---
_id: '5377'
abstract:
- lang: eng
text: 'Two-player games on graphs are central in many problems in formal verification
and program analysis such as synthesis and verification of open systems. In this
work we consider solving recursive game graphs (or pushdown game graphs) that
can model the control flow of sequential programs with recursion. While pushdown
games have been studied before with qualitative objectives, such as reachability
and ω-regular objectives, in this work we study for the first time such games
with the most well-studied quantitative objective, namely, mean-payoff objectives.
In pushdown games two types of strategies are relevant: (1) global strategies,
that depend on the entire global history; and (2) modular strategies, that have
only local memory and thus do not depend on the context of invocation, but only
on the history of the current invocation of the module. Our main results are as
follows: (1) One-player pushdown games with mean-payoff objectives under global
strategies are decidable in polynomial time. (2) Two- player pushdown games with
mean-payoff objectives under global strategies are undecidable. (3) One-player
pushdown games with mean-payoff objectives under modular strategies are NP- hard.
(4) Two-player pushdown games with mean-payoff objectives under modular strategies
can be solved in NP (i.e., both one-player and two-player pushdown games with
mean-payoff objectives under modular strategies are NP-complete). We also establish
the optimal strategy complexity showing that global strategies for mean-payoff
objectives require infinite memory even in one-player pushdown games; and memoryless
modular strategies are sufficient in two- player pushdown games. Finally we also
show that all the problems have the same complexity if the stack boundedness condition
is added, where along with the mean-payoff objective the player must also ensure
that the stack height is bounded.'
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: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Velner Y. Mean-Payoff Pushdown Games. IST Austria; 2012.
doi:10.15479/AT:IST-2012-0002
apa: Chatterjee, K., & Velner, Y. (2012). Mean-payoff pushdown games.
IST Austria. https://doi.org/10.15479/AT:IST-2012-0002
chicago: Chatterjee, Krishnendu, and Yaron Velner. Mean-Payoff Pushdown Games.
IST Austria, 2012. https://doi.org/10.15479/AT:IST-2012-0002.
ieee: K. Chatterjee and Y. Velner, Mean-payoff pushdown games. IST Austria,
2012.
ista: Chatterjee K, Velner Y. 2012. Mean-payoff pushdown games, IST Austria, 33p.
mla: Chatterjee, Krishnendu, and Yaron Velner. Mean-Payoff Pushdown Games.
IST Austria, 2012, doi:10.15479/AT:IST-2012-0002.
short: K. Chatterjee, Y. Velner, Mean-Payoff Pushdown Games, IST Austria, 2012.
date_created: 2018-12-12T11:38:59Z
date_published: 2012-07-02T00:00:00Z
date_updated: 2023-02-23T11:05:50Z
day: '02'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2012-0002
file:
- access_level: open_access
checksum: a03c08c1589dbb0c96183a8bcf3ab240
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:00Z
date_updated: 2020-07-14T12:46:38Z
file_id: '5522'
file_name: IST-2012-002_IST-2012-0002.pdf
file_size: 592098
relation: main_file
file_date_updated: 2020-07-14T12:46:38Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '33'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '10'
related_material:
record:
- id: '2956'
relation: later_version
status: public
status: public
title: Mean-payoff pushdown games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '5378'
abstract:
- lang: eng
text: 'One central issue in the formal design and analysis of reactive systems is
the notion of refinement that asks whether all behaviors of the implementation
is allowed by the specification. The local interpretation of behavior leads to
the notion of simulation. Alternating transition systems (ATSs) provide a general
model for composite reactive systems, and the simulation relation for ATSs is
known as alternating simulation. The simulation relation for fair transition systems
is called fair simulation. In this work our main contributions are as follows:
(1) We present an improved algorithm for fair simulation with Büchi fairness constraints;
our algorithm requires O(n3 · m) time as compared to the previous known O(n6)-time
algorithm, where n is the number of states and m is the number of transitions.
(2) We present a game based algorithm for alternating simulation that requires
O(m2)-time as compared to the previous known O((n · m)2)-time algorithm, where
n is the number of states and m is the size of transition relation. (3) We present
an iterative algorithm for alternating simulation that matches the time complexity
of the game based algorithm, but is more space efficient than the game based algorithm.'
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: Siddhesh
full_name: Chaubal, Siddhesh
last_name: Chaubal
- first_name: Pritish
full_name: Kamath, Pritish
last_name: Kamath
citation:
ama: Chatterjee K, Chaubal S, Kamath P. Faster Algorithms for Alternating Refinement
Relations. IST Austria; 2012. doi:10.15479/AT:IST-2012-0001
apa: Chatterjee, K., Chaubal, S., & Kamath, P. (2012). Faster algorithms
for alternating refinement relations. IST Austria. https://doi.org/10.15479/AT:IST-2012-0001
chicago: Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. Faster
Algorithms for Alternating Refinement Relations. IST Austria, 2012. https://doi.org/10.15479/AT:IST-2012-0001.
ieee: K. Chatterjee, S. Chaubal, and P. Kamath, Faster algorithms for alternating
refinement relations. IST Austria, 2012.
ista: Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating
refinement relations, IST Austria, 21p.
mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Alternating Refinement
Relations. IST Austria, 2012, doi:10.15479/AT:IST-2012-0001.
short: K. Chatterjee, S. Chaubal, P. Kamath, Faster Algorithms for Alternating Refinement
Relations, IST Austria, 2012.
date_created: 2018-12-12T11:38:59Z
date_published: 2012-07-04T00:00:00Z
date_updated: 2023-02-23T12:21:38Z
day: '04'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2012-0001
file:
- access_level: open_access
checksum: ec8d1857cc7095d3de5107a0162ced37
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:28Z
date_updated: 2020-07-14T12:46:39Z
file_id: '5489'
file_name: IST-2012-0001_IST-2012-0001.pdf
file_size: 394256
relation: main_file
file_date_updated: 2020-07-14T12:46:39Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '21'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '14'
related_material:
record:
- id: '497'
relation: later_version
status: public
status: public
title: Faster algorithms for alternating refinement relations
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '5396'
abstract:
- lang: eng
text: We consider the problem of inference in agraphical model with binary variables.
While in theory it is arguably preferable to compute marginal probabilities, in
practice researchers often use MAP inference due to the availability of efficient
discrete optimization algorithms. We bridge the gap between the two approaches
by introducing the Discrete Marginals technique in which approximate marginals
are obtained by minimizing an objective function with unary and pair-wise terms
over a discretized domain. This allows the use of techniques originally devel-oped
for MAP-MRF inference and learning. We explore two ways to set up the objective
function - by discretizing the Bethe free energy and by learning it from training
data. Experimental results show that for certain types of graphs a learned function
can out-perform the Bethe approximation. We also establish a link between the
Bethe free energy and submodular functions.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Filip
full_name: Korc, Filip
id: 476A2FD6-F248-11E8-B48F-1D18A9856A87
last_name: Korc
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Korc F, Kolmogorov V, Lampert C. Approximating Marginals Using Discrete
Energy Minimization. IST Austria; 2012. doi:10.15479/AT:IST-2012-0003
apa: Korc, F., Kolmogorov, V., & Lampert, C. (2012). Approximating marginals
using discrete energy minimization. IST Austria. https://doi.org/10.15479/AT:IST-2012-0003
chicago: Korc, Filip, Vladimir Kolmogorov, and Christoph Lampert. Approximating
Marginals Using Discrete Energy Minimization. IST Austria, 2012. https://doi.org/10.15479/AT:IST-2012-0003.
ieee: F. Korc, V. Kolmogorov, and C. Lampert, Approximating marginals using discrete
energy minimization. IST Austria, 2012.
ista: Korc F, Kolmogorov V, Lampert C. 2012. Approximating marginals using discrete
energy minimization, IST Austria, 13p.
mla: Korc, Filip, et al. Approximating Marginals Using Discrete Energy Minimization.
IST Austria, 2012, doi:10.15479/AT:IST-2012-0003.
short: F. Korc, V. Kolmogorov, C. Lampert, Approximating Marginals Using Discrete
Energy Minimization, IST Austria, 2012.
date_created: 2018-12-12T11:39:06Z
date_published: 2012-07-23T00:00:00Z
date_updated: 2023-02-23T11:13:22Z
day: '23'
ddc:
- '000'
department:
- _id: VlKo
- _id: ChLa
doi: 10.15479/AT:IST-2012-0003
file:
- access_level: open_access
checksum: 7e0ba85ad123b13223aaf6cdde2d288c
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:29Z
date_updated: 2020-07-14T12:46:44Z
file_id: '5490'
file_name: IST-2012-0003_IST-2012-0003.pdf
file_size: 618744
relation: main_file
file_date_updated: 2020-07-14T12:46:44Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '13'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '36'
related_material:
record:
- id: '3124'
relation: earlier_version
status: public
status: public
title: Approximating marginals using discrete energy minimization
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '5398'
abstract:
- lang: eng
text: This document is created as a part of the project “Repository for Research
Data on IST Austria”. It summarises the actual state of research data at IST Austria,
based on survey results. It supports the choice of appropriate software, which
would best fit the requirements of their users, the researchers.
author:
- first_name: Jana
full_name: Porsche, Jana
id: 3252EDC2-F248-11E8-B48F-1D18A9856A87
last_name: Porsche
citation:
ama: Porsche J. Actual State of Research Data @ ISTAustria. IST Austria;
2012.
apa: Porsche, J. (2012). Actual state of research data @ ISTAustria. IST
Austria.
chicago: Porsche, Jana. Actual State of Research Data @ ISTAustria. IST Austria,
2012.
ieee: J. Porsche, Actual state of research data @ ISTAustria. IST Austria,
2012.
ista: Porsche J. 2012. Actual state of research data @ ISTAustria, IST Austria,p.
mla: Porsche, Jana. Actual State of Research Data @ ISTAustria. IST Austria,
2012.
short: J. Porsche, Actual State of Research Data @ ISTAustria, IST Austria, 2012.
date_created: 2018-12-12T11:39:06Z
date_published: 2012-11-12T00:00:00Z
date_updated: 2020-07-14T23:04:49Z
day: '12'
ddc:
- '020'
department:
- _id: E-Lib
file:
- access_level: open_access
checksum: e0a7c041eea1ca4b70ab6f9ec5177f4e
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:11Z
date_updated: 2020-07-14T12:46:44Z
file_id: '5472'
file_name: IST-2012-103-v1+1_Actual_state_of_research_data_@_IST_Austria.pdf
file_size: 238544
relation: main_file
file_date_updated: 2020-07-14T12:46:44Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication_status: published
publisher: IST Austria
pubrep_id: '103'
status: public
title: Actual state of research data @ ISTAustria
type: report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '5745'
article_processing_charge: No
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
last_name: Gupta
citation:
ama: 'Gupta A. Improved Single Pass Algorithms for Resolution Proof Reduction. In:
Automated Technology for Verification and Analysis. Vol 7561. LNCS. Berlin,
Heidelberg: Springer Berlin Heidelberg; 2012:107-121. doi:10.1007/978-3-642-33386-6_10'
apa: 'Gupta, A. (2012). Improved Single Pass Algorithms for Resolution Proof Reduction.
In Automated Technology for Verification and Analysis (Vol. 7561, pp. 107–121).
Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-33386-6_10'
chicago: 'Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof
Reduction.” In Automated Technology for Verification and Analysis, 7561:107–21.
LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. https://doi.org/10.1007/978-3-642-33386-6_10.'
ieee: 'A. Gupta, “Improved Single Pass Algorithms for Resolution Proof Reduction,”
in Automated Technology for Verification and Analysis, vol. 7561, Berlin,
Heidelberg: Springer Berlin Heidelberg, 2012, pp. 107–121.'
ista: 'Gupta A. 2012.Improved Single Pass Algorithms for Resolution Proof Reduction.
In: Automated Technology for Verification and Analysis. vol. 7561, 107–121.'
mla: Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.”
Automated Technology for Verification and Analysis, vol. 7561, Springer
Berlin Heidelberg, 2012, pp. 107–21, doi:10.1007/978-3-642-33386-6_10.
short: A. Gupta, in:, Automated Technology for Verification and Analysis, Springer
Berlin Heidelberg, Berlin, Heidelberg, 2012, pp. 107–121.
conference:
end_date: 2012-10-06
location: Thiruvananthapuram, Kerala, India
name: ATVA 2012
start_date: 2012-10-03
date_created: 2018-12-18T13:01:46Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2023-09-05T14:15:29Z
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-33386-6_10
ec_funded: 1
file:
- access_level: open_access
checksum: 68415837a315de3cc4d120f6019d752c
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T13:07:35Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5746'
file_name: 2012_ATVA_Gupta.pdf
file_size: 465502
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 7561'
language:
- iso: eng
oa: 1
oa_version: None
page: 107-121
place: Berlin, Heidelberg
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: Automated Technology for Verification and Analysis
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783642333859'
- '9783642333866'
issn:
- 0302-9743
publication_status: published
publisher: Springer Berlin Heidelberg
pubrep_id: '180'
quality_controlled: '1'
series_title: LNCS
status: public
title: Improved Single Pass Algorithms for Resolution Proof Reduction
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7561
year: '2012'
...
---
_id: '6588'
abstract:
- lang: eng
text: First we note that the best polynomial approximation to vertical bar x vertical
bar on the set, which consists of an interval on the positive half-axis and a
point on the negative half-axis, can be given by means of the classical Chebyshev
polynomials. Then we explore the cases when a solution of the related problem
on two intervals can be given in elementary functions.
acknowledgement: "This work is supported by the Austrian Science Fund (FWF), Project
P22025-N18.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: Pausinger F. Elementary solutions of the Bernstein problem on two intervals.
Journal of Mathematical Physics, Analysis, Geometry. 2012;8(1):63-78.
apa: Pausinger, F. (2012). Elementary solutions of the Bernstein problem on two
intervals. Journal of Mathematical Physics, Analysis, Geometry. B. Verkin
Institute for Low Temperature Physics and Engineering.
chicago: Pausinger, Florian. “Elementary Solutions of the Bernstein Problem on Two
Intervals.” Journal of Mathematical Physics, Analysis, Geometry. B. Verkin
Institute for Low Temperature Physics and Engineering, 2012.
ieee: F. Pausinger, “Elementary solutions of the Bernstein problem on two intervals,”
Journal of Mathematical Physics, Analysis, Geometry, vol. 8, no. 1. B.
Verkin Institute for Low Temperature Physics and Engineering, pp. 63–78, 2012.
ista: Pausinger F. 2012. Elementary solutions of the Bernstein problem on two intervals.
Journal of Mathematical Physics, Analysis, Geometry. 8(1), 63–78.
mla: Pausinger, Florian. “Elementary Solutions of the Bernstein Problem on Two Intervals.”
Journal of Mathematical Physics, Analysis, Geometry, vol. 8, no. 1, B.
Verkin Institute for Low Temperature Physics and Engineering, 2012, pp. 63–78.
short: F. Pausinger, Journal of Mathematical Physics, Analysis, Geometry 8 (2012)
63–78.
date_created: 2019-06-27T08:16:56Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2023-10-16T09:41:31Z
day: '01'
department:
- _id: HeEd
external_id:
isi:
- '000301173600004'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://mi.mathnet.ru/eng/jmag525
month: '01'
oa: 1
oa_version: Published Version
page: 63-78
publication: Journal of Mathematical Physics, Analysis, Geometry
publication_identifier:
issn:
- 1812-9471
publication_status: published
publisher: B. Verkin Institute for Low Temperature Physics and Engineering
quality_controlled: '1'
scopus_import: '1'
status: public
title: Elementary solutions of the Bernstein problem on two intervals
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2012'
...
---
_id: '13075'
abstract:
- lang: eng
text: Little is known about the stability of trophic relationships in complex natural
communities over evolutionary timescales. Here, we use sequence data from 18 nuclear
loci to reconstruct and compare the intraspecific histories of major Pleistocene
refugial populations in the Middle East, the Balkans and Iberia in a guild of
four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota
and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood
method to numerically estimate models of divergence between three populations
from multilocus data. We investigate the power of this framework on simulated
data, and - using triplet alignments of intronic loci - quantify the support for
all possible divergence relationships between refugial populations in the four
parasitoids. Although an East to West order of population divergence has highest
support in all but one species, we cannot rule out alternative population tree
topologies. Comparing the estimated times of population splits between species,
we find that one species, M. amaenus, has a significantly older history than the
rest of the guild and must have arrived in central Europe at least one glacial
cycle prior to other guild members. This suggests that although all four species
may share a common origin in the East, they expanded westwards into Europe at
different times.
article_processing_charge: No
author:
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
- first_name: George
full_name: Melika, George
last_name: Melika
citation:
ama: 'Lohse K, Barton NH, Stone G, Melika G. Data from: A likelihood-based comparison
of population histories in a parasitoid guild. 2012. doi:10.5061/DRYAD.0G0FS'
apa: 'Lohse, K., Barton, N. H., Stone, G., & Melika, G. (2012). Data from: A
likelihood-based comparison of population histories in a parasitoid guild. Dryad.
https://doi.org/10.5061/DRYAD.0G0FS'
chicago: 'Lohse, Konrad, Nicholas H Barton, Graham Stone, and George Melika. “Data
from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild.”
Dryad, 2012. https://doi.org/10.5061/DRYAD.0G0FS.'
ieee: 'K. Lohse, N. H. Barton, G. Stone, and G. Melika, “Data from: A likelihood-based
comparison of population histories in a parasitoid guild.” Dryad, 2012.'
ista: 'Lohse K, Barton NH, Stone G, Melika G. 2012. Data from: A likelihood-based
comparison of population histories in a parasitoid guild, Dryad, 10.5061/DRYAD.0G0FS.'
mla: 'Lohse, Konrad, et al. Data from: A Likelihood-Based Comparison of Population
Histories in a Parasitoid Guild. Dryad, 2012, doi:10.5061/DRYAD.0G0FS.'
short: K. Lohse, N.H. Barton, G. Stone, G. Melika, (2012).
date_created: 2023-05-23T17:01:02Z
date_published: 2012-06-08T00:00:00Z
date_updated: 2025-05-28T11:56:58Z
day: '08'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.0G0FS
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.0g0fs
month: '06'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2968'
relation: used_in_publication
status: public
status: public
title: 'Data from: A likelihood-based comparison of population histories in a parasitoid
guild'
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_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '1384'
abstract:
- lang: eng
text: 'Software model checking, as an undecidable problem, has three possible outcomes:
(1) the program satisfies the specification, (2) the program does not satisfy
the specification, and (3) the model checker fails. The third outcome usually
manifests itself in a space-out, time-out, or one component of the verification
tool giving up; in all of these failing cases, significant computation is performed
by the verification tool before the failure, but no result is reported. We propose
to reformulate the model-checking problem as follows, in order to have the verification
tool report a summary of the performed work even in case of failure: given a program
and a specification, the model checker returns a condition Ψ - usually a state
predicate - such that the program satisfies the specification under the condition
Ψ - that is, as long as the program does not leave the states in which Ψ is satisfied.
In our experiments, we investigated as one major application of conditional model
checking the sequential combination of model checkers with information passing.
We give the condition that one model checker produces, as input to a second conditional
model checker, such that the verification problem for the second is restricted
to the part of the state space that is not covered by the condition, i.e., the
second model checker works on the problems that the first model checker could
not solve. Our experiments demonstrate that repeated application of conditional
model checkers, passing information from one model checker to the next, can significantly
improve the verification results and performance, i.e., we can now verify programs
that we could not verify before.'
acknowledgement: This research was supported by the Canadian NSERC grant RGPIN 341819-07, the ERC Advanced Grant
QUAREM, and the Austrian Science Fund NFN RiSE.
article_number: '57'
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- 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: Mehmet
full_name: Keremoglu, Mehmet
last_name: Keremoglu
- first_name: Philipp
full_name: Wendler, Philipp
last_name: Wendler
citation:
ama: 'Beyer D, Henzinger TA, Keremoglu M, Wendler P. Conditional model checking:
A technique to pass information between verifiers. In: Proceedings of the ACM
SIGSOFT 20th International Symposium on the Foundations of Software Engineering.
ACM; 2012. doi:10.1145/2393596.2393664'
apa: 'Beyer, D., Henzinger, T. A., Keremoglu, M., & Wendler, P. (2012). Conditional
model checking: A technique to pass information between verifiers. In Proceedings
of the ACM SIGSOFT 20th International Symposium on the Foundations of Software
Engineering. Cary, NC, USA: ACM. https://doi.org/10.1145/2393596.2393664'
chicago: 'Beyer, Dirk, Thomas A Henzinger, Mehmet Keremoglu, and Philipp Wendler.
“Conditional Model Checking: A Technique to Pass Information between Verifiers.”
In Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations
of Software Engineering. ACM, 2012. https://doi.org/10.1145/2393596.2393664.'
ieee: 'D. Beyer, T. A. Henzinger, M. Keremoglu, and P. Wendler, “Conditional model
checking: A technique to pass information between verifiers,” in Proceedings
of the ACM SIGSOFT 20th International Symposium on the Foundations of Software
Engineering, Cary, NC, USA, 2012.'
ista: 'Beyer D, Henzinger TA, Keremoglu M, Wendler P. 2012. Conditional model checking:
A technique to pass information between verifiers. Proceedings of the ACM SIGSOFT
20th International Symposium on the Foundations of Software Engineering. FSE:
Foundations of Software Engineering, 57.'
mla: 'Beyer, Dirk, et al. “Conditional Model Checking: A Technique to Pass Information
between Verifiers.” Proceedings of the ACM SIGSOFT 20th International Symposium
on the Foundations of Software Engineering, 57, ACM, 2012, doi:10.1145/2393596.2393664.'
short: D. Beyer, T.A. Henzinger, M. Keremoglu, P. Wendler, in:, Proceedings of the
ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering,
ACM, 2012.
conference:
end_date: 2012-11-16
location: Cary, NC, USA
name: 'FSE: Foundations of Software Engineering'
start_date: 2012-11-11
date_created: 2018-12-11T11:51:42Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2021-01-12T06:50:18Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/2393596.2393664
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1109.6926
month: '11'
oa: 1
oa_version: Preprint
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 ACM SIGSOFT 20th International Symposium on the Foundations
of Software Engineering
publication_status: published
publisher: ACM
publist_id: '5826'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Conditional model checking: A technique to pass information between verifiers'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '9451'
abstract:
- lang: eng
text: The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes
DNA demethylation before fertilization, but the targeting preferences, mechanism,
and biological significance of this process remain unclear. Here, we show that
active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for
all of the demethylation in the central cell and preferentially targets small,
AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative
cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation
of similar sequences, and lack of DEMETER in vegetative cells causes reduced small
RNA–directed DNA methylation of transposons in sperm. Our results demonstrate
that demethylation in companion cells reinforces transposon methylation in plant
gametes and likely contributes to stable silencing of transposable elements across
generations.
article_processing_charge: No
article_type: original
author:
- first_name: Christian A.
full_name: Ibarra, Christian A.
last_name: Ibarra
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
last_name: Feng
- first_name: Vera K.
full_name: Schoft, Vera K.
last_name: Schoft
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Rie
full_name: Uzawa, Rie
last_name: Uzawa
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Nina
full_name: Chumak, Nina
last_name: Chumak
- first_name: Adriana
full_name: Machlicova, Adriana
last_name: Machlicova
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Denisse
full_name: Rojas, Denisse
last_name: Rojas
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Hisashi
full_name: Tamaru, Hisashi
last_name: Tamaru
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion
cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364.
doi:10.1126/science.1224839
apa: Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues,
J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells
reinforces transposon methylation in gametes. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.1224839
chicago: Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie
Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in
Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science.
American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839.
ieee: C. A. Ibarra et al., “Active DNA demethylation in plant companion cells
reinforces transposon methylation in gametes,” Science, vol. 337, no. 6100.
American Association for the Advancement of Science, pp. 1360–1364, 2012.
ista: Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A,
Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman
D. 2012. Active DNA demethylation in plant companion cells reinforces transposon
methylation in gametes. Science. 337(6100), 1360–1364.
mla: Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells
Reinforces Transposon Methylation in Gametes.” Science, vol. 337, no. 6100,
American Association for the Advancement of Science, 2012, pp. 1360–64, doi:10.1126/science.1224839.
short: C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues,
A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H.
Tamaru, D. Zilberman, Science 337 (2012) 1360–1364.
date_created: 2021-06-04T07:51:31Z
date_published: 2012-09-14T00:00:00Z
date_updated: 2021-12-14T08:28:51Z
day: '14'
ddc:
- '580'
department:
- _id: DaZi
doi: 10.1126/science.1224839
extern: '1'
external_id:
pmid:
- '22984074'
has_accepted_license: '1'
intvolume: ' 337'
issue: '6100'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/
month: '09'
oa: 1
oa_version: Published Version
page: 1360-1364
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Active DNA demethylation in plant companion cells reinforces transposon methylation
in gametes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 337
year: '2012'
...
---
_id: '9497'
abstract:
- lang: eng
text: The regulation of eukaryotic chromatin relies on interactions between many
epigenetic factors, including histone modifications, DNA methylation, and the
incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic
histone variants that is enriched at the transcriptional start sites of genes,
has been implicated in a variety of chromosomal processes. Recently, we reported
a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic
hallmark of heterochromatin that has also been found in the bodies of active genes
in plants and animals. Here, we investigate the basis of this anticorrelation
using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide
bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only
a minor effect on the level or profile of DNA methylation in genes, and we propose
that the global anticorrelation between DNA methylation and H2A.Z is primarily
caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic
mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at
the TSS, is correlated with lower transcription levels and higher measures of
gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are
disproportionately associated with response to environmental and developmental
stimuli. We propose that H2A.Z deposition in gene bodies promotes variability
in levels and patterns of gene expression, and that a major function of genic
DNA methylation is to exclude H2A.Z from constitutively expressed genes.
article_number: e1002988
article_processing_charge: No
article_type: original
author:
- first_name: Devin
full_name: Coleman-Derr, Devin
last_name: Coleman-Derr
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene
bodies regulates responsive genes. PLoS Genetics. 2012;8(10). doi:10.1371/journal.pgen.1002988
apa: Coleman-Derr, D., & Zilberman, D. (2012). Deposition of histone variant
H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. Public
Library of Science. https://doi.org/10.1371/journal.pgen.1002988
chicago: Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant
H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics. Public
Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002988.
ieee: D. Coleman-Derr and D. Zilberman, “Deposition of histone variant H2A.Z within
gene bodies regulates responsive genes,” PLoS Genetics, vol. 8, no. 10.
Public Library of Science, 2012.
ista: Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within
gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988.
mla: Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z
within Gene Bodies Regulates Responsive Genes.” PLoS Genetics, vol. 8,
no. 10, e1002988, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002988.
short: D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012).
date_created: 2021-06-07T10:55:27Z
date_published: 2012-10-11T00:00:00Z
date_updated: 2021-12-14T08:29:57Z
day: '11'
department:
- _id: DaZi
doi: 10.1371/journal.pgen.1002988
extern: '1'
external_id:
pmid:
- '23071449'
intvolume: ' 8'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pgen.1002988
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
eissn:
- 1553-7404
issn:
- 1553-7390
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Deposition of histone variant H2A.Z within gene bodies regulates responsive
genes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 8
year: '2012'
...
---
_id: '9499'
abstract:
- lang: eng
text: EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative
development. Loss of function mutants in the EMF1 gene mimic the phenotype caused
by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors
that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb
Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of
lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination.
Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with
known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the
EMF1 functions and its mechanism of action, we performed genome-wide mapping of
EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1
binding pattern is similar to that of H3K27me3 modification on the chromosomal
and genic level. ChIPOTLe peak finding and clustering analyses both show that
the highly trimethylated genes also have high enrichment levels of EMF1 binding,
termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced
to allow vegetative growth, and with genes specifying cell fates during growth
and differentiation. H3K27me3 marks not only these genes but also some genes that
are involved in endosperm development and maternal effects. Transcriptome analysis,
coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants
showed that EMF1 represses gene activities via diverse mechanisms and plays a
novel role in the PcG mechanism.
article_number: e1002512
article_processing_charge: No
article_type: original
author:
- first_name: Sang Yeol
full_name: Kim, Sang Yeol
last_name: Kim
- first_name: Jungeun
full_name: Lee, Jungeun
last_name: Lee
- first_name: Leor
full_name: Eshed-Williams, Leor
last_name: Eshed-Williams
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Z. Renee
full_name: Sung, Z. Renee
last_name: Sung
citation:
ama: Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate
to repress key regulators of Arabidopsis development. PLoS Genetics. 2012;8(3).
doi:10.1371/journal.pgen.1002512
apa: Kim, S. Y., Lee, J., Eshed-Williams, L., Zilberman, D., & Sung, Z. R. (2012).
EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development.
PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002512
chicago: Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and
Z. Renee Sung. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis
Development.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002512.
ieee: S. Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, and Z. R. Sung, “EMF1
and PRC2 cooperate to repress key regulators of Arabidopsis development,” PLoS
Genetics, vol. 8, no. 3. Public Library of Science, 2012.
ista: Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. 2012. EMF1 and PRC2
cooperate to repress key regulators of Arabidopsis development. PLoS Genetics.
8(3), e1002512.
mla: Kim, Sang Yeol, et al. “EMF1 and PRC2 Cooperate to Repress Key Regulators of
Arabidopsis Development.” PLoS Genetics, vol. 8, no. 3, e1002512, Public
Library of Science, 2012, doi:10.1371/journal.pgen.1002512.
short: S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics
8 (2012).
date_created: 2021-06-07T11:07:56Z
date_published: 2012-03-22T00:00:00Z
date_updated: 2021-12-14T08:31:14Z
day: '22'
department:
- _id: DaZi
doi: 10.1371/journal.pgen.1002512
extern: '1'
external_id:
pmid:
- '22457632'
intvolume: ' 8'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pgen.1002512
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
eissn:
- 1553-7404
issn:
- 1553-7390
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 8
year: '2012'
...
---
_id: '9528'
abstract:
- lang: eng
text: Accumulating evidence points toward diverse functions for plant chromatin.
Remarkable progress has been made over the last few years in elucidating the mechanisms
for a number of these functions. Activity of the histone demethylase IBM1 accurately
targets DNA methylation to silent repeats and transposable elements, not to genes.
A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes
in sensing precise differences in ambient temperature and consequent gene regulation.
Precise maintenance of chromosome number is assured by a histone modification
that suppresses inappropriate DNA replication and by centromeric histone H3 regulation
of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS
C, the expression of which quantitatively measures the duration of cold exposure,
functioning as memory of winter. These findings are a testament to the power of
using plants to research chromatin organization, and demonstrate examples of how
chromatin functions to achieve biological accuracy, precision, and memory.
article_processing_charge: No
article_type: review
author:
- first_name: Jason T.
full_name: Huff, Jason T.
last_name: Huff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory
by plant chromatin organization. Current Opinion in Genetics and Development.
2012;22(2):132-138. doi:10.1016/j.gde.2012.01.007
apa: Huff, J. T., & Zilberman, D. (2012). Regulation of biological accuracy,
precision, and memory by plant chromatin organization. Current Opinion in Genetics
and Development. Elsevier. https://doi.org/10.1016/j.gde.2012.01.007
chicago: Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy,
Precision, and Memory by Plant Chromatin Organization.” Current Opinion in
Genetics and Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.01.007.
ieee: J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision,
and memory by plant chromatin organization,” Current Opinion in Genetics and
Development, vol. 22, no. 2. Elsevier, pp. 132–138, 2012.
ista: Huff JT, Zilberman D. 2012. Regulation of biological accuracy, precision,
and memory by plant chromatin organization. Current Opinion in Genetics and Development.
22(2), 132–138.
mla: Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision,
and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and
Development, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:10.1016/j.gde.2012.01.007.
short: J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012)
132–138.
date_created: 2021-06-08T08:58:52Z
date_published: 2012-04-01T00:00:00Z
date_updated: 2021-12-14T08:32:38Z
department:
- _id: DaZi
doi: 10.1016/j.gde.2012.01.007
extern: '1'
external_id:
pmid:
- '22336527'
intvolume: ' 22'
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
page: 132-138
pmid: 1
publication: Current Opinion in Genetics and Development
publication_identifier:
issn:
- 0959-437X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Regulation of biological accuracy, precision, and memory by plant chromatin
organization
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 22
year: '2012'
...
---
_id: '9535'
abstract:
- lang: eng
text: The most well-studied function of DNA methylation in eukaryotic cells is the
transcriptional silencing of genes and transposons. More recent results showed
that many eukaryotes methylate the bodies of genes as well and that this methylation
correlates with transcriptional activity rather than repression. The purpose of
gene body methylation remains mysterious, but is potentially related to the histone
variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions
of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and
other investigators have shown that this relationship is likely to be the result
of an ancient but unknown mechanism by which DNA methylation prevents the incorporation
of H2A.Z. Recently, we discovered strong correlations between the presence of
H2A.Z within gene bodies, the degree to which a gene's expression varies across
tissue types or environmental conditions, and transcriptional misregulation in
an h2a.z mutant. We propose that one basal function of gene body methylation is
the establishment of constitutive expression patterns within housekeeping genes
by excluding H2A.Z from their bodies.
article_processing_charge: No
article_type: review
author:
- first_name: D.
full_name: Coleman-Derr, D.
last_name: Coleman-Derr
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of
constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology.
2012;77:147-154. doi:10.1101/sqb.2012.77.014944
apa: Coleman-Derr, D., & Zilberman, D. (2012). DNA methylation, H2A.Z, and the
regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative
Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/sqb.2012.77.014944
chicago: Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the
Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative
Biology. Cold Spring Harbor Laboratory Press, 2012. https://doi.org/10.1101/sqb.2012.77.014944.
ieee: D. Coleman-Derr and D. Zilberman, “DNA methylation, H2A.Z, and the regulation
of constitutive expression,” Cold Spring Harbor Symposia on Quantitative Biology,
vol. 77. Cold Spring Harbor Laboratory Press, pp. 147–154, 2012.
ista: Coleman-Derr D, Zilberman D. 2012. DNA methylation, H2A.Z, and the regulation
of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology.
77, 147–154.
mla: Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation
of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology,
vol. 77, Cold Spring Harbor Laboratory Press, 2012, pp. 147–54, doi:10.1101/sqb.2012.77.014944.
short: D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative
Biology 77 (2012) 147–154.
date_created: 2021-06-08T13:01:23Z
date_published: 2012-12-18T00:00:00Z
date_updated: 2021-12-14T08:33:09Z
day: '18'
department:
- _id: DaZi
doi: 10.1101/sqb.2012.77.014944
extern: '1'
external_id:
pmid:
- '23250988'
intvolume: ' 77'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/sqb.2012.77.014944
month: '12'
oa: 1
oa_version: Published Version
page: 147-154
pmid: 1
publication: Cold Spring Harbor Symposia on Quantitative Biology
publication_identifier:
eissn:
- 1943-4456
issn:
- 0091-7451
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation, H2A.Z, and the regulation of constitutive expression
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 77
year: '2012'
...
---
_id: '12198'
abstract:
- lang: eng
text: The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes
DNA demethylation before fertilization, but the targeting preferences, mechanism,
and biological significance of this process remain unclear. Here, we show that
active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for
all of the demethylation in the central cell and preferentially targets small,
AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative
cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation
of similar sequences, and lack of DEMETER in vegetative cells causes reduced small
RNA–directed DNA methylation of transposons in sperm. Our results demonstrate
that demethylation in companion cells reinforces transposon methylation in plant
gametes and likely contributes to stable silencing of transposable elements across
generations.
acknowledgement: We thank S. Harmer for assistance with the analysis of histone modifications,
the BioOptics team at the Vienna Biocenter Campus for sorting sperm and vegetative
cell nuclei, K. Slotkin for the LAT52p-amiRNA=GFP plasmid, and G. Drews for the
DD45p-GFP transgenic line. This work was partially funded by an NIH grant (GM69415)
to R.L.F., NSF grants (MCB-0918821 and IOS-1025890) to R.L.F. and D.Z., a Young
Investigator Grant from the Arnold and Mabel Beckman Foundation to D.Z., an Austrian
Science Fund (FWF) grant P21389-B03 to H.T., a Ruth L. Kirschstein NIH Predoctoral
Fellowship (GM093633) to C.A.I., a Fulbright Scholarship to J.A.R., a fellowship
from the Jane Coffin Childs Memorial Fund to A.Z., and a Robert and Colleen Haas
Scholarship to D.R. Sequencing data are deposited in GEO (GSE38935).
article_processing_charge: No
article_type: original
author:
- first_name: Christian A.
full_name: Ibarra, Christian A.
last_name: Ibarra
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Vera K.
full_name: Schoft, Vera K.
last_name: Schoft
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Rie
full_name: Uzawa, Rie
last_name: Uzawa
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Nina
full_name: Chumak, Nina
last_name: Chumak
- first_name: Adriana
full_name: Machlicova, Adriana
last_name: Machlicova
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Denisse
full_name: Rojas, Denisse
last_name: Rojas
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Hisashi
full_name: Tamaru, Hisashi
last_name: Tamaru
- first_name: Daniel
full_name: Zilberman, Daniel
last_name: Zilberman
citation:
ama: Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion
cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364.
doi:10.1126/science.1224839
apa: Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues,
J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells
reinforces transposon methylation in gametes. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.1224839
chicago: Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie
Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in
Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science.
American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839.
ieee: C. A. Ibarra et al., “Active DNA demethylation in plant companion cells
reinforces transposon methylation in gametes,” Science, vol. 337, no. 6100.
American Association for the Advancement of Science, pp. 1360–1364, 2012.
ista: Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A,
Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman
D. 2012. Active DNA demethylation in plant companion cells reinforces transposon
methylation in gametes. Science. 337(6100), 1360–1364.
mla: Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells
Reinforces Transposon Methylation in Gametes.” Science, vol. 337, no. 6100,
American Association for the Advancement of Science, 2012, pp. 1360–64, doi:10.1126/science.1224839.
short: C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues,
A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H.
Tamaru, D. Zilberman, Science 337 (2012) 1360–1364.
date_created: 2023-01-16T09:21:24Z
date_published: 2012-09-14T00:00:00Z
date_updated: 2023-10-16T09:27:26Z
day: '14'
department:
- _id: XiFe
doi: 10.1126/science.1224839
external_id:
pmid:
- '22984074'
intvolume: ' 337'
issue: '6100'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/
month: '09'
oa: 1
oa_version: Published Version
page: 1360-1364
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Active DNA demethylation in plant companion cells reinforces transposon methylation
in gametes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 337
year: '2012'
...
---
_id: '9755'
abstract:
- lang: eng
text: Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated
disease defences at the individual and colony level. An intriguing yet little
understood phenomenon is that social contact to pathogen-exposed individuals reduces
susceptibility of previously naive nestmates to this pathogen. We tested whether
such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium
anisopliae is based on active upregulation of the immune system of nestmates following
contact to an infectious individual or passive protection via transfer of immune
effectors among group members—that is, active versus passive immunisation. We
found no evidence for involvement of passive immunisation via transfer of antimicrobials
among colony members. Instead, intensive allogrooming behaviour between naive
and pathogen-exposed ants before fungal conidia firmly attached to their cuticle
suggested passage of the pathogen from the exposed individuals to their nestmates.
By tracing fluorescence-labelled conidia we indeed detected frequent pathogen
transfer to the nestmates, where they caused low-level infections as revealed
by growth of small numbers of fungal colony forming units from their dissected
body content. These infections rarely led to death, but instead promoted an enhanced
ability to inhibit fungal growth and an active upregulation of immune genes involved
in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there
was no upregulation of the gene cathepsin L, which is associated with antibacterial
and antiviral defences, and we found no increased antibacterial activity of nestmates
of fungus-exposed ants. This indicates that social immunisation after fungal exposure
is specific, similar to recent findings for individual-level immune priming in
invertebrates. Epidemiological modeling further suggests that active social immunisation
is adaptive, as it leads to faster elimination of the disease and lower death
rates than passive immunisation. Interestingly, humans have also utilised the
protective effect of low-level infections to fight smallpox by intentional transfer
of low pathogen doses (“variolation” or “inoculation”).
article_processing_charge: No
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Meghan
full_name: Vyleta, Meghan
id: 418901AA-F248-11E8-B48F-1D18A9856A87
last_name: Vyleta
- first_name: Fabian
full_name: Theis, Fabian
last_name: Theis
- first_name: Miriam
full_name: Stock, Miriam
id: 42462816-F248-11E8-B48F-1D18A9856A87
last_name: Stock
- first_name: Martina
full_name: Klatt, Martina
id: E60F29C6-E9AE-11E9-AF6E-D190C7302F38
last_name: Klatt
- first_name: Verena
full_name: Drescher, Verena
last_name: Drescher
- first_name: Carsten
full_name: Marr, Carsten
last_name: Marr
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Konrad M, Vyleta M, Theis F, et al. Data from: Social transfer of pathogenic
fungus promotes active immunisation in ant colonies. 2012. doi:10.5061/dryad.sv37s'
apa: 'Konrad, M., Vyleta, M., Theis, F., Stock, M., Klatt, M., Drescher, V., … Cremer,
S. (2012). Data from: Social transfer of pathogenic fungus promotes active immunisation
in ant colonies. Dryad. https://doi.org/10.5061/dryad.sv37s'
chicago: 'Konrad, Matthias, Meghan Vyleta, Fabian Theis, Miriam Stock, Martina Klatt,
Verena Drescher, Carsten Marr, Line V Ugelvig, and Sylvia Cremer. “Data from:
Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.”
Dryad, 2012. https://doi.org/10.5061/dryad.sv37s.'
ieee: 'M. Konrad et al., “Data from: Social transfer of pathogenic fungus
promotes active immunisation in ant colonies.” Dryad, 2012.'
ista: 'Konrad M, Vyleta M, Theis F, Stock M, Klatt M, Drescher V, Marr C, Ugelvig
LV, Cremer S. 2012. Data from: Social transfer of pathogenic fungus promotes active
immunisation in ant colonies, Dryad, 10.5061/dryad.sv37s.'
mla: 'Konrad, Matthias, et al. Data from: Social Transfer of Pathogenic Fungus
Promotes Active Immunisation in Ant Colonies. Dryad, 2012, doi:10.5061/dryad.sv37s.'
short: M. Konrad, M. Vyleta, F. Theis, M. Stock, M. Klatt, V. Drescher, C. Marr,
L.V. Ugelvig, S. Cremer, (2012).
date_created: 2021-07-30T08:39:13Z
date_published: 2012-09-27T00:00:00Z
date_updated: 2023-02-23T11:18:41Z
day: '27'
department:
- _id: SyCr
doi: 10.5061/dryad.sv37s
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.sv37s
month: '09'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '3242'
relation: used_in_publication
status: public
status: public
title: 'Data from: Social transfer of pathogenic fungus promotes active immunisation
in ant colonies'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2012'
...
---
_id: '9757'
abstract:
- lang: eng
text: To fight infectious diseases, host immune defences are employed at multiple
levels. Sanitary behaviour, such as pathogen avoidance and removal, acts as a
first line of defence to prevent infection [1] before activation of the physiological
immune system. Insect societies have evolved a wide range of collective hygiene
measures and intensive health care towards pathogen-exposed group members [2].
One of the most common behaviours is allogrooming, in which nestmates remove infectious
particles from the body surfaces of exposed individuals [3]. Here we show that,
in invasive garden ants, grooming of fungus-exposed brood is effective beyond
the sheer mechanical removal of fungal conidiospores as it also includes chemical
disinfection through the application of poison produced by the ants themselves.
Formic acid is the main active component of the poison. It inhibits fungal growth
of conidiospores remaining on the brood surface after grooming and also those
collected in the mouth of the grooming ant. This dual function is achieved by
uptake of the poison droplet into the mouth through acidopore self-grooming and
subsequent application onto the infectious brood via brood grooming. This extraordinary
behaviour extends current understanding of grooming and the establishment of social
immunity in insect societies.
article_processing_charge: No
author:
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Barbara
full_name: Mitteregger, Barbara
id: 479DDAAC-E9CD-11E9-9B5F-82450873F7A1
last_name: Mitteregger
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. Data from:
Ants disinfect fungus-exposed brood by oral uptake and spread of their poison.
2012. doi:10.5061/dryad.61649'
apa: 'Tragust, S., Mitteregger, B., Barone, V., Konrad, M., Ugelvig, L. V., &
Cremer, S. (2012). Data from: Ants disinfect fungus-exposed brood by oral uptake
and spread of their poison. Dryad. https://doi.org/10.5061/dryad.61649'
chicago: 'Tragust, Simon, Barbara Mitteregger, Vanessa Barone, Matthias Konrad,
Line V Ugelvig, and Sylvia Cremer. “Data from: Ants Disinfect Fungus-Exposed Brood
by Oral Uptake and Spread of Their Poison.” Dryad, 2012. https://doi.org/10.5061/dryad.61649.'
ieee: 'S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L. V. Ugelvig, and S. Cremer,
“Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their
poison.” Dryad, 2012.'
ista: 'Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. 2012.
Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their
poison, Dryad, 10.5061/dryad.61649.'
mla: 'Tragust, Simon, et al. Data from: Ants Disinfect Fungus-Exposed Brood by
Oral Uptake and Spread of Their Poison. Dryad, 2012, doi:10.5061/dryad.61649.'
short: S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer,
(2012).
date_created: 2021-07-30T12:31:31Z
date_published: 2012-12-14T00:00:00Z
date_updated: 2023-02-23T11:04:28Z
day: '14'
department:
- _id: SyCr
doi: 10.5061/dryad.61649
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.61649
month: '12'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2926'
relation: used_in_publication
status: public
status: public
title: 'Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of
their poison'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2012'
...
---
_id: '9758'
abstract:
- lang: eng
text: 'We propose a two-step procedure for estimating multiple migration rates in
an approximate Bayesian computation (ABC) framework, accounting for global nuisance
parameters. The approach is not limited to migration, but generally of interest
for inference problems with multiple parameters and a modular structure (e.g.
independent sets of demes or loci). We condition on a known, but complex demographic
model of a spatially subdivided population, motivated by the reintroduction of
Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters
ancestral mutation rate and male mating skew have been estimated for the whole
population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step,
we estimate in this study the migration rates independently for clusters of demes
putatively connected by migration. For large clusters (many migration rates),
ABC faces the problem of too many summary statistics. We therefore assess by simulation
if estimation per pair of demes is a valid alternative. We find that the trade-off
between reduced dimensionality for the pairwise estimation on the one hand and
lower accuracy due to the assumption of pairwise independence on the other depends
on the number of migration rates to be inferred: the accuracy of the pairwise
approach increases with the number of parameters, relative to the joint estimation
approach. To distinguish between low and zero migration, we perform ABC-type model
comparison between a model with migration and one without. Applying the approach
to microsatellite data from Alpine ibex, we find no evidence for substantial gene
flow via migration, except for one pair of demes in one direction.'
article_processing_charge: No
author:
- first_name: Simon
full_name: Aeschbacher, Simon
id: 2D35326E-F248-11E8-B48F-1D18A9856A87
last_name: Aeschbacher
- first_name: Andreas
full_name: Futschik, Andreas
last_name: Futschik
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
citation:
ama: 'Aeschbacher S, Futschik A, Beaumont M. Data from: Approximate Bayesian computation
for modular inference problems with many parameters: the example of migration
rates. 2012. doi:10.5061/dryad.274b1'
apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2012). Data from: Approximate
Bayesian computation for modular inference problems with many parameters: the
example of migration rates. Dryad. https://doi.org/10.5061/dryad.274b1'
chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Data from: Approximate
Bayesian Computation for Modular Inference Problems with Many Parameters: The
Example of Migration Rates.” Dryad, 2012. https://doi.org/10.5061/dryad.274b1.'
ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Data from: Approximate Bayesian
computation for modular inference problems with many parameters: the example of
migration rates.” Dryad, 2012.'
ista: 'Aeschbacher S, Futschik A, Beaumont M. 2012. Data from: Approximate Bayesian
computation for modular inference problems with many parameters: the example of
migration rates, Dryad, 10.5061/dryad.274b1.'
mla: 'Aeschbacher, Simon, et al. Data from: Approximate Bayesian Computation
for Modular Inference Problems with Many Parameters: The Example of Migration
Rates. Dryad, 2012, doi:10.5061/dryad.274b1.'
short: S. Aeschbacher, A. Futschik, M. Beaumont, (2012).
date_created: 2021-07-30T12:36:39Z
date_published: 2012-11-14T00:00:00Z
date_updated: 2023-02-23T11:05:19Z
day: '14'
department:
- _id: NiBa
doi: 10.5061/dryad.274b1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.274b1
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2944'
relation: used_in_publication
status: public
status: public
title: 'Data from: Approximate Bayesian computation for modular inference problems
with many parameters: the example of migration rates'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2012'
...
---
_id: '3836'
abstract:
- lang: eng
text: Hierarchical Timing Language (HTL) is a coordination language for distributed,
hard real-time applications. HTL is a hierarchical extension of Giotto and, like
its predecessor, based on the logical execution time (LET) paradigm of real-time
programming. Giotto is compiled into code for a virtual machine, called the EmbeddedMachine
(or E machine). If HTL is targeted to the E machine, then the hierarchicalprogram
structure needs to be flattened; the flattening makes separatecompilation difficult,
and may result in E machinecode of exponential size. In this paper, we propose
a generalization of the E machine, which supports a hierarchicalprogram structure
at runtime through real-time trigger mechanisms that are arranged in a tree. We
present the generalized E machine, and a modular compiler for HTL that generates
code of linear size. The compiler may generate code for any part of a given HTL
program separately in any order.
author:
- first_name: Arkadeb
full_name: Ghosal, Arkadeb
last_name: Ghosal
- first_name: Daniel
full_name: Iercan, Daniel
last_name: Iercan
- first_name: Christoph
full_name: Kirsch, Christoph
last_name: Kirsch
- 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: Alberto
full_name: Sangiovanni Vincentelli, Alberto
last_name: Sangiovanni Vincentelli
citation:
ama: Ghosal A, Iercan D, Kirsch C, Henzinger TA, Sangiovanni Vincentelli A. Separate
compilation of hierarchical real-time programs into linear-bounded embedded machine
code. Science of Computer Programming. 2012;77(2):96-112. doi:10.1016/j.scico.2010.06.004
apa: Ghosal, A., Iercan, D., Kirsch, C., Henzinger, T. A., & Sangiovanni Vincentelli,
A. (2012). Separate compilation of hierarchical real-time programs into linear-bounded
embedded machine code. Science of Computer Programming. Elsevier. https://doi.org/10.1016/j.scico.2010.06.004
chicago: Ghosal, Arkadeb, Daniel Iercan, Christoph Kirsch, Thomas A Henzinger, and
Alberto Sangiovanni Vincentelli. “Separate Compilation of Hierarchical Real-Time
Programs into Linear-Bounded Embedded Machine Code.” Science of Computer Programming.
Elsevier, 2012. https://doi.org/10.1016/j.scico.2010.06.004.
ieee: A. Ghosal, D. Iercan, C. Kirsch, T. A. Henzinger, and A. Sangiovanni Vincentelli,
“Separate compilation of hierarchical real-time programs into linear-bounded embedded
machine code,” Science of Computer Programming, vol. 77, no. 2. Elsevier,
pp. 96–112, 2012.
ista: Ghosal A, Iercan D, Kirsch C, Henzinger TA, Sangiovanni Vincentelli A. 2012.
Separate compilation of hierarchical real-time programs into linear-bounded embedded
machine code. Science of Computer Programming. 77(2), 96–112.
mla: Ghosal, Arkadeb, et al. “Separate Compilation of Hierarchical Real-Time Programs
into Linear-Bounded Embedded Machine Code.” Science of Computer Programming,
vol. 77, no. 2, Elsevier, 2012, pp. 96–112, doi:10.1016/j.scico.2010.06.004.
short: A. Ghosal, D. Iercan, C. Kirsch, T.A. Henzinger, A. Sangiovanni Vincentelli,
Science of Computer Programming 77 (2012) 96–112.
date_created: 2018-12-11T12:05:26Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2021-01-12T07:52:32Z
day: '01'
department:
- _id: ToHe
doi: 10.1016/j.scico.2010.06.004
intvolume: ' 77'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 96 - 112
publication: Science of Computer Programming
publication_status: published
publisher: Elsevier
publist_id: '2370'
quality_controlled: '1'
scopus_import: 1
status: public
title: Separate compilation of hierarchical real-time programs into linear-bounded
embedded machine code
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2012'
...
---
_id: '3846'
abstract:
- lang: eng
text: We summarize classical and recent results about two-player games played on
graphs with ω-regular objectives. These games have applications in the verification
and synthesis of reactive systems. Important distinctions are whether a graph
game is turn-based or concurrent; deterministic or stochastic; zero-sum or not.
We cluster known results and open problems according to these classifications.
acknowledgement: This research was supported in part by the ONR grant N00014-02-1-0671,
by the AFOSR MURI grant F49620-00-1-0327, and by the NSF grants CCR-9988172, CCR-0085949,
and CCR-0225610.
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: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Chatterjee K, Henzinger TA. A survey of stochastic ω regular games. Journal
of Computer and System Sciences. 2012;78(2):394-413. doi:10.1016/j.jcss.2011.05.002
apa: Chatterjee, K., & Henzinger, T. A. (2012). A survey of stochastic ω regular
games. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2011.05.002
chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “A Survey of Stochastic
ω Regular Games.” Journal of Computer and System Sciences. Elsevier, 2012.
https://doi.org/10.1016/j.jcss.2011.05.002.
ieee: K. Chatterjee and T. A. Henzinger, “A survey of stochastic ω regular games,”
Journal of Computer and System Sciences, vol. 78, no. 2. Elsevier, pp.
394–413, 2012.
ista: Chatterjee K, Henzinger TA. 2012. A survey of stochastic ω regular games.
Journal of Computer and System Sciences. 78(2), 394–413.
mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. “A Survey of Stochastic ω
Regular Games.” Journal of Computer and System Sciences, vol. 78, no. 2,
Elsevier, 2012, pp. 394–413, doi:10.1016/j.jcss.2011.05.002.
short: K. Chatterjee, T.A. Henzinger, Journal of Computer and System Sciences 78
(2012) 394–413.
date_created: 2018-12-11T12:05:29Z
date_published: 2012-03-02T00:00:00Z
date_updated: 2022-05-24T08:00:54Z
day: '02'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1016/j.jcss.2011.05.002
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url: https://doi.org/10.1016/j.jcss.2011.05.002
month: '03'
oa: 1
oa_version: Submitted Version
page: 394 - 413
publication: Journal of Computer and System Sciences
publication_status: published
publisher: Elsevier
publist_id: '2341'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A survey of stochastic ω regular games
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
year: '2012'
...
---
_id: '3163'
abstract:
- lang: eng
text: We study multi-label prediction for structured output sets, a problem that
occurs, for example, in object detection in images, secondary structure prediction
in computational biology, and graph matching with symmetries. Conventional multilabel
classification techniques are typically not applicable in this situation, because
they require explicit enumeration of the label set, which is infeasible in case
of structured outputs. Relying on techniques originally designed for single-label
structured prediction, in particular structured support vector machines, results
in reduced prediction accuracy, or leads to infeasible optimization problems.
In this work we derive a maximum-margin training formulation for multi-label structured
prediction that remains computationally tractable while achieving high prediction
accuracy. It also shares most beneficial properties with single-label maximum-margin
approaches, in particular formulation as a convex optimization problem, efficient
working set training, and PAC-Bayesian generalization bounds.
author:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Lampert C. Maximum margin multi-label structured prediction. In: Neural Information
Processing Systems; 2011.'
apa: 'Lampert, C. (2011). Maximum margin multi-label structured prediction. Presented
at the NIPS: Neural Information Processing Systems, Granada, Spain: Neural Information
Processing Systems.'
chicago: Lampert, Christoph. “Maximum Margin Multi-Label Structured Prediction.”
Neural Information Processing Systems, 2011.
ieee: 'C. Lampert, “Maximum margin multi-label structured prediction,” presented
at the NIPS: Neural Information Processing Systems, Granada, Spain, 2011.'
ista: 'Lampert C. 2011. Maximum margin multi-label structured prediction. NIPS:
Neural Information Processing Systems.'
mla: Lampert, Christoph. Maximum Margin Multi-Label Structured Prediction.
Neural Information Processing Systems, 2011.
short: C. Lampert, in:, Neural Information Processing Systems, 2011.
conference:
end_date: 2011-12-14
location: Granada, Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2011-12-12
date_created: 2018-12-11T12:01:45Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2023-10-17T11:47:35Z
day: '01'
department:
- _id: ChLa
language:
- iso: eng
month: '12'
oa_version: None
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '3522'
quality_controlled: '1'
related_material:
record:
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relation: later_version
status: public
scopus_import: 1
status: public
title: Maximum margin multi-label structured prediction
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...