---
_id: '1440'
acknowledgement: The author thanks Banerjee et al. (2016) for providing coordinates
prior to public release and apologizes to colleagues whose work was not cited or
discussed due to the limited space available. The author is supported by grants
from EU FP7 (CIG-303564), HFSP (RGY0084_2012), and FWF (W1232).
article_processing_charge: No
author:
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: 'Janovjak HL. Light at the end of the protein: Crystal structure of a C-terminal
light-sensing domain. Structure. 2016;24(2):213-215. doi:10.1016/j.str.2016.01.002'
apa: 'Janovjak, H. L. (2016). Light at the end of the protein: Crystal structure
of a C-terminal light-sensing domain. Structure. Cell Press. https://doi.org/10.1016/j.str.2016.01.002'
chicago: 'Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure
of a C-Terminal Light-Sensing Domain.” Structure. Cell Press, 2016. https://doi.org/10.1016/j.str.2016.01.002.'
ieee: 'H. L. Janovjak, “Light at the end of the protein: Crystal structure of a
C-terminal light-sensing domain,” Structure, vol. 24, no. 2. Cell Press,
pp. 213–215, 2016.'
ista: 'Janovjak HL. 2016. Light at the end of the protein: Crystal structure of
a C-terminal light-sensing domain. Structure. 24(2), 213–215.'
mla: 'Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of
a C-Terminal Light-Sensing Domain.” Structure, vol. 24, no. 2, Cell Press,
2016, pp. 213–15, doi:10.1016/j.str.2016.01.002.'
short: H.L. Janovjak, Structure 24 (2016) 213–215.
corr_author: '1'
date_created: 2018-12-11T11:52:02Z
date_published: 2016-02-02T00:00:00Z
date_updated: 2025-09-18T11:43:50Z
day: '02'
department:
- _id: HaJa
doi: 10.1016/j.str.2016.01.002
ec_funded: 1
external_id:
isi:
- '000373567700001'
intvolume: ' 24'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 213 - 215
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
- _id: 255A6082-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Structure
publication_status: published
publisher: Cell Press
publist_id: '5756'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Light at the end of the protein: Crystal structure of a C-terminal light-sensing
domain'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 24
year: '2016'
...
---
_id: '1446'
abstract:
- lang: eng
text: The accuracy of interdisciplinarity measurements is directly related to the
quality of the underlying bibliographic data. Existing indicators of interdisciplinarity
are not capable of reflecting the inaccuracies introduced by incorrect and incomplete
records because correct and complete bibliographic data can rarely be obtained.
This is the case for the Rao–Stirling index, which cannot handle references that
are not categorized into disciplinary fields. We introduce a method that addresses
this problem. It extends the Rao–Stirling index to acknowledge missing data by
calculating its interval of uncertainty using computational optimization. The
evaluation of our method indicates that the uncertainty interval is not only useful
for estimating the inaccuracy of interdisciplinarity measurements, but it also
delivers slightly more accurate aggregated interdisciplinarity measurements than
the Rao–Stirling index.
article_processing_charge: No
author:
- first_name: Maria
full_name: Calatrava Moreno, Maria
last_name: Calatrava Moreno
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Hannes
full_name: Werthner, Hannes
last_name: Werthner
citation:
ama: Calatrava Moreno M, Auzinger T, Werthner H. On the uncertainty of interdisciplinarity
measurements due to incomplete bibliographic data. Scientometrics. 2016;107(1):213-232.
doi:10.1007/s11192-016-1842-4
apa: Calatrava Moreno, M., Auzinger, T., & Werthner, H. (2016). On the uncertainty
of interdisciplinarity measurements due to incomplete bibliographic data. Scientometrics.
Springer. https://doi.org/10.1007/s11192-016-1842-4
chicago: Calatrava Moreno, Maria, Thomas Auzinger, and Hannes Werthner. “On the
Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic
Data.” Scientometrics. Springer, 2016. https://doi.org/10.1007/s11192-016-1842-4.
ieee: M. Calatrava Moreno, T. Auzinger, and H. Werthner, “On the uncertainty of
interdisciplinarity measurements due to incomplete bibliographic data,” Scientometrics,
vol. 107, no. 1. Springer, pp. 213–232, 2016.
ista: Calatrava Moreno M, Auzinger T, Werthner H. 2016. On the uncertainty of interdisciplinarity
measurements due to incomplete bibliographic data. Scientometrics. 107(1), 213–232.
mla: Calatrava Moreno, Maria, et al. “On the Uncertainty of Interdisciplinarity
Measurements Due to Incomplete Bibliographic Data.” Scientometrics, vol.
107, no. 1, Springer, 2016, pp. 213–32, doi:10.1007/s11192-016-1842-4.
short: M. Calatrava Moreno, T. Auzinger, H. Werthner, Scientometrics 107 (2016)
213–232.
date_created: 2018-12-11T11:52:04Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2025-09-18T11:42:34Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1007/s11192-016-1842-4
external_id:
isi:
- '000373187000011'
file:
- access_level: open_access
checksum: 32d46268588b87d9b686492018e6a2b2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:56Z
date_updated: 2020-07-14T12:44:55Z
file_id: '4848'
file_name: IST-2016-530-v1+1_s11192-016-1842-4.pdf
file_size: 806035
relation: main_file
file_date_updated: 2020-07-14T12:44:55Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 213 - 232
publication: Scientometrics
publication_status: published
publisher: Springer
publist_id: '5750'
pubrep_id: '530'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s11192-016-1902-9
scopus_import: '1'
status: public
title: On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 107
year: '2016'
...
---
_id: '1448'
abstract:
- lang: eng
text: We develop a new and systematic method for proving entropic Ricci curvature
lower bounds for Markov chains on discrete sets. Using different methods, such
bounds have recently been obtained in several examples (e.g., 1-dimensional birth
and death chains, product chains, Bernoulli–Laplace models, and random transposition
models). However, a general method to obtain discrete Ricci bounds had been lacking.
Our method covers all of the examples above. In addition we obtain new Ricci curvature
bounds for zero-range processes on the complete graph. The method is inspired
by recent work of Caputo, Dai Pra and Posta on discrete functional inequalities.
acknowledgement: "Supported by the German Research Foundation through the Collaborative
Research Center 1060\r\nThe Mathematics of Emergent Effects and the Hausdorff Center
for Mathematics. Part of this work has been done while M. Fathi visited J. Maas
at the University of Bonn in July 2014.We would like to thank the referees for their
careful reading of the manuscript. "
article_processing_charge: No
arxiv: 1
author:
- first_name: Max
full_name: Fathi, Max
last_name: Fathi
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
citation:
ama: Fathi M, Maas J. Entropic Ricci curvature bounds for discrete interacting systems.
The Annals of Applied Probability. 2016;26(3):1774-1806. doi:10.1214/15-AAP1133
apa: Fathi, M., & Maas, J. (2016). Entropic Ricci curvature bounds for discrete
interacting systems. The Annals of Applied Probability. Institute of Mathematical
Statistics. https://doi.org/10.1214/15-AAP1133
chicago: Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete
Interacting Systems.” The Annals of Applied Probability. Institute of Mathematical
Statistics, 2016. https://doi.org/10.1214/15-AAP1133.
ieee: M. Fathi and J. Maas, “Entropic Ricci curvature bounds for discrete interacting
systems,” The Annals of Applied Probability, vol. 26, no. 3. Institute
of Mathematical Statistics, pp. 1774–1806, 2016.
ista: Fathi M, Maas J. 2016. Entropic Ricci curvature bounds for discrete interacting
systems. The Annals of Applied Probability. 26(3), 1774–1806.
mla: Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting
Systems.” The Annals of Applied Probability, vol. 26, no. 3, Institute
of Mathematical Statistics, 2016, pp. 1774–806, doi:10.1214/15-AAP1133.
short: M. Fathi, J. Maas, The Annals of Applied Probability 26 (2016) 1774–1806.
corr_author: '1'
date_created: 2018-12-11T11:52:05Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2025-09-18T11:41:58Z
day: '01'
department:
- _id: JaMa
doi: 10.1214/15-AAP1133
external_id:
arxiv:
- '1501.00562'
isi:
- '000378215800016'
intvolume: ' 26'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.00562
month: '06'
oa: 1
oa_version: Preprint
page: 1774 - 1806
publication: The Annals of Applied Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '5748'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Entropic Ricci curvature bounds for discrete interacting systems
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 26
year: '2016'
...
---
_id: '1794'
abstract:
- lang: eng
text: We consider Conditional random fields (CRFs) with pattern-based potentials
defined on a chain. In this model the energy of a string (labeling) (Formula presented.)
is the sum of terms over intervals [i, j] where each term is non-zero only if
the substring (Formula presented.) equals a prespecified pattern w. Such CRFs
can be naturally applied to many sequence tagging problems. We present efficient
algorithms for the three standard inference tasks in a CRF, namely computing (i)
the partition function, (ii) marginals, and (iii) computing the MAP. Their complexities
are respectively (Formula presented.), (Formula presented.) and (Formula presented.)
where L is the combined length of input patterns, (Formula presented.) is the
maximum length of a pattern, and D is the input alphabet. This improves on the
previous algorithms of Ye et al. (NIPS, 2009) whose complexities are respectively
(Formula presented.), (Formula presented.) and (Formula presented.), where (Formula
presented.) is the number of input patterns. In addition, we give an efficient
algorithm for sampling, and revisit the case of MAP with non-positive weights.
acknowledgement: This work has been partially supported by the European Research Council
under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant
agreement no. 616160.
article_processing_charge: No
arxiv: 1
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Rustem
full_name: Takhanov, Rustem
id: 2CCAC26C-F248-11E8-B48F-1D18A9856A87
last_name: Takhanov
citation:
ama: Kolmogorov V, Takhanov R. Inference algorithms for pattern-based CRFs on sequence
data. Algorithmica. 2016;76(1):17-46. doi:10.1007/s00453-015-0017-7
apa: Kolmogorov, V., & Takhanov, R. (2016). Inference algorithms for pattern-based
CRFs on sequence data. Algorithmica. Springer. https://doi.org/10.1007/s00453-015-0017-7
chicago: Kolmogorov, Vladimir, and Rustem Takhanov. “Inference Algorithms for Pattern-Based
CRFs on Sequence Data.” Algorithmica. Springer, 2016. https://doi.org/10.1007/s00453-015-0017-7.
ieee: V. Kolmogorov and R. Takhanov, “Inference algorithms for pattern-based CRFs
on sequence data,” Algorithmica, vol. 76, no. 1. Springer, pp. 17–46, 2016.
ista: Kolmogorov V, Takhanov R. 2016. Inference algorithms for pattern-based CRFs
on sequence data. Algorithmica. 76(1), 17–46.
mla: Kolmogorov, Vladimir, and Rustem Takhanov. “Inference Algorithms for Pattern-Based
CRFs on Sequence Data.” Algorithmica, vol. 76, no. 1, Springer, 2016, pp.
17–46, doi:10.1007/s00453-015-0017-7.
short: V. Kolmogorov, R. Takhanov, Algorithmica 76 (2016) 17–46.
corr_author: '1'
date_created: 2018-12-11T11:54:02Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2025-09-29T14:28:47Z
day: '01'
department:
- _id: VlKo
doi: 10.1007/s00453-015-0017-7
ec_funded: 1
external_id:
arxiv:
- '1210.0508'
isi:
- '000381149500002'
intvolume: ' 76'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1210.0508
month: '09'
oa: 1
oa_version: Preprint
page: 17 - 46
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Algorithmica
publication_status: published
publisher: Springer
publist_id: '5316'
quality_controlled: '1'
related_material:
record:
- id: '2272'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Inference algorithms for pattern-based CRFs on sequence data
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 76
year: '2016'
...
---
_id: '1833'
abstract:
- lang: eng
text: 'Relational models for contingency tables are generalizations of log-linear
models, allowing effects associated with arbitrary subsets of cells in the table,
and not necessarily containing the overall effect, that is, a common parameter
in every cell. Similarly to log-linear models, relational models can be extended
to non-negative distributions, but the extension requires more complex methods.
An extended relational model is defined as an algebraic variety, and it turns
out to be the closure of the original model with respect to the Bregman divergence.
In the extended relational model, the MLE of the cell parameters always exists
and is unique, but some of its properties may be different from those of the MLE
under log-linear models. The MLE can be computed using a generalized iterative
scaling procedure based on Bregman projections. '
article_processing_charge: No
arxiv: 1
author:
- first_name: Anna
full_name: Klimova, Anna
id: 31934120-F248-11E8-B48F-1D18A9856A87
last_name: Klimova
- first_name: Tamás
full_name: Rudas, Tamás
last_name: Rudas
citation:
ama: Klimova A, Rudas T. On the closure of relational models. Journal of Multivariate
Analysis. 2016;143:440-452. doi:10.1016/j.jmva.2015.10.005
apa: Klimova, A., & Rudas, T. (2016). On the closure of relational models. Journal
of Multivariate Analysis. Elsevier. https://doi.org/10.1016/j.jmva.2015.10.005
chicago: Klimova, Anna, and Tamás Rudas. “On the Closure of Relational Models.”
Journal of Multivariate Analysis. Elsevier, 2016. https://doi.org/10.1016/j.jmva.2015.10.005.
ieee: A. Klimova and T. Rudas, “On the closure of relational models,” Journal
of Multivariate Analysis, vol. 143. Elsevier, pp. 440–452, 2016.
ista: Klimova A, Rudas T. 2016. On the closure of relational models. Journal of
Multivariate Analysis. 143, 440–452.
mla: Klimova, Anna, and Tamás Rudas. “On the Closure of Relational Models.” Journal
of Multivariate Analysis, vol. 143, Elsevier, 2016, pp. 440–52, doi:10.1016/j.jmva.2015.10.005.
short: A. Klimova, T. Rudas, Journal of Multivariate Analysis 143 (2016) 440–452.
corr_author: '1'
date_created: 2018-12-11T11:54:15Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2025-09-18T10:47:32Z
day: '01'
department:
- _id: CaUh
doi: 10.1016/j.jmva.2015.10.005
external_id:
arxiv:
- '1501.00600'
isi:
- '000366885300029'
intvolume: ' 143'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.00600
month: '01'
oa: 1
oa_version: Preprint
page: 440 - 452
publication: Journal of Multivariate Analysis
publication_status: published
publisher: Elsevier
publist_id: '5270'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the closure of relational models
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 143
year: '2016'
...
---
_id: '1227'
abstract:
- lang: eng
text: Many biological systems can be modeled as multiaffine hybrid systems. Due
to the nonlinearity of multiaffine systems, it is difficult to verify their properties
of interest directly. A common strategy to tackle this problem is to construct
and analyze a discrete overapproximation of the original system. However, the
conservativeness of a discrete abstraction significantly determines the level
of confidence we can have in the properties of the original system. In this paper,
in order to reduce the conservativeness of a discrete abstraction, we propose
a new method based on a sufficient and necessary decision condition for computing
discrete transitions between states in the abstract system. We assume the state
space partition of a multiaffine system to be based on a set of multivariate polynomials.
Hence, a rectangular partition defined in terms of polynomials of the form (xi
− c) is just a simple case of multivariate polynomial partition, and the new decision
condition applies naturally. We analyze and demonstrate the improvement of our
method over the existing methods using some examples.
acknowledgement: This research was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23
(Wittgenstein Award).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
- 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: Yu
full_name: Jiang, Yu
last_name: Jiang
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
citation:
ama: 'Kong H, Bartocci E, Bogomolov S, et al. Discrete abstraction of multiaffine
systems. In: Vol 9957. Springer; 2016:128-144. doi:10.1007/978-3-319-47151-8_9'
apa: 'Kong, H., Bartocci, E., Bogomolov, S., Grosu, R., Henzinger, T. A., Jiang,
Y., & Schilling, C. (2016). Discrete abstraction of multiaffine systems (Vol.
9957, pp. 128–144). Presented at the HSB: Hybrid Systems Biology, Grenoble, France:
Springer. https://doi.org/10.1007/978-3-319-47151-8_9'
chicago: Kong, Hui, Ezio Bartocci, Sergiy Bogomolov, Radu Grosu, Thomas A Henzinger,
Yu Jiang, and Christian Schilling. “Discrete Abstraction of Multiaffine Systems,”
9957:128–44. Springer, 2016. https://doi.org/10.1007/978-3-319-47151-8_9.
ieee: 'H. Kong et al., “Discrete abstraction of multiaffine systems,” presented
at the HSB: Hybrid Systems Biology, Grenoble, France, 2016, vol. 9957, pp. 128–144.'
ista: 'Kong H, Bartocci E, Bogomolov S, Grosu R, Henzinger TA, Jiang Y, Schilling
C. 2016. Discrete abstraction of multiaffine systems. HSB: Hybrid Systems Biology,
LNCS, vol. 9957, 128–144.'
mla: Kong, Hui, et al. Discrete Abstraction of Multiaffine Systems. Vol.
9957, Springer, 2016, pp. 128–44, doi:10.1007/978-3-319-47151-8_9.
short: H. Kong, E. Bartocci, S. Bogomolov, R. Grosu, T.A. Henzinger, Y. Jiang, C.
Schilling, in:, Springer, 2016, pp. 128–144.
conference:
end_date: 2016-10-21
location: Grenoble, France
name: 'HSB: Hybrid Systems Biology'
start_date: 2016-10-20
date_created: 2018-12-11T11:50:49Z
date_published: 2016-09-25T00:00:00Z
date_updated: 2025-09-22T09:24:50Z
day: '25'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-319-47151-8_9
external_id:
isi:
- '000389928100009'
file:
- access_level: open_access
checksum: 994e164b558c47bacf8dc066dd27c8fc
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:49Z
date_updated: 2020-07-14T12:44:39Z
file_id: '4840'
file_name: IST-2017-781-v1+1_main.pdf
file_size: 683955
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 9957'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 128 - 144
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '6107'
pubrep_id: '781'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Discrete abstraction of multiaffine systems
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9957
year: '2016'
...
---
_id: '1231'
abstract:
- lang: eng
text: 'We study the time-and memory-complexities of the problem of computing labels
of (multiple) randomly selected challenge-nodes in a directed acyclic graph. The
w-bit label of a node is the hash of the labels of its parents, and the hash function
is modeled as a random oracle. Specific instances of this problem underlie both
proofs of space [Dziembowski et al. CRYPTO’15] as well as popular memory-hard
functions like scrypt. As our main tool, we introduce the new notion of a probabilistic
parallel entangled pebbling game, a new type of combinatorial pebbling game on
a graph, which is closely related to the labeling game on the same graph. As a
first application of our framework, we prove that for scrypt, when the underlying
hash function is invoked n times, the cumulative memory complexity (CMC) (a notion
recently introduced by Alwen and Serbinenko (STOC’15) to capture amortized memory-hardness
for parallel adversaries) is at least Ω(w · (n/ log(n))2). This bound holds for
adversaries that can store many natural functions of the labels (e.g., linear
combinations), but still not arbitrary functions thereof. We then introduce and
study a combinatorial quantity, and show how a sufficiently small upper bound
on it (which we conjecture) extends our CMC bound for scrypt to hold against arbitrary
adversaries. We also show that such an upper bound solves the main open problem
for proofs-of-space protocols: namely, establishing that the time complexity of
computing the label of a random node in a graph on n nodes (given an initial kw-bit
state) reduces tightly to the time complexity for black pebbling on the same graph
(given an initial k-node pebbling).'
acknowledgement: "Joël Alwen, Chethan Kamath, and Krzysztof Pietrzak’s research is
partially supported by an ERC starting grant (259668-PSPC). Vladimir Kolmogorov
is partially supported by an ERC consolidator grant (616160-DOICV). Binyi Chen was
partially supported by NSF grants CNS-1423566 and CNS-1514526, and a gift from the
Gareatis Foundation. Stefano Tessaro was partially supported by NSF grants CNS-1423566,
CNS-1528178, a Hellman Fellowship, and the Glen and Susanne Culler Chair.\r\n\r\nThis
work was done in part while the authors were visiting the Simons Institute for the
Theory of Computing, supported by the Simons Foundation and by the DIMACS/Simons
Collaboration in Cryptography through NSF grant CNS-1523467."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Binyi
full_name: Chen, Binyi
last_name: Chen
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- 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: Stefano
full_name: Tessaro, Stefano
last_name: Tessaro
citation:
ama: 'Alwen JF, Chen B, Kamath Hosdurg C, Kolmogorov V, Pietrzak KZ, Tessaro S.
On the complexity of scrypt and proofs of space in the parallel random oracle
model. In: Vol 9666. Springer; 2016:358-387. doi:10.1007/978-3-662-49896-5_13'
apa: 'Alwen, J. F., Chen, B., Kamath Hosdurg, C., Kolmogorov, V., Pietrzak, K. Z.,
& Tessaro, S. (2016). On the complexity of scrypt and proofs of space in the
parallel random oracle model (Vol. 9666, pp. 358–387). Presented at the EUROCRYPT:
Theory and Applications of Cryptographic Techniques, Vienna, Austria: Springer.
https://doi.org/10.1007/978-3-662-49896-5_13'
chicago: Alwen, Joel F, Binyi Chen, Chethan Kamath Hosdurg, Vladimir Kolmogorov,
Krzysztof Z Pietrzak, and Stefano Tessaro. “On the Complexity of Scrypt and Proofs
of Space in the Parallel Random Oracle Model,” 9666:358–87. Springer, 2016. https://doi.org/10.1007/978-3-662-49896-5_13.
ieee: 'J. F. Alwen, B. Chen, C. Kamath Hosdurg, V. Kolmogorov, K. Z. Pietrzak, and
S. Tessaro, “On the complexity of scrypt and proofs of space in the parallel random
oracle model,” presented at the EUROCRYPT: Theory and Applications of Cryptographic
Techniques, Vienna, Austria, 2016, vol. 9666, pp. 358–387.'
ista: 'Alwen JF, Chen B, Kamath Hosdurg C, Kolmogorov V, Pietrzak KZ, Tessaro S.
2016. On the complexity of scrypt and proofs of space in the parallel random oracle
model. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol.
9666, 358–387.'
mla: Alwen, Joel F., et al. On the Complexity of Scrypt and Proofs of Space in
the Parallel Random Oracle Model. Vol. 9666, Springer, 2016, pp. 358–87, doi:10.1007/978-3-662-49896-5_13.
short: J.F. Alwen, B. Chen, C. Kamath Hosdurg, V. Kolmogorov, K.Z. Pietrzak, S.
Tessaro, in:, Springer, 2016, pp. 358–387.
conference:
end_date: 2016-05-12
location: Vienna, Austria
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
start_date: 2016-05-08
date_created: 2018-12-11T11:50:51Z
date_published: 2016-04-28T00:00:00Z
date_updated: 2025-09-22T09:22:54Z
day: '28'
department:
- _id: KrPi
- _id: VlKo
doi: 10.1007/978-3-662-49896-5_13
ec_funded: 1
external_id:
isi:
- '000389727200013'
intvolume: ' 9666'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/100
month: '04'
oa: 1
oa_version: Submitted Version
page: 358 - 387
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_status: published
publisher: Springer
publist_id: '6103'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the complexity of scrypt and proofs of space in the parallel random oracle
model
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9666
year: '2016'
...
---
_id: '1232'
abstract:
- lang: eng
text: Mitochondrial electron transport chain complexes are organized into supercomplexes
responsible for carrying out cellular respiration. Here we present three architectures
of mammalian (ovine) supercomplexes determined by cryo-electron microscopy. We
identify two distinct arrangements of supercomplex CICIII 2 CIV (the respirasome)
- a major 'tight' form and a minor 'loose' form (resolved at the resolution of
5.8 Å and 6.7 Å, respectively), which may represent different stages in supercomplex
assembly or disassembly. We have also determined an architecture of supercomplex
CICIII 2 at 7.8 Å resolution. All observed density can be attributed to the known
80 subunits of the individual complexes, including 132 transmembrane helices.
The individual complexes form tight interactions that vary between the architectures,
with complex IV subunit COX7a switching contact from complex III to complex I.
The arrangement of active sites within the supercomplex may help control reactive
oxygen species production. To our knowledge, these are the first complete architectures
of the dominant, physiologically relevant state of the electron transport chain.
acknowledgement: We thank the MRC LMB Cambridge for the use of the Titan Krios microscope.
Data processing was performed using the IST high-performance computer cluster. J.A.L.
holds a long-term fellowship from FEBS. K.F. is partially funded by a MRC UK PhD
fellowship.
article_processing_charge: No
author:
- first_name: James A
full_name: Letts, James A
id: 322DA418-F248-11E8-B48F-1D18A9856A87
last_name: Letts
orcid: 0000-0002-9864-3586
- first_name: Karol
full_name: Fiedorczuk, Karol
id: 5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0
last_name: Fiedorczuk
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Letts JA, Fiedorczuk K, Sazanov LA. The architecture of respiratory supercomplexes.
Nature. 2016;537(7622):644-648. doi:10.1038/nature19774
apa: Letts, J. A., Fiedorczuk, K., & Sazanov, L. A. (2016). The architecture
of respiratory supercomplexes. Nature. Nature Publishing Group. https://doi.org/10.1038/nature19774
chicago: Letts, James A, Karol Fiedorczuk, and Leonid A Sazanov. “The Architecture
of Respiratory Supercomplexes.” Nature. Nature Publishing Group, 2016.
https://doi.org/10.1038/nature19774.
ieee: J. A. Letts, K. Fiedorczuk, and L. A. Sazanov, “The architecture of respiratory
supercomplexes,” Nature, vol. 537, no. 7622. Nature Publishing Group, pp.
644–648, 2016.
ista: Letts JA, Fiedorczuk K, Sazanov LA. 2016. The architecture of respiratory
supercomplexes. Nature. 537(7622), 644–648.
mla: Letts, James A., et al. “The Architecture of Respiratory Supercomplexes.” Nature,
vol. 537, no. 7622, Nature Publishing Group, 2016, pp. 644–48, doi:10.1038/nature19774.
short: J.A. Letts, K. Fiedorczuk, L.A. Sazanov, Nature 537 (2016) 644–648.
date_created: 2018-12-11T11:50:51Z
date_published: 2016-09-29T00:00:00Z
date_updated: 2025-09-22T09:22:23Z
day: '29'
department:
- _id: LeSa
doi: 10.1038/nature19774
external_id:
isi:
- '000384331700042'
intvolume: ' 537'
isi: 1
issue: '7622'
language:
- iso: eng
month: '09'
oa_version: None
page: 644 - 648
project:
- _id: 2593EBD6-B435-11E9-9278-68D0E5697425
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6102'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The architecture of respiratory supercomplexes
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 537
year: '2016'
...
---
_id: '1233'
abstract:
- lang: eng
text: About three decades ago it was realized that implementing private channels
between parties which can be adaptively corrupted requires an encryption scheme
that is secure against selective opening attacks. Whether standard (IND-CPA) security
implies security against selective opening attacks has been a major open question
since. The only known reduction from selective opening to IND-CPA security loses
an exponential factor. A polynomial reduction is only known for the very special
case where the distribution considered in the selective opening security experiment
is a product distribution, i.e., the messages are sampled independently from each
other. In this paper we give a reduction whose loss is quantified via the dependence
graph (where message dependencies correspond to edges) of the underlying message
distribution. In particular, for some concrete distributions including Markov
distributions, our reduction is polynomial.
acknowledgement: G. Fuchsbauer and K. Pietrzak are supported by the European Research
Council, ERC Starting Grant (259668-PSPC). F. Heuer is funded by a Sofja Kovalevskaja
Award of the Alexander von Humboldt Foundation and DFG SPP 1736, Algorithms for
BIG DATA. E. Kiltz is supported by a Sofja Kovalevskaja Award of the Alexander von
Humboldt Foundation, the German Israel Foundation, and ERC Project ERCC (FP7/615074).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Felix
full_name: Heuer, Felix
last_name: Heuer
- first_name: Eike
full_name: Kiltz, Eike
last_name: Kiltz
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Fuchsbauer G, Heuer F, Kiltz E, Pietrzak KZ. Standard security does imply
security against selective opening for markov distributions. In: Vol 9562. Springer;
2016:282-305. doi:10.1007/978-3-662-49096-9_12'
apa: 'Fuchsbauer, G., Heuer, F., Kiltz, E., & Pietrzak, K. Z. (2016). Standard
security does imply security against selective opening for markov distributions
(Vol. 9562, pp. 282–305). Presented at the TCC: Theory of Cryptography Conference,
Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-662-49096-9_12'
chicago: Fuchsbauer, Georg, Felix Heuer, Eike Kiltz, and Krzysztof Z Pietrzak. “Standard
Security Does Imply Security against Selective Opening for Markov Distributions,”
9562:282–305. Springer, 2016. https://doi.org/10.1007/978-3-662-49096-9_12.
ieee: 'G. Fuchsbauer, F. Heuer, E. Kiltz, and K. Z. Pietrzak, “Standard security
does imply security against selective opening for markov distributions,” presented
at the TCC: Theory of Cryptography Conference, Tel Aviv, Israel, 2016, vol. 9562,
pp. 282–305.'
ista: 'Fuchsbauer G, Heuer F, Kiltz E, Pietrzak KZ. 2016. Standard security does
imply security against selective opening for markov distributions. TCC: Theory
of Cryptography Conference, LNCS, vol. 9562, 282–305.'
mla: Fuchsbauer, Georg, et al. Standard Security Does Imply Security against
Selective Opening for Markov Distributions. Vol. 9562, Springer, 2016, pp.
282–305, doi:10.1007/978-3-662-49096-9_12.
short: G. Fuchsbauer, F. Heuer, E. Kiltz, K.Z. Pietrzak, in:, Springer, 2016, pp.
282–305.
conference:
end_date: 2016-01-13
location: Tel Aviv, Israel
name: 'TCC: Theory of Cryptography Conference'
start_date: 2016-01-10
date_created: 2018-12-11T11:50:51Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2025-09-22T09:21:52Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-662-49096-9_12
ec_funded: 1
external_id:
isi:
- '000376041100012'
intvolume: ' 9562'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2015/853
month: '01'
oa: 1
oa_version: Submitted Version
page: 282 - 305
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '6100'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Standard security does imply security against selective opening for markov
distributions
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9562
year: '2016'
...
---
_id: '1237'
abstract:
- lang: eng
text: 'Bitmap images of arbitrary dimension may be formally perceived as unions
of m-dimensional boxes aligned with respect to a rectangular grid in ℝm. Cohomology
and homology groups are well known topological invariants of such sets. Cohomological
operations, such as the cup product, provide higher-order algebraic topological
invariants, especially important for digital images of dimension higher than 3.
If such an operation is determined at the level of simplicial chains [see e.g.
González-Díaz, Real, Homology, Homotopy Appl, 2003, 83-93], then it is effectively
computable. However, decomposing a cubical complex into a simplicial one deleteriously
affects the efficiency of such an approach. In order to avoid this overhead, a
direct cubical approach was applied in [Pilarczyk, Real, Adv. Comput. Math., 2015,
253-275] for the cup product in cohomology, and implemented in the ChainCon software
package [http://www.pawelpilarczyk.com/chaincon/]. We establish a formula for
the Steenrod square operations [see Steenrod, Annals of Mathematics. Second Series,
1947, 290-320] directly at the level of cubical chains, and we prove the correctness
of this formula. An implementation of this formula is programmed in C++ within
the ChainCon software framework. We provide a few examples and discuss the effectiveness
of this approach. One specific application follows from the fact that Steenrod
squares yield tests for the topological extension problem: Can a given map A →
Sd to a sphere Sd be extended to a given super-complex X of A? In particular,
the ROB-SAT problem, which is to decide for a given function f: X → ℝm and a value
r > 0 whether every g: X → ℝm with ∥g - f ∥∞ ≤ r has a root, reduces to the
extension problem.'
acknowledgement: The research conducted by both authors has received funding from
the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework
Programme (FP7/2007-2013) under REA grant agreements no. 291734 (for M. K.) and
no. 622033 (for P. P.).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
citation:
ama: 'Krcál M, Pilarczyk P. Computation of cubical Steenrod squares. In: Vol 9667.
Springer; 2016:140-151. doi:10.1007/978-3-319-39441-1_13'
apa: 'Krcál, M., & Pilarczyk, P. (2016). Computation of cubical Steenrod squares
(Vol. 9667, pp. 140–151). Presented at the CTIC: Computational Topology in Image
Context, Marseille, France: Springer. https://doi.org/10.1007/978-3-319-39441-1_13'
chicago: Krcál, Marek, and Pawel Pilarczyk. “Computation of Cubical Steenrod Squares,”
9667:140–51. Springer, 2016. https://doi.org/10.1007/978-3-319-39441-1_13.
ieee: 'M. Krcál and P. Pilarczyk, “Computation of cubical Steenrod squares,” presented
at the CTIC: Computational Topology in Image Context, Marseille, France, 2016,
vol. 9667, pp. 140–151.'
ista: 'Krcál M, Pilarczyk P. 2016. Computation of cubical Steenrod squares. CTIC:
Computational Topology in Image Context, LNCS, vol. 9667, 140–151.'
mla: Krcál, Marek, and Pawel Pilarczyk. Computation of Cubical Steenrod Squares.
Vol. 9667, Springer, 2016, pp. 140–51, doi:10.1007/978-3-319-39441-1_13.
short: M. Krcál, P. Pilarczyk, in:, Springer, 2016, pp. 140–151.
conference:
end_date: 2016-06-17
location: Marseille, France
name: 'CTIC: Computational Topology in Image Context'
start_date: 2016-06-15
date_created: 2018-12-11T11:50:52Z
date_published: 2016-06-02T00:00:00Z
date_updated: 2025-09-22T09:19:17Z
day: '02'
department:
- _id: UlWa
- _id: HeEd
doi: 10.1007/978-3-319-39441-1_13
ec_funded: 1
external_id:
isi:
- '000389805800013'
intvolume: ' 9667'
isi: 1
language:
- iso: eng
month: '06'
oa_version: None
page: 140 - 151
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 255F06BE-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '622033'
name: Persistent Homology - Images, Data and Maps
publication_status: published
publisher: Springer
publist_id: '6096'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computation of cubical Steenrod squares
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9667
year: '2016'
...
---
_id: '1238'
abstract:
- lang: eng
text: The dynamic localization of endosomal compartments labeled with targeted fluorescent
protein tags is routinely followed by time lapse fluorescence microscopy approaches
and single particle tracking algorithms. In this way trajectories of individual
endosomes can be mapped and linked to physiological processes as cell growth.
However, other aspects of dynamic behavior including endosomal interactions are
difficult to follow in this manner. Therefore, we characterized the localization
and dynamic properties of early and late endosomes throughout the entire course
of root hair formation by means of spinning disc time lapse imaging and post-acquisition
automated multitracking and quantitative analysis. Our results show differential
motile behavior of early and late endosomes and interactions of late endosomes
that may be specified to particular root hair domains. Detailed data analysis
revealed a particular transient interaction between late endosomes—termed herein
as dancing-endosomes—which is not concluding to vesicular fusion. Endosomes preferentially
located in the root hair tip interacted as dancing-endosomes and traveled short
distances during this interaction. Finally, sizes of early and late endosomes
were addressed by means of super-resolution structured illumination microscopy
(SIM) to corroborate measurements on the spinning disc. This is a first study
providing quantitative microscopic data on dynamic spatio-temporal interactions
of endosomes during root hair tip growth.
acknowledgement: "This work was supported by National Program for Sustainability I
(grant no. LO1204) provided by the Czech Ministry of Education and by Institutional
Fund of Palacký University Olomouc (GK and OŠ).\r\nWe thank Sabine Fischer for help
with the statistics."
article_number: '1262'
article_processing_charge: No
author:
- first_name: Daniel
full_name: Von Wangenheim, Daniel
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Amparo
full_name: Rosero, Amparo
last_name: Rosero
- first_name: George
full_name: Komis, George
last_name: Komis
- first_name: Olga
full_name: Šamajová, Olga
last_name: Šamajová
- first_name: Miroslav
full_name: Ovečka, Miroslav
last_name: Ovečka
- first_name: Boris
full_name: Voigt, Boris
last_name: Voigt
- first_name: Jozef
full_name: Šamaj, Jozef
last_name: Šamaj
citation:
ama: von Wangenheim D, Rosero A, Komis G, et al. Endosomal interactions during root
hair growth. Frontiers in Plant Science. 2016;6(JAN2016). doi:10.3389/fpls.2015.01262
apa: von Wangenheim, D., Rosero, A., Komis, G., Šamajová, O., Ovečka, M., Voigt,
B., & Šamaj, J. (2016). Endosomal interactions during root hair growth. Frontiers
in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2015.01262
chicago: Wangenheim, Daniel von, Amparo Rosero, George Komis, Olga Šamajová, Miroslav
Ovečka, Boris Voigt, and Jozef Šamaj. “Endosomal Interactions during Root Hair
Growth.” Frontiers in Plant Science. Frontiers Research Foundation, 2016.
https://doi.org/10.3389/fpls.2015.01262.
ieee: D. von Wangenheim et al., “Endosomal interactions during root hair
growth,” Frontiers in Plant Science, vol. 6, no. JAN2016. Frontiers Research
Foundation, 2016.
ista: von Wangenheim D, Rosero A, Komis G, Šamajová O, Ovečka M, Voigt B, Šamaj
J. 2016. Endosomal interactions during root hair growth. Frontiers in Plant Science.
6(JAN2016), 1262.
mla: von Wangenheim, Daniel, et al. “Endosomal Interactions during Root Hair Growth.”
Frontiers in Plant Science, vol. 6, no. JAN2016, 1262, Frontiers Research
Foundation, 2016, doi:10.3389/fpls.2015.01262.
short: D. von Wangenheim, A. Rosero, G. Komis, O. Šamajová, M. Ovečka, B. Voigt,
J. Šamaj, Frontiers in Plant Science 6 (2016).
date_created: 2018-12-11T11:50:53Z
date_published: 2016-01-29T00:00:00Z
date_updated: 2025-09-22T09:18:11Z
day: '29'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.3389/fpls.2015.01262
external_id:
isi:
- '000368891500001'
file:
- access_level: open_access
checksum: 3127eab844d53564bf47e2b6b42f1ca0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:36Z
date_updated: 2020-07-14T12:44:41Z
file_id: '4760'
file_name: IST-2016-710-v1+1_fpls-06-01262.pdf
file_size: 1640550
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: JAN2016
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Frontiers in Plant Science
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '6094'
pubrep_id: '710'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Endosomal interactions during root hair growth
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2016'
...
---
_id: '1239'
abstract:
- lang: eng
text: Nonadherent polarized cells have been observed to have a pearlike, elongated
shape. Using a minimal model that describes the cell cortex as a thin layer of
contractile active gel, we show that the anisotropy of active stresses, controlled
by cortical viscosity and filament ordering, can account for this morphology.
The predicted shapes can be determined from the flow pattern only; they prove
to be independent of the mechanism at the origin of the cortical flow, and are
only weakly sensitive to the cytoplasmic rheology. In the case of actin flows
resulting from a contractile instability, we propose a phase diagram of three-dimensional
cell shapes that encompasses nonpolarized spherical, elongated, as well as oblate
shapes, all of which have been observed in experiment.
acknowledgement: 'V. R. acknowledges support by the Austrian Science Fund (FWF): (Grant
No. T560-B17).'
article_number: '028102'
article_processing_charge: No
author:
- first_name: Andrew
full_name: Callan Jones, Andrew
last_name: Callan Jones
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Raphaël
full_name: Voituriez, Raphaël
last_name: Voituriez
citation:
ama: Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. Cortical
flow-driven shapes of nonadherent cells. Physical Review Letters. 2016;116(2).
doi:10.1103/PhysRevLett.116.028102
apa: Callan Jones, A., Ruprecht, V., Wieser, S., Heisenberg, C.-P. J., & Voituriez,
R. (2016). Cortical flow-driven shapes of nonadherent cells. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.116.028102
chicago: Callan Jones, Andrew, Verena Ruprecht, Stefan Wieser, Carl-Philipp J Heisenberg,
and Raphaël Voituriez. “Cortical Flow-Driven Shapes of Nonadherent Cells.” Physical
Review Letters. American Physical Society, 2016. https://doi.org/10.1103/PhysRevLett.116.028102.
ieee: A. Callan Jones, V. Ruprecht, S. Wieser, C.-P. J. Heisenberg, and R. Voituriez,
“Cortical flow-driven shapes of nonadherent cells,” Physical Review Letters,
vol. 116, no. 2. American Physical Society, 2016.
ista: Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. 2016.
Cortical flow-driven shapes of nonadherent cells. Physical Review Letters. 116(2),
028102.
mla: Callan Jones, Andrew, et al. “Cortical Flow-Driven Shapes of Nonadherent Cells.”
Physical Review Letters, vol. 116, no. 2, 028102, American Physical Society,
2016, doi:10.1103/PhysRevLett.116.028102.
short: A. Callan Jones, V. Ruprecht, S. Wieser, C.-P.J. Heisenberg, R. Voituriez,
Physical Review Letters 116 (2016).
date_created: 2018-12-11T11:50:53Z
date_published: 2016-01-15T00:00:00Z
date_updated: 2025-09-22T09:18:45Z
day: '15'
department:
- _id: CaHe
doi: 10.1103/PhysRevLett.116.028102
external_id:
isi:
- '000368286300022'
intvolume: ' 116'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
project:
- _id: 2529486C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T 560-B17
name: Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6095'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cortical flow-driven shapes of nonadherent cells
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 116
year: '2016'
...
---
_id: '1240'
abstract:
- lang: eng
text: 'Background: Long non-coding RNAs (lncRNAs) are increasingly implicated as
gene regulators and may ultimately be more numerous than protein-coding genes
in the human genome. Despite large numbers of reported lncRNAs, reference annotations
are likely incomplete due to their lower and tighter tissue-specific expression
compared to mRNAs. An unexplored factor potentially confounding lncRNA identification
is inter-individual expression variability. Here, we characterize lncRNA natural
expression variability in human primary granulocytes. Results: We annotate granulocyte
lncRNAs and mRNAs in RNA-seq data from 10 healthy individuals, identifying multiple
lncRNAs absent from reference annotations, and use this to investigate three known
features (higher tissue-specificity, lower expression, and reduced splicing efficiency)
of lncRNAs relative to mRNAs. Expression variability was examined in seven individuals
sampled three times at 1- or more than 1-month intervals. We show that lncRNAs
display significantly more inter-individual expression variability compared to
mRNAs. We confirm this finding in two independent human datasets by analyzing
multiple tissues from the GTEx project and lymphoblastoid cell lines from the
GEUVADIS project. Using the latter dataset we also show that including more human
donors into the transcriptome annotation pipeline allows identification of an
increasing number of lncRNAs, but minimally affects mRNA gene number. Conclusions:
A comprehensive annotation of lncRNAs is known to require an approach that is
sensitive to low and tight tissue-specific expression. Here we show that increased
inter-individual expression variability is an additional general lncRNA feature
to consider when creating a comprehensive annotation of human lncRNAs or proposing
their use as prognostic or disease markers.'
acknowledgement: "This study was partly funded by the Austrian Science Fund (FWF F43-B09,
FWF W1207-B09). PMG is a recipient of a DOC Fellowship of the Austrian Academy of
Sciences.\r\nWe thank Ruth Klement, Tomasz Kulinski, Elisangela Valente, Elisabeth
Salzer,\r\nand Roland Jäger for technical/bioinformatic assistance and advice, the
CeMM\r\nIT department and José Manuel Molero for help and advice on software usage,\r\nthe
Biomedical Sequencing Facility (http://biomedical-sequencing.at/) for\r\nsequencing
and advice, Jacques Colinge, Daniel Andergassen, and Tomasz\r\nKulinski for discussions,
Quanah Hudson and Jörg Menche for reading and\r\ncommenting on the manuscript."
article_number: '14'
article_processing_charge: No
author:
- first_name: Aleksandra
full_name: Kornienko, Aleksandra
last_name: Kornienko
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Philipp
full_name: Guenzl, Philipp
last_name: Guenzl
- first_name: Heinz
full_name: Gisslinger, Heinz
last_name: Gisslinger
- first_name: Bettina
full_name: Gisslinger, Bettina
last_name: Gisslinger
- first_name: Ciara
full_name: Cleary, Ciara
last_name: Cleary
- first_name: Robert
full_name: Kralovics, Robert
last_name: Kralovics
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Denise
full_name: Barlow, Denise
last_name: Barlow
citation:
ama: Kornienko A, Dotter C, Guenzl P, et al. Long non-coding RNAs display higher
natural expression variation than protein-coding genes in healthy humans. Genome
Biology. 2016;17(1). doi:10.1186/s13059-016-0873-8
apa: Kornienko, A., Dotter, C., Guenzl, P., Gisslinger, H., Gisslinger, B., Cleary,
C., … Barlow, D. (2016). Long non-coding RNAs display higher natural expression
variation than protein-coding genes in healthy humans. Genome Biology.
BioMed Central. https://doi.org/10.1186/s13059-016-0873-8
chicago: Kornienko, Aleksandra, Christoph Dotter, Philipp Guenzl, Heinz Gisslinger,
Bettina Gisslinger, Ciara Cleary, Robert Kralovics, Florian Pauler, and Denise
Barlow. “Long Non-Coding RNAs Display Higher Natural Expression Variation than
Protein-Coding Genes in Healthy Humans.” Genome Biology. BioMed Central,
2016. https://doi.org/10.1186/s13059-016-0873-8.
ieee: A. Kornienko et al., “Long non-coding RNAs display higher natural expression
variation than protein-coding genes in healthy humans,” Genome Biology,
vol. 17, no. 1. BioMed Central, 2016.
ista: Kornienko A, Dotter C, Guenzl P, Gisslinger H, Gisslinger B, Cleary C, Kralovics
R, Pauler F, Barlow D. 2016. Long non-coding RNAs display higher natural expression
variation than protein-coding genes in healthy humans. Genome Biology. 17(1),
14.
mla: Kornienko, Aleksandra, et al. “Long Non-Coding RNAs Display Higher Natural
Expression Variation than Protein-Coding Genes in Healthy Humans.” Genome Biology,
vol. 17, no. 1, 14, BioMed Central, 2016, doi:10.1186/s13059-016-0873-8.
short: A. Kornienko, C. Dotter, P. Guenzl, H. Gisslinger, B. Gisslinger, C. Cleary,
R. Kralovics, F. Pauler, D. Barlow, Genome Biology 17 (2016).
date_created: 2018-12-11T11:50:53Z
date_published: 2016-01-29T00:00:00Z
date_updated: 2025-09-22T09:17:40Z
day: '29'
ddc:
- '576'
department:
- _id: GaNo
doi: 10.1186/s13059-016-0873-8
external_id:
isi:
- '000368904100001'
file:
- access_level: open_access
checksum: a268beee1a690801c83ec6729f9ebc5b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:05Z
date_updated: 2020-07-14T12:44:41Z
file_id: '4789'
file_name: IST-2016-709-v1+1_s13059-016-0873-8.pdf
file_size: 2914601
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Genome Biology
publication_status: published
publisher: BioMed Central
publist_id: '6093'
pubrep_id: '709'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long non-coding RNAs display higher natural expression variation than protein-coding
genes in healthy humans
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 17
year: '2016'
...
---
_id: '1241'
abstract:
- lang: eng
text: 'How likely is it that a population escapes extinction through adaptive evolution?
The answer to this question is of great relevance in conservation biology, where
we aim at species’ rescue and the maintenance of biodiversity, and in agriculture
and medicine, where we seek to hamper the emergence of pesticide or drug resistance.
By reshuffling the genome, recombination has two antagonistic effects on the probability
of evolutionary rescue: It generates and it breaks up favorable gene combinations.
Which of the two effects prevails depends on the fitness effects of mutations
and on the impact of stochasticity on the allele frequencies. In this article,
we analyze a mathematical model for rescue after a sudden environmental change
when adaptation is contingent on mutations at two loci. The analysis reveals a
complex nonlinear dependence of population survival on recombination. We moreover
find that, counterintuitively, a fast eradication of the wild type can promote
rescue in the presence of recombination. The model also shows that two-step rescue
is not unlikely to happen and can even be more likely than single-step rescue
(where adaptation relies on a single mutation), depending on the circumstances.'
acknowledgement: This work was made possible by a “For Women in Science” fellowship
(L’Oréal Österreich in cooperation with the Austrian Commission for the United Nations
Educational, Scientific, and Cultural Organization and the Austrian Academy of Sciences
with financial support from the Federal Ministry for Science and Research Austria)
and European Research Council grant 250152 (to Nick Barton).
article_processing_charge: No
author:
- first_name: Hildegard
full_name: Uecker, Hildegard
id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
last_name: Uecker
orcid: 0000-0001-9435-2813
- first_name: Joachim
full_name: Hermisson, Joachim
last_name: Hermisson
citation:
ama: Uecker H, Hermisson J. The role of recombination in evolutionary rescue. Genetics.
2016;202(2):721-732. doi:10.1534/genetics.115.180299
apa: Uecker, H., & Hermisson, J. (2016). The role of recombination in evolutionary
rescue. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.180299
chicago: Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in
Evolutionary Rescue.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.180299.
ieee: H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,”
Genetics, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016.
ista: Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue.
Genetics. 202(2), 721–732.
mla: Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary
Rescue.” Genetics, vol. 202, no. 2, Genetics Society of America, 2016,
pp. 721–32, doi:10.1534/genetics.115.180299.
short: H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.
date_created: 2018-12-11T11:50:54Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2025-09-22T09:17:06Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.115.180299
ec_funded: 1
external_id:
isi:
- '000371304600028'
intvolume: ' 202'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://biorxiv.org/content/early/2015/07/06/022020.abstract
month: '02'
oa: 1
oa_version: Preprint
page: 721 - 732
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 25B67606-B435-11E9-9278-68D0E5697425
name: Evolutionary rescue
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '6091'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The role of recombination in evolutionary rescue
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 202
year: '2016'
...
---
_id: '1242'
abstract:
- lang: eng
text: A crucial step in the regulation of gene expression is binding of transcription
factor (TF) proteins to regulatory sites along the DNA. But transcription factors
act at nanomolar concentrations, and noise due to random arrival of these molecules
at their binding sites can severely limit the precision of regulation. Recent
work on the optimization of information flow through regulatory networks indicates
that the lower end of the dynamic range of concentrations is simply inaccessible,
overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain
proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest
a scheme in which transcription factors also act as indirect translational regulators,
binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule
acts as an independent sensor of the input concentration, and averaging over these
multiple sensors reduces the noise. We analyze information flow through this scheme
and identify conditions under which it outperforms direct transcriptional regulation.
Our results suggest that the dual role of homeodomain proteins is not just a historical
accident, but a solution to a crucial physics problem in the regulation of gene
expression.
acknowledgement: "We thank T. Gregor, A. Prochaintz, and others for\r\nhelpful discussions.
This work was supported in part by\r\nGrants No. PHY-1305525 and No. CCF-0939370
from the\r\nUS National Science Foundation and by the W.M. Keck\r\nFoundation. A.M.W.
acknowledges the support by European\r\nResearch Council (ERC) Grant No. MCCIG PCIG10–GA-\r\n2011–303561.
G.T. and T.R.S. were supported by Austrian\r\nScience Fund (FWF) Grant No. P28844S."
article_number: '022404'
article_processing_charge: No
arxiv: 1
author:
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Aleksandra
full_name: Walczak, Aleksandra
last_name: Walczak
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of
transcription factor action by translational regulation. Physical Review E
Statistical Nonlinear and Soft Matter Physics. 2016;93(2). doi:10.1103/PhysRevE.93.022404
apa: Sokolowski, T. R., Walczak, A., Bialek, W., & Tkačik, G. (2016). Extending
the dynamic range of transcription factor action by translational regulation.
Physical Review E Statistical Nonlinear and Soft Matter Physics. American
Institute of Physics. https://doi.org/10.1103/PhysRevE.93.022404
chicago: Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik.
“Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.”
Physical Review E Statistical Nonlinear and Soft Matter Physics. American
Institute of Physics, 2016. https://doi.org/10.1103/PhysRevE.93.022404.
ieee: T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic
range of transcription factor action by translational regulation,” Physical
Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2. American
Institute of Physics, 2016.
ista: Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic
range of transcription factor action by translational regulation. Physical Review
E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404.
mla: Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription
Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear
and Soft Matter Physics, vol. 93, no. 2, 022404, American Institute of Physics,
2016, doi:10.1103/PhysRevE.93.022404.
short: T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical
Nonlinear and Soft Matter Physics 93 (2016).
date_created: 2018-12-11T11:50:54Z
date_published: 2016-02-04T00:00:00Z
date_updated: 2025-09-22T09:16:30Z
day: '04'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.93.022404
external_id:
arxiv:
- '1507.02562'
isi:
- '000369439100005'
intvolume: ' 93'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.02562
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '6088'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extending the dynamic range of transcription factor action by translational
regulation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 93
year: '2016'
...
---
_id: '1244'
abstract:
- lang: eng
text: Cell polarity refers to a functional spatial organization of proteins that
is crucial for the control of essential cellular processes such as growth and
division. To establish polarity, cells rely on elaborate regulation networks that
control the distribution of proteins at the cell membrane. In fission yeast cells,
a microtubule-dependent network has been identified that polarizes the distribution
of signaling proteins that restricts growth to cell ends and targets the cytokinetic
machinery to the middle of the cell. Although many molecular components have been
shown to play a role in this network, it remains unknown which molecular functionalities
are minimally required to establish a polarized protein distribution in this system.
Here we show that a membrane-binding protein fragment, which distributes homogeneously
in wild-type fission yeast cells, can be made to concentrate at cell ends by attaching
it to a cytoplasmic microtubule end-binding protein. This concentration results
in a polarized pattern of chimera proteins with a spatial extension that is very
reminiscent of natural polarity patterns in fission yeast. However, chimera levels
fluctuate in response to microtubule dynamics, and disruption of microtubules
leads to disappearance of the pattern. Numerical simulations confirm that the
combined functionality of membrane anchoring and microtubule tip affinity is in
principle sufficient to create polarized patterns. Our chimera protein may thus
represent a simple molecular functionality that is able to polarize the membrane,
onto which additional layers of molecular complexity may be built to provide the
temporal robustness that is typical of natural polarity patterns.
acknowledgement: "We thank Sophie Martin, Ken Sawin, Stephen Huisman,\r\nand Damian
Brunner for strains; Julianne\r\nTeapal, Marcel Janson, Sergio Rincon,\r\nand Phong
Tran for technical assistance; Andrew Mugler and Bela Mulder for\r\ndiscussions;
and Sander Tans, Phong Tran,\r\nand Anne Paoletti for critical reading\r\nof the
manuscript. This work is part of the research program of the\r\n“\r\nStichting\r\nvoor
Fundamenteel Onderzoek de Materie,\r\n”\r\nwhich is financially supported by\r\nthe\r\n“\r\nNederlandse
organisatie voor Wete\r\nnschappelijk Onderzoek (NWO).\r\n”"
article_processing_charge: No
author:
- first_name: Pierre
full_name: Recouvreux, Pierre
last_name: Recouvreux
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Aristea
full_name: Grammoustianou, Aristea
last_name: Grammoustianou
- first_name: Pieter
full_name: Tenwolde, Pieter
last_name: Tenwolde
- first_name: Marileen
full_name: Dogterom, Marileen
last_name: Dogterom
citation:
ama: Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. Chimera
proteins with affinity for membranes and microtubule tips polarize in the membrane
of fission yeast cells. PNAS. 2016;113(7):1811-1816. doi:10.1073/pnas.1419248113
apa: Recouvreux, P., Sokolowski, T. R., Grammoustianou, A., Tenwolde, P., &
Dogterom, M. (2016). Chimera proteins with affinity for membranes and microtubule
tips polarize in the membrane of fission yeast cells. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.1419248113
chicago: Recouvreux, Pierre, Thomas R Sokolowski, Aristea Grammoustianou, Pieter
Tenwolde, and Marileen Dogterom. “Chimera Proteins with Affinity for Membranes
and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” PNAS.
National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1419248113.
ieee: P. Recouvreux, T. R. Sokolowski, A. Grammoustianou, P. Tenwolde, and M. Dogterom,
“Chimera proteins with affinity for membranes and microtubule tips polarize in
the membrane of fission yeast cells,” PNAS, vol. 113, no. 7. National Academy
of Sciences, pp. 1811–1816, 2016.
ista: Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. 2016.
Chimera proteins with affinity for membranes and microtubule tips polarize in
the membrane of fission yeast cells. PNAS. 113(7), 1811–1816.
mla: Recouvreux, Pierre, et al. “Chimera Proteins with Affinity for Membranes and
Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” PNAS,
vol. 113, no. 7, National Academy of Sciences, 2016, pp. 1811–16, doi:10.1073/pnas.1419248113.
short: P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom,
PNAS 113 (2016) 1811–1816.
date_created: 2018-12-11T11:50:55Z
date_published: 2016-02-16T00:00:00Z
date_updated: 2025-09-22T09:15:17Z
day: '16'
department:
- _id: GaTk
doi: 10.1073/pnas.1419248113
external_id:
isi:
- '000370220000046'
intvolume: ' 113'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763754/
month: '02'
oa: 1
oa_version: Submitted Version
page: 1811 - 1816
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6085'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chimera proteins with affinity for membranes and microtubule tips polarize
in the membrane of fission yeast cells
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 113
year: '2016'
...
---
_id: '1245'
abstract:
- lang: eng
text: 'To facilitate collaboration in massive online classrooms, instructors must
make many decisions. For instance, the following parameters need to be decided
when designing a peer-feedback system where students review each others'' essays:
the number of students each student must provide feedback to, an algorithm to
map feedback providers to receivers, constraints that ensure students do not become
free-riders (receiving feedback but not providing it), the best times to receive
feedback to improve learning etc. While instructors can answer these questions
by running experiments or invoking past experience, game-theoretic models with
data from online learning platforms can identify better initial designs for further
improvements. As an example, we explore the design space of a peer feedback system
by modeling it using game theory. Our simulations show that incentivizing students
to provide feedback requires the value obtained from receiving a feedback to exceed
the cost of providing it by a large factor (greater than 7). Furthermore, hiding
feedback from low-effort students incentivizes them to provide more feedback.'
acknowledgement: 'ERC Start Grant Graph Games 279307 supported this research. '
article_processing_charge: No
author:
- first_name: Vineet
full_name: Pandey, Vineet
last_name: Pandey
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Pandey V, Chatterjee K. Game-theoretic models identify useful principles for
peer collaboration in online learning platforms. In: Proceedings of the ACM
Conference on Computer Supported Cooperative Work. Vol 26. ACM; 2016:365-368.
doi:10.1145/2818052.2869122'
apa: 'Pandey, V., & Chatterjee, K. (2016). Game-theoretic models identify useful
principles for peer collaboration in online learning platforms. In Proceedings
of the ACM Conference on Computer Supported Cooperative Work (Vol. 26, pp.
365–368). San Francisco, CA, USA: ACM. https://doi.org/10.1145/2818052.2869122'
chicago: Pandey, Vineet, and Krishnendu Chatterjee. “Game-Theoretic Models Identify
Useful Principles for Peer Collaboration in Online Learning Platforms.” In Proceedings
of the ACM Conference on Computer Supported Cooperative Work, 26:365–68. ACM,
2016. https://doi.org/10.1145/2818052.2869122.
ieee: V. Pandey and K. Chatterjee, “Game-theoretic models identify useful principles
for peer collaboration in online learning platforms,” in Proceedings of the
ACM Conference on Computer Supported Cooperative Work, San Francisco, CA,
USA, 2016, vol. 26, no. Februar-2016, pp. 365–368.
ista: 'Pandey V, Chatterjee K. 2016. Game-theoretic models identify useful principles
for peer collaboration in online learning platforms. Proceedings of the ACM Conference
on Computer Supported Cooperative Work. CSCW: Computer Supported Cooperative Work
and Social Computing vol. 26, 365–368.'
mla: Pandey, Vineet, and Krishnendu Chatterjee. “Game-Theoretic Models Identify
Useful Principles for Peer Collaboration in Online Learning Platforms.” Proceedings
of the ACM Conference on Computer Supported Cooperative Work, vol. 26, no.
Februar-2016, ACM, 2016, pp. 365–68, doi:10.1145/2818052.2869122.
short: V. Pandey, K. Chatterjee, in:, Proceedings of the ACM Conference on Computer
Supported Cooperative Work, ACM, 2016, pp. 365–368.
conference:
end_date: 2016-03-02
location: San Francisco, CA, USA
name: 'CSCW: Computer Supported Cooperative Work and Social Computing'
start_date: 2016-02-26
date_created: 2018-12-11T11:50:55Z
date_published: 2016-02-27T00:00:00Z
date_updated: 2025-09-22T09:14:46Z
day: '27'
department:
- _id: KrCh
doi: 10.1145/2818052.2869122
ec_funded: 1
external_id:
isi:
- '000468137600088'
intvolume: ' 26'
isi: 1
issue: Februar-2016
language:
- iso: eng
month: '02'
oa_version: None
page: 365 - 368
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the ACM Conference on Computer Supported Cooperative Work
publication_status: published
publisher: ACM
publist_id: '6083'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Game-theoretic models identify useful principles for peer collaboration in
online learning platforms
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 26
year: '2016'
...
---
_id: '1246'
abstract:
- lang: eng
text: Near-field imaging is a powerful tool to investigate the complex structure
of light at the nanoscale. Recent advances in near-field imaging have indicated
the possibility for the complete reconstruction of both electric and magnetic
components of the evanescent field. Here we study the electro-magnetic field structure
of surface plasmon polariton waves propagating along subwavelength gold nanowires
by performing phase- and polarization-resolved near-field microscopy in collection
mode. By applying the optical reciprocity theorem, we describe the signal collected
by the probe as an overlap integral of the nanowire's evanescent field and the
probe's response function. As a result, we find that the probe's sensitivity to
the magnetic field is approximately equal to its sensitivity to the electric field.
Through rigorous modeling of the nanowire mode as well as the aperture probe response
function, we obtain a good agreement between experimentally measured signals and
a numerical model. Our findings provide a better understanding of aperture-based
near-field imaging of the nanoscopic plasmonic and photonic structures and are
helpful for the interpretation of future near-field experiments.
acknowledgement: 'This work is supported part of the research program of the Netherlands
Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization
for Scientific Research (NWO), and part of this work has been funded by the project
‘SPANGL4Q’, which acknowledges the financial support of the Future and Emerging
Technologies (FET) program within the Seventh Framework Programme for Research of
the European Commission, under FETOpen grant number: FP7-284743. L.K. acknowledges
funding from ERC Advanced, Investigator Grant (no. 240438-CONSTANS).'
article_number: '22665'
article_processing_charge: No
author:
- first_name: Irina
full_name: Kabakova, Irina
last_name: Kabakova
- first_name: Anouk
full_name: De Hoogh, Anouk
last_name: De Hoogh
- first_name: Ruben
full_name: Van Der Wel, Ruben
last_name: Van Der Wel
- first_name: Matthias
full_name: Wulf, Matthias
id: 45598606-F248-11E8-B48F-1D18A9856A87
last_name: Wulf
orcid: 0000-0001-6613-1378
- first_name: Boris
full_name: Le Feber, Boris
last_name: Le Feber
- first_name: Laurens
full_name: Kuipers, Laurens
last_name: Kuipers
citation:
ama: Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. Imaging
of electric and magnetic fields near plasmonic nanowires. Scientific Reports.
2016;6. doi:10.1038/srep22665
apa: Kabakova, I., De Hoogh, A., Van Der Wel, R., Wulf, M., Le Feber, B., &
Kuipers, L. (2016). Imaging of electric and magnetic fields near plasmonic nanowires.
Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep22665
chicago: Kabakova, Irina, Anouk De Hoogh, Ruben Van Der Wel, Matthias Wulf, Boris
Le Feber, and Laurens Kuipers. “Imaging of Electric and Magnetic Fields near Plasmonic
Nanowires.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep22665.
ieee: I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, and L. Kuipers,
“Imaging of electric and magnetic fields near plasmonic nanowires,” Scientific
Reports, vol. 6. Nature Publishing Group, 2016.
ista: Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. 2016.
Imaging of electric and magnetic fields near plasmonic nanowires. Scientific Reports.
6, 22665.
mla: Kabakova, Irina, et al. “Imaging of Electric and Magnetic Fields near Plasmonic
Nanowires.” Scientific Reports, vol. 6, 22665, Nature Publishing Group,
2016, doi:10.1038/srep22665.
short: I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, L. Kuipers,
Scientific Reports 6 (2016).
date_created: 2018-12-11T11:50:55Z
date_published: 2016-03-07T00:00:00Z
date_updated: 2025-09-22T09:14:06Z
day: '07'
ddc:
- '539'
department:
- _id: JoFi
doi: 10.1038/srep22665
external_id:
isi:
- '000371407500001'
file:
- access_level: open_access
checksum: ca76236cb1aae22cb90c65313e2c5e98
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:11Z
date_updated: 2020-07-14T12:44:41Z
file_id: '5061'
file_name: IST-2016-707-v1+1_srep22665.pdf
file_size: 1425165
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6082'
pubrep_id: '707'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Imaging of electric and magnetic fields near plasmonic nanowires
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2016'
...
---
_id: '1247'
abstract:
- lang: eng
text: The shaping of organs in plants depends on the intercellular flow of the phytohormone
auxin, of which the directional signaling is determined by the polar subcellular
localization of PIN-FORMED (PIN) auxin transport proteins. Phosphorylation dynamics
of PIN proteins are affected by the protein phosphatase 2A (PP2A) and the PINOID
kinase, which act antagonistically to mediate their apical-basal polar delivery.
Here, we identified the ROTUNDA3 (RON3) protein as a regulator of the PP2A phosphatase
activity in Arabidopsis thaliana. The RON3 gene was map-based cloned starting
from the ron3-1 leaf mutant and found to be a unique, plant-specific gene coding
for a protein with high and dispersed proline content. The ron3-1 and ron3-2 mutant
phenotypes [i.e., reduced apical dominance, primary root length, lateral root
emergence, and growth; increased ectopic stages II, IV, and V lateral root primordia;
decreased auxin maxima in indole-3-acetic acid (IAA)-treated root apical meristems;
hypergravitropic root growth and response; increased IAA levels in shoot apices;
and reduced auxin accumulation in root meristems] support a role for RON3 in auxin
biology. The affinity-purified PP2A complex with RON3 as bait suggested that RON3
might act in PIN transporter trafficking. Indeed, pharmacological interference
with vesicle trafficking processes revealed that single ron3-2 and double ron3-2
rcn1 mutants have altered PIN polarity and endocytosis in specific cells. Our
data indicate that RON3 contributes to auxin-mediated development by playing a
role in PIN recycling and polarity establishment through regulation of the PP2A
complex activity.
acknowledgement: "This work was supported by the Ghent University Special Research
Fund (M.K.), the European Research Council (Project ERC-2011-StG-20101109-PSDP)
(to J.F.), and the Körber European Science Foun-\r\ndation (J.F.). S.D.G. is indebted
to the Agency for Science and Technology for\r\na predoctoral fellowship."
article_processing_charge: No
author:
- first_name: Michael
full_name: Karampelias, Michael
last_name: Karampelias
- first_name: Pia
full_name: Neyt, Pia
last_name: Neyt
- first_name: Steven
full_name: De Groeve, Steven
last_name: De Groeve
- first_name: Stijn
full_name: Aesaert, Stijn
last_name: Aesaert
- first_name: Griet
full_name: Coussens, Griet
last_name: Coussens
- first_name: Jakub
full_name: Rolčík, Jakub
last_name: Rolčík
- first_name: Leonardo
full_name: Bruno, Leonardo
last_name: Bruno
- first_name: Nancy
full_name: De Winne, Nancy
last_name: De Winne
- first_name: Annemie
full_name: Van Minnebruggen, Annemie
last_name: Van Minnebruggen
- first_name: Marc
full_name: Van Montagu, Marc
last_name: Van Montagu
- first_name: Maria
full_name: Ponce, Maria
last_name: Ponce
- first_name: José
full_name: Micol, José
last_name: Micol
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Mieke
full_name: Van Lijsebettens, Mieke
last_name: Van Lijsebettens
citation:
ama: Karampelias M, Neyt P, De Groeve S, et al. ROTUNDA3 function in plant development
by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS.
2016;113(10):2768-2773. doi:10.1073/pnas.1501343112
apa: Karampelias, M., Neyt, P., De Groeve, S., Aesaert, S., Coussens, G., Rolčík,
J., … Van Lijsebettens, M. (2016). ROTUNDA3 function in plant development by phosphatase
2A-mediated regulation of auxin transporter recycling. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.1501343112
chicago: Karampelias, Michael, Pia Neyt, Steven De Groeve, Stijn Aesaert, Griet
Coussens, Jakub Rolčík, Leonardo Bruno, et al. “ROTUNDA3 Function in Plant Development
by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” PNAS.
National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1501343112.
ieee: M. Karampelias et al., “ROTUNDA3 function in plant development by phosphatase
2A-mediated regulation of auxin transporter recycling,” PNAS, vol. 113,
no. 10. National Academy of Sciences, pp. 2768–2773, 2016.
ista: Karampelias M, Neyt P, De Groeve S, Aesaert S, Coussens G, Rolčík J, Bruno
L, De Winne N, Van Minnebruggen A, Van Montagu M, Ponce M, Micol J, Friml J, De
Jaeger G, Van Lijsebettens M. 2016. ROTUNDA3 function in plant development by
phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. 113(10),
2768–2773.
mla: Karampelias, Michael, et al. “ROTUNDA3 Function in Plant Development by Phosphatase
2A-Mediated Regulation of Auxin Transporter Recycling.” PNAS, vol. 113,
no. 10, National Academy of Sciences, 2016, pp. 2768–73, doi:10.1073/pnas.1501343112.
short: M. Karampelias, P. Neyt, S. De Groeve, S. Aesaert, G. Coussens, J. Rolčík,
L. Bruno, N. De Winne, A. Van Minnebruggen, M. Van Montagu, M. Ponce, J. Micol,
J. Friml, G. De Jaeger, M. Van Lijsebettens, PNAS 113 (2016) 2768–2773.
date_created: 2018-12-11T11:50:56Z
date_published: 2016-03-08T00:00:00Z
date_updated: 2025-09-22T09:13:28Z
day: '08'
department:
- _id: JiFr
doi: 10.1073/pnas.1501343112
ec_funded: 1
external_id:
isi:
- '000372013300055'
intvolume: ' 113'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791031/
month: '03'
oa: 1
oa_version: Submitted Version
page: 2768 - 2773
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6081'
quality_controlled: '1'
scopus_import: '1'
status: public
title: ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation
of auxin transporter recycling
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 113
year: '2016'
...
---
_id: '1248'
abstract:
- lang: eng
text: Life depends as much on the flow of information as on the flow of energy.
Here we review the many efforts to make this intuition precise. Starting with
the building blocks of information theory, we explore examples where it has been
possible to measure, directly, the flow of information in biological networks,
or more generally where information-theoretic ideas have been used to guide the
analysis of experiments. Systems of interest range from single molecules (the
sequence diversity in families of proteins) to groups of organisms (the distribution
of velocities in flocks of birds), and all scales in between. Many of these analyses
are motivated by the idea that biological systems may have evolved to optimize
the gathering and representation of information, and we review the experimental
evidence for this optimization, again across a wide range of scales.
acknowledgement: "Our work was supported in part by the US\r\nNational Science Foundation
(PHY–1305525 and CCF–\r\n0939370), by the Austrian Science Foundation (FWF\r\nP25651),
by the Human Frontiers Science Program, and\r\nby the Simons and Swartz Foundations."
article_processing_charge: No
arxiv: 1
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: William
full_name: Bialek, William
last_name: Bialek
citation:
ama: Tkačik G, Bialek W. Information processing in living systems. Annual Review
of Condensed Matter Physics. 2016;7:89-117. doi:10.1146/annurev-conmatphys-031214-014803
apa: Tkačik, G., & Bialek, W. (2016). Information processing in living systems.
Annual Review of Condensed Matter Physics. Annual Reviews. https://doi.org/10.1146/annurev-conmatphys-031214-014803
chicago: Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.”
Annual Review of Condensed Matter Physics. Annual Reviews, 2016. https://doi.org/10.1146/annurev-conmatphys-031214-014803.
ieee: G. Tkačik and W. Bialek, “Information processing in living systems,” Annual
Review of Condensed Matter Physics, vol. 7. Annual Reviews, pp. 89–117, 2016.
ista: Tkačik G, Bialek W. 2016. Information processing in living systems. Annual
Review of Condensed Matter Physics. 7, 89–117.
mla: Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.”
Annual Review of Condensed Matter Physics, vol. 7, Annual Reviews, 2016,
pp. 89–117, doi:10.1146/annurev-conmatphys-031214-014803.
short: G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016)
89–117.
date_created: 2018-12-11T11:50:56Z
date_published: 2016-03-10T00:00:00Z
date_updated: 2025-09-22T09:12:56Z
day: '10'
department:
- _id: GaTk
doi: 10.1146/annurev-conmatphys-031214-014803
external_id:
arxiv:
- '1412.8752'
isi:
- '000372188500005'
intvolume: ' 7'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1412.8752
month: '03'
oa: 1
oa_version: Preprint
page: 89 - 117
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: Annual Review of Condensed Matter Physics
publication_status: published
publisher: Annual Reviews
publist_id: '6080'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Information processing in living systems
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 7
year: '2016'
...