---
_id: '3917'
abstract:
- lang: eng
text: Male dimorphism is not genetically determined, but is induced by environmental
conditions particularly decreasing temperature and density.
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
citation:
ama: 'Cremer S, Heinze J. Zwischen Hochzeitsflug und Brudermord: reproduktive Taktiken
bei Ameisenmännchen. Blick in die Wissenschaft. 2003;12(15):32-36.'
apa: 'Cremer, S., & Heinze, J. (2003). Zwischen Hochzeitsflug und Brudermord:
reproduktive Taktiken bei Ameisenmännchen. Blick in Die Wissenschaft. Schnell
und Steiner.'
chicago: 'Cremer, Sylvia, and Jürgen Heinze. “Zwischen Hochzeitsflug Und Brudermord:
Reproduktive Taktiken Bei Ameisenmännchen.” Blick in Die Wissenschaft.
Schnell und Steiner, 2003.'
ieee: 'S. Cremer and J. Heinze, “Zwischen Hochzeitsflug und Brudermord: reproduktive
Taktiken bei Ameisenmännchen,” Blick in die Wissenschaft, vol. 12, no.
15. Schnell und Steiner, pp. 32–36, 2003.'
ista: 'Cremer S, Heinze J. 2003. Zwischen Hochzeitsflug und Brudermord: reproduktive
Taktiken bei Ameisenmännchen. Blick in die Wissenschaft. 12(15), 32–36.'
mla: 'Cremer, Sylvia, and Jürgen Heinze. “Zwischen Hochzeitsflug Und Brudermord:
Reproduktive Taktiken Bei Ameisenmännchen.” Blick in Die Wissenschaft,
vol. 12, no. 15, Schnell und Steiner, 2003, pp. 32–36.'
short: S. Cremer, J. Heinze, Blick in Die Wissenschaft 12 (2003) 32–36.
date_created: 2018-12-11T12:05:53Z
date_published: 2003-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:11Z
day: '01'
extern: '1'
intvolume: ' 12'
issue: '15'
language:
- iso: eng
month: '01'
oa_version: None
page: 32 - 36
publication: Blick in die Wissenschaft
publication_status: published
publisher: Schnell und Steiner
publist_id: '2235'
status: public
title: 'Zwischen Hochzeitsflug und Brudermord: reproduktive Taktiken bei Ameisenmännchen'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2003'
...
---
_id: '4416'
abstract:
- lang: eng
text: "Methods for the formal specification and verification of systems are indispensible
for the development of complex yet correct systems. In formal verification, the
designer describes the system in a modeling language with a well-defined semantics,
and this system description is analyzed against a set of correctness requirements.
Model checking is an algorithmic technique to check that a system description
indeed satisfies correctness requirements given as logical specifications. While
successful in hardware verification, the potential for model checking for software
and embedded systems has not yet been realized. This is because traditional model
checking focuses on systems modeled as finite state-transition graphs. While a
natural model for hardware (especially synchronous hardware), state-transition
graphs often do not capture software and embedded systems at an appropriate level
of granularity. This dissertation considers two orthogonal extensions to finite
state-transition graphs making model checking techniques applicable to both a
wider class of systems and a wider class of properties.\r\n\r\nThe first direction
is an extension to infinite-state structures finitely represented using constraints
and operations on constraints. Infinite state arises when we wish to model variables
with unbounded range (e.g., integers), or data structures, or real time. We provide
a uniform framework of symbolic region algebras to study model checking of infinite-state
systems. We also provide sufficient language-independent termination conditions
for symbolic model checking algorithms on infinite state systems.\r\n\r\nThe second
direction supplements verification with game theoretic reasoning. Games are natural
models for interactions between components. We study game theoretic behavior with
winning conditions given by temporal logic objectives both in the deterministic
and in the probabilistic context. For deterministic games, we provide an extremal
model characterization of fixpoint algorithms that link solutions of verification
problems to solutions for games. For probabilistic games we study fixpoint characterization
of winning probabilities for games with omega-regular winning objectives, and
construct (epsilon-)optimal winning strategies."
article_processing_charge: No
author:
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
citation:
ama: Majumdar R. Symbolic algorithms for verification and control. 2003:1-201.
apa: Majumdar, R. (2003). Symbolic algorithms for verification and control.
University of California, Berkeley.
chicago: Majumdar, Ritankar. “Symbolic Algorithms for Verification and Control.”
University of California, Berkeley, 2003.
ieee: R. Majumdar, “Symbolic algorithms for verification and control,” University
of California, Berkeley, 2003.
ista: Majumdar R. 2003. Symbolic algorithms for verification and control. University
of California, Berkeley.
mla: Majumdar, Ritankar. Symbolic Algorithms for Verification and Control.
University of California, Berkeley, 2003, pp. 1–201.
short: R. Majumdar, Symbolic Algorithms for Verification and Control, University
of California, Berkeley, 2003.
date_created: 2018-12-11T12:08:44Z
date_published: 2003-12-01T00:00:00Z
date_updated: 2021-01-12T07:56:49Z
day: '01'
extern: '1'
language:
- iso: eng
month: '12'
oa_version: None
page: 1 - 201
publication_status: published
publisher: University of California, Berkeley
publist_id: '313'
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
title: Symbolic algorithms for verification and control
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2003'
...
---
_id: '4425'
abstract:
- lang: eng
text: "Giotto provides a time-triggered programmer’s model for the implementation
of embedded control systems with hard real-time constraints. Giotto’s precise
semantics and predictabil- ity make it suitable for safety-critical applications.\r\nGiotto
is based around the idea that time-triggered task invocation together with time-triggered
mode switching can form a useful programming model for real-time systems. To substantiate
this claim, we describe the use of Giotto to refactor the software of a small,
autonomous helicopter. The ease with which Giotto expresses the existing software
provides evidence that Giotto is an appropriate programming language for control
systems.\r\nSince Giotto is a real-time programming language, ensuring that Giotto
programs meet their deadlines is crucial. To study precedence-constrained Giotto
scheduling, we first examine single-mode, single-processor scheduling. We extend
to an infinite, periodic setting the classical problem of meeting deadlines for
a set of tasks with release times, deadlines, precedence constraints, and preemption.
We then develop an algorithm for scheduling Giotto programs on a single processor
by representing Giotto programs as instances of the extended scheduling problem.\r\nNext,
we study multi-mode, single-processor Giotto scheduling. This problem is different
from classical scheduling problems, since in our precedence-constrained approach,
the deadlines of tasks may vary depending on the mode switching behavior of the
program. We present conditional scheduling models which capture this varying-deadline
behavior. We develop polynomial-time algorithms for some conditional scheduling
models, and prove oth- ers to be computationally hard. We show how to represent
multi-mode Giotto programs as instances of the model, resulting in an algorithm
for scheduling multi-mode Giotto programs on a single processor.\r\nFinally, we
show that the problem of scheduling Giotto programs for multiple net- worked processors
is strongly NP-hard."
article_processing_charge: No
author:
- first_name: Benjamin
full_name: Horowitz, Benjamin
last_name: Horowitz
citation:
ama: 'Horowitz B. Giotto: A time-triggered language for embedded programming. 2003:1-237.'
apa: 'Horowitz, B. (2003). Giotto: A time-triggered language for embedded programming.
University of California, Berkeley.'
chicago: 'Horowitz, Benjamin. “Giotto: A Time-Triggered Language for Embedded Programming.”
University of California, Berkeley, 2003.'
ieee: 'B. Horowitz, “Giotto: A time-triggered language for embedded programming,”
University of California, Berkeley, 2003.'
ista: 'Horowitz B. 2003. Giotto: A time-triggered language for embedded programming.
University of California, Berkeley.'
mla: 'Horowitz, Benjamin. Giotto: A Time-Triggered Language for Embedded Programming.
University of California, Berkeley, 2003, pp. 1–237.'
short: 'B. Horowitz, Giotto: A Time-Triggered Language for Embedded Programming,
University of California, Berkeley, 2003.'
date_created: 2018-12-11T12:08:47Z
date_published: 2003-10-01T00:00:00Z
date_updated: 2021-01-12T07:56:53Z
day: '01'
extern: '1'
language:
- iso: eng
month: '10'
oa_version: None
page: 1 - 237
publication_status: published
publisher: University of California, Berkeley
publist_id: '305'
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
title: 'Giotto: A time-triggered language for embedded programming'
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2003'
...
---
_id: '576'
abstract:
- lang: eng
text: 'We study the free expansion of a pancake-shaped Bose-condensed gas, which
is initially trapped under harmonic confinement and containing a vortex at its
centre. In the case of a radial expansion holding the axial confinement fixed
we consider various models for the interactions, depending on the thickness of
the condensate relative to the value of the scattering length. We are thus able
to evaluate different scattering regimes ranging from quasi-three-dimensional
(Q3D) to strictly two-dimensional (2D). We find that as the system goes from Q3D
to 2D the expansion rate of the condensate increases whereas that of the vortex
core decreases. In the Q3D scattering regime we also examine a fully free expansion
in 3D and find oscillatory behaviour for the vortex core radius: an initial fast
expansion of the vortex core is followed by a slowing down. Such a nonuniform
expansion rate of the vortex core implies that the timing of its observation should
be chosen appropriately.'
author:
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Patrizia
full_name: Vignolo, Patrizia
last_name: Vignolo
- first_name: Anna
full_name: Minguzzi, Anna
last_name: Minguzzi
- first_name: Bilal
full_name: Tanatar, Bilal
last_name: Tanatar
- first_name: Mario
full_name: Tosi, Mario P
last_name: Tosi
citation:
ama: 'Hosten O, Vignolo P, Minguzzi A, Tanatar B, Tosi M. Free expansion of two-dimensional
condensates with a vortex. Journal of Physics B: Atomic, Molecular and Optical
Physics. 2003;36(12):2455-2463. doi:10.1088/0953-4075/36/12/306'
apa: 'Hosten, O., Vignolo, P., Minguzzi, A., Tanatar, B., & Tosi, M. (2003).
Free expansion of two-dimensional condensates with a vortex. Journal of Physics
B: Atomic, Molecular and Optical Physics. IOP Publishing Ltd. https://doi.org/10.1088/0953-4075/36/12/306'
chicago: 'Hosten, Onur, Patrizia Vignolo, Anna Minguzzi, Bilal Tanatar, and Mario
Tosi. “Free Expansion of Two-Dimensional Condensates with a Vortex.” Journal
of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing Ltd.,
2003. https://doi.org/10.1088/0953-4075/36/12/306.'
ieee: 'O. Hosten, P. Vignolo, A. Minguzzi, B. Tanatar, and M. Tosi, “Free expansion
of two-dimensional condensates with a vortex,” Journal of Physics B: Atomic,
Molecular and Optical Physics, vol. 36, no. 12. IOP Publishing Ltd., pp. 2455–2463,
2003.'
ista: 'Hosten O, Vignolo P, Minguzzi A, Tanatar B, Tosi M. 2003. Free expansion
of two-dimensional condensates with a vortex. Journal of Physics B: Atomic, Molecular
and Optical Physics. 36(12), 2455–2463.'
mla: 'Hosten, Onur, et al. “Free Expansion of Two-Dimensional Condensates with a
Vortex.” Journal of Physics B: Atomic, Molecular and Optical Physics, vol.
36, no. 12, IOP Publishing Ltd., 2003, pp. 2455–63, doi:10.1088/0953-4075/36/12/306.'
short: 'O. Hosten, P. Vignolo, A. Minguzzi, B. Tanatar, M. Tosi, Journal of Physics
B: Atomic, Molecular and Optical Physics 36 (2003) 2455–2463.'
date_created: 2018-12-11T11:47:16Z
date_published: 2003-06-28T00:00:00Z
date_updated: 2021-01-12T08:03:20Z
day: '28'
doi: 10.1088/0953-4075/36/12/306
extern: 1
intvolume: ' 36'
issue: '12'
month: '06'
page: 2455 - 2463
publication: 'Journal of Physics B: Atomic, Molecular and Optical Physics'
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '7239'
quality_controlled: 0
status: public
title: Free expansion of two-dimensional condensates with a vortex
type: journal_article
volume: 36
year: '2003'
...
---
_id: '6156'
abstract:
- lang: eng
text: 'Social and solitary feeding in natural Caenorhabditis elegans isolates are
associated with two alleles of the orphan G-protein-coupled receptor (GPCR) NPR-1:
social feeders contain NPR-1 215F, whereas solitary feeders contain NPR-1 215V.
Here we identify FMRFamide-related neuropeptides (FaRPs) encoded by the flp-18
and flp-21 genes as NPR-1 ligands and show that these peptides can differentially
activate the NPR-1 215F and NPR-1 215V receptors. Multicopy overexpression of
flp-21 transformed wild social animals into solitary feeders. Conversely, a flp-21
deletion partially phenocopied the npr-1(null) phenotype, which is consistent
with NPR-1 activation by FLP-21 in vivo but also implicates other ligands for
NPR-1. Phylogenetic studies indicate that the dominant npr-1 215V allele likely
arose from an ancestral npr-1 215F gene in C. elegans. Our data suggest a model
in which solitary feeding evolved in an ancestral social strain of C. elegans
by a gain-of-function mutation that modified the response of NPR-1 to FLP-18 and
FLP-21 ligands.'
author:
- first_name: Candida
full_name: Rogers, Candida
last_name: Rogers
- first_name: Vincenzina
full_name: Reale, Vincenzina
last_name: Reale
- first_name: Kyuhyung
full_name: Kim, Kyuhyung
last_name: Kim
- first_name: Heather
full_name: Chatwin, Heather
last_name: Chatwin
- first_name: Chris
full_name: Li, Chris
last_name: Li
- first_name: Peter
full_name: Evans, Peter
last_name: Evans
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Rogers C, Reale V, Kim K, et al. Inhibition of Caenorhabditis elegans social
feeding by FMRFamide-related peptide activation of NPR-1. Nature Neuroscience.
2003;6(11):1178-1185. doi:10.1038/nn1140
apa: Rogers, C., Reale, V., Kim, K., Chatwin, H., Li, C., Evans, P., & de Bono,
M. (2003). Inhibition of Caenorhabditis elegans social feeding by FMRFamide-related
peptide activation of NPR-1. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/nn1140
chicago: Rogers, Candida, Vincenzina Reale, Kyuhyung Kim, Heather Chatwin, Chris
Li, Peter Evans, and Mario de Bono. “Inhibition of Caenorhabditis Elegans Social
Feeding by FMRFamide-Related Peptide Activation of NPR-1.” Nature Neuroscience.
Springer Nature, 2003. https://doi.org/10.1038/nn1140.
ieee: C. Rogers et al., “Inhibition of Caenorhabditis elegans social feeding
by FMRFamide-related peptide activation of NPR-1,” Nature Neuroscience,
vol. 6, no. 11. Springer Nature, pp. 1178–1185, 2003.
ista: Rogers C, Reale V, Kim K, Chatwin H, Li C, Evans P, de Bono M. 2003. Inhibition
of Caenorhabditis elegans social feeding by FMRFamide-related peptide activation
of NPR-1. Nature Neuroscience. 6(11), 1178–1185.
mla: Rogers, Candida, et al. “Inhibition of Caenorhabditis Elegans Social Feeding
by FMRFamide-Related Peptide Activation of NPR-1.” Nature Neuroscience,
vol. 6, no. 11, Springer Nature, 2003, pp. 1178–85, doi:10.1038/nn1140.
short: C. Rogers, V. Reale, K. Kim, H. Chatwin, C. Li, P. Evans, M. de Bono, Nature
Neuroscience 6 (2003) 1178–1185.
date_created: 2019-03-21T09:47:53Z
date_published: 2003-10-12T00:00:00Z
date_updated: 2021-01-12T08:06:25Z
day: '12'
doi: 10.1038/nn1140
extern: '1'
external_id:
pmid:
- '14555955'
intvolume: ' 6'
issue: '11'
language:
- iso: eng
month: '10'
oa_version: None
page: 1178-1185
pmid: 1
publication: Nature Neuroscience
publication_identifier:
issn:
- 1097-6256
- 1546-1726
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Inhibition of Caenorhabditis elegans social feeding by FMRFamide-related peptide
activation of NPR-1
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2003'
...
---
_id: '6157'
abstract:
- lang: eng
text: In many animal species individuals aggregate to live in groups. A range of
experimental approaches in different animals, including studies of social feeding
in nematodes, maternal behavior in rats and sheep, and pair-bonding in voles,
are providing insights into the neural bases for these behaviors. These studies
are delineating multiple neural circuits and gene networks in the brain that interact
in ways that are as yet poorly understood to coordinate social behavior.
author:
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: de Bono M. Molecular approaches to aggregation behavior and social attachment.
Journal of Neurobiology. 2003;54(1):78-92. doi:10.1002/neu.10162
apa: de Bono, M. (2003). Molecular approaches to aggregation behavior and social
attachment. Journal of Neurobiology. Wiley. https://doi.org/10.1002/neu.10162
chicago: Bono, Mario de. “Molecular Approaches to Aggregation Behavior and Social
Attachment.” Journal of Neurobiology. Wiley, 2003. https://doi.org/10.1002/neu.10162.
ieee: M. de Bono, “Molecular approaches to aggregation behavior and social attachment,”
Journal of Neurobiology, vol. 54, no. 1. Wiley, pp. 78–92, 2003.
ista: de Bono M. 2003. Molecular approaches to aggregation behavior and social attachment.
Journal of Neurobiology. 54(1), 78–92.
mla: de Bono, Mario. “Molecular Approaches to Aggregation Behavior and Social Attachment.”
Journal of Neurobiology, vol. 54, no. 1, Wiley, 2003, pp. 78–92, doi:10.1002/neu.10162.
short: M. de Bono, Journal of Neurobiology 54 (2003) 78–92.
date_created: 2019-03-21T09:52:31Z
date_published: 2003-01-01T00:00:00Z
date_updated: 2021-01-12T08:06:26Z
day: '01'
doi: 10.1002/neu.10162
extern: '1'
external_id:
pmid:
- '12486699'
intvolume: ' 54'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 78-92
pmid: 1
publication: Journal of Neurobiology
publication_identifier:
issn:
- 0022-3034
- 1097-4695
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Molecular approaches to aggregation behavior and social attachment
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2003'
...
---
_id: '847'
abstract:
- lang: eng
text: The accumulation of genome-wide information on single nucleotide polymorphisms
in humans provides an unprecedented opportunity to detect the evolutionary forces
responsible for heterogeneity of the level of genetic variability across loci.
Previous studies have shown that history of recombination events has produced
long haplotype blocks in the human genome, which contribute to this heterogeneity.
Other factors, however, such as natural selection or the heterogeneity of mutation
rates across loci, may also lead to heterogeneity of genetic variability. We compared
synonymous and non-synonymous variability within human genes with their divergence
from murine orthologs. We separately analyzed the non-synonymous variants predicted
to damage protein structure or function and the variants predicted to be functionally
benign. The predictions were based on comparative sequence analysis and, in some
cases, on the analysis of protein structure. A strong correlation between non-synonymous,
benign variability and non-synonymous human-mouse divergence suggests that selection
played an important role in shaping the pattern of variability in coding regions
of human genes. However, the lack of correlation between deleterious variability
and evolutionary divergence shows that a substantial proportion of the observed
non-synonymous single-nucleotide polymorphisms reduces fitness and never reaches
fixation. Evolutionary and medical implications of the impact of selection on
human polymorphisms are discussed.
acknowledgement: We are grateful to Alexey Kondrashov and Alison Wellman for the careful
reading of the manuscript and providing us with their valuable comments.
author:
- first_name: Shamil
full_name: Sunyaev, Shamil R
last_name: Sunyaev
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Peer
full_name: Bork, Peer
last_name: Bork
- first_name: Vasily
full_name: Ramensky, Vasily
last_name: Ramensky
citation:
ama: Sunyaev S, Kondrashov F, Bork P, Ramensky V. Impact of selection, mutation
rate and genetic drift on human genetic variation. Human Molecular Genetics.
2003;12(24):3325-3330. doi:10.1093/hmg/ddg359
apa: Sunyaev, S., Kondrashov, F., Bork, P., & Ramensky, V. (2003). Impact of
selection, mutation rate and genetic drift on human genetic variation. Human
Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddg359
chicago: Sunyaev, Shamil, Fyodor Kondrashov, Peer Bork, and Vasily Ramensky. “Impact
of Selection, Mutation Rate and Genetic Drift on Human Genetic Variation.” Human
Molecular Genetics. Oxford University Press, 2003. https://doi.org/10.1093/hmg/ddg359.
ieee: S. Sunyaev, F. Kondrashov, P. Bork, and V. Ramensky, “Impact of selection,
mutation rate and genetic drift on human genetic variation,” Human Molecular
Genetics, vol. 12, no. 24. Oxford University Press, pp. 3325–3330, 2003.
ista: Sunyaev S, Kondrashov F, Bork P, Ramensky V. 2003. Impact of selection, mutation
rate and genetic drift on human genetic variation. Human Molecular Genetics. 12(24),
3325–3330.
mla: Sunyaev, Shamil, et al. “Impact of Selection, Mutation Rate and Genetic Drift
on Human Genetic Variation.” Human Molecular Genetics, vol. 12, no. 24,
Oxford University Press, 2003, pp. 3325–30, doi:10.1093/hmg/ddg359.
short: S. Sunyaev, F. Kondrashov, P. Bork, V. Ramensky, Human Molecular Genetics
12 (2003) 3325–3330.
date_created: 2018-12-11T11:48:49Z
date_published: 2003-12-15T00:00:00Z
date_updated: 2021-01-12T08:19:29Z
day: '15'
doi: 10.1093/hmg/ddg359
extern: 1
intvolume: ' 12'
issue: '24'
month: '12'
page: 3325 - 3330
publication: Human Molecular Genetics
publication_status: published
publisher: Oxford University Press
publist_id: '6803'
quality_controlled: 0
status: public
title: Impact of selection, mutation rate and genetic drift on human genetic variation
type: journal_article
volume: 12
year: '2003'
...
---
_id: '876'
abstract:
- lang: eng
text: Alternative splicing is thought to be a major source of functional diversity
in animal proteins. We analyzed the evolutionary conservation of proteins encoded
by alternatively spliced genes and predicted the ancestral state for 73 cases
of alternative splicing (25 insertions and 48 deletions). The amino acid sequences
of most of the inserts in proteins produced by alternative splicing are as conserved
as the surrounding sequences. Thus, alternative splicing often creates novel isoforms
by the insertion of new, functional protein sequences that probably originated
from noncoding sequences of introns.
acknowledgement: We thank Peer Bork, Mikhail Gelfand, Alexey Kondrashov, David Lipman
and Shamil Sunyaev for critical reading of the manuscript and useful suggestions
and the Koonin group members for helpful discussions.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Eugene
full_name: Koonin, Eugene V
last_name: Koonin
citation:
ama: 'Kondrashov F, Koonin E. Evolution of alternative splicing: Deletions, insertions
and origin of functional parts of proteins from intron sequences. Trends in
Genetics. 2003;19(3):115-119. doi:10.1016/S0168-9525(02)00029-X'
apa: 'Kondrashov, F., & Koonin, E. (2003). Evolution of alternative splicing:
Deletions, insertions and origin of functional parts of proteins from intron sequences.
Trends in Genetics. Elsevier. https://doi.org/10.1016/S0168-9525(02)00029-X'
chicago: 'Kondrashov, Fyodor, and Eugene Koonin. “Evolution of Alternative Splicing:
Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences.”
Trends in Genetics. Elsevier, 2003. https://doi.org/10.1016/S0168-9525(02)00029-X.'
ieee: 'F. Kondrashov and E. Koonin, “Evolution of alternative splicing: Deletions,
insertions and origin of functional parts of proteins from intron sequences,”
Trends in Genetics, vol. 19, no. 3. Elsevier, pp. 115–119, 2003.'
ista: 'Kondrashov F, Koonin E. 2003. Evolution of alternative splicing: Deletions,
insertions and origin of functional parts of proteins from intron sequences. Trends
in Genetics. 19(3), 115–119.'
mla: 'Kondrashov, Fyodor, and Eugene Koonin. “Evolution of Alternative Splicing:
Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences.”
Trends in Genetics, vol. 19, no. 3, Elsevier, 2003, pp. 115–19, doi:10.1016/S0168-9525(02)00029-X.'
short: F. Kondrashov, E. Koonin, Trends in Genetics 19 (2003) 115–119.
date_created: 2018-12-11T11:48:58Z
date_published: 2003-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:58Z
day: '01'
doi: 10.1016/S0168-9525(02)00029-X
extern: 1
intvolume: ' 19'
issue: '3'
month: '01'
page: 115 - 119
publication: Trends in Genetics
publication_status: published
publisher: Elsevier
publist_id: '6776'
quality_controlled: 0
status: public
title: 'Evolution of alternative splicing: Deletions, insertions and origin of functional
parts of proteins from intron sequences'
type: journal_article
volume: 19
year: '2003'
...
---
_id: '9495'
abstract:
- lang: eng
text: RNA interference is a conserved process in which double-stranded RNA is processed
into 21–25 nucleotide siRNAs that trigger posttranscriptional gene silencing.
In addition, plants display a phenomenon termed RNA-directed DNA methylation (RdDM)
in which DNA with sequence identity to silenced RNA is de novo methylated at its
cytosine residues. This methylation is not only at canonical CpG sites but also
at cytosines in CpNpG and asymmetric sequence contexts. In this report, we study
the role of the DRM and CMT3 DNA methyltransferase genes in the initiation and
maintenance of RdDM. Neither drm nor cmt3 mutants affected the maintenance of
preestablished RNA-directed CpG methylation. However, drm mutants showed a nearly
complete loss of asymmetric methylation and a partial loss of CpNpG methylation.
The remaining asymmetric and CpNpG methylation was dependent on the activity of
CMT3, showing that DRM and CMT3 act redundantly to maintain non-CpG methylation.
These DNA methyltransferases appear to act downstream of siRNAs, since drm1 drm2
cmt3 triple mutants show a lack of non-CpG methylation but elevated levels of
siRNAs. Finally, we demonstrate that DRM activity is required for the initial
establishment of RdDM in all sequence contexts including CpG, CpNpG, and asymmetric
sites.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaofeng
full_name: Cao, Xiaofeng
last_name: Cao
- first_name: Werner
full_name: Aufsatz, Werner
last_name: Aufsatz
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: M.Florian
full_name: Mette, M.Florian
last_name: Mette
- first_name: Michael S.
full_name: Huang, Michael S.
last_name: Huang
- first_name: Marjori
full_name: Matzke, Marjori
last_name: Matzke
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Cao X, Aufsatz W, Zilberman D, et al. Role of the DRM and CMT3 methyltransferases
in RNA-directed DNA methylation. Current Biology. 2003;13(24):2212-2217.
doi:10.1016/j.cub.2003.11.052
apa: Cao, X., Aufsatz, W., Zilberman, D., Mette, M. F., Huang, M. S., Matzke, M.,
& Jacobsen, S. E. (2003). Role of the DRM and CMT3 methyltransferases in RNA-directed
DNA methylation. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2003.11.052
chicago: Cao, Xiaofeng, Werner Aufsatz, Daniel Zilberman, M.Florian Mette, Michael
S. Huang, Marjori Matzke, and Steven E. Jacobsen. “Role of the DRM and CMT3 Methyltransferases
in RNA-Directed DNA Methylation.” Current Biology. Elsevier, 2003. https://doi.org/10.1016/j.cub.2003.11.052.
ieee: X. Cao et al., “Role of the DRM and CMT3 methyltransferases in RNA-directed
DNA methylation,” Current Biology, vol. 13, no. 24. Elsevier, pp. 2212–2217,
2003.
ista: Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE.
2003. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation.
Current Biology. 13(24), 2212–2217.
mla: Cao, Xiaofeng, et al. “Role of the DRM and CMT3 Methyltransferases in RNA-Directed
DNA Methylation.” Current Biology, vol. 13, no. 24, Elsevier, 2003, pp.
2212–17, doi:10.1016/j.cub.2003.11.052.
short: X. Cao, W. Aufsatz, D. Zilberman, M.F. Mette, M.S. Huang, M. Matzke, S.E.
Jacobsen, Current Biology 13 (2003) 2212–2217.
date_created: 2021-06-07T10:43:02Z
date_published: 2003-12-16T00:00:00Z
date_updated: 2021-12-14T08:41:38Z
day: '16'
department:
- _id: DaZi
doi: 10.1016/j.cub.2003.11.052
extern: '1'
external_id:
pmid:
- '14680640'
intvolume: ' 13'
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2003.11.052
month: '12'
oa: 1
oa_version: Published Version
page: 2212-2217
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 13
year: '2003'
...
---
_id: '8519'
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Kaloshin V. The existential Hilbert 16-th problem and an estimate for cyclicity
of elementary polycycles. Inventiones mathematicae. 2003;151(3):451-512.
doi:10.1007/s00222-002-0244-9
apa: Kaloshin, V. (2003). The existential Hilbert 16-th problem and an estimate
for cyclicity of elementary polycycles. Inventiones Mathematicae. Springer
Nature. https://doi.org/10.1007/s00222-002-0244-9
chicago: Kaloshin, Vadim. “The Existential Hilbert 16-Th Problem and an Estimate
for Cyclicity of Elementary Polycycles.” Inventiones Mathematicae. Springer
Nature, 2003. https://doi.org/10.1007/s00222-002-0244-9.
ieee: V. Kaloshin, “The existential Hilbert 16-th problem and an estimate for cyclicity
of elementary polycycles,” Inventiones mathematicae, vol. 151, no. 3. Springer
Nature, pp. 451–512, 2003.
ista: Kaloshin V. 2003. The existential Hilbert 16-th problem and an estimate for
cyclicity of elementary polycycles. Inventiones mathematicae. 151(3), 451–512.
mla: Kaloshin, Vadim. “The Existential Hilbert 16-Th Problem and an Estimate for
Cyclicity of Elementary Polycycles.” Inventiones Mathematicae, vol. 151,
no. 3, Springer Nature, 2003, pp. 451–512, doi:10.1007/s00222-002-0244-9.
short: V. Kaloshin, Inventiones Mathematicae 151 (2003) 451–512.
date_created: 2020-09-18T10:49:26Z
date_published: 2003-03-01T00:00:00Z
date_updated: 2021-01-12T08:19:50Z
day: '01'
doi: 10.1007/s00222-002-0244-9
extern: '1'
intvolume: ' 151'
issue: '3'
keyword:
- General Mathematics
language:
- iso: eng
month: '03'
oa_version: None
page: 451-512
publication: Inventiones mathematicae
publication_identifier:
issn:
- 0020-9910
- 1432-1297
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: The existential Hilbert 16-th problem and an estimate for cyclicity of elementary
polycycles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 151
year: '2003'
...
---
_id: '9455'
abstract:
- lang: eng
text: Proteins of the ARGONAUTE family are important in diverse posttranscriptional
RNA-mediated gene-silencing systems as well as in transcriptional gene silencing
in Drosophila and fission yeast and in programmed DNA elimination in Tetrahymena.
We cloned ARGONAUTE4 (AGO4) from a screen for mutants that suppress silencing
of the Arabidopsis SUPERMAN(SUP) gene. The ago4-1 mutant reactivated silentSUP
alleles and decreased CpNpG and asymmetric DNA methylation as well as histone
H3 lysine-9 methylation. In addition,ago4-1 blocked histone and DNA methylation
and the accumulation of 25-nucleotide small interfering RNAs (siRNAs) that correspond
to the retroelement AtSN1. These results suggest that AGO4 and long siRNAs direct
chromatin modifications, including histone methylation and non-CpG DNA methylation.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: ' Xiaofeng'
full_name: Cao, Xiaofeng
last_name: Cao
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Zilberman D, Cao Xiaofeng, Jacobsen SE. ARGONAUTE4 control of locus-specific
siRNA accumulation and DNA and histone methylation. Science. 2003;299(5607):716-719.
doi:10.1126/science.1079695
apa: Zilberman, D., Cao, Xiaofeng, & Jacobsen, S. E. (2003). ARGONAUTE4 control
of locus-specific siRNA accumulation and DNA and histone methylation. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.1079695
chicago: Zilberman, Daniel, Xiaofeng Cao, and Steven E. Jacobsen. “ARGONAUTE4 Control
of Locus-Specific SiRNA Accumulation and DNA and Histone Methylation.” Science.
American Association for the Advancement of Science, 2003. https://doi.org/10.1126/science.1079695.
ieee: D. Zilberman, Xiaofeng Cao, and S. E. Jacobsen, “ARGONAUTE4 control of locus-specific
siRNA accumulation and DNA and histone methylation,” Science, vol. 299,
no. 5607. American Association for the Advancement of Science, pp. 716–719, 2003.
ista: Zilberman D, Cao Xiaofeng, Jacobsen SE. 2003. ARGONAUTE4 control of locus-specific
siRNA accumulation and DNA and histone methylation. Science. 299(5607), 716–719.
mla: Zilberman, Daniel, et al. “ARGONAUTE4 Control of Locus-Specific SiRNA Accumulation
and DNA and Histone Methylation.” Science, vol. 299, no. 5607, American
Association for the Advancement of Science, 2003, pp. 716–19, doi:10.1126/science.1079695.
short: D. Zilberman, Xiaofeng Cao, S.E. Jacobsen, Science 299 (2003) 716–719.
date_created: 2021-06-04T11:26:26Z
date_published: 2003-01-31T00:00:00Z
date_updated: 2021-12-14T08:43:30Z
day: '31'
department:
- _id: DaZi
doi: 10.1126/science.1079695
extern: '1'
external_id:
pmid:
- '12522258'
intvolume: ' 299'
issue: '5607'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '01'
oa_version: None
page: 716-719
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: ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone
methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 299
year: '2003'
...
---
_id: '4628'
abstract:
- lang: eng
text: 'Discounting the future means that the value, today, of a unit payoffis 1
if the payoffo ccurs today, a if it occurs tomorrow, a 2 if it occurs the day
after tomorrow, and so on, for some real-valued discount factor 0 < a <
1. Discounting (or inflation) is a key paradigm in economics and has been studied
in Markov decision processes as well as game theory. We submit that discounting
also has a natural place in systems engineering: for nonterminating systems, a
potential bug in the far-away future is less troubling than a potential bug today.
We therefore develop a systems theory with discounting. Our theory includes several
basic elements: discounted versions of system properties that correspond to the
ω-regular properties, fixpoint-based algorithms for checking discounted properties,
and a quantitative notion of bisimilarity for capturing the difference between
two states with respect to discounted properties. We present the theory in a general
form that applies to probabilistic systems as well as multicomponent systems (games),
but it readily specializes to classical transition systems. We show that discounting,
besides its natural practical appeal, has also several mathematical benefits.
First, the resulting theory is robust, in that small perturbations of a system
can cause only small changes in the properties of the system. Second, the theory
is computational, in that the values of discounted properties, as well as the
discounted bisimilarity distance between states, can be computed to any desired
degree of precision.'
acknowledgement: This research was supported in part by the NSF CAREER award CCR-0132780,
the DARPA grant F33615-C-98-3614, the NSF grants CCR-9988172, CCR-0234690 and CCR-0225610,
and the ONR grant N00014-02-1-0671.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Luca
full_name: De Alfaro, Luca
last_name: De Alfaro
- 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: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
citation:
ama: 'De Alfaro L, Henzinger TA, Majumdar R. Discounting the future in systems theory.
In: Proceedings of the 30th International Colloquium on Automata, Languages
and Programming. Vol 2719. Springer; 2003:1022-1037. doi:10.1007/3-540-45061-0_79'
apa: 'De Alfaro, L., Henzinger, T. A., & Majumdar, R. (2003). Discounting the
future in systems theory. In Proceedings of the 30th International Colloquium
on Automata, Languages and Programming (Vol. 2719, pp. 1022–1037). Eindhoven,
The Netherlands: Springer. https://doi.org/10.1007/3-540-45061-0_79'
chicago: De Alfaro, Luca, Thomas A Henzinger, and Ritankar Majumdar. “Discounting
the Future in Systems Theory.” In Proceedings of the 30th International Colloquium
on Automata, Languages and Programming, 2719:1022–37. Springer, 2003. https://doi.org/10.1007/3-540-45061-0_79.
ieee: L. De Alfaro, T. A. Henzinger, and R. Majumdar, “Discounting the future in
systems theory,” in Proceedings of the 30th International Colloquium on Automata,
Languages and Programming, Eindhoven, The Netherlands, 2003, vol. 2719, pp.
1022–1037.
ista: 'De Alfaro L, Henzinger TA, Majumdar R. 2003. Discounting the future in systems
theory. Proceedings of the 30th International Colloquium on Automata, Languages
and Programming. ICALP: Automata, Languages and Programming, LNCS, vol. 2719,
1022–1037.'
mla: De Alfaro, Luca, et al. “Discounting the Future in Systems Theory.” Proceedings
of the 30th International Colloquium on Automata, Languages and Programming,
vol. 2719, Springer, 2003, pp. 1022–37, doi:10.1007/3-540-45061-0_79.
short: L. De Alfaro, T.A. Henzinger, R. Majumdar, in:, Proceedings of the 30th International
Colloquium on Automata, Languages and Programming, Springer, 2003, pp. 1022–1037.
conference:
end_date: 2003-07-04
location: Eindhoven, The Netherlands
name: 'ICALP: Automata, Languages and Programming'
start_date: 2003-06-30
date_created: 2018-12-11T12:09:50Z
date_published: 2003-06-25T00:00:00Z
date_updated: 2023-07-26T13:07:31Z
day: '25'
doi: 10.1007/3-540-45061-0_79
extern: '1'
intvolume: ' 2719'
language:
- iso: eng
month: '06'
oa_version: None
page: 1022 - 1037
publication: Proceedings of the 30th International Colloquium on Automata, Languages
and Programming
publication_identifier:
isbn:
- '9783540404934'
publication_status: published
publisher: Springer
publist_id: '77'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Discounting the future in systems theory
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2719
year: '2003'
...
---
_id: '13436'
abstract:
- lang: eng
text: Cross-metathesis reactions of α,β-unsaturated sulfones and sulfoxides in the
presence of molybdenum and ruthenium pre-catalysts were tested. A selective metahesis
reaction was achieved between functionalized terminal olefins and vinyl sulfones
by using the ‘second generation’ ruthenium catalysts 1c–h while the highly active
Schrock catalyst 1b was found to be functional group incompatible with vinyl sulfones.
The cross-metathesis products were isolated in good yields with an excellent (E)-selectivity.
Both the molybdenum and ruthenium-based complexes were, however, incompatible
with α,β- and β,γ-unsaturated sulfoxides.
article_processing_charge: No
article_type: original
author:
- first_name: Anna
full_name: Michrowska, Anna
last_name: Michrowska
- first_name: Michał
full_name: Bieniek, Michał
last_name: Bieniek
- first_name: Mikhail
full_name: Kim, Mikhail
last_name: Kim
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Karol
full_name: Grela, Karol
last_name: Grela
citation:
ama: Michrowska A, Bieniek M, Kim M, Klajn R, Grela K. Cross-metathesis reaction
of vinyl sulfones and sulfoxides. Tetrahedron. 2003;59(25):4525-4531. doi:10.1016/s0040-4020(03)00682-3
apa: Michrowska, A., Bieniek, M., Kim, M., Klajn, R., & Grela, K. (2003). Cross-metathesis
reaction of vinyl sulfones and sulfoxides. Tetrahedron. Elsevier. https://doi.org/10.1016/s0040-4020(03)00682-3
chicago: Michrowska, Anna, Michał Bieniek, Mikhail Kim, Rafal Klajn, and Karol Grela.
“Cross-Metathesis Reaction of Vinyl Sulfones and Sulfoxides.” Tetrahedron.
Elsevier, 2003. https://doi.org/10.1016/s0040-4020(03)00682-3.
ieee: A. Michrowska, M. Bieniek, M. Kim, R. Klajn, and K. Grela, “Cross-metathesis
reaction of vinyl sulfones and sulfoxides,” Tetrahedron, vol. 59, no. 25.
Elsevier, pp. 4525–4531, 2003.
ista: Michrowska A, Bieniek M, Kim M, Klajn R, Grela K. 2003. Cross-metathesis reaction
of vinyl sulfones and sulfoxides. Tetrahedron. 59(25), 4525–4531.
mla: Michrowska, Anna, et al. “Cross-Metathesis Reaction of Vinyl Sulfones and Sulfoxides.”
Tetrahedron, vol. 59, no. 25, Elsevier, 2003, pp. 4525–31, doi:10.1016/s0040-4020(03)00682-3.
short: A. Michrowska, M. Bieniek, M. Kim, R. Klajn, K. Grela, Tetrahedron 59 (2003)
4525–4531.
date_created: 2023-08-01T10:39:34Z
date_published: 2003-06-16T00:00:00Z
date_updated: 2023-08-08T12:44:17Z
day: '16'
doi: 10.1016/s0040-4020(03)00682-3
extern: '1'
intvolume: ' 59'
issue: '25'
keyword:
- Organic Chemistry
- Drug Discovery
- Biochemistry
language:
- iso: eng
month: '06'
oa_version: None
page: 4525-4531
publication: Tetrahedron
publication_identifier:
eissn:
- 1464-5416
issn:
- 0040-4020
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cross-metathesis reaction of vinyl sulfones and sulfoxides
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 59
year: '2003'
...
---
_id: '4561'
abstract:
- lang: eng
text: 'We present a formalism for specifying component interfaces that expose component
requirements on limited resources. The formalism permits an algorithmic check
if two or more components, when put together, exceed the available resources.
Moreover, the formalism can be used to compute the quantity of resources necessary
for satisfying the requirements of a collection of components. The formalism can
be instantiated in several ways. For example, several components may draw power
from the same source. Then, the formalism supports compatibility checks such as:
can two components, when put together, achieve their tasks without ever exceeding
the available amount of peak power? or, can they achieve their tasks by using
no more than the initially available amount of energy (i.e., power accumulated
over time)? The corresponding quantitative questions that our algorithms answer
are the following: what is the amount of peak power needed for two components
to be put together? what is the corresponding amount of initial energy? To solve
these questions, we model interfaces with resource requirements as games with
quantitative objectives. The games are played on state spaces where each state
is labeled by a number (representing, e.g., power consumption), and a play produces
an infinite path of labels. The objective may be, for example, to minimize the
largest label that occurs during a play. We illustrate our approach by modeling
compatibility questions for the components of robot control software, and of wireless
sensor networks.'
acknowledgement: This research was supported in part by the DARPA grant F33615-00-C-1693,
the MARCO grant 98-DT-660, the ONR grant N00014-02-1-0671, and the NSF grants CCR-0085949,
CCR-0132780, CCR-0234690, and CCR-9988172.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Arindam
full_name: Chakrabarti, Arindam
last_name: Chakrabarti
- first_name: Luca
full_name: De Alfaro, Luca
last_name: De Alfaro
- 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: Mariëlle
full_name: Stoelinga, Mariëlle
last_name: Stoelinga
citation:
ama: 'Chakrabarti A, De Alfaro L, Henzinger TA, Stoelinga M. Resource interfaces.
In: Third International Conference on Embedded Software. Vol 2855. ACM;
2003:117-133. doi:10.1007/978-3-540-45212-6_9'
apa: 'Chakrabarti, A., De Alfaro, L., Henzinger, T. A., & Stoelinga, M. (2003).
Resource interfaces. In Third International Conference on Embedded Software
(Vol. 2855, pp. 117–133). Philadelphia, PA, USA: ACM. https://doi.org/10.1007/978-3-540-45212-6_9'
chicago: Chakrabarti, Arindam, Luca De Alfaro, Thomas A Henzinger, and Mariëlle
Stoelinga. “Resource Interfaces.” In Third International Conference on Embedded
Software, 2855:117–33. ACM, 2003. https://doi.org/10.1007/978-3-540-45212-6_9.
ieee: A. Chakrabarti, L. De Alfaro, T. A. Henzinger, and M. Stoelinga, “Resource
interfaces,” in Third International Conference on Embedded Software, Philadelphia,
PA, USA, 2003, vol. 2855, pp. 117–133.
ista: 'Chakrabarti A, De Alfaro L, Henzinger TA, Stoelinga M. 2003. Resource interfaces.
Third International Conference on Embedded Software. EMSOFT: Embedded Software
, LNCS, vol. 2855, 117–133.'
mla: Chakrabarti, Arindam, et al. “Resource Interfaces.” Third International
Conference on Embedded Software, vol. 2855, ACM, 2003, pp. 117–33, doi:10.1007/978-3-540-45212-6_9.
short: A. Chakrabarti, L. De Alfaro, T.A. Henzinger, M. Stoelinga, in:, Third International
Conference on Embedded Software, ACM, 2003, pp. 117–133.
conference:
end_date: 2003-10-15
location: Philadelphia, PA, USA
name: 'EMSOFT: Embedded Software '
start_date: 2003-10-13
date_created: 2018-12-11T12:09:29Z
date_published: 2003-09-29T00:00:00Z
date_updated: 2024-01-08T10:48:11Z
day: '29'
doi: 10.1007/978-3-540-45212-6_9
extern: '1'
intvolume: ' 2855'
language:
- iso: eng
month: '09'
oa_version: None
page: 117 - 133
publication: Third International Conference on Embedded Software
publication_identifier:
isbn:
- '9783540202233'
publication_status: published
publisher: ACM
publist_id: '148'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Resource interfaces
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2855
year: '2003'
...
---
_id: '4630'
abstract:
- lang: eng
text: We consider concurrent two-person games played in real time, in which the
players decide both which action to play, and when to play it. Such timed games
differ from untimed games in two essential ways. First, players can take each
other by surprise, because actions are played with delays that cannot be anticipated
by the opponent. Second, a player should not be able to win the game by preventing
time from diverging. We present a model of timed games that preserves the element
of surprise and accounts for time divergence in a way that treats both players
symmetrically and applies to all ω-regular winning conditions. We prove that the
ability to take each other by surprise adds extra power to the players. For the
case that the games are specified in the style of timed automata, we provide symbolic
algorithms for their solution with respect to all ω-regular winning conditions.
We also show that for these timed games, memory strategies are more powerful than
memoryless strategies already in the case of reachability objectives.
acknowledgement: Supported in part by the AFOSR MURI grant F49620-00-1-0327, the DARPA
grant F33615-C-98-3614, the MARCO grant 98-DT-660, -the ONR grant N00014-02-1-0671,
the NSF grants CCR-9988172, CCR-0225610, and CCR-0234690, the NSF CAREER award CCR-0132780,
and the MIUR grant MEFISTO.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Luca
full_name: De Alfaro, Luca
last_name: De Alfaro
- first_name: Marco
full_name: Faella, Marco
last_name: Faella
- 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: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
- first_name: Mariëlle
full_name: Stoelinga, Mariëlle
last_name: Stoelinga
citation:
ama: 'De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. The element
of surprise in timed games. In: Proceedings of the 14th International Conference
on Concurrency Theory. Vol 2761. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2003:144-158. doi:10.1007/978-3-540-45187-7_9'
apa: 'De Alfaro, L., Faella, M., Henzinger, T. A., Majumdar, R., & Stoelinga,
M. (2003). The element of surprise in timed games. In Proceedings of the 14th
International Conference on Concurrency Theory (Vol. 2761, pp. 144–158). Marseille,
France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-540-45187-7_9'
chicago: De Alfaro, Luca, Marco Faella, Thomas A Henzinger, Ritankar Majumdar, and
Mariëlle Stoelinga. “The Element of Surprise in Timed Games.” In Proceedings
of the 14th International Conference on Concurrency Theory, 2761:144–58. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2003. https://doi.org/10.1007/978-3-540-45187-7_9.
ieee: L. De Alfaro, M. Faella, T. A. Henzinger, R. Majumdar, and M. Stoelinga, “The
element of surprise in timed games,” in Proceedings of the 14th International
Conference on Concurrency Theory, Marseille, France, 2003, vol. 2761, pp.
144–158.
ista: 'De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. 2003. The element
of surprise in timed games. Proceedings of the 14th International Conference on
Concurrency Theory. CONCUR: Concurrency Theory, LNCS, vol. 2761, 144–158.'
mla: De Alfaro, Luca, et al. “The Element of Surprise in Timed Games.” Proceedings
of the 14th International Conference on Concurrency Theory, vol. 2761, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2003, pp. 144–58, doi:10.1007/978-3-540-45187-7_9.
short: L. De Alfaro, M. Faella, T.A. Henzinger, R. Majumdar, M. Stoelinga, in:,
Proceedings of the 14th International Conference on Concurrency Theory, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2003, pp. 144–158.
conference:
end_date: 2003-09-05
location: Marseille, France
name: 'CONCUR: Concurrency Theory'
start_date: 2003-09-03
date_created: 2018-12-11T12:09:51Z
date_published: 2003-08-21T00:00:00Z
date_updated: 2024-01-08T10:05:30Z
day: '21'
doi: 10.1007/978-3-540-45187-7_9
extern: '1'
intvolume: ' 2761'
language:
- iso: eng
month: '08'
oa_version: None
page: 144 - 158
publication: Proceedings of the 14th International Conference on Concurrency Theory
publication_identifier:
isbn:
- '9783540407539'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '78'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The element of surprise in timed games
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2761
year: '2003'
...
---
_id: '4468'
abstract:
- lang: eng
text: Giotto is a high-level programming language for time-triggered control applications.
The authors begin with a conceptual overview of its methodology, discuss the Giotto
helicopter project, and summarize available Giotto implementations.
acknowledgement: We thank Niklaus Wirth and Walter Schaufelberger for their advice
and support of the reengineering effort of the ETH Zurich helicopter control system
using Giotto. This research was supported in part by DARPA SEC grant F33615-C-98–3614,
MARCO GSRC grant 98-DT-660, and AFOSR MURI grant F49620–00-1–0327. A preliminary
version of this article appeared as [1].
article_processing_charge: No
article_type: original
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Christoph
full_name: Kirsch, Christoph
last_name: Kirsch
- first_name: Marco
full_name: Sanvido, Marco
last_name: Sanvido
- first_name: Wolfgang
full_name: Pree, Wolfgang
last_name: Pree
citation:
ama: Henzinger TA, Kirsch C, Sanvido M, Pree W. From control models to real-time
code using Giotto. IEEE Control Systems Magazine. 2003;23(1):50-64. doi:10.1109/MCS.2003.1172829
apa: Henzinger, T. A., Kirsch, C., Sanvido, M., & Pree, W. (2003). From control
models to real-time code using Giotto. IEEE Control Systems Magazine. IEEE.
https://doi.org/10.1109/MCS.2003.1172829
chicago: Henzinger, Thomas A, Christoph Kirsch, Marco Sanvido, and Wolfgang Pree.
“From Control Models to Real-Time Code Using Giotto.” IEEE Control Systems
Magazine. IEEE, 2003. https://doi.org/10.1109/MCS.2003.1172829.
ieee: T. A. Henzinger, C. Kirsch, M. Sanvido, and W. Pree, “From control models
to real-time code using Giotto,” IEEE Control Systems Magazine, vol. 23,
no. 1. IEEE, pp. 50–64, 2003.
ista: Henzinger TA, Kirsch C, Sanvido M, Pree W. 2003. From control models to real-time
code using Giotto. IEEE Control Systems Magazine. 23(1), 50–64.
mla: Henzinger, Thomas A., et al. “From Control Models to Real-Time Code Using Giotto.”
IEEE Control Systems Magazine, vol. 23, no. 1, IEEE, 2003, pp. 50–64, doi:10.1109/MCS.2003.1172829.
short: T.A. Henzinger, C. Kirsch, M. Sanvido, W. Pree, IEEE Control Systems Magazine
23 (2003) 50–64.
date_created: 2018-12-11T12:09:00Z
date_published: 2003-01-29T00:00:00Z
date_updated: 2024-01-08T10:54:53Z
day: '29'
doi: 10.1109/MCS.2003.1172829
extern: '1'
intvolume: ' 23'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 50 - 64
publication: IEEE Control Systems Magazine
publication_identifier:
issn:
- '1066-033X '
publication_status: published
publisher: IEEE
publist_id: '260'
quality_controlled: '1'
scopus_import: '1'
status: public
title: From control models to real-time code using Giotto
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 23
year: '2003'
...
---
_id: '4465'
abstract:
- lang: eng
text: Giotto is a principled, tool-supported design methodology for implementing
embedded control systems on platforms of possibly distributed sensors, actuators,
CPUs, and networks. Giotto is based on the principle that time-triggered task
invocations plus time-triggered mode switches can form the abstract essence of
programming real-time control systems. Giotto consists of a programming language
with a formal semantics, and a retargetable compiler and runtime library. Giotto
supports the automation of control system design by strictly separating platform-independent
functionality and timing concerns from platform-dependent scheduling and communication
issues. The time-triggered predictability of Giotto makes it particularly suitable
for safety-critical applications with hard real-time constraints. We illustrate
the platform independence and time-triggered execution of Giotto by coordinating
a heterogeneous flock of Intel x86 robots and Lego Mindstorms robots.
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Benjamin
full_name: Horowitz, Benjamin
last_name: Horowitz
- first_name: Christoph
full_name: Kirsch, Christoph
last_name: Kirsch
citation:
ama: 'Henzinger TA, Horowitz B, Kirsch C. Embedded control systems development with
Giotto. In: Software-Enabled Control: Information Technology for Dynamical
Systems. Wiley-Blackwell; 2003:123-146. doi:10.1002/047172288X.ch8'
apa: 'Henzinger, T. A., Horowitz, B., & Kirsch, C. (2003). Embedded control
systems development with Giotto. In Software-Enabled Control: Information Technology
for Dynamical Systems (pp. 123–146). Wiley-Blackwell. https://doi.org/10.1002/047172288X.ch8'
chicago: 'Henzinger, Thomas A, Benjamin Horowitz, and Christoph Kirsch. “Embedded
Control Systems Development with Giotto.” In Software-Enabled Control: Information
Technology for Dynamical Systems, 123–46. Wiley-Blackwell, 2003. https://doi.org/10.1002/047172288X.ch8.'
ieee: 'T. A. Henzinger, B. Horowitz, and C. Kirsch, “Embedded control systems development
with Giotto,” in Software-Enabled Control: Information Technology for Dynamical
Systems, Wiley-Blackwell, 2003, pp. 123–146.'
ista: 'Henzinger TA, Horowitz B, Kirsch C. 2003.Embedded control systems development
with Giotto. In: Software-Enabled Control: Information Technology for Dynamical
Systems. , 123–146.'
mla: 'Henzinger, Thomas A., et al. “Embedded Control Systems Development with Giotto.”
Software-Enabled Control: Information Technology for Dynamical Systems,
Wiley-Blackwell, 2003, pp. 123–46, doi:10.1002/047172288X.ch8.'
short: 'T.A. Henzinger, B. Horowitz, C. Kirsch, in:, Software-Enabled Control: Information
Technology for Dynamical Systems, Wiley-Blackwell, 2003, pp. 123–146.'
date_created: 2018-12-11T12:08:59Z
date_published: 2003-05-20T00:00:00Z
date_updated: 2024-01-08T12:24:01Z
day: '20'
doi: 10.1002/047172288X.ch8
extern: '1'
language:
- iso: eng
month: '05'
oa_version: None
page: 123 - 146
publication: 'Software-Enabled Control: Information Technology for Dynamical Systems'
publication_identifier:
isbn:
- '9780471234364 '
publication_status: published
publisher: Wiley-Blackwell
publist_id: '262'
quality_controlled: '1'
status: public
title: Embedded control systems development with Giotto
type: book_chapter
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
year: '2003'
...
---
_id: '4466'
abstract:
- lang: eng
text: One source of complexity in the μ-calculus is its ability to specify an unbounded
number of switches between universal (AX) and existential (EX) branching modes.
We therefore study the problems of satisfiability, validity, model checking, and
implication for the universal and existential fragments of the μ-calculus, in
which only one branching mode is allowed. The universal fragment is rich enough
to express most specifications of interest, and therefore improved algorithms
are of practical importance. We show that while the satisfiability and validity
problems become indeed simpler for the existential and universal fragments, this
is, unfortunately, not the case for model checking and implication. We also show
the corresponding results for the alternationfree fragment of the μ-calculus,
where no alternations between least and greatest fixed points are allowed. Our
results imply that efforts to find a polynomial-time model-checking algorithm
for the μ-calculus can be replaced by efforts to find such an algorithm for the
universal or existential fragment.
acknowledgement: This work was supported in part by NSF grant CCR-9988172, the AFOSR
MURI grant F49620-00-1-0327, and a Microsoft Research Fellowship.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
citation:
ama: 'Henzinger TA, Kupferman O, Majumdar R. On the universal and existential fragments
of the mu-calculus. In: Proceedings of the 9th International Conference on
Tools and Algorithms for the Construction and Analysis of Systems . Vol 2619.
Springer; 2003:49-64. doi:10.1007/3-540-36577-X_5'
apa: 'Henzinger, T. A., Kupferman, O., & Majumdar, R. (2003). On the universal
and existential fragments of the mu-calculus. In Proceedings of the 9th International
Conference on Tools and Algorithms for the Construction and Analysis of Systems
(Vol. 2619, pp. 49–64). Warsaw, Poland: Springer. https://doi.org/10.1007/3-540-36577-X_5'
chicago: Henzinger, Thomas A, Orna Kupferman, and Ritankar Majumdar. “On the Universal
and Existential Fragments of the Mu-Calculus.” In Proceedings of the 9th International
Conference on Tools and Algorithms for the Construction and Analysis of Systems
, 2619:49–64. Springer, 2003. https://doi.org/10.1007/3-540-36577-X_5.
ieee: T. A. Henzinger, O. Kupferman, and R. Majumdar, “On the universal and existential
fragments of the mu-calculus,” in Proceedings of the 9th International Conference
on Tools and Algorithms for the Construction and Analysis of Systems , Warsaw,
Poland, 2003, vol. 2619, pp. 49–64.
ista: 'Henzinger TA, Kupferman O, Majumdar R. 2003. On the universal and existential
fragments of the mu-calculus. Proceedings of the 9th International Conference
on Tools and Algorithms for the Construction and Analysis of Systems . TACAS:
Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol.
2619, 49–64.'
mla: Henzinger, Thomas A., et al. “On the Universal and Existential Fragments of
the Mu-Calculus.” Proceedings of the 9th International Conference on Tools
and Algorithms for the Construction and Analysis of Systems , vol. 2619, Springer,
2003, pp. 49–64, doi:10.1007/3-540-36577-X_5.
short: T.A. Henzinger, O. Kupferman, R. Majumdar, in:, Proceedings of the 9th International
Conference on Tools and Algorithms for the Construction and Analysis of Systems
, Springer, 2003, pp. 49–64.
conference:
end_date: 2003-04-11
location: Warsaw, Poland
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2003-04-07
date_created: 2018-12-11T12:08:59Z
date_published: 2003-03-14T00:00:00Z
date_updated: 2024-01-08T13:17:35Z
day: '14'
doi: 10.1007/3-540-36577-X_5
extern: '1'
intvolume: ' 2619'
language:
- iso: eng
month: '03'
oa_version: None
page: 49 - 64
publication: 'Proceedings of the 9th International Conference on Tools and Algorithms
for the Construction and Analysis of Systems '
publication_identifier:
isbn:
- '9783540008989'
publication_status: published
publisher: Springer
publist_id: '263'
quality_controlled: '1'
status: public
title: On the universal and existential fragments of the mu-calculus
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2619
year: '2003'
...
---
_id: '4467'
abstract:
- lang: eng
text: 'BLAST (the Berkeley Lazy Abstraction Software verification Tool) is a verification
system for checking safety properties of C programs using automatic property-driven
construction and model checking of software abstractions. Blast implements an
abstract-model check-refine loop to check for reachability of a specified label
in the program. The abstract model is built on the fly using predicate abstraction.
This model is then checked for reachability. If there is no (abstract) path to
the specified error label, Blast reports that the system is safe and produces
a succinct proof. Otherwise, it checks if the path is feasible using symbolic
execution of the program. If the path is feasible, Blast outputs the path as an
error trace, otherwise, it uses the infeasibility of the path to refine the abstract
model. Blast short-circuits the loop from abstraction to verification to refinement,
integrating the three steps tightly through “lazy abstraction” [5]. This integration
can offer significant advantages in performance by avoiding the repetition of
work from one iteration of the loop to the next. '
acknowledgement: This work was supported in part by the NSF grants CCR-0085949 and
CCR-9988172, the DARPA PCES grant F33615-00-C-1693, the MARCO GSRC grant 98-DT-660,
and a Microsoft Research Fellowship.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
- first_name: Grégoire
full_name: Sutre, Grégoire
last_name: Sutre
citation:
ama: 'Henzinger TA, Jhala R, Majumdar R, Sutre G. Software verification with BLAST.
In: Proceedings of the 10th International SPIN Workshop . Vol 2648. Springer;
2003:235-239. doi:10.1007/3-540-44829-2_17'
apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Sutre, G. (2003). Software
verification with BLAST. In Proceedings of the 10th International SPIN Workshop
(Vol. 2648, pp. 235–239). Portland, OR, USA: Springer. https://doi.org/10.1007/3-540-44829-2_17'
chicago: Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Grégoire Sutre.
“Software Verification with BLAST.” In Proceedings of the 10th International
SPIN Workshop , 2648:235–39. Springer, 2003. https://doi.org/10.1007/3-540-44829-2_17.
ieee: T. A. Henzinger, R. Jhala, R. Majumdar, and G. Sutre, “Software verification
with BLAST,” in Proceedings of the 10th International SPIN Workshop , Portland,
OR, USA, 2003, vol. 2648, pp. 235–239.
ista: 'Henzinger TA, Jhala R, Majumdar R, Sutre G. 2003. Software verification with
BLAST. Proceedings of the 10th International SPIN Workshop . SPIN: Model Checking
Software, LNCS, vol. 2648, 235–239.'
mla: Henzinger, Thomas A., et al. “Software Verification with BLAST.” Proceedings
of the 10th International SPIN Workshop , vol. 2648, Springer, 2003, pp. 235–39,
doi:10.1007/3-540-44829-2_17.
short: T.A. Henzinger, R. Jhala, R. Majumdar, G. Sutre, in:, Proceedings of the
10th International SPIN Workshop , Springer, 2003, pp. 235–239.
conference:
end_date: 2003-05-10
location: Portland, OR, USA
name: 'SPIN: Model Checking Software'
start_date: 2003-05-09
date_created: 2018-12-11T12:09:00Z
date_published: 2003-04-28T00:00:00Z
date_updated: 2024-01-08T14:05:29Z
day: '28'
doi: 10.1007/3-540-44829-2_17
extern: '1'
intvolume: ' 2648'
language:
- iso: eng
month: '04'
oa_version: None
page: 235 - 239
publication: 'Proceedings of the 10th International SPIN Workshop '
publication_identifier:
isbn:
- '9783540401179'
publication_status: published
publisher: Springer
publist_id: '264'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Software verification with BLAST
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2648
year: '2003'
...
---
_id: '4463'
abstract:
- lang: eng
text: We present an algorithm called TAR (“Thread-modular Abstraction Refinement”)
for model checking safety properties of concurrent software. The TAR algorithm
uses thread-modular assume-guarantee reasoning to overcome the exponential complexity
in the control state of multithreaded programs. Thread modularity means that TAR
explores the state space of one thread at a time, making assumptions about how
the environment can interfere. The TAR algorithm uses counterexample-guided predicate-abstraction
refinement to overcome the usually infinite complexity in the data state of C
programs. A successive approximation scheme automatically infers the necessary
precision on data variables as well as suitable environment assumptions. The scheme
is novel in that transition relations are approximated from above, while at the
same time environment assumptions are approximated from below. In our software
verification tool BLAST we have implemented a fully automatic race checker for
multithreaded C programs which is based on the TAR algorithm. This tool has verified
a wide variety of commonly used locking idioms, including locking schemes that
are not amenable to existing dynamic and static race checkers such as ERASER or
WARLOCK.
acknowledgement: This work was supported in part by the NSF grants CCR-0085949 and
CCR-0234690, the DARPA grant F33615-00-C-1693, and the MARCO grant 98-DT-660.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
- first_name: Shaz
full_name: Qadeer, Shaz
last_name: Qadeer
citation:
ama: 'Henzinger TA, Jhala R, Majumdar R, Qadeer S. Thread-modular abstraction refinement.
In: Proceedings of the 15th International Conference on Computer Aided Verification.
Vol 2725. Springer; 2003:262-274. doi:10.1007/978-3-540-45069-6_27'
apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Qadeer, S. (2003). Thread-modular
abstraction refinement. In Proceedings of the 15th International Conference
on Computer Aided Verification (Vol. 2725, pp. 262–274). Boulder, CO, USA:
Springer. https://doi.org/10.1007/978-3-540-45069-6_27'
chicago: Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Shaz Qadeer.
“Thread-Modular Abstraction Refinement.” In Proceedings of the 15th International
Conference on Computer Aided Verification, 2725:262–74. Springer, 2003. https://doi.org/10.1007/978-3-540-45069-6_27.
ieee: T. A. Henzinger, R. Jhala, R. Majumdar, and S. Qadeer, “Thread-modular abstraction
refinement,” in Proceedings of the 15th International Conference on Computer
Aided Verification, Boulder, CO, USA, 2003, vol. 2725, pp. 262–274.
ista: 'Henzinger TA, Jhala R, Majumdar R, Qadeer S. 2003. Thread-modular abstraction
refinement. Proceedings of the 15th International Conference on Computer Aided
Verification. CAV: Computer Aided Verification, LNCS, vol. 2725, 262–274.'
mla: Henzinger, Thomas A., et al. “Thread-Modular Abstraction Refinement.” Proceedings
of the 15th International Conference on Computer Aided Verification, vol.
2725, Springer, 2003, pp. 262–74, doi:10.1007/978-3-540-45069-6_27.
short: T.A. Henzinger, R. Jhala, R. Majumdar, S. Qadeer, in:, Proceedings of the
15th International Conference on Computer Aided Verification, Springer, 2003,
pp. 262–274.
conference:
end_date: 2003-07-12
location: Boulder, CO, USA
name: 'CAV: Computer Aided Verification'
start_date: 2003-07-08
date_created: 2018-12-11T12:08:59Z
date_published: 2003-06-27T00:00:00Z
date_updated: 2024-01-10T11:05:53Z
day: '27'
doi: 10.1007/978-3-540-45069-6_27
extern: '1'
intvolume: ' 2725'
language:
- iso: eng
month: '06'
oa_version: None
page: 262 - 274
publication: Proceedings of the 15th International Conference on Computer Aided Verification
publication_identifier:
isbn:
- '9783540405245'
publication_status: published
publisher: Springer
publist_id: '266'
quality_controlled: '1'
status: public
title: Thread-modular abstraction refinement
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2725
year: '2003'
...
---
_id: '4462'
abstract:
- lang: eng
text: 'A major hurdle in the algorithmic verification and control of systems is
the need to find suitable abstract models, which omit enough details to overcome
the state-explosion problem, but retain enough details to exhibit satisfaction
or controllability with respect to the specification. The paradigm of counterexample-guided
abstraction refinement suggests a fully automatic way of finding suitable abstract
models: one starts with a coarse abstraction, attempts to verify or control the
abstract model, and if this attempt fails and the abstract counterexample does
not correspond to a concrete counterexample, then one uses the spurious counterexample
to guide the refinement of the abstract model. We present a counterexample-guided
refinement algorithm for solving ω-regular control objectives. The main difficulty
is that in control, unlike in verification, counterexamples are strategies in
a game between system and controller. In the case that the controller has no choices,
our scheme subsumes known counterexample-guided refinement algorithms for the
verification of ω-regular specifications. Our algorithm is useful in all situations
where ω-regular games need to be solved, such as supervisory control, sequential
and program synthesis, and modular verification. The algorithm is fully symbolic,
and therefore applicable also to infinite-state systems.'
acknowledgement: This research was supported in part by the DARPA SEC grant F33615-C-98-3614,
the ONR grant N00014-02-1-0671, and the NSF grants CCR-9988172, CCR-0085949, and
CCR-0225610.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
citation:
ama: 'Henzinger TA, Jhala R, Majumdar R. Counterexample-guided control. In: Proceedings
of the 30th International Colloquium on Automata, Languages and Programming.
Vol 2719. Springer; 2003:886-902. doi:10.1007/3-540-45061-0_69'
apa: 'Henzinger, T. A., Jhala, R., & Majumdar, R. (2003). Counterexample-guided
control. In Proceedings of the 30th International Colloquium on Automata, Languages
and Programming (Vol. 2719, pp. 886–902). Eindhoven, The Netherlands: Springer.
https://doi.org/10.1007/3-540-45061-0_69'
chicago: Henzinger, Thomas A, Ranjit Jhala, and Ritankar Majumdar. “Counterexample-Guided
Control.” In Proceedings of the 30th International Colloquium on Automata,
Languages and Programming, 2719:886–902. Springer, 2003. https://doi.org/10.1007/3-540-45061-0_69.
ieee: T. A. Henzinger, R. Jhala, and R. Majumdar, “Counterexample-guided control,”
in Proceedings of the 30th International Colloquium on Automata, Languages
and Programming, Eindhoven, The Netherlands, 2003, vol. 2719, pp. 886–902.
ista: 'Henzinger TA, Jhala R, Majumdar R. 2003. Counterexample-guided control. Proceedings
of the 30th International Colloquium on Automata, Languages and Programming. ICALP:
Automata, Languages and Programming, LNCS, vol. 2719, 886–902.'
mla: Henzinger, Thomas A., et al. “Counterexample-Guided Control.” Proceedings
of the 30th International Colloquium on Automata, Languages and Programming,
vol. 2719, Springer, 2003, pp. 886–902, doi:10.1007/3-540-45061-0_69.
short: T.A. Henzinger, R. Jhala, R. Majumdar, in:, Proceedings of the 30th International
Colloquium on Automata, Languages and Programming, Springer, 2003, pp. 886–902.
conference:
end_date: 2003-07-04
location: Eindhoven, The Netherlands
name: 'ICALP: Automata, Languages and Programming'
start_date: 2003-06-30
date_created: 2018-12-11T12:08:58Z
date_published: 2003-06-25T00:00:00Z
date_updated: 2024-01-10T11:19:41Z
day: '25'
doi: 10.1007/3-540-45061-0_69
extern: '1'
intvolume: ' 2719'
language:
- iso: eng
month: '06'
oa_version: None
page: 886 - 902
publication: Proceedings of the 30th International Colloquium on Automata, Languages
and Programming
publication_identifier:
isbn:
- '9783540404934'
publication_status: published
publisher: Springer
publist_id: '265'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Counterexample-guided control
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2719
year: '2003'
...
---
_id: '4464'
abstract:
- lang: eng
text: We introduce the paradigm of schedule-carrying code (SCC). A hard real-time
program can be executed on a given platform only if there exists a feasible schedule
for the real-time tasks of the program. Traditionally, a scheduler determines
the existence of a feasible schedule according to some scheduling strategy. With
SCC, a compiler proves the existence of a feasible schedule by generating executable
code that is attached to the program and represents its schedule. An SCC executable
is a real-time program that carries its schedule as code, which is produced once
and can be revalidated and executed with each use. We evaluate SCC both in theory
and practice. In theory, we give two scenarios, of nonpreemptive and distributed
scheduling for Giotto programs, where the generation of a feasible schedule is
hard, while the validation of scheduling instructions that are attached to the
programs is easy. In practice, we implement SCC and show that explicit scheduling
instructions can reduce the scheduling overhead up to 35% and can provide an efficient,
flexible, and verifiable means for compiling Giotto programs on complex architectures,
such as the TTA.
acknowledgement: This work was supported by the AFOSR MURI grant F49620-00-1-0327,
the California MICRO grant 01-037, the DARPA grant F33615-C-98-3614, the MARCO grant
98-DT-660, and the NSF grants CCR-0208875, CCR-0085949, and CCR-0225610.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Christoph
full_name: Kirsch, Christoph
last_name: Kirsch
- first_name: Slobodan
full_name: Matic, Slobodan
last_name: Matic
citation:
ama: 'Henzinger TA, Kirsch C, Matic S. Schedule-carrying code. In: Proceedings
of the 3rd International Conference on Embedded Software. Vol 2855. ACM; 2003:241-256.
doi:10.1007/978-3-540-45212-6_16'
apa: 'Henzinger, T. A., Kirsch, C., & Matic, S. (2003). Schedule-carrying code.
In Proceedings of the 3rd International Conference on Embedded Software
(Vol. 2855, pp. 241–256). Philadelphia, PA, USA: ACM. https://doi.org/10.1007/978-3-540-45212-6_16'
chicago: Henzinger, Thomas A, Christoph Kirsch, and Slobodan Matic. “Schedule-Carrying
Code.” In Proceedings of the 3rd International Conference on Embedded Software,
2855:241–56. ACM, 2003. https://doi.org/10.1007/978-3-540-45212-6_16.
ieee: T. A. Henzinger, C. Kirsch, and S. Matic, “Schedule-carrying code,” in Proceedings
of the 3rd International Conference on Embedded Software, Philadelphia, PA,
USA, 2003, vol. 2855, pp. 241–256.
ista: 'Henzinger TA, Kirsch C, Matic S. 2003. Schedule-carrying code. Proceedings
of the 3rd International Conference on Embedded Software. EMSOFT: Embedded Software
, LNCS, vol. 2855, 241–256.'
mla: Henzinger, Thomas A., et al. “Schedule-Carrying Code.” Proceedings of the
3rd International Conference on Embedded Software, vol. 2855, ACM, 2003, pp.
241–56, doi:10.1007/978-3-540-45212-6_16.
short: T.A. Henzinger, C. Kirsch, S. Matic, in:, Proceedings of the 3rd International
Conference on Embedded Software, ACM, 2003, pp. 241–256.
conference:
end_date: 2003-10-15
location: Philadelphia, PA, USA
name: 'EMSOFT: Embedded Software '
start_date: 2003-10-13
date_created: 2018-12-11T12:08:59Z
date_published: 2003-09-29T00:00:00Z
date_updated: 2024-01-10T11:33:57Z
day: '29'
doi: 10.1007/978-3-540-45212-6_16
extern: '1'
intvolume: ' 2855'
language:
- iso: eng
month: '09'
oa_version: None
page: 241 - 256
publication: Proceedings of the 3rd International Conference on Embedded Software
publication_identifier:
isbn:
- '9783540202233'
publication_status: published
publisher: ACM
publist_id: '267'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Schedule-carrying code
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2855
year: '2003'
...
---
_id: '4460'
abstract:
- lang: eng
text: "Symbolic model checking, which enables the automatic verification of large
systems, proceeds by calculating expressions that represent state sets. Traditionally,
symbolic model-checking tools are based on back- ward state traversal; their basic
operation is the function pre, which, given a set of states, returns the set of
all predecessor states. This is because specifiers usually employ formalisms with
future-time modalities, which are naturally evaluated by iterating applications
of pre. It has been shown experimentally that symbolic model checking can perform
significantly better if it is based, instead, on forward state traversal; in this
case, the basic operation is the function post, which, given a set of states,
returns the set of all successor states. This is because forward state traversal
can ensure that only parts of the state space that are reachable from an initial
state and relevant for the satisfaction or violation of the specification are
explored; that is, errors can be detected as soon as possible.\r\nIn this paper,
we investigate which specifications can be checked by symbolic forward state traversal.
We formulate the problems of symbolic backward and forward model checking by means
of two μ-calculi. The pre-μ calculus is based on the pre operation, and the post-μ
calculus is based on the post operation. These two μ-calculi induce query logics,
which augment fixpoint expressions with a boolean emptiness query. Using query
logics, we are able to relate and compare the symbolic backward and forward approaches.
In particular, we prove that all ω-regular (linear-time) specifications can be
expressed as post-μ queries, and therefore checked using symbolic forward state
traversal. On the other hand, we show that there are simple branching-time specifications
that cannot be checked in this way."
acknowledgement: This research was supported in part by the SRC contract 99-TJ-683.003
and the NSF grant CCR-9988172.
article_processing_charge: No
article_type: original
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
- first_name: Shaz
full_name: Qadeer, Shaz
last_name: Qadeer
citation:
ama: Henzinger TA, Kupferman O, Qadeer S. From pre-historic to post-modern symbolic
model checking. Formal Methods in System Design. 2003;23(3):303-327. doi:10.1023/A:1026228213080
apa: Henzinger, T. A., Kupferman, O., & Qadeer, S. (2003). From pre-historic
to post-modern symbolic model checking. Formal Methods in System Design.
Springer. https://doi.org/10.1023/A:1026228213080
chicago: Henzinger, Thomas A, Orna Kupferman, and Shaz Qadeer. “From Pre-Historic
to Post-Modern Symbolic Model Checking.” Formal Methods in System Design.
Springer, 2003. https://doi.org/10.1023/A:1026228213080.
ieee: T. A. Henzinger, O. Kupferman, and S. Qadeer, “From pre-historic to post-modern
symbolic model checking,” Formal Methods in System Design, vol. 23, no.
3. Springer, pp. 303–327, 2003.
ista: Henzinger TA, Kupferman O, Qadeer S. 2003. From pre-historic to post-modern
symbolic model checking. Formal Methods in System Design. 23(3), 303–327.
mla: Henzinger, Thomas A., et al. “From Pre-Historic to Post-Modern Symbolic Model
Checking.” Formal Methods in System Design, vol. 23, no. 3, Springer, 2003,
pp. 303–27, doi:10.1023/A:1026228213080.
short: T.A. Henzinger, O. Kupferman, S. Qadeer, Formal Methods in System Design
23 (2003) 303–327.
date_created: 2018-12-11T12:08:58Z
date_published: 2003-06-20T00:00:00Z
date_updated: 2024-01-10T11:50:31Z
day: '20'
doi: 10.1023/A:1026228213080
extern: '1'
intvolume: ' 23'
issue: '3'
language:
- iso: eng
month: '06'
oa_version: None
page: 303 - 327
publication: Formal Methods in System Design
publication_identifier:
issn:
- 0925-9856
publication_status: published
publisher: Springer
publist_id: '268'
quality_controlled: '1'
scopus_import: '1'
status: public
title: From pre-historic to post-modern symbolic model checking
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 23
year: '2003'
...
---
_id: '4469'
abstract:
- lang: eng
text: Giotto provides an abstract programmer's model for the implementation of embedded
control systems with hard real-time constraints. A typical control application
consists of periodic software tasks together with a mode-switching logic for enabling
and disabling tasks. Giotto specifies time-triggered sensor readings, task invocations,
actuator updates, and mode switches independent of any implementation platform.
Giotto can be annotated with platform constraints such as task-to-host mappings,
and task and communication schedules. The annotations are directives for the Giotto
compiler, but they do not alter the functionality and timing of a Giotto program.
By separating the platform-independent from the platform-dependent concerns, Giotto
enables a great deal of flexibility in choosing control platforms as well as a
great deal of automation in the validation and synthesis of control software.
The time-triggered nature of Giotto achieves timing predictability, which makes
Giotto particularly suitable for safety-critical applications.
acknowledgement: The authors would like to thank R. Majumdar for implementing a prototype
Giotto compiler for Lego Mindstorms robots. They would like to thank D. Derevyanko
and W. Williams for building the Intel x86 robots; and E. Lee and X. Liu for help
with implementing Giotto as a “model of computation” in Ptolemy II [26]. Finally,
they would also like to thank M. Sanvido for his suggestions on the design of the
Giotto drivers; and P. Griffiths for implementing the functionality code of the
electronic throttle controller.
article_processing_charge: No
article_type: original
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Benjamin
full_name: Horowitz, Benjamin
last_name: Horowitz
- first_name: Christoph
full_name: Kirsch, Christoph
last_name: Kirsch
citation:
ama: 'Henzinger TA, Horowitz B, Kirsch C. Giotto: A time-triggered language for
embedded programming. Proceedings of the IEEE. 2003;91(1):84-99. doi:10.1109/JPROC.2002.805825'
apa: 'Henzinger, T. A., Horowitz, B., & Kirsch, C. (2003). Giotto: A time-triggered
language for embedded programming. Proceedings of the IEEE. IEEE. https://doi.org/10.1109/JPROC.2002.805825'
chicago: 'Henzinger, Thomas A, Benjamin Horowitz, and Christoph Kirsch. “Giotto:
A Time-Triggered Language for Embedded Programming.” Proceedings of the IEEE.
IEEE, 2003. https://doi.org/10.1109/JPROC.2002.805825.'
ieee: 'T. A. Henzinger, B. Horowitz, and C. Kirsch, “Giotto: A time-triggered language
for embedded programming,” Proceedings of the IEEE, vol. 91, no. 1. IEEE,
pp. 84–99, 2003.'
ista: 'Henzinger TA, Horowitz B, Kirsch C. 2003. Giotto: A time-triggered language
for embedded programming. Proceedings of the IEEE. 91(1), 84–99.'
mla: 'Henzinger, Thomas A., et al. “Giotto: A Time-Triggered Language for Embedded
Programming.” Proceedings of the IEEE, vol. 91, no. 1, IEEE, 2003, pp.
84–99, doi:10.1109/JPROC.2002.805825.'
short: T.A. Henzinger, B. Horowitz, C. Kirsch, Proceedings of the IEEE 91 (2003)
84–99.
date_created: 2018-12-11T12:09:00Z
date_published: 2003-01-29T00:00:00Z
date_updated: 2024-01-10T11:55:18Z
day: '29'
doi: 10.1109/JPROC.2002.805825
extern: '1'
intvolume: ' 91'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 84 - 99
publication: Proceedings of the IEEE
publication_identifier:
issn:
- '0018-9219 '
publication_status: published
publisher: IEEE
publist_id: '261'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Giotto: A time-triggered language for embedded programming'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 91
year: '2003'
...
---
_id: '4338'
abstract:
- lang: eng
text: 'Mosaic hybrid zones arise when ecologically differentiated taxa hybridize
across a network of habitat patches. Frequent interbreeding across a small-scale
patchwork can erode species differences that might have been preserved in a clinal
hybrid zone. In particular, the rapid breakdown of neutral divergence sets an
upper limit to the time for which differences at marker loci can persist. We present
here a case study of a mosaic hybrid zone between the fire-bellied toads Bombina
bombina and B. variegata (Anura: Discoglossidae) near Apahida in Romania. In our
20 × 20 km study area, we detected no evidence of a clinal transition but found
a strong association between aquatic habitat and mean allele frequencies at four
molecular markers. In particular, pure populations of B. bombina in ponds appear
to cause massive introgression into the surrounding B. variegata gene pool found
in temporary aquatic sites. Nevertheless, the genetic structure of these hybrid
populations was remarkably similar to those of a previously studied transect near
Pescenica (Croatia), which had both clinal and mosaic features: estimates of heterozygote
deficit and linkage disequilibrium in each country are similar. In Apahida, the
observed strong linkage disequilibria should stem from an imperfect habitat preference
that guides most (but not all) adults into the habitats to which they are adapted.
In the absence of a clinal structure, the inferred migration rate between habitats
implies that associations between selected loci and neutral markers should break
down rapidly. Although plausible selection strengths can maintain differentiation
at those loci adapting the toads to either permanent or temporary breeding sites,
the divergence at neutral markers must be transient. The hybrid zone may be approaching
a state in which the gene pools are homogenized at all but the selected loci,
not dissimilar from an early stage of sympatric divergence.'
acknowledgement: "We thank G. Mara and T. Galbena for enthusiastic field\r\nassistance,
A. Hofmann and R. Sieglstetter for access to their\r\nunpublished data, B. Fo¨rg-Brey
and G. Praetzel for help in\r\nthe lab. Helpful comments on a previous version of
the man-\r\nuscript were provided by R. Ennos, J. Szymura, F. Balloux,\r\nJ. Bridle,
L. Kruuk, F. Bonhomme, M. Arnold, and two anon-\r\nymous reviewers. We also thank
A. Pinggera for providing\r\nthe cover illustration. This work was supported by
Natural\r\nEnvironment Research Council studentships to THV and TRS\r\nand Deutsche
Forschungsgemeinschaft grant Nu 51/2-1 to BN."
article_processing_charge: No
article_type: original
author:
- first_name: Timothy
full_name: Vines, Timothy
last_name: Vines
- first_name: S C
full_name: Kohler, S C
last_name: Kohler
- first_name: M
full_name: Thiel, M
last_name: Thiel
- first_name: Ioan
full_name: Ghira, Ioan
last_name: Ghira
- first_name: T R
full_name: Sands, T R
last_name: Sands
- first_name: Catriona
full_name: Maccallum, Catriona
last_name: Maccallum
- 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: Beate
full_name: Nürnberger, Beate
last_name: Nürnberger
citation:
ama: Vines T, Kohler SC, Thiel M, et al. On the maintenance of reproductive isolation
in a mosaic hybrid zone between the toads Bombina bombina and B. variegata. Evolution.
2003;57(8):1876-1888. doi:10.1111/j.0014-3820.2003.tb00595.x
apa: Vines, T., Kohler, S. C., Thiel, M., Ghira, I., Sands, T. R., Maccallum, C.,
… Nürnberger, B. (2003). On the maintenance of reproductive isolation in a mosaic
hybrid zone between the toads Bombina bombina and B. variegata. Evolution.
Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2003.tb00595.x
chicago: Vines, Timothy, S C Kohler, M Thiel, Ioan Ghira, T R Sands, Catriona Maccallum,
Nicholas H Barton, and Beate Nürnberger. “On the Maintenance of Reproductive Isolation
in a Mosaic Hybrid Zone between the Toads Bombina Bombina and B. Variegata.” Evolution.
Wiley-Blackwell, 2003. https://doi.org/10.1111/j.0014-3820.2003.tb00595.x.
ieee: T. Vines et al., “On the maintenance of reproductive isolation in a
mosaic hybrid zone between the toads Bombina bombina and B. variegata,” Evolution,
vol. 57, no. 8. Wiley-Blackwell, pp. 1876–1888, 2003.
ista: Vines T, Kohler SC, Thiel M, Ghira I, Sands TR, Maccallum C, Barton NH, Nürnberger
B. 2003. On the maintenance of reproductive isolation in a mosaic hybrid zone
between the toads Bombina bombina and B. variegata. Evolution. 57(8), 1876–1888.
mla: Vines, Timothy, et al. “On the Maintenance of Reproductive Isolation in a Mosaic
Hybrid Zone between the Toads Bombina Bombina and B. Variegata.” Evolution,
vol. 57, no. 8, Wiley-Blackwell, 2003, pp. 1876–88, doi:10.1111/j.0014-3820.2003.tb00595.x.
short: T. Vines, S.C. Kohler, M. Thiel, I. Ghira, T.R. Sands, C. Maccallum, N.H.
Barton, B. Nürnberger, Evolution 57 (2003) 1876–1888.
date_created: 2018-12-11T12:08:20Z
date_published: 2003-08-01T00:00:00Z
date_updated: 2024-01-23T09:16:43Z
day: '01'
doi: 10.1111/j.0014-3820.2003.tb00595.x
extern: '1'
intvolume: ' 57'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 1876 - 1888
publication: Evolution
publication_identifier:
issn:
- 0014-3820
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1692'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the maintenance of reproductive isolation in a mosaic hybrid zone between
the toads Bombina bombina and B. variegata
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 57
year: '2003'
...
---
_id: '4350'
abstract:
- lang: eng
text: 'The phylogeny of Crocodylia offers an unusual twist on the usual molecules
versus morphology story. The true gharial (Gavialis gangeticus) and the false
gharial (Tomistoma schlegelii), as their common names imply, have appeared in
all cladistic morphological analyses as distantly related species, convergent
upon a similar morphology. In contrast, all previous molecular studies have shown
them to be sister taxa. We present the first phylogenetic study of Crocodylia
using a nuclear gene. We cloned and sequenced the c-myc proto-oncogene from Alligator
mississippiensis to facilitate primer design and then sequenced an 1,100-base
pair fragment that includes both coding and noncoding regions and informative
indels for one species in each extant crocodylian genus and six avian outgroups.
Phylogenetic analyses using parsimony, maximum likelihood, and Bayesian inference
all strongly agreed on the same tree, which is identical to the tree found in
previous molecular analyses: Gavialis and Tomistoma are sister taxa and together
are the sister group of Crocodylidae. Kishino-Hasegawa tests rejected the morphological
tree in favor of the molecular tree. We excluded long-branch attraction and variation
in base composition among taxa as explanations for this topology. To explore the
causes of discrepancy between molecular and morphological estimates of crocodylian
phylogeny, we examined puzzling features of the morphological data using a priori
partitions of the data based on anatomical regions and investigated the effects
of different coding schemes for two obvious morphological similarities of the
two gharials.'
acknowledgement: "We thank Lou Densmore and Herb Dessauer for crocodylian tissue\r\nsamples.
Dave Swofford, Jim Wilgenbusch, and Kevin de Queiroz gave\r\nus much helpful advice.
Dave also allowed us to use an experimental\r\nversion of PAUP∗ with partitioned
likelihood, and Jim also provided\r\nprograms to make possible partitioned model
KH tests. Chris Brochu\r\nand Lou Densmore sent us preprints of their papers in
press, and Chris\r\nprovided an unpublished version of his morphological data set.
Allan\r\nBaker, Lou Densmore, and an anonymous reviewer provided useful\r\ncomments
on the manuscript. We especially wish to acknowledge Chris\r\nBrochu’s help; although
we remain in disagreement on many points,\r\nhis comments on several previous drafts
have greatly improved this\r\npaper."
article_processing_charge: No
article_type: original
author:
- first_name: John
full_name: Harshman, John
last_name: Harshman
- first_name: Christopher
full_name: Huddleston, Christopher
last_name: Huddleston
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Thomas
full_name: Parsons, Thomas
last_name: Parsons
- first_name: Michael
full_name: Braun, Michael
last_name: Braun
citation:
ama: 'Harshman J, Huddleston C, Bollback JP, Parsons T, Braun M. True and false
gharials: A nuclear gene phylogeny of crocodylia. Systematic Biology. 2003;52(3):386-402.
doi:10.1080/10635150390197028'
apa: 'Harshman, J., Huddleston, C., Bollback, J. P., Parsons, T., & Braun, M.
(2003). True and false gharials: A nuclear gene phylogeny of crocodylia. Systematic
Biology. Oxford University Press. https://doi.org/10.1080/10635150390197028'
chicago: 'Harshman, John, Christopher Huddleston, Jonathan P Bollback, Thomas Parsons,
and Michael Braun. “True and False Gharials: A Nuclear Gene Phylogeny of Crocodylia.”
Systematic Biology. Oxford University Press, 2003. https://doi.org/10.1080/10635150390197028.'
ieee: 'J. Harshman, C. Huddleston, J. P. Bollback, T. Parsons, and M. Braun, “True
and false gharials: A nuclear gene phylogeny of crocodylia,” Systematic Biology,
vol. 52, no. 3. Oxford University Press, pp. 386–402, 2003.'
ista: 'Harshman J, Huddleston C, Bollback JP, Parsons T, Braun M. 2003. True and
false gharials: A nuclear gene phylogeny of crocodylia. Systematic Biology. 52(3),
386–402.'
mla: 'Harshman, John, et al. “True and False Gharials: A Nuclear Gene Phylogeny
of Crocodylia.” Systematic Biology, vol. 52, no. 3, Oxford University Press,
2003, pp. 386–402, doi:10.1080/10635150390197028.'
short: J. Harshman, C. Huddleston, J.P. Bollback, T. Parsons, M. Braun, Systematic
Biology 52 (2003) 386–402.
date_created: 2018-12-11T12:08:24Z
date_published: 2003-06-01T00:00:00Z
date_updated: 2024-01-23T08:53:58Z
day: '01'
doi: 10.1080/10635150390197028
extern: '1'
external_id:
pmid:
- ' 12775527'
intvolume: ' 52'
issue: '3'
language:
- iso: eng
month: '06'
oa_version: None
page: 386 - 402
pmid: 1
publication: Systematic Biology
publication_identifier:
issn:
- '0039-7989 '
publication_status: published
publisher: Oxford University Press
publist_id: '1110'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'True and false gharials: A nuclear gene phylogeny of crocodylia'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 52
year: '2003'
...
---
_id: '4348'
abstract:
- lang: eng
text: Many questions in evolutionary biology are best addressed by comparing traits
in different species. Often such studies involve mapping characters on phylogenetic
trees. Mapping characters on trees allows the nature, number, and timing of the
transformations to be identified. The parsimony method is the only method available
for mapping morphological characters on phylogenies. Although the parsimony method
often makes reasonable reconstructions of the history of a character, it has a
number of limitations. These limitations include the inability to consider more
than a single change along a branch on a tree and the uncoupling of evolutionary
time from amount of character change. We extended a method described by Nielsen
(2002, Syst. Biol. 51:729-739) to the mapping of morphological characters under
continuous-time Markov models and demonstrate here the utility of the method for
mapping characters on trees and for identifying character correlation.
acknowledgement: "We thank J. Kohn, D. Stern, and M. Hart for sending the alignments\r\nused
in this study. J.P.H. was supported by NSF grants DEB-0075406\r\nand MCB-0075404.
R.N. was supported by NSF grant DEB-0089487."
article_processing_charge: No
article_type: original
author:
- first_name: John
full_name: Huelsenbeck, John
last_name: Huelsenbeck
- first_name: Rasmus
full_name: Nielsen, Rasmus
last_name: Nielsen
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Huelsenbeck J, Nielsen R, Bollback JP. Stochastic mapping of morphological
characters. Systematic Biology. 2003;52(2):131-158. doi:10.1080/10635150390192780
apa: Huelsenbeck, J., Nielsen, R., & Bollback, J. P. (2003). Stochastic mapping
of morphological characters. Systematic Biology. Oxford University Press.
https://doi.org/10.1080/10635150390192780
chicago: Huelsenbeck, John, Rasmus Nielsen, and Jonathan P Bollback. “Stochastic
Mapping of Morphological Characters.” Systematic Biology. Oxford University
Press, 2003. https://doi.org/10.1080/10635150390192780.
ieee: J. Huelsenbeck, R. Nielsen, and J. P. Bollback, “Stochastic mapping of morphological
characters,” Systematic Biology, vol. 52, no. 2. Oxford University Press,
pp. 131–158, 2003.
ista: Huelsenbeck J, Nielsen R, Bollback JP. 2003. Stochastic mapping of morphological
characters. Systematic Biology. 52(2), 131–158.
mla: Huelsenbeck, John, et al. “Stochastic Mapping of Morphological Characters.”
Systematic Biology, vol. 52, no. 2, Oxford University Press, 2003, pp.
131–58, doi:10.1080/10635150390192780.
short: J. Huelsenbeck, R. Nielsen, J.P. Bollback, Systematic Biology 52 (2003) 131–158.
date_created: 2018-12-11T12:08:24Z
date_published: 2003-04-01T00:00:00Z
date_updated: 2024-01-23T09:10:59Z
day: '01'
doi: 10.1080/10635150390192780
extern: '1'
external_id:
pmid:
- '12746144 '
intvolume: ' 52'
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
page: 131 - 158
pmid: 1
publication: Systematic Biology
publication_identifier:
issn:
- '0039-7989 '
publication_status: published
publisher: Oxford University Press
publist_id: '1111'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stochastic mapping of morphological characters
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 52
year: '2003'
...
---
_id: '4254'
abstract:
- lang: eng
text: Chromosomal rearrangements can promote reproductive isolation by reducing
recombination along a large section of the genome. We model the effects of the
genetic barrier to gene flow caused by a chromosomal rearrangement on the rate
of accumulation of postzygotic isolation genes in parapatry. We find that, if
reproductive isolation is produced by the accumulation in parapatry of sets of
alleles compatible within but incompatible across species, chromosomal rearrangements
are far more likely to favor it than classical genetic barriers without chromosomal
changes. New evidence of the role of chromosomal rearrangements in parapatric
speciation suggests that postzygotic isolation is often due to the accumulation
of such incompatibilities. The model makes testable qualitative predictions about
the genetic signature of speciation.
acknowledgement: "We thank A. Andrés, C. Bartolomé, J. Bertranpetit, F. Calafell,
B. Charlesworth, D. Charlesworth, F. Depaulis, S. Gavrilets, T. Johnson, P. Keightley,
M. Kirkpatrik, A. Kondrashov, H. Laayouni, X. Maside, M. Noor, D. Ortiz-Barrientos,\r\nL.
Rieseberg, and T. Vines for valuable discussion and criticism. The detailed comments
of B. Charlesworth, D. Charlesworth, and F. Depaulis greatly improved the original
manuscript. AN is particularly grateful to X. Maside, who was a patient guide through
the jungle of speciation. This work was supported by the NERC grant GR3/11635 (United
Kingdom). AN is funded by the Ramón y Cajal Program (Spain)."
article_processing_charge: No
article_type: original
author:
- first_name: Arcadio
full_name: Navarro, Arcadio
last_name: Navarro
- 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: 'Navarro A, Barton NH. Accumulating postzygotic isolation genes in parapatry:
a new twist on chromosomal speciation. Evolution; International Journal of
Organic Evolution. 2003;57(3):447-459. doi:10.1111/j.0014-3820.2003.tb01537.x'
apa: 'Navarro, A., & Barton, N. H. (2003). Accumulating postzygotic isolation
genes in parapatry: a new twist on chromosomal speciation. Evolution; International
Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2003.tb01537.x'
chicago: 'Navarro, Arcadio, and Nicholas H Barton. “Accumulating Postzygotic Isolation
Genes in Parapatry: A New Twist on Chromosomal Speciation.” Evolution; International
Journal of Organic Evolution. Wiley-Blackwell, 2003. https://doi.org/10.1111/j.0014-3820.2003.tb01537.x.'
ieee: 'A. Navarro and N. H. Barton, “Accumulating postzygotic isolation genes in
parapatry: a new twist on chromosomal speciation,” Evolution; International
Journal of Organic Evolution, vol. 57, no. 3. Wiley-Blackwell, pp. 447–459,
2003.'
ista: 'Navarro A, Barton NH. 2003. Accumulating postzygotic isolation genes in parapatry:
a new twist on chromosomal speciation. Evolution; International Journal of Organic
Evolution. 57(3), 447–459.'
mla: 'Navarro, Arcadio, and Nicholas H. Barton. “Accumulating Postzygotic Isolation
Genes in Parapatry: A New Twist on Chromosomal Speciation.” Evolution; International
Journal of Organic Evolution, vol. 57, no. 3, Wiley-Blackwell, 2003, pp. 447–59,
doi:10.1111/j.0014-3820.2003.tb01537.x.'
short: A. Navarro, N.H. Barton, Evolution; International Journal of Organic Evolution
57 (2003) 447–459.
date_created: 2018-12-11T12:07:52Z
date_published: 2003-03-01T00:00:00Z
date_updated: 2024-01-23T10:21:57Z
day: '01'
doi: 10.1111/j.0014-3820.2003.tb01537.x
extern: '1'
external_id:
pmid:
- '12703935 '
intvolume: ' 57'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 447 - 459
pmid: 1
publication: Evolution; International Journal of Organic Evolution
publication_identifier:
issn:
- 0014-3820
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1840'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal
speciation'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 57
year: '2003'
...
---
_id: '4257'
abstract:
- lang: eng
text: Variation within a species may be structured both geographically and by genetic
background. We review the effects of such structuring on neutral variants, using
a framework based on the coalescent process. Short-term effects of sex differences
and age structure can be averaged out using fast timescale approximations, allowing
a simple general treatment of effective population size and migration. We consider
the effects of geographic structure on variation within and between local populations,
first in general terms, and then for specific migration models. We discuss the
close parallels between geographic structure and stable types of genetic structure
caused by selection, including balancing selection and background selection. The
effects of departures from stability, such as selective sweeps and population
bottlenecks, are also described. Methods for distinguishing population history
from the effects of ongoing gene flow are discussed. We relate the theoretical
results to observed patterns of variation in natural populations.
article_processing_charge: No
article_type: original
author:
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
- first_name: Deborah
full_name: Charlesworth, Deborah
last_name: Charlesworth
- 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: Charlesworth B, Charlesworth D, Barton NH. The effects of genetic and geographic
structure on neutral variation. Annual Review of Ecology and Systematics.
2003;34:99-125. doi:10.1146/annurev.ecolsys.34.011802.132359
apa: Charlesworth, B., Charlesworth, D., & Barton, N. H. (2003). The effects
of genetic and geographic structure on neutral variation. Annual Review of
Ecology and Systematics. Annual Reviews. https://doi.org/10.1146/annurev.ecolsys.34.011802.132359
chicago: Charlesworth, Brian, Deborah Charlesworth, and Nicholas H Barton. “The
Effects of Genetic and Geographic Structure on Neutral Variation.” Annual Review
of Ecology and Systematics. Annual Reviews, 2003. https://doi.org/10.1146/annurev.ecolsys.34.011802.132359.
ieee: B. Charlesworth, D. Charlesworth, and N. H. Barton, “The effects of genetic
and geographic structure on neutral variation,” Annual Review of Ecology and
Systematics, vol. 34. Annual Reviews, pp. 99–125, 2003.
ista: Charlesworth B, Charlesworth D, Barton NH. 2003. The effects of genetic and
geographic structure on neutral variation. Annual Review of Ecology and Systematics.
34, 99–125.
mla: Charlesworth, Brian, et al. “The Effects of Genetic and Geographic Structure
on Neutral Variation.” Annual Review of Ecology and Systematics, vol. 34,
Annual Reviews, 2003, pp. 99–125, doi:10.1146/annurev.ecolsys.34.011802.132359.
short: B. Charlesworth, D. Charlesworth, N.H. Barton, Annual Review of Ecology and
Systematics 34 (2003) 99–125.
date_created: 2018-12-11T12:07:53Z
date_published: 2003-11-01T00:00:00Z
date_updated: 2024-01-23T10:15:44Z
day: '01'
doi: 10.1146/annurev.ecolsys.34.011802.132359
extern: '1'
intvolume: ' 34'
language:
- iso: eng
month: '11'
oa_version: None
page: 99 - 125
publication: Annual Review of Ecology and Systematics
publication_identifier:
issn:
- 1543-592X
publication_status: published
publisher: Annual Reviews
publist_id: '1839'
quality_controlled: '1'
status: public
title: The effects of genetic and geographic structure on neutral variation
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 34
year: '2003'
...
---
_id: '4256'
abstract:
- lang: eng
text: Artificial Life models may shed new light on the long-standing challenge for
evolutionary biology of explaining the origins of complex organs. Real progress
on this issue, however, requires Artificial Life researchers to take seriously
the tools and insights from population genetics.
article_processing_charge: No
article_type: original
author:
- 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: Willem
full_name: Zuidema, Willem
last_name: Zuidema
citation:
ama: Barton NH, Zuidema W. The erratic path towards complexity. Current Biology.
2003;13(16):R649-R651. doi:10.1016/S0960-9822(03)00573-6
apa: Barton, N. H., & Zuidema, W. (2003). The erratic path towards complexity.
Current Biology. Cell Press. https://doi.org/10.1016/S0960-9822(03)00573-6
chicago: Barton, Nicholas H, and Willem Zuidema. “The Erratic Path towards Complexity.”
Current Biology. Cell Press, 2003. https://doi.org/10.1016/S0960-9822(03)00573-6.
ieee: N. H. Barton and W. Zuidema, “The erratic path towards complexity,” Current
Biology, vol. 13, no. 16. Cell Press, pp. R649–R651, 2003.
ista: Barton NH, Zuidema W. 2003. The erratic path towards complexity. Current Biology.
13(16), R649–R651.
mla: Barton, Nicholas H., and Willem Zuidema. “The Erratic Path towards Complexity.”
Current Biology, vol. 13, no. 16, Cell Press, 2003, pp. R649–51, doi:10.1016/S0960-9822(03)00573-6.
short: N.H. Barton, W. Zuidema, Current Biology 13 (2003) R649–R651.
date_created: 2018-12-11T12:07:53Z
date_published: 2003-08-19T00:00:00Z
date_updated: 2024-01-23T09:41:33Z
day: '19'
doi: 10.1016/S0960-9822(03)00573-6
extern: '1'
intvolume: ' 13'
issue: '16'
language:
- iso: eng
month: '08'
oa_version: Published Version
page: R649 - R651
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Cell Press
publist_id: '1838'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The erratic path towards complexity
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 13
year: '2003'
...
---
_id: '4255'
abstract:
- lang: eng
text: 'Humans and their closest evolutionary relatives, the chimpanzees, differ
in ∼1.24% of their genomic DNA sequences. The fraction of these changes accumulated
during the speciation processes that have separated the two lineages may be of
special relevance in understanding the basis of their differences. We analyzed
human and chimpanzee sequence data to search for the patterns of divergence and
polymorphism predicted by a theoretical model of speciation. According to the
model, positively selected changes should accumulate in chromosomes that present
fixed structural differences, such as inversions, between the two species. Protein
evolution was more than 2.2 times faster in chromosomes that had undergone structural
rearrangements compared with colinear chromosomes. Also, nucleotide variability
is slightly lower in rearranged chromosomes. These patterns of divergence and
polymorphism may be, at least in part, the molecular footprint of speciation events
in the human and chimpanzee lineages. '
article_processing_charge: No
article_type: original
author:
- first_name: Arcadio
full_name: Navarro, Arcadio
last_name: Navarro
- 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: Navarro A, Barton NH. Chromosomal speciation and molecular divergence -- Accelerated
evolution in rearranged chromosomes. Science. 2003;300(5617):321-324. doi:10.1126/science.1080600
apa: Navarro, A., & Barton, N. H. (2003). Chromosomal speciation and molecular
divergence -- Accelerated evolution in rearranged chromosomes. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.1080600
chicago: Navarro, Arcadio, and Nicholas H Barton. “Chromosomal Speciation and Molecular
Divergence -- Accelerated Evolution in Rearranged Chromosomes.” Science.
American Association for the Advancement of Science, 2003. https://doi.org/10.1126/science.1080600 .
ieee: A. Navarro and N. H. Barton, “Chromosomal speciation and molecular divergence
-- Accelerated evolution in rearranged chromosomes,” Science, vol. 300,
no. 5617. American Association for the Advancement of Science, pp. 321–324, 2003.
ista: Navarro A, Barton NH. 2003. Chromosomal speciation and molecular divergence
-- Accelerated evolution in rearranged chromosomes. Science. 300(5617), 321–324.
mla: Navarro, Arcadio, and Nicholas H. Barton. “Chromosomal Speciation and Molecular
Divergence -- Accelerated Evolution in Rearranged Chromosomes.” Science,
vol. 300, no. 5617, American Association for the Advancement of Science, 2003,
pp. 321–24, doi:10.1126/science.1080600
.
short: A. Navarro, N.H. Barton, Science 300 (2003) 321–324.
date_created: 2018-12-11T12:07:53Z
date_published: 2003-04-11T00:00:00Z
date_updated: 2024-02-26T13:37:51Z
day: '11'
doi: '10.1126/science.1080600 '
extern: '1'
external_id:
pmid:
- ' 12690198'
intvolume: ' 300'
issue: '5617'
language:
- iso: eng
month: '04'
oa_version: None
page: 321 - 324
pmid: 1
publication: Science
publication_identifier:
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '1841'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromosomal speciation and molecular divergence -- Accelerated evolution in
rearranged chromosomes
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 300
year: '2003'
...
---
_id: '4146'
abstract:
- lang: eng
text: During vertebrate gastrulation, highly coordinated cellular rearrangements
lead to the formation of the three germ layers, ectoderm, mesoderm and endoderm.
In zebrafish, silberblick (slb)/wnt11 regulates normal gastrulation movements
by activating a signalling pathway similar to the Frizzled-signalling pathway,
which establishes epithelial planar cell polarity (PCP) in Drosophila. However,
the cellular mechanisms by which slb/wnt11 functions during zebrafish gastrulation
are still unclear. Using high-resolution two-photon confocal imaging followed
by computer-assisted reconstruction and motion analysis, we have analysed the
movement and morphology of individual cells in three dimensions during the course
of gastrulation. We show that in slb-mutant embryos, hypoblast cells within the
forming germ ring have slower, less directed migratory movements at the onset
of gastrulation. These aberrant cell movements are accompanied by defects in the
orientation of cellular processes along the individual movement directions of
these cells. We conclude that slb/wnt11-mediated orientation of cellular processes
plays a role in facilitating and stabilising movements of hypoblast cells in the
germ ring, thereby pointing at a novel function of the slb/wnt11 signalling pathway
for the regulation of migratory cell movements at early stages of gastrulation.
acknowledgement: 'We thank Jennifer Geiger, Mathias Köppen, Christian Dahmann and
Marcos Gonzalez-Gaitan for helpful comments on earlier versions of this manuscript,Beate
Kilian for technical assistance, Ugur Yalcin, Katrin Anczok and Viktor Schnabel
for help with the image analysis, Vinzenz Link for programming Excel Macros and
Harald Brush-Janovjak for extensive reviews of the statistics part of this work.
We are grateful to Kurt Anderson and Jan Peychl for help with the confocal microscopy.
P.J.H., E.V. and D.R.S. are supported by NIH grant HD-18577, The W.M Keck Foundation
and the Developmental Studies Hybridoma Bank(DSHB), P.J.H. by The American Cancer
Society (grant # PF-01-110-01-CSM),M.L.C. and S.W.W. by the Wellcome Trust, M.T.
by an MRC Career Development Award, and F.U. and C.P.H. by an Emmy-Noether-Fellowship
from the DFG.'
article_processing_charge: No
article_type: original
author:
- first_name: Florian
full_name: Ulrich, Florian
last_name: Ulrich
- first_name: Miguel
full_name: Concha, Miguel
last_name: Concha
- first_name: Paul
full_name: Heid, Paul
last_name: Heid
- first_name: Ed
full_name: Voss, Ed
last_name: Voss
- first_name: Sabine
full_name: Witzel, Sabine
last_name: Witzel
- first_name: Henry
full_name: Roehl, Henry
last_name: Roehl
- first_name: Masazumi
full_name: Tada, Masazumi
last_name: Tada
- first_name: Stephen
full_name: Wilson, Stephen
last_name: Wilson
- first_name: Richard
full_name: Adams, Richard
last_name: Adams
- first_name: David
full_name: Soll, David
last_name: Soll
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Ulrich F, Concha M, Heid P, et al. Slb/Wnt11 controls hypoblast cell migration
and morphogenesis at the onset of zebrafish gastrulation. Development.
2003;130(22):5375-5384. doi:10.1242/dev.00758
apa: Ulrich, F., Concha, M., Heid, P., Voss, E., Witzel, S., Roehl, H., … Heisenberg,
C.-P. J. (2003). Slb/Wnt11 controls hypoblast cell migration and morphogenesis
at the onset of zebrafish gastrulation. Development. Company of Biologists.
https://doi.org/10.1242/dev.00758
chicago: Ulrich, Florian, Miguel Concha, Paul Heid, Ed Voss, Sabine Witzel, Henry
Roehl, Masazumi Tada, et al. “Slb/Wnt11 Controls Hypoblast Cell Migration and
Morphogenesis at the Onset of Zebrafish Gastrulation.” Development. Company
of Biologists, 2003. https://doi.org/10.1242/dev.00758.
ieee: F. Ulrich et al., “Slb/Wnt11 controls hypoblast cell migration and
morphogenesis at the onset of zebrafish gastrulation,” Development, vol.
130, no. 22. Company of Biologists, pp. 5375–5384, 2003.
ista: Ulrich F, Concha M, Heid P, Voss E, Witzel S, Roehl H, Tada M, Wilson S, Adams
R, Soll D, Heisenberg C-PJ. 2003. Slb/Wnt11 controls hypoblast cell migration
and morphogenesis at the onset of zebrafish gastrulation. Development. 130(22),
5375–5384.
mla: Ulrich, Florian, et al. “Slb/Wnt11 Controls Hypoblast Cell Migration and Morphogenesis
at the Onset of Zebrafish Gastrulation.” Development, vol. 130, no. 22,
Company of Biologists, 2003, pp. 5375–84, doi:10.1242/dev.00758.
short: F. Ulrich, M. Concha, P. Heid, E. Voss, S. Witzel, H. Roehl, M. Tada, S.
Wilson, R. Adams, D. Soll, C.-P.J. Heisenberg, Development 130 (2003) 5375–5384.
date_created: 2018-12-11T12:07:13Z
date_published: 2003-11-15T00:00:00Z
date_updated: 2024-02-27T10:14:21Z
day: '15'
doi: 10.1242/dev.00758
extern: '1'
external_id:
pmid:
- ' PMC1414802'
intvolume: ' 130'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1414802/
month: '11'
oa: 1
oa_version: None
page: 5375 - 5384
pmid: 1
publication: Development
publication_identifier:
issn:
- 1011-6370
publication_status: published
publisher: Company of Biologists
publist_id: '1975'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Slb/Wnt11 controls hypoblast cell migration and morphogenesis at the onset
of zebrafish gastrulation
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 130
year: '2003'
...
---
_id: '4169'
abstract:
- lang: eng
text: 'Background: During vertebrate gastrulation, cell polarization and migration
are core components in the cellular rearrangements that lead to the formation
of the three germ layers, ectoderm, mesoderm, and endoderm. Previous studies have
implicated the Wnt/planar cell polarity (PCP) signaling pathway in controlling
cell morphology and movement during gastrulation. However, cell polarization and
directed cell migration are reduced but not completely abolished in the absence
of Wnt/PCP signals; this observation indicates that other signaling pathways must
be involved. Results: We show that Phosphoinositide 3-Kinases (PI3Ks) are required
at the onset of zebrafish gastrulation in mesendodermal cells for process formation
and cell polarization. Platelet Derived Growth Factor (PDGF) functions upstream
of PI3K, while Protein Kinase B (PKB), a downstream effector of PI3K activity,
localizes to the leading edge of migrating mesendodermal cells. In the absence
of PI3K activity, PKB localization and cell polarization are strongly reduced
in mesendodermal cells and are followed by slower but still highly coordinated
and directed movements of these cells. Conclusions: We have identified a novel
role of a signaling pathway comprised of PDGF, PI3K, and PKB in the control of
morphogenetic cell movements during gastrulation. Furthermore, our findings provide
insight into the relationship between cell polarization and directed cell migration
at the onset of zebrafish gastrulation.'
acknowledgement: 'We would like to thank Jennifer Geiger, Juan Hurl& Hannu Mansu-koski,
Florian Raible, Marino Zerial, Steve Wilson, and Kurt Anderson for critical reading
of earlier versions of this manuscript. We thank Erez Raz, Bart Vanhaesebroeck,
and Lukas Roth for sending us the pCS2-PH-GFP-nos, the p1IOCAAX, and the pCS2-actin-GFP
constructs, respectively. We are grateful to Marino Zerial and his lab for encouraging
us to start this work and providing us with the dnP13K construct and to Florian
Ulrich and Franziska Friedrich for help with the confocal microscope and artwork,
respectively. We thank Gunter Junghanns and Evelyn Lehmann for excellent fish care.
C.-P.H. is supported by an Emmy-Noother-Fellowship from the Deutsche Forschungsgemeinschaft. '
article_processing_charge: No
article_type: original
author:
- first_name: Juan
full_name: Montero, Juan
last_name: Montero
- first_name: Beate
full_name: Kilian, Beate
last_name: Kilian
- first_name: Joanne
full_name: Chan, Joanne
last_name: Chan
- first_name: Peter
full_name: Bayliss, Peter
last_name: Bayliss
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Montero J, Kilian B, Chan J, Bayliss P, Heisenberg C-PJ. Phosphoinositide 3-kinase
is required for process outgrowth and cell polarization of gastrulating mesendodermal
cells. Current Biology. 2003;13(15):1279-1289. doi:10.1016/S0960-9822(03)00505-0
apa: Montero, J., Kilian, B., Chan, J., Bayliss, P., & Heisenberg, C.-P. J.
(2003). Phosphoinositide 3-kinase is required for process outgrowth and cell polarization
of gastrulating mesendodermal cells. Current Biology. Cell Press. https://doi.org/10.1016/S0960-9822(03)00505-0
chicago: Montero, Juan, Beate Kilian, Joanne Chan, Peter Bayliss, and Carl-Philipp
J Heisenberg. “Phosphoinositide 3-Kinase Is Required for Process Outgrowth and
Cell Polarization of Gastrulating Mesendodermal Cells.” Current Biology.
Cell Press, 2003. https://doi.org/10.1016/S0960-9822(03)00505-0.
ieee: J. Montero, B. Kilian, J. Chan, P. Bayliss, and C.-P. J. Heisenberg, “Phosphoinositide
3-kinase is required for process outgrowth and cell polarization of gastrulating
mesendodermal cells,” Current Biology, vol. 13, no. 15. Cell Press, pp.
1279–1289, 2003.
ista: Montero J, Kilian B, Chan J, Bayliss P, Heisenberg C-PJ. 2003. Phosphoinositide
3-kinase is required for process outgrowth and cell polarization of gastrulating
mesendodermal cells. Current Biology. 13(15), 1279–1289.
mla: Montero, Juan, et al. “Phosphoinositide 3-Kinase Is Required for Process Outgrowth
and Cell Polarization of Gastrulating Mesendodermal Cells.” Current Biology,
vol. 13, no. 15, Cell Press, 2003, pp. 1279–89, doi:10.1016/S0960-9822(03)00505-0.
short: J. Montero, B. Kilian, J. Chan, P. Bayliss, C.-P.J. Heisenberg, Current Biology
13 (2003) 1279–1289.
date_created: 2018-12-11T12:07:22Z
date_published: 2003-08-05T00:00:00Z
date_updated: 2024-02-27T10:03:37Z
day: '05'
doi: 10.1016/S0960-9822(03)00505-0
extern: '1'
external_id:
pmid:
- ' 12906787'
intvolume: ' 13'
issue: '15'
language:
- iso: eng
month: '08'
oa_version: None
page: 1279 - 1289
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Cell Press
publist_id: '1950'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phosphoinositide 3-kinase is required for process outgrowth and cell polarization
of gastrulating mesendodermal cells
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 13
year: '2003'
...
---
_id: '4185'
abstract:
- lang: eng
text: Wnt genes play important roles in regulating patterning and morphogenesis
during vertebrate gastrulation. In zebrafish, slb/wnt11 is required for convergence
and extension movements, but not cell fate specification during gastrulation.
To determine if other Wnt genes functionally interact with slb/wnt11, we analysed
the role of ppt/wnt5 during zebrafish gastrulation. ppt/wnt5 is maternally provided
and zygotically expressed at all stages during gastrulation. The analysis of ppt
mutant embryos reveals that Ppt/Wnt5 regulates cell elongation and convergent
extension movements in posterior regions of the gastrula, while its function in
more anterior regions is largely redundant to that of Slb/Wnt11. Frizzled-2 functions
downstream of ppt/wnt5, indicating that it might act as a receptor for Ppt/Wnt5
in this process. The characterisation of the role of Ppt/Wnt5 provides insight
into the functional diversity of Wnt genes in regulating vertebrate gastrulation
movements. (C) 2003 Elsevier Science Ireland Ltd. All rights reserved.
acknowledgement: We thank Michael Brand, Florian Raible, Gerlinde Reim, Tobias Langenberg,
Jennifer Geiger and Kate Poole for helpful comments on earlier versions of this
manuscript. We are grateful to Henry Roehl and Christiane Nüsslein Volhard for sending
us the ppt mutant stock. M.T. was supported by a Career Development Fellowship from
the MRC. B.K., H.M. and C.P.H. are supported by an Emmy Noether-Fellowship from
the DFG.
article_processing_charge: No
article_type: original
author:
- first_name: Beate
full_name: Kilian, Beate
last_name: Kilian
- first_name: Hannu
full_name: Mansukoski, Hannu
last_name: Mansukoski
- first_name: Filipa
full_name: Barbosa, Filipa
last_name: Barbosa
- first_name: Florian
full_name: Ulrich, Florian
last_name: Ulrich
- first_name: Masazumi
full_name: Tada, Masazumi
last_name: Tada
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Kilian B, Mansukoski H, Barbosa F, Ulrich F, Tada M, Heisenberg C-PJ. The role
of Ppt/Wnt5 in regulating cell shape and movement during zebrafish gastrulation.
Mechanisms of Development. 2003;120(4):467-476. doi:10.1016/S0925-4773(03)00004-2
apa: Kilian, B., Mansukoski, H., Barbosa, F., Ulrich, F., Tada, M., & Heisenberg,
C.-P. J. (2003). The role of Ppt/Wnt5 in regulating cell shape and movement during
zebrafish gastrulation. Mechanisms of Development. Elsevier. https://doi.org/10.1016/S0925-4773(03)00004-2
chicago: Kilian, Beate, Hannu Mansukoski, Filipa Barbosa, Florian Ulrich, Masazumi
Tada, and Carl-Philipp J Heisenberg. “The Role of Ppt/Wnt5 in Regulating Cell
Shape and Movement during Zebrafish Gastrulation.” Mechanisms of Development.
Elsevier, 2003. https://doi.org/10.1016/S0925-4773(03)00004-2.
ieee: B. Kilian, H. Mansukoski, F. Barbosa, F. Ulrich, M. Tada, and C.-P. J. Heisenberg,
“The role of Ppt/Wnt5 in regulating cell shape and movement during zebrafish gastrulation,”
Mechanisms of Development, vol. 120, no. 4. Elsevier, pp. 467–476, 2003.
ista: Kilian B, Mansukoski H, Barbosa F, Ulrich F, Tada M, Heisenberg C-PJ. 2003.
The role of Ppt/Wnt5 in regulating cell shape and movement during zebrafish gastrulation.
Mechanisms of Development. 120(4), 467–476.
mla: Kilian, Beate, et al. “The Role of Ppt/Wnt5 in Regulating Cell Shape and Movement
during Zebrafish Gastrulation.” Mechanisms of Development, vol. 120, no.
4, Elsevier, 2003, pp. 467–76, doi:10.1016/S0925-4773(03)00004-2.
short: B. Kilian, H. Mansukoski, F. Barbosa, F. Ulrich, M. Tada, C.-P.J. Heisenberg,
Mechanisms of Development 120 (2003) 467–476.
date_created: 2018-12-11T12:07:27Z
date_published: 2003-04-01T00:00:00Z
date_updated: 2024-02-27T09:46:39Z
day: '01'
doi: 10.1016/S0925-4773(03)00004-2
extern: '1'
external_id:
pmid:
- '12676324 '
intvolume: ' 120'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 467 - 476
pmid: 1
publication: Mechanisms of Development
publication_identifier:
issn:
- 0925-4773
publication_status: published
publisher: Elsevier
publist_id: '1934'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The role of Ppt/Wnt5 in regulating cell shape and movement during zebrafish
gastrulation
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 120
year: '2003'
...
---
_id: '3992'
abstract:
- lang: eng
text: Computing the volume occupied by individual atoms in macromolecular structures
has been the subject of research for several decades. This interest has grown
in the recent years, because weighted volumes are widely used in implicit solvent
models. Applications of the latter in molecular mechanics simulations require
that the derivatives of these weighted volumes be known. In this article, we give
a formula for the volume derivative of a molecule modeled as a space-filling diagram
made up of balls in motion. The formula is given in terms of the weights, radii,
and distances between the centers as well as the sizes of the facets of the power
diagram restricted to the space-filling diagram. Special attention is given to
the detection and treatment of singularities as well as discontinuities of the
derivative.
article_processing_charge: No
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Patrice
full_name: Koehl, Patrice
last_name: Koehl
citation:
ama: Edelsbrunner H, Koehl P. The weighted-volume derivative of a space-filling
diagram. PNAS. 2003;100(5):2203-2208. doi:10.1073/pnas.0537830100
apa: Edelsbrunner, H., & Koehl, P. (2003). The weighted-volume derivative of
a space-filling diagram. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0537830100
chicago: Edelsbrunner, Herbert, and Patrice Koehl. “The Weighted-Volume Derivative
of a Space-Filling Diagram.” PNAS. National Academy of Sciences, 2003.
https://doi.org/10.1073/pnas.0537830100.
ieee: H. Edelsbrunner and P. Koehl, “The weighted-volume derivative of a space-filling
diagram,” PNAS, vol. 100, no. 5. National Academy of Sciences, pp. 2203–2208,
2003.
ista: Edelsbrunner H, Koehl P. 2003. The weighted-volume derivative of a space-filling
diagram. PNAS. 100(5), 2203–2208.
mla: Edelsbrunner, Herbert, and Patrice Koehl. “The Weighted-Volume Derivative of
a Space-Filling Diagram.” PNAS, vol. 100, no. 5, National Academy of Sciences,
2003, pp. 2203–08, doi:10.1073/pnas.0537830100.
short: H. Edelsbrunner, P. Koehl, PNAS 100 (2003) 2203–2208.
date_created: 2018-12-11T12:06:19Z
date_published: 2003-03-04T00:00:00Z
date_updated: 2024-02-27T12:31:59Z
day: '04'
doi: 10.1073/pnas.0537830100
extern: '1'
external_id:
pmid:
- '12601153'
intvolume: ' 100'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC151318/
month: '03'
oa: 1
oa_version: Published Version
page: 2203 - 2208
pmid: 1
publication: PNAS
publication_identifier:
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
publist_id: '2133'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The weighted-volume derivative of a space-filling diagram
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 100
year: '2003'
...
---
_id: '3999'
abstract:
- lang: eng
text: We introduce relaxed scheduling as a paradigm for mesh maintenance and demonstrate
its applicability to triangulating a skin surface in R-3.
acknowledgement: NSF under grant CCR-00- 86013.
alternative_title:
- LNCS
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
- first_name: Alper
full_name: Üngör, Alper
last_name: Üngör
citation:
ama: 'Edelsbrunner H, Üngör A. Relaxed scheduling in dynamic skin triangulation.
In: Proceedings of the Japanese Conference on Discrete and Computational Geometry
. Vol 2866. Springer; 2003:135-151. doi:10.1007/978-3-540-44400-8_14'
apa: 'Edelsbrunner, H., & Üngör, A. (2003). Relaxed scheduling in dynamic skin
triangulation. In Proceedings of the Japanese Conference on Discrete and Computational
Geometry (Vol. 2866, pp. 135–151). Tokyo, Japan: Springer. https://doi.org/10.1007/978-3-540-44400-8_14'
chicago: Edelsbrunner, Herbert, and Alper Üngör. “Relaxed Scheduling in Dynamic
Skin Triangulation.” In Proceedings of the Japanese Conference on Discrete
and Computational Geometry , 2866:135–51. Springer, 2003. https://doi.org/10.1007/978-3-540-44400-8_14.
ieee: H. Edelsbrunner and A. Üngör, “Relaxed scheduling in dynamic skin triangulation,”
in Proceedings of the Japanese Conference on Discrete and Computational Geometry
, Tokyo, Japan, 2003, vol. 2866, pp. 135–151.
ista: 'Edelsbrunner H, Üngör A. 2003. Relaxed scheduling in dynamic skin triangulation.
Proceedings of the Japanese Conference on Discrete and Computational Geometry
. JCDCG: Japanese Conference on Discrete and Computational Geometry, LNCS, vol.
2866, 135–151.'
mla: Edelsbrunner, Herbert, and Alper Üngör. “Relaxed Scheduling in Dynamic Skin
Triangulation.” Proceedings of the Japanese Conference on Discrete and Computational
Geometry , vol. 2866, Springer, 2003, pp. 135–51, doi:10.1007/978-3-540-44400-8_14.
short: H. Edelsbrunner, A. Üngör, in:, Proceedings of the Japanese Conference on
Discrete and Computational Geometry , Springer, 2003, pp. 135–151.
conference:
end_date: 2002-12-09
location: Tokyo, Japan
name: 'JCDCG: Japanese Conference on Discrete and Computational Geometry'
start_date: 2002-12-06
date_created: 2018-12-11T12:06:21Z
date_published: 2003-12-16T00:00:00Z
date_updated: 2024-02-27T11:07:15Z
day: '16'
doi: 10.1007/978-3-540-44400-8_14
extern: '1'
intvolume: ' 2866'
language:
- iso: eng
month: '12'
oa_version: None
page: 135 - 151
publication: 'Proceedings of the Japanese Conference on Discrete and Computational
Geometry '
publication_identifier:
isbn:
- '9783540207764'
publication_status: published
publisher: Springer
publist_id: '2127'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Relaxed scheduling in dynamic skin triangulation
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2866
year: '2003'
...
---
_id: '3997'
abstract:
- lang: eng
text: We combine topological and geometric methods to construct a multi-resolution
data structure for functions over two-dimensional domains. Starting with the Morse-Smale
complex, we construct a topological hierarchy by progressively canceling critical
points in pairs. Concurrently, we create a geometric hierarchy by adapting the
geometry to the changes in topology. The data structure supports mesh traversal
operations similarly to traditional multi-resolution representations.
acknowledgement: This work was performed under the auspices of the U. S. Department
of Energy by University of California Lawrence Livermore National Laboratory under
contract No. W-7405-Eng-48. H. Edelsbrunner is partially supported by the National
Science Foundation (NFS) under grants EIA-99-72879 and CCR-00-86013. B. Hamann is
supported by the NSF under contract ACI 9624034, through the LSSDSV program under
contract ACI 9982251, and through the NPACI; the National Institute of Mental Health
and the NSF under contract NIMH 2 P20 MH60975-06A2; the Lawrence Livermore National
Laboratory under ASCI ASAP Level-2 Memorandum Agreement B347878 and under Memorandum
Agreement B503159.
article_processing_charge: No
author:
- first_name: Peer
full_name: Bremer, Peer
last_name: Bremer
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Bernd
full_name: Hamann, Bernd
last_name: Hamann
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
citation:
ama: 'Bremer P, Edelsbrunner H, Hamann B, Pascucci V. A multi-resolution data structure
for two-dimensional Morse-Smale functions. In: Proceedings of the 14th IEEE
Conference on Visualization . IEEE; 2003:139-146. doi:10.1109/VISUAL.2003.1250365'
apa: 'Bremer, P., Edelsbrunner, H., Hamann, B., & Pascucci, V. (2003). A multi-resolution
data structure for two-dimensional Morse-Smale functions. In Proceedings of
the 14th IEEE Conference on Visualization (pp. 139–146). Seattle, WA, USA
: IEEE. https://doi.org/10.1109/VISUAL.2003.1250365'
chicago: Bremer, Peer, Herbert Edelsbrunner, Bernd Hamann, and Valerio Pascucci.
“A Multi-Resolution Data Structure for Two-Dimensional Morse-Smale Functions.”
In Proceedings of the 14th IEEE Conference on Visualization , 139–46. IEEE,
2003. https://doi.org/10.1109/VISUAL.2003.1250365.
ieee: P. Bremer, H. Edelsbrunner, B. Hamann, and V. Pascucci, “A multi-resolution
data structure for two-dimensional Morse-Smale functions,” in Proceedings of
the 14th IEEE Conference on Visualization , Seattle, WA, USA , 2003, pp. 139–146.
ista: 'Bremer P, Edelsbrunner H, Hamann B, Pascucci V. 2003. A multi-resolution
data structure for two-dimensional Morse-Smale functions. Proceedings of the 14th
IEEE Conference on Visualization . VIS: IEEE Visualization, 139–146.'
mla: Bremer, Peer, et al. “A Multi-Resolution Data Structure for Two-Dimensional
Morse-Smale Functions.” Proceedings of the 14th IEEE Conference on Visualization
, IEEE, 2003, pp. 139–46, doi:10.1109/VISUAL.2003.1250365.
short: P. Bremer, H. Edelsbrunner, B. Hamann, V. Pascucci, in:, Proceedings of the
14th IEEE Conference on Visualization , IEEE, 2003, pp. 139–146.
conference:
end_date: 2003-10-24
location: 'Seattle, WA, USA '
name: 'VIS: IEEE Visualization'
start_date: 2003-10-19
date_created: 2018-12-11T12:06:21Z
date_published: 2003-08-01T00:00:00Z
date_updated: 2024-02-27T11:12:50Z
day: '01'
doi: 10.1109/VISUAL.2003.1250365
extern: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 139 - 146
publication: 'Proceedings of the 14th IEEE Conference on Visualization '
publication_identifier:
isbn:
- '0780381203'
publication_status: published
publisher: IEEE
publist_id: '2131'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A multi-resolution data structure for two-dimensional Morse-Smale functions
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
year: '2003'
...
---
_id: '4168'
abstract:
- lang: eng
text: Recent studies show that signaling through integrin receptors is required
for normal cell movements during Xenopus gastrulation. Integrins function in this
process by modulating the activity of cadherin adhesion molecules within tissues
undergoing convergence and extension movements.
article_processing_charge: No
article_type: original
author:
- first_name: Juan
full_name: Montero, Juan
last_name: Montero
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Montero J, Heisenberg C-PJ. Adhesive crosstalk in gastrulation. Developmental
Cell. 2003;5(2):190-191. doi:10.1016/S1534-5807(03)00235-1
apa: Montero, J., & Heisenberg, C.-P. J. (2003). Adhesive crosstalk in gastrulation.
Developmental Cell. Cell Press. https://doi.org/10.1016/S1534-5807(03)00235-1
chicago: Montero, Juan, and Carl-Philipp J Heisenberg. “Adhesive Crosstalk in Gastrulation.”
Developmental Cell. Cell Press, 2003. https://doi.org/10.1016/S1534-5807(03)00235-1.
ieee: J. Montero and C.-P. J. Heisenberg, “Adhesive crosstalk in gastrulation,”
Developmental Cell, vol. 5, no. 2. Cell Press, pp. 190–191, 2003.
ista: Montero J, Heisenberg C-PJ. 2003. Adhesive crosstalk in gastrulation. Developmental
Cell. 5(2), 190–191.
mla: Montero, Juan, and Carl-Philipp J. Heisenberg. “Adhesive Crosstalk in Gastrulation.”
Developmental Cell, vol. 5, no. 2, Cell Press, 2003, pp. 190–91, doi:10.1016/S1534-5807(03)00235-1.
short: J. Montero, C.-P.J. Heisenberg, Developmental Cell 5 (2003) 190–191.
date_created: 2018-12-11T12:07:21Z
date_published: 2003-08-01T00:00:00Z
date_updated: 2024-02-27T09:54:53Z
day: '01'
doi: 10.1016/S1534-5807(03)00235-1
extern: '1'
external_id:
pmid:
- '12919669 '
intvolume: ' 5'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
page: 190 - 191
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Cell Press
publist_id: '1949'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adhesive crosstalk in gastrulation
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 5
year: '2003'
...
---
_id: '3991'
abstract:
- lang: eng
text: We give analytic inclusion-exclusion formulas for the area and perimeter derivatives
of a union of finitely many disks in the plane.
acknowledgement: Partially supported by NSF under grant DMS-98-73945 and CCR-00-86013.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Ho
full_name: Cheng, Ho
last_name: Cheng
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Cheng H, Edelsbrunner H. Area and perimeter derivatives of a union of disks.
In: Computer Science in Perspective: Essays Dedicated to Thomas Ottmann.
Vol 2598. Springer; 2003:88-97. doi:10.1007/3-540-36477-3_7'
apa: 'Cheng, H., & Edelsbrunner, H. (2003). Area and perimeter derivatives of
a union of disks. In Computer Science in Perspective: Essays Dedicated to Thomas
Ottmann (Vol. 2598, pp. 88–97). Springer. https://doi.org/10.1007/3-540-36477-3_7'
chicago: 'Cheng, Ho, and Herbert Edelsbrunner. “Area and Perimeter Derivatives of
a Union of Disks.” In Computer Science in Perspective: Essays Dedicated to
Thomas Ottmann, 2598:88–97. Springer, 2003. https://doi.org/10.1007/3-540-36477-3_7.'
ieee: 'H. Cheng and H. Edelsbrunner, “Area and perimeter derivatives of a union
of disks,” in Computer Science in Perspective: Essays Dedicated to Thomas Ottmann,
vol. 2598, Springer, 2003, pp. 88–97.'
ista: 'Cheng H, Edelsbrunner H. 2003.Area and perimeter derivatives of a union of
disks. In: Computer Science in Perspective: Essays Dedicated to Thomas Ottmann.
LNCS, vol. 2598, 88–97.'
mla: 'Cheng, Ho, and Herbert Edelsbrunner. “Area and Perimeter Derivatives of a
Union of Disks.” Computer Science in Perspective: Essays Dedicated to Thomas
Ottmann, vol. 2598, Springer, 2003, pp. 88–97, doi:10.1007/3-540-36477-3_7.'
short: 'H. Cheng, H. Edelsbrunner, in:, Computer Science in Perspective: Essays
Dedicated to Thomas Ottmann, Springer, 2003, pp. 88–97.'
date_created: 2018-12-11T12:06:18Z
date_published: 2003-02-17T00:00:00Z
date_updated: 2024-02-27T12:15:02Z
day: '17'
doi: 10.1007/3-540-36477-3_7
extern: '1'
intvolume: ' 2598'
language:
- iso: eng
month: '02'
oa_version: None
page: 88 - 97
publication: 'Computer Science in Perspective: Essays Dedicated to Thomas Ottmann'
publication_identifier:
isbn:
- '9783540005797'
publication_status: published
publisher: Springer
publist_id: '2132'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Area and perimeter derivatives of a union of disks
type: book_chapter
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2598
year: '2003'
...