---
OA_place: repository
OA_type: green
_id: '3877'
abstract:
- lang: eng
text: The synthesis problem asks to construct a reactive finite-state system from
an omega-regular specification. Initial specifications are often unrealizable,
which means that there is no system that implements the specification. A common
reason for unrealizability is that assumptions on the environment of the system
are incomplete. We study the problem of correcting an unrealizable specification
phi by computing an environment assumption psi such that the new specification
psi -> phi is realizable. Our aim is to construct an assumption psi that constrains
only the environment and is as weak as possible. We present a two-step algorithm
for computing assumptions. The algorithm operates on the game graph that is used
to answer the realizability question. First, we compute a safety assumption that
removes a minimal set of environment edges from the graph. Second, we compute
a liveness assumption that puts fairness conditions on some of the remaining environment
edges. We show that the problem of finding a minimal set of fair edges is computationally
hard, and we use probabilistic games to compute a locally minimal fairness assumption.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
citation:
ama: 'Chatterjee K, Henzinger TA, Jobstmann B. Environment assumptions for synthesis.
In: 19th International Conference on Concurrency Theory. Vol 5201. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2008:147-161. doi:10.1007/978-3-540-85361-9_14'
apa: 'Chatterjee, K., Henzinger, T. A., & Jobstmann, B. (2008). Environment
assumptions for synthesis. In 19th International Conference on Concurrency
Theory (Vol. 5201, pp. 147–161). Toronto, Canada: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.1007/978-3-540-85361-9_14'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Barbara Jobstmann. “Environment
Assumptions for Synthesis.” In 19th International Conference on Concurrency
Theory, 5201:147–61. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008.
https://doi.org/10.1007/978-3-540-85361-9_14.
ieee: K. Chatterjee, T. A. Henzinger, and B. Jobstmann, “Environment assumptions
for synthesis,” in 19th International Conference on Concurrency Theory,
Toronto, Canada, 2008, vol. 5201, pp. 147–161.
ista: 'Chatterjee K, Henzinger TA, Jobstmann B. 2008. Environment assumptions for
synthesis. 19th International Conference on Concurrency Theory. CONCUR: Concurrency
Theory, LNCS, vol. 5201, 147–161.'
mla: Chatterjee, Krishnendu, et al. “Environment Assumptions for Synthesis.” 19th
International Conference on Concurrency Theory, vol. 5201, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2008, pp. 147–61, doi:10.1007/978-3-540-85361-9_14.
short: K. Chatterjee, T.A. Henzinger, B. Jobstmann, in:, 19th International Conference
on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008,
pp. 147–161.
conference:
end_date: 2008-08-22
location: Toronto, Canada
name: 'CONCUR: Concurrency Theory'
start_date: 2008-08-19
date_created: 2018-12-11T12:05:39Z
date_published: 2008-07-30T00:00:00Z
date_updated: 2026-05-29T10:20:36Z
day: '30'
doi: 10.1007/978-3-540-85361-9_14
extern: '1'
external_id:
arxiv:
- '0805.4167'
intvolume: ' 5201'
language:
- iso: eng
month: '07'
oa_version: Preprint
page: 147 - 161
publication: 19th International Conference on Concurrency Theory
publication_identifier:
eissn:
- 1611-3349
issn:
- 0302-9743
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '2295'
status: public
title: Environment assumptions for synthesis
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5201
year: '2008'
...
---
OA_type: closed access
_id: '3878'
abstract:
- lang: eng
text: We study the problem of generating a test sequence that achieves maximal coverage
for a reactive system under test. We formulate the problem as a repeated game
between the tester and the system, where the system state space is partitioned
according to some coverage criterion and the objective of the tester is to maximize
the set of partitions (or coverage goals) visited during the game. We show the
complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete,
but is NP-complete for deterministic systems. For the special case of non-deterministic
systems with a re-initializing “reset” action, which represent running a new test
input on a re-initialized system, we show that the complexity is coNP-complete.
Our proof technique for reset games uses randomized testing strategies that circumvent
the exponentially large memory requirement of deterministic testing strategies.
acknowledgement: This research was supported in part by the NSF grants CCR-0132780
and CNS-0720884.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Luca
full_name: De Alfaro, Luca
last_name: De Alfaro
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
citation:
ama: 'Chatterjee K, De Alfaro L, Majumdar R. The complexity of coverage. In: 6th
Asian Symposium on Programming Language and Systems. Vol 5356. Springer Nature;
2008:91-106. doi:10.1007/978-3-540-89330-1_7'
apa: 'Chatterjee, K., De Alfaro, L., & Majumdar, R. (2008). The complexity of
coverage. In 6th Asian Symposium on Programming Language and Systems (Vol.
5356, pp. 91–106). Bangalore, India: Springer Nature. https://doi.org/10.1007/978-3-540-89330-1_7'
chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Ritankar Majumdar. “The Complexity
of Coverage.” In 6th Asian Symposium on Programming Language and Systems,
5356:91–106. Springer Nature, 2008. https://doi.org/10.1007/978-3-540-89330-1_7.
ieee: K. Chatterjee, L. De Alfaro, and R. Majumdar, “The complexity of coverage,”
in 6th Asian Symposium on Programming Language and Systems, Bangalore,
India, 2008, vol. 5356, pp. 91–106.
ista: 'Chatterjee K, De Alfaro L, Majumdar R. 2008. The complexity of coverage.
6th Asian Symposium on Programming Language and Systems. APLAS: Asian Symposium
on Programming Languages and Systems, LNCS, vol. 5356, 91–106.'
mla: Chatterjee, Krishnendu, et al. “The Complexity of Coverage.” 6th Asian Symposium
on Programming Language and Systems, vol. 5356, Springer Nature, 2008, pp.
91–106, doi:10.1007/978-3-540-89330-1_7.
short: K. Chatterjee, L. De Alfaro, R. Majumdar, in:, 6th Asian Symposium on Programming
Language and Systems, Springer Nature, 2008, pp. 91–106.
conference:
end_date: 2008-12-11
location: Bangalore, India
name: 'APLAS: Asian Symposium on Programming Languages and Systems'
start_date: 2008-12-09
date_created: 2018-12-11T12:05:40Z
date_published: 2008-12-03T00:00:00Z
date_updated: 2026-05-29T09:59:46Z
day: '03'
doi: 10.1007/978-3-540-89330-1_7
extern: '1'
external_id:
arxiv:
- '0804.4525'
intvolume: ' 5356'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0804.4525
month: '12'
oa: 1
oa_version: None
page: 91 - 106
publication: 6th Asian Symposium on Programming Language and Systems
publication_identifier:
eissn:
- 1611-3349
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
publist_id: '2292'
status: public
title: The complexity of coverage
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5356
year: '2008'
...
---
OA_type: closed access
_id: '3879'
abstract:
- lang: eng
text: Quantitative generalizations of classical languages, which assign to each
word a real number instead of a boolean value, have applications in modeling resource-constrained
computation. We use weighted automata (finite automata with transition weights)
to define several natural classes of quantitative languages over finite and infinite
words; in particular, the real value of an infinite run is computed as the maximum,
limsup, liminf, limit average, or discounted sum of the transition weights. We
define the classical decision problems of automata theory (emptiness, universality,
language inclusion, and language equivalence) in the quantitative setting and
study their computational complexity. As the decidability of language inclusion
remains open for some classes of weighted automata, we introduce a notion of quantitative
simulation that is decidable and implies language inclusion. We also give a complete
characterization of the expressive power of the various classes of weighted automata.
In particular, we show that most classes of weighted automata cannot be determinized.
acknowledgement: Research supported in part by the NSF grants CCR-0132780, CNS-0720884,
and CCR-0225610, by the Swiss National Science Foundation, and by the European COMBEST
project.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, Doyen L, Henzinger TA. Quantitative languages. In: 22nd International
Workshop on Computer Science Logic. Vol 5213. Springer Nature; 2008:385-400.
doi:10.1007/978-3-540-87531-4_28'
apa: 'Chatterjee, K., Doyen, L., & Henzinger, T. A. (2008). Quantitative languages.
In 22nd International Workshop on Computer Science Logic (Vol. 5213, pp.
385–400). Bertinoro, Italy: Springer Nature. https://doi.org/10.1007/978-3-540-87531-4_28'
chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Quantitative
Languages.” In 22nd International Workshop on Computer Science Logic, 5213:385–400.
Springer Nature, 2008. https://doi.org/10.1007/978-3-540-87531-4_28.
ieee: K. Chatterjee, L. Doyen, and T. A. Henzinger, “Quantitative languages,” in
22nd International Workshop on Computer Science Logic, Bertinoro, Italy,
2008, vol. 5213, pp. 385–400.
ista: 'Chatterjee K, Doyen L, Henzinger TA. 2008. Quantitative languages. 22nd International
Workshop on Computer Science Logic. CSL: Computer Science Logic, LNCS, vol. 5213,
385–400.'
mla: Chatterjee, Krishnendu, et al. “Quantitative Languages.” 22nd International
Workshop on Computer Science Logic, vol. 5213, Springer Nature, 2008, pp.
385–400, doi:10.1007/978-3-540-87531-4_28.
short: K. Chatterjee, L. Doyen, T.A. Henzinger, in:, 22nd International Workshop
on Computer Science Logic, Springer Nature, 2008, pp. 385–400.
conference:
end_date: 2008-09-19
location: Bertinoro, Italy
name: 'CSL: Computer Science Logic'
start_date: 2008-09-16
date_created: 2018-12-11T12:05:40Z
date_published: 2008-09-10T00:00:00Z
date_updated: 2026-05-29T10:05:43Z
day: '10'
doi: 10.1007/978-3-540-87531-4_28
extern: '1'
intvolume: ' 5213'
language:
- iso: eng
month: '09'
oa_version: None
page: 385 - 400
publication: 22nd International Workshop on Computer Science Logic
publication_identifier:
eissn:
- 1611-3349
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
publist_id: '2293'
status: public
title: Quantitative languages
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5213
year: '2008'
...
---
OA_type: closed access
_id: '3880'
abstract:
- lang: eng
text: We consider imperfect-information parity games in which strategies rely on
observations that provide imperfect information about the history of a play. To
solve such games, i.e., to determine the winning regions of players and corresponding
winning strategies, one can use the subset construction to build an equivalent
perfect-information game. Recently, an algorithm that avoids the inefficient subset
construction has been proposed. The algorithm performs a fixed-point computation
in a lattice of antichains, thus maintaining a succinct representation of state
sets. However, this representation does not allow to recover winning strategies.
In this paper, we build on the antichain approach to develop an algorithm for
constructing the winning strategies in parity games of imperfect information.
We have implemented this algorithm as a prototype. To our knowledge, this is the
first implementation of a procedure for solving imperfect-information parity games
on graphs.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Dietmar
full_name: Berwanger, Dietmar
last_name: Berwanger
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- 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: Sangram
full_name: Raje, Sangram
last_name: Raje
citation:
ama: 'Berwanger D, Chatterjee K, Doyen L, Henzinger TA, Raje S. Strategy construction
for parity games with imperfect information. In: 19th International Conference,
CONCUR 2008. Vol 5201. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2008:325-339. doi:10.1007/978-3-540-85361-9'
apa: 'Berwanger, D., Chatterjee, K., Doyen, L., Henzinger, T. A., & Raje, S.
(2008). Strategy construction for parity games with imperfect information. In
19th International Conference, CONCUR 2008 (Vol. 5201, pp. 325–339). Toronto,
Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-540-85361-9'
chicago: Berwanger, Dietmar, Krishnendu Chatterjee, Laurent Doyen, Thomas A Henzinger,
and Sangram Raje. “Strategy Construction for Parity Games with Imperfect Information.”
In 19th International Conference, CONCUR 2008, 5201:325–39. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2008. https://doi.org/10.1007/978-3-540-85361-9.
ieee: D. Berwanger, K. Chatterjee, L. Doyen, T. A. Henzinger, and S. Raje, “Strategy
construction for parity games with imperfect information,” in 19th International
Conference, CONCUR 2008, Toronto, Canada, 2008, vol. 5201, pp. 325–339.
ista: 'Berwanger D, Chatterjee K, Doyen L, Henzinger TA, Raje S. 2008. Strategy
construction for parity games with imperfect information. 19th International Conference,
CONCUR 2008. CONCUR: Concurrency Theory, LNCS, vol. 5201, 325–339.'
mla: Berwanger, Dietmar, et al. “Strategy Construction for Parity Games with Imperfect
Information.” 19th International Conference, CONCUR 2008, vol. 5201, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 325–39, doi:10.1007/978-3-540-85361-9.
short: D. Berwanger, K. Chatterjee, L. Doyen, T.A. Henzinger, S. Raje, in:, 19th
International Conference, CONCUR 2008, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2008, pp. 325–339.
conference:
end_date: 2008-08-22
location: Toronto, Canada
name: 'CONCUR: Concurrency Theory'
start_date: 2008-08-19
date_created: 2018-12-11T12:05:40Z
date_published: 2008-07-30T00:00:00Z
date_updated: 2026-05-29T09:53:33Z
day: '30'
doi: 10.1007/978-3-540-85361-9
extern: '1'
intvolume: ' 5201'
language:
- iso: eng
month: '07'
oa_version: None
page: 325 - 339
publication: 19th International Conference, CONCUR 2008
publication_identifier:
eissn:
- 1611-3349
issn:
- 0302-9743
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '2291'
related_material:
record:
- id: '3863'
relation: later_version
status: public
status: public
title: Strategy construction for parity games with imperfect information
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5201
year: '2008'
...
---
OA_place: publisher
OA_type: gold
_id: '3903'
abstract:
- lang: eng
text: "Background\r\n\r\nThe invasive garden ant, Lasius neglectus, is the most
recently detected pest ant and the first known invasive ant able to become established
and thrive in the temperate regions of Eurasia. In this study, we aim to reconstruct
the invasion history of this ant in Europe analysing 14 populations with three
complementary approaches: genetic microsatellite analysis, chemical analysis of
cuticular hydrocarbon profiles and behavioural observations of aggression behaviour.
We evaluate the relative informative power of the three methodological approaches
and estimate both the number of independent introduction events from a yet unknown
native range somewhere in the Black Sea area, and the invasive potential of the
existing introduced populations.\r\n\r\nResults\r\n\r\nThree clusters of genetically
similar populations were detected, and all but one population had a similar chemical
profile. Aggression between populations could be predicted from their genetic
and chemical distance, and two major clusters of non-aggressive groups of populations
were found. However, populations of L. neglectus did not separate into clear supercolonial
associations, as is typical for other invasive ants.\r\n\r\nConclusion\r\n\r\nThe
three methodological approaches gave consistent and complementary results. All
joint evidence supports the inference that the 14 introduced populations of L.
neglectus in Europe likely arose from only very few independent introductions
from the native range, and that new infestations were typically started through
introductions from other invasive populations. This indicates that existing introduced
populations have a very high invasive potential when the ants are inadvertently
spread by human transport. "
article_processing_charge: No
article_type: original
author:
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Falko
full_name: Drijfhout, Falko
last_name: Drijfhout
- first_name: Daniel
full_name: Kronauer, Daniel
last_name: Kronauer
- first_name: Jacobus
full_name: Boomsma, Jacobus
last_name: Boomsma
- first_name: Jes
full_name: Pedersen, Jes
last_name: Pedersen
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Ugelvig LV, Drijfhout F, Kronauer D, Boomsma J, Pedersen J, Cremer S. The
introduction history of invasive garden ants in Europe: integrating genetic, chemical
and behavioural approaches. BMC Biology. 2008;6(11). doi:10.1186/1741-7007-6-11'
apa: 'Ugelvig, L. V., Drijfhout, F., Kronauer, D., Boomsma, J., Pedersen, J., &
Cremer, S. (2008). The introduction history of invasive garden ants in Europe:
integrating genetic, chemical and behavioural approaches. BMC Biology.
Springer Nature. https://doi.org/10.1186/1741-7007-6-11'
chicago: 'Ugelvig, Line V, Falko Drijfhout, Daniel Kronauer, Jacobus Boomsma, Jes
Pedersen, and Sylvia Cremer. “The Introduction History of Invasive Garden Ants
in Europe: Integrating Genetic, Chemical and Behavioural Approaches.” BMC Biology.
Springer Nature, 2008. https://doi.org/10.1186/1741-7007-6-11.'
ieee: 'L. V. Ugelvig, F. Drijfhout, D. Kronauer, J. Boomsma, J. Pedersen, and S.
Cremer, “The introduction history of invasive garden ants in Europe: integrating
genetic, chemical and behavioural approaches,” BMC Biology, vol. 6, no.
11. Springer Nature, 2008.'
ista: 'Ugelvig LV, Drijfhout F, Kronauer D, Boomsma J, Pedersen J, Cremer S. 2008.
The introduction history of invasive garden ants in Europe: integrating genetic,
chemical and behavioural approaches. BMC Biology. 6(11).'
mla: 'Ugelvig, Line V., et al. “The Introduction History of Invasive Garden Ants
in Europe: Integrating Genetic, Chemical and Behavioural Approaches.” BMC Biology,
vol. 6, no. 11, Springer Nature, 2008, doi:10.1186/1741-7007-6-11.'
short: L.V. Ugelvig, F. Drijfhout, D. Kronauer, J. Boomsma, J. Pedersen, S. Cremer,
BMC Biology 6 (2008).
date_created: 2018-12-11T12:05:48Z
date_published: 2008-02-26T00:00:00Z
date_updated: 2026-05-29T09:45:56Z
day: '26'
doi: 10.1186/1741-7007-6-11
extern: '1'
external_id:
pmid:
- '18302731'
intvolume: ' 6'
issue: '11'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '02'
oa_version: None
pmid: 1
publication: BMC Biology
publication_identifier:
eissn:
- 1741-7007
publication_status: published
publisher: Springer Nature
publist_id: '2249'
status: public
title: 'The introduction history of invasive garden ants in Europe: integrating genetic,
chemical and behavioural approaches'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2008'
...
---
OA_type: closed access
_id: '3905'
abstract:
- lang: eng
text: Winged and wingless males coexist in the ant Cardiocondyla obscurior. Wingless
(“ergatoid”) males never leave their maternal colony and fight remorselessly among
each other for the access to emerging females. The peaceful winged males disperse
after about 10 days, but beforehand also mate in the nest. In the first 5 days
of their life, winged males perform a chemical female mimicry that protects them
against attack and even makes them sexually attractive to ergatoid males. When
older, the chemical profile of winged males no longer matches that of virgin females;
nevertheless, they are still tolerated, which so far has been puzzling. Contrasting
this general pattern, we have identified a single aberrant colony in which all
winged males were attacked and killed by the ergatoid males. A comparative analysis
of the morphology and chemical profile of these untypical attacked winged males
and the tolerated males from several normal colonies revealed that normal old
males are still performing some chemical mimicry to the virgin queens, though
less perfect than in their young ages. The anomalous attacked winged males, on
the other hand, had a very different odour to the females. Our study thus exemplifies
that the analysis of rare malfunctioning can add valuable insight on functioning
under normal conditions and allows the conclusion that older winged males from
normal colonies of the ant C. obscurior are guarded through an imperfect chemical
female mimicry, still close enough to protect against attacks by the wingless
fighters yet dissimilar enough not to elicit their sexual interest.
article_processing_charge: No
article_type: original
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Patrizia
full_name: D'Ettorre, Patrizia
last_name: D'Ettorre
- first_name: Falko
full_name: Drijfhout, Falko
last_name: Drijfhout
- first_name: Matthew
full_name: Sledge, Matthew
last_name: Sledge
- first_name: Stefano
full_name: Turillazzi, Stefano
last_name: Turillazzi
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
citation:
ama: Cremer S, D’Ettorre P, Drijfhout F, Sledge M, Turillazzi S, Heinze J. Imperfect
chemical female mimicry in males of the ant Cardiocondyla obscurior. Naturwissenschaften.
2008;95(11):1101-1105. doi:10.1007/s00114-008-0430-8
apa: Cremer, S., D’Ettorre, P., Drijfhout, F., Sledge, M., Turillazzi, S., &
Heinze, J. (2008). Imperfect chemical female mimicry in males of the ant Cardiocondyla
obscurior. Naturwissenschaften. Springer Nature. https://doi.org/10.1007/s00114-008-0430-8
chicago: Cremer, Sylvia, Patrizia D’Ettorre, Falko Drijfhout, Matthew Sledge, Stefano
Turillazzi, and Jürgen Heinze. “Imperfect Chemical Female Mimicry in Males of
the Ant Cardiocondyla Obscurior.” Naturwissenschaften. Springer Nature,
2008. https://doi.org/10.1007/s00114-008-0430-8.
ieee: S. Cremer, P. D’Ettorre, F. Drijfhout, M. Sledge, S. Turillazzi, and J. Heinze,
“Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior,”
Naturwissenschaften, vol. 95, no. 11. Springer Nature, pp. 1101–1105, 2008.
ista: Cremer S, D’Ettorre P, Drijfhout F, Sledge M, Turillazzi S, Heinze J. 2008.
Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior.
Naturwissenschaften. 95(11), 1101–1105.
mla: Cremer, Sylvia, et al. “Imperfect Chemical Female Mimicry in Males of the Ant
Cardiocondyla Obscurior.” Naturwissenschaften, vol. 95, no. 11, Springer
Nature, 2008, pp. 1101–05, doi:10.1007/s00114-008-0430-8.
short: S. Cremer, P. D’Ettorre, F. Drijfhout, M. Sledge, S. Turillazzi, J. Heinze,
Naturwissenschaften 95 (2008) 1101–1105.
date_created: 2018-12-11T12:05:48Z
date_published: 2008-08-05T00:00:00Z
date_updated: 2026-05-29T09:32:36Z
day: '05'
doi: 10.1007/s00114-008-0430-8
extern: '1'
external_id:
pmid:
- '18679638'
intvolume: ' 95'
issue: '11'
language:
- iso: eng
month: '08'
oa_version: None
page: 1101 - 1105
pmid: 1
publication: Naturwissenschaften
publication_identifier:
eissn:
- 1432-1904
issn:
- 0028-1042
publication_status: published
publisher: Springer Nature
publist_id: '2246'
status: public
title: Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 95
year: '2008'
...
---
OA_type: gold
_id: '3906'
acknowledgement: 'Funding was obtained from the European Community: FP5 EU research-training
network ‘INSECTS’ (JJB SC PD FPD DPH) and FP6 Individual Marie Curie EIF grant (SC),
the Alexander-von-Humboldt Foundation (Feodor-Lynen postdoctoral stipend to SC),
the Danish Natural Science Research Council (JSP), the Danish National Research
Foundation (JJB DRN JSP), and the Austrian Science Fund (BCS FMS CS HK).'
article_number: e3838
article_processing_charge: No
article_type: original
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Falko
full_name: Drijfhout, Falko
last_name: Drijfhout
- first_name: Birgit
full_name: Schlick Steiner, Birgit
last_name: Schlick Steiner
- first_name: Florian
full_name: Steiner, Florian
last_name: Steiner
- first_name: Bernhard
full_name: Seifert, Bernhard
last_name: Seifert
- first_name: David
full_name: Hughes, David
last_name: Hughes
- first_name: Andreas
full_name: Schulz, Andreas
last_name: Schulz
- first_name: Klaus
full_name: Petersen, Klaus
last_name: Petersen
- first_name: Heino
full_name: Konrad, Heino
last_name: Konrad
- first_name: Christian
full_name: Stauffer, Christian
last_name: Stauffer
- first_name: Kadri
full_name: Kiran, Kadri
last_name: Kiran
- first_name: Xavier
full_name: Espadaler, Xavier
last_name: Espadaler
- first_name: Patrizia
full_name: D'Ettorre, Patrizia
last_name: D'Ettorre
- first_name: Nihat
full_name: Aktaç, Nihat
last_name: Aktaç
- first_name: Jørgen
full_name: Eilenberg, Jørgen
last_name: Eilenberg
- first_name: Graeme
full_name: Jones, Graeme
last_name: Jones
- first_name: David
full_name: Nash, David
last_name: Nash
- first_name: Jes
full_name: Pedersen, Jes
last_name: Pedersen
- first_name: Jacobus
full_name: Boomsma, Jacobus
last_name: Boomsma
citation:
ama: Cremer S, Ugelvig LV, Drijfhout F, et al. The evolution of invasiveness in
garden ants. PLoS One. 2008;3(12). doi:10.1371/journal.pone.0003838
apa: Cremer, S., Ugelvig, L. V., Drijfhout, F., Schlick Steiner, B., Steiner, F.,
Seifert, B., … Boomsma, J. (2008). The evolution of invasiveness in garden ants.
PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0003838
chicago: Cremer, Sylvia, Line V Ugelvig, Falko Drijfhout, Birgit Schlick Steiner,
Florian Steiner, Bernhard Seifert, David Hughes, et al. “The Evolution of Invasiveness
in Garden Ants.” PLoS One. Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0003838.
ieee: S. Cremer et al., “The evolution of invasiveness in garden ants,” PLoS
One, vol. 3, no. 12. Public Library of Science, 2008.
ista: Cremer S, Ugelvig LV, Drijfhout F, Schlick Steiner B, Steiner F, Seifert B,
Hughes D, Schulz A, Petersen K, Konrad H, Stauffer C, Kiran K, Espadaler X, D’Ettorre
P, Aktaç N, Eilenberg J, Jones G, Nash D, Pedersen J, Boomsma J. 2008. The evolution
of invasiveness in garden ants. PLoS One. 3(12), e3838.
mla: Cremer, Sylvia, et al. “The Evolution of Invasiveness in Garden Ants.” PLoS
One, vol. 3, no. 12, e3838, Public Library of Science, 2008, doi:10.1371/journal.pone.0003838.
short: S. Cremer, L.V. Ugelvig, F. Drijfhout, B. Schlick Steiner, F. Steiner, B.
Seifert, D. Hughes, A. Schulz, K. Petersen, H. Konrad, C. Stauffer, K. Kiran,
X. Espadaler, P. D’Ettorre, N. Aktaç, J. Eilenberg, G. Jones, D. Nash, J. Pedersen,
J. Boomsma, PLoS One 3 (2008).
date_created: 2018-12-11T12:05:49Z
date_published: 2008-12-03T00:00:00Z
date_updated: 2026-05-29T09:35:45Z
day: '03'
doi: 10.1371/journal.pone.0003838
extern: '1'
external_id:
pmid:
- '19050762'
intvolume: ' 3'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
pmid: 1
publication: PLoS One
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
publist_id: '2247'
status: public
title: The evolution of invasiveness in garden ants
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 3
year: '2008'
...
---
OA_type: closed access
_id: '3907'
abstract:
- lang: eng
text: 'Wingless males of the ant genus Cardiocondyla engage in fatal fighting for
access to female sexual nestmates. Older, heavily sclerotized males are usually
capable of eliminating all younger rivals, whose cuticle is still soft. In Cardiocondyla
sp. A, this type of local mate competition (LMC) has turned the standard pattern
of brood production of social insects upside down, in that mother queens in multi-queen
colonies produce extremely long-lived sons very early in the life cycle of the
colony. Here, we investigated the emergence pattern of sexuals in two species
with LMC, in which males are much less long-lived. Queens of Cardiocondyla obscurior
and Cardiocondyla minutior reared their first sons significantly earlier in multi-queen
than in single-queen societies. In addition, first female sexuals also emerged
earlier in multi-queen colonies, so that early males had mating opportunities.
Hence, the timing of sexual production appears to be well predicted by evolutionary
theory, in particular by local mate and queen–queen competition. '
article_processing_charge: No
article_type: original
author:
- first_name: Masaki
full_name: Suefuji, Masaki
last_name: Suefuji
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Jan
full_name: Oettler, Jan
last_name: Oettler
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
citation:
ama: Suefuji M, Cremer S, Oettler J, Heinze J. Queen number influences the timing
of the sexual production in colonies of Cardiocondyla ants. Biology Letters.
2008;4(6):670-673. doi:10.1098/rsbl.2008.0355
apa: Suefuji, M., Cremer, S., Oettler, J., & Heinze, J. (2008). Queen number
influences the timing of the sexual production in colonies of Cardiocondyla ants.
Biology Letters. The Royal Society. https://doi.org/10.1098/rsbl.2008.0355
chicago: Suefuji, Masaki, Sylvia Cremer, Jan Oettler, and Jürgen Heinze. “Queen
Number Influences the Timing of the Sexual Production in Colonies of Cardiocondyla
Ants.” Biology Letters. The Royal Society, 2008. https://doi.org/10.1098/rsbl.2008.0355.
ieee: M. Suefuji, S. Cremer, J. Oettler, and J. Heinze, “Queen number influences
the timing of the sexual production in colonies of Cardiocondyla ants,” Biology
Letters, vol. 4, no. 6. The Royal Society, pp. 670–673, 2008.
ista: Suefuji M, Cremer S, Oettler J, Heinze J. 2008. Queen number influences the
timing of the sexual production in colonies of Cardiocondyla ants. Biology Letters.
4(6), 670–673.
mla: Suefuji, Masaki, et al. “Queen Number Influences the Timing of the Sexual Production
in Colonies of Cardiocondyla Ants.” Biology Letters, vol. 4, no. 6, The
Royal Society, 2008, pp. 670–73, doi:10.1098/rsbl.2008.0355.
short: M. Suefuji, S. Cremer, J. Oettler, J. Heinze, Biology Letters 4 (2008) 670–673.
date_created: 2018-12-11T12:05:49Z
date_published: 2008-12-23T00:00:00Z
date_updated: 2026-06-02T08:58:39Z
day: '23'
doi: 10.1098/rsbl.2008.0355
extern: '1'
external_id:
pmid:
- '18700195'
intvolume: ' 4'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 670 - 673
pmid: 1
publication: Biology Letters
publication_identifier:
eissn:
- 1744-957X
issn:
- 1744-9561
publication_status: published
publisher: The Royal Society
publist_id: '2248'
quality_controlled: '1'
status: public
title: Queen number influences the timing of the sexual production in colonies of
Cardiocondyla ants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2008'
...
---
OA_type: closed access
_id: '3939'
abstract:
- lang: eng
text: The priming of a T cell results from its physical interaction with a dendritic
cell (DC) that presents the cognate antigenic peptide. The success rate of such
interactions is extremely low, because the precursor frequency of a naive T cell
recognizing a specific antigen is in the range of 1:10(5)-10(6). To make this
principle practicable, encounter frequencies between DCs and T cells are maximized
within lymph nodes (LNs) that are compact immunological projections of the peripheral
tissue they drain. But LNs are more than passive meeting places for DCs that immigrated
from the tissue and lymphocytes that recirculated via the blood. The microanatomy
of the LN stroma actively organizes the cellular encounters by providing preformed
migration tracks that create dynamic but highly ordered movement patterns. LN
architecture further acts as a sophisticated filtration system that sieves the
incoming interstitial fluid at different levels and guarantees that immunologically
relevant antigens are loaded on DCs or B cells while inert substances are channeled
back into the blood circulation. This review focuses on the non-hematopoietic
infrastructure of the lymph node. We describe the association between fibroblastic
reticular cell, conduit, DC, and T cell as the essential functional unit of the
T-cell cortex.
article_processing_charge: No
article_type: original
author:
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Lämmermann T, Sixt MK. The microanatomy of T-cell responses. Immunological
Reviews. 2008;221(1):26-43. doi:10.1111/j.1600-065X.2008.00592.x
apa: Lämmermann, T., & Sixt, M. K. (2008). The microanatomy of T-cell responses.
Immunological Reviews. Wiley-Blackwell. https://doi.org/10.1111/j.1600-065X.2008.00592.x
chicago: Lämmermann, Tim, and Michael K Sixt. “The Microanatomy of T-Cell Responses.”
Immunological Reviews. Wiley-Blackwell, 2008. https://doi.org/10.1111/j.1600-065X.2008.00592.x.
ieee: T. Lämmermann and M. K. Sixt, “The microanatomy of T-cell responses,” Immunological
Reviews, vol. 221, no. 1. Wiley-Blackwell, pp. 26–43, 2008.
ista: Lämmermann T, Sixt MK. 2008. The microanatomy of T-cell responses. Immunological
Reviews. 221(1), 26–43.
mla: Lämmermann, Tim, and Michael K. Sixt. “The Microanatomy of T-Cell Responses.”
Immunological Reviews, vol. 221, no. 1, Wiley-Blackwell, 2008, pp. 26–43,
doi:10.1111/j.1600-065X.2008.00592.x.
short: T. Lämmermann, M.K. Sixt, Immunological Reviews 221 (2008) 26–43.
date_created: 2018-12-11T12:06:00Z
date_published: 2008-02-07T00:00:00Z
date_updated: 2026-05-29T09:27:21Z
day: '07'
doi: 10.1111/j.1600-065X.2008.00592.x
extern: '1'
external_id:
pmid:
- '18275473'
intvolume: ' 221'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 26 - 43
pmid: 1
publication: Immunological Reviews
publication_identifier:
eissn:
- 1600-065X
issn:
- 0105-2896
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2187'
status: public
title: The microanatomy of T-cell responses
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 221
year: '2008'
...
---
OA_type: closed access
_id: '3940'
abstract:
- lang: eng
text: Until recently little information was available on the molecular details of
the extracellular matrix (ECM) of secondary lymphoid tissues. There is now growing
evidence that these ECMs are unique structures, combining characteristics of basement
membranes and interstitial or fibrillar matrices, resulting in scaffolds that
are strong and highly flexible and, in certain secondary lymphoid compartments,
also forming conduit networks for rapid fluid transport. This review will address
the structural characteristics of the ECM of the murine spleen and its potential
role as an organizer of immune cell compartments, with reference to the lymph
node where relevant.
article_processing_charge: No
article_type: review
author:
- first_name: Zerina
full_name: Lokmic, Zerina
last_name: Lokmic
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Susanna
full_name: Cardell, Susanna
last_name: Cardell
- first_name: Rupert
full_name: Hallmann, Rupert
last_name: Hallmann
- first_name: Lydia
full_name: Sorokin, Lydia
last_name: Sorokin
citation:
ama: Lokmic Z, Lämmermann T, Sixt MK, Cardell S, Hallmann R, Sorokin L. The extracellular
matrix of the spleen as a potential organizer of immune cell compartments. Seminars
in Immunology. 2008;20(1):4-13. doi:10.1016/j.smim.2007.12.009
apa: Lokmic, Z., Lämmermann, T., Sixt, M. K., Cardell, S., Hallmann, R., & Sorokin,
L. (2008). The extracellular matrix of the spleen as a potential organizer of
immune cell compartments. Seminars in Immunology. Academic Press. https://doi.org/10.1016/j.smim.2007.12.009
chicago: Lokmic, Zerina, Tim Lämmermann, Michael K Sixt, Susanna Cardell, Rupert
Hallmann, and Lydia Sorokin. “The Extracellular Matrix of the Spleen as a Potential
Organizer of Immune Cell Compartments.” Seminars in Immunology. Academic
Press, 2008. https://doi.org/10.1016/j.smim.2007.12.009.
ieee: Z. Lokmic, T. Lämmermann, M. K. Sixt, S. Cardell, R. Hallmann, and L. Sorokin,
“The extracellular matrix of the spleen as a potential organizer of immune cell
compartments,” Seminars in Immunology, vol. 20, no. 1. Academic Press,
pp. 4–13, 2008.
ista: Lokmic Z, Lämmermann T, Sixt MK, Cardell S, Hallmann R, Sorokin L. 2008. The
extracellular matrix of the spleen as a potential organizer of immune cell compartments.
Seminars in Immunology. 20(1), 4–13.
mla: Lokmic, Zerina, et al. “The Extracellular Matrix of the Spleen as a Potential
Organizer of Immune Cell Compartments.” Seminars in Immunology, vol. 20,
no. 1, Academic Press, 2008, pp. 4–13, doi:10.1016/j.smim.2007.12.009.
short: Z. Lokmic, T. Lämmermann, M.K. Sixt, S. Cardell, R. Hallmann, L. Sorokin,
Seminars in Immunology 20 (2008) 4–13.
date_created: 2018-12-11T12:06:00Z
date_published: 2008-02-01T00:00:00Z
date_updated: 2026-05-29T09:29:25Z
day: '01'
doi: 10.1016/j.smim.2007.12.009
extern: '1'
external_id:
pmid:
- '18243017'
intvolume: ' 20'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 4 - 13
pmid: 1
publication: Seminars in Immunology
publication_identifier:
eissn:
- 1096-3618
issn:
- 1044-5323
publication_status: published
publisher: Academic Press
publist_id: '2188'
status: public
title: The extracellular matrix of the spleen as a potential organizer of immune cell
compartments
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 20
year: '2008'
...
---
OA_type: closed access
_id: '3941'
abstract:
- lang: eng
text: All metazoan cells carry transmembrane receptors of the integrin family, which
couple the contractile force of the actomyosin cytoskeleton to the extracellular
environment. In agreement with this principle, rapidly migrating leukocytes use
integrin-mediated adhesion when moving over two-dimensional surfaces. As migration
on two-dimensional substrates naturally overemphasizes the role of adhesion, the
contribution of integrins during three-dimensional movement of leukocytes within
tissues has remained controversial. We studied the interplay between adhesive,
contractile and protrusive forces during interstitial leukocyte chemotaxis in
vivo and in vitro. We ablated all integrin heterodimers from murine leukocytes,
and show here that functional integrins do not contribute to migration in three-dimensional
environments. Instead, these cells migrate by the sole force of actin-network
expansion, which promotes protrusive flowing of the leading edge. Myosin II-dependent
contraction is only required on passage through narrow gaps, where a squeezing
contraction of the trailing edge propels the rigid nucleus.
article_processing_charge: No
article_type: original
author:
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Bernhard
full_name: Bader, Bernhard
last_name: Bader
- first_name: Susan
full_name: Monkley, Susan
last_name: Monkley
- first_name: Tim
full_name: Worbs, Tim
last_name: Worbs
- first_name: Roland
full_name: Wedlich Söldner, Roland
last_name: Wedlich Söldner
- first_name: Karin
full_name: Hirsch, Karin
last_name: Hirsch
- first_name: Markus
full_name: Keller, Markus
last_name: Keller
- first_name: Reinhold
full_name: Förster, Reinhold
last_name: Förster
- first_name: David
full_name: Critchley, David
last_name: Critchley
- first_name: Reinhard
full_name: Fässler, Reinhard
last_name: Fässler
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Lämmermann T, Bader B, Monkley S, et al. Rapid leukocyte migration by integrin-independent
flowing and squeezing. Nature. 2008;453(7191):51-55. doi:10.1038/nature06887
apa: Lämmermann, T., Bader, B., Monkley, S., Worbs, T., Wedlich Söldner, R., Hirsch,
K., … Sixt, M. K. (2008). Rapid leukocyte migration by integrin-independent flowing
and squeezing. Nature. Nature Publishing Group. https://doi.org/10.1038/nature06887
chicago: Lämmermann, Tim, Bernhard Bader, Susan Monkley, Tim Worbs, Roland Wedlich
Söldner, Karin Hirsch, Markus Keller, et al. “Rapid Leukocyte Migration by Integrin-Independent
Flowing and Squeezing.” Nature. Nature Publishing Group, 2008. https://doi.org/10.1038/nature06887.
ieee: T. Lämmermann et al., “Rapid leukocyte migration by integrin-independent
flowing and squeezing,” Nature, vol. 453, no. 7191. Nature Publishing Group,
pp. 51–55, 2008.
ista: Lämmermann T, Bader B, Monkley S, Worbs T, Wedlich Söldner R, Hirsch K, Keller
M, Förster R, Critchley D, Fässler R, Sixt MK. 2008. Rapid leukocyte migration
by integrin-independent flowing and squeezing. Nature. 453(7191), 51–55.
mla: Lämmermann, Tim, et al. “Rapid Leukocyte Migration by Integrin-Independent
Flowing and Squeezing.” Nature, vol. 453, no. 7191, Nature Publishing Group,
2008, pp. 51–55, doi:10.1038/nature06887.
short: T. Lämmermann, B. Bader, S. Monkley, T. Worbs, R. Wedlich Söldner, K. Hirsch,
M. Keller, R. Förster, D. Critchley, R. Fässler, M.K. Sixt, Nature 453 (2008)
51–55.
date_created: 2018-12-11T12:06:00Z
date_published: 2008-05-01T00:00:00Z
date_updated: 2026-05-29T09:25:29Z
day: '01'
doi: 10.1038/nature06887
extern: '1'
external_id:
pmid:
- '18451854'
intvolume: ' 453'
issue: '7191'
language:
- iso: eng
month: '05'
oa_version: None
page: 51 - 55
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Nature Publishing Group
publist_id: '2186'
status: public
title: Rapid leukocyte migration by integrin-independent flowing and squeezing
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 453
year: '2008'
...
---
OA_type: closed access
_id: '3942'
abstract:
- lang: eng
text: Recent in vitro studies have suggested a role for sialylation in chemokine
receptor binding to its ligand (Bannert, N., S. Craig, M. Farzan, D. Sogah, N.V.
Santo, H. Choe, and J. Sodroski. 2001. J. Exp. Med. 194:1661-1673). This prompted
us to investigate chemokine-induced leukocyte adhesion in inflamed cremaster muscle
venules of alpha2,3 sialyltransferase (ST3Gal-IV)-deficient mice. We found a marked
reduction in leukocyte adhesion to inflamed microvessels upon injection of the
CXCR2 ligands CXCL1 (keratinocyte-derived chemokine) or CXCL8 (interleukin 8).
In addition, extravasation of ST3Gal-IV(-/-) neutrophils into thioglycollate-pretreated
peritoneal cavities was significantly decreased. In vitro assays revealed that
CXCL8 binding to isolated ST3Gal-IV(-/-) neutrophils was markedly impaired. Furthermore,
CXCL1-mediated adhesion of ST3Gal-IV(-/-) leukocytes at physiological flow conditions,
as well as transendothelial migration of ST3Gal-IV(-/-) leukocytes in response
to CXCL1, was significantly reduced. In human neutrophils, enzymatic desialylation
decreased binding of CXCR2 ligands to the neutrophil surface and diminished neutrophil
degranulation in response to these chemokines. In addition, binding of alpha2,3-linked
sialic acid-specific Maackia amurensis lectin II to purified CXCR2 from neuraminidase-treated
CXCR2-transfected HEK293 cells was markedly impaired. Collectively, we provide
substantial evidence that sialylation by ST3Gal-IV significantly contributes to
CXCR2-mediated leukocyte adhesion during inflammation in vivo.
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Frommhold, David
last_name: Frommhold
- first_name: Andreas
full_name: Ludwig, Andreas
last_name: Ludwig
- first_name: M Gabriele
full_name: Bixel, M Gabriele
last_name: Bixel
- first_name: Alexander
full_name: Zarbock, Alexander
last_name: Zarbock
- first_name: Inna
full_name: Babushkina, Inna
last_name: Babushkina
- first_name: Melitta
full_name: Weissinger, Melitta
last_name: Weissinger
- first_name: Sandra
full_name: Cauwenberghs, Sandra
last_name: Cauwenberghs
- first_name: Lesley
full_name: Ellies, Lesley
last_name: Ellies
- first_name: Jamey
full_name: Marth, Jamey
last_name: Marth
- first_name: Annette
full_name: Beck Sickinger, Annette
last_name: Beck Sickinger
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Bärbel
full_name: Lange Sperandio, Bärbel
last_name: Lange Sperandio
- first_name: Alma
full_name: Zernecke, Alma
last_name: Zernecke
- first_name: Ernst
full_name: Brandt, Ernst
last_name: Brandt
- first_name: Christian
full_name: Weber, Christian
last_name: Weber
- first_name: Dietmar
full_name: Vestweber, Dietmar
last_name: Vestweber
- first_name: Klaus
full_name: Ley, Klaus
last_name: Ley
- first_name: Markus
full_name: Sperandio, Markus
last_name: Sperandio
citation:
ama: Frommhold D, Ludwig A, Bixel MG, et al. Sialyltransferase ST3Gal-IV controls
CXCR2-mediated firm leukocyte arrest during inflammation. The Journal of Experimental
Medicine. 2008;205(6):1435-1446. doi:10.1084/jem.20070846
apa: Frommhold, D., Ludwig, A., Bixel, M. G., Zarbock, A., Babushkina, I., Weissinger,
M., … Sperandio, M. (2008). Sialyltransferase ST3Gal-IV controls CXCR2-mediated
firm leukocyte arrest during inflammation. The Journal of Experimental Medicine.
Rockefeller University Press. https://doi.org/10.1084/jem.20070846
chicago: Frommhold, David, Andreas Ludwig, M Gabriele Bixel, Alexander Zarbock,
Inna Babushkina, Melitta Weissinger, Sandra Cauwenberghs, et al. “Sialyltransferase
ST3Gal-IV Controls CXCR2-Mediated Firm Leukocyte Arrest during Inflammation.”
The Journal of Experimental Medicine. Rockefeller University Press, 2008.
https://doi.org/10.1084/jem.20070846.
ieee: D. Frommhold et al., “Sialyltransferase ST3Gal-IV controls CXCR2-mediated
firm leukocyte arrest during inflammation,” The Journal of Experimental Medicine,
vol. 205, no. 6. Rockefeller University Press, pp. 1435–1446, 2008.
ista: Frommhold D, Ludwig A, Bixel MG, Zarbock A, Babushkina I, Weissinger M, Cauwenberghs
S, Ellies L, Marth J, Beck Sickinger A, Sixt MK, Lange Sperandio B, Zernecke A,
Brandt E, Weber C, Vestweber D, Ley K, Sperandio M. 2008. Sialyltransferase ST3Gal-IV
controls CXCR2-mediated firm leukocyte arrest during inflammation. The Journal
of Experimental Medicine. 205(6), 1435–1446.
mla: Frommhold, David, et al. “Sialyltransferase ST3Gal-IV Controls CXCR2-Mediated
Firm Leukocyte Arrest during Inflammation.” The Journal of Experimental Medicine,
vol. 205, no. 6, Rockefeller University Press, 2008, pp. 1435–46, doi:10.1084/jem.20070846.
short: D. Frommhold, A. Ludwig, M.G. Bixel, A. Zarbock, I. Babushkina, M. Weissinger,
S. Cauwenberghs, L. Ellies, J. Marth, A. Beck Sickinger, M.K. Sixt, B. Lange Sperandio,
A. Zernecke, E. Brandt, C. Weber, D. Vestweber, K. Ley, M. Sperandio, The Journal
of Experimental Medicine 205 (2008) 1435–1446.
date_created: 2018-12-11T12:06:01Z
date_published: 2008-06-02T00:00:00Z
date_updated: 2026-05-29T09:23:50Z
day: '02'
doi: 10.1084/jem.20070846
extern: '1'
external_id:
pmid:
- '18519646'
intvolume: ' 205'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 1435 - 1446
pmid: 1
publication: The Journal of Experimental Medicine
publication_identifier:
eissn:
- 1540-9538
issn:
- 0022-1007
publication_status: published
publisher: Rockefeller University Press
publist_id: '2185'
status: public
title: Sialyltransferase ST3Gal-IV controls CXCR2-mediated firm leukocyte arrest during
inflammation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 205
year: '2008'
...
---
OA_type: free access
_id: '3943'
abstract:
- lang: eng
text: Neutrophil granulocytes form the body's first line of antibacterial defense,
but they also contribute to tissue injury and noninfectious, chronic inflammation.
Proteinase 3 (PR3) and neutrophil elastase (NE) are 2 abundant neutrophil serine
proteases implicated in antimicrobial defense with overlapping and potentially
redundant substrate specificity. Here, we unraveled a cooperative role for PR3
and NE in neutrophil activation and noninfectious inflammation in vivo, which
we believe to be novel. Mice lacking both PR3 and NE demonstrated strongly diminished
immune complex-mediated (IC-mediated) neutrophil infiltration in vivo as well
as reduced activation of isolated neutrophils by ICs in vitro. In contrast, in
mice lacking just NE, neutrophil recruitment to ICs was only marginally impaired.
The defects in mice lacking both PR3 and NE were directly linked to the accumulation
of antiinflammatory progranulin (PGRN). Both PR3 and NE cleaved PGRN in vitro
and during neutrophil activation and inflammation in vivo. Local administration
of recombinant PGRN potently inhibited neutrophilic inflammation in vivo, demonstrating
that PGRN represents a crucial inflammation-suppressing mediator. We conclude
that PR3 and NE enhance neutrophil-dependent inflammation by eliminating the local
antiinflammatory activity of PGRN. Our results support the use of serine protease
inhibitors as antiinflammatory agents.
article_processing_charge: No
article_type: original
author:
- first_name: Kai
full_name: Kessenbrock, Kai
last_name: Kessenbrock
- first_name: Leopold
full_name: Fröhlich, Leopold
last_name: Fröhlich
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Heiko
full_name: Pfister, Heiko
last_name: Pfister
- first_name: Andrew
full_name: Bateman, Andrew
last_name: Bateman
- first_name: Azzaq
full_name: Belaaouaj, Azzaq
last_name: Belaaouaj
- first_name: Johannes
full_name: Ring, Johannes
last_name: Ring
- first_name: Markus
full_name: Ollert, Markus
last_name: Ollert
- first_name: Reinhard
full_name: Fässler, Reinhard
last_name: Fässler
- first_name: Dieter
full_name: Jenne, Dieter
last_name: Jenne
citation:
ama: Kessenbrock K, Fröhlich L, Sixt MK, et al. Proteinase 3 and neutrophil elastase
enhance inflammation in mice by inactivating antiinflammatory progranulin. The
Journal of Clinical Investigation. 2008;118(7):2438-2447. doi:10.1172/JCI34694
apa: Kessenbrock, K., Fröhlich, L., Sixt, M. K., Lämmermann, T., Pfister, H., Bateman,
A., … Jenne, D. (2008). Proteinase 3 and neutrophil elastase enhance inflammation
in mice by inactivating antiinflammatory progranulin. The Journal of Clinical
Investigation. American Society for Clinical Investigation. https://doi.org/10.1172/JCI34694
chicago: Kessenbrock, Kai, Leopold Fröhlich, Michael K Sixt, Tim Lämmermann, Heiko
Pfister, Andrew Bateman, Azzaq Belaaouaj, et al. “Proteinase 3 and Neutrophil
Elastase Enhance Inflammation in Mice by Inactivating Antiinflammatory Progranulin.”
The Journal of Clinical Investigation. American Society for Clinical Investigation,
2008. https://doi.org/10.1172/JCI34694.
ieee: K. Kessenbrock et al., “Proteinase 3 and neutrophil elastase enhance
inflammation in mice by inactivating antiinflammatory progranulin,” The Journal
of Clinical Investigation, vol. 118, no. 7. American Society for Clinical
Investigation, pp. 2438–2447, 2008.
ista: Kessenbrock K, Fröhlich L, Sixt MK, Lämmermann T, Pfister H, Bateman A, Belaaouaj
A, Ring J, Ollert M, Fässler R, Jenne D. 2008. Proteinase 3 and neutrophil elastase
enhance inflammation in mice by inactivating antiinflammatory progranulin. The
Journal of Clinical Investigation. 118(7), 2438–2447.
mla: Kessenbrock, Kai, et al. “Proteinase 3 and Neutrophil Elastase Enhance Inflammation
in Mice by Inactivating Antiinflammatory Progranulin.” The Journal of Clinical
Investigation, vol. 118, no. 7, American Society for Clinical Investigation,
2008, pp. 2438–47, doi:10.1172/JCI34694.
short: K. Kessenbrock, L. Fröhlich, M.K. Sixt, T. Lämmermann, H. Pfister, A. Bateman,
A. Belaaouaj, J. Ring, M. Ollert, R. Fässler, D. Jenne, The Journal of Clinical
Investigation 118 (2008) 2438–2447.
date_created: 2018-12-11T12:06:01Z
date_published: 2008-06-20T00:00:00Z
date_updated: 2026-05-29T09:19:48Z
day: '20'
doi: 10.1172/JCI34694
extern: '1'
external_id:
pmid:
- '18568075'
intvolume: ' 118'
issue: '7'
language:
- iso: eng
month: '06'
oa_version: None
page: 2438 - 2447
pmid: 1
publication: The Journal of Clinical Investigation
publication_identifier:
eissn:
- 1558-8238
issn:
- 0021-9738
publication_status: published
publisher: American Society for Clinical Investigation
publist_id: '2183'
status: public
title: Proteinase 3 and neutrophil elastase enhance inflammation in mice by inactivating
antiinflammatory progranulin
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 118
year: '2008'
...
---
OA_type: closed access
_id: '3944'
abstract:
- lang: eng
text: Live imaging of the actin cytoskeleton is crucial for the study of many fundamental
biological processes, but current approaches to visualize actin have several limitations.
Here we describe Lifeact, a 17-amino-acid peptide, which stained filamentous actin
(F-actin) structures in eukaryotic cells and tissues. Lifeact did not interfere
with actin dynamics in vitro and in vivo and in its chemically modified peptide
form allowed visualization of actin dynamics in nontransfectable cells.
article_processing_charge: No
article_type: original
author:
- first_name: Julia
full_name: Riedl, Julia
last_name: Riedl
- first_name: Alvaro
full_name: Crevenna, Alvaro
last_name: Crevenna
- first_name: Kai
full_name: Kessenbrock, Kai
last_name: Kessenbrock
- first_name: Jerry
full_name: Yu, Jerry
last_name: Yu
- first_name: Dorothee
full_name: Neukirchen, Dorothee
last_name: Neukirchen
- first_name: Michal
full_name: Bista, Michal
last_name: Bista
- first_name: Frank
full_name: Bradke, Frank
last_name: Bradke
- first_name: Dieter
full_name: Jenne, Dieter
last_name: Jenne
- first_name: Tad
full_name: Holak, Tad
last_name: Holak
- first_name: Zena
full_name: Werb, Zena
last_name: Werb
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Roland
full_name: Wedlich Soldner, Roland
last_name: Wedlich Soldner
citation:
ama: 'Riedl J, Crevenna A, Kessenbrock K, et al. Lifeact: a versatile marker to
visualize F-actin. Nature Methods. 2008;5(7):605-607. doi:10.1038/nmeth.1220'
apa: 'Riedl, J., Crevenna, A., Kessenbrock, K., Yu, J., Neukirchen, D., Bista, M.,
… Wedlich Soldner, R. (2008). Lifeact: a versatile marker to visualize F-actin.
Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.1220'
chicago: 'Riedl, Julia, Alvaro Crevenna, Kai Kessenbrock, Jerry Yu, Dorothee Neukirchen,
Michal Bista, Frank Bradke, et al. “Lifeact: A Versatile Marker to Visualize F-Actin.”
Nature Methods. Nature Publishing Group, 2008. https://doi.org/10.1038/nmeth.1220.'
ieee: 'J. Riedl et al., “Lifeact: a versatile marker to visualize F-actin,”
Nature Methods, vol. 5, no. 7. Nature Publishing Group, pp. 605–607, 2008.'
ista: 'Riedl J, Crevenna A, Kessenbrock K, Yu J, Neukirchen D, Bista M, Bradke F,
Jenne D, Holak T, Werb Z, Sixt MK, Wedlich Soldner R. 2008. Lifeact: a versatile
marker to visualize F-actin. Nature Methods. 5(7), 605–607.'
mla: 'Riedl, Julia, et al. “Lifeact: A Versatile Marker to Visualize F-Actin.” Nature
Methods, vol. 5, no. 7, Nature Publishing Group, 2008, pp. 605–07, doi:10.1038/nmeth.1220.'
short: J. Riedl, A. Crevenna, K. Kessenbrock, J. Yu, D. Neukirchen, M. Bista, F.
Bradke, D. Jenne, T. Holak, Z. Werb, M.K. Sixt, R. Wedlich Soldner, Nature Methods
5 (2008) 605–607.
date_created: 2018-12-11T12:06:02Z
date_published: 2008-06-08T00:00:00Z
date_updated: 2026-05-29T09:21:50Z
day: '08'
doi: 10.1038/nmeth.1220
extern: '1'
external_id:
pmid:
- '18536722'
intvolume: ' 5'
issue: '7'
language:
- iso: eng
month: '06'
oa_version: None
page: 605 - 607
pmid: 1
publication: Nature Methods
publication_identifier:
eissn:
- 1548-7105
issn:
- 1548-7091
publication_status: published
publisher: Nature Publishing Group
publist_id: '2184'
status: public
title: 'Lifeact: a versatile marker to visualize F-actin'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5
year: '2008'
...
---
OA_type: closed access
_id: '3945'
abstract:
- lang: eng
text: Langerhans cells and dermal dendritic cells migrate to the draining lymph
nodes through dermal lymphatic vessels. They do so in the steady-state and under
inflammatory conditions. Peripheral T cell tolerance or T cell priming, respectively,
are the consequences of migration. The nature of dendritic cell-containing vessels
was mostly defined by electron microscopy or by their lack of blood endothelial
markers. Selective markers for murine lymph endothelium were hitherto rare or
not available. Here, we utilised recently developed antibodies against the murine
hyaluronan receptor, LYVE-1, to study the lymph vessel network in mouse skin in
more detail. In hairless skin from the ears, lymph vessels were spread out in
a horizontal plane. They formed anastomoses, and they possessed frequent blind
endings that were occasionally open. Lymph vessels were wider than blood vessels,
which were identified by their strong CD31 expression. In body wall skin LYVE-1
reactive vessels did not extend laterally but they dived straight down into the
deeper dermis. There, they are connected to each other and formed a network similar
to ear skin. The number and width of lymph vessels did not grossly change upon
inflammatory stimuli such as skin explant culture or tape stripping. There were
also no marked changes in caliber in response to the TLR 7/8 ligand Imiquimod.
Double-labelling experiments of cultured skin showed that most of the strongly
cell surface MHC II-expressing (i.e. activated) dendritic cells were confined
to the lymph vessels. Langerin/CD207(+) cells within this population appeared
later than dermal dendritic cells, i.e. langerin-negative cells. Comparable results
were obtained after stimulating the skin in vivo with the TLR 7/8 ligand Imiquimod
or by tape stripping. In untreated skin (i.e. steady state) a few MHC II(+) and
Langerin/CD207(+) cells, presumably migrating skin dendritic cells including epidermal
Langerhans cells, were consistently observed within the lymph vessels. The novel
antibody reagents may serve as important tools to further study the dendritic
cell traffic in the skin under physiological conditions as well as in conditions
of adoptive dendritic cell transfer in immunotherapy.
article_processing_charge: No
article_type: original
author:
- first_name: Christoph
full_name: Tripp, Christoph
last_name: Tripp
- first_name: Bernhard
full_name: Haid, Bernhard
last_name: Haid
- first_name: Vincent
full_name: Flacher, Vincent
last_name: Flacher
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Hannes
full_name: Peter, Hannes
last_name: Peter
- first_name: Julia
full_name: Farkas, Julia
last_name: Farkas
- first_name: Robert
full_name: Gschwentner, Robert
last_name: Gschwentner
- first_name: Lydia
full_name: Sorokin, Lydia
last_name: Sorokin
- first_name: Nikolaus
full_name: Romani, Nikolaus
last_name: Romani
- first_name: Patrizia
full_name: Stoitzner, Patrizia
last_name: Stoitzner
citation:
ama: Tripp C, Haid B, Flacher V, et al. The lymph vessel network in mouse skin visualised
with antibodies against the hyaluronan receptor LYVE-1. Immunobiology.
2008;213(9-10):715-728. doi:10.1016/j.imbio.2008.07.025
apa: Tripp, C., Haid, B., Flacher, V., Sixt, M. K., Peter, H., Farkas, J., … Stoitzner,
P. (2008). The lymph vessel network in mouse skin visualised with antibodies against
the hyaluronan receptor LYVE-1. Immunobiology. Elsevier. https://doi.org/10.1016/j.imbio.2008.07.025
chicago: Tripp, Christoph, Bernhard Haid, Vincent Flacher, Michael K Sixt, Hannes
Peter, Julia Farkas, Robert Gschwentner, Lydia Sorokin, Nikolaus Romani, and Patrizia
Stoitzner. “The Lymph Vessel Network in Mouse Skin Visualised with Antibodies
against the Hyaluronan Receptor LYVE-1.” Immunobiology. Elsevier, 2008.
https://doi.org/10.1016/j.imbio.2008.07.025.
ieee: C. Tripp et al., “The lymph vessel network in mouse skin visualised
with antibodies against the hyaluronan receptor LYVE-1,” Immunobiology,
vol. 213, no. 9–10. Elsevier, pp. 715–728, 2008.
ista: Tripp C, Haid B, Flacher V, Sixt MK, Peter H, Farkas J, Gschwentner R, Sorokin
L, Romani N, Stoitzner P. 2008. The lymph vessel network in mouse skin visualised
with antibodies against the hyaluronan receptor LYVE-1. Immunobiology. 213(9–10),
715–728.
mla: Tripp, Christoph, et al. “The Lymph Vessel Network in Mouse Skin Visualised
with Antibodies against the Hyaluronan Receptor LYVE-1.” Immunobiology,
vol. 213, no. 9–10, Elsevier, 2008, pp. 715–28, doi:10.1016/j.imbio.2008.07.025.
short: C. Tripp, B. Haid, V. Flacher, M.K. Sixt, H. Peter, J. Farkas, R. Gschwentner,
L. Sorokin, N. Romani, P. Stoitzner, Immunobiology 213 (2008) 715–728.
date_created: 2018-12-11T12:06:02Z
date_published: 2008-08-30T00:00:00Z
date_updated: 2026-05-29T09:17:45Z
day: '30'
doi: 10.1016/j.imbio.2008.07.025
extern: '1'
external_id:
pmid:
- '18926287'
intvolume: ' 213'
issue: 9-10
language:
- iso: eng
month: '08'
oa_version: None
page: 715 - 728
pmid: 1
publication: Immunobiology
publication_identifier:
eissn:
- 1878-3279
issn:
- 0171-2985
publication_status: published
publisher: Elsevier
publist_id: '2182'
status: public
title: The lymph vessel network in mouse skin visualised with antibodies against the
hyaluronan receptor LYVE-1
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 213
year: '2008'
...
---
_id: '3969'
abstract:
- lang: eng
text: Persistent homology is an algebraic tool for measuring topological features
of shapes and functions. It casts the multi-scale organization we frequently observe
in nature into a mathematical formalism. Here we give a record of the short history
of persistent homology and present its basic concepts. Besides the mathematics
we focus on algorithms and mention the various connections to applications, including
to biomolecules, biological networks, data analysis, and geometric modeling.
acknowledgement: Supported in part by DARPA under grants HR0011-05-1-0007 and HR0011-05-0057
and by the NSF under grant DBI-06-06873.
alternative_title:
- Contemporary Mathematics
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: John
full_name: Harer, John
last_name: Harer
citation:
ama: 'Edelsbrunner H, Harer J. Persistent homology - a survey. In: Surveys on
Discrete and Computational Geometry: Twenty Years Later. American Mathematical
Society; 2008:257-282.'
apa: 'Edelsbrunner, H., & Harer, J. (2008). Persistent homology - a survey.
In Surveys on Discrete and Computational Geometry: Twenty Years Later (pp.
257–282). American Mathematical Society.'
chicago: 'Edelsbrunner, Herbert, and John Harer. “Persistent Homology - a Survey.”
In Surveys on Discrete and Computational Geometry: Twenty Years Later,
257–82. American Mathematical Society, 2008.'
ieee: 'H. Edelsbrunner and J. Harer, “Persistent homology - a survey,” in Surveys
on Discrete and Computational Geometry: Twenty Years Later, American Mathematical
Society, 2008, pp. 257–282.'
ista: 'Edelsbrunner H, Harer J. 2008.Persistent homology - a survey. In: Surveys
on Discrete and Computational Geometry: Twenty Years Later. Contemporary Mathematics,
, 257–282.'
mla: 'Edelsbrunner, Herbert, and John Harer. “Persistent Homology - a Survey.” Surveys
on Discrete and Computational Geometry: Twenty Years Later, American Mathematical
Society, 2008, pp. 257–82.'
short: 'H. Edelsbrunner, J. Harer, in:, Surveys on Discrete and Computational Geometry:
Twenty Years Later, American Mathematical Society, 2008, pp. 257–282.'
date_created: 2018-12-11T12:06:11Z
date_published: 2008-03-28T00:00:00Z
date_updated: 2026-05-21T11:47:36Z
day: '28'
extern: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 257 - 282
publication: 'Surveys on Discrete and Computational Geometry: Twenty Years Later'
publication_status: published
publisher: American Mathematical Society
publist_id: '2156'
status: public
title: Persistent homology - a survey
type: book_chapter
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2008'
...
---
OA_place: publisher
OA_type: gold
_id: '3970'
abstract:
- lang: eng
text: 'While genome-wide gene expression data are generated at an increasing rate,
the repertoire of approaches for pattern discovery in these data is still limited.
Identifying subtle patterns of interest in large amounts of data (tens of thousands
of profiles) associated with a certain level of noise remains a challenge. A microarray
time series was recently generated to study the transcriptional program of the
mouse segmentation clock, a biological oscillator associated with the periodic
formation of the segments of the body axis. A method related to Fourier analysis,
the Lomb-Scargle periodogram, was used to detect periodic profiles in the dataset,
leading to the identification of a novel set of cyclic genes associated with the
segmentation clock. Here, we applied to the same microarray time series dataset
four distinct mathematical methods to identify significant patterns in gene expression
profiles. These methods are called: Phase consistency, Address reduction, Cyclohedron
test and Stable persistence, and are based on different conceptual frameworks
that are either hypothesis- or data-driven. Some of the methods, unlike Fourier
transforms, are not dependent on the assumption of periodicity of the pattern
of interest. Remarkably, these methods identified blindly the expression profiles
of known cyclic genes as the most significant patterns in the dataset. Many candidate
genes predicted by more than one approach appeared to be true positive cyclic
genes and will be of particular interest for future research. In addition, these
methods predicted novel candidate cyclic genes that were consistent with previous
biological knowledge and experimental validation in mouse embryos. Our results
demonstrate the utility of these novel pattern detection strategies, notably for
detection of periodic profiles, and suggest that combining several distinct mathematical
approaches to analyze microarray datasets is a valuable strategy for identifying
genes that exhibit novel, interesting transcriptional patterns.'
acknowledgement: This research was partially supported by DARPA grant HR 0011-05-1-0057.
HE and YM mathematical work was supported by DARPA grant HR0011-05-1-0007. AS research
was supported by a Lucent Technologies Bell Labs Graduate Research. Fellowship;
AK and MR research was supported by NIH grant GM U54 GM74942; and SA research was
supported by Association pour la Recherche sur le Cancer (ARC), France. OP, AM,
MLD, EG and GH research was supported by the Stowers Institute for Medical Research.
OP is a Howard Hughes Medical Institute Investigator.
article_processing_charge: No
article_type: original
author:
- first_name: Mary
full_name: Dequéant, Mary
last_name: Dequéant
- first_name: Sebastian
full_name: Ahnert, Sebastian
last_name: Ahnert
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Thomas
full_name: Fink, Thomas
last_name: Fink
- first_name: Earl
full_name: Glynn, Earl
last_name: Glynn
- first_name: Gaye
full_name: Hattem, Gaye
last_name: Hattem
- first_name: Andrzej
full_name: Kudlicki, Andrzej
last_name: Kudlicki
- first_name: Yuriy
full_name: Mileyko, Yuriy
last_name: Mileyko
- first_name: Jason
full_name: Morton, Jason
last_name: Morton
- first_name: Arcady
full_name: Mushegian, Arcady
last_name: Mushegian
- first_name: Lior
full_name: Pachter, Lior
last_name: Pachter
- first_name: Maga
full_name: Rowicka, Maga
last_name: Rowicka
- first_name: Anne
full_name: Shiu, Anne
last_name: Shiu
- first_name: Bernd
full_name: Sturmfels, Bernd
last_name: Sturmfels
- first_name: Olivier
full_name: Pourquie, Olivier
last_name: Pourquie
citation:
ama: Dequéant M, Ahnert S, Edelsbrunner H, et al. Comparison of pattern detection
methods in microarray time series of the segmentation clock. PLoS One.
2008;3(8). doi:10.1371/journal.pone.0002856
apa: Dequéant, M., Ahnert, S., Edelsbrunner, H., Fink, T., Glynn, E., Hattem, G.,
… Pourquie, O. (2008). Comparison of pattern detection methods in microarray time
series of the segmentation clock. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0002856
chicago: Dequéant, Mary, Sebastian Ahnert, Herbert Edelsbrunner, Thomas Fink, Earl
Glynn, Gaye Hattem, Andrzej Kudlicki, et al. “Comparison of Pattern Detection
Methods in Microarray Time Series of the Segmentation Clock.” PLoS One.
Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0002856.
ieee: M. Dequéant et al., “Comparison of pattern detection methods in microarray
time series of the segmentation clock,” PLoS One, vol. 3, no. 8. Public
Library of Science, 2008.
ista: Dequéant M, Ahnert S, Edelsbrunner H, Fink T, Glynn E, Hattem G, Kudlicki
A, Mileyko Y, Morton J, Mushegian A, Pachter L, Rowicka M, Shiu A, Sturmfels B,
Pourquie O. 2008. Comparison of pattern detection methods in microarray time series
of the segmentation clock. PLoS One. 3(8).
mla: Dequéant, Mary, et al. “Comparison of Pattern Detection Methods in Microarray
Time Series of the Segmentation Clock.” PLoS One, vol. 3, no. 8, Public
Library of Science, 2008, doi:10.1371/journal.pone.0002856.
short: M. Dequéant, S. Ahnert, H. Edelsbrunner, T. Fink, E. Glynn, G. Hattem, A.
Kudlicki, Y. Mileyko, J. Morton, A. Mushegian, L. Pachter, M. Rowicka, A. Shiu,
B. Sturmfels, O. Pourquie, PLoS One 3 (2008).
date_created: 2018-12-11T12:06:11Z
date_published: 2008-08-06T00:00:00Z
date_updated: 2026-05-29T09:10:12Z
day: '06'
doi: 10.1371/journal.pone.0002856
extern: '1'
external_id:
pmid:
- '18682743'
intvolume: ' 3'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
pmid: 1
publication: PLoS One
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
publist_id: '2157'
status: public
title: Comparison of pattern detection methods in microarray time series of the segmentation
clock
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 3
year: '2008'
...
---
OA_type: free access
_id: '3971'
abstract:
- lang: eng
text: The Reeb graph is a useful tool in visualizing real-valued data obtained from
computational simulations of physical processes. We characterize the evolution
of the Reeb graph of a time-varying continuous function defined in three-dimensional
space. We show how to maintain the Reeb graph over time and compress the entire
sequence of Reeb graphs into a single, partially persistent data structure, and
augment this data structure with Betti numbers to describe the topology of level
sets and with path seeds to assist in the fast extraction of level sets for visualization.
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: John
full_name: Harer, John
last_name: Harer
- first_name: Ajith
full_name: Mascarenhas, Ajith
last_name: Mascarenhas
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
- first_name: Jack
full_name: Snoeyink, Jack
last_name: Snoeyink
citation:
ama: 'Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. Time-varying
Reeb graphs for continuous space-time data. Computational Geometry: Theory
and Applications. 2008;41(3):149-166. doi:10.1016/j.comgeo.2007.11.001'
apa: 'Edelsbrunner, H., Harer, J., Mascarenhas, A., Pascucci, V., & Snoeyink,
J. (2008). Time-varying Reeb graphs for continuous space-time data. Computational
Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2007.11.001'
chicago: 'Edelsbrunner, Herbert, John Harer, Ajith Mascarenhas, Valerio Pascucci,
and Jack Snoeyink. “Time-Varying Reeb Graphs for Continuous Space-Time Data.”
Computational Geometry: Theory and Applications. Elsevier, 2008. https://doi.org/10.1016/j.comgeo.2007.11.001.'
ieee: 'H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, and J. Snoeyink,
“Time-varying Reeb graphs for continuous space-time data,” Computational Geometry:
Theory and Applications, vol. 41, no. 3. Elsevier, pp. 149–166, 2008.'
ista: 'Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. 2008. Time-varying
Reeb graphs for continuous space-time data. Computational Geometry: Theory and
Applications. 41(3), 149–166.'
mla: 'Edelsbrunner, Herbert, et al. “Time-Varying Reeb Graphs for Continuous Space-Time
Data.” Computational Geometry: Theory and Applications, vol. 41, no. 3,
Elsevier, 2008, pp. 149–66, doi:10.1016/j.comgeo.2007.11.001.'
short: 'H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, J. Snoeyink, Computational
Geometry: Theory and Applications 41 (2008) 149–166.'
date_created: 2018-12-11T12:06:12Z
date_published: 2008-11-01T00:00:00Z
date_updated: 2026-05-29T09:15:13Z
day: '01'
doi: 10.1016/j.comgeo.2007.11.001
extern: '1'
intvolume: ' 41'
issue: '3'
language:
- iso: eng
month: '11'
oa_version: None
page: 149 - 166
publication: 'Computational Geometry: Theory and Applications'
publication_identifier:
eissn:
- 1879-081X
issn:
- 0925-7721
publication_status: published
publisher: Elsevier
publist_id: '2158'
status: public
title: Time-varying Reeb graphs for continuous space-time data
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 41
year: '2008'
...
---
_id: '3974'
abstract:
- lang: eng
text: Generalizing the concept of a Reeb graph, the Reeb space of a multivariate
continuous mapping identifies points of the domain that belong to a common component
of the preimage of a point in the range. We study the local and global structure
of this space for generic, piecewise linear mappings on a combinatorial manifold.
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: John
full_name: Harer, John
last_name: Harer
- first_name: Amit
full_name: Patel, Amit
id: 34A254A0-F248-11E8-B48F-1D18A9856A87
last_name: Patel
citation:
ama: 'Edelsbrunner H, Harer J, Patel A. Reeb spaces of piecewise linear mappings.
In: Proceedings of the Twenty-Fourth Annual Symposium on Computational Geometry.
Association for Computing Machinery; 2008:242-250. doi:10.1145/1377676.1377720'
apa: 'Edelsbrunner, H., Harer, J., & Patel, A. (2008). Reeb spaces of piecewise
linear mappings. In Proceedings of the twenty-fourth annual symposium on Computational
geometry (pp. 242–250). College Park, MD, United States: Association for Computing
Machinery. https://doi.org/10.1145/1377676.1377720'
chicago: Edelsbrunner, Herbert, John Harer, and Amit Patel. “Reeb Spaces of Piecewise
Linear Mappings.” In Proceedings of the Twenty-Fourth Annual Symposium on Computational
Geometry, 242–50. Association for Computing Machinery, 2008. https://doi.org/10.1145/1377676.1377720.
ieee: H. Edelsbrunner, J. Harer, and A. Patel, “Reeb spaces of piecewise linear
mappings,” in Proceedings of the twenty-fourth annual symposium on Computational
geometry, College Park, MD, United States, 2008, pp. 242–250.
ista: 'Edelsbrunner H, Harer J, Patel A. 2008. Reeb spaces of piecewise linear mappings.
Proceedings of the twenty-fourth annual symposium on Computational geometry. SCG:
Symposium on Computational Geometry, 242–250.'
mla: Edelsbrunner, Herbert, et al. “Reeb Spaces of Piecewise Linear Mappings.” Proceedings
of the Twenty-Fourth Annual Symposium on Computational Geometry, Association
for Computing Machinery, 2008, pp. 242–50, doi:10.1145/1377676.1377720.
short: H. Edelsbrunner, J. Harer, A. Patel, in:, Proceedings of the Twenty-Fourth
Annual Symposium on Computational Geometry, Association for Computing Machinery,
2008, pp. 242–250.
conference:
end_date: 2008-06-11
location: College Park, MD, United States
name: 'SCG: Symposium on Computational Geometry'
start_date: 2008-06-09
date_created: 2018-12-11T12:06:13Z
date_published: 2008-06-09T00:00:00Z
date_updated: 2026-05-29T09:01:13Z
day: '09'
doi: 10.1145/1377676.1377720
extern: '1'
language:
- iso: eng
month: '06'
oa_version: None
page: 242 - 250
publication: Proceedings of the twenty-fourth annual symposium on Computational geometry
publication_identifier:
isbn:
- '9781605580715'
publication_status: published
publisher: Association for Computing Machinery
publist_id: '2155'
status: public
title: Reeb spaces of piecewise linear mappings
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2008'
...
---
_id: '4135'
abstract:
- lang: eng
text: There have been several attempts to build a unified framework for macroecological
patterns. However, these have mostly been based either on questionable assumptions
or have had to be parameterized to obtain realistic predictions. Here, we propose
a new model explicitly considering patterns of aggregated species distributions
on multiple spatial scales, the property which lies behind all spatial macroecological
patterns, using the idea we term ‘generalized fractals’. Species’ spatial distributions
were modelled by a random hierarchical process in which the original ‘habitat’
patches were randomly replaced by sets of smaller patches nested within them,
and the statistical properties of modelled species assemblages were compared with
macroecological patterns in observed bird data. Without parameterization based
on observed patterns, this simple model predicts realistic patterns of species
abundance, distribution and diversity, including fractal-like spatial distributions,
the frequency distribution of species occupancies/abundances and the species–area
relationship. Although observed macroecological patterns may differ in some quantitative
properties, our concept of random hierarchical aggregation can be considered as
an appropriate null model of fundamental macroecological patterns which can potentially
be modified to accommodate ecologically important variables.
article_processing_charge: No
author:
- first_name: D.
full_name: Storch, D.
last_name: Storch
- first_name: A.
full_name: Šizling, A.
last_name: Šizling
- first_name: J.
full_name: Reif, J.
last_name: Reif
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: E.
full_name: Šizlingová, E.
last_name: Šizlingová
- first_name: K.
full_name: Gaston, K.
last_name: Gaston
citation:
ama: 'Storch D, Šizling A, Reif J, Polechova J, Šizlingová E, Gaston K. The quest
for a null model for macroecological patterns: Geometry of species distributions
at multiple spatial scales. Ecology Letters. 2008;11(8):771-784. doi:10.1111/j.1461-0248.2008.01206.x'
apa: 'Storch, D., Šizling, A., Reif, J., Polechova, J., Šizlingová, E., & Gaston,
K. (2008). The quest for a null model for macroecological patterns: Geometry of
species distributions at multiple spatial scales. Ecology Letters. Wiley.
https://doi.org/10.1111/j.1461-0248.2008.01206.x'
chicago: 'Storch, D., A. Šizling, J. Reif, Jitka Polechova, E. Šizlingová, and K.
Gaston. “The Quest for a Null Model for Macroecological Patterns: Geometry of
Species Distributions at Multiple Spatial Scales.” Ecology Letters. Wiley,
2008. https://doi.org/10.1111/j.1461-0248.2008.01206.x.'
ieee: 'D. Storch, A. Šizling, J. Reif, J. Polechova, E. Šizlingová, and K. Gaston,
“The quest for a null model for macroecological patterns: Geometry of species
distributions at multiple spatial scales,” Ecology Letters, vol. 11, no.
8. Wiley, pp. 771–784, 2008.'
ista: 'Storch D, Šizling A, Reif J, Polechova J, Šizlingová E, Gaston K. 2008. The
quest for a null model for macroecological patterns: Geometry of species distributions
at multiple spatial scales. Ecology Letters. 11(8), 771–784.'
mla: 'Storch, D., et al. “The Quest for a Null Model for Macroecological Patterns:
Geometry of Species Distributions at Multiple Spatial Scales.” Ecology Letters,
vol. 11, no. 8, Wiley, 2008, pp. 771–84, doi:10.1111/j.1461-0248.2008.01206.x.'
short: D. Storch, A. Šizling, J. Reif, J. Polechova, E. Šizlingová, K. Gaston, Ecology
Letters 11 (2008) 771–784.
date_created: 2018-12-11T12:07:09Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2025-07-02T05:52:43Z
day: '01'
doi: 10.1111/j.1461-0248.2008.01206.x
extern: '1'
intvolume: ' 11'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 771 - 784
publication: Ecology Letters
publication_status: published
publisher: Wiley
publist_id: '1985'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The quest for a null model for macroecological patterns: Geometry of species
distributions at multiple spatial scales'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2008'
...