---
_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
- access_level: closed
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
license: https://creativecommons.org/licenses/by/4.0/
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: 2024-03-28T23:30:28Z
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'
...