---
_id: '1666'
abstract:
- lang: eng
text: Evolution of gene regulation is crucial for our understanding of the phenotypic
differences between species, populations and individuals. Sequence-specific binding
of transcription factors to the regulatory regions on the DNA is a key regulatory
mechanism that determines gene expression and hence heritable phenotypic variation.
We use a biophysical model for directional selection on gene expression to estimate
the rates of gain and loss of transcription factor binding sites (TFBS) in finite
populations under both point and insertion/deletion mutations. Our results show
that these rates are typically slow for a single TFBS in an isolated DNA region,
unless the selection is extremely strong. These rates decrease drastically with
increasing TFBS length or increasingly specific protein-DNA interactions, making
the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation
timescales. Similarly, evolution converges to the stationary distribution of binding
sequences very slowly, making the equilibrium assumption questionable. The availability
of longer regulatory sequences in which multiple binding sites can evolve simultaneously,
the presence of “pre-sites” or partially decayed old sites in the initial sequence,
and biophysical cooperativity between transcription factors, can all facilitate
gain of TFBS and reconcile theoretical calculations with timescales inferred from
comparative genomics.
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding
site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639
apa: Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of
transcription factor binding site evolution. PLoS Genetics. Public Library
of Science. https://doi.org/10.1371/journal.pgen.1005639
chicago: Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics
of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public
Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.
ieee: M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription
factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public
Library of Science, 2015.
ista: Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor
binding site evolution. PLoS Genetics. 11(11).
mla: Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.”
PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.
short: M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).
date_created: 2018-12-11T11:53:21Z
date_published: 2015-11-06T00:00:00Z
date_updated: 2023-09-07T11:53:49Z
day: '06'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pgen.1005639
ec_funded: 1
file:
- access_level: open_access
checksum: a4e72fca5ccf40ddacf4d08c8e46b554
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:58Z
date_updated: 2020-07-14T12:45:10Z
file_id: '4657'
file_name: IST-2016-463-v1+1_journal.pgen.1005639.pdf
file_size: 2580778
relation: main_file
file_date_updated: 2020-07-14T12:45:10Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '5483'
pubrep_id: '463'
quality_controlled: '1'
related_material:
record:
- id: '9712'
relation: research_data
status: public
- id: '1131'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Dynamics of transcription factor binding site evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '1502'
abstract:
- lang: eng
text: We extend the theory of input-output conformance with operators for merge
and quotient. The former is useful when testing against multiple requirements
or views. The latter can be used to generate tests for patches of an already tested
system. Both operators can combine systems with different action alphabets, which
is usually the case when constructing complex systems and specifications from
parts, for instance different views as well as newly defined functionality of
a~previous version of the system.
acknowledgement: "This research was funded in part by the European Research Council
(ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF)
projects S11402-N23(RiSE) and Z211-N23 (Wittgestein Award), by People Programme
(Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013)
under REA grant agreement 291734, and by the ARTEMIS JU under grant agreement 295373
(nSafeCer). Jan Křetínský has been partially supported by the Czech Science Foundation,
grant No. P202/12/G061. Nikola Beneš has been supported by the\r\nMEYS project
No. CZ.1.07/2.3.00/30.0009 Employment of Newly Graduated Doctors of Science for
Scientific Excellence."
alternative_title:
- 'Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based
Software Engineering '
author:
- first_name: Nikola
full_name: Beneš, Nikola
last_name: Beneš
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- 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: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Dejan
full_name: Nickovic, Dejan
last_name: Nickovic
citation:
ama: 'Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. Complete composition
operators for IOCO-testing theory. In: ACM; 2015:101-110. doi:10.1145/2737166.2737175'
apa: 'Beneš, N., Daca, P., Henzinger, T. A., Kretinsky, J., & Nickovic, D. (2015).
Complete composition operators for IOCO-testing theory (pp. 101–110). Presented
at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada: ACM.
https://doi.org/10.1145/2737166.2737175'
chicago: Beneš, Nikola, Przemyslaw Daca, Thomas A Henzinger, Jan Kretinsky, and
Dejan Nickovic. “Complete Composition Operators for IOCO-Testing Theory,” 101–10.
ACM, 2015. https://doi.org/10.1145/2737166.2737175.
ieee: 'N. Beneš, P. Daca, T. A. Henzinger, J. Kretinsky, and D. Nickovic, “Complete
composition operators for IOCO-testing theory,” presented at the CBSE: Component-Based
Software Engineering , Montreal, QC, Canada, 2015, pp. 101–110.'
ista: 'Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. 2015. Complete composition
operators for IOCO-testing theory. CBSE: Component-Based Software Engineering
, Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based
Software Engineering , , 101–110.'
mla: Beneš, Nikola, et al. Complete Composition Operators for IOCO-Testing Theory.
ACM, 2015, pp. 101–10, doi:10.1145/2737166.2737175.
short: N. Beneš, P. Daca, T.A. Henzinger, J. Kretinsky, D. Nickovic, in:, ACM, 2015,
pp. 101–110.
conference:
end_date: 2015-05-08
location: Montreal, QC, Canada
name: 'CBSE: Component-Based Software Engineering '
start_date: 2015-05-04
date_created: 2018-12-11T11:52:24Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1145/2737166.2737175
ec_funded: 1
file:
- access_level: open_access
checksum: c6ce681035c163a158751f240cb7d389
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:46Z
date_updated: 2020-07-14T12:44:59Z
file_id: '5303'
file_name: IST-2016-625-v1+1_conf-cbse-BenesDHKN15.pdf
file_size: 467561
relation: main_file
file_date_updated: 2020-07-14T12:44:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 101 - 110
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_identifier:
isbn:
- 978-1-4503-3471-6
publication_status: published
publisher: ACM
publist_id: '5676'
pubrep_id: '625'
quality_controlled: '1'
related_material:
record:
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Complete composition operators for IOCO-testing theory
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1501'
abstract:
- lang: eng
text: 'We consider Markov decision processes (MDPs) which are a standard model for
probabilistic systems. We focus on qualitative properties for MDPs that can express
that desired behaviors of the system arise almost-surely (with probability 1)
or with positive probability. We introduce a new simulation relation to capture
the refinement relation of MDPs with respect to qualitative properties, and present
discrete graph algorithms with quadratic complexity to compute the simulation
relation. We present an automated technique for assume-guarantee style reasoning
for compositional analysis of two-player games by giving a counterexample guided
abstraction-refinement approach to compute our new simulation relation. We show
a tight link between two-player games and MDPs, and as a consequence the results
for games are lifted to MDPs with qualitative properties. We have implemented
our algorithms and show that the compositional analysis leads to significant improvements. '
acknowledgement: 'The research was partly supported by Austrian Science Fund (FWF)
Grant No. P23499- N23, FWF NFN Grant No. S11407-N23, FWF Grant S11403-N23 (RiSE),
and FWF Grant Z211-N23 (Wittgenstein Award), ERC Start Grant (279307: Graph Games),
Microsoft faculty fellows award, the ERC Advanced Grant QUAREM (Quantitative Reactive
Modeling).'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
citation:
ama: Chatterjee K, Chmelik M, Daca P. CEGAR for compositional analysis of qualitative
properties in Markov decision processes. Formal Methods in System Design.
2015;47(2):230-264. doi:10.1007/s10703-015-0235-2
apa: Chatterjee, K., Chmelik, M., & Daca, P. (2015). CEGAR for compositional
analysis of qualitative properties in Markov decision processes. Formal Methods
in System Design. Springer. https://doi.org/10.1007/s10703-015-0235-2
chicago: Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for
Compositional Analysis of Qualitative Properties in Markov Decision Processes.”
Formal Methods in System Design. Springer, 2015. https://doi.org/10.1007/s10703-015-0235-2.
ieee: K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for compositional analysis
of qualitative properties in Markov decision processes,” Formal Methods in
System Design, vol. 47, no. 2. Springer, pp. 230–264, 2015.
ista: Chatterjee K, Chmelik M, Daca P. 2015. CEGAR for compositional analysis of
qualitative properties in Markov decision processes. Formal Methods in System
Design. 47(2), 230–264.
mla: Chatterjee, Krishnendu, et al. “CEGAR for Compositional Analysis of Qualitative
Properties in Markov Decision Processes.” Formal Methods in System Design,
vol. 47, no. 2, Springer, 2015, pp. 230–64, doi:10.1007/s10703-015-0235-2.
short: K. Chatterjee, M. Chmelik, P. Daca, Formal Methods in System Design 47 (2015)
230–264.
date_created: 2018-12-11T11:52:23Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/s10703-015-0235-2
ec_funded: 1
intvolume: ' 47'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1405.0835
month: '10'
oa: 1
oa_version: Preprint
page: 230 - 264
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: Formal Methods in System Design
publication_status: published
publisher: Springer
publist_id: '5677'
quality_controlled: '1'
related_material:
record:
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: CEGAR for compositional analysis of qualitative properties in Markov decision
processes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2015'
...
---
_id: '1602'
abstract:
- lang: eng
text: Interprocedural analysis is at the heart of numerous applications in programming
languages, such as alias analysis, constant propagation, etc. Recursive state
machines (RSMs) are standard models for interprocedural analysis. We consider
a general framework with RSMs where the transitions are labeled from a semiring,
and path properties are algebraic with semiring operations. RSMs with algebraic
path properties can model interprocedural dataflow analysis problems, the shortest
path problem, the most probable path problem, etc. The traditional algorithms
for interprocedural analysis focus on path properties where the starting point
is fixed as the entry point of a specific method. In this work, we consider possible
multiple queries as required in many applications such as in alias analysis. The
study of multiple queries allows us to bring in a very important algorithmic distinction
between the resource usage of the one-time preprocessing vs for each individual
query. The second aspect that we consider is that the control flow graphs for
most programs have constant treewidth. Our main contributions are simple and implementable
algorithms that supportmultiple queries for algebraic path properties for RSMs
that have constant treewidth. Our theoretical results show that our algorithms
have small additional one-time preprocessing, but can answer subsequent queries
significantly faster as compared to the current best-known solutions for several
important problems, such as interprocedural reachability and shortest path. We
provide a prototype implementation for interprocedural reachability and intraprocedural
shortest path that gives a significant speed-up on several benchmarks.
acknowledgement: We thank anonymous reviewers for helpful comments to improve the
presentation of the paper.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Prateesh
full_name: Goyal, Prateesh
last_name: Goyal
citation:
ama: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. Faster algorithms for
algebraic path properties in recursive state machines with constant treewidth.
ACM SIGPLAN Notices. 2015;50(1):97-109. doi:10.1145/2676726.2676979
apa: 'Chatterjee, K., Ibsen-Jensen, R., Pavlogiannis, A., & Goyal, P. (2015).
Faster algorithms for algebraic path properties in recursive state machines with
constant treewidth. ACM SIGPLAN Notices. Mumbai, India: ACM. https://doi.org/10.1145/2676726.2676979'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Andreas Pavlogiannis, and
Prateesh Goyal. “Faster Algorithms for Algebraic Path Properties in Recursive
State Machines with Constant Treewidth.” ACM SIGPLAN Notices. ACM, 2015.
https://doi.org/10.1145/2676726.2676979.
ieee: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, and P. Goyal, “Faster algorithms
for algebraic path properties in recursive state machines with constant treewidth,”
ACM SIGPLAN Notices, vol. 50, no. 1. ACM, pp. 97–109, 2015.
ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. 2015. Faster algorithms
for algebraic path properties in recursive state machines with constant treewidth.
ACM SIGPLAN Notices. 50(1), 97–109.
mla: Chatterjee, Krishnendu, et al. “Faster Algorithms for Algebraic Path Properties
in Recursive State Machines with Constant Treewidth.” ACM SIGPLAN Notices,
vol. 50, no. 1, ACM, 2015, pp. 97–109, doi:10.1145/2676726.2676979.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, P. Goyal, ACM SIGPLAN Notices
50 (2015) 97–109.
conference:
end_date: 2015-01-17
location: Mumbai, India
name: 'SIGPLAN: Symposium on Principles of Programming Languages'
start_date: 2015-01-15
date_created: 2018-12-11T11:52:58Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-09-07T12:01:58Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/2676726.2676979
ec_funded: 1
external_id:
arxiv:
- '1410.7724'
intvolume: ' 50'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1410.7724
month: '01'
oa: 1
oa_version: Preprint
page: 97 - 109
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: ACM SIGPLAN Notices
publication_status: published
publisher: ACM
publist_id: '5565'
quality_controlled: '1'
related_material:
record:
- id: '821'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Faster algorithms for algebraic path properties in recursive state machines
with constant treewidth
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2015'
...
---
_id: '1604'
abstract:
- lang: eng
text: We consider the quantitative analysis problem for interprocedural control-flow
graphs (ICFGs). The input consists of an ICFG, a positive weight function that
assigns every transition a positive integer-valued number, and a labelling of
the transitions (events) as good, bad, and neutral events. The weight function
assigns to each transition a numerical value that represents ameasure of how good
or bad an event is. The quantitative analysis problem asks whether there is a
run of the ICFG where the ratio of the sum of the numerical weights of good events
versus the sum of weights of bad events in the long-run is at least a given threshold
(or equivalently, to compute the maximal ratio among all valid paths in the ICFG).
The quantitative analysis problem for ICFGs can be solved in polynomial time,
and we present an efficient and practical algorithm for the problem. We show that
several problems relevant for static program analysis, such as estimating the
worst-case execution time of a program or the average energy consumption of a
mobile application, can be modeled in our framework. We have implemented our algorithm
as a tool in the Java Soot framework. We demonstrate the effectiveness of our
approach with two case studies. First, we show that our framework provides a sound
approach (no false positives) for the analysis of inefficiently-used containers.
Second, we show that our approach can also be used for static profiling of programs
which reasons about methods that are frequently invoked. Our experimental results
show that our tool scales to relatively large benchmarks, and discovers relevant
and useful information that can be used to optimize performance of the programs.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Pavlogiannis A, Velner Y. Quantitative interprocedural analysis.
Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 2015;50(1):539-551.
doi:10.1145/2676726.2676968
apa: 'Chatterjee, K., Pavlogiannis, A., & Velner, Y. (2015). Quantitative interprocedural
analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . Mumbai, India:
ACM. https://doi.org/10.1145/2676726.2676968'
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. “Quantitative
Interprocedural Analysis.” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT
. ACM, 2015. https://doi.org/10.1145/2676726.2676968.
ieee: K. Chatterjee, A. Pavlogiannis, and Y. Velner, “Quantitative interprocedural
analysis,” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT , vol. 50,
no. 1. ACM, pp. 539–551, 2015.
ista: Chatterjee K, Pavlogiannis A, Velner Y. 2015. Quantitative interprocedural
analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 50(1), 539–551.
mla: Chatterjee, Krishnendu, et al. “Quantitative Interprocedural Analysis.” Proceedings
of the 42nd Annual ACM SIGPLAN-SIGACT , vol. 50, no. 1, ACM, 2015, pp. 539–51,
doi:10.1145/2676726.2676968.
short: K. Chatterjee, A. Pavlogiannis, Y. Velner, Proceedings of the 42nd Annual
ACM SIGPLAN-SIGACT 50 (2015) 539–551.
conference:
end_date: 2015-01-17
location: Mumbai, India
name: 'SIGPLAN: Symposium on Principles of Programming Languages'
start_date: 2015-01-15
date_created: 2018-12-11T11:52:59Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-09-07T12:01:59Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/2676726.2676968
ec_funded: 1
intvolume: ' 50'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 539 - 551
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: 'Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT '
publication_identifier:
isbn:
- 978-1-4503-3300-9
publication_status: published
publisher: ACM
publist_id: '5563'
pubrep_id: '523'
quality_controlled: '1'
related_material:
record:
- id: '5445'
relation: earlier_version
status: public
- id: '821'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Quantitative interprocedural analysis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2015'
...
---
_id: '1607'
abstract:
- lang: eng
text: We consider the core algorithmic problems related to verification of systems
with respect to three classical quantitative properties, namely, the mean-payoff
property, the ratio property, and the minimum initial credit for energy property.
The algorithmic problem given a graph and a quantitative property asks to compute
the optimal value (the infimum value over all traces) from every node of the graph.
We consider graphs with constant treewidth, and it is well-known that the control-flow
graphs of most programs have constant treewidth. Let n denote the number of nodes
of a graph, m the number of edges (for constant treewidth graphs m=O(n)) and W
the largest absolute value of the weights. Our main theoretical results are as
follows. First, for constant treewidth graphs we present an algorithm that approximates
the mean-payoff value within a multiplicative factor of ϵ in time O(n⋅log(n/ϵ))
and linear space, as compared to the classical algorithms that require quadratic
time. Second, for the ratio property we present an algorithm that for constant
treewidth graphs works in time O(n⋅log(|a⋅b|))=O(n⋅log(n⋅W)), when the output
is ab, as compared to the previously best known algorithm with running time O(n2⋅log(n⋅W)).
Third, for the minimum initial credit problem we show that (i) for general graphs
the problem can be solved in O(n2⋅m) time and the associated decision problem
can be solved in O(n⋅m) time, improving the previous known O(n3⋅m⋅log(n⋅W)) and
O(n2⋅m) bounds, respectively; and (ii) for constant treewidth graphs we present
an algorithm that requires O(n⋅logn) time, improving the previous known O(n4⋅log(n⋅W))
bound. We have implemented some of our algorithms and show that they present a
significant speedup on standard benchmarks.
acknowledgement: 'The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant
(279307: Graph Games), and Microsoft faculty fellows award.'
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative
verification in constant treewidth graphs. In: Vol 9206. Springer; 2015:140-157.
doi:10.1007/978-3-319-21690-4_9'
apa: 'Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster algorithms
for quantitative verification in constant treewidth graphs (Vol. 9206, pp. 140–157).
Presented at the CAV: Computer Aided Verification, San Francisco, CA, USA: Springer.
https://doi.org/10.1007/978-3-319-21690-4_9'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
“Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs,”
9206:140–57. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_9.
ieee: 'K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for
quantitative verification in constant treewidth graphs,” presented at the CAV:
Computer Aided Verification, San Francisco, CA, USA, 2015, vol. 9206, pp. 140–157.'
ista: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for
quantitative verification in constant treewidth graphs. CAV: Computer Aided Verification,
LNCS, vol. 9206, 140–157.'
mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification
in Constant Treewidth Graphs. Vol. 9206, Springer, 2015, pp. 140–57, doi:10.1007/978-3-319-21690-4_9.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Springer, 2015, pp.
140–157.
conference:
end_date: 2015-07-24
location: San Francisco, CA, USA
name: 'CAV: Computer Aided Verification'
start_date: 2015-07-18
date_created: 2018-12-11T11:52:59Z
date_published: 2015-07-16T00:00:00Z
date_updated: 2023-09-07T12:01:59Z
day: '16'
department:
- _id: KrCh
doi: 10.1007/978-3-319-21690-4_9
ec_funded: 1
intvolume: ' 9206'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1504.07384
month: '07'
oa: 1
oa_version: Preprint
page: 140 - 157
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '5560'
quality_controlled: '1'
related_material:
record:
- id: '5430'
relation: earlier_version
status: public
- id: '5437'
relation: earlier_version
status: public
- id: '821'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Faster algorithms for quantitative verification in constant treewidth graphs
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9206
year: '2015'
...
---
_id: '1714'
abstract:
- lang: eng
text: 'We present a flexible framework for the automated competitive analysis of
on-line scheduling algorithms for firm-deadline real-time tasks based on multi-objective
graphs: Given a task set and an on-line scheduling algorithm specified as a labeled
transition system, along with some optional safety, liveness, and/or limit-average
constraints for the adversary, we automatically compute the competitive ratio
of the algorithm w.r.t. A clairvoyant scheduler. We demonstrate the flexibility
and power of our approach by comparing the competitive ratio of several on-line
algorithms, including Dover, that have been proposed in the past, for various
task sets. Our experimental results reveal that none of these algorithms is universally
optimal, in the sense that there are task sets where other schedulers provide
better performance. Our framework is hence a very useful design tool for selecting
optimal algorithms for a given application.'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Alexander
full_name: Kößler, Alexander
last_name: Kößler
- first_name: Ulrich
full_name: Schmid, Ulrich
last_name: Schmid
citation:
ama: 'Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. A framework for automated
competitive analysis of on-line scheduling of firm-deadline tasks. In: Real-Time
Systems Symposium. Vol 2015. IEEE; 2015:118-127. doi:10.1109/RTSS.2014.9'
apa: 'Chatterjee, K., Pavlogiannis, A., Kößler, A., & Schmid, U. (2015). A framework
for automated competitive analysis of on-line scheduling of firm-deadline tasks.
In Real-Time Systems Symposium (Vol. 2015, pp. 118–127). Rome, Italy: IEEE.
https://doi.org/10.1109/RTSS.2014.9'
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, Alexander Kößler, and Ulrich
Schmid. “A Framework for Automated Competitive Analysis of On-Line Scheduling
of Firm-Deadline Tasks.” In Real-Time Systems Symposium, 2015:118–27. IEEE,
2015. https://doi.org/10.1109/RTSS.2014.9.
ieee: K. Chatterjee, A. Pavlogiannis, A. Kößler, and U. Schmid, “A framework for
automated competitive analysis of on-line scheduling of firm-deadline tasks,”
in Real-Time Systems Symposium, Rome, Italy, 2015, vol. 2015, no. January,
pp. 118–127.
ista: 'Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. 2015. A framework for automated
competitive analysis of on-line scheduling of firm-deadline tasks. Real-Time Systems
Symposium. RTSS: Real-Time Systems Symposium vol. 2015, 118–127.'
mla: Chatterjee, Krishnendu, et al. “A Framework for Automated Competitive Analysis
of On-Line Scheduling of Firm-Deadline Tasks.” Real-Time Systems Symposium,
vol. 2015, no. January, IEEE, 2015, pp. 118–27, doi:10.1109/RTSS.2014.9.
short: K. Chatterjee, A. Pavlogiannis, A. Kößler, U. Schmid, in:, Real-Time Systems
Symposium, IEEE, 2015, pp. 118–127.
conference:
end_date: 2014-12-05
location: Rome, Italy
name: 'RTSS: Real-Time Systems Symposium'
start_date: 2014-12-02
date_created: 2018-12-11T11:53:37Z
date_published: 2015-01-15T00:00:00Z
date_updated: 2023-09-07T12:01:59Z
day: '15'
department:
- _id: KrCh
doi: 10.1109/RTSS.2014.9
intvolume: ' 2015'
issue: January
language:
- iso: eng
month: '01'
oa_version: None
page: 118 - 127
publication: Real-Time Systems Symposium
publication_status: published
publisher: IEEE
publist_id: '5417'
quality_controlled: '1'
related_material:
record:
- id: '5423'
relation: earlier_version
status: public
- id: '821'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: A framework for automated competitive analysis of on-line scheduling of firm-deadline
tasks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015
year: '2015'
...
---
_id: '1633'
abstract:
- lang: eng
text: "We present a method for simulating brittle fracture under the assumptions
of quasi-static linear elastic fracture mechanics (LEFM). Using the boundary element
method (BEM) and Lagrangian crack-fronts, we produce highly detailed fracture
surfaces. The computational cost of the BEM is alleviated by using a low-resolution
mesh and interpolating the resulting stress intensity factors when propagating
the high-resolution crack-front.\r\n\r\nOur system produces physics-based fracture
surfaces with high spatial and temporal resolution, taking spatial variation of
material toughness and/or strength into account. It also allows for crack initiation
to be handled separately from crack propagation, which is not only more reasonable
from a physics perspective, but can also be used to control the simulation.\r\n\r\nSeparating
the resolution of the crack-front from the resolution of the computational mesh
increases the efficiency and therefore the amount of visual detail on the resulting
fracture surfaces. The BEM also allows us to re-use previously computed blocks
of the system matrix."
article_number: '151'
author:
- first_name: David
full_name: Hahn, David
id: 357A6A66-F248-11E8-B48F-1D18A9856A87
last_name: Hahn
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Hahn D, Wojtan C. High-resolution brittle fracture simulation with boundary
elements. In: Vol 34. ACM; 2015. doi:10.1145/2766896'
apa: 'Hahn, D., & Wojtan, C. (2015). High-resolution brittle fracture simulation
with boundary elements (Vol. 34). Presented at the SIGGRAPH: Special Interest
Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United
States: ACM. https://doi.org/10.1145/2766896'
chicago: Hahn, David, and Chris Wojtan. “High-Resolution Brittle Fracture Simulation
with Boundary Elements,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766896.
ieee: 'D. Hahn and C. Wojtan, “High-resolution brittle fracture simulation with
boundary elements,” presented at the SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol.
34, no. 4.'
ista: 'Hahn D, Wojtan C. 2015. High-resolution brittle fracture simulation with
boundary elements. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques vol. 34, 151.'
mla: Hahn, David, and Chris Wojtan. High-Resolution Brittle Fracture Simulation
with Boundary Elements. Vol. 34, no. 4, 151, ACM, 2015, doi:10.1145/2766896.
short: D. Hahn, C. Wojtan, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:09Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2023-09-07T12:02:56Z
day: '27'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2766896
ec_funded: 1
file:
- access_level: open_access
checksum: 955aee971983f6b6152bcc1c9b4a7c20
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:13Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5131'
file_name: IST-2016-609-v1+1_FractureBEM.pdf
file_size: 20154270
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication_status: published
publisher: ACM
publist_id: '5522'
pubrep_id: '609'
quality_controlled: '1'
related_material:
record:
- id: '839'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: High-resolution brittle fracture simulation with boundary elements
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1537'
abstract:
- lang: eng
text: 3D amoeboid cell migration is central to many developmental and disease-related
processes such as cancer metastasis. Here, we identify a unique prototypic amoeboid
cell migration mode in early zebrafish embryos, termed stable-bleb migration.
Stable-bleb cells display an invariant polarized balloon-like shape with exceptional
migration speed and persistence. Progenitor cells can be reversibly transformed
into stable-bleb cells irrespective of their primary fate and motile characteristics
by increasing myosin II activity through biochemical or mechanical stimuli. Using
a combination of theory and experiments, we show that, in stable-bleb cells, cortical
contractility fluctuations trigger a stochastic switch into amoeboid motility,
and a positive feedback between cortical flows and gradients in contractility
maintains stable-bleb cell polarization. We further show that rearward cortical
flows drive stable-bleb cell migration in various adhesive and non-adhesive environments,
unraveling a highly versatile amoeboid migration phenotype.
acknowledged_ssus:
- _id: SSU
acknowledgement: 'We would like to thank R. Hausschild and E. Papusheva for technical
assistance and the service facilities at the IST Austria for continuous support.
The caRhoA plasmid was a kind gift of T. Kudoh and A. Takesono. We thank M. Piel
and E. Paluch for exchanging unpublished data. '
author:
- 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: Andrew
full_name: Callan Jones, Andrew
last_name: Callan Jones
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Hitoshi
full_name: Morita, Hitoshi
id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87
last_name: Morita
- first_name: Keisuke
full_name: Sako, Keisuke
id: 3BED66BE-F248-11E8-B48F-1D18A9856A87
last_name: Sako
orcid: 0000-0002-6453-8075
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Monika
full_name: Ritsch Marte, Monika
last_name: Ritsch Marte
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Raphaël
full_name: Voituriez, Raphaël
last_name: Voituriez
- 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
citation:
ama: Ruprecht V, Wieser S, Callan Jones A, et al. Cortical contractility triggers
a stochastic switch to fast amoeboid cell motility. Cell. 2015;160(4):673-685.
doi:10.1016/j.cell.2015.01.008
apa: Ruprecht, V., Wieser, S., Callan Jones, A., Smutny, M., Morita, H., Sako, K.,
… Heisenberg, C.-P. J. (2015). Cortical contractility triggers a stochastic switch
to fast amoeboid cell motility. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.01.008
chicago: Ruprecht, Verena, Stefan Wieser, Andrew Callan Jones, Michael Smutny, Hitoshi
Morita, Keisuke Sako, Vanessa Barone, et al. “Cortical Contractility Triggers
a Stochastic Switch to Fast Amoeboid Cell Motility.” Cell. Cell Press,
2015. https://doi.org/10.1016/j.cell.2015.01.008.
ieee: V. Ruprecht et al., “Cortical contractility triggers a stochastic switch
to fast amoeboid cell motility,” Cell, vol. 160, no. 4. Cell Press, pp.
673–685, 2015.
ista: Ruprecht V, Wieser S, Callan Jones A, Smutny M, Morita H, Sako K, Barone V,
Ritsch Marte M, Sixt MK, Voituriez R, Heisenberg C-PJ. 2015. Cortical contractility
triggers a stochastic switch to fast amoeboid cell motility. Cell. 160(4), 673–685.
mla: Ruprecht, Verena, et al. “Cortical Contractility Triggers a Stochastic Switch
to Fast Amoeboid Cell Motility.” Cell, vol. 160, no. 4, Cell Press, 2015,
pp. 673–85, doi:10.1016/j.cell.2015.01.008.
short: V. Ruprecht, S. Wieser, A. Callan Jones, M. Smutny, H. Morita, K. Sako, V.
Barone, M. Ritsch Marte, M.K. Sixt, R. Voituriez, C.-P.J. Heisenberg, Cell 160
(2015) 673–685.
date_created: 2018-12-11T11:52:35Z
date_published: 2015-02-12T00:00:00Z
date_updated: 2023-09-07T12:05:08Z
day: '12'
ddc:
- '570'
department:
- _id: CaHe
- _id: MiSi
doi: 10.1016/j.cell.2015.01.008
file:
- access_level: open_access
checksum: 228d3edf40627d897b3875088a0ac51f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:21Z
date_updated: 2020-07-14T12:45:01Z
file_id: '5003'
file_name: IST-2016-484-v1+1_1-s2.0-S0092867415000094-main.pdf
file_size: 4362653
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 160'
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 673 - 685
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
- _id: 2527D5CC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 812-B12
name: Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '5634'
pubrep_id: '484'
quality_controlled: '1'
related_material:
record:
- id: '961'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Cortical contractility triggers a stochastic switch to fast amoeboid cell motility
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 160
year: '2015'
...
---
_id: '1591'
abstract:
- lang: eng
text: Auxin participates in a multitude of developmental processes, as well as responses
to environmental cues. Compared with other plant hormones, auxin exhibits a unique
property, as it undergoes directional, cell-to-cell transport facilitated by plasma
membrane-localized transport proteins. Among them, a prominent role has been ascribed
to the PIN family of auxin efflux facilitators. PIN proteins direct polar auxin
transport on account of their asymmetric subcellular localizations. In this review,
we provide an overview of the multiple developmental roles of PIN proteins, including
the atypical endoplasmic reticulum-localized members of the family, and look at
the family from an evolutionary perspective. Next, we cover the cell biological
and molecular aspects of PIN function, in particular the establishment of their
polar subcellular localization. Hormonal and environmental inputs into the regulation
of PIN action are summarized as well.
author:
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Adamowski M, Friml J. PIN-dependent auxin transport: Action, regulation, and
evolution. Plant Cell. 2015;27(1):20-32. doi:10.1105/tpc.114.134874'
apa: 'Adamowski, M., & Friml, J. (2015). PIN-dependent auxin transport: Action,
regulation, and evolution. Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.114.134874'
chicago: 'Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action,
Regulation, and Evolution.” Plant Cell. American Society of Plant Biologists,
2015. https://doi.org/10.1105/tpc.114.134874.'
ieee: 'M. Adamowski and J. Friml, “PIN-dependent auxin transport: Action, regulation,
and evolution,” Plant Cell, vol. 27, no. 1. American Society of Plant Biologists,
pp. 20–32, 2015.'
ista: 'Adamowski M, Friml J. 2015. PIN-dependent auxin transport: Action, regulation,
and evolution. Plant Cell. 27(1), 20–32.'
mla: 'Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action,
Regulation, and Evolution.” Plant Cell, vol. 27, no. 1, American Society
of Plant Biologists, 2015, pp. 20–32, doi:10.1105/tpc.114.134874.'
short: M. Adamowski, J. Friml, Plant Cell 27 (2015) 20–32.
date_created: 2018-12-11T11:52:54Z
date_published: 2015-01-20T00:00:00Z
date_updated: 2023-09-07T12:06:09Z
day: '20'
department:
- _id: JiFr
doi: 10.1105/tpc.114.134874
external_id:
pmid:
- '25604445'
intvolume: ' 27'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330589/
month: '01'
oa: 1
oa_version: Submitted Version
page: 20 - 32
pmid: 1
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '5580'
quality_controlled: '1'
related_material:
record:
- id: '938'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: 'PIN-dependent auxin transport: Action, regulation, and evolution'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2015'
...
---
_id: '1677'
abstract:
- lang: eng
text: We consider real symmetric and complex Hermitian random matrices with the
additional symmetry hxy = hN-y,N-x. The matrix elements are independent (up to
the fourfold symmetry) and not necessarily identically distributed. This ensemble
naturally arises as the Fourier transform of a Gaussian orthogonal ensemble. Italso
occurs as the flip matrix model - an approximation of the two-dimensional Anderson
model at small disorder. We show that the density of states converges to the Wigner
semicircle law despite the new symmetry type. We also prove the local version
of the semicircle law on the optimal scale.
article_number: '103301'
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
citation:
ama: Alt J. The local semicircle law for random matrices with a fourfold symmetry.
Journal of Mathematical Physics. 2015;56(10). doi:10.1063/1.4932606
apa: Alt, J. (2015). The local semicircle law for random matrices with a fourfold
symmetry. Journal of Mathematical Physics. American Institute of Physics.
https://doi.org/10.1063/1.4932606
chicago: Alt, Johannes. “The Local Semicircle Law for Random Matrices with a Fourfold
Symmetry.” Journal of Mathematical Physics. American Institute of Physics,
2015. https://doi.org/10.1063/1.4932606.
ieee: J. Alt, “The local semicircle law for random matrices with a fourfold symmetry,”
Journal of Mathematical Physics, vol. 56, no. 10. American Institute of
Physics, 2015.
ista: Alt J. 2015. The local semicircle law for random matrices with a fourfold
symmetry. Journal of Mathematical Physics. 56(10), 103301.
mla: Alt, Johannes. “The Local Semicircle Law for Random Matrices with a Fourfold
Symmetry.” Journal of Mathematical Physics, vol. 56, no. 10, 103301, American
Institute of Physics, 2015, doi:10.1063/1.4932606.
short: J. Alt, Journal of Mathematical Physics 56 (2015).
date_created: 2018-12-11T11:53:25Z
date_published: 2015-10-09T00:00:00Z
date_updated: 2023-09-07T12:38:08Z
day: '09'
department:
- _id: LaEr
doi: 10.1063/1.4932606
ec_funded: 1
intvolume: ' 56'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1506.04683
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Journal of Mathematical Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5472'
quality_controlled: '1'
related_material:
record:
- id: '149'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: The local semicircle law for random matrices with a fourfold symmetry
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 56
year: '2015'
...
---
_id: '1678'
abstract:
- lang: eng
text: High-throughput live-cell screens are intricate elements of systems biology
studies and drug discovery pipelines. Here, we demonstrate an optogenetics-assisted
method that avoids the need for chemical activators and reporters, reduces the
number of operational steps and increases information content in a cell-based
small-molecule screen against human protein kinases, including an orphan receptor
tyrosine kinase. This blueprint for all-optical screening can be adapted to many
drug targets and cellular processes.
acknowledgement: 'This work was supported by grants from the European Union Seventh
Framework Programme (CIG-303564 to H.J. and ERC-StG-311166 to S.M.B.N.), the Human
Frontier Science Program (RGY0084_2012 to H.J.) and the Herzfelder Foundation (to
M.G.). A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by the graduate
program MolecularDrugTargets (Austrian Science Fund (FWF): W 1232) and a FemTech
fellowship (3580812 Austrian Research Promotion Agency).'
author:
- first_name: Álvaro
full_name: Inglés Prieto, Álvaro
id: 2A9DB292-F248-11E8-B48F-1D18A9856A87
last_name: Inglés Prieto
orcid: 0000-0002-5409-8571
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
- first_name: Markus
full_name: Muellner, Markus
last_name: Muellner
- first_name: Matthias
full_name: Nowak, Matthias
id: 30845DAA-F248-11E8-B48F-1D18A9856A87
last_name: Nowak
- first_name: Sebastian
full_name: Nijman, Sebastian
last_name: Nijman
- first_name: Michael
full_name: Grusch, Michael
last_name: Grusch
- 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: Inglés Prieto Á, Gschaider-Reichhart E, Muellner M, et al. Light-assisted small-molecule
screening against protein kinases. Nature Chemical Biology. 2015;11(12):952-954.
doi:10.1038/nchembio.1933
apa: Inglés Prieto, Á., Gschaider-Reichhart, E., Muellner, M., Nowak, M., Nijman,
S., Grusch, M., & Janovjak, H. L. (2015). Light-assisted small-molecule screening
against protein kinases. Nature Chemical Biology. Nature Publishing Group.
https://doi.org/10.1038/nchembio.1933
chicago: Inglés Prieto, Álvaro, Eva Gschaider-Reichhart, Markus Muellner, Matthias
Nowak, Sebastian Nijman, Michael Grusch, and Harald L Janovjak. “Light-Assisted
Small-Molecule Screening against Protein Kinases.” Nature Chemical Biology.
Nature Publishing Group, 2015. https://doi.org/10.1038/nchembio.1933.
ieee: Á. Inglés Prieto et al., “Light-assisted small-molecule screening against
protein kinases,” Nature Chemical Biology, vol. 11, no. 12. Nature Publishing
Group, pp. 952–954, 2015.
ista: Inglés Prieto Á, Gschaider-Reichhart E, Muellner M, Nowak M, Nijman S, Grusch
M, Janovjak HL. 2015. Light-assisted small-molecule screening against protein
kinases. Nature Chemical Biology. 11(12), 952–954.
mla: Inglés Prieto, Álvaro, et al. “Light-Assisted Small-Molecule Screening against
Protein Kinases.” Nature Chemical Biology, vol. 11, no. 12, Nature Publishing
Group, 2015, pp. 952–54, doi:10.1038/nchembio.1933.
short: Á. Inglés Prieto, E. Gschaider-Reichhart, M. Muellner, M. Nowak, S. Nijman,
M. Grusch, H.L. Janovjak, Nature Chemical Biology 11 (2015) 952–954.
date_created: 2018-12-11T11:53:25Z
date_published: 2015-10-12T00:00:00Z
date_updated: 2023-09-07T12:49:09Z
day: '12'
ddc:
- '571'
department:
- _id: HaJa
- _id: LifeSc
doi: 10.1038/nchembio.1933
ec_funded: 1
file:
- access_level: open_access
checksum: e9fb251dfcb7cd209b83f17867e61321
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:51Z
date_updated: 2020-07-14T12:45:12Z
file_id: '4842'
file_name: IST-2017-837-v1+1_ingles-prieto.pdf
file_size: 1308364
relation: main_file
file_date_updated: 2020-07-14T12:45:12Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '12'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 952 - 954
project:
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors (HFSP Young Investigator)
- _id: 255A6082-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '5471'
pubrep_id: '837'
quality_controlled: '1'
related_material:
record:
- id: '418'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Light-assisted small-molecule screening against protein kinases
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '1576'
abstract:
- lang: eng
text: 'Gene expression is controlled primarily by interactions between transcription
factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured
well by thermodynamic models of regulation. These models, however, neglect regulatory
crosstalk: the possibility that noncognate TFs could initiate transcription, with
potentially disastrous effects for the cell. Here, we estimate the importance
of crosstalk, suggest that its avoidance strongly constrains equilibrium models
of TF binding, and propose an alternative nonequilibrium scheme that implements
kinetic proofreading to suppress erroneous initiation. This proposal is consistent
with the observed covalent modifications of the transcriptional apparatus and
predicts increased noise in gene expression as a trade-off for improved specificity.
Using information theory, we quantify this trade-off to find when optimal proofreading
architectures are favored over their equilibrium counterparts. Such architectures
exhibit significant super-Poisson noise at low expression in steady state.'
article_number: '248101'
author:
- first_name: Sarah A
full_name: Cepeda Humerez, Sarah A
id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
last_name: Cepeda Humerez
- first_name: Georg
full_name: Rieckh, Georg
id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
last_name: Rieckh
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Cepeda Humerez SA, Rieckh G, Tkačik G. Stochastic proofreading mechanism alleviates
crosstalk in transcriptional regulation. Physical Review Letters. 2015;115(24).
doi:10.1103/PhysRevLett.115.248101
apa: Cepeda Humerez, S. A., Rieckh, G., & Tkačik, G. (2015). Stochastic proofreading
mechanism alleviates crosstalk in transcriptional regulation. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.115.248101
chicago: Cepeda Humerez, Sarah A, Georg Rieckh, and Gašper Tkačik. “Stochastic Proofreading
Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review
Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.115.248101.
ieee: S. A. Cepeda Humerez, G. Rieckh, and G. Tkačik, “Stochastic proofreading mechanism
alleviates crosstalk in transcriptional regulation,” Physical Review Letters,
vol. 115, no. 24. American Physical Society, 2015.
ista: Cepeda Humerez SA, Rieckh G, Tkačik G. 2015. Stochastic proofreading mechanism
alleviates crosstalk in transcriptional regulation. Physical Review Letters. 115(24),
248101.
mla: Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates
Crosstalk in Transcriptional Regulation.” Physical Review Letters, vol.
115, no. 24, 248101, American Physical Society, 2015, doi:10.1103/PhysRevLett.115.248101.
short: S.A. Cepeda Humerez, G. Rieckh, G. Tkačik, Physical Review Letters 115 (2015).
date_created: 2018-12-11T11:52:49Z
date_published: 2015-12-08T00:00:00Z
date_updated: 2023-09-07T12:55:21Z
day: '08'
department:
- _id: GaTk
doi: 10.1103/PhysRevLett.115.248101
ec_funded: 1
intvolume: ' 115'
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1504.05716
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5595'
quality_controlled: '1'
related_material:
record:
- id: '6473'
relation: part_of_dissertation
status: public
scopus_import: 1
status: public
title: Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2015'
...
---
_id: '8183'
abstract:
- lang: eng
text: "We study conditions under which a finite simplicial complex $K$ can be mapped
to $\\mathbb R^d$ without higher-multiplicity intersections. An almost $r$-embedding
is a map $f: K\\to \\mathbb R^d$ such that the images of any $r$\r\npairwise disjoint
simplices of $K$ do not have a common point. We show that if $r$ is not a prime
power and $d\\geq 2r+1$, then there is a counterexample to the topological Tverberg
conjecture, i.e., there is an almost $r$-embedding of\r\nthe $(d+1)(r-1)$-simplex
in $\\mathbb R^d$. This improves on previous constructions of counterexamples
(for $d\\geq 3r$) based on a series of papers by M. \\\"Ozaydin, M. Gromov, P.
Blagojevi\\'c, F. Frick, G. Ziegler, and the second and fourth present authors.
The counterexamples are obtained by proving the following algebraic criterion
in codimension 2: If $r\\ge3$ and if $K$ is a finite $2(r-1)$-complex then there
exists an almost $r$-embedding $K\\to \\mathbb R^{2r}$ if and only if there exists
a general position PL map $f:K\\to \\mathbb R^{2r}$ such that the algebraic intersection
number of the $f$-images of any $r$ pairwise disjoint simplices of $K$ is zero.
This result can be restated in terms of cohomological obstructions or equivariant
maps, and extends an analogous codimension 3 criterion by the second and fourth
authors. As another application we classify ornaments $f:S^3 \\sqcup S^3\\sqcup
S^3\\to \\mathbb R^5$ up to ornament\r\nconcordance. It follows from work of M.
Freedman, V. Krushkal and P. Teichner that the analogous criterion for $r=2$ is
false. We prove a lemma on singular higher-dimensional Borromean rings, yielding
an elementary proof of the counterexample."
acknowledgement: We would like to thank A. Klyachko, V. Krushkal, S. Melikhov, M.
Tancer, P. Teichner and anonymous referees for helpful discussions.
article_number: '1511.03501'
article_processing_charge: No
author:
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
- first_name: A.
full_name: Skopenkov, A.
last_name: Skopenkov
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity
intersections, III. Codimension 2. arXiv.
apa: Avvakumov, S., Mabillard, I., Skopenkov, A., & Wagner, U. (n.d.). Eliminating
higher-multiplicity intersections, III. Codimension 2. arXiv.
chicago: Avvakumov, Sergey, Isaac Mabillard, A. Skopenkov, and Uli Wagner. “Eliminating
Higher-Multiplicity Intersections, III. Codimension 2.” ArXiv, n.d.
ieee: S. Avvakumov, I. Mabillard, A. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity
intersections, III. Codimension 2,” arXiv. .
ista: Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity
intersections, III. Codimension 2. arXiv, 1511.03501.
mla: Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections, III.
Codimension 2.” ArXiv, 1511.03501.
short: S. Avvakumov, I. Mabillard, A. Skopenkov, U. Wagner, ArXiv (n.d.).
date_created: 2020-07-30T10:45:19Z
date_published: 2015-11-15T00:00:00Z
date_updated: 2023-09-07T13:12:17Z
day: '15'
department:
- _id: UlWa
external_id:
arxiv:
- '1511.03501'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.03501
month: '11'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '9308'
relation: later_version
status: public
- id: '10220'
relation: later_version
status: public
- id: '8156'
relation: dissertation_contains
status: public
status: public
title: Eliminating higher-multiplicity intersections, III. Codimension 2
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5441'
abstract:
- lang: eng
text: We study algorithmic questions for concurrent systems where the transitions
are labeled from a complete, closed semiring, and path properties are algebraic
with semiring operations. The algebraic path properties can model dataflow analysis
problems, the shortest path problem, and many other natural problems that arise
in program analysis. We consider that each component of the concurrent system
is a graph with constant treewidth, a property satisfied by the controlflow graphs
of most programs. We allow for multiple possible queries, which arise naturally
in demand driven dataflow analysis. The study of multiple queries allows us to
consider the tradeoff between the resource usage of the one-time preprocessing
and for each individual query. The traditional approach constructs the product
graph of all components and applies the best-known graph algorithm on the product.
In this approach, even the answer to a single query requires the transitive closure
(i.e., the results of all possible queries), which provides no room for tradeoff
between preprocessing and query time. Our main contributions are algorithms that
significantly improve the worst-case running time of the traditional approach,
and provide various tradeoffs depending on the number of queries. For example,
in a concurrent system of two components, the traditional approach requires hexic
time in the worst case for answering one query as well as computing the transitive
closure, whereas we show that with one-time preprocessing in almost cubic time,
each subsequent query can be answered in at most linear time, and even the transitive
closure can be computed in almost quartic time. Furthermore, we establish conditional
optimality results showing that the worst-case running time of our algorithms
cannot be improved without achieving major breakthroughs in graph algorithms (i.e.,
improving the worst-case bound for the shortest path problem in general graphs).
Preliminary experimental results show that our algorithms perform favorably on
several benchmarks.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Amir
full_name: Goharshady, Amir
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. Algorithms
for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components.
IST Austria; 2015. doi:10.15479/AT:IST-2015-340-v1-1
apa: Chatterjee, K., Ibsen-Jensen, R., Goharshady, A. K., & Pavlogiannis, A.
(2015). Algorithms for algebraic path properties in concurrent systems of constant
treewidth components. IST Austria. https://doi.org/10.15479/AT:IST-2015-340-v1-1
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Amir Kafshdar Goharshady,
and Andreas Pavlogiannis. Algorithms for Algebraic Path Properties in Concurrent
Systems of Constant Treewidth Components. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-340-v1-1.
ieee: K. Chatterjee, R. Ibsen-Jensen, A. K. Goharshady, and A. Pavlogiannis, Algorithms
for algebraic path properties in concurrent systems of constant treewidth components.
IST Austria, 2015.
ista: Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. 2015. Algorithms
for algebraic path properties in concurrent systems of constant treewidth components,
IST Austria, 24p.
mla: Chatterjee, Krishnendu, et al. Algorithms for Algebraic Path Properties
in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015,
doi:10.15479/AT:IST-2015-340-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, A.K. Goharshady, A. Pavlogiannis, Algorithms
for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components,
IST Austria, 2015.
date_created: 2018-12-12T11:39:21Z
date_published: 2015-07-11T00:00:00Z
date_updated: 2023-09-19T14:36:19Z
day: '11'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-340-v1-1
file:
- access_level: open_access
checksum: df383dc62c94d7b2ea639aba088a76c6
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:09Z
date_updated: 2020-07-14T12:46:56Z
file_id: '5531'
file_name: IST-2015-340-v1+1_main.pdf
file_size: 861396
relation: main_file
file_date_updated: 2020-07-14T12:46:56Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '24'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '340'
related_material:
record:
- id: '1437'
relation: later_version
status: public
- id: '5442'
relation: earlier_version
status: public
- id: '6009'
relation: later_version
status: public
status: public
title: Algorithms for algebraic path properties in concurrent systems of constant
treewidth components
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5442'
abstract:
- lang: eng
text: "We study algorithmic questions for concurrent systems where the transitions
are labeled from a complete, closed semiring, and path properties are algebraic
with semiring operations. The algebraic path properties can model dataflow analysis
problems, the shortest path problem, and many other natural properties that arise
in program analysis.\r\nWe consider that each component of the concurrent system
is a graph with constant treewidth, and it is known that the controlflow graphs
of most programs have constant treewidth. We allow for multiple possible queries,
which arise naturally in demand driven dataflow analysis problems (e.g., alias
analysis). The study of multiple queries allows us to consider the tradeoff between
the resource usage of the \\emph{one-time} preprocessing and for \\emph{each individual}
query. The traditional approaches construct the product graph of all components
and apply the best-known graph algorithm on the product. In the traditional approach,
even the answer to a single query requires the transitive closure computation
(i.e., the results of all possible queries), which provides no room for tradeoff
between preprocessing and query time.\r\n\r\nOur main contributions are algorithms
that significantly improve the worst-case running time of the traditional approach,
and provide various tradeoffs depending on the number of queries. For example,
in a concurrent system of two components, the traditional approach requires hexic
time in the worst case for answering one query as well as computing the transitive
closure, whereas we show that with one-time preprocessing in almost cubic time,
\r\neach subsequent query can be answered in at most linear time, and even the
transitive closure can be computed in almost quartic time. Furthermore, we establish
conditional optimality results that show that the worst-case running times of
our algorithms cannot be improved without achieving major breakthroughs in graph
algorithms (such as improving \r\nthe worst-case bounds for the shortest path
problem in general graphs whose current best-known bound has not been improved
in five decades). Finally, we provide a prototype implementation of our algorithms
which significantly outperforms the existing algorithmic methods on several benchmarks."
alternative_title:
- IST Austria Technical Report
author:
- first_name: '1'
full_name: Anonymous, 1
last_name: Anonymous
- first_name: '2'
full_name: Anonymous, 2
last_name: Anonymous
- first_name: '3'
full_name: Anonymous, 3
last_name: Anonymous
- first_name: '4'
full_name: Anonymous, 4
last_name: Anonymous
citation:
ama: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. Algorithms for Algebraic
Path Properties in Concurrent Systems of Constant Treewidth Components. IST
Austria; 2015.
apa: Anonymous, 1, Anonymous, 2, Anonymous, 3, & Anonymous, 4. (2015). Algorithms
for algebraic path properties in concurrent systems of constant treewidth components.
IST Austria.
chicago: Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. Algorithms
for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components.
IST Austria, 2015.
ieee: 1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, Algorithms for
algebraic path properties in concurrent systems of constant treewidth components.
IST Austria, 2015.
ista: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2015. Algorithms for algebraic
path properties in concurrent systems of constant treewidth components, IST Austria,
22p.
mla: Anonymous, 1, et al. Algorithms for Algebraic Path Properties in Concurrent
Systems of Constant Treewidth Components. IST Austria, 2015.
short: 1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Algorithms for Algebraic
Path Properties in Concurrent Systems of Constant Treewidth Components, IST Austria,
2015.
date_created: 2018-12-12T11:39:21Z
date_published: 2015-07-14T00:00:00Z
date_updated: 2023-09-19T14:36:19Z
day: '14'
ddc:
- '000'
file:
- access_level: open_access
checksum: 98fd936102f3e057fc321ef6d316001d
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:37Z
date_updated: 2020-07-14T12:46:57Z
file_id: '5498'
file_name: IST-2015-343-v2+1_main.pdf
file_size: 658747
relation: main_file
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checksum: b31d09b1241b59c75e1f42dadf09d258
content_type: text/plain
creator: dernst
date_created: 2019-04-16T12:36:08Z
date_updated: 2020-07-14T12:46:57Z
file_id: '6316'
file_name: IST-2015-343-v2+2_anonymous.txt
file_size: 139
relation: main_file
file_date_updated: 2020-07-14T12:46:57Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '22'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '344'
related_material:
record:
- id: '1437'
relation: later_version
status: public
- id: '5441'
relation: later_version
status: public
- id: '6009'
relation: later_version
status: public
scopus_import: 1
status: public
title: Algorithms for algebraic path properties in concurrent systems of constant
treewidth components
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1689'
abstract:
- lang: eng
text: We consider the problem of computing the set of initial states of a dynamical
system such that there exists a control strategy to ensure that the trajectories
satisfy a temporal logic specification with probability 1 (almost-surely). We
focus on discrete-time, stochastic linear dynamics and specifications given as
formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over
linear predicates in the states of the system. We propose a solution based on
iterative abstraction-refinement, and turn-based 2-player probabilistic games.
While the theoretical guarantee of our algorithm after any finite number of iterations
is only a partial solution, we show that if our algorithm terminates, then the
result is the set of satisfying initial states. Moreover, for any (partial) solution
our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction
of the temporal logic specification. We demonstrate our approach on an illustrative
case study.
author:
- first_name: Mária
full_name: Svoreňová, Mária
last_name: Svoreňová
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ivana
full_name: Cěrná, Ivana
last_name: Cěrná
- first_name: Cǎlin
full_name: Belta, Cǎlin
last_name: Belta
citation:
ama: 'Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal
logic control for stochastic linear systems using abstraction refinement of probabilistic
games. In: Proceedings of the 18th International Conference on Hybrid Systems:
Computation and Control. ACM; 2015:259-268. doi:10.1145/2728606.2728608'
apa: 'Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., &
Belta, C. (2015). Temporal logic control for stochastic linear systems using abstraction
refinement of probabilistic games. In Proceedings of the 18th International
Conference on Hybrid Systems: Computation and Control (pp. 259–268). Seattle,
WA, United States: ACM. https://doi.org/10.1145/2728606.2728608'
chicago: 'Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee,
Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems
Using Abstraction Refinement of Probabilistic Games.” In Proceedings of the
18th International Conference on Hybrid Systems: Computation and Control,
259–68. ACM, 2015. https://doi.org/10.1145/2728606.2728608.'
ieee: 'M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta,
“Temporal logic control for stochastic linear systems using abstraction refinement
of probabilistic games,” in Proceedings of the 18th International Conference
on Hybrid Systems: Computation and Control, Seattle, WA, United States, 2015,
pp. 259–268.'
ista: 'Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2015.
Temporal logic control for stochastic linear systems using abstraction refinement
of probabilistic games. Proceedings of the 18th International Conference on Hybrid
Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control,
259–268.'
mla: 'Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems
Using Abstraction Refinement of Probabilistic Games.” Proceedings of the 18th
International Conference on Hybrid Systems: Computation and Control, ACM,
2015, pp. 259–68, doi:10.1145/2728606.2728608.'
short: 'M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta,
in:, Proceedings of the 18th International Conference on Hybrid Systems: Computation
and Control, ACM, 2015, pp. 259–268.'
conference:
end_date: 2015-04-16
location: Seattle, WA, United States
name: 'HSCC: Hybrid Systems - Computation and Control'
start_date: 2015-04-14
date_created: 2018-12-11T11:53:29Z
date_published: 2015-04-14T00:00:00Z
date_updated: 2023-09-20T09:43:09Z
day: '14'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1145/2728606.2728608
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.5387
month: '04'
oa: 1
oa_version: Preprint
page: 259 - 268
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: 'Proceedings of the 18th International Conference on Hybrid Systems:
Computation and Control'
publication_status: published
publisher: ACM
publist_id: '5456'
related_material:
record:
- id: '1407'
relation: later_version
status: public
scopus_import: 1
status: public
title: Temporal logic control for stochastic linear systems using abstraction refinement
of probabilistic games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1729'
abstract:
- lang: eng
text: We present a computer-aided programming approach to concurrency. The approach
allows programmers to program assuming a friendly, non-preemptive scheduler, and
our synthesis procedure inserts synchronization to ensure that the final program
works even with a preemptive scheduler. The correctness specification is implicit,
inferred from the non-preemptive behavior. Let us consider sequences of calls
that the program makes to an external interface. The specification requires that
any such sequence produced under a preemptive scheduler should be included in
the set of such sequences produced under a non-preemptive scheduler. The solution
is based on a finitary abstraction, an algorithm for bounded language inclusion
modulo an independence relation, and rules for inserting synchronization. We apply
the approach to device-driver programming, where the driver threads call the software
interface of the device and the API provided by the operating system. Our experiments
demonstrate that our synthesis method is precise and efficient, and, since it
does not require explicit specifications, is more practical than the conventional
approach based on user-provided assertions.
alternative_title:
- LNCS
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Edmund
full_name: Clarke, Edmund
last_name: Clarke
- 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: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Leonid
full_name: Ryzhyk, Leonid
last_name: Ryzhyk
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling
using synchronization synthesis. 2015;9207:180-197. doi:10.1007/978-3-319-21668-3_11
apa: 'Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta,
R., & Tarrach, T. (2015). From non-preemptive to preemptive scheduling using
synchronization synthesis. Presented at the CAV: Computer Aided Verification,
San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21668-3_11'
chicago: Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid
Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive
Scheduling Using Synchronization Synthesis.” Lecture Notes in Computer Science.
Springer, 2015. https://doi.org/10.1007/978-3-319-21668-3_11.
ieee: P. Cerny et al., “From non-preemptive to preemptive scheduling using
synchronization synthesis,” vol. 9207. Springer, pp. 180–197, 2015.
ista: Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach
T. 2015. From non-preemptive to preemptive scheduling using synchronization synthesis.
9207, 180–197.
mla: Cerny, Pavol, et al. From Non-Preemptive to Preemptive Scheduling Using
Synchronization Synthesis. Vol. 9207, Springer, 2015, pp. 180–97, doi:10.1007/978-3-319-21668-3_11.
short: P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta,
T. Tarrach, 9207 (2015) 180–197.
conference:
end_date: 2015-07-24
location: San Francisco, CA, United States
name: 'CAV: Computer Aided Verification'
start_date: 2015-07-18
date_created: 2018-12-11T11:53:42Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-09-20T11:13:50Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-21668-3_11
ec_funded: 1
file:
- access_level: local
checksum: 6ff58ac220e2f20cb001ba35d4924495
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:53Z
date_updated: 2020-07-14T12:45:13Z
file_id: '4715'
file_name: IST-2015-336-v1+1_long_version.pdf
file_size: 481922
relation: main_file
file_date_updated: 2020-07-14T12:45:13Z
has_accepted_license: '1'
intvolume: ' 9207'
language:
- iso: eng
month: '07'
oa_version: Submitted Version
page: 180 - 197
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _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: '5398'
pubrep_id: '336'
quality_controlled: '1'
related_material:
record:
- id: '1130'
relation: dissertation_contains
status: public
- id: '1338'
relation: later_version
status: public
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: From non-preemptive to preemptive scheduling using synchronization synthesis
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9207
year: '2015'
...
---
_id: '1835'
abstract:
- lang: eng
text: The behaviour of gene regulatory networks (GRNs) is typically analysed using
simulation-based statistical testing-like methods. In this paper, we demonstrate
that we can replace this approach by a formal verification-like method that gives
higher assurance and scalability. We focus on Wagner’s weighted GRN model with
varying weights, which is used in evolutionary biology. In the model, weight parameters
represent the gene interaction strength that may change due to genetic mutations.
For a property of interest, we synthesise the constraints over the parameter space
that represent the set of GRNs satisfying the property. We experimentally show
that our parameter synthesis procedure computes the mutational robustness of GRNs
–an important problem of interest in evolutionary biology– more efficiently than
the classical simulation method. We specify the property in linear temporal logics.
We employ symbolic bounded model checking and SMT solving to compute the space
of GRNs that satisfy the property, which amounts to synthesizing a set of linear
constraints on the weights.
acknowledgement: "SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2
148797.\r\n"
alternative_title:
- LNCS
author:
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- 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: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking
gene regulatory networks. 2015;9035:469-483. doi:10.1007/978-3-662-46681-0_47
apa: 'Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &
Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS:
Tools and Algorithms for the Construction and Analysis of Systems, London, United
Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_47'
chicago: Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago
Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture
Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_47.
ieee: M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov,
“Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.
ista: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model
checking gene regulatory networks. 9035, 469–483.
mla: Giacobbe, Mirco, et al. Model Checking Gene Regulatory Networks. Vol.
9035, Springer, 2015, pp. 469–83, doi:10.1007/978-3-662-46681-0_47.
short: M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035
(2015) 469–483.
conference:
end_date: 2015-04-18
location: London, United Kingdom
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2015-04-11
date_created: 2018-12-11T11:54:16Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-09-20T11:06:03Z
day: '01'
department:
- _id: ToHe
- _id: CaGu
- _id: NiBa
doi: 10.1007/978-3-662-46681-0_47
ec_funded: 1
intvolume: ' 9035'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.7704
month: '04'
oa: 1
oa_version: Preprint
page: 469 - 483
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '5267'
quality_controlled: '1'
related_material:
record:
- id: '1351'
relation: later_version
status: public
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Model checking gene regulatory networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9035
year: '2015'
...
---
_id: '1509'
abstract:
- lang: eng
text: The Auxin Binding Protein1 (ABP1) has been identified based on its ability
to bind auxin with high affinity and studied for a long time as a prime candidate
for the extracellular auxin receptor responsible for mediating in particular the
fast non-transcriptional auxin responses. However, the contradiction between the
embryo-lethal phenotypes of the originally described Arabidopsis T-DNA insertional
knock-out alleles (abp1-1 and abp1-1s) and the wild type-like phenotypes of other
recently described loss-of-function alleles (abp1-c1 and abp1-TD1) questions the
biological importance of ABP1 and relevance of the previous genetic studies. Here
we show that there is no hidden copy of the ABP1 gene in the Arabidopsis genome
but the embryo-lethal phenotypes of abp1-1 and abp1-1s alleles are very similar
to the knock-out phenotypes of the neighboring gene, BELAYA SMERT (BSM). Furthermore,
the allelic complementation test between bsm and abp1 alleles shows that the embryo-lethality
in the abp1-1 and abp1-1s alleles is caused by the off-target disruption of the
BSM locus by the T-DNA insertions. This clarifies the controversy of different
phenotypes among published abp1 knock-out alleles and asks for reflections on
the developmental role of ABP1.
acknowledgement: "This work was supported by ERC Independent Research grant (ERC-2011-StG-20101109-PSDP
to JF). JM internship was supported by the grant “Action Austria – Slovakia”.\r\nData
associated with the article are available under the terms of the Creative Commons
Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication). \r\n\r\nData
availability: \r\nF1000Research: Dataset 1. Dataset 1, 10.5256/f1000research.7143.d104552\r\n\r\nF1000Research:
Dataset 2. Dataset 2, 10.5256/f1000research.7143.d104553\r\n\r\nF1000Research: Dataset
3. Dataset 3, 10.5256/f1000research.7143.d104554"
article_processing_charge: No
author:
- first_name: Jaroslav
full_name: Michalko, Jaroslav
id: 483727CA-F248-11E8-B48F-1D18A9856A87
last_name: Michalko
- first_name: Marta
full_name: Dravecka, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Dravecka
orcid: 0000-0002-2519-8004
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Michalko J, Lukacisinova M, Bollenbach MT, Friml J. Embryo-lethal phenotypes
in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000
Research . 2015;4. doi:10.12688/f1000research.7143.1
apa: Michalko, J., Lukacisinova, M., Bollenbach, M. T., & Friml, J. (2015).
Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring
BSM gene. F1000 Research . F1000 Research. https://doi.org/10.12688/f1000research.7143.1
chicago: Michalko, Jaroslav, Marta Lukacisinova, Mark Tobias Bollenbach, and Jiří
Friml. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of
the Neighboring BSM Gene.” F1000 Research . F1000 Research, 2015. https://doi.org/10.12688/f1000research.7143.1.
ieee: J. Michalko, M. Lukacisinova, M. T. Bollenbach, and J. Friml, “Embryo-lethal
phenotypes in early abp1 mutants are due to disruption of the neighboring BSM
gene,” F1000 Research , vol. 4. F1000 Research, 2015.
ista: Michalko J, Lukacisinova M, Bollenbach MT, Friml J. 2015. Embryo-lethal phenotypes
in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000
Research . 4.
mla: Michalko, Jaroslav, et al. “Embryo-Lethal Phenotypes in Early Abp1 Mutants
Are Due to Disruption of the Neighboring BSM Gene.” F1000 Research , vol.
4, F1000 Research, 2015, doi:10.12688/f1000research.7143.1.
short: J. Michalko, M. Lukacisinova, M.T. Bollenbach, J. Friml, F1000 Research 4
(2015).
date_created: 2018-12-11T11:52:26Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2023-10-10T14:10:24Z
day: '01'
ddc:
- '570'
department:
- _id: JiFr
- _id: ToBo
doi: 10.12688/f1000research.7143.1
ec_funded: 1
file:
- access_level: open_access
checksum: 8beae5cbe988e1060265ae7de2ee8306
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:12Z
date_updated: 2020-07-14T12:44:59Z
file_id: '5198'
file_name: IST-2016-497-v1+1_10.12688_f1000research.7143.1_20151102.pdf
file_size: 4414248
relation: main_file
file_date_updated: 2020-07-14T12:44:59Z
has_accepted_license: '1'
intvolume: ' 4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: 'F1000 Research '
publication_status: published
publisher: F1000 Research
publist_id: '5668'
pubrep_id: '497'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the
neighboring BSM gene
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2015'
...
---
_id: '1681'
abstract:
- lang: eng
text: In many social situations, individuals endeavor to find the single best possible
partner, but are constrained to evaluate the candidates in sequence. Examples
include the search for mates, economic partnerships, or any other long-term ties
where the choice to interact involves two parties. Surprisingly, however, previous
theoretical work on mutual choice problems focuses on finding equilibrium solutions,
while ignoring the evolutionary dynamics of decisions. Empirically, this may be
of high importance, as some equilibrium solutions can never be reached unless
the population undergoes radical changes and a sufficient number of individuals
change their decisions simultaneously. To address this question, we apply a mutual
choice sequential search problem in an evolutionary game-theoretical model that
allows one to find solutions that are favored by evolution. As an example, we
study the influence of sequential search on the evolutionary dynamics of cooperation.
For this, we focus on the classic snowdrift game and the prisoner’s dilemma game.
article_processing_charge: No
article_type: original
author:
- first_name: Tadeas
full_name: Priklopil, Tadeas
id: 3C869AA0-F248-11E8-B48F-1D18A9856A87
last_name: Priklopil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Priklopil T, Chatterjee K. Evolution of decisions in population games with
sequentially searching individuals. Games. 2015;6(4):413-437. doi:10.3390/g6040413
apa: Priklopil, T., & Chatterjee, K. (2015). Evolution of decisions in population
games with sequentially searching individuals. Games. MDPI. https://doi.org/10.3390/g6040413
chicago: Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in
Population Games with Sequentially Searching Individuals.” Games. MDPI,
2015. https://doi.org/10.3390/g6040413.
ieee: T. Priklopil and K. Chatterjee, “Evolution of decisions in population games
with sequentially searching individuals,” Games, vol. 6, no. 4. MDPI, pp.
413–437, 2015.
ista: Priklopil T, Chatterjee K. 2015. Evolution of decisions in population games
with sequentially searching individuals. Games. 6(4), 413–437.
mla: Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population
Games with Sequentially Searching Individuals.” Games, vol. 6, no. 4, MDPI,
2015, pp. 413–37, doi:10.3390/g6040413.
short: T. Priklopil, K. Chatterjee, Games 6 (2015) 413–437.
date_created: 2018-12-11T11:53:26Z
date_published: 2015-09-29T00:00:00Z
date_updated: 2023-10-17T11:42:52Z
day: '29'
ddc:
- '000'
department:
- _id: NiBa
- _id: KrCh
doi: 10.3390/g6040413
ec_funded: 1
file:
- access_level: open_access
checksum: 912e1acbaf201100f447a43e4d5958bd
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:41Z
date_updated: 2020-07-14T12:45:12Z
file_id: '4959'
file_name: IST-2016-448-v1+1_games-06-00413.pdf
file_size: 518832
relation: main_file
file_date_updated: 2020-07-14T12:45:12Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '4'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 413 - 437
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Games
publication_identifier:
eissn:
- 2073-4336
publication_status: published
publisher: MDPI
publist_id: '5467'
pubrep_id: '448'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution of decisions in population games with sequentially searching individuals
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '1655'
abstract:
- lang: eng
text: Quantifying behaviors of robots which were generated autonomously from task-independent
objective functions is an important prerequisite for objective comparisons of
algorithms and movements of animals. The temporal sequence of such a behavior
can be considered as a time series and hence complexity measures developed for
time series are natural candidates for its quantification. The predictive information
and the excess entropy are such complexity measures. They measure the amount of
information the past contains about the future and thus quantify the nonrandom
structure in the temporal sequence. However, when using these measures for systems
with continuous states one has to deal with the fact that their values will depend
on the resolution with which the systems states are observed. For deterministic
systems both measures will diverge with increasing resolution. We therefore propose
a new decomposition of the excess entropy in resolution dependent and resolution
independent parts and discuss how they depend on the dimensionality of the dynamics,
correlations and the noise level. For the practical estimation we propose to use
estimates based on the correlation integral instead of the direct estimation of
the mutual information based on next neighbor statistics because the latter allows
less control of the scale dependencies. Using our algorithm we are able to show
how autonomous learning generates behavior of increasing complexity with increasing
learning duration.
acknowledgement: This work was supported by the DFG priority program 1527 (Autonomous
Learning) and by the European Community’s Seventh Framework Programme (FP7/2007-2013)
under grant agreement no. 318723 (MatheMACS) and from the People Programme (Marie
Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013)
under REA grant agreement no. 291734.
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: Eckehard
full_name: Olbrich, Eckehard
last_name: Olbrich
citation:
ama: Martius GS, Olbrich E. Quantifying emergent behavior of autonomous robots.
Entropy. 2015;17(10):7266-7297. doi:10.3390/e17107266
apa: Martius, G. S., & Olbrich, E. (2015). Quantifying emergent behavior of
autonomous robots. Entropy. MDPI. https://doi.org/10.3390/e17107266
chicago: Martius, Georg S, and Eckehard Olbrich. “Quantifying Emergent Behavior
of Autonomous Robots.” Entropy. MDPI, 2015. https://doi.org/10.3390/e17107266.
ieee: G. S. Martius and E. Olbrich, “Quantifying emergent behavior of autonomous
robots,” Entropy, vol. 17, no. 10. MDPI, pp. 7266–7297, 2015.
ista: Martius GS, Olbrich E. 2015. Quantifying emergent behavior of autonomous robots.
Entropy. 17(10), 7266–7297.
mla: Martius, Georg S., and Eckehard Olbrich. “Quantifying Emergent Behavior of
Autonomous Robots.” Entropy, vol. 17, no. 10, MDPI, 2015, pp. 7266–97,
doi:10.3390/e17107266.
short: G.S. Martius, E. Olbrich, Entropy 17 (2015) 7266–7297.
date_created: 2018-12-11T11:53:17Z
date_published: 2015-10-23T00:00:00Z
date_updated: 2023-10-17T11:42:00Z
day: '23'
ddc:
- '000'
department:
- _id: ChLa
- _id: GaTk
doi: 10.3390/e17107266
ec_funded: 1
file:
- access_level: open_access
checksum: 945d99631a96e0315acb26dc8541dcf9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:25Z
date_updated: 2020-07-14T12:45:08Z
file_id: '4943'
file_name: IST-2016-464-v1+1_entropy-17-07266.pdf
file_size: 6455007
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 17'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 7266 - 7297
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Entropy
publication_status: published
publisher: MDPI
publist_id: '5495'
pubrep_id: '464'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantifying emergent behavior of autonomous robots
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2015'
...
---
_id: '1834'
abstract:
- lang: eng
text: Huge body of evidences demonstrated that volatile anesthetics affect the hippocampal
neurogenesis and neurocognitive functions, and most of them showed impairment
at anesthetic dose. Here, we investigated the effect of low dose (1.8%) sevoflurane
on hippocampal neurogenesis and dentate gyrus-dependent learning. Neonatal rats
at postnatal day 4 to 6 (P4-6) were treated with 1.8% sevoflurane for 6 hours.
Neurogenesis was quantified by bromodeoxyuridine labeling and electrophysiology
recording. Four and seven weeks after treatment, the Morris water maze and contextual-fear
discrimination learning tests were performed to determine the influence on spatial
learning and pattern separation. A 6-hour treatment with 1.8% sevoflurane promoted
hippocampal neurogenesis and increased the survival of newborn cells and the proportion
of immature granular cells in the dentate gyrus of neonatal rats. Sevoflurane-treated
rats performed better during the training days of the Morris water maze test and
in contextual-fear discrimination learning test. These results suggest that a
subanesthetic dose of sevoflurane promotes hippocampal neurogenesis in neonatal
rats and facilitates their performance in dentate gyrus-dependent learning tasks.
article_processing_charge: No
article_type: original
author:
- first_name: Chong
full_name: Chen, Chong
id: 3DFD581A-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Chao
full_name: Wang, Chao
last_name: Wang
- first_name: Xuan
full_name: Zhao, Xuan
last_name: Zhao
- first_name: Tao
full_name: Zhou, Tao
last_name: Zhou
- first_name: Dao
full_name: Xu, Dao
last_name: Xu
- first_name: Zhi
full_name: Wang, Zhi
last_name: Wang
- first_name: Ying
full_name: Wang, Ying
last_name: Wang
citation:
ama: Chen C, Wang C, Zhao X, et al. Low-dose sevoflurane promoteshippocampal neurogenesis
and facilitates the development of dentate gyrus-dependent learning in neonatal
rats. ASN Neuro. 2015;7(2). doi:10.1177/1759091415575845
apa: Chen, C., Wang, C., Zhao, X., Zhou, T., Xu, D., Wang, Z., & Wang, Y. (2015).
Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development
of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. SAGE Publications.
https://doi.org/10.1177/1759091415575845
chicago: Chen, Chong, Chao Wang, Xuan Zhao, Tao Zhou, Dao Xu, Zhi Wang, and Ying
Wang. “Low-Dose Sevoflurane Promoteshippocampal Neurogenesis and Facilitates the
Development of Dentate Gyrus-Dependent Learning in Neonatal Rats.” ASN Neuro.
SAGE Publications, 2015. https://doi.org/10.1177/1759091415575845.
ieee: C. Chen et al., “Low-dose sevoflurane promoteshippocampal neurogenesis
and facilitates the development of dentate gyrus-dependent learning in neonatal
rats,” ASN Neuro, vol. 7, no. 2. SAGE Publications, 2015.
ista: Chen C, Wang C, Zhao X, Zhou T, Xu D, Wang Z, Wang Y. 2015. Low-dose sevoflurane
promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent
learning in neonatal rats. ASN Neuro. 7(2).
mla: Chen, Chong, et al. “Low-Dose Sevoflurane Promoteshippocampal Neurogenesis
and Facilitates the Development of Dentate Gyrus-Dependent Learning in Neonatal
Rats.” ASN Neuro, vol. 7, no. 2, SAGE Publications, 2015, doi:10.1177/1759091415575845.
short: C. Chen, C. Wang, X. Zhao, T. Zhou, D. Xu, Z. Wang, Y. Wang, ASN Neuro 7
(2015).
date_created: 2018-12-11T11:54:16Z
date_published: 2015-04-13T00:00:00Z
date_updated: 2023-10-18T06:47:30Z
day: '13'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1177/1759091415575845
file:
- access_level: open_access
checksum: 53e16bd3fc2ae2c0d7de9164626c37aa
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:08Z
date_updated: 2020-07-14T12:45:18Z
file_id: '5057'
file_name: IST-2016-456-v1+1_ASN_Neuro-2015-Chen-.pdf
file_size: 1146814
relation: main_file
file_date_updated: 2020-07-14T12:45:18Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '04'
oa: 1
oa_version: Published Version
publication: ASN Neuro
publication_status: published
publisher: SAGE Publications
publist_id: '5269'
pubrep_id: '456'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development
of dentate gyrus-dependent learning in neonatal rats
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2015'
...
---
_id: '1635'
abstract:
- lang: eng
text: We calculate a Ricci curvature lower bound for some classical examples of
random walks, namely, a chain on a slice of the n-dimensional discrete cube (the
so-called Bernoulli-Laplace model) and the random transposition shuffle of the
symmetric group of permutations on n letters.
article_processing_charge: No
article_type: original
author:
- first_name: Matthias
full_name: Erbar, Matthias
last_name: Erbar
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Prasad
full_name: Tetali, Prasad
last_name: Tetali
citation:
ama: Erbar M, Maas J, Tetali P. Discrete Ricci curvature bounds for Bernoulli-Laplace
and random transposition models. Annales de la faculté des sciences de Toulouse.
2015;24(4):781-800. doi:10.5802/afst.1464
apa: Erbar, M., Maas, J., & Tetali, P. (2015). Discrete Ricci curvature bounds
for Bernoulli-Laplace and random transposition models. Annales de La Faculté
Des Sciences de Toulouse. Faculté des sciences de Toulouse. https://doi.org/10.5802/afst.1464
chicago: Erbar, Matthias, Jan Maas, and Prasad Tetali. “Discrete Ricci Curvature
Bounds for Bernoulli-Laplace and Random Transposition Models.” Annales de La
Faculté Des Sciences de Toulouse. Faculté des sciences de Toulouse, 2015.
https://doi.org/10.5802/afst.1464.
ieee: M. Erbar, J. Maas, and P. Tetali, “Discrete Ricci curvature bounds for Bernoulli-Laplace
and random transposition models,” Annales de la faculté des sciences de Toulouse,
vol. 24, no. 4. Faculté des sciences de Toulouse, pp. 781–800, 2015.
ista: Erbar M, Maas J, Tetali P. 2015. Discrete Ricci curvature bounds for Bernoulli-Laplace
and random transposition models. Annales de la faculté des sciences de Toulouse.
24(4), 781–800.
mla: Erbar, Matthias, et al. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace
and Random Transposition Models.” Annales de La Faculté Des Sciences de Toulouse,
vol. 24, no. 4, Faculté des sciences de Toulouse, 2015, pp. 781–800, doi:10.5802/afst.1464.
short: M. Erbar, J. Maas, P. Tetali, Annales de La Faculté Des Sciences de Toulouse
24 (2015) 781–800.
date_created: 2018-12-11T11:53:10Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-10-18T07:48:28Z
day: '01'
department:
- _id: JaMa
doi: 10.5802/afst.1464
external_id:
arxiv:
- '1409.8605'
intvolume: ' 24'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1409.8605
month: '01'
oa: 1
oa_version: Preprint
page: 781 - 800
publication: Annales de la faculté des sciences de Toulouse
publication_status: published
publisher: Faculté des sciences de Toulouse
publist_id: '5520'
quality_controlled: '1'
status: public
title: Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition
models
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2015'
...
---
_id: '14303'
abstract:
- lang: eng
text: Scaffolded DNA origami enables the fabrication of a variety of complex nanostructures
that promise utility in diverse fields of application, ranging from biosensing
over advanced therapeutics to metamaterials. The broad applicability of DNA origami
as a material beyond the level of proof-of-concept studies critically depends,
among other factors, on the availability of large amounts of pure single-stranded
scaffold DNA. Here, we present a method for the efficient production of M13 bacteriophage-derived
genomic DNA using high-cell-density fermentation of Escherichia coli in stirred-tank
bioreactors. We achieve phage titers of up to 1.6 × 1014 plaque-forming units
per mL. Downstream processing yields up to 410 mg of high-quality single-stranded
DNA per one liter reaction volume, thus upgrading DNA origami-based nanotechnology
from the milligram to the gram scale.
article_processing_charge: No
article_type: letter_note
author:
- first_name: B
full_name: Kick, B
last_name: Kick
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: H
full_name: Dietz, H
last_name: Dietz
- first_name: D
full_name: Weuster-Botz, D
last_name: Weuster-Botz
citation:
ama: Kick B, Praetorius FM, Dietz H, Weuster-Botz D. Efficient production of single-stranded
phage DNA as scaffolds for DNA origami. Nano Letters. 2015;15(7):4672-4676.
doi:10.1021/acs.nanolett.5b01461
apa: Kick, B., Praetorius, F. M., Dietz, H., & Weuster-Botz, D. (2015). Efficient
production of single-stranded phage DNA as scaffolds for DNA origami. Nano
Letters. ACS Publications. https://doi.org/10.1021/acs.nanolett.5b01461
chicago: Kick, B, Florian M Praetorius, H Dietz, and D Weuster-Botz. “Efficient
Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” Nano
Letters. ACS Publications, 2015. https://doi.org/10.1021/acs.nanolett.5b01461.
ieee: B. Kick, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Efficient production
of single-stranded phage DNA as scaffolds for DNA origami,” Nano Letters,
vol. 15, no. 7. ACS Publications, pp. 4672–4676, 2015.
ista: Kick B, Praetorius FM, Dietz H, Weuster-Botz D. 2015. Efficient production
of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. 15(7),
4672–4676.
mla: Kick, B., et al. “Efficient Production of Single-Stranded Phage DNA as Scaffolds
for DNA Origami.” Nano Letters, vol. 15, no. 7, ACS Publications, 2015,
pp. 4672–76, doi:10.1021/acs.nanolett.5b01461.
short: B. Kick, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Nano Letters 15 (2015)
4672–4676.
date_created: 2023-09-06T12:52:47Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-11-07T11:56:32Z
day: '01'
doi: 10.1021/acs.nanolett.5b01461
extern: '1'
external_id:
pmid:
- '26028443'
intvolume: ' 15'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/acs.nanolett.5b01461
month: '06'
oa: 1
oa_version: Published Version
page: 4672-4676
pmid: 1
publication: Nano Letters
publication_identifier:
eissn:
- 1530-6992
issn:
- 1530-6984
publication_status: published
publisher: ACS Publications
quality_controlled: '1'
status: public
title: Efficient production of single-stranded phage DNA as scaffolds for DNA origami
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2015'
...
---
_id: '1603'
abstract:
- lang: eng
text: "For deterministic systems, a counterexample to a property can simply be an
error trace, whereas counterexamples in probabilistic systems are necessarily
more complex. For instance, a set of erroneous traces with a sufficient cumulative
probability mass can be used. Since these are too large objects to understand
and manipulate, compact representations such as subchains have been considered.
In the case of probabilistic systems with non-determinism, the situation is even
more complex. While a subchain for a given strategy (or scheduler, resolving non-determinism)
is a straightforward choice, we take a different approach. Instead, we focus on
the strategy itself, and extract the most important decisions it makes, and present
its succinct representation.\r\nThe key tools we employ to achieve this are (1)
introducing a concept of importance of a state w.r.t. the strategy, and (2) learning
using decision trees. There are three main consequent advantages of our approach.
Firstly, it exploits the quantitative information on states, stressing the more
important decisions. Secondly, it leads to a greater variability and degree of
freedom in representing the strategies. Thirdly, the representation uses a self-explanatory
data structure. In summary, our approach produces more succinct and more explainable
strategies, as opposed to e.g. binary decision diagrams. Finally, our experimental
results show that we can extract several rules describing the strategy even for
very large systems that do not fit in memory, and based on the rules explain the
erroneous behaviour."
acknowledgement: This research was funded in part by Austrian Science Fund (FWF) Grant
No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE) and Z211-N23 (Wittgenstein Award),
European Research Council (ERC) Grant No 279307 (Graph Games), ERC Grant No 267989
(QUAREM), the Czech Science Foundation Grant No P202/12/G061, and People Programme
(Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013)
REA Grant No 291734.
alternative_title:
- LNCS
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Andreas
full_name: Fellner, Andreas
id: 42BABFB4-F248-11E8-B48F-1D18A9856A87
last_name: Fellner
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: 'Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. Counterexample
explanation by learning small strategies in Markov decision processes. In: Vol
9206. Springer; 2015:158-177. doi:10.1007/978-3-319-21690-4_10'
apa: 'Brázdil, T., Chatterjee, K., Chmelik, M., Fellner, A., & Kretinsky, J.
(2015). Counterexample explanation by learning small strategies in Markov decision
processes (Vol. 9206, pp. 158–177). Presented at the CAV: Computer Aided Verification,
San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21690-4_10'
chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Andreas Fellner,
and Jan Kretinsky. “Counterexample Explanation by Learning Small Strategies in
Markov Decision Processes,” 9206:158–77. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_10.
ieee: 'T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, and J. Kretinsky, “Counterexample
explanation by learning small strategies in Markov decision processes,” presented
at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015,
vol. 9206, pp. 158–177.'
ista: 'Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. 2015. Counterexample
explanation by learning small strategies in Markov decision processes. CAV: Computer
Aided Verification, LNCS, vol. 9206, 158–177.'
mla: Brázdil, Tomáš, et al. Counterexample Explanation by Learning Small Strategies
in Markov Decision Processes. Vol. 9206, Springer, 2015, pp. 158–77, doi:10.1007/978-3-319-21690-4_10.
short: T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, J. Kretinsky, in:, Springer,
2015, pp. 158–177.
conference:
end_date: 2015-07-24
location: San Francisco, CA, United States
name: 'CAV: Computer Aided Verification'
start_date: 2015-07-18
date_created: 2018-12-11T11:52:58Z
date_published: 2015-07-16T00:00:00Z
date_updated: 2024-02-21T13:52:07Z
day: '16'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-21690-4_10
ec_funded: 1
intvolume: ' 9206'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1502.02834
month: '07'
oa: 1
oa_version: Preprint
page: 158 - 177
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_identifier:
eisbn:
- 978-3-319-21690-4
publication_status: published
publisher: Springer
publist_id: '5564'
quality_controlled: '1'
related_material:
record:
- id: '5549'
relation: research_paper
status: public
scopus_import: 1
status: public
title: Counterexample explanation by learning small strategies in Markov decision
processes
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9206
year: '2015'
...
---
_id: '5549'
abstract:
- lang: eng
text: "This repository contains the experimental part of the CAV 2015 publication
Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.\r\nWe
extended the probabilistic model checker PRISM to represent strategies of Markov
Decision Processes as Decision Trees.\r\nThe archive contains a java executable
version of the extended tool (prism_dectree.jar) together with a few examples
of the PRISM benchmark library.\r\nTo execute the program, please have a look
at the README.txt, which provides instructions and further information on the
archive.\r\nThe archive contains scripts that (if run often enough) reproduces
the data presented in the publication."
article_processing_charge: No
author:
- first_name: Andreas
full_name: Fellner, Andreas
id: 42BABFB4-F248-11E8-B48F-1D18A9856A87
last_name: Fellner
citation:
ama: 'Fellner A. Experimental part of CAV 2015 publication: Counterexample Explanation
by Learning Small Strategies in Markov Decision Processes. 2015. doi:10.15479/AT:ISTA:28'
apa: 'Fellner, A. (2015). Experimental part of CAV 2015 publication: Counterexample
Explanation by Learning Small Strategies in Markov Decision Processes. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:28'
chicago: 'Fellner, Andreas. “Experimental Part of CAV 2015 Publication: Counterexample
Explanation by Learning Small Strategies in Markov Decision Processes.” Institute
of Science and Technology Austria, 2015. https://doi.org/10.15479/AT:ISTA:28.'
ieee: 'A. Fellner, “Experimental part of CAV 2015 publication: Counterexample Explanation
by Learning Small Strategies in Markov Decision Processes.” Institute of Science
and Technology Austria, 2015.'
ista: 'Fellner A. 2015. Experimental part of CAV 2015 publication: Counterexample
Explanation by Learning Small Strategies in Markov Decision Processes, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:28.'
mla: 'Fellner, Andreas. Experimental Part of CAV 2015 Publication: Counterexample
Explanation by Learning Small Strategies in Markov Decision Processes. Institute
of Science and Technology Austria, 2015, doi:10.15479/AT:ISTA:28.'
short: A. Fellner, (2015).
contributor:
- first_name: Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
datarep_id: '28'
date_created: 2018-12-12T12:31:29Z
date_published: 2015-08-13T00:00:00Z
date_updated: 2024-02-21T13:52:07Z
day: '13'
ddc:
- '004'
department:
- _id: KrCh
- _id: ToHe
doi: 10.15479/AT:ISTA:28
ec_funded: 1
file:
- access_level: open_access
checksum: b8bcb43c0893023cda66c1b69c16ac62
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:31Z
date_updated: 2020-07-14T12:47:00Z
file_id: '5597'
file_name: IST-2015-28-v1+2_Fellner_DataRep.zip
file_size: 49557109
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
has_accepted_license: '1'
keyword:
- Markov Decision Process
- Decision Tree
- Probabilistic Verification
- Counterexample Explanation
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publisher: Institute of Science and Technology Austria
publist_id: '5564'
related_material:
record:
- id: '1603'
relation: popular_science
status: public
status: public
title: 'Experimental part of CAV 2015 publication: Counterexample Explanation by Learning
Small Strategies in Markov Decision Processes'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1512'
abstract:
- lang: eng
text: 'We show that very weak topological assumptions are enough to ensure the existence
of a Helly-type theorem. More precisely, we show that for any non-negative integers
b and d there exists an integer h(b,d) such that the following holds. If F is
a finite family of subsets of R^d such that the ith reduced Betti number (with
Z_2 coefficients in singular homology) of the intersection of any proper subfamily
G of F is at most b for every non-negative integer i less or equal to (d-1)/2,
then F has Helly number at most h(b,d). These topological conditions are sharp:
not controlling any of these first Betti numbers allow for families with unbounded
Helly number. Our proofs combine homological non-embeddability results with a
Ramsey-based approach to build, given an arbitrary simplicial complex K, some
well-behaved chain map from C_*(K) to C_*(R^d). Both techniques are of independent
interest.'
acknowledgement: "PP, ZP and MT were partially supported by the Charles University
Grant GAUK 421511. ZP was\r\npartially supported by the Charles University Grant
SVV-2014-260103. ZP and MT were partially\r\nsupported by the ERC Advanced Grant
No. 267165 and by the project CE-ITI (GACR P202/12/G061)\r\nof the Czech Science
Foundation. UW was partially supported by the Swiss National Science Foundation\r\n(grants
SNSF-200020-138230 and SNSF-PP00P2-138948). Part of this work was done when XG was
affiliated with INRIA Nancy Grand-Est and when MT was affiliated with Institutionen
för matematik, Kungliga Tekniska Högskolan, then IST Austria."
alternative_title:
- LIPIcs
article_processing_charge: No
author:
- first_name: Xavier
full_name: Goaoc, Xavier
last_name: Goaoc
- first_name: Pavel
full_name: Paták, Pavel
last_name: Paták
- first_name: Zuzana
full_name: Patakova, Zuzana
last_name: Patakova
orcid: 0000-0002-3975-1683
- first_name: Martin
full_name: Tancer, Martin
last_name: Tancer
orcid: 0000-0002-1191-6714
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Bounding Helly numbers via
Betti numbers. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2015:507-521. doi:10.4230/LIPIcs.SOCG.2015.507'
apa: 'Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2015). Bounding
Helly numbers via Betti numbers (Vol. 34, pp. 507–521). Presented at the SoCG:
Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.507'
chicago: Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner.
“Bounding Helly Numbers via Betti Numbers,” 34:507–21. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.507.
ieee: 'X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Bounding Helly
numbers via Betti numbers,” presented at the SoCG: Symposium on Computational
Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 507–521.'
ista: 'Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2015. Bounding Helly numbers
via Betti numbers. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34,
507–521.'
mla: Goaoc, Xavier, et al. Bounding Helly Numbers via Betti Numbers. Vol.
34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–21, doi:10.4230/LIPIcs.SOCG.2015.507.
short: X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2015, pp. 507–521.
conference:
end_date: 2015-06-25
location: Eindhoven, Netherlands
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2015-06-22
date_created: 2018-12-11T11:52:27Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2024-02-28T12:59:37Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SOCG.2015.507
file:
- access_level: open_access
checksum: e6881df44d87fe0c2529c9f7b2724614
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:09Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4794'
file_name: IST-2016-501-v1+1_46.pdf
file_size: 633712
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 34'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 507 - 521
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5665'
pubrep_id: '501'
quality_controlled: '1'
related_material:
record:
- id: '424'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Bounding Helly numbers via Betti numbers
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '271'
abstract:
- lang: eng
text: We show that a non-singular integral form of degree d is soluble non-trivially
over the integers if and only if it is soluble non-trivially over the reals and
the p-adic numbers, provided that the form has at least (d-\sqrt{d}/2)2^d variables.
This improves on a longstanding result of Birch.
acknowledgement: While working on this paper the authors were supported by the Leverhulme
Trust and ERC grant 306457.
article_processing_charge: No
article_type: original
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Sean
full_name: Prendiville, Sean
last_name: Prendiville
citation:
ama: Browning TD, Prendiville S. Improvements in Birch’s theorem on forms in many
variables. Journal fur die Reine und Angewandte Mathematik. 2017(731):203-234.
doi:10.1515/crelle-2014-0122
apa: Browning, T. D., & Prendiville, S. (n.d.). Improvements in Birch’s theorem
on forms in many variables. Journal Fur Die Reine Und Angewandte Mathematik.
Walter de Gruyter. https://doi.org/10.1515/crelle-2014-0122
chicago: Browning, Timothy D, and Sean Prendiville. “Improvements in Birch’s Theorem
on Forms in Many Variables.” Journal Fur Die Reine Und Angewandte Mathematik.
Walter de Gruyter, n.d. https://doi.org/10.1515/crelle-2014-0122.
ieee: T. D. Browning and S. Prendiville, “Improvements in Birch’s theorem on forms
in many variables,” Journal fur die Reine und Angewandte Mathematik, vol.
2017, no. 731. Walter de Gruyter, pp. 203–234.
ista: Browning TD, Prendiville S. Improvements in Birch’s theorem on forms in many
variables. Journal fur die Reine und Angewandte Mathematik. 2017(731), 203–234.
mla: Browning, Timothy D., and Sean Prendiville. “Improvements in Birch’s Theorem
on Forms in Many Variables.” Journal Fur Die Reine Und Angewandte Mathematik,
vol. 2017, no. 731, Walter de Gruyter, pp. 203–34, doi:10.1515/crelle-2014-0122.
short: T.D. Browning, S. Prendiville, Journal Fur Die Reine Und Angewandte Mathematik
2017 (n.d.) 203–234.
date_created: 2018-12-11T11:45:32Z
date_published: 2015-02-20T00:00:00Z
date_updated: 2024-03-05T12:09:22Z
day: '20'
doi: 10.1515/crelle-2014-0122
extern: '1'
external_id:
arxiv:
- '1402.4489'
intvolume: ' 2017'
issue: '731'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1402.4489
month: '02'
oa: 1
oa_version: Preprint
page: 203 - 234
publication: Journal fur die Reine und Angewandte Mathematik
publication_identifier:
issn:
- 0075-4102
publication_status: submitted
publisher: Walter de Gruyter
publist_id: '7631'
quality_controlled: '1'
related_material:
record:
- id: '256'
relation: later_version
status: public
status: public
title: Improvements in Birch's theorem on forms in many variables
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2017
year: '2015'
...
---
_id: '1675'
abstract:
- lang: eng
text: Proofs of work (PoW) have been suggested by Dwork and Naor (Crypto’92) as
protection to a shared resource. The basic idea is to ask the service requestor
to dedicate some non-trivial amount of computational work to every request. The
original applications included prevention of spam and protection against denial
of service attacks. More recently, PoWs have been used to prevent double spending
in the Bitcoin digital currency system. In this work, we put forward an alternative
concept for PoWs - so-called proofs of space (PoS), where a service requestor
must dedicate a significant amount of disk space as opposed to computation. We
construct secure PoS schemes in the random oracle model (with one additional mild
assumption required for the proof to go through), using graphs with high “pebbling
complexity” and Merkle hash-trees. We discuss some applications, including follow-up
work where a decentralized digital currency scheme called Spacecoin is constructed
that uses PoS (instead of wasteful PoW like in Bitcoin) to prevent double spending.
The main technical contribution of this work is the construction of (directed,
loop-free) graphs on N vertices with in-degree O(log logN) such that even if one
places Θ(N) pebbles on the nodes of the graph, there’s a constant fraction of
nodes that needs Θ(N) steps to be pebbled (where in every step one can put a pebble
on a node if all its parents have a pebble).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Stefan
full_name: Dziembowski, Stefan
last_name: Dziembowski
- first_name: Sebastian
full_name: Faust, Sebastian
last_name: Faust
- 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
citation:
ama: 'Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. Proofs of space. In: 35th
Annual Cryptology Conference. Vol 9216. Springer; 2015:585-605. doi:10.1007/978-3-662-48000-7_29'
apa: 'Dziembowski, S., Faust, S., Kolmogorov, V., & Pietrzak, K. Z. (2015).
Proofs of space. In 35th Annual Cryptology Conference (Vol. 9216, pp. 585–605).
Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-48000-7_29'
chicago: Dziembowski, Stefan, Sebastian Faust, Vladimir Kolmogorov, and Krzysztof
Z Pietrzak. “Proofs of Space.” In 35th Annual Cryptology Conference, 9216:585–605.
Springer, 2015. https://doi.org/10.1007/978-3-662-48000-7_29.
ieee: S. Dziembowski, S. Faust, V. Kolmogorov, and K. Z. Pietrzak, “Proofs of space,”
in 35th Annual Cryptology Conference, Santa Barbara, CA, United States,
2015, vol. 9216, pp. 585–605.
ista: 'Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. 2015. Proofs of space.
35th Annual Cryptology Conference. CRYPTO: International Cryptology Conference,
LNCS, vol. 9216, 585–605.'
mla: Dziembowski, Stefan, et al. “Proofs of Space.” 35th Annual Cryptology Conference,
vol. 9216, Springer, 2015, pp. 585–605, doi:10.1007/978-3-662-48000-7_29.
short: S. Dziembowski, S. Faust, V. Kolmogorov, K.Z. Pietrzak, in:, 35th Annual
Cryptology Conference, Springer, 2015, pp. 585–605.
conference:
end_date: 2015-08-20
location: Santa Barbara, CA, United States
name: 'CRYPTO: International Cryptology Conference'
start_date: 2015-08-16
date_created: 2018-12-11T11:53:24Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2024-03-20T08:31:49Z
day: '01'
department:
- _id: VlKo
- _id: KrPi
doi: 10.1007/978-3-662-48000-7_29
ec_funded: 1
intvolume: ' 9216'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2013/796.pdf
month: '08'
oa: 1
oa_version: Preprint
page: 585 - 605
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: 35th Annual Cryptology Conference
publication_identifier:
isbn:
- '9783662479995'
issn:
- 0302-9743
publication_status: published
publisher: Springer
publist_id: '5474'
pubrep_id: '671'
quality_controlled: '1'
related_material:
record:
- id: '2274'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Proofs of space
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9216
year: '2015'
...
---
_id: '15160'
abstract:
- lang: eng
text: The circadian clock orchestrates global changes in transcriptional regulation
on a daily basis via the bHLH-PAS transcription factor CLOCK:BMAL1. Pathways driven
by other bHLH-PAS transcription factors have a homologous repressor that modulates
activity on a tissue-specific basis, but none have been identified for CLOCK:BMAL1.
We show here that the cancer/testis antigen PASD1 fulfills this role to suppress
circadian rhythms. PASD1 is evolutionarily related to CLOCK and interacts with
the CLOCK:BMAL1 complex to repress transcriptional activation. Expression of PASD1
is restricted to germline tissues in healthy individuals but can be induced in
cells of somatic origin upon oncogenic transformation. Reducing PASD1 in human
cancer cells significantly increases the amplitude of transcriptional oscillations
to generate more robust circadian rhythms. Our results describe a function for
a germline-specific protein in regulation of the circadian clock and provide a
molecular link from oncogenic transformation to suppression of circadian rhythms.
article_processing_charge: No
article_type: original
author:
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Stacy L.
full_name: Harvey, Stacy L.
last_name: Harvey
- first_name: Patrick J.
full_name: Sammons, Patrick J.
last_name: Sammons
- first_name: Amanda P.
full_name: Anderson, Amanda P.
last_name: Anderson
- first_name: Hema M.
full_name: Kopalle, Hema M.
last_name: Kopalle
- first_name: Alison H.
full_name: Banham, Alison H.
last_name: Banham
- first_name: Carrie L.
full_name: Partch, Carrie L.
last_name: Partch
citation:
ama: Michael AK, Harvey SL, Sammons PJ, et al. Cancer/Testis antigen PASD1 silences
the circadian clock. Molecular Cell. 2015;58(5):743-754. doi:10.1016/j.molcel.2015.03.031
apa: Michael, A. K., Harvey, S. L., Sammons, P. J., Anderson, A. P., Kopalle, H.
M., Banham, A. H., & Partch, C. L. (2015). Cancer/Testis antigen PASD1 silences
the circadian clock. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2015.03.031
chicago: Michael, Alicia K., Stacy L. Harvey, Patrick J. Sammons, Amanda P. Anderson,
Hema M. Kopalle, Alison H. Banham, and Carrie L. Partch. “Cancer/Testis Antigen
PASD1 Silences the Circadian Clock.” Molecular Cell. Elsevier, 2015. https://doi.org/10.1016/j.molcel.2015.03.031.
ieee: A. K. Michael et al., “Cancer/Testis antigen PASD1 silences the circadian
clock,” Molecular Cell, vol. 58, no. 5. Elsevier, pp. 743–754, 2015.
ista: Michael AK, Harvey SL, Sammons PJ, Anderson AP, Kopalle HM, Banham AH, Partch
CL. 2015. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular
Cell. 58(5), 743–754.
mla: Michael, Alicia K., et al. “Cancer/Testis Antigen PASD1 Silences the Circadian
Clock.” Molecular Cell, vol. 58, no. 5, Elsevier, 2015, pp. 743–54, doi:10.1016/j.molcel.2015.03.031.
short: A.K. Michael, S.L. Harvey, P.J. Sammons, A.P. Anderson, H.M. Kopalle, A.H.
Banham, C.L. Partch, Molecular Cell 58 (2015) 743–754.
date_created: 2024-03-21T07:58:08Z
date_published: 2015-06-04T00:00:00Z
date_updated: 2024-03-25T11:52:26Z
day: '04'
doi: 10.1016/j.molcel.2015.03.031
extern: '1'
intvolume: ' 58'
issue: '5'
keyword:
- Cell Biology
- Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.molcel.2015.03.031
month: '06'
oa: 1
oa_version: Published Version
page: 743-754
publication: Molecular Cell
publication_identifier:
issn:
- 1097-2765
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cancer/Testis antigen PASD1 silences the circadian clock
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2015'
...
---
_id: '15159'
abstract:
- lang: eng
text: It is widely recognized that BMAL1 is an essential subunit of the primary
transcription factor that drives rhythmic circadian transcription in the nucleus.
In a surprising turn, Lipton et al. now show that BMAL1 rhythmically interacts
with translational machinery in the cytosol to stimulate protein synthesis in
response to mTOR signaling.
article_processing_charge: No
article_type: original
author:
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Hande
full_name: Asimgil, Hande
last_name: Asimgil
- first_name: Carrie L.
full_name: Partch, Carrie L.
last_name: Partch
citation:
ama: Michael AK, Asimgil H, Partch CL. Cytosolic BMAL1 moonlights as a translation
factor. Trends in Biochemical Sciences. 2015;40(9):489-490. doi:10.1016/j.tibs.2015.07.006
apa: Michael, A. K., Asimgil, H., & Partch, C. L. (2015). Cytosolic BMAL1 moonlights
as a translation factor. Trends in Biochemical Sciences. Elsevier. https://doi.org/10.1016/j.tibs.2015.07.006
chicago: Michael, Alicia K., Hande Asimgil, and Carrie L. Partch. “Cytosolic BMAL1
Moonlights as a Translation Factor.” Trends in Biochemical Sciences. Elsevier,
2015. https://doi.org/10.1016/j.tibs.2015.07.006.
ieee: A. K. Michael, H. Asimgil, and C. L. Partch, “Cytosolic BMAL1 moonlights as
a translation factor,” Trends in Biochemical Sciences, vol. 40, no. 9.
Elsevier, pp. 489–490, 2015.
ista: Michael AK, Asimgil H, Partch CL. 2015. Cytosolic BMAL1 moonlights as a translation
factor. Trends in Biochemical Sciences. 40(9), 489–490.
mla: Michael, Alicia K., et al. “Cytosolic BMAL1 Moonlights as a Translation Factor.”
Trends in Biochemical Sciences, vol. 40, no. 9, Elsevier, 2015, pp. 489–90,
doi:10.1016/j.tibs.2015.07.006.
short: A.K. Michael, H. Asimgil, C.L. Partch, Trends in Biochemical Sciences 40
(2015) 489–490.
date_created: 2024-03-21T07:57:44Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2024-03-25T11:53:58Z
day: '01'
doi: 10.1016/j.tibs.2015.07.006
extern: '1'
intvolume: ' 40'
issue: '9'
keyword:
- Molecular Biology
- Biochemistry
language:
- iso: eng
month: '09'
oa_version: None
page: 489-490
publication: Trends in Biochemical Sciences
publication_identifier:
issn:
- 0968-0004
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cytosolic BMAL1 moonlights as a translation factor
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2015'
...
---
_id: '1619'
abstract:
- lang: eng
text: The emergence of drug resistant pathogens is a serious public health problem.
It is a long-standing goal to predict rates of resistance evolution and design
optimal treatment strategies accordingly. To this end, it is crucial to reveal
the underlying causes of drug-specific differences in the evolutionary dynamics
leading to resistance. However, it remains largely unknown why the rates of resistance
evolution via spontaneous mutations and the diversity of mutational paths vary
substantially between drugs. Here we comprehensively quantify the distribution
of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics,
in the presence of eight antibiotics representing the main modes of action. Using
precise high-throughput fitness measurements for genome-wide Escherichia coli
gene deletion strains, we find that the width of the DFE varies dramatically between
antibiotics and, contrary to conventional wisdom, for some drugs the DFE width
is lower than in the absence of stress. We show that this previously underappreciated
divergence in DFE width among antibiotics is largely caused by their distinct
drug-specific dose-response characteristics. Unlike the DFE, the magnitude of
the changes in tolerated drug concentration resulting from genome-wide mutations
is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin,
i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin
than for other drugs. A population genetics model predicts that resistance evolution
for drugs with this property is severely limited and confined to reproducible
mutational paths. We tested this prediction in laboratory evolution experiments
using the “morbidostat”, a device for evolving bacteria in well-controlled drug
environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible
mutations—an almost paradoxical behavior since this drug causes DNA damage and
increases the mutation rate. Overall, we identified novel quantitative characteristics
of the evolutionary landscape that provide the conceptual foundation for predicting
the dynamics of drug resistance evolution.
article_number: e1002299
author:
- first_name: Guillaume
full_name: Chevereau, Guillaume
id: 424D78A0-F248-11E8-B48F-1D18A9856A87
last_name: Chevereau
- first_name: Marta
full_name: Dravecka, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Dravecka
orcid: 0000-0002-2519-8004
- first_name: Tugce
full_name: Batur, Tugce
last_name: Batur
- first_name: Aysegul
full_name: Guvenek, Aysegul
last_name: Guvenek
- first_name: Dilay
full_name: Ayhan, Dilay
last_name: Ayhan
- first_name: Erdal
full_name: Toprak, Erdal
last_name: Toprak
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Chevereau G, Lukacisinova M, Batur T, et al. Quantifying the determinants of
evolutionary dynamics leading to drug resistance. PLoS Biology. 2015;13(11).
doi:10.1371/journal.pbio.1002299
apa: Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D., Toprak,
E., & Bollenbach, M. T. (2015). Quantifying the determinants of evolutionary
dynamics leading to drug resistance. PLoS Biology. Public Library of Science.
https://doi.org/10.1371/journal.pbio.1002299
chicago: Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek,
Dilay Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Quantifying the Determinants
of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology. Public
Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.
ieee: G. Chevereau et al., “Quantifying the determinants of evolutionary
dynamics leading to drug resistance,” PLoS Biology, vol. 13, no. 11. Public
Library of Science, 2015.
ista: Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan D, Toprak E, Bollenbach
MT. 2015. Quantifying the determinants of evolutionary dynamics leading to drug
resistance. PLoS Biology. 13(11), e1002299.
mla: Chevereau, Guillaume, et al. “Quantifying the Determinants of Evolutionary
Dynamics Leading to Drug Resistance.” PLoS Biology, vol. 13, no. 11, e1002299,
Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.
short: G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D. Ayhan, E. Toprak,
M.T. Bollenbach, PLoS Biology 13 (2015).
date_created: 2018-12-11T11:53:04Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2024-03-27T23:30:28Z
day: '18'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1371/journal.pbio.1002299
ec_funded: 1
file:
- access_level: open_access
checksum: 0e82e3279f50b15c6c170c042627802b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:00Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4723'
file_name: IST-2016-468-v1+1_journal.pbio.1002299.pdf
file_size: 1387760
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5547'
pubrep_id: '468'
quality_controlled: '1'
related_material:
record:
- id: '9711'
relation: research_data
status: public
- id: '9765'
relation: research_data
status: public
- id: '6263'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Quantifying the determinants of evolutionary dynamics leading to drug resistance
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2015'
...
---
_id: '10382'
abstract:
- lang: eng
text: 'Protein oligomers have been implicated as toxic agents in a wide range of
amyloid-related diseases. However, it has remained unsolved whether the oligomers
are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct.
Analogously, it has not been resolved if the amyloid nucleation process is a classical
one-step nucleation process or a two-step process involving prenucleation clusters.
We use coarse-grained computer simulations to study the effect of nonspecific
attractions between peptides on the primary nucleation process underlying amyloid
fibrillization. We find that, for peptides that do not attract, the classical
one-step nucleation mechanism is possible but only at nonphysiologically high
peptide concentrations. At low peptide concentrations, which mimic the physiologically
relevant regime, attractive interpeptide interactions are essential for fibril
formation. Nucleation then inevitably takes place through a two-step mechanism
involving prefibrillar oligomers. We show that oligomers not only help peptides
meet each other but also, create an environment that facilitates the conversion
of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically
does not proceed through the most prevalent oligomers but through an oligomer
size that is only observed in rare fluctuations, which is why such aggregates
might be hard to capture experimentally. Finally, we find that the nucleation
of amyloid fibrils cannot be described by classical nucleation theory: in the
two-step mechanism, the critical nucleus size increases with increases in both
concentration and interpeptide interactions, which is in direct contrast with
predictions from classical nucleation theory.'
acknowledgement: We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs,
for helpful discussions. A.Š. acknowledges support from the Human Frontier Science
Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical
Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the
Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology
and Biological Sciences Research Council. D.F. acknowledges European Research Council
Advanced Grant 227758.
article_processing_charge: No
article_type: original
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Yassmine C.
full_name: Chebaro, Yassmine C.
last_name: Chebaro
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions
in amyloid nucleation. Proceedings of the National Academy of Sciences.
2014;111(50):17869-17874. doi:10.1073/pnas.1410159111
apa: Šarić, A., Chebaro, Y. C., Knowles, T. P. J., & Frenkel, D. (2014). Crucial
role of nonspecific interactions in amyloid nucleation. Proceedings of the
National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1410159111
chicago: Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel.
“Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410159111.
ieee: A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of
nonspecific interactions in amyloid nucleation,” Proceedings of the National
Academy of Sciences, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874,
2014.
ista: Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific
interactions in amyloid nucleation. Proceedings of the National Academy of Sciences.
111(50), 17869–17874.
mla: Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid
Nucleation.” Proceedings of the National Academy of Sciences, vol. 111,
no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:10.1073/pnas.1410159111.
short: A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National
Academy of Sciences 111 (2014) 17869–17874.
date_created: 2021-11-29T13:09:53Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2021-11-29T13:29:05Z
day: '01'
doi: 10.1073/pnas.1410159111
extern: '1'
external_id:
arxiv:
- '1412.0897'
pmid:
- '25453085'
intvolume: ' 111'
issue: '50'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pnas.org/content/111/50/17869
month: '12'
oa: 1
oa_version: Published Version
page: 17869-17874
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Crucial role of nonspecific interactions in amyloid nucleation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2014'
...
---
_id: '10383'
abstract:
- lang: eng
text: We use numerical simulations to compute the equation of state of a suspension
of spherical self-propelled nanoparticles in two and three dimensions. We study
in detail the effect of excluded volume interactions and confinement as a function
of the system's temperature, concentration, and strength of the propulsion. We
find a striking nonmonotonic dependence of the pressure on the temperature and
provide simple scaling arguments to predict and explain the occurrence of such
anomalous behavior. We explicitly show how our results have important implications
for the effective forces on passive components suspended in a bath of active particles.
article_number: '052303'
article_processing_charge: No
article_type: original
author:
- first_name: S. A.
full_name: Mallory, S. A.
last_name: Mallory
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: C.
full_name: Valeriani, C.
last_name: Valeriani
- first_name: A.
full_name: Cacciuto, A.
last_name: Cacciuto
citation:
ama: Mallory SA, Šarić A, Valeriani C, Cacciuto A. Anomalous thermomechanical properties
of a self-propelled colloidal fluid. Physical Review E. 2014;89(5). doi:10.1103/physreve.89.052303
apa: Mallory, S. A., Šarić, A., Valeriani, C., & Cacciuto, A. (2014). Anomalous
thermomechanical properties of a self-propelled colloidal fluid. Physical Review
E. American Physical Society. https://doi.org/10.1103/physreve.89.052303
chicago: Mallory, S. A., Anđela Šarić, C. Valeriani, and A. Cacciuto. “Anomalous
Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” Physical
Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.89.052303.
ieee: S. A. Mallory, A. Šarić, C. Valeriani, and A. Cacciuto, “Anomalous thermomechanical
properties of a self-propelled colloidal fluid,” Physical Review E, vol.
89, no. 5. American Physical Society, 2014.
ista: Mallory SA, Šarić A, Valeriani C, Cacciuto A. 2014. Anomalous thermomechanical
properties of a self-propelled colloidal fluid. Physical Review E. 89(5), 052303.
mla: Mallory, S. A., et al. “Anomalous Thermomechanical Properties of a Self-Propelled
Colloidal Fluid.” Physical Review E, vol. 89, no. 5, 052303, American Physical
Society, 2014, doi:10.1103/physreve.89.052303.
short: S.A. Mallory, A. Šarić, C. Valeriani, A. Cacciuto, Physical Review E 89 (2014).
date_created: 2021-11-29T13:10:33Z
date_published: 2014-05-06T00:00:00Z
date_updated: 2021-11-29T13:29:01Z
day: '06'
doi: 10.1103/physreve.89.052303
extern: '1'
external_id:
arxiv:
- '1310.0826'
pmid:
- '25353796'
intvolume: ' 89'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1310.0826
month: '05'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review E
publication_identifier:
eissn:
- 1550-2376
issn:
- 1539-3755
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anomalous thermomechanical properties of a self-propelled colloidal fluid
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 89
year: '2014'
...
---
_id: '1058'
abstract:
- lang: eng
text: Diffraction-unlimited far-field super-resolution fluorescence (nanoscopy)
methods typically rely on transiently transferring fluorophores between two states,
whereby this transfer is usually laid out as a switch. However, depending on whether
this is induced in a spatially controlled manner using a pattern of light (coordinate-targeted)
or stochastically on a single-molecule basis, specific requirements on the fluorophores
are imposed. Therefore, the fluorophores are usually utilized just for one class
of methods only. In this study we demonstrate that the reversibly switchable fluorescent
protein Dreiklang enables live-cell recordings in both spatially controlled and
stochastic modes. We show that the Dreiklang chromophore entails three different
light-induced switching mechanisms, namely a reversible photochemical one, off-switching
by stimulated emission, and a reversible transfer to a long-lived dark state from
the S1 state, all of which can be utilized to overcome the diffraction barrier.
We also find that for the single-molecule- based stochastic GSDIM approach (ground-state
depletion followed by individual molecule return), Dreiklang provides a larger
number of on-off localization events as compared to its progenitor Citrine. Altogether,
Dreiklang is a versatile probe for essentially all popular forms of live-cell
fluorescence nanoscopy.
article_processing_charge: No
author:
- first_name: Nickels
full_name: Jensen, Nickels
last_name: Jensen
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Katrin
full_name: Willig, Katrin
last_name: Willig
- first_name: Flavie
full_name: Lavoie Cardinal, Flavie
last_name: Lavoie Cardinal
- first_name: Tanja
full_name: Brakemann, Tanja
last_name: Brakemann
- first_name: Stefan
full_name: Hell, Stefan
last_name: Hell
- first_name: Stefan
full_name: Jakobs, Stefan
last_name: Jakobs
citation:
ama: Jensen N, Danzl JG, Willig K, et al. Coordinate-targeted and coordinate-stochastic
super-resolution microscopy with the reversibly switchable fluorescent protein
dreiklang. ChemPhysChem. 2014;15(4):756-762. doi:10.1002/cphc.201301034
apa: Jensen, N., Danzl, J. G., Willig, K., Lavoie Cardinal, F., Brakemann, T., Hell,
S., & Jakobs, S. (2014). Coordinate-targeted and coordinate-stochastic super-resolution
microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem.
Wiley-Blackwell. https://doi.org/10.1002/cphc.201301034
chicago: Jensen, Nickels, Johann G Danzl, Katrin Willig, Flavie Lavoie Cardinal,
Tanja Brakemann, Stefan Hell, and Stefan Jakobs. “Coordinate-Targeted and Coordinate-Stochastic
Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein
Dreiklang.” ChemPhysChem. Wiley-Blackwell, 2014. https://doi.org/10.1002/cphc.201301034.
ieee: N. Jensen et al., “Coordinate-targeted and coordinate-stochastic super-resolution
microscopy with the reversibly switchable fluorescent protein dreiklang,” ChemPhysChem,
vol. 15, no. 4. Wiley-Blackwell, pp. 756–762, 2014.
ista: Jensen N, Danzl JG, Willig K, Lavoie Cardinal F, Brakemann T, Hell S, Jakobs
S. 2014. Coordinate-targeted and coordinate-stochastic super-resolution microscopy
with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 15(4),
756–762.
mla: Jensen, Nickels, et al. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution
Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem,
vol. 15, no. 4, Wiley-Blackwell, 2014, pp. 756–62, doi:10.1002/cphc.201301034.
short: N. Jensen, J.G. Danzl, K. Willig, F. Lavoie Cardinal, T. Brakemann, S. Hell,
S. Jakobs, ChemPhysChem 15 (2014) 756–762.
date_created: 2018-12-11T11:49:55Z
date_published: 2014-03-17T00:00:00Z
date_updated: 2021-01-12T06:47:58Z
day: '17'
doi: 10.1002/cphc.201301034
extern: '1'
intvolume: ' 15'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 756 - 762
publication: ChemPhysChem
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6332'
status: public
title: Coordinate-targeted and coordinate-stochastic super-resolution microscopy with
the reversibly switchable fluorescent protein dreiklang
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2014'
...
---
_id: '10815'
abstract:
- lang: eng
text: In the last several decades, developmental biology has clarified the molecular
mechanisms of embryogenesis and organogenesis. In particular, it has demonstrated
that the “tool-kit genes” essential for regulating developmental processes are
not only highly conserved among species, but are also used as systems at various
times and places in an organism to control distinct developmental events. Therefore,
mutations in many of these tool-kit genes may cause congenital diseases involving
morphological abnormalities. This link between genes and abnormal morphological
phenotypes underscores the importance of understanding how cells behave and contribute
to morphogenesis as a result of gene function. Recent improvements in live imaging
and in quantitative analyses of cellular dynamics will advance our understanding
of the cellular pathogenesis of congenital diseases associated with aberrant morphologies.
In these studies, it is critical to select an appropriate model organism for the
particular phenomenon of interest.
acknowledgement: The authors thank all the members of the Division of Morphogenesis,
National Institute for Basic Biology, for their contributions to the research, their
encouragement, and helpful discussions, particularly Dr M. Suzuki for his critical
reading of the manuscript. We also thank the Model Animal Research and Spectrography
and Bioimaging Facilities, NIBB Core Research Facilities, for technical support.
M.H. was supported by a research fellowship from the Japan Society for the Promotion
of Science (JSPS). Our work introduced in this review was supported by a Grant-in-Aid
for Scientific Research on Innovative Areas from the Ministry of Education, Culture,
Sports, Science, and Technology (MEXT), Japan, to N.U.
article_processing_charge: No
article_type: original
author:
- first_name: Masakazu
full_name: Hashimoto, Masakazu
last_name: Hashimoto
- first_name: Hitoshi
full_name: Morita, Hitoshi
id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87
last_name: Morita
- first_name: Naoto
full_name: Ueno, Naoto
last_name: Ueno
citation:
ama: Hashimoto M, Morita H, Ueno N. Molecular and cellular mechanisms of development
underlying congenital diseases. Congenital Anomalies. 2014;54(1):1-7. doi:10.1111/cga.12039
apa: Hashimoto, M., Morita, H., & Ueno, N. (2014). Molecular and cellular mechanisms
of development underlying congenital diseases. Congenital Anomalies. Wiley.
https://doi.org/10.1111/cga.12039
chicago: Hashimoto, Masakazu, Hitoshi Morita, and Naoto Ueno. “Molecular and Cellular
Mechanisms of Development Underlying Congenital Diseases.” Congenital Anomalies.
Wiley, 2014. https://doi.org/10.1111/cga.12039.
ieee: M. Hashimoto, H. Morita, and N. Ueno, “Molecular and cellular mechanisms of
development underlying congenital diseases,” Congenital Anomalies, vol.
54, no. 1. Wiley, pp. 1–7, 2014.
ista: Hashimoto M, Morita H, Ueno N. 2014. Molecular and cellular mechanisms of
development underlying congenital diseases. Congenital Anomalies. 54(1), 1–7.
mla: Hashimoto, Masakazu, et al. “Molecular and Cellular Mechanisms of Development
Underlying Congenital Diseases.” Congenital Anomalies, vol. 54, no. 1,
Wiley, 2014, pp. 1–7, doi:10.1111/cga.12039.
short: M. Hashimoto, H. Morita, N. Ueno, Congenital Anomalies 54 (2014) 1–7.
date_created: 2022-03-04T08:17:25Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2022-03-04T08:26:05Z
day: '01'
department:
- _id: CaHe
doi: 10.1111/cga.12039
external_id:
pmid:
- '24666178'
intvolume: ' 54'
issue: '1'
keyword:
- Developmental Biology
- Embryology
- General Medicine
- Pediatrics
- Perinatology
- and Child Health
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/cga.12039
month: '02'
oa: 1
oa_version: None
page: 1-7
pmid: 1
publication: Congenital Anomalies
publication_identifier:
issn:
- 0914-3505
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular and cellular mechanisms of development underlying congenital diseases
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2014'
...
---
_id: '10811'
abstract:
- lang: eng
text: Auxin is an important signaling compound in plants and vital for plant development
and growth. The present book, Auxin and its Role in Plant Development, provides
the reader with detailed and comprehensive insight into the functioning of the
molecule on the whole and specifically in plant development. In the first part,
the functioning, metabolism and signaling pathways of auxin in plants are explained,
the second part depicts the specific role of auxin in plant development and the
third part describes the interaction and functioning of the signaling compound upon
stimuli of the environment. Each chapter is written by international experts in
the respective field and designed for scientists and researchers in plant biology,
plant development and cell biology to summarize the recent progress in understanding
the role of auxin and suggest future perspectives for auxin research.
article_processing_charge: No
citation:
ama: 'Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development.
1st ed. Vienna: Springer Nature; 2014. doi:10.1007/978-3-7091-1526-8'
apa: 'Zažímalová, E., Petrášek, J., & Benková, E. (Eds.). (2014). Auxin and
Its Role in Plant Development (1st ed.). Vienna: Springer Nature. https://doi.org/10.1007/978-3-7091-1526-8'
chicago: 'Zažímalová, Eva, Jan Petrášek, and Eva Benková, eds. Auxin and Its
Role in Plant Development. 1st ed. Vienna: Springer Nature, 2014. https://doi.org/10.1007/978-3-7091-1526-8.'
ieee: 'E. Zažímalová, J. Petrášek, and E. Benková, Eds., Auxin and Its Role in
Plant Development, 1st ed. Vienna: Springer Nature, 2014.'
ista: 'Zažímalová E, Petrášek J, Benková E eds. 2014. Auxin and Its Role in Plant
Development 1st ed., Vienna: Springer Nature, 444p.'
mla: Zažímalová, Eva, et al., editors. Auxin and Its Role in Plant Development.
1st ed., Springer Nature, 2014, doi:10.1007/978-3-7091-1526-8.
short: E. Zažímalová, J. Petrášek, E. Benková, eds., Auxin and Its Role in Plant
Development, 1st ed., Springer Nature, Vienna, 2014.
date_created: 2022-03-03T11:52:44Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2022-03-04T07:38:15Z
day: '01'
department:
- _id: EvBe
doi: 10.1007/978-3-7091-1526-8
edition: '1'
editor:
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
language:
- iso: eng
month: '04'
oa_version: None
page: '444'
place: Vienna
publication_identifier:
eisbn:
- '9783709115268'
isbn:
- '9783709115251'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Auxin and Its Role in Plant Development
type: book_editor
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '10884'
abstract:
- lang: eng
text: "We revisit the parameterized model checking problem for token-passing systems
and specifications in indexed CTL ∗ \\X. Emerson and Namjoshi (1995, 2003) have
shown that parameterized model checking of indexed CTL ∗ \\X in uni-directional
token rings can be reduced to checking rings up to some cutoff size. Clarke et
al. (2004) have shown a similar result for general topologies and indexed LTL
\\X, provided processes cannot choose the directions for sending or receiving
the token.\r\nWe unify and substantially extend these results by systematically
exploring fragments of indexed CTL ∗ \\X with respect to general topologies.
For each fragment we establish whether a cutoff exists, and for some concrete
topologies, such as rings, cliques and stars, we infer small cutoffs. Finally,
we show that the problem becomes undecidable, and thus no cutoffs exist, if processes
are allowed to choose the directions in which they send or from which they receive
the token."
acknowledgement: "This work was supported by the Austrian Science Fund through grant
P23499-N23\r\nand through the RiSE network (S11403, S11405, S11406, S11407-N23);
ERC Starting Grant (279307: Graph Games); Vienna Science and Technology Fund (WWTF)\r\ngrants
PROSEED, ICT12-059, and VRG11-005."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Benjamin
full_name: Aminof, Benjamin
id: 4A55BD00-F248-11E8-B48F-1D18A9856A87
last_name: Aminof
- first_name: Swen
full_name: Jacobs, Swen
last_name: Jacobs
- first_name: Ayrat
full_name: Khalimov, Ayrat
last_name: Khalimov
- first_name: Sasha
full_name: Rubin, Sasha
id: 2EC51194-F248-11E8-B48F-1D18A9856A87
last_name: Rubin
citation:
ama: 'Aminof B, Jacobs S, Khalimov A, Rubin S. Parameterized model checking of token-passing
systems. In: Verification, Model Checking, and Abstract Interpretation.
Vol 8318. Springer Nature; 2014:262-281. doi:10.1007/978-3-642-54013-4_15'
apa: 'Aminof, B., Jacobs, S., Khalimov, A., & Rubin, S. (2014). Parameterized
model checking of token-passing systems. In Verification, Model Checking, and
Abstract Interpretation (Vol. 8318, pp. 262–281). San Diego, CA, United States:
Springer Nature. https://doi.org/10.1007/978-3-642-54013-4_15'
chicago: Aminof, Benjamin, Swen Jacobs, Ayrat Khalimov, and Sasha Rubin. “Parameterized
Model Checking of Token-Passing Systems.” In Verification, Model Checking,
and Abstract Interpretation, 8318:262–81. Springer Nature, 2014. https://doi.org/10.1007/978-3-642-54013-4_15.
ieee: B. Aminof, S. Jacobs, A. Khalimov, and S. Rubin, “Parameterized model checking
of token-passing systems,” in Verification, Model Checking, and Abstract Interpretation,
San Diego, CA, United States, 2014, vol. 8318, pp. 262–281.
ista: 'Aminof B, Jacobs S, Khalimov A, Rubin S. 2014. Parameterized model checking
of token-passing systems. Verification, Model Checking, and Abstract Interpretation.
VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318,
262–281.'
mla: Aminof, Benjamin, et al. “Parameterized Model Checking of Token-Passing Systems.”
Verification, Model Checking, and Abstract Interpretation, vol. 8318, Springer
Nature, 2014, pp. 262–81, doi:10.1007/978-3-642-54013-4_15.
short: B. Aminof, S. Jacobs, A. Khalimov, S. Rubin, in:, Verification, Model Checking,
and Abstract Interpretation, Springer Nature, 2014, pp. 262–281.
conference:
end_date: 2014-01-21
location: San Diego, CA, United States
name: 'VMCAI: Verifcation, Model Checking, and Abstract Interpretation'
start_date: 2014-01-19
date_created: 2022-03-18T13:01:22Z
date_published: 2014-01-30T00:00:00Z
date_updated: 2022-05-17T08:36:01Z
day: '30'
department:
- _id: KrCh
doi: 10.1007/978-3-642-54013-4_15
ec_funded: 1
external_id:
arxiv:
- '1311.4425'
intvolume: ' 8318'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1311.4425'
month: '01'
oa: 1
oa_version: Preprint
page: 262-281
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Verification, Model Checking, and Abstract Interpretation
publication_identifier:
eisbn:
- '9783642540134'
eissn:
- 1611-3349
isbn:
- '9783642540127'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Parameterized model checking of token-passing systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8318
year: '2014'
...
---
_id: '10893'
abstract:
- lang: eng
text: Saddle periodic orbits are an essential and stable part of the topological
skeleton of a 3D vector field. Nevertheless, there is currently no efficient algorithm
to robustly extract these features. In this chapter, we present a novel technique
to extract saddle periodic orbits. Exploiting the analytic properties of such
an orbit, we propose a scalar measure based on the finite-time Lyapunov exponent
(FTLE) that indicates its presence. Using persistent homology, we can then extract
the robust cycles of this field. These cycles thereby represent the saddle periodic
orbits of the given vector field. We discuss the different existing FTLE approximation
schemes regarding their applicability to this specific problem and propose an
adapted version of FTLE called Normalized Velocity Separation. Finally, we evaluate
our method using simple analytic vector field data.
acknowledgement: First, we thank the reviewers of this paper for their ideas and critical
comments. In addition, we thank Ronny Peikert and Filip Sadlo for a fruitful discussions.
This research is supported by the European Commission under the TOPOSYS project
FP7-ICT-318493-STREP, the European Social Fund (ESF App. No. 100098251), and the
European Science Foundation under the ACAT Research Network Program.
article_processing_charge: No
author:
- first_name: Jens
full_name: Kasten, Jens
last_name: Kasten
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Wieland
full_name: Reich, Wieland
last_name: Reich
- first_name: Gerik
full_name: Scheuermann, Gerik
last_name: Scheuermann
citation:
ama: 'Kasten J, Reininghaus J, Reich W, Scheuermann G. Toward the extraction of
saddle periodic orbits. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological
Methods in Data Analysis and Visualization III . Vol 1. Mathematics and Visualization.
Cham: Springer; 2014:55-69. doi:10.1007/978-3-319-04099-8_4'
apa: 'Kasten, J., Reininghaus, J., Reich, W., & Scheuermann, G. (2014). Toward
the extraction of saddle periodic orbits. In P.-T. Bremer, I. Hotz, V. Pascucci,
& R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization
III (Vol. 1, pp. 55–69). Cham: Springer. https://doi.org/10.1007/978-3-319-04099-8_4'
chicago: 'Kasten, Jens, Jan Reininghaus, Wieland Reich, and Gerik Scheuermann. “Toward
the Extraction of Saddle Periodic Orbits.” In Topological Methods in Data Analysis
and Visualization III , edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci,
and Ronald Peikert, 1:55–69. Mathematics and Visualization. Cham: Springer, 2014.
https://doi.org/10.1007/978-3-319-04099-8_4.'
ieee: 'J. Kasten, J. Reininghaus, W. Reich, and G. Scheuermann, “Toward the extraction
of saddle periodic orbits,” in Topological Methods in Data Analysis and Visualization
III , vol. 1, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Cham:
Springer, 2014, pp. 55–69.'
ista: 'Kasten J, Reininghaus J, Reich W, Scheuermann G. 2014.Toward the extraction
of saddle periodic orbits. In: Topological Methods in Data Analysis and Visualization
III . vol. 1, 55–69.'
mla: Kasten, Jens, et al. “Toward the Extraction of Saddle Periodic Orbits.” Topological
Methods in Data Analysis and Visualization III , edited by Peer-Timo Bremer
et al., vol. 1, Springer, 2014, pp. 55–69, doi:10.1007/978-3-319-04099-8_4.
short: J. Kasten, J. Reininghaus, W. Reich, G. Scheuermann, in:, P.-T. Bremer, I.
Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and
Visualization III , Springer, Cham, 2014, pp. 55–69.
date_created: 2022-03-21T07:11:23Z
date_published: 2014-03-19T00:00:00Z
date_updated: 2022-06-21T12:01:47Z
day: '19'
department:
- _id: HeEd
doi: 10.1007/978-3-319-04099-8_4
ec_funded: 1
editor:
- first_name: Peer-Timo
full_name: Bremer, Peer-Timo
last_name: Bremer
- first_name: Ingrid
full_name: Hotz, Ingrid
last_name: Hotz
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
- first_name: Ronald
full_name: Peikert, Ronald
last_name: Peikert
intvolume: ' 1'
language:
- iso: eng
month: '03'
oa_version: None
page: 55-69
place: Cham
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: 'Topological Methods in Data Analysis and Visualization III '
publication_identifier:
eisbn:
- '9783319040998'
eissn:
- 2197-666X
isbn:
- '9783319040981'
issn:
- 1612-3786
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
series_title: Mathematics and Visualization
status: public
title: Toward the extraction of saddle periodic orbits
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2014'
...
---
_id: '11080'
abstract:
- lang: eng
text: The spindle assembly checkpoint prevents separation of sister chromatids until
each kinetochore is attached to the mitotic spindle. Rodriguez-Bravo et al. report
that the nuclear pore complex scaffolds spindle assembly checkpoint signaling
in interphase, providing a store of inhibitory signals that limits the speed of
the subsequent mitosis.
article_processing_charge: No
article_type: original
author:
- first_name: Abigail
full_name: Buchwalter, Abigail
last_name: Buchwalter
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Buchwalter A, Hetzer M. Nuclear pores set the speed limit for mitosis. Cell.
2014;156(5):868-869. doi:10.1016/j.cell.2014.02.004
apa: Buchwalter, A., & Hetzer, M. (2014). Nuclear pores set the speed limit
for mitosis. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.02.004
chicago: Buchwalter, Abigail, and Martin Hetzer. “Nuclear Pores Set the Speed Limit
for Mitosis.” Cell. Elsevier, 2014. https://doi.org/10.1016/j.cell.2014.02.004.
ieee: A. Buchwalter and M. Hetzer, “Nuclear pores set the speed limit for mitosis,”
Cell, vol. 156, no. 5. Elsevier, pp. 868–869, 2014.
ista: Buchwalter A, Hetzer M. 2014. Nuclear pores set the speed limit for mitosis.
Cell. 156(5), 868–869.
mla: Buchwalter, Abigail, and Martin Hetzer. “Nuclear Pores Set the Speed Limit
for Mitosis.” Cell, vol. 156, no. 5, Elsevier, 2014, pp. 868–69, doi:10.1016/j.cell.2014.02.004.
short: A. Buchwalter, M. Hetzer, Cell 156 (2014) 868–869.
date_created: 2022-04-07T07:50:04Z
date_published: 2014-02-27T00:00:00Z
date_updated: 2022-07-18T08:44:33Z
day: '27'
doi: 10.1016/j.cell.2014.02.004
extern: '1'
external_id:
pmid:
- '24581486'
intvolume: ' 156'
issue: '5'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2014.02.004
month: '02'
oa: 1
oa_version: Published Version
page: 868-869
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nuclear pores set the speed limit for mitosis
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 156
year: '2014'
...
---
_id: '11082'
abstract:
- lang: eng
text: The nuclear pore complex (NPC) plays a critical role in gene expression by
mediating import of transcription regulators into the nucleus and export of RNA
transcripts to the cytoplasm. Emerging evidence suggests that in addition to mediating
transport, a subset of nucleoporins (Nups) engage in transcriptional activation
and elongation at genomic loci that are not associated with NPCs. The underlying
mechanism and regulation of Nup mobility on and off nuclear pores remain unclear.
Here we show that Nup50 is a mobile Nup with a pronounced presence both at the
NPC and in the nucleoplasm that can move between these different localizations.
Strikingly, the dynamic behavior of Nup50 in both locations is dependent on active
transcription by RNA polymerase II and requires the N-terminal half of the protein,
which contains importin α– and Nup153-binding domains. However, Nup50 dynamics
are independent of importin α, Nup153, and Nup98, even though the latter two proteins
also exhibit transcription-dependent mobility. Of interest, depletion of Nup50
from C2C12 myoblasts does not affect cell proliferation but inhibits differentiation
into myotubes. Taken together, our results suggest a transport-independent role
for Nup50 in chromatin biology that occurs away from the NPC.
article_processing_charge: No
article_type: original
author:
- first_name: Abigail L.
full_name: Buchwalter, Abigail L.
last_name: Buchwalter
- first_name: Yun
full_name: Liang, Yun
last_name: Liang
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Buchwalter AL, Liang Y, Hetzer M. Nup50 is required for cell differentiation
and exhibits transcription-dependent dynamics. Molecular Biology of the Cell.
2014;25(16):2472-2484. doi:10.1091/mbc.e14-04-0865
apa: Buchwalter, A. L., Liang, Y., & Hetzer, M. (2014). Nup50 is required for
cell differentiation and exhibits transcription-dependent dynamics. Molecular
Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.e14-04-0865
chicago: Buchwalter, Abigail L., Yun Liang, and Martin Hetzer. “Nup50 Is Required
for Cell Differentiation and Exhibits Transcription-Dependent Dynamics.” Molecular
Biology of the Cell. American Society for Cell Biology, 2014. https://doi.org/10.1091/mbc.e14-04-0865.
ieee: A. L. Buchwalter, Y. Liang, and M. Hetzer, “Nup50 is required for cell differentiation
and exhibits transcription-dependent dynamics,” Molecular Biology of the Cell,
vol. 25, no. 16. American Society for Cell Biology, pp. 2472–2484, 2014.
ista: Buchwalter AL, Liang Y, Hetzer M. 2014. Nup50 is required for cell differentiation
and exhibits transcription-dependent dynamics. Molecular Biology of the Cell.
25(16), 2472–2484.
mla: Buchwalter, Abigail L., et al. “Nup50 Is Required for Cell Differentiation
and Exhibits Transcription-Dependent Dynamics.” Molecular Biology of the Cell,
vol. 25, no. 16, American Society for Cell Biology, 2014, pp. 2472–84, doi:10.1091/mbc.e14-04-0865.
short: A.L. Buchwalter, Y. Liang, M. Hetzer, Molecular Biology of the Cell 25 (2014)
2472–2484.
date_created: 2022-04-07T07:50:24Z
date_published: 2014-08-15T00:00:00Z
date_updated: 2022-07-18T08:45:20Z
day: '15'
doi: 10.1091/mbc.e14-04-0865
extern: '1'
intvolume: ' 25'
issue: '16'
keyword:
- Cell Biology
- Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1091/mbc.e14-04-0865
month: '08'
oa: 1
oa_version: Published Version
page: 2472-2484
publication: Molecular Biology of the Cell
publication_identifier:
issn:
- 1059-1524
- 1939-4586
publication_status: published
publisher: American Society for Cell Biology
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nup50 is required for cell differentiation and exhibits transcription-dependent
dynamics
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 25
year: '2014'
...
---
_id: '11081'
abstract:
- lang: eng
text: In eukaryotic cells the nuclear genome is enclosed by the nuclear envelope
(NE). In metazoans, the NE breaks down in mitosis and it has been assumed that
the physical barrier separating nucleoplasm and cytoplasm remains intact during
the rest of the cell cycle and cell differentiation. However, recent studies suggest
that nonmitotic NE remodeling plays a critical role in development, virus infection,
laminopathies, and cancer. Although the mechanisms underlying these NE restructuring
events are currently being defined, one common theme is activation of protein
kinase C family members in the interphase nucleus to disrupt the nuclear lamina,
demonstrating the importance of the lamina in maintaining nuclear integrity.
article_processing_charge: No
article_type: review
author:
- first_name: Emily
full_name: Hatch, Emily
last_name: Hatch
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Hatch E, Hetzer M. Breaching the nuclear envelope in development and disease.
Journal of Cell Biology. 2014;205(2):133-141. doi:10.1083/jcb.201402003
apa: Hatch, E., & Hetzer, M. (2014). Breaching the nuclear envelope in development
and disease. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201402003
chicago: Hatch, Emily, and Martin Hetzer. “Breaching the Nuclear Envelope in Development
and Disease.” Journal of Cell Biology. Rockefeller University Press, 2014.
https://doi.org/10.1083/jcb.201402003.
ieee: E. Hatch and M. Hetzer, “Breaching the nuclear envelope in development and
disease,” Journal of Cell Biology, vol. 205, no. 2. Rockefeller University
Press, pp. 133–141, 2014.
ista: Hatch E, Hetzer M. 2014. Breaching the nuclear envelope in development and
disease. Journal of Cell Biology. 205(2), 133–141.
mla: Hatch, Emily, and Martin Hetzer. “Breaching the Nuclear Envelope in Development
and Disease.” Journal of Cell Biology, vol. 205, no. 2, Rockefeller University
Press, 2014, pp. 133–41, doi:10.1083/jcb.201402003.
short: E. Hatch, M. Hetzer, Journal of Cell Biology 205 (2014) 133–141.
date_created: 2022-04-07T07:50:13Z
date_published: 2014-04-21T00:00:00Z
date_updated: 2022-07-18T08:45:09Z
day: '21'
doi: 10.1083/jcb.201402003
extern: '1'
external_id:
pmid:
- '24751535'
intvolume: ' 205'
issue: '2'
keyword:
- Cell Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1083/jcb.201402003
month: '04'
oa: 1
oa_version: Published Version
page: 133-141
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
issn:
- 1540-8140
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Breaching the nuclear envelope in development and disease
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 205
year: '2014'
...
---
_id: '11583'
abstract:
- lang: eng
text: 'Candidate galaxies at redshifts of z ∼ 10 are now being found in extremely
deep surveys, probing very small areas. As a consequence, candidates are very
faint, making spectroscopic confirmation practically impossible. In order to overcome
such limitations, we have undertaken the CF-HiZELS survey, which is a large-area,
medium-depth near-infrared narrow-band survey targeted at z = 8.8 Lyman α (Lyα)
emitters (LAEs) and covering 10 deg2 in part of the SSA22 field with the Canada–France–Hawaii
Telescope (CFHT). We surveyed a comoving volume of 4.7 × 106 Mpc3 to a Lyα luminosity
limit of 6.3 × 1043舁erg舁s−1. We look for Lyα candidates by applying the following
criteria: (i) clear emission-line source, (ii) no optical detections (ugriz from
CFHTLS), (iii) no visible detection in the optical stack (ugriz > 27), (iv) visually
checked reliable NBJ and J detections and (v) J − K ≤ 0. We compute photometric
redshifts and remove a significant amount of dusty lower redshift line-emitters
at z ∼ 1.4 or 2.2. A total of 13 Lyα candidates were found, of which two are marked
as strong candidates, but the majority have very weak constraints on their spectral
energy distributions. Using follow-up observations with SINFONI/VLT, we are able
to exclude the most robust candidates as LAEs. We put a strong constraint on the
Lyα luminosity function at z ∼ 9 and make realistic predictions for ongoing and
future surveys. Our results show that surveys for the highest redshift LAEs are
susceptible of multiple contaminations and that spectroscopic follow-up is absolutely
necessary.'
acknowledgement: We thank the anonymous referee for the comments and suggestions which
improved both the quality and clarity of this work. DS acknowledges financial support
from the Netherlands Organisation for Scientific Research (NWO) through a Veni fellowship.
IRS acknowledges support from STFC (ST/I001573/1), a Leverhulme Fellowship, the
ERC Advanced Investigator programme DUSTYGAL 321334 and a Royal Society/Wolfson
Merit Award. PNB acknowledges support from the Leverhulme Trust. JWK acknowledges
the support from the Creative Research Initiative Program, no. 2008- 0060544, of
the National Research Foundation of Korea (NRF) funded by the Korean government
(MSIP). JPUF and BMJ acknowledge support from the ERC-StG grant EGGS-278202. The
Dark Cosmology Centre is funded by the Danish National Research Foundation. This
work is based in part on data obtained as part of the UKIRT Infrared Deep Sky Survey.
Based on observations obtained with MegaPrime/MegaCam, a joint project of CFHT and
CEA/IRFU, at the Canada–France–Hawaii Telescope (CFHT) which is operated by the
National Research Council (NRC) of Canada, the Institut National des Science de
l’Univers of the Centre National de la Recherche Scientifique (CNRS) of France and
the University of Hawaii. This work is based in part on data products produced at
Terapix available at the Canadian Astronomy Data Centre as part of the Canada-France-Hawaii
Telescope Legacy Survey, a collaborative project of NRC and CNRS. This work was
only possible due to OPTICON/FP7 and the access that it granted to the CFHT telescope.
The authors also wish to acknowledge the CFHTLS and UKIDSS surveys for their excellent
legacy and complementary value – without such high-quality data sets, this research
would not have been possible.
article_processing_charge: No
article_type: original
author:
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: David
full_name: Sobral, David
last_name: Sobral
- first_name: A. M.
full_name: Swinbank, A. M.
last_name: Swinbank
- first_name: Ian
full_name: Smail, Ian
last_name: Smail
- first_name: P. N.
full_name: Best, P. N.
last_name: Best
- first_name: Jae-Woo
full_name: Kim, Jae-Woo
last_name: Kim
- first_name: Marijn
full_name: Franx, Marijn
last_name: Franx
- first_name: Bo
full_name: Milvang-Jensen, Bo
last_name: Milvang-Jensen
- first_name: Johan
full_name: Fynbo, Johan
last_name: Fynbo
citation:
ama: 'Matthee JJ, Sobral D, Swinbank AM, et al. A 10 deg2 Lyman α survey at z=8.8
with spectroscopic follow-up: Strong constraints on the luminosity function and
implications for other surveys. Monthly Notices of the Royal Astronomical Society.
2014;440(3):2375-2387. doi:10.1093/mnras/stu392'
apa: 'Matthee, J. J., Sobral, D., Swinbank, A. M., Smail, I., Best, P. N., Kim,
J.-W., … Fynbo, J. (2014). A 10 deg2 Lyman α survey at z=8.8 with spectroscopic
follow-up: Strong constraints on the luminosity function and implications for
other surveys. Monthly Notices of the Royal Astronomical Society. Oxford
University Press. https://doi.org/10.1093/mnras/stu392'
chicago: 'Matthee, Jorryt J, David Sobral, A. M. Swinbank, Ian Smail, P. N. Best,
Jae-Woo Kim, Marijn Franx, Bo Milvang-Jensen, and Johan Fynbo. “A 10 Deg2 Lyman
α Survey at Z=8.8 with Spectroscopic Follow-up: Strong Constraints on the Luminosity
Function and Implications for Other Surveys.” Monthly Notices of the Royal
Astronomical Society. Oxford University Press, 2014. https://doi.org/10.1093/mnras/stu392.'
ieee: 'J. J. Matthee et al., “A 10 deg2 Lyman α survey at z=8.8 with spectroscopic
follow-up: Strong constraints on the luminosity function and implications for
other surveys,” Monthly Notices of the Royal Astronomical Society, vol.
440, no. 3. Oxford University Press, pp. 2375–2387, 2014.'
ista: 'Matthee JJ, Sobral D, Swinbank AM, Smail I, Best PN, Kim J-W, Franx M, Milvang-Jensen
B, Fynbo J. 2014. A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up:
Strong constraints on the luminosity function and implications for other surveys.
Monthly Notices of the Royal Astronomical Society. 440(3), 2375–2387.'
mla: 'Matthee, Jorryt J., et al. “A 10 Deg2 Lyman α Survey at Z=8.8 with Spectroscopic
Follow-up: Strong Constraints on the Luminosity Function and Implications for
Other Surveys.” Monthly Notices of the Royal Astronomical Society, vol.
440, no. 3, Oxford University Press, 2014, pp. 2375–87, doi:10.1093/mnras/stu392.'
short: J.J. Matthee, D. Sobral, A.M. Swinbank, I. Smail, P.N. Best, J.-W. Kim, M.
Franx, B. Milvang-Jensen, J. Fynbo, Monthly Notices of the Royal Astronomical
Society 440 (2014) 2375–2387.
date_created: 2022-07-14T12:33:24Z
date_published: 2014-05-21T00:00:00Z
date_updated: 2022-08-19T08:30:30Z
day: '21'
doi: 10.1093/mnras/stu392
extern: '1'
external_id:
arxiv:
- '1402.6697'
intvolume: ' 440'
issue: '3'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: evolution'
- 'galaxies: high-redshift'
- 'cosmology: observations'
- dark ages
- reionization
- first stars
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1402.6697
month: '05'
oa: 1
oa_version: Preprint
page: 2375-2387
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints
on the luminosity function and implications for other surveys'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 440
year: '2014'
...
---
_id: '11582'
abstract:
- lang: eng
text: We have observed a sample of typical z ∼ 1 star-forming galaxies, selected
from the HiZELS survey, with the new K-band Multi-Object Spectrograph (KMOS) near-infrared,
multi-integral field unit instrument on the Very Large Telescope (VLT), in order
to obtain their dynamics and metallicity gradients. The majority of our galaxies
have a metallicity gradient consistent with being flat or negative (i.e. higher
metallicity cores than outskirts). Intriguingly, we find a trend between metallicity
gradient and specific star formation rate (sSFR), such that galaxies with a high
sSFR tend to have relatively metal poor centres, a result which is strengthened
when combined with data sets from the literature. This result appears to explain
the discrepancies reported between different high-redshift studies and varying
claims for evolution. From a galaxy evolution perspective, the trend we see would
mean that a galaxy's sSFR is governed by the amount of metal-poor gas that can
be funnelled into its core, triggered either by merging or through efficient accretion.
In fact, merging may play a significant role as it is the starburst galaxies at
all epochs, which have the more positive metallicity gradients. Our results may
help to explain the origin of the fundamental metallicity relation, in which galaxies
at a fixed mass are observed to have lower metallicities at higher star formation
rates, especially if the metallicity is measured in an aperture encompassing only
the central regions of the galaxy. Finally, we note that this study demonstrates
the power of KMOS as an efficient instrument for large-scale resolved galaxy surveys.
acknowledgement: First, we acknowledge the referee for their comments, which have
improved the clarity of this paper. JPS and IRS acknowledge support from STFC (ST/I001573/1).
IRS also acknowledges support from the ERC Advanced Investigator programme DUSTYGAL
and a Royal Society/Wolfson Merit Award. DS acknowledges financial support from
NWO through a Veni fellowship and from FCT through the award of an FCT-IF starting
grant. PNB acknowledges STFC for financial support.
article_processing_charge: No
article_type: original
author:
- first_name: John P.
full_name: Stott, John P.
last_name: Stott
- first_name: David
full_name: Sobral, David
last_name: Sobral
- first_name: A. M.
full_name: Swinbank, A. M.
last_name: Swinbank
- first_name: Ian
full_name: Smail, Ian
last_name: Smail
- first_name: Richard
full_name: Bower, Richard
last_name: Bower
- first_name: Philip N.
full_name: Best, Philip N.
last_name: Best
- first_name: Ray M.
full_name: Sharples, Ray M.
last_name: Sharples
- first_name: James E.
full_name: Geach, James E.
last_name: Geach
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
citation:
ama: Stott JP, Sobral D, Swinbank AM, et al. A relationship between specific star
formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS.
Monthly Notices of the Royal Astronomical Society. 2014;443(3):2695-2704.
doi:10.1093/mnras/stu1343
apa: Stott, J. P., Sobral, D., Swinbank, A. M., Smail, I., Bower, R., Best, P. N.,
… Matthee, J. J. (2014). A relationship between specific star formation rate and
metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices
of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stu1343
chicago: Stott, John P., David Sobral, A. M. Swinbank, Ian Smail, Richard Bower,
Philip N. Best, Ray M. Sharples, James E. Geach, and Jorryt J Matthee. “A Relationship
between Specific Star Formation Rate and Metallicity Gradient within z ∼ 1 Galaxies
from KMOS-HiZELS.” Monthly Notices of the Royal Astronomical Society. Oxford
University Press, 2014. https://doi.org/10.1093/mnras/stu1343.
ieee: J. P. Stott et al., “A relationship between specific star formation
rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS,” Monthly
Notices of the Royal Astronomical Society, vol. 443, no. 3. Oxford University
Press, pp. 2695–2704, 2014.
ista: Stott JP, Sobral D, Swinbank AM, Smail I, Bower R, Best PN, Sharples RM, Geach
JE, Matthee JJ. 2014. A relationship between specific star formation rate and
metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices of
the Royal Astronomical Society. 443(3), 2695–2704.
mla: Stott, John P., et al. “A Relationship between Specific Star Formation Rate
and Metallicity Gradient within z ∼ 1 Galaxies from KMOS-HiZELS.” Monthly Notices
of the Royal Astronomical Society, vol. 443, no. 3, Oxford University Press,
2014, pp. 2695–704, doi:10.1093/mnras/stu1343.
short: J.P. Stott, D. Sobral, A.M. Swinbank, I. Smail, R. Bower, P.N. Best, R.M.
Sharples, J.E. Geach, J.J. Matthee, Monthly Notices of the Royal Astronomical
Society 443 (2014) 2695–2704.
date_created: 2022-07-14T12:16:10Z
date_published: 2014-09-21T00:00:00Z
date_updated: 2022-08-19T08:27:25Z
day: '21'
doi: 10.1093/mnras/stu1343
extern: '1'
external_id:
arxiv:
- '1407.1047'
intvolume: ' 443'
issue: '3'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: abundances'
- 'galaxies: evolution'
- 'galaxies: kinematics and dynamics'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1407.1047
month: '09'
oa: 1
oa_version: Preprint
page: 2695-2704
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: A relationship between specific star formation rate and metallicity gradient
within z ∼ 1 galaxies from KMOS-HiZELS
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 443
year: '2014'
...
---
_id: '11750'
abstract:
- lang: eng
text: We report on the magnetic properties of a hot-pressed FeSb 2 sample. We find
a significant increase in the magnetic susceptibility in our sample when compared
with the values previously reported for the polycrystalline sample. The pronounced
Curie tail at low temperature corresponds to 0.2% of Fe 2+ impurities per mole.
In the intrinsic conductivity region, the susceptibility due to free carriers
shows thermally activated behavior and is consistent with the data reported for
single crystal FeSb 2 . Based on our data and analysis, while the enhanced magnetic
susceptibility in our sample comes mainly from a small amount of unreacted Fe,
the contribution from the enhanced carrier density due to lattice and strain defects
arising from the ball milling process is also significant. Existence of an unreacted
Fe phase is evidenced by small coercivity values of ~100 observed at 50 and 300
K.
article_number: '6675864'
article_processing_charge: No
article_type: original
author:
- first_name: Mani
full_name: Pokharel, Mani
last_name: Pokharel
- first_name: Huaizhou
full_name: Zhao, Huaizhou
last_name: Zhao
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: Zhifeng
full_name: Ren, Zhifeng
last_name: Ren
- first_name: Cyril
full_name: Opeil, Cyril
last_name: Opeil
citation:
ama: Pokharel M, Zhao H, Modic KA, Ren Z, Opeil C. Magnetic properties of hot-pressed
FeSb2. IEEE Transactions on Magnetics. 2014;50(5). doi:10.1109/TMAG.2013.2292607
apa: Pokharel, M., Zhao, H., Modic, K. A., Ren, Z., & Opeil, C. (2014). Magnetic
properties of hot-pressed FeSb2. IEEE Transactions on Magnetics. Institute
of Electrical and Electronics Engineers. https://doi.org/10.1109/TMAG.2013.2292607
chicago: Pokharel, Mani, Huaizhou Zhao, Kimberly A Modic, Zhifeng Ren, and Cyril
Opeil. “Magnetic Properties of Hot-Pressed FeSb2.” IEEE Transactions on Magnetics.
Institute of Electrical and Electronics Engineers, 2014. https://doi.org/10.1109/TMAG.2013.2292607.
ieee: M. Pokharel, H. Zhao, K. A. Modic, Z. Ren, and C. Opeil, “Magnetic properties
of hot-pressed FeSb2,” IEEE Transactions on Magnetics, vol. 50, no. 5.
Institute of Electrical and Electronics Engineers, 2014.
ista: Pokharel M, Zhao H, Modic KA, Ren Z, Opeil C. 2014. Magnetic properties of
hot-pressed FeSb2. IEEE Transactions on Magnetics. 50(5), 6675864.
mla: Pokharel, Mani, et al. “Magnetic Properties of Hot-Pressed FeSb2.” IEEE
Transactions on Magnetics, vol. 50, no. 5, 6675864, Institute of Electrical
and Electronics Engineers, 2014, doi:10.1109/TMAG.2013.2292607.
short: M. Pokharel, H. Zhao, K.A. Modic, Z. Ren, C. Opeil, IEEE Transactions on
Magnetics 50 (2014).
date_created: 2022-08-08T08:26:02Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2022-08-11T09:51:22Z
day: '01'
doi: 10.1109/TMAG.2013.2292607
extern: '1'
intvolume: ' 50'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
publication: IEEE Transactions on Magnetics
publication_identifier:
eissn:
- 1941-0069
issn:
- 0018-9464
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Magnetic properties of hot-pressed FeSb2
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2014'
...
---
_id: '11789'
abstract:
- lang: eng
text: "We study a weighted online bipartite matching problem: G(V 1, V 2, E) is
a weighted bipartite graph where V 1 is known beforehand and the vertices of V
2 arrive online. The goal is to match vertices of V 2 as they arrive to vertices
in V 1, so as to maximize the sum of weights of edges in the matching. If assignments
to V 1 cannot be changed, no bounded competitive ratio is achievable. We study
the weighted online matching problem with free disposal, where vertices in V 1
can be assigned multiple times, but only get credit for the maximum weight edge
assigned to them over the course of the algorithm. For this problem, the greedy
algorithm is 0.5-competitive and determining whether a better competitive ratio
is achievable is a well known open problem.\r\n\r\nWe identify an interesting
special case where the edge weights are decomposable as the product of two factors,
one corresponding to each end point of the edge. This is analogous to the well
studied related machines model in the scheduling literature, although the objective
functions are different. For this case of decomposable edge weights, we design
a 0.5664 competitive randomized algorithm in complete bipartite graphs. We show
that such instances with decomposable weights are non-trivial by establishing
upper bounds of 0.618 for deterministic and 0.8 for randomized algorithms.\r\n\r\nA
tight competitive ratio of 1 − 1/e ≈ 0.632 was known previously for both the 0-1
case as well as the case where edge weights depend on the offline vertices only,
but for these cases, reassignments cannot change the quality of the solution.
Beating 0.5 for weighted matching where reassignments are necessary has been a
significant challenge. We thus give the first online algorithm with competitive
ratio strictly better than 0.5 for a non-trivial case of weighted matching with
free disposal."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Moses
full_name: Charikar, Moses
last_name: Charikar
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Huy L.
full_name: Nguyễn, Huy L.
last_name: Nguyễn
citation:
ama: 'Charikar M, Henzinger MH, Nguyễn HL. Online bipartite matching with decomposable
weights. In: 22nd Annual European Symposium on Algorithms. Vol 8737. Springer
Nature; 2014:260-271. doi:10.1007/978-3-662-44777-2_22'
apa: 'Charikar, M., Henzinger, M. H., & Nguyễn, H. L. (2014). Online bipartite
matching with decomposable weights. In 22nd Annual European Symposium on Algorithms
(Vol. 8737, pp. 260–271). Wroclaw, Poland: Springer Nature. https://doi.org/10.1007/978-3-662-44777-2_22'
chicago: Charikar, Moses, Monika H Henzinger, and Huy L. Nguyễn. “Online Bipartite
Matching with Decomposable Weights.” In 22nd Annual European Symposium on Algorithms,
8737:260–71. Springer Nature, 2014. https://doi.org/10.1007/978-3-662-44777-2_22.
ieee: M. Charikar, M. H. Henzinger, and H. L. Nguyễn, “Online bipartite matching
with decomposable weights,” in 22nd Annual European Symposium on Algorithms,
Wroclaw, Poland, 2014, vol. 8737, pp. 260–271.
ista: 'Charikar M, Henzinger MH, Nguyễn HL. 2014. Online bipartite matching with
decomposable weights. 22nd Annual European Symposium on Algorithms. ESA: Annual
European Symposium on Algorithms, LNCS, vol. 8737, 260–271.'
mla: Charikar, Moses, et al. “Online Bipartite Matching with Decomposable Weights.”
22nd Annual European Symposium on Algorithms, vol. 8737, Springer Nature,
2014, pp. 260–71, doi:10.1007/978-3-662-44777-2_22.
short: M. Charikar, M.H. Henzinger, H.L. Nguyễn, in:, 22nd Annual European Symposium
on Algorithms, Springer Nature, 2014, pp. 260–271.
conference:
end_date: 2014-09-10
location: Wroclaw, Poland
name: 'ESA: Annual European Symposium on Algorithms'
start_date: 2014-09-08
date_created: 2022-08-11T10:41:47Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2023-02-13T11:16:24Z
day: '01'
doi: 10.1007/978-3-662-44777-2_22
extern: '1'
external_id:
arxiv:
- '1409.2139'
intvolume: ' 8737'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1409.2139
month: '09'
oa: 1
oa_version: Preprint
page: 260 - 271
publication: 22nd Annual European Symposium on Algorithms
publication_identifier:
isbn:
- 978-366244776-5
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Online bipartite matching with decomposable weights
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8737
year: '2014'
...
---
_id: '11790'
abstract:
- lang: eng
text: "Assume a seller wants to sell a digital product in a social network where
a buyer’s valuation of the item has positive network externalities from her neighbors
that already have the item. The goal of the seller is to maximize his revenue.
Previous work on this problem [7] studies the case where clients are offered the
item in sequence and have to pay personalized prices. This is highly infeasible
in large scale networks such as the Facebook graph: (1) Offering items to the
clients one after the other consumes a large amount of time, and (2) price-discrimination
of clients could appear unfair to them and result in negative client reaction
or could conflict with legal requirements.\r\n\r\nWe study a setting dealing with
these issues. Specifically, the item is offered in parallel to multiple clients
at the same time and at the same price. This is called a round. We show that with
O(logn) rounds, where n is the number of clients, a constant factor of the revenue
with price discrimination can be achieved and that this is not possible with o(logn)
rounds. Moreover we show that it is APX-hard to maximize the revenue and we give
constant factor approximation algorithms for various further settings of limited
price discrimination."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Luděk
full_name: Cigler, Luděk
last_name: Cigler
- first_name: Wolfgang
full_name: Dvořák, Wolfgang
last_name: Dvořák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Martin
full_name: Starnberger, Martin
last_name: Starnberger
citation:
ama: 'Cigler L, Dvořák W, Henzinger MH, Starnberger M. Limiting price discrimination
when selling products with positive network externalities. In: 10th International
Conference of Web and Internet Economics. Vol 8877. Springer Nature; 2014:44-57.
doi:10.1007/978-3-319-13129-0_4'
apa: 'Cigler, L., Dvořák, W., Henzinger, M. H., & Starnberger, M. (2014). Limiting
price discrimination when selling products with positive network externalities.
In 10th International Conference of Web and Internet Economics (Vol. 8877,
pp. 44–57). Beijing, China: Springer Nature. https://doi.org/10.1007/978-3-319-13129-0_4'
chicago: Cigler, Luděk, Wolfgang Dvořák, Monika H Henzinger, and Martin Starnberger.
“Limiting Price Discrimination When Selling Products with Positive Network Externalities.”
In 10th International Conference of Web and Internet Economics, 8877:44–57.
Springer Nature, 2014. https://doi.org/10.1007/978-3-319-13129-0_4.
ieee: L. Cigler, W. Dvořák, M. H. Henzinger, and M. Starnberger, “Limiting price
discrimination when selling products with positive network externalities,” in
10th International Conference of Web and Internet Economics, Beijing, China,
2014, vol. 8877, pp. 44–57.
ista: 'Cigler L, Dvořák W, Henzinger MH, Starnberger M. 2014. Limiting price discrimination
when selling products with positive network externalities. 10th International
Conference of Web and Internet Economics. WINE: International Conference on Web
and Internet Economics, LNCS, vol. 8877, 44–57.'
mla: Cigler, Luděk, et al. “Limiting Price Discrimination When Selling Products
with Positive Network Externalities.” 10th International Conference of Web
and Internet Economics, vol. 8877, Springer Nature, 2014, pp. 44–57, doi:10.1007/978-3-319-13129-0_4.
short: L. Cigler, W. Dvořák, M.H. Henzinger, M. Starnberger, in:, 10th International
Conference of Web and Internet Economics, Springer Nature, 2014, pp. 44–57.
conference:
end_date: 2014-12-17
location: Beijing, China
name: 'WINE: International Conference on Web and Internet Economics'
start_date: 2014-12-14
date_created: 2022-08-11T10:58:44Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2023-02-13T11:18:30Z
day: '01'
doi: 10.1007/978-3-319-13129-0_4
extern: '1'
intvolume: ' 8877'
language:
- iso: eng
month: '12'
oa_version: None
page: 44 - 57
publication: 10th International Conference of Web and Internet Economics
publication_identifier:
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Limiting price discrimination when selling products with positive network externalities
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8877
year: '2014'
...
---
_id: '118'
abstract:
- lang: eng
text: While the penetration of objects into granular media is well-studied, there
is little understanding of how objects settle in gravities, geff, different from
that of Earth - a scenario potentially relevant to the geomorphology of planets
and asteroids and also to their exploration using man-made devices. By conducting
experiments in an accelerating frame, we explore geff ranging from 0.4 g to 1.2
g. Surprisingly, we find that the rest depth is independent of geff and also that
the time required for the object to come to rest scales like geff-1/2. With discrete
element modeling simulations, we reproduce the experimental results and extend
the range of geff to objects as small as asteroids and as large as Jupiter. Our
results shed light on the initial stage of sedimentation into dry granular media
across a range of celestial bodies and also have implications for the design of
man-made, extraterrestrial vehicles and structures. Key Points The settling depth
in granular media is independent of gravity The settling time scales like g-1/2
Layering driven by granular sedimentation should be similar.
acknowledgement: 'The Spanish MINECO project FIS2011-26675, the PIUNA program (U.
Navarra), and the Project 29942WL (Fonds de Solidarité Prioritaire France-Cuba)
have partially supported this research. '
author:
- first_name: Ernesto
full_name: Altshuler, Ernesto
last_name: Altshuler
- first_name: H
full_name: Torres, H
last_name: Torres
- first_name: A
full_name: González_Pita, A
last_name: González_Pita
- first_name: Colina G
full_name: Sánchez, Colina G
last_name: Sánchez
- first_name: Carlos
full_name: Pérez Penichet, Carlos
last_name: Pérez Penichet
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: Rauól
full_name: Hidalgo, Rauól
last_name: Hidalgo
citation:
ama: Altshuler E, Torres H, González_Pita A, et al. Settling into dry granular media
in different gravities. Geophysical Research Letters. 2014;41(9):3032-3037.
doi:10.1002/2014GL059229
apa: Altshuler, E., Torres, H., González_Pita, A., Sánchez, C. G., Pérez Penichet,
C., Waitukaitis, S. R., & Hidalgo, R. (2014). Settling into dry granular media
in different gravities. Geophysical Research Letters. Wiley-Blackwell.
https://doi.org/10.1002/2014GL059229
chicago: Altshuler, Ernesto, H Torres, A González_Pita, Colina G Sánchez, Carlos
Pérez Penichet, Scott R Waitukaitis, and Rauól Hidalgo. “Settling into Dry Granular
Media in Different Gravities.” Geophysical Research Letters. Wiley-Blackwell,
2014. https://doi.org/10.1002/2014GL059229.
ieee: E. Altshuler et al., “Settling into dry granular media in different
gravities,” Geophysical Research Letters, vol. 41, no. 9. Wiley-Blackwell,
pp. 3032–3037, 2014.
ista: Altshuler E, Torres H, González_Pita A, Sánchez CG, Pérez Penichet C, Waitukaitis
SR, Hidalgo R. 2014. Settling into dry granular media in different gravities.
Geophysical Research Letters. 41(9), 3032–3037.
mla: Altshuler, Ernesto, et al. “Settling into Dry Granular Media in Different Gravities.”
Geophysical Research Letters, vol. 41, no. 9, Wiley-Blackwell, 2014, pp.
3032–37, doi:10.1002/2014GL059229.
short: E. Altshuler, H. Torres, A. González_Pita, C.G. Sánchez, C. Pérez Penichet,
S.R. Waitukaitis, R. Hidalgo, Geophysical Research Letters 41 (2014) 3032–3037.
date_created: 2018-12-11T11:44:43Z
date_published: 2014-05-16T00:00:00Z
date_updated: 2021-01-12T06:48:53Z
day: '16'
doi: 10.1002/2014GL059229
extern: '1'
intvolume: ' 41'
issue: '9'
language:
- iso: eng
month: '05'
oa_version: None
page: 3032 - 3037
publication: Geophysical Research Letters
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7936'
quality_controlled: '1'
status: public
title: Settling into dry granular media in different gravities
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 41
year: '2014'
...
---
_id: '11855'
abstract:
- lang: eng
text: 'The decremental single-source shortest paths (SSSP) problem concerns maintaining
the distances between a given source node s to every node in an n-node m-edge
graph G undergoing edge deletions. While its static counterpart can be easily
solved in near-linear time, this decremental problem is much more challenging
even in the undirected unweighted case. In this case, the classic O(mn) total
update time of Even and Shiloach (JACM 1981) has been the fastest known algorithm
for three decades. With the loss of a (1 + ε)-approximation factor, the running
time was recently improved to O(n 2+o(1) ) by Bernstein and Roditty (SODA 2011),
and more recently to O(n 1.8+o(1) + m 1+o(1) ) by Henzinger, Krinninger, and Nanongkai
(SODA 2014). In this paper, we finally bring the running time of this case down
to near-linear: We give a (1 + ε)-approximation algorithm with O(m 1+o(1) ) total
update time, thus obtaining near-linear time. Moreover, we obtain O(m 1+o(1) log
W) time for the weighted case, where the edge weights are integers from 1 to W.
The only prior work on weighted graphs in o(mn log W) time is the O(mn 0.986 log
W)-time algorithm by Henzinger, Krinninger, and Nanongkai (STOC 2014) which works
for the general weighted directed case. In contrast to the previous results which
rely on maintaining a sparse emulator, our algorithm relies on maintaining a so-called
sparse (d, ε)-hop set introduced by Cohen (JACM 2000) in the PRAM literature.
A (d, ε)-hop set of a graph G = (V, E) is a set E'' of weighted edges such that
the distance between any pair of nodes in G can be (1 + ε)-approximated by their
d-hop distance (given by a path containing at most d edges) on G''=(V, E∪E'').
Our algorithm can maintain an (n o(1) , ε)-hop set of near-linear size in near-linear
time under edge deletions. It is the first of its kind to the best of our knowledge.
To maintain the distances on this hop set, we develop a monotone bounded-hop Even-Shiloach
tree. It results from extending and combining the monotone Even-Shiloach tree
of Henzinger, Krinninger, and Nanongkai (FOCS 2013) with the bounded-hop SSSP
technique of Bernstein (STOC 2013). These two new tools might be of independent
interest.'
article_processing_charge: No
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Henzinger MH, Krinninger S, Nanongkai D. Decremental single-source shortest
paths on undirected graphs in near-linear total update time. In: 55th Annual
Symposium on Foundations of Computer Science. Institute of Electrical and
Electronics Engineers; 2014:146-155. doi:10.1109/focs.2014.24'
apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Decremental
single-source shortest paths on undirected graphs in near-linear total update
time. In 55th Annual Symposium on Foundations of Computer Science (pp.
146–155). Philadelphia, PA, United States: Institute of Electrical and Electronics
Engineers. https://doi.org/10.1109/focs.2014.24'
chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Decremental
Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update
Time.” In 55th Annual Symposium on Foundations of Computer Science, 146–55.
Institute of Electrical and Electronics Engineers, 2014. https://doi.org/10.1109/focs.2014.24.
ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Decremental single-source
shortest paths on undirected graphs in near-linear total update time,” in 55th
Annual Symposium on Foundations of Computer Science, Philadelphia, PA, United
States, 2014, pp. 146–155.
ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2014. Decremental single-source
shortest paths on undirected graphs in near-linear total update time. 55th Annual
Symposium on Foundations of Computer Science. FOCS: Annual Symposium on Foundations
of Computer Science, 146–155.'
mla: Henzinger, Monika H., et al. “Decremental Single-Source Shortest Paths on Undirected
Graphs in near-Linear Total Update Time.” 55th Annual Symposium on Foundations
of Computer Science, Institute of Electrical and Electronics Engineers, 2014,
pp. 146–55, doi:10.1109/focs.2014.24.
short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 55th Annual Symposium on
Foundations of Computer Science, Institute of Electrical and Electronics Engineers,
2014, pp. 146–155.
conference:
end_date: 2014-10-21
location: Philadelphia, PA, United States
name: 'FOCS: Annual Symposium on Foundations of Computer Science'
start_date: 2014-10-18
date_created: 2022-08-16T08:14:33Z
date_published: 2014-10-01T00:00:00Z
date_updated: 2023-02-21T16:27:34Z
day: '01'
doi: 10.1109/focs.2014.24
extern: '1'
external_id:
arxiv:
- '1402.0054'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1402.0054
month: '10'
oa: 1
oa_version: Preprint
page: 146-155
publication: 55th Annual Symposium on Foundations of Computer Science
publication_identifier:
eisbn:
- 978-1-4799-6517-5
issn:
- 0272-5428
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
related_material:
record:
- id: '11768'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Decremental single-source shortest paths on undirected graphs in near-linear
total update time
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '11870'
abstract:
- lang: eng
text: "We consider dynamic algorithms for maintaining Single-Source Reachability
(SSR) and approximate Single-Source Shortest Paths (SSSP) on n-node m-edge directed
graphs under edge deletions (decremental algorithms). The previous fastest algorithm
for SSR and SSSP goes back three decades to Even and Shiloach (JACM 1981); it
has O(1) query time and O(mn) total update time (i.e., linear amortized update
time if all edges are deleted). This algorithm serves as a building block for
several other dynamic algorithms. The question whether its total update time can
be improved is a major, long standing, open problem.\r\n\r\nIn this paper, we
answer this question affirmatively. We obtain a randomized algorithm which, in
a simplified form, achieves an Õ(mn0.984) expected total update time for SSR and
(1 + ε)-approximate SSSP, where Õ(·) hides poly log n. We also extend our algorithm
to achieve roughly the same running time for Strongly Connected Components (SCC),
improving the algorithm of Roditty and Zwick (FOCS 2002), and an algorithm that
improves the Õ (mn log W)-time algorithm of Bernstein (STOC 2013) for approximating
SSSP on weighted directed graphs, where the edge weights are integers from 1 to
W. All our algorithms have constant query time in the worst case."
article_number: 674 - 683
article_processing_charge: No
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Henzinger MH, Krinninger S, Nanongkai D. Sublinear-time decremental algorithms
for single-source reachability and shortest paths on directed graphs. In: 46th
Annual ACM Symposium on Theory of Computing. Association for Computing Machinery;
2014. doi:10.1145/2591796.2591869'
apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Sublinear-time
decremental algorithms for single-source reachability and shortest paths on directed
graphs. In 46th Annual ACM Symposium on Theory of Computing. New York,
NY, United States: Association for Computing Machinery. https://doi.org/10.1145/2591796.2591869'
chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Sublinear-Time
Decremental Algorithms for Single-Source Reachability and Shortest Paths on Directed
Graphs.” In 46th Annual ACM Symposium on Theory of Computing. Association
for Computing Machinery, 2014. https://doi.org/10.1145/2591796.2591869.
ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Sublinear-time decremental
algorithms for single-source reachability and shortest paths on directed graphs,”
in 46th Annual ACM Symposium on Theory of Computing, New York, NY, United
States, 2014.
ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2014. Sublinear-time decremental
algorithms for single-source reachability and shortest paths on directed graphs.
46th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of
Computing, 674–683.'
mla: Henzinger, Monika H., et al. “Sublinear-Time Decremental Algorithms for Single-Source
Reachability and Shortest Paths on Directed Graphs.” 46th Annual ACM Symposium
on Theory of Computing, 674–683, Association for Computing Machinery, 2014,
doi:10.1145/2591796.2591869.
short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 46th Annual ACM Symposium
on Theory of Computing, Association for Computing Machinery, 2014.
conference:
end_date: 2014-06-03
location: New York, NY, United States
name: 'STOC: Symposium on Theory of Computing'
start_date: 2014-05-31
date_created: 2022-08-16T09:41:57Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2023-02-17T11:18:52Z
day: '01'
doi: 10.1145/2591796.2591869
extern: '1'
external_id:
arxiv:
- '1504.07959'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.07959
month: '05'
oa: 1
oa_version: Preprint
publication: 46th Annual ACM Symposium on Theory of Computing
publication_identifier:
isbn:
- 978-145032710-7
issn:
- 0737-8017
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sublinear-time decremental algorithms for single-source reachability and shortest
paths on directed graphs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '11876'
abstract:
- lang: eng
text: "We study dynamic (1 + ∊)-approximation algorithms for the single-source shortest
paths problem in an unweighted undirected n-node m-edge graph under edge deletions.
The fastest algorithm for this problem is an algorithm with O(n2+o(1)) total update
time and constant query time by Bernstein and Roditty (SODA 2011). In this paper,
we improve the total update time to O(n1.8+o(1) + m1+o(1)) while keeping the query
time constant. This running time is essentially tight when m = Ω(n1.8) since we
need Ω(m) time even in the static setting. For smaller values of m, the running
time of our algorithm is subquadratic, and is the first that breaks through the
quadratic time barrier.\r\n\r\nIn obtaining this result, we develop a fast algorithm
for what we call center cover data structure. We also make non-trivial extensions
to our previous techniques called lazy-update and monotone Even-Shiloach trees
(ICALP 2013 and FOCS 2013). As by-products of our new techniques, we obtain two
new results for the decremental all-pairs shortest-paths problem. Our first result
is the first approximation algorithm whose total update time is faster than Õ(mn)
for all values of m. Our second result is a new trade-off between the total update
time and the additive approximation guarantee."
article_processing_charge: No
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Henzinger MH, Krinninger S, Nanongkai D. A subquadratic-time algorithm for
decremental single-source shortest paths. In: 25th Annual ACM-SIAM Symposium
on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2014:1053-1072.
doi:10.1137/1.9781611973402.79'
apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). A subquadratic-time
algorithm for decremental single-source shortest paths. In 25th Annual ACM-SIAM
Symposium on Discrete Algorithms (pp. 1053–1072). Portland, OR, United States:
Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973402.79'
chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “A Subquadratic-Time
Algorithm for Decremental Single-Source Shortest Paths.” In 25th Annual ACM-SIAM
Symposium on Discrete Algorithms, 1053–72. Society for Industrial and Applied
Mathematics, 2014. https://doi.org/10.1137/1.9781611973402.79.
ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “A subquadratic-time algorithm
for decremental single-source shortest paths,” in 25th Annual ACM-SIAM Symposium
on Discrete Algorithms, Portland, OR, United States, 2014, pp. 1053–1072.
ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2014. A subquadratic-time algorithm
for decremental single-source shortest paths. 25th Annual ACM-SIAM Symposium on
Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1053–1072.'
mla: Henzinger, Monika H., et al. “A Subquadratic-Time Algorithm for Decremental
Single-Source Shortest Paths.” 25th Annual ACM-SIAM Symposium on Discrete Algorithms,
Society for Industrial and Applied Mathematics, 2014, pp. 1053–72, doi:10.1137/1.9781611973402.79.
short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 25th Annual ACM-SIAM Symposium
on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014,
pp. 1053–1072.
conference:
end_date: 2014-01-07
location: Portland, OR, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2014-01-05
date_created: 2022-08-16T12:58:31Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-17T11:58:42Z
day: '01'
doi: 10.1137/1.9781611973402.79
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1137/1.9781611973402.79
month: '01'
oa: 1
oa_version: Published Version
page: 1053-1072
publication: 25th Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
eisbn:
- 978-1-61197-340-2
isbn:
- 978-1-61197-338-9
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: A subquadratic-time algorithm for decremental single-source shortest paths
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '11875'
abstract:
- lang: eng
text: We present the first deterministic data structures for maintaining approximate
minimum vertex cover and maximum matching in a fully dynamic graph in time per
update. In particular, for minimum vertex cover we provide deterministic data
structures for maintaining a (2 + ε) approximation in O(log n/ε2) amortized time
per update. For maximum matching, we show how to maintain a (3 + e) approximation
in O(m1/3/ε2) amortized time per update, and a (4 + ε) approximation in O(m1/3/ε2)
worst-case time per update. Our data structure for fully dynamic minimum vertex
cover is essentially near-optimal and settles an open problem by Onak and Rubinfeld
[13].
article_processing_charge: No
author:
- first_name: Sayan
full_name: Bhattacharya, Sayan
last_name: Bhattacharya
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Giuseppe F.
full_name: Italiano, Giuseppe F.
last_name: Italiano
citation:
ama: 'Bhattacharya S, Henzinger MH, Italiano GF. Deterministic fully dynamic data
structures for vertex cover and matching. In: 26th Annual ACM-SIAM Symposium
on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2014:785-804.
doi:10.1137/1.9781611973730.54'
apa: 'Bhattacharya, S., Henzinger, M. H., & Italiano, G. F. (2014). Deterministic
fully dynamic data structures for vertex cover and matching. In 26th Annual
ACM-SIAM Symposium on Discrete Algorithms (pp. 785–804). San Diego, CA, United
States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973730.54'
chicago: Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe F. Italiano. “Deterministic
Fully Dynamic Data Structures for Vertex Cover and Matching.” In 26th Annual
ACM-SIAM Symposium on Discrete Algorithms, 785–804. Society for Industrial
and Applied Mathematics, 2014. https://doi.org/10.1137/1.9781611973730.54.
ieee: S. Bhattacharya, M. H. Henzinger, and G. F. Italiano, “Deterministic fully
dynamic data structures for vertex cover and matching,” in 26th Annual ACM-SIAM
Symposium on Discrete Algorithms, San Diego, CA, United States, 2014, pp.
785–804.
ista: 'Bhattacharya S, Henzinger MH, Italiano GF. 2014. Deterministic fully dynamic
data structures for vertex cover and matching. 26th Annual ACM-SIAM Symposium
on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 785–804.'
mla: Bhattacharya, Sayan, et al. “Deterministic Fully Dynamic Data Structures for
Vertex Cover and Matching.” 26th Annual ACM-SIAM Symposium on Discrete Algorithms,
Society for Industrial and Applied Mathematics, 2014, pp. 785–804, doi:10.1137/1.9781611973730.54.
short: S. Bhattacharya, M.H. Henzinger, G.F. Italiano, in:, 26th Annual ACM-SIAM
Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics,
2014, pp. 785–804.
conference:
end_date: 2015-01-06
location: San Diego, CA, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2015-01-04
date_created: 2022-08-16T12:36:42Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-21T16:32:06Z
day: '01'
doi: 10.1137/1.9781611973730.54
extern: '1'
external_id:
arxiv:
- '1412.1318'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1412.1318
month: '01'
oa: 1
oa_version: Preprint
page: 785-804
publication: 26th Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
eisbn:
- 978-1-61197-373-0
isbn:
- 978-1-61197-374-7
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
record:
- id: '11890'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Deterministic fully dynamic data structures for vertex cover and matching
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '119'
abstract:
- lang: eng
text: Observations of flowing granular matter have suggested that same-material
tribocharging depends on particle size, typically rendering large grains positive
and small ones negative. Models assuming the transfer of trapped electrons can
account for this trend, but have not been validated. Tracking individual grains
in an electric field, we show quantitatively that charge is transferred based
on size between materially identical grains. However, the surface density of trapped
electrons, measured independently by thermoluminescence techniques, is orders
of magnitude too small to account for the scale of charge transferred. This reveals
that trapped electrons are not a necessary ingredient for same-material tribocharging.
acknowledgement: This work was supported by the NSF through DMR-1309611. Access to
the shared experimental facilities provided by the NSF-supported Chicago MRSEC (DMR-0820054)
is gratefully acknowledged. S. L. F. and J. L. P. acknowledge funding from UIC NSF
Grants No. 0850830 and No. 0602308. S. R. W. acknowledges support from a University
of Chicago Millikan Fellowship and from Mrs. Joan Winstein through the Winstein
Prize for Instrumentation.
article_number: '218001'
author:
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: Victor
full_name: Lee, Victor
last_name: Lee
- first_name: James
full_name: Pierson, James
last_name: Pierson
- first_name: Steven
full_name: Forman, Steven
last_name: Forman
- first_name: Heinrich
full_name: Jaeger, Heinrich
last_name: Jaeger
citation:
ama: Waitukaitis SR, Lee V, Pierson J, Forman S, Jaeger H. Size-dependent same-material
tribocharging in insulating grains. APS Physics, Physical Review Letters.
2014;112(21). doi:10.1103/PhysRevLett.112.218001
apa: Waitukaitis, S. R., Lee, V., Pierson, J., Forman, S., & Jaeger, H. (2014).
Size-dependent same-material tribocharging in insulating grains. APS Physics,
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.112.218001
chicago: Waitukaitis, Scott R, Victor Lee, James Pierson, Steven Forman, and Heinrich
Jaeger. “Size-Dependent Same-Material Tribocharging in Insulating Grains.” APS
Physics, Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.112.218001.
ieee: S. R. Waitukaitis, V. Lee, J. Pierson, S. Forman, and H. Jaeger, “Size-dependent
same-material tribocharging in insulating grains,” APS Physics, Physical Review
Letters, vol. 112, no. 21. American Physical Society, 2014.
ista: Waitukaitis SR, Lee V, Pierson J, Forman S, Jaeger H. 2014. Size-dependent
same-material tribocharging in insulating grains. APS Physics, Physical Review
Letters. 112(21), 218001.
mla: Waitukaitis, Scott R., et al. “Size-Dependent Same-Material Tribocharging in
Insulating Grains.” APS Physics, Physical Review Letters, vol. 112, no.
21, 218001, American Physical Society, 2014, doi:10.1103/PhysRevLett.112.218001.
short: S.R. Waitukaitis, V. Lee, J. Pierson, S. Forman, H. Jaeger, APS Physics,
Physical Review Letters 112 (2014).
date_created: 2018-12-11T11:44:44Z
date_published: 2014-05-30T00:00:00Z
date_updated: 2021-01-12T06:48:58Z
day: '30'
doi: 10.1103/PhysRevLett.112.218001
extern: '1'
external_id:
arxiv:
- '1309.2578'
intvolume: ' 112'
issue: '21'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1309.2578
month: '05'
oa: 1
oa_version: Submitted Version
publication: APS Physics, Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7935'
quality_controlled: '1'
status: public
title: Size-dependent same-material tribocharging in insulating grains
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2014'
...
---
_id: '11968'
abstract:
- lang: eng
text: 'Membrane phospholipids typically contain fatty acids (FAs) of 16 and 18 carbon
atoms. This particular chain length is evolutionarily highly conserved and presumably
provides maximum stability and dynamic properties to biological membranes in response
to nutritional or environmental cues. Here, we show that the relative proportion
of C16 versus C18 FAs is regulated by the activity of acetyl-CoA carboxylase (Acc1),
the first and rate-limiting enzyme of FA de novo synthesis. Acc1 activity is attenuated
by AMPK/Snf1-dependent phosphorylation, which is required to maintain an appropriate
acyl-chain length distribution. Moreover, we find that the transcriptional repressor
Opi1 preferentially binds to C16 over C18 phosphatidic acid (PA) species: thus,
C16-chain containing PA sequesters Opi1 more effectively to the ER, enabling AMPK/Snf1
control of PA acyl-chain length to determine the degree of derepression of Opi1
target genes. These findings reveal an unexpected regulatory link between the
major energy-sensing kinase, membrane lipid composition, and transcription.'
article_processing_charge: No
article_type: original
author:
- first_name: Harald F.
full_name: Hofbauer, Harald F.
last_name: Hofbauer
- first_name: Florian H.
full_name: Schopf, Florian H.
last_name: Schopf
- first_name: Hannes
full_name: Schleifer, Hannes
last_name: Schleifer
- first_name: Oskar L.
full_name: Knittelfelder, Oskar L.
last_name: Knittelfelder
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: Gerald N.
full_name: Rechberger, Gerald N.
last_name: Rechberger
- first_name: Heimo
full_name: Wolinski, Heimo
last_name: Wolinski
- first_name: Maria L.
full_name: Gaspar, Maria L.
last_name: Gaspar
- first_name: C. Oliver
full_name: Kappe, C. Oliver
last_name: Kappe
- first_name: Johannes
full_name: Stadlmann, Johannes
last_name: Stadlmann
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Alexandra
full_name: Zenz, Alexandra
last_name: Zenz
- first_name: Karl
full_name: Lohner, Karl
last_name: Lohner
- first_name: Oksana
full_name: Tehlivets, Oksana
last_name: Tehlivets
- first_name: Susan A.
full_name: Henry, Susan A.
last_name: Henry
- first_name: Sepp D.
full_name: Kohlwein, Sepp D.
last_name: Kohlwein
citation:
ama: Hofbauer HF, Schopf FH, Schleifer H, et al. Regulation of gene expression through
a transcriptional repressor that senses acyl-chain length in membrane phospholipids.
Developmental Cell. 2014;29(6):P729-739. doi:10.1016/j.devcel.2014.04.025
apa: Hofbauer, H. F., Schopf, F. H., Schleifer, H., Knittelfelder, O. L., Pieber,
B., Rechberger, G. N., … Kohlwein, S. D. (2014). Regulation of gene expression
through a transcriptional repressor that senses acyl-chain length in membrane
phospholipids. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2014.04.025
chicago: Hofbauer, Harald F., Florian H. Schopf, Hannes Schleifer, Oskar L. Knittelfelder,
Bartholomäus Pieber, Gerald N. Rechberger, Heimo Wolinski, et al. “Regulation
of Gene Expression through a Transcriptional Repressor That Senses Acyl-Chain
Length in Membrane Phospholipids.” Developmental Cell. Elsevier, 2014.
https://doi.org/10.1016/j.devcel.2014.04.025.
ieee: H. F. Hofbauer et al., “Regulation of gene expression through a transcriptional
repressor that senses acyl-chain length in membrane phospholipids,” Developmental
Cell, vol. 29, no. 6. Elsevier, pp. P729-739, 2014.
ista: Hofbauer HF, Schopf FH, Schleifer H, Knittelfelder OL, Pieber B, Rechberger
GN, Wolinski H, Gaspar ML, Kappe CO, Stadlmann J, Mechtler K, Zenz A, Lohner K,
Tehlivets O, Henry SA, Kohlwein SD. 2014. Regulation of gene expression through
a transcriptional repressor that senses acyl-chain length in membrane phospholipids.
Developmental Cell. 29(6), P729-739.
mla: Hofbauer, Harald F., et al. “Regulation of Gene Expression through a Transcriptional
Repressor That Senses Acyl-Chain Length in Membrane Phospholipids.” Developmental
Cell, vol. 29, no. 6, Elsevier, 2014, pp. P729-739, doi:10.1016/j.devcel.2014.04.025.
short: H.F. Hofbauer, F.H. Schopf, H. Schleifer, O.L. Knittelfelder, B. Pieber,
G.N. Rechberger, H. Wolinski, M.L. Gaspar, C.O. Kappe, J. Stadlmann, K. Mechtler,
A. Zenz, K. Lohner, O. Tehlivets, S.A. Henry, S.D. Kohlwein, Developmental Cell
29 (2014) P729-739.
date_created: 2022-08-25T08:42:42Z
date_published: 2014-06-23T00:00:00Z
date_updated: 2023-02-21T10:09:45Z
day: '23'
doi: 10.1016/j.devcel.2014.04.025
extern: '1'
external_id:
pmid:
- '24960695'
intvolume: ' 29'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2014.04.025
month: '06'
oa: 1
oa_version: Published Version
page: P729-739
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Regulation of gene expression through a transcriptional repressor that senses
acyl-chain length in membrane phospholipids
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2014'
...
---
_id: '11967'
abstract:
- lang: eng
text: An experimentally easy to perform method for the generation of alumina-supported
Fe3O4 nanoparticles [(6±1) nm size, 0.67 wt %]and the use of this material in
hydrazine-mediated heterogeneously catalyzed reductions of nitroarenes to anilines
under batch and continuous-flow conditions is presented. The bench-stable, reusable
nano-Fe3O4@Al2O3 catalyst can selectively reduce functionalized nitroarenes at
1 mol % catalyst loading by using a 20 mol % excess of hydrazine hydrate in an
elevated temperature regime (150 °C, reaction time 2–6 min in batch). For continuous-flow
processing, the catalyst material is packed into dedicated cartridges and used
in a commercially available high-temperature/-pressure flow device. In continuous
mode, reaction times can be reduced to less than 1 min at 150 °C (30 bar back
pressure) in a highly intensified process. The nano-Fe3O4@Al2O3 catalyst demonstrated
stable reduction of nitrobenzene (0.5 M in MeOH) for more than 10 h on stream
at a productivity of 30 mmol h−1 (0.72 mol per day). Importantly, virtually no
leaching of the catalytically active material could be observed by inductively
coupled plasma MS monitoring.
article_processing_charge: No
article_type: original
author:
- first_name: Mojtaba Mirhosseini
full_name: Moghaddam, Mojtaba Mirhosseini
last_name: Moghaddam
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: Toma
full_name: Glasnov, Toma
last_name: Glasnov
- first_name: C. Oliver
full_name: Kappe, C. Oliver
last_name: Kappe
citation:
ama: Moghaddam MM, Pieber B, Glasnov T, Kappe CO. Immobilized iron oxide nanoparticles
as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous
flow. ChemSusChem. 2014;7(11):3122-3131. doi:10.1002/cssc.201402455
apa: Moghaddam, M. M., Pieber, B., Glasnov, T., & Kappe, C. O. (2014). Immobilized
iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated
nitro reductions in continuous flow. ChemSusChem. Wiley. https://doi.org/10.1002/cssc.201402455
chicago: Moghaddam, Mojtaba Mirhosseini, Bartholomäus Pieber, Toma Glasnov, and
C. Oliver Kappe. “Immobilized Iron Oxide Nanoparticles as Stable and Reusable
Catalysts for Hydrazine-Mediated Nitro Reductions in Continuous Flow.” ChemSusChem.
Wiley, 2014. https://doi.org/10.1002/cssc.201402455.
ieee: M. M. Moghaddam, B. Pieber, T. Glasnov, and C. O. Kappe, “Immobilized iron
oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro
reductions in continuous flow,” ChemSusChem, vol. 7, no. 11. Wiley, pp.
3122–3131, 2014.
ista: Moghaddam MM, Pieber B, Glasnov T, Kappe CO. 2014. Immobilized iron oxide
nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions
in continuous flow. ChemSusChem. 7(11), 3122–3131.
mla: Moghaddam, Mojtaba Mirhosseini, et al. “Immobilized Iron Oxide Nanoparticles
as Stable and Reusable Catalysts for Hydrazine-Mediated Nitro Reductions in Continuous
Flow.” ChemSusChem, vol. 7, no. 11, Wiley, 2014, pp. 3122–31, doi:10.1002/cssc.201402455.
short: M.M. Moghaddam, B. Pieber, T. Glasnov, C.O. Kappe, ChemSusChem 7 (2014) 3122–3131.
date_created: 2022-08-25T08:36:54Z
date_published: 2014-11-01T00:00:00Z
date_updated: 2023-02-21T10:09:42Z
day: '01'
doi: 10.1002/cssc.201402455
extern: '1'
external_id:
pmid:
- '25209099'
intvolume: ' 7'
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 3122-3131
pmid: 1
publication: ChemSusChem
publication_identifier:
eissn:
- 1864-564X
issn:
- 1864-5631
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated
nitro reductions in continuous flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2014'
...
---
_id: '11987'
abstract:
- lang: eng
text: A method for the direct lithiation of terminal alkynes and heterocycles with
subsequent carboxylation in a continuous flow format was developed. This method
provides carboxylic acids at ambient conditions within less than five seconds
with only little excess of the organometallic base and CO2.
article_number: '13430'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: Toma
full_name: Glasnov, Toma
last_name: Glasnov
- first_name: C. O.
full_name: Kappe, C. O.
last_name: Kappe
citation:
ama: 'Pieber B, Glasnov T, Kappe CO. Flash carboxylation: Fast lithiation–carboxylation
sequence at room temperature in continuous flow. RSC Advances. 2014;4(26).
doi:10.1039/c4ra01442a'
apa: 'Pieber, B., Glasnov, T., & Kappe, C. O. (2014). Flash carboxylation: Fast
lithiation–carboxylation sequence at room temperature in continuous flow. RSC
Advances. Royal Society of Chemistry. https://doi.org/10.1039/c4ra01442a'
chicago: 'Pieber, Bartholomäus, Toma Glasnov, and C. O. Kappe. “Flash Carboxylation:
Fast Lithiation–Carboxylation Sequence at Room Temperature in Continuous Flow.”
RSC Advances. Royal Society of Chemistry, 2014. https://doi.org/10.1039/c4ra01442a.'
ieee: 'B. Pieber, T. Glasnov, and C. O. Kappe, “Flash carboxylation: Fast lithiation–carboxylation
sequence at room temperature in continuous flow,” RSC Advances, vol. 4,
no. 26. Royal Society of Chemistry, 2014.'
ista: 'Pieber B, Glasnov T, Kappe CO. 2014. Flash carboxylation: Fast lithiation–carboxylation
sequence at room temperature in continuous flow. RSC Advances. 4(26), 13430.'
mla: 'Pieber, Bartholomäus, et al. “Flash Carboxylation: Fast Lithiation–Carboxylation
Sequence at Room Temperature in Continuous Flow.” RSC Advances, vol. 4,
no. 26, 13430, Royal Society of Chemistry, 2014, doi:10.1039/c4ra01442a.'
short: B. Pieber, T. Glasnov, C.O. Kappe, RSC Advances 4 (2014).
date_created: 2022-08-25T11:48:19Z
date_published: 2014-03-03T00:00:00Z
date_updated: 2023-02-21T10:10:31Z
day: '03'
doi: 10.1039/c4ra01442a
extern: '1'
intvolume: ' 4'
issue: '26'
language:
- iso: eng
month: '03'
oa_version: None
publication: RSC Advances
publication_identifier:
eissn:
- 2046-2069
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature
in continuous flow'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2014'
...
---
_id: '1309'
abstract:
- lang: eng
text: We show that weak solutions of the Derrida-Lebowitz-Speer-Spohn (DLSS) equation
display infinite speed of support propagation. We apply our method to the case
of the quantum drift-diffusion equation which augments the DLSS equation with
a drift term and possibly a second-order diffusion term. The proof is accomplished
using weighted entropy estimates, Hardy's inequality and a family of singular
weight functions to derive a differential inequality; the differential inequality
shows exponential growth of the weighted entropy, with the growth constant blowing
up very fast as the singularity of the weight becomes sharper. To the best of
our knowledge, this is the first example of a nonnegativity-preserving higher-order
parabolic equation displaying infinite speed of support propagation.
author:
- first_name: Julian L
full_name: Julian Fischer
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: Fischer JL. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift-diffusion models. Nonlinear Differential Equations
and Applications. 2014;21(1):27-50. doi:10.1007/s00030-013-0235-0
apa: Fischer, J. L. (2014). Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift-diffusion models. Nonlinear Differential Equations
and Applications. Birkhäuser. https://doi.org/10.1007/s00030-013-0235-0
chicago: Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn
Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations
and Applications. Birkhäuser, 2014. https://doi.org/10.1007/s00030-013-0235-0.
ieee: J. L. Fischer, “Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift-diffusion models,” Nonlinear Differential Equations
and Applications, vol. 21, no. 1. Birkhäuser, pp. 27–50, 2014.
ista: Fischer JL. 2014. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift-diffusion models. Nonlinear Differential Equations
and Applications. 21(1), 27–50.
mla: Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn
Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations
and Applications, vol. 21, no. 1, Birkhäuser, 2014, pp. 27–50, doi:10.1007/s00030-013-0235-0.
short: J.L. Fischer, Nonlinear Differential Equations and Applications 21 (2014)
27–50.
date_created: 2018-12-11T11:51:17Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:47Z
day: '01'
doi: 10.1007/s00030-013-0235-0
extern: 1
intvolume: ' 21'
issue: '1'
month: '01'
page: 27 - 50
publication: Nonlinear Differential Equations and Applications
publication_status: published
publisher: Birkhäuser
publist_id: '5960'
quality_controlled: 0
status: public
title: Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift-diffusion models
type: journal_article
volume: 21
year: '2014'
...
---
_id: '1312'
abstract:
- lang: eng
text: We derive upper bounds on the waiting time of solutions to the thin-film equation
in the regime of weak slippage n ∈ [2, 32\11). In particular, we give sufficient
conditions on the initial data for instantaneous forward motion of the free boundary.
For n ∈ (2, 32\11), our estimates are sharp, for n = 2, they are sharp up to a
logarithmic correction term. Note that the case n = 2 corresponds-with a grain
of salt-to the assumption of the Navier slip condition at the fluid-solid interface.
We also obtain results in the regime of strong slippage n ∈ (1,2); however, in
this regime we expect them not to be optimal. Our method is based on weighted
backward entropy estimates, Hardy's inequality and singular weight functions;
we deduce a differential inequality which would enforce blowup of the weighted
entropy if the contact line were to remain stationary for too long.
author:
- first_name: Julian L
full_name: Julian Fischer
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: 'Fischer JL. Upper bounds on waiting times for the Thin-film equation: The
case of weak slippage. Archive for Rational Mechanics and Analysis. 2014;211(3):771-818.
doi:10.1007/s00205-013-0690-0'
apa: 'Fischer, J. L. (2014). Upper bounds on waiting times for the Thin-film equation:
The case of weak slippage. Archive for Rational Mechanics and Analysis.
Springer. https://doi.org/10.1007/s00205-013-0690-0'
chicago: 'Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation:
The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis.
Springer, 2014. https://doi.org/10.1007/s00205-013-0690-0.'
ieee: 'J. L. Fischer, “Upper bounds on waiting times for the Thin-film equation:
The case of weak slippage,” Archive for Rational Mechanics and Analysis,
vol. 211, no. 3. Springer, pp. 771–818, 2014.'
ista: 'Fischer JL. 2014. Upper bounds on waiting times for the Thin-film equation:
The case of weak slippage. Archive for Rational Mechanics and Analysis. 211(3),
771–818.'
mla: 'Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation:
The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis,
vol. 211, no. 3, Springer, 2014, pp. 771–818, doi:10.1007/s00205-013-0690-0.'
short: J.L. Fischer, Archive for Rational Mechanics and Analysis 211 (2014) 771–818.
date_created: 2018-12-11T11:51:18Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:48Z
day: '01'
doi: 10.1007/s00205-013-0690-0
extern: 1
intvolume: ' 211'
issue: '3'
month: '01'
page: 771 - 818
publication: Archive for Rational Mechanics and Analysis
publication_status: published
publisher: Springer
publist_id: '5959'
quality_controlled: 0
status: public
title: 'Upper bounds on waiting times for the Thin-film equation: The case of weak
slippage'
type: journal_article
volume: 211
year: '2014'
...
---
_id: '1375'
abstract:
- lang: eng
text: 'We consider directed graphs where each edge is labeled with an integer weight
and study the fundamental algorithmic question of computing the value of a cycle
with minimum mean weight. Our contributions are twofold: (1) First we show that
the algorithmic question is reducible to the problem of a logarithmic number of
min-plus matrix multiplications of n×n-matrices, where n is the number of vertices
of the graph. (2) Second, when the weights are nonnegative, we present the first
(1+ε)-approximation algorithm for the problem and the running time of our algorithm
is Õ(nωlog3(nW/ε)/ε),1 where O(nω) is the time required for the classic n×n-matrix
multiplication and W is the maximum value of the weights. With an additional O(log(nW/ε))
factor in space a cycle with approximately optimal weight can be computed within
the same time bound.'
article_processing_charge: No
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Veronika
full_name: Loitzenbauer, Veronika
last_name: Loitzenbauer
- first_name: Michael
full_name: Raskin, Michael
last_name: Raskin
citation:
ama: Chatterjee K, Henzinger MH, Krinninger S, Loitzenbauer V, Raskin M. Approximating
the minimum cycle mean. Theoretical Computer Science. 2014;547(C):104-116.
doi:10.1016/j.tcs.2014.06.031
apa: Chatterjee, K., Henzinger, M. H., Krinninger, S., Loitzenbauer, V., & Raskin,
M. (2014). Approximating the minimum cycle mean. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2014.06.031
chicago: Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, Veronika
Loitzenbauer, and Michael Raskin. “Approximating the Minimum Cycle Mean.” Theoretical
Computer Science. Elsevier, 2014. https://doi.org/10.1016/j.tcs.2014.06.031.
ieee: K. Chatterjee, M. H. Henzinger, S. Krinninger, V. Loitzenbauer, and M. Raskin,
“Approximating the minimum cycle mean,” Theoretical Computer Science, vol.
547, no. C. Elsevier, pp. 104–116, 2014.
ista: Chatterjee K, Henzinger MH, Krinninger S, Loitzenbauer V, Raskin M. 2014.
Approximating the minimum cycle mean. Theoretical Computer Science. 547(C), 104–116.
mla: Chatterjee, Krishnendu, et al. “Approximating the Minimum Cycle Mean.” Theoretical
Computer Science, vol. 547, no. C, Elsevier, 2014, pp. 104–16, doi:10.1016/j.tcs.2014.06.031.
short: K. Chatterjee, M.H. Henzinger, S. Krinninger, V. Loitzenbauer, M. Raskin,
Theoretical Computer Science 547 (2014) 104–116.
date_created: 2018-12-11T11:51:40Z
date_published: 2014-08-28T00:00:00Z
date_updated: 2022-09-09T11:50:58Z
day: '28'
department:
- _id: KrCh
doi: 10.1016/j.tcs.2014.06.031
ec_funded: 1
external_id:
arxiv:
- '1307.4473'
intvolume: ' 547'
issue: C
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1307.4473
month: '08'
oa: 1
oa_version: Preprint
page: 104 - 116
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Theoretical Computer Science
publication_status: published
publisher: Elsevier
publist_id: '5836'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Approximating the minimum cycle mean
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 547
year: '2014'
...
---
_id: '1392'
abstract:
- lang: eng
text: Fault-tolerant distributed algorithms play an important role in ensuring the
reliability of many software applications. In this paper we consider distributed
algorithms whose computations are organized in rounds. To verify the correctness
of such algorithms, we reason about (i) properties (such as invariants) of the
state, (ii) the transitions controlled by the algorithm, and (iii) the communication
graph. We introduce a logic that addresses these points, and contains set comprehensions
with cardinality constraints, function symbols to describe the local states of
each process, and a limited form of quantifier alternation to express the verification
conditions. We show its use in automating the verification of consensus algorithms.
In particular, we give a semi-decision procedure for the unsatisfiability problem
of the logic and identify a decidable fragment. We successfully applied our framework
to verify the correctness of a variety of consensus algorithms tolerant to both
benign faults (message loss, process crashes) and value faults (message corruption).
acknowledgement: Supported by the Vienna Science and Technology Fund (WWTF) through
grant PROSEED.
alternative_title:
- LNCS
author:
- first_name: Cezara
full_name: Dragoi, Cezara
id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87
last_name: Dragoi
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Helmut
full_name: Veith, Helmut
last_name: Veith
- first_name: Josef
full_name: Widder, Josef
last_name: Widder
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: 'Dragoi C, Henzinger TA, Veith H, Widder J, Zufferey D. A logic-based framework
for verifying consensus algorithms. In: Vol 8318. Springer; 2014:161-181. doi:10.1007/978-3-642-54013-4_10'
apa: 'Dragoi, C., Henzinger, T. A., Veith, H., Widder, J., & Zufferey, D. (2014).
A logic-based framework for verifying consensus algorithms (Vol. 8318, pp. 161–181).
Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation,
San Diego, USA: Springer. https://doi.org/10.1007/978-3-642-54013-4_10'
chicago: Dragoi, Cezara, Thomas A Henzinger, Helmut Veith, Josef Widder, and Damien
Zufferey. “A Logic-Based Framework for Verifying Consensus Algorithms,” 8318:161–81.
Springer, 2014. https://doi.org/10.1007/978-3-642-54013-4_10.
ieee: 'C. Dragoi, T. A. Henzinger, H. Veith, J. Widder, and D. Zufferey, “A logic-based
framework for verifying consensus algorithms,” presented at the VMCAI: Verification,
Model Checking and Abstract Interpretation, San Diego, USA, 2014, vol. 8318, pp.
161–181.'
ista: 'Dragoi C, Henzinger TA, Veith H, Widder J, Zufferey D. 2014. A logic-based
framework for verifying consensus algorithms. VMCAI: Verification, Model Checking
and Abstract Interpretation, LNCS, vol. 8318, 161–181.'
mla: Dragoi, Cezara, et al. A Logic-Based Framework for Verifying Consensus Algorithms.
Vol. 8318, Springer, 2014, pp. 161–81, doi:10.1007/978-3-642-54013-4_10.
short: C. Dragoi, T.A. Henzinger, H. Veith, J. Widder, D. Zufferey, in:, Springer,
2014, pp. 161–181.
conference:
end_date: 2014-01-21
location: San Diego, USA
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2014-01-19
date_created: 2018-12-11T11:51:45Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:22Z
day: '01'
ddc:
- '000'
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-54013-4_10
ec_funded: 1
file:
- access_level: open_access
checksum: bffa33d39be77df0da39defe97eabf84
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:06Z
date_updated: 2020-07-14T12:44:48Z
file_id: '4859'
file_name: IST-2014-179-v1+1_vmcai14.pdf
file_size: 444138
relation: main_file
file_date_updated: 2020-07-14T12:44:48Z
has_accepted_license: '1'
intvolume: ' 8318'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 161 - 181
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Springer
publist_id: '5817'
pubrep_id: '179'
quality_controlled: '1'
scopus_import: 1
status: public
title: A logic-based framework for verifying consensus algorithms
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8318
year: '2014'
...
---
_id: '1393'
abstract:
- lang: eng
text: 'Probabilistic programs are usual functional or imperative programs with two
added constructs: (1) the ability to draw values at random from distributions,
and (2) the ability to condition values of variables in a program via observations.
Models from diverse application areas such as computer vision, coding theory,
cryptographic protocols, biology and reliability analysis can be written as probabilistic
programs. Probabilistic inference is the problem of computing an explicit representation
of the probability distribution implicitly specified by a probabilistic program.
Depending on the application, the desired output from inference may vary-we may
want to estimate the expected value of some function f with respect to the distribution,
or the mode of the distribution, or simply a set of samples drawn from the distribution.
In this paper, we describe connections this research area called \Probabilistic
Programming" has with programming languages and software engineering, and
this includes language design, and the static and dynamic analysis of programs.
We survey current state of the art and speculate on promising directions for future
research.'
article_processing_charge: No
author:
- first_name: Andrew
full_name: Gordon, Andrew
last_name: Gordon
- 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: Aditya
full_name: Nori, Aditya
last_name: Nori
- first_name: Sriram
full_name: Rajamani, Sriram
last_name: Rajamani
citation:
ama: 'Gordon A, Henzinger TA, Nori A, Rajamani S. Probabilistic programming. In:
Proceedings of the on Future of Software Engineering. ACM; 2014:167-181.
doi:10.1145/2593882.2593900'
apa: 'Gordon, A., Henzinger, T. A., Nori, A., & Rajamani, S. (2014). Probabilistic
programming. In Proceedings of the on Future of Software Engineering (pp.
167–181). Hyderabad, India: ACM. https://doi.org/10.1145/2593882.2593900'
chicago: Gordon, Andrew, Thomas A Henzinger, Aditya Nori, and Sriram Rajamani. “Probabilistic
Programming.” In Proceedings of the on Future of Software Engineering,
167–81. ACM, 2014. https://doi.org/10.1145/2593882.2593900.
ieee: A. Gordon, T. A. Henzinger, A. Nori, and S. Rajamani, “Probabilistic programming,”
in Proceedings of the on Future of Software Engineering, Hyderabad, India,
2014, pp. 167–181.
ista: 'Gordon A, Henzinger TA, Nori A, Rajamani S. 2014. Probabilistic programming.
Proceedings of the on Future of Software Engineering. FOSE: Future of Software
Engineering, 167–181.'
mla: Gordon, Andrew, et al. “Probabilistic Programming.” Proceedings of the on
Future of Software Engineering, ACM, 2014, pp. 167–81, doi:10.1145/2593882.2593900.
short: A. Gordon, T.A. Henzinger, A. Nori, S. Rajamani, in:, Proceedings of the
on Future of Software Engineering, ACM, 2014, pp. 167–181.
conference:
end_date: 2014-06-07
location: Hyderabad, India
name: 'FOSE: Future of Software Engineering'
start_date: 2014-05-31
date_created: 2018-12-11T11:51:45Z
date_published: 2014-05-31T00:00:00Z
date_updated: 2021-01-12T06:50:22Z
day: '31'
department:
- _id: ToHe
doi: 10.1145/2593882.2593900
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/2593882.2593900
month: '05'
oa: 1
oa_version: Published Version
page: 167 - 181
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Proceedings of the on Future of Software Engineering
publication_status: published
publisher: ACM
publist_id: '5816'
quality_controlled: '1'
scopus_import: 1
status: public
title: Probabilistic programming
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1404'
abstract:
- lang: eng
text: "The co-evolution of hosts and pathogens is characterized by continuous adaptations
of both parties. Pathogens of social insects need to adapt towards disease defences
at two levels: 1) individual immunity of each colony member consisting of behavioural
defence strategies as well as humoral and cellular immune responses and 2) social
immunity that is collectively performed by all group members comprising behavioural,
physiological and organisational defence strategies.\r\n\r\nTo disentangle the
selection pressure on pathogens by the collective versus individual level of disease
defence in social insects, we performed an evolution experiment using the Argentine
Ant, Linepithema humile, as a host and a mixture of the general insect pathogenic
fungus Metarhizium spp. (6 strains) as a pathogen. We allowed pathogen evolution
over 10 serial host passages to two different evolution host treatments: (1) only
individual host immunity in a single host treatment, and (2) simultaneously acting
individual and social immunity in a social host treatment, in which an exposed
ant was accompanied by two untreated nestmates.\r\n\r\nBefore starting the pathogen
evolution experiment, the 6 Metarhizium spp. strains were characterised concerning
conidiospore size killing rates in singly and socially reared ants, their competitiveness
under coinfecting conditions and their influence on ant behaviour. We analysed
how the ancestral atrain mixture changed in conidiospere size, killing rate and
strain composition dependent on host treatment (single or social hosts) during
10 passages and found that killing rate and conidiospere size of the pathogen
increased under both evolution regimes, but different depending on host treatment.\r\n\r\nTesting
the evolved strain mixtures that evolved under either the single or social host
treatment under both single and social current rearing conditions in a full factorial
design experiment revealed that the additional collective defences in insect societies
add new selection pressure for their coevolving pathogens that compromise their
ability to adapt to its host at the group level. To our knowledge, this is the
first study directly measuring the influence of social immunity on pathogen evolution."
acknowledgement: This work was funded by the DFG and the ERC.
alternative_title:
- IST Austria Thesis
author:
- first_name: Miriam
full_name: Stock, Miriam
id: 42462816-F248-11E8-B48F-1D18A9856A87
last_name: Stock
citation:
ama: Stock M. Evolution of a fungal pathogen towards individual versus social immunity
in ants. 2014.
apa: Stock, M. (2014). Evolution of a fungal pathogen towards individual versus
social immunity in ants. IST Austria.
chicago: Stock, Miriam. “Evolution of a Fungal Pathogen towards Individual versus
Social Immunity in Ants.” IST Austria, 2014.
ieee: M. Stock, “Evolution of a fungal pathogen towards individual versus social
immunity in ants,” IST Austria, 2014.
ista: Stock M. 2014. Evolution of a fungal pathogen towards individual versus social
immunity in ants. IST Austria.
mla: Stock, Miriam. Evolution of a Fungal Pathogen towards Individual versus
Social Immunity in Ants. IST Austria, 2014.
short: M. Stock, Evolution of a Fungal Pathogen towards Individual versus Social
Immunity in Ants, IST Austria, 2014.
date_created: 2018-12-11T11:51:49Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T06:50:30Z
day: '01'
department:
- _id: SyCr
language:
- iso: eng
month: '04'
oa_version: None
page: '101'
publication_status: published
publisher: IST Austria
publist_id: '5803'
status: public
supervisor:
- first_name: Sylvia M
full_name: Cremer, Sylvia M
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: Evolution of a fungal pathogen towards individual versus social immunity in
ants
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1516'
abstract:
- lang: eng
text: "We present a rigorous derivation of the BCS gap equation for superfluid fermionic
gases with point interactions. Our starting point is the BCS energy functional,
whose minimizer we investigate in the limit when the range of the interaction
potential goes to zero.\r\n"
article_processing_charge: No
author:
- first_name: Gerhard
full_name: Bräunlich, Gerhard
last_name: Bräunlich
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Bräunlich G, Hainzl C, Seiringer R. On the BCS gap equation for superfluid
fermionic gases. In: Proceedings of the QMath12 Conference. World Scientific
Publishing; 2014:127-137. doi:10.1142/9789814618144_0007'
apa: 'Bräunlich, G., Hainzl, C., & Seiringer, R. (2014). On the BCS gap equation
for superfluid fermionic gases. In Proceedings of the QMath12 Conference
(pp. 127–137). Berlin, Germany: World Scientific Publishing. https://doi.org/10.1142/9789814618144_0007'
chicago: Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “On the BCS
Gap Equation for Superfluid Fermionic Gases.” In Proceedings of the QMath12
Conference, 127–37. World Scientific Publishing, 2014. https://doi.org/10.1142/9789814618144_0007.
ieee: G. Bräunlich, C. Hainzl, and R. Seiringer, “On the BCS gap equation for superfluid
fermionic gases,” in Proceedings of the QMath12 Conference, Berlin, Germany,
2014, pp. 127–137.
ista: 'Bräunlich G, Hainzl C, Seiringer R. 2014. On the BCS gap equation for superfluid
fermionic gases. Proceedings of the QMath12 Conference. QMath: Mathematical Results
in Quantum Physics, 127–137.'
mla: Bräunlich, Gerhard, et al. “On the BCS Gap Equation for Superfluid Fermionic
Gases.” Proceedings of the QMath12 Conference, World Scientific Publishing,
2014, pp. 127–37, doi:10.1142/9789814618144_0007.
short: G. Bräunlich, C. Hainzl, R. Seiringer, in:, Proceedings of the QMath12 Conference,
World Scientific Publishing, 2014, pp. 127–137.
conference:
end_date: 2013-09-13
location: Berlin, Germany
name: 'QMath: Mathematical Results in Quantum Physics'
start_date: 2013-09-10
date_created: 2018-12-11T11:52:28Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:51:19Z
day: '01'
department:
- _id: RoSe
doi: 10.1142/9789814618144_0007
external_id:
arxiv:
- '1403.2563'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.2563
month: '01'
oa: 1
oa_version: Preprint
page: 127 - 137
publication: Proceedings of the QMath12 Conference
publication_status: published
publisher: World Scientific Publishing
publist_id: '5661'
quality_controlled: '1'
status: public
title: On the BCS gap equation for superfluid fermionic gases
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1629'
abstract:
- lang: eng
text: We propose a method for propagating edit operations in 2D vector graphics,
based on geometric relationship functions. These functions quantify the geometric
relationship of a point to a polygon, such as the distance to the boundary or
the direction to the closest corner vertex. The level sets of the relationship
functions describe points with the same relationship to a polygon. For a given
query point, we first determine a set of relationships to local features, construct
all level sets for these relationships, and accumulate them. The maxima of the
resulting distribution are points with similar geometric relationships. We show
extensions to handle mirror symmetries, and discuss the use of relationship functions
as local coordinate systems. Our method can be applied, for example, to interactive
floorplan editing, and it is especially useful for large layouts, where individual
edits would be cumbersome. We demonstrate populating 2D layouts with tens to hundreds
of objects by propagating relatively few edit operations.
article_number: '15'
author:
- first_name: Paul
full_name: Guerrero, Paul
last_name: Guerrero
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Michael
full_name: Wimmer, Michael
last_name: Wimmer
- first_name: Peter
full_name: Wonka, Peter
last_name: Wonka
citation:
ama: Guerrero P, Jeschke S, Wimmer M, Wonka P. Edit propagation using geometric
relationship functions. ACM Transactions on Graphics. 2014;33(2). doi:10.1145/2591010
apa: Guerrero, P., Jeschke, S., Wimmer, M., & Wonka, P. (2014). Edit propagation
using geometric relationship functions. ACM Transactions on Graphics. ACM.
https://doi.org/10.1145/2591010
chicago: Guerrero, Paul, Stefan Jeschke, Michael Wimmer, and Peter Wonka. “Edit
Propagation Using Geometric Relationship Functions.” ACM Transactions on Graphics.
ACM, 2014. https://doi.org/10.1145/2591010.
ieee: P. Guerrero, S. Jeschke, M. Wimmer, and P. Wonka, “Edit propagation using
geometric relationship functions,” ACM Transactions on Graphics, vol. 33,
no. 2. ACM, 2014.
ista: Guerrero P, Jeschke S, Wimmer M, Wonka P. 2014. Edit propagation using geometric
relationship functions. ACM Transactions on Graphics. 33(2), 15.
mla: Guerrero, Paul, et al. “Edit Propagation Using Geometric Relationship Functions.”
ACM Transactions on Graphics, vol. 33, no. 2, 15, ACM, 2014, doi:10.1145/2591010.
short: P. Guerrero, S. Jeschke, M. Wimmer, P. Wonka, ACM Transactions on Graphics
33 (2014).
date_created: 2018-12-11T11:53:08Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2021-01-12T06:52:06Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2591010
file:
- access_level: open_access
checksum: 7f91e588a4e888610313b98271e6418e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:22Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4876'
file_name: IST-2016-577-v1+1_2014.TOG.Paul.EditingPropagation.final.pdf
file_size: 9832561
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 33'
issue: '2'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '5526'
pubrep_id: '577'
quality_controlled: '1'
status: public
title: Edit propagation using geometric relationship functions
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2014'
...
---
_id: '10793'
abstract:
- lang: eng
text: "The Hanani–Tutte theorem is a classical result proved for the first time
in the 1930s that characterizes planar graphs as graphs that admit a drawing in
the plane in which every pair of edges not sharing a vertex cross an even number
of times. We generalize this classical result to clustered graphs with two disjoint
clusters, and show that a straightforward extension of our result to flat clustered
graphs with three or more disjoint clusters is not possible.\r\n\r\nWe also give
a new and short proof for a related result by Di Battista and Frati based on the
matroid intersection algorithm."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Jan
full_name: Kynčl, Jan
last_name: Kynčl
- first_name: Igor
full_name: Malinović, Igor
last_name: Malinović
- first_name: Dömötör
full_name: Pálvölgyi, Dömötör
last_name: Pálvölgyi
citation:
ama: 'Fulek R, Kynčl J, Malinović I, Pálvölgyi D. Clustered planarity testing revisited.
In: International Symposium on Graph Drawing. Vol 8871. Cham: Springer
Nature; 2014:428-436. doi:10.1007/978-3-662-45803-7_36'
apa: 'Fulek, R., Kynčl, J., Malinović, I., & Pálvölgyi, D. (2014). Clustered
planarity testing revisited. In International Symposium on Graph Drawing
(Vol. 8871, pp. 428–436). Cham: Springer Nature. https://doi.org/10.1007/978-3-662-45803-7_36'
chicago: 'Fulek, Radoslav, Jan Kynčl, Igor Malinović, and Dömötör Pálvölgyi. “Clustered
Planarity Testing Revisited.” In International Symposium on Graph Drawing,
8871:428–36. Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-662-45803-7_36.'
ieee: R. Fulek, J. Kynčl, I. Malinović, and D. Pálvölgyi, “Clustered planarity testing
revisited,” in International Symposium on Graph Drawing, 2014, vol. 8871,
pp. 428–436.
ista: Fulek R, Kynčl J, Malinović I, Pálvölgyi D. 2014. Clustered planarity testing
revisited. International Symposium on Graph Drawing. , LNCS, vol. 8871, 428–436.
mla: Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” International
Symposium on Graph Drawing, vol. 8871, Springer Nature, 2014, pp. 428–36,
doi:10.1007/978-3-662-45803-7_36.
short: R. Fulek, J. Kynčl, I. Malinović, D. Pálvölgyi, in:, International Symposium
on Graph Drawing, Springer Nature, Cham, 2014, pp. 428–436.
date_created: 2022-02-25T10:32:14Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T10:08:04Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/978-3-662-45803-7_36
external_id:
arxiv:
- '1305.4519'
intvolume: ' 8871'
language:
- iso: eng
month: '01'
oa_version: Preprint
page: 428-436
place: Cham
publication: International Symposium on Graph Drawing
publication_identifier:
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '1642'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Clustered planarity testing revisited
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8871
year: '2014'
...
---
_id: '1643'
abstract:
- lang: eng
text: We extend the notion of verifiable random functions (VRF) to constrained VRFs,
which generalize the concept of constrained pseudorandom functions, put forward
by Boneh and Waters (Asiacrypt’13), and independently by Kiayias et al. (CCS’13)
and Boyle et al. (PKC’14), who call them delegatable PRFs and functional PRFs,
respectively. In a standard VRF the secret key sk allows one to evaluate a pseudorandom
function at any point of its domain; in addition, it enables computation of a
non-interactive proof that the function value was computed correctly. In a constrained
VRF from the key sk one can derive constrained keys skS for subsets S of the domain,
which allow computation of function values and proofs only at points in S. After
formally defining constrained VRFs, we derive instantiations from the multilinear-maps-based
constrained PRFs by Boneh and Waters, yielding a VRF with constrained keys for
any set that can be decided by a polynomial-size circuit. Our VRFs have the same
function values as the Boneh-Waters PRFs and are proved secure under the same
hardness assumption, showing that verifiability comes at no cost. Constrained
(functional) VRFs were stated as an open problem by Boyle et al.
alternative_title:
- LNCS
author:
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
citation:
ama: 'Fuchsbauer G. Constrained Verifiable Random Functions . In: Abdalla M, De
Prisco R, eds. SCN 2014. Vol 8642. Springer; 2014:95-114. doi:10.1007/978-3-319-10879-7_7'
apa: 'Fuchsbauer, G. (2014). Constrained Verifiable Random Functions . In M. Abdalla
& R. De Prisco (Eds.), SCN 2014 (Vol. 8642, pp. 95–114). Amalfi, Italy:
Springer. https://doi.org/10.1007/978-3-319-10879-7_7'
chicago: Fuchsbauer, Georg. “Constrained Verifiable Random Functions .” In SCN
2014, edited by Michel Abdalla and Roberto De Prisco, 8642:95–114. Springer,
2014. https://doi.org/10.1007/978-3-319-10879-7_7.
ieee: G. Fuchsbauer, “Constrained Verifiable Random Functions ,” in SCN 2014,
Amalfi, Italy, 2014, vol. 8642, pp. 95–114.
ista: 'Fuchsbauer G. 2014. Constrained Verifiable Random Functions . SCN 2014. SCN:
Security and Cryptography for Networks, LNCS, vol. 8642, 95–114.'
mla: Fuchsbauer, Georg. “Constrained Verifiable Random Functions .” SCN 2014,
edited by Michel Abdalla and Roberto De Prisco, vol. 8642, Springer, 2014, pp.
95–114, doi:10.1007/978-3-319-10879-7_7.
short: G. Fuchsbauer, in:, M. Abdalla, R. De Prisco (Eds.), SCN 2014, Springer,
2014, pp. 95–114.
conference:
end_date: 2014-09-05
location: Amalfi, Italy
name: 'SCN: Security and Cryptography for Networks'
start_date: 2014-09-03
date_created: 2018-12-11T11:53:13Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:12Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-319-10879-7_7
ec_funded: 1
editor:
- first_name: Michel
full_name: Abdalla, Michel
last_name: Abdalla
- first_name: Roberto
full_name: De Prisco, Roberto
last_name: De Prisco
intvolume: ' 8642'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprint.iacr.org/2014/537
month: '01'
oa: 1
oa_version: Submitted Version
page: 95 - 114
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: SCN 2014
publication_status: published
publisher: Springer
publist_id: '5509'
scopus_import: 1
status: public
title: 'Constrained Verifiable Random Functions '
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8642
year: '2014'
...
---
_id: '1702'
abstract:
- lang: eng
text: In this paper we present INTERHORN, a solver for recursion-free Horn clauses.
The main application domain of INTERHORN lies in solving interpolation problems
arising in software verification. We show how a range of interpolation problems,
including path, transition, nested, state/transition and well-founded interpolation
can be handled directly by INTERHORN. By detailing these interpolation problems
and their Horn clause representations, we hope to encourage the emergence of a
common back-end interpolation interface useful for diverse verification tools.
alternative_title:
- EPTCS
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Corneliu
full_name: Popeea, Corneliu
last_name: Popeea
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
citation:
ama: 'Gupta A, Popeea C, Rybalchenko A. Generalised interpolation by solving recursion
free-horn clauses. In: Electronic Proceedings in Theoretical Computer Science,
EPTCS. Vol 169. Open Publishing; 2014:31-38. doi:10.4204/EPTCS.169.5'
apa: 'Gupta, A., Popeea, C., & Rybalchenko, A. (2014). Generalised interpolation
by solving recursion free-horn clauses. In Electronic Proceedings in Theoretical
Computer Science, EPTCS (Vol. 169, pp. 31–38). Vienna, Austria: Open Publishing.
https://doi.org/10.4204/EPTCS.169.5'
chicago: Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Generalised
Interpolation by Solving Recursion Free-Horn Clauses.” In Electronic Proceedings
in Theoretical Computer Science, EPTCS, 169:31–38. Open Publishing, 2014.
https://doi.org/10.4204/EPTCS.169.5.
ieee: A. Gupta, C. Popeea, and A. Rybalchenko, “Generalised interpolation by solving
recursion free-horn clauses,” in Electronic Proceedings in Theoretical Computer
Science, EPTCS, Vienna, Austria, 2014, vol. 169, pp. 31–38.
ista: 'Gupta A, Popeea C, Rybalchenko A. 2014. Generalised interpolation by solving
recursion free-horn clauses. Electronic Proceedings in Theoretical Computer Science,
EPTCS. HCVS: Horn Clauses for Verification and Synthesis, EPTCS, vol. 169, 31–38.'
mla: Gupta, Ashutosh, et al. “Generalised Interpolation by Solving Recursion Free-Horn
Clauses.” Electronic Proceedings in Theoretical Computer Science, EPTCS,
vol. 169, Open Publishing, 2014, pp. 31–38, doi:10.4204/EPTCS.169.5.
short: A. Gupta, C. Popeea, A. Rybalchenko, in:, Electronic Proceedings in Theoretical
Computer Science, EPTCS, Open Publishing, 2014, pp. 31–38.
conference:
end_date: 2014-07-17
location: Vienna, Austria
name: 'HCVS: Horn Clauses for Verification and Synthesis'
start_date: 2014-07-17
date_created: 2018-12-11T11:53:33Z
date_published: 2014-12-02T00:00:00Z
date_updated: 2021-01-12T06:52:38Z
day: '02'
department:
- _id: ToHe
doi: 10.4204/EPTCS.169.5
intvolume: ' 169'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1303.7378v2
month: '12'
oa: 1
oa_version: Submitted Version
page: 31 - 38
publication: Electronic Proceedings in Theoretical Computer Science, EPTCS
publication_status: published
publisher: Open Publishing
publist_id: '5435'
quality_controlled: '1'
status: public
title: Generalised interpolation by solving recursion free-horn clauses
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 169
year: '2014'
...
---
_id: '1708'
abstract:
- lang: eng
text: It has been long argued that, because of inherent ambiguity and noise, the
brain needs to represent uncertainty in the form of probability distributions.
The neural encoding of such distributions remains however highly controversial.
Here we present a novel circuit model for representing multidimensional real-valued
distributions using a spike based spatio-temporal code. Our model combines the
computational advantages of the currently competing models for probabilistic codes
and exhibits realistic neural responses along a variety of classic measures. Furthermore,
the model highlights the challenges associated with interpreting neural activity
in relation to behavioral uncertainty and points to alternative population-level
approaches for the experimental validation of distributed representations.
author:
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
- first_name: Sophie
full_name: Denève, Sophie
last_name: Denève
citation:
ama: 'Savin C, Denève S. Spatio-temporal representations of uncertainty in spiking
neural networks. In: Vol 3. Neural Information Processing Systems; 2014:2024-2032.'
apa: 'Savin, C., & Denève, S. (2014). Spatio-temporal representations of uncertainty
in spiking neural networks (Vol. 3, pp. 2024–2032). Presented at the NIPS: Neural
Information Processing Systems, Montreal, Canada: Neural Information Processing
Systems.'
chicago: Savin, Cristina, and Sophie Denève. “Spatio-Temporal Representations of
Uncertainty in Spiking Neural Networks,” 3:2024–32. Neural Information Processing
Systems, 2014.
ieee: 'C. Savin and S. Denève, “Spatio-temporal representations of uncertainty in
spiking neural networks,” presented at the NIPS: Neural Information Processing
Systems, Montreal, Canada, 2014, vol. 3, no. January, pp. 2024–2032.'
ista: 'Savin C, Denève S. 2014. Spatio-temporal representations of uncertainty in
spiking neural networks. NIPS: Neural Information Processing Systems vol. 3, 2024–2032.'
mla: Savin, Cristina, and Sophie Denève. Spatio-Temporal Representations of Uncertainty
in Spiking Neural Networks. Vol. 3, no. January, Neural Information Processing
Systems, 2014, pp. 2024–32.
short: C. Savin, S. Denève, in:, Neural Information Processing Systems, 2014, pp.
2024–2032.
conference:
end_date: 2014-12-13
location: Montreal, Canada
name: 'NIPS: Neural Information Processing Systems'
start_date: 2014-12-08
date_created: 2018-12-11T11:53:35Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:40Z
day: '01'
department:
- _id: GaTk
intvolume: ' 3'
issue: January
language:
- iso: eng
main_file_link:
- url: http://papers.nips.cc/paper/5343-spatio-temporal-representations-of-uncertainty-in-spiking-neural-networks.pdf
month: '01'
oa_version: None
page: 2024 - 2032
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '5427'
quality_controlled: '1'
scopus_import: 1
status: public
title: Spatio-temporal representations of uncertainty in spiking neural networks
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2014'
...
---
_id: '1761'
abstract:
- lang: eng
text: Metal silicides formed by means of thermal annealing processes are employed
as contact materials in microelectronics. Control of the structure of silicide/silicon
interfaces becomes a critical issue when the characteristic size of the device
is reduced below a few tens of nanometers. Here, we report on silicide clustering
occurring within the channel of PtSi/Si/PtSi Schottky-barrier transistors. This
phenomenon is investigated through atomistic simulations and low-temperature resonant-tunneling
spectroscopy. Our results provide evidence for the segregation of a PtSi cluster
with a diameter of a few nanometers from the silicide contact. The cluster acts
as a metallic quantum dot giving rise to distinct signatures of quantum transport
through its discrete energy states.
acknowledgement: This work was supported by the Agence Nationale de la Recherche and
by the EU through the ERC Starting Grant HybridNano
author:
- first_name: Massimo
full_name: Mongillo, Massimo
last_name: Mongillo
- first_name: Panayotis
full_name: Spathis, Panayotis N
last_name: Spathis
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Silvano
full_name: De Franceschi, Silvano
last_name: De Franceschi
- first_name: Pascal
full_name: Gentile, Pascal
last_name: Gentile
- first_name: Riccardo
full_name: Rurali, Riccardo
last_name: Rurali
- first_name: Xavier
full_name: Cartoixà, Xavier
last_name: Cartoixà
citation:
ama: Mongillo M, Spathis P, Katsaros G, et al. PtSi clustering in silicon probed
by transport spectroscopy. Physical Review X. 2014;3(4). doi:10.1103/PhysRevX.3.041025
apa: Mongillo, M., Spathis, P., Katsaros, G., De Franceschi, S., Gentile, P., Rurali,
R., & Cartoixà, X. (2014). PtSi clustering in silicon probed by transport
spectroscopy. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.3.041025
chicago: Mongillo, Massimo, Panayotis Spathis, Georgios Katsaros, Silvano De Franceschi,
Pascal Gentile, Riccardo Rurali, and Xavier Cartoixà. “PtSi Clustering in Silicon
Probed by Transport Spectroscopy.” Physical Review X. American Physical
Society, 2014. https://doi.org/10.1103/PhysRevX.3.041025.
ieee: M. Mongillo et al., “PtSi clustering in silicon probed by transport
spectroscopy,” Physical Review X, vol. 3, no. 4. American Physical Society,
2014.
ista: Mongillo M, Spathis P, Katsaros G, De Franceschi S, Gentile P, Rurali R, Cartoixà
X. 2014. PtSi clustering in silicon probed by transport spectroscopy. Physical
Review X. 3(4).
mla: Mongillo, Massimo, et al. “PtSi Clustering in Silicon Probed by Transport Spectroscopy.”
Physical Review X, vol. 3, no. 4, American Physical Society, 2014, doi:10.1103/PhysRevX.3.041025.
short: M. Mongillo, P. Spathis, G. Katsaros, S. De Franceschi, P. Gentile, R. Rurali,
X. Cartoixà, Physical Review X 3 (2014).
date_created: 2018-12-11T11:53:52Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:02Z
day: '01'
doi: 10.1103/PhysRevX.3.041025
extern: 1
intvolume: ' 3'
issue: '4'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1407.5413
month: '01'
oa: 1
publication: Physical Review X
publication_status: published
publisher: American Physical Society
publist_id: '5363'
quality_controlled: 0
status: public
title: PtSi clustering in silicon probed by transport spectroscopy
type: journal_article
volume: 3
year: '2014'
...
---
_id: '1791'
abstract:
- lang: eng
text: Acute gene inactivation using short hairpin RNA (shRNA, knockdown) in developing
brain is a powerful technique to study genetic function; however, discrepancies
between knockdown and knockout murine phenotypes have left unanswered questions.
For example, doublecortin (Dcx) knockdown but not knockout shows a neocortical
neuronal migration phenotype. Here we report that in utero electroporation of
shRNA, but not siRNA or miRNA, to Dcx demonstrates a migration phenotype in Dcx
knockouts akin to the effect in wild-type mice, suggestingshRNA-mediated off-target
toxicity. This effect wasnot limited to Dcx, as it was observed in Dclk1 knockouts,
as well as with a fraction of scrambled shRNAs, suggesting a sequence-dependent
but not sequence-specific effect. Profiling RNAs from electroporated cells showed
a defect in endogenous let7 miRNA levels, and disruption of let7 or Dicer recapitulated
the migration defect. The results suggest that shRNA-mediated knockdown can produce
untoward migration effects by altering endogenous miRNA pathways.
acknowledgement: This work was supported by the National Institutes of Health R01NS41537.
G.K. was supported by an EMBO Long Term Fellowship, S.L.B. by the A.P. Giannini
Fellowship, and A.G.F. by the Brain Behavior Research Foundation
author:
- first_name: Seungtae
full_name: Baek, SeungTae
last_name: Baek
- first_name: Géraldine
full_name: Kerjan, Géraldine
last_name: Kerjan
- first_name: Stephanie
full_name: Bielas, Stephanie L
last_name: Bielas
- first_name: Jieun
full_name: Lee, Jieun
last_name: Lee
- first_name: Ali
full_name: Fenstermaker, Ali G
last_name: Fenstermaker
- first_name: Gaia
full_name: Gaia Novarino
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Joseph
full_name: Gleeson, Joseph G
last_name: Gleeson
citation:
ama: Baek S, Kerjan G, Bielas S, et al. Off-target effect of doublecortin family
shRNA on neuronal migration associated with endogenous MicroRNA dysregulation.
Neuron. 2014;82(6):1255-1262. doi:10.1016/j.neuron.2014.04.036
apa: Baek, S., Kerjan, G., Bielas, S., Lee, J., Fenstermaker, A., Novarino, G.,
& Gleeson, J. (2014). Off-target effect of doublecortin family shRNA on neuronal
migration associated with endogenous MicroRNA dysregulation. Neuron. Elsevier.
https://doi.org/10.1016/j.neuron.2014.04.036
chicago: Baek, Seungtae, Géraldine Kerjan, Stephanie Bielas, Jieun Lee, Ali Fenstermaker,
Gaia Novarino, and Joseph Gleeson. “Off-Target Effect of Doublecortin Family ShRNA
on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron.
Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.036.
ieee: S. Baek et al., “Off-target effect of doublecortin family shRNA on
neuronal migration associated with endogenous MicroRNA dysregulation,” Neuron,
vol. 82, no. 6. Elsevier, pp. 1255–1262, 2014.
ista: Baek S, Kerjan G, Bielas S, Lee J, Fenstermaker A, Novarino G, Gleeson J.
2014. Off-target effect of doublecortin family shRNA on neuronal migration associated
with endogenous MicroRNA dysregulation. Neuron. 82(6), 1255–1262.
mla: Baek, Seungtae, et al. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal
Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron, vol.
82, no. 6, Elsevier, 2014, pp. 1255–62, doi:10.1016/j.neuron.2014.04.036.
short: S. Baek, G. Kerjan, S. Bielas, J. Lee, A. Fenstermaker, G. Novarino, J. Gleeson,
Neuron 82 (2014) 1255–1262.
date_created: 2018-12-11T11:54:01Z
date_published: 2014-06-18T00:00:00Z
date_updated: 2021-01-12T06:53:13Z
day: '18'
doi: 10.1016/j.neuron.2014.04.036
extern: 1
intvolume: ' 82'
issue: '6'
month: '06'
page: 1255 - 1262
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '5322'
quality_controlled: 0
status: public
title: Off-target effect of doublecortin family shRNA on neuronal migration associated
with endogenous MicroRNA dysregulation
type: journal_article
volume: 82
year: '2014'
...
---
_id: '1806'
abstract:
- lang: eng
text: The generation of asymmetry, at both cellular and tissue level, is one of
the most essential capabilities of all eukaryotic organisms. It mediates basically
all multicellular development ranging from embryogenesis and de novo organ formation
till responses to various environmental stimuli. In plants, the awe-inspiring
number of such processes is regulated by phytohormone auxin and its directional,
cell-to-cell transport. The mediators of this transport, PIN auxin transporters,
are asymmetrically localized at the plasma membrane, and this polar localization
determines the directionality of intercellular auxin flow. Thus, auxin transport
contributes crucially to the generation of local auxin gradients or maxima, which
instruct given cell to change its developmental program. Here, we introduce and
discuss the molecular components and cellular mechanisms regulating the generation
and maintenance of cellular PIN polarity, as the general hallmarks of cell polarity
in plants.
author:
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Baster P, Friml J. Auxin on the road navigated by cellular PIN polarity. In:
Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development.
Springer; 2014:143-170. doi:10.1007/978-3-7091-1526-8_8'
apa: Baster, P., & Friml, J. (2014). Auxin on the road navigated by cellular
PIN polarity. In E. Zažímalová, J. Petrášek, & E. Benková (Eds.), Auxin
and Its Role in Plant Development (pp. 143–170). Springer. https://doi.org/10.1007/978-3-7091-1526-8_8
chicago: Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular
PIN Polarity.” In Auxin and Its Role in Plant Development, edited by Eva
Zažímalová, Jan Petrášek, and Eva Benková, 143–70. Springer, 2014. https://doi.org/10.1007/978-3-7091-1526-8_8.
ieee: P. Baster and J. Friml, “Auxin on the road navigated by cellular PIN polarity,”
in Auxin and Its Role in Plant Development, E. Zažímalová, J. Petrášek,
and E. Benková, Eds. Springer, 2014, pp. 143–170.
ista: 'Baster P, Friml J. 2014.Auxin on the road navigated by cellular PIN polarity.
In: Auxin and Its Role in Plant Development. , 143–170.'
mla: Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN
Polarity.” Auxin and Its Role in Plant Development, edited by Eva Zažímalová
et al., Springer, 2014, pp. 143–70, doi:10.1007/978-3-7091-1526-8_8.
short: P. Baster, J. Friml, in:, E. Zažímalová, J. Petrášek, E. Benková (Eds.),
Auxin and Its Role in Plant Development, Springer, 2014, pp. 143–170.
date_created: 2018-12-11T11:54:07Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T06:53:19Z
day: '01'
department:
- _id: JiFr
doi: 10.1007/978-3-7091-1526-8_8
editor:
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
language:
- iso: eng
month: '04'
oa_version: None
page: 143 - 170
publication: Auxin and Its Role in Plant Development
publication_status: published
publisher: Springer
publist_id: '5304'
quality_controlled: '1'
scopus_import: 1
status: public
title: Auxin on the road navigated by cellular PIN polarity
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1816'
abstract:
- lang: eng
text: Watermarking techniques for vector graphics dislocate vertices in order to
embed imperceptible, yet detectable, statistical features into the input data.
The embedding process may result in a change of the topology of the input data,
e.g., by introducing self-intersections, which is undesirable or even disastrous
for many applications. In this paper we present a watermarking framework for two-dimensional
vector graphics that employs conventional watermarking techniques but still provides
the guarantee that the topology of the input data is preserved. The geometric
part of this framework computes so-called maximum perturbation regions (MPR) of
vertices. We propose two efficient algorithms to compute MPRs based on Voronoi
diagrams and constrained triangulations. Furthermore, we present two algorithms
to conditionally correct the watermarked data in order to increase the watermark
embedding capacity and still guarantee topological correctness. While we focus
on the watermarking of input formed by straight-line segments, one of our approaches
can also be extended to circular arcs. We conclude the paper by demonstrating
and analyzing the applicability of our framework in conjunction with two well-known
watermarking techniques.
acknowledgement: 'Work by Martin Held and Stefan Huber was supported by Austrian Science
Fund (FWF): L367-N15 and P25816-N15.'
author:
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Martin
full_name: Held, Martin
last_name: Held
- first_name: Peter
full_name: Meerwald, Peter
last_name: Meerwald
- first_name: Roland
full_name: Kwitt, Roland
last_name: Kwitt
citation:
ama: Huber S, Held M, Meerwald P, Kwitt R. Topology-preserving watermarking of vector
graphics. International Journal of Computational Geometry and Applications.
2014;24(1):61-86. doi:10.1142/S0218195914500034
apa: Huber, S., Held, M., Meerwald, P., & Kwitt, R. (2014). Topology-preserving
watermarking of vector graphics. International Journal of Computational Geometry
and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195914500034
chicago: Huber, Stefan, Martin Held, Peter Meerwald, and Roland Kwitt. “Topology-Preserving
Watermarking of Vector Graphics.” International Journal of Computational Geometry
and Applications. World Scientific Publishing, 2014. https://doi.org/10.1142/S0218195914500034.
ieee: S. Huber, M. Held, P. Meerwald, and R. Kwitt, “Topology-preserving watermarking
of vector graphics,” International Journal of Computational Geometry and Applications,
vol. 24, no. 1. World Scientific Publishing, pp. 61–86, 2014.
ista: Huber S, Held M, Meerwald P, Kwitt R. 2014. Topology-preserving watermarking
of vector graphics. International Journal of Computational Geometry and Applications.
24(1), 61–86.
mla: Huber, Stefan, et al. “Topology-Preserving Watermarking of Vector Graphics.”
International Journal of Computational Geometry and Applications, vol.
24, no. 1, World Scientific Publishing, 2014, pp. 61–86, doi:10.1142/S0218195914500034.
short: S. Huber, M. Held, P. Meerwald, R. Kwitt, International Journal of Computational
Geometry and Applications 24 (2014) 61–86.
date_created: 2018-12-11T11:54:10Z
date_published: 2014-03-16T00:00:00Z
date_updated: 2021-01-12T06:53:23Z
day: '16'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1142/S0218195914500034
file:
- access_level: open_access
checksum: be45c133ab4d43351260e21beaa8f4b1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:43Z
date_updated: 2020-07-14T12:45:17Z
file_id: '4704'
file_name: IST-2016-443-v1+1_S0218195914500034.pdf
file_size: 991734
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 24'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 61 - 86
publication: International Journal of Computational Geometry and Applications
publication_status: published
publisher: World Scientific Publishing
publist_id: '5290'
pubrep_id: '443'
quality_controlled: '1'
scopus_import: 1
status: public
title: Topology-preserving watermarking of vector graphics
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: 24
year: '2014'
...
---
_id: '1821'
abstract:
- lang: eng
text: We review recent progress towards a rigorous understanding of the Bogoliubov
approximation for bosonic quantum many-body systems. We focus, in particular,
on the excitation spectrum of a Bose gas in the mean-field (Hartree) limit. A
list of open problems will be discussed at the end.
article_number: '1.4881536'
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Seiringer R. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation.
Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4881536
apa: Seiringer, R. (2014). Bose gases, Bose-Einstein condensation, and the Bogoliubov
approximation. Journal of Mathematical Physics. American Institute of Physics.
https://doi.org/10.1063/1.4881536
chicago: Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov
Approximation.” Journal of Mathematical Physics. American Institute of
Physics, 2014. https://doi.org/10.1063/1.4881536.
ieee: R. Seiringer, “Bose gases, Bose-Einstein condensation, and the Bogoliubov
approximation,” Journal of Mathematical Physics, vol. 55, no. 7. American
Institute of Physics, 2014.
ista: Seiringer R. 2014. Bose gases, Bose-Einstein condensation, and the Bogoliubov
approximation. Journal of Mathematical Physics. 55(7), 1.4881536.
mla: Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov
Approximation.” Journal of Mathematical Physics, vol. 55, no. 7, 1.4881536,
American Institute of Physics, 2014, doi:10.1063/1.4881536.
short: R. Seiringer, Journal of Mathematical Physics 55 (2014).
date_created: 2018-12-11T11:54:11Z
date_published: 2014-06-26T00:00:00Z
date_updated: 2021-01-12T06:53:25Z
day: '26'
ddc:
- '510'
- '530'
department:
- _id: RoSe
doi: 10.1063/1.4881536
file:
- access_level: open_access
checksum: ed0efc93c10f1341155f0316af617b82
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:49Z
date_updated: 2020-07-14T12:45:17Z
file_id: '5172'
file_name: IST-2016-532-v1+1_J._Mathematical_Phys._2014_Seiringer.pdf
file_size: 269171
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 55'
issue: '7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication: Journal of Mathematical Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5285'
pubrep_id: '532'
quality_controlled: '1'
scopus_import: 1
status: public
title: Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2014'
...
---
_id: '1822'
article_number: '075101'
author:
- first_name: Vojkan
full_name: Jakšić, Vojkan
last_name: Jakšić
- first_name: Claude
full_name: Pillet, Claude
last_name: Pillet
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Jakšić V, Pillet C, Seiringer R. Introduction. Journal of Mathematical Physics.
2014;55(7). doi:10.1063/1.4884877
apa: Jakšić, V., Pillet, C., & Seiringer, R. (2014). Introduction. Journal
of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4884877
chicago: Jakšić, Vojkan, Claude Pillet, and Robert Seiringer. “Introduction.” Journal
of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4884877.
ieee: V. Jakšić, C. Pillet, and R. Seiringer, “Introduction,” Journal of Mathematical
Physics, vol. 55, no. 7. American Institute of Physics, 2014.
ista: Jakšić V, Pillet C, Seiringer R. 2014. Introduction. Journal of Mathematical
Physics. 55(7), 075101.
mla: Jakšić, Vojkan, et al. “Introduction.” Journal of Mathematical Physics,
vol. 55, no. 7, 075101, American Institute of Physics, 2014, doi:10.1063/1.4884877.
short: V. Jakšić, C. Pillet, R. Seiringer, Journal of Mathematical Physics 55 (2014).
date_created: 2018-12-11T11:54:12Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2021-01-12T06:53:25Z
day: '01'
department:
- _id: RoSe
doi: 10.1063/1.4884877
intvolume: ' 55'
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
publication: Journal of Mathematical Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5284'
quality_controlled: '1'
scopus_import: 1
status: public
title: Introduction
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2014'
...
---
_id: '1829'
abstract:
- lang: eng
text: Hitting and batting tasks, such as tennis forehands, ping-pong strokes, or
baseball batting, depend on predictions where the ball can be intercepted and
how it can properly be returned to the opponent. These predictions get more accurate
over time, hence the behaviors need to be continuously modified. As a result,
movement templates with a learned global shape need to be adapted during the execution
so that the racket reaches a target position and velocity that will return the
ball over to the other side of the net or court. It requires altering learned
movements to hit a varying target with the necessary velocity at a specific instant
in time. Such a task cannot be incorporated straightforwardly in most movement
representations suitable for learning. For example, the standard formulation of
the dynamical system based motor primitives (introduced by Ijspeert et al (2002b))
does not satisfy this property despite their flexibility which has allowed learning
tasks ranging from locomotion to kendama. In order to fulfill this requirement,
we reformulate the Ijspeert framework to incorporate the possibility of specifying
a desired hitting point and a desired hitting velocity while maintaining all advantages
of the original formulation.We show that the proposed movement template formulation
works well in two scenarios, i.e., for hitting a ball on a string with a table
tennis racket at a specified velocity and for returning balls launched by a ball
gun successfully over the net using forehand movements.
alternative_title:
- Springer Tracts in Advanced Robotics
author:
- first_name: Katharina
full_name: Muelling, Katharina
last_name: Muelling
- first_name: Oliver
full_name: Kroemer, Oliver
last_name: Kroemer
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
citation:
ama: 'Muelling K, Kroemer O, Lampert C, Schölkopf B. Movement templates for learning
of hitting and batting. In: Kober J, Peters J, eds. Learning Motor Skills.
Vol 97. From Algorithms to Robot Experiments. Springer; 2014:69-82. doi:10.1007/978-3-319-03194-1_3'
apa: Muelling, K., Kroemer, O., Lampert, C., & Schölkopf, B. (2014). Movement
templates for learning of hitting and batting. In J. Kober & J. Peters (Eds.),
Learning Motor Skills (Vol. 97, pp. 69–82). Springer. https://doi.org/10.1007/978-3-319-03194-1_3
chicago: Muelling, Katharina, Oliver Kroemer, Christoph Lampert, and Bernhard Schölkopf.
“Movement Templates for Learning of Hitting and Batting.” In Learning Motor
Skills, edited by Jens Kober and Jan Peters, 97:69–82. From Algorithms to
Robot Experiments. Springer, 2014. https://doi.org/10.1007/978-3-319-03194-1_3.
ieee: K. Muelling, O. Kroemer, C. Lampert, and B. Schölkopf, “Movement templates
for learning of hitting and batting,” in Learning Motor Skills, vol. 97,
J. Kober and J. Peters, Eds. Springer, 2014, pp. 69–82.
ista: 'Muelling K, Kroemer O, Lampert C, Schölkopf B. 2014.Movement templates for
learning of hitting and batting. In: Learning Motor Skills. Springer Tracts in
Advanced Robotics, vol. 97, 69–82.'
mla: Muelling, Katharina, et al. “Movement Templates for Learning of Hitting and
Batting.” Learning Motor Skills, edited by Jens Kober and Jan Peters, vol.
97, Springer, 2014, pp. 69–82, doi:10.1007/978-3-319-03194-1_3.
short: K. Muelling, O. Kroemer, C. Lampert, B. Schölkopf, in:, J. Kober, J. Peters
(Eds.), Learning Motor Skills, Springer, 2014, pp. 69–82.
date_created: 2018-12-11T11:54:14Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:28Z
day: '01'
department:
- _id: ChLa
doi: 10.1007/978-3-319-03194-1_3
editor:
- first_name: Jens
full_name: Kober, Jens
last_name: Kober
- first_name: Jan
full_name: Peters, Jan
last_name: Peters
intvolume: ' 97'
language:
- iso: eng
month: '01'
oa_version: None
page: 69 - 82
publication: Learning Motor Skills
publication_status: published
publisher: Springer
publist_id: '5274'
quality_controlled: '1'
scopus_import: 1
series_title: From Algorithms to Robot Experiments
status: public
title: Movement templates for learning of hitting and batting
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 97
year: '2014'
...
---
_id: '1844'
abstract:
- lang: eng
text: 'Local protein interactions ("molecular context" effects) dictate
amino acid replacements and can be described in terms of site-specific, energetic
preferences for any different amino acid. It has been recently debated whether
these preferences remain approximately constant during evolution or whether, due
to coevolution of sites, they change strongly. Such research highlights an unresolved
and fundamental issue with far-reaching implications for phylogenetic analysis
and molecular evolution modeling. Here, we take advantage of the recent availability
of phenotypically supported laboratory resurrections of Precambrian thioredoxins
and β-lactamases to experimentally address the change of site-specific amino acid
preferences over long geological timescales. Extensive mutational analyses support
the notion that evolutionary adjustment to a new amino acid may occur, but to
a large extent this is insufficient to erase the primitive preference for amino
acid replacements. Generally, site-specific amino acid preferences appear to remain
conserved throughout evolutionary history despite local sequence divergence. We
show such preference conservation to be readily understandable in molecular terms
and we provide crystallographic evidence for an intriguing structural-switch mechanism:
Energetic preference for an ancestral amino acid in a modern protein can be linked
to reorganization upon mutation to the ancestral local structure around the mutated
site. Finally, we point out that site-specific preference conservation naturally
leads to one plausible evolutionary explanation for the existence of intragenic
global suppressor mutations.'
author:
- first_name: Valeria
full_name: Risso, Valeria
last_name: Risso
- first_name: Fadia
full_name: Manssour Triedo, Fadia
last_name: Manssour Triedo
- first_name: Asuncion
full_name: Delgado Delgado, Asuncion
last_name: Delgado Delgado
- first_name: Rocio
full_name: Arco, Rocio
last_name: Arco
- first_name: Alicia
full_name: Barroso Deljesús, Alicia
last_name: Barroso Deljesús
- first_name: Álvaro
full_name: Inglés Prieto, Álvaro
id: 2A9DB292-F248-11E8-B48F-1D18A9856A87
last_name: Inglés Prieto
orcid: 0000-0002-5409-8571
- first_name: Raquel
full_name: Godoy Ruiz, Raquel
last_name: Godoy Ruiz
- first_name: Josè
full_name: Gavira, Josè
last_name: Gavira
- first_name: Eric
full_name: Gaucher, Eric
last_name: Gaucher
- first_name: Beatriz
full_name: Ibarra Molero, Beatriz
last_name: Ibarra Molero
- first_name: Jose
full_name: Sánchez Ruiz, Jose
last_name: Sánchez Ruiz
citation:
ama: Risso V, Manssour Triedo F, Delgado Delgado A, et al. Mutational studies on
resurrected ancestral proteins reveal conservation of site-specific amino acid
preferences throughout evolutionary history. Molecular Biology and Evolution.
2014;32(2):440-455. doi:10.1093/molbev/msu312
apa: Risso, V., Manssour Triedo, F., Delgado Delgado, A., Arco, R., Barroso Deljesús,
A., Inglés Prieto, Á., … Sánchez Ruiz, J. (2014). Mutational studies on resurrected
ancestral proteins reveal conservation of site-specific amino acid preferences
throughout evolutionary history. Molecular Biology and Evolution. Oxford
University Press. https://doi.org/10.1093/molbev/msu312
chicago: Risso, Valeria, Fadia Manssour Triedo, Asuncion Delgado Delgado, Rocio
Arco, Alicia Barroso Deljesús, Álvaro Inglés Prieto, Raquel Godoy Ruiz, et al.
“Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific
Amino Acid Preferences throughout Evolutionary History.” Molecular Biology
and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu312.
ieee: V. Risso et al., “Mutational studies on resurrected ancestral proteins
reveal conservation of site-specific amino acid preferences throughout evolutionary
history,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University
Press, pp. 440–455, 2014.
ista: Risso V, Manssour Triedo F, Delgado Delgado A, Arco R, Barroso Deljesús A,
Inglés Prieto Á, Godoy Ruiz R, Gavira J, Gaucher E, Ibarra Molero B, Sánchez Ruiz
J. 2014. Mutational studies on resurrected ancestral proteins reveal conservation
of site-specific amino acid preferences throughout evolutionary history. Molecular
Biology and Evolution. 32(2), 440–455.
mla: Risso, Valeria, et al. “Mutational Studies on Resurrected Ancestral Proteins
Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary
History.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University
Press, 2014, pp. 440–55, doi:10.1093/molbev/msu312.
short: V. Risso, F. Manssour Triedo, A. Delgado Delgado, R. Arco, A. Barroso Deljesús,
Á. Inglés Prieto, R. Godoy Ruiz, J. Gavira, E. Gaucher, B. Ibarra Molero, J. Sánchez
Ruiz, Molecular Biology and Evolution 32 (2014) 440–455.
date_created: 2018-12-11T11:54:19Z
date_published: 2014-11-12T00:00:00Z
date_updated: 2021-01-12T06:53:34Z
day: '12'
ddc:
- '571'
department:
- _id: HaJa
doi: 10.1093/molbev/msu312
file:
- access_level: open_access
checksum: 06215318e66be8f3e0c33abb07e9d3da
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:56Z
date_updated: 2020-07-14T12:45:19Z
file_id: '5247'
file_name: IST-2016-430-v1+1_Mol_Biol_Evol-2015-Risso-440-55.pdf
file_size: 1545246
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 32'
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 440 - 455
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '5257'
pubrep_id: '430'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mutational studies on resurrected ancestral proteins reveal conservation of
site-specific amino acid preferences throughout evolutionary history
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2014'
...
---
_id: '1842'
abstract:
- lang: eng
text: We prove polynomial upper bounds of geometric Ramsey numbers of pathwidth-2
outerplanar triangulations in both convex and general cases. We also prove that
the geometric Ramsey numbers of the ladder graph on 2n vertices are bounded by
O(n3) and O(n10), in the convex and general case, respectively. We then apply
similar methods to prove an (Formula presented.) upper bound on the Ramsey number
of a path with n ordered vertices.
acknowledgement: Marek Krčál was supported by the ERC Advanced Grant No. 267165.
author:
- first_name: Josef
full_name: Cibulka, Josef
last_name: Cibulka
- first_name: Pu
full_name: Gao, Pu
last_name: Gao
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
- first_name: Tomáš
full_name: Valla, Tomáš
last_name: Valla
- first_name: Pavel
full_name: Valtr, Pavel
last_name: Valtr
citation:
ama: Cibulka J, Gao P, Krcál M, Valla T, Valtr P. On the geometric ramsey number
of outerplanar graphs. Discrete & Computational Geometry. 2014;53(1):64-79.
doi:10.1007/s00454-014-9646-x
apa: Cibulka, J., Gao, P., Krcál, M., Valla, T., & Valtr, P. (2014). On the
geometric ramsey number of outerplanar graphs. Discrete & Computational
Geometry. Springer. https://doi.org/10.1007/s00454-014-9646-x
chicago: Cibulka, Josef, Pu Gao, Marek Krcál, Tomáš Valla, and Pavel Valtr. “On
the Geometric Ramsey Number of Outerplanar Graphs.” Discrete & Computational
Geometry. Springer, 2014. https://doi.org/10.1007/s00454-014-9646-x.
ieee: J. Cibulka, P. Gao, M. Krcál, T. Valla, and P. Valtr, “On the geometric ramsey
number of outerplanar graphs,” Discrete & Computational Geometry, vol.
53, no. 1. Springer, pp. 64–79, 2014.
ista: Cibulka J, Gao P, Krcál M, Valla T, Valtr P. 2014. On the geometric ramsey
number of outerplanar graphs. Discrete & Computational Geometry. 53(1), 64–79.
mla: Cibulka, Josef, et al. “On the Geometric Ramsey Number of Outerplanar Graphs.”
Discrete & Computational Geometry, vol. 53, no. 1, Springer, 2014,
pp. 64–79, doi:10.1007/s00454-014-9646-x.
short: J. Cibulka, P. Gao, M. Krcál, T. Valla, P. Valtr, Discrete & Computational
Geometry 53 (2014) 64–79.
date_created: 2018-12-11T11:54:18Z
date_published: 2014-11-14T00:00:00Z
date_updated: 2021-01-12T06:53:33Z
day: '14'
department:
- _id: UlWa
- _id: HeEd
doi: 10.1007/s00454-014-9646-x
intvolume: ' 53'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1310.7004
month: '11'
oa: 1
oa_version: Submitted Version
page: 64 - 79
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '5260'
scopus_import: 1
status: public
title: On the geometric ramsey number of outerplanar graphs
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2014'
...
---
_id: '1854'
abstract:
- lang: eng
text: In this paper, we present a method for non-rigid, partial shape matching in
vector graphics. Given a user-specified query region in a 2D shape, similar regions
are found, even if they are non-linearly distorted. Furthermore, a non-linear
mapping is established between the query regions and these matches, which allows
the automatic transfer of editing operations such as texturing. This is achieved
by a two-step approach. First, pointwise correspondences between the query region
and the whole shape are established. The transformation parameters of these correspondences
are registered in an appropriate transformation space. For transformations between
similar regions, these parameters form surfaces in transformation space, which
are extracted in the second step of our method. The extracted regions may be related
to the query region by a non-rigid transform, enabling non-rigid shape matching.
In this paper, we present a method for non-rigid, partial shape matching in vector
graphics. Given a user-specified query region in a 2D shape, similar regions are
found, even if they are non-linearly distorted. Furthermore, a non-linear mapping
is established between the query regions and these matches, which allows the automatic
transfer of editing operations such as texturing. This is achieved by a two-step
approach. First, pointwise correspondences between the query region and the whole
shape are established. The transformation parameters of these correspondences
are registered in an appropriate transformation space. For transformations between
similar regions, these parameters form surfaces in transformation space, which
are extracted in the second step of our method. The extracted regions may be related
to the query region by a non-rigid transform, enabling non-rigid shape matching.
author:
- first_name: Paul
full_name: Guerrero, Paul
last_name: Guerrero
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Michael
full_name: Wimmer, Michael
last_name: Wimmer
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
citation:
ama: Guerrero P, Auzinger T, Wimmer M, Jeschke S. Partial shape matching using transformation
parameter similarity. Computer Graphics Forum. 2014;34(1):239-252. doi:10.1111/cgf.12509
apa: Guerrero, P., Auzinger, T., Wimmer, M., & Jeschke, S. (2014). Partial shape
matching using transformation parameter similarity. Computer Graphics Forum.
Wiley. https://doi.org/10.1111/cgf.12509
chicago: Guerrero, Paul, Thomas Auzinger, Michael Wimmer, and Stefan Jeschke. “Partial
Shape Matching Using Transformation Parameter Similarity.” Computer Graphics
Forum. Wiley, 2014. https://doi.org/10.1111/cgf.12509.
ieee: P. Guerrero, T. Auzinger, M. Wimmer, and S. Jeschke, “Partial shape matching
using transformation parameter similarity,” Computer Graphics Forum, vol.
34, no. 1. Wiley, pp. 239–252, 2014.
ista: Guerrero P, Auzinger T, Wimmer M, Jeschke S. 2014. Partial shape matching
using transformation parameter similarity. Computer Graphics Forum. 34(1), 239–252.
mla: Guerrero, Paul, et al. “Partial Shape Matching Using Transformation Parameter
Similarity.” Computer Graphics Forum, vol. 34, no. 1, Wiley, 2014, pp.
239–52, doi:10.1111/cgf.12509.
short: P. Guerrero, T. Auzinger, M. Wimmer, S. Jeschke, Computer Graphics Forum
34 (2014) 239–252.
date_created: 2018-12-11T11:54:22Z
date_published: 2014-11-05T00:00:00Z
date_updated: 2021-01-12T06:53:38Z
day: '05'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1111/cgf.12509
file:
- access_level: open_access
checksum: 91946bfc509c77f5fd3151a3ff2b2c8f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:58Z
date_updated: 2020-07-14T12:45:19Z
file_id: '5182'
file_name: IST-2016-574-v1+1_Guerrero-2014-TPS-paper.pdf
file_size: 24817484
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 239 - 252
publication: Computer Graphics Forum
publication_status: published
publisher: Wiley
publist_id: '5246'
pubrep_id: '574'
quality_controlled: '1'
scopus_import: 1
status: public
title: Partial shape matching using transformation parameter similarity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2014'
...
---
_id: '1852'
abstract:
- lang: eng
text: To control morphogenesis, molecular regulatory networks have to interfere
with the mechanical properties of the individual cells of developing organs and
tissues, but how this is achieved is not well known. We study this issue here
in the shoot meristem of higher plants, a group of undifferentiated cells where
complex changes in growth rates and directions lead to the continuous formation
of new organs [1, 2]. Here, we show that the plant hormone auxin plays an important
role in this process via a dual, local effect on the extracellular matrix, the
cell wall, which determines cell shape. Our study reveals that auxin not only
causes a limited reduction in wall stiffness but also directly interferes with
wall anisotropy via the regulation of cortical microtubule dynamics. We further
show that to induce growth isotropy and organ outgrowth, auxin somehow interferes
with the cortical microtubule-ordering activity of a network of proteins, including
AUXIN BINDING PROTEIN 1 and KATANIN 1. Numerical simulations further indicate
that the induced isotropy is sufficient to amplify the effects of the relatively
minor changes in wall stiffness to promote organogenesis and the establishment
of new growth axes in a robust manner.
acknowledgement: 'This work was funded by grants from EraSysBio+ (iSAM) and ERC (Morphodynamics). '
author:
- first_name: Massimiliano
full_name: Sassi, Massimiliano
last_name: Sassi
- first_name: Olivier
full_name: Ali, Olivier
last_name: Ali
- first_name: Frédéric
full_name: Boudon, Frédéric
last_name: Boudon
- first_name: Gladys
full_name: Cloarec, Gladys
last_name: Cloarec
- first_name: Ursula
full_name: Abad, Ursula
last_name: Abad
- first_name: Coralie
full_name: Cellier, Coralie
last_name: Cellier
- first_name: Xu
full_name: Chen, Xu
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Benjamin
full_name: Gilles, Benjamin
last_name: Gilles
- first_name: Pascale
full_name: Milani, Pascale
last_name: Milani
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Teva
full_name: Vernoux, Teva
last_name: Vernoux
- first_name: Christophe
full_name: Godin, Christophe
last_name: Godin
- first_name: Olivier
full_name: Hamant, Olivier
last_name: Hamant
- first_name: Jan
full_name: Traas, Jan
last_name: Traas
citation:
ama: Sassi M, Ali O, Boudon F, et al. An auxin-mediated shift toward growth isotropy
promotes organ formation at the shoot meristem in Arabidopsis. Current Biology.
2014;24(19):2335-2342. doi:10.1016/j.cub.2014.08.036
apa: Sassi, M., Ali, O., Boudon, F., Cloarec, G., Abad, U., Cellier, C., … Traas,
J. (2014). An auxin-mediated shift toward growth isotropy promotes organ formation
at the shoot meristem in Arabidopsis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.08.036
chicago: Sassi, Massimiliano, Olivier Ali, Frédéric Boudon, Gladys Cloarec, Ursula
Abad, Coralie Cellier, Xu Chen, et al. “An Auxin-Mediated Shift toward Growth
Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current
Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.08.036.
ieee: M. Sassi et al., “An auxin-mediated shift toward growth isotropy promotes
organ formation at the shoot meristem in Arabidopsis,” Current Biology,
vol. 24, no. 19. Cell Press, pp. 2335–2342, 2014.
ista: Sassi M, Ali O, Boudon F, Cloarec G, Abad U, Cellier C, Chen X, Gilles B,
Milani P, Friml J, Vernoux T, Godin C, Hamant O, Traas J. 2014. An auxin-mediated
shift toward growth isotropy promotes organ formation at the shoot meristem in
Arabidopsis. Current Biology. 24(19), 2335–2342.
mla: Sassi, Massimiliano, et al. “An Auxin-Mediated Shift toward Growth Isotropy
Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current Biology,
vol. 24, no. 19, Cell Press, 2014, pp. 2335–42, doi:10.1016/j.cub.2014.08.036.
short: M. Sassi, O. Ali, F. Boudon, G. Cloarec, U. Abad, C. Cellier, X. Chen, B.
Gilles, P. Milani, J. Friml, T. Vernoux, C. Godin, O. Hamant, J. Traas, Current
Biology 24 (2014) 2335–2342.
date_created: 2018-12-11T11:54:22Z
date_published: 2014-10-06T00:00:00Z
date_updated: 2021-01-12T06:53:37Z
day: '06'
department:
- _id: JiFr
doi: 10.1016/j.cub.2014.08.036
intvolume: ' 24'
issue: '19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-01074821
month: '10'
oa: 1
oa_version: Submitted Version
page: 2335 - 2342
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '5248'
quality_controlled: '1'
scopus_import: 1
status: public
title: An auxin-mediated shift toward growth isotropy promotes organ formation at
the shoot meristem in Arabidopsis
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2014'
...
---
_id: '1853'
abstract:
- lang: eng
text: Wireless sensor networks (WSNs) composed of low-power, low-cost sensor nodes
are expected to form the backbone of future intelligent networks for a broad range
of civil, industrial and military applications. These sensor nodes are often deployed
through random spreading, and function in dynamic environments. Many applications
of WSNs such as pollution tracking, forest fire detection, and military surveillance
require knowledge of the location of constituent nodes. But the use of technologies
such as GPS on all nodes is prohibitive due to power and cost constraints. So,
the sensor nodes need to autonomously determine their locations. Most localization
techniques use anchor nodes with known locations to determine the position of
remaining nodes. Localization techniques have two conflicting requirements. On
one hand, an ideal localization technique should be computationally simple and
on the other hand, it must be resistant to attacks that compromise anchor nodes.
In this paper, we propose a computationally light-weight game theoretic secure
localization technique and demonstrate its effectiveness in comparison to existing
techniques.
author:
- first_name: Susmit
full_name: Jha, Susmit
last_name: Jha
- first_name: Stavros
full_name: Tripakis, Stavros
last_name: Tripakis
- first_name: Sanjit
full_name: Seshia, Sanjit
last_name: Seshia
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Jha S, Tripakis S, Seshia S, Chatterjee K. Game theoretic secure localization
in wireless sensor networks. In: IEEE; 2014:85-90. doi:10.1109/IOT.2014.7030120'
apa: 'Jha, S., Tripakis, S., Seshia, S., & Chatterjee, K. (2014). Game theoretic
secure localization in wireless sensor networks (pp. 85–90). Presented at the
IOT: Internet of Things, Cambridge, USA: IEEE. https://doi.org/10.1109/IOT.2014.7030120'
chicago: Jha, Susmit, Stavros Tripakis, Sanjit Seshia, and Krishnendu Chatterjee.
“Game Theoretic Secure Localization in Wireless Sensor Networks,” 85–90. IEEE,
2014. https://doi.org/10.1109/IOT.2014.7030120.
ieee: 'S. Jha, S. Tripakis, S. Seshia, and K. Chatterjee, “Game theoretic secure
localization in wireless sensor networks,” presented at the IOT: Internet of Things,
Cambridge, USA, 2014, pp. 85–90.'
ista: 'Jha S, Tripakis S, Seshia S, Chatterjee K. 2014. Game theoretic secure localization
in wireless sensor networks. IOT: Internet of Things, 85–90.'
mla: Jha, Susmit, et al. Game Theoretic Secure Localization in Wireless Sensor
Networks. IEEE, 2014, pp. 85–90, doi:10.1109/IOT.2014.7030120.
short: S. Jha, S. Tripakis, S. Seshia, K. Chatterjee, in:, IEEE, 2014, pp. 85–90.
conference:
end_date: 2014-10-08
location: Cambridge, USA
name: 'IOT: Internet of Things'
start_date: 2014-10-06
date_created: 2018-12-11T11:54:22Z
date_published: 2014-02-03T00:00:00Z
date_updated: 2021-01-12T06:53:38Z
day: '03'
department:
- _id: KrCh
doi: 10.1109/IOT.2014.7030120
language:
- iso: eng
month: '02'
oa_version: None
page: 85 - 90
publication_status: published
publisher: IEEE
publist_id: '5247'
quality_controlled: '1'
status: public
title: Game theoretic secure localization in wireless sensor networks
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1862'
abstract:
- lang: eng
text: The prominent and evolutionarily ancient role of the plant hormone auxin is
the regulation of cell expansion. Cell expansion requires ordered arrangement
of the cytoskeleton but molecular mechanisms underlying its regulation by signalling
molecules including auxin are unknown. Here we show in the model plant Arabidopsis
thaliana that in elongating cells exogenous application of auxin or redistribution
of endogenous auxin induces very rapid microtubule re-orientation from transverse
to longitudinal, coherent with the inhibition of cell expansion. This fast auxin
effect requires auxin binding protein 1 (ABP1) and involves a contribution of
downstream signalling components such as ROP6 GTPase, ROP-interactive protein
RIC1 and the microtubule-severing protein katanin. These components are required
for rapid auxin-and ABP1-mediated re-orientation of microtubules to regulate cell
elongation in roots and dark-grown hypocotyls as well as asymmetric growth during
gravitropic responses.
acknowledgement: We thank R. Dixit for performing complementary experiments, D. W.
Ehrhardt and T. Hashimoto for providing the seeds of TUB6–RFP and EB1b–GFP respectively,
E. Zazimalova, J. Petrasek and M. Fendrych for discussing the manuscript and J.
Leung for text optimization. This work was supported by the European Research Council
(project ERC-2011-StG-20101109-PSDP, to J.F.), ANR blanc AuxiWall project (ANR-11-BSV5-0007,
to C.P.-R. and L.G.) and the Agency for Innovation by Science and Technology (IWT)
(to H.R.). This work benefited from the facilities and expertise of the Imagif Cell
Biology platform (http://www.imagif.cnrs.fr), which is supported by the Conseil
Général de l’Essonne.
article_processing_charge: No
article_type: original
author:
- first_name: Xu
full_name: Chen, Xu
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Laurie
full_name: Grandont, Laurie
last_name: Grandont
- first_name: Hongjiang
full_name: Li, Hongjiang
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Sébastien
full_name: Paque, Sébastien
last_name: Paque
- first_name: Anas
full_name: Abuzeineh, Anas
last_name: Abuzeineh
- first_name: Hana
full_name: Rakusova, Hana
id: 4CAAA450-78D2-11EA-8E57-B40A396E08BA
last_name: Rakusova
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Catherine
full_name: Perrot Rechenmann, Catherine
last_name: Perrot Rechenmann
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Chen X, Grandont L, Li H, et al. Inhibition of cell expansion by rapid ABP1-mediated
auxin effect on microtubules. Nature. 2014;516(729):90-93. doi:10.1038/nature13889
apa: Chen, X., Grandont, L., Li, H., Hauschild, R., Paque, S., Abuzeineh, A., …
Friml, J. (2014). Inhibition of cell expansion by rapid ABP1-mediated auxin effect
on microtubules. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13889
chicago: Chen, Xu, Laurie Grandont, Hongjiang Li, Robert Hauschild, Sébastien Paque,
Anas Abuzeineh, Hana Rakusova, Eva Benková, Catherine Perrot Rechenmann, and Jiří
Friml. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.”
Nature. Nature Publishing Group, 2014. https://doi.org/10.1038/nature13889.
ieee: X. Chen et al., “Inhibition of cell expansion by rapid ABP1-mediated
auxin effect on microtubules,” Nature, vol. 516, no. 729. Nature Publishing
Group, pp. 90–93, 2014.
ista: Chen X, Grandont L, Li H, Hauschild R, Paque S, Abuzeineh A, Rakusova H, Benková
E, Perrot Rechenmann C, Friml J. 2014. Inhibition of cell expansion by rapid ABP1-mediated
auxin effect on microtubules. Nature. 516(729), 90–93.
mla: Chen, Xu, et al. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin
Effect on Microtubules.” Nature, vol. 516, no. 729, Nature Publishing Group,
2014, pp. 90–93, doi:10.1038/nature13889.
short: X. Chen, L. Grandont, H. Li, R. Hauschild, S. Paque, A. Abuzeineh, H. Rakusova,
E. Benková, C. Perrot Rechenmann, J. Friml, Nature 516 (2014) 90–93.
date_created: 2018-12-11T11:54:25Z
date_published: 2014-12-04T00:00:00Z
date_updated: 2022-05-23T08:26:44Z
day: '04'
department:
- _id: JiFr
- _id: Bio
- _id: EvBe
doi: 10.1038/nature13889
ec_funded: 1
external_id:
pmid:
- '25409144'
intvolume: ' 516'
issue: '729'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257754/
month: '12'
oa: 1
oa_version: Submitted Version
page: 90 - 93
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Nature Publishing Group
publist_id: '5237'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 516
year: '2014'
...
---
_id: '1869'
abstract:
- lang: eng
text: Boolean controllers for systems with complex datapaths are often very difficult
to implement correctly, in particular when concurrency is involved. Yet, in many
instances it is easy to formally specify correctness. For example, the specification
for the controller of a pipelined processor only has to state that the pipelined
processor gives the same results as a non-pipelined reference design. This makes
such controllers a good target for automated synthesis. However, an efficient
abstraction for the complex datapath elements is needed, as a bit-precise description
is often infeasible. We present Suraq, the first controller synthesis tool which
uses uninterpreted functions for the abstraction. Quantified firstorder formulas
(with specific quantifier structure) serve as the specification language from
which Suraq synthesizes Boolean controllers. Suraq transforms the specification
into an unsatisfiable SMT formula, and uses Craig interpolation to compute its
results. Using Suraq, we were able to synthesize a controller (consisting of two
Boolean signals) for a five-stage pipelined DLX processor in roughly one hour
and 15 minutes.
acknowledgement: The work presented in this paper was supported in part by the European
Research Council (ERC) under grant agreement QUAINT (I774-N23)
alternative_title:
- LNCS
author:
- first_name: Georg
full_name: Hofferek, Georg
last_name: Hofferek
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
citation:
ama: 'Hofferek G, Gupta A. Suraq - a controller synthesis tool using uninterpreted
functions. In: Yahav E, ed. HVC 2014. Vol 8855. Springer; 2014:68-74. doi:10.1007/978-3-319-13338-6_6'
apa: 'Hofferek, G., & Gupta, A. (2014). Suraq - a controller synthesis tool
using uninterpreted functions. In E. Yahav (Ed.), HVC 2014 (Vol. 8855,
pp. 68–74). Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-13338-6_6'
chicago: Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool
Using Uninterpreted Functions.” In HVC 2014, edited by Eran Yahav, 8855:68–74.
Springer, 2014. https://doi.org/10.1007/978-3-319-13338-6_6.
ieee: G. Hofferek and A. Gupta, “Suraq - a controller synthesis tool using uninterpreted
functions,” in HVC 2014, Haifa, Israel, 2014, vol. 8855, pp. 68–74.
ista: 'Hofferek G, Gupta A. 2014. Suraq - a controller synthesis tool using uninterpreted
functions. HVC 2014. HVC: Haifa Verification Conference, LNCS, vol. 8855, 68–74.'
mla: Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using
Uninterpreted Functions.” HVC 2014, edited by Eran Yahav, vol. 8855, Springer,
2014, pp. 68–74, doi:10.1007/978-3-319-13338-6_6.
short: G. Hofferek, A. Gupta, in:, E. Yahav (Ed.), HVC 2014, Springer, 2014, pp.
68–74.
conference:
end_date: 2014-11-20
location: Haifa, Israel
name: 'HVC: Haifa Verification Conference'
start_date: 2014-11-18
date_created: 2018-12-11T11:54:27Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:44Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-319-13338-6_6
ec_funded: 1
editor:
- first_name: Eran
full_name: Yahav, Eran
last_name: Yahav
intvolume: ' 8855'
language:
- iso: eng
month: '01'
oa_version: None
page: 68 - 74
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: HVC 2014
publication_status: published
publisher: Springer
publist_id: '5228'
quality_controlled: '1'
status: public
title: Suraq - a controller synthesis tool using uninterpreted functions
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8855
year: '2014'
...
---
_id: '1872'
abstract:
- lang: eng
text: Extensionality axioms are common when reasoning about data collections, such
as arrays and functions in program analysis, or sets in mathematics. An extensionality
axiom asserts that two collections are equal if they consist of the same elements
at the same indices. Using extensionality is often required to show that two collections
are equal. A typical example is the set theory theorem (∀x)(∀y)x∪y = y ∪x. Interestingly,
while humans have no problem with proving such set identities using extensionality,
they are very hard for superposition theorem provers because of the calculi they
use. In this paper we show how addition of a new inference rule, called extensionality
resolution, allows first-order theorem provers to easily solve problems no modern
first-order theorem prover can solve. We illustrate this by running the VAMPIRE
theorem prover with extensionality resolution on a number of set theory and array
problems. Extensionality resolution helps VAMPIRE to solve problems from the TPTP
library of first-order problems that were never solved before by any prover.
acknowledgement: This research was supported in part by the Austrian National Research
Network RiSE (S11410-N23).
alternative_title:
- LNCS
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
- first_name: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
- first_name: Andrei
full_name: Voronkov, Andrei
last_name: Voronkov
citation:
ama: 'Gupta A, Kovács L, Kragl B, Voronkov A. Extensional crisis and proving identity.
In: Cassez F, Raskin J-F, eds. ATVA 2014. Vol 8837. Springer; 2014:185-200.
doi:10.1007/978-3-319-11936-6_14'
apa: 'Gupta, A., Kovács, L., Kragl, B., & Voronkov, A. (2014). Extensional crisis
and proving identity. In F. Cassez & J.-F. Raskin (Eds.), ATVA 2014
(Vol. 8837, pp. 185–200). Sydney, Australia: Springer. https://doi.org/10.1007/978-3-319-11936-6_14'
chicago: Gupta, Ashutosh, Laura Kovács, Bernhard Kragl, and Andrei Voronkov. “Extensional
Crisis and Proving Identity.” In ATVA 2014, edited by Franck Cassez and
Jean-François Raskin, 8837:185–200. Springer, 2014. https://doi.org/10.1007/978-3-319-11936-6_14.
ieee: A. Gupta, L. Kovács, B. Kragl, and A. Voronkov, “Extensional crisis and proving
identity,” in ATVA 2014, Sydney, Australia, 2014, vol. 8837, pp. 185–200.
ista: 'Gupta A, Kovács L, Kragl B, Voronkov A. 2014. Extensional crisis and proving
identity. ATVA 2014. ATVA: Automated Technology for Verification and Analysis,
LNCS, vol. 8837, 185–200.'
mla: Gupta, Ashutosh, et al. “Extensional Crisis and Proving Identity.” ATVA
2014, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer,
2014, pp. 185–200, doi:10.1007/978-3-319-11936-6_14.
short: A. Gupta, L. Kovács, B. Kragl, A. Voronkov, in:, F. Cassez, J.-F. Raskin
(Eds.), ATVA 2014, Springer, 2014, pp. 185–200.
conference:
end_date: 2014-11-07
location: Sydney, Australia
name: 'ATVA: Automated Technology for Verification and Analysis'
start_date: 2014-11-03
date_created: 2018-12-11T11:54:28Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:45Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-11936-6_14
ec_funded: 1
editor:
- first_name: Franck
full_name: Cassez, Franck
last_name: Cassez
- first_name: Jean-François
full_name: Raskin, Jean-François
last_name: Raskin
file:
- access_level: open_access
checksum: af4bd3fc1f4c93075e4dc5cbf625fe7b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:15Z
date_updated: 2020-07-14T12:45:19Z
file_id: '4801'
file_name: IST-2016-641-v1+1_atva2014.pdf
file_size: 244294
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 8837'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 185 - 200
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication: ATVA 2014
publication_status: published
publisher: Springer
publist_id: '5226'
pubrep_id: '641'
quality_controlled: '1'
scopus_import: 1
status: public
title: Extensional crisis and proving identity
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8837
year: '2014'
...
---
_id: '1870'
abstract:
- lang: eng
text: We investigate the problem of checking if a finite-state transducer is robust
to uncertainty in its input. Our notion of robustness is based on the analytic
notion of Lipschitz continuity - a transducer is K-(Lipschitz) robust if the perturbation
in its output is at most K times the perturbation in its input. We quantify input
and output perturbation using similarity functions. We show that K-robustness
is undecidable even for deterministic transducers. We identify a class of functional
transducers, which admits a polynomial time automata-theoretic decision procedure
for K-robustness. This class includes Mealy machines and functional letter-to-letter
transducers. We also study K-robustness of nondeterministic transducers. Since
a nondeterministic transducer generates a set of output words for each input word,
we quantify output perturbation using setsimilarity functions. We show that K-robustness
of nondeterministic transducers is undecidable, even for letter-to-letter transducers.
We identify a class of set-similarity functions which admit decidable K-robustness
of letter-to-letter transducers.
alternative_title:
- LIPIcs
author:
- 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: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
citation:
ama: 'Henzinger TA, Otop J, Samanta R. Lipschitz robustness of finite-state transducers.
In: Leibniz International Proceedings in Informatics, LIPIcs. Vol 29. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2014:431-443. doi:10.4230/LIPIcs.FSTTCS.2014.431'
apa: 'Henzinger, T. A., Otop, J., & Samanta, R. (2014). Lipschitz robustness
of finite-state transducers. In Leibniz International Proceedings in Informatics,
LIPIcs (Vol. 29, pp. 431–443). Delhi, India: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431'
chicago: Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness
of Finite-State Transducers.” In Leibniz International Proceedings in Informatics,
LIPIcs, 29:431–43. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014.
https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431.
ieee: T. A. Henzinger, J. Otop, and R. Samanta, “Lipschitz robustness of finite-state
transducers,” in Leibniz International Proceedings in Informatics, LIPIcs,
Delhi, India, 2014, vol. 29, pp. 431–443.
ista: 'Henzinger TA, Otop J, Samanta R. 2014. Lipschitz robustness of finite-state
transducers. Leibniz International Proceedings in Informatics, LIPIcs. FSTTCS:
Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol.
29, 431–443.'
mla: Henzinger, Thomas A., et al. “Lipschitz Robustness of Finite-State Transducers.”
Leibniz International Proceedings in Informatics, LIPIcs, vol. 29, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 431–43, doi:10.4230/LIPIcs.FSTTCS.2014.431.
short: T.A. Henzinger, J. Otop, R. Samanta, in:, Leibniz International Proceedings
in Informatics, LIPIcs, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014,
pp. 431–443.
conference:
end_date: 2014-12-17
location: Delhi, India
name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science'
start_date: 2014-12-15
date_created: 2018-12-11T11:54:27Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2021-01-12T06:53:45Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.FSTTCS.2014.431
file:
- access_level: open_access
checksum: 7b1aff1710a8bffb7080ec07f62d9a17
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:11Z
date_updated: 2020-07-14T12:45:19Z
file_id: '4734'
file_name: IST-2017-804-v1+1_37.pdf
file_size: 562151
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 29'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 431 - 443
publication: Leibniz International Proceedings in Informatics, LIPIcs
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5227'
pubrep_id: '804'
quality_controlled: '1'
status: public
title: Lipschitz robustness of finite-state transducers
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2014'
...
---
_id: '1875'
abstract:
- lang: eng
text: We present a formal framework for repairing infinite-state, imperative, sequential
programs, with (possibly recursive) procedures and multiple assertions; the framework
can generate repaired programs by modifying the original erroneous program in
multiple program locations, and can ensure the readability of the repaired program
using user-defined expression templates; the framework also generates a set of
inductive assertions that serve as a proof of correctness of the repaired program.
As a step toward integrating programmer intent and intuition in automated program
repair, we present a cost-aware formulation - given a cost function associated
with permissible statement modifications, the goal is to ensure that the total
program modification cost does not exceed a given repair budget. As part of our
predicate abstractionbased solution framework, we present a sound and complete
algorithm for repair of Boolean programs. We have developed a prototype tool based
on SMT solving and used it successfully to repair diverse errors in benchmark
C programs.
alternative_title:
- LNCS
author:
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
- first_name: Oswaldo
full_name: Olivo, Oswaldo
last_name: Olivo
- first_name: Emerson
full_name: Allen, Emerson
last_name: Allen
citation:
ama: 'Samanta R, Olivo O, Allen E. Cost-aware automatic program repair. In: Müller-Olm
M, Seidl H, eds. Vol 8723. Springer; 2014:268-284. doi:10.1007/978-3-319-10936-7_17'
apa: 'Samanta, R., Olivo, O., & Allen, E. (2014). Cost-aware automatic program
repair. In M. Müller-Olm & H. Seidl (Eds.) (Vol. 8723, pp. 268–284). Presented
at the SAS: Static Analysis Symposium, Munich, Germany: Springer. https://doi.org/10.1007/978-3-319-10936-7_17'
chicago: Samanta, Roopsha, Oswaldo Olivo, and Emerson Allen. “Cost-Aware Automatic
Program Repair.” edited by Markus Müller-Olm and Helmut Seidl, 8723:268–84. Springer,
2014. https://doi.org/10.1007/978-3-319-10936-7_17.
ieee: 'R. Samanta, O. Olivo, and E. Allen, “Cost-aware automatic program repair,”
presented at the SAS: Static Analysis Symposium, Munich, Germany, 2014, vol. 8723,
pp. 268–284.'
ista: 'Samanta R, Olivo O, Allen E. 2014. Cost-aware automatic program repair. SAS:
Static Analysis Symposium, LNCS, vol. 8723, 268–284.'
mla: Samanta, Roopsha, et al. Cost-Aware Automatic Program Repair. Edited
by Markus Müller-Olm and Helmut Seidl, vol. 8723, Springer, 2014, pp. 268–84,
doi:10.1007/978-3-319-10936-7_17.
short: R. Samanta, O. Olivo, E. Allen, in:, M. Müller-Olm, H. Seidl (Eds.), Springer,
2014, pp. 268–284.
conference:
end_date: 2014-09-14
location: Munich, Germany
name: 'SAS: Static Analysis Symposium'
start_date: 2014-09-11
date_created: 2018-12-11T11:54:29Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2021-01-12T06:53:46Z
day: '01'
ddc:
- '000'
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-319-10936-7_17
editor:
- first_name: Markus
full_name: Müller-Olm, Markus
last_name: Müller-Olm
- first_name: Helmut
full_name: Seidl, Helmut
last_name: Seidl
file:
- access_level: open_access
checksum: 78ec4ea1bdecc676cd3e8cad35c6182c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:51Z
date_updated: 2020-07-14T12:45:19Z
file_id: '4650'
file_name: IST-2014-313-v1+1_SOE.SAS14.pdf
file_size: 409485
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 8723'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 268 - 284
publication_status: published
publisher: Springer
publist_id: '5221'
pubrep_id: '313'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cost-aware automatic program repair
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8723
year: '2014'
...
---
_id: '1876'
abstract:
- lang: eng
text: We study densities of functionals over uniformly bounded triangulations of
a Delaunay set of vertices, and prove that the minimum is attained for the Delaunay
triangulation if this is the case for finite sets.
article_processing_charge: No
article_type: original
author:
- first_name: Nikolai
full_name: Dolbilin, Nikolai
last_name: Dolbilin
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Alexey
full_name: Glazyrin, Alexey
last_name: Glazyrin
- first_name: Oleg
full_name: Musin, Oleg
last_name: Musin
citation:
ama: Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. Functionals on triangulations
of delaunay sets. Moscow Mathematical Journal. 2014;14(3):491-504. doi:10.17323/1609-4514-2014-14-3-491-504
apa: Dolbilin, N., Edelsbrunner, H., Glazyrin, A., & Musin, O. (2014). Functionals
on triangulations of delaunay sets. Moscow Mathematical Journal. Independent
University of Moscow. https://doi.org/10.17323/1609-4514-2014-14-3-491-504
chicago: Dolbilin, Nikolai, Herbert Edelsbrunner, Alexey Glazyrin, and Oleg Musin.
“Functionals on Triangulations of Delaunay Sets.” Moscow Mathematical Journal.
Independent University of Moscow, 2014. https://doi.org/10.17323/1609-4514-2014-14-3-491-504.
ieee: N. Dolbilin, H. Edelsbrunner, A. Glazyrin, and O. Musin, “Functionals on triangulations
of delaunay sets,” Moscow Mathematical Journal, vol. 14, no. 3. Independent
University of Moscow, pp. 491–504, 2014.
ista: Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. 2014. Functionals on triangulations
of delaunay sets. Moscow Mathematical Journal. 14(3), 491–504.
mla: Dolbilin, Nikolai, et al. “Functionals on Triangulations of Delaunay Sets.”
Moscow Mathematical Journal, vol. 14, no. 3, Independent University of
Moscow, 2014, pp. 491–504, doi:10.17323/1609-4514-2014-14-3-491-504.
short: N. Dolbilin, H. Edelsbrunner, A. Glazyrin, O. Musin, Moscow Mathematical
Journal 14 (2014) 491–504.
date_created: 2018-12-11T11:54:29Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2022-03-03T11:47:09Z
day: '01'
department:
- _id: HeEd
doi: 10.17323/1609-4514-2014-14-3-491-504
external_id:
arxiv:
- '1211.7053'
intvolume: ' 14'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1211.7053
month: '07'
oa: 1
oa_version: Submitted Version
page: 491 - 504
publication: Moscow Mathematical Journal
publication_identifier:
issn:
- '16093321'
publication_status: published
publisher: Independent University of Moscow
publist_id: '5220'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Functionals on triangulations of delaunay sets
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2014'
...
---
_id: '1877'
abstract:
- lang: eng
text: During inflammation, lymph nodes swell with an influx of immune cells. New
findings identify a signalling pathway that induces relaxation in the contractile
cells that give structure to these organs.
article_type: letter_note
author:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Kari
full_name: Vaahtomeri, Kari
id: 368EE576-F248-11E8-B48F-1D18A9856A87
last_name: Vaahtomeri
orcid: 0000-0001-7829-3518
citation:
ama: 'Sixt MK, Vaahtomeri K. Physiology: Relax and come in. Nature. 2014;514(7523):441-442.
doi:10.1038/514441a'
apa: 'Sixt, M. K., & Vaahtomeri, K. (2014). Physiology: Relax and come in. Nature.
Springer Nature. https://doi.org/10.1038/514441a'
chicago: 'Sixt, Michael K, and Kari Vaahtomeri. “Physiology: Relax and Come In.”
Nature. Springer Nature, 2014. https://doi.org/10.1038/514441a.'
ieee: 'M. K. Sixt and K. Vaahtomeri, “Physiology: Relax and come in,” Nature,
vol. 514, no. 7523. Springer Nature, pp. 441–442, 2014.'
ista: 'Sixt MK, Vaahtomeri K. 2014. Physiology: Relax and come in. Nature. 514(7523),
441–442.'
mla: 'Sixt, Michael K., and Kari Vaahtomeri. “Physiology: Relax and Come In.” Nature,
vol. 514, no. 7523, Springer Nature, 2014, pp. 441–42, doi:10.1038/514441a.'
short: M.K. Sixt, K. Vaahtomeri, Nature 514 (2014) 441–442.
date_created: 2018-12-11T11:54:30Z
date_published: 2014-10-23T00:00:00Z
date_updated: 2021-01-12T06:53:47Z
day: '23'
department:
- _id: MiSi
doi: 10.1038/514441a
intvolume: ' 514'
issue: '7523'
language:
- iso: eng
month: '10'
oa_version: None
page: 441 - 442
publication: Nature
publication_status: published
publisher: Springer Nature
publist_id: '5219'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Physiology: Relax and come in'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 514
year: '2014'
...
---
_id: '1886'
abstract:
- lang: eng
text: 'Information processing in the sensory periphery is shaped by natural stimulus
statistics. In the periphery, a transmission bottleneck constrains performance;
thus efficient coding implies that natural signal components with a predictably
wider range should be compressed. In a different regime—when sampling limitations
constrain performance—efficient coding implies that more resources should be allocated
to informative features that are more variable. We propose that this regime is
relevant for sensory cortex when it extracts complex features from limited numbers
of sensory samples. To test this prediction, we use central visual processing
as a model: we show that visual sensitivity for local multi-point spatial correlations,
described by dozens of independently-measured parameters, can be quantitatively
predicted from the structure of natural images. This suggests that efficient coding
applies centrally, where it extends to higher-order sensory features and operates
in a regime in which sensitivity increases with feature variability.'
article_number: e03722
author:
- first_name: Ann
full_name: Hermundstad, Ann
last_name: Hermundstad
- first_name: John
full_name: Briguglio, John
last_name: Briguglio
- first_name: Mary
full_name: Conte, Mary
last_name: Conte
- first_name: Jonathan
full_name: Victor, Jonathan
last_name: Victor
- first_name: Vijay
full_name: Balasubramanian, Vijay
last_name: Balasubramanian
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G.
Variance predicts salience in central sensory processing. eLife. 2014;(November).
doi:10.7554/eLife.03722
apa: Hermundstad, A., Briguglio, J., Conte, M., Victor, J., Balasubramanian, V.,
& Tkačik, G. (2014). Variance predicts salience in central sensory processing.
ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.03722
chicago: Hermundstad, Ann, John Briguglio, Mary Conte, Jonathan Victor, Vijay Balasubramanian,
and Gašper Tkačik. “Variance Predicts Salience in Central Sensory Processing.”
ELife. eLife Sciences Publications, 2014. https://doi.org/10.7554/eLife.03722.
ieee: A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and
G. Tkačik, “Variance predicts salience in central sensory processing,” eLife,
no. November. eLife Sciences Publications, 2014.
ista: Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G.
2014. Variance predicts salience in central sensory processing. eLife. (November),
e03722.
mla: Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.”
ELife, no. November, e03722, eLife Sciences Publications, 2014, doi:10.7554/eLife.03722.
short: A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G.
Tkačik, ELife (2014).
date_created: 2018-12-11T11:54:32Z
date_published: 2014-11-14T00:00:00Z
date_updated: 2021-01-12T06:53:50Z
day: '14'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.7554/eLife.03722
file:
- access_level: open_access
checksum: 766ac8999ac6e3364f10065a06024b8f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:04Z
date_updated: 2020-07-14T12:45:20Z
file_id: '4922'
file_name: IST-2016-420-v1+1_e03722.full.pdf
file_size: 5117086
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
issue: November
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
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: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '5209'
pubrep_id: '420'
quality_controlled: '1'
scopus_import: 1
status: public
title: Variance predicts salience in central sensory processing
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1890'
abstract:
- lang: eng
text: To search for a target in a complex environment is an everyday behavior that
ends with finding the target. When we search for two identical targets, however,
we must continue the search after finding the first target and memorize its location.
We used fixation-related potentials to investigate the neural correlates of different
stages of the search, that is, before and after finding the first target. Having
found the first target influenced subsequent distractor processing. Compared to
distractor fixations before the first target fixation, a negative shift was observed
for three subsequent distractor fixations. These results suggest that processing
a target in continued search modulates the brain's response, either transiently
by reflecting temporary working memory processes or permanently by reflecting
working memory retention.
acknowledgement: 'Funded by Austrian Science Fund (FWF) Grant Number: P 22189-B18;
European Union within the 6th Framework Programme Grant Number: 517590; State government
of Styria Grant Number: PN 4055'
author:
- first_name: Christof
full_name: Körner, Christof
last_name: Körner
- first_name: Verena
full_name: Braunstein, Verena
last_name: Braunstein
- first_name: Matthias
full_name: Stangl, Matthias
last_name: Stangl
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Christa
full_name: Neuper, Christa
last_name: Neuper
- first_name: Anja
full_name: Ischebeck, Anja
last_name: Ischebeck
citation:
ama: 'Körner C, Braunstein V, Stangl M, Schlögl A, Neuper C, Ischebeck A. Sequential
effects in continued visual search: Using fixation-related potentials to compare
distractor processing before and after target detection. Psychophysiology.
2014;51(4):385-395. doi:10.1111/psyp.12062'
apa: 'Körner, C., Braunstein, V., Stangl, M., Schlögl, A., Neuper, C., & Ischebeck,
A. (2014). Sequential effects in continued visual search: Using fixation-related
potentials to compare distractor processing before and after target detection.
Psychophysiology. Wiley-Blackwell. https://doi.org/10.1111/psyp.12062'
chicago: 'Körner, Christof, Verena Braunstein, Matthias Stangl, Alois Schlögl, Christa
Neuper, and Anja Ischebeck. “Sequential Effects in Continued Visual Search: Using
Fixation-Related Potentials to Compare Distractor Processing before and after
Target Detection.” Psychophysiology. Wiley-Blackwell, 2014. https://doi.org/10.1111/psyp.12062.'
ieee: 'C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, and A. Ischebeck,
“Sequential effects in continued visual search: Using fixation-related potentials
to compare distractor processing before and after target detection,” Psychophysiology,
vol. 51, no. 4. Wiley-Blackwell, pp. 385–395, 2014.'
ista: 'Körner C, Braunstein V, Stangl M, Schlögl A, Neuper C, Ischebeck A. 2014.
Sequential effects in continued visual search: Using fixation-related potentials
to compare distractor processing before and after target detection. Psychophysiology.
51(4), 385–395.'
mla: 'Körner, Christof, et al. “Sequential Effects in Continued Visual Search: Using
Fixation-Related Potentials to Compare Distractor Processing before and after
Target Detection.” Psychophysiology, vol. 51, no. 4, Wiley-Blackwell, 2014,
pp. 385–95, doi:10.1111/psyp.12062.'
short: C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, A. Ischebeck,
Psychophysiology 51 (2014) 385–395.
date_created: 2018-12-11T11:54:34Z
date_published: 2014-02-11T00:00:00Z
date_updated: 2021-01-12T06:53:52Z
day: '11'
ddc:
- '000'
department:
- _id: ScienComp
- _id: PeJo
doi: 10.1111/psyp.12062
file:
- access_level: open_access
checksum: 4255b6185e774acce1d99f8e195c564d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:44Z
date_updated: 2020-07-14T12:45:20Z
file_id: '5233'
file_name: IST-2016-442-v1+1_K-rner_et_al-2014-Psychophysiology.pdf
file_size: 543243
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
intvolume: ' 51'
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 385 - 395
publication: Psychophysiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5205'
pubrep_id: '442'
scopus_import: 1
status: public
title: 'Sequential effects in continued visual search: Using fixation-related potentials
to compare distractor processing before and after target detection'
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2014'
...
---
_id: '1892'
abstract:
- lang: eng
text: Behavioural variation among conspecifics is typically contingent on individual
state or environmental conditions. Sex-specific genetic polymorphisms are enigmatic
because they lack conditionality, and genes causing adaptive trait variation in
one sex may reduce Darwinian fitness in the other. One way to avoid such genetic
antagonism is to control sex-specific traits by inheritance via sex chromosomes.
Here, controlled laboratory crossings suggest that in snail-brooding cichlid fish
a single locus, two-allele polymorphism located on a sex-linked chromosome of
heterogametic males generates an extreme reproductive dimorphism. Both natural
and sexual selection are responsible for exceptionally large body size of bourgeois
males, creating a niche for a miniature male phenotype to evolve. This extreme
intrasexual dimorphism results from selection on opposite size thresholds caused
by a single ecological factor, empty snail shells used as breeding substrate.
Paternity analyses reveal that in the field parasitic dwarf males sire the majority
of offspring in direct sperm competition with large nest owners exceeding their
size more than 40 times. Apparently, use of empty snail shells as breeding substrate
and single locus sex-linked inheritance of growth are the major ecological and
genetic mechanisms responsible for the extreme intrasexual diversity observed
in Lamprologus callipterus.
acknowledgement: "This research was supported by grants of the Swiss National Science
Foundation to M.T.\r\nWe thank Tetsu Sato for providing field samples, Olivier Goffinet
for field assistance, Dolores Schütz for vital help in the field and with the manuscript,
David Lank, Barbara Taborsky, Suzanne Alonzo and two anonymous referees for comments
on earlier manuscript versions, and the Fisheries Department, Ministry of Agriculture
and Livestock of Zambia, for permission and support."
article_number: '20140253'
article_processing_charge: No
article_type: original
author:
- first_name: Sabine
full_name: Ocana, Sabine
last_name: Ocana
- first_name: Patrick
full_name: Meidl, Patrick
id: 4709BCE6-F248-11E8-B48F-1D18A9856A87
last_name: Meidl
- first_name: Danielle
full_name: Bonfils, Danielle
last_name: Bonfils
- first_name: Michael
full_name: Taborsky, Michael
last_name: Taborsky
citation:
ama: Ocana S, Meidl P, Bonfils D, Taborsky M. Y-linked Mendelian inheritance of
giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the
Royal Society of London Series B Biological Sciences. 2014;281(1794). doi:10.1098/rspb.2014.0253
apa: Ocana, S., Meidl, P., Bonfils, D., & Taborsky, M. (2014). Y-linked Mendelian
inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings
of the Royal Society of London Series B Biological Sciences. The Royal Society.
https://doi.org/10.1098/rspb.2014.0253
chicago: Ocana, Sabine, Patrick Meidl, Danielle Bonfils, and Michael Taborsky. “Y-Linked
Mendelian Inheritance of Giant and Dwarf Male Morphs in Shell-Brooding Cichlids.”
Proceedings of the Royal Society of London Series B Biological Sciences.
The Royal Society, 2014. https://doi.org/10.1098/rspb.2014.0253.
ieee: S. Ocana, P. Meidl, D. Bonfils, and M. Taborsky, “Y-linked Mendelian inheritance
of giant and dwarf male morphs in shell-brooding cichlids,” Proceedings of
the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794.
The Royal Society, 2014.
ista: Ocana S, Meidl P, Bonfils D, Taborsky M. 2014. Y-linked Mendelian inheritance
of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the
Royal Society of London Series B Biological Sciences. 281(1794), 20140253.
mla: Ocana, Sabine, et al. “Y-Linked Mendelian Inheritance of Giant and Dwarf Male
Morphs in Shell-Brooding Cichlids.” Proceedings of the Royal Society of London
Series B Biological Sciences, vol. 281, no. 1794, 20140253, The Royal Society,
2014, doi:10.1098/rspb.2014.0253.
short: S. Ocana, P. Meidl, D. Bonfils, M. Taborsky, Proceedings of the Royal Society
of London Series B Biological Sciences 281 (2014).
date_created: 2018-12-11T11:54:34Z
date_published: 2014-11-07T00:00:00Z
date_updated: 2022-06-07T09:12:32Z
day: '07'
department:
- _id: CampIT
doi: 10.1098/rspb.2014.0253
external_id:
pmid:
- '25232141'
intvolume: ' 281'
issue: '1794'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211437/
month: '11'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: The Royal Society
publist_id: '5203'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding
cichlids
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 281
year: '2014'
...
---
_id: '1891'
abstract:
- lang: eng
text: We provide theoretical tests of a novel experimental technique to determine
mechanostability of proteins based on stretching a mechanically protected protein
by single-molecule force spectroscopy. This technique involves stretching a homogeneous
or heterogeneous chain of reference proteins (single-molecule markers) in which
one of them acts as host to the guest protein under study. The guest protein is
grafted into the host through genetic engineering. It is expected that unraveling
of the host precedes the unraveling of the guest removing ambiguities in the reading
of the force-extension patterns of the guest protein. We study examples of such
systems within a coarse-grained structure-based model. We consider systems with
various ratios of mechanostability for the host and guest molecules and compare
them to experimental results involving cohesin I as the guest molecule. For a
comparison, we also study the force-displacement patterns in proteins that are
linked in a serial fashion. We find that the mechanostability of the guest is
similar to that of the isolated or serially linked protein. We also demonstrate
that the ideal configuration of this strategy would be one in which the host is
much more mechanostable than the single-molecule markers. We finally show that
it is troublesome to use the highly stable cystine knot proteins as a host to
graft a guest in stretching studies because this would involve a cleaving procedure.
acknowledgement: Grant Nr. 2011/01/N/ST3/02475
author:
- first_name: Mateusz
full_name: Chwastyk, Mateusz
last_name: Chwastyk
- first_name: Albert
full_name: Galera Prat, Albert
last_name: Galera Prat
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Àngel
full_name: Gómez Sicilia, Àngel
last_name: Gómez Sicilia
- first_name: Mariano
full_name: Carrión Vázquez, Mariano
last_name: Carrión Vázquez
- first_name: Marek
full_name: Cieplak, Marek
last_name: Cieplak
citation:
ama: 'Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M,
Cieplak M. Theoretical tests of the mechanical protection strategy in protein
nanomechanics. Proteins: Structure, Function and Bioinformatics. 2014;82(5):717-726.
doi:10.1002/prot.24436'
apa: 'Chwastyk, M., Galera Prat, A., Sikora, M. K., Gómez Sicilia, À., Carrión Vázquez,
M., & Cieplak, M. (2014). Theoretical tests of the mechanical protection strategy
in protein nanomechanics. Proteins: Structure, Function and Bioinformatics.
Wiley-Blackwell. https://doi.org/10.1002/prot.24436'
chicago: 'Chwastyk, Mateusz, Albert Galera Prat, Mateusz K Sikora, Àngel Gómez Sicilia,
Mariano Carrión Vázquez, and Marek Cieplak. “Theoretical Tests of the Mechanical
Protection Strategy in Protein Nanomechanics.” Proteins: Structure, Function
and Bioinformatics. Wiley-Blackwell, 2014. https://doi.org/10.1002/prot.24436.'
ieee: 'M. Chwastyk, A. Galera Prat, M. K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez,
and M. Cieplak, “Theoretical tests of the mechanical protection strategy in protein
nanomechanics,” Proteins: Structure, Function and Bioinformatics, vol.
82, no. 5. Wiley-Blackwell, pp. 717–726, 2014.'
ista: 'Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M,
Cieplak M. 2014. Theoretical tests of the mechanical protection strategy in protein
nanomechanics. Proteins: Structure, Function and Bioinformatics. 82(5), 717–726.'
mla: 'Chwastyk, Mateusz, et al. “Theoretical Tests of the Mechanical Protection
Strategy in Protein Nanomechanics.” Proteins: Structure, Function and Bioinformatics,
vol. 82, no. 5, Wiley-Blackwell, 2014, pp. 717–26, doi:10.1002/prot.24436.'
short: 'M. Chwastyk, A. Galera Prat, M.K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez,
M. Cieplak, Proteins: Structure, Function and Bioinformatics 82 (2014) 717–726.'
date_created: 2018-12-11T11:54:34Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2021-01-12T06:53:52Z
day: '01'
department:
- _id: CaHe
doi: 10.1002/prot.24436
intvolume: ' 82'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 717 - 726
publication: 'Proteins: Structure, Function and Bioinformatics'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5204'
scopus_import: 1
status: public
title: Theoretical tests of the mechanical protection strategy in protein nanomechanics
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 82
year: '2014'
...
---
_id: '1884'
abstract:
- lang: eng
text: Unbiased high-throughput massively parallel sequencing methods have transformed
the process of discovery of novel putative driver gene mutations in cancer. In
chronic lymphocytic leukemia (CLL), these methods have yielded several unexpected
findings, including the driver genes SF3B1, NOTCH1 and POT1. Recent analysis,
utilizing down-sampling of existing datasets, has shown that the discovery process
of putative drivers is far from complete across cancer. In CLL, while driver gene
mutations affecting >10% of patients were efficiently discovered with previously
published CLL cohorts of up to 160 samples subjected to whole exome sequencing
(WES), this sample size has only 0.78 power to detect drivers affecting 5% of
patients, and only 0.12 power for drivers affecting 2% of patients. These calculations
emphasize the need to apply unbiased WES to larger patient cohorts.
author:
- first_name: Dan
full_name: Landau, Dan
last_name: Landau
- first_name: Chip
full_name: Stewart, Chip
last_name: Stewart
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Michael
full_name: Lawrence, Michael
last_name: Lawrence
- first_name: Carrie
full_name: Sougnez, Carrie
last_name: Sougnez
- first_name: Jennifer
full_name: Brown, Jennifer
last_name: Brown
- first_name: Armando
full_name: Lopez Guillermo, Armando
last_name: Lopez Guillermo
- first_name: Stacey
full_name: Gabriel, Stacey
last_name: Gabriel
- first_name: Eric
full_name: Lander, Eric
last_name: Lander
- first_name: Donna
full_name: Neuberg, Donna
last_name: Neuberg
- first_name: Carlos
full_name: López Otín, Carlos
last_name: López Otín
- first_name: Elias
full_name: Campo, Elias
last_name: Campo
- first_name: Gad
full_name: Getz, Gad
last_name: Getz
- first_name: Catherine
full_name: Wu, Catherine
last_name: Wu
citation:
ama: 'Landau D, Stewart C, Reiter J, et al. Novel putative driver gene mutations
in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole
exome sequencing of 262 primary CLL aamples. Blood. 2014;124(21):1952-1952.'
apa: 'Landau, D., Stewart, C., Reiter, J., Lawrence, M., Sougnez, C., Brown, J.,
… Wu, C. (2014). Novel putative driver gene mutations in chronic lymphocytic leukemia
(CLL): results from a combined analysis of whole exome sequencing of 262 primary
CLL aamples. Blood. American Society of Hematology.'
chicago: 'Landau, Dan, Chip Stewart, Johannes Reiter, Michael Lawrence, Carrie Sougnez,
Jennifer Brown, Armando Lopez Guillermo, et al. “Novel Putative Driver Gene Mutations
in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole
Exome Sequencing of 262 Primary CLL Aamples.” Blood. American Society of
Hematology, 2014.'
ieee: 'D. Landau et al., “Novel putative driver gene mutations in chronic
lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing
of 262 primary CLL aamples,” Blood, vol. 124, no. 21. American Society
of Hematology, pp. 1952–1952, 2014.'
ista: 'Landau D, Stewart C, Reiter J, Lawrence M, Sougnez C, Brown J, Lopez Guillermo
A, Gabriel S, Lander E, Neuberg D, López Otín C, Campo E, Getz G, Wu C. 2014.
Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results
from a combined analysis of whole exome sequencing of 262 primary CLL aamples.
Blood. 124(21), 1952–1952.'
mla: 'Landau, Dan, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic
Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of
262 Primary CLL Aamples.” Blood, vol. 124, no. 21, American Society of
Hematology, 2014, pp. 1952–1952.'
short: D. Landau, C. Stewart, J. Reiter, M. Lawrence, C. Sougnez, J. Brown, A. Lopez
Guillermo, S. Gabriel, E. Lander, D. Neuberg, C. López Otín, E. Campo, G. Getz,
C. Wu, Blood 124 (2014) 1952–1952.
date_created: 2018-12-11T11:54:32Z
date_published: 2014-12-04T00:00:00Z
date_updated: 2021-01-12T06:53:50Z
day: '04'
department:
- _id: KrCh
intvolume: ' 124'
issue: '21'
language:
- iso: eng
main_file_link:
- url: http://www.bloodjournal.org/content/124/21/1952?sso-checked=true
month: '12'
oa_version: None
page: 1952 - 1952
publication: Blood
publication_status: published
publisher: American Society of Hematology
publist_id: '5211'
status: public
title: 'Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL):
results from a combined analysis of whole exome sequencing of 262 primary CLL aamples'
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 124
year: '2014'
...
---
_id: '1889'
abstract:
- lang: eng
text: We study translation-invariant quasi-free states for a system of fermions
with two-particle interactions. The associated energy functional is similar to
the BCS functional but also includes direct and exchange energies. We show that
for suitable short-range interactions, these latter terms only lead to a renormalization
of the chemical potential, with the usual properties of the BCS functional left
unchanged. Our analysis thus represents a rigorous justification of part of the
BCS approximation. We give bounds on the critical temperature below which the
system displays superfluidity.
acknowledgement: We would like to thank Max Lein and Andreas Deuchert for valuable
suggestions and remarks. Partial financial support by the NSERC (R.S.) is gratefully
acknowledged.
article_number: '1450012'
article_processing_charge: No
article_type: original
author:
- first_name: Gerhard
full_name: Bräunlich, Gerhard
last_name: Bräunlich
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Bräunlich G, Hainzl C, Seiringer R. Translation-invariant quasi-free states
for fermionic systems and the BCS approximation. Reviews in Mathematical Physics.
2014;26(7). doi:10.1142/S0129055X14500123
apa: Bräunlich, G., Hainzl, C., & Seiringer, R. (2014). Translation-invariant
quasi-free states for fermionic systems and the BCS approximation. Reviews
in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X14500123
chicago: Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Translation-Invariant
Quasi-Free States for Fermionic Systems and the BCS Approximation.” Reviews
in Mathematical Physics. World Scientific Publishing, 2014. https://doi.org/10.1142/S0129055X14500123.
ieee: G. Bräunlich, C. Hainzl, and R. Seiringer, “Translation-invariant quasi-free
states for fermionic systems and the BCS approximation,” Reviews in Mathematical
Physics, vol. 26, no. 7. World Scientific Publishing, 2014.
ista: Bräunlich G, Hainzl C, Seiringer R. 2014. Translation-invariant quasi-free
states for fermionic systems and the BCS approximation. Reviews in Mathematical
Physics. 26(7), 1450012.
mla: Bräunlich, Gerhard, et al. “Translation-Invariant Quasi-Free States for Fermionic
Systems and the BCS Approximation.” Reviews in Mathematical Physics, vol.
26, no. 7, 1450012, World Scientific Publishing, 2014, doi:10.1142/S0129055X14500123.
short: G. Bräunlich, C. Hainzl, R. Seiringer, Reviews in Mathematical Physics 26
(2014).
date_created: 2018-12-11T11:54:33Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2022-06-07T09:03:09Z
day: '01'
department:
- _id: RoSe
doi: 10.1142/S0129055X14500123
external_id:
arxiv:
- '1305.5135'
intvolume: ' 26'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1305.5135
month: '08'
oa: 1
oa_version: Submitted Version
publication: Reviews in Mathematical Physics
publication_status: published
publisher: World Scientific Publishing
publist_id: '5206'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Translation-invariant quasi-free states for fermionic systems and the BCS approximation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2014'
...
---
_id: '1894'
abstract:
- lang: eng
text: 'Background: Bacterial Dsb enzymes are involved in the oxidative folding of
many proteins, through the formation of disulfide bonds between their cysteine
residues. The Dsb protein network has been well characterized in cells of the
model microorganism Escherichia coli. To gain insight into the functioning of
the Dsb system in epsilon-Proteobacteria, where it plays an important role in
the colonization process, we studied two homologs of the main Escherichia coli
Dsb oxidase (EcDsbA) that are present in the cells of the enteric pathogen Campylobacter
jejuni, the most frequently reported bacterial cause of human enteritis in the
world. Methods and Results: Phylogenetic analysis suggests the horizontal transfer
of the epsilon-Proteobacterial DsbAs from a common ancestor to gamma-Proteobacteria,
which then gave rise to the DsbL lineage. Phenotype and enzymatic assays suggest
that the two C. jejuni DsbAs play different roles in bacterial cells and have
divergent substrate spectra. CjDsbA1 is essential for the motility and autoagglutination
phenotypes, while CjDsbA2 has no impact on those processes. CjDsbA1 plays a critical
role in the oxidative folding that ensures the activity of alkaline phosphatase
CjPhoX, whereas CjDsbA2 is crucial for the activity of arylsulfotransferase CjAstA,
encoded within the dsbA2-dsbB-astA operon. Conclusions: Our results show that
CjDsbA1 is the primary thiol-oxidoreductase affecting life processes associated
with bacterial spread and host colonization, as well as ensuring the oxidative
folding of particular protein substrates. In contrast, CjDsbA2 activity does not
affect the same processes and so far its oxidative folding activity has been demonstrated
for one substrate, arylsulfotransferase CjAstA. The results suggest the cooperation
between CjDsbA2 and CjDsbB. In the case of the CjDsbA1, this cooperation is not
exclusive and there is probably another protein to be identified in C. jejuni
cells that acts to re-oxidize CjDsbA1. Altogether the data presented here constitute
the considerable insight to the Epsilonproteobacterial Dsb systems, which have
been poorly understood so far.'
article_number: e106247
author:
- first_name: Anna
full_name: Grabowska, Anna
last_name: Grabowska
- first_name: Ewa
full_name: Wywiał, Ewa
last_name: Wywiał
- first_name: Stanislaw
full_name: Dunin Horkawicz, Stanislaw
last_name: Dunin Horkawicz
- first_name: Anna
full_name: Łasica, Anna
last_name: Łasica
- first_name: Marc
full_name: Wösten, Marc
last_name: Wösten
- first_name: Anna A
full_name: Nagy-Staron, Anna A
id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87
last_name: Nagy-Staron
- first_name: Renata
full_name: Godlewska, Renata
last_name: Godlewska
- first_name: Katarzyna
full_name: Bocian Ostrzycka, Katarzyna
last_name: Bocian Ostrzycka
- first_name: Katarzyna
full_name: Pieńkowska, Katarzyna
last_name: Pieńkowska
- first_name: Paweł
full_name: Łaniewski, Paweł
last_name: Łaniewski
- first_name: Janusz
full_name: Bujnicki, Janusz
last_name: Bujnicki
- first_name: Jos
full_name: Van Putten, Jos
last_name: Van Putten
- first_name: Elzbieta
full_name: Jagusztyn Krynicka, Elzbieta
last_name: Jagusztyn Krynicka
citation:
ama: Grabowska A, Wywiał E, Dunin Horkawicz S, et al. Functional and bioinformatics
analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase,
DsbA. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0106247
apa: Grabowska, A., Wywiał, E., Dunin Horkawicz, S., Łasica, A., Wösten, M., Nagy-Staron,
A. A., … Jagusztyn Krynicka, E. (2014). Functional and bioinformatics analysis
of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA.
PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0106247
chicago: Grabowska, Anna, Ewa Wywiał, Stanislaw Dunin Horkawicz, Anna Łasica, Marc
Wösten, Anna A Nagy-Staron, Renata Godlewska, et al. “Functional and Bioinformatics
Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase,
DsbA.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0106247.
ieee: A. Grabowska et al., “Functional and bioinformatics analysis of two
Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA,” PLoS
One, vol. 9, no. 9. Public Library of Science, 2014.
ista: Grabowska A, Wywiał E, Dunin Horkawicz S, Łasica A, Wösten M, Nagy-Staron
AA, Godlewska R, Bocian Ostrzycka K, Pieńkowska K, Łaniewski P, Bujnicki J, Van
Putten J, Jagusztyn Krynicka E. 2014. Functional and bioinformatics analysis of
two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA.
PLoS One. 9(9), e106247.
mla: Grabowska, Anna, et al. “Functional and Bioinformatics Analysis of Two Campylobacter
Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” PLoS One,
vol. 9, no. 9, e106247, Public Library of Science, 2014, doi:10.1371/journal.pone.0106247.
short: A. Grabowska, E. Wywiał, S. Dunin Horkawicz, A. Łasica, M. Wösten, A.A. Nagy-Staron,
R. Godlewska, K. Bocian Ostrzycka, K. Pieńkowska, P. Łaniewski, J. Bujnicki, J.
Van Putten, E. Jagusztyn Krynicka, PLoS One 9 (2014).
date_created: 2018-12-11T11:54:35Z
date_published: 2014-09-02T00:00:00Z
date_updated: 2021-01-12T06:53:54Z
day: '02'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1371/journal.pone.0106247
file:
- access_level: open_access
checksum: 7d02c3da7f72b82bb5d7932d80c3251f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:19Z
date_updated: 2020-07-14T12:45:20Z
file_id: '5205'
file_name: IST-2016-438-v1+1_journal.pone.0106247.pdf
file_size: 4248801
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5201'
pubrep_id: '438'
quality_controlled: '1'
scopus_import: 1
status: public
title: Functional and bioinformatics analysis of two Campylobacter jejuni homologs
of the thiol-disulfide oxidoreductase, DsbA
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2014'
...
---
_id: '1895'
abstract:
- lang: eng
text: Major histocompatibility complex class I (MHCI) molecules were recently identified
as novel regulators of synaptic plasticity. These molecules are expressed in various
brain areas, especially in regions undergoing activity-dependent synaptic plasticity,
but their role in the nucleus accumbens (NAc) is unknown. In this study, we investigated
the effects of genetic disruption of MHCI function, through deletion of β2-microblobulin,
which causes lack of cell surface expression of MHCI. First, we confirmed that
MHCI molecules are expressed in the NAc core in wild-type mice. Second, we performed
electrophysiological recordings with NAc core slices from wild-type and β2-microglobulin
knock-out mice lacking cell surface expression of MHCI. We found that low frequency
stimulation induced long-term depression in wild-type but not knock-out mice,
whereas high frequency stimulation induced long-term potentiation in both genotypes,
with a larger magnitude in knock-out mice. Furthermore, we demonstrated that knock-out
mice showed more persistent behavioral sensitization to cocaine, which is a NAc-related
behavior. Using this model, we analyzed the density of total AMPA receptors and
their subunits GluR1 and GluR2 in the NAc core, by SDS-digested freeze-fracture
replica labeling. After repeated cocaine exposure, the density of GluR1 was increased,
but there was no change in total AMPA receptors and GluR2 levels in wildtype mice.
In contrast, following repeated cocaine exposure, increased densities of total
AMPA receptors, GluR1 and GluR2 were observed in knock-out mice. These results
indicate that functional deficiency of MHCI enhances synaptic potentiation, induced
by electrical and pharmacological stimulation.
acknowledgement: This work was supported in part by a Grant-in-Aid for Scientific
Research on Innovative Areas (Comprehensive Brain Science Network) and (B) 17330153,
from the Ministry of Education, Culture, Sports, Science and Technology of Japan.
article_number: e107099
author:
- first_name: Mitsuhiro
full_name: Edamura, Mitsuhiro
last_name: Edamura
- first_name: Gen
full_name: Murakami, Gen
last_name: Murakami
- first_name: Hongrui
full_name: Meng, Hongrui
last_name: Meng
- first_name: Makoto
full_name: Itakura, Makoto
last_name: Itakura
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Atsuo
full_name: Fukuda, Atsuo
last_name: Fukuda
- first_name: Daiichiro
full_name: Nakahara, Daiichiro
last_name: Nakahara
citation:
ama: Edamura M, Murakami G, Meng H, et al. Functional deficiency of MHC class i
enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One.
2014;9(9). doi:10.1371/journal.pone.0107099
apa: Edamura, M., Murakami, G., Meng, H., Itakura, M., Shigemoto, R., Fukuda, A.,
& Nakahara, D. (2014). Functional deficiency of MHC class i enhances LTP and
abolishes LTD in the nucleus accumbens of mice. PLoS One. Public Library
of Science. https://doi.org/10.1371/journal.pone.0107099
chicago: Edamura, Mitsuhiro, Gen Murakami, Hongrui Meng, Makoto Itakura, Ryuichi
Shigemoto, Atsuo Fukuda, and Daiichiro Nakahara. “Functional Deficiency of MHC
Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS
One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0107099.
ieee: M. Edamura et al., “Functional deficiency of MHC class i enhances LTP
and abolishes LTD in the nucleus accumbens of mice,” PLoS One, vol. 9,
no. 9. Public Library of Science, 2014.
ista: Edamura M, Murakami G, Meng H, Itakura M, Shigemoto R, Fukuda A, Nakahara
D. 2014. Functional deficiency of MHC class i enhances LTP and abolishes LTD in
the nucleus accumbens of mice. PLoS One. 9(9), e107099.
mla: Edamura, Mitsuhiro, et al. “Functional Deficiency of MHC Class i Enhances LTP
and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS One, vol. 9,
no. 9, e107099, Public Library of Science, 2014, doi:10.1371/journal.pone.0107099.
short: M. Edamura, G. Murakami, H. Meng, M. Itakura, R. Shigemoto, A. Fukuda, D.
Nakahara, PLoS One 9 (2014).
date_created: 2018-12-11T11:54:35Z
date_published: 2014-09-30T00:00:00Z
date_updated: 2021-01-12T06:53:54Z
day: '30'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1371/journal.pone.0107099
file:
- access_level: open_access
checksum: 1f3be936be93114596d61ba44cacee69
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:01Z
date_updated: 2020-07-14T12:45:20Z
file_id: '4724'
file_name: IST-2016-439-v1+1_journal.pone.0107099.pdf
file_size: 6262085
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5200'
pubrep_id: '439'
scopus_import: 1
status: public
title: Functional deficiency of MHC class i enhances LTP and abolishes LTD in the
nucleus accumbens of mice
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2014'
...
---
_id: '1893'
abstract:
- lang: eng
text: Phosphatidylinositol (PtdIns) is a structural phospholipid that can be phosphorylated
into various lipid signaling molecules, designated polyphosphoinositides (PPIs).
The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol
is performed by a set of organelle-specific kinases and phosphatases, and the
characteristic head groups make these molecules ideal for regulating biological
processes in time and space. In yeast and mammals, PtdIns3P and PtdIns(3,5)P2
play crucial roles in trafficking toward the lytic compartments, whereas the role
in plants is not yet fully understood. Here we identified the role of a land plant-specific
subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during
vacuolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize
to the tonoplast along with PtdIns3P, the presumable product of their activity.
In SAC gain- and loss-of-function mutants, the levels of PtdIns monophosphates
and bisphosphates were changed, with opposite effects on the morphology of storage
and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover,
multiple sac knockout mutants had an increased number of smaller storage and lytic
vacuoles, whereas extralarge vacuoles were observed in the overexpression lines,
correlating with various growth and developmental defects. The fragmented vacuolar
phenotype of sac mutants could be mimicked by treating wild-type seedlings with
PtdIns(3,5)P2, corroborating that this PPI is important for vacuole morphology.
Taken together, these results provide evidence that PPIs, together with their
metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar
morphology and function in plants.
acknowledgement: This work was supported by grants from the Research Foundation-Flanders
(Odysseus).
author:
- first_name: Petra
full_name: Nováková, Petra
id: 44E59624-F248-11E8-B48F-1D18A9856A87
last_name: Nováková
- first_name: Sibylle
full_name: Hirsch, Sibylle
last_name: Hirsch
- first_name: Elena
full_name: Feraru, Elena
last_name: Feraru
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Ringo
full_name: Van Wijk, Ringo
last_name: Van Wijk
- first_name: Tom
full_name: Viaene, Tom
last_name: Viaene
- first_name: Mareike
full_name: Heilmann, Mareike
last_name: Heilmann
- first_name: Jennifer
full_name: Lerche, Jennifer
last_name: Lerche
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Mugurel
full_name: Feraru, Mugurel
last_name: Feraru
- first_name: Peter
full_name: Grones, Peter
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Marc
full_name: Van Montagu, Marc
last_name: Van Montagu
- first_name: Ingo
full_name: Heilmann, Ingo
last_name: Heilmann
- first_name: Teun
full_name: Munnik, Teun
last_name: Munnik
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Marhavá P, Hirsch S, Feraru E, et al. SAC phosphoinositide phosphatases at
the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 2014;111(7):2818-2823.
doi:10.1073/pnas.1324264111
apa: Marhavá, P., Hirsch, S., Feraru, E., Tejos, R., Van Wijk, R., Viaene, T., …
Friml, J. (2014). SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar
function in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1324264111
chicago: Marhavá, Petra, Sibylle Hirsch, Elena Feraru, Ricardo Tejos, Ringo Van
Wijk, Tom Viaene, Mareike Heilmann, et al. “SAC Phosphoinositide Phosphatases
at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” PNAS. National
Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1324264111.
ieee: P. Marhavá et al., “SAC phosphoinositide phosphatases at the tonoplast
mediate vacuolar function in Arabidopsis,” PNAS, vol. 111, no. 7. National
Academy of Sciences, pp. 2818–2823, 2014.
ista: Marhavá P, Hirsch S, Feraru E, Tejos R, Van Wijk R, Viaene T, Heilmann M,
Lerche J, De Rycke R, Feraru M, Grones P, Van Montagu M, Heilmann I, Munnik T,
Friml J. 2014. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar
function in Arabidopsis. PNAS. 111(7), 2818–2823.
mla: Marhavá, Petra, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast
Mediate Vacuolar Function in Arabidopsis.” PNAS, vol. 111, no. 7, National
Academy of Sciences, 2014, pp. 2818–23, doi:10.1073/pnas.1324264111.
short: P. Marhavá, S. Hirsch, E. Feraru, R. Tejos, R. Van Wijk, T. Viaene, M. Heilmann,
J. Lerche, R. De Rycke, M. Feraru, P. Grones, M. Van Montagu, I. Heilmann, T.
Munnik, J. Friml, PNAS 111 (2014) 2818–2823.
date_created: 2018-12-11T11:54:34Z
date_published: 2014-02-18T00:00:00Z
date_updated: 2021-01-12T06:53:53Z
day: '18'
department:
- _id: JiFr
doi: 10.1073/pnas.1324264111
ec_funded: 1
intvolume: ' 111'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932866/
month: '02'
oa: 1
oa_version: Submitted Version
page: 2818 - 2823
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: '5202'
scopus_import: 1
status: public
title: SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function
in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2014'
...
---
_id: '1896'
abstract:
- lang: eng
text: 'Biopolymer length regulation is a complex process that involves a large number
of biological, chemical, and physical subprocesses acting simultaneously across
multiple spatial and temporal scales. An illustrative example important for genomic
stability is the length regulation of telomeres - nucleoprotein structures at
the ends of linear chromosomes consisting of tandemly repeated DNA sequences and
a specialized set of proteins. Maintenance of telomeres is often facilitated by
the enzyme telomerase but, particularly in telomerase-free systems, the maintenance
of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms
mediated by recombination. Various linear and circular DNA structures were identified
to participate in ALT, however, dynamics of the whole process is still poorly
understood. We propose a chemical kinetics model of ALT with kinetic rates systematically
derived from the biophysics of DNA diffusion and looping. The reaction system
is reduced to a coagulation-fragmentation system by quasi-steady-state approximation.
The detailed treatment of kinetic rates yields explicit formulas for expected
size distributions of telomeres that demonstrate the key role played by the J
factor, a quantitative measure of bending of polymers. The results are in agreement
with experimental data and point out interesting phenomena: an appearance of very
long telomeric circles if the total telomere density exceeds a critical value
(excess mass) and a nonlinear response of the telomere size distributions to the
amount of telomeric DNA in the system. The results can be of general importance
for understanding dynamics of telomeres in telomerase-independent systems as this
mode of telomere maintenance is similar to the situation in tumor cells lacking
telomerase activity. Furthermore, due to its universality, the model may also
serve as a prototype of an interaction between linear and circular DNA structures
in various settings.'
acknowledgement: The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and
K.B.).
article_number: '032701'
article_processing_charge: No
author:
- first_name: Richard
full_name: Kollár, Richard
last_name: Kollár
- first_name: Katarína
full_name: Bod'ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'ová
orcid: 0000-0002-7214-0171
- first_name: Jozef
full_name: Nosek, Jozef
last_name: Nosek
- first_name: Ľubomír
full_name: Tomáška, Ľubomír
last_name: Tomáška
citation:
ama: Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism
of telomere length maintenance. Physical Review E Statistical Nonlinear and
Soft Matter Physics. 2014;89(3). doi:10.1103/PhysRevE.89.032701
apa: Kollár, R., Bodova, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model
of alternative mechanism of telomere length maintenance. Physical Review E
Statistical Nonlinear and Soft Matter Physics. American Institute of Physics.
https://doi.org/10.1103/PhysRevE.89.032701
chicago: Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical
Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review
E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics,
2014. https://doi.org/10.1103/PhysRevE.89.032701.
ieee: R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative
mechanism of telomere length maintenance,” Physical Review E Statistical Nonlinear
and Soft Matter Physics, vol. 89, no. 3. American Institute of Physics, 2014.
ista: Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative
mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear
and Soft Matter Physics. 89(3), 032701.
mla: Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere
Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter
Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701.
short: R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical
Nonlinear and Soft Matter Physics 89 (2014).
date_created: 2018-12-11T11:54:35Z
date_published: 2014-03-04T00:00:00Z
date_updated: 2022-08-01T10:50:10Z
day: '04'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1103/PhysRevE.89.032701
intvolume: ' 89'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1402.0430
month: '03'
oa: 1
oa_version: Submitted Version
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5198'
scopus_import: '1'
status: public
title: Mathematical model of alternative mechanism of telomere length maintenance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2014'
...
---
_id: '1897'
abstract:
- lang: eng
text: GNOM is one of the most characterized membrane trafficking regulators in plants,
with crucial roles in development. GNOM encodes an ARF-guanine nucleotide exchange
factor (ARF-GEF) that activates small GTPases of the ARF (ADP ribosylation factor)
class to mediate vesicle budding at endomembranes. The crucial role of GNOM in
recycling of PIN auxin transporters and other proteins to the plasma membrane
was identified in studies using the ARF-GEF inhibitor brefeldin A (BFA). GNOM,
the most prominent regulator of recycling in plants, has been proposed to act
and localize at so far elusive recycling endosomes. Here, we report the GNOM localization
in context of its cellular function in Arabidopsis thaliana. State-of-the-art
imaging, pharmacological interference, and ultrastructure analysis show that GNOM
predominantly localizes to Golgi apparatus. Super-resolution confocal live imaging
microscopy identified GNOM and its closest homolog GNOM-like 1 at distinct subdomains
on Golgi cisternae. Short-term BFA treatment stabilizes GNOM at the Golgi apparatus,
whereas prolonged exposures results in GNOM translocation to trans-Golgi network
(TGN)/early endosomes (EEs). Malformed TGN/EE in gnom mutants suggests a role
for GNOM in maintaining TGN/EE function. Our results redefine the subcellular
action of GNOM and reevaluate the identity and function of recycling endosomes
in plants.
acknowledgement: This work was supported by the Odysseus Program of the Research Foundation-Flanders
(J.F.).
author:
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Marisa
full_name: Otegui, Marisa
last_name: Otegui
- first_name: Natsumaro
full_name: Kutsuna, Natsumaro
last_name: Kutsuna
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Tomoko
full_name: Dainobu, Tomoko
last_name: Dainobu
- first_name: Michael
full_name: Karampelias, Michael
last_name: Karampelias
- first_name: Masaru
full_name: Fujimoto, Masaru
last_name: Fujimoto
- first_name: Elena
full_name: Feraru, Elena
last_name: Feraru
- first_name: Daisuke
full_name: Miki, Daisuke
last_name: Miki
- first_name: Hiroo
full_name: Fukuda, Hiroo
last_name: Fukuda
- first_name: Akihiko
full_name: Nakano, Akihiko
last_name: Nakano
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Naramoto S, Otegui M, Kutsuna N, et al. Insights into the localization and
function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus
in Arabidopsis. Plant Cell. 2014;26(7):3062-3076. doi:10.1105/tpc.114.125880
apa: Naramoto, S., Otegui, M., Kutsuna, N., De Rycke, R., Dainobu, T., Karampelias,
M., … Friml, J. (2014). Insights into the localization and function of the membrane
trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant
Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.125880
chicago: Naramoto, Satoshi, Marisa Otegui, Natsumaro Kutsuna, Riet De Rycke, Tomoko
Dainobu, Michael Karampelias, Masaru Fujimoto, et al. “Insights into the Localization
and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus
in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2014.
https://doi.org/10.1105/tpc.114.125880.
ieee: S. Naramoto et al., “Insights into the localization and function of
the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis,”
Plant Cell, vol. 26, no. 7. American Society of Plant Biologists, pp. 3062–3076,
2014.
ista: Naramoto S, Otegui M, Kutsuna N, De Rycke R, Dainobu T, Karampelias M, Fujimoto
M, Feraru E, Miki D, Fukuda H, Nakano A, Friml J. 2014. Insights into the localization
and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus
in Arabidopsis. Plant Cell. 26(7), 3062–3076.
mla: Naramoto, Satoshi, et al. “Insights into the Localization and Function of the
Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.”
Plant Cell, vol. 26, no. 7, American Society of Plant Biologists, 2014,
pp. 3062–76, doi:10.1105/tpc.114.125880.
short: S. Naramoto, M. Otegui, N. Kutsuna, R. De Rycke, T. Dainobu, M. Karampelias,
M. Fujimoto, E. Feraru, D. Miki, H. Fukuda, A. Nakano, J. Friml, Plant Cell 26
(2014) 3062–3076.
date_created: 2018-12-11T11:54:36Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2021-01-12T06:53:55Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.114.125880
intvolume: ' 26'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145132/
month: '07'
oa: 1
oa_version: Submitted Version
page: 3062 - 3076
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '5199'
scopus_import: 1
status: public
title: Insights into the localization and function of the membrane trafficking regulator
GNOM ARF-GEF at the Golgi apparatus in Arabidopsis
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2014'
...
---
_id: '1899'
abstract:
- lang: eng
text: Asymmetric cell divisions allow stem cells to balance proliferation and differentiation.
During embryogenesis, murine epidermis expands rapidly from a single layer of
unspecified basal layer progenitors to a stratified, differentiated epithelium.
Morphogenesis involves perpendicular (asymmetric) divisions and the spindle orientation
protein LGN, but little is known about how the apical localization of LGN is regulated.
Here, we combine conventional genetics and lentiviral-mediated in vivo RNAi to
explore the functions of the LGN-interacting proteins Par3, mInsc and Gα i3. Whereas
loss of each gene alone leads to randomized division angles, combined loss of
Gnai3 and mInsc causes a phenotype of mostly planar divisions, akin to loss of
LGN. These findings lend experimental support for the hitherto untested model
that Par3-mInsc and Gα i3 act cooperatively to polarize LGN and promote perpendicular
divisions. Finally, we uncover a developmental switch between delamination-driven
early stratification and spindle-orientation-dependent differentiation that occurs
around E15, revealing a two-step mechanism underlying epidermal maturation.
article_processing_charge: No
article_type: original
author:
- first_name: Scott
full_name: Williams, Scott
last_name: Williams
- first_name: Lyndsay
full_name: Ratliff, Lyndsay
last_name: Ratliff
- first_name: Maria P
full_name: Postiglione, Maria P
id: 2C67902A-F248-11E8-B48F-1D18A9856A87
last_name: Postiglione
- first_name: Juergen
full_name: Knoblich, Juergen
last_name: Knoblich
- first_name: Elaine
full_name: Fuchs, Elaine
last_name: Fuchs
citation:
ama: Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. Par3-mInsc and
Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature
Cell Biology. 2014;16(8):758-769. doi:10.1038/ncb3001
apa: Williams, S., Ratliff, L., Postiglione, M. P., Knoblich, J., & Fuchs, E.
(2014). Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions
through LGN. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3001
chicago: Williams, Scott, Lyndsay Ratliff, Maria P Postiglione, Juergen Knoblich,
and Elaine Fuchs. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal
Cell Divisions through LGN.” Nature Cell Biology. Nature Publishing Group,
2014. https://doi.org/10.1038/ncb3001.
ieee: S. Williams, L. Ratliff, M. P. Postiglione, J. Knoblich, and E. Fuchs, “Par3-mInsc
and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN,”
Nature Cell Biology, vol. 16, no. 8. Nature Publishing Group, pp. 758–769,
2014.
ista: Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. 2014. Par3-mInsc
and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN.
Nature Cell Biology. 16(8), 758–769.
mla: Williams, Scott, et al. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented
Epidermal Cell Divisions through LGN.” Nature Cell Biology, vol. 16, no.
8, Nature Publishing Group, 2014, pp. 758–69, doi:10.1038/ncb3001.
short: S. Williams, L. Ratliff, M.P. Postiglione, J. Knoblich, E. Fuchs, Nature
Cell Biology 16 (2014) 758–769.
date_created: 2018-12-11T11:54:36Z
date_published: 2014-07-13T00:00:00Z
date_updated: 2021-01-12T06:53:55Z
day: '13'
department:
- _id: SiHi
doi: 10.1038/ncb3001
external_id:
pmid:
- '25016959'
intvolume: ' 16'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159251/
month: '07'
oa: 1
oa_version: Submitted Version
page: 758 - 769
pmid: 1
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '5196'
quality_controlled: '1'
scopus_import: 1
status: public
title: Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions
through LGN
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2014'
...