---
_id: '3779'
abstract:
- lang: eng
text: Crosses between closely related species give two contrasting results. One
result is that species hybrids may be inferior to their parents, for example,
being less fertile [1]. The other is that F1 hybrids may display superior performance
(heterosis), for example with increased vigour [2]. Although various hypotheses
have been proposed to account for these two aspects of hybridisation, their biological
basis is still poorly understood [3]. To gain further insights into this issue,
we analysed the role that variation in gene expression may play. We took a conserved
trait, flower asymmetry in Antirrhinum, and determined the extent to which the
underlying regulatory genes varied in expression among closely related species.
We show that expression of both genes analysed, CYC and RAD, varies significantly
between species because of cis-acting differences. By making a quantitative genotype-phenotype
map, using a range of mutant alleles, we demonstrate that the species lie on a
plateau in gene expression-morphology space, so that the variation has no detectable
phenotypic effect. However, phenotypic differences can be revealed by shifting
genotypes off the plateau through genetic crosses. Our results can be readily
explained if genomes are free to evolve within an effectively neutral zone in
gene expression space. The consequences of this drift will be negligible for individual
loci, but when multiple loci across the genome are considered, we show that the
variation may have significant effects on phenotype and fitness, causing a significant
drift load. By considering these consequences for various gene-expression-fitness
landscapes, we conclude that F1 hybrids might be expected to show increased performance
with regard to conserved traits, such as basic physiology, but reduced performance
with regard to others. Thus, our study provides a new way of explaining how various
aspects of hybrid performance may arise through natural variation in gene activity.
acknowledgement: "This was supported by a Marie Curie grant for early stage training
and the BBSRC-John Innes Centre PhD Rotation Program.\r\nWe would like to thank
X. Feng and A. Hudson for assistance with introgressions and genotyping; A. Green,
A. Bangham and J. Pateman for advice and assistance on shape model procedures; F.
Alderson and S.Mitchell from JIC horticultural services; P.J. Wittkopp for protocols
and advice on pyrosequencing; and R. Sablowski for discussions and comments.\r\n"
article_number: e1000429
author:
- first_name: Ulises
full_name: Rosas, Ulises
last_name: Rosas
- 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: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Pierre
full_name: Barbier De Reuille, Pierre
last_name: Barbier De Reuille
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Cryptic variation
between species and the basis of hybrid performance. PLoS Biology. 2010;8(7).
doi:10.1371/journal.pbio.1000429
apa: Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E.
(2010). Cryptic variation between species and the basis of hybrid performance.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429
chicago: Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille,
and Enrico Coen. “Cryptic Variation between Species and the Basis of Hybrid Performance.”
PLoS Biology. Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000429.
ieee: U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Cryptic
variation between species and the basis of hybrid performance,” PLoS Biology,
vol. 8, no. 7. Public Library of Science, 2010.
ista: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Cryptic
variation between species and the basis of hybrid performance. PLoS Biology. 8(7),
e1000429.
mla: Rosas, Ulises, et al. “Cryptic Variation between Species and the Basis of Hybrid
Performance.” PLoS Biology, vol. 8, no. 7, e1000429, Public Library of
Science, 2010, doi:10.1371/journal.pbio.1000429.
short: U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, PLoS Biology
8 (2010).
date_created: 2018-12-11T12:05:07Z
date_published: 2010-07-20T00:00:00Z
date_updated: 2023-02-23T14:07:34Z
day: '20'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.1000429
file:
- access_level: open_access
checksum: ee1ce2fb283a6b4127544ae532d0b4a1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:11Z
date_updated: 2020-07-14T12:46:15Z
file_id: '5060'
file_name: IST-2015-366-v1+1_journal.pbio.1000429.pdf
file_size: 1089530
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '2448'
pubrep_id: '366'
quality_controlled: '1'
related_material:
record:
- id: '9764'
relation: research_data
status: public
scopus_import: 1
status: public
title: Cryptic variation between species and the basis of hybrid performance
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2010'
...
---
_id: '3782'
abstract:
- lang: eng
text: In cortex surface segmentation, the extracted surface is required to have
a particular topology, namely, a two-sphere. We present a new method for removing
topology noise of a curve or surface within the level set framework, and thus
produce a cortical surface with correct topology. We define a new energy term
which quantifies topology noise. We then show how to minimize this term by computing
its functional derivative with respect to the level set function. This method
differs from existing methods in that it is inherently continuous and not digital;
and in the way that our energy directly relates to the topology of the underlying
curve or surface, versus existing knot-based measures which are related in a more
indirect fashion. The proposed flow is validated empirically.
acknowledgement: "Partially supported by the Austri an Science Fund unde r grant P20134-N13.\r\nWe
thank Helena Molina-Abril for very helpful discussion. We thank anonymous reviewers
for helpful comments."
alternative_title:
- LNCS
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Daniel
full_name: Freedman, Daniel
last_name: Freedman
citation:
ama: 'Chen C, Freedman D. Topology noise removal for curve and surface evolution.
In: Conference Proceedings MCV 2010. Vol 6533. Springer; 2010:31-42. doi:10.1007/978-3-642-18421-5_4'
apa: 'Chen, C., & Freedman, D. (2010). Topology noise removal for curve and
surface evolution. In Conference proceedings MCV 2010 (Vol. 6533, pp.
31–42). Beijing, China: Springer. https://doi.org/10.1007/978-3-642-18421-5_4'
chicago: Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve and
Surface Evolution.” In Conference Proceedings MCV 2010, 6533:31–42. Springer,
2010. https://doi.org/10.1007/978-3-642-18421-5_4.
ieee: C. Chen and D. Freedman, “Topology noise removal for curve and surface evolution,”
in Conference proceedings MCV 2010, Beijing, China, 2010, vol. 6533, pp.
31–42.
ista: 'Chen C, Freedman D. 2010. Topology noise removal for curve and surface evolution. Conference
proceedings MCV 2010. MCV: Medical Computer Vision, LNCS, vol. 6533, 31–42.'
mla: Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve and Surface
Evolution.” Conference Proceedings MCV 2010, vol. 6533, Springer, 2010,
pp. 31–42, doi:10.1007/978-3-642-18421-5_4.
short: C. Chen, D. Freedman, in:, Conference Proceedings MCV 2010, Springer, 2010,
pp. 31–42.
conference:
end_date: 2010-09-20
location: Beijing, China
name: 'MCV: Medical Computer Vision'
start_date: 2010-09-20
date_created: 2018-12-11T12:05:08Z
date_published: 2010-12-31T00:00:00Z
date_updated: 2021-01-12T07:52:10Z
day: '31'
department:
- _id: HeEd
doi: 10.1007/978-3-642-18421-5_4
intvolume: ' 6533'
language:
- iso: eng
month: '12'
oa_version: None
page: 31 - 42
publication: ' Conference proceedings MCV 2010'
publication_status: published
publisher: Springer
publist_id: '2445'
quality_controlled: '1'
scopus_import: 1
status: public
title: Topology noise removal for curve and surface evolution
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6533
year: '2010'
...
---
_id: '3783'
abstract:
- lang: eng
text: MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that
facilitates several tasks when scoring microsatellites. It implements new subroutines
in R and PERL and takes advantage of features provided by previously developed
freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification
through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite
markers according to their multiplex group, fluorochrome type, and size range.
After peak selection, binning of alleles can be carried out 1) automatically through
AlleloBin or 2) by manual bin definition through Binator. In both cases, several
features for quality checking and further binning improvement are provided. The
genotype table can then be converted into input files for several population genetics
programs through CREATE. Finally, Hardy–Weinberg equilibrium tests and confidence
intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT
is the only freely available public-domain software that facilitates full multiplex
microsatellite scoring, from electropherogram files to user-defined text files
to be used with population genetics software. MICROSATELIGHT has been created
for the Windows XP operating system and has been successfully tested under Windows
7. It is available at http://sourceforge.net/projects/microsatelight/.
acknowledgement: "Ministerio de Educación y Ciencia (CGL2006-13423, CTM2007-66635).
M.P. and FP are part of the research group 2009SGR-636 of the Generalitat de Catalunya.
F.P. acknowledges an EU-Synthesys grant (GB-TAF-4474).\r\n\r\nThanks to José Gabriel
Segarra-Moragues (Centro de Investigaciones sobre Desertificación) for sending us
pictures with several types of stuttering and Pedro Simões and Gemma Calàbria (Universitat
de Barcelona) for testing this software. Finally, thanks are due to 2 anonymous
referees for their valuable comments. These comments certainly helped to improve
the manuscript."
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Fernando
full_name: González Candelas, Fernando
last_name: González Candelas
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
citation:
ama: Palero F, González Candelas F, Pascual M. Microsatelight – Pipeline to expedite
microsatellite analysis. Journal of Heredity. 2010;102(2):247-249. doi:10.1093/jhered/esq111
apa: Palero, F., González Candelas, F., & Pascual, M. (2010). Microsatelight
– Pipeline to expedite microsatellite analysis. Journal of Heredity. Oxford
University Press. https://doi.org/10.1093/jhered/esq111
chicago: Palero, Ferran, Fernando González Candelas, and Marta Pascual. “Microsatelight
– Pipeline to Expedite Microsatellite Analysis.” Journal of Heredity. Oxford
University Press, 2010. https://doi.org/10.1093/jhered/esq111.
ieee: F. Palero, F. González Candelas, and M. Pascual, “Microsatelight – Pipeline
to expedite microsatellite analysis,” Journal of Heredity, vol. 102, no.
2. Oxford University Press, pp. 247–249, 2010.
ista: Palero F, González Candelas F, Pascual M. 2010. Microsatelight – Pipeline
to expedite microsatellite analysis. Journal of Heredity. 102(2), 247–249.
mla: Palero, Ferran, et al. “Microsatelight – Pipeline to Expedite Microsatellite
Analysis.” Journal of Heredity, vol. 102, no. 2, Oxford University Press,
2010, pp. 247–49, doi:10.1093/jhered/esq111.
short: F. Palero, F. González Candelas, M. Pascual, Journal of Heredity 102 (2010)
247–249.
date_created: 2018-12-11T12:05:09Z
date_published: 2010-12-02T00:00:00Z
date_updated: 2021-01-12T07:52:10Z
day: '02'
department:
- _id: NiBa
doi: 10.1093/jhered/esq111
intvolume: ' 102'
issue: '2'
language:
- iso: eng
month: '12'
oa_version: None
page: 247 - 249
publication: Journal of Heredity
publication_status: published
publisher: Oxford University Press
publist_id: '2444'
quality_controlled: '1'
scopus_import: 1
status: public
title: Microsatelight – Pipeline to expedite microsatellite analysis
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 102
year: '2010'
...
---
_id: '3785'
abstract:
- lang: eng
text: Most fisheries involving spiny lobsters of the genus Palinurus have been over
exploited during the last decades, so there is a raising concern about management
decisions for these valuable resources. A total of 13 microsatellite DNA loci
recently developed in Palinurus elephas were assayed in order to assess genetic diversity levels in every known species of the genus. Microsatellite markers gave
amplifications and showed polymorphism in all species, with gene diversity values varying from 0.65060.077 SD (Palinurus
barbarae) to 0.79260.051 SD (Palinurus elephas). Most importantly, when depth
distribution was taken into account, shallower waters pecies consistently showed
larger historical effective population sizes than their deeper-water counterparts. This
could explain why deeper-water species are more sensitive to overfishing, and
would indicate that overexploitation may have a larger impact on their long-term
genetic diversity.
article_processing_charge: No
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
- first_name: E.
full_name: Macpherson, E.
last_name: Macpherson
- first_name: C.
full_name: Matthee, C.
last_name: Matthee
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
citation:
ama: 'Palero F, Abello P, Macpherson E, Matthee C, Pascual M. Genetic diversity
levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata).
Journal of Crustacean Biology. 2010;30(4):658-663. doi:10.1651/09-3192.1'
apa: 'Palero, F., Abello, P., Macpherson, E., Matthee, C., & Pascual, M. (2010).
Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus
(Decapoda: Achelata). Journal of Crustacean Biology. Oxford University
Press. https://doi.org/10.1651/09-3192.1'
chicago: 'Palero, Ferran, Pere Abello, E. Macpherson, C. Matthee, and Marta Pascual.
“Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus
(Decapoda: Achelata).” Journal of Crustacean Biology. Oxford University
Press, 2010. https://doi.org/10.1651/09-3192.1.'
ieee: 'F. Palero, P. Abello, E. Macpherson, C. Matthee, and M. Pascual, “Genetic
diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda:
Achelata),” Journal of Crustacean Biology, vol. 30, no. 4. Oxford University
Press, pp. 658–663, 2010.'
ista: 'Palero F, Abello P, Macpherson E, Matthee C, Pascual M. 2010. Genetic diversity
levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata).
Journal of Crustacean Biology. 30(4), 658–663.'
mla: 'Palero, Ferran, et al. “Genetic Diversity Levels in Fishery-Exploited Spiny
Lobsters of the Genus Palinurus (Decapoda: Achelata).” Journal of Crustacean
Biology, vol. 30, no. 4, Oxford University Press, 2010, pp. 658–63, doi:10.1651/09-3192.1.'
short: F. Palero, P. Abello, E. Macpherson, C. Matthee, M. Pascual, Journal of Crustacean
Biology 30 (2010) 658–663.
date_created: 2018-12-11T12:05:09Z
date_published: 2010-10-01T00:00:00Z
date_updated: 2023-10-16T09:51:05Z
day: '01'
department:
- _id: NiBa
doi: 10.1651/09-3192.1
intvolume: ' 30'
issue: '4'
language:
- iso: eng
month: '10'
oa_version: None
page: 658 - 663
publication: Journal of Crustacean Biology
publication_identifier:
eissn:
- 1937-240X
issn:
- 0278-0372
publication_status: published
publisher: Oxford University Press
publist_id: '2442'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Genetic diversity levels in fishery-exploited spiny lobsters of the Genus
Palinurus (Decapoda: Achelata)'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2010'
...
---
_id: '3786'
abstract:
- lang: eng
text: Four rare palinurid phyllosoma larvae, one mid-stage and three final stage,
were found among the unclassified collections in the Crustacea Section, Natural
History Museum, London. Detailed morphological analysis of the larvae indicated
that they belong to several Palinustus species given the presence of incipient
blunt-horns, length of antennula, length ratio of segments of antennular peduncle,
distribution of pereiopod spines, and shape of uropods and telson. Moreover, the
size of the final-stage larvae agrees with that expected given the size of the
recently described puerulus stage of Palinustus mossambicus. This constitutes
the first description of a complete phyllosoma assigned to Palinustus species.
The phyllosoma described in the present study include the largest Palinuridae
larva ever found.
article_processing_charge: No
article_type: original
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Guillermo
full_name: Guerao, Guillermo
last_name: Guerao
- first_name: Paul
full_name: Clark, Paul
last_name: Clark
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
citation:
ama: 'Palero F, Guerao G, Clark P, Abello P. Final-stage phyllosoma of Palinustus
A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first
complete description. Zootaxa. 2010;2403(1):42-58. doi:10.11646/zootaxa.2403.1.4'
apa: 'Palero, F., Guerao, G., Clark, P., & Abello, P. (2010). Final-stage phyllosoma
of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The
first complete description. Zootaxa. Magnolia Press. https://doi.org/10.11646/zootaxa.2403.1.4'
chicago: 'Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Final-Stage
Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata:
Palinuridae)-The First Complete Description.” Zootaxa. Magnolia Press,
2010. https://doi.org/10.11646/zootaxa.2403.1.4.'
ieee: 'F. Palero, G. Guerao, P. Clark, and P. Abello, “Final-stage phyllosoma of
Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The
first complete description,” Zootaxa, vol. 2403, no. 1. Magnolia Press,
pp. 42–58, 2010.'
ista: 'Palero F, Guerao G, Clark P, Abello P. 2010. Final-stage phyllosoma of Palinustus
A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first
complete description. Zootaxa. 2403(1), 42–58.'
mla: 'Palero, Ferran, et al. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards,
1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.”
Zootaxa, vol. 2403, no. 1, Magnolia Press, 2010, pp. 42–58, doi:10.11646/zootaxa.2403.1.4.'
short: F. Palero, G. Guerao, P. Clark, P. Abello, Zootaxa 2403 (2010) 42–58.
date_created: 2018-12-11T12:05:10Z
date_published: 2010-03-19T00:00:00Z
date_updated: 2022-03-21T08:22:58Z
day: '19'
department:
- _id: NiBa
doi: 10.11646/zootaxa.2403.1.4
intvolume: ' 2403'
issue: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 42 - 58
publication: Zootaxa
publication_status: published
publisher: Magnolia Press
publist_id: '2441'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda:
Achelata: Palinuridae)-The first complete description'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2403
year: '2010'
...
---
_id: '3787'
abstract:
- lang: eng
text: DNA samples were extracted from ethanol and formalin-fixed decapod crustacean
tissue using a new method based on Tetramethylsilane (TMS)-Chelex. It is shown
that neither an indigestible matrix of cross-linked protein nor soluble PCR inhibitors
impede PCR success when dealing with formalin-fixed material. Instead, amplification
success from formalin-fixed tissue appears to depend on the presence of unmodified
DNA in the extracted sample. A staining method that facilitates the targeting
of samples with a high content of unmodified DNA is provided.
acknowledgement: "The authors would like to thank two anonymous reviewers for their
remarks, which helped to improve the manuscript. This project was supported by the
Marine Biodiversity and Ecosystem Functioning Network of Excellence MarBEF (Contract
no. GOCE-CT-2003-505446) of the 6th European Framework Programme(FP6), the Zoology
Research Fund, Department of Zoology, NHM, London, a Research Grant from the Royal
Society to S.T., and a pre-doctoral fellowship awarded by the Autonomous Government
of Catalonia to F.P.(2006FIC-00082). This research received support from the SYNTHESYS
Project http://www.synthesys. info/ which is financed by European Community Research
Infrastructure Action under the FP6 “Structuring the European Research Area” Programme.
Many thanks are due to J. Fortuño for suggesting TMS as an alternative to critical
point drying, P.Crabb for helping with the UV-light photography setting and our
colleagues/friends in the Whale Basement Molecular Laboratories, Department of Zoology
NHM \r\n\r\n"
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Sally
full_name: Hall, Sally
last_name: Hall
- first_name: Paul
full_name: Clark, Paul
last_name: Clark
- first_name: David
full_name: Johnston, David
last_name: Johnston
- first_name: Jackie
full_name: Mackenzie Dodds, Jackie
last_name: Mackenzie Dodds
- first_name: Sven
full_name: Thatje, Sven
last_name: Thatje
citation:
ama: 'Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. DNA extraction
from formalin-fixed tissue: new light from the deep sea. Scientia Marina.
2010;74(3):465-470. doi:10.3989/scimar.2010.74n3465'
apa: 'Palero, F., Hall, S., Clark, P., Johnston, D., Mackenzie Dodds, J., &
Thatje, S. (2010). DNA extraction from formalin-fixed tissue: new light from the
deep sea. Scientia Marina. Consejo Superior de Investigaciones Científicas.
https://doi.org/10.3989/scimar.2010.74n3465'
chicago: 'Palero, Ferran, Sally Hall, Paul Clark, David Johnston, Jackie Mackenzie
Dodds, and Sven Thatje. “DNA Extraction from Formalin-Fixed Tissue: New Light
from the Deep Sea.” Scientia Marina. Consejo Superior de Investigaciones
Científicas, 2010. https://doi.org/10.3989/scimar.2010.74n3465.'
ieee: 'F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, and S. Thatje,
“DNA extraction from formalin-fixed tissue: new light from the deep sea,” Scientia
Marina, vol. 74, no. 3. Consejo Superior de Investigaciones Científicas, pp.
465–470, 2010.'
ista: 'Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. 2010.
DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia
Marina. 74(3), 465–470.'
mla: 'Palero, Ferran, et al. “DNA Extraction from Formalin-Fixed Tissue: New Light
from the Deep Sea.” Scientia Marina, vol. 74, no. 3, Consejo Superior de
Investigaciones Científicas, 2010, pp. 465–70, doi:10.3989/scimar.2010.74n3465.'
short: F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, S. Thatje,
Scientia Marina 74 (2010) 465–470.
date_created: 2018-12-11T12:05:10Z
date_published: 2010-09-01T00:00:00Z
date_updated: 2021-01-12T07:52:11Z
day: '01'
department:
- _id: NiBa
doi: 10.3989/scimar.2010.74n3465
intvolume: ' 74'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprints.soton.ac.uk/68731/
month: '09'
oa: 1
oa_version: Submitted Version
page: 465 - 470
publication: Scientia Marina
publication_status: published
publisher: Consejo Superior de Investigaciones Científicas
publist_id: '2440'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'DNA extraction from formalin-fixed tissue: new light from the deep sea'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2010'
...
---
_id: '3788'
abstract:
- lang: eng
text: Cell sorting is a widespread phenomenon pivotal to the early development of
multicellular organisms. In vitro cell sorting studies have been instrumental
in revealing the cellular properties driving this process. However, these studies
have as yet been limited to two-dimensional analysis of three-dimensional cell
sorting events. Here we describe a method to record the sorting of primary zebrafish
ectoderm and mesoderm germ layer progenitor cells in three dimensions over time,
and quantitatively analyze their sorting behavior using an order parameter related
to heterotypic interface length. We investigate the cell population size dependence
of sorted aggregates and find that the germ layer progenitor cells engulfed in
the final configuration display a relationship between total interfacial length
and system size according to a simple geometrical argument, subject to a finite-size
effect.
author:
- first_name: Abigail
full_name: Klopper, Abigail
last_name: Klopper
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Stephan
full_name: Grill, Stephan
last_name: Grill
- 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: 'Klopper A, Krens G, Grill S, Heisenberg C-PJ. Finite-size corrections to scaling
behavior in sorted cell aggregates. The European Physical Journal E: Soft Matter
and Biological Physics. 2010;33(2):99-103. doi:10.1140/epje/i2010-10642-y'
apa: 'Klopper, A., Krens, G., Grill, S., & Heisenberg, C.-P. J. (2010). Finite-size
corrections to scaling behavior in sorted cell aggregates. The European Physical
Journal E: Soft Matter and Biological Physics. Springer. https://doi.org/10.1140/epje/i2010-10642-y'
chicago: 'Klopper, Abigail, Gabriel Krens, Stephan Grill, and Carl-Philipp J Heisenberg.
“Finite-Size Corrections to Scaling Behavior in Sorted Cell Aggregates.” The
European Physical Journal E: Soft Matter and Biological Physics. Springer,
2010. https://doi.org/10.1140/epje/i2010-10642-y.'
ieee: 'A. Klopper, G. Krens, S. Grill, and C.-P. J. Heisenberg, “Finite-size corrections
to scaling behavior in sorted cell aggregates,” The European Physical Journal
E: Soft Matter and Biological Physics, vol. 33, no. 2. Springer, pp. 99–103,
2010.'
ista: 'Klopper A, Krens G, Grill S, Heisenberg C-PJ. 2010. Finite-size corrections
to scaling behavior in sorted cell aggregates. The European Physical Journal E:
Soft Matter and Biological Physics. 33(2), 99–103.'
mla: 'Klopper, Abigail, et al. “Finite-Size Corrections to Scaling Behavior in Sorted
Cell Aggregates.” The European Physical Journal E: Soft Matter and Biological
Physics, vol. 33, no. 2, Springer, 2010, pp. 99–103, doi:10.1140/epje/i2010-10642-y.'
short: 'A. Klopper, G. Krens, S. Grill, C.-P.J. Heisenberg, The European Physical
Journal E: Soft Matter and Biological Physics 33 (2010) 99–103.'
date_created: 2018-12-11T12:05:10Z
date_published: 2010-09-18T00:00:00Z
date_updated: 2021-01-12T07:52:12Z
day: '18'
department:
- _id: CaHe
doi: 10.1140/epje/i2010-10642-y
intvolume: ' 33'
issue: '2'
language:
- iso: eng
month: '09'
oa_version: None
page: 99 - 103
publication: 'The European Physical Journal E: Soft Matter and Biological Physics'
publication_status: published
publisher: Springer
publist_id: '2439'
scopus_import: 1
status: public
title: Finite-size corrections to scaling behavior in sorted cell aggregates
type: journal_article
user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2010'
...
---
_id: '3789'
abstract:
- lang: eng
text: 'The development of multicellular organisms is dependent on the tight coordination
between tissue growth and morphogenesis. The stereotypical orientation of cell
divisions has been proposed to be a fundamental mechanism by which proliferating
and growing tissues take shape. However, the actual contribution of stereotypical
division orientation (SDO) to tissue morphogenesis is unclear. In zebrafish, cell
divisions with stereotypical orientation have been implicated in both body-axis
elongation and neural rod formation [1, 2], although there is little direct evidence
for a critical function of SDO in either of these processes. Here we show that
SDO is required for formation of the neural rod midline during neurulation but
dispensable for elongation of the body axis during gastrulation. Our data indicate
that SDO during both gastrulation and neurulation is dependent on the noncanonical
Wnt receptor Frizzled 7 (Fz7) and that interfering with cell division orientation
leads to severe defects in neural rod midline formation but not body-axis elongation.
These findings suggest a novel function for Fz7-controlled cell division orientation
in neural rod midline formation during neurulation. '
acknowledgement: "This work was supported by grants from the Fundacion Caja Madrid
to E.Q.H. and the Institute of Science and Technology Austria, the Max-Planck-Society,
and the Deutsche Forschungsgemeinschaft to C.P.H.\r\nWe are grateful to Jon Clarke,
Andy Oates, and Garrett Greenan for reading earlier versions of this manuscript.
We thank J. Peychl, H. Ibarra, and P. Pitrone for excellent assistance and advice
in multi-photon microscopy and D. White for assistance during the image-processing
steps. We also thank D. Panhans for technical assistance, the whole Heisenberg laboratory
for useful comments and discussions, and E. Lehmann, J. Hückmann, and G. Junghans
for excellent fish care. "
author:
- first_name: Elena
full_name: Quesada-Hernández, Elena
id: EA35229E-E909-11E9-8DF8-C90C5D5AF86E
last_name: Quesada-Hernández
- first_name: Luca
full_name: Caneparo, Luca
last_name: Caneparo
- first_name: Sylvia
full_name: Schneider, Sylvia
id: 1FAC36B0-E90A-11E9-9D2F-EF31CE0C9C2F
last_name: Schneider
- first_name: Sylke
full_name: Winkler, Sylke
last_name: Winkler
- first_name: Michael
full_name: Liebling, Michael
last_name: Liebling
- first_name: Scott
full_name: Fraser, Scott
last_name: Fraser
- 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: Quesada-Hernández E, Caneparo L, Schneider S, et al. Stereotypical cell division
orientation controls neural rod midline formation in zebrafish. Current Biology.
2010;20(21):1966-1972. doi:10.1016/j.cub.2010.10.009
apa: Quesada-Hernández, E., Caneparo, L., Schneider, S., Winkler, S., Liebling,
M., Fraser, S., & Heisenberg, C.-P. J. (2010). Stereotypical cell division
orientation controls neural rod midline formation in zebrafish. Current Biology.
Cell Press. https://doi.org/10.1016/j.cub.2010.10.009
chicago: Quesada-Hernández, Elena, Luca Caneparo, Sylvia Schneider, Sylke Winkler,
Michael Liebling, Scott Fraser, and Carl-Philipp J Heisenberg. “Stereotypical
Cell Division Orientation Controls Neural Rod Midline Formation in Zebrafish.”
Current Biology. Cell Press, 2010. https://doi.org/10.1016/j.cub.2010.10.009.
ieee: E. Quesada-Hernández et al., “Stereotypical cell division orientation
controls neural rod midline formation in zebrafish,” Current Biology, vol.
20, no. 21. Cell Press, pp. 1966–1972, 2010.
ista: Quesada-Hernández E, Caneparo L, Schneider S, Winkler S, Liebling M, Fraser
S, Heisenberg C-PJ. 2010. Stereotypical cell division orientation controls neural
rod midline formation in zebrafish. Current Biology. 20(21), 1966–1972.
mla: Quesada-Hernández, Elena, et al. “Stereotypical Cell Division Orientation Controls
Neural Rod Midline Formation in Zebrafish.” Current Biology, vol. 20, no.
21, Cell Press, 2010, pp. 1966–72, doi:10.1016/j.cub.2010.10.009.
short: E. Quesada-Hernández, L. Caneparo, S. Schneider, S. Winkler, M. Liebling,
S. Fraser, C.-P.J. Heisenberg, Current Biology 20 (2010) 1966–1972.
date_created: 2018-12-11T12:05:11Z
date_published: 2010-11-09T00:00:00Z
date_updated: 2021-01-12T07:52:12Z
day: '09'
department:
- _id: CaHe
doi: 10.1016/j.cub.2010.10.009
intvolume: ' 20'
issue: '21'
language:
- iso: eng
month: '11'
oa_version: None
page: 1966 - 1972
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '2438'
quality_controlled: '1'
scopus_import: 1
status: public
title: Stereotypical cell division orientation controls neural rod midline formation
in zebrafish
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2010'
...
---
_id: '3790'
abstract:
- lang: eng
text: Cell shape and motility are primarily controlled by cellular mechanics. The
attachment of the plasma membrane to the underlying actomyosin cortex has been
proposed to be important for cellular processes involving membrane deformation.
However, little is known about the actual function of membrane-to-cortex attachment
(MCA) in cell protrusion formation and migration, in particular in the context
of the developing embryo. Here, we use a multidisciplinary approach to study MCA
in zebrafish mesoderm and endoderm (mesendoderm) germ layer progenitor cells,
which migrate using a combination of different protrusion types, namely, lamellipodia,
filopodia, and blebs, during zebrafish gastrulation. By interfering with the activity
of molecules linking the cortex to the membrane and measuring resulting changes
in MCA by atomic force microscopy, we show that reducing MCA in mesendoderm progenitors
increases the proportion of cellular blebs and reduces the directionality of cell
migration. We propose that MCA is a key parameter controlling the relative proportions
of different cell protrusion types in mesendoderm progenitors, and thus is key
in controlling directed migration during gastrulation.
acknowledgement: "We would like to thank A. G. Clark, S. Grill, A. Oates, E. Raz,
L. Rohde, and M. Zerial for reading earlier versions of the manuscript. We are grateful
to W. Zachariae, Y. Arboleda-Estudillo, S. Schneider, P. Stockinger, D. Panhans,
M. Biro, J. C. Olaya, and the BIOTEC/MPI-CBG zebrafish and imaging facilities for
help and advice at various stages of this project and to J. Helenius for help with
programming. This work was supported by grants from the Boehringer Ingelheim Fonds
to MK, the Polish Ministry of Science and Higher Education to E. P., and the Deutsche
Forschungsgemeinschaft (HE 3231/6-1 and PA 1590/1-1) to CPH and EP.\r\n"
article_number: e1000544
author:
- first_name: Alba
full_name: Diz Muñoz, Alba
last_name: Diz Muñoz
- first_name: Michael
full_name: Krieg, Michael
last_name: Krieg
- first_name: Martin
full_name: Bergert, Martin
last_name: Bergert
- first_name: Itziar
full_name: Ibarlucea Benitez, Itziar
last_name: Ibarlucea Benitez
- first_name: Daniel
full_name: Müller, Daniel
last_name: Müller
- first_name: Ewa
full_name: Paluch, Ewa
last_name: Paluch
- 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: Diz Muñoz A, Krieg M, Bergert M, et al. Control of directed cell migration
in vivo by membrane-to-cortex attachment. PLoS Biology. 2010;8(11). doi:10.1371/journal.pbio.1000544
apa: Diz Muñoz, A., Krieg, M., Bergert, M., Ibarlucea Benitez, I., Müller, D., Paluch,
E., & Heisenberg, C.-P. J. (2010). Control of directed cell migration in vivo
by membrane-to-cortex attachment. PLoS Biology. Public Library of Science.
https://doi.org/10.1371/journal.pbio.1000544
chicago: Diz Muñoz, Alba, Michael Krieg, Martin Bergert, Itziar Ibarlucea Benitez,
Daniel Müller, Ewa Paluch, and Carl-Philipp J Heisenberg. “Control of Directed
Cell Migration in Vivo by Membrane-to-Cortex Attachment.” PLoS Biology.
Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000544.
ieee: A. Diz Muñoz et al., “Control of directed cell migration in vivo by
membrane-to-cortex attachment,” PLoS Biology, vol. 8, no. 11. Public Library
of Science, 2010.
ista: Diz Muñoz A, Krieg M, Bergert M, Ibarlucea Benitez I, Müller D, Paluch E,
Heisenberg C-PJ. 2010. Control of directed cell migration in vivo by membrane-to-cortex
attachment. PLoS Biology. 8(11), e1000544.
mla: Diz Muñoz, Alba, et al. “Control of Directed Cell Migration in Vivo by Membrane-to-Cortex
Attachment.” PLoS Biology, vol. 8, no. 11, e1000544, Public Library of
Science, 2010, doi:10.1371/journal.pbio.1000544.
short: A. Diz Muñoz, M. Krieg, M. Bergert, I. Ibarlucea Benitez, D. Müller, E. Paluch,
C.-P.J. Heisenberg, PLoS Biology 8 (2010).
date_created: 2018-12-11T12:05:11Z
date_published: 2010-11-30T00:00:00Z
date_updated: 2021-01-12T07:52:13Z
day: '30'
ddc:
- '576'
department:
- _id: CaHe
doi: 10.1371/journal.pbio.1000544
file:
- access_level: open_access
checksum: 52d18c90ca6b02234cea5e8b399b7f46
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:24Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4685'
file_name: IST-2015-365-v1+1_journal.pbio.1000544.pdf
file_size: 799506
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '2437'
pubrep_id: '365'
quality_controlled: '1'
scopus_import: 1
status: public
title: Control of directed cell migration in vivo by membrane-to-cortex attachment
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2010'
...
---
_id: '3793'
abstract:
- lang: eng
text: "Recent progress in per-pixel object class labeling of natural images can
be attributed to the use of multiple types of image features and sound statistical
learning approaches. Within the latter, Conditional Random Fields (CRF) are prominently
used for their ability to represent interactions between random variables. Despite
their popularity in computer vision, parameter learning for CRFs has remained
difficult, popular approaches being cross-validation and piecewise training.\r\nIn
this work, we propose a simple yet expressive tree-structured CRF based on a recent
hierarchical image segmentation method. Our model combines and weights multiple
image features within a hierarchical representation and allows simple and efficient
globally-optimal learning of ≈ 105 parameters. The tractability of our model allows
us to pose and answer some of the open questions regarding parameter learning
applying to CRF-based approaches. The key findings for learning CRF models are,
from the obvious to the surprising, i) multiple image features always help, ii)
the limiting dimension with respect to current models is the amount of training
data, iii) piecewise training is competitive, iv) current methods for max-margin
training fail for models with many parameters.\r\n"
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Nowozin, Sebastian
last_name: Nowozin
- first_name: Peter
full_name: Gehler, Peter
last_name: Gehler
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Nowozin S, Gehler P, Lampert C. On parameter learning in CRF-based approaches
to object class image segmentation. In: Vol 6316. Springer; 2010:98-111. doi:10.1007/978-3-642-15567-3_8'
apa: 'Nowozin, S., Gehler, P., & Lampert, C. (2010). On parameter learning in
CRF-based approaches to object class image segmentation (Vol. 6316, pp. 98–111).
Presented at the ECCV: European Conference on Computer Vision, Heraklion, Crete,
Greece: Springer. https://doi.org/10.1007/978-3-642-15567-3_8'
chicago: Nowozin, Sebastian, Peter Gehler, and Christoph Lampert. “On Parameter
Learning in CRF-Based Approaches to Object Class Image Segmentation,” 6316:98–111.
Springer, 2010. https://doi.org/10.1007/978-3-642-15567-3_8.
ieee: 'S. Nowozin, P. Gehler, and C. Lampert, “On parameter learning in CRF-based
approaches to object class image segmentation,” presented at the ECCV: European
Conference on Computer Vision, Heraklion, Crete, Greece, 2010, vol. 6316, pp.
98–111.'
ista: 'Nowozin S, Gehler P, Lampert C. 2010. On parameter learning in CRF-based
approaches to object class image segmentation. ECCV: European Conference on Computer
Vision, LNCS, vol. 6316, 98–111.'
mla: Nowozin, Sebastian, et al. On Parameter Learning in CRF-Based Approaches
to Object Class Image Segmentation. Vol. 6316, Springer, 2010, pp. 98–111,
doi:10.1007/978-3-642-15567-3_8.
short: S. Nowozin, P. Gehler, C. Lampert, in:, Springer, 2010, pp. 98–111.
conference:
end_date: 2010-09-11
location: Heraklion, Crete, Greece
name: 'ECCV: European Conference on Computer Vision'
start_date: 2010-09-05
date_created: 2018-12-11T12:05:12Z
date_published: 2010-11-04T00:00:00Z
date_updated: 2021-01-12T07:52:14Z
day: '04'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.1007/978-3-642-15567-3_8
file:
- access_level: open_access
checksum: 3716e10e161f7c714fd17ec193a223c3
content_type: application/pdf
creator: dernst
date_created: 2020-05-19T16:27:34Z
date_updated: 2020-07-14T12:46:16Z
file_id: '7871'
file_name: 2010_ECCV_Nowozin.pdf
file_size: 4087332
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 6316'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 98 - 111
publication_status: published
publisher: Springer
publist_id: '2431'
quality_controlled: '1'
scopus_import: 1
status: public
title: On parameter learning in CRF-based approaches to object class image segmentation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6316
year: '2010'
...
---
_id: '3794'
abstract:
- lang: eng
text: 'We study the problem of multimodal dimensionality reduction assuming that
data samples can be missing at training time, and not all data modalities may
be present at application time. Maximum covariance analysis, as a generalization
of PCA, has many desirable properties, but its application to practical problems
is limited by its need for perfectly paired data. We overcome this limitation
by a latent variable approach that allows working with weakly paired data and
is still able to efficiently process large datasets using standard numerical routines.
The resulting weakly paired maximum covariance analysis often finds better representations
than alternative methods, as we show in two exemplary tasks: texture discrimination
and transfer learning.'
alternative_title:
- LNCS
author:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Oliver
full_name: Krömer, Oliver
last_name: Krömer
citation:
ama: 'Lampert C, Krömer O. Weakly-paired maximum covariance analysis for multimodal
dimensionality reduction and transfer learning. In: Vol 6312. Springer; 2010:566-579.
doi:10.1007/978-3-642-15552-9_41'
apa: 'Lampert, C., & Krömer, O. (2010). Weakly-paired maximum covariance analysis
for multimodal dimensionality reduction and transfer learning (Vol. 6312, pp.
566–579). Presented at the ECCV: European Conference on Computer Vision, Heraklion,
Crete, Greece: Springer. https://doi.org/10.1007/978-3-642-15552-9_41'
chicago: Lampert, Christoph, and Oliver Krömer. “Weakly-Paired Maximum Covariance
Analysis for Multimodal Dimensionality Reduction and Transfer Learning,” 6312:566–79.
Springer, 2010. https://doi.org/10.1007/978-3-642-15552-9_41.
ieee: 'C. Lampert and O. Krömer, “Weakly-paired maximum covariance analysis for
multimodal dimensionality reduction and transfer learning,” presented at the ECCV:
European Conference on Computer Vision, Heraklion, Crete, Greece, 2010, vol. 6312,
pp. 566–579.'
ista: 'Lampert C, Krömer O. 2010. Weakly-paired maximum covariance analysis for
multimodal dimensionality reduction and transfer learning. ECCV: European Conference
on Computer Vision, LNCS, vol. 6312, 566–579.'
mla: Lampert, Christoph, and Oliver Krömer. Weakly-Paired Maximum Covariance
Analysis for Multimodal Dimensionality Reduction and Transfer Learning. Vol.
6312, Springer, 2010, pp. 566–79, doi:10.1007/978-3-642-15552-9_41.
short: C. Lampert, O. Krömer, in:, Springer, 2010, pp. 566–579.
conference:
end_date: 2010-09-11
location: Heraklion, Crete, Greece
name: 'ECCV: European Conference on Computer Vision'
start_date: 2010-09-05
date_created: 2018-12-11T12:05:12Z
date_published: 2010-11-10T00:00:00Z
date_updated: 2021-01-12T07:52:14Z
day: '10'
department:
- _id: ChLa
doi: 10.1007/978-3-642-15552-9_41
intvolume: ' 6312'
language:
- iso: eng
main_file_link:
- url: http://www.ics.forth.gr/eccv2010/intro.php
month: '11'
oa_version: None
page: 566 - 579
publication_status: published
publisher: Springer
publist_id: '2433'
quality_controlled: '1'
scopus_import: 1
status: public
title: Weakly-paired maximum covariance analysis for multimodal dimensionality reduction
and transfer learning
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6312
year: '2010'
...
---
_id: '3795'
abstract:
- lang: eng
text: 'The (apparent) contour of a smooth mapping from a 2-manifold to the plane,
f: M → R2 , is the set of critical values, that is, the image of the points at
which the gradients of the two component functions are linearly dependent. Assuming
M is compact and orientable and measuring difference with the erosion distance,
we prove that the contour is stable.'
acknowledgement: This research is partially supported by the Defense Advanced Research
Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.
alternative_title:
- Mathematics and Visualization
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Dmitriy
full_name: Morozov, Dmitriy
last_name: Morozov
- first_name: Amit
full_name: Patel, Amit
id: 34A254A0-F248-11E8-B48F-1D18A9856A87
last_name: Patel
citation:
ama: 'Edelsbrunner H, Morozov D, Patel A. The stability of the apparent contour
of an orientable 2-manifold. In: Topological Data Analysis and Visualization:
Theory, Algorithms and Applications. Springer; 2010:27-42. doi:10.1007/978-3-642-15014-2_3'
apa: 'Edelsbrunner, H., Morozov, D., & Patel, A. (2010). The stability of the
apparent contour of an orientable 2-manifold. In Topological Data Analysis
and Visualization: Theory, Algorithms and Applications (pp. 27–42). Springer.
https://doi.org/10.1007/978-3-642-15014-2_3'
chicago: 'Edelsbrunner, Herbert, Dmitriy Morozov, and Amit Patel. “The Stability
of the Apparent Contour of an Orientable 2-Manifold.” In Topological Data Analysis
and Visualization: Theory, Algorithms and Applications, 27–42. Springer, 2010.
https://doi.org/10.1007/978-3-642-15014-2_3.'
ieee: 'H. Edelsbrunner, D. Morozov, and A. Patel, “The stability of the apparent
contour of an orientable 2-manifold,” in Topological Data Analysis and Visualization:
Theory, Algorithms and Applications, Springer, 2010, pp. 27–42.'
ista: 'Edelsbrunner H, Morozov D, Patel A. 2010.The stability of the apparent contour
of an orientable 2-manifold. In: Topological Data Analysis and Visualization:
Theory, Algorithms and Applications. Mathematics and Visualization, , 27–42.'
mla: 'Edelsbrunner, Herbert, et al. “The Stability of the Apparent Contour of an
Orientable 2-Manifold.” Topological Data Analysis and Visualization: Theory,
Algorithms and Applications, Springer, 2010, pp. 27–42, doi:10.1007/978-3-642-15014-2_3.'
short: 'H. Edelsbrunner, D. Morozov, A. Patel, in:, Topological Data Analysis and
Visualization: Theory, Algorithms and Applications, Springer, 2010, pp. 27–42.'
date_created: 2018-12-11T12:05:13Z
date_published: 2010-12-22T00:00:00Z
date_updated: 2021-01-12T07:52:15Z
day: '22'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/978-3-642-15014-2_3
file:
- access_level: open_access
checksum: f03a44c3d1c3e2d4fedb3b94404f3fd5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:40Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4896'
file_name: IST-2016-538-v1+1_2011-B-02-ApparentContour.pdf
file_size: 210710
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 27 - 42
publication: 'Topological Data Analysis and Visualization: Theory, Algorithms and
Applications'
publication_status: published
publisher: Springer
publist_id: '2428'
pubrep_id: '538'
quality_controlled: '1'
scopus_import: 1
status: public
title: The stability of the apparent contour of an orientable 2-manifold
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '3832'
abstract:
- lang: eng
text: A recent paper by von Engelhardt et al. identifies a novel auxiliary subunit
of native AMPARs, termedCKAMP44. Unlike other auxiliary subunits, CKAMP44 accelerates
desensitization and prolongs recovery from desensitization. CKAMP44 is highly
expressed in hippocampal dentate gyrus granule cells and decreases the paired-pulse
ratio at perforant path input synapses. Thus, both principal and auxiliary AMPAR
subunits control the time course of signaling at glutamatergic synapses.
article_processing_charge: No
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: 'Guzmán J, Jonas PM. Beyond TARPs: The growing list of auxiliary AMPAR subunits.
Neuron. 2010;66(1):8-10. doi:10.1016/j.neuron.2010.04.003'
apa: 'Guzmán, J., & Jonas, P. M. (2010). Beyond TARPs: The growing list of auxiliary
AMPAR subunits. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2010.04.003'
chicago: 'Guzmán, José, and Peter M Jonas. “Beyond TARPs: The Growing List of Auxiliary
AMPAR Subunits.” Neuron. Elsevier, 2010. https://doi.org/10.1016/j.neuron.2010.04.003.'
ieee: 'J. Guzmán and P. M. Jonas, “Beyond TARPs: The growing list of auxiliary AMPAR
subunits,” Neuron, vol. 66, no. 1. Elsevier, pp. 8–10, 2010.'
ista: 'Guzmán J, Jonas PM. 2010. Beyond TARPs: The growing list of auxiliary AMPAR
subunits. Neuron. 66(1), 8–10.'
mla: 'Guzmán, José, and Peter M. Jonas. “Beyond TARPs: The Growing List of Auxiliary
AMPAR Subunits.” Neuron, vol. 66, no. 1, Elsevier, 2010, pp. 8–10, doi:10.1016/j.neuron.2010.04.003.'
short: J. Guzmán, P.M. Jonas, Neuron 66 (2010) 8–10.
date_created: 2018-12-11T12:05:25Z
date_published: 2010-04-15T00:00:00Z
date_updated: 2021-01-12T07:52:31Z
day: '15'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2010.04.003
external_id:
pmid:
- '20399724'
intvolume: ' 66'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/20399724
month: '04'
oa: 1
oa_version: Published Version
page: 8 - 10
pmid: 1
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2377'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Beyond TARPs: The growing list of auxiliary AMPAR subunits'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2010'
...
---
_id: '3833'
article_processing_charge: No
author:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Stefan
full_name: Hefft, Stefan
last_name: Hefft
citation:
ama: 'Jonas PM, Hefft S. GABA release at terminals of CCK-interneurons: synchrony,
asynchrony and modulation by cannabinoid receptors (commentary on Ali &
Todorova). The European Journal of Neuroscience. 2010;31(7):1194-1195.
doi:10.1111/j.1460-9568.2010.07189.x'
apa: 'Jonas, P. M., & Hefft, S. (2010). GABA release at terminals of CCK-interneurons:
synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali
& Todorova). The European Journal of Neuroscience. Wiley-Blackwell.
https://doi.org/10.1111/j.1460-9568.2010.07189.x'
chicago: 'Jonas, Peter M, and Stefan Hefft. “GABA Release at Terminals of CCK-Interneurons:
Synchrony, Asynchrony and Modulation by Cannabinoid Receptors (Commentary on Ali
& Todorova).” The European Journal of Neuroscience. Wiley-Blackwell,
2010. https://doi.org/10.1111/j.1460-9568.2010.07189.x.'
ieee: 'P. M. Jonas and S. Hefft, “GABA release at terminals of CCK-interneurons:
synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali
& Todorova),” The European Journal of Neuroscience, vol. 31, no.
7. Wiley-Blackwell, pp. 1194–1195, 2010.'
ista: 'Jonas PM, Hefft S. 2010. GABA release at terminals of CCK-interneurons: synchrony,
asynchrony and modulation by cannabinoid receptors (commentary on Ali &
Todorova). The European Journal of Neuroscience. 31(7), 1194–1195.'
mla: 'Jonas, Peter M., and Stefan Hefft. “GABA Release at Terminals of CCK-Interneurons:
Synchrony, Asynchrony and Modulation by Cannabinoid Receptors (Commentary on Ali
& Todorova).” The European Journal of Neuroscience, vol. 31, no.
7, Wiley-Blackwell, 2010, pp. 1194–95, doi:10.1111/j.1460-9568.2010.07189.x.'
short: P.M. Jonas, S. Hefft, The European Journal of Neuroscience 31 (2010) 1194–1195.
date_created: 2018-12-11T12:05:25Z
date_published: 2010-03-19T00:00:00Z
date_updated: 2021-01-12T07:52:31Z
day: '19'
department:
- _id: PeJo
doi: 10.1111/j.1460-9568.2010.07189.x
intvolume: ' 31'
issue: '7'
language:
- iso: eng
month: '03'
oa_version: None
page: 1194 - 1195
publication: The European Journal of Neuroscience
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2378'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'GABA release at terminals of CCK-interneurons: synchrony, asynchrony and modulation
by cannabinoid receptors (commentary on Ali & Todorova)'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2010'
...
---
_id: '3834'
abstract:
- lang: eng
text: "Background\r\n\r\nThe chemical master equation (CME) is a system of ordinary
differential equations that describes the evolution of a network of chemical reactions
as a stochastic process. Its solution yields the probability density vector of
the system at each point in time. Solving the CME numerically is in many cases
computationally expensive or even infeasible as the number of reachable states
can be very large or infinite. We introduce the sliding window method, which computes
an approximate solution of the CME by performing a sequence of local analysis
steps. In each step, only a manageable subset of states is considered, representing
a "window" into the state space. In subsequent steps, the window follows
the direction in which the probability mass moves, until the time period of interest
has elapsed. We construct the window based on a deterministic approximation of
the future behavior of the system by estimating upper and lower bounds on the
populations of the chemical species.\r\nResults\r\n\r\nIn order to show the effectiveness
of our approach, we apply it to several examples previously described in the literature.
The experimental results show that the proposed method speeds up the analysis
considerably, compared to a global analysis, while still providing high accuracy.\r\n\r\n\r\nConclusions\r\n\r\nThe
sliding window method is a novel approach to address the performance problems
of numerical algorithms for the solution of the chemical master equation. The
method efficiently approximates the probability distributions at the time points
of interest for a variety of chemically reacting systems, including systems for
which no upper bound on the population sizes of the chemical species is known
a priori."
acknowledgement: This research has been partially funded by the Swiss National Science
Foundation under grant 205321-111840 and by the Cluster of Excellence on Multimodal
Computing and Interaction at Saarland University.
author:
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
- first_name: Rushil
full_name: Goel, Rushil
last_name: Goel
- first_name: Maria
full_name: Mateescu, Maria
id: 3B43276C-F248-11E8-B48F-1D18A9856A87
last_name: Mateescu
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Wolf V, Goel R, Mateescu M, Henzinger TA. Solving the chemical master equation
using sliding windows. BMC Systems Biology. 2010;4(42):1-19. doi:10.1186/1752-0509-4-42
apa: Wolf, V., Goel, R., Mateescu, M., & Henzinger, T. A. (2010). Solving the
chemical master equation using sliding windows. BMC Systems Biology. BioMed
Central. https://doi.org/10.1186/1752-0509-4-42
chicago: Wolf, Verena, Rushil Goel, Maria Mateescu, and Thomas A Henzinger. “Solving
the Chemical Master Equation Using Sliding Windows.” BMC Systems Biology.
BioMed Central, 2010. https://doi.org/10.1186/1752-0509-4-42.
ieee: V. Wolf, R. Goel, M. Mateescu, and T. A. Henzinger, “Solving the chemical
master equation using sliding windows,” BMC Systems Biology, vol. 4, no.
42. BioMed Central, pp. 1–19, 2010.
ista: Wolf V, Goel R, Mateescu M, Henzinger TA. 2010. Solving the chemical master
equation using sliding windows. BMC Systems Biology. 4(42), 1–19.
mla: Wolf, Verena, et al. “Solving the Chemical Master Equation Using Sliding Windows.”
BMC Systems Biology, vol. 4, no. 42, BioMed Central, 2010, pp. 1–19, doi:10.1186/1752-0509-4-42.
short: V. Wolf, R. Goel, M. Mateescu, T.A. Henzinger, BMC Systems Biology 4 (2010)
1–19.
date_created: 2018-12-11T12:05:25Z
date_published: 2010-04-08T00:00:00Z
date_updated: 2021-01-12T07:52:32Z
day: '08'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1186/1752-0509-4-42
file:
- access_level: open_access
checksum: 220239fae76f7b03c4d7f05d74ef426f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:29Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5217'
file_name: IST-2012-72-v1+1_Solving_the_chemical_master_equation_using_sliding_windows.pdf
file_size: 1919130
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '42'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1 - 19
publication: BMC Systems Biology
publication_status: published
publisher: BioMed Central
publist_id: '2374'
pubrep_id: '72'
quality_controlled: '1'
scopus_import: 1
status: public
title: Solving the chemical master equation using sliding windows
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2010'
...
---
_id: '3838'
abstract:
- lang: eng
text: We present a numerical approximation technique for the analysis of continuous-time
Markov chains that describe net- works of biochemical reactions and play an important
role in the stochastic modeling of biological systems. Our approach is based on
the construction of a stochastic hybrid model in which certain discrete random
variables of the original Markov chain are approximated by continuous deterministic
variables. We compute the solution of the stochastic hybrid model using a numerical
algorithm that discretizes time and in each step performs a mutual update of the
transient prob- ability distribution of the discrete stochastic variables and
the values of the continuous deterministic variables. We im- plemented the algorithm
and we demonstrate its usefulness and efficiency on several case studies from
systems biology.
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: Maria
full_name: Mateescu, Maria
last_name: Mateescu
- first_name: Linar
full_name: Mikeev, Linar
last_name: Mikeev
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
citation:
ama: 'Henzinger TA, Mateescu M, Mikeev L, Wolf V. Hybrid numerical solution of the
chemical master equation. In: Springer; 2010:55-65. doi:10.1145/1839764.1839772'
apa: 'Henzinger, T. A., Mateescu, M., Mikeev, L., & Wolf, V. (2010). Hybrid
numerical solution of the chemical master equation (pp. 55–65). Presented at the
CMSB: Computational Methods in Systems Biology, Trento, Italy: Springer. https://doi.org/10.1145/1839764.1839772'
chicago: Henzinger, Thomas A, Maria Mateescu, Linar Mikeev, and Verena Wolf. “Hybrid
Numerical Solution of the Chemical Master Equation,” 55–65. Springer, 2010. https://doi.org/10.1145/1839764.1839772.
ieee: 'T. A. Henzinger, M. Mateescu, L. Mikeev, and V. Wolf, “Hybrid numerical solution
of the chemical master equation,” presented at the CMSB: Computational Methods
in Systems Biology, Trento, Italy, 2010, pp. 55–65.'
ista: 'Henzinger TA, Mateescu M, Mikeev L, Wolf V. 2010. Hybrid numerical solution
of the chemical master equation. CMSB: Computational Methods in Systems Biology,
55–65.'
mla: Henzinger, Thomas A., et al. Hybrid Numerical Solution of the Chemical Master
Equation. Springer, 2010, pp. 55–65, doi:10.1145/1839764.1839772.
short: T.A. Henzinger, M. Mateescu, L. Mikeev, V. Wolf, in:, Springer, 2010, pp.
55–65.
conference:
end_date: 2010-10-01
location: Trento, Italy
name: 'CMSB: Computational Methods in Systems Biology'
start_date: 2010-09-29
date_created: 2018-12-11T12:05:27Z
date_published: 2010-09-29T00:00:00Z
date_updated: 2021-01-12T07:52:33Z
day: '29'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1145/1839764.1839772
file:
- access_level: open_access
checksum: 81cb6f0babd97151b171d1ce86582831
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:55Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5179'
file_name: IST-2012-68-v1+1_Hybrid_Numerical_Solution_of_the_Chemical_Master_Equation.pdf
file_size: 671790
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 55 - 65
publication_status: published
publisher: Springer
publist_id: '2356'
pubrep_id: '68'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hybrid numerical solution of the chemical master equation
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '3839'
abstract:
- lang: eng
text: We present a loop property generation method for loops iterating over multi-dimensional
arrays. When used on matrices, our method is able to infer their shapes (also
called types), such as upper-triangular, diagonal, etc. To gen- erate loop properties,
we first transform a nested loop iterating over a multi- dimensional array into
an equivalent collection of unnested loops. Then, we in- fer quantified loop invariants
for each unnested loop using a generalization of a recurrence-based invariant
generation technique. These loop invariants give us conditions on matrices from
which we can derive matrix types automatically us- ing theorem provers. Invariant
generation is implemented in the software package Aligator and types are derived
by theorem provers and SMT solvers, including Vampire and Z3. When run on the
Java matrix package JAMA, our tool was able to infer automatically all matrix
types describing the matrix shapes guaranteed by JAMA’s API.
acknowledgement: The research was supported by the Swiss NSF.
alternative_title:
- LNCS
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: Thibaud
full_name: Hottelier, Thibaud
last_name: Hottelier
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
- first_name: Andrei
full_name: Voronkov, Andrei
last_name: Voronkov
citation:
ama: 'Henzinger TA, Hottelier T, Kovács L, Voronkov A. Invariant and type inference
for matrices. In: Vol 5944. Springer; 2010:163-179. doi:10.1007/978-3-642-11319-2_14'
apa: 'Henzinger, T. A., Hottelier, T., Kovács, L., & Voronkov, A. (2010). Invariant
and type inference for matrices (Vol. 5944, pp. 163–179). Presented at the VMCAI:
Verification, Model Checking and Abstract Interpretation, Madrid, Spain: Springer.
https://doi.org/10.1007/978-3-642-11319-2_14'
chicago: Henzinger, Thomas A, Thibaud Hottelier, Laura Kovács, and Andrei Voronkov.
“Invariant and Type Inference for Matrices,” 5944:163–79. Springer, 2010. https://doi.org/10.1007/978-3-642-11319-2_14.
ieee: 'T. A. Henzinger, T. Hottelier, L. Kovács, and A. Voronkov, “Invariant and
type inference for matrices,” presented at the VMCAI: Verification, Model Checking
and Abstract Interpretation, Madrid, Spain, 2010, vol. 5944, pp. 163–179.'
ista: 'Henzinger TA, Hottelier T, Kovács L, Voronkov A. 2010. Invariant and type
inference for matrices. VMCAI: Verification, Model Checking and Abstract Interpretation,
LNCS, vol. 5944, 163–179.'
mla: Henzinger, Thomas A., et al. Invariant and Type Inference for Matrices.
Vol. 5944, Springer, 2010, pp. 163–79, doi:10.1007/978-3-642-11319-2_14.
short: T.A. Henzinger, T. Hottelier, L. Kovács, A. Voronkov, in:, Springer, 2010,
pp. 163–179.
conference:
end_date: 2010-01-19
location: Madrid, Spain
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2010-01-17
date_created: 2018-12-11T12:05:27Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:33Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-11319-2_14
file:
- access_level: open_access
checksum: da69b13a2d9a7a316c909e09c1090cef
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:09Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4989'
file_name: IST-2012-69-v1+1_Invariant_and_type_inference_for_matrices.pdf
file_size: 251265
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 5944'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 163 - 179
publication_status: published
publisher: Springer
publist_id: '2357'
pubrep_id: '69'
quality_controlled: '1'
scopus_import: 1
status: public
title: Invariant and type inference for matrices
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 5944
year: '2010'
...
---
_id: '3840'
abstract:
- lang: eng
text: 'Classical formalizations of systems and properties are boolean: given a system
and a property, the property is either true or false of the system. Correspondingly,
classical methods for system analysis determine the truth value of a property,
preferably giving a proof if the property is true, and a counterexample if the
property is false; classical methods for system synthesis construct a system for
which a property is true; classical methods for system transformation, composition,
and abstraction aim to preserve the truth of properties. The boolean view is prevalent
even if the system, the property, or both refer to numerical quantities, such
as the times or probabilities of events. For example, a timed automaton either
satisfies or violates a formula of a real-time logic; a stochastic process either
satisfies or violates a formula of a probabilistic logic. The classical black-and-white
view partitions the world into "correct" and "incorrect" systems, offering few
nuances. In reality, of several systems that satisfy a property in the boolean
sense, often some are more desirable than others, and of the many systems that
violate a property, usually some are less objectionable than others. For instance,
among the systems that satisfy the response property that every request be granted,
we may prefer systems that grant requests quickly (the quicker, the better), or
we may prefer systems that issue few unnecessary grants (the fewer, the better);
and among the systems that violate the response property, we may prefer systems
that serve many initial requests (the more, the better), or we may prefer systems
that serve many requests in the long run (the greater the fraction of served to
unserved requests, the better). Formally, while a boolean notion of correctness
is given by a preorder on systems and properties, a quantitative notion of correctness
is defined by a directed metric on systems and properties, where the distance
between a system and a property provides a measure of "fit" or "desirability."
There are many ways how such distances can be defined. In a linear-time framework,
one assigns numerical values to individual behaviors before assigning values to
systems and properties, which are sets of behaviors. For example, the value of
a single behavior may be a discounted value, which is largely determined by a
prefix of the behavior, e.g., by the number of requests that are granted before
the first request that is not granted; or a limit value, which is independent
of any finite prefix. A limit value may be an average, such as the average response
time over an infinite sequence of requests and grants, or a supremum, such as
the worst-case response time. Similarly, the value of a set of behaviors may be
an extremum or an average across the values of all behaviors in the set: in this
way one can measure the worst of all possible average-case response times, or
the average of all possible worst-case response times, etc. Accordingly, the distance
between two sets of behaviors may be defined as the worst or average difference
between the values of corresponding behaviors. In summary, we propagate replacing
boolean specifications for the correctness of systems with quantitative measures
for the desirability of systems. In quantitative analysis, the aim is to compute
the distance between a system and a property (or between two systems, or two properties);
in quantitative synthesis, the objective is to construct a system that has minimal
distance from a given property. Multiple quantitative measures can be prioritized
(e.g., combined lexicographically into a single measure) or studied along the
Pareto curve. Quantitative transformations, compositions, and abstractions of
systems are useful if they allow us to bound the induced change in distance from
a property. We present some initial results in some of these directions. We also
give some potential applications, which not only generalize tradiditional correctness
concerns in the functional, timed, and probabilistic domains, but also capture
such system measures as resource use, performance, cost, reliability, and robustness.'
acknowledgement: This talk surveys joint work with Roderick Bloem, Krishnendu Chatterjee,
Laurent Doyen, and Barbara Jobstmann.
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Henzinger TA. From boolean to quantitative notions of correctness. In: Vol
45. ACM; 2010:157-158. doi:10.1145/1706299.1706319'
apa: 'Henzinger, T. A. (2010). From boolean to quantitative notions of correctness
(Vol. 45, pp. 157–158). Presented at the POPL: Principles of Programming Languages,
Madrid, Spain: ACM. https://doi.org/10.1145/1706299.1706319'
chicago: Henzinger, Thomas A. “From Boolean to Quantitative Notions of Correctness,”
45:157–58. ACM, 2010. https://doi.org/10.1145/1706299.1706319.
ieee: 'T. A. Henzinger, “From boolean to quantitative notions of correctness,” presented
at the POPL: Principles of Programming Languages, Madrid, Spain, 2010, vol. 45,
no. 1, pp. 157–158.'
ista: 'Henzinger TA. 2010. From boolean to quantitative notions of correctness.
POPL: Principles of Programming Languages vol. 45, 157–158.'
mla: Henzinger, Thomas A. From Boolean to Quantitative Notions of Correctness.
Vol. 45, no. 1, ACM, 2010, pp. 157–58, doi:10.1145/1706299.1706319.
short: T.A. Henzinger, in:, ACM, 2010, pp. 157–158.
conference:
end_date: 2010-01-23
location: Madrid, Spain
name: 'POPL: Principles of Programming Languages'
start_date: 2010-01-17
date_created: 2018-12-11T12:05:27Z
date_published: 2010-01-17T00:00:00Z
date_updated: 2021-01-12T07:52:34Z
day: '17'
department:
- _id: ToHe
doi: 10.1145/1706299.1706319
intvolume: ' 45'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 157 - 158
publication_status: published
publisher: ACM
publist_id: '2354'
quality_controlled: '1'
scopus_import: 1
status: public
title: From boolean to quantitative notions of correctness
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2010'
...
---
_id: '3842'
abstract:
- lang: eng
text: Within systems biology there is an increasing interest in the stochastic behavior
of biochemical reaction networks. An appropriate stochastic description is provided
by the chemical master equation, which represents a continuous-time Markov chain
(CTMC). The uniformization technique is an efficient method to compute probability
distributions of a CTMC if the number of states is manageable. However, the size
of a CTMC that represents a biochemical reaction network is usually far beyond
what is feasible. In this paper we present an on-the-fly variant of uniformization,
where we improve the original algorithm at the cost of a small approximation error.
By means of several examples, we show that our approach is particularly well-suited
for biochemical reaction networks.
author:
- first_name: Frédéric
full_name: Didier, Frédéric
last_name: Didier
- 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: Maria
full_name: Mateescu, Maria
last_name: Mateescu
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
citation:
ama: Didier F, Henzinger TA, Mateescu M, Wolf V. Fast adaptive uniformization of
the chemical master equation. IET Systems Biology. 2010;4(6):441-452. doi:10.1049/iet-syb.2010.0005
apa: Didier, F., Henzinger, T. A., Mateescu, M., & Wolf, V. (2010). Fast adaptive
uniformization of the chemical master equation. IET Systems Biology. Institution
of Engineering and Technology. https://doi.org/10.1049/iet-syb.2010.0005
chicago: Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf.
“Fast Adaptive Uniformization of the Chemical Master Equation.” IET Systems
Biology. Institution of Engineering and Technology, 2010. https://doi.org/10.1049/iet-syb.2010.0005.
ieee: F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization
of the chemical master equation,” IET Systems Biology, vol. 4, no. 6. Institution
of Engineering and Technology, pp. 441–452, 2010.
ista: Didier F, Henzinger TA, Mateescu M, Wolf V. 2010. Fast adaptive uniformization
of the chemical master equation. IET Systems Biology. 4(6), 441–452.
mla: Didier, Frédéric, et al. “Fast Adaptive Uniformization of the Chemical Master
Equation.” IET Systems Biology, vol. 4, no. 6, Institution of Engineering
and Technology, 2010, pp. 441–52, doi:10.1049/iet-syb.2010.0005.
short: F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, IET Systems Biology 4 (2010)
441–452.
date_created: 2018-12-11T12:05:28Z
date_published: 2010-11-15T00:00:00Z
date_updated: 2023-02-23T11:45:08Z
day: '15'
ddc:
- '570'
department:
- _id: ToHe
doi: 10.1049/iet-syb.2010.0005
file:
- access_level: open_access
checksum: 9a3bde48f43203991a0b3c6a277c2f5b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:02Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5254'
file_name: IST-2012-66-v1+1_Fast_adaptive_uniformization_of_the_chemical_master_equation.pdf
file_size: 222890
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 441 - 452
publication: IET Systems Biology
publication_status: published
publisher: Institution of Engineering and Technology
publist_id: '2349'
pubrep_id: '66'
quality_controlled: '1'
related_material:
record:
- id: '3843'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Fast adaptive uniformization of the chemical master equation
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2010'
...
---
_id: '3845'
abstract:
- lang: eng
text: This paper presents Aligators, a tool for the generation of universally quantified
array invariants. Aligators leverages recurrence solving and algebraic techniques
to carry out inductive reasoning over array content. The Aligators’ loop extraction
module allows treatment of multi-path loops by exploiting their commutativity
and serializability properties. Our experience in applying Aligators on a collection
of loops from open source software projects indicates the applicability of recurrence
and algebraic solving techniques for reasoning about arrays.
alternative_title:
- LNCS
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: Thibaud
full_name: Hottelier, Thibaud
last_name: Hottelier
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
citation:
ama: 'Henzinger TA, Hottelier T, Kovács L, Rybalchenko A. Aligators for arrays.
In: Vol 6397. Springer; 2010:348-356. doi:10.1007/978-3-642-16242-8_25'
apa: 'Henzinger, T. A., Hottelier, T., Kovács, L., & Rybalchenko, A. (2010).
Aligators for arrays (Vol. 6397, pp. 348–356). Presented at the LPAR: Logic for
Programming, Artificial Intelligence, and Reasoning, Yogyakarta, Indonesia: Springer.
https://doi.org/10.1007/978-3-642-16242-8_25'
chicago: Henzinger, Thomas A, Thibaud Hottelier, Laura Kovács, and Andrey Rybalchenko.
“Aligators for Arrays,” 6397:348–56. Springer, 2010. https://doi.org/10.1007/978-3-642-16242-8_25.
ieee: 'T. A. Henzinger, T. Hottelier, L. Kovács, and A. Rybalchenko, “Aligators
for arrays,” presented at the LPAR: Logic for Programming, Artificial Intelligence,
and Reasoning, Yogyakarta, Indonesia, 2010, vol. 6397, pp. 348–356.'
ista: 'Henzinger TA, Hottelier T, Kovács L, Rybalchenko A. 2010. Aligators for arrays.
LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS, vol.
6397, 348–356.'
mla: Henzinger, Thomas A., et al. Aligators for Arrays. Vol. 6397, Springer,
2010, pp. 348–56, doi:10.1007/978-3-642-16242-8_25.
short: T.A. Henzinger, T. Hottelier, L. Kovács, A. Rybalchenko, in:, Springer, 2010,
pp. 348–356.
conference:
end_date: 2010-10-15
location: Yogyakarta, Indonesia
name: 'LPAR: Logic for Programming, Artificial Intelligence, and Reasoning'
start_date: 2010-10-10
date_created: 2018-12-11T12:05:29Z
date_published: 2010-10-01T00:00:00Z
date_updated: 2021-01-12T07:52:37Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-16242-8_25
file:
- access_level: open_access
checksum: 913af269da6710f2174f470b48ab7a82
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:05Z
date_updated: 2020-07-14T12:46:17Z
file_id: '4790'
file_name: IST-2012-64-v1+1_Aligators_for_arrays.pdf
file_size: 186143
relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
intvolume: ' 6397'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 348 - 356
publication_status: published
publisher: Springer
publist_id: '2342'
pubrep_id: '64'
quality_controlled: '1'
scopus_import: 1
status: public
title: Aligators for arrays
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6397
year: '2010'
...