---
_id: '3962'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Holger
full_name: Pflicke, Holger
id: CAA57A9A-5B61-11E9-B130-E0C1E1F2C83D
last_name: Pflicke
citation:
ama: Pflicke H. Dendritic cell migration across basement membranes in the skin.
2010.
apa: Pflicke, H. (2010). Dendritic cell migration across basement membranes
in the skin. Institute of Science and Technology Austria.
chicago: Pflicke, Holger. “ Dendritic Cell Migration across Basement Membranes
in the Skin.” Institute of Science and Technology Austria, 2010.
ieee: H. Pflicke, “ Dendritic cell migration across basement membranes in the skin,”
Institute of Science and Technology Austria, 2010.
ista: Pflicke H. 2010. Dendritic cell migration across basement membranes in the
skin. Institute of Science and Technology Austria.
mla: Pflicke, Holger. Dendritic Cell Migration across Basement Membranes in
the Skin. Institute of Science and Technology Austria, 2010.
short: H. Pflicke, Dendritic Cell Migration across Basement Membranes in the Skin,
Institute of Science and Technology Austria, 2010.
date_created: 2018-12-11T12:06:08Z
date_published: 2010-07-01T00:00:00Z
date_updated: 2023-09-07T11:28:47Z
day: '01'
degree_awarded: PhD
department:
- _id: CaHe
- _id: GradSch
language:
- iso: eng
month: '07'
oa_version: None
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '2165'
status: public
supervisor:
- 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
title: "\uFEFF\uFEFFDendritic cell migration across basement membranes in the skin"
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2010'
...
---
_id: '3963'
abstract:
- lang: eng
text: Almost all species of the orchid genus Ophrys are pollinated by sexual deception.
The orchids mimic the sex pheromone of receptive female insects, mainly hymenopterans,
in order to attract males seeking to copulate. Most Ophrys species have achromatic
flowers, but some exhibit a coloured perianth and a bright, conspicuous labellum
pattern. We recently showed that the pink perianth of Ophrys heldreichii flowers
increases detectability by its pollinator, males of the long-horned bee Eucera
berlandi. Here we tested the hypothesis that the bright, complex labellum pattern
mimics the female of the pollinator to increase attractiveness toward males. In
a dual-choice test we offered E. berlandi males an O. heldreichii flower and a
flower from O. dictynnae, which also exhibits a pinkish perianth but no conspicuous
labellum pattern. Both flowers were housed in UV-transmitting acrylic glass boxes
to exclude olfactory signals. Males significantly preferred O. heldreichii to
O. dictynnae flowers. In a second experiment, we replaced the perianth of both
flowers with identical artificial perianths made from pink card, so that only
the labellum differed between the two flower stimuli. Males then chose between
both stimuli at random, suggesting that the presence of a labellum pattern does
not affect their choice. Spectral measurements revealed higher colour contrast
with the background of the perianth of O. heldreichii compared to O. dictynnae,
but no difference in green receptor-specific contrast or brightness. Our results
show that male choice is guided by the chromatic contrast of the perianth during
the initial flower approach but is not affected by the presence of a labellum
pattern. Instead, we hypothesise that the labellum pattern is involved in aversive
learning during post-copulatory behaviour and used by the orchid as a strategy
to increase outcrossing.
article_processing_charge: No
author:
- first_name: M.
full_name: Streinzer, M.
last_name: Streinzer
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
- first_name: H.
full_name: Paulus, H.
last_name: Paulus
- first_name: J.
full_name: Spaethe, J.
last_name: Spaethe
citation:
ama: Streinzer M, Ellis T, Paulus H, Spaethe J. Visual discrimination between two
sexually deceptive Ophrys species by a bee pollinator. Arthropod-Plant Interactions.
2010;4(3):141-148. doi:10.1007/s11829-010-9093-4
apa: Streinzer, M., Ellis, T., Paulus, H., & Spaethe, J. (2010). Visual discrimination
between two sexually deceptive Ophrys species by a bee pollinator. Arthropod-Plant
Interactions. Springer. https://doi.org/10.1007/s11829-010-9093-4
chicago: Streinzer, M., Thomas Ellis, H. Paulus, and J. Spaethe. “Visual Discrimination
between Two Sexually Deceptive Ophrys Species by a Bee Pollinator.” Arthropod-Plant
Interactions. Springer, 2010. https://doi.org/10.1007/s11829-010-9093-4.
ieee: M. Streinzer, T. Ellis, H. Paulus, and J. Spaethe, “Visual discrimination
between two sexually deceptive Ophrys species by a bee pollinator,” Arthropod-Plant
Interactions, vol. 4, no. 3. Springer, pp. 141–148, 2010.
ista: Streinzer M, Ellis T, Paulus H, Spaethe J. 2010. Visual discrimination between
two sexually deceptive Ophrys species by a bee pollinator. Arthropod-Plant Interactions.
4(3), 141–148.
mla: Streinzer, M., et al. “Visual Discrimination between Two Sexually Deceptive
Ophrys Species by a Bee Pollinator.” Arthropod-Plant Interactions, vol.
4, no. 3, Springer, 2010, pp. 141–48, doi:10.1007/s11829-010-9093-4.
short: M. Streinzer, T. Ellis, H. Paulus, J. Spaethe, Arthropod-Plant Interactions
4 (2010) 141–148.
date_created: 2018-12-11T12:06:08Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:30Z
day: '01'
doi: 10.1007/s11829-010-9093-4
extern: '1'
intvolume: ' 4'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '01'
oa_version: None
page: 141 - 148
publication: Arthropod-Plant Interactions
publication_status: published
publisher: Springer
publist_id: '2164'
status: public
title: Visual discrimination between two sexually deceptive Ophrys species by a bee
pollinator
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2010'
...
---
_id: '3964'
abstract:
- lang: eng
text: We prove two stability results for Lipschitz functions on triangulable, compact
metric spaces and consider applications of both to problems in systems biology.
Given two functions, the first result is formulated in terms of the Wasserstein
distance between their persistence diagrams and the second in terms of their total
persistence.
acknowledgement: This research is partially supported by the Defense Advanced Research
Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057 and by
CNRS under grant PICS-3416.
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: Yuriy
full_name: Mileyko, Yuriy
last_name: Mileyko
citation:
ama: Cohen Steiner D, Edelsbrunner H, Harer J, Mileyko Y. Lipschitz functions have
L_p-stable persistence. Foundations of Computational Mathematics. 2010;10(2):127-139.
doi:10.1007/s10208-010-9060-6
apa: Cohen Steiner, D., Edelsbrunner, H., Harer, J., & Mileyko, Y. (2010). Lipschitz
functions have L_p-stable persistence. Foundations of Computational Mathematics.
Springer. https://doi.org/10.1007/s10208-010-9060-6
chicago: Cohen Steiner, David, Herbert Edelsbrunner, John Harer, and Yuriy Mileyko.
“Lipschitz Functions Have L_p-Stable Persistence.” Foundations of Computational
Mathematics. Springer, 2010. https://doi.org/10.1007/s10208-010-9060-6.
ieee: D. Cohen Steiner, H. Edelsbrunner, J. Harer, and Y. Mileyko, “Lipschitz functions
have L_p-stable persistence,” Foundations of Computational Mathematics,
vol. 10, no. 2. Springer, pp. 127–139, 2010.
ista: Cohen Steiner D, Edelsbrunner H, Harer J, Mileyko Y. 2010. Lipschitz functions
have L_p-stable persistence. Foundations of Computational Mathematics. 10(2),
127–139.
mla: Cohen Steiner, David, et al. “Lipschitz Functions Have L_p-Stable Persistence.”
Foundations of Computational Mathematics, vol. 10, no. 2, Springer, 2010,
pp. 127–39, doi:10.1007/s10208-010-9060-6.
short: D. Cohen Steiner, H. Edelsbrunner, J. Harer, Y. Mileyko, Foundations of Computational
Mathematics 10 (2010) 127–139.
date_created: 2018-12-11T12:06:09Z
date_published: 2010-01-28T00:00:00Z
date_updated: 2021-01-12T07:53:31Z
day: '28'
doi: 10.1007/s10208-010-9060-6
extern: 1
intvolume: ' 10'
issue: '2'
month: '01'
page: 127 - 139
publication: Foundations of Computational Mathematics
publication_status: published
publisher: Springer
publist_id: '2163'
quality_controlled: 0
status: public
title: Lipschitz functions have L_p-stable persistence
type: journal_article
volume: 10
year: '2010'
...
---
_id: '4134'
abstract:
- lang: eng
text: 'All species are restricted in their distribution. Currently, ecological models
can only explain such limits if patches vary in quality, leading to asymmetrical
dispersal, or if genetic variation is too low at the margins for adaptation. However,
population genetic models suggest that the increase in genetic variance resulting
from dispersal should allow adaptation to almost any ecological gradient. Clearly
therefore, these models miss something that prevents evolution in natural populations.
We developed an individual-based simulation to explore stochastic effects in these
models. At high carrying capacities, our simulations largely agree with deterministic
predictions. However, when carrying capacity is low, the population fails to establish
for a wide range of parameter values where adaptation was expected from previous
models. Stochastic or transient effects appear critical around the boundaries
in parameter space between simulation behaviours. Dispersal, gradient steepness,
and population density emerge as key factors determining adaptation on an ecological
gradient. '
acknowledgement: We are very grateful to Nick Barton.
author:
- first_name: Jon
full_name: Bridle, Jon
last_name: Bridle
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Masakado
full_name: Kawata, Masakado
last_name: Kawata
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: Bridle J, Polechova J, Kawata M, Butlin R. Why is adaptation prevented at ecological
margins? New insights from individual-based simulations. Ecology Letters.
2010;13(4):485-494. doi:10.1111/j.1461-0248.2010.01442.x
apa: Bridle, J., Polechova, J., Kawata, M., & Butlin, R. (2010). Why is adaptation
prevented at ecological margins? New insights from individual-based simulations.
Ecology Letters. Wiley-Blackwell. https://doi.org/10.1111/j.1461-0248.2010.01442.x
chicago: Bridle, Jon, Jitka Polechova, Masakado Kawata, and Roger Butlin. “Why Is
Adaptation Prevented at Ecological Margins? New Insights from Individual-Based
Simulations.” Ecology Letters. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1461-0248.2010.01442.x.
ieee: J. Bridle, J. Polechova, M. Kawata, and R. Butlin, “Why is adaptation prevented
at ecological margins? New insights from individual-based simulations,” Ecology
Letters, vol. 13, no. 4. Wiley-Blackwell, pp. 485–494, 2010.
ista: Bridle J, Polechova J, Kawata M, Butlin R. 2010. Why is adaptation prevented
at ecological margins? New insights from individual-based simulations. Ecology
Letters. 13(4), 485–494.
mla: Bridle, Jon, et al. “Why Is Adaptation Prevented at Ecological Margins? New
Insights from Individual-Based Simulations.” Ecology Letters, vol. 13,
no. 4, Wiley-Blackwell, 2010, pp. 485–94, doi:10.1111/j.1461-0248.2010.01442.x.
short: J. Bridle, J. Polechova, M. Kawata, R. Butlin, Ecology Letters 13 (2010)
485–494.
date_created: 2018-12-11T12:07:08Z
date_published: 2010-03-15T00:00:00Z
date_updated: 2021-01-12T07:54:45Z
day: '15'
department:
- _id: NiBa
doi: 10.1111/j.1461-0248.2010.01442.x
ec_funded: 1
intvolume: ' 13'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 485 - 494
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Ecology Letters
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1987'
quality_controlled: '1'
scopus_import: 1
status: public
title: Why is adaptation prevented at ecological margins? New insights from individual-based
simulations
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2010'
...
---
_id: '4157'
abstract:
- lang: eng
text: Integrin- and cadherin-mediated adhesion is central for cell and tissue morphogenesis,
allowing cells and tissues to change shape without loosing integrity. Studies
predominantly in cell culture showed that mechanosensation through adhesion structures
is achieved by force-mediated modulation of their molecular composition. The specific
molecular composition of adhesion sites in turn determines their signalling activity
and dynamic reorganization. Here, we will review how adhesion sites respond to
mecanical stimuli, and how spatially and temporally regulated signalling from
different adhesion sites controls cell migration and tissue morphogenesis.
acknowledged_ssus:
- _id: Bio
author:
- first_name: Ekaterina
full_name: Papusheva, Ekaterina
id: 41DB591E-F248-11E8-B48F-1D18A9856A87
last_name: Papusheva
- 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: 'Papusheva E, Heisenberg C-PJ. Spatial organization of adhesion: force-dependent
regulation and function in tissue morphogenesis. EMBO Journal. 2010;29(16):2753-2768.
doi:10.1038/emboj.2010.182'
apa: 'Papusheva, E., & Heisenberg, C.-P. J. (2010). Spatial organization of
adhesion: force-dependent regulation and function in tissue morphogenesis. EMBO
Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2010.182'
chicago: 'Papusheva, Ekaterina, and Carl-Philipp J Heisenberg. “Spatial Organization
of Adhesion: Force-Dependent Regulation and Function in Tissue Morphogenesis.”
EMBO Journal. Wiley-Blackwell, 2010. https://doi.org/10.1038/emboj.2010.182.'
ieee: 'E. Papusheva and C.-P. J. Heisenberg, “Spatial organization of adhesion:
force-dependent regulation and function in tissue morphogenesis,” EMBO Journal,
vol. 29, no. 16. Wiley-Blackwell, pp. 2753–2768, 2010.'
ista: 'Papusheva E, Heisenberg C-PJ. 2010. Spatial organization of adhesion: force-dependent
regulation and function in tissue morphogenesis. EMBO Journal. 29(16), 2753–2768.'
mla: 'Papusheva, Ekaterina, and Carl-Philipp J. Heisenberg. “Spatial Organization
of Adhesion: Force-Dependent Regulation and Function in Tissue Morphogenesis.”
EMBO Journal, vol. 29, no. 16, Wiley-Blackwell, 2010, pp. 2753–68, doi:10.1038/emboj.2010.182.'
short: E. Papusheva, C.-P.J. Heisenberg, EMBO Journal 29 (2010) 2753–2768.
date_created: 2018-12-11T12:07:17Z
date_published: 2010-08-18T00:00:00Z
date_updated: 2021-01-12T07:54:55Z
day: '18'
department:
- _id: Bio
- _id: CaHe
doi: 10.1038/emboj.2010.182
external_id:
pmid:
- '20717145'
intvolume: ' 29'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2924654/
month: '08'
oa: 1
oa_version: Submitted Version
page: 2753 - 2768
pmid: 1
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1962'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Spatial organization of adhesion: force-dependent regulation and function
in tissue morphogenesis'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2010'
...
---
_id: '4163'
abstract:
- lang: eng
text: Organ formation requires the precise assembly of progenitor cells into a functional
multicellular structure. Mechanical forces probably participate in this process
but how they influence organ morphogenesis is still unclear. Here, we show that
Wnt11- and Prickle1a-mediated planar cell polarity (PCP) signalling coordinates
the formation of the zebrafish ciliated laterality organ (Kupffer's vesicle) by
regulating adhesion properties between organ progenitor cells (the dorsal forerunner
cells, DFCs). Combined inhibition of Wnt11 and Prickle1a reduces DFC cell-cell
adhesion and impairs their compaction and arrangement during vesicle lumen formation.
This leads to the formation of a mis-shapen vesicle with small fragmented lumina
and shortened cilia, resulting in severely impaired organ function and, as a consequence,
randomised laterality of both molecular and visceral asymmetries. Our results
reveal a novel role for PCP-dependent cell adhesion in coordinating the supracellular
organisation of progenitor cells during vertebrate laterality organ formation.
article_processing_charge: No
author:
- first_name: Pablo
full_name: Oteíza, Pablo
last_name: Oteíza
- first_name: Mathias
full_name: Koeppen, Mathias
last_name: Koeppen
- first_name: Michael
full_name: Krieg, Michael
last_name: Krieg
- first_name: Eduardo
full_name: Pulgar, Eduardo
last_name: Pulgar
- first_name: Cecilia
full_name: Farias, Cecilia
last_name: Farias
- first_name: Cristina
full_name: Melo, Cristina
last_name: Melo
- first_name: Steffen
full_name: Preibisch, Steffen
last_name: Preibisch
- first_name: Daniel
full_name: Mueller, Daniel
last_name: Mueller
- first_name: Masazumi
full_name: Tada, Masazumi
last_name: Tada
- first_name: Steffen
full_name: Hartel, Steffen
last_name: Hartel
- 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
- first_name: Miguel
full_name: Concha, Miguel
last_name: Concha
citation:
ama: Oteíza P, Koeppen M, Krieg M, et al. Planar cell polarity signalling regulates
cell adhesion properties in progenitors of the zebrafish laterality organ. Development.
2010;137(20):3459-3468. doi:10.1242/dev.049981
apa: Oteíza, P., Koeppen, M., Krieg, M., Pulgar, E., Farias, C., Melo, C., … Concha,
M. (2010). Planar cell polarity signalling regulates cell adhesion properties
in progenitors of the zebrafish laterality organ. Development. Company
of Biologists. https://doi.org/10.1242/dev.049981
chicago: Oteíza, Pablo, Mathias Koeppen, Michael Krieg, Eduardo Pulgar, Cecilia
Farias, Cristina Melo, Steffen Preibisch, et al. “Planar Cell Polarity Signalling
Regulates Cell Adhesion Properties in Progenitors of the Zebrafish Laterality
Organ.” Development. Company of Biologists, 2010. https://doi.org/10.1242/dev.049981.
ieee: P. Oteíza et al., “Planar cell polarity signalling regulates cell adhesion
properties in progenitors of the zebrafish laterality organ,” Development,
vol. 137, no. 20. Company of Biologists, pp. 3459–3468, 2010.
ista: Oteíza P, Koeppen M, Krieg M, Pulgar E, Farias C, Melo C, Preibisch S, Mueller
D, Tada M, Hartel S, Heisenberg C-PJ, Concha M. 2010. Planar cell polarity signalling
regulates cell adhesion properties in progenitors of the zebrafish laterality
organ. Development. 137(20), 3459–3468.
mla: Oteíza, Pablo, et al. “Planar Cell Polarity Signalling Regulates Cell Adhesion
Properties in Progenitors of the Zebrafish Laterality Organ.” Development,
vol. 137, no. 20, Company of Biologists, 2010, pp. 3459–68, doi:10.1242/dev.049981.
short: P. Oteíza, M. Koeppen, M. Krieg, E. Pulgar, C. Farias, C. Melo, S. Preibisch,
D. Mueller, M. Tada, S. Hartel, C.-P.J. Heisenberg, M. Concha, Development 137
(2010) 3459–3468.
date_created: 2018-12-11T12:07:20Z
date_published: 2010-10-15T00:00:00Z
date_updated: 2021-01-12T07:54:58Z
day: '15'
doi: 10.1242/dev.049981
extern: '1'
intvolume: ' 137'
issue: '20'
language:
- iso: eng
month: '10'
oa_version: None
page: 3459 - 3468
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '1958'
status: public
title: Planar cell polarity signalling regulates cell adhesion properties in progenitors
of the zebrafish laterality organ
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 137
year: '2010'
...
---
_id: '4187'
abstract:
- lang: eng
text: Cell migration is central to embryonic development, homeostasis and disease(1),
processes in which cells move as part of a group or individually. Whereas the
mechanisms controlling single-cell migration in vitro are relatively well understood(2-4),
less is known about the mechanisms promoting the motility of individual cells
in vivo. In particular, it is not clear how cells that form blebs in their migration
use those protrusions to bring about movement in the context of the three-dimensional
cellular environment(5,6). Here we show that the motility of chemokine-guided
germ cells within the zebrafish embryo requires the function of the small Rho
GTPases Rac1 and RhoA, as well as E-cadherin-mediated cell-cell adhesion. Using
fluorescence resonance energy transfer we demonstrate that Rac1 and RhoA are activated
in the cell front. At this location, Rac1 is responsible for the formation of
actin-rich structures, and RhoA promotes retrograde actin flow. We propose that
these actin-rich structures undergoing retrograde flow are essential for the generation
of E-cadherin-mediated traction forces between the germ cells and the surrounding
tissue and are therefore crucial for cell motility in vivo.
author:
- first_name: Elena
full_name: Kardash, Elena
last_name: Kardash
- first_name: Michal
full_name: Reichman-Fried, Michal
last_name: Reichman Fried
- first_name: Jean
full_name: Maître, Jean-Léon
last_name: Maître
- first_name: Bijan
full_name: Boldajipour, Bijan
last_name: Boldajipour
- first_name: Ekaterina
full_name: Ekaterina Papusheva
id: 41DB591E-F248-11E8-B48F-1D18A9856A87
last_name: Papusheva
- first_name: Esther
full_name: Messerschmidt, Esther-Maria
last_name: Messerschmidt
- first_name: Carl
full_name: Heisenberg, Carl-Philipp
last_name: Heisenberg
- first_name: Erez
full_name: Raz, Erez
last_name: Raz
citation:
ama: Kardash E, Reichman Fried M, Maître J, et al. A role for Rho GTPases and cell-cell
adhesion in single-cell motility in vivo. Nature Cell Biology. 2010;12(1):47-53.
doi:10.1038/ncb2003
apa: Kardash, E., Reichman Fried, M., Maître, J., Boldajipour, B., Papusheva, E.,
Messerschmidt, E., … Raz, E. (2010). A role for Rho GTPases and cell-cell adhesion
in single-cell motility in vivo. Nature Cell Biology. Nature Publishing
Group. https://doi.org/10.1038/ncb2003
chicago: Kardash, Elena, Michal Reichman Fried, Jean Maître, Bijan Boldajipour,
Ekaterina Papusheva, Esther Messerschmidt, Carl Heisenberg, and Erez Raz. “A Role
for Rho GTPases and Cell-Cell Adhesion in Single-Cell Motility in Vivo.” Nature
Cell Biology. Nature Publishing Group, 2010. https://doi.org/10.1038/ncb2003.
ieee: E. Kardash et al., “A role for Rho GTPases and cell-cell adhesion in
single-cell motility in vivo,” Nature Cell Biology, vol. 12, no. 1. Nature
Publishing Group, pp. 47–53, 2010.
ista: Kardash E, Reichman Fried M, Maître J, Boldajipour B, Papusheva E, Messerschmidt
E, Heisenberg C, Raz E. 2010. A role for Rho GTPases and cell-cell adhesion in
single-cell motility in vivo. Nature Cell Biology. 12(1), 47–53.
mla: Kardash, Elena, et al. “A Role for Rho GTPases and Cell-Cell Adhesion in Single-Cell
Motility in Vivo.” Nature Cell Biology, vol. 12, no. 1, Nature Publishing
Group, 2010, pp. 47–53, doi:10.1038/ncb2003.
short: E. Kardash, M. Reichman Fried, J. Maître, B. Boldajipour, E. Papusheva, E.
Messerschmidt, C. Heisenberg, E. Raz, Nature Cell Biology 12 (2010) 47–53.
date_created: 2018-12-11T12:07:28Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:09Z
day: '01'
doi: 10.1038/ncb2003
extern: 1
intvolume: ' 12'
issue: '1'
month: '01'
page: 47 - 53
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '1932'
quality_controlled: 0
status: public
title: A role for Rho GTPases and cell-cell adhesion in single-cell motility in vivo
type: journal_article
volume: 12
year: '2010'
...
---
_id: '4221'
abstract:
- lang: eng
text: Collective cell migration, the simultaneous movement of multiple cells that
are connected by cell-cell adhesion, is ubiquitous in development, tissue repair,
and tumor metastasis [1, 2]. It has been hypothesized that the directionality
of cell movement during collective migration emerges as a collective property
[3, 4]. Here we determine how movement directionality is established in collective
mesendoderm migration during zebrafish gastrulation. By interfering with two key
features of collective migration, (1) having neighboring cells and (2) adhering
to them, we show that individual mesendoderm cells are capable of normal directed
migration when moving as single cells but require cell-cell adhesion to participate
in coordinated and directed migration when moving as part of a group. We conclude
that movement directionality is not a de novo collective property of mesendoderm
cells but rather a property of single mesendoderm cells that requires cell-cell
adhesion during collective migration.
article_processing_charge: No
author:
- first_name: Yohanna
full_name: Arboleda Estudillo, Yohanna
last_name: Arboleda Estudillo
- first_name: Michael
full_name: Krieg, Michael
last_name: Krieg
- first_name: Jan
full_name: Stuehmer, Jan
last_name: Stuehmer
- first_name: Nicholas
full_name: Licata, Nicholas
last_name: Licata
- first_name: Daniel
full_name: Mueller, Daniel
last_name: Mueller
- 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: Arboleda Estudillo Y, Krieg M, Stuehmer J, Licata N, Mueller D, Heisenberg
C-PJ. Movement directionality in collective migration of germ layer progenitors.
Current Biology. 2010;20(2):161-169. doi:10.1016/j.cub.2009.11.036
apa: Arboleda Estudillo, Y., Krieg, M., Stuehmer, J., Licata, N., Mueller, D., &
Heisenberg, C.-P. J. (2010). Movement directionality in collective migration of
germ layer progenitors. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2009.11.036
chicago: Arboleda Estudillo, Yohanna, Michael Krieg, Jan Stuehmer, Nicholas Licata,
Daniel Mueller, and Carl-Philipp J Heisenberg. “Movement Directionality in Collective
Migration of Germ Layer Progenitors.” Current Biology. Cell Press, 2010.
https://doi.org/10.1016/j.cub.2009.11.036.
ieee: Y. Arboleda Estudillo, M. Krieg, J. Stuehmer, N. Licata, D. Mueller, and C.-P.
J. Heisenberg, “Movement directionality in collective migration of germ layer
progenitors,” Current Biology, vol. 20, no. 2. Cell Press, pp. 161–169,
2010.
ista: Arboleda Estudillo Y, Krieg M, Stuehmer J, Licata N, Mueller D, Heisenberg
C-PJ. 2010. Movement directionality in collective migration of germ layer progenitors.
Current Biology. 20(2), 161–169.
mla: Arboleda Estudillo, Yohanna, et al. “Movement Directionality in Collective
Migration of Germ Layer Progenitors.” Current Biology, vol. 20, no. 2,
Cell Press, 2010, pp. 161–69, doi:10.1016/j.cub.2009.11.036.
short: Y. Arboleda Estudillo, M. Krieg, J. Stuehmer, N. Licata, D. Mueller, C.-P.J.
Heisenberg, Current Biology 20 (2010) 161–169.
date_created: 2018-12-11T12:07:40Z
date_published: 2010-01-26T00:00:00Z
date_updated: 2021-01-12T07:55:25Z
day: '26'
doi: 10.1016/j.cub.2009.11.036
extern: '1'
intvolume: ' 20'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 161 - 169
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '1897'
status: public
title: Movement directionality in collective migration of germ layer progenitors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2010'
...
---
_id: '4243'
abstract:
- lang: eng
text: We investigate a new model for populations evolving in a spatial continuum.
This model can be thought of as a spatial version of the Lambda-Fleming-Viot process.
It explicitly incorporates both small scale reproduction events and large scale
extinction-recolonisation events. The lineages ancestral to a sample from a population
evolving according to this model can be described in terms of a spatial version
of the Lambda-coalescent. Using a technique of Evans (1997), we prove existence
and uniqueness in law for the model. We then investigate the asymptotic behaviour
of the genealogy of a finite number of individuals sampled uniformly at random
(or more generally `far enough apart') from a two-dimensional torus of sidelength
L as L tends to infinity. Under appropriate conditions (and on a suitable timescale)
we can obtain as limiting genealogical processes a Kingman coalescent, a more
general Lambda-coalescent or a system of coalescing Brownian motions (with a non-local
coalescence mechanism).
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: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: Barton NH, Etheridge A, Véber A. A new model for evolution in a spatial continuum.
Electronic Journal of Probability. 2010;15(7):162-216. doi:10.1214/EJP.v15-741
apa: Barton, N. H., Etheridge, A., & Véber, A. (2010). A new model for evolution
in a spatial continuum. Electronic Journal of Probability. Institute of
Mathematical Statistics. https://doi.org/10.1214/EJP.v15-741
chicago: Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “A New Model
for Evolution in a Spatial Continuum.” Electronic Journal of Probability.
Institute of Mathematical Statistics, 2010. https://doi.org/10.1214/EJP.v15-741.
ieee: N. H. Barton, A. Etheridge, and A. Véber, “A new model for evolution in a
spatial continuum,” Electronic Journal of Probability, vol. 15, no. 7.
Institute of Mathematical Statistics, pp. 162–216, 2010.
ista: Barton NH, Etheridge A, Véber A. 2010. A new model for evolution in a spatial
continuum. Electronic Journal of Probability. 15(7), 162–216.
mla: Barton, Nicholas H., et al. “A New Model for Evolution in a Spatial Continuum.”
Electronic Journal of Probability, vol. 15, no. 7, Institute of Mathematical
Statistics, 2010, pp. 162–216, doi:10.1214/EJP.v15-741.
short: N.H. Barton, A. Etheridge, A. Véber, Electronic Journal of Probability 15
(2010) 162–216.
date_created: 2018-12-11T12:07:48Z
date_published: 2010-02-03T00:00:00Z
date_updated: 2021-01-12T07:55:34Z
day: '03'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1214/EJP.v15-741
file:
- access_level: open_access
checksum: bab577546dd4e8f882e9a9dd645cd01e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:21Z
date_updated: 2020-07-14T12:46:26Z
file_id: '5140'
file_name: IST-2015-369-v1+1_741-2535-1-PB.pdf
file_size: 450171
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '7'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 162 - 216
publication: Electronic Journal of Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '1863'
pubrep_id: '369'
quality_controlled: '1'
scopus_import: 1
status: public
title: A new model for evolution in a spatial continuum
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2010'
...
---
_id: '4339'
abstract:
- lang: ger
text: Mit diesem Buch möchten wir einen Überblick der aktuellen Diskussion zum Thema
Bibliothek 2.0 geben und den Stand der tatsächlichen Umsetzung der Web 2.0-Ansätze
in deutschsprachigen Bibliotheken beleuchten. An dieser Stelle ist die Frage erlaubt,
warum es zu einer Zeit, in der es bereits die ersten "Web 3.0"- Konferenzen gibt,
eines Handbuches der Bibliothek 2.0 noch bedarf. Und warum es überhaupt ein deutschsprachiges
Handbuch zur Bibliothek 2.0 braucht, wo es doch bereits verschiedenste Publikationen
zu diesem Thema aus anderen Ländern, insbesondere des angloamerikanischen Raums
gibt. Ist dazu nicht bereits alles gesagt?
author:
- first_name: Julia
full_name: Bergmann, Julia
last_name: Bergmann
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
citation:
ama: 'Bergmann J, Danowski P. Ist Bibliothek 2.0 überhaupt noch relevant? – Eine
Einleitung in das Handbuch. In: Bergmann J, Danowski P, eds. Handbuch Bibliothek
2.0. Bibliotheks- und Informationspraxis 41. De Gruyter; 2010:5-20. doi:10.1515/9783110232103'
apa: Bergmann, J., & Danowski, P. (2010). Ist Bibliothek 2.0 überhaupt noch
relevant? – Eine Einleitung in das Handbuch. In J. Bergmann & P. Danowski
(Eds.), Handbuch Bibliothek 2.0 (pp. 5–20). De Gruyter. https://doi.org/10.1515/9783110232103
chicago: Bergmann, Julia, and Patrick Danowski. “Ist Bibliothek 2.0 Überhaupt Noch
Relevant? – Eine Einleitung in Das Handbuch.” In Handbuch Bibliothek 2.0,
edited by Julia Bergmann and Patrick Danowski, 5–20. Bibliotheks- Und Informationspraxis
41. De Gruyter, 2010. https://doi.org/10.1515/9783110232103.
ieee: J. Bergmann and P. Danowski, “Ist Bibliothek 2.0 überhaupt noch relevant?
– Eine Einleitung in das Handbuch,” in Handbuch Bibliothek 2.0, J. Bergmann
and P. Danowski, Eds. De Gruyter, 2010, pp. 5–20.
ista: 'Bergmann J, Danowski P. 2010.Ist Bibliothek 2.0 überhaupt noch relevant?
– Eine Einleitung in das Handbuch. In: Handbuch Bibliothek 2.0. , 5–20.'
mla: Bergmann, Julia, and Patrick Danowski. “Ist Bibliothek 2.0 Überhaupt Noch Relevant?
– Eine Einleitung in Das Handbuch.” Handbuch Bibliothek 2.0, edited by
Julia Bergmann and Patrick Danowski, De Gruyter, 2010, pp. 5–20, doi:10.1515/9783110232103.
short: J. Bergmann, P. Danowski, in:, J. Bergmann, P. Danowski (Eds.), Handbuch
Bibliothek 2.0, De Gruyter, 2010, pp. 5–20.
date_created: 2018-12-11T12:08:21Z
date_published: 2010-09-23T00:00:00Z
date_updated: 2021-01-12T07:56:15Z
day: '23'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.1515/9783110232103
editor:
- first_name: Julia
full_name: Bergmann, Julia
last_name: Bergmann
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
file:
- access_level: open_access
checksum: d42cedd48fffa85d75046f396a309fc3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:06Z
date_updated: 2020-07-14T12:46:27Z
file_id: '5123'
file_name: IST-2012-12-v1+1_9783110232103.5.pdf
file_size: 567580
relation: main_file
file_date_updated: 2020-07-14T12:46:27Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 5 - 20
publication: Handbuch Bibliothek 2.0
publication_status: published
publisher: De Gruyter
publist_id: '1235'
pubrep_id: '12'
quality_controlled: '1'
series_title: Bibliotheks- und Informationspraxis 41
status: public
title: Ist Bibliothek 2.0 überhaupt noch relevant? – Eine Einleitung in das Handbuch
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '4340'
abstract:
- lang: eng
text: "More and more libraries starting semantic web projects. The question about
the license of the data\r\nis not discussed or the discussion is deferred to the
end of project. in this paper is discussed why\r\nthe question of the license
is so important in context of the semantic web that is should be one of the\r\nfirst
aspects in a semantic web project. Also it will be shown why a public domain weaver
is the\r\nonly solution that fulfill the the special requirements of the semantic
web and that guaranties the\r\nreuseablitly of semantic library data for a sustainability
of the projects. "
author:
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
citation:
ama: Danowski P. Open Bibliographic Data. Elsevier; 2010.
apa: Danowski, P. (2010). Open bibliographic data. European Library Automation
Group (ELAG) 2010. Elsevier.
chicago: Danowski, Patrick. Open Bibliographic Data. European Library
Automation Group (ELAG) 2010. Elsevier, 2010.
ieee: P. Danowski, Open bibliographic data. Elsevier, 2010.
ista: Danowski P. 2010. Open bibliographic data, Elsevier,p.
mla: Danowski, Patrick. “Open Bibliographic Data.” European Library Automation
Group (ELAG) 2010, Elsevier, 2010.
short: P. Danowski, Open Bibliographic Data, Elsevier, 2010.
conference:
name: 'ELAG: European Library Automation Group'
date_created: 2018-12-11T12:08:21Z
date_published: 2010-06-10T00:00:00Z
date_updated: 2020-07-14T23:07:19Z
day: '10'
ddc:
- '020'
extern: '1'
file:
- access_level: open_access
checksum: 7061756135333d73b26a84526fa654f5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:01Z
date_updated: 2020-07-14T12:46:27Z
file_id: '5118'
file_name: IST-2012-51-v1+1_149-danowski-en.pdf
file_size: 94982
relation: main_file
file_date_updated: 2020-07-14T12:46:27Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.slideshare.net/PatrickD/open-bibliographic-data-elag2010
month: '06'
oa: 1
oa_version: None
publication: European Library Automation Group (ELAG) 2010
publication_status: published
publisher: Elsevier
publist_id: '1234'
status: public
title: Open bibliographic data
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: other_academic_publication
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '4341'
abstract:
- lang: eng
text: More and more libraries starting semantic web projects. The question about
the license of the data is not discussed or the discussion is deferred to the
end of project. in this paper is discussed why the question of the license is
so important in context of the semantic web that is should be one of the first
aspects in a semantic web project. Also it will be shown why a public domain weaver
is the only solution that fulfill the the special requirements of the semantic
web and that guaranties the reuseablitly of semantic library data for a sustainability
of the projects.
alternative_title:
- 'IFLA '
author:
- first_name: Patrick
full_name: Patrick Danowski
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
citation:
ama: 'Danowski P. Step one: blow up the silo! - Open bibliographic data, the first
step towards Linked Open Data. In: IFLA; 2010.'
apa: 'Danowski, P. (2010). Step one: blow up the silo! - Open bibliographic data,
the first step towards Linked Open Data. Presented at the WLIC: World Library
and Information Congress, IFLA.'
chicago: 'Danowski, Patrick. “Step One: Blow up the Silo! - Open Bibliographic Data,
the First Step towards Linked Open Data.” IFLA, 2010.'
ieee: 'P. Danowski, “Step one: blow up the silo! - Open bibliographic data, the
first step towards Linked Open Data,” presented at the WLIC: World Library and
Information Congress, 2010.'
ista: 'Danowski P. 2010. Step one: blow up the silo! - Open bibliographic data,
the first step towards Linked Open Data. WLIC: World Library and Information Congress,
IFLA , .'
mla: 'Danowski, Patrick. Step One: Blow up the Silo! - Open Bibliographic Data,
the First Step towards Linked Open Data. IFLA, 2010.'
short: P. Danowski, in:, IFLA, 2010.
conference:
name: 'WLIC: World Library and Information Congress'
date_created: 2018-12-11T12:08:21Z
date_published: 2010-08-01T00:00:00Z
date_updated: 2021-01-12T07:56:16Z
day: '01'
extern: 1
main_file_link:
- open_access: '0'
url: http://www.ifla.org/files/hq/papers/ifla76/149-danowski-en.pdf
month: '08'
publication_status: published
publisher: IFLA
publist_id: '1233'
pubrep_id: '51'
quality_controlled: 0
status: public
title: 'Step one: blow up the silo! - Open bibliographic data, the first step towards
Linked Open Data'
type: conference
year: '2010'
...
---
_id: '4346'
abstract:
- lang: eng
text: With the term "Library 2.0" the editors mean an institution which applies
the principles of the Web 2.0 such as openness, re-use, collaboration and interaction
in the entire organization. Libraries are extending their service offerings and
work processes to include the potential of Web 2.0 technologies. This changes
the job description and self-image of librarians. The collective volume offers
a complete overview of the topic Library 2.0 and the current state of developments
from a technological, sociological, information theoretical and practice-oriented
perspective.
alternative_title:
- Bibliotheks- und Informationspraxis
article_processing_charge: No
citation:
ama: Danowski P, Bergmann J, eds. Handbuch Bibliothek 2.0. Vol 41. De Gruyter;
2010. doi:10.1515/9783110232103
apa: Danowski, P., & Bergmann, J. (Eds.). (2010). Handbuch Bibliothek 2.0
(Vol. 41). De Gruyter. https://doi.org/10.1515/9783110232103
chicago: Danowski, Patrick, and Julia Bergmann, eds. Handbuch Bibliothek 2.0.
Vol. 41. Bibliothekspraxis. De Gruyter, 2010. https://doi.org/10.1515/9783110232103.
ieee: P. Danowski and J. Bergmann, Eds., Handbuch Bibliothek 2.0, vol. 41.
De Gruyter, 2010.
ista: Danowski P, Bergmann J eds. 2010. Handbuch Bibliothek 2.0, De Gruyter, 405p.
mla: Danowski, Patrick, and Julia Bergmann, editors. Handbuch Bibliothek 2.0.
Vol. 41, De Gruyter, 2010, doi:10.1515/9783110232103.
short: P. Danowski, J. Bergmann, eds., Handbuch Bibliothek 2.0, De Gruyter, 2010.
date_created: 2018-12-11T12:08:23Z
date_published: 2010-09-01T00:00:00Z
date_updated: 2021-12-22T14:41:57Z
day: '01'
department:
- _id: E-Lib
doi: 10.1515/9783110232103
editor:
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
- first_name: Julia
full_name: Bergmann, Julia
last_name: Bergmann
language:
- iso: ger
main_file_link:
- open_access: '1'
url: https://www.degruyter.com/document/doi/10.1515/9783110232103/html
month: '09'
oa: 1
oa_version: Published Version
page: '405'
publication_identifier:
eisbn:
- 9-783-1102-3210-3
isbn:
- 9-783-1102-3209-7
publication_status: published
publisher: De Gruyter
publist_id: '1228'
quality_controlled: '1'
series_title: Bibliothekspraxis
status: public
title: Handbuch Bibliothek 2.0
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: book_editor
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: ' 41'
year: '2010'
...
---
_id: '4358'
abstract:
- lang: eng
text: Phenotypic biotyping has traditionally been used to differentiate bacteria
occupying distinct ecological niches such as host species. For example, the capacity
of Staphylococcus aureus from sheep to coagulate ruminant plasma, reported over
60 years ago, led to the description of small ruminant and bovine S. aureus ecovars.
The great majority of small ruminant isolates are represented by a single, widespread
clonal complex (CC133) of S. aureus, but its evolutionary origin and the molecular
basis for its host tropism remain unknown. Here, we provide evidence that the
CC133 clone evolved as the result of a human to ruminant host jump followed by
adaptive genome diversification. Comparative whole-genome sequencing revealed
molecular evidence for host adaptation including gene decay and diversification
of proteins involved in host-pathogen interactions. Importantly, several novel
mobile genetic elements encoding virulence proteins with attenuated or enhanced
activity in ruminants were widely distributed in CC133 isolates, suggesting a
key role in its host-specific interactions. To investigate this further, we examined
the activity of a novel staphylococcal pathogenicity island (SaPIov2) found in
the great majority of CC133 isolates which encodes a variant of the chromosomally
encoded von Willebrand-binding protein (vWbp(Sov2)), previously demonstrated to
have coagulase activity for human plasma. Remarkably, we discovered that SaPIov2
confers the ability to coagulate ruminant plasma suggesting an important role
in ruminant disease pathogenesis and revealing the origin of a defining phenotype
of the classical S. aureus biotyping scheme. Taken together, these data provide
broad new insights into the origin and molecular basis of S. aureus ruminant host
specificity.
author:
- first_name: Caitriona
full_name: Guinane, Caitriona M
last_name: Guinane
- first_name: Nouri
full_name: Ben Zakour, Nouri L
last_name: Ben Zakour
- first_name: Maria
full_name: Tormo-Mas, Maria A
last_name: Tormo Mas
- first_name: Lucy
full_name: Weinert, Lucy A
last_name: Weinert
- first_name: Bethan
full_name: Lowder, Bethan V
last_name: Lowder
- first_name: Robyn
full_name: Cartwright, Robyn A
last_name: Cartwright
- first_name: Davida
full_name: Smyth, Davida S
last_name: Smyth
- first_name: Cyril
full_name: Smyth, Cyril J
last_name: Smyth
- first_name: Jodi
full_name: Lindsay, Jodi A
last_name: Lindsay
- first_name: Katherine
full_name: Gould, Katherine A
last_name: Gould
- first_name: Adam
full_name: Witney, Adam
last_name: Witney
- first_name: Jason
full_name: Hinds, Jason
last_name: Hinds
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Andrew
full_name: Rambaut, Andrew
last_name: Rambaut
- first_name: Jose
full_name: Penades, Jose R
last_name: Penades
- first_name: J Ross
full_name: Fitzgerald, J Ross
last_name: Fitzgerald
citation:
ama: Guinane C, Ben Zakour N, Tormo Mas M, et al. Evolutionary genomics of Staphylococcus
aureus reveals insights into the origin and molecular basis of ruminant host adaptation.
Genome Biology and Evolution. 2010;2:454-466. doi:10.1093/gbe/evq031
apa: Guinane, C., Ben Zakour, N., Tormo Mas, M., Weinert, L., Lowder, B., Cartwright,
R., … Fitzgerald, J. R. (2010). Evolutionary genomics of Staphylococcus aureus
reveals insights into the origin and molecular basis of ruminant host adaptation.
Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evq031
chicago: Guinane, Caitriona, Nouri Ben Zakour, Maria Tormo Mas, Lucy Weinert, Bethan
Lowder, Robyn Cartwright, Davida Smyth, et al. “Evolutionary Genomics of Staphylococcus
Aureus Reveals Insights into the Origin and Molecular Basis of Ruminant Host Adaptation.”
Genome Biology and Evolution. Oxford University Press, 2010. https://doi.org/10.1093/gbe/evq031.
ieee: C. Guinane et al., “Evolutionary genomics of Staphylococcus aureus
reveals insights into the origin and molecular basis of ruminant host adaptation,”
Genome Biology and Evolution, vol. 2. Oxford University Press, pp. 454–466,
2010.
ista: Guinane C, Ben Zakour N, Tormo Mas M, Weinert L, Lowder B, Cartwright R, Smyth
D, Smyth C, Lindsay J, Gould K, Witney A, Hinds J, Bollback JP, Rambaut A, Penades
J, Fitzgerald JR. 2010. Evolutionary genomics of Staphylococcus aureus reveals
insights into the origin and molecular basis of ruminant host adaptation. Genome
Biology and Evolution. 2, 454–466.
mla: Guinane, Caitriona, et al. “Evolutionary Genomics of Staphylococcus Aureus
Reveals Insights into the Origin and Molecular Basis of Ruminant Host Adaptation.”
Genome Biology and Evolution, vol. 2, Oxford University Press, 2010, pp.
454–66, doi:10.1093/gbe/evq031.
short: C. Guinane, N. Ben Zakour, M. Tormo Mas, L. Weinert, B. Lowder, R. Cartwright,
D. Smyth, C. Smyth, J. Lindsay, K. Gould, A. Witney, J. Hinds, J.P. Bollback,
A. Rambaut, J. Penades, J.R. Fitzgerald, Genome Biology and Evolution 2 (2010)
454–466.
date_created: 2018-12-11T12:08:27Z
date_published: 2010-06-09T00:00:00Z
date_updated: 2021-01-12T07:56:23Z
day: '09'
doi: 10.1093/gbe/evq031
extern: 1
intvolume: ' 2'
month: '06'
page: 454 - 466
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '1100'
quality_controlled: 0
status: public
title: Evolutionary genomics of Staphylococcus aureus reveals insights into the origin
and molecular basis of ruminant host adaptation
type: journal_article
volume: 2
year: '2010'
...
---
_id: '4361'
abstract:
- lang: eng
text: Depth-bounded processes form the most expressive known fragment of the π-calculus
for which interesting verification problems are still decidable. In this paper
we develop an adequate domain of limits for the well-structured transition systems
that are induced by depth-bounded processes. An immediate consequence of our result
is that there exists a forward algorithm that decides the covering problem for
this class. Unlike backward algorithms, the forward algorithm terminates even
if the depth of the process is not known a priori. More importantly, our result
suggests a whole spectrum of forward algorithms that enable the effective verification
of a large class of mobile systems.
alternative_title:
- LNCS
author:
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
- 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: 'Wies T, Zufferey D, Henzinger TA. Forward analysis of depth-bounded processes.
In: Ong L, ed. Vol 6014. Springer; 2010:94-108. doi:10.1007/978-3-642-12032-9_8'
apa: 'Wies, T., Zufferey, D., & Henzinger, T. A. (2010). Forward analysis of
depth-bounded processes. In L. Ong (Ed.) (Vol. 6014, pp. 94–108). Presented at
the FoSSaCS: Foundations of Software Science and Computation Structures, Paphos,
Cyprus: Springer. https://doi.org/10.1007/978-3-642-12032-9_8'
chicago: Wies, Thomas, Damien Zufferey, and Thomas A Henzinger. “Forward Analysis
of Depth-Bounded Processes.” edited by Luke Ong, 6014:94–108. Springer, 2010.
https://doi.org/10.1007/978-3-642-12032-9_8.
ieee: 'T. Wies, D. Zufferey, and T. A. Henzinger, “Forward analysis of depth-bounded
processes,” presented at the FoSSaCS: Foundations of Software Science and Computation
Structures, Paphos, Cyprus, 2010, vol. 6014, pp. 94–108.'
ista: 'Wies T, Zufferey D, Henzinger TA. 2010. Forward analysis of depth-bounded
processes. FoSSaCS: Foundations of Software Science and Computation Structures,
LNCS, vol. 6014, 94–108.'
mla: Wies, Thomas, et al. Forward Analysis of Depth-Bounded Processes. Edited
by Luke Ong, vol. 6014, Springer, 2010, pp. 94–108, doi:10.1007/978-3-642-12032-9_8.
short: T. Wies, D. Zufferey, T.A. Henzinger, in:, L. Ong (Ed.), Springer, 2010,
pp. 94–108.
conference:
end_date: 2010-03-28
location: Paphos, Cyprus
name: 'FoSSaCS: Foundations of Software Science and Computation Structures'
start_date: 2010-03-20
date_created: 2018-12-11T12:08:27Z
date_published: 2010-03-01T00:00:00Z
date_updated: 2023-09-07T11:36:36Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1007/978-3-642-12032-9_8
editor:
- first_name: Luke
full_name: Ong, Luke
last_name: Ong
file:
- access_level: open_access
checksum: 3e610de84937d821316362658239134a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:17Z
date_updated: 2020-07-14T12:46:27Z
file_id: '4677'
file_name: IST-2012-50-v1+1_Forward_analysis_of_depth-bounded_processes.pdf
file_size: 240766
relation: main_file
file_date_updated: 2020-07-14T12:46:27Z
has_accepted_license: '1'
intvolume: ' 6014'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 94 - 108
publication_status: published
publisher: Springer
publist_id: '1099'
pubrep_id: '50'
quality_controlled: '1'
related_material:
record:
- id: '1405'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Forward analysis of depth-bounded processes
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6014
year: '2010'
...
---
_id: '4362'
abstract:
- lang: eng
text: Software transactional memories (STMs) promise simple and efficient concurrent
programming. Several correctness properties have been proposed for STMs. Based
on a bounded conflict graph algorithm for verifying correctness of STMs, we develop
TRACER, a tool for runtime verification of STM implementations. The novelty of
TRACER lies in the way it combines coarse and precise runtime analyses to guarantee
sound and complete verification in an efficient manner. We implement TRACER in
the TL2 STM implementation. We evaluate the performance of TRACER on STAMP benchmarks.
While a precise runtime verification technique based on conflict graphs results
in an average slowdown of 60x, the two-level approach of TRACER performs complete
verification with an average slowdown of around 25x across different benchmarks.
alternative_title:
- LNCS
author:
- first_name: Vasu
full_name: Singh, Vasu
id: 4DAE2708-F248-11E8-B48F-1D18A9856A87
last_name: Singh
citation:
ama: 'Singh V. Runtime verification for software transactional memories. In: Sokolsky
O, Rosu G, Tilmann N, et al., eds. Vol 6418. Springer; 2010:421-435. doi:10.1007/978-3-642-16612-9_32'
apa: 'Singh, V. (2010). Runtime verification for software transactional memories.
In O. Sokolsky, G. Rosu, N. Tilmann, H. Barringer, Y. Falcone, B. Finkbeiner,
… G. Pace (Eds.) (Vol. 6418, pp. 421–435). Presented at the RV: International
Conference on Runtime Verification, St. Julians, Malta: Springer. https://doi.org/10.1007/978-3-642-16612-9_32'
chicago: Singh, Vasu. “Runtime Verification for Software Transactional Memories.”
edited by Oleg Sokolsky, Grigore Rosu, Nikolai Tilmann, Howard Barringer, Ylies
Falcone, Bernd Finkbeiner, Klaus Havelund, Insup Lee, and Gordon Pace, 6418:421–35.
Springer, 2010. https://doi.org/10.1007/978-3-642-16612-9_32.
ieee: 'V. Singh, “Runtime verification for software transactional memories,” presented
at the RV: International Conference on Runtime Verification, St. Julians, Malta,
2010, vol. 6418, pp. 421–435.'
ista: 'Singh V. 2010. Runtime verification for software transactional memories.
RV: International Conference on Runtime Verification, LNCS, vol. 6418, 421–435.'
mla: Singh, Vasu. Runtime Verification for Software Transactional Memories.
Edited by Oleg Sokolsky et al., vol. 6418, Springer, 2010, pp. 421–35, doi:10.1007/978-3-642-16612-9_32.
short: V. Singh, in:, O. Sokolsky, G. Rosu, N. Tilmann, H. Barringer, Y. Falcone,
B. Finkbeiner, K. Havelund, I. Lee, G. Pace (Eds.), Springer, 2010, pp. 421–435.
conference:
end_date: 2010-11-04
location: St. Julians, Malta
name: 'RV: International Conference on Runtime Verification'
start_date: 2010-11-01
date_created: 2018-12-11T12:08:28Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:25Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-642-16612-9_32
editor:
- first_name: Oleg
full_name: Sokolsky, Oleg
last_name: Sokolsky
- first_name: Grigore
full_name: Rosu, Grigore
last_name: Rosu
- first_name: Nikolai
full_name: Tilmann, Nikolai
last_name: Tilmann
- first_name: Howard
full_name: Barringer, Howard
last_name: Barringer
- first_name: Ylies
full_name: Falcone, Ylies
last_name: Falcone
- first_name: Bernd
full_name: Finkbeiner, Bernd
last_name: Finkbeiner
- first_name: Klaus
full_name: Havelund, Klaus
last_name: Havelund
- first_name: Insup
full_name: Lee, Insup
last_name: Lee
- first_name: Gordon
full_name: Pace, Gordon
last_name: Pace
intvolume: ' 6418'
language:
- iso: eng
month: '01'
oa_version: None
page: 421 - 435
publication_status: published
publisher: Springer
publist_id: '1096'
quality_controlled: '1'
scopus_import: 1
status: public
title: Runtime verification for software transactional memories
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6418
year: '2010'
...
---
_id: '4364'
author:
- first_name: Andreas
full_name: Podelski,Andreas
last_name: Podelski
- first_name: Thomas
full_name: Thomas Wies
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
citation:
ama: 'Podelski A, Wies T. Counterexample-guided focus. In: ACM; 2010:249-260. doi:10.1145/1707801.1706330'
apa: 'Podelski, A., & Wies, T. (2010). Counterexample-guided focus (pp. 249–260).
Presented at the POPL: Principles of Programming Languages, ACM. https://doi.org/10.1145/1707801.1706330'
chicago: Podelski, Andreas, and Thomas Wies. “Counterexample-Guided Focus,” 249–60.
ACM, 2010. https://doi.org/10.1145/1707801.1706330.
ieee: 'A. Podelski and T. Wies, “Counterexample-guided focus,” presented at the
POPL: Principles of Programming Languages, 2010, pp. 249–260.'
ista: 'Podelski A, Wies T. 2010. Counterexample-guided focus. POPL: Principles of
Programming Languages, 249–260.'
mla: Podelski, Andreas, and Thomas Wies. Counterexample-Guided Focus. ACM,
2010, pp. 249–60, doi:10.1145/1707801.1706330.
short: A. Podelski, T. Wies, in:, ACM, 2010, pp. 249–260.
conference:
name: 'POPL: Principles of Programming Languages'
date_created: 2018-12-11T12:08:28Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:26Z
day: '01'
doi: 10.1145/1707801.1706330
extern: 1
month: '01'
page: 249 - 260
publication_status: published
publisher: ACM
publist_id: '1093'
quality_controlled: 0
status: public
title: Counterexample-guided focus
type: conference
year: '2010'
...
---
_id: '4369'
abstract:
- lang: eng
text: In this paper we propose a novel technique for constructing timed automata
from properties expressed in the logic mtl, under bounded-variability assumptions.
We handle full mtl and include all future operators. Our construction is based
on separation of the continuous time monitoring of the input sequence and discrete
predictions regarding the future. The separation of the continuous from the discrete
allows us to determinize our automata in an exponential construction that does
not increase the number of clocks. This leads to a doubly exponential construction
from mtl to deterministic timed automata, compared with triply exponential using
existing approaches. We offer an alternative to the existing approach to linear
real-time model checking, which has never been implemented. It further offers
a unified framework for model checking, runtime monitoring, and synthesis, in
an approach that can reuse tools, implementations, and insights from the discrete
setting.
alternative_title:
- LNCS
author:
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Nir
full_name: Piterman, Nir
last_name: Piterman
citation:
ama: 'Nickovic D, Piterman N. From MTL to deterministic timed automata. In: Henzinger
TA, Chatterjee K, eds. Vol 6246. Springer; 2010:152-167. doi:10.1007/978-3-642-15297-9_13'
apa: 'Nickovic, D., & Piterman, N. (2010). From MTL to deterministic timed automata.
In T. A. Henzinger & K. Chatterjee (Eds.) (Vol. 6246, pp. 152–167). Presented
at the FORMATS: Formal Modeling and Analysis of Timed Systems, Klosterneuburg,
Austria: Springer. https://doi.org/10.1007/978-3-642-15297-9_13'
chicago: Nickovic, Dejan, and Nir Piterman. “From MTL to Deterministic Timed Automata.”
edited by Thomas A. Henzinger and Krishnendu Chatterjee, 6246:152–67. Springer,
2010. https://doi.org/10.1007/978-3-642-15297-9_13.
ieee: 'D. Nickovic and N. Piterman, “From MTL to deterministic timed automata,”
presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Klosterneuburg,
Austria, 2010, vol. 6246, pp. 152–167.'
ista: 'Nickovic D, Piterman N. 2010. From MTL to deterministic timed automata. FORMATS:
Formal Modeling and Analysis of Timed Systems, LNCS, vol. 6246, 152–167.'
mla: Nickovic, Dejan, and Nir Piterman. From MTL to Deterministic Timed Automata.
Edited by Thomas A. Henzinger and Krishnendu Chatterjee, vol. 6246, Springer,
2010, pp. 152–67, doi:10.1007/978-3-642-15297-9_13.
short: D. Nickovic, N. Piterman, in:, T.A. Henzinger, K. Chatterjee (Eds.), Springer,
2010, pp. 152–167.
conference:
end_date: 2010-09-10
location: Klosterneuburg, Austria
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
start_date: 2010-09-08
date_created: 2018-12-11T12:08:30Z
date_published: 2010-09-08T00:00:00Z
date_updated: 2021-01-12T07:56:27Z
day: '08'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1007/978-3-642-15297-9_13
ec_funded: 1
editor:
- first_name: Thomas A.
full_name: Henzinger, Thomas A.
last_name: Henzinger
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
last_name: Chatterjee
file:
- access_level: open_access
checksum: b0ca5f5fbe8a3d20ccbc6f51a344a459
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:43Z
date_updated: 2020-07-14T12:46:27Z
file_id: '5028'
file_name: IST-2012-49-v1+1_From_MTL_to_deterministic_timed_automata.pdf
file_size: 249789
relation: main_file
file_date_updated: 2020-07-14T12:46:27Z
has_accepted_license: '1'
intvolume: ' 6246'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 152 - 167
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_status: published
publisher: Springer
publist_id: '1090'
pubrep_id: '49'
quality_controlled: '1'
scopus_import: 1
status: public
title: From MTL to deterministic timed automata
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6246
year: '2010'
...
---
_id: '4378'
abstract:
- lang: eng
text: 'Techniques such as verification condition generation, predicate abstraction,
and expressive type systems reduce software verification to proving formulas in
expressive logics. Programs and their specifications often make use of data structures
such as sets, multisets, algebraic data types, or graphs. Consequently, formulas
generated from verification also involve such data structures. To automate the
proofs of such formulas we propose a logic (a “calculus”) of such data structures.
We build the calculus by starting from decidable logics of individual data structures,
and connecting them through functions and sets, in ways that go beyond the frameworks
such as Nelson-Oppen. The result are new decidable logics that can simultaneously
specify properties of different kinds of data structures and overcome the limitations
of the individual logics. Several of our decidable logics include abstraction
functions that map a data structure into its more abstract view (a tree into a
multiset, a multiset into a set), into a numerical quantity (the size or the height),
or into the truth value of a candidate data structure invariant (sortedness, or
the heap property). For algebraic data types, we identify an asymptotic many-to-one
condition on the abstraction function that guarantees the existence of a decision
procedure. In addition to the combination based on abstraction functions, we can
combine multiple data structure theories if they all reduce to the same data structure
logic. As an instance of this approach, we describe a decidable logic whose formulas
are propositional combinations of formulas in: weak monadic second-order logic
of two successors, two-variable logic with counting, multiset algebra with Presburger
arithmetic, the Bernays-Schönfinkel-Ramsey class of first-order logic, and the
logic of algebraic data types with the set content function. The subformulas in
this combination can share common variables that refer to sets of objects along
with the common set algebra operations. Such sound and complete combination is
possible because the relations on sets definable in the component logics are all
expressible in Boolean Algebra with Presburger Arithmetic. Presburger arithmetic
and its new extensions play an important role in our decidability results. In
several cases, when we combine logics that belong to NP, we can prove the satisfiability
for the combined logic is still in NP.'
alternative_title:
- LNCS
author:
- first_name: Viktor
full_name: Kuncak, Viktor
last_name: Kuncak
- first_name: Ruzica
full_name: Piskac, Ruzica
last_name: Piskac
- first_name: Philippe
full_name: Suter, Philippe
last_name: Suter
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
citation:
ama: 'Kuncak V, Piskac R, Suter P, Wies T. Building a calculus of data structures.
In: Barthe G, Hermenegildo M, eds. Vol 5944. Springer; 2010:26-44. doi:10.1007/978-3-642-11319-2_6'
apa: 'Kuncak, V., Piskac, R., Suter, P., & Wies, T. (2010). Building a calculus
of data structures. In G. Barthe & M. Hermenegildo (Eds.) (Vol. 5944, pp.
26–44). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation,
Madrid, Spain: Springer. https://doi.org/10.1007/978-3-642-11319-2_6'
chicago: Kuncak, Viktor, Ruzica Piskac, Philippe Suter, and Thomas Wies. “Building
a Calculus of Data Structures.” edited by Gilles Barthe and Manuel Hermenegildo,
5944:26–44. Springer, 2010. https://doi.org/10.1007/978-3-642-11319-2_6.
ieee: 'V. Kuncak, R. Piskac, P. Suter, and T. Wies, “Building a calculus of data
structures,” presented at the VMCAI: Verification, Model Checking and Abstract
Interpretation, Madrid, Spain, 2010, vol. 5944, pp. 26–44.'
ista: 'Kuncak V, Piskac R, Suter P, Wies T. 2010. Building a calculus of data structures.
VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 5944,
26–44.'
mla: Kuncak, Viktor, et al. Building a Calculus of Data Structures. Edited
by Gilles Barthe and Manuel Hermenegildo, vol. 5944, Springer, 2010, pp. 26–44,
doi:10.1007/978-3-642-11319-2_6.
short: V. Kuncak, R. Piskac, P. Suter, T. Wies, in:, G. Barthe, M. Hermenegildo
(Eds.), Springer, 2010, pp. 26–44.
conference:
end_date: 2010-01-19
location: Madrid, Spain
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2010-01-17
date_created: 2018-12-11T12:08:33Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:31Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-642-11319-2_6
editor:
- first_name: Gilles
full_name: Barthe, Gilles
last_name: Barthe
- first_name: Manuel
full_name: Hermenegildo, Manuel
last_name: Hermenegildo
intvolume: ' 5944'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://infoscience.epfl.ch/record/161290/
month: '01'
oa: 1
oa_version: Submitted Version
page: 26 - 44
publication_status: published
publisher: Springer
publist_id: '1081'
quality_controlled: '1'
scopus_import: 1
status: public
title: Building a calculus of data structures
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 5944
year: '2010'
...
---
_id: '4379'
abstract:
- lang: eng
text: |
The formal specification component of verification can be exported to simulation through the idea of property checkers. The essence of this approach is the automatic construction of an observer from the specification in the form of a program that can be interfaced with a simulator and alert the user if the property is violated by a simulation trace. Although not complete, this lighter approach to formal verification has been effectively used in software and digital hardware to detect errors. Recently, the idea of property checkers has been extended to analog and mixed-signal systems.
In this paper, we apply the property-based checking methodology to an industrial and realistic example of a DDR2 memory interface. The properties describing the DDR2 analog behavior are expressed in the formal specification language stl/psl in form of assertions. The simulation traces generated from an actual DDR2 interface design are checked with respect to the stl/psl assertions using the amt tool. The focus of this paper is on the translation of the official (informal and descriptive) specification of two non-trivial DDR2 properties into stl/psl assertions. We study both the benefits and the current limits of such approach.
acknowledgement: We would like to thank Tom Giovannini from Rambus, Inc. for his detailed
explana- tions of the DDR2 specification and for providing us with simulation traces.
We would also like to thank Oded Maler from Verimag for discussions on the STL/PSL
language and its extensions.
author:
- first_name: Kevin
full_name: Jones, Kevin D
last_name: Jones
- first_name: Victor
full_name: Konrad,Victor
last_name: Konrad
- first_name: Dejan
full_name: Dejan Nickovic
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
citation:
ama: 'Jones K, Konrad V, Nickovic D. Analog property checkers: a DDR2 case study.
Formal Methods in System Design. 2010;36(2):114-130. doi:10.1007/s10703-009-0085-x'
apa: 'Jones, K., Konrad, V., & Nickovic, D. (2010). Analog property checkers:
a DDR2 case study. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-009-0085-x'
chicago: 'Jones, Kevin, Victor Konrad, and Dejan Nickovic. “Analog Property Checkers:
A DDR2 Case Study.” Formal Methods in System Design. Springer, 2010. https://doi.org/10.1007/s10703-009-0085-x.'
ieee: 'K. Jones, V. Konrad, and D. Nickovic, “Analog property checkers: a DDR2 case
study,” Formal Methods in System Design, vol. 36, no. 2. Springer, pp.
114–130, 2010.'
ista: 'Jones K, Konrad V, Nickovic D. 2010. Analog property checkers: a DDR2 case
study. Formal Methods in System Design. 36(2), 114–130.'
mla: 'Jones, Kevin, et al. “Analog Property Checkers: A DDR2 Case Study.” Formal
Methods in System Design, vol. 36, no. 2, Springer, 2010, pp. 114–30, doi:10.1007/s10703-009-0085-x.'
short: K. Jones, V. Konrad, D. Nickovic, Formal Methods in System Design 36 (2010)
114–130.
date_created: 2018-12-11T12:08:33Z
date_published: 2010-06-01T00:00:00Z
date_updated: 2021-01-12T07:56:31Z
day: '01'
doi: 10.1007/s10703-009-0085-x
extern: 1
intvolume: ' 36'
issue: '2'
main_file_link:
- open_access: '1'
url: http://openaccess.city.ac.uk/1066/
month: '06'
oa: 1
page: 114 - 130
publication: Formal Methods in System Design
publication_status: published
publisher: Springer
publist_id: '1080'
quality_controlled: 0
status: public
title: 'Analog property checkers: a DDR2 case study'
type: journal_article
volume: 36
year: '2010'
...