---
_id: '3843'
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).\r\nStandard Uniformization (SU) is an efficient method for
the transient analysis of CTMCs. For systems with very different time scales,
such as biochemical reaction networks, SU is computationally expensive. In these
cases, a variant of SU, called adaptive uniformization (AU), is known to reduce
the large number of iterations needed by SU. The additional difficulty of AU is
that it requires the solution of a birth process.\r\nIn this paper we present
an on-the-fly variant of AU, where we improve the original algorithm for AU 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."
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.
article_processing_charge: No
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
id: 3B43276C-F248-11E8-B48F-1D18A9856A87
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. In: Vol 4. IEEE; 2009:118-127. doi:10.1109/HiBi.2009.23'
apa: 'Didier, F., Henzinger, T. A., Mateescu, M., & Wolf, V. (2009). Fast adaptive
uniformization of the chemical master equation (Vol. 4, pp. 118–127). Presented
at the HIBI: High-Performance Computational Systems Biology, Trento, Italy: IEEE.
https://doi.org/10.1109/HiBi.2009.23'
chicago: Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf.
“Fast Adaptive Uniformization of the Chemical Master Equation,” 4:118–27. IEEE,
2009. https://doi.org/10.1109/HiBi.2009.23.
ieee: 'F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization
of the chemical master equation,” presented at the HIBI: High-Performance Computational
Systems Biology, Trento, Italy, 2009, vol. 4, no. 6, pp. 118–127.'
ista: 'Didier F, Henzinger TA, Mateescu M, Wolf V. 2009. Fast adaptive uniformization
of the chemical master equation. HIBI: High-Performance Computational Systems
Biology vol. 4, 118–127.'
mla: Didier, Frédéric, et al. Fast Adaptive Uniformization of the Chemical Master
Equation. Vol. 4, no. 6, IEEE, 2009, pp. 118–27, doi:10.1109/HiBi.2009.23.
short: F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2009, pp. 118–127.
conference:
end_date: 2009-10-16
location: Trento, Italy
name: 'HIBI: High-Performance Computational Systems Biology'
start_date: 2009-10-14
date_created: 2018-12-11T12:05:28Z
date_published: 2009-10-30T00:00:00Z
date_updated: 2023-02-23T11:45:05Z
day: '30'
ddc:
- '000'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1109/HiBi.2009.23
file:
- access_level: open_access
checksum: 9a3bde48f43203991a0b3c6a277c2f5b
content_type: application/pdf
creator: dernst
date_created: 2020-05-19T16:33:55Z
date_updated: 2020-07-14T12:46:17Z
file_id: '7874'
file_name: 2009_HIBI_Didier.pdf
file_size: 222890
relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '6'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 118 - 127
publication_status: published
publisher: IEEE
publist_id: '2348'
quality_controlled: '1'
related_material:
record:
- id: '3842'
relation: later_version
status: public
scopus_import: 1
status: public
title: Fast adaptive uniformization of the chemical master equation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2009'
...
---
_id: '3844'
abstract:
- lang: eng
text: The Hierarchical Timing Language (HTL) is a real-time coordination language
for distributed control systems. HTL programs must be checked for well-formedness,
race freedom, transmission safety (schedulability of inter-host communication),
and time safety (schedulability of host computation). We present a modular abstract
syntax and semantics for HTL, modular checks of well-formedness, race freedom,
and transmission safety, and modular code distribution. Our contributions here
complement previous results on HTL time safety and modular code generation. Modularity
in HTL can be utilized in easy program composition as well as fast program analysis
and code generation, but also in so-called runtime patching, where program components
may be modified at runtime.
acknowledgement: Supported by the EU ArtistDesign Network of Excellence on Embedded
Systems Design, the EU project COMBEST, the Austrian Science Funds P18913-N15 and
V00125, and Fundacao para a Ciencia e Tecnologia funds SFRH/BD/29461/2006 and PTDC/EIA/71462/2006
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Christoph
full_name: Kirsch, Christoph
last_name: Kirsch
- first_name: Eduardo
full_name: Marques, Eduardo
last_name: Marques
- first_name: Ana
full_name: Sokolova, Ana
last_name: Sokolova
citation:
ama: 'Henzinger TA, Kirsch C, Marques E, Sokolova A. Distributed, modular HTL. In:
IEEE; 2009:171-180. doi:10.1109/RTSS.2009.9'
apa: 'Henzinger, T. A., Kirsch, C., Marques, E., & Sokolova, A. (2009). Distributed,
modular HTL (pp. 171–180). Presented at the RTSS: Real-Time Systems Symposium,
Washington, DC, United States: IEEE. https://doi.org/10.1109/RTSS.2009.9'
chicago: Henzinger, Thomas A, Christoph Kirsch, Eduardo Marques, and Ana Sokolova.
“Distributed, Modular HTL,” 171–80. IEEE, 2009. https://doi.org/10.1109/RTSS.2009.9.
ieee: 'T. A. Henzinger, C. Kirsch, E. Marques, and A. Sokolova, “Distributed, modular
HTL,” presented at the RTSS: Real-Time Systems Symposium, Washington, DC, United
States, 2009, pp. 171–180.'
ista: 'Henzinger TA, Kirsch C, Marques E, Sokolova A. 2009. Distributed, modular
HTL. RTSS: Real-Time Systems Symposium, 171–180.'
mla: Henzinger, Thomas A., et al. Distributed, Modular HTL. IEEE, 2009, pp.
171–80, doi:10.1109/RTSS.2009.9.
short: T.A. Henzinger, C. Kirsch, E. Marques, A. Sokolova, in:, IEEE, 2009, pp.
171–180.
conference:
end_date: 2009-12-04
location: Washington, DC, United States
name: 'RTSS: Real-Time Systems Symposium'
start_date: 2009-12-01
date_created: 2018-12-11T12:05:28Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:36Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1109/RTSS.2009.9
ec_funded: 1
file:
- access_level: open_access
checksum: b2b15a5ef71eb50d62eaa5aea7efd8c4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:56Z
date_updated: 2020-07-14T12:46:17Z
file_id: '4655'
file_name: IST-2012-65-v1+1_Distributed_modular_Htl.pdf
file_size: 526458
relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 171 - 180
project:
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
publication_status: published
publisher: IEEE
publist_id: '2346'
pubrep_id: '65'
quality_controlled: '1'
status: public
title: Distributed, modular HTL
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2009'
...
---
_id: '3869'
abstract:
- lang: eng
text: 'We investigate logics and equivalence relations that capture the qualitative
behavior of Markov Decision Processes (MDPs). We present Qualitative Randomized
CTL (QRCTL): formulas of this logic can express the fact that certain temporal
properties hold over all paths, or with probability 0 or 1, but they do not distinguish
among intermediate probability values. We present a symbolic, polynomial time
model-checking algorithm for QRCTL on MDPs. The logic QRCTL induces an equivalence
relation over states of an MDP that we call qualitative equivalence: informally,
two states are qualitatively equivalent if the sets of formulas that hold with
probability 0 or 1 at the two states are the same. We show that for finite alternating
MDPs, where nondeterministic and probabilistic choices occur in different states,
qualitative equivalence coincides with alternating bisimulation, and can thus
be computed via efficient partition-refinement algorithms. On the other hand,
in non-alternating MDPs the equivalence relations cannot be computed via partition-refinement
algorithms, but rather, they require non-local computation. Finally, we consider
QRCTL*, that extends QRCTL with nested temporal operators in the same manner in
which CTL* extends CTL. We show that QRCTL and QRCTL* induce the same qualitative
equivalence on alternating MDPs, while on non-alternating MDPs, the equivalence
arising from QRCTL* can be strictly finer. We also provide a full characterization
of the relation between qualitative equivalence, bisimulation, and alternating
bisimulation, according to whether the MDPs are finite, and to whether their transition
relations are finitely-branching.'
acknowledgement: A preliminary version of this paper appeared in the proceedings of
the 4th International Conference on the Quantitative Evaluation of Systems (QEST
2007).
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
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: Marco
full_name: Faella, Marco
last_name: Faella
- first_name: Axel
full_name: Legay, Axel
last_name: Legay
citation:
ama: Chatterjee K, De Alfaro L, Faella M, Legay A. Qualitative logics and equivalences
for probabilistic systems. Logical Methods in Computer Science. 2009;5(2).
doi:10.2168/LMCS-5(2:7)2009
apa: Chatterjee, K., De Alfaro, L., Faella, M., & Legay, A. (2009). Qualitative
logics and equivalences for probabilistic systems. Logical Methods in Computer
Science. International Federation of Computational Logic. https://doi.org/10.2168/LMCS-5(2:7)2009
chicago: Chatterjee, Krishnendu, Luca De Alfaro, Marco Faella, and Axel Legay. “Qualitative
Logics and Equivalences for Probabilistic Systems.” Logical Methods in Computer
Science. International Federation of Computational Logic, 2009. https://doi.org/10.2168/LMCS-5(2:7)2009.
ieee: K. Chatterjee, L. De Alfaro, M. Faella, and A. Legay, “Qualitative logics
and equivalences for probabilistic systems,” Logical Methods in Computer Science,
vol. 5, no. 2. International Federation of Computational Logic, 2009.
ista: Chatterjee K, De Alfaro L, Faella M, Legay A. 2009. Qualitative logics and
equivalences for probabilistic systems. Logical Methods in Computer Science. 5(2).
mla: Chatterjee, Krishnendu, et al. “Qualitative Logics and Equivalences for Probabilistic
Systems.” Logical Methods in Computer Science, vol. 5, no. 2, International
Federation of Computational Logic, 2009, doi:10.2168/LMCS-5(2:7)2009.
short: K. Chatterjee, L. De Alfaro, M. Faella, A. Legay, Logical Methods in Computer
Science 5 (2009).
date_created: 2018-12-11T12:05:37Z
date_published: 2009-05-04T00:00:00Z
date_updated: 2021-01-12T07:52:49Z
day: '04'
doi: 10.2168/LMCS-5(2:7)2009
extern: 1
intvolume: ' 5'
issue: '2'
month: '05'
publication: Logical Methods in Computer Science
publication_status: published
publisher: International Federation of Computational Logic
publist_id: '2308'
quality_controlled: 0
status: public
title: Qualitative logics and equivalences for probabilistic systems
type: journal_article
volume: 5
year: '2009'
...
---
_id: '3870'
abstract:
- lang: eng
text: Games on graphs with omega-regular objectives provide a model for the control
and synthesis of reactive systems. Every omega-regular objective can be decomposed
into a safety part and a liveness part. The liveness part ensures that something
good happens “eventually.” Two main strengths of the classical, infinite-limit
formulation of liveness are robustness (independence from the granularity of transitions)
and simplicity (abstraction of complicated time bounds). However, the classical
liveness formulation suffers from the drawback that the time until something good
happens may be unbounded. A stronger formulation of liveness, so-called finitary
liveness, overcomes this drawback, while still retaining robustness and simplicity.
Finitary liveness requires that there exists an unknown, fixed bound b such that
something good happens within b transitions. While for one-shot liveness (reachability)
objectives, classical and finitary liveness coincide, for repeated liveness (Buchi)
objectives, the finitary formulation is strictly stronger. In this work we study
games with finitary parity and Streett objectives. We prove the determinacy of
these games, present algorithms for solving these games, and characterize the
memory requirements of winning strategies. We show that finitary parity games
can be solved in polynomial time, which is not known for infinitary parity games.
For finitary Streett games, we give an EXPTIME algorithm and show that the problem
is NP-hard. Our algorithms can be used, for example, for synthesizing controllers
that do not let the response time of a system increase without bound.
acknowledgement: "This research was supported in part by the AFOSR MURI grant F49620-00-1-0327,
the NSF grants CCR-0132780, CNS-0720884, and CCR- 225610, by the Swiss National
Science Foundation, by the COMBEST project of the European Union, and EU-TMR network
Games.\r\nWe thank anonymous reviewers for useful comments."
article_number: '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: Florian
full_name: Horn, Florian
id: 37327ACE-F248-11E8-B48F-1D18A9856A87
last_name: Horn
citation:
ama: Chatterjee K, Henzinger TA, Horn F. Finitary winning in omega-regular games.
ACM Transactions on Computational Logic (TOCL). 2009;11(1). doi:10.1145/1614431.1614432
apa: Chatterjee, K., Henzinger, T. A., & Horn, F. (2009). Finitary winning in
omega-regular games. ACM Transactions on Computational Logic (TOCL). ACM.
https://doi.org/10.1145/1614431.1614432
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “Finitary
Winning in Omega-Regular Games.” ACM Transactions on Computational Logic (TOCL).
ACM, 2009. https://doi.org/10.1145/1614431.1614432.
ieee: K. Chatterjee, T. A. Henzinger, and F. Horn, “Finitary winning in omega-regular
games,” ACM Transactions on Computational Logic (TOCL), vol. 11, no. 1.
ACM, 2009.
ista: Chatterjee K, Henzinger TA, Horn F. 2009. Finitary winning in omega-regular
games. ACM Transactions on Computational Logic (TOCL). 11(1), 1.
mla: Chatterjee, Krishnendu, et al. “Finitary Winning in Omega-Regular Games.” ACM
Transactions on Computational Logic (TOCL), vol. 11, no. 1, 1, ACM, 2009,
doi:10.1145/1614431.1614432.
short: K. Chatterjee, T.A. Henzinger, F. Horn, ACM Transactions on Computational
Logic (TOCL) 11 (2009).
date_created: 2018-12-11T12:05:37Z
date_published: 2009-10-01T00:00:00Z
date_updated: 2021-01-12T07:52:50Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1145/1614431.1614432
ec_funded: 1
file:
- access_level: open_access
checksum: 139c4586d24f11e5da31fb3a0cf96ef4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:08Z
date_updated: 2020-07-14T12:46:20Z
file_id: '5125'
file_name: IST-2012-53-v1+1_Finitary_winning_in_omega-regular_games.pdf
file_size: 180082
relation: main_file
file_date_updated: 2020-07-14T12:46:20Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
publication: ACM Transactions on Computational Logic (TOCL)
publication_status: published
publisher: ACM
publist_id: '2309'
pubrep_id: '53'
quality_controlled: '1'
scopus_import: 1
status: public
title: Finitary winning in omega-regular games
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2009'
...
---
_id: '3871'
abstract:
- lang: eng
text: 'Nondeterministic weighted automata are finite automata with numerical weights
oil transitions. They define quantitative languages 1, that assign to each word
v; a real number L(w). The value of ail infinite word w is computed as the maximal
value of all runs over w, and the value of a run as the supremum, limsup liminf,
limit average, or discounted sum of the transition weights. We introduce probabilistic
weighted antomata, in which the transitions are chosen in a randomized (rather
than nondeterministic) fashion. Under almost-sure semantics (resp. positive semantics),
the value of a word v) is the largest real v such that the runs over w have value
at least v with probability I (resp. positive probability). We study the classical
questions of automata theory for probabilistic weighted automata: emptiness and
universality, expressiveness, and closure under various operations oil languages.
For quantitative languages, emptiness university axe defined as whether the value
of some (resp. every) word exceeds a given threshold. We prove some, of these
questions to he decidable, and others undecidable. Regarding expressive power,
we show that probabilities allow its to define a wide variety of new classes of
quantitative languages except for discounted-sum automata, where probabilistic
choice is no more expressive than nondeterminism. Finally we live ail almost complete
picture of the closure of various classes of probabilistic weighted automata for
the following, provide, is operations oil quantitative languages: maximum, sum.
and numerical complement.'
acknowledgement: This research was supported in part by the Swiss National Science
Foundation under the Indo-Swiss Joint Research Programme, by the European Network
of Excellence on Embedded Systems Design (ArtistDesign), by the European projects
Combest, Quasimodo, and Gasics, by the PAI program Moves funded by the Belgian Federal
Government, and by the CFV (Federated Center in Verification ) funded by the F.R.S.-FNRS.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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. Probabilistic weighted automata. In:
Vol 5710. Springer; 2009:244-258. doi:10.1007/978-3-642-04081-8_17'
apa: 'Chatterjee, K., Doyen, L., & Henzinger, T. A. (2009). Probabilistic weighted
automata (Vol. 5710, pp. 244–258). Presented at the CONCUR: Concurrency Theory,
Bologna, Italy: Springer. https://doi.org/10.1007/978-3-642-04081-8_17'
chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Probabilistic
Weighted Automata,” 5710:244–58. Springer, 2009. https://doi.org/10.1007/978-3-642-04081-8_17.
ieee: 'K. Chatterjee, L. Doyen, and T. A. Henzinger, “Probabilistic weighted automata,”
presented at the CONCUR: Concurrency Theory, Bologna, Italy, 2009, vol. 5710,
pp. 244–258.'
ista: 'Chatterjee K, Doyen L, Henzinger TA. 2009. Probabilistic weighted automata.
CONCUR: Concurrency Theory, LNCS, vol. 5710, 244–258.'
mla: Chatterjee, Krishnendu, et al. Probabilistic Weighted Automata. Vol.
5710, Springer, 2009, pp. 244–58, doi:10.1007/978-3-642-04081-8_17.
short: K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 244–258.
conference:
end_date: 2009-09-04
location: Bologna, Italy
name: 'CONCUR: Concurrency Theory'
start_date: 2009-09-01
date_created: 2018-12-11T12:05:37Z
date_published: 2009-09-01T00:00:00Z
date_updated: 2021-01-12T07:52:50Z
day: '01'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.1007/978-3-642-04081-8_17
ec_funded: 1
file:
- access_level: open_access
checksum: af973ddbcf131b8810c6bff2c055ff56
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:46Z
date_updated: 2020-07-14T12:46:20Z
file_id: '4771'
file_name: IST-2012-52-v1+1_Probabilistic_Weighted_Automata.pdf
file_size: 200161
relation: main_file
file_date_updated: 2020-07-14T12:46:20Z
has_accepted_license: '1'
intvolume: ' 5710'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 244 - 258
project:
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
publication_status: published
publisher: Springer
publist_id: '2304'
pubrep_id: '52'
quality_controlled: '1'
scopus_import: 1
status: public
title: Probabilistic weighted automata
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5710
year: '2009'
...
---
_id: '3946'
abstract:
- lang: eng
text: We compare anti-parasite defences at the level of multicellular organisms
and insect societies, and find that selection by parasites at these two organisational
levels is often very similar and has created a number of parallel evolutionary
solutions in the host's immune response. The defence mechanisms of both individuals
and insect colonies start with border defences to prevent parasite intake and
are followed by soma defences that prevent the establishment and spread of the
parasite between the body's cells or the social insect workers. Lastly, germ line
defences are employed to inhibit infection of the reproductive tissue of organisms
or the reproductive individuals in colonies. We further find sophisticated self/non-self-recognition
systems operating at both levels, which appear to be vital in maintaining the
integrity of the body or colony as a reproductive entity. We then expand on the
regulation of immune responses and end with a contemplation of how evolution may
shape the different immune components, both within and between levels. The aim
of this review is to highlight common evolutionary principles acting in disease
defence at the level of both individual organisms and societies, thereby linking
the fields of physiological and ecological immunology.
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- 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: Cremer S, Sixt MK. Analogies in the evolution of individual and social immunity.
Philosophical Transactions of the Royal Society of London Series B, Biological
Sciences. 2009;364(1513):129-142. doi:10.1098/rstb.2008.0166
apa: Cremer, S., & Sixt, M. K. (2009). Analogies in the evolution of individual
and social immunity. Philosophical Transactions of the Royal Society of London.
Series B, Biological Sciences. Royal Society, The. https://doi.org/10.1098/rstb.2008.0166
chicago: Cremer, Sylvia, and Michael K Sixt. “Analogies in the Evolution of Individual
and Social Immunity.” Philosophical Transactions of the Royal Society of London.
Series B, Biological Sciences. Royal Society, The, 2009. https://doi.org/10.1098/rstb.2008.0166.
ieee: S. Cremer and M. K. Sixt, “Analogies in the evolution of individual and social
immunity,” Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences, vol. 364, no. 1513. Royal Society, The, pp. 129–142,
2009.
ista: Cremer S, Sixt MK. 2009. Analogies in the evolution of individual and social
immunity. Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences. 364(1513), 129–142.
mla: Cremer, Sylvia, and Michael K. Sixt. “Analogies in the Evolution of Individual
and Social Immunity.” Philosophical Transactions of the Royal Society of London.
Series B, Biological Sciences, vol. 364, no. 1513, Royal Society, The, 2009,
pp. 129–42, doi:10.1098/rstb.2008.0166.
short: S. Cremer, M.K. Sixt, Philosophical Transactions of the Royal Society of
London. Series B, Biological Sciences 364 (2009) 129–142.
date_created: 2018-12-11T12:06:02Z
date_published: 2009-01-12T00:00:00Z
date_updated: 2021-01-12T07:53:23Z
day: '12'
doi: 10.1098/rstb.2008.0166
extern: '1'
intvolume: ' 364'
issue: '1513'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666697/
month: '01'
oa: 1
oa_version: None
page: 129 - 142
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '2181'
status: public
title: Analogies in the evolution of individual and social immunity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 364
year: '2009'
...
---
_id: '3947'
abstract:
- lang: eng
text: Mature dendritic cells (DCs) moving from the skin to the lymph node are a
prototypic example of rapidly migrating amoeboid leukocytes. Interstitial DC migration
is directionally guided by chemokines, but independent of specific adhesive interactions
with the tissue as well as pericellular proteolysis. Instead, the protrusive flow
of the actin cytoskeleton directly drives a basal mode of locomotion that is occasionally
supported by actomyosin contractions at the trailing edge to propel the cell's
rigid nucleus. We here delete the small GTPase Cdc42 in DCs and find that actin
flow and actomyosin contraction are still initiated in response to chemotactic
cues. Accordingly, the cells are able to polarize and form protrusions. However,
in the absence of Cdc42 the protrusions are temporally and spatially dysregulated,
which leads to impaired leading edge coordination. Although this defect still
allows the cells to move on 2-dimensional surfaces, their in vivo motility is
completely abrogated. We show that this difference is entirely caused by the geometric
complexity of the environment, as multiple competing protrusions lead to instantaneous
entanglement within 3-dimensional extracellular matrix scaffolds. This demonstrates
that the decisive factor for migrating DCs is not specific interaction with the
extracellular environment, but adequate coordination of cytoskeletal flow.
acknowledgement: |-
We thank Sylvia Cremer for help with statistics and critical reading of the paper and Reinhard Fässler for continuous support.
This work was supported by the German Research Foundation (Bonn, Germany), the Peter Hans Hofschneider Foundation for Experimental Biomedicine (Zürich, Switzerland), and the Max Planck Society (Munich, Germany).
author:
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Jörg
full_name: Jörg Renkawitz
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Xunwei
full_name: Wu, Xunwei
last_name: Wu
- first_name: Karin
full_name: Hirsch, Karin
last_name: Hirsch
- first_name: Cord
full_name: Brakebusch, Cord
last_name: Brakebusch
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Lämmermann T, Renkawitz J, Wu X, Hirsch K, Brakebusch C, Sixt MK. Cdc42-dependent
leading edge coordination is essential for interstitial dendritic cell migration
(Plenary Paper). Blood. 2009;113(23):5703-5710. doi:10.1182/blood-2008-11-191882
apa: Lämmermann, T., Renkawitz, J., Wu, X., Hirsch, K., Brakebusch, C., & Sixt,
M. K. (2009). Cdc42-dependent leading edge coordination is essential for interstitial
dendritic cell migration (Plenary Paper). Blood. American Society of Hematology.
https://doi.org/10.1182/blood-2008-11-191882
chicago: Lämmermann, Tim, Jörg Renkawitz, Xunwei Wu, Karin Hirsch, Cord Brakebusch,
and Michael K Sixt. “Cdc42-Dependent Leading Edge Coordination Is Essential for
Interstitial Dendritic Cell Migration (Plenary Paper).” Blood. American
Society of Hematology, 2009. https://doi.org/10.1182/blood-2008-11-191882.
ieee: T. Lämmermann, J. Renkawitz, X. Wu, K. Hirsch, C. Brakebusch, and M. K. Sixt,
“Cdc42-dependent leading edge coordination is essential for interstitial dendritic
cell migration (Plenary Paper),” Blood, vol. 113, no. 23. American Society
of Hematology, pp. 5703–5710, 2009.
ista: Lämmermann T, Renkawitz J, Wu X, Hirsch K, Brakebusch C, Sixt MK. 2009. Cdc42-dependent
leading edge coordination is essential for interstitial dendritic cell migration
(Plenary Paper). Blood. 113(23), 5703–5710.
mla: Lämmermann, Tim, et al. “Cdc42-Dependent Leading Edge Coordination Is Essential
for Interstitial Dendritic Cell Migration (Plenary Paper).” Blood, vol.
113, no. 23, American Society of Hematology, 2009, pp. 5703–10, doi:10.1182/blood-2008-11-191882.
short: T. Lämmermann, J. Renkawitz, X. Wu, K. Hirsch, C. Brakebusch, M.K. Sixt,
Blood 113 (2009) 5703–5710.
date_created: 2018-12-11T12:06:03Z
date_published: 2009-06-04T00:00:00Z
date_updated: 2021-01-12T07:53:23Z
day: '04'
doi: 10.1182/blood-2008-11-191882
extern: 1
intvolume: ' 113'
issue: '23'
month: '06'
page: 5703 - 5710
publication: Blood
publication_status: published
publisher: American Society of Hematology
publist_id: '2179'
quality_controlled: 0
status: public
title: Cdc42-dependent leading edge coordination is essential for interstitial dendritic
cell migration (Plenary Paper)
type: journal_article
volume: 113
year: '2009'
...
---
_id: '3948'
abstract:
- lang: eng
text: Inhibiting the alpha(4) subunit of the integrin heterodimers alpha(4)beta(1)
and alpha(4)beta(7) with the monoclonal antibody natalizumab is an effective treatment
for multiple sclerosis (MS). However, the pharmacological action of natalizumab
is not understood conclusively. Previous studies suggested that natalizumab inhibits
activation, proliferation, or extravasation of inflammatory cells. To specify
which mechanisms, cell types, and alpha(4) heterodimers are affected by the antibody
treatment, we studied MS-like experimental autoimmune encephalomyelitis (EAE)
in mice lacking the beta(1)-integrin gene either in all hematopoietic cells or
selectively in T lymphocytes. Our results show that T cells critically rely on
beta(1) integrins to accumulate in the central nervous system (CNS) during EAE,
whereas CNS infiltration of beta(1)-deficient myeloid cells remains unaffected,
suggesting that T cells are the main target of anti-alpha(4)-antibody blockade.
We demonstrate that beta(1)-integrin expression on encephalitogenic T cells is
critical for EAE development, and we therefore exclude alpha(4)beta(7) as a target
integrin of the antibody treatment. T cells lacking beta(1) integrin are unable
to firmly adhere to CNS endothelium in vivo, whereas their priming and expansion
remain unaffected. Collectively, these results suggest that the primary action
of natalizumab is interference with T cell extravasation via inhibition of alpha(4)beta(1)
integrins.
author:
- first_name: Martina
full_name: Bauer, Martina
last_name: Bauer
- first_name: Cord
full_name: Brakebusch, Cord
last_name: Brakebusch
- first_name: Caroline
full_name: Coisne, Caroline
last_name: Coisne
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Hartmut
full_name: Wekerle, Hartmut
last_name: Wekerle
- first_name: Britta
full_name: Engelhardt, Britta
last_name: Engelhardt
- first_name: Reinhard
full_name: Fässler, Reinhard
last_name: Fässler
citation:
ama: Bauer M, Brakebusch C, Coisne C, et al. β1 integrins differentially control
extravasation of inflammatory cell subsets into the CNS during autoimmunity. PNAS.
2009;106(6):1920-1925. doi:10.1073/pnas.0808909106
apa: Bauer, M., Brakebusch, C., Coisne, C., Sixt, M. K., Wekerle, H., Engelhardt,
B., & Fässler, R. (2009). β1 integrins differentially control extravasation
of inflammatory cell subsets into the CNS during autoimmunity. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.0808909106
chicago: Bauer, Martina, Cord Brakebusch, Caroline Coisne, Michael K Sixt, Hartmut
Wekerle, Britta Engelhardt, and Reinhard Fässler. “Β1 Integrins Differentially
Control Extravasation of Inflammatory Cell Subsets into the CNS during Autoimmunity.”
PNAS. National Academy of Sciences, 2009. https://doi.org/10.1073/pnas.0808909106.
ieee: M. Bauer et al., “β1 integrins differentially control extravasation
of inflammatory cell subsets into the CNS during autoimmunity,” PNAS, vol.
106, no. 6. National Academy of Sciences, pp. 1920–1925, 2009.
ista: Bauer M, Brakebusch C, Coisne C, Sixt MK, Wekerle H, Engelhardt B, Fässler
R. 2009. β1 integrins differentially control extravasation of inflammatory cell
subsets into the CNS during autoimmunity. PNAS. 106(6), 1920–1925.
mla: Bauer, Martina, et al. “Β1 Integrins Differentially Control Extravasation of
Inflammatory Cell Subsets into the CNS during Autoimmunity.” PNAS, vol.
106, no. 6, National Academy of Sciences, 2009, pp. 1920–25, doi:10.1073/pnas.0808909106.
short: M. Bauer, C. Brakebusch, C. Coisne, M.K. Sixt, H. Wekerle, B. Engelhardt,
R. Fässler, PNAS 106 (2009) 1920–1925.
date_created: 2018-12-11T12:06:03Z
date_published: 2009-02-10T00:00:00Z
date_updated: 2021-01-12T07:53:24Z
day: '10'
doi: 10.1073/pnas.0808909106
extern: 1
intvolume: ' 106'
issue: '6'
month: '02'
page: 1920 - 1925
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2180'
quality_controlled: 0
status: public
title: β1 integrins differentially control extravasation of inflammatory cell subsets
into the CNS during autoimmunity
type: journal_article
volume: 106
year: '2009'
...
---
_id: '3949'
abstract:
- lang: eng
text: Adhesion and motility of mammalian leukocytes are essential requirements for
innate and adaptive immune defense mechanisms. We show here that the guanine nucleotide
exchange factor cytohesin-1, which had previously been demonstrated to be an important
component of beta-2 integrin activation in lymphocytes, regulates the activation
of the small GTPase RhoA in primary dendritic cells (DCs). Cytohesin-1 and RhoA
are both required for the induction of chemokine-dependent conformational changes
of the integrin beta-2 subunit of DCs during adhesion under physiological flow
conditions. Furthermore, use of RNAi in murine bone marrow DCs (BM-DCs) revealed
that interference with cytohesin-1 signaling impairs migration of wild-type dendritic
cells in complex 3D environments and in vivo. This phenotype was not observed
in the complete absence of integrins. We thus demonstrate an essential role of
cytohesin-1/RhoA during ameboid migration in the presence of integrins and further
suggest that DCs without integrins switch to a different migration mode.
author:
- first_name: Thomas
full_name: Quast, Thomas
last_name: Quast
- first_name: Barbara
full_name: Tappertzhofen, Barbara
last_name: Tappertzhofen
- first_name: Cora
full_name: Schild, Cora
last_name: Schild
- first_name: Jessica
full_name: Grell, Jessica
last_name: Grell
- first_name: Niklas
full_name: Czeloth, Niklas
last_name: Czeloth
- first_name: Reinhold
full_name: Förster, Reinhold
last_name: Förster
- first_name: Ronen
full_name: Alon, Ronen
last_name: Alon
- first_name: Line
full_name: Fraemohs, Line
last_name: Fraemohs
- first_name: Katrin
full_name: Dreck, Katrin
last_name: Dreck
- first_name: Christian
full_name: Weber, Christian
last_name: Weber
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Waldemar
full_name: Kolanus, Waldemar
last_name: Kolanus
citation:
ama: Quast T, Tappertzhofen B, Schild C, et al. Cytohesin-1 controls the activation
of RhoA and modulates integrin-dependent adhesion and migration of dendritic cells.
Blood. 2009;113(23):5801-5810. doi:10.1182/blood-2008-08-176123
apa: Quast, T., Tappertzhofen, B., Schild, C., Grell, J., Czeloth, N., Förster,
R., … Kolanus, W. (2009). Cytohesin-1 controls the activation of RhoA and modulates
integrin-dependent adhesion and migration of dendritic cells. Blood. American
Society of Hematology. https://doi.org/10.1182/blood-2008-08-176123
chicago: Quast, Thomas, Barbara Tappertzhofen, Cora Schild, Jessica Grell, Niklas
Czeloth, Reinhold Förster, Ronen Alon, et al. “Cytohesin-1 Controls the Activation
of RhoA and Modulates Integrin-Dependent Adhesion and Migration of Dendritic Cells.”
Blood. American Society of Hematology, 2009. https://doi.org/10.1182/blood-2008-08-176123.
ieee: T. Quast et al., “Cytohesin-1 controls the activation of RhoA and modulates
integrin-dependent adhesion and migration of dendritic cells,” Blood, vol.
113, no. 23. American Society of Hematology, pp. 5801–5810, 2009.
ista: Quast T, Tappertzhofen B, Schild C, Grell J, Czeloth N, Förster R, Alon R,
Fraemohs L, Dreck K, Weber C, Lämmermann T, Sixt MK, Kolanus W. 2009. Cytohesin-1
controls the activation of RhoA and modulates integrin-dependent adhesion and
migration of dendritic cells. Blood. 113(23), 5801–5810.
mla: Quast, Thomas, et al. “Cytohesin-1 Controls the Activation of RhoA and Modulates
Integrin-Dependent Adhesion and Migration of Dendritic Cells.” Blood, vol.
113, no. 23, American Society of Hematology, 2009, pp. 5801–10, doi:10.1182/blood-2008-08-176123.
short: T. Quast, B. Tappertzhofen, C. Schild, J. Grell, N. Czeloth, R. Förster,
R. Alon, L. Fraemohs, K. Dreck, C. Weber, T. Lämmermann, M.K. Sixt, W. Kolanus,
Blood 113 (2009) 5801–5810.
date_created: 2018-12-11T12:06:03Z
date_published: 2009-06-04T00:00:00Z
date_updated: 2021-01-12T07:53:24Z
day: '04'
doi: 10.1182/blood-2008-08-176123
extern: 1
intvolume: ' 113'
issue: '23'
month: '06'
page: 5801 - 5810
publication: Blood
publication_status: published
publisher: American Society of Hematology
publist_id: '2177'
quality_controlled: 0
status: public
title: Cytohesin-1 controls the activation of RhoA and modulates integrin-dependent
adhesion and migration of dendritic cells
type: journal_article
volume: 113
year: '2009'
...
---
_id: '3950'
abstract:
- lang: eng
text: Integrin activation is essential for the function of all blood cells, including
platelets and leukocytes. The blood cell-specific FERM domain protein Kindlin-3
is required for the activation of the beta1 and beta3 integrins on platelets.
Impaired activation of beta1, beta2 and beta3 integrins on platelets and leukocytes
is the hallmark of a rare autosomal recessive leukocyte adhesion deficiency syndrome
in humans called LAD-III, characterized by severe bleeding and impaired adhesion
of leukocytes to inflamed endothelia. Here we show that Kindlin-3 also binds the
beta2 integrin cytoplasmic domain and is essential for neutrophil binding and
spreading on beta2 integrin-dependent ligands such as intercellular adhesion molecule-1
and the complement C3 activation product iC3b. Moreover, loss of Kindlin-3 expression
abolished firm adhesion and arrest of neutrophils on activated endothelial cells
in vitro and in vivo, whereas selectin-mediated rolling was unaffected. Thus,
Kindlin-3 is essential to activate the beta1, beta2 and beta3 integrin classes,
and loss of Kindlin-3 function is sufficient to cause a LAD-III-like phenotype
in mice.
author:
- first_name: Markus
full_name: Moser, Markus
last_name: Moser
- first_name: Martina
full_name: Bauer, Martina
last_name: Bauer
- first_name: Stephan
full_name: Schmid, Stephan
last_name: Schmid
- first_name: Raphael
full_name: Ruppert, Raphael
last_name: Ruppert
- first_name: Sarah
full_name: Schmidt, Sarah
last_name: Schmidt
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Hao
full_name: Wang, Hao-Ven
last_name: Wang
- first_name: Markus
full_name: Sperandio, Markus
last_name: Sperandio
- first_name: Reinhard
full_name: Fässler, Reinhard
last_name: Fässler
citation:
ama: Moser M, Bauer M, Schmid S, et al. Kindlin-3 is required for β2 integrin-mediated
leukocyte adhesion to endothelial cells. Nature Medicine. 2009;15(3):300-305.
doi:10.1038/nm.1921
apa: Moser, M., Bauer, M., Schmid, S., Ruppert, R., Schmidt, S., Sixt, M. K., …
Fässler, R. (2009). Kindlin-3 is required for β2 integrin-mediated leukocyte adhesion
to endothelial cells. Nature Medicine. Nature Publishing Group. https://doi.org/10.1038/nm.1921
chicago: Moser, Markus, Martina Bauer, Stephan Schmid, Raphael Ruppert, Sarah Schmidt,
Michael K Sixt, Hao Wang, Markus Sperandio, and Reinhard Fässler. “Kindlin-3 Is
Required for Β2 Integrin-Mediated Leukocyte Adhesion to Endothelial Cells.” Nature
Medicine. Nature Publishing Group, 2009. https://doi.org/10.1038/nm.1921.
ieee: M. Moser et al., “Kindlin-3 is required for β2 integrin-mediated leukocyte
adhesion to endothelial cells,” Nature Medicine, vol. 15, no. 3. Nature
Publishing Group, pp. 300–305, 2009.
ista: Moser M, Bauer M, Schmid S, Ruppert R, Schmidt S, Sixt MK, Wang H, Sperandio
M, Fässler R. 2009. Kindlin-3 is required for β2 integrin-mediated leukocyte adhesion
to endothelial cells. Nature Medicine. 15(3), 300–305.
mla: Moser, Markus, et al. “Kindlin-3 Is Required for Β2 Integrin-Mediated Leukocyte
Adhesion to Endothelial Cells.” Nature Medicine, vol. 15, no. 3, Nature
Publishing Group, 2009, pp. 300–05, doi:10.1038/nm.1921.
short: M. Moser, M. Bauer, S. Schmid, R. Ruppert, S. Schmidt, M.K. Sixt, H. Wang,
M. Sperandio, R. Fässler, Nature Medicine 15 (2009) 300–305.
date_created: 2018-12-11T12:06:04Z
date_published: 2009-02-22T00:00:00Z
date_updated: 2021-01-12T07:53:25Z
day: '22'
doi: 10.1038/nm.1921
extern: 1
intvolume: ' 15'
issue: '3'
month: '02'
page: 300 - 305
publication: Nature Medicine
publication_status: published
publisher: Nature Publishing Group
publist_id: '2178'
quality_controlled: 0
status: public
title: Kindlin-3 is required for β2 integrin-mediated leukocyte adhesion to endothelial
cells
type: journal_article
volume: 15
year: '2009'
...
---
_id: '3951'
abstract:
- lang: eng
text: The morphological term 'amoeboid' migration subsumes a number of rather distinct
biophysical modes of cellular locomotion that range from blebbing motility to
entirely actin-polymerization-based gliding. Here, we discuss the diverse principles
of force generation and force transduction that lead to the distinct amoeboid
phenotypes. We argue that shifting the balance between actin protrusion, actomyosin
contraction, and adhesion to the extracellular substrate can explain the different
modes of amoeboid movement and that blebbing and gliding are barely extreme variants
of one common migration strategy. Depending on the cell type, physiological conditions
or experimental manipulation, amoeboid cells can adopt the distinct mechanical
modes of amoeboid migration.
author:
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Lämmermann T, Sixt MK. Mechanical modes of “amoeboid” cell migration. Current
Opinion in Cell Biology. 2009;21(5):636-644. doi:10.1016/j.ceb.2009.05.003
apa: Lämmermann, T., & Sixt, M. K. (2009). Mechanical modes of “amoeboid” cell
migration. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2009.05.003
chicago: Lämmermann, Tim, and Michael K Sixt. “Mechanical Modes of ‘amoeboid’ Cell
Migration.” Current Opinion in Cell Biology. Elsevier, 2009. https://doi.org/10.1016/j.ceb.2009.05.003.
ieee: T. Lämmermann and M. K. Sixt, “Mechanical modes of ‘amoeboid’ cell migration,”
Current Opinion in Cell Biology, vol. 21, no. 5. Elsevier, pp. 636–644,
2009.
ista: Lämmermann T, Sixt MK. 2009. Mechanical modes of ‘amoeboid’ cell migration.
Current Opinion in Cell Biology. 21(5), 636–644.
mla: Lämmermann, Tim, and Michael K. Sixt. “Mechanical Modes of ‘amoeboid’ Cell
Migration.” Current Opinion in Cell Biology, vol. 21, no. 5, Elsevier,
2009, pp. 636–44, doi:10.1016/j.ceb.2009.05.003.
short: T. Lämmermann, M.K. Sixt, Current Opinion in Cell Biology 21 (2009) 636–644.
date_created: 2018-12-11T12:06:04Z
date_published: 2009-10-01T00:00:00Z
date_updated: 2021-01-12T07:53:25Z
day: '01'
doi: 10.1016/j.ceb.2009.05.003
extern: 1
intvolume: ' 21'
issue: '5'
month: '10'
page: 636 - 644
publication: Current Opinion in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '2176'
quality_controlled: 0
status: public
title: Mechanical modes of 'amoeboid' cell migration
type: journal_article
volume: 21
year: '2009'
...
---
_id: '3952'
abstract:
- lang: eng
text: The mammalian actin-binding protein 1 (mAbp1, Hip-55, SH3P7) is phosphorylated
by the nonreceptor tyrosine kinase Syk that has a fundamental effect for several
beta(2) integrin (CD11/CD18)-mediated neutrophil functions. Live cell imaging
showed a dynamic enrichment of enhanced green fluorescence protein-tagged mAbp1
at the phagocytic cup of neutrophil-like differentiated HL-60 cells during beta(2)
integrin-mediated phagocytosis of serum-opsonized Escherichia coli. The genetic
absence of Syk or its pharmacologic inhibition using piceatannol abrogated the
proper localization of mAbp1 at the phagocytic cup. The genetic absence or down-regulation
of mAbp1 using the RNA interference technique significantly compromised beta(2)
integrin-mediated phagocytosis of serum-opsonized E coli or Salmonella typhimurium
in vitro as well as clearance of S typhimurium infection in vivo. Moreover, the
genetic absence of mAbp1 almost completely abrogated firm neutrophil adhesion
under physiologic shear stress conditions in vitro as well as leukocyte adhesion
and extravasation in inflamed cremaster muscle venules of mice treated with tumor-necrosis
factor alpha. Functional analysis showed that the down-regulation of mAbp1 diminished
the number of beta(2) integrin clusters in the high-affinity conformation under
flow conditions. These unanticipated results define mAbp1 as a novel molecular
player in integrin biology that is critical for phagocytosis and firm neutrophil
adhesion under flow conditions.
author:
- first_name: Jürgen
full_name: Schymeinsky, Jürgen
last_name: Schymeinsky
- first_name: Ronald
full_name: Gerstl, Ronald
last_name: Gerstl
- first_name: Ingrid
full_name: Mannigel, Ingrid
last_name: Mannigel
- first_name: Katy
full_name: Niedung, Katy
last_name: Niedung
- first_name: David
full_name: Frommhold, David
last_name: Frommhold
- first_name: Klaus
full_name: Panthel, Klaus
last_name: Panthel
- first_name: Jürgen
full_name: Heesemann, Jürgen
last_name: Heesemann
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Thomas
full_name: Quast, Thomas
last_name: Quast
- first_name: Waldemar
full_name: Kolanus, Waldemar
last_name: Kolanus
- first_name: Attila
full_name: Mocsai, Attila
last_name: Mocsai
- first_name: Jürgen
full_name: Wienands, Jürgen
last_name: Wienands
- first_name: Markus
full_name: Sperandio, Markus
last_name: Sperandio
- first_name: Barbara
full_name: Walzog, Barbara
last_name: Walzog
citation:
ama: 'Schymeinsky J, Gerstl R, Mannigel I, et al. A fundamental role of mAbp1 in
neutrophils: impact on β(2) integrin-mediated phagocytosis and adhesion in vivo.
Blood. 2009;114(19):4209-4220. doi:10.1182/blood-2009-02-206169'
apa: 'Schymeinsky, J., Gerstl, R., Mannigel, I., Niedung, K., Frommhold, D., Panthel,
K., … Walzog, B. (2009). A fundamental role of mAbp1 in neutrophils: impact on
β(2) integrin-mediated phagocytosis and adhesion in vivo. Blood. American
Society of Hematology. https://doi.org/10.1182/blood-2009-02-206169'
chicago: 'Schymeinsky, Jürgen, Ronald Gerstl, Ingrid Mannigel, Katy Niedung, David
Frommhold, Klaus Panthel, Jürgen Heesemann, et al. “A Fundamental Role of MAbp1
in Neutrophils: Impact on β(2) Integrin-Mediated Phagocytosis and Adhesion in
Vivo.” Blood. American Society of Hematology, 2009. https://doi.org/10.1182/blood-2009-02-206169.'
ieee: 'J. Schymeinsky et al., “A fundamental role of mAbp1 in neutrophils:
impact on β(2) integrin-mediated phagocytosis and adhesion in vivo,” Blood,
vol. 114, no. 19. American Society of Hematology, pp. 4209–4220, 2009.'
ista: 'Schymeinsky J, Gerstl R, Mannigel I, Niedung K, Frommhold D, Panthel K, Heesemann
J, Sixt MK, Quast T, Kolanus W, Mocsai A, Wienands J, Sperandio M, Walzog B. 2009.
A fundamental role of mAbp1 in neutrophils: impact on β(2) integrin-mediated phagocytosis
and adhesion in vivo. Blood. 114(19), 4209–4220.'
mla: 'Schymeinsky, Jürgen, et al. “A Fundamental Role of MAbp1 in Neutrophils: Impact
on β(2) Integrin-Mediated Phagocytosis and Adhesion in Vivo.” Blood, vol.
114, no. 19, American Society of Hematology, 2009, pp. 4209–20, doi:10.1182/blood-2009-02-206169.'
short: J. Schymeinsky, R. Gerstl, I. Mannigel, K. Niedung, D. Frommhold, K. Panthel,
J. Heesemann, M.K. Sixt, T. Quast, W. Kolanus, A. Mocsai, J. Wienands, M. Sperandio,
B. Walzog, Blood 114 (2009) 4209–4220.
date_created: 2018-12-11T12:06:04Z
date_published: 2009-11-05T00:00:00Z
date_updated: 2021-01-12T07:53:26Z
day: '05'
doi: 10.1182/blood-2009-02-206169
extern: 1
intvolume: ' 114'
issue: '19'
month: '11'
page: 4209 - 4220
publication: Blood
publication_status: published
publisher: American Society of Hematology
publist_id: '2175'
quality_controlled: 0
status: public
title: 'A fundamental role of mAbp1 in neutrophils: impact on β(2) integrin-mediated
phagocytosis and adhesion in vivo'
type: journal_article
volume: 114
year: '2009'
...
---
_id: '3953'
abstract:
- lang: eng
text: CD4(+)CD25(+) regulatory T cell (Treg) entry into secondary lymphoid organs
and local expansion is critical for their immunosuppressive function. Long-term
application of the sphingosine-1 phosphate receptor agonist FTY720 exerts pleiotropic
anti-inflammatory effects, whereas short-term FTY720 boosts antiviral immunity.
In this study, we provide evidence that FTY720 potently inhibits Treg proliferation
in vitro and in vivo without affecting their viability, phenotype, or in vitro
immunosuppression. In contrast, adoptively transferred Treg exposed ex vivo to
FTY720 lost their protective effects in murine models of acute glomerulonephritis
and acute graft-vs-host disease. On a cellular level, FTY720 inhibits IL-2-induced
STAT-5 phosphorylation, paralleled by a loss of FoxP3 expression during Treg expansion
in vitro. Notably, loss of in vivo immunosuppression is not due to impaired migration
to or localization within secondary lymphoid organs. We could even show a selective
trapping of adoptively transferred Treg in inflammatory lymph nodes by FTY720.
Finally, Treg isolated from animals systemically exposed to FTY720 also exhibit
a significantly impaired proliferative response upon restimulation when compared
with Treg isolated from solvent-treated animals. In summary, our data suggest
that sphingosine-1 phosphate receptor-mediated signals induced by FTY720 abrogate
their in vivo immunosuppressive potential by blocking IL-2 induced expansion,
which is indispensable for their in vivo immunosuppressive activity.
author:
- first_name: Anna
full_name: Wolf, Anna Maria
last_name: Wolf
- first_name: Kathrin
full_name: Eller, Kathrin
last_name: Eller
- first_name: Robert
full_name: Zeiser, Robert
last_name: Zeiser
- first_name: Christoph
full_name: Dürr, Christoph
last_name: Dürr
- first_name: Ulrike
full_name: Gerlach, Ulrike V
last_name: Gerlach
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Lydia
full_name: Markut, Lydia
last_name: Markut
- first_name: Guenther
full_name: Gastl, Guenther
last_name: Gastl
- first_name: Alexander
full_name: Rosenkranz, Alexander R
last_name: Rosenkranz
- first_name: Dominik
full_name: Wolf, Dominik
last_name: Wolf
citation:
ama: Wolf A, Eller K, Zeiser R, et al. The sphingosine 1-phosphate receptor agonist
FTY720 potently inhibits regulatory T cell proliferation in vitro and in vivo.
Journal of Immunology. 2009;183(6):3751-3760. doi:10.4049/jimmunol.0901011
apa: Wolf, A., Eller, K., Zeiser, R., Dürr, C., Gerlach, U., Sixt, M. K., … Wolf,
D. (2009). The sphingosine 1-phosphate receptor agonist FTY720 potently inhibits
regulatory T cell proliferation in vitro and in vivo. Journal of Immunology.
American Association of Immunologists. https://doi.org/10.4049/jimmunol.0901011
chicago: Wolf, Anna, Kathrin Eller, Robert Zeiser, Christoph Dürr, Ulrike Gerlach,
Michael K Sixt, Lydia Markut, Guenther Gastl, Alexander Rosenkranz, and Dominik
Wolf. “The Sphingosine 1-Phosphate Receptor Agonist FTY720 Potently Inhibits Regulatory
T Cell Proliferation in Vitro and in Vivo.” Journal of Immunology. American
Association of Immunologists, 2009. https://doi.org/10.4049/jimmunol.0901011.
ieee: A. Wolf et al., “The sphingosine 1-phosphate receptor agonist FTY720
potently inhibits regulatory T cell proliferation in vitro and in vivo,” Journal
of Immunology, vol. 183, no. 6. American Association of Immunologists, pp.
3751–3760, 2009.
ista: Wolf A, Eller K, Zeiser R, Dürr C, Gerlach U, Sixt MK, Markut L, Gastl G,
Rosenkranz A, Wolf D. 2009. The sphingosine 1-phosphate receptor agonist FTY720
potently inhibits regulatory T cell proliferation in vitro and in vivo. Journal
of Immunology. 183(6), 3751–3760.
mla: Wolf, Anna, et al. “The Sphingosine 1-Phosphate Receptor Agonist FTY720 Potently
Inhibits Regulatory T Cell Proliferation in Vitro and in Vivo.” Journal of
Immunology, vol. 183, no. 6, American Association of Immunologists, 2009,
pp. 3751–60, doi:10.4049/jimmunol.0901011.
short: A. Wolf, K. Eller, R. Zeiser, C. Dürr, U. Gerlach, M.K. Sixt, L. Markut,
G. Gastl, A. Rosenkranz, D. Wolf, Journal of Immunology 183 (2009) 3751–3760.
date_created: 2018-12-11T12:06:05Z
date_published: 2009-09-15T00:00:00Z
date_updated: 2021-01-12T07:53:26Z
day: '15'
doi: 10.4049/jimmunol.0901011
extern: 1
intvolume: ' 183'
issue: '6'
month: '09'
page: 3751 - 3760
publication: Journal of Immunology
publication_status: published
publisher: American Association of Immunologists
publist_id: '2174'
quality_controlled: 0
status: public
title: The sphingosine 1-phosphate receptor agonist FTY720 potently inhibits regulatory
T cell proliferation in vitro and in vivo
type: journal_article
volume: 183
year: '2009'
...
---
_id: '3954'
abstract:
- lang: eng
text: The leading front of a cell can either protrude as an actin-free membrane
bleb that is inflated by actomyosin-driven contractile forces, or as an actin-rich
pseudopodium, a site where polymerizing actin filaments push out the membrane.
Pushing filaments can only cause the membrane to protrude if the expanding actin
network experiences a retrograde counter-force, which is usually provided by transmembrane
receptors of the integrin family. Here we show that chemotactic dendritic cells
mechanically adapt to the adhesive properties of their substrate by switching
between integrin-mediated and integrin-independent locomotion. We found that on
engaging the integrin-actin clutch, actin polymerization was entirely turned into
protrusion, whereas on disengagement actin underwent slippage and retrograde flow.
Remarkably, accelerated retrograde flow was balanced by an increased actin polymerization
rate; therefore, cell shape and protrusion velocity remained constant on alternating
substrates. Due to this adaptive response in polymerization dynamics, tracks of
adhesive substrate did not dictate the path of the cells. Instead, directional
guidance was exclusively provided by a soluble gradient of chemoattractant, which
endowed these 'amoeboid' cells with extraordinary flexibility, enabling them to
traverse almost every type of tissue.
acknowledgement: We thank S. Cremer for statistical analysis, K. Hirsch for technical
assistance, D. Critchley for talin1-deficient mice and R. Fässler for integrindeficient
mice, discussions and critical reading of the manuscript. This work was supported
by the German Research Foundation, the Peter Hans Hofschneider Foundation for Experimental
Biomedicine, the Max Planck Society, the Alexander von Humboldt Foundation and the
allergology programme of the Landesstiftung Baden-Württemberg.
author:
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Kathrin
full_name: Schumann, Kathrin
id: F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F
last_name: Schumann
- first_name: Michele
full_name: Weber, Michele
id: 3A3FC708-F248-11E8-B48F-1D18A9856A87
last_name: Weber
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Holger
full_name: Pflicke, Holger
last_name: Pflicke
- first_name: Matthieu
full_name: Piel, Matthieu
last_name: Piel
- first_name: Julien
full_name: Polleux, Julien
last_name: Polleux
- first_name: Joachim
full_name: Spatz, Joachim
last_name: Spatz
- 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: Renkawitz J, Schumann K, Weber M, et al. Adaptive force transmission in amoeboid
cell migration. Nature Cell Biology. 2009;11(12):1438-1443. doi:10.1038/ncb1992
apa: Renkawitz, J., Schumann, K., Weber, M., Lämmermann, T., Pflicke, H., Piel,
M., … Sixt, M. K. (2009). Adaptive force transmission in amoeboid cell migration.
Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb1992
chicago: Renkawitz, Jörg, Kathrin Schumann, Michele Weber, Tim Lämmermann, Holger
Pflicke, Matthieu Piel, Julien Polleux, Joachim Spatz, and Michael K Sixt. “Adaptive
Force Transmission in Amoeboid Cell Migration.” Nature Cell Biology. Nature
Publishing Group, 2009. https://doi.org/10.1038/ncb1992.
ieee: J. Renkawitz et al., “Adaptive force transmission in amoeboid cell
migration,” Nature Cell Biology, vol. 11, no. 12. Nature Publishing Group,
pp. 1438–1443, 2009.
ista: Renkawitz J, Schumann K, Weber M, Lämmermann T, Pflicke H, Piel M, Polleux
J, Spatz J, Sixt MK. 2009. Adaptive force transmission in amoeboid cell migration.
Nature Cell Biology. 11(12), 1438–1443.
mla: Renkawitz, Jörg, et al. “Adaptive Force Transmission in Amoeboid Cell Migration.”
Nature Cell Biology, vol. 11, no. 12, Nature Publishing Group, 2009, pp.
1438–43, doi:10.1038/ncb1992.
short: J. Renkawitz, K. Schumann, M. Weber, T. Lämmermann, H. Pflicke, M. Piel,
J. Polleux, J. Spatz, M.K. Sixt, Nature Cell Biology 11 (2009) 1438–1443.
date_created: 2018-12-11T12:06:05Z
date_published: 2009-11-15T00:00:00Z
date_updated: 2021-01-12T07:53:27Z
day: '15'
doi: 10.1038/ncb1992
extern: '1'
intvolume: ' 11'
issue: '12'
language:
- iso: eng
month: '11'
oa_version: None
page: 1438 - 1443
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '2173'
status: public
title: Adaptive force transmission in amoeboid cell migration
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2009'
...
---
_id: '3955'
abstract:
- lang: eng
text: Although both processes occur at similar rates, leukocyte extravasation from
the blood circulation is well investigated, whereas intravasation into lymphatic
vessels has hardly been studied. In contrast to a common assumption-that intra-
and extravasation follow similar molecular principles-we previously showed that
lymphatic entry of dendritic cells (DCs) does not require integrin-mediated adhesive
interactions. In this study, we demonstrate that DC-entry is also independent
of pericellular proteolysis, raising the question of whether lymphatic vessels
offer preexisting entry routes. We find that the perilymphatic basement membrane
of initial lymphatic vessels is discontinuous and therefore leaves gaps for entering
cells. Using a newly developed in situ live cell imaging approach that allows
us to dynamically visualize the cells and their extracellular environment, we
demonstrate that DCs enter through these discontinuities, which are transiently
mechanically dilated by the passaging cells. We further show that penetration
of the underlying lymphatic endothelial layer occurs through flap valves lacking
continuous intercellular junctions. Together, we demonstrate free cellular communication
between interstitium and lymphatic lumen.
author:
- first_name: Holger
full_name: Pflicke, Holger
last_name: Pflicke
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Pflicke H, Sixt MK. Preformed portals facilitate dendritic cell entry into
afferent lymphatic vessels. The Journal of Experimental Medicine. 2009;206(13):2925-2935.
doi:10.1084/jem.20091739
apa: Pflicke, H., & Sixt, M. K. (2009). Preformed portals facilitate dendritic
cell entry into afferent lymphatic vessels. The Journal of Experimental Medicine.
Rockefeller University Press. https://doi.org/10.1084/jem.20091739
chicago: Pflicke, Holger, and Michael K Sixt. “Preformed Portals Facilitate Dendritic
Cell Entry into Afferent Lymphatic Vessels.” The Journal of Experimental Medicine.
Rockefeller University Press, 2009. https://doi.org/10.1084/jem.20091739.
ieee: H. Pflicke and M. K. Sixt, “Preformed portals facilitate dendritic cell entry
into afferent lymphatic vessels,” The Journal of Experimental Medicine,
vol. 206, no. 13. Rockefeller University Press, pp. 2925–2935, 2009.
ista: Pflicke H, Sixt MK. 2009. Preformed portals facilitate dendritic cell entry
into afferent lymphatic vessels. The Journal of Experimental Medicine. 206(13),
2925–2935.
mla: Pflicke, Holger, and Michael K. Sixt. “Preformed Portals Facilitate Dendritic
Cell Entry into Afferent Lymphatic Vessels.” The Journal of Experimental Medicine,
vol. 206, no. 13, Rockefeller University Press, 2009, pp. 2925–35, doi:10.1084/jem.20091739.
short: H. Pflicke, M.K. Sixt, The Journal of Experimental Medicine 206 (2009) 2925–2935.
date_created: 2018-12-11T12:06:05Z
date_published: 2009-12-07T00:00:00Z
date_updated: 2021-01-12T07:53:27Z
day: '07'
doi: 10.1084/jem.20091739
extern: 1
intvolume: ' 206'
issue: '13'
month: '12'
page: 2925 - 2935
publication: The Journal of Experimental Medicine
publication_status: published
publisher: Rockefeller University Press
publist_id: '2172'
quality_controlled: 0
status: public
title: Preformed portals facilitate dendritic cell entry into afferent lymphatic vessels
type: journal_article
volume: 206
year: '2009'
...
---
_id: '3966'
abstract:
- lang: eng
text: 'Persistent homology has proven to be a useful tool in a variety of contexts,
including the recognition and measurement of shape characteristics of surfaces
in ℝ3. Persistence pairs homology classes that are born and die in a filtration
of a topological space, but does not pair its actual homology classes. For the
sublevelset filtration of a surface in ℝ3, persistence has been extended to a
pairing of essential classes using Reeb graphs. In this paper, we give an algebraic
formulation that extends persistence to essential homology for any filtered space,
present an algorithm to calculate it, and describe how it aids our ability to
recognize shape features for codimension 1 submanifolds of Euclidean space. The
extension derives from Poincaré duality but generalizes to nonmanifold spaces.
We prove stability for general triangulated spaces and duality as well as symmetry
for triangulated manifolds. '
acknowledgement: Research by all three authors is partially supported by DARPA under
grant HR0011-05-1-0007. Research by the second author is also partially supported
by NSF under grant CCR-00-86013.
author:
- first_name: David
full_name: Cohen-Steiner, David
last_name: Cohen Steiner
- first_name: Herbert
full_name: Herbert Edelsbrunner
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: Cohen Steiner D, Edelsbrunner H, Harer J. Extending persistence using Poincare
and Lefschetz duality. Foundations of Computational Mathematics. 2009;9(1):79-103.
doi:10.1007/s10208-008-9027-z
apa: Cohen Steiner, D., Edelsbrunner, H., & Harer, J. (2009). Extending persistence
using Poincare and Lefschetz duality. Foundations of Computational Mathematics.
Springer. https://doi.org/10.1007/s10208-008-9027-z
chicago: Cohen Steiner, David, Herbert Edelsbrunner, and John Harer. “Extending
Persistence Using Poincare and Lefschetz Duality.” Foundations of Computational
Mathematics. Springer, 2009. https://doi.org/10.1007/s10208-008-9027-z.
ieee: D. Cohen Steiner, H. Edelsbrunner, and J. Harer, “Extending persistence using
Poincare and Lefschetz duality,” Foundations of Computational Mathematics,
vol. 9, no. 1. Springer, pp. 79–103, 2009.
ista: Cohen Steiner D, Edelsbrunner H, Harer J. 2009. Extending persistence using
Poincare and Lefschetz duality. Foundations of Computational Mathematics. 9(1),
79–103.
mla: Cohen Steiner, David, et al. “Extending Persistence Using Poincare and Lefschetz
Duality.” Foundations of Computational Mathematics, vol. 9, no. 1, Springer,
2009, pp. 79–103, doi:10.1007/s10208-008-9027-z.
short: D. Cohen Steiner, H. Edelsbrunner, J. Harer, Foundations of Computational
Mathematics 9 (2009) 79–103.
date_created: 2018-12-11T12:06:10Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:32Z
day: '01'
doi: 10.1007/s10208-008-9027-z
extern: 1
intvolume: ' 9'
issue: '1'
month: '01'
page: 79 - 103
publication: Foundations of Computational Mathematics
publication_status: published
publisher: Springer
publist_id: '2162'
quality_controlled: 0
status: public
title: Extending persistence using Poincare and Lefschetz duality
type: journal_article
volume: 9
year: '2009'
...
---
_id: '3967'
abstract:
- lang: eng
text: Motivated by the measurement of local homology and of functions on noisy domains,
we extend the notion of persistent homology to sequences of kernels, images, and
cokernels of maps induced by inclusions in a filtration of pairs of spaces. Specifically,
we note that persistence in this context is well defined, we prove that the persistence
diagrams are stable, and we explain how to compute them.
author:
- first_name: David
full_name: Cohen-Steiner, David
last_name: Cohen Steiner
- first_name: Herbert
full_name: Herbert Edelsbrunner
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: Dmitriy
full_name: Morozov, Dmitriy
last_name: Morozov
citation:
ama: 'Cohen Steiner D, Edelsbrunner H, Harer J, Morozov D. Persistent homology for
kernels, images, and cokernels. In: SIAM; 2009:1011-1020.'
apa: 'Cohen Steiner, D., Edelsbrunner, H., Harer, J., & Morozov, D. (2009).
Persistent homology for kernels, images, and cokernels (pp. 1011–1020). Presented
at the SODA: Symposium on Discrete Algorithms, SIAM.'
chicago: Cohen Steiner, David, Herbert Edelsbrunner, John Harer, and Dmitriy Morozov.
“Persistent Homology for Kernels, Images, and Cokernels,” 1011–20. SIAM, 2009.
ieee: 'D. Cohen Steiner, H. Edelsbrunner, J. Harer, and D. Morozov, “Persistent
homology for kernels, images, and cokernels,” presented at the SODA: Symposium
on Discrete Algorithms, 2009, pp. 1011–1020.'
ista: 'Cohen Steiner D, Edelsbrunner H, Harer J, Morozov D. 2009. Persistent homology
for kernels, images, and cokernels. SODA: Symposium on Discrete Algorithms, 1011–1020.'
mla: Cohen Steiner, David, et al. Persistent Homology for Kernels, Images, and
Cokernels. SIAM, 2009, pp. 1011–20.
short: D. Cohen Steiner, H. Edelsbrunner, J. Harer, D. Morozov, in:, SIAM, 2009,
pp. 1011–1020.
conference:
name: 'SODA: Symposium on Discrete Algorithms'
date_created: 2018-12-11T12:06:10Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:32Z
day: '01'
extern: 1
month: '01'
page: 1011 - 1020
publication_status: published
publisher: SIAM
publist_id: '2159'
quality_controlled: 0
status: public
title: Persistent homology for kernels, images, and cokernels
type: conference
year: '2009'
...
---
_id: '3968'
abstract:
- lang: eng
text: We describe an algorithm for segmenting three-dimensional medical imaging
data modeled as a continuous function on a 3-manifold. It is related to watershed
algorithms developed in image processing but is closer to its mathematical roots,
which are Morse theory and homological algebra. It allows for the implicit treatment
of an underlying mesh, thus combining the structural integrity of its mathematical
foundations with the computational efficiency of image processing.
acknowledgement: This research was partially supported by Geomagic, Inc., and by the
Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0007
and HR0011-05-1-0057.
alternative_title:
- LNCS
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. The persistent Morse complex segmentation of a 3-manifold.
In: Vol 5903. Springer; 2009:36-50. doi:10.1007/978-3-642-10470-1_4'
apa: 'Edelsbrunner, H., & Harer, J. (2009). The persistent Morse complex segmentation
of a 3-manifold (Vol. 5903, pp. 36–50). Presented at the 3DPH: Modelling the Physiological
Human, Zermatt, Switzerland: Springer. https://doi.org/10.1007/978-3-642-10470-1_4'
chicago: Edelsbrunner, Herbert, and John Harer. “The Persistent Morse Complex Segmentation
of a 3-Manifold,” 5903:36–50. Springer, 2009. https://doi.org/10.1007/978-3-642-10470-1_4.
ieee: 'H. Edelsbrunner and J. Harer, “The persistent Morse complex segmentation
of a 3-manifold,” presented at the 3DPH: Modelling the Physiological Human, Zermatt,
Switzerland, 2009, vol. 5903, pp. 36–50.'
ista: 'Edelsbrunner H, Harer J. 2009. The persistent Morse complex segmentation
of a 3-manifold. 3DPH: Modelling the Physiological Human, LNCS, vol. 5903, 36–50.'
mla: Edelsbrunner, Herbert, and John Harer. The Persistent Morse Complex Segmentation
of a 3-Manifold. Vol. 5903, Springer, 2009, pp. 36–50, doi:10.1007/978-3-642-10470-1_4.
short: H. Edelsbrunner, J. Harer, in:, Springer, 2009, pp. 36–50.
conference:
end_date: 2009-12-02
location: Zermatt, Switzerland
name: '3DPH: Modelling the Physiological Human'
start_date: 2009-11-29
date_created: 2018-12-11T12:06:10Z
date_published: 2009-11-17T00:00:00Z
date_updated: 2021-01-12T07:53:32Z
day: '17'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/978-3-642-10470-1_4
file:
- access_level: open_access
checksum: 11fc85bcc19bab1f020e706a4b8a4660
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:33Z
date_updated: 2020-07-14T12:46:21Z
file_id: '4694'
file_name: IST-2016-535-v1+1_2009-P-04-3ManifoldSegmentation.pdf
file_size: 165090
relation: main_file
file_date_updated: 2020-07-14T12:46:21Z
has_accepted_license: '1'
intvolume: ' 5903'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 36 - 50
publication_status: published
publisher: Springer
publist_id: '2160'
pubrep_id: '535'
quality_controlled: '1'
scopus_import: 1
status: public
title: The persistent Morse complex segmentation of a 3-manifold
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5903
year: '2009'
...
---
_id: '4136'
abstract:
- lang: eng
text: 'Populations living in a spatially and temporally changing environment can
adapt to the changing optimum and/or migrate toward favorable habitats. Here we
extend previous analyses with a static optimum to allow the environment to vary
in time as well as in space. The model follows both population dynamics and the
trait mean under stabilizing selection, and the outcomes can be understood by
comparing the loads due to genetic variance, dispersal, and temporal change. With
fixed genetic variance, we obtain two regimes: (1) adaptation that is uniform
along the environmental gradient and that responds to the moving optimum as expected
for panmictic populations and when the spatial gradient is sufficiently steep,
and (2) a population with limited range that adapts more slowly than the environmental
optimum changes in both time and space; the population therefore becomes locally
extinct and migrates toward suitable habitat. We also use a population‐genetic
model with many loci to allow genetic variance to evolve, and we show that the
only solution now has uniform adaptation.'
article_processing_charge: No
article_type: original
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- 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: Glenn
full_name: Marion, Glenn
last_name: Marion
citation:
ama: 'Polechova J, Barton NH, Marion G. Species’ range: Adaptation in space and
time. American Naturalist. 2009;174(5):E186-E204. doi:10.1086/605958'
apa: 'Polechova, J., Barton, N. H., & Marion, G. (2009). Species’ range: Adaptation
in space and time. American Naturalist. University of Chicago Press. https://doi.org/10.1086/605958'
chicago: 'Polechova, Jitka, Nicholas H Barton, and Glenn Marion. “Species’ Range:
Adaptation in Space and Time.” American Naturalist. University of Chicago
Press, 2009. https://doi.org/10.1086/605958.'
ieee: 'J. Polechova, N. H. Barton, and G. Marion, “Species’ range: Adaptation in
space and time,” American Naturalist, vol. 174, no. 5. University of Chicago
Press, pp. E186–E204, 2009.'
ista: 'Polechova J, Barton NH, Marion G. 2009. Species’ range: Adaptation in space
and time. American Naturalist. 174(5), E186–E204.'
mla: 'Polechova, Jitka, et al. “Species’ Range: Adaptation in Space and Time.” American
Naturalist, vol. 174, no. 5, University of Chicago Press, 2009, pp. E186–204,
doi:10.1086/605958.'
short: J. Polechova, N.H. Barton, G. Marion, American Naturalist 174 (2009) E186–E204.
date_created: 2018-12-11T12:07:09Z
date_published: 2009-11-05T00:00:00Z
date_updated: 2021-01-12T07:54:46Z
day: '05'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1086/605958
external_id:
pmid:
- ' 19788353'
intvolume: ' 174'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.doi.org/10.1086/605958
month: '11'
oa: 1
oa_version: Published Version
page: E186 - E204
pmid: 1
publication: American Naturalist
publication_status: published
publisher: University of Chicago Press
publist_id: '1986'
pubrep_id: '552'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1086/659642
scopus_import: 1
status: public
title: 'Species'' range: Adaptation in space and time'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 174
year: '2009'
...
---
_id: '4143'
abstract:
- lang: eng
text: 'The migration of single cells and epithelial sheets is of great importance
for gastrulation and organ formation in developing embryos and, if misregulated,
can have dire consequences e.g. during cancer metastasis. A keystone of cell migration
is the regulation of adhesive contacts, which are dynamically assembled and disassembled
via endocytosis. Here, we discuss some of the basic concepts about the function
of endocytic trafficking during cell migration: transport of integrins from the
cell rear to the leading edge in fibroblasts; confinement of signalling to the
front of single cells by endocytic transport of growth factors; regulation of
movement coherence in multicellular sheets by cadherin turnover; and shaping of
extracellular chemokine gradients. Taken together, endocytosis enables migrating
cells and tissues to dynamically modulate their adhesion and signalling, allowing
them to efficiently migrate through their extracellular environment.'
article_processing_charge: No
author:
- first_name: Florian
full_name: Ulrich, Florian
last_name: Ulrich
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Ulrich F, Heisenberg C-PJ. Trafficking and cell migration. Traffic.
2009;10(7):811-818. doi:10.1111/j.1600-0854.2009.00929.x
apa: Ulrich, F., & Heisenberg, C.-P. J. (2009). Trafficking and cell migration.
Traffic. Wiley-Blackwell. https://doi.org/10.1111/j.1600-0854.2009.00929.x
chicago: Ulrich, Florian, and Carl-Philipp J Heisenberg. “Trafficking and Cell Migration.”
Traffic. Wiley-Blackwell, 2009. https://doi.org/10.1111/j.1600-0854.2009.00929.x.
ieee: F. Ulrich and C.-P. J. Heisenberg, “Trafficking and cell migration,” Traffic,
vol. 10, no. 7. Wiley-Blackwell, pp. 811–818, 2009.
ista: Ulrich F, Heisenberg C-PJ. 2009. Trafficking and cell migration. Traffic.
10(7), 811–818.
mla: Ulrich, Florian, and Carl-Philipp J. Heisenberg. “Trafficking and Cell Migration.”
Traffic, vol. 10, no. 7, Wiley-Blackwell, 2009, pp. 811–18, doi:10.1111/j.1600-0854.2009.00929.x.
short: F. Ulrich, C.-P.J. Heisenberg, Traffic 10 (2009) 811–818.
date_created: 2018-12-11T12:07:12Z
date_published: 2009-05-20T00:00:00Z
date_updated: 2021-01-12T07:54:49Z
day: '20'
doi: 10.1111/j.1600-0854.2009.00929.x
extern: '1'
intvolume: ' 10'
issue: '7'
language:
- iso: eng
month: '05'
oa_version: None
page: 811 - 818
publication: Traffic
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1976'
status: public
title: Trafficking and cell migration
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2009'
...