---
_id: '9739'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Ben
full_name: Adlam, Ben
last_name: Adlam
- first_name: Martin
full_name: Novak, Martin
last_name: Novak
citation:
ama: Chatterjee K, Pavlogiannis A, Adlam B, Novak M. Detailed proofs for “The time
scale of evolutionary innovation.” 2014. doi:10.1371/journal.pcbi.1003818.s001
apa: Chatterjee, K., Pavlogiannis, A., Adlam, B., & Novak, M. (2014). Detailed
proofs for “The time scale of evolutionary innovation.” Public Library of Science.
https://doi.org/10.1371/journal.pcbi.1003818.s001
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Novak.
“Detailed Proofs for ‘The Time Scale of Evolutionary Innovation.’” Public Library
of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003818.s001.
ieee: K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for
‘The time scale of evolutionary innovation.’” Public Library of Science, 2014.
ista: Chatterjee K, Pavlogiannis A, Adlam B, Novak M. 2014. Detailed proofs for
“The time scale of evolutionary innovation”, Public Library of Science, 10.1371/journal.pcbi.1003818.s001.
mla: Chatterjee, Krishnendu, et al. Detailed Proofs for “The Time Scale of Evolutionary
Innovation.” Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003818.s001.
short: K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014).
date_created: 2021-07-28T08:13:57Z
date_published: 2014-09-11T00:00:00Z
date_updated: 2023-02-23T10:25:37Z
day: '11'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1003818.s001
month: '09'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '2039'
relation: used_in_publication
status: public
status: public
title: Detailed proofs for “The time scale of evolutionary innovation”
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9740'
abstract:
- lang: eng
text: The fitness effects of symbionts on their hosts can be context-dependent,
with usually benign symbionts causing detrimental effects when their hosts are
stressed, or typically parasitic symbionts providing protection towards their
hosts (e.g. against pathogen infection). Here, we studied the novel association
between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia
formicarum for potential costs and benefits. We tested ants with different Laboulbenia
levels for their survival and immunity under resource limitation and exposure
to the obligate killing entomopathogen Metarhizium brunneum. While survival of
L. neglectus workers under starvation was significantly decreased with increasing
Laboulbenia levels, host survival under Metarhizium exposure increased with higher
levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection,
which seems to be driven mechanistically by both improved sanitary behaviours
and an upregulated immune system. Ants with high Laboulbenia levels showed significantly
longer self-grooming and elevated expression of immune genes relevant for wound
repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase),
compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont
Laboulbenia formicarum weakens its ant host by either direct resource exploitation
or the costs of an upregulated behavioural and immunological response, which,
however, provides a prophylactic protection upon later exposure to pathogens.
article_processing_charge: No
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Konrad M, Grasse AV, Tragust S, Cremer S. Data from: Anti-pathogen protection
versus survival costs mediated by an ectosymbiont in an ant host. 2014. doi:10.5061/dryad.vm0vc'
apa: 'Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2014). Data from:
Anti-pathogen protection versus survival costs mediated by an ectosymbiont in
an ant host. Dryad. https://doi.org/10.5061/dryad.vm0vc'
chicago: 'Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Data
from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont
in an Ant Host.” Dryad, 2014. https://doi.org/10.5061/dryad.vm0vc.'
ieee: 'M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Data from: Anti-pathogen
protection versus survival costs mediated by an ectosymbiont in an ant host.”
Dryad, 2014.'
ista: 'Konrad M, Grasse AV, Tragust S, Cremer S. 2014. Data from: Anti-pathogen
protection versus survival costs mediated by an ectosymbiont in an ant host, Dryad,
10.5061/dryad.vm0vc.'
mla: 'Konrad, Matthias, et al. Data from: Anti-Pathogen Protection versus Survival
Costs Mediated by an Ectosymbiont in an Ant Host. Dryad, 2014, doi:10.5061/dryad.vm0vc.'
short: M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, (2014).
date_created: 2021-07-28T08:38:40Z
date_published: 2014-11-13T00:00:00Z
date_updated: 2023-02-23T10:23:32Z
day: '13'
department:
- _id: SyCr
doi: 10.5061/dryad.vm0vc
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.vm0vc
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1993'
relation: used_in_publication
status: public
status: public
title: 'Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont
in an ant host'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9741'
abstract:
- lang: eng
text: In rapidly changing environments, selection history may impact the dynamics
of adaptation. Mutations selected in one environment may result in pleiotropic
fitness trade-offs in subsequent novel environments, slowing the rates of adaptation.
Epistatic interactions between mutations selected in sequential stressful environments
may slow or accelerate subsequent rates of adaptation, depending on the nature
of that interaction. We explored the dynamics of adaptation during sequential
exposure to herbicides with different modes of action in Chlamydomonas reinhardtii.
Evolution of resistance to two of the herbicides was largely independent of selection
history. For carbetamide, previous adaptation to other herbicide modes of action
positively impacted the likelihood of adaptation to this herbicide. Furthermore,
while adaptation to all individual herbicides was associated with pleiotropic
fitness costs in stress-free environments, we observed that accumulation of resistance
mechanisms was accompanied by a reduction in overall fitness costs. We suggest
that antagonistic epistasis may be a driving mechanism that enables populations
to more readily adapt in novel environments. These findings highlight the potential
for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug
and -pesticide resistance, as well as the potential for epistatic interactions
between adaptive mutations to facilitate evolutionary rescue in rapidly changing
environments.
article_processing_charge: No
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
citation:
ama: 'Lagator M, Colegrave N, Neve P. Data from: Selection history and epistatic
interactions impact dynamics of adaptation to novel environmental stresses. 2014.
doi:10.5061/dryad.85dn7'
apa: 'Lagator, M., Colegrave, N., & Neve, P. (2014). Data from: Selection history
and epistatic interactions impact dynamics of adaptation to novel environmental
stresses. Dryad. https://doi.org/10.5061/dryad.85dn7'
chicago: 'Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History
and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental
Stresses.” Dryad, 2014. https://doi.org/10.5061/dryad.85dn7.'
ieee: 'M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and
epistatic interactions impact dynamics of adaptation to novel environmental stresses.”
Dryad, 2014.'
ista: 'Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic
interactions impact dynamics of adaptation to novel environmental stresses, Dryad,
10.5061/dryad.85dn7.'
mla: 'Lagator, Mato, et al. Data from: Selection History and Epistatic Interactions
Impact Dynamics of Adaptation to Novel Environmental Stresses. Dryad, 2014,
doi:10.5061/dryad.85dn7.'
short: M. Lagator, N. Colegrave, P. Neve, (2014).
date_created: 2021-07-28T08:48:06Z
date_published: 2014-08-21T00:00:00Z
date_updated: 2023-02-23T10:25:31Z
day: '21'
department:
- _id: CaGu
doi: 10.5061/dryad.85dn7
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.85dn7
month: '08'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2036'
relation: used_in_publication
status: public
status: public
title: 'Data from: Selection history and epistatic interactions impact dynamics of
adaptation to novel environmental stresses'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9747'
abstract:
- lang: eng
text: Understanding the effects of sex and migration on adaptation to novel environments
remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas
reinhardtii, we investigated how sex and migration affected rates of evolutionary
rescue in a sink environment, and subsequent changes in fitness following evolutionary
rescue. We show that sex and migration affect both the rate of evolutionary rescue
and subsequent adaptation. However, their combined effects change as the populations
adapt to a sink habitat. Both sex and migration independently increased rates
of evolutionary rescue, but the effect of sex on subsequent fitness improvements,
following initial rescue, changed with migration, as sex was beneficial in the
absence of migration but constraining adaptation when combined with migration.
These results suggest that sex and migration are beneficial during the initial
stages of adaptation, but can become detrimental as the population adapts to its
environment.
article_processing_charge: No
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Andrew
full_name: Morgan, Andrew
last_name: Morgan
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
citation:
ama: 'Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration
in adaptation to sink environments. 2014. doi:10.5061/dryad.s42n1'
apa: 'Lagator, M., Morgan, A., Neve, P., & Colegrave, N. (2014). Data from:
Role of sex and migration in adaptation to sink environments. Dryad. https://doi.org/10.5061/dryad.s42n1'
chicago: 'Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from:
Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. https://doi.org/10.5061/dryad.s42n1.'
ieee: 'M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex
and migration in adaptation to sink environments.” Dryad, 2014.'
ista: 'Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and
migration in adaptation to sink environments, Dryad, 10.5061/dryad.s42n1.'
mla: 'Lagator, Mato, et al. Data from: Role of Sex and Migration in Adaptation
to Sink Environments. Dryad, 2014, doi:10.5061/dryad.s42n1.'
short: M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014).
date_created: 2021-07-28T15:32:55Z
date_published: 2014-04-17T00:00:00Z
date_updated: 2023-02-23T10:27:31Z
day: '17'
department:
- _id: CaGu
doi: 10.5061/dryad.s42n1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.s42n1
month: '04'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2083'
relation: used_in_publication
status: public
status: public
title: 'Data from: Role of sex and migration in adaptation to sink environments'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9752'
abstract:
- lang: eng
text: Redundancies and correlations in the responses of sensory neurons may seem
to waste neural resources, but they can also carry cues about structured stimuli
and may help the brain to correct for response errors. To investigate the effect
of stimulus structure on redundancy in retina, we measured simultaneous responses
from populations of retinal ganglion cells presented with natural and artificial
stimuli that varied greatly in correlation structure; these stimuli and recordings
are publicly available online. Responding to spatio-temporally structured stimuli
such as natural movies, pairs of ganglion cells were modestly more correlated
than in response to white noise checkerboards, but they were much less correlated
than predicted by a non-adapting functional model of retinal response. Meanwhile,
responding to stimuli with purely spatial correlations, pairs of ganglion cells
showed increased correlations consistent with a static, non-adapting receptive
field and nonlinearity. We found that in response to spatio-temporally correlated
stimuli, ganglion cells had faster temporal kernels and tended to have stronger
surrounds. These properties of individual cells, along with gain changes that
opposed changes in effective contrast at the ganglion cell input, largely explained
the pattern of pairwise correlations across stimuli where receptive field measurements
were possible.
article_processing_charge: No
author:
- first_name: Kristina
full_name: Simmons, Kristina
last_name: Simmons
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Jan
full_name: Homann, Jan
last_name: Homann
- first_name: Heather
full_name: Yee, Heather
last_name: Yee
- first_name: Stephanie
full_name: Palmer, Stephanie
last_name: Palmer
- first_name: Philip
full_name: Nelson, Philip
last_name: Nelson
- first_name: Vijay
full_name: Balasubramanian, Vijay
last_name: Balasubramanian
citation:
ama: 'Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus
correlations by the retina. 2014. doi:10.5061/dryad.246qg'
apa: 'Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., …
Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations
by the retina. Dryad. https://doi.org/10.5061/dryad.246qg'
chicago: 'Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather
Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation
of Stimulus Correlations by the Retina.” Dryad, 2014. https://doi.org/10.5061/dryad.246qg.'
ieee: 'K. Simmons et al., “Data from: Transformation of stimulus correlations
by the retina.” Dryad, 2014.'
ista: 'Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian
V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad,
10.5061/dryad.246qg.'
mla: 'Simmons, Kristina, et al. Data from: Transformation of Stimulus Correlations
by the Retina. Dryad, 2014, doi:10.5061/dryad.246qg.'
short: K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson,
V. Balasubramanian, (2014).
date_created: 2021-07-30T08:13:52Z
date_published: 2014-11-07T00:00:00Z
date_updated: 2023-02-23T10:35:57Z
day: '07'
department:
- _id: GaTk
doi: 10.5061/dryad.246qg
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.246qg
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2277'
relation: used_in_publication
status: public
status: public
title: 'Data from: Transformation of stimulus correlations by the retina'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9753'
abstract:
- lang: eng
text: 'Background: The brood of ants and other social insects is highly susceptible
to pathogens, particularly those that penetrate the soft larval and pupal cuticle.
We here test whether the presence of a pupal cocoon, which occurs in some ant
species but not in others, affects the sanitary brood care and fungal infection
patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We
use a) a comparative approach analysing four species with either naked or cocooned
pupae and b) a within-species analysis of a single ant species, in which both
pupal types co-exist in the same colony. Results: We found that the presence of
a cocoon did not compromise fungal pathogen detection by the ants and that species
with cocooned pupae increased brood grooming after pathogen exposure. All tested
ant species further removed brood from their nests, which was predominantly expressed
towards larvae and naked pupae treated with the live fungal pathogen. In contrast,
cocooned pupae exposed to live fungus were not removed at higher rates than cocooned
pupae exposed to dead fungus or a sham control. Consistent with this, exposure
to the live fungus caused high numbers of infections and fungal outgrowth in larvae
and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed
the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion:
Our study suggests that the pupal cocoon has a protective effect against fungal
infection, causing an adaptive change in sanitary behaviours by the ants. It further
demonstrates that brood removal - originally described for honeybees as “hygienic
behaviour” – is a widespread sanitary behaviour in ants, which likely has important
implications on disease dynamics in social insect colonies.'
article_processing_charge: No
author:
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Michel
full_name: Chapuisat, Michel
last_name: Chapuisat
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Data from: Pupal cocoons
affect sanitary brood care and limit fungal infections in ant colonies. 2014.
doi:10.5061/dryad.nc0gc'
apa: 'Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., & Cremer, S. (2014).
Data from: Pupal cocoons affect sanitary brood care and limit fungal infections
in ant colonies. Dryad. https://doi.org/10.5061/dryad.nc0gc'
chicago: 'Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia
Cremer. “Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal
Infections in Ant Colonies.” Dryad, 2014. https://doi.org/10.5061/dryad.nc0gc.'
ieee: 'S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Data
from: Pupal cocoons affect sanitary brood care and limit fungal infections in
ant colonies.” Dryad, 2014.'
ista: 'Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2014. Data from:
Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies,
Dryad, 10.5061/dryad.nc0gc.'
mla: 'Tragust, Simon, et al. Data from: Pupal Cocoons Affect Sanitary Brood Care
and Limit Fungal Infections in Ant Colonies. Dryad, 2014, doi:10.5061/dryad.nc0gc.'
short: S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, (2014).
date_created: 2021-07-30T08:24:11Z
date_published: 2014-10-08T00:00:00Z
date_updated: 2023-02-23T10:36:17Z
day: '08'
department:
- _id: SyCr
doi: 10.5061/dryad.nc0gc
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.nc0gc
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2284'
relation: used_in_publication
status: public
status: public
title: 'Data from: Pupal cocoons affect sanitary brood care and limit fungal infections
in ant colonies'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9888'
abstract:
- lang: eng
text: Detailed description of the experimental prodedures, data analyses and additional
statistical analyses of the results.
article_processing_charge: No
author:
- first_name: Stephan
full_name: Wolf, Stephan
last_name: Wolf
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Ka
full_name: Lim, Ka
last_name: Lim
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Suzanne
full_name: Clark, Suzanne
last_name: Clark
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
- first_name: Juliet
full_name: Osborne, Juliet
last_name: Osborne
citation:
ama: Wolf S, Mcmahon D, Lim K, et al. Supporting information. 2014. doi:10.1371/journal.pone.0103989.s003
apa: Wolf, S., Mcmahon, D., Lim, K., Pull, C., Clark, S., Paxton, R., & Osborne,
J. (2014). Supporting information. Public Library of Science. https://doi.org/10.1371/journal.pone.0103989.s003
chicago: Wolf, Stephan, Dino Mcmahon, Ka Lim, Christopher Pull, Suzanne Clark, Robert
Paxton, and Juliet Osborne. “Supporting Information.” Public Library of Science,
2014. https://doi.org/10.1371/journal.pone.0103989.s003.
ieee: S. Wolf et al., “Supporting information.” Public Library of Science,
2014.
ista: Wolf S, Mcmahon D, Lim K, Pull C, Clark S, Paxton R, Osborne J. 2014. Supporting
information, Public Library of Science, 10.1371/journal.pone.0103989.s003.
mla: Wolf, Stephan, et al. Supporting Information. Public Library of Science,
2014, doi:10.1371/journal.pone.0103989.s003.
short: S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, (2014).
date_created: 2021-08-11T14:17:53Z
date_updated: 2023-02-23T10:27:38Z
day: '06'
department:
- _id: SyCr
doi: 10.1371/journal.pone.0103989.s003
month: '08'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '2086'
relation: used_in_publication
status: public
status: public
title: Supporting information
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9931'
abstract:
- lang: eng
text: Gene duplication is important in evolution, because it provides new raw material
for evolutionary adaptations. Several existing hypotheses about the causes of
duplicate retention and diversification differ in their emphasis on gene dosage,
subfunctionalization, and neofunctionalization. Little experimental data exist
on the relative importance of gene expression changes and changes in coding regions
for the evolution of duplicate genes. Furthermore, we do not know how strongly
the environment could affect this importance. To address these questions, we performed
evolution experiments with the TEM-1 beta lactamase gene in Escherichia coli to
study the initial stages of duplicate gene evolution in the laboratory. We mimicked
tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid.
We then subjected these copies to repeated cycles of mutagenesis and selection
in various environments that contained antibiotics in different combinations and
concentrations. Our experiments showed that gene dosage is the most important
factor in the initial stages of duplicate gene evolution, and overshadows the
importance of point mutations in the coding region.
acknowledgement: We thank the Functional Genomics Center Zurich for its service in
generating sequencing data, M. Ackermann and E. Hayden for helpful discussions,
A. de Visser for comments on earlier versions of this manuscript, and M. Moser for
help with quantitative PCR. This work was supported by Swiss National Science Foundation
(grant 315230–129708), as well as through the YeastX project of SystemsX.ch, and
the University Priority Research Program in Systems Biology at the University of
Zurich. RD acknowledges support from the Forschungskredit program of the University
of Zurich. The authors declare no conflict of interest.
article_processing_charge: No
article_type: original
author:
- first_name: Riddhiman
full_name: Dhar, Riddhiman
last_name: Dhar
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Andreas
full_name: Wagner, Andreas
last_name: Wagner
citation:
ama: Dhar R, Bergmiller T, Wagner A. Increased gene dosage plays a predominant role
in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution.
2014;68(6):1775-1791. doi:10.1111/evo.12373
apa: Dhar, R., Bergmiller, T., & Wagner, A. (2014). Increased gene dosage plays
a predominant role in the initial stages of evolution of duplicate TEM-1 beta
lactamase genes. Evolution. Wiley. https://doi.org/10.1111/evo.12373
chicago: Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Increased Gene
Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate
TEM-1 Beta Lactamase Genes.” Evolution. Wiley, 2014. https://doi.org/10.1111/evo.12373.
ieee: R. Dhar, T. Bergmiller, and A. Wagner, “Increased gene dosage plays a predominant
role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes,”
Evolution, vol. 68, no. 6. Wiley, pp. 1775–1791, 2014.
ista: Dhar R, Bergmiller T, Wagner A. 2014. Increased gene dosage plays a predominant
role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes.
Evolution. 68(6), 1775–1791.
mla: Dhar, Riddhiman, et al. “Increased Gene Dosage Plays a Predominant Role in
the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” Evolution,
vol. 68, no. 6, Wiley, 2014, pp. 1775–91, doi:10.1111/evo.12373.
short: R. Dhar, T. Bergmiller, A. Wagner, Evolution 68 (2014) 1775–1791.
date_created: 2021-08-17T09:03:09Z
date_published: 2014-06-03T00:00:00Z
date_updated: 2023-02-23T14:13:27Z
day: '03'
department:
- _id: CaGu
doi: 10.1111/evo.12373
external_id:
pmid:
- '24495000'
intvolume: ' 68'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 1775-1791
pmid: 1
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '9932'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Increased gene dosage plays a predominant role in the initial stages of evolution
of duplicate TEM-1 beta lactamase genes
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 68
year: '2014'
...
---
_id: '9932'
abstract:
- lang: eng
text: Gene duplication is important in evolution, because it provides new raw material
for evolutionary adaptations. Several existing hypotheses about the causes of
duplicate retention and diversification differ in their emphasis on gene dosage,
sub-functionalization, and neo-functionalization. Little experimental data exists
on the relative importance of gene expression changes and changes in coding regions
for the evolution of duplicate genes. Furthermore, we do not know how strongly
the environment could affect this importance. To address these questions, we performed
evolution experiments with the TEM-1 beta lactamase gene in E. coli to study the
initial stages of duplicate gene evolution in the laboratory. We mimicked tandem
duplication by inserting two copies of the TEM-1 gene on the same plasmid. We
then subjected these copies to repeated cycles of mutagenesis and selection in
various environments that contained antibiotics in different combinations and
concentrations. Our experiments showed that gene dosage is the most important
factor in the initial stages of duplicate gene evolution, and overshadows the
importance of point mutations in the coding region.
article_processing_charge: No
author:
- first_name: Riddhiman
full_name: Dhar, Riddhiman
last_name: Dhar
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Andreas
full_name: Wagner, Andreas
last_name: Wagner
citation:
ama: 'Dhar R, Bergmiller T, Wagner A. Data from: Increased gene dosage plays a predominant
role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes.
2014. doi:10.5061/dryad.jc402'
apa: 'Dhar, R., Bergmiller, T., & Wagner, A. (2014). Data from: Increased gene
dosage plays a predominant role in the initial stages of evolution of duplicate
TEM-1 beta lactamase genes. Dryad. https://doi.org/10.5061/dryad.jc402'
chicago: 'Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Data from: Increased
Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate
TEM-1 Beta Lactamase Genes.” Dryad, 2014. https://doi.org/10.5061/dryad.jc402.'
ieee: 'R. Dhar, T. Bergmiller, and A. Wagner, “Data from: Increased gene dosage
plays a predominant role in the initial stages of evolution of duplicate TEM-1
beta lactamase genes.” Dryad, 2014.'
ista: 'Dhar R, Bergmiller T, Wagner A. 2014. Data from: Increased gene dosage plays
a predominant role in the initial stages of evolution of duplicate TEM-1 beta
lactamase genes, Dryad, 10.5061/dryad.jc402.'
mla: 'Dhar, Riddhiman, et al. Data from: Increased Gene Dosage Plays a Predominant
Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.
Dryad, 2014, doi:10.5061/dryad.jc402.'
short: R. Dhar, T. Bergmiller, A. Wagner, (2014).
date_created: 2021-08-17T09:11:40Z
date_published: 2014-01-27T00:00:00Z
date_updated: 2023-02-23T14:13:24Z
day: '27'
department:
- _id: CaGu
doi: 10.5061/dryad.jc402
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.jc402
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9931'
relation: used_in_publication
status: public
status: public
title: 'Data from: Increased gene dosage plays a predominant role in the initial stages
of evolution of duplicate TEM-1 beta lactamase genes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '2443'
abstract:
- lang: eng
text: The mode of action of auxin is based on its non-uniform distribution within
tissues and organs. Despite the wide use of several auxin analogues in research
and agriculture, little is known about the specificity of different auxin-related
transport and signalling processes towards these compounds. Using seedlings of
Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2),
the physiological activity of several auxin analogues was investigated, together
with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis
and to be transported across the plasma membrane. This study shows that the specificity
criteria for different auxin-related processes vary widely. Notably, the special
behaviour of some synthetic auxin analogues suggests that they might be useful
tools in investigations of the molecular mechanism of auxin action. Thus, due
to their differential stimulatory effects on DR5 expression, indole-3-propionic
(IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of
TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin
signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate
between transcriptional and non-transcriptional pathways of auxin signalling.
The results demonstrate that the major determinants for the auxin-like physiological
potential of a particular compound are very complex and involve its chemical and
metabolic stability, its ability to distribute in tissues in a polar manner and
its activity towards auxin signalling machinery.
acknowledgement: The authors thank Dr Christian Luschnig (University of Natural Resources
and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor
Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds
and, last but not least, to Dr David Morris for critical reading of the manuscript.
We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance.
This work was supported by the Grant Agency of the Czech Republic (P305/11/0797
to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project
CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European
Research Council starting independent research grant ERC-2011-StG-20101109-PSDP
(to J.F.).
article_processing_charge: No
article_type: original
author:
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Martin
full_name: Kubeš, Martin
last_name: Kubeš
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Petre
full_name: Dobrev, Petre
last_name: Dobrev
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
citation:
ama: 'Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along
the auxin response chain: A study using auxin analogues. New Phytologist.
2013;200(4):1034-1048. doi:10.1111/nph.12437'
apa: 'Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová,
E. (2013). Defining the selectivity of processes along the auxin response chain:
A study using auxin analogues. New Phytologist. Wiley. https://doi.org/10.1111/nph.12437'
chicago: 'Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev,
Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes
along the Auxin Response Chain: A Study Using Auxin Analogues.” New Phytologist.
Wiley, 2013. https://doi.org/10.1111/nph.12437.'
ieee: 'S. Simon et al., “Defining the selectivity of processes along the
auxin response chain: A study using auxin analogues,” New Phytologist,
vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.'
ista: 'Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová
E. 2013. Defining the selectivity of processes along the auxin response chain:
A study using auxin analogues. New Phytologist. 200(4), 1034–1048.'
mla: 'Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin
Response Chain: A Study Using Auxin Analogues.” New Phytologist, vol. 200,
no. 4, Wiley, 2013, pp. 1034–48, doi:10.1111/nph.12437.'
short: S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek,
E. Zažímalová, New Phytologist 200 (2013) 1034–1048.
date_created: 2018-12-11T11:57:41Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2025-05-07T11:12:32Z
day: '01'
department:
- _id: JiFr
doi: 10.1111/nph.12437
ec_funded: 1
intvolume: ' 200'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/nph.12437
month: '12'
oa: 1
oa_version: Published Version
page: 1034 - 1048
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: New Phytologist
publication_status: published
publisher: Wiley
publist_id: '4460'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Defining the selectivity of processes along the auxin response chain: A study
using auxin analogues'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 200
year: '2013'
...
---
_id: '2444'
abstract:
- lang: eng
text: 'We consider two core algorithmic problems for probabilistic verification:
the maximal end-component decomposition and the almost-sure reachability set computation
for Markov decision processes (MDPs). For MDPs with treewidth k, we present two
improved static algorithms for both the problems that run in time O(n·k 2.38·2k
) and O(m·logn· k), respectively, where n is the number of states and m is the
number of edges, significantly improving the previous known O(n·k·√n· k) bound
for low treewidth. We also present decremental algorithms for both problems for
MDPs with constant treewidth that run in amortized logarithmic time, which is
a huge improvement over the previously known algorithms that require amortized
linear time.'
alternative_title:
- LNCS
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Jakub
full_name: Ła̧Cki, Jakub
last_name: Ła̧Cki
citation:
ama: Chatterjee K, Ła̧Cki J. Faster algorithms for Markov decision processes with
low treewidth. 2013;8044:543-558. doi:10.1007/978-3-642-39799-8_36
apa: 'Chatterjee, K., & Ła̧Cki, J. (2013). Faster algorithms for Markov decision
processes with low treewidth. Presented at the CAV: Computer Aided Verification,
St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_36'
chicago: Chatterjee, Krishnendu, and Jakub Ła̧Cki. “Faster Algorithms for Markov
Decision Processes with Low Treewidth.” Lecture Notes in Computer Science. Springer,
2013. https://doi.org/10.1007/978-3-642-39799-8_36.
ieee: K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes
with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013.
ista: Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes
with low treewidth. 8044, 543–558.
mla: Chatterjee, Krishnendu, and Jakub Ła̧Cki. Faster Algorithms for Markov Decision
Processes with Low Treewidth. Vol. 8044, Springer, 2013, pp. 543–58, doi:10.1007/978-3-642-39799-8_36.
short: K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558.
conference:
end_date: 2013-07-19
location: St. Petersburg, Russia
name: 'CAV: Computer Aided Verification'
start_date: 2013-07-13
date_created: 2018-12-11T11:57:42Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2020-08-11T10:09:47Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-642-39799-8_36
ec_funded: 1
external_id:
arxiv:
- '1304.0084'
intvolume: ' 8044'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1304.0084
month: '07'
oa: 1
oa_version: Preprint
page: 543 - 558
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '4459'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Faster algorithms for Markov decision processes with low treewidth
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8044
year: '2013'
...
---
_id: '2445'
abstract:
- lang: eng
text: We develop program synthesis techniques that can help programmers fix concurrency-related
bugs. We make two new contributions to synthesis for concurrency, the first improving
the efficiency of the synthesized code, and the second improving the efficiency
of the synthesis procedure itself. The first contribution is to have the synthesis
procedure explore a variety of (sequential) semantics-preserving program transformations.
Classically, only one such transformation has been considered, namely, the insertion
of synchronization primitives (such as locks). Based on common manual bug-fixing
techniques used by Linux device-driver developers, we explore additional, more
efficient transformations, such as the reordering of independent instructions.
The second contribution is to speed up the counterexample-guided removal of concurrency
bugs within the synthesis procedure by considering partial-order traces (instead
of linear traces) as counterexamples. A partial-order error trace represents a
set of linear (interleaved) traces of a concurrent program all of which lead to
the same error. By eliminating a partial-order error trace, we eliminate in a
single iteration of the synthesis procedure all linearizations of the partial-order
trace. We evaluated our techniques on several simplified examples of real concurrency
bugs that occurred in Linux device drivers.
alternative_title:
- LNCS
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- 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: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Leonid
full_name: Ryzhyk, Leonid
last_name: Ryzhyk
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: 'Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. Efficient synthesis
for concurrency by semantics-preserving transformations. In: Vol 8044. Springer;
2013:951-967. doi:10.1007/978-3-642-39799-8_68'
apa: 'Cerny, P., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., & Tarrach,
T. (2013). Efficient synthesis for concurrency by semantics-preserving transformations
(Vol. 8044, pp. 951–967). Presented at the CAV: Computer Aided Verification, St.
Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_68'
chicago: Cerny, Pavol, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, and
Thorsten Tarrach. “Efficient Synthesis for Concurrency by Semantics-Preserving
Transformations,” 8044:951–67. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_68.
ieee: 'P. Cerny, T. A. Henzinger, A. Radhakrishna, L. Ryzhyk, and T. Tarrach, “Efficient
synthesis for concurrency by semantics-preserving transformations,” presented
at the CAV: Computer Aided Verification, St. Petersburg, Russia, 2013, vol. 8044,
pp. 951–967.'
ista: 'Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. 2013. Efficient
synthesis for concurrency by semantics-preserving transformations. CAV: Computer
Aided Verification, LNCS, vol. 8044, 951–967.'
mla: Cerny, Pavol, et al. Efficient Synthesis for Concurrency by Semantics-Preserving
Transformations. Vol. 8044, Springer, 2013, pp. 951–67, doi:10.1007/978-3-642-39799-8_68.
short: P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer,
2013, pp. 951–967.
conference:
end_date: 2013-07-19
location: St. Petersburg, Russia
name: 'CAV: Computer Aided Verification'
start_date: 2013-07-13
date_created: 2018-12-11T11:57:42Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2023-09-07T11:57:01Z
day: '01'
ddc:
- '000'
- '004'
department:
- _id: ToHe
doi: 10.1007/978-3-642-39799-8_68
ec_funded: 1
file:
- access_level: open_access
checksum: 70c70ca5487faba82262c63e1b678a27
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:37Z
date_updated: 2020-07-14T12:45:40Z
file_id: '5158'
file_name: IST-2014-199-v1+1_cav2013-final.pdf
file_size: 365548
relation: main_file
file_date_updated: 2020-07-14T12:45:40Z
has_accepted_license: '1'
intvolume: ' 8044'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 951 - 967
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '4458'
pubrep_id: '199'
quality_controlled: '1'
related_material:
record:
- id: '1130'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Efficient synthesis for concurrency by semantics-preserving transformations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8044
year: '2013'
...
---
_id: '2446'
abstract:
- lang: eng
text: The model-checking problem for probabilistic systems crucially relies on the
translation of LTL to deterministic Rabin automata (DRW). Our recent Safraless
translation [KE12, GKE12] for the LTL(F,G) fragment produces smaller automata
as compared to the traditional approach. In this work, instead of DRW we consider
deterministic automata with acceptance condition given as disjunction of generalized
Rabin pairs (DGRW). The Safraless translation of LTL(F,G) formulas to DGRW results
in smaller automata as compared to DRW. We present algorithms for probabilistic
model-checking as well as game solving for DGRW conditions. Our new algorithms
lead to improvement both in terms of theoretical bounds as well as practical evaluation.
We compare PRISM with and without our new translation, and show that the new translation
leads to significant improvements.
alternative_title:
- LNCS
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Gaiser, Andreas
last_name: Gaiser
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: Chatterjee K, Gaiser A, Kretinsky J. Automata with generalized Rabin pairs
for probabilistic model checking and LTL synthesis. 2013;8044:559-575. doi:10.1007/978-3-642-39799-8_37
apa: 'Chatterjee, K., Gaiser, A., & Kretinsky, J. (2013). Automata with generalized
Rabin pairs for probabilistic model checking and LTL synthesis. Presented at the
CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_37'
chicago: Chatterjee, Krishnendu, Andreas Gaiser, and Jan Kretinsky. “Automata with
Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis.” Lecture
Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_37.
ieee: K. Chatterjee, A. Gaiser, and J. Kretinsky, “Automata with generalized Rabin
pairs for probabilistic model checking and LTL synthesis,” vol. 8044. Springer,
pp. 559–575, 2013.
ista: Chatterjee K, Gaiser A, Kretinsky J. 2013. Automata with generalized Rabin
pairs for probabilistic model checking and LTL synthesis. 8044, 559–575.
mla: Chatterjee, Krishnendu, et al. Automata with Generalized Rabin Pairs for
Probabilistic Model Checking and LTL Synthesis. Vol. 8044, Springer, 2013,
pp. 559–75, doi:10.1007/978-3-642-39799-8_37.
short: K. Chatterjee, A. Gaiser, J. Kretinsky, 8044 (2013) 559–575.
conference:
end_date: 2013-07-19
location: St. Petersburg, Russia
name: 'CAV: Computer Aided Verification'
start_date: 2013-07-13
date_created: 2018-12-11T11:57:42Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2020-08-11T10:09:47Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-642-39799-8_37
ec_funded: 1
external_id:
arxiv:
- '1304.5281'
intvolume: ' 8044'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1304.5281
month: '07'
oa: 1
oa_version: Preprint
page: 559 - 575
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '4457'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Automata with generalized Rabin pairs for probabilistic model checking and
LTL synthesis
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8044
year: '2013'
...
---
_id: '2447'
abstract:
- lang: eng
text: "Separation logic (SL) has gained widespread popularity because of its ability
to succinctly express complex invariants of a program’s heap configurations. Several
specialized provers have been developed for decidable SL fragments. However, these
provers cannot be easily extended or combined with solvers for other theories
that are important in program verification, e.g., linear arithmetic. In this paper,
we present a reduction of decidable SL fragments to a decidable first-order theory
that fits well into the satisfiability modulo theories (SMT) framework. We show
how to use this reduction to automate satisfiability, entailment, frame inference,
and abduction problems for separation logic using SMT solvers. Our approach provides
a simple method of integrating separation logic into existing verification tools
that provide SMT backends, and an elegant way of combining SL fragments with other
decidable first-order theories. We implemented this approach in a verification
tool and applied it to heap-manipulating programs whose verification involves
reasoning in theory combinations.\r\n"
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Ruzica
full_name: Piskac, Ruzica
last_name: Piskac
- 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
citation:
ama: Piskac R, Wies T, Zufferey D. Automating separation logic using SMT. 2013;8044:773-789.
doi:10.1007/978-3-642-39799-8_54
apa: 'Piskac, R., Wies, T., & Zufferey, D. (2013). Automating separation logic
using SMT. Presented at the CAV: Computer Aided Verification, St. Petersburg,
Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_54'
chicago: Piskac, Ruzica, Thomas Wies, and Damien Zufferey. “Automating Separation
Logic Using SMT.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_54.
ieee: R. Piskac, T. Wies, and D. Zufferey, “Automating separation logic using SMT,”
vol. 8044. Springer, pp. 773–789, 2013.
ista: Piskac R, Wies T, Zufferey D. 2013. Automating separation logic using SMT.
8044, 773–789.
mla: Piskac, Ruzica, et al. Automating Separation Logic Using SMT. Vol. 8044,
Springer, 2013, pp. 773–89, doi:10.1007/978-3-642-39799-8_54.
short: R. Piskac, T. Wies, D. Zufferey, 8044 (2013) 773–789.
conference:
end_date: 2013-07-19
location: St. Petersburg, Russia
name: 'CAV: Computer Aided Verification'
start_date: 2013-07-13
date_created: 2018-12-11T11:57:43Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2020-08-11T10:09:47Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-642-39799-8_54
file:
- access_level: open_access
checksum: 2e866932ab688f47ecd504acb4d5c7d4
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T11:13:01Z
date_updated: 2020-07-14T12:45:41Z
file_id: '7859'
file_name: 2013_CAV_Piskac.pdf
file_size: 309182
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 8044'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 773 - 789
publication_status: published
publisher: Springer
publist_id: '4456'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Automating separation logic using SMT
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8044
year: '2013'
...
---
_id: '2448'
abstract:
- lang: eng
text: Cell-to-cell directional flow of the phytohormone auxin is primarily established
by polar localization of the PIN auxin transporters, a process tightly regulated
at multiple levels by auxin itself. We recently reported that, in the context
of strong auxin flows, activity of the vacuolar ZIFL1.1 transporter is required
for fine-tuning of polar auxin transport rates in the Arabidopsis root. In particular,
ZIFL1.1 function protects plasma-membrane stability of the PIN2 carrier in epidermal
root tip cells under conditions normally triggering PIN2 degradation. Here, we
show that ZIFL1.1 activity at the root tip also promotes PIN1 plasma-membrane
abundance in central cylinder cells, thus supporting the notion that ZIFL1.1 acts
as a general positive modulator of polar auxin transport in roots.
article_number: e25688
article_processing_charge: No
article_type: original
author:
- first_name: Estelle
full_name: Remy, Estelle
last_name: Remy
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Paula
full_name: Duque, Paula
last_name: Duque
citation:
ama: Remy E, Baster P, Friml J, Duque P. ZIFL1.1 transporter modulates polar auxin
transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root
tip. Plant Signaling & Behavior. 2013;8(10). doi:10.4161/psb.25688
apa: Remy, E., Baster, P., Friml, J., & Duque, P. (2013). ZIFL1.1 transporter
modulates polar auxin transport by stabilizing membrane abundance of multiple
PINs in Arabidopsis root tip. Plant Signaling & Behavior. Taylor &
Francis. https://doi.org/10.4161/psb.25688
chicago: Remy, Estelle, Pawel Baster, Jiří Friml, and Paula Duque. “ZIFL1.1 Transporter
Modulates Polar Auxin Transport by Stabilizing Membrane Abundance of Multiple
PINs in Arabidopsis Root Tip.” Plant Signaling & Behavior. Taylor &
Francis, 2013. https://doi.org/10.4161/psb.25688.
ieee: E. Remy, P. Baster, J. Friml, and P. Duque, “ZIFL1.1 transporter modulates
polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis
root tip,” Plant Signaling & Behavior, vol. 8, no. 10. Taylor &
Francis, 2013.
ista: Remy E, Baster P, Friml J, Duque P. 2013. ZIFL1.1 transporter modulates polar
auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis
root tip. Plant Signaling & Behavior. 8(10), e25688.
mla: Remy, Estelle, et al. “ZIFL1.1 Transporter Modulates Polar Auxin Transport
by Stabilizing Membrane Abundance of Multiple PINs in Arabidopsis Root Tip.” Plant
Signaling & Behavior, vol. 8, no. 10, e25688, Taylor & Francis, 2013,
doi:10.4161/psb.25688.
short: E. Remy, P. Baster, J. Friml, P. Duque, Plant Signaling & Behavior 8
(2013).
date_created: 2018-12-11T11:57:43Z
date_published: 2013-07-10T00:00:00Z
date_updated: 2025-05-07T11:12:32Z
day: '10'
department:
- _id: JiFr
doi: 10.4161/psb.25688
ec_funded: 1
external_id:
pmid:
- '23857365'
intvolume: ' 8'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091088/
month: '07'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Plant Signaling & Behavior
publication_status: published
publisher: Taylor & Francis
publist_id: '4455'
quality_controlled: '1'
scopus_import: '1'
status: public
title: ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane
abundance of multiple PINs in Arabidopsis root tip
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2013'
...
---
_id: '2449'
abstract:
- lang: eng
text: 'Intracellular protein routing is mediated by vesicular transport which is
tightly regulated in eukaryotes. The protein and lipid homeostasis depends on
coordinated delivery of de novo synthesized or recycled cargoes to the plasma
membrane by exocytosis and their subsequent removal by rerouting them for recycling
or degradation. Here, we report the characterization of protein affected trafficking
3 (pat3) mutant that we identified by an epifluorescence-based forward genetic
screen for mutants defective in subcellular distribution of Arabidopsis auxin
transporter PIN1–GFP. While pat3 displays largely normal plant morphology and
development in nutrient-rich conditions, it shows strong ectopic intracellular
accumulations of different plasma membrane cargoes in structures that resemble
prevacuolar compartments (PVC) with an aberrant morphology. Genetic mapping revealed
that pat3 is defective in vacuolar protein sorting 35A (VPS35A), a putative subunit
of the retromer complex that mediates retrograde trafficking between the PVC and
trans-Golgi network. Similarly, a mutant defective in another retromer subunit,
vps29, shows comparable subcellular defects in PVC morphology and protein accumulation.
Thus, our data provide evidence that the retromer components VPS35A and VPS29
are essential for normal PVC morphology and normal trafficking of plasma membrane
proteins in plants. In addition, we show that, out of the three VPS35 retromer
subunits present in Arabidopsis thaliana genome, the VPS35 homolog A plays a prevailing
role in trafficking to the lytic vacuole, presenting another level of complexity
in the retromer-dependent vacuolar sorting. '
author:
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Murguel
full_name: Feraru, Murguel
last_name: Feraru
- first_name: Sibylle
full_name: Hirsch, Sibylle
last_name: Hirsch
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Claudiu
full_name: Nicuales, Claudiu
last_name: Nicuales
- first_name: Jelle
full_name: Van Leene, Jelle
last_name: Van Leene
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Nodzyński T, Feraru M, Hirsch S, et al. Retromer subunits VPS35A and VPS29
mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant.
2013;6(6):1849-1862. doi:10.1093/mp/sst044
apa: Nodzyński, T., Feraru, M., Hirsch, S., De Rycke, R., Nicuales, C., Van Leene,
J., … Friml, J. (2013). Retromer subunits VPS35A and VPS29 mediate prevacuolar
compartment (PVC) function in Arabidopsis. Molecular Plant. Cell Press.
https://doi.org/10.1093/mp/sst044
chicago: Nodzyński, Tomasz, Murguel Feraru, Sibylle Hirsch, Riet De Rycke, Claudiu
Nicuales, Jelle Van Leene, Geert De Jaeger, Steffen Vanneste, and Jiří Friml.
“Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function
in Arabidopsis.” Molecular Plant. Cell Press, 2013. https://doi.org/10.1093/mp/sst044.
ieee: T. Nodzyński et al., “Retromer subunits VPS35A and VPS29 mediate prevacuolar
compartment (PVC) function in Arabidopsis,” Molecular Plant, vol. 6, no.
6. Cell Press, pp. 1849–1862, 2013.
ista: Nodzyński T, Feraru M, Hirsch S, De Rycke R, Nicuales C, Van Leene J, De Jaeger
G, Vanneste S, Friml J. 2013. Retromer subunits VPS35A and VPS29 mediate prevacuolar
compartment (PVC) function in Arabidopsis. Molecular Plant. 6(6), 1849–1862.
mla: Nodzyński, Tomasz, et al. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar
Compartment (PVC) Function in Arabidopsis.” Molecular Plant, vol. 6, no.
6, Cell Press, 2013, pp. 1849–62, doi:10.1093/mp/sst044.
short: T. Nodzyński, M. Feraru, S. Hirsch, R. De Rycke, C. Nicuales, J. Van Leene,
G. De Jaeger, S. Vanneste, J. Friml, Molecular Plant 6 (2013) 1849–1862.
date_created: 2018-12-11T11:57:44Z
date_published: 2013-11-01T00:00:00Z
date_updated: 2021-01-12T06:57:33Z
day: '01'
department:
- _id: JiFr
doi: 10.1093/mp/sst044
intvolume: ' 6'
issue: '6'
language:
- iso: eng
month: '11'
oa_version: None
page: 1849 - 1862
publication: Molecular Plant
publication_status: published
publisher: Cell Press
publist_id: '4454'
quality_controlled: '1'
scopus_import: 1
status: public
title: Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function
in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2013'
...
---
_id: '2466'
abstract:
- lang: eng
text: 'We introduce a new method for efficiently simulating liquid with extreme
amounts of spatial adaptivity. Our method combines several key components to drastically
speed up the simulation of large-scale fluid phenomena: We leverage an alternative
Eulerian tetrahedral mesh discretization to significantly reduce the complexity
of the pressure solve while increasing the robustness with respect to element
quality and removing the possibility of locking. Next, we enable subtle free-surface
phenomena by deriving novel second-order boundary conditions consistent with our
discretization. We couple this discretization with a spatially adaptive Fluid-Implicit
Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations
that can undergo sharp changes in spatial resolution while minimizing artifacts.
Along the way, we provide a new method for generating a smooth and detailed surface
from a set of particles with variable sizes. Finally, we explore several new sizing
functions for determining spatially adaptive simulation resolutions, and we show
how to couple them to our simulator. We combine each of these elements to produce
a simulation algorithm that is capable of creating animations at high maximum
resolutions while avoiding common pitfalls like inaccurate boundary conditions
and inefficient computation.'
article_number: '103'
article_processing_charge: No
author:
- first_name: Ryoichi
full_name: Ando, Ryoichi
last_name: Ando
- first_name: Nils
full_name: Thuerey, Nils
last_name: Thuerey
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
date_created: 2018-12-11T11:57:50Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2024-11-19T11:56:45Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2461912.2461982
file:
- access_level: open_access
checksum: aeea6b0ff2b27c695aeb8408c7d2fc50
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:25Z
date_updated: 2020-07-14T12:45:41Z
file_id: '5279'
file_name: IST-2016-605-v1+1_tetflip_fixed.pdf
file_size: 8601561
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 32'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '4436'
pubrep_id: '605'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Highly adaptive liquid simulations on tetrahedral meshes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2013'
...
---
_id: '2467'
abstract:
- lang: eng
text: This paper presents a method for computing topology changes for triangle meshes
in an interactive geometric modeling environment. Most triangle meshes in practice
do not exhibit desirable geometric properties, so we develop a solution that is
independent of standard assumptions and robust to geometric errors. Specifically,
we provide the first method for topology change applicable to arbitrary non-solid,
non-manifold, non-closed, self-intersecting surfaces. We prove that this new method
for topology change produces the expected conventional results when applied to
solid (closed, manifold, non-self-intersecting) surfaces---that is, we prove a
backwards-compatibility property relative to prior work. Beyond solid surfaces,
we present empirical evidence that our method remains tolerant to a variety of
surface aberrations through the incorporation of a novel error correction scheme.
Finally, we demonstrate how topology change applied to non-solid objects enables
wholly new and useful behaviors.
article_number: '34'
author:
- first_name: Gilbert
full_name: Bernstein, Gilbert
last_name: Bernstein
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Bernstein G, Wojtan C. Putting holes in holey geometry: Topology change for
arbitrary surfaces. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2462027'
apa: 'Bernstein, G., & Wojtan, C. (2013). Putting holes in holey geometry: Topology
change for arbitrary surfaces. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2462027'
chicago: 'Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry:
Topology Change for Arbitrary Surfaces.” ACM Transactions on Graphics.
ACM, 2013. https://doi.org/10.1145/2461912.2462027.'
ieee: 'G. Bernstein and C. Wojtan, “Putting holes in holey geometry: Topology change
for arbitrary surfaces,” ACM Transactions on Graphics, vol. 32, no. 4.
ACM, 2013.'
ista: 'Bernstein G, Wojtan C. 2013. Putting holes in holey geometry: Topology change
for arbitrary surfaces. ACM Transactions on Graphics. 32(4), 34.'
mla: 'Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology
Change for Arbitrary Surfaces.” ACM Transactions on Graphics, vol. 32,
no. 4, 34, ACM, 2013, doi:10.1145/2461912.2462027.'
short: G. Bernstein, C. Wojtan, ACM Transactions on Graphics 32 (2013).
date_created: 2018-12-11T11:57:50Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2023-02-23T10:44:16Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2461912.2462027
file:
- access_level: open_access
checksum: 9c8425d62246996ca632c5a01870515b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:43Z
date_updated: 2020-07-14T12:45:41Z
file_id: '4768'
file_name: IST-2016-604-v1+1_toptop2013.pdf
file_size: 3514674
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 32'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '4435'
pubrep_id: '604'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Putting holes in holey geometry: Topology change for arbitrary surfaces'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2013'
...
---
_id: '2468'
abstract:
- lang: eng
text: Our work concerns the combination of an Eulerian liquid simulation with a
high-resolution surface tracker (e.g. the level set method or a Lagrangian triangle
mesh). The naive application of a high-resolution surface tracker to a low-resolution
velocity field can produce many visually disturbing physical and topological artifacts
that limit their use in practice. We address these problems by defining an error
function which compares the current state of the surface tracker to the set of
physically valid surface states. By reducing this error with a gradient descent
technique, we introduce a novel physics-based surface fairing method. Similarly,
by treating this error function as a potential energy, we derive a new surface
correction force that mimics the vortex sheet equations. We demonstrate our results
with both level set and mesh-based surface trackers.
article_number: '68'
author:
- first_name: Morten
full_name: Bojsen-Hansen, Morten
id: 439F0C8C-F248-11E8-B48F-1D18A9856A87
last_name: Bojsen-Hansen
orcid: 0000-0002-4417-3224
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Bojsen-Hansen M, Wojtan C. Liquid surface tracking with error compensation.
ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461991
apa: Bojsen-Hansen, M., & Wojtan, C. (2013). Liquid surface tracking with error
compensation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461991
chicago: Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with
Error Compensation.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461991.
ieee: M. Bojsen-Hansen and C. Wojtan, “Liquid surface tracking with error compensation,”
ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013.
ista: Bojsen-Hansen M, Wojtan C. 2013. Liquid surface tracking with error compensation.
ACM Transactions on Graphics. 32(4), 68.
mla: Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error
Compensation.” ACM Transactions on Graphics, vol. 32, no. 4, 68, ACM, 2013,
doi:10.1145/2461912.2461991.
short: M. Bojsen-Hansen, C. Wojtan, ACM Transactions on Graphics 32 (2013).
date_created: 2018-12-11T11:57:50Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2023-02-23T10:44:18Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2461912.2461991
file:
- access_level: open_access
checksum: 53d905e0180e23ef3e813b969ffed4e1
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date_created: 2018-12-12T10:09:37Z
date_updated: 2020-07-14T12:45:41Z
file_id: '4761'
file_name: IST-2016-603-v1+1_liquidError_web.pdf
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has_accepted_license: '1'
intvolume: ' 32'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '4434'
pubrep_id: '603'
quality_controlled: '1'
scopus_import: 1
status: public
title: Liquid surface tracking with error compensation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2013'
...
---
_id: '2469'
abstract:
- lang: eng
text: Cadherins are transmembrane proteins that mediate cell–cell adhesion in animals.
By regulating contact formation and stability, cadherins play a crucial role in
tissue morphogenesis and homeostasis. Here, we review the three major unctions
of cadherins in cell–cell contact formation and stability. Two of those functions
lead to a decrease in interfacial ension at the forming cell–cell contact, thereby
promoting contact expansion — first, by providing adhesion tension that lowers
interfacial tension at the cell–cell contact, and second, by signaling to the
actomyosin cytoskeleton in order to reduce cortex tension and thus interfacial
tension at the contact. The third function of cadherins in cell–cell contact formation
is to stabilize the contact by resisting mechanical forces that pull on the contact.
author:
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
- 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: Maître J-L, Heisenberg C-PJ. Three functions of cadherins in cell adhesion.
Current Biology. 2013;23(14):R626-R633. doi:10.1016/j.cub.2013.06.019
apa: Maître, J.-L., & Heisenberg, C.-P. J. (2013). Three functions of cadherins
in cell adhesion. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.06.019
chicago: Maître, Jean-Léon, and Carl-Philipp J Heisenberg. “Three Functions of Cadherins
in Cell Adhesion.” Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.06.019.
ieee: J.-L. Maître and C.-P. J. Heisenberg, “Three functions of cadherins in cell
adhesion,” Current Biology, vol. 23, no. 14. Cell Press, pp. R626–R633,
2013.
ista: Maître J-L, Heisenberg C-PJ. 2013. Three functions of cadherins in cell adhesion.
Current Biology. 23(14), R626–R633.
mla: Maître, Jean-Léon, and Carl-Philipp J. Heisenberg. “Three Functions of Cadherins
in Cell Adhesion.” Current Biology, vol. 23, no. 14, Cell Press, 2013,
pp. R626–33, doi:10.1016/j.cub.2013.06.019.
short: J.-L. Maître, C.-P.J. Heisenberg, Current Biology 23 (2013) R626–R633.
date_created: 2018-12-11T11:57:51Z
date_published: 2013-07-22T00:00:00Z
date_updated: 2021-01-12T06:57:40Z
day: '22'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1016/j.cub.2013.06.019
external_id:
pmid:
- '23885883'
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creator: dernst
date_created: 2019-01-24T15:40:22Z
date_updated: 2020-07-14T12:45:41Z
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file_name: 2013_CurrentBiology_Maitre.pdf
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relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 23'
issue: '14'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: R626 - R633
pmid: 1
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '4433'
quality_controlled: '1'
scopus_import: 1
status: public
title: Three functions of cadherins in cell adhesion
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2013'
...