---
_id: '2028'
abstract:
- lang: eng
text: 'Understanding the dynamics of noisy neurons remains an important challenge
in neuroscience. Here, we describe a simple probabilistic model that accurately
describes the firing behavior in a large class (type II) of neurons. To demonstrate
the usefulness of this model, we show how it accurately predicts the interspike
interval (ISI) distributions, bursting patterns and mean firing rates found by:
(1) simulations of the classic Hodgkin-Huxley model with channel noise, (2) experimental
data from squid giant axon with a noisy input current and (3) experimental data
on noisy firing from a neuron within the suprachiasmatic nucleus (SCN). This simple
model has 6 parameters, however, in some cases, two of these parameters are coupled
and only 5 parameters account for much of the known behavior. From these parameters,
many properties of spiking can be found through simple calculation. Thus, we show
how the complex effects of noise can be understood through a simple and general
probabilistic model.'
acknowledgement: 'This work is supported by AFOSR grant FA 9550-11-1-0165, program
grant RPG 24/2012 from the Human Frontiers of Science (DBF) and travel support from
the European Commission Marie Curie International Reintegration Grant PIRG04-GA-2008-239429
(KB). DP was supported by NIHR01 GM104987 and the Wyss Institute of Biologically
Inspired Engineering. '
article_processing_charge: No
author:
- first_name: Katarina
full_name: Bodova, Katarina
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bodova
orcid: 0000-0002-7214-0171
- first_name: David
full_name: Paydarfar, David
last_name: Paydarfar
- first_name: Daniel
full_name: Forger, Daniel
last_name: Forger
citation:
ama: Bodova K, Paydarfar D, Forger D. Characterizing spiking in noisy type II neurons.
Journal of Theoretical Biology. 2014;365:40-54. doi:10.1016/j.jtbi.2014.09.041
apa: Bodova, K., Paydarfar, D., & Forger, D. (2014). Characterizing spiking
in noisy type II neurons. Journal of Theoretical Biology. Academic Press.
https://doi.org/10.1016/j.jtbi.2014.09.041
chicago: Bodova, Katarina, David Paydarfar, and Daniel Forger. “Characterizing Spiking
in Noisy Type II Neurons.” Journal of Theoretical Biology. Academic Press,
2014. https://doi.org/10.1016/j.jtbi.2014.09.041.
ieee: K. Bodova, D. Paydarfar, and D. Forger, “Characterizing spiking in noisy type
II neurons,” Journal of Theoretical Biology, vol. 365. Academic Press,
pp. 40–54, 2014.
ista: Bodova K, Paydarfar D, Forger D. 2014. Characterizing spiking in noisy type
II neurons. Journal of Theoretical Biology. 365, 40–54.
mla: Bodova, Katarina, et al. “Characterizing Spiking in Noisy Type II Neurons.”
Journal of Theoretical Biology, vol. 365, Academic Press, 2014, pp. 40–54,
doi:10.1016/j.jtbi.2014.09.041.
short: K. Bodova, D. Paydarfar, D. Forger, Journal of Theoretical Biology 365 (2014)
40–54.
corr_author: '1'
das_tickbox: '1'
date_created: 2018-12-11T11:55:18Z
date_published: 2014-10-12T00:00:00Z
date_updated: 2026-07-07T13:13:09Z
day: '12'
ddc:
- '570'
department:
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doi: 10.1016/j.jtbi.2014.09.041
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creator: system
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date_updated: 2020-07-14T12:45:25Z
file_id: '5316'
file_name: IST-2016-444-v1+1_1-s2.0-S0022519314005888-main.pdf
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license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: 40 - 54
publication: Journal of Theoretical Biology
publication_status: published
publisher: Academic Press
publist_id: '5043'
pubrep_id: '444'
quality_controlled: '1'
related_material:
link:
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url: https://doi.org/10.1016/j.jtbi.2015.03.013
scopus_import: '1'
status: public
title: Characterizing spiking in noisy type II neurons
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 365
year: '2014'
...
---
_id: '5415'
abstract:
- lang: eng
text: 'Recently there has been a significant effort to add quantitative properties
in formal verification and synthesis. While weighted automata over finite and
infinite words provide a natural and flexible framework to express quantitative
properties, perhaps surprisingly, several basic system properties such as average
response time cannot be expressed with weighted automata. In this work, we introduce
nested weighted automata as a new formalism for expressing important quantitative
properties such as average response time. We establish an almost complete decidability
picture for the basic decision problems for nested weighted automata, and illustrate
its applicability in several domains. '
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: Chatterjee K, Henzinger TA, Otop J. Nested Weighted Automata. IST Austria;
2014. doi:10.15479/AT:IST-2014-170-v1-1
apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2014). Nested weighted
automata. IST Austria. https://doi.org/10.15479/AT:IST-2014-170-v1-1
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. Nested Weighted
Automata. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-170-v1-1.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, Nested weighted automata.
IST Austria, 2014.
ista: Chatterjee K, Henzinger TA, Otop J. 2014. Nested weighted automata, IST Austria,
27p.
mla: Chatterjee, Krishnendu, et al. Nested Weighted Automata. IST Austria,
2014, doi:10.15479/AT:IST-2014-170-v1-1.
short: K. Chatterjee, T.A. Henzinger, J. Otop, Nested Weighted Automata, IST Austria,
2014.
date_created: 2018-12-12T11:39:12Z
date_published: 2014-02-19T00:00:00Z
date_updated: 2026-07-07T14:01:10Z
day: '19'
ddc:
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department:
- _id: KrCh
- _id: ToHe
doi: 10.15479/AT:IST-2014-170-v1-1
file:
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checksum: 31f90dcf2cf899c3f8c6427cfcc2b3c7
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language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '27'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '170'
related_material:
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relation: later_version
status: public
- id: '1656'
relation: later_version
status: public
- id: '467'
relation: later_version
status: public
status: public
title: Nested weighted automata
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2038'
abstract:
- lang: eng
text: Recently, there has been an effort to add quantitative objectives to formal
verification and synthesis. We introduce and investigate the extension of temporal
logics with quantitative atomic assertions. At the heart of quantitative objectives
lies the accumulation of values along a computation. It is often the accumulated
sum, as with energy objectives, or the accumulated average, as with mean-payoff
objectives. We investigate the extension of temporal logics with the prefix-accumulation
assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric (or Boolean) variable
of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the
accumulated sum and average of the values of v from the beginning of the computation
up to the current point in time. We also allow the path-accumulation assertions
LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an
entire infinite computation. We study the border of decidability for such quantitative
extensions of various temporal logics. In particular, we show that extending the
fragment of CTL that has only the EX, EF, AX, and AG temporal modalities with
both prefix-accumulation assertions, or extending LTL with both path-accumulation
assertions, results in temporal logics whose model-checking problem is decidable.
Moreover, the prefix-accumulation assertions may be generalized with "controlled
accumulation," allowing, for example, to specify constraints on the average
waiting time between a request and a grant. On the negative side, we show that
this branching-time logic is, in a sense, the maximal logic with one or both of
the prefix-accumulation assertions that permits a decidable model-checking procedure.
Extending a temporal logic that has the EG or EU modalities, such as CTL or LTL,
makes the problem undecidable.
acknowledgement: The research was supported in part by ERC Starting grant 278410 (QUALITY).
article_number: '27'
article_processing_charge: No
article_type: original
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: Boker U, Chatterjee K, Henzinger TA, Kupferman O. Temporal specifications with
accumulative values. ACM Transactions on Computational Logic. 2014;15(4).
doi:10.1145/2629686
apa: Boker, U., Chatterjee, K., Henzinger, T. A., & Kupferman, O. (2014). Temporal
specifications with accumulative values. ACM Transactions on Computational
Logic. ACM. https://doi.org/10.1145/2629686
chicago: Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman.
“Temporal Specifications with Accumulative Values.” ACM Transactions on Computational
Logic. ACM, 2014. https://doi.org/10.1145/2629686.
ieee: U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, “Temporal specifications
with accumulative values,” ACM Transactions on Computational Logic, vol.
15, no. 4. ACM, 2014.
ista: Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2014. Temporal specifications
with accumulative values. ACM Transactions on Computational Logic. 15(4), 27.
mla: Boker, Udi, et al. “Temporal Specifications with Accumulative Values.” ACM
Transactions on Computational Logic, vol. 15, no. 4, 27, ACM, 2014, doi:10.1145/2629686.
short: U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, ACM Transactions on
Computational Logic 15 (2014).
das_tickbox: '1'
date_created: 2018-12-11T11:55:21Z
date_published: 2014-09-16T00:00:00Z
date_updated: 2026-07-07T14:01:43Z
day: '16'
ddc:
- '000'
- '004'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1145/2629686
ec_funded: 1
external_id:
isi:
- '000345570700002'
file:
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checksum: 354c41d37500b56320afce94cf9a99c2
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creator: system
date_created: 2018-12-12T10:10:59Z
date_updated: 2020-07-14T12:45:26Z
file_id: '4851'
file_name: IST-2014-192-v1+1_AccumulativeValues.pdf
file_size: 346184
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file_date_updated: 2020-07-14T12:45:26Z
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intvolume: ' 15'
isi: 1
issue: '4'
language:
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month: '09'
oa: 1
oa_version: Submitted Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _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: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: ACM Transactions on Computational Logic
publication_status: published
publisher: ACM
publist_id: '5013'
pubrep_id: '192'
quality_controlled: '1'
related_material:
record:
- id: '5385'
relation: earlier_version
status: public
- id: '3356'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Temporal specifications with accumulative values
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2014'
...
---
OA_place: repository
OA_type: green
_id: '1903'
abstract:
- lang: eng
text: 'We consider two-player zero-sum partial-observation stochastic games on graphs.
Based on the information available to the players these games can be classified
as follows: (a) general partial-observation (both players have partial view of
the game); (b) one-sided partial-observation (one player has partial-observation
and the other player has complete-observation); and (c) perfect-observation (both
players have complete view of the game). The one-sided partial-observation games
subsumes the important special case of one-player partial-observation stochastic
games (or partial-observation Markov decision processes (POMDPs)). Based on the
randomization available for the strategies, (a) the players may not be allowed
to use randomization (pure strategies), or (b) they may choose a probability distribution
over actions but the actual random choice is external and not visible to the player
(actions invisible), or (c) they may use full randomization. We consider all these
classes of games with reachability, and parity objectives that can express all
ω-regular objectives. The analysis problems are classified into the qualitative
analysis that asks for the existence of a strategy that ensures the objective
with probability 1; and the quantitative analysis that asks for the existence
of a strategy that ensures the objective with probability at least λ (0,1). In
this talk we will cover a wide range of results: for perfect-observation games;
for POMDPs; for one-sided partial-observation games; and for general partial-observation
games.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Chatterjee K. Partial-observation stochastic reachability and parity games.
In: Vol 8634. Springer; 2014:1-4. doi:10.1007/978-3-662-44522-8_1'
apa: 'Chatterjee, K. (2014). Partial-observation stochastic reachability and parity
games (Vol. 8634, pp. 1–4). Presented at the MFCS: Mathematical Foundations of
Computer Science, Budapest, Hungary: Springer. https://doi.org/10.1007/978-3-662-44522-8_1'
chicago: Chatterjee, Krishnendu. “Partial-Observation Stochastic Reachability and
Parity Games,” 8634:1–4. Springer, 2014. https://doi.org/10.1007/978-3-662-44522-8_1.
ieee: 'K. Chatterjee, “Partial-observation stochastic reachability and parity games,”
presented at the MFCS: Mathematical Foundations of Computer Science, Budapest,
Hungary, 2014, vol. 8634, no. PART 1, pp. 1–4.'
ista: 'Chatterjee K. 2014. Partial-observation stochastic reachability and parity
games. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 8634, 1–4.'
mla: Chatterjee, Krishnendu. Partial-Observation Stochastic Reachability and
Parity Games. Vol. 8634, no. PART 1, Springer, 2014, pp. 1–4, doi:10.1007/978-3-662-44522-8_1.
short: K. Chatterjee, in:, Springer, 2014, pp. 1–4.
conference:
end_date: 2014-08-29
location: Budapest, Hungary
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2014-08-25
corr_author: '1'
date_created: 2018-12-11T11:54:38Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2026-07-07T14:01:25Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-662-44522-8_1
ec_funded: 1
intvolume: ' 8634'
issue: PART 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.15479/AT:IST-2011-0007
month: '01'
oa: 1
oa_version: Preprint
page: 1 - 4
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_status: published
publisher: Springer
publist_id: '5192'
pubrep_id: '141'
quality_controlled: '1'
related_material:
record:
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relation: earlier_version
status: public
- id: '2211'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Partial-observation stochastic reachability and parity games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8634
year: '2014'
...
---
_id: '2211'
abstract:
- lang: eng
text: 'In two-player finite-state stochastic games of partial observation on graphs,
in every state of the graph, the players simultaneously choose an action, and
their joint actions determine a probability distribution over the successor states.
The game is played for infinitely many rounds and thus the players construct an
infinite path in the graph. We consider reachability objectives where the first
player tries to ensure a target state to be visited almost-surely (i.e., with
probability 1) or positively (i.e., with positive probability), no matter the
strategy of the second player. We classify such games according to the information
and to the power of randomization available to the players. On the basis of information,
the game can be one-sided with either (a) player 1, or (b) player 2 having partial
observation (and the other player has perfect observation), or two-sided with
(c) both players having partial observation. On the basis of randomization, (a)
the players may not be allowed to use randomization (pure strategies), or (b)
they may choose a probability distribution over actions but the actual random
choice is external and not visible to the player (actions invisible), or (c) they
may use full randomization. Our main results for pure strategies are as follows:
(1) For one-sided games with player 2 having perfect observation we show that
(in contrast to full randomized strategies) belief-based (subset-construction
based) strategies are not sufficient, and we present an exponential upper bound
on memory both for almost-sure and positive winning strategies; we show that the
problem of deciding the existence of almost-sure and positive winning strategies
for player 1 is EXPTIME-complete and present symbolic algorithms that avoid the
explicit exponential construction. (2) For one-sided games with player 1 having
perfect observation we show that nonelementarymemory is both necessary and sufficient
for both almost-sure and positive winning strategies. (3) We show that for the
general (two-sided) case finite-memory strategies are sufficient for both positive
and almost-sure winning, and at least nonelementary memory is required. We establish
the equivalence of the almost-sure winning problems for pure strategies and for
randomized strategies with actions invisible. Our equivalence result exhibit serious
flaws in previous results of the literature: we show a nonelementary memory lower
bound for almost-sure winning whereas an exponential upper bound was previously
claimed.'
article_number: '16'
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: 'Chatterjee K, Doyen L. Partial-observation stochastic games: How to win when
belief fails. ACM Transactions on Computational Logic. 2014;15(2). doi:10.1145/2579821'
apa: 'Chatterjee, K., & Doyen, L. (2014). Partial-observation stochastic games:
How to win when belief fails. ACM Transactions on Computational Logic.
ACM. https://doi.org/10.1145/2579821'
chicago: 'Chatterjee, Krishnendu, and Laurent Doyen. “Partial-Observation Stochastic
Games: How to Win When Belief Fails.” ACM Transactions on Computational Logic.
ACM, 2014. https://doi.org/10.1145/2579821.'
ieee: 'K. Chatterjee and L. Doyen, “Partial-observation stochastic games: How to
win when belief fails,” ACM Transactions on Computational Logic, vol. 15,
no. 2. ACM, 2014.'
ista: 'Chatterjee K, Doyen L. 2014. Partial-observation stochastic games: How to
win when belief fails. ACM Transactions on Computational Logic. 15(2), 16.'
mla: 'Chatterjee, Krishnendu, and Laurent Doyen. “Partial-Observation Stochastic
Games: How to Win When Belief Fails.” ACM Transactions on Computational Logic,
vol. 15, no. 2, 16, ACM, 2014, doi:10.1145/2579821.'
short: K. Chatterjee, L. Doyen, ACM Transactions on Computational Logic 15 (2014).
das_tickbox: '1'
date_created: 2018-12-11T11:56:21Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2026-07-07T14:01:26Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/2579821
external_id:
arxiv:
- '1107.2141'
isi:
- '000336005000006'
intvolume: ' 15'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1107.2141
month: '04'
oa: 1
oa_version: Preprint
publication: ACM Transactions on Computational Logic
publication_status: published
publisher: ACM
publist_id: '4759'
quality_controlled: '1'
related_material:
record:
- id: '5381'
relation: earlier_version
status: public
- id: '1903'
relation: earlier_version
status: public
- id: '2955'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'Partial-observation stochastic games: How to win when belief fails'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2014'
...
---
_id: '2054'
abstract:
- lang: eng
text: 'We study two-player concurrent games on finite-state graphs played for an
infinite number of rounds, where in each round, the two players (player 1 and
player 2) choose their moves independently and simultaneously; the current state
and the two moves determine the successor state. The objectives are ω-regular
winning conditions specified as parity objectives. We consider the qualitative
analysis problems: the computation of the almost-sure and limit-sure winning set
of states, where player 1 can ensure to win with probability 1 and with probability
arbitrarily close to 1, respectively. In general the almost-sure and limit-sure
winning strategies require both infinite-memory as well as infinite-precision
(to describe probabilities). While the qualitative analysis problem for concurrent
parity games with infinite-memory, infinite-precision randomized strategies was
studied before, we study the bounded-rationality problem for qualitative analysis
of concurrent parity games, where the strategy set for player 1 is restricted
to bounded-resource strategies. In terms of precision, strategies can be deterministic,
uniform, finite-precision, or infinite-precision; and in terms of memory, strategies
can be memoryless, finite-memory, or infinite-memory. We present a precise and
complete characterization of the qualitative winning sets for all combinations
of classes of strategies. In particular, we show that uniform memoryless strategies
are as powerful as finite-precision infinite-memory strategies, and infinite-precision
memoryless strategies are as powerful as infinite-precision finite-memory strategies.
We show that the winning sets can be computed in (n2d+3) time, where n is the
size of the game structure and 2d is the number of priorities (or colors), and
our algorithms are symbolic. The membership problem of whether a state belongs
to a winning set can be decided in NP ∩ coNP. Our symbolic algorithms are based
on a characterization of the winning sets as μ-calculus formulas, however, our
μ-calculus formulas are crucially different from the ones for concurrent parity
games (without bounded rationality); and our memoryless witness strategy constructions
are significantly different from the infinite-memory witness strategy constructions
for concurrent parity games.'
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Chatterjee K. Qualitative concurrent parity games: Bounded rationality. In:
Baldan P, Gorla D, eds. Lecture Notes in Computer Science (Including Subseries
Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).
Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:544-559. doi:10.1007/978-3-662-44584-6_37'
apa: 'Chatterjee, K. (2014). Qualitative concurrent parity games: Bounded rationality.
In P. Baldan & D. Gorla (Eds.), Lecture Notes in Computer Science (including
subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
(Vol. 8704, pp. 544–559). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für
Informatik. https://doi.org/10.1007/978-3-662-44584-6_37'
chicago: 'Chatterjee, Krishnendu. “Qualitative Concurrent Parity Games: Bounded
Rationality.” In Lecture Notes in Computer Science (Including Subseries Lecture
Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited
by Paolo Baldan and Daniele Gorla, 8704:544–59. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_37.'
ieee: 'K. Chatterjee, “Qualitative concurrent parity games: Bounded rationality,”
in Lecture Notes in Computer Science (including subseries Lecture Notes in
Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy,
2014, vol. 8704, pp. 544–559.'
ista: 'Chatterjee K. 2014. Qualitative concurrent parity games: Bounded rationality.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial
Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory,
LNCS, vol. 8704, 544–559.'
mla: 'Chatterjee, Krishnendu. “Qualitative Concurrent Parity Games: Bounded Rationality.”
Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial
Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan
and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2014, pp. 544–59, doi:10.1007/978-3-662-44584-6_37.'
short: K. Chatterjee, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer
Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture
Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014,
pp. 544–559.
conference:
end_date: 2014-09-05
location: Rome, Italy
name: 'CONCUR: Concurrency Theory'
start_date: 2014-09-02
corr_author: '1'
date_created: 2018-12-11T11:55:27Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2026-07-07T14:02:37Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-662-44584-6_37
ec_funded: 1
editor:
- first_name: Paolo
full_name: Baldan, Paolo
last_name: Baldan
- first_name: Daniele
full_name: Gorla, Daniele
last_name: Gorla
intvolume: ' 8704'
language:
- iso: eng
month: '09'
oa_version: None
page: 544 - 559
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: Lecture Notes in Computer Science (including subseries Lecture Notes
in Artificial Intelligence and Lecture Notes in Bioinformatics)
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '4992'
quality_controlled: '1'
related_material:
record:
- id: '3354'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'Qualitative concurrent parity games: Bounded rationality'
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8704
year: '2014'
...
---
_id: '535'
abstract:
- lang: eng
text: Energy games belong to a class of turn-based two-player infinite-duration
games played on a weighted directed graph. It is one of the rare and intriguing
combinatorial problems that lie in NP∩co-NP, but are not known to be in P. The
existence of polynomial-time algorithms has been a major open problem for decades
and apart from pseudopolynomial algorithms there is no algorithm that solves any
non-trivial subclass in polynomial time. In this paper, we give several results
based on the weight structures of the graph. First, we identify a notion of penalty
and present a polynomial-time algorithm when the penalty is large. Our algorithm
is the first polynomial-time algorithm on a large class of weighted graphs. It
includes several worst-case instances on which previous algorithms, such as value
iteration and random facet algorithms, require at least sub-exponential time.
Our main technique is developing the first non-trivial approximation algorithm
and showing how to convert it to an exact algorithm. Moreover, we show that in
a practical case in verification where weights are clustered around a constant
number of values, the energy game problem can be solved in polynomial time. We
also show that the problem is still as hard as in general when the clique-width
is bounded or the graph is strongly ergodic, suggesting that restricting the graph
structure does not necessarily help.
article_processing_charge: No
article_type: original
arxiv: 1
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: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: Chatterjee K, Henzinger M, Krinninger S, Nanongkai D. Polynomial-time algorithms
for energy games with special weight structures. Algorithmica. 2014;70(3):457-492.
doi:10.1007/s00453-013-9843-7
apa: Chatterjee, K., Henzinger, M., Krinninger, S., & Nanongkai, D. (2014).
Polynomial-time algorithms for energy games with special weight structures. Algorithmica.
Springer. https://doi.org/10.1007/s00453-013-9843-7
chicago: Chatterjee, Krishnendu, Monika Henzinger, Sebastian Krinninger, and Danupon
Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.”
Algorithmica. Springer, 2014. https://doi.org/10.1007/s00453-013-9843-7.
ieee: K. Chatterjee, M. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time
algorithms for energy games with special weight structures,” Algorithmica,
vol. 70, no. 3. Springer, pp. 457–492, 2014.
ista: Chatterjee K, Henzinger M, Krinninger S, Nanongkai D. 2014. Polynomial-time
algorithms for energy games with special weight structures. Algorithmica. 70(3),
457–492.
mla: Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games
with Special Weight Structures.” Algorithmica, vol. 70, no. 3, Springer,
2014, pp. 457–92, doi:10.1007/s00453-013-9843-7.
short: K. Chatterjee, M. Henzinger, S. Krinninger, D. Nanongkai, Algorithmica 70
(2014) 457–492.
date_created: 2018-12-11T11:47:01Z
date_published: 2014-11-01T00:00:00Z
date_updated: 2026-07-08T05:50:38Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/s00453-013-9843-7
ec_funded: 1
external_id:
arxiv:
- '1604.08234'
isi:
- '000340552300005'
intvolume: ' 70'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.08234
month: '11'
oa: 1
oa_version: Preprint
page: 457 - 492
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: Algorithmica
publication_status: published
publisher: Springer
publist_id: '7282'
quality_controlled: '1'
related_material:
record:
- id: '10905'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Polynomial-time algorithms for energy games with special weight structures
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 70
year: '2014'
...
---
_id: '1872'
abstract:
- lang: eng
text: Extensionality axioms are common when reasoning about data collections, such
as arrays and functions in program analysis, or sets in mathematics. An extensionality
axiom asserts that two collections are equal if they consist of the same elements
at the same indices. Using extensionality is often required to show that two collections
are equal. A typical example is the set theory theorem (∀x)(∀y)x∪y = y ∪x. Interestingly,
while humans have no problem with proving such set identities using extensionality,
they are very hard for superposition theorem provers because of the calculi they
use. In this paper we show how addition of a new inference rule, called extensionality
resolution, allows first-order theorem provers to easily solve problems no modern
first-order theorem prover can solve. We illustrate this by running the VAMPIRE
theorem prover with extensionality resolution on a number of set theory and array
problems. Extensionality resolution helps VAMPIRE to solve problems from the TPTP
library of first-order problems that were never solved before by any prover.
acknowledgement: This research was supported in part by the Austrian National Research
Network RiSE (S11410-N23).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
- first_name: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
- first_name: Andrei
full_name: Voronkov, Andrei
last_name: Voronkov
citation:
ama: 'Gupta A, Kovács L, Kragl B, Voronkov A. Extensional crisis and proving identity.
In: 12th International Symposium on Automated Technology for Verification and
Analysis. Vol 8837. Springer; 2014:185-200. doi:10.1007/978-3-319-11936-6_14'
apa: 'Gupta, A., Kovács, L., Kragl, B., & Voronkov, A. (2014). Extensional crisis
and proving identity. In 12th International Symposium on Automated Technology
for Verification and Analysis (Vol. 8837, pp. 185–200). Sydney, Australia:
Springer. https://doi.org/10.1007/978-3-319-11936-6_14'
chicago: Gupta, Ashutosh, Laura Kovács, Bernhard Kragl, and Andrei Voronkov. “Extensional
Crisis and Proving Identity.” In 12th International Symposium on Automated
Technology for Verification and Analysis, 8837:185–200. Springer, 2014. https://doi.org/10.1007/978-3-319-11936-6_14.
ieee: A. Gupta, L. Kovács, B. Kragl, and A. Voronkov, “Extensional crisis and proving
identity,” in 12th International Symposium on Automated Technology for Verification
and Analysis, Sydney, Australia, 2014, vol. 8837, pp. 185–200.
ista: 'Gupta A, Kovács L, Kragl B, Voronkov A. 2014. Extensional crisis and proving
identity. 12th International Symposium on Automated Technology for Verification
and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS,
vol. 8837, 185–200.'
mla: Gupta, Ashutosh, et al. “Extensional Crisis and Proving Identity.” 12th
International Symposium on Automated Technology for Verification and Analysis,
vol. 8837, Springer, 2014, pp. 185–200, doi:10.1007/978-3-319-11936-6_14.
short: A. Gupta, L. Kovács, B. Kragl, A. Voronkov, in:, 12th International Symposium
on Automated Technology for Verification and Analysis, Springer, 2014, pp. 185–200.
conference:
end_date: 2014-11-07
location: Sydney, Australia
name: 'ATVA: Automated Technology for Verification and Analysis'
start_date: 2014-11-03
das_tickbox: '1'
date_created: 2018-12-11T11:54:28Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2026-07-08T06:49:33Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-11936-6_14
ec_funded: 1
file:
- access_level: open_access
checksum: af4bd3fc1f4c93075e4dc5cbf625fe7b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:15Z
date_updated: 2020-07-14T12:45:19Z
file_id: '4801'
file_name: IST-2016-641-v1+1_atva2014.pdf
file_size: 244294
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 8837'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 185 - 200
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication: 12th International Symposium on Automated Technology for Verification
and Analysis
publication_status: published
publisher: Springer
publist_id: '5226'
pubrep_id: '641'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extensional crisis and proving identity
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8837
year: '2014'
...
---
_id: '1999'
abstract:
- lang: eng
text: Selection for disease control is believed to have contributed to shape the
organisation of insect societies — leading to interaction patterns that mitigate
disease transmission risk within colonies, conferring them ‘organisational immunity’.
Recent studies combining epidemiological models with social network analysis have
identified general properties of interaction networks that may hinder propagation
of infection within groups. These can be prophylactic and/or induced upon pathogen
exposure. Here we review empirical evidence for these two types of organisational
immunity in social insects and describe the individual-level behaviours that underlie
it. We highlight areas requiring further investigation, and emphasise the need
for tighter links between theory and empirical research and between individual-level
and collective-level analyses.
article_processing_charge: No
author:
- first_name: Nathalie
full_name: Stroeymeyt, Nathalie
last_name: Stroeymeyt
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Stroeymeyt N, Casillas Perez BE, Cremer S. Organisational immunity in social
insects. Current Opinion in Insect Science. 2014;5(1):1-15. doi:10.1016/j.cois.2014.09.001
apa: Stroeymeyt, N., Casillas Perez, B. E., & Cremer, S. (2014). Organisational
immunity in social insects. Current Opinion in Insect Science. Elsevier.
https://doi.org/10.1016/j.cois.2014.09.001
chicago: Stroeymeyt, Nathalie, Barbara E Casillas Perez, and Sylvia Cremer. “Organisational
Immunity in Social Insects.” Current Opinion in Insect Science. Elsevier,
2014. https://doi.org/10.1016/j.cois.2014.09.001.
ieee: N. Stroeymeyt, B. E. Casillas Perez, and S. Cremer, “Organisational immunity
in social insects,” Current Opinion in Insect Science, vol. 5, no. 1. Elsevier,
pp. 1–15, 2014.
ista: Stroeymeyt N, Casillas Perez BE, Cremer S. 2014. Organisational immunity in
social insects. Current Opinion in Insect Science. 5(1), 1–15.
mla: Stroeymeyt, Nathalie, et al. “Organisational Immunity in Social Insects.” Current
Opinion in Insect Science, vol. 5, no. 1, Elsevier, 2014, pp. 1–15, doi:10.1016/j.cois.2014.09.001.
short: N. Stroeymeyt, B.E. Casillas Perez, S. Cremer, Current Opinion in Insect
Science 5 (2014) 1–15.
corr_author: '1'
date_created: 2018-12-11T11:55:08Z
date_published: 2014-11-01T00:00:00Z
date_updated: 2026-07-13T22:30:58Z
day: '01'
department:
- _id: SyCr
doi: 10.1016/j.cois.2014.09.001
ec_funded: 1
external_id:
isi:
- '000209578900002'
intvolume: ' 5'
isi: 1
issue: '1'
language:
- iso: eng
month: '11'
oa_version: None
page: 1 - 15
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
publication: Current Opinion in Insect Science
publication_status: published
publisher: Elsevier
publist_id: '5080'
quality_controlled: '1'
related_material:
record:
- id: '6383'
relation: dissertation_contains
- id: '6435'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Organisational immunity in social insects
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5
year: '2014'
...
---
_id: '10895'
abstract:
- lang: eng
text: 'Due to their sessile lifestyles, plants need to deal with the limitations
and stresses imposed by the changing environment. Plants cope with these by a
remarkable developmental flexibility, which is embedded in their strategy to survive.
Plants can adjust their size, shape and number of organs, bend according to gravity
and light, and regenerate tissues that were damaged, utilizing a coordinating,
intercellular signal, the plant hormone, auxin. Another versatile signal is the
cation, Ca2+, which is a crucial second messenger for many rapid cellular processes
during responses to a wide range of endogenous and environmental signals, such
as hormones, light, drought stress and others. Auxin is a good candidate for one
of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling
is poorly understood. Here, we will provide an overview of possible developmental
and physiological roles, as well as mechanisms underlying the interconnection
of Ca2+ and auxin signaling. '
article_processing_charge: No
article_type: original
author:
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Vanneste S, Friml J. Calcium: The missing link in auxin action. Plants.
2013;2(4):650-675. doi:10.3390/plants2040650'
apa: 'Vanneste, S., & Friml, J. (2013). Calcium: The missing link in auxin action.
Plants. MDPI. https://doi.org/10.3390/plants2040650'
chicago: 'Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin
Action.” Plants. MDPI, 2013. https://doi.org/10.3390/plants2040650.'
ieee: 'S. Vanneste and J. Friml, “Calcium: The missing link in auxin action,” Plants,
vol. 2, no. 4. MDPI, pp. 650–675, 2013.'
ista: 'Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants.
2(4), 650–675.'
mla: 'Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.”
Plants, vol. 2, no. 4, MDPI, 2013, pp. 650–75, doi:10.3390/plants2040650.'
short: S. Vanneste, J. Friml, Plants 2 (2013) 650–675.
corr_author: '1'
date_created: 2022-03-21T07:13:49Z
date_published: 2013-10-21T00:00:00Z
date_updated: 2024-10-09T21:01:52Z
day: '21'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3390/plants2040650
external_id:
pmid:
- '27137397'
file:
- access_level: open_access
checksum: fb4ff2e820e344e253c9197544610be6
content_type: application/pdf
creator: dernst
date_created: 2022-03-21T12:12:56Z
date_updated: 2022-03-21T12:12:56Z
file_id: '10916'
file_name: 2013_Plants_Vanneste.pdf
file_size: 670188
relation: main_file
success: 1
file_date_updated: 2022-03-21T12:12:56Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '4'
keyword:
- Plant Science
- Ecology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '10'
oa: 1
oa_version: Published Version
page: 650-675
pmid: 1
publication: Plants
publication_identifier:
issn:
- 2223-7747
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Calcium: The missing link in auxin action'
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: 2
year: '2013'
...
---
_id: '10897'
abstract:
- lang: eng
text: Taking images is an efficient way to collect data about the physical world.
It can be done fast and in exquisite detail. By definition, image processing is
the field that concerns itself with the computation aimed at harnessing the information
contained in images [10]. This talk is concerned with topological information.
Our main thesis is that persistent homology [5] is a useful method to quantify
and summarize topological information, building a bridge that connects algebraic
topology with applications. We provide supporting evidence for this thesis by
touching upon four technical developments in the overlap between persistent homology
and image processing.
acknowledgement: This research is partially supported by the European Science Foundation
(ESF) under the Research Network Programme, the European Union under the Toposys
Project FP7-ICT-318493-STREP, the Russian Government under the Mega Project 11.G34.31.0053.
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Edelsbrunner H. Persistent homology in image processing. In: Graph-Based
Representations in Pattern Recognition. Vol 7877. LNCS. Berlin, Heidelberg:
Springer Nature; 2013:182-183. doi:10.1007/978-3-642-38221-5_19'
apa: 'Edelsbrunner, H. (2013). Persistent homology in image processing. In Graph-Based
Representations in Pattern Recognition (Vol. 7877, pp. 182–183). Berlin, Heidelberg:
Springer Nature. https://doi.org/10.1007/978-3-642-38221-5_19'
chicago: 'Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” In Graph-Based
Representations in Pattern Recognition, 7877:182–83. LNCS. Berlin, Heidelberg:
Springer Nature, 2013. https://doi.org/10.1007/978-3-642-38221-5_19.'
ieee: H. Edelsbrunner, “Persistent homology in image processing,” in Graph-Based
Representations in Pattern Recognition, Vienna, Austria, 2013, vol. 7877,
pp. 182–183.
ista: 'Edelsbrunner H. 2013. Persistent homology in image processing. Graph-Based
Representations in Pattern Recognition. GbRPR: Graph-based Representations in
Pattern RecognitionLNCS vol. 7877, 182–183.'
mla: Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” Graph-Based
Representations in Pattern Recognition, vol. 7877, Springer Nature, 2013,
pp. 182–83, doi:10.1007/978-3-642-38221-5_19.
short: H. Edelsbrunner, in:, Graph-Based Representations in Pattern Recognition,
Springer Nature, Berlin, Heidelberg, 2013, pp. 182–183.
conference:
end_date: 2013-05-17
location: Vienna, Austria
name: 'GbRPR: Graph-based Representations in Pattern Recognition'
start_date: 2013-05-15
corr_author: '1'
date_created: 2022-03-21T07:30:33Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2025-04-15T08:37:54Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-642-38221-5_19
ec_funded: 1
intvolume: ' 7877'
language:
- iso: eng
month: '06'
oa_version: None
page: 182-183
place: Berlin, Heidelberg
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Graph-Based Representations in Pattern Recognition
publication_identifier:
eisbn:
- '9783642382215'
eissn:
- 1611-3349
isbn:
- '9783642382208'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: Persistent homology in image processing
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7877
year: '2013'
...
---
_id: '10898'
abstract:
- lang: eng
text: A prominent remedy to multicore scalability issues in concurrent data structure
implementations is to relax the sequential specification of the data structure.
We present distributed queues (DQ), a new family of relaxed concurrent queue implementations.
DQs implement relaxed queues with linearizable emptiness check and either configurable
or bounded out-of-order behavior or pool behavior. Our experiments show that DQs
outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue
as well as pool implementations that we considered.
acknowledgement: This work has been supported by the European Research Council advanced
grant on Quantitative Reactive Modeling (QUAREM) and the National Research Network
RiSE on Rigorous Systems Engineering (Austrian Science Fund S11402-N23 and S11404-N23).
article_number: '17'
article_processing_charge: No
author:
- first_name: Andreas
full_name: Haas, Andreas
last_name: Haas
- first_name: Michael
full_name: Lippautz, Michael
last_name: Lippautz
- 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: Hannes
full_name: Payer, Hannes
last_name: Payer
- first_name: Ana
full_name: Sokolova, Ana
last_name: Sokolova
- first_name: Christoph M.
full_name: Kirsch, Christoph M.
last_name: Kirsch
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
citation:
ama: 'Haas A, Lippautz M, Henzinger TA, et al. Distributed queues in shared memory:
Multicore performance and scalability through quantitative relaxation. In: Proceedings
of the ACM International Conference on Computing Frontiers - CF ’13. ACM;
2013. doi:10.1145/2482767.2482789'
apa: 'Haas, A., Lippautz, M., Henzinger, T. A., Payer, H., Sokolova, A., Kirsch,
C. M., & Sezgin, A. (2013). Distributed queues in shared memory: Multicore
performance and scalability through quantitative relaxation. In Proceedings
of the ACM International Conference on Computing Frontiers - CF ’13. Ischia,
Italy: ACM. https://doi.org/10.1145/2482767.2482789'
chicago: 'Haas, Andreas, Michael Lippautz, Thomas A Henzinger, Hannes Payer, Ana
Sokolova, Christoph M. Kirsch, and Ali Sezgin. “Distributed Queues in Shared Memory:
Multicore Performance and Scalability through Quantitative Relaxation.” In Proceedings
of the ACM International Conference on Computing Frontiers - CF ’13. ACM,
2013. https://doi.org/10.1145/2482767.2482789.'
ieee: 'A. Haas et al., “Distributed queues in shared memory: Multicore performance
and scalability through quantitative relaxation,” in Proceedings of the ACM
International Conference on Computing Frontiers - CF ’13, Ischia, Italy, 2013,
no. 5.'
ista: 'Haas A, Lippautz M, Henzinger TA, Payer H, Sokolova A, Kirsch CM, Sezgin
A. 2013. Distributed queues in shared memory: Multicore performance and scalability
through quantitative relaxation. Proceedings of the ACM International Conference
on Computing Frontiers - CF ’13. CF: Conference on Computing Frontiers, 17.'
mla: 'Haas, Andreas, et al. “Distributed Queues in Shared Memory: Multicore Performance
and Scalability through Quantitative Relaxation.” Proceedings of the ACM International
Conference on Computing Frontiers - CF ’13, no. 5, 17, ACM, 2013, doi:10.1145/2482767.2482789.'
short: A. Haas, M. Lippautz, T.A. Henzinger, H. Payer, A. Sokolova, C.M. Kirsch,
A. Sezgin, in:, Proceedings of the ACM International Conference on Computing Frontiers
- CF ’13, ACM, 2013.
conference:
end_date: 2013-05-16
location: Ischia, Italy
name: 'CF: Conference on Computing Frontiers'
start_date: 2013-05-14
date_created: 2022-03-21T07:33:22Z
date_published: 2013-05-14T00:00:00Z
date_updated: 2025-05-14T11:23:58Z
day: '14'
department:
- _id: ToHe
doi: 10.1145/2482767.2482789
ec_funded: 1
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
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: Proceedings of the ACM International Conference on Computing Frontiers
- CF '13
publication_identifier:
isbn:
- 978-145032053-5
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Distributed queues in shared memory: Multicore performance and scalability
through quantitative relaxation'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '10899'
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Differentiation. In: Encyclopedia of Biodiversity. 2nd ed.
Elsevier; 2013:508-515. doi:10.1016/b978-0-12-384719-5.00031-9'
apa: Barton, N. H. (2013). Differentiation. In Encyclopedia of Biodiversity
(2nd ed., pp. 508–515). Elsevier. https://doi.org/10.1016/b978-0-12-384719-5.00031-9
chicago: Barton, Nicholas H. “Differentiation.” In Encyclopedia of Biodiversity,
2nd ed., 508–15. Elsevier, 2013. https://doi.org/10.1016/b978-0-12-384719-5.00031-9.
ieee: N. H. Barton, “Differentiation,” in Encyclopedia of Biodiversity, 2nd
ed., Elsevier, 2013, pp. 508–515.
ista: 'Barton NH. 2013.Differentiation. In: Encyclopedia of Biodiversity. , 508–515.'
mla: Barton, Nicholas H. “Differentiation.” Encyclopedia of Biodiversity,
2nd ed., Elsevier, 2013, pp. 508–15, doi:10.1016/b978-0-12-384719-5.00031-9.
short: N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013,
pp. 508–515.
corr_author: '1'
date_created: 2022-03-21T07:46:22Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2024-10-09T21:02:37Z
day: '01'
department:
- _id: NiBa
doi: 10.1016/b978-0-12-384719-5.00031-9
edition: '2'
keyword:
- Adaptive landscape
- Cline
- Coalescent process
- Gene flow
- Hybrid zone
- Local adaptation
- Natural selection
- Neutral theory
- Population structure
- Speciation
language:
- iso: eng
month: '01'
oa_version: None
page: 508-515
publication: Encyclopedia of Biodiversity
publication_identifier:
isbn:
- 978-0-12-384720-1
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Differentiation
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '10900'
abstract:
- lang: eng
text: Leukocyte migration through the interstitial space is crucial for the maintenance
of tolerance and immunity. The main cues for leukocyte trafficking are chemokines
thought to directionally guide these cells towards their targets. However, model
systems that facilitate quantification of chemokine-guided leukocyte migration
in vivo are uncommon. Here we describe an ex vivo crawl-in assay using explanted
mouse ears that allows the visualization of chemokine-dependent dendritic cell
(DC) motility in the dermal interstitium in real time. We present methods for
the preparation of mouse ear sheets and their use in multidimensional confocal
imaging experiments to monitor and analyze the directional migration of fluorescently
labelled DCs through the dermis and into afferent lymphatic vessels. The assay
provides a more physiological approach to study leukocyte migration than in vitro
three-dimensional (3D) or 2-dimensional (2D) migration assays such as collagen
gels and transwell assays.
acknowledgement: We would like to thank Alexander Eichner and Ingrid de Vries for
discussion and critical reading of the manuscript, and Mary Frank for assistance
with the recording of videos and images in Fig. 1. M.S. is supported through funding
from the German Research Foundation (DFG). M.W. acknowledges the Alexander von Humboldt
Foundation for funding.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Michele
full_name: Weber, Michele
id: 3A3FC708-F248-11E8-B48F-1D18A9856A87
last_name: Weber
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: 'Weber M, Sixt MK. Live Cell Imaging of Chemotactic Dendritic Cell Migration
in Explanted Mouse Ear Preparations. In: Cardona A, Ubogu E, eds. Chemokines.
Vol 1013. MIMB. Totowa, NJ: Humana Press; 2013:215-226. doi:10.1007/978-1-62703-426-5_14'
apa: 'Weber, M., & Sixt, M. K. (2013). Live Cell Imaging of Chemotactic Dendritic
Cell Migration in Explanted Mouse Ear Preparations. In A. Cardona & E. Ubogu
(Eds.), Chemokines (Vol. 1013, pp. 215–226). Totowa, NJ: Humana Press.
https://doi.org/10.1007/978-1-62703-426-5_14'
chicago: 'Weber, Michele, and Michael K Sixt. “Live Cell Imaging of Chemotactic
Dendritic Cell Migration in Explanted Mouse Ear Preparations.” In Chemokines,
edited by Astrid Cardona and Eroboghene Ubogu, 1013:215–26. MIMB. Totowa, NJ:
Humana Press, 2013. https://doi.org/10.1007/978-1-62703-426-5_14.'
ieee: 'M. Weber and M. K. Sixt, “Live Cell Imaging of Chemotactic Dendritic Cell
Migration in Explanted Mouse Ear Preparations,” in Chemokines, vol. 1013,
A. Cardona and E. Ubogu, Eds. Totowa, NJ: Humana Press, 2013, pp. 215–226.'
ista: 'Weber M, Sixt MK. 2013.Live Cell Imaging of Chemotactic Dendritic Cell Migration
in Explanted Mouse Ear Preparations. In: Chemokines. Methods in Molecular Biology,
vol. 1013, 215–226.'
mla: Weber, Michele, and Michael K. Sixt. “Live Cell Imaging of Chemotactic Dendritic
Cell Migration in Explanted Mouse Ear Preparations.” Chemokines, edited
by Astrid Cardona and Eroboghene Ubogu, vol. 1013, Humana Press, 2013, pp. 215–26,
doi:10.1007/978-1-62703-426-5_14.
short: M. Weber, M.K. Sixt, in:, A. Cardona, E. Ubogu (Eds.), Chemokines, Humana
Press, Totowa, NJ, 2013, pp. 215–226.
corr_author: '1'
date_created: 2022-03-21T07:47:41Z
date_published: 2013-04-03T00:00:00Z
date_updated: 2024-10-09T21:02:37Z
day: '03'
department:
- _id: MiSi
doi: 10.1007/978-1-62703-426-5_14
editor:
- first_name: Astrid
full_name: Cardona, Astrid
last_name: Cardona
- first_name: Eroboghene
full_name: Ubogu, Eroboghene
last_name: Ubogu
external_id:
pmid:
- '23625502'
intvolume: ' 1013'
language:
- iso: eng
month: '04'
oa_version: None
page: 215-226
place: Totowa, NJ
pmid: 1
publication: Chemokines
publication_identifier:
eisbn:
- '9781627034265'
eissn:
- 1940-6029
isbn:
- '9781627034258'
issn:
- 1064-3745
publication_status: published
publisher: Humana Press
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse
Ear Preparations
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 1013
year: '2013'
...
---
_id: '10902'
abstract:
- lang: eng
text: We consider how to edit strings from a source language so that the edited
strings belong to a target language, where the languages are given as deterministic
finite automata. Non-streaming (or offline) transducers perform edits given the
whole source string. We show that the class of deterministic one-pass transducers
with registers along with increment and min operation suffices for computing optimal
edit distance, whereas the same class of transducers without the min operation
is not sufficient. Streaming (or online) transducers perform edits as the letters
of the source string are received. We present a polynomial time algorithm for
the partial-repair problem that given a bound α asks for the construction of a
deterministic streaming transducer (if one exists) that ensures that the ‘maximum
fraction’ η of the strings of the source language are edited, within cost α, to
the target language.
acknowledgement: 'The research was supported by Austrian Science Fund (FWF) Grant
No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph
Games), and Microsoft faculty fellows award. Thanks to Gabriele Puppis for suggesting
the problem of identifying a deterministic transducer to compute the optimal cost,
and to Martin Chmelik for his comments on the introduction.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Siddhesh
full_name: Chaubal, Siddhesh
last_name: Chaubal
- first_name: Sasha
full_name: Rubin, Sasha
id: 2EC51194-F248-11E8-B48F-1D18A9856A87
last_name: Rubin
citation:
ama: 'Chatterjee K, Chaubal S, Rubin S. How to travel between languages. In: 7th
International Conference on Language and Automata Theory and Applications.
Vol 7810. LNCS. Berlin, Heidelberg: Springer Nature; 2013:214-225. doi:10.1007/978-3-642-37064-9_20'
apa: 'Chatterjee, K., Chaubal, S., & Rubin, S. (2013). How to travel between
languages. In 7th International Conference on Language and Automata Theory
and Applications (Vol. 7810, pp. 214–225). Berlin, Heidelberg: Springer Nature.
https://doi.org/10.1007/978-3-642-37064-9_20'
chicago: 'Chatterjee, Krishnendu, Siddhesh Chaubal, and Sasha Rubin. “How to Travel
between Languages.” In 7th International Conference on Language and Automata
Theory and Applications, 7810:214–25. LNCS. Berlin, Heidelberg: Springer Nature,
2013. https://doi.org/10.1007/978-3-642-37064-9_20.'
ieee: K. Chatterjee, S. Chaubal, and S. Rubin, “How to travel between languages,”
in 7th International Conference on Language and Automata Theory and Applications,
Bilbao, Spain, 2013, vol. 7810, pp. 214–225.
ista: 'Chatterjee K, Chaubal S, Rubin S. 2013. How to travel between languages.
7th International Conference on Language and Automata Theory and Applications.
LATA: Language and Automata Theory and ApplicationsLNCS, LNCS, vol. 7810, 214–225.'
mla: Chatterjee, Krishnendu, et al. “How to Travel between Languages.” 7th International
Conference on Language and Automata Theory and Applications, vol. 7810, Springer
Nature, 2013, pp. 214–25, doi:10.1007/978-3-642-37064-9_20.
short: K. Chatterjee, S. Chaubal, S. Rubin, in:, 7th International Conference on
Language and Automata Theory and Applications, Springer Nature, Berlin, Heidelberg,
2013, pp. 214–225.
conference:
end_date: 2013-04-05
location: Bilbao, Spain
name: 'LATA: Language and Automata Theory and Applications'
start_date: 2013-04-02
corr_author: '1'
date_created: 2022-03-21T07:56:21Z
date_published: 2013-04-15T00:00:00Z
date_updated: 2025-07-10T11:50:03Z
day: '15'
department:
- _id: KrCh
doi: 10.1007/978-3-642-37064-9_20
ec_funded: 1
intvolume: ' 7810'
language:
- iso: eng
month: '04'
oa_version: None
page: 214-225
place: Berlin, Heidelberg
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: 7th International Conference on Language and Automata Theory and Applications
publication_identifier:
eisbn:
- '9783642370649'
eissn:
- 1611-3349
isbn:
- '9783642370632'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: How to travel between languages
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7810
year: '2013'
...
---
_id: '11083'
abstract:
- lang: eng
text: Nuclear pore complex (NPC) proteins are known for their critical roles in
regulating nucleocytoplasmic traffic of macromolecules across the nuclear envelope.
However, recent findings suggest that some nucleoporins (Nups), including Nup98,
have additional functions in developmental gene regulation. Nup98, which exhibits
transcription-dependent mobility at the NPC but can also bind chromatin away from
the nuclear envelope, is frequently involved in chromosomal translocations in
a subset of patients suffering from acute myeloid leukemia (AML). A common paradigm
suggests that Nup98 translocations cause aberrant transcription when they are
recuited to aberrant genomic loci. Importantly, this model fails to account for
the potential loss of wild type (WT) Nup98 function in the presence of Nup98 translocation
mutants. Here we examine how the cell might regulate Nup98 nucleoplasmic protein
levels to control transcription in healthy cells. In addition, we discuss the
possibility that dominant negative Nup98 fusion proteins disrupt the transcriptional
activity of WT Nup98 in the nucleoplasm to drive AML.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Tobias M.
full_name: Franks, Tobias M.
last_name: Franks
- 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: Franks TM, Hetzer M. The role of Nup98 in transcription regulation in healthy
and diseased cells. Trends in Cell Biology. 2013;23(3):112-117. doi:10.1016/j.tcb.2012.10.013
apa: Franks, T. M., & Hetzer, M. (2013). The role of Nup98 in transcription
regulation in healthy and diseased cells. Trends in Cell Biology. Elsevier.
https://doi.org/10.1016/j.tcb.2012.10.013
chicago: Franks, Tobias M., and Martin Hetzer. “The Role of Nup98 in Transcription
Regulation in Healthy and Diseased Cells.” Trends in Cell Biology. Elsevier,
2013. https://doi.org/10.1016/j.tcb.2012.10.013.
ieee: T. M. Franks and M. Hetzer, “The role of Nup98 in transcription regulation
in healthy and diseased cells,” Trends in Cell Biology, vol. 23, no. 3.
Elsevier, pp. 112–117, 2013.
ista: Franks TM, Hetzer M. 2013. The role of Nup98 in transcription regulation in
healthy and diseased cells. Trends in Cell Biology. 23(3), 112–117.
mla: Franks, Tobias M., and Martin Hetzer. “The Role of Nup98 in Transcription Regulation
in Healthy and Diseased Cells.” Trends in Cell Biology, vol. 23, no. 3,
Elsevier, 2013, pp. 112–17, doi:10.1016/j.tcb.2012.10.013.
short: T.M. Franks, M. Hetzer, Trends in Cell Biology 23 (2013) 112–117.
date_created: 2022-04-07T07:50:33Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2024-10-14T11:23:44Z
day: '01'
doi: 10.1016/j.tcb.2012.10.013
extern: '1'
external_id:
pmid:
- '23246429'
intvolume: ' 23'
issue: '3'
keyword:
- Cell Biology
language:
- iso: eng
month: '03'
oa_version: None
page: 112-117
pmid: 1
publication: Trends in Cell Biology
publication_identifier:
issn:
- 0962-8924
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The role of Nup98 in transcription regulation in healthy and diseased cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2013'
...
---
_id: '11084'
abstract:
- lang: eng
text: Protein turnover is an effective way of maintaining a functional proteome,
as old and potentially damaged polypeptides are destroyed and replaced by newly
synthesized copies. An increasing number of intracellular proteins, however, have
been identified that evade this turnover process and instead are maintained over
a cell's lifetime. This diverse group of long-lived proteins might be particularly
prone to accumulation of damage and thus have a crucial role in the functional
deterioration of key regulatory processes during ageing.
article_processing_charge: No
article_type: original
author:
- first_name: Brandon H.
full_name: Toyama, Brandon H.
last_name: Toyama
- 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: 'Toyama BH, Hetzer M. Protein homeostasis: Live long, won’t prosper. Nature
Reviews Molecular Cell Biology. 2013;14:55-61. doi:10.1038/nrm3496'
apa: 'Toyama, B. H., & Hetzer, M. (2013). Protein homeostasis: Live long, won’t
prosper. Nature Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/nrm3496'
chicago: 'Toyama, Brandon H., and Martin Hetzer. “Protein Homeostasis: Live Long,
Won’t Prosper.” Nature Reviews Molecular Cell Biology. Springer Nature,
2013. https://doi.org/10.1038/nrm3496.'
ieee: 'B. H. Toyama and M. Hetzer, “Protein homeostasis: Live long, won’t prosper,”
Nature Reviews Molecular Cell Biology, vol. 14. Springer Nature, pp. 55–61,
2013.'
ista: 'Toyama BH, Hetzer M. 2013. Protein homeostasis: Live long, won’t prosper.
Nature Reviews Molecular Cell Biology. 14, 55–61.'
mla: 'Toyama, Brandon H., and Martin Hetzer. “Protein Homeostasis: Live Long, Won’t
Prosper.” Nature Reviews Molecular Cell Biology, vol. 14, Springer Nature,
2013, pp. 55–61, doi:10.1038/nrm3496.'
short: B.H. Toyama, M. Hetzer, Nature Reviews Molecular Cell Biology 14 (2013) 55–61.
date_created: 2022-04-07T07:50:43Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2024-10-14T11:24:09Z
day: '01'
doi: 10.1038/nrm3496
extern: '1'
external_id:
pmid:
- '23258296'
intvolume: ' 14'
keyword:
- Cell Biology
- Molecular Biology
language:
- iso: eng
month: '01'
oa_version: None
page: 55-61
pmid: 1
publication: Nature Reviews Molecular Cell Biology
publication_identifier:
issn:
- 1471-0072
- 1471-0080
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Protein homeostasis: Live long, won''t prosper'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2013'
...
---
_id: '11085'
abstract:
- lang: eng
text: During mitotic exit, missegregated chromosomes can recruit their own nuclear
envelope (NE) to form micronuclei (MN). MN have reduced functioning compared to
primary nuclei in the same cell, although the two compartments appear to be structurally
comparable. Here we show that over 60% of MN undergo an irreversible loss of compartmentalization
during interphase due to NE collapse. This disruption of the MN, which is induced
by defects in nuclear lamina assembly, drastically reduces nuclear functions and
can trigger massive DNA damage. MN disruption is associated with chromatin compaction
and invasion of endoplasmic reticulum (ER) tubules into the chromatin. We identified
disrupted MN in both major subtypes of human non-small-cell lung cancer, suggesting
that disrupted MN could be a useful objective biomarker for genomic instability
in solid tumors. Our study shows that NE collapse is a key event underlying MN
dysfunction and establishes a link between aberrant NE organization and aneuploidy.
article_processing_charge: No
article_type: original
author:
- first_name: Emily M.
full_name: Hatch, Emily M.
last_name: Hatch
- first_name: Andrew H.
full_name: Fischer, Andrew H.
last_name: Fischer
- first_name: Thomas J.
full_name: Deerinck, Thomas J.
last_name: Deerinck
- 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 EM, Fischer AH, Deerinck TJ, Hetzer M. Catastrophic nuclear envelope
collapse in cancer cell micronuclei. Cell. 2013;154(1):47-60. doi:10.1016/j.cell.2013.06.007
apa: Hatch, E. M., Fischer, A. H., Deerinck, T. J., & Hetzer, M. (2013). Catastrophic
nuclear envelope collapse in cancer cell micronuclei. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.06.007
chicago: Hatch, Emily M., Andrew H. Fischer, Thomas J. Deerinck, and Martin Hetzer.
“Catastrophic Nuclear Envelope Collapse in Cancer Cell Micronuclei.” Cell.
Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.06.007.
ieee: E. M. Hatch, A. H. Fischer, T. J. Deerinck, and M. Hetzer, “Catastrophic nuclear
envelope collapse in cancer cell micronuclei,” Cell, vol. 154, no. 1. Elsevier,
pp. 47–60, 2013.
ista: Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. 2013. Catastrophic nuclear envelope
collapse in cancer cell micronuclei. Cell. 154(1), 47–60.
mla: Hatch, Emily M., et al. “Catastrophic Nuclear Envelope Collapse in Cancer Cell
Micronuclei.” Cell, vol. 154, no. 1, Elsevier, 2013, pp. 47–60, doi:10.1016/j.cell.2013.06.007.
short: E.M. Hatch, A.H. Fischer, T.J. Deerinck, M. Hetzer, Cell 154 (2013) 47–60.
date_created: 2022-04-07T07:50:51Z
date_published: 2013-07-03T00:00:00Z
date_updated: 2024-10-14T11:24:29Z
day: '03'
doi: 10.1016/j.cell.2013.06.007
extern: '1'
external_id:
pmid:
- '23827674'
intvolume: ' 154'
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2013.06.007
month: '07'
oa: 1
oa_version: Published Version
page: 47-60
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Catastrophic nuclear envelope collapse in cancer cell micronuclei
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 154
year: '2013'
...
---
_id: '11086'
abstract:
- lang: eng
text: Faithful execution of developmental gene expression programs occurs at multiple
levels and involves many different components such as transcription factors, histone-modification
enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins,
well known components that control nucleo-cytoplasmic trafficking, have wide-ranging
functions in developmental gene regulation that potentially extend beyond their
role in nuclear transport. Whether the unexpected role of nuclear pore proteins
in transcription regulation, which initially has been described in fungi and flies,
also applies to human cells is unknown. Here we show at a genome-wide level that
the nuclear pore protein NUP98 associates with developmentally regulated genes
active during human embryonic stem cell differentiation. Overexpression of a dominant
negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes.
In addition, we identify two modes of developmental gene regulation by NUP98 that
are differentiated by the spatial localization of NUP98 target genes. Genes in
the initial stage of developmental induction can associate with NUP98 that is
embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that
are highly induced can interact with NUP98 in the nuclear interior, away from
the nuclear pores. This work demonstrates for the first time that NUP98 dynamically
associates with the human genome during differentiation, revealing a role of a
nuclear pore protein in regulating developmental gene expression programs.
article_number: e1003308
article_processing_charge: No
article_type: original
author:
- first_name: Yun
full_name: Liang, Yun
last_name: Liang
- first_name: Tobias M.
full_name: Franks, Tobias M.
last_name: Franks
- first_name: Maria C.
full_name: Marchetto, Maria C.
last_name: Marchetto
- first_name: Fred H.
full_name: Gage, Fred H.
last_name: Gage
- 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: Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. Dynamic association of
NUP98 with the human genome. PLoS Genetics. 2013;9(2). doi:10.1371/journal.pgen.1003308
apa: Liang, Y., Franks, T. M., Marchetto, M. C., Gage, F. H., & Hetzer, M. (2013).
Dynamic association of NUP98 with the human genome. PLoS Genetics. Public
Library of Science. https://doi.org/10.1371/journal.pgen.1003308
chicago: Liang, Yun, Tobias M. Franks, Maria C. Marchetto, Fred H. Gage, and Martin
Hetzer. “Dynamic Association of NUP98 with the Human Genome.” PLoS Genetics.
Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003308.
ieee: Y. Liang, T. M. Franks, M. C. Marchetto, F. H. Gage, and M. Hetzer, “Dynamic
association of NUP98 with the human genome,” PLoS Genetics, vol. 9, no.
2. Public Library of Science, 2013.
ista: Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. 2013. Dynamic association
of NUP98 with the human genome. PLoS Genetics. 9(2), e1003308.
mla: Liang, Yun, et al. “Dynamic Association of NUP98 with the Human Genome.” PLoS
Genetics, vol. 9, no. 2, e1003308, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003308.
short: Y. Liang, T.M. Franks, M.C. Marchetto, F.H. Gage, M. Hetzer, PLoS Genetics
9 (2013).
date_created: 2022-04-07T07:50:59Z
date_published: 2013-02-28T00:00:00Z
date_updated: 2024-10-14T11:24:40Z
day: '28'
doi: 10.1371/journal.pgen.1003308
extern: '1'
external_id:
pmid:
- '23468646'
intvolume: ' 9'
issue: '2'
keyword:
- Cancer Research
- Genetics (clinical)
- Genetics
- Molecular Biology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pgen.1003308
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic association of NUP98 with the human genome
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '11087'
abstract:
- lang: eng
text: Intracellular proteins with long lifespans have recently been linked to age-dependent
defects, ranging from decreased fertility to the functional decline of neurons.
Why long-lived proteins exist in metabolically active cellular environments and
how they are maintained over time remains poorly understood. Here, we provide
a system-wide identification of proteins with exceptional lifespans in the rat
brain. These proteins are inefficiently replenished despite being translated robustly
throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence,
we found that nuclear pore complexes (NPCs) are maintained over a cell’s life
through slow but finite exchange of even its most stable subcomplexes. This maintenance
is limited, however, as some nucleoporin levels decrease during aging, providing
a rationale for the previously observed age-dependent deterioration of NPC function.
Our identification of a long-lived proteome reveals cellular components that are
at increased risk for damage accumulation, linking long-term protein persistence
to the cellular aging process.
article_processing_charge: No
article_type: original
author:
- first_name: Brandon H.
full_name: Toyama, Brandon H.
last_name: Toyama
- first_name: Jeffrey N.
full_name: Savas, Jeffrey N.
last_name: Savas
- first_name: Sung Kyu
full_name: Park, Sung Kyu
last_name: Park
- first_name: Michael S.
full_name: Harris, Michael S.
last_name: Harris
- first_name: Nicholas T.
full_name: Ingolia, Nicholas T.
last_name: Ingolia
- first_name: John R.
full_name: Yates, John R.
last_name: Yates
- 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: Toyama BH, Savas JN, Park SK, et al. Identification of long-lived proteins
reveals exceptional stability of essential cellular structures. Cell. 2013;154(5):971-982.
doi:10.1016/j.cell.2013.07.037
apa: Toyama, B. H., Savas, J. N., Park, S. K., Harris, M. S., Ingolia, N. T., Yates,
J. R., & Hetzer, M. (2013). Identification of long-lived proteins reveals
exceptional stability of essential cellular structures. Cell. Elsevier.
https://doi.org/10.1016/j.cell.2013.07.037
chicago: Toyama, Brandon H., Jeffrey N. Savas, Sung Kyu Park, Michael S. Harris,
Nicholas T. Ingolia, John R. Yates, and Martin Hetzer. “Identification of Long-Lived
Proteins Reveals Exceptional Stability of Essential Cellular Structures.” Cell.
Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.07.037.
ieee: B. H. Toyama et al., “Identification of long-lived proteins reveals
exceptional stability of essential cellular structures,” Cell, vol. 154,
no. 5. Elsevier, pp. 971–982, 2013.
ista: Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, Yates JR, Hetzer M. 2013.
Identification of long-lived proteins reveals exceptional stability of essential
cellular structures. Cell. 154(5), 971–982.
mla: Toyama, Brandon H., et al. “Identification of Long-Lived Proteins Reveals Exceptional
Stability of Essential Cellular Structures.” Cell, vol. 154, no. 5, Elsevier,
2013, pp. 971–82, doi:10.1016/j.cell.2013.07.037.
short: B.H. Toyama, J.N. Savas, S.K. Park, M.S. Harris, N.T. Ingolia, J.R. Yates,
M. Hetzer, Cell 154 (2013) 971–982.
date_created: 2022-04-07T07:51:08Z
date_published: 2013-08-29T00:00:00Z
date_updated: 2025-12-15T10:02:46Z
day: '29'
department:
- _id: MaHe
doi: 10.1016/j.cell.2013.07.037
extern: '1'
external_id:
pmid:
- '23993091'
intvolume: ' 154'
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.2013.07.037
month: '08'
oa: 1
oa_version: Published Version
page: 971-982
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Identification of long-lived proteins reveals exceptional stability of essential
cellular structures
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 154
year: '2013'
...