---
_id: '3745'
abstract:
- lang: eng
text: The precision of biochemical signaling is limited by randomness in the diffusive
arrival of molecules at their targets. For proteins binding to specific sites
on DNA and regulating transcription, the ability of the proteins to diffuse in
one dimension by sliding along the length of the DNA, in addition to their diffusion
in bulk solution, would seem to generate a larger target for DNA binding, consequently
reducing the noise in the occupancy of the regulatory site. Here we show that
this effect is largely canceled by the enhanced temporal correlations in one-dimensional
diffusion. With realistic parameters, sliding along DNA has surprisingly little
effect on the physical limits to the precision of transcriptional regulation.
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Tkačik G, Bialek W. Diffusion, dimensionality, and noise in transcriptional
regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics.
2009;79(5). doi:10.1103/PhysRevE.79.051901
apa: Tkačik, G., & Bialek, W. (2009). Diffusion, dimensionality, and noise in
transcriptional regulation. Physical Review E Statistical Nonlinear and Soft
Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.79.051901
chicago: Tkačik, Gašper, and William Bialek. “Diffusion, Dimensionality, and Noise
in Transcriptional Regulation.” Physical Review E Statistical Nonlinear and
Soft Matter Physics. American Institute of Physics, 2009. https://doi.org/10.1103/PhysRevE.79.051901.
ieee: G. Tkačik and W. Bialek, “Diffusion, dimensionality, and noise in transcriptional
regulation,” Physical Review E Statistical Nonlinear and Soft Matter Physics,
vol. 79, no. 5. American Institute of Physics, 2009.
ista: Tkačik G, Bialek W. 2009. Diffusion, dimensionality, and noise in transcriptional
regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 79(5).
mla: Tkačik, Gašper, and William Bialek. “Diffusion, Dimensionality, and Noise in
Transcriptional Regulation.” Physical Review E Statistical Nonlinear and Soft
Matter Physics, vol. 79, no. 5, American Institute of Physics, 2009, doi:10.1103/PhysRevE.79.051901.
short: G. Tkačik, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter
Physics 79 (2009).
date_created: 2018-12-11T12:04:56Z
date_published: 2009-05-04T00:00:00Z
date_updated: 2021-01-12T07:51:54Z
day: '04'
doi: 10.1103/PhysRevE.79.051901
extern: 1
intvolume: ' 79'
issue: '5'
month: '05'
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '2483'
quality_controlled: 0
status: public
title: Diffusion, dimensionality, and noise in transcriptional regulation
type: journal_article
volume: 79
year: '2009'
...
---
_id: '3747'
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: 'Tkačik G, Bialek W. Cell Biology: Networks, regulation, pathways. In: Meyers
R, ed. Encyclopedia of Complexity and Systems Science. Springer; 2009:719-741.
doi:10.1007/978-0-387-30440-3_48'
apa: 'Tkačik, G., & Bialek, W. (2009). Cell Biology: Networks, regulation, pathways.
In R. Meyers (Ed.), Encyclopedia of Complexity and Systems Science (pp.
719–741). Springer. https://doi.org/10.1007/978-0-387-30440-3_48'
chicago: 'Tkačik, Gašper, and William Bialek. “Cell Biology: Networks, Regulation,
Pathways.” In Encyclopedia of Complexity and Systems Science, edited by
R. Meyers, 719–41. Springer, 2009. https://doi.org/10.1007/978-0-387-30440-3_48.'
ieee: 'G. Tkačik and W. Bialek, “Cell Biology: Networks, regulation, pathways,”
in Encyclopedia of Complexity and Systems Science, R. Meyers, Ed. Springer,
2009, pp. 719–741.'
ista: 'Tkačik G, Bialek W. 2009.Cell Biology: Networks, regulation, pathways. In:
Encyclopedia of Complexity and Systems Science. , 719–741.'
mla: 'Tkačik, Gašper, and William Bialek. “Cell Biology: Networks, Regulation, Pathways.”
Encyclopedia of Complexity and Systems Science, edited by R. Meyers, Springer,
2009, pp. 719–41, doi:10.1007/978-0-387-30440-3_48.'
short: G. Tkačik, W. Bialek, in:, R. Meyers (Ed.), Encyclopedia of Complexity and
Systems Science, Springer, 2009, pp. 719–741.
date_created: 2018-12-11T12:04:56Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:51:54Z
day: '01'
doi: 10.1007/978-0-387-30440-3_48
editor:
- first_name: R.
full_name: Meyers,R. A.
last_name: Meyers
extern: 1
month: '01'
page: 719 - 741
publication: Encyclopedia of Complexity and Systems Science
publication_status: published
publisher: Springer
publist_id: '2481'
quality_controlled: 0
status: public
title: 'Cell Biology: Networks, regulation, pathways'
type: book_chapter
year: '2009'
...
---
_id: '3764'
abstract:
- lang: eng
text: 'We present a method for accurately tracking the moving surface of deformable
materials in a manner that gracefully handles topological changes. We employ a
Lagrangian surface tracking method, and we use a triangle mesh for our surface
representation so that fine features can be retained. We make topological changes
to the mesh by first identifying merging or splitting events at a particular grid
resolution, and then locally creating new pieces of the mesh in the affected cells
using a standard isosurface creation method. We stitch the new, topologically
simplified portion of the mesh to the rest of the mesh at the cell boundaries.
Our method detects and treats topological events with an emphasis on the preservation
of detailed features, while simultaneously simplifying those portions of the material
that are not visible. Our surface tracker is not tied to a particular method for
simulating deformable materials. In particular, we show results from two significantly
different simulators: a Lagrangian FEM simulator with tetrahedral elements, and
an Eulerian grid-based fluid simulator. Although our surface tracking method is
generic, it is particularly well-suited for simulations that exhibit fine surface
details and numerous topological events. Highlights of our results include merging
of viscoplastic materials with complex geometry, a taffy-pulling animation with
many fold and merge events, and stretching and slicing of stiff plastic material.'
article_processing_charge: No
author:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Nils
full_name: Thürey, Nils
last_name: Thürey
- first_name: Markus
full_name: Gross, Markus
last_name: Gross
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
citation:
ama: Wojtan C, Thürey N, Gross M, Turk G. Deforming meshes that split and merge.
ACM Transactions on Graphics. 2009;28(3). doi:10.1145/1531326.1531382
apa: Wojtan, C., Thürey, N., Gross, M., & Turk, G. (2009). Deforming meshes
that split and merge. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/1531326.1531382
chicago: Wojtan, Chris, Nils Thürey, Markus Gross, and Greg Turk. “Deforming Meshes
That Split and Merge.” ACM Transactions on Graphics. ACM, 2009. https://doi.org/10.1145/1531326.1531382.
ieee: C. Wojtan, N. Thürey, M. Gross, and G. Turk, “Deforming meshes that split
and merge,” ACM Transactions on Graphics, vol. 28, no. 3. ACM, 2009.
ista: Wojtan C, Thürey N, Gross M, Turk G. 2009. Deforming meshes that split and
merge. ACM Transactions on Graphics. 28(3).
mla: Wojtan, Chris, et al. “Deforming Meshes That Split and Merge.” ACM Transactions
on Graphics, vol. 28, no. 3, ACM, 2009, doi:10.1145/1531326.1531382.
short: C. Wojtan, N. Thürey, M. Gross, G. Turk, ACM Transactions on Graphics 28
(2009).
date_created: 2018-12-11T12:05:02Z
date_published: 2009-08-01T00:00:00Z
date_updated: 2023-02-23T11:41:39Z
day: '01'
doi: 10.1145/1531326.1531382
extern: '1'
intvolume: ' 28'
issue: '3'
language:
- iso: eng
month: '08'
oa_version: None
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '2466'
status: public
title: Deforming meshes that split and merge
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2009'
...
---
_id: '3768'
acknowledgement: 10.1093/bioinformatics/btn539
author:
- first_name: Anne
full_name: Anne Kupczok
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Arndt
full_name: von Haeseler,Arndt
last_name: Von Haeseler
citation:
ama: Kupczok A, Von Haeseler A. Comment on “{A} congruence index for testing topological
similarity between trees”. Bioinformatics. 2009;25(1):147-149. doi:4199
apa: Kupczok, A., & Von Haeseler, A. (2009). Comment on “{A} congruence index
for testing topological similarity between trees”. Bioinformatics. Oxford
University Press. https://doi.org/4199
chicago: Kupczok, Anne, and Arndt Von Haeseler. “Comment on ‘{A} Congruence Index
for Testing Topological Similarity between Trees’.” Bioinformatics. Oxford
University Press, 2009. https://doi.org/4199.
ieee: A. Kupczok and A. Von Haeseler, “Comment on ‘{A} congruence index for testing
topological similarity between trees’.,” Bioinformatics, vol. 25, no. 1.
Oxford University Press, pp. 147–149, 2009.
ista: Kupczok A, Von Haeseler A. 2009. Comment on ‘{A} congruence index for testing
topological similarity between trees’. Bioinformatics. 25(1), 147–149.
mla: Kupczok, Anne, and Arndt Von Haeseler. “Comment on ‘{A} Congruence Index for
Testing Topological Similarity between Trees’.” Bioinformatics, vol. 25,
no. 1, Oxford University Press, 2009, pp. 147–49, doi:4199.
short: A. Kupczok, A. Von Haeseler, Bioinformatics 25 (2009) 147–149.
date_created: 2018-12-11T12:05:04Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:03Z
day: '01'
doi: '4199'
extern: 1
intvolume: ' 25'
issue: '1'
month: '01'
page: 147 - 149
publication: Bioinformatics
publication_status: published
publisher: Oxford University Press
publist_id: '2459'
quality_controlled: 0
status: public
title: Comment on '{A} congruence index for testing topological similarity between
trees'.
type: journal_article
volume: 25
year: '2009'
...
---
_id: '3775'
abstract:
- lang: eng
text: There is a close analogy between statistical thermodynamics and the evolution
of allele frequencies under mutation, selection and random drift. Wright's formula
for the stationary distribution of allele frequencies is analogous to the Boltzmann
distribution in statistical physics. Population size, 2N, plays the role of the
inverse temperature, 1/kT, and determines the magnitude of random fluctuations.
Log mean fitness, View the MathML source, tends to increase under selection, and
is analogous to a (negative) energy; a potential function, U, increases under
mutation in a similar way. An entropy, SH, can be defined which measures the deviation
from the distribution of allele frequencies expected under random drift alone;
the sum View the MathML source gives a free fitness that increases as the population
evolves towards its stationary distribution. Usually, we observe the distribution
of a few quantitative traits that depend on the frequencies of very many alleles.
The mean and variance of such traits are analogous to observable quantities in
statistical thermodynamics. Thus, we can define an entropy, SΩ, which measures
the volume of allele frequency space that is consistent with the observed trait
distribution. The stationary distribution of the traits is View the MathML source;
this applies with arbitrary epistasis and dominance. The entropies SΩ, SH are
distinct, but converge when there are so many alleles that traits fluctuate close
to their expectations. Populations tend to evolve towards states that can be realised
in many ways (i.e., large SΩ), which may lead to a substantial drop below the
adaptive peak; we illustrate this point with a simple model of genetic redundancy.
This analogy with statistical thermodynamics brings together previous ideas in
a general framework, and justifies a maximum entropy approximation to the dynamics
of quantitative traits.
acknowledgement: "This work was supported by a Royal Society/Wolfson Award, and by
grants EP/T11753/01, EP/C546318/01 from the EPSRC.\r\nWe are grateful to M. Cates,
H.P. de Vladar and G. Sella, and to two anonymous referees, for their helpful comments."
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jason
full_name: Coe, Jason
last_name: Coe
citation:
ama: Barton NH, Coe J. On the application of statistical physics to evolutionary
biology. Journal of Theoretical Biology. 2009;259(2):317-324. doi:10.1016/j.jtbi.2009.03.019
apa: Barton, N. H., & Coe, J. (2009). On the application of statistical physics
to evolutionary biology. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2009.03.019
chicago: Barton, Nicholas H, and Jason Coe. “On the Application of Statistical Physics
to Evolutionary Biology.” Journal of Theoretical Biology. Elsevier, 2009.
https://doi.org/10.1016/j.jtbi.2009.03.019.
ieee: N. H. Barton and J. Coe, “On the application of statistical physics to evolutionary
biology,” Journal of Theoretical Biology, vol. 259, no. 2. Elsevier, pp.
317–324, 2009.
ista: Barton NH, Coe J. 2009. On the application of statistical physics to evolutionary
biology. Journal of Theoretical Biology. 259(2), 317–324.
mla: Barton, Nicholas H., and Jason Coe. “On the Application of Statistical Physics
to Evolutionary Biology.” Journal of Theoretical Biology, vol. 259, no.
2, Elsevier, 2009, pp. 317–24, doi:10.1016/j.jtbi.2009.03.019.
short: N.H. Barton, J. Coe, Journal of Theoretical Biology 259 (2009) 317–324.
date_created: 2018-12-11T12:05:06Z
date_published: 2009-07-21T00:00:00Z
date_updated: 2021-01-12T07:52:06Z
day: '21'
department:
- _id: NiBa
doi: 10.1016/j.jtbi.2009.03.019
intvolume: ' 259'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-00554594/document
month: '07'
oa: 1
oa_version: Submitted Version
page: 317 - 324
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '2452'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the application of statistical physics to evolutionary biology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 259
year: '2009'
...
---
_id: '3780'
abstract:
- lang: eng
text: Why are sinistral snails so rare? Two main hypotheses are that selection acts
against the establishment of new coiling morphs, because dextral and sinistral
snails have trouble mating, or else a developmental constraint prevents the establishment
of sinistrals. We therefore used an isolate of the snail Lymnaea stagnalis, in
which sinistrals are rare, and populations of Partula suturalis, in which sinistrals
are common, as well as a mathematical model, to understand the circumstances by
which new morphs evolve. The main finding is that the sinistral genotype is associated
with reduced egg viability in L. stagnalis, but in P. suturalis individuals of
sinistral and dextral genotype appear equally fecund, implying a lack of a constraint.
As positive frequency-dependent selection against the rare chiral morph in P.
suturalis also operates over a narrow range (< 3%), the results suggest a model
for chiral evolution in snails in which weak positive frequency-dependent selection
may be overcome by a negative frequency-dependent selection, such as reproductive
character displacement. In snails, there is not always a developmental constraint.
As the direction of cleavage, and thus the directional asymmetry of the entire
body, does not generally vary in other Spiralia (annelids, echiurans, vestimentiferans,
sipunculids and nemerteans), it remains an open question as to whether this is
because of a constraint and/or because most taxa do not have a conspicuous external
asymmetry (like a shell) upon which selection can act.
acknowledgement: We owe a great debt to Jim Murray for his many contributions to the
study of Partula, in the field, in the laboratory, in the interpretation of data,
and in generating new ideas about evolution. With pleasure and respect we dedicate
this paper to him. Jim Murray played a leading role in making the collections used
here. We are very grateful also to Ann Clarke and Elizabeth Murray for help with
collecting, to Lorna Stewart for snail dissections, to Joris Koene for the gift
of snails, to Natasha Constant for entering the data, and Takahiro Asami, Edmund
Gittenberger and Gerhard Falkner for establishing the sinistral stock of L. stagnalis.
Comments from an anonymous referee, A. Richard Palmer and the editorial board improved
the manuscript. Work in the field was supported by the Royal Society, The Carnegie
Trust, the Percy Sladen Trust and the National Science Foundation. The Science Research
Council (B/SR/4144), the National Science Foundation (GB-4188), the Royal Society
and the University of Nottingham supported work in the laboratory.
author:
- first_name: Angus
full_name: Davison, Angus
last_name: Davison
- 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: Bryan
full_name: Clarke, Bryan
last_name: Clarke
citation:
ama: 'Davison A, Barton NH, Clarke B. The effect of chirality phenotype and genotype
on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications
for the evolution of sinistral snails. Journal of Evolutionary Biology.
2009;22(8):1624-1635. doi:10.1111/j.1420-9101.2009.01770.x'
apa: 'Davison, A., Barton, N. H., & Clarke, B. (2009). The effect of chirality
phenotype and genotype on the fecundity and viability of Partula suturalis and
Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal
of Evolutionary Biology. Wiley. https://doi.org/10.1111/j.1420-9101.2009.01770.x'
chicago: 'Davison, Angus, Nicholas H Barton, and Bryan Clarke. “The Effect of Chirality
Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and
Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” Journal
of Evolutionary Biology. Wiley, 2009. https://doi.org/10.1111/j.1420-9101.2009.01770.x.'
ieee: 'A. Davison, N. H. Barton, and B. Clarke, “The effect of chirality phenotype
and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis:
Implications for the evolution of sinistral snails,” Journal of Evolutionary
Biology, vol. 22, no. 8. Wiley, pp. 1624–1635, 2009.'
ista: 'Davison A, Barton NH, Clarke B. 2009. The effect of chirality phenotype and
genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis:
Implications for the evolution of sinistral snails. Journal of Evolutionary Biology.
22(8), 1624–1635.'
mla: 'Davison, Angus, et al. “The Effect of Chirality Phenotype and Genotype on
the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications
for the Evolution of Sinistral Snails.” Journal of Evolutionary Biology,
vol. 22, no. 8, Wiley, 2009, pp. 1624–35, doi:10.1111/j.1420-9101.2009.01770.x.'
short: A. Davison, N.H. Barton, B. Clarke, Journal of Evolutionary Biology 22 (2009)
1624–1635.
date_created: 2018-12-11T12:05:08Z
date_published: 2009-08-01T00:00:00Z
date_updated: 2021-01-12T07:52:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/j.1420-9101.2009.01770.x
file:
- access_level: open_access
checksum: f70c15c6ab9306121d4153a3be0d2346
content_type: application/pdf
creator: dernst
date_created: 2019-02-22T09:21:44Z
date_updated: 2020-07-14T12:46:15Z
file_id: '6044'
file_name: Davison_JEB_v31_2009.pdf
file_size: 2583812
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 22'
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 1624 - 1635
publication: Journal of Evolutionary Biology
publication_status: published
publisher: Wiley
publist_id: '2447'
pubrep_id: '553'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The effect of chirality phenotype and genotype on the fecundity and viability
of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral
snails'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2009'
...
---
_id: '3828'
abstract:
- lang: eng
text: 'Glutamate receptors of the AMPA-subtype (AMPARs), together with the transmembrane
AMPAR regulatory proteins (TARPs), mediate fast excitatory synaptic transmission
in the mammalian brain. Here, we show by proteomic analysis that the majority
of AMPARs in the rat brain are coassembled with two members of the cornichon family
of transmembrane proteins, rather than with the TARPs. Coassembly with cornichon
homologs 2 and 3 affects AMPARs in two ways: Cornichons increase surface expression
of AMPARs, and they alter channel gating by markedly slowing deactivation and
desensitization kinetics. These results demonstrate that cornichons are intrinsic
auxiliary subunits of native AMPARs and provide previously unknown molecular determinants
for glutamatergic neurotransmission in the central nervous system.'
author:
- first_name: Jochen
full_name: Schwenk, Jochen
last_name: Schwenk
- first_name: Nadine
full_name: Harmel, Nadine
last_name: Harmel
- first_name: Gerd
full_name: Zolles, Gerd
last_name: Zolles
- first_name: Wolfgang
full_name: Bildl, Wolfgang
last_name: Bildl
- first_name: Ákos
full_name: Kulik, Ákos
last_name: Kulik
- first_name: Bernd
full_name: Heimrich, Bernd
last_name: Heimrich
- first_name: Osamu
full_name: Chisaka, Osamu
last_name: Chisaka
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Uwe
full_name: Schulte, Uwe
last_name: Schulte
- first_name: Bernd
full_name: Fakler, Bernd
last_name: Fakler
- first_name: Nikolaj
full_name: Klocker, Nikolaj
last_name: Klocker
citation:
ama: Schwenk J, Harmel N, Zolles G, et al. Functional proteomics identify cornichon
proteins as auxiliary subunits of AMPA receptors. Science. 2009;323(5919):1313-1319.
doi:10.1126/science.1167852
apa: Schwenk, J., Harmel, N., Zolles, G., Bildl, W., Kulik, Á., Heimrich, B., …
Klocker, N. (2009). Functional proteomics identify cornichon proteins as auxiliary
subunits of AMPA receptors. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1167852
chicago: Schwenk, Jochen, Nadine Harmel, Gerd Zolles, Wolfgang Bildl, Ákos Kulik,
Bernd Heimrich, Osamu Chisaka, et al. “Functional Proteomics Identify Cornichon
Proteins as Auxiliary Subunits of AMPA Receptors.” Science. American Association
for the Advancement of Science, 2009. https://doi.org/10.1126/science.1167852.
ieee: J. Schwenk et al., “Functional proteomics identify cornichon proteins
as auxiliary subunits of AMPA receptors,” Science, vol. 323, no. 5919.
American Association for the Advancement of Science, pp. 1313–9, 2009.
ista: Schwenk J, Harmel N, Zolles G, Bildl W, Kulik Á, Heimrich B, Chisaka O, Jonas
PM, Schulte U, Fakler B, Klocker N. 2009. Functional proteomics identify cornichon
proteins as auxiliary subunits of AMPA receptors. Science. 323(5919), 1313–9.
mla: Schwenk, Jochen, et al. “Functional Proteomics Identify Cornichon Proteins
as Auxiliary Subunits of AMPA Receptors.” Science, vol. 323, no. 5919,
American Association for the Advancement of Science, 2009, pp. 1313–19, doi:10.1126/science.1167852.
short: J. Schwenk, N. Harmel, G. Zolles, W. Bildl, Á. Kulik, B. Heimrich, O. Chisaka,
P.M. Jonas, U. Schulte, B. Fakler, N. Klocker, Science 323 (2009) 1313–9.
date_created: 2018-12-11T12:05:23Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:29Z
day: '01'
doi: 10.1126/science.1167852
extern: 1
intvolume: ' 323'
issue: '5919'
month: '01'
page: 1313 - 9
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '2382'
quality_controlled: 0
status: public
title: Functional proteomics identify cornichon proteins as auxiliary subunits of
AMPA receptors
type: journal_article
volume: 323
year: '2009'
...
---
_id: '3835'
abstract:
- lang: eng
text: Many specifications include assumptions on the environment. If the environment
satisfies the assumptions then a correct system reacts as intended. However, when
the environment deviates from its expected behavior, a correct system can behave
arbitrarily. We want to synthesize robust systems that degrade gracefully, i.e.,
a small number of environment failures should induce a small number of system
failures. We define ratio games and show that an optimal robust system corresponds
to the winning strategy of a ratio game, where the system minimizes the ratio
of system errors to environment errors. We show that ratio games can be solved
in pseudopolynomial time.
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 Combest,
Quasimodo, and Gasics projects, 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.
article_processing_charge: No
author:
- first_name: Roderick
full_name: Bloem, Roderick
last_name: Bloem
- first_name: Karin
full_name: Greimel, Karin
last_name: Greimel
- 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: 'Bloem R, Greimel K, Henzinger TA, Jobstmann B. Synthesizing robust systems.
In: Springer; 2009:85-92. doi:10.1109/FMCAD.2009.5351139'
apa: 'Bloem, R., Greimel, K., Henzinger, T. A., & Jobstmann, B. (2009). Synthesizing
robust systems (pp. 85–92). Presented at the FMCAD: Formal Methods in Computer-Aided
Design, Springer. https://doi.org/10.1109/FMCAD.2009.5351139'
chicago: Bloem, Roderick, Karin Greimel, Thomas A Henzinger, and Barbara Jobstmann.
“Synthesizing Robust Systems,” 85–92. Springer, 2009. https://doi.org/10.1109/FMCAD.2009.5351139.
ieee: 'R. Bloem, K. Greimel, T. A. Henzinger, and B. Jobstmann, “Synthesizing robust
systems,” presented at the FMCAD: Formal Methods in Computer-Aided Design, 2009,
pp. 85–92.'
ista: 'Bloem R, Greimel K, Henzinger TA, Jobstmann B. 2009. Synthesizing robust
systems. FMCAD: Formal Methods in Computer-Aided Design, 85–92.'
mla: Bloem, Roderick, et al. Synthesizing Robust Systems. Springer, 2009,
pp. 85–92, doi:10.1109/FMCAD.2009.5351139.
short: R. Bloem, K. Greimel, T.A. Henzinger, B. Jobstmann, in:, Springer, 2009,
pp. 85–92.
conference:
name: 'FMCAD: Formal Methods in Computer-Aided Design'
date_created: 2018-12-11T12:05:26Z
date_published: 2009-12-11T00:00:00Z
date_updated: 2022-03-21T08:25:44Z
day: '11'
doi: 10.1109/FMCAD.2009.5351139
extern: '1'
language:
- iso: eng
month: '12'
oa_version: None
page: 85 - 92
publication_status: published
publisher: Springer
publist_id: '2373'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synthesizing robust systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2009'
...
---
_id: '3837'
abstract:
- lang: eng
text: In this paper we extend the work of Alfaro, Henzinger et al. on interface
theories for component-based design. Existing interface theories often fail to
capture functional relations between the inputs and outputs of an interface. For
example, a simple synchronous interface that takes as input a number n ≥ 0 and
returns, at the same time, as output n + 1, cannot be expressed in existing theories.
In this paper we provide a theory of relational interfaces, where such input-output
relations can be captured. Our theory supports synchronous interfaces, both stateless
and stateful. It includes explicit notions of environments and pluggability, and
satisfies fundamental properties such as preservation of refinement by composition,
and characterization of pluggability by refinement. We achieve these properties
by making reasonable restrictions on feedback loops in interface compositions.
acknowledgement: 'This work is supported by the Center for Hybrid and Embedded Software
Systems (CHESS) at UC Berkeley, which receives support from the National Science
Foundation (NSF awards #0720882 (CSR-EHS: PRET) and #0720841 (CSR-CPS)), the U.S.
Army Research Office (ARO #W911NF-07-2-0019), the U.S. Air Force Office of Scientific
Research (MURI #FA9550-06-0312), the Air Force Research Lab (AFRL), the State of
California Micro Program, and the following companies: Agilent, Bosch, Lockheed-Martin,
National Instruments, Thales and Toyota. This work is also supported by the COMBEST
and ArtistDesign projects of the European Union, and the Swiss National Science
Foundation. '
author:
- first_name: Stavros
full_name: Tripakis, Stavros
last_name: Tripakis
- first_name: Ben
full_name: Lickly, Ben
last_name: Lickly
- 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: Edward
full_name: Lee, Edward
last_name: Lee
citation:
ama: 'Tripakis S, Lickly B, Henzinger TA, Lee E. On relational interfaces. In: EMSOFT
’09 Proceedings of the Seventh ACM International Conference on Embedded Software.
ACM; 2009:67-76. doi:10.1145/1629335.1629346'
apa: 'Tripakis, S., Lickly, B., Henzinger, T. A., & Lee, E. (2009). On relational
interfaces. In EMSOFT ’09 Proceedings of the seventh ACM international conference
on Embedded software (pp. 67–76). Grenoble, France: ACM. https://doi.org/10.1145/1629335.1629346'
chicago: Tripakis, Stavros, Ben Lickly, Thomas A Henzinger, and Edward Lee. “On
Relational Interfaces.” In EMSOFT ’09 Proceedings of the Seventh ACM International
Conference on Embedded Software, 67–76. ACM, 2009. https://doi.org/10.1145/1629335.1629346.
ieee: S. Tripakis, B. Lickly, T. A. Henzinger, and E. Lee, “On relational interfaces,”
in EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded
software, Grenoble, France, 2009, pp. 67–76.
ista: 'Tripakis S, Lickly B, Henzinger TA, Lee E. 2009. On relational interfaces.
EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded
software. EMSOFT: Embedded Software , 67–76.'
mla: Tripakis, Stavros, et al. “On Relational Interfaces.” EMSOFT ’09 Proceedings
of the Seventh ACM International Conference on Embedded Software, ACM, 2009,
pp. 67–76, doi:10.1145/1629335.1629346.
short: S. Tripakis, B. Lickly, T.A. Henzinger, E. Lee, in:, EMSOFT ’09 Proceedings
of the Seventh ACM International Conference on Embedded Software, ACM, 2009, pp.
67–76.
conference:
end_date: 2009-10-16
location: Grenoble, France
name: 'EMSOFT: Embedded Software '
start_date: 2009-10-12
date_created: 2018-12-11T12:05:26Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:33Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1145/1629335.1629346
ec_funded: 1
file:
- access_level: open_access
checksum: 3a70e21527dfaad2f198549ae5710786
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:57Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5045'
file_name: IST-2012-70-v1+1_On_Relational_Interfaces.pdf
file_size: 310902
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 67 - 76
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
publication: EMSOFT '09 Proceedings of the seventh ACM international conference on
Embedded software
publication_status: published
publisher: ACM
publist_id: '2360'
pubrep_id: '70'
quality_controlled: '1'
status: public
title: On relational interfaces
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2009'
...
---
_id: '3841'
abstract:
- lang: eng
text: 'We compare several languages for specifying Markovian population models such
as queuing networks and chemical reaction networks. These languages —matrix descriptions,
stochastic Petri nets, stoichiometric equations, stochastic process algebras,
and guarded command models— all describe continuous-time Markov chains, but they
differ according to important properties, such as compositionality, expressiveness
and succinctness, executability, ease of use, and the support they provide for
checking the well-formedness of a model and for analyzing a model. '
acknowledgement: This research was supported in part by the Excellence Cluster on
Multimodal Computing and Interaction and the Swiss National Science Foundation.
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
citation:
ama: 'Henzinger TA, Jobstmann B, Wolf V. Formalisms for specifying Markovian population
models. In: Vol 5797. Springer; 2009:3-23. doi:10.1007/978-3-642-04420-5_2'
apa: 'Henzinger, T. A., Jobstmann, B., & Wolf, V. (2009). Formalisms for specifying
Markovian population models (Vol. 5797, pp. 3–23). Presented at the RP: Reachability
Problems, Palaiseau, France: Springer. https://doi.org/10.1007/978-3-642-04420-5_2'
chicago: Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for
Specifying Markovian Population Models,” 5797:3–23. Springer, 2009. https://doi.org/10.1007/978-3-642-04420-5_2.
ieee: 'T. A. Henzinger, B. Jobstmann, and V. Wolf, “Formalisms for specifying Markovian
population models,” presented at the RP: Reachability Problems, Palaiseau, France,
2009, vol. 5797, pp. 3–23.'
ista: 'Henzinger TA, Jobstmann B, Wolf V. 2009. Formalisms for specifying Markovian
population models. RP: Reachability Problems, LNCS, vol. 5797, 3–23.'
mla: Henzinger, Thomas A., et al. Formalisms for Specifying Markovian Population
Models. Vol. 5797, Springer, 2009, pp. 3–23, doi:10.1007/978-3-642-04420-5_2.
short: T.A. Henzinger, B. Jobstmann, V. Wolf, in:, Springer, 2009, pp. 3–23.
conference:
end_date: 2009-09-25
location: Palaiseau, France
name: 'RP: Reachability Problems'
start_date: 2009-09-23
date_created: 2018-12-11T12:05:28Z
date_published: 2009-09-07T00:00:00Z
date_updated: 2023-02-23T11:24:49Z
day: '07'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-04420-5_2
file:
- access_level: open_access
checksum: df88431872586c773fbcfea37d7b36a2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:41Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4702'
file_name: IST-2012-67-v1+1_Formalisms_for_specifying_Markovian_population_models.pdf
file_size: 222840
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 5797'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 3 - 23
publication_status: published
publisher: Springer
publist_id: '2352'
pubrep_id: '67'
quality_controlled: '1'
related_material:
record:
- id: '3381'
relation: later_version
status: public
scopus_import: 1
status: public
title: Formalisms for specifying Markovian population models
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5797
year: '2009'
...
---
_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'
...