
---
_id: '829'
abstract:
- lang: eng
text: The architecture of a plant's root system, established postembryonically,
results from both coordinated root growth and lateral root branching. The plant
hormones auxin and cytokinin are central endogenous signaling molecules that regulate
lateral root organogenesis positively and negatively, respectively. Tight control
and mutual balance of their antagonistic activities are particularly important
during the early phases of lateral root organogenesis to ensure continuous lateral
root initiation (LRI) and proper development of lateral root primordia (LRP).
Here, we show that the early phases of lateral root organogenesis, including priming
and initiation, take place in root zones with a repressed cytokinin response.
Accordingly, ectopic overproduction of cytokinin in the root basal meristem most
efficiently inhibits LRI. Enhanced cytokinin responses in pericycle cells between
existing LRP might restrict LRI near existing LRP and, when compromised, ectopic
LRI occurs. Furthermore, our results demonstrate that young LRP are more sensitive
to perturbations in the cytokinin activity than are developmentally more advanced
primordia. We hypothesize that the effect of cytokinin on the development of primordia
possibly depends on the robustness and stability of the auxin gradient.
acknowledgement: We thank Jen Sheen, Dolf Weijers, Tatsuo Kakimoto, Stephen Depuydt,
and Laurent Laplaze for sharing published material, Jiri Friml for discussions,
and Martine De Cock and Annick Bleys for help in preparing the manuscript. This
work was supported by a Starting Independent Research grant from the European Research
Council (ERC-2007-Stg-207362-HCPO) and the project CZ.1.07/2.3.00/20.0043 to the
Central European Institute of Technology to E.B. and grants from the Ministry of
Education, Youth, and Sports of the Czech Republic (MSM 6198959216) and the Centre
of the Region Haná for Biotechnological and Agricultural Research (ED0007/01/01)
to P.T.
author:
- first_name: Agnieszka
full_name: Bielach, Agnieszka
last_name: Bielach
- first_name: Katerina
full_name: Podlesakova, Katerina
last_name: Podlesakova
- first_name: Peter
full_name: Peter Marhavy
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Jérôme
full_name: Duclercq, Jérôme
last_name: Duclercq
- first_name: Candela
full_name: Candela Cuesta
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Bruno
full_name: Muller, Bruno
last_name: Muller
- first_name: Wim
full_name: Grunewald, Wim
last_name: Grunewald
- first_name: Petr
full_name: Tarkowski, Petr
last_name: Tarkowski
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Bielach A, Podlesakova K, Marhavý P, et al. Spatiotemporal regulation of lateral
root organogenesis in Arabidopsis by cytokinin. The Plant Cell. 2012;24(10):3967-3981.
doi:10.1105/tpc.112.103044
apa: Bielach, A., Podlesakova, K., Marhavý, P., Duclercq, J., Cuesta, C., Muller,
B., … Benková, E. (2012). Spatiotemporal regulation of lateral root organogenesis
in Arabidopsis by cytokinin. The Plant Cell. American Society of Plant
Biologists. https://doi.org/10.1105/tpc.112.103044
chicago: Bielach, Agnieszka, Katerina Podlesakova, Peter Marhavý, Jérôme Duclercq,
Candela Cuesta, Bruno Muller, Wim Grunewald, Petr Tarkowski, and Eva Benková.
“Spatiotemporal Regulation of Lateral Root Organogenesis in Arabidopsis by Cytokinin.”
The Plant Cell. American Society of Plant Biologists, 2012. https://doi.org/10.1105/tpc.112.103044.
ieee: A. Bielach et al., “Spatiotemporal regulation of lateral root organogenesis
in Arabidopsis by cytokinin,” The Plant Cell, vol. 24, no. 10. American
Society of Plant Biologists, pp. 3967–3981, 2012.
ista: Bielach A, Podlesakova K, Marhavý P, Duclercq J, Cuesta C, Muller B, Grunewald
W, Tarkowski P, Benková E. 2012. Spatiotemporal regulation of lateral root organogenesis
in Arabidopsis by cytokinin. The Plant Cell. 24(10), 3967–3981.
mla: Bielach, Agnieszka, et al. “Spatiotemporal Regulation of Lateral Root Organogenesis
in Arabidopsis by Cytokinin.” The Plant Cell, vol. 24, no. 10, American
Society of Plant Biologists, 2012, pp. 3967–81, doi:10.1105/tpc.112.103044.
short: A. Bielach, K. Podlesakova, P. Marhavý, J. Duclercq, C. Cuesta, B. Muller,
W. Grunewald, P. Tarkowski, E. Benková, The Plant Cell 24 (2012) 3967–3981.
date_created: 2018-12-11T11:48:43Z
date_published: 2012-10-01T00:00:00Z
date_updated: 2021-01-12T08:17:55Z
day: '01'
doi: 10.1105/tpc.112.103044
extern: 1
intvolume: ' 24'
issue: '10'
month: '10'
page: 3967 - 3981
publication: The Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6819'
quality_controlled: 0
status: public
title: Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin
type: journal_article
volume: 24
year: '2012'
...
---
_id: '846'
abstract:
- lang: eng
text: Whether or not evolutionary change is inherently irreversible remains a controversial
topic. Some examples of evolutionary irreversibility are known; however, this
question has not been comprehensively addressed at the molecular level. Here,
we use data from 221 human genes with known pathogenic mutations to estimate the
rate of irreversibility in protein evolution. For these genes, we reconstruct
ancestral amino acid sequences along the mammalian phylogeny and identify ancestral
amino acid states that match known pathogenic mutations. Such cases represent
inherent evolutionary irreversibility because, at the present moment, reversals
to these ancestral amino acid states are impossible for the human lineage. We
estimate that approximately 10% of all amino acid substitutions along the mammalian
phylogeny are irreversible, such that a return to the ancestral amino acid state
would lead to a pathogenic phenotype. For a subset of 51 genes with high rates
of irreversibility, as much as 40% of all amino acid evolution was estimated to
be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes,
the molecular nature of the high rate of irreversibility in proteins is best explained
by evolution with a high prevalence of compensatory, epistatic interactions between
amino acid sites. Under such mode of protein evolution, once an amino acid substitution
is fixed, the probability of its reversal declines as the protein sequence accumulates
changes that affect the phenotypic manifestation of the ancestral state. The prevalence
of epistasis in evolution indicates that the observed high rate of irreversibility
in protein evolution is an inherent property of protein structure and function.
acknowledgement: This work was supported by Plan Nacional grant BFU2009-09271 from
the Spanish Ministry of Science and Innovation and by FPU (Formación del Profesorado
Universitario) program grant AP2008-01888 from the Spanish Ministry of Education
to O.S. F.A.K. is a European Molecular Biology Organization Young Investigator and
Howard Hughes Medical Institute International Early Career Scientist.
author:
- first_name: Onuralp
full_name: Soylemez, Onuralp
last_name: Soylemez
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Soylemez O, Kondrashov F. Estimating the rate of irreversibility in protein
evolution. Genome Biology and Evolution. 2012;4(12):1213-1222. doi:10.1093/gbe/evs096
apa: Soylemez, O., & Kondrashov, F. (2012). Estimating the rate of irreversibility
in protein evolution. Genome Biology and Evolution. Oxford University Press.
https://doi.org/10.1093/gbe/evs096
chicago: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility
in Protein Evolution.” Genome Biology and Evolution. Oxford University
Press, 2012. https://doi.org/10.1093/gbe/evs096.
ieee: O. Soylemez and F. Kondrashov, “Estimating the rate of irreversibility in
protein evolution,” Genome Biology and Evolution, vol. 4, no. 12. Oxford
University Press, pp. 1213–1222, 2012.
ista: Soylemez O, Kondrashov F. 2012. Estimating the rate of irreversibility in
protein evolution. Genome Biology and Evolution. 4(12), 1213–1222.
mla: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility
in Protein Evolution.” Genome Biology and Evolution, vol. 4, no. 12, Oxford
University Press, 2012, pp. 1213–22, doi:10.1093/gbe/evs096.
short: O. Soylemez, F. Kondrashov, Genome Biology and Evolution 4 (2012) 1213–1222.
date_created: 2018-12-11T11:48:49Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '01'
doi: 10.1093/gbe/evs096
extern: 1
intvolume: ' 4'
issue: '12'
month: '01'
page: 1213 - 1222
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6802'
quality_controlled: 0
status: public
title: Estimating the rate of irreversibility in protein evolution
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
volume: 4
year: '2012'
...
---
_id: '8463'
abstract:
- lang: eng
text: The 1H dipolar network, which is the major obstacle for applying proton detection
in the solid-state, can be reduced by deuteration, employing the RAP (Reduced
Adjoining Protonation) labeling scheme, which yields random protonation at non-exchangeable
sites. We present here a systematic study on the optimal degree of random sidechain
protonation in RAP samples as a function of the MAS (magic angle spinning) frequency.
In particular, we compare 1H sensitivity and linewidth of a microcrystalline protein,
the SH3 domain of chicken α-spectrin, for samples, prepared with 5–25 % H2O in
the E. coli growth medium, in the MAS frequency range of 20–60 kHz. At an external
field of 19.96 T (850 MHz), we find that using a proton concentration between
15 and 25 % in the M9 medium yields the best compromise in terms of sensitivity
and resolution, with an achievable average 1H linewidth on the order of 40–50
Hz. Comparing sensitivities at a MAS frequency of 60 versus 20 kHz, a gain in
sensitivity by a factor of 4–4.5 is observed in INEPT-based 1H detected 1D 1H,13C
correlation experiments. In total, we find that spectra recorded with a 1.3 mm
rotor at 60 kHz have almost the same sensitivity as spectra recorded with a fully
packed 3.2 mm rotor at 20 kHz, even though ~20× less material is employed. The
improved sensitivity is attributed to 1H line narrowing due to fast MAS and to
the increased efficiency of the 1.3 mm coil.
article_processing_charge: No
article_type: original
author:
- first_name: Sam
full_name: Asami, Sam
last_name: Asami
- first_name: Kathrin
full_name: Szekely, Kathrin
last_name: Szekely
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Beat H.
full_name: Meier, Beat H.
last_name: Meier
- first_name: Bernd
full_name: Reif, Bernd
last_name: Reif
citation:
ama: Asami S, Szekely K, Schanda P, Meier BH, Reif B. Optimal degree of protonation
for 1H detection of aliphatic sites in randomly deuterated proteins as a function
of the MAS frequency. Journal of Biomolecular NMR. 2012;54(2):155-168.
doi:10.1007/s10858-012-9659-9
apa: Asami, S., Szekely, K., Schanda, P., Meier, B. H., & Reif, B. (2012). Optimal
degree of protonation for 1H detection of aliphatic sites in randomly deuterated
proteins as a function of the MAS frequency. Journal of Biomolecular NMR.
Springer Nature. https://doi.org/10.1007/s10858-012-9659-9
chicago: Asami, Sam, Kathrin Szekely, Paul Schanda, Beat H. Meier, and Bernd Reif.
“Optimal Degree of Protonation for 1H Detection of Aliphatic Sites in Randomly
Deuterated Proteins as a Function of the MAS Frequency.” Journal of Biomolecular
NMR. Springer Nature, 2012. https://doi.org/10.1007/s10858-012-9659-9.
ieee: S. Asami, K. Szekely, P. Schanda, B. H. Meier, and B. Reif, “Optimal degree
of protonation for 1H detection of aliphatic sites in randomly deuterated proteins
as a function of the MAS frequency,” Journal of Biomolecular NMR, vol.
54, no. 2. Springer Nature, pp. 155–168, 2012.
ista: Asami S, Szekely K, Schanda P, Meier BH, Reif B. 2012. Optimal degree of protonation
for 1H detection of aliphatic sites in randomly deuterated proteins as a function
of the MAS frequency. Journal of Biomolecular NMR. 54(2), 155–168.
mla: Asami, Sam, et al. “Optimal Degree of Protonation for 1H Detection of Aliphatic
Sites in Randomly Deuterated Proteins as a Function of the MAS Frequency.” Journal
of Biomolecular NMR, vol. 54, no. 2, Springer Nature, 2012, pp. 155–68, doi:10.1007/s10858-012-9659-9.
short: S. Asami, K. Szekely, P. Schanda, B.H. Meier, B. Reif, Journal of Biomolecular
NMR 54 (2012) 155–168.
date_created: 2020-09-18T10:09:18Z
date_published: 2012-08-23T00:00:00Z
date_updated: 2021-01-12T08:19:27Z
day: '23'
doi: 10.1007/s10858-012-9659-9
extern: '1'
intvolume: ' 54'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
page: 155-168
publication: Journal of Biomolecular NMR
publication_identifier:
issn:
- 0925-2738
- 1573-5001
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Optimal degree of protonation for 1H detection of aliphatic sites in randomly
deuterated proteins as a function of the MAS frequency
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2012'
...
---
_id: '8465'
abstract:
- lang: eng
text: We demonstrate that conformational exchange processes in proteins on microsecond-to-millisecond
time scales can be detected and quantified by solid-state NMR spectroscopy. We
show two independent approaches that measure the effect of conformational exchange
on transverse relaxation parameters, namely Carr–Purcell–Meiboom–Gill relaxation-dispersion
experiments and measurement of differential multiple-quantum coherence decay.
Long coherence lifetimes, as required for these experiments, are achieved by the
use of highly deuterated samples and fast magic-angle spinning. The usefulness
of the approaches is demonstrated by application to microcrystalline ubiquitin.
We detect a conformational exchange process in a region of the protein for which
dynamics have also been observed in solution. Interestingly, quantitative analysis
of the data reveals that the exchange process is more than 1 order of magnitude
slower than in solution, and this points to the impact of the crystalline environment
on free energy barriers.
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Tollinger, Martin
last_name: Tollinger
- first_name: Astrid C.
full_name: Sivertsen, Astrid C.
last_name: Sivertsen
- first_name: Beat H.
full_name: Meier, Beat H.
last_name: Meier
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. Site-resolved measurement
of microsecond-to-millisecond conformational-exchange processes in proteins by
solid-state NMR spectroscopy. Journal of the American Chemical Society.
2012;134(36):14800-14807. doi:10.1021/ja303591y
apa: Tollinger, M., Sivertsen, A. C., Meier, B. H., Ernst, M., & Schanda, P.
(2012). Site-resolved measurement of microsecond-to-millisecond conformational-exchange
processes in proteins by solid-state NMR spectroscopy. Journal of the American
Chemical Society. American Chemical Society. https://doi.org/10.1021/ja303591y
chicago: Tollinger, Martin, Astrid C. Sivertsen, Beat H. Meier, Matthias Ernst,
and Paul Schanda. “Site-Resolved Measurement of Microsecond-to-Millisecond Conformational-Exchange
Processes in Proteins by Solid-State NMR Spectroscopy.” Journal of the American
Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja303591y.
ieee: M. Tollinger, A. C. Sivertsen, B. H. Meier, M. Ernst, and P. Schanda, “Site-resolved
measurement of microsecond-to-millisecond conformational-exchange processes in
proteins by solid-state NMR spectroscopy,” Journal of the American Chemical
Society, vol. 134, no. 36. American Chemical Society, pp. 14800–14807, 2012.
ista: Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. 2012. Site-resolved
measurement of microsecond-to-millisecond conformational-exchange processes in
proteins by solid-state NMR spectroscopy. Journal of the American Chemical Society.
134(36), 14800–14807.
mla: Tollinger, Martin, et al. “Site-Resolved Measurement of Microsecond-to-Millisecond
Conformational-Exchange Processes in Proteins by Solid-State NMR Spectroscopy.”
Journal of the American Chemical Society, vol. 134, no. 36, American Chemical
Society, 2012, pp. 14800–07, doi:10.1021/ja303591y.
short: M. Tollinger, A.C. Sivertsen, B.H. Meier, M. Ernst, P. Schanda, Journal of
the American Chemical Society 134 (2012) 14800–14807.
date_created: 2020-09-18T10:10:20Z
date_published: 2012-08-21T00:00:00Z
date_updated: 2021-01-12T08:19:27Z
day: '21'
doi: 10.1021/ja303591y
extern: '1'
intvolume: ' 134'
issue: '36'
language:
- iso: eng
month: '08'
oa_version: None
page: 14800-14807
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Site-resolved measurement of microsecond-to-millisecond conformational-exchange
processes in proteins by solid-state NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 134
year: '2012'
...
---
_id: '8466'
abstract:
- lang: eng
text: Recent advances in NMR spectroscopy and the availability of high magnetic
field strengths now offer the possibility to record real-time 3D NMR spectra of
short-lived protein states, e.g., states that become transiently populated during
protein folding. Here we present a strategy for obtaining sequential NMR assignments
as well as atom-resolved information on structural and dynamic features within
a folding intermediate of the amyloidogenic protein β2-microglobulin that has
a half-lifetime of only 20 min.
article_processing_charge: No
article_type: original
author:
- first_name: Enrico
full_name: Rennella, Enrico
last_name: Rennella
- first_name: Thomas
full_name: Cutuil, Thomas
last_name: Cutuil
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Vincent
full_name: Forge, Vincent
last_name: Forge
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B. Real-time NMR
characterization of structure and dynamics in a transiently populated protein
folding intermediate. Journal of the American Chemical Society. 2012;134(19):8066-8069.
doi:10.1021/ja302598j
apa: Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Forge, V., & Brutscher,
B. (2012). Real-time NMR characterization of structure and dynamics in a transiently
populated protein folding intermediate. Journal of the American Chemical Society.
American Chemical Society. https://doi.org/10.1021/ja302598j
chicago: Rennella, Enrico, Thomas Cutuil, Paul Schanda, Isabel Ayala, Vincent Forge,
and Bernhard Brutscher. “Real-Time NMR Characterization of Structure and Dynamics
in a Transiently Populated Protein Folding Intermediate.” Journal of the American
Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja302598j.
ieee: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, and B. Brutscher,
“Real-time NMR characterization of structure and dynamics in a transiently populated
protein folding intermediate,” Journal of the American Chemical Society,
vol. 134, no. 19. American Chemical Society, pp. 8066–8069, 2012.
ista: Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B. 2012. Real-time
NMR characterization of structure and dynamics in a transiently populated protein
folding intermediate. Journal of the American Chemical Society. 134(19), 8066–8069.
mla: Rennella, Enrico, et al. “Real-Time NMR Characterization of Structure and Dynamics
in a Transiently Populated Protein Folding Intermediate.” Journal of the American
Chemical Society, vol. 134, no. 19, American Chemical Society, 2012, pp. 8066–69,
doi:10.1021/ja302598j.
short: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, B. Brutscher, Journal
of the American Chemical Society 134 (2012) 8066–8069.
date_created: 2020-09-18T10:10:28Z
date_published: 2012-05-03T00:00:00Z
date_updated: 2021-01-12T08:19:28Z
day: '03'
doi: 10.1021/ja302598j
extern: '1'
intvolume: ' 134'
issue: '19'
language:
- iso: eng
month: '05'
oa_version: None
page: 8066-8069
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Real-time NMR characterization of structure and dynamics in a transiently populated
protein folding intermediate
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 134
year: '2012'
...
---
_id: '8467'
abstract:
- lang: eng
text: Partial deuteration is a powerful tool to increase coherence life times and
spectral resolution in proton solid-state NMR. The J coupling to deuterium needs,
however, to be decoupled to maintain the good resolution in the (usually indirect)
13C dimension(s). We present a simple and reversible way to expand a commercial
1.3 mm HCN MAS probe with a 2H channel with sufficient field strength for J-decoupling
of deuterium, namely 2–3 kHz. The coil is placed at the outside of the stator
and requires no significant modifications to the probe. The performance and the
realizable gains in sensitivity and resolution are demonstrated using perdeuterated
ubiquitin, with selectively CHD2-labeled methyl groups.
article_processing_charge: No
article_type: original
author:
- first_name: Matthias
full_name: Huber, Matthias
last_name: Huber
- first_name: Oliver
full_name: With, Oliver
last_name: With
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: René
full_name: Verel, René
last_name: Verel
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
- first_name: Beat H.
full_name: Meier, Beat H.
last_name: Meier
citation:
ama: Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. A supplementary coil
for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance.
2012;214:76-80. doi:10.1016/j.jmr.2011.10.010
apa: Huber, M., With, O., Schanda, P., Verel, R., Ernst, M., & Meier, B. H.
(2012). A supplementary coil for 2H decoupling with commercial HCN MAS probes.
Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2011.10.010
chicago: Huber, Matthias, Oliver With, Paul Schanda, René Verel, Matthias Ernst,
and Beat H. Meier. “A Supplementary Coil for 2H Decoupling with Commercial HCN
MAS Probes.” Journal of Magnetic Resonance. Elsevier, 2012. https://doi.org/10.1016/j.jmr.2011.10.010.
ieee: M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, and B. H. Meier, “A supplementary
coil for 2H decoupling with commercial HCN MAS probes,” Journal of Magnetic
Resonance, vol. 214. Elsevier, pp. 76–80, 2012.
ista: Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. 2012. A supplementary
coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance.
214, 76–80.
mla: Huber, Matthias, et al. “A Supplementary Coil for 2H Decoupling with Commercial
HCN MAS Probes.” Journal of Magnetic Resonance, vol. 214, Elsevier, 2012,
pp. 76–80, doi:10.1016/j.jmr.2011.10.010.
short: M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, B.H. Meier, Journal of
Magnetic Resonance 214 (2012) 76–80.
date_created: 2020-09-18T10:10:36Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T08:19:28Z
day: '01'
doi: 10.1016/j.jmr.2011.10.010
extern: '1'
intvolume: ' 214'
language:
- iso: eng
month: '01'
oa_version: None
page: 76-80
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: A supplementary coil for 2H decoupling with commercial HCN MAS probes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 214
year: '2012'
...
---
_id: '8502'
abstract:
- lang: eng
text: 'The famous ergodic hypothesis suggests that for a typical Hamiltonian on
a typical energy surface nearly all trajectories are dense. KAM theory disproves
it. Ehrenfest (The Conceptual Foundations of the Statistical Approach in Mechanics.
Ithaca, NY: Cornell University Press, 1959) and Birkhoff (Collected Math Papers.
Vol 2, New York: Dover, pp 462–465, 1968) stated the quasi-ergodic hypothesis
claiming that a typical Hamiltonian on a typical energy surface has a dense orbit.
This question is wide open. Herman (Proceedings of the International Congress
of Mathematicians, Vol II (Berlin, 1998). Doc Math 1998, Extra Vol II, Berlin:
Int Math Union, pp 797–808, 1998) proposed to look for an example of a Hamiltonian
near H0(I)=⟨I,I⟩2 with a dense orbit on the unit energy surface. In this paper
we construct a Hamiltonian H0(I)+εH1(θ,I,ε) which has an orbit dense in a set
of maximal Hausdorff dimension equal to 5 on the unit energy surface.'
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: Maria
full_name: Saprykina, Maria
last_name: Saprykina
citation:
ama: Kaloshin V, Saprykina M. An example of a nearly integrable Hamiltonian system
with a trajectory dense in a set of maximal Hausdorff dimension. Communications
in Mathematical Physics. 2012;315(3):643-697. doi:10.1007/s00220-012-1532-x
apa: Kaloshin, V., & Saprykina, M. (2012). An example of a nearly integrable
Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension.
Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-012-1532-x
chicago: Kaloshin, Vadim, and Maria Saprykina. “An Example of a Nearly Integrable
Hamiltonian System with a Trajectory Dense in a Set of Maximal Hausdorff Dimension.”
Communications in Mathematical Physics. Springer Nature, 2012. https://doi.org/10.1007/s00220-012-1532-x.
ieee: V. Kaloshin and M. Saprykina, “An example of a nearly integrable Hamiltonian
system with a trajectory dense in a set of maximal Hausdorff dimension,” Communications
in Mathematical Physics, vol. 315, no. 3. Springer Nature, pp. 643–697, 2012.
ista: Kaloshin V, Saprykina M. 2012. An example of a nearly integrable Hamiltonian
system with a trajectory dense in a set of maximal Hausdorff dimension. Communications
in Mathematical Physics. 315(3), 643–697.
mla: Kaloshin, Vadim, and Maria Saprykina. “An Example of a Nearly Integrable Hamiltonian
System with a Trajectory Dense in a Set of Maximal Hausdorff Dimension.” Communications
in Mathematical Physics, vol. 315, no. 3, Springer Nature, 2012, pp. 643–97,
doi:10.1007/s00220-012-1532-x.
short: V. Kaloshin, M. Saprykina, Communications in Mathematical Physics 315 (2012)
643–697.
date_created: 2020-09-18T10:47:16Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2021-01-12T08:19:44Z
day: '01'
doi: 10.1007/s00220-012-1532-x
extern: '1'
intvolume: ' 315'
issue: '3'
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '11'
oa_version: None
page: 643-697
publication: Communications in Mathematical Physics
publication_identifier:
issn:
- 0010-3616
- 1432-0916
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: An example of a nearly integrable Hamiltonian system with a trajectory dense
in a set of maximal Hausdorff dimension
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 315
year: '2012'
...
---
_id: '8503'
abstract:
- lang: eng
text: We prove there are finitely many isometry classes of planar central configurations
(also called relative equilibria) in the Newtonian 5-body problem, except perhaps
if the 5-tuple of positive masses belongs to a given codimension 2 subvariety
of the mass space.
article_processing_charge: No
article_type: original
author:
- first_name: Alain
full_name: Albouy, Alain
last_name: Albouy
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Albouy A, Kaloshin V. Finiteness of central configurations of five bodies in
the plane. Annals of Mathematics. 2012;176(1):535-588. doi:10.4007/annals.2012.176.1.10
apa: Albouy, A., & Kaloshin, V. (2012). Finiteness of central configurations
of five bodies in the plane. Annals of Mathematics. Princeton University
Press. https://doi.org/10.4007/annals.2012.176.1.10
chicago: Albouy, Alain, and Vadim Kaloshin. “Finiteness of Central Configurations
of Five Bodies in the Plane.” Annals of Mathematics. Princeton University
Press, 2012. https://doi.org/10.4007/annals.2012.176.1.10.
ieee: A. Albouy and V. Kaloshin, “Finiteness of central configurations of five bodies
in the plane,” Annals of Mathematics, vol. 176, no. 1. Princeton University
Press, pp. 535–588, 2012.
ista: Albouy A, Kaloshin V. 2012. Finiteness of central configurations of five bodies
in the plane. Annals of Mathematics. 176(1), 535–588.
mla: Albouy, Alain, and Vadim Kaloshin. “Finiteness of Central Configurations of
Five Bodies in the Plane.” Annals of Mathematics, vol. 176, no. 1, Princeton
University Press, 2012, pp. 535–88, doi:10.4007/annals.2012.176.1.10.
short: A. Albouy, V. Kaloshin, Annals of Mathematics 176 (2012) 535–588.
date_created: 2020-09-18T10:47:24Z
date_published: 2012-07-01T00:00:00Z
date_updated: 2021-01-12T08:19:44Z
day: '01'
doi: 10.4007/annals.2012.176.1.10
extern: '1'
intvolume: ' 176'
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 535-588
publication: Annals of Mathematics
publication_identifier:
issn:
- 0003-486X
publication_status: published
publisher: Princeton University Press
quality_controlled: '1'
status: public
title: Finiteness of central configurations of five bodies in the plane
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 176
year: '2012'
...
---
_id: '8504'
abstract:
- lang: eng
text: In this paper we present a surprising example of a Cr unimodal map of an interval
f:I→I whose number of periodic points Pn(f)=∣{x∈I:fnx=x}∣ grows faster than any
ahead given sequence along a subsequence nk=3k. This example also shows that ‘non-flatness’
of critical points is necessary for the Martens–de Melo–van Strien theorem [M.
Martens, W. de Melo and S. van Strien. Julia–Fatou–Sullivan theory for real one-dimensional
dynamics. Acta Math.168(3–4) (1992), 273–318] to hold.
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: O. S.
full_name: KOZLOVSKI, O. S.
last_name: KOZLOVSKI
citation:
ama: Kaloshin V, KOZLOVSKI OS. A Cr unimodal map with an arbitrary fast growth of
the number of periodic points. Ergodic Theory and Dynamical Systems. 2012;32(1):159-165.
doi:10.1017/s0143385710000817
apa: Kaloshin, V., & KOZLOVSKI, O. S. (2012). A Cr unimodal map with an arbitrary
fast growth of the number of periodic points. Ergodic Theory and Dynamical
Systems. Cambridge University Press. https://doi.org/10.1017/s0143385710000817
chicago: Kaloshin, Vadim, and O. S. KOZLOVSKI. “A Cr Unimodal Map with an Arbitrary
Fast Growth of the Number of Periodic Points.” Ergodic Theory and Dynamical
Systems. Cambridge University Press, 2012. https://doi.org/10.1017/s0143385710000817.
ieee: V. Kaloshin and O. S. KOZLOVSKI, “A Cr unimodal map with an arbitrary fast
growth of the number of periodic points,” Ergodic Theory and Dynamical Systems,
vol. 32, no. 1. Cambridge University Press, pp. 159–165, 2012.
ista: Kaloshin V, KOZLOVSKI OS. 2012. A Cr unimodal map with an arbitrary fast growth
of the number of periodic points. Ergodic Theory and Dynamical Systems. 32(1),
159–165.
mla: Kaloshin, Vadim, and O. S. KOZLOVSKI. “A Cr Unimodal Map with an Arbitrary
Fast Growth of the Number of Periodic Points.” Ergodic Theory and Dynamical
Systems, vol. 32, no. 1, Cambridge University Press, 2012, pp. 159–65, doi:10.1017/s0143385710000817.
short: V. Kaloshin, O.S. KOZLOVSKI, Ergodic Theory and Dynamical Systems 32 (2012)
159–165.
date_created: 2020-09-18T10:47:33Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2021-01-12T08:19:44Z
day: '01'
doi: 10.1017/s0143385710000817
extern: '1'
intvolume: ' 32'
issue: '1'
keyword:
- Applied Mathematics
- General Mathematics
language:
- iso: eng
month: '02'
oa_version: None
page: 159-165
publication: Ergodic Theory and Dynamical Systems
publication_identifier:
issn:
- 0143-3857
- 1469-4417
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
status: public
title: A Cr unimodal map with an arbitrary fast growth of the number of periodic points
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2012'
...