---
_id: '1171'
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Tkačik G. Understanding regulatory networks requires more than computing a
multitude of graph statistics: Comment on "Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function"
by O. C. Martin et al. Physics of Life Reviews. 2016;17:166-167. doi:10.1016/j.plrev.2016.06.005'
apa: 'Tkačik, G. (2016). Understanding regulatory networks requires more than computing
a multitude of graph statistics: Comment on "Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function"
by O. C. Martin et al. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.005'
chicago: 'Tkačik, Gašper. “Understanding Regulatory Networks Requires More than
Computing a Multitude of Graph Statistics: Comment on "Drivers of Structural
Features in Gene Regulatory Networks: From Biophysical Constraints to Biological
Function" by O. C. Martin et Al.” Physics of Life Reviews. Elsevier,
2016. https://doi.org/10.1016/j.plrev.2016.06.005.'
ieee: 'G. Tkačik, “Understanding regulatory networks requires more than computing
a multitude of graph statistics: Comment on "Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function"
by O. C. Martin et al.,” Physics of Life Reviews, vol. 17. Elsevier, pp.
166–167, 2016.'
ista: 'Tkačik G. 2016. Understanding regulatory networks requires more than computing
a multitude of graph statistics: Comment on "Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function"
by O. C. Martin et al. Physics of Life Reviews. 17, 166–167.'
mla: 'Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing
a Multitude of Graph Statistics: Comment on "Drivers of Structural Features
in Gene Regulatory Networks: From Biophysical Constraints to Biological Function"
by O. C. Martin et Al.” Physics of Life Reviews, vol. 17, Elsevier, 2016,
pp. 166–67, doi:10.1016/j.plrev.2016.06.005.'
short: G. Tkačik, Physics of Life Reviews 17 (2016) 166–167.
date_created: 2018-12-11T11:50:32Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:48:50Z
day: '01'
department:
- _id: GaTk
doi: 10.1016/j.plrev.2016.06.005
intvolume: ' 17'
language:
- iso: eng
month: '07'
oa_version: None
page: 166 - 167
publication: Physics of Life Reviews
publication_status: published
publisher: Elsevier
publist_id: '6185'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Understanding regulatory networks requires more than computing a multitude
of graph statistics: Comment on "Drivers of structural features in gene regulatory
networks: From biophysical constraints to biological function" by O. C. Martin
et al.'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1172'
abstract:
- lang: eng
text: A central issue in cell biology is the physico-chemical basis of organelle
biogenesis in intracellular trafficking pathways, its most impressive manifestation
being the biogenesis of Golgi cisternae. At a basic level, such morphologically
and chemically distinct compartments should arise from an interplay between the
molecular transport and chemical maturation. Here, we formulate analytically tractable,
minimalist models, that incorporate this interplay between transport and chemical
progression in physical space, and explore the conditions for de novo biogenesis
of distinct cisternae. We propose new quantitative measures that can discriminate
between the various models of transport in a qualitative manner-this includes
measures of the dynamics in steady state and the dynamical response to perturbations
of the kind amenable to live-cell imaging.
acknowledgement: H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund
Thattai for critical discussions and suggestions.
article_number: '38840'
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Mustansir
full_name: Barma, Mustansir
last_name: Barma
- first_name: Madan
full_name: Rao, Madan
last_name: Rao
citation:
ama: Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis
and transport through Golgi-like cisternae. Scientific Reports. 2016;6.
doi:10.1038/srep38840
apa: Sachdeva, H., Barma, M., & Rao, M. (2016). Nonequilibrium description of
de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/srep38840
chicago: Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description
of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific
Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38840.
ieee: H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo
biogenesis and transport through Golgi-like cisternae,” Scientific Reports,
vol. 6. Nature Publishing Group, 2016.
ista: Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis
and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.
mla: Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis
and Transport through Golgi-like Cisternae.” Scientific Reports, vol. 6,
38840, Nature Publishing Group, 2016, doi:10.1038/srep38840.
short: H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).
date_created: 2018-12-11T11:50:32Z
date_published: 2016-12-19T00:00:00Z
date_updated: 2021-01-12T06:48:50Z
day: '19'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1038/srep38840
file:
- access_level: open_access
checksum: cb378732da885ea4959ec5b845fb6e52
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:56Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4977'
file_name: IST-2017-737-v1+1_srep38840.pdf
file_size: 760967
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6183'
pubrep_id: '737'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nonequilibrium description of de novo biogenesis and transport through Golgi-like
cisternae
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1177'
abstract:
- lang: eng
text: Boldyreva, Palacio and Warinschi introduced a multiple forking game as an
extension of general forking. The notion of (multiple) forking is a useful abstraction
from the actual simulation of cryptographic scheme to the adversary in a security
reduction, and is achieved through the intermediary of a so-called wrapper algorithm.
Multiple forking has turned out to be a useful tool in the security argument of
several cryptographic protocols. However, a reduction employing multiple forking
incurs a significant degradation of (Formula presented.) , where (Formula presented.)
denotes the upper bound on the underlying random oracle calls and (Formula presented.)
, the number of forkings. In this work we take a closer look at the reasons for
the degradation with a tighter security bound in mind. We nail down the exact
set of conditions for success in the multiple forking game. A careful analysis
of the cryptographic schemes and corresponding security reduction employing multiple
forking leads to the formulation of ‘dependence’ and ‘independence’ conditions
pertaining to the output of the wrapper in different rounds. Based on the (in)dependence
conditions we propose a general framework of multiple forking and a General Multiple
Forking Lemma. Leveraging (in)dependence to the full allows us to improve the
degradation factor in the multiple forking game by a factor of (Formula presented.).
By implication, the cost of a single forking involving two random oracles (augmented
forking) matches that involving a single random oracle (elementary forking). Finally,
we study the effect of these observations on the concrete security of existing
schemes employing multiple forking. We conclude that by careful design of the
protocol (and the wrapper in the security reduction) it is possible to harness
our observations to the full extent.
acknowledgement: "We are grateful to the anonymous reviewers for their insightful
comments. The\r\ndetailed reports helped us a lot to address the technical mistakes
as well as to improve the overall presentation of the paper."
author:
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Sanjit
full_name: Chatterjee, Sanjit
last_name: Chatterjee
citation:
ama: 'Kamath Hosdurg C, Chatterjee S. A closer look at multiple-forking: Leveraging
(in)dependence for a tighter bound. Algorithmica. 2016;74(4):1321-1362.
doi:10.1007/s00453-015-9997-6'
apa: 'Kamath Hosdurg, C., & Chatterjee, S. (2016). A closer look at multiple-forking:
Leveraging (in)dependence for a tighter bound. Algorithmica. Springer.
https://doi.org/10.1007/s00453-015-9997-6'
chicago: 'Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking:
Leveraging (in)Dependence for a Tighter Bound.” Algorithmica. Springer,
2016. https://doi.org/10.1007/s00453-015-9997-6.'
ieee: 'C. Kamath Hosdurg and S. Chatterjee, “A closer look at multiple-forking:
Leveraging (in)dependence for a tighter bound,” Algorithmica, vol. 74,
no. 4. Springer, pp. 1321–1362, 2016.'
ista: 'Kamath Hosdurg C, Chatterjee S. 2016. A closer look at multiple-forking:
Leveraging (in)dependence for a tighter bound. Algorithmica. 74(4), 1321–1362.'
mla: 'Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking:
Leveraging (in)Dependence for a Tighter Bound.” Algorithmica, vol. 74,
no. 4, Springer, 2016, pp. 1321–62, doi:10.1007/s00453-015-9997-6.'
short: C. Kamath Hosdurg, S. Chatterjee, Algorithmica 74 (2016) 1321–1362.
date_created: 2018-12-11T11:50:33Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:48:52Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/s00453-015-9997-6
intvolume: ' 74'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprint.iacr.org/2013/651
month: '04'
oa: 1
oa_version: Submitted Version
page: 1321 - 1362
publication: Algorithmica
publication_status: published
publisher: Springer
publist_id: '6177'
quality_controlled: '1'
status: public
title: 'A closer look at multiple-forking: Leveraging (in)dependence for a tighter
bound'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2016'
...
---
_id: '1179'
abstract:
- lang: eng
text: "Computational notions of entropy have recently found many applications, including
leakage-resilient cryptography, deterministic encryption or memory delegation.
The two main types of results which make computational notions so useful are (1)
Chain rules, which quantify by how much the computational entropy of a variable
decreases if conditioned on some other variable (2) Transformations, which quantify
to which extend one type of entropy implies another.\r\n\r\nSuch chain rules and
transformations typically lose a significant amount in quality of the entropy,
and are the reason why applying these results one gets rather weak quantitative
security bounds. In this paper we for the first time prove lower bounds in this
context, showing that existing results for transformations are, unfortunately,
basically optimal for non-adaptive black-box reductions (and it’s hard to imagine
how non black-box reductions or adaptivity could be useful here.)\r\n\r\nA variable
X has k bits of HILL entropy of quality (ϵ,s)\r\nif there exists a variable Y
with k bits min-entropy which cannot be distinguished from X with advantage ϵ\r\n\r\nby
distinguishing circuits of size s. A weaker notion is Metric entropy, where we
switch quantifiers, and only require that for every distinguisher of size s, such
a Y exists.\r\n\r\nWe first describe our result concerning transformations. By
definition, HILL implies Metric without any loss in quality. Metric entropy often
comes up in applications, but must be transformed to HILL for meaningful security
guarantees. The best known result states that if a variable X has k bits of Metric
entropy of quality (ϵ,s)\r\n, then it has k bits of HILL with quality (2ϵ,s⋅ϵ2).
We show that this loss of a factor Ω(ϵ−2)\r\n\r\nin circuit size is necessary.
In fact, we show the stronger result that this loss is already necessary when
transforming so called deterministic real valued Metric entropy to randomised
boolean Metric (both these variants of Metric entropy are implied by HILL without
loss in quality).\r\n\r\nThe chain rule for HILL entropy states that if X has
k bits of HILL entropy of quality (ϵ,s)\r\n, then for any variable Z of length
m, X conditioned on Z has k−m bits of HILL entropy with quality (ϵ,s⋅ϵ2/2m). We
show that a loss of Ω(2m/ϵ) in circuit size necessary here. Note that this still
leaves a gap of ϵ between the known bound and our lower bound."
acknowledgement: "K. Pietrzak—Supported by the European Research Council consolidator
grant (682815-TOCNeT).\r\nM. Skórski—Supported by the National Science Center, Poland
(2015/17/N/ST6/03564)."
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Skorski
full_name: Maciej, Skorski
last_name: Maciej
citation:
ama: 'Pietrzak KZ, Maciej S. Pseudoentropy: Lower-bounds for chain rules and transformations.
In: Vol 9985. Springer; 2016:183-203. doi:10.1007/978-3-662-53641-4_8'
apa: 'Pietrzak, K. Z., & Maciej, S. (2016). Pseudoentropy: Lower-bounds for
chain rules and transformations (Vol. 9985, pp. 183–203). Presented at the TCC:
Theory of Cryptography Conference, Beijing, China: Springer. https://doi.org/10.1007/978-3-662-53641-4_8'
chicago: 'Pietrzak, Krzysztof Z, and Skorski Maciej. “Pseudoentropy: Lower-Bounds
for Chain Rules and Transformations,” 9985:183–203. Springer, 2016. https://doi.org/10.1007/978-3-662-53641-4_8.'
ieee: 'K. Z. Pietrzak and S. Maciej, “Pseudoentropy: Lower-bounds for chain rules
and transformations,” presented at the TCC: Theory of Cryptography Conference,
Beijing, China, 2016, vol. 9985, pp. 183–203.'
ista: 'Pietrzak KZ, Maciej S. 2016. Pseudoentropy: Lower-bounds for chain rules
and transformations. TCC: Theory of Cryptography Conference, LNCS, vol. 9985,
183–203.'
mla: 'Pietrzak, Krzysztof Z., and Skorski Maciej. Pseudoentropy: Lower-Bounds
for Chain Rules and Transformations. Vol. 9985, Springer, 2016, pp. 183–203,
doi:10.1007/978-3-662-53641-4_8.'
short: K.Z. Pietrzak, S. Maciej, in:, Springer, 2016, pp. 183–203.
conference:
end_date: 2016-11-03
location: Beijing, China
name: 'TCC: Theory of Cryptography Conference'
start_date: 2016-10-31
date_created: 2018-12-11T11:50:34Z
date_published: 2016-10-22T00:00:00Z
date_updated: 2021-01-12T06:48:53Z
day: '22'
department:
- _id: KrPi
doi: 10.1007/978-3-662-53641-4_8
ec_funded: 1
intvolume: ' 9985'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/159
month: '10'
oa: 1
oa_version: Preprint
page: 183 - 203
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_status: published
publisher: Springer
publist_id: '6175'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Pseudoentropy: Lower-bounds for chain rules and transformations'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9985
year: '2016'
...
---
_id: '7763'
abstract:
- lang: eng
text: An orthogonal wavelet basis is characterized by its approximation order, which
relates to the ability of the basis to represent general smooth functions on a
given scale. It is known, though perhaps not widely known, that there are ways
of exceeding the approximation order, i.e., achieving higher-order error in the
discretized wavelet transform and its inverse. The focus here is on the development
of a practical formulation to accomplish this first for 1D smooth functions, then
for 1D functions with discontinuities and then for multidimensional (here 2D)
functions with discontinuities. It is shown how to transcend both the wavelet
approximation order and the 2D Gibbs phenomenon in representing electromagnetic
fields at discontinuous dielectric interfaces that do not simply follow the wavelet-basis
grid.
article_processing_charge: No
article_type: original
author:
- first_name: Richard
full_name: Lombardini, Richard
last_name: Lombardini
- first_name: Ramiro
full_name: Acevedo, Ramiro
last_name: Acevedo
- first_name: Alexander
full_name: Kuczala, Alexander
last_name: Kuczala
- first_name: Kerry P.
full_name: Keys, Kerry P.
last_name: Keys
- 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: Bruce R.
full_name: Johnson, Bruce R.
last_name: Johnson
citation:
ama: Lombardini R, Acevedo R, Kuczala A, Keys KP, Goodrich CP, Johnson BR. Higher-order
wavelet reconstruction/differentiation filters and Gibbs phenomena. Journal
of Computational Physics. 2016;305:244-262. doi:10.1016/j.jcp.2015.10.035
apa: Lombardini, R., Acevedo, R., Kuczala, A., Keys, K. P., Goodrich, C. P., &
Johnson, B. R. (2016). Higher-order wavelet reconstruction/differentiation filters
and Gibbs phenomena. Journal of Computational Physics. Elsevier. https://doi.org/10.1016/j.jcp.2015.10.035
chicago: Lombardini, Richard, Ramiro Acevedo, Alexander Kuczala, Kerry P. Keys,
Carl Peter Goodrich, and Bruce R. Johnson. “Higher-Order Wavelet Reconstruction/Differentiation
Filters and Gibbs Phenomena.” Journal of Computational Physics. Elsevier,
2016. https://doi.org/10.1016/j.jcp.2015.10.035.
ieee: R. Lombardini, R. Acevedo, A. Kuczala, K. P. Keys, C. P. Goodrich, and B.
R. Johnson, “Higher-order wavelet reconstruction/differentiation filters and Gibbs
phenomena,” Journal of Computational Physics, vol. 305. Elsevier, pp. 244–262,
2016.
ista: Lombardini R, Acevedo R, Kuczala A, Keys KP, Goodrich CP, Johnson BR. 2016.
Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena.
Journal of Computational Physics. 305, 244–262.
mla: Lombardini, Richard, et al. “Higher-Order Wavelet Reconstruction/Differentiation
Filters and Gibbs Phenomena.” Journal of Computational Physics, vol. 305,
Elsevier, 2016, pp. 244–62, doi:10.1016/j.jcp.2015.10.035.
short: R. Lombardini, R. Acevedo, A. Kuczala, K.P. Keys, C.P. Goodrich, B.R. Johnson,
Journal of Computational Physics 305 (2016) 244–262.
date_created: 2020-04-30T11:40:41Z
date_published: 2016-01-15T00:00:00Z
date_updated: 2021-01-12T08:15:22Z
day: '15'
doi: 10.1016/j.jcp.2015.10.035
extern: '1'
intvolume: ' 305'
language:
- iso: eng
month: '01'
oa_version: None
page: 244-262
publication: Journal of Computational Physics
publication_identifier:
issn:
- 0021-9991
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 305
year: '2016'
...
---
_id: '7764'
abstract:
- lang: eng
text: States of self stress, organizations of internal forces in many-body systems
that are in equilibrium with an absence of external forces, can be thought of
as the constitutive building blocks of the elastic response of a material. In
overconstrained disordered packings they have a natural mathematical correspondence
with the zero-energy vibrational modes in underconstrained systems. While substantial
attention in the literature has been paid to diverging length scales associated
with zero- and finite-energy vibrational modes in jammed systems, less is known
about the spatial structure of the states of self stress. In this work we define
a natural way in which a unique state of self stress can be associated with each
bond in a disordered spring network derived from a jammed packing, and then investigate
the spatial structure of these bond-localized states of self stress. This allows
for an understanding of how the elastic properties of a system would change upon
changing the strength or even existence of any bond in the system.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel M.
full_name: Sussman, Daniel M.
last_name: Sussman
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
citation:
ama: Sussman DM, Goodrich CP, Liu AJ. Spatial structure of states of self stress
in jammed systems. Soft Matter. 2016;12(17):3982-3990. doi:10.1039/c6sm00094k
apa: Sussman, D. M., Goodrich, C. P., & Liu, A. J. (2016). Spatial structure
of states of self stress in jammed systems. Soft Matter. Royal Society
of Chemistry. https://doi.org/10.1039/c6sm00094k
chicago: Sussman, Daniel M., Carl Peter Goodrich, and Andrea J. Liu. “Spatial Structure
of States of Self Stress in Jammed Systems.” Soft Matter. Royal Society
of Chemistry, 2016. https://doi.org/10.1039/c6sm00094k.
ieee: D. M. Sussman, C. P. Goodrich, and A. J. Liu, “Spatial structure of states
of self stress in jammed systems,” Soft Matter, vol. 12, no. 17. Royal
Society of Chemistry, pp. 3982–3990, 2016.
ista: Sussman DM, Goodrich CP, Liu AJ. 2016. Spatial structure of states of self
stress in jammed systems. Soft Matter. 12(17), 3982–3990.
mla: Sussman, Daniel M., et al. “Spatial Structure of States of Self Stress in Jammed
Systems.” Soft Matter, vol. 12, no. 17, Royal Society of Chemistry, 2016,
pp. 3982–90, doi:10.1039/c6sm00094k.
short: D.M. Sussman, C.P. Goodrich, A.J. Liu, Soft Matter 12 (2016) 3982–3990.
date_created: 2020-04-30T11:40:56Z
date_published: 2016-03-14T00:00:00Z
date_updated: 2021-01-12T08:15:22Z
day: '14'
doi: 10.1039/c6sm00094k
extern: '1'
intvolume: ' 12'
issue: '17'
language:
- iso: eng
month: '03'
oa_version: None
page: 3982-3990
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
related_material:
link:
- relation: other
url: https://doi.org/10.1039/c6sm02496c
status: public
title: Spatial structure of states of self stress in jammed systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2016'
...
---
_id: '785'
abstract:
- lang: eng
text: High memory contention is generally agreed to be a worst-case scenario for
concurrent data structures. There has been a significant amount of research effort
spent investigating designs which minimize contention, and several programming
techniques have been proposed to mitigate its effects. However, there are currently
few architectural mechanisms to allow scaling contended data structures at high
thread counts. In this paper, we investigate hardware support for scalable contended
data structures. We propose Lease/Release, a simple addition to standard directory-based
MSI cache coherence protocols, allowing participants to lease memory, at the granularity
of cache lines, by delaying coherence messages for a short, bounded period of
time. Our analysis shows that Lease/Release can significantly reduce the overheads
of contention for both non-blocking (lock-free) and lock-based data structure
implementations, while ensuring that no deadlocks are introduced. We validate
Lease/Release empirically on the Graphite multiprocessor simulator, on a range
of data structures, including queue, stack, and priority queue implementations,
as well as on transactional applications. Results show that Lease/Release consistently
improves both throughput and energy usage, by up to 5x, both for lock-free and
lock-based data structure designs.
acknowledgement: We would like to thank Richard Black, Miguel Castro, Dave Dice, Aleksandar
Dragojevic, Maurice Herlihy, Ant Rowstron, Nir Shavit, and Vasileios Trigonakis,
as well as the anonymous reviewers, for helpful suggestions during the development
of this paper.
article_processing_charge: No
author:
- first_name: Syed
full_name: Haider, Syed
last_name: Haider
- first_name: William
full_name: Hasenplaugh, William
last_name: Hasenplaugh
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Haider S, Hasenplaugh W, Alistarh D-A. Lease/Release: Architectural support
for scaling contended data structures. In: Vol 12-16-March-2016. ACM; 2016. doi:10.1145/2851141.2851155'
apa: 'Haider, S., Hasenplaugh, W., & Alistarh, D.-A. (2016). Lease/Release:
Architectural support for scaling contended data structures (Vol. 12-16-March-2016).
Presented at the PPoPP: Principles and Practice of Parallel Pogramming, ACM. https://doi.org/10.1145/2851141.2851155'
chicago: 'Haider, Syed, William Hasenplaugh, and Dan-Adrian Alistarh. “Lease/Release:
Architectural Support for Scaling Contended Data Structures,” Vol. 12-16-March-2016.
ACM, 2016. https://doi.org/10.1145/2851141.2851155.'
ieee: 'S. Haider, W. Hasenplaugh, and D.-A. Alistarh, “Lease/Release: Architectural
support for scaling contended data structures,” presented at the PPoPP: Principles
and Practice of Parallel Pogramming, 2016, vol. 12-16-March-2016.'
ista: 'Haider S, Hasenplaugh W, Alistarh D-A. 2016. Lease/Release: Architectural
support for scaling contended data structures. PPoPP: Principles and Practice
of Parallel Pogramming vol. 12-16-March-2016.'
mla: 'Haider, Syed, et al. Lease/Release: Architectural Support for Scaling Contended
Data Structures. Vol. 12-16-March-2016, ACM, 2016, doi:10.1145/2851141.2851155.'
short: S. Haider, W. Hasenplaugh, D.-A. Alistarh, in:, ACM, 2016.
conference:
name: 'PPoPP: Principles and Practice of Parallel Pogramming'
date_created: 2018-12-11T11:48:29Z
date_published: 2016-02-27T00:00:00Z
date_updated: 2022-03-18T12:56:29Z
day: '27'
doi: 10.1145/2851141.2851155
extern: '1'
language:
- iso: eng
month: '02'
oa_version: None
publication_status: published
publisher: ACM
publist_id: '6871'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Lease/Release: Architectural support for scaling contended data structures'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12-16-March-2016
year: '2016'
...
---
_id: '786'
abstract:
- lang: eng
text: Lock-free concurrent algorithms guarantee that some concurrent operation will
always make progress in a finite number of steps. Yet programmers prefer to treat
concurrent code as if it were wait-free, guaranteeing that all operations always
make progress. Unfortunately, designing wait-free algorithms is generally a very
complex task, and the resulting algorithms are not always efficient. Although
obtaining efficient wait-free algorithms has been a long-time goal for the theory
community, most nonblocking commercial code is only lock-free. This article suggests
a simple solution to this problem.We show that for a large class of lock-free
algorithms, under scheduling conditions that approximate those found in commercial
hardware architectures, lock-free algorithms behave as if they are wait-free.
In other words, programmers can continue to design simple lock-free algorithms
instead of complex wait-free ones, and in practice, they will get wait-free progress.
Our main contribution is a new way of analyzing a general class of lock-free algorithms
under a stochastic scheduler. Our analysis relates the individual performance
of processes to the global performance of the system using Markov chain lifting
between a complex per-process chain and a simpler system progress chain. We show
that lock-free algorithms are not only wait-free with probability 1 but that in
fact a general subset of lock-free algorithms can be closely bounded in terms
of the average number of steps required until an operation completes. To the best
of our knowledge, this is the first attempt to analyze progress conditions, typically
stated in relation to a worst-case adversary, in a stochastic model capturing
their expected asymptotic behavior.
acknowledgement: Part of this work was performed while the first author was a postdoctoral
associate at MIT CSAIL, where he was supported by the SNF Postdoctoral Fellows Program,
NSF grant CCF-1217921, DoE ASCR grant ER26116/DE-SC0008923, and by grants from the
Oracle and Intel corporations. The second author was supported in part by ISF grant
1696/14. The third author was supported in part by NSF grants CCF-1217921, CCF-1301926,
IIS-1447786, and CCF-1561807, and the U.S. Department of Energy under grant DE-SC0008923,
and by equipment grants from Intel Corporation.
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: Keren
full_name: Censor Hillel, Keren
last_name: Censor Hillel
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: Alistarh D-A, Censor Hillel K, Shavit N. Are lock free concurrent algorithms
practically wait free . Journal of the ACM. 2016;63(4). doi:10.1145/2903136
apa: Alistarh, D.-A., Censor Hillel, K., & Shavit, N. (2016). Are lock free
concurrent algorithms practically wait free . Journal of the ACM. ACM.
https://doi.org/10.1145/2903136
chicago: Alistarh, Dan-Adrian, Keren Censor Hillel, and Nir Shavit. “Are Lock Free
Concurrent Algorithms Practically Wait Free .” Journal of the ACM. ACM,
2016. https://doi.org/10.1145/2903136.
ieee: D.-A. Alistarh, K. Censor Hillel, and N. Shavit, “Are lock free concurrent
algorithms practically wait free ,” Journal of the ACM, vol. 63, no. 4.
ACM, 2016.
ista: Alistarh D-A, Censor Hillel K, Shavit N. 2016. Are lock free concurrent algorithms
practically wait free . Journal of the ACM. 63(4).
mla: Alistarh, Dan-Adrian, et al. “Are Lock Free Concurrent Algorithms Practically
Wait Free .” Journal of the ACM, vol. 63, no. 4, ACM, 2016, doi:10.1145/2903136.
short: D.-A. Alistarh, K. Censor Hillel, N. Shavit, Journal of the ACM 63 (2016).
date_created: 2018-12-11T11:48:29Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2023-02-23T13:19:04Z
day: '01'
doi: 10.1145/2903136
extern: '1'
external_id:
arxiv:
- '1311.3200'
intvolume: ' 63'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1311.3200
month: '09'
oa: 1
oa_version: Preprint
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '6870'
quality_controlled: '1'
status: public
title: 'Are lock free concurrent algorithms practically wait free '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 63
year: '2016'
...
---
_id: '8020'
abstract:
- lang: eng
text: Balance of cortical excitation and inhibition (EI) is thought to be disrupted
in several neuropsychiatric conditions, yet it is not clear how it is maintained
in the healthy human brain. When EI balance is disturbed during learning and memory
in animal models, it can be restabilized via formation of inhibitory replicas
of newly formed excitatory connections. Here we assess evidence for such selective
inhibitory rebalancing in humans. Using fMRI repetition suppression we measure
newly formed cortical associations in the human brain. We show that expression
of these associations reduces over time despite persistence in behavior, consistent
with inhibitory rebalancing. To test this, we modulated excitation/inhibition
balance with transcranial direct current stimulation (tDCS). Using ultra-high-field
(7T) MRI and spectroscopy, we show that reducing GABA allows cortical associations
to be re-expressed. This suggests that in humans associative memories are stored
in balanced excitatory-inhibitory ensembles that lie dormant unless latent inhibitory
connections are unmasked.
article_processing_charge: No
article_type: original
author:
- first_name: H.C.
full_name: Barron, H.C.
last_name: Barron
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: U.E.
full_name: Emir, U.E.
last_name: Emir
- first_name: T.R.
full_name: Makin, T.R.
last_name: Makin
- first_name: J.
full_name: O’Shea, J.
last_name: O’Shea
- first_name: S.
full_name: Clare, S.
last_name: Clare
- first_name: S.
full_name: Jbabdi, S.
last_name: Jbabdi
- first_name: R.J.
full_name: Dolan, R.J.
last_name: Dolan
- first_name: T.E.J.
full_name: Behrens, T.E.J.
last_name: Behrens
citation:
ama: Barron HC, Vogels TP, Emir UE, et al. Unmasking latent inhibitory connections
in human cortex to reveal dormant cortical memories. Neuron. 2016;90(1):191-203.
doi:10.1016/j.neuron.2016.02.031
apa: Barron, H. C., Vogels, T. P., Emir, U. E., Makin, T. R., O’Shea, J., Clare,
S., … Behrens, T. E. J. (2016). Unmasking latent inhibitory connections in human
cortex to reveal dormant cortical memories. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2016.02.031
chicago: Barron, H.C., Tim P Vogels, U.E. Emir, T.R. Makin, J. O’Shea, S. Clare,
S. Jbabdi, R.J. Dolan, and T.E.J. Behrens. “Unmasking Latent Inhibitory Connections
in Human Cortex to Reveal Dormant Cortical Memories.” Neuron. Elsevier,
2016. https://doi.org/10.1016/j.neuron.2016.02.031.
ieee: H. C. Barron et al., “Unmasking latent inhibitory connections in human
cortex to reveal dormant cortical memories,” Neuron, vol. 90, no. 1. Elsevier,
pp. 191–203, 2016.
ista: Barron HC, Vogels TP, Emir UE, Makin TR, O’Shea J, Clare S, Jbabdi S, Dolan
RJ, Behrens TEJ. 2016. Unmasking latent inhibitory connections in human cortex
to reveal dormant cortical memories. Neuron. 90(1), 191–203.
mla: Barron, H. C., et al. “Unmasking Latent Inhibitory Connections in Human Cortex
to Reveal Dormant Cortical Memories.” Neuron, vol. 90, no. 1, Elsevier,
2016, pp. 191–203, doi:10.1016/j.neuron.2016.02.031.
short: H.C. Barron, T.P. Vogels, U.E. Emir, T.R. Makin, J. O’Shea, S. Clare, S.
Jbabdi, R.J. Dolan, T.E.J. Behrens, Neuron 90 (2016) 191–203.
date_created: 2020-06-25T13:05:33Z
date_published: 2016-04-06T00:00:00Z
date_updated: 2021-01-12T08:16:34Z
day: '06'
ddc:
- '570'
doi: 10.1016/j.neuron.2016.02.031
extern: '1'
external_id:
pmid:
- '26996082'
file:
- access_level: open_access
checksum: 9ce7a1c64986dce0435c070285a7ef9b
content_type: application/pdf
creator: cziletti
date_created: 2020-07-09T09:57:04Z
date_updated: 2020-07-14T12:48:08Z
file_id: '8104'
file_name: 2016_Neuron_Barron.pdf
file_size: 5334136
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
intvolume: ' 90'
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 191-203
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Unmasking latent inhibitory connections in human cortex to reveal dormant cortical
memories
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 90
year: '2016'
...
---
_id: '8094'
abstract:
- lang: eng
text: 'With the accelerated development of robot technologies, optimal control becomes
one of the central themes of research. In traditional approaches, the controller,
by its internal functionality, finds appropriate actions on the basis of the history
of sensor values, guided by the goals, intentions, objectives, learning schemes,
and so forth. The idea is that the controller controls the world---the body plus
its environment---as reliably as possible. This paper focuses on new lines of
self-organization for developmental robotics. We apply the recently developed
differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder
system from the Myorobotics toolkit. In the experiments, we observe a vast variety
of self-organized behavior patterns: when left alone, the arm realizes pseudo-random
sequences of different poses. By applying physical forces, the system can be entrained
into definite motion patterns like wiping a table. Most interestingly, after attaching
an object, the controller gets in a functional resonance with the object''s internal
dynamics, starting to shake spontaneously bottles half-filled with water or sensitively
driving an attached pendulum into a circular mode. When attached to the crank
of a wheel the neural system independently discovers how to rotate it. In this
way, the robot discovers affordances of objects its body is interacting with.'
article_processing_charge: No
author:
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
- first_name: Rafael
full_name: Hostettler, Rafael
last_name: Hostettler
- first_name: Alois
full_name: Knoll, Alois
last_name: Knoll
- first_name: Ralf
full_name: Der, Ralf
last_name: Der
citation:
ama: 'Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon
driven arm by differential extrinsic plasticity. In: Proceedings of the Artificial
Life Conference 2016. Vol 28. MIT Press; 2016:142-143. doi:10.7551/978-0-262-33936-0-ch029'
apa: 'Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Self-organized
control of an tendon driven arm by differential extrinsic plasticity. In Proceedings
of the Artificial Life Conference 2016 (Vol. 28, pp. 142–143). Cancun, Mexico:
MIT Press. https://doi.org/10.7551/978-0-262-33936-0-ch029'
chicago: Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized
Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In Proceedings
of the Artificial Life Conference 2016, 28:142–43. MIT Press, 2016. https://doi.org/10.7551/978-0-262-33936-0-ch029.
ieee: G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control
of an tendon driven arm by differential extrinsic plasticity,” in Proceedings
of the Artificial Life Conference 2016, Cancun, Mexico, 2016, vol. 28, pp.
142–143.
ista: 'Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of
an tendon driven arm by differential extrinsic plasticity. Proceedings of the
Artificial Life Conference 2016. ALIFE 2016: 15th International Conference on
the Synthesis and Simulation of Living Systems vol. 28, 142–143.'
mla: Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by
Differential Extrinsic Plasticity.” Proceedings of the Artificial Life Conference
2016, vol. 28, MIT Press, 2016, pp. 142–43, doi:10.7551/978-0-262-33936-0-ch029.
short: G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial
Life Conference 2016, MIT Press, 2016, pp. 142–143.
conference:
end_date: 2016-07-08
location: Cancun, Mexico
name: 'ALIFE 2016: 15th International Conference on the Synthesis and Simulation
of Living Systems'
start_date: 2016-07-04
date_created: 2020-07-05T22:00:47Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2021-01-12T08:16:53Z
day: '01'
ddc:
- '610'
department:
- _id: ChLa
- _id: GaTk
doi: 10.7551/978-0-262-33936-0-ch029
ec_funded: 1
file:
- access_level: open_access
checksum: cff63e7a4b8ac466ba51a9c84153a940
content_type: application/pdf
creator: cziletti
date_created: 2020-07-06T12:59:09Z
date_updated: 2020-07-14T12:48:09Z
file_id: '8096'
file_name: 2016_ProcALIFE_Martius.pdf
file_size: 678670
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
intvolume: ' 28'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 142-143
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Proceedings of the Artificial Life Conference 2016
publication_identifier:
isbn:
- '9780262339360'
publication_status: published
publisher: MIT Press
quality_controlled: '1'
scopus_import: 1
status: public
title: Self-organized control of an tendon driven arm by differential extrinsic plasticity
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 28
year: '2016'
...
---
_id: '8128'
abstract:
- lang: eng
text: The stimulus selectivity of synaptic currents in cortical neurons often shows
a co-tuning of excitation and inhibition, but the mechanisms that underlie the
emergence and plasticity of this co-tuning are not fully understood. Using a computational
model, we show that an interaction of excitatory and inhibitory synaptic plasticity
reproduces both the developmental and – when combined with a disinhibitory gate
– the adult plasticity of excitatory and inhibitory receptive fields in auditory
cortex. The co-tuning arises from inhibitory plasticity that balances excitation
and inhibition, while excitatory stimulus selectivity can result from two different
mechanisms. Inhibitory inputs with a broad stimulus tuning introduce a sliding
threshold as in Bienenstock-Cooper-Munro rules, introducing an excitatory stimulus
selectivity at the cost of a broader inhibitory receptive field. Alternatively,
input asymmetries can be amplified by synaptic competition. The latter leaves
any receptive field plasticity transient, a prediction we verify in recordings
in auditory cortex.
article_processing_charge: No
author:
- first_name: Claudia
full_name: Clopath, Claudia
last_name: Clopath
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Robert C.
full_name: Froemke, Robert C.
last_name: Froemke
- first_name: Henning
full_name: Sprekeler, Henning
last_name: Sprekeler
citation:
ama: Clopath C, Vogels TP, Froemke RC, Sprekeler H. Receptive field formation by
interacting excitatory and inhibitory synaptic plasticity. bioRxiv. 2016.
apa: Clopath, C., Vogels, T. P., Froemke, R. C., & Sprekeler, H. (2016). Receptive
field formation by interacting excitatory and inhibitory synaptic plasticity.
bioRxiv. Cold Spring Harbor Laboratory.
chicago: Clopath, Claudia, Tim P Vogels, Robert C. Froemke, and Henning Sprekeler.
“Receptive Field Formation by Interacting Excitatory and Inhibitory Synaptic Plasticity.”
BioRxiv. Cold Spring Harbor Laboratory, 2016.
ieee: C. Clopath, T. P. Vogels, R. C. Froemke, and H. Sprekeler, “Receptive field
formation by interacting excitatory and inhibitory synaptic plasticity,” bioRxiv.
Cold Spring Harbor Laboratory, 2016.
ista: Clopath C, Vogels TP, Froemke RC, Sprekeler H. 2016. Receptive field formation
by interacting excitatory and inhibitory synaptic plasticity. bioRxiv, .
mla: Clopath, Claudia, et al. “Receptive Field Formation by Interacting Excitatory
and Inhibitory Synaptic Plasticity.” BioRxiv, Cold Spring Harbor Laboratory,
2016.
short: C. Clopath, T.P. Vogels, R.C. Froemke, H. Sprekeler, BioRxiv (2016).
date_created: 2020-07-16T12:26:55Z
date_published: 2016-07-29T00:00:00Z
date_updated: 2021-01-12T08:17:02Z
day: '29'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/066589 '
month: '07'
oa: 1
oa_version: Preprint
page: '43'
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
status: public
title: Receptive field formation by interacting excitatory and inhibitory synaptic
plasticity
type: preprint
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
year: '2016'
...
---
_id: '813'
abstract:
- lang: eng
text: The Gag polyprotein of retroviruses drives immature virus assembly by forming
hexameric protein lattices. The assembly is primarily mediated by protein-protein
interactions between capsid (CA) domains and by interactions between nucleocapsid
(NC) domains and RNA. Specific interactions between NC and the viral RNA are required
for genome packaging. Previously reported cryoelectron microscopy analysis of
immature Mason-Pfizer monkey virus (M-PMV) particles suggested that a basic region
(residues RKK) in CA may serve as an additional binding site for nucleic acids.
Here, we have introduced mutations into the RKK region in both bacterial and proviral
M-PMV vectors and have assessed their impact on M-PMV assembly, structure, RNA
binding, budding/release, nuclear trafficking, and infectivity using in vitro
and in vivo systems. Our data indicate that the RKK region binds and structures
nucleic acid that serves to promote virus particle assembly in the cytoplasm.
Moreover, the RKK region appears to be important for recruitment of viral genomic
RNA into Gag particles, and this function could be linked to changes in nuclear
trafficking. Together these observations suggest that in M-PMV, direct interactions
between CA and nucleic acid play important functions in the late stages of the
viral life cycle.
acknowledgement: |-
Work in the laboratory of John A. G. Briggs was funded by Deutsche
Forschungsgemeinschaft (DFG) (BR 3635/2-1). This work, including the
efforts of Tomas Ruml, was funded by the Grant Agency of the Czech
Republic (14-15326S) and the Czech Ministry of Education (NPU I sus-
tainability projects LO1302 and LO1304).
author:
- first_name: Tibor
full_name: Füzik, Tibor
last_name: Füzik
- first_name: Růžena
full_name: ' Píchalová, Růžena'
last_name: Píchalová
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Karolína
full_name: Strohalmová, Karolína
last_name: Strohalmová
- first_name: Ivana
full_name: Křížová, Ivana
last_name: Křížová
- first_name: Romana
full_name: Hadravová, Romana
last_name: Hadravová
- first_name: Michaela
full_name: Rumlová, Michaela
last_name: Rumlová
- first_name: John
full_name: Briggs, John A
last_name: Briggs
- first_name: Pavel
full_name: Ulbrich, Pavel
last_name: Ulbrich
- first_name: Tomáš
full_name: Ruml, Tomáš
last_name: Ruml
citation:
ama: Füzik T, Píchalová R, Schur FK, et al. Nucleic acid binding by Mason-Pfizer
monkey virus CA promotes virus assembly and genome packaging. Journal of Virology.
2016;90(9):4593-4603. doi:10.1128/JVI.03197-15
apa: Füzik, T., Píchalová, R., Schur, F. K., Strohalmová, K., Křížová, I., Hadravová,
R., … Ruml, T. (2016). Nucleic acid binding by Mason-Pfizer monkey virus CA promotes
virus assembly and genome packaging. Journal of Virology. ASM. https://doi.org/10.1128/JVI.03197-15
chicago: Füzik, Tibor, Růžena Píchalová, Florian KM Schur, Karolína Strohalmová,
Ivana Křížová, Romana Hadravová, Michaela Rumlová, John Briggs, Pavel Ulbrich,
and Tomáš Ruml. “Nucleic Acid Binding by Mason-Pfizer Monkey Virus CA Promotes
Virus Assembly and Genome Packaging.” Journal of Virology. ASM, 2016. https://doi.org/10.1128/JVI.03197-15.
ieee: T. Füzik et al., “Nucleic acid binding by Mason-Pfizer monkey virus
CA promotes virus assembly and genome packaging,” Journal of Virology,
vol. 90, no. 9. ASM, pp. 4593–4603, 2016.
ista: Füzik T, Píchalová R, Schur FK, Strohalmová K, Křížová I, Hadravová R, Rumlová
M, Briggs J, Ulbrich P, Ruml T. 2016. Nucleic acid binding by Mason-Pfizer monkey
virus CA promotes virus assembly and genome packaging. Journal of Virology. 90(9),
4593–4603.
mla: Füzik, Tibor, et al. “Nucleic Acid Binding by Mason-Pfizer Monkey Virus CA
Promotes Virus Assembly and Genome Packaging.” Journal of Virology, vol.
90, no. 9, ASM, 2016, pp. 4593–603, doi:10.1128/JVI.03197-15.
short: T. Füzik, R. Píchalová, F.K. Schur, K. Strohalmová, I. Křížová, R. Hadravová,
M. Rumlová, J. Briggs, P. Ulbrich, T. Ruml, Journal of Virology 90 (2016) 4593–4603.
date_created: 2018-12-11T11:48:38Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2021-01-12T08:17:03Z
day: '01'
doi: 10.1128/JVI.03197-15
extern: 1
intvolume: ' 90'
issue: '9'
month: '05'
page: 4593 - 4603
publication: Journal of Virology
publication_status: published
publisher: ASM
publist_id: '6835'
quality_controlled: 0
status: public
title: Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly
and genome packaging
type: journal_article
volume: 90
year: '2016'
...
---
_id: '816'
abstract:
- lang: eng
text: Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic
cleavage of the viral Gag polyprotein induces structural maturation. Maturation
can be blocked by maturation inhibitors (MIs), thereby abolishing infectivity.
The CA (capsid) and SP1 (spacer peptide 1) region of Gag is the key regulator
of assembly and maturation and is the target of MIs.We applied optimized cryo-electron
tomography and subtomogram averaging to resolve this region within assembled immature
HIV-1 particles at 3.9 angstrom resolution and built an atomic model. The structure
reveals a network of intra- And intermolecular interactions mediating immature
HIV-1 assembly. The proteolytic cleavage site between CA and SP1 is inaccessible
to protease.We suggest that MIs prevent CA-SP1 cleavage by stabilizing the structure,
and MI resistance develops by destabilizing CA-SP1.
acknowledgement: The authors thank B. Glass for preparation of the immature HIV-1
(D25A) sample; J. Plitzko and D. Tegunov for providing the K2Align software; and
S. Mattei, N. Hoffman, F. Thommen, A. Sonnen, and S. Dodonova for technical assistance
and/or discussion. This study was supported by Deutsche Forschungsgemeinschaft grants
BR 3635/2-1 (to J.A.G.B.) and KR 906/7-1 (to H.-G.K.). The Briggs laboratory acknowledges
financial support from the European Molecular Biology Laboratory (EMBL) and from
the Chica und Heinz Schaller Stiftung. W.W. was supported by a European Molecular
Biology Organization Long-Term Fellowship (ALTF 748-2014). A.J.J. acknowledges support
by the EMBL Interdisciplinary Postdoc Program under the Marie Curie Action COFUND
(PCOFUND-GA-2008-229597) and by the Joachim Herz Stiftung. This study was technically
supported by the EMBL information technology services unit and the EMBL Proteomics
Core Facility. F.K.M.S., M.O., H.-G.K., and J.A.G.B. designed the experiments, with
J.M.K. assisting in the design of those involving mass spectrometry. F.K.M.S. and
M.O. prepared samples. W.J.H.H. implemented tomography acquisition schemes. F.K.M.S.
and W.J.H.H. acquired the data. F.K.M.S. and W.W. processed images. F.K.M.S., A.J.J.,
and C.S. refined the model. F.K.M.S., M.O., and J.A.G.B. analyzed the data. F.K.M.S.
and J.A.G.B. wrote the manuscript with support from all authors. Representative
tomograms and the final electron microscopy structures have been deposited in the
Electron Microscopy Data Bank with accession numbers EMD-4015, EMD-4016, EMD-4017,
EMD-4018, EMD-4019, and EMD-4020. The refined HIV-1 CA-SP1 model has been deposited
in the Protein Data Bank with accession number 5L93.
author:
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Martin
full_name: Martin Obr
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
- first_name: Wim
full_name: Hagen, Wim J
last_name: Hagen
- first_name: William
full_name: Wan, William
last_name: Wan
- first_name: Arjen
full_name: Jakobi, Arjen J
last_name: Jakobi
- first_name: Joanna
full_name: Kirkpatrick, Joanna M
last_name: Kirkpatrick
- first_name: Carsten
full_name: Sachse, Carsten
last_name: Sachse
- 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, Obr M, Hagen W, et al. An atomic model of HIV-1 capsid-SP1 reveals
structures regulating assembly and maturation. Science. 2016;353(6298):506-508.
doi:10.1126/science.aaf9620
apa: Schur, F. K., Obr, M., Hagen, W., Wan, W., Jakobi, A., Kirkpatrick, J., … Briggs,
J. (2016). An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly
and maturation. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.aaf9620
chicago: Schur, Florian KM, Martin Obr, Wim Hagen, William Wan, Arjen Jakobi, Joanna
Kirkpatrick, Carsten Sachse, Hans Kraüsslich, and John Briggs. “An Atomic Model
of HIV-1 Capsid-SP1 Reveals Structures Regulating Assembly and Maturation.” Science.
American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aaf9620.
ieee: F. K. Schur et al., “An atomic model of HIV-1 capsid-SP1 reveals structures
regulating assembly and maturation,” Science, vol. 353, no. 6298. American
Association for the Advancement of Science, pp. 506–508, 2016.
ista: Schur FK, Obr M, Hagen W, Wan W, Jakobi A, Kirkpatrick J, Sachse C, Kraüsslich
H, Briggs J. 2016. An atomic model of HIV-1 capsid-SP1 reveals structures regulating
assembly and maturation. Science. 353(6298), 506–508.
mla: Schur, Florian KM, et al. “An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures
Regulating Assembly and Maturation.” Science, vol. 353, no. 6298, American
Association for the Advancement of Science, 2016, pp. 506–08, doi:10.1126/science.aaf9620.
short: F.K. Schur, M. Obr, W. Hagen, W. Wan, A. Jakobi, J. Kirkpatrick, C. Sachse,
H. Kraüsslich, J. Briggs, Science 353 (2016) 506–508.
date_created: 2018-12-11T11:48:39Z
date_published: 2016-07-29T00:00:00Z
date_updated: 2021-01-12T08:17:12Z
day: '29'
doi: 10.1126/science.aaf9620
extern: 1
intvolume: ' 353'
issue: '6298'
month: '07'
page: 506 - 508
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6834'
quality_controlled: 0
status: public
title: An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly
and maturation
type: journal_article
volume: 353
year: '2016'
...
---
_id: '8241'
abstract:
- lang: eng
text: 'Background: Anticancer vaccines could represent a valuable complementary
strategy to established therapies, especially in settings of early stage and minimal
residual disease. HER-2 is an important target for immunotherapy and addressed
by the monoclonal antibody trastuzumab. We have previously generated HER-2 mimotope
peptides from phage display libraries. The synthesized peptides were coupled to
carriers and applied for epitope-specific induction of trastuzumab-like IgG. For
simplification and to avoid methodological limitations of synthesis and coupling
chemistry, we herewith present a novel and optimized approach by using adeno-associated
viruses (AAV) as effective and high-density mimotope-display system, which can
be directly used for vaccination. Methods: An AAV capsid display library was constructed
by genetically incorporating random peptides in a plasmid encoding the wild-type
AAV2 capsid protein. AAV clones, expressing peptides specifically reactive to
trastuzumab, were employed to immunize BALB/c mice. Antibody titers against human
HER-2 were determined, and the isotype composition and functional properties of
these were tested. Finally, prophylactically immunized mice were challenged with
human HER-2 transfected mouse D2F2/E2 cells. Results: HER-2 mimotope AAV-vaccines
induced antibodies specific to human HER-2. Two clones were selected for immunization
of mice, which were subsequently grafted D2F2/E2 cells. Both mimotope AAV clones
delayed the growth of tumors significantly, as compared to controls. Conclusion:
In this study, a novel mimotope AAV-based platform was created allowing the isolation
of mimotopes, which can be directly used as anticancer vaccines. The example of
trastuzumab AAV-mimotopes demonstrates that this vaccine strategy could help to
establish active immunotherapy for breast-cancer patients.'
article_number: e1171446
article_processing_charge: No
article_type: original
author:
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
- first_name: Krisztina
full_name: Manzano-Szalai, Krisztina
last_name: Manzano-Szalai
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: Kathrin
full_name: Thell, Kathrin
last_name: Thell
- first_name: Anna
full_name: Bentley-Lukschal, Anna
last_name: Bentley-Lukschal
- first_name: Caroline
full_name: Stremnitzer, Caroline
last_name: Stremnitzer
- first_name: Franziska
full_name: Roth-Walter, Franziska
last_name: Roth-Walter
- first_name: Margit
full_name: Weghofer, Margit
last_name: Weghofer
- first_name: Mirko
full_name: Ritter, Mirko
last_name: Ritter
- first_name: Kerstin
full_name: Pino Tossi, Kerstin
last_name: Pino Tossi
- first_name: Markus
full_name: Hörer, Markus
last_name: Hörer
- first_name: Uwe
full_name: Michaelis, Uwe
last_name: Michaelis
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: Singer J, Manzano-Szalai K, Singer J, et al. Proof of concept study with an
HER-2 mimotope anticancer vaccine deduced from a novel AAV-mimotope library platform.
OncoImmunology. 2016;5(7). doi:10.1080/2162402x.2016.1171446
apa: Singer, J., Manzano-Szalai, K., Singer, J., Thell, K., Bentley-Lukschal, A.,
Stremnitzer, C., … Jensen-Jarolim, E. (2016). Proof of concept study with an HER-2
mimotope anticancer vaccine deduced from a novel AAV-mimotope library platform.
OncoImmunology. Taylor & Francis. https://doi.org/10.1080/2162402x.2016.1171446
chicago: Singer, Josef, Krisztina Manzano-Szalai, Judit Singer, Kathrin Thell, Anna
Bentley-Lukschal, Caroline Stremnitzer, Franziska Roth-Walter, et al. “Proof of
Concept Study with an HER-2 Mimotope Anticancer Vaccine Deduced from a Novel AAV-Mimotope
Library Platform.” OncoImmunology. Taylor & Francis, 2016. https://doi.org/10.1080/2162402x.2016.1171446.
ieee: J. Singer et al., “Proof of concept study with an HER-2 mimotope anticancer
vaccine deduced from a novel AAV-mimotope library platform,” OncoImmunology,
vol. 5, no. 7. Taylor & Francis, 2016.
ista: Singer J, Manzano-Szalai K, Singer J, Thell K, Bentley-Lukschal A, Stremnitzer
C, Roth-Walter F, Weghofer M, Ritter M, Pino Tossi K, Hörer M, Michaelis U, Jensen-Jarolim
E. 2016. Proof of concept study with an HER-2 mimotope anticancer vaccine deduced
from a novel AAV-mimotope library platform. OncoImmunology. 5(7), e1171446.
mla: Singer, Josef, et al. “Proof of Concept Study with an HER-2 Mimotope Anticancer
Vaccine Deduced from a Novel AAV-Mimotope Library Platform.” OncoImmunology,
vol. 5, no. 7, e1171446, Taylor & Francis, 2016, doi:10.1080/2162402x.2016.1171446.
short: J. Singer, K. Manzano-Szalai, J. Singer, K. Thell, A. Bentley-Lukschal, C.
Stremnitzer, F. Roth-Walter, M. Weghofer, M. Ritter, K. Pino Tossi, M. Hörer,
U. Michaelis, E. Jensen-Jarolim, OncoImmunology 5 (2016).
date_created: 2020-08-10T11:54:03Z
date_published: 2016-06-30T00:00:00Z
date_updated: 2021-01-12T08:17:41Z
day: '30'
doi: 10.1080/2162402x.2016.1171446
extern: '1'
intvolume: ' 5'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1080/2162402X.2016.1171446
month: '06'
oa: 1
oa_version: Published Version
publication: OncoImmunology
publication_identifier:
issn:
- 2162-402X
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
status: public
title: Proof of concept study with an HER-2 mimotope anticancer vaccine deduced from
a novel AAV-mimotope library platform
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2016'
...
---
_id: '8300'
abstract:
- lang: eng
text: The integration of social networking concepts into Internet of Things systems
is a burgeoning topic of research that promises to support novel and more powerful
applications. In this paper we focus on the design and implementation of a highly
scalable Trust and Reputation Model for the Internet of Things based on the social
approach that the COSMOS project introduces, as part of its final results. We
create our model by combining popular solutions proposed for Peer-to-Peer and
mobile ad-hoc networks and adapting them on the Internet of Things concept. Each
Thing can compute the Trust index of another Thing based on its own experiences,
while it has the capability of determining its Reputation Index either by consulting
its other “friends” (Followees) or referring to the Platform, a management system
used in COSMOS. The model is tested through simulations of the proposed social
system, demonstrating the ability of TRM-SIoT to achieve the Social Exclusion
of malicious nodes and collectives from the network, with low computational overhead
and high scalability. Furthermore, due to the adaptive nature of the system, Social
Reintegration of these nodes is also possible.
article_number: '7733612'
article_processing_charge: No
author:
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Orfefs
full_name: Voutyras, Orfefs
last_name: Voutyras
- first_name: Theodora
full_name: Varvarigou, Theodora
last_name: Varvarigou
citation:
ama: 'Kokoris Kogias E, Voutyras O, Varvarigou T. TRM-SIoT: A scalable hybrid trust
& reputation model for the social Internet of Things. In: 2016 IEEE 21st
International Conference on Emerging Technologies and Factory Automation.
IEEE; 2016. doi:10.1109/etfa.2016.7733612'
apa: 'Kokoris Kogias, E., Voutyras, O., & Varvarigou, T. (2016). TRM-SIoT: A
scalable hybrid trust & reputation model for the social Internet of Things.
In 2016 IEEE 21st International Conference on Emerging Technologies and Factory
Automation. Berlin, Germany: IEEE. https://doi.org/10.1109/etfa.2016.7733612'
chicago: 'Kokoris Kogias, Eleftherios, Orfefs Voutyras, and Theodora Varvarigou.
“TRM-SIoT: A Scalable Hybrid Trust & Reputation Model for the Social Internet
of Things.” In 2016 IEEE 21st International Conference on Emerging Technologies
and Factory Automation. IEEE, 2016. https://doi.org/10.1109/etfa.2016.7733612.'
ieee: 'E. Kokoris Kogias, O. Voutyras, and T. Varvarigou, “TRM-SIoT: A scalable
hybrid trust & reputation model for the social Internet of Things,” in 2016
IEEE 21st International Conference on Emerging Technologies and Factory Automation,
Berlin, Germany, 2016.'
ista: 'Kokoris Kogias E, Voutyras O, Varvarigou T. 2016. TRM-SIoT: A scalable hybrid
trust & reputation model for the social Internet of Things. 2016 IEEE 21st
International Conference on Emerging Technologies and Factory Automation. ETFA:
Conference on Emerging Technologies and Factory Automation, 7733612.'
mla: 'Kokoris Kogias, Eleftherios, et al. “TRM-SIoT: A Scalable Hybrid Trust &
Reputation Model for the Social Internet of Things.” 2016 IEEE 21st International
Conference on Emerging Technologies and Factory Automation, 7733612, IEEE,
2016, doi:10.1109/etfa.2016.7733612.'
short: E. Kokoris Kogias, O. Voutyras, T. Varvarigou, in:, 2016 IEEE 21st International
Conference on Emerging Technologies and Factory Automation, IEEE, 2016.
conference:
end_date: 2016-09-09
location: Berlin, Germany
name: 'ETFA: Conference on Emerging Technologies and Factory Automation'
start_date: 2016-09-06
date_created: 2020-08-26T11:48:54Z
date_published: 2016-09-09T00:00:00Z
date_updated: 2021-01-12T08:17:59Z
day: '09'
doi: 10.1109/etfa.2016.7733612
extern: '1'
language:
- iso: eng
month: '09'
oa_version: None
publication: 2016 IEEE 21st International Conference on Emerging Technologies and
Factory Automation
publication_identifier:
isbn:
- '9781509013142'
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: 'TRM-SIoT: A scalable hybrid trust & reputation model for the social Internet
of Things'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '8302'
abstract:
- lang: eng
text: While showing great promise, Bitcoin requires users to wait tens of minutes
for transactions to commit, and even then, offering only probabilistic guarantees.
This paper introduces ByzCoin, a novel Byzantine consensus protocol that leverages
scalable collective signing to commit Bitcoin transactions irreversibly within
seconds. ByzCoin achieves Byzantine consensus while preserving Bitcoin’s open
membership by dynamically forming hash power-proportionate consensus groups that
represent recently-successful block miners. ByzCoin employs communication trees
to optimize transaction commitment and verification under normal operation while
guaranteeing safety and liveness under Byzantine faults, up to a near-optimal
tolerance of f faulty group members among 3f + 2 total. ByzCoin mitigates double
spending and selfish mining attacks by producing collectively signed transaction
blocks within one minute of transaction submission. Tree-structured communication
further reduces this latency to less than 30 seconds. Due to these optimizations,
ByzCoin achieves a throughput higher than Paypal currently handles, with a confirmation
latency of 15-20 seconds.
article_processing_charge: No
arxiv: 1
author:
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Philipp
full_name: Jovanovic, Philipp
last_name: Jovanovic
- first_name: Nicolas
full_name: Gailly, Nicolas
last_name: Gailly
- first_name: Ismail
full_name: Khoffi, Ismail
last_name: Khoffi
- first_name: Linus
full_name: Gasser, Linus
last_name: Gasser
- first_name: Bryan
full_name: Ford, Bryan
last_name: Ford
citation:
ama: 'Kokoris Kogias E, Jovanovic P, Gailly N, Khoffi I, Gasser L, Ford B. Enhancing
bitcoin security and performance with strong consistency via collective signing.
In: Proceedings of the 25th USENIX Conference on Security Symposium. USENIX
Association; 2016:279–296.'
apa: 'Kokoris Kogias, E., Jovanovic, P., Gailly, N., Khoffi, I., Gasser, L., &
Ford, B. (2016). Enhancing bitcoin security and performance with strong consistency
via collective signing. In Proceedings of the 25th USENIX Conference on Security
Symposium (pp. 279–296). Austin, TX, United States: USENIX Association.'
chicago: Kokoris Kogias, Eleftherios, Philipp Jovanovic, Nicolas Gailly, Ismail
Khoffi, Linus Gasser, and Bryan Ford. “Enhancing Bitcoin Security and Performance
with Strong Consistency via Collective Signing.” In Proceedings of the 25th
USENIX Conference on Security Symposium, 279–296. USENIX Association, 2016.
ieee: E. Kokoris Kogias, P. Jovanovic, N. Gailly, I. Khoffi, L. Gasser, and B. Ford,
“Enhancing bitcoin security and performance with strong consistency via collective
signing,” in Proceedings of the 25th USENIX Conference on Security Symposium,
Austin, TX, United States, 2016, pp. 279–296.
ista: 'Kokoris Kogias E, Jovanovic P, Gailly N, Khoffi I, Gasser L, Ford B. 2016.
Enhancing bitcoin security and performance with strong consistency via collective
signing. Proceedings of the 25th USENIX Conference on Security Symposium. SEC:
Security Symposium, 279–296.'
mla: Kokoris Kogias, Eleftherios, et al. “Enhancing Bitcoin Security and Performance
with Strong Consistency via Collective Signing.” Proceedings of the 25th USENIX
Conference on Security Symposium, USENIX Association, 2016, pp. 279–296.
short: E. Kokoris Kogias, P. Jovanovic, N. Gailly, I. Khoffi, L. Gasser, B. Ford,
in:, Proceedings of the 25th USENIX Conference on Security Symposium, USENIX Association,
2016, pp. 279–296.
conference:
end_date: 2016-08-12
location: Austin, TX, United States
name: 'SEC: Security Symposium'
start_date: 2016-08-10
date_created: 2020-08-26T12:08:35Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2021-01-12T08:18:00Z
day: '01'
extern: '1'
external_id:
arxiv:
- '1602.06997'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.06997
month: '09'
oa: 1
oa_version: Published Version
page: 279–296
publication: Proceedings of the 25th USENIX Conference on Security Symposium
publication_identifier:
isbn:
- '9781931971324'
publication_status: published
publisher: USENIX Association
quality_controlled: '1'
status: public
title: Enhancing bitcoin security and performance with strong consistency via collective
signing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '8452'
abstract:
- lang: eng
text: During spore formation in Bacillus subtilis a transenvelope complex is assembled
across the double membrane that separates the mother cell and forespore. This
complex (called the “A–Q complex”) is required to maintain forespore development
and is composed of proteins with remote homology to components of type II, III,
and IV secretion systems found in Gram-negative bacteria. Here, we show that one
of these proteins, SpoIIIAG, which has remote homology to ring-forming proteins
found in type III secretion systems, assembles into an oligomeric ring in the
periplasmic-like space between the two membranes. Three-dimensional reconstruction
of images generated by cryo-electron microscopy indicates that the SpoIIIAG ring
has a cup-and-saucer architecture with a 6-nm central pore. Structural modeling
of SpoIIIAG generated a 24-member ring with dimensions similar to those of the
EM-derived saucer. Point mutations in the predicted oligomeric interface disrupted
ring formation in vitro and impaired forespore gene expression and efficient spore
formation in vivo. Taken together, our data provide strong support for the model
in which the A–Q transenvelope complex contains a conduit that connects the mother
cell and forespore. We propose that a set of stacked rings spans the intermembrane
space, as has been found for type III secretion systems.
article_processing_charge: No
article_type: original
author:
- first_name: Christopher D. A.
full_name: Rodrigues, Christopher D. A.
last_name: Rodrigues
- first_name: Xavier
full_name: Henry, Xavier
last_name: Henry
- first_name: Emmanuelle
full_name: Neumann, Emmanuelle
last_name: Neumann
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Laure
full_name: Bellard, Laure
last_name: Bellard
- first_name: Yann
full_name: Fichou, Yann
last_name: Fichou
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Guy
full_name: Schoehn, Guy
last_name: Schoehn
- first_name: David Z.
full_name: Rudner, David Z.
last_name: Rudner
- first_name: Cecile
full_name: Morlot, Cecile
last_name: Morlot
citation:
ama: Rodrigues CDA, Henry X, Neumann E, et al. A ring-shaped conduit connects the
mother cell and forespore during sporulation in Bacillus subtilis. Proceedings
of the National Academy of Sciences. 2016;113(41):11585-11590. doi:10.1073/pnas.1609604113
apa: Rodrigues, C. D. A., Henry, X., Neumann, E., Kurauskas, V., Bellard, L., Fichou,
Y., … Morlot, C. (2016). A ring-shaped conduit connects the mother cell and forespore
during sporulation in Bacillus subtilis. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1609604113
chicago: Rodrigues, Christopher D. A., Xavier Henry, Emmanuelle Neumann, Vilius
Kurauskas, Laure Bellard, Yann Fichou, Paul Schanda, Guy Schoehn, David Z. Rudner,
and Cecile Morlot. “A Ring-Shaped Conduit Connects the Mother Cell and Forespore
during Sporulation in Bacillus Subtilis.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1609604113.
ieee: C. D. A. Rodrigues et al., “A ring-shaped conduit connects the mother
cell and forespore during sporulation in Bacillus subtilis,” Proceedings of
the National Academy of Sciences, vol. 113, no. 41. National Academy of Sciences,
pp. 11585–11590, 2016.
ista: Rodrigues CDA, Henry X, Neumann E, Kurauskas V, Bellard L, Fichou Y, Schanda
P, Schoehn G, Rudner DZ, Morlot C. 2016. A ring-shaped conduit connects the mother
cell and forespore during sporulation in Bacillus subtilis. Proceedings of the
National Academy of Sciences. 113(41), 11585–11590.
mla: Rodrigues, Christopher D. A., et al. “A Ring-Shaped Conduit Connects the Mother
Cell and Forespore during Sporulation in Bacillus Subtilis.” Proceedings of
the National Academy of Sciences, vol. 113, no. 41, National Academy of Sciences,
2016, pp. 11585–90, doi:10.1073/pnas.1609604113.
short: C.D.A. Rodrigues, X. Henry, E. Neumann, V. Kurauskas, L. Bellard, Y. Fichou,
P. Schanda, G. Schoehn, D.Z. Rudner, C. Morlot, Proceedings of the National Academy
of Sciences 113 (2016) 11585–11590.
date_created: 2020-09-18T10:06:58Z
date_published: 2016-09-28T00:00:00Z
date_updated: 2021-01-12T08:19:22Z
day: '28'
doi: 10.1073/pnas.1609604113
extern: '1'
intvolume: ' 113'
issue: '41'
language:
- iso: eng
month: '09'
oa_version: None
page: 11585-11590
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: A ring-shaped conduit connects the mother cell and forespore during sporulation
in Bacillus subtilis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '8453'
abstract:
- lang: eng
text: Transverse relaxation rate measurements in magic-angle spinning solid-state
nuclear magnetic resonance provide information about molecular motions occurring
on nanosecond-to-millisecond (ns–ms) time scales. The measurement of heteronuclear
(13C, 15N) relaxation rate constants in the presence of a spin-lock radiofrequency
field (R1ρ relaxation) provides access to such motions, and an increasing number
of studies involving R1ρ relaxation in proteins have been reported. However, two
factors that influence the observed relaxation rate constants have so far been
neglected, namely, (1) the role of CSA/dipolar cross-correlated relaxation (CCR)
and (2) the impact of fast proton spin flips (i.e., proton spin diffusion and
relaxation). We show that CSA/D CCR in R1ρ experiments is measurable and that
the CCR rate constant depends on ns–ms motions; it can thus provide insight into
dynamics. We find that proton spin diffusion attenuates this CCR due to its decoupling
effect on the doublet components. For measurements of dynamics, the use of R1ρ
rate constants has practical advantages over the use of CCR rates, and this article
reveals factors that have so far been disregarded and which are important for
accurate measurements and interpretation.
article_processing_charge: No
article_type: original
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Emmanuelle
full_name: Weber, Emmanuelle
last_name: Weber
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Dominique
full_name: Marion, Dominique
last_name: Marion
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Kurauskas V, Weber E, Hessel A, Ayala I, Marion D, Schanda P. Cross-correlated
relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning
R1ρ NMR measurements: Application to protein backbone dynamics measurements. The
Journal of Physical Chemistry B. 2016;120(34):8905-8913. doi:10.1021/acs.jpcb.6b06129'
apa: 'Kurauskas, V., Weber, E., Hessel, A., Ayala, I., Marion, D., & Schanda,
P. (2016). Cross-correlated relaxation of dipolar coupling and chemical-shift
anisotropy in magic-angle spinning R1ρ NMR measurements: Application to protein
backbone dynamics measurements. The Journal of Physical Chemistry B. American
Chemical Society. https://doi.org/10.1021/acs.jpcb.6b06129'
chicago: 'Kurauskas, Vilius, Emmanuelle Weber, Audrey Hessel, Isabel Ayala, Dominique
Marion, and Paul Schanda. “Cross-Correlated Relaxation of Dipolar Coupling and
Chemical-Shift Anisotropy in Magic-Angle Spinning R1ρ NMR Measurements: Application
to Protein Backbone Dynamics Measurements.” The Journal of Physical Chemistry
B. American Chemical Society, 2016. https://doi.org/10.1021/acs.jpcb.6b06129.'
ieee: 'V. Kurauskas, E. Weber, A. Hessel, I. Ayala, D. Marion, and P. Schanda, “Cross-correlated
relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning
R1ρ NMR measurements: Application to protein backbone dynamics measurements,”
The Journal of Physical Chemistry B, vol. 120, no. 34. American Chemical
Society, pp. 8905–8913, 2016.'
ista: 'Kurauskas V, Weber E, Hessel A, Ayala I, Marion D, Schanda P. 2016. Cross-correlated
relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning
R1ρ NMR measurements: Application to protein backbone dynamics measurements. The
Journal of Physical Chemistry B. 120(34), 8905–8913.'
mla: 'Kurauskas, Vilius, et al. “Cross-Correlated Relaxation of Dipolar Coupling
and Chemical-Shift Anisotropy in Magic-Angle Spinning R1ρ NMR Measurements: Application
to Protein Backbone Dynamics Measurements.” The Journal of Physical Chemistry
B, vol. 120, no. 34, American Chemical Society, 2016, pp. 8905–13, doi:10.1021/acs.jpcb.6b06129.'
short: V. Kurauskas, E. Weber, A. Hessel, I. Ayala, D. Marion, P. Schanda, The Journal
of Physical Chemistry B 120 (2016) 8905–8913.
date_created: 2020-09-18T10:07:07Z
date_published: 2016-08-08T00:00:00Z
date_updated: 2021-01-12T08:19:22Z
day: '08'
doi: 10.1021/acs.jpcb.6b06129
extern: '1'
intvolume: ' 120'
issue: '34'
keyword:
- Physical and Theoretical Chemistry
- Materials Chemistry
- Surfaces
- Coatings and Films
language:
- iso: eng
month: '08'
oa_version: None
page: 8905-8913
publication: The Journal of Physical Chemistry B
publication_identifier:
issn:
- 1520-6106
- 1520-5207
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: 'Cross-correlated relaxation of dipolar coupling and chemical-shift anisotropy
in magic-angle spinning R1ρ NMR measurements: Application to protein backbone dynamics
measurements'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2016'
...
---
_id: '8454'
abstract:
- lang: eng
text: Magic-angle spinning solid-state NMR spectroscopy is an important technique
to study molecular structure, dynamics and interactions, and is rapidly gaining
importance in biomolecular sciences. Here we provide an overview of experimental
approaches to study molecular dynamics by MAS solid-state NMR, with an emphasis
on the underlying theoretical concepts and differences of MAS solid-state NMR
compared to solution-state NMR. The theoretical foundations of nuclear spin relaxation
are revisited, focusing on the particularities of spin relaxation in solid samples
under magic-angle spinning. We discuss the range of validity of Redfield theory,
as well as the inherent multi-exponential behavior of relaxation in solids. Experimental
challenges for measuring relaxation parameters in MAS solid-state NMR and a few
recently proposed relaxation approaches are discussed, which provide information
about time scales and amplitudes of motions ranging from picoseconds to milliseconds.
We also discuss the theoretical basis and experimental measurements of anisotropic
interactions (chemical-shift anisotropies, dipolar and quadrupolar couplings),
which give direct information about the amplitude of motions. The potential of
combining relaxation data with such measurements of dynamically-averaged anisotropic
interactions is discussed. Although the focus of this review is on the theoretical
foundations of dynamics studies rather than their application, we close by discussing
a small number of recent dynamics studies, where the dynamic properties of proteins
in crystals are compared to those in solution.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
citation:
ama: 'Schanda P, Ernst M. Studying dynamics by magic-angle spinning solid-state
NMR spectroscopy: Principles and applications to biomolecules. Progress in
Nuclear Magnetic Resonance Spectroscopy. 2016;96(8):1-46. doi:10.1016/j.pnmrs.2016.02.001'
apa: 'Schanda, P., & Ernst, M. (2016). Studying dynamics by magic-angle spinning
solid-state NMR spectroscopy: Principles and applications to biomolecules. Progress
in Nuclear Magnetic Resonance Spectroscopy. Elsevier. https://doi.org/10.1016/j.pnmrs.2016.02.001'
chicago: 'Schanda, Paul, and Matthias Ernst. “Studying Dynamics by Magic-Angle Spinning
Solid-State NMR Spectroscopy: Principles and Applications to Biomolecules.” Progress
in Nuclear Magnetic Resonance Spectroscopy. Elsevier, 2016. https://doi.org/10.1016/j.pnmrs.2016.02.001.'
ieee: 'P. Schanda and M. Ernst, “Studying dynamics by magic-angle spinning solid-state
NMR spectroscopy: Principles and applications to biomolecules,” Progress in
Nuclear Magnetic Resonance Spectroscopy, vol. 96, no. 8. Elsevier, pp. 1–46,
2016.'
ista: 'Schanda P, Ernst M. 2016. Studying dynamics by magic-angle spinning solid-state
NMR spectroscopy: Principles and applications to biomolecules. Progress in Nuclear
Magnetic Resonance Spectroscopy. 96(8), 1–46.'
mla: 'Schanda, Paul, and Matthias Ernst. “Studying Dynamics by Magic-Angle Spinning
Solid-State NMR Spectroscopy: Principles and Applications to Biomolecules.” Progress
in Nuclear Magnetic Resonance Spectroscopy, vol. 96, no. 8, Elsevier, 2016,
pp. 1–46, doi:10.1016/j.pnmrs.2016.02.001.'
short: P. Schanda, M. Ernst, Progress in Nuclear Magnetic Resonance Spectroscopy
96 (2016) 1–46.
date_created: 2020-09-18T10:07:17Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:23Z
day: '01'
doi: 10.1016/j.pnmrs.2016.02.001
extern: '1'
intvolume: ' 96'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 1-46
publication: Progress in Nuclear Magnetic Resonance Spectroscopy
publication_identifier:
issn:
- 0079-6565
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Studying dynamics by magic-angle spinning solid-state NMR spectroscopy: Principles
and applications to biomolecules'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 96
year: '2016'
...
---
_id: '8455'
abstract:
- lang: eng
text: Solid-state NMR spectroscopy allows the characterization of the structure,
interactions and dynamics of insoluble and/or very large proteins. Sensitivity
and resolution are often major challenges for obtaining atomic-resolution information,
in particular for very large protein complexes. Here we show that the use of deuterated,
specifically CH3-labelled proteins result in significant sensitivity gains compared
to previously employed CHD2 labelling, while line widths increase only marginally.
We apply this labelling strategy to a 468 kDa-large dodecameric aminopeptidase,
TET2, and the 1.6 MDa-large 50S ribosome subunit of Thermus thermophilus.
article_processing_charge: No
article_type: original
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Elodie
full_name: Crublet, Elodie
last_name: Crublet
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Rime
full_name: Kerfah, Rime
last_name: Kerfah
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Jérôme
full_name: Boisbouvier, Jérôme
last_name: Boisbouvier
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Kurauskas V, Crublet E, Macek P, et al. Sensitive proton-detected solid-state
NMR spectroscopy of large proteins with selective CH3labelling: Application to
the 50S ribosome subunit. Chemical Communications. 2016;52(61):9558-9561.
doi:10.1039/c6cc04484k'
apa: 'Kurauskas, V., Crublet, E., Macek, P., Kerfah, R., Gauto, D. F., Boisbouvier,
J., & Schanda, P. (2016). Sensitive proton-detected solid-state NMR spectroscopy
of large proteins with selective CH3labelling: Application to the 50S ribosome
subunit. Chemical Communications. Royal Society of Chemistry. https://doi.org/10.1039/c6cc04484k'
chicago: 'Kurauskas, Vilius, Elodie Crublet, Pavel Macek, Rime Kerfah, Diego F.
Gauto, Jérôme Boisbouvier, and Paul Schanda. “Sensitive Proton-Detected Solid-State
NMR Spectroscopy of Large Proteins with Selective CH3labelling: Application to
the 50S Ribosome Subunit.” Chemical Communications. Royal Society of Chemistry,
2016. https://doi.org/10.1039/c6cc04484k.'
ieee: 'V. Kurauskas et al., “Sensitive proton-detected solid-state NMR spectroscopy
of large proteins with selective CH3labelling: Application to the 50S ribosome
subunit,” Chemical Communications, vol. 52, no. 61. Royal Society of Chemistry,
pp. 9558–9561, 2016.'
ista: 'Kurauskas V, Crublet E, Macek P, Kerfah R, Gauto DF, Boisbouvier J, Schanda
P. 2016. Sensitive proton-detected solid-state NMR spectroscopy of large proteins
with selective CH3labelling: Application to the 50S ribosome subunit. Chemical
Communications. 52(61), 9558–9561.'
mla: 'Kurauskas, Vilius, et al. “Sensitive Proton-Detected Solid-State NMR Spectroscopy
of Large Proteins with Selective CH3labelling: Application to the 50S Ribosome
Subunit.” Chemical Communications, vol. 52, no. 61, Royal Society of Chemistry,
2016, pp. 9558–61, doi:10.1039/c6cc04484k.'
short: V. Kurauskas, E. Crublet, P. Macek, R. Kerfah, D.F. Gauto, J. Boisbouvier,
P. Schanda, Chemical Communications 52 (2016) 9558–9561.
date_created: 2020-09-18T10:07:29Z
date_published: 2016-07-04T00:00:00Z
date_updated: 2021-01-12T08:19:23Z
day: '04'
doi: 10.1039/c6cc04484k
extern: '1'
intvolume: ' 52'
issue: '61'
keyword:
- Materials Chemistry
- Electronic
- Optical and Magnetic Materials
- General Chemistry
- Surfaces
- Coatings and Films
- Metals and Alloys
- Ceramics and Composites
- Catalysis
language:
- iso: eng
month: '07'
oa_version: None
page: 9558-9561
publication: Chemical Communications
publication_identifier:
issn:
- 1359-7345
- 1364-548X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: 'Sensitive proton-detected solid-state NMR spectroscopy of large proteins with
selective CH3labelling: Application to the 50S ribosome subunit'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2016'
...