---
_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
arxiv: 1
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: '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'
...
---
OA_place: repository
OA_type: green
_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.”
article_processing_charge: No
arxiv: 1
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: Proceedings of the 42nd International Colloquium on Automata,
Languages and Programming. Vol 9135. Springer Nature; 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. In Proceedings of the 42nd International
Colloquium on Automata, Languages and Programming (Vol. 9135, pp. 479–491).
Kyoto, Japan: Springer Nature. 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.” In Proceedings of the 42nd International
Colloquium on Automata, Languages and Programming, 9135:479–91. Springer Nature,
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,” in Proceedings of the 42nd International Colloquium
on Automata, Languages and Programming, Kyoto, Japan, 2015, vol. 9135, pp.
479–491.
ista: 'Alistarh D-A, Gelashvili R. 2015. Polylogarithmic-time leader election in
population protocols. Proceedings of the 42nd International Colloquium on Automata,
Languages and Programming. 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.” Proceedings of the 42nd International Colloquium
on Automata, Languages and Programming, vol. 9135, Springer Nature, 2015,
pp. 479–91, doi:10.1007/978-3-662-47666-6_38.
short: D.-A. Alistarh, R. Gelashvili, in:, Proceedings of the 42nd International
Colloquium on Automata, Languages and Programming, Springer Nature, 2015, pp.
479–491.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'ICALP: International Colloquium on Automota, Languages and Programming'
start_date: 2015-07-06
date_created: 2018-12-11T11:48:28Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2026-05-19T13:03:42Z
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: Proceedings of the 42nd International Colloquium on Automata, Languages
and Programming
publication_identifier:
eisbn:
- '9783662476666'
isbn:
- '9783662476659'
publication_status: published
publisher: Springer Nature
publist_id: '6877'
status: public
title: Polylogarithmic-time leader election in population protocols
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
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'
...
---
OA_place: publisher
OA_type: free access
_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: Proceedings of the 2015 ACM Symposium on Principles of Distributed
Computing. Vol 2015-July. Association for Computing Machinery; 2015:251-260.
doi:10.1145/2767386.2767430'
apa: 'Alistarh, D.-A., Sauerwald, T., & Vojnović, M. (2015). Lock-Free algorithms
under stochastic schedulers. In Proceedings of the 2015 ACM Symposium on Principles
of Distributed Computing (Vol. 2015–July, pp. 251–260). New York, NY, United
States: Association for Computing Machinery. https://doi.org/10.1145/2767386.2767430'
chicago: Alistarh, Dan-Adrian, Thomas Sauerwald, and Milan Vojnović. “Lock-Free
Algorithms under Stochastic Schedulers.” In Proceedings of the 2015 ACM Symposium
on Principles of Distributed Computing, 2015–July:251–60. Association for
Computing Machinery, 2015. https://doi.org/10.1145/2767386.2767430.
ieee: D.-A. Alistarh, T. Sauerwald, and M. Vojnović, “Lock-Free algorithms under
stochastic schedulers,” in Proceedings of the 2015 ACM Symposium on Principles
of Distributed Computing, New York, NY, United States, 2015, vol. 2015–July,
pp. 251–260.
ista: 'Alistarh D-A, Sauerwald T, Vojnović M. 2015. Lock-Free algorithms under stochastic
schedulers. Proceedings of the 2015 ACM Symposium on Principles of Distributed
Computing. PODC: Principles of Distributed Computing vol. 2015–July, 251–260.'
mla: Alistarh, Dan-Adrian, et al. “Lock-Free Algorithms under Stochastic Schedulers.”
Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing,
vol. 2015–July, Association for Computing Machinery, 2015, pp. 251–60, doi:10.1145/2767386.2767430.
short: D.-A. Alistarh, T. Sauerwald, M. Vojnović, in:, Proceedings of the 2015 ACM
Symposium on Principles of Distributed Computing, Association for Computing Machinery,
2015, pp. 251–260.
conference:
end_date: 2015-7-23
location: New York, NY, United States
name: 'PODC: Principles of Distributed Computing'
start_date: 2015-07-21
date_created: 2018-12-11T11:48:28Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2026-05-19T13:21:59Z
day: '21'
doi: 10.1145/2767386.2767430
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://dx.doi.org/10.1145/2767386.2767430
month: '07'
oa: 1
oa_version: Accepted Version
page: 251 - 260
publication: Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing
publication_identifier:
eisbn:
- '9781450336178'
publication_status: published
publisher: Association for Computing Machinery
publist_id: '6874'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lock-Free algorithms under stochastic schedulers
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 2015-July
year: '2015'
...
---
OA_place: publisher
OA_type: free access
_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
arxiv: 1
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: Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing.
Association for Computing Machinery; 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. In Proceedings of the 2015 ACM Symposium on Principles
of Distributed Computing (pp. 365–374). New York, NY, United States: Association
for Computing Machinery. 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.” In Proceedings of the 2015 ACM Symposium
on Principles of Distributed Computing, 365–74. Association for Computing
Machinery, 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,” in Proceedings of the 2015 ACM Symposium on Principles
of Distributed Computing, New York, NY, United States, 2015, pp. 365–374.
ista: 'Alistarh D-A, Gelashvili R, Vladu A. 2015. How to elect a leader faster than
a tournament. Proceedings of the 2015 ACM Symposium on Principles of Distributed
Computing. PODC: Principles of Distributed Computing, 365–374.'
mla: Alistarh, Dan-Adrian, et al. “How to Elect a Leader Faster than a Tournament.”
Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing,
Association for Computing Machinery, 2015, pp. 365–74, doi:10.1145/2767386.2767420.
short: D.-A. Alistarh, R. Gelashvili, A. Vladu, in:, Proceedings of the 2015 ACM
Symposium on Principles of Distributed Computing, Association for Computing Machinery,
2015, pp. 365–374.
conference:
end_date: 2015-07-23
location: New York, NY, United States
name: 'PODC: Principles of Distributed Computing'
start_date: 2015-07-21
date_created: 2018-12-11T11:48:28Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2026-05-19T13:27:49Z
day: '21'
doi: 10.1145/2767386.2767420
extern: '1'
external_id:
arxiv:
- '1411.1001'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/2767386.2767420
month: '07'
oa: 1
oa_version: Accepted Version
page: 365 - 374
publication: Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing
publication_identifier:
isbn:
- '9781450336178'
publication_status: published
publisher: Association for Computing Machinery
publist_id: '6875'
quality_controlled: '1'
scopus_import: '1'
status: public
title: How to elect a leader faster than a tournament
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2015'
...
---
_id: '784'
abstract:
- lang: eng
text: We demonstrate an optical switch design that can scale up to a thousand ports
with high per-port bandwidth (25 Gbps+) and low switching latency (40 ns). Our
design uses a broadcast and select architecture, based on a passive star coupler
and fast tunable transceivers. In addition we employ time division multiplexing
to achieve very low switching latency. Our demo shows the feasibility of the switch
data plane using a small testbed, comprising two transmitters and a receiver,
connected through a star coupler.
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Hitesh
full_name: Ballani, Hitesh
last_name: Ballani
- first_name: Paolo
full_name: Costa, Paolo
last_name: Costa
- first_name: Adam
full_name: Funnell, Adam
last_name: Funnell
- first_name: Joshua
full_name: Benjamin, Joshua
last_name: Benjamin
- first_name: Philip
full_name: Watts, Philip
last_name: Watts
- first_name: Benn
full_name: Thomsen, Benn
last_name: Thomsen
citation:
ama: 'Alistarh D-A, Ballani H, Costa P, et al. A high-radix, low-latency optical
switch for data centers. In: ACM; 2015:367-368. doi:10.1145/2785956.2790035'
apa: 'Alistarh, D.-A., Ballani, H., Costa, P., Funnell, A., Benjamin, J., Watts,
P., & Thomsen, B. (2015). A high-radix, low-latency optical switch for data
centers (pp. 367–368). Presented at the SIGCOMM: Special Interest Group on Data
Communication, London, United Kindgdom: ACM. https://doi.org/10.1145/2785956.2790035'
chicago: Alistarh, Dan-Adrian, Hitesh Ballani, Paolo Costa, Adam Funnell, Joshua
Benjamin, Philip Watts, and Benn Thomsen. “A High-Radix, Low-Latency Optical Switch
for Data Centers,” 367–68. ACM, 2015. https://doi.org/10.1145/2785956.2790035.
ieee: 'D.-A. Alistarh et al., “A high-radix, low-latency optical switch for
data centers,” presented at the SIGCOMM: Special Interest Group on Data Communication,
London, United Kindgdom, 2015, pp. 367–368.'
ista: 'Alistarh D-A, Ballani H, Costa P, Funnell A, Benjamin J, Watts P, Thomsen
B. 2015. A high-radix, low-latency optical switch for data centers. SIGCOMM: Special
Interest Group on Data Communication, 367–368.'
mla: Alistarh, Dan-Adrian, et al. A High-Radix, Low-Latency Optical Switch for
Data Centers. ACM, 2015, pp. 367–68, doi:10.1145/2785956.2790035.
short: D.-A. Alistarh, H. Ballani, P. Costa, A. Funnell, J. Benjamin, P. Watts,
B. Thomsen, in:, ACM, 2015, pp. 367–368.
conference:
end_date: 2015-08-21
location: London, United Kindgdom
name: 'SIGCOMM: Special Interest Group on Data Communication'
start_date: 2015-08-17
date_created: 2018-12-11T11:48:29Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:18:57Z
day: '01'
doi: 10.1145/2785956.2790035
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 367 - 368
publication_identifier:
isbn:
- 978-1-4503-3542-3
publication_status: published
publisher: ACM
publist_id: '6872'
quality_controlled: '1'
status: public
title: A high-radix, low-latency optical switch for data centers
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '802'
abstract:
- lang: eng
text: Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at
the plasma membrane of various eukaryotes with the important exception of mammals.
In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man)
linked at position 2 of the inositol. However, several pathogenic fungi additionally
synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at
this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC
core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC,
which is the most abundant GIPC synthesized by this fungus. In this study, we
identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate
its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted
deletion of the gene encoding GntA in A. fumigatus resulted in complete absence
of zwitterionic GIPC; a phenotype that could be reverted by episomal expression
of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was
substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces
cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore
shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid
product resistant to saponification and to digestion by phosphatidylinositol-phospholipase
C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation
of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis.
article_processing_charge: No
author:
- first_name: Jakob
full_name: Engel, Jakob
last_name: Engel
- first_name: Philipp S
full_name: Schmalhorst, Philipp S
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Anke
full_name: Kruger, Anke
last_name: Kruger
- first_name: Christina
full_name: Muller, Christina
last_name: Muller
- first_name: Falk
full_name: Buettner, Falk
last_name: Buettner
- first_name: Françoise
full_name: Routier, Françoise
last_name: Routier
citation:
ama: Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. Characterization
of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic
glycoinositolphosphoceramide biosynthesis. Glycobiology. 2015;25(12):1423-1430.
doi:10.1093/glycob/cwv059
apa: Engel, J., Schmalhorst, P. S., Kruger, A., Muller, C., Buettner, F., &
Routier, F. (2015). Characterization of an N-acetylglucosaminyltransferase involved
in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis.
Glycobiology. Oxford University Press. https://doi.org/10.1093/glycob/cwv059
chicago: Engel, Jakob, Philipp S Schmalhorst, Anke Kruger, Christina Muller, Falk
Buettner, and Françoise Routier. “Characterization of an N-Acetylglucosaminyltransferase
Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.”
Glycobiology. Oxford University Press, 2015. https://doi.org/10.1093/glycob/cwv059.
ieee: J. Engel, P. S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, and F. Routier,
“Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis,” Glycobiology,
vol. 25, no. 12. Oxford University Press, pp. 1423–1430, 2015.
ista: Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. 2015.
Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology.
25(12), 1423–1430.
mla: Engel, Jakob, et al. “Characterization of an N-Acetylglucosaminyltransferase
Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.”
Glycobiology, vol. 25, no. 12, Oxford University Press, 2015, pp. 1423–30,
doi:10.1093/glycob/cwv059.
short: J. Engel, P.S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, F. Routier,
Glycobiology 25 (2015) 1423–1430.
date_created: 2018-12-11T11:48:35Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2025-09-23T08:14:24Z
day: '01'
department:
- _id: CaHe
doi: 10.1093/glycob/cwv059
external_id:
isi:
- '000368443700010'
pmid:
- '26306635'
intvolume: ' 25'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 1423 - 1430
pmid: 1
publication: Glycobiology
publication_status: published
publisher: Oxford University Press
publist_id: '6851'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 25
year: '2015'
...
---
OA_type: closed access
_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.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Wim
full_name: Hagen, Wim
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
last_name: Kraüsslich
- first_name: John
full_name: Briggs, John
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. Springer Nature. 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. Springer Nature, 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. Springer
Nature, 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, Springer
Nature, 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: 2026-05-19T08:19:41Z
day: '22'
doi: 10.1038/nature13838
extern: '1'
external_id:
pmid:
- '25363765'
intvolume: ' 517'
issue: '7535'
language:
- iso: eng
month: '01'
oa_version: None
page: 505 - 508
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
publist_id: '6836'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 517
year: '2015'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_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"
article_processing_charge: No
article_type: original
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: 2026-05-18T12:47:51Z
day: '22'
doi: 10.1128/JVI.01502-15
extern: '1'
external_id:
pmid:
- '26223638'
intvolume: ' 89'
issue: '20'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.1128/jvi.01502-15
month: '09'
oa: 1
oa_version: Published Version
page: 10294 - 10302
pmid: 1
publication: Journal of Virology
publication_identifier:
eissn:
- 1098-5514
issn:
- 0022-538X
publication_status: published
publisher: ASM
publist_id: '6837'
quality_controlled: '1'
scopus_import: '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
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 89
year: '2015'
...
---
_id: '8183'
abstract:
- lang: eng
text: "We study conditions under which a finite simplicial complex $K$ can be mapped
to $\\mathbb R^d$ without higher-multiplicity intersections. An almost $r$-embedding
is a map $f: K\\to \\mathbb R^d$ such that the images of any $r$\r\npairwise disjoint
simplices of $K$ do not have a common point. We show that if $r$ is not a prime
power and $d\\geq 2r+1$, then there is a counterexample to the topological Tverberg
conjecture, i.e., there is an almost $r$-embedding of\r\nthe $(d+1)(r-1)$-simplex
in $\\mathbb R^d$. This improves on previous constructions of counterexamples
(for $d\\geq 3r$) based on a series of papers by M. \\\"Ozaydin, M. Gromov, P.
Blagojevi\\'c, F. Frick, G. Ziegler, and the second and fourth present authors.
The counterexamples are obtained by proving the following algebraic criterion
in codimension 2: If $r\\ge3$ and if $K$ is a finite $2(r-1)$-complex then there
exists an almost $r$-embedding $K\\to \\mathbb R^{2r}$ if and only if there exists
a general position PL map $f:K\\to \\mathbb R^{2r}$ such that the algebraic intersection
number of the $f$-images of any $r$ pairwise disjoint simplices of $K$ is zero.
This result can be restated in terms of cohomological obstructions or equivariant
maps, and extends an analogous codimension 3 criterion by the second and fourth
authors. As another application we classify ornaments $f:S^3 \\sqcup S^3\\sqcup
S^3\\to \\mathbb R^5$ up to ornament\r\nconcordance. It follows from work of M.
Freedman, V. Krushkal and P. Teichner that the analogous criterion for $r=2$ is
false. We prove a lemma on singular higher-dimensional Borromean rings, yielding
an elementary proof of the counterexample."
acknowledgement: We would like to thank A. Klyachko, V. Krushkal, S. Melikhov, M.
Tancer, P. Teichner and anonymous referees for helpful discussions.
article_number: '1511.03501'
article_processing_charge: No
arxiv: 1
author:
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
orcid: 0000-0002-7840-5062
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
- first_name: A.
full_name: Skopenkov, A.
last_name: Skopenkov
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity
intersections, III. Codimension 2. arXiv. doi:10.48550/arXiv.1511.03501
apa: Avvakumov, S., Mabillard, I., Skopenkov, A., & Wagner, U. (n.d.). Eliminating
higher-multiplicity intersections, III. Codimension 2. arXiv. https://doi.org/10.48550/arXiv.1511.03501
chicago: Avvakumov, Sergey, Isaac Mabillard, A. Skopenkov, and Uli Wagner. “Eliminating
Higher-Multiplicity Intersections, III. Codimension 2.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1511.03501.
ieee: S. Avvakumov, I. Mabillard, A. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity
intersections, III. Codimension 2,” arXiv. .
ista: Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity
intersections, III. Codimension 2. arXiv, 1511.03501.
mla: Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections, III.
Codimension 2.” ArXiv, 1511.03501, doi:10.48550/arXiv.1511.03501.
short: S. Avvakumov, I. Mabillard, A. Skopenkov, U. Wagner, ArXiv (n.d.).
corr_author: '1'
date_created: 2020-07-30T10:45:19Z
date_published: 2015-11-15T00:00:00Z
date_updated: 2026-04-08T07:25:54Z
day: '15'
department:
- _id: UlWa
doi: 10.48550/arXiv.1511.03501
external_id:
arxiv:
- '1511.03501'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.03501
month: '11'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: draft
related_material:
record:
- id: '9308'
relation: later_version
status: public
- id: '10220'
relation: later_version
status: public
- id: '8156'
relation: dissertation_contains
status: public
status: public
title: Eliminating higher-multiplicity intersections, III. Codimension 2
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_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\r\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). "
article_processing_charge: No
article_type: original
author:
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Eva
full_name: Benková, Eva
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: 2026-05-19T09:39:29Z
day: '20'
doi: 10.21769/BioProtoc.1446
extern: '1'
external_id:
pmid:
- '27331080'
intvolume: ' 5'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.21769/BioProtoc.1446
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Bio-protocol
publication_identifier:
eissn:
- 2331-8325
publication_status: published
publisher: Bio-protocol LLC
publist_id: '6816'
quality_controlled: '1'
status: public
title: Real time analysis of lateral root organogenesis in arabidopsis
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 5
year: '2015'
...
---
OA_place: publisher
OA_type: gold
_id: '8456'
abstract:
- lang: eng
text: The large majority of three-dimensional structures of biological macromolecules
have been determined by X-ray diffraction of crystalline samples. High-resolution
structure determination crucially depends on the homogeneity of the protein crystal.
Overall ‘rocking’ motion of molecules in the crystal is expected to influence
diffraction quality, and such motion may therefore affect the process of solving
crystal structures. Yet, so far overall molecular motion has not directly been
observed in protein crystals, and the timescale of such dynamics remains unclear.
Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics
simulations to directly characterize the rigid-body motion of a protein in different
crystal forms. For ubiquitin crystals investigated in this study we determine
the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude
of rocking varies from one crystal form to another and is correlated with the
resolution obtainable in X-ray diffraction experiments.
article_number: '8361'
article_processing_charge: Yes
article_type: original
author:
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Yi
full_name: Xue, Yi
last_name: Xue
- first_name: Nicolas
full_name: Coquelle, Nicolas
last_name: Coquelle
- first_name: Jens D.
full_name: Haller, Jens D.
last_name: Haller
- first_name: Tairan
full_name: Yuwen, Tairan
last_name: Yuwen
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Oleg
full_name: Mikhailovskii, Oleg
last_name: Mikhailovskii
- first_name: Dieter
full_name: Willbold, Dieter
last_name: Willbold
- first_name: Jacques-Philippe
full_name: Colletier, Jacques-Philippe
last_name: Colletier
- first_name: Nikolai R.
full_name: Skrynnikov, Nikolai R.
last_name: Skrynnikov
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Ma P, Xue Y, Coquelle N, et al. Observing the overall rocking motion of a protein
in a crystal. Nature Communications. 2015;6. doi:10.1038/ncomms9361
apa: Ma, P., Xue, Y., Coquelle, N., Haller, J. D., Yuwen, T., Ayala, I., … Schanda,
P. (2015). Observing the overall rocking motion of a protein in a crystal. Nature
Communications. Springer Nature. https://doi.org/10.1038/ncomms9361
chicago: Ma, Peixiang, Yi Xue, Nicolas Coquelle, Jens D. Haller, Tairan Yuwen, Isabel
Ayala, Oleg Mikhailovskii, et al. “Observing the Overall Rocking Motion of a Protein
in a Crystal.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms9361.
ieee: P. Ma et al., “Observing the overall rocking motion of a protein in
a crystal,” Nature Communications, vol. 6. Springer Nature, 2015.
ista: Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold
D, Colletier J-P, Skrynnikov NR, Schanda P. 2015. Observing the overall rocking
motion of a protein in a crystal. Nature Communications. 6, 8361.
mla: Ma, Peixiang, et al. “Observing the Overall Rocking Motion of a Protein in
a Crystal.” Nature Communications, vol. 6, 8361, Springer Nature, 2015,
doi:10.1038/ncomms9361.
short: P. Ma, Y. Xue, N. Coquelle, J.D. Haller, T. Yuwen, I. Ayala, O. Mikhailovskii,
D. Willbold, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications
6 (2015).
date_created: 2020-09-18T10:07:36Z
date_published: 2015-10-05T00:00:00Z
date_updated: 2025-01-22T14:39:22Z
day: '05'
doi: 10.1038/ncomms9361
extern: '1'
intvolume: ' 6'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/ncomms9361
month: '10'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Observing the overall rocking motion of a protein in a crystal
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '8457'
abstract:
- lang: eng
text: We review recent advances in methodologies to study microseconds‐to‐milliseconds
exchange processes in biological molecules using magic‐angle spinning solid‐state
nuclear magnetic resonance (MAS ssNMR) spectroscopy. The particularities of MAS
ssNMR, as compared to solution‐state NMR, are elucidated using numerical simulations
and experimental data. These simulations reveal the potential of MAS NMR to provide
detailed insight into short‐lived conformations of biological molecules. Recent
studies of conformational exchange dynamics in microcrystalline ubiquitin are
discussed.
article_processing_charge: No
article_type: original
author:
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Ma P, Schanda P. Conformational exchange processes in biological systems:
Detection by solid-state NMR. eMagRes. 2015;4(3):699-708. doi:10.1002/9780470034590.emrstm1418'
apa: 'Ma, P., & Schanda, P. (2015). Conformational exchange processes in biological
systems: Detection by solid-state NMR. EMagRes. Wiley. https://doi.org/10.1002/9780470034590.emrstm1418'
chicago: 'Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in
Biological Systems: Detection by Solid-State NMR.” EMagRes. Wiley, 2015.
https://doi.org/10.1002/9780470034590.emrstm1418.'
ieee: 'P. Ma and P. Schanda, “Conformational exchange processes in biological systems:
Detection by solid-state NMR,” eMagRes, vol. 4, no. 3. Wiley, pp. 699–708,
2015.'
ista: 'Ma P, Schanda P. 2015. Conformational exchange processes in biological systems:
Detection by solid-state NMR. eMagRes. 4(3), 699–708.'
mla: 'Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological
Systems: Detection by Solid-State NMR.” EMagRes, vol. 4, no. 3, Wiley,
2015, pp. 699–708, doi:10.1002/9780470034590.emrstm1418.'
short: P. Ma, P. Schanda, EMagRes 4 (2015) 699–708.
date_created: 2020-09-18T10:07:45Z
date_published: 2015-09-10T00:00:00Z
date_updated: 2021-01-12T08:19:24Z
day: '10'
doi: 10.1002/9780470034590.emrstm1418
extern: '1'
intvolume: ' 4'
issue: '3'
language:
- iso: eng
month: '09'
oa_version: None
page: 699-708
publication: eMagRes
publication_identifier:
isbn:
- '9780470034590'
- '9780470058213'
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: 'Conformational exchange processes in biological systems: Detection by solid-state
NMR'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2015'
...
---
_id: '848'
abstract:
- lang: eng
text: The nature of factors governing the tempo and mode of protein evolution is
a fundamental issue in evolutionary biology. Specifically, whether or not interactions
between different sites, or epistasis, are important in directing the course of
evolution became one of the central questions. Several recent reports have scrutinized
patterns of long-term protein evolution claiming them to be compatible only with
an epistatic fitness landscape. However, these claims have not yet been substantiated
with a formal model of protein evolution. Here, we formulate a simple covarion-like
model of protein evolution focusing on the rate at which the fitness impact of
amino acids at a site changes with time. We then apply the model to the data on
convergent and divergent protein evolution to test whether or not the incorporation
of epistatic interactions is necessary to explain the data. We find that convergent
evolution cannot be explained without the incorporation of epistasis and the rate
at which an amino acid state switches from being acceptable at a site to being
deleterious is faster than the rate of amino acid substitution. Specifically,
for proteins that have persisted in modern prokaryotic organisms since the last
universal common ancestor for one amino acid substitution approximately ten amino
acid states switch from being accessible to being deleterious, or vice versa.
Thus, molecular evolution can only be perceived in the context of rapid turnover
of which amino acids are available for evolution.
article_processing_charge: No
author:
- first_name: Dinara
full_name: Usmanova, Dinara
last_name: Usmanova
- first_name: Luca
full_name: Ferretti, Luca
last_name: Ferretti
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Peter
full_name: Vlasov, Peter
last_name: Vlasov
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. A model of
substitution trajectories in sequence space and long-term protein evolution. Molecular
Biology and Evolution. 2015;32(2):542-554. doi:10.1093/molbev/msu318
apa: Usmanova, D., Ferretti, L., Povolotskaya, I., Vlasov, P., & Kondrashov,
F. (2015). A model of substitution trajectories in sequence space and long-term
protein evolution. Molecular Biology and Evolution. Oxford University Press.
https://doi.org/10.1093/molbev/msu318
chicago: Usmanova, Dinara, Luca Ferretti, Inna Povolotskaya, Peter Vlasov, and Fyodor
Kondrashov. “A Model of Substitution Trajectories in Sequence Space and Long-Term
Protein Evolution.” Molecular Biology and Evolution. Oxford University
Press, 2015. https://doi.org/10.1093/molbev/msu318.
ieee: D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A
model of substitution trajectories in sequence space and long-term protein evolution,”
Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press,
pp. 542–554, 2015.
ista: Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. 2015. A model
of substitution trajectories in sequence space and long-term protein evolution.
Molecular Biology and Evolution. 32(2), 542–554.
mla: Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence
Space and Long-Term Protein Evolution.” Molecular Biology and Evolution,
vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:10.1093/molbev/msu318.
short: D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular
Biology and Evolution 32 (2015) 542–554.
date_created: 2018-12-11T11:48:49Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2025-09-22T14:32:37Z
day: '01'
doi: 10.1093/molbev/msu318
extern: '1'
external_id:
isi:
- '000350050700020'
intvolume: ' 32'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 542 - 554
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6804'
quality_controlled: '1'
status: public
title: A model of substitution trajectories in sequence space and long-term protein
evolution
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 32
year: '2015'
...
---
_id: '8495'
abstract:
- lang: eng
text: 'In this note, we consider the dynamics associated to a perturbation of an
integrable Hamiltonian system in action-angle coordinates in any number of degrees
of freedom and we prove the following result of ``micro-diffusion'''': under generic
assumptions on $ h$ and $ f$, there exists an orbit of the system for which the
drift of its action variables is at least of order $ \sqrt {\varepsilon }$, after
a time of order $ \sqrt {\varepsilon }^{-1}$. The assumptions, which are essentially
minimal, are that there exists a resonant point for $ h$ and that the corresponding
averaged perturbation is non-constant. The conclusions, although very weak when
compared to usual instability phenomena, are also essentially optimal within this
setting.'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Abed
full_name: Bounemoura, Abed
last_name: Bounemoura
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Bounemoura A, Kaloshin V. A note on micro-instability for Hamiltonian systems
close to integrable. Proceedings of the American Mathematical Society.
2015;144(4):1553-1560. doi:10.1090/proc/12796
apa: Bounemoura, A., & Kaloshin, V. (2015). A note on micro-instability for
Hamiltonian systems close to integrable. Proceedings of the American Mathematical
Society. American Mathematical Society. https://doi.org/10.1090/proc/12796
chicago: Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for
Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical
Society. American Mathematical Society, 2015. https://doi.org/10.1090/proc/12796.
ieee: A. Bounemoura and V. Kaloshin, “A note on micro-instability for Hamiltonian
systems close to integrable,” Proceedings of the American Mathematical Society,
vol. 144, no. 4. American Mathematical Society, pp. 1553–1560, 2015.
ista: Bounemoura A, Kaloshin V. 2015. A note on micro-instability for Hamiltonian
systems close to integrable. Proceedings of the American Mathematical Society.
144(4), 1553–1560.
mla: Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian
Systems Close to Integrable.” Proceedings of the American Mathematical Society,
vol. 144, no. 4, American Mathematical Society, 2015, pp. 1553–60, doi:10.1090/proc/12796.
short: A. Bounemoura, V. Kaloshin, Proceedings of the American Mathematical Society
144 (2015) 1553–1560.
date_created: 2020-09-18T10:46:14Z
date_published: 2015-12-21T00:00:00Z
date_updated: 2021-01-12T08:19:40Z
day: '21'
doi: 10.1090/proc/12796
extern: '1'
intvolume: ' 144'
issue: '4'
language:
- iso: eng
month: '12'
oa_version: None
page: 1553-1560
publication: Proceedings of the American Mathematical Society
publication_identifier:
issn:
- 0002-9939
- 1088-6826
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
status: public
title: A note on micro-instability for Hamiltonian systems close to integrable
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 144
year: '2015'
...
---
_id: '8498'
abstract:
- lang: eng
text: "In the present note we announce a proof of a strong form of Arnold diffusion
for smooth convex Hamiltonian systems. Let ${\\mathbb T}^2$ be a 2-dimensional
torus and B2 be the unit ball around the origin in ${\\mathbb R}^2$ . Fix ρ >
0. Our main result says that for a 'generic' time-periodic perturbation of an
integrable system of two degrees of freedom $H_0(p)+\\varepsilon H_1(\\theta,p,t),\\quad
\\ \\theta\\in {\\mathbb T}^2,\\ p\\in B^2,\\ t\\in {\\mathbb T}={\\mathbb R}/{\\mathbb
Z}$ , with a strictly convex H0, there exists a ρ-dense orbit (θε, pε, t)(t) in
${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ , namely, a ρ-neighborhood of
the orbit contains ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ .\r\n\r\nOur
proof is a combination of geometric and variational methods. The fundamental elements
of the construction are the usage of crumpled normally hyperbolic invariant cylinders
from [9], flower and simple normally hyperbolic invariant manifolds from [36]
as well as their kissing property at a strong double resonance. This allows us
to build a 'connected' net of three-dimensional normally hyperbolic invariant
manifolds. To construct diffusing orbits along this net we employ a version of
the Mather variational method [41] equipped with weak KAM theory [28], proposed
by Bernard in [7]."
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: K
full_name: Zhang, K
last_name: Zhang
citation:
ama: Kaloshin V, Zhang K. Arnold diffusion for smooth convex systems of two and
a half degrees of freedom. Nonlinearity. 2015;28(8):2699-2720. doi:10.1088/0951-7715/28/8/2699
apa: Kaloshin, V., & Zhang, K. (2015). Arnold diffusion for smooth convex systems
of two and a half degrees of freedom. Nonlinearity. IOP Publishing. https://doi.org/10.1088/0951-7715/28/8/2699
chicago: Kaloshin, Vadim, and K Zhang. “Arnold Diffusion for Smooth Convex Systems
of Two and a Half Degrees of Freedom.” Nonlinearity. IOP Publishing, 2015.
https://doi.org/10.1088/0951-7715/28/8/2699.
ieee: V. Kaloshin and K. Zhang, “Arnold diffusion for smooth convex systems of two
and a half degrees of freedom,” Nonlinearity, vol. 28, no. 8. IOP Publishing,
pp. 2699–2720, 2015.
ista: Kaloshin V, Zhang K. 2015. Arnold diffusion for smooth convex systems of two
and a half degrees of freedom. Nonlinearity. 28(8), 2699–2720.
mla: Kaloshin, Vadim, and K. Zhang. “Arnold Diffusion for Smooth Convex Systems
of Two and a Half Degrees of Freedom.” Nonlinearity, vol. 28, no. 8, IOP
Publishing, 2015, pp. 2699–720, doi:10.1088/0951-7715/28/8/2699.
short: V. Kaloshin, K. Zhang, Nonlinearity 28 (2015) 2699–2720.
date_created: 2020-09-18T10:46:43Z
date_published: 2015-06-30T00:00:00Z
date_updated: 2021-01-12T08:19:41Z
day: '30'
doi: 10.1088/0951-7715/28/8/2699
extern: '1'
intvolume: ' 28'
issue: '8'
keyword:
- Mathematical Physics
- General Physics and Astronomy
- Applied Mathematics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '06'
oa_version: None
page: 2699-2720
publication: Nonlinearity
publication_identifier:
issn:
- 0951-7715
- 1361-6544
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
status: public
title: Arnold diffusion for smooth convex systems of two and a half degrees of freedom
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2015'
...
---
_id: '8499'
abstract:
- lang: eng
text: "We consider the cubic defocusing nonlinear Schrödinger equation in the two
dimensional torus. Fix s>1. Recently Colliander, Keel, Staffilani, Tao and Takaoka
proved the existence of solutions with s-Sobolev norm growing in time.\r\n\r\nWe
establish the existence of solutions with polynomial time estimates. More exactly,
there is c>0 such that for any K≫1 we find a solution u and a time T such that
∥u(T)∥Hs≥K∥u(0)∥Hs. Moreover, the time T satisfies the polynomial bound 0Journal of the European Mathematical Society. 2015;17(1):71-149.
doi:10.4171/jems/499
apa: Guardia, M., & Kaloshin, V. (2015). Growth of Sobolev norms in the cubic
defocusing nonlinear Schrödinger equation. Journal of the European Mathematical
Society. European Mathematical Society Publishing House. https://doi.org/10.4171/jems/499
chicago: Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic
Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical
Society. European Mathematical Society Publishing House, 2015. https://doi.org/10.4171/jems/499.
ieee: M. Guardia and V. Kaloshin, “Growth of Sobolev norms in the cubic defocusing
nonlinear Schrödinger equation,” Journal of the European Mathematical Society,
vol. 17, no. 1. European Mathematical Society Publishing House, pp. 71–149, 2015.
ista: Guardia M, Kaloshin V. 2015. Growth of Sobolev norms in the cubic defocusing
nonlinear Schrödinger equation. Journal of the European Mathematical Society.
17(1), 71–149.
mla: Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic
Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical
Society, vol. 17, no. 1, European Mathematical Society Publishing House, 2015,
pp. 71–149, doi:10.4171/jems/499.
short: M. Guardia, V. Kaloshin, Journal of the European Mathematical Society 17
(2015) 71–149.
date_created: 2020-09-18T10:46:50Z
date_published: 2015-02-05T00:00:00Z
date_updated: 2021-01-12T08:19:41Z
day: '05'
doi: 10.4171/jems/499
extern: '1'
intvolume: ' 17'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 71-149
publication: Journal of the European Mathematical Society
publication_identifier:
issn:
- 1435-9855
publication_status: published
publisher: European Mathematical Society Publishing House
quality_controlled: '1'
status: public
title: Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2015'
...
---
OA_place: publisher
OA_type: free access
_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.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Colin
full_name: Kretz, Colin
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
last_name: Desch
- first_name: David
full_name: Siemieniak, David
last_name: Siemieniak
- first_name: Kärt
full_name: Tomberg, Kärt
last_name: Tomberg
- first_name: Fyodor
full_name: Kondrashov, Fyodor
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
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: 2026-05-19T13:15:29Z
day: '28'
doi: 10.1073/pnas.1511328112
extern: '1'
external_id:
pmid:
- ' 26170332'
intvolume: ' 112'
issue: '30'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1511328112
month: '07'
oa: 1
oa_version: Accepted Version
page: 9328 - 9333
pmid: 1
publication: PNAS
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
publist_id: '6783'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Massively parallel enzyme kinetics reveals the substrate recognition landscape
of the metalloprotease ADAMTS13
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 112
year: '2015'
...