---
_id: '7767'
abstract:
- lang: eng
text: We present a model of soft active particles that leads to a rich array of
collective behavior found also in dense biological swarms of bacteria and other
unicellular organisms. Our model uses only local interactions, such as Vicsek-type
nearest-neighbor alignment, short-range repulsion, and a local boundary term.
Changing the relative strength of these interactions leads to migrating swarms,
rotating swarms, and jammed swarms, as well as swarms that exhibit run-and-tumble
motion, alternating between migration and either rotating or jammed states. Interestingly,
although a migrating swarm moves slower than an individual particle, the diffusion
constant can be up to three orders of magnitude larger, suggesting that collective
motion can be highly advantageous, for example, when searching for food.
article_number: '032706'
article_processing_charge: No
article_type: original
author:
- first_name: Ruben
full_name: van Drongelen, Ruben
last_name: van Drongelen
- first_name: Anshuman
full_name: Pal, Anshuman
last_name: Pal
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
citation:
ama: van Drongelen R, Pal A, Goodrich CP, Idema T. Collective dynamics of soft active
particles. Physical Review E. 2015;91(3). doi:10.1103/physreve.91.032706
apa: van Drongelen, R., Pal, A., Goodrich, C. P., & Idema, T. (2015). Collective
dynamics of soft active particles. Physical Review E. American Physical
Society. https://doi.org/10.1103/physreve.91.032706
chicago: Drongelen, Ruben van, Anshuman Pal, Carl Peter Goodrich, and Timon Idema.
“Collective Dynamics of Soft Active Particles.” Physical Review E. American
Physical Society, 2015. https://doi.org/10.1103/physreve.91.032706.
ieee: R. van Drongelen, A. Pal, C. P. Goodrich, and T. Idema, “Collective dynamics
of soft active particles,” Physical Review E, vol. 91, no. 3. American
Physical Society, 2015.
ista: van Drongelen R, Pal A, Goodrich CP, Idema T. 2015. Collective dynamics of
soft active particles. Physical Review E. 91(3), 032706.
mla: van Drongelen, Ruben, et al. “Collective Dynamics of Soft Active Particles.”
Physical Review E, vol. 91, no. 3, 032706, American Physical Society, 2015,
doi:10.1103/physreve.91.032706.
short: R. van Drongelen, A. Pal, C.P. Goodrich, T. Idema, Physical Review E 91 (2015).
date_created: 2020-04-30T11:41:38Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2021-01-12T08:15:24Z
day: '01'
doi: 10.1103/physreve.91.032706
extern: '1'
intvolume: ' 91'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Collective dynamics of soft active particles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2015'
...
---
_id: '777'
abstract:
- lang: eng
text: 'In many applications, the data is of rich structure that can be represented
by a hypergraph, where the data items are represented by vertices and the associations
among items are represented by hyperedges. Equivalently, we are given an input
bipartite graph with two types of vertices: items, and associations (which we
refer to as topics). We consider the problem of partitioning the set of items
into a given number of components such that the maximum number of topics covered
by a component is minimized. This is a clustering problem with various applications,
e.g. partitioning of a set of information objects such as documents, images, and
videos, and load balancing in the context of modern computation platforms.Inthis
paper, we focus on the streaming computation model for this problem, in which
items arrive online one at a time and each item must be assigned irrevocably to
a component at its arrival time. Motivated by scalability requirements, we focus
on the class of streaming computation algorithms with memory limited to be at
most linear in the number of components. We show that a greedy assignment strategy
is able to recover a hidden co-clustering of items under a natural set of recovery
conditions. We also report results of an extensive empirical evaluation, which
demonstrate that this greedy strategy yields superior performance when compared
with alternative approaches.'
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Jennifer
full_name: Iglesias, Jennifer
last_name: Iglesias
- first_name: Milan
full_name: Vojnović, Milan
last_name: Vojnović
citation:
ama: 'Alistarh D-A, Iglesias J, Vojnović M. Streaming min-max hypergraph partitioning.
In: Vol 2015-January. Neural Information Processing Systems; 2015:1900-1908.'
apa: 'Alistarh, D.-A., Iglesias, J., & Vojnović, M. (2015). Streaming min-max
hypergraph partitioning (Vol. 2015–January, pp. 1900–1908). Presented at the NIPS:
Neural Information Processing Systems, Neural Information Processing Systems.'
chicago: Alistarh, Dan-Adrian, Jennifer Iglesias, and Milan Vojnović. “Streaming
Min-Max Hypergraph Partitioning,” 2015–January:1900–1908. Neural Information Processing
Systems, 2015.
ieee: 'D.-A. Alistarh, J. Iglesias, and M. Vojnović, “Streaming min-max hypergraph
partitioning,” presented at the NIPS: Neural Information Processing Systems, 2015,
vol. 2015–January, pp. 1900–1908.'
ista: 'Alistarh D-A, Iglesias J, Vojnović M. 2015. Streaming min-max hypergraph
partitioning. NIPS: Neural Information Processing Systems vol. 2015–January, 1900–1908.'
mla: Alistarh, Dan-Adrian, et al. Streaming Min-Max Hypergraph Partitioning.
Vol. 2015–January, Neural Information Processing Systems, 2015, pp. 1900–08.
short: D.-A. Alistarh, J. Iglesias, M. Vojnović, in:, Neural Information Processing
Systems, 2015, pp. 1900–1908.
conference:
name: 'NIPS: Neural Information Processing Systems'
date_created: 2018-12-11T11:48:27Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:17:09Z
day: '01'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://papers.nips.cc/paper/5897-streaming-min-max-hypergraph-partitioning
month: '01'
oa_version: None
page: 1900 - 1908
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '6879'
status: public
title: Streaming min-max hypergraph partitioning
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-January
year: '2015'
...
---
_id: '7779'
abstract:
- lang: eng
text: "The fact that a disordered material is not constrained in its properties
in\r\nthe same way as a crystal presents significant and yet largely untapped\r\npotential
for novel material design. However, unlike their crystalline\r\ncounterparts,
disordered solids are not well understood. One of the primary\r\nobstacles is
the lack of a theoretical framework for thinking about disorder\r\nand its relation
to mechanical properties. To this end, we study an idealized\r\nsystem of frictionless
athermal soft spheres that, when compressed, undergoes a\r\njamming phase transition
with diverging length scales and clean power-law\r\nsignatures. This critical
point is the cornerstone of a much larger \"jamming\r\nscenario\" that has the
potential to provide the essential theoretical\r\nfoundation necessary for a unified
understanding of the mechanics of disordered\r\nsolids. We begin by showing that
jammed sphere packings have a valid linear\r\nregime despite the presence of \"contact
nonlinearities.\" We then investigate\r\nthe critical nature of the transition,
focusing on diverging length scales and\r\nfinite-size effects. Next, we argue
that jamming plays the same role for\r\ndisordered solids as the perfect crystal
plays for crystalline solids. Not only\r\ncan it be considered an idealized starting
point for understanding disordered\r\nmaterials, but it can even influence systems
that have a relatively high amount\r\nof crystalline order. The behavior of solids
can thus be thought of as existing\r\non a spectrum, with the perfect crystal
and the jamming transition at opposing\r\nends. Finally, we introduce a new principle
wherein the contribution of an\r\nindividual bond to one global property is independent
of its contribution to\r\nanother. This principle allows the different global
responses of a disordered\r\nsystem to be manipulated independently and provides
a great deal of flexibility\r\nin designing materials with unique, textured and
tunable properties."
article_processing_charge: No
arxiv: 1
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
citation:
ama: 'Goodrich CP. Unearthing the anticrystal: Criticality in the linear response
of disordered solids. arXiv:151008820. 2015.'
apa: 'Goodrich, C. P. (2015). Unearthing the anticrystal: Criticality in the linear
response of disordered solids. arXiv:1510.08820.'
chicago: 'Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the
Linear Response of Disordered Solids.” ArXiv:1510.08820, 2015.'
ieee: 'C. P. Goodrich, “Unearthing the anticrystal: Criticality in the linear response
of disordered solids,” arXiv:1510.08820. 2015.'
ista: 'Goodrich CP. 2015. Unearthing the anticrystal: Criticality in the linear
response of disordered solids. arXiv:1510.08820, .'
mla: 'Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear
Response of Disordered Solids.” ArXiv:1510.08820, 2015.'
short: C.P. Goodrich, ArXiv:1510.08820 (2015).
date_created: 2020-04-30T12:16:18Z
date_published: 2015-10-29T00:00:00Z
date_updated: 2021-01-12T08:15:28Z
day: '29'
extern: '1'
external_id:
arxiv:
- '1510.08820'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1510.08820
month: '10'
oa: 1
oa_version: Preprint
page: '242'
publication: arXiv:1510.08820
publication_status: published
status: public
title: 'Unearthing the anticrystal: Criticality in the linear response of disordered
solids'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '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'
...
---
_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.”
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: Vol 9135. Springer; 2015:479-491. doi:10.1007/978-3-662-47666-6_38'
apa: 'Alistarh, D.-A., & Gelashvili, R. (2015). Polylogarithmic-time leader
election in population protocols (Vol. 9135, pp. 479–491). Presented at the ICALP:
International Colloquium on Automota, Languages and Programming, Springer. https://doi.org/10.1007/978-3-662-47666-6_38'
chicago: Alistarh, Dan-Adrian, and Rati Gelashvili. “Polylogarithmic-Time Leader
Election in Population Protocols,” 9135:479–91. Springer, 2015. https://doi.org/10.1007/978-3-662-47666-6_38.
ieee: 'D.-A. Alistarh and R. Gelashvili, “Polylogarithmic-time leader election in
population protocols,” presented at the ICALP: International Colloquium on Automota,
Languages and Programming, 2015, vol. 9135, pp. 479–491.'
ista: 'Alistarh D-A, Gelashvili R. 2015. Polylogarithmic-time leader election in
population protocols. ICALP: International Colloquium on Automota, Languages and
Programming vol. 9135, 479–491.'
mla: Alistarh, Dan-Adrian, and Rati Gelashvili. Polylogarithmic-Time Leader Election
in Population Protocols. Vol. 9135, Springer, 2015, pp. 479–91, doi:10.1007/978-3-662-47666-6_38.
short: D.-A. Alistarh, R. Gelashvili, in:, Springer, 2015, pp. 479–491.
conference:
name: 'ICALP: International Colloquium on Automota, Languages and Programming'
date_created: 2018-12-11T11:48:28Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:18:11Z
day: '01'
doi: 10.1007/978-3-662-47666-6_38
extern: '1'
external_id:
arxiv:
- '1502.05745'
intvolume: ' 9135'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1502.05745
month: '01'
oa: 1
oa_version: Preprint
page: 479 - 491
publication_status: published
publisher: Springer
publist_id: '6877'
status: public
title: Polylogarithmic-time leader election in population protocols
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9135
year: '2015'
...
---
_id: '781'
abstract:
- lang: eng
text: 'Population protocols, roughly defined as systems consisting of large numbers
of simple identical agents, interacting at random and updating their state following
simple rules, are an important research topic at the intersection of distributed
computing and biology. One of the fundamental tasks that a population protocol
may solve is majority: each node starts in one of two states; the goal is for
all nodes to reach a correct consensus on which of the two states was initially
the majority. Despite considerable research effort, known protocols for this problem
are either exact but slow (taking linear parallel time to converge), or fast but
approximate (with non-zero probability of error). In this paper, we show that
this trade-off between preciasion and speed is not inherent. We present a new
protocol called Average and Conquer (AVC) that solves majority ex-actly in expected
parallel convergence time O(log n/(sε) + log n log s), where n is the number of
nodes, εn is the initial node advantage of the majority state, and s = Ω(log n
log log n) is the number of states the protocol employs. This shows that the majority
problem can be solved exactly in time poly-logarithmic in n, provided that the
memory per node is s = Ω(1/ε + lognlog1/ε). On the negative side, we establish
a lower bound of Ω(1/ε) on the expected paraallel convergence time for the case
of four memory states per node, and a lower bound of Ω(logn) parallel time for
protocols using any number of memory states per node.per node, and a lower bound
of (log n) parallel time for protocols using any number of memory states per node.'
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Milan
full_name: Vojnović, Milan
last_name: Vojnović
citation:
ama: 'Alistarh D-A, Gelashvili R, Vojnović M. Fast and exact majority in population
protocols. In: Vol 2015-July. ACM; 2015:47-56. doi:10.1145/2767386.2767429'
apa: 'Alistarh, D.-A., Gelashvili, R., & Vojnović, M. (2015). Fast and exact
majority in population protocols (Vol. 2015–July, pp. 47–56). Presented at the
PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767429'
chicago: Alistarh, Dan-Adrian, Rati Gelashvili, and Milan Vojnović. “Fast and Exact
Majority in Population Protocols,” 2015–July:47–56. ACM, 2015. https://doi.org/10.1145/2767386.2767429.
ieee: 'D.-A. Alistarh, R. Gelashvili, and M. Vojnović, “Fast and exact majority
in population protocols,” presented at the PODC: Principles of Distributed Computing,
2015, vol. 2015–July, pp. 47–56.'
ista: 'Alistarh D-A, Gelashvili R, Vojnović M. 2015. Fast and exact majority in
population protocols. PODC: Principles of Distributed Computing vol. 2015–July,
47–56.'
mla: Alistarh, Dan-Adrian, et al. Fast and Exact Majority in Population Protocols.
Vol. 2015–July, ACM, 2015, pp. 47–56, doi:10.1145/2767386.2767429.
short: D.-A. Alistarh, R. Gelashvili, M. Vojnović, in:, ACM, 2015, pp. 47–56.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:28Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2023-02-23T13:18:35Z
day: '21'
doi: 10.1145/2767386.2767429
extern: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 47 - 56
publication_status: published
publisher: ACM
publist_id: '6873'
status: public
title: Fast and exact majority in population protocols
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-July
year: '2015'
...
---
_id: '782'
abstract:
- lang: eng
text: 'In this work, we consider the following random process, mo- Tivated by the
analysis of lock-free concurrent algorithms under high memory contention. In each
round, a new scheduling step is allocated to one of n threads, according to a
distribution p = (p1; p2; : : : ; pn), where thread i is scheduled with probability
pi. When some thread first reaches a set threshold of executed steps, it registers
a win, completing its current operation, and resets its step count to 1. At the
same time, threads whose step count was close to the threshold also get reset
because of the win, but to 0 steps, being penalized for almost winning. We are
interested in two questions: how often does some thread complete an operation
(system latency), and how often does a specific thread complete an operation (individual
latency)? We provide asymptotically tight bounds for the system and individual
latency of this general concurrency pattern, for arbitrary scheduling distributions
p. Surprisingly, a sim- ple characterization exists: in expectation, the system
will complete a new operation every Θ(1/p 2) steps, while thread i will complete
a new operation every Θ(1/2=p i ) steps. The proof is interesting in its own right,
as it requires a careful analysis of how the higher norms of the vector p inuence
the thread step counts and latencies in this random process. Our result offers
a simple connection between the scheduling distribution and the average performance
of concurrent algorithms, which has several applications.'
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Thomas
full_name: Sauerwald, Thomas
last_name: Sauerwald
- first_name: Milan
full_name: Vojnović, Milan
last_name: Vojnović
citation:
ama: 'Alistarh D-A, Sauerwald T, Vojnović M. Lock-Free algorithms under stochastic
schedulers. In: Vol 2015-July. ACM; 2015:251-260. doi:10.1145/2767386.2767430'
apa: 'Alistarh, D.-A., Sauerwald, T., & Vojnović, M. (2015). Lock-Free algorithms
under stochastic schedulers (Vol. 2015–July, pp. 251–260). Presented at the PODC:
Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767430'
chicago: Alistarh, Dan-Adrian, Thomas Sauerwald, and Milan Vojnović. “Lock-Free
Algorithms under Stochastic Schedulers,” 2015–July:251–60. ACM, 2015. https://doi.org/10.1145/2767386.2767430.
ieee: 'D.-A. Alistarh, T. Sauerwald, and M. Vojnović, “Lock-Free algorithms under
stochastic schedulers,” presented at the PODC: Principles of Distributed Computing,
2015, vol. 2015–July, pp. 251–260.'
ista: 'Alistarh D-A, Sauerwald T, Vojnović M. 2015. Lock-Free algorithms under stochastic
schedulers. PODC: Principles of Distributed Computing vol. 2015–July, 251–260.'
mla: Alistarh, Dan-Adrian, et al. Lock-Free Algorithms under Stochastic Schedulers.
Vol. 2015–July, ACM, 2015, pp. 251–60, doi:10.1145/2767386.2767430.
short: D.-A. Alistarh, T. Sauerwald, M. Vojnović, in:, ACM, 2015, pp. 251–260.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:28Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2023-02-23T13:18:50Z
day: '21'
doi: 10.1145/2767386.2767430
extern: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 251 - 260
publication_status: published
publisher: ACM
publist_id: '6874'
status: public
title: Lock-Free algorithms under stochastic schedulers
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-July
year: '2015'
...
---
_id: '783'
abstract:
- lang: eng
text: 'The problem of electing a leader from among n contenders is one of the fundamental
questions in distributed computing. In its simplest formulation, the task is as
follows: given n processors, all participants must eventually return a win or
lose indication, such that a single contender may win. Despite a considerable
amount of work on leader election, the following question is still open: can we
elect a leader in an asynchronous fault-prone system faster than just running
a Θ(log n)-time tournament, against a strong adaptive adversary? In this paper,
we answer this question in the affirmative, improving on a decades-old upper bound.
We introduce two new algorithmic ideas to reduce the time complexity of electing
a leader to O(log∗ n), using O(n2) point-to-point messages. A non-trivial application
of our algorithm is a new upper bound for the tight renaming problem, assigning
n items to the n participants in expected O(log2 n) time and O(n2) messages. We
complement our results with lower bound of Ω(n2) messages for solving these two
problems, closing the question of their message complexity.'
acknowledgement: "Support is gratefully acknowledged from the National Science Foundation
under grants CCF-1217921, CCF-1301926,\r\nand IIS-1447786, the Department of
\ Energy under grant\r\nER26116/DE-SC0008923, and the Oracle and Intel corporations.\r\nThe
authors would like to thank Prof. Nir Shavit for ad-\r\nvice and encouragement
during this work, and the anonymous reviewers for their very useful suggestions."
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Adrian
full_name: Vladu, Adrian
last_name: Vladu
citation:
ama: 'Alistarh D-A, Gelashvili R, Vladu A. How to elect a leader faster than a tournament.
In: Vol 2015-July. ACM; 2015:365-374. doi:10.1145/2767386.2767420'
apa: 'Alistarh, D.-A., Gelashvili, R., & Vladu, A. (2015). How to elect a leader
faster than a tournament (Vol. 2015–July, pp. 365–374). Presented at the PODC:
Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767420'
chicago: Alistarh, Dan-Adrian, Rati Gelashvili, and Adrian Vladu. “How to Elect
a Leader Faster than a Tournament,” 2015–July:365–74. ACM, 2015. https://doi.org/10.1145/2767386.2767420.
ieee: 'D.-A. Alistarh, R. Gelashvili, and A. Vladu, “How to elect a leader faster
than a tournament,” presented at the PODC: Principles of Distributed Computing,
2015, vol. 2015–July, pp. 365–374.'
ista: 'Alistarh D-A, Gelashvili R, Vladu A. 2015. How to elect a leader faster than
a tournament. PODC: Principles of Distributed Computing vol. 2015–July, 365–374.'
mla: Alistarh, Dan-Adrian, et al. How to Elect a Leader Faster than a Tournament.
Vol. 2015–July, ACM, 2015, pp. 365–74, doi:10.1145/2767386.2767420.
short: D.-A. Alistarh, R. Gelashvili, A. Vladu, in:, ACM, 2015, pp. 365–374.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:28Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2023-02-23T13:18:55Z
day: '21'
doi: 10.1145/2767386.2767420
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1411.1001
month: '07'
oa: 1
oa_version: None
page: 365 - 374
publication_status: published
publisher: ACM
publist_id: '6875'
status: public
title: How to elect a leader faster than a tournament
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-July
year: '2015'
...
---
_id: '784'
abstract:
- lang: eng
text: We demonstrate an optical switch design that can scale up to a thousand ports
with high per-port bandwidth (25 Gbps+) and low switching latency (40 ns). Our
design uses a broadcast and select architecture, based on a passive star coupler
and fast tunable transceivers. In addition we employ time division multiplexing
to achieve very low switching latency. Our demo shows the feasibility of the switch
data plane using a small testbed, comprising two transmitters and a receiver,
connected through a star coupler.
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Hitesh
full_name: Ballani, Hitesh
last_name: Ballani
- first_name: Paolo
full_name: Costa, Paolo
last_name: Costa
- first_name: Adam
full_name: Funnell, Adam
last_name: Funnell
- first_name: Joshua
full_name: Benjamin, Joshua
last_name: Benjamin
- first_name: Philip
full_name: Watts, Philip
last_name: Watts
- first_name: Benn
full_name: Thomsen, Benn
last_name: Thomsen
citation:
ama: 'Alistarh D-A, Ballani H, Costa P, et al. A high-radix, low-latency optical
switch for data centers. In: ACM; 2015:367-368. doi:10.1145/2785956.2790035'
apa: 'Alistarh, D.-A., Ballani, H., Costa, P., Funnell, A., Benjamin, J., Watts,
P., & Thomsen, B. (2015). A high-radix, low-latency optical switch for data
centers (pp. 367–368). Presented at the SIGCOMM: Special Interest Group on Data
Communication, London, United Kindgdom: ACM. https://doi.org/10.1145/2785956.2790035'
chicago: Alistarh, Dan-Adrian, Hitesh Ballani, Paolo Costa, Adam Funnell, Joshua
Benjamin, Philip Watts, and Benn Thomsen. “A High-Radix, Low-Latency Optical Switch
for Data Centers,” 367–68. ACM, 2015. https://doi.org/10.1145/2785956.2790035.
ieee: 'D.-A. Alistarh et al., “A high-radix, low-latency optical switch for
data centers,” presented at the SIGCOMM: Special Interest Group on Data Communication,
London, United Kindgdom, 2015, pp. 367–368.'
ista: 'Alistarh D-A, Ballani H, Costa P, Funnell A, Benjamin J, Watts P, Thomsen
B. 2015. A high-radix, low-latency optical switch for data centers. SIGCOMM: Special
Interest Group on Data Communication, 367–368.'
mla: Alistarh, Dan-Adrian, et al. A High-Radix, Low-Latency Optical Switch for
Data Centers. ACM, 2015, pp. 367–68, doi:10.1145/2785956.2790035.
short: D.-A. Alistarh, H. Ballani, P. Costa, A. Funnell, J. Benjamin, P. Watts,
B. Thomsen, in:, ACM, 2015, pp. 367–368.
conference:
end_date: 2015-08-21
location: London, United Kindgdom
name: 'SIGCOMM: Special Interest Group on Data Communication'
start_date: 2015-08-17
date_created: 2018-12-11T11:48:29Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:18:57Z
day: '01'
doi: 10.1145/2785956.2790035
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 367 - 368
publication_identifier:
isbn:
- 978-1-4503-3542-3
publication_status: published
publisher: ACM
publist_id: '6872'
quality_controlled: '1'
status: public
title: A high-radix, low-latency optical switch for data centers
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '802'
abstract:
- lang: eng
text: Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at
the plasma membrane of various eukaryotes with the important exception of mammals.
In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man)
linked at position 2 of the inositol. However, several pathogenic fungi additionally
synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at
this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC
core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC,
which is the most abundant GIPC synthesized by this fungus. In this study, we
identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate
its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted
deletion of the gene encoding GntA in A. fumigatus resulted in complete absence
of zwitterionic GIPC; a phenotype that could be reverted by episomal expression
of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was
substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces
cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore
shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid
product resistant to saponification and to digestion by phosphatidylinositol-phospholipase
C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation
of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis.
author:
- first_name: Jakob
full_name: Engel, Jakob
last_name: Engel
- first_name: Philipp S
full_name: Schmalhorst, Philipp S
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Anke
full_name: Kruger, Anke
last_name: Kruger
- first_name: Christina
full_name: Muller, Christina
last_name: Muller
- first_name: Falk
full_name: Buettner, Falk
last_name: Buettner
- first_name: Françoise
full_name: Routier, Françoise
last_name: Routier
citation:
ama: Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. Characterization
of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic
glycoinositolphosphoceramide biosynthesis. Glycobiology. 2015;25(12):1423-1430.
doi:10.1093/glycob/cwv059
apa: Engel, J., Schmalhorst, P. S., Kruger, A., Muller, C., Buettner, F., &
Routier, F. (2015). Characterization of an N-acetylglucosaminyltransferase involved
in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis.
Glycobiology. Oxford University Press. https://doi.org/10.1093/glycob/cwv059
chicago: Engel, Jakob, Philipp S Schmalhorst, Anke Kruger, Christina Muller, Falk
Buettner, and Françoise Routier. “Characterization of an N-Acetylglucosaminyltransferase
Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.”
Glycobiology. Oxford University Press, 2015. https://doi.org/10.1093/glycob/cwv059.
ieee: J. Engel, P. S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, and F. Routier,
“Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis,” Glycobiology,
vol. 25, no. 12. Oxford University Press, pp. 1423–1430, 2015.
ista: Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. 2015.
Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology.
25(12), 1423–1430.
mla: Engel, Jakob, et al. “Characterization of an N-Acetylglucosaminyltransferase
Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.”
Glycobiology, vol. 25, no. 12, Oxford University Press, 2015, pp. 1423–30,
doi:10.1093/glycob/cwv059.
short: J. Engel, P.S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, F. Routier,
Glycobiology 25 (2015) 1423–1430.
date_created: 2018-12-11T11:48:35Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T08:16:33Z
day: '01'
department:
- _id: CaHe
doi: 10.1093/glycob/cwv059
external_id:
pmid:
- '26306635'
intvolume: ' 25'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 1423 - 1430
pmid: 1
publication: Glycobiology
publication_status: published
publisher: Oxford University Press
publist_id: '6851'
quality_controlled: '1'
scopus_import: 1
status: public
title: Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2015'
...
---
_id: '814'
abstract:
- lang: eng
text: Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages.
First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein
lattice at the plasma membrane of the infected cell, inducing budding and release
of an immature particle. Second, Gag is cleaved by the viral protease, leading
to internal rearrangement of the virus into the mature, infectious form. Immature
and mature HIV-1 particles are heterogeneous in size and morphology, preventing
high-resolution analysis of their protein arrangement in situ by conventional
structural biology methods. Here we apply cryo-electron tomography and sub-tomogram
averaging methods to resolve the structure of the capsid lattice within intact
immature HIV-1 particles at subnanometre resolution, allowing unambiguous positioning
of all α-helices. The resulting model reveals tertiary and quaternary structural
interactions that mediate HIV-1 assembly. Strikingly, these interactions differ
from those predicted by the current model based on in vitro-assembled arrays of
Gag-derived proteins from Mason-Pfizer monkey virus. To validate this difference,
we solve the structure of the capsid lattice within intact immature Mason-Pfizer
monkey virus particles. Comparison with the immature HIV-1 structure reveals that
retroviral capsid proteins, while having conserved tertiary structures, adopt
different quaternary arrangements during virus assembly. The approach demonstrated
here should be applicable to determine structures of other proteins at subnanometre
resolution within heterogeneous environments.
acknowledgement: This study was supported by Deutsche Forschungsgemeinschaft grants
BR 3635/2-1 to J.A.G.B., KR 906/7-1 to H.-G.K. and by Grant Agency of the Czech
Republic 14-15326S to M.R. The Briggs laboratory acknowledges financial support
from the European Molecular Biology Laboratory and from the Chica und Heinz Schaller
Stiftung. We thank B. Glass, M. Anders and S. Mattei for preparation of samples,
and R. Hadravova, K. H. Bui, F. Thommen, M. Schorb, S. Dodonova, S. Glatt, P. Ulbrich
and T. Bharat for technical support and/or discussion. This study was technically
supported by the European Molecular Biology Laboratory IT services unit.
author:
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Wim
full_name: Hagen, Wim J
last_name: Hagen
- first_name: Michaela
full_name: Rumlová, Michaela
last_name: Rumlová
- first_name: Tomáš
full_name: Ruml, Tomáš
last_name: Ruml
- first_name: B
full_name: Müller B
last_name: Müller
- first_name: Hans
full_name: Kraüsslich, Hans Georg
last_name: Kraüsslich
- first_name: John
full_name: Briggs, John A
last_name: Briggs
citation:
ama: Schur FK, Hagen W, Rumlová M, et al. Structure of the immature HIV-1 capsid
in intact virus particles at 8.8 Å resolution. Nature. 2015;517(7535):505-508.
doi:10.1038/nature13838
apa: Schur, F. K., Hagen, W., Rumlová, M., Ruml, T., Müller, B., Kraüsslich, H.,
& Briggs, J. (2015). Structure of the immature HIV-1 capsid in intact virus
particles at 8.8 Å resolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13838
chicago: Schur, Florian KM, Wim Hagen, Michaela Rumlová, Tomáš Ruml, B Müller, Hans
Kraüsslich, and John Briggs. “Structure of the Immature HIV-1 Capsid in Intact
Virus Particles at 8.8 Å Resolution.” Nature. Nature Publishing Group,
2015. https://doi.org/10.1038/nature13838.
ieee: F. K. Schur et al., “Structure of the immature HIV-1 capsid in intact
virus particles at 8.8 Å resolution,” Nature, vol. 517, no. 7535. Nature
Publishing Group, pp. 505–508, 2015.
ista: Schur FK, Hagen W, Rumlová M, Ruml T, Müller B, Kraüsslich H, Briggs J. 2015.
Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution.
Nature. 517(7535), 505–508.
mla: Schur, Florian KM, et al. “Structure of the Immature HIV-1 Capsid in Intact
Virus Particles at 8.8 Å Resolution.” Nature, vol. 517, no. 7535, Nature
Publishing Group, 2015, pp. 505–08, doi:10.1038/nature13838.
short: F.K. Schur, W. Hagen, M. Rumlová, T. Ruml, B. Müller, H. Kraüsslich, J. Briggs,
Nature 517 (2015) 505–508.
date_created: 2018-12-11T11:48:39Z
date_published: 2015-01-22T00:00:00Z
date_updated: 2021-01-12T08:17:08Z
day: '22'
doi: 10.1038/nature13838
extern: 1
intvolume: ' 517'
issue: '7535'
month: '01'
page: 505 - 508
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6836'
quality_controlled: 0
status: public
title: Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution
type: journal_article
volume: 517
year: '2015'
...
---
_id: '815'
abstract:
- lang: eng
text: "The polyprotein Gag is the primary structural component of retroviruses.
Gag consists of independently folded domains connected by flexible linkers. Interactions
between the conserved capsid (CA) domains of Gag mediate formation of hexameric
protein lattices that drive assembly of immature virus particles. Proteolytic
cleavage of Gag by the viral protease (PR) is required for maturation of retroviruses
from an immature form into an infectious form. Within the assembled Gag lattices
of HIV-1 and Mason- Pfizer monkey virus (M-PMV), the C-terminal domain of CA adopts
similar quaternary arrangements, while the N-terminal domain of CA is packed in
very different manners. Here, we have used cryo-electron tomography and subtomogram
averaging to study in vitro-assembled, immature virus-like Rous sarcoma virus
(RSV) Gag particles and have determined the structure of CA and the surrounding
regions to a resolution of ~8 Å. We found that the C-terminal domain of RSV CA
is arranged similarly to HIV-1 and M-PMV, whereas the N-terminal domain of CA
adopts a novel arrangement in which the upstream p10 domain folds back into the
CA lattice. In this position the cleavage site between CA and p10 appears to be
inaccessible to PR. Below CA, an extended density is consistent with the presence
of a six-helix bundle formed by the spacer-peptide region. We have also assessed
the affect of lattice assembly on proteolytic processing by exogenous PR. The
cleavage between p10 and CA is indeed inhibited in the assembled lattice, a finding
consistent with structural regulation of proteolytic maturation.\r\n"
author:
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Robert
full_name: Dick, Robert
last_name: Dick
- first_name: Wim
full_name: Hagen, Wim
last_name: Hagen
- first_name: Volker
full_name: Vogt, Volker
last_name: Vogt
- first_name: John
full_name: Briggs, John
last_name: Briggs
citation:
ama: Schur FK, Dick R, Hagen W, Vogt V, Briggs J. The structure of immature virus
like Rous sarcoma virus gag particles reveals a structural role for the p10 domain
in assembly. Journal of Virology. 2015;89(20):10294-10302. doi:10.1128/JVI.01502-15
apa: Schur, F. K., Dick, R., Hagen, W., Vogt, V., & Briggs, J. (2015). The structure
of immature virus like Rous sarcoma virus gag particles reveals a structural role
for the p10 domain in assembly. Journal of Virology. ASM. https://doi.org/10.1128/JVI.01502-15
chicago: Schur, Florian KM, Robert Dick, Wim Hagen, Volker Vogt, and John Briggs.
“The Structure of Immature Virus like Rous Sarcoma Virus Gag Particles Reveals
a Structural Role for the P10 Domain in Assembly.” Journal of Virology.
ASM, 2015. https://doi.org/10.1128/JVI.01502-15.
ieee: F. K. Schur, R. Dick, W. Hagen, V. Vogt, and J. Briggs, “The structure of
immature virus like Rous sarcoma virus gag particles reveals a structural role
for the p10 domain in assembly,” Journal of Virology, vol. 89, no. 20.
ASM, pp. 10294–10302, 2015.
ista: Schur FK, Dick R, Hagen W, Vogt V, Briggs J. 2015. The structure of immature
virus like Rous sarcoma virus gag particles reveals a structural role for the
p10 domain in assembly. Journal of Virology. 89(20), 10294–10302.
mla: Schur, Florian KM, et al. “The Structure of Immature Virus like Rous Sarcoma
Virus Gag Particles Reveals a Structural Role for the P10 Domain in Assembly.”
Journal of Virology, vol. 89, no. 20, ASM, 2015, pp. 10294–302, doi:10.1128/JVI.01502-15.
short: F.K. Schur, R. Dick, W. Hagen, V. Vogt, J. Briggs, Journal of Virology 89
(2015) 10294–10302.
date_created: 2018-12-11T11:48:39Z
date_published: 2015-09-22T00:00:00Z
date_updated: 2021-01-12T08:17:09Z
day: '22'
doi: 10.1128/JVI.01502-15
extern: '1'
external_id:
pmid:
- '26223638'
intvolume: ' 89'
issue: '20'
language:
- iso: eng
month: '09'
oa_version: None
page: 10294 - 10302
pmid: 1
publication: Journal of Virology
publication_status: published
publisher: ASM
publist_id: '6837'
quality_controlled: '1'
status: public
title: The structure of immature virus like Rous sarcoma virus gag particles reveals
a structural role for the p10 domain in assembly
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2015'
...
---
_id: '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
- 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.
apa: Avvakumov, S., Mabillard, I., Skopenkov, A., & Wagner, U. (n.d.). Eliminating
higher-multiplicity intersections, III. Codimension 2. arXiv.
chicago: Avvakumov, Sergey, Isaac Mabillard, A. Skopenkov, and Uli Wagner. “Eliminating
Higher-Multiplicity Intersections, III. Codimension 2.” ArXiv, n.d.
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.
short: S. Avvakumov, I. Mabillard, A. Skopenkov, U. Wagner, ArXiv (n.d.).
date_created: 2020-07-30T10:45:19Z
date_published: 2015-11-15T00:00:00Z
date_updated: 2023-09-07T13:12:17Z
day: '15'
department:
- _id: UlWa
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: submitted
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: '1481'
abstract:
- lang: eng
text: 'Simple board games, like Tic-Tac-Toe and CONNECT-4, play an important role
not only in the development of mathematical and logical skills, but also in the
emotional and social development. In this paper, we address the problem of generating
targeted starting positions for such games. This can facilitate new approaches
for bringing novice players to mastery, and also leads to discovery of interesting
game variants. We present an approach that generates starting states of varying
hardness levels for player 1 in a two-player board game, given rules of the board
game, the desired number of steps required for player 1 to win, and the expertise
levels of the two players. Our approach leverages symbolic methods and iterative
simulation to efficiently search the extremely large state space. We present experimental
results that include discovery of states of varying hardness levels for several
simple grid-based board games. The presence of such states for standard game variants
like 4×4 Tic-Tac-Toe opens up new games to be played that have never been played
as the default start state is heavily biased. '
acknowledgement: "A Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/146.\r\n"
article_processing_charge: No
author:
- first_name: Umair
full_name: Ahmed, Umair
last_name: Ahmed
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Sumit
full_name: Gulwani, Sumit
last_name: Gulwani
citation:
ama: 'Ahmed U, Chatterjee K, Gulwani S. Automatic generation of alternative starting
positions for simple traditional board games. In: Proceedings of the Twenty-Ninth
AAAI Conference on Artificial Intelligence. Vol 2. AAAI Press; 2015:745-752.'
apa: 'Ahmed, U., Chatterjee, K., & Gulwani, S. (2015). Automatic generation
of alternative starting positions for simple traditional board games. In Proceedings
of the Twenty-Ninth AAAI Conference on Artificial Intelligence (Vol. 2, pp.
745–752). Austin, TX, USA: AAAI Press.'
chicago: Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. “Automatic Generation
of Alternative Starting Positions for Simple Traditional Board Games.” In Proceedings
of the Twenty-Ninth AAAI Conference on Artificial Intelligence, 2:745–52.
AAAI Press, 2015.
ieee: U. Ahmed, K. Chatterjee, and S. Gulwani, “Automatic generation of alternative
starting positions for simple traditional board games,” in Proceedings of the
Twenty-Ninth AAAI Conference on Artificial Intelligence, Austin, TX, USA,
2015, vol. 2, pp. 745–752.
ista: 'Ahmed U, Chatterjee K, Gulwani S. 2015. Automatic generation of alternative
starting positions for simple traditional board games. Proceedings of the Twenty-Ninth
AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence
vol. 2, 745–752.'
mla: Ahmed, Umair, et al. “Automatic Generation of Alternative Starting Positions
for Simple Traditional Board Games.” Proceedings of the Twenty-Ninth AAAI Conference
on Artificial Intelligence, vol. 2, AAAI Press, 2015, pp. 745–52.
short: U. Ahmed, K. Chatterjee, S. Gulwani, in:, Proceedings of the Twenty-Ninth
AAAI Conference on Artificial Intelligence, AAAI Press, 2015, pp. 745–752.
conference:
end_date: 2015-01-30
location: Austin, TX, USA
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2015-01-25
date_created: 2018-12-11T11:52:16Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T12:25:07Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
intvolume: ' 2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.aaai.org/ocs/index.php/AAAI/AAAI15/paper/download/9523/9300
month: '01'
oa: 1
oa_version: None
page: 745 - 752
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence
publication_status: published
publisher: AAAI Press
publist_id: '5713'
quality_controlled: '1'
related_material:
record:
- id: '5410'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Automatic generation of alternative starting positions for simple traditional
board games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2015'
...
---
_id: '1483'
abstract:
- lang: eng
text: Topological data analysis offers a rich source of valuable information to
study vision problems. Yet, so far we lack a theoretically sound connection to
popular kernel-based learning techniques, such as kernel SVMs or kernel PCA. In
this work, we establish such a connection by designing a multi-scale kernel for
persistence diagrams, a stable summary representation of topological features
in data. We show that this kernel is positive definite and prove its stability
with respect to the 1-Wasserstein distance. Experiments on two benchmark datasets
for 3D shape classification/retrieval and texture recognition show considerable
performance gains of the proposed method compared to an alternative approach that
is based on the recently introduced persistence landscapes.
author:
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
- first_name: Roland
full_name: Kwitt, Roland
last_name: Kwitt
citation:
ama: 'Reininghaus J, Huber S, Bauer U, Kwitt R. A stable multi-scale kernel for
topological machine learning. In: IEEE; 2015:4741-4748. doi:10.1109/CVPR.2015.7299106'
apa: 'Reininghaus, J., Huber, S., Bauer, U., & Kwitt, R. (2015). A stable multi-scale
kernel for topological machine learning (pp. 4741–4748). Presented at the CVPR:
Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. https://doi.org/10.1109/CVPR.2015.7299106'
chicago: Reininghaus, Jan, Stefan Huber, Ulrich Bauer, and Roland Kwitt. “A Stable
Multi-Scale Kernel for Topological Machine Learning,” 4741–48. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7299106.
ieee: 'J. Reininghaus, S. Huber, U. Bauer, and R. Kwitt, “A stable multi-scale kernel
for topological machine learning,” presented at the CVPR: Computer Vision and
Pattern Recognition, Boston, MA, USA, 2015, pp. 4741–4748.'
ista: 'Reininghaus J, Huber S, Bauer U, Kwitt R. 2015. A stable multi-scale kernel
for topological machine learning. CVPR: Computer Vision and Pattern Recognition,
4741–4748.'
mla: Reininghaus, Jan, et al. A Stable Multi-Scale Kernel for Topological Machine
Learning. IEEE, 2015, pp. 4741–48, doi:10.1109/CVPR.2015.7299106.
short: J. Reininghaus, S. Huber, U. Bauer, R. Kwitt, in:, IEEE, 2015, pp. 4741–4748.
conference:
end_date: 2015-06-12
location: Boston, MA, USA
name: 'CVPR: Computer Vision and Pattern Recognition'
start_date: 2015-06-07
date_created: 2018-12-11T11:52:17Z
date_published: 2015-10-14T00:00:00Z
date_updated: 2021-01-12T06:51:03Z
day: '14'
department:
- _id: HeEd
doi: 10.1109/CVPR.2015.7299106
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1412.6821
month: '10'
oa: 1
oa_version: Preprint
page: 4741 - 4748
publication_identifier:
eisbn:
- '978-1-4673-6964-0 '
publication_status: published
publisher: IEEE
publist_id: '5709'
scopus_import: 1
status: public
title: A stable multi-scale kernel for topological machine learning
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1495'
abstract:
- lang: eng
text: 'Motivated by biological questions, we study configurations of equal-sized
disks in the Euclidean plane that neither pack nor cover. Measuring the quality
by the probability that a random point lies in exactly one disk, we show that
the regular hexagonal grid gives the maximum among lattice configurations. '
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Mabel
full_name: Iglesias Ham, Mabel
id: 41B58C0C-F248-11E8-B48F-1D18A9856A87
last_name: Iglesias Ham
- first_name: Vitaliy
full_name: Kurlin, Vitaliy
last_name: Kurlin
citation:
ama: 'Edelsbrunner H, Iglesias Ham M, Kurlin V. Relaxed disk packing. In: Proceedings
of the 27th Canadian Conference on Computational Geometry. Vol 2015-August.
Queen’s University; 2015:128-135.'
apa: 'Edelsbrunner, H., Iglesias Ham, M., & Kurlin, V. (2015). Relaxed disk
packing. In Proceedings of the 27th Canadian Conference on Computational Geometry
(Vol. 2015–August, pp. 128–135). Ontario, Canada: Queen’s University.'
chicago: Edelsbrunner, Herbert, Mabel Iglesias Ham, and Vitaliy Kurlin. “Relaxed
Disk Packing.” In Proceedings of the 27th Canadian Conference on Computational
Geometry, 2015–August:128–35. Queen’s University, 2015.
ieee: H. Edelsbrunner, M. Iglesias Ham, and V. Kurlin, “Relaxed disk packing,” in
Proceedings of the 27th Canadian Conference on Computational Geometry,
Ontario, Canada, 2015, vol. 2015–August, pp. 128–135.
ista: 'Edelsbrunner H, Iglesias Ham M, Kurlin V. 2015. Relaxed disk packing. Proceedings
of the 27th Canadian Conference on Computational Geometry. CCCG: Canadian Conference
on Computational Geometry vol. 2015–August, 128–135.'
mla: Edelsbrunner, Herbert, et al. “Relaxed Disk Packing.” Proceedings of the
27th Canadian Conference on Computational Geometry, vol. 2015–August, Queen’s
University, 2015, pp. 128–35.
short: H. Edelsbrunner, M. Iglesias Ham, V. Kurlin, in:, Proceedings of the 27th
Canadian Conference on Computational Geometry, Queen’s University, 2015, pp. 128–135.
conference:
end_date: 2015-08-12
location: Ontario, Canada
name: 'CCCG: Canadian Conference on Computational Geometry'
start_date: 2015-08-10
date_created: 2018-12-11T11:52:21Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:09Z
day: '01'
department:
- _id: HeEd
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1505.03402
month: '08'
oa: 1
oa_version: Submitted Version
page: 128-135
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Proceedings of the 27th Canadian Conference on Computational Geometry
publication_status: published
publisher: Queen's University
publist_id: '5684'
quality_controlled: '1'
scopus_import: 1
status: public
title: Relaxed disk packing
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2015-August
year: '2015'
...
---
_id: '1497'
abstract:
- lang: eng
text: Detecting allelic biases from high-throughput sequencing data requires an
approach that maximises sensitivity while minimizing false positives. Here, we
present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which
uses high-throughput sequencing data from reciprocal crosses of two genetically
distinct mouse strains to detect allele-specific expression and chromatin modifications.
Allelome.PRO extends approaches used in previous studies that exclusively analyzed
imprinted expression to give a complete picture of the ‘allelome’ by automatically
categorising the allelic expression of all genes in a given cell type into imprinted,
strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity
to analyze lowly expressed transcripts, together with a robust false discovery
rate empirically calculated from variation in the sequencing data. We used RNA-seq
data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine
a biologically relevant allelic ratio cutoff, and define for the first time an
entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment
of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This
approach can be easily extended to analyze histone marks of active enhancers,
or transcription factor binding sites and therefore provides a powerful tool to
identify candidate cis regulatory elements genome wide.
acknowledgement: "Austrian Science Fund [FWF P25185-B22, FWF F4302- B09, FWFW1207-B09].
Funding for open access charge: Austrian Science Fund.\r\nWe thank Florian Breitwieser
for advice during the early stages of this project. High-throughput sequencing was
conducted by the Biomedical Sequencing Facility (BSF) at CeMM in Vienna."
article_number: e146
author:
- first_name: Daniel
full_name: Andergassen, Daniel
last_name: Andergassen
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
- first_name: Tomasz
full_name: Kulinski, Tomasz
last_name: Kulinski
- first_name: Philipp
full_name: Guenzl, Philipp
last_name: Guenzl
- first_name: Philipp
full_name: Bammer, Philipp
last_name: Bammer
- first_name: Denise
full_name: Barlow, Denise
last_name: Barlow
- first_name: Florian
full_name: Pauler, Florian
last_name: Pauler
- first_name: Quanah
full_name: Hudson, Quanah
last_name: Hudson
citation:
ama: Andergassen D, Dotter C, Kulinski T, et al. Allelome.PRO, a pipeline to define
allele-specific genomic features from high-throughput sequencing data. Nucleic
Acids Research. 2015;43(21). doi:10.1093/nar/gkv727
apa: Andergassen, D., Dotter, C., Kulinski, T., Guenzl, P., Bammer, P., Barlow,
D., … Hudson, Q. (2015). Allelome.PRO, a pipeline to define allele-specific genomic
features from high-throughput sequencing data. Nucleic Acids Research.
Oxford University Press. https://doi.org/10.1093/nar/gkv727
chicago: Andergassen, Daniel, Christoph Dotter, Tomasz Kulinski, Philipp Guenzl,
Philipp Bammer, Denise Barlow, Florian Pauler, and Quanah Hudson. “Allelome.PRO,
a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing
Data.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv727.
ieee: D. Andergassen et al., “Allelome.PRO, a pipeline to define allele-specific
genomic features from high-throughput sequencing data,” Nucleic Acids Research,
vol. 43, no. 21. Oxford University Press, 2015.
ista: Andergassen D, Dotter C, Kulinski T, Guenzl P, Bammer P, Barlow D, Pauler
F, Hudson Q. 2015. Allelome.PRO, a pipeline to define allele-specific genomic
features from high-throughput sequencing data. Nucleic Acids Research. 43(21),
e146.
mla: Andergassen, Daniel, et al. “Allelome.PRO, a Pipeline to Define Allele-Specific
Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research,
vol. 43, no. 21, e146, Oxford University Press, 2015, doi:10.1093/nar/gkv727.
short: D. Andergassen, C. Dotter, T. Kulinski, P. Guenzl, P. Bammer, D. Barlow,
F. Pauler, Q. Hudson, Nucleic Acids Research 43 (2015).
date_created: 2018-12-11T11:52:22Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2021-01-12T06:51:09Z
day: '21'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1093/nar/gkv727
file:
- access_level: open_access
checksum: 385b83854fd0eb2e4f386867da2823e2
content_type: application/pdf
creator: dernst
date_created: 2018-12-20T14:18:57Z
date_updated: 2020-07-14T12:44:58Z
file_id: '5768'
file_name: 2015_NucleicAcidsRes_Andergassen.pdf
file_size: 6863297
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 43'
issue: '21'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Nucleic Acids Research
publication_status: published
publisher: Oxford University Press
publist_id: '5682'
quality_controlled: '1'
scopus_import: 1
status: public
title: Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput
sequencing data
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2015'
...
---
_id: '1498'
abstract:
- lang: eng
text: Fault-tolerant distributed algorithms play an important role in many critical/high-availability
applications. These algorithms are notoriously difficult to implement correctly,
due to asynchronous communication and the occurrence of faults, such as the network
dropping messages or computers crashing. Nonetheless there is surprisingly little
language and verification support to build distributed systems based on fault-tolerant
algorithms. In this paper, we present some of the challenges that a designer has
to overcome to implement a fault-tolerant distributed system. Then we review different
models that have been proposed to reason about distributed algorithms and sketch
how such a model can form the basis for a domain-specific programming language.
Adopting a high-level programming model can simplify the programmer's life and
make the code amenable to automated verification, while still compiling to efficiently
executable code. We conclude by summarizing the current status of an ongoing language
design and implementation project that is based on this idea.
alternative_title:
- LIPIcs
author:
- first_name: Cezara
full_name: Dragoi, Cezara
id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87
last_name: Dragoi
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: Dragoi C, Henzinger TA, Zufferey D. The need for language support for fault-tolerant
distributed systems. 2015;32:90-102. doi:10.4230/LIPIcs.SNAPL.2015.90
apa: 'Dragoi, C., Henzinger, T. A., & Zufferey, D. (2015). The need for language
support for fault-tolerant distributed systems. Presented at the SNAPL: Summit
oN Advances in Programming Languages, Asilomar, CA, United States: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90'
chicago: Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “The Need for
Language Support for Fault-Tolerant Distributed Systems.” Leibniz International
Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2015. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90.
ieee: C. Dragoi, T. A. Henzinger, and D. Zufferey, “The need for language support
for fault-tolerant distributed systems,” vol. 32. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, pp. 90–102, 2015.
ista: Dragoi C, Henzinger TA, Zufferey D. 2015. The need for language support for
fault-tolerant distributed systems. 32, 90–102.
mla: Dragoi, Cezara, et al. The Need for Language Support for Fault-Tolerant
Distributed Systems. Vol. 32, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2015, pp. 90–102, doi:10.4230/LIPIcs.SNAPL.2015.90.
short: C. Dragoi, T.A. Henzinger, D. Zufferey, 32 (2015) 90–102.
conference:
end_date: 2015-05-06
location: Asilomar, CA, United States
name: 'SNAPL: Summit oN Advances in Programming Languages'
start_date: 2015-05-03
date_created: 2018-12-11T11:52:22Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2020-08-11T10:09:14Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.SNAPL.2015.90
ec_funded: 1
file:
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checksum: cf5e94baa89a2dc4c5de01abc676eda8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:02Z
date_updated: 2020-07-14T12:44:58Z
file_id: '5050'
file_name: IST-2016-499-v1+1_9.pdf
file_size: 489362
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 32'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 90 - 102
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
isbn:
- '978-3-939897-80-4 '
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5681'
pubrep_id: '499'
quality_controlled: '1'
scopus_import: 1
series_title: Leibniz International Proceedings in Informatics
status: public
title: The need for language support for fault-tolerant distributed systems
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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year: '2015'
...
---
_id: '1499'
abstract:
- lang: eng
text: "We consider weighted automata with both positive and negative integer weights
on edges and\r\nstudy the problem of synchronization using adaptive strategies
that may only observe whether\r\nthe current weight-level is negative or nonnegative.
We show that the synchronization problem is decidable in polynomial time for deterministic
weighted automata."
acknowledgement: "The research leading to these results has received funding from
the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement
601148 (CASSTING), EU FP7 FET project SENSATION, Sino-Danish Basic Research Center
IDAE4CPS, the European Research Council (ERC) under grant agreement 267989 (QUAREM),
the Austrian Science Fund (FWF) project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein
Award), the Czech Science Foundation under grant agreement P202/12/G061, and People
Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme
(FP7/2007-2013) REA Grant No 291734."
alternative_title:
- LIPIcs
author:
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Kim
full_name: Larsen, Kim
last_name: Larsen
- first_name: Simon
full_name: Laursen, Simon
last_name: Laursen
- first_name: Jiří
full_name: Srba, Jiří
last_name: Srba
citation:
ama: 'Kretinsky J, Larsen K, Laursen S, Srba J. Polynomial time decidability of
weighted synchronization under partial observability. In: Vol 42. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik; 2015:142-154. doi:10.4230/LIPIcs.CONCUR.2015.142'
apa: 'Kretinsky, J., Larsen, K., Laursen, S., & Srba, J. (2015). Polynomial
time decidability of weighted synchronization under partial observability (Vol.
42, pp. 142–154). Presented at the CONCUR: Concurrency Theory, Madrid, Spain:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142'
chicago: Kretinsky, Jan, Kim Larsen, Simon Laursen, and Jiří Srba. “Polynomial Time
Decidability of Weighted Synchronization under Partial Observability,” 42:142–54.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142.
ieee: 'J. Kretinsky, K. Larsen, S. Laursen, and J. Srba, “Polynomial time decidability
of weighted synchronization under partial observability,” presented at the CONCUR:
Concurrency Theory, Madrid, Spain, 2015, vol. 42, pp. 142–154.'
ista: 'Kretinsky J, Larsen K, Laursen S, Srba J. 2015. Polynomial time decidability
of weighted synchronization under partial observability. CONCUR: Concurrency Theory,
LIPIcs, vol. 42, 142–154.'
mla: Kretinsky, Jan, et al. Polynomial Time Decidability of Weighted Synchronization
under Partial Observability. Vol. 42, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2015, pp. 142–54, doi:10.4230/LIPIcs.CONCUR.2015.142.
short: J. Kretinsky, K. Larsen, S. Laursen, J. Srba, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2015, pp. 142–154.
conference:
end_date: 2015-09-04
location: Madrid, Spain
name: 'CONCUR: Concurrency Theory'
start_date: 2015-09-01
date_created: 2018-12-11T11:52:22Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:51:10Z
day: '01'
ddc:
- '000'
- '003'
department:
- _id: ToHe
- _id: KrCh
doi: 10.4230/LIPIcs.CONCUR.2015.142
ec_funded: 1
file:
- access_level: open_access
checksum: 49eb5021caafaabe5356c65b9c5f8c9c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:12Z
date_updated: 2020-07-14T12:44:58Z
file_id: '4672'
file_name: IST-2016-498-v1+1_32.pdf
file_size: 623563
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 42'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 142 - 154
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5680'
pubrep_id: '498'
quality_controlled: '1'
scopus_import: 1
status: public
title: Polynomial time decidability of weighted synchronization under partial observability
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2015'
...