---
_id: '9722'
article_processing_charge: No
author:
- first_name: Anna
full_name: Lovrics, Anna
last_name: Lovrics
- first_name: Yu
full_name: Gao, Yu
last_name: Gao
- first_name: Bianka
full_name: Juhász, Bianka
last_name: Juhász
- first_name: István
full_name: Bock, István
last_name: Bock
- first_name: Helen M.
full_name: Byrne, Helen M.
last_name: Byrne
- first_name: András
full_name: Dinnyés, András
last_name: Dinnyés
- first_name: Krisztián
full_name: Kovács, Krisztián
id: 2AB5821E-F248-11E8-B48F-1D18A9856A87
last_name: Kovács
citation:
ama: Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression
states when Dbx2 inhibits Nkx2.2. 2014. doi:10.1371/journal.pone.0111430.s006
apa: Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., &
Kovács, K. (2014). Transition probability between TF expression states when Dbx2
inhibits Nkx2.2. Public Library of Science. https://doi.org/10.1371/journal.pone.0111430.s006
chicago: Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András
Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States
When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0111430.s006.
ieee: A. Lovrics et al., “Transition probability between TF expression states
when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014.
ista: Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition
probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library
of Science, 10.1371/journal.pone.0111430.s006.
mla: Lovrics, Anna, et al. Transition Probability between TF Expression States
When Dbx2 Inhibits Nkx2.2. Public Library of Science, 2014, doi:10.1371/journal.pone.0111430.s006.
short: A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács,
(2014).
date_created: 2021-07-26T14:35:00Z
date_published: 2014-11-14T00:00:00Z
date_updated: 2023-02-23T10:24:07Z
day: '14'
department:
- _id: JoCs
doi: 10.1371/journal.pone.0111430.s006
month: '11'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '2004'
relation: used_in_publication
status: public
status: public
title: Transition probability between TF expression states when Dbx2 inhibits Nkx2.2
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_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: '977'
abstract:
- lang: eng
text: We propose a method for detecting many-body localization (MBL) in disordered
spin systems. The method involves pulsed coherent spin manipulations that probe
the dephasing of a given spin due to its entanglement with a set of distant spins.
It allows one to distinguish the MBL phase from a noninteracting localized phase
and a delocalized phase. In particular, we show that for a properly chosen pulse
sequence the MBL phase exhibits a characteristic power-law decay reflecting its
slow growth of entanglement. We find that this power-law decay is robust with
respect to thermal and disorder averaging, provide numerical simulations supporting
our results, and discuss possible experimental realizations in solid-state and
cold-atom systems.
acknowledgement: |-
We thank E. Altman, Y. Bahri, I. Bloch, T. Giamarchi, D. Huse, V. Oganesyan, A. Pal, D. Pekker, and G. Refael for insightful discussions. The authors acknowledge support from the Harvard Quantum Optics Center, Harvard-MIT CUA, the DARPA OLE program, AFOSR Quantum Simulation MURI, ARO-MURI on Atomtronics, the ARO-MURI Quism program, the Austrian Science Fund (FWF) Project No. J 3361-N20, NSERC grant, and Sloan Research Fellowship. Simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University and the Research Computing Center at Harvard University. Research at Perimeter Institute was supported by the Government of Canada and by the Province of Ontario.
M. S., M. K., and S. G. contributed equally to this work.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Michael
full_name: Knap, Michael J
last_name: Knap
- first_name: Sarang
full_name: Gopalakrishnan, Sarang
last_name: Gopalakrishnan
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Norman
full_name: Yao, Norman Y
last_name: Yao
- first_name: Chris
full_name: Laumann, Chris R
last_name: Laumann
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
- first_name: Mikhail
full_name: Lukin, Mikhail D
last_name: Lukin
- first_name: Eugene
full_name: Demler, Eugene A
last_name: Demler
citation:
ama: Serbyn M, Knap M, Gopalakrishnan S, et al. Interferometric probes of many-body
localization. Physical Review Letters. 2014;113(14). doi:10.1103/PhysRevLett.113.147204
apa: Serbyn, M., Knap, M., Gopalakrishnan, S., Papić, Z., Yao, N., Laumann, C.,
… Demler, E. (2014). Interferometric probes of many-body localization. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.113.147204
chicago: Serbyn, Maksym, Michael Knap, Sarang Gopalakrishnan, Zlatko Papić, Norman
Yao, Chris Laumann, Dmitry Abanin, Mikhail Lukin, and Eugene Demler. “Interferometric
Probes of Many-Body Localization.” Physical Review Letters. American Physical
Society, 2014. https://doi.org/10.1103/PhysRevLett.113.147204.
ieee: M. Serbyn et al., “Interferometric probes of many-body localization,”
Physical Review Letters, vol. 113, no. 14. American Physical Society, 2014.
ista: Serbyn M, Knap M, Gopalakrishnan S, Papić Z, Yao N, Laumann C, Abanin D, Lukin
M, Demler E. 2014. Interferometric probes of many-body localization. Physical
Review Letters. 113(14).
mla: Serbyn, Maksym, et al. “Interferometric Probes of Many-Body Localization.”
Physical Review Letters, vol. 113, no. 14, American Physical Society, 2014,
doi:10.1103/PhysRevLett.113.147204.
short: M. Serbyn, M. Knap, S. Gopalakrishnan, Z. Papić, N. Yao, C. Laumann, D. Abanin,
M. Lukin, E. Demler, Physical Review Letters 113 (2014).
date_created: 2018-12-11T11:49:30Z
date_published: 2014-10-03T00:00:00Z
date_updated: 2021-01-12T08:22:22Z
day: '03'
doi: 10.1103/PhysRevLett.113.147204
extern: 1
intvolume: ' 113'
issue: '14'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.0693
month: '10'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6421'
quality_controlled: 0
status: public
title: Interferometric probes of many-body localization
type: journal_article
volume: 113
year: '2014'
...
---
_id: '978'
abstract:
- lang: eng
text: The newly discovered topological crystalline insulators feature a complex
band structure involving multiple Dirac cones, and are potentially highly tunable
by external electric field, temperature or strain. Theoretically, it has been
predicted that the various Dirac cones, which are offset in energy and momentum,
might harbour vastly different orbital character. However, their orbital texture,
which is of immense importance in determining a variety of a materialâ €™ s properties
remains elusive. Here, we unveil the orbital texture of Pb 1â ̂'x Sn x Se, a prototypical
topological crystalline insulator. By using Fourier-transform scanning tunnelling
spectroscopy we measure the interference patterns produced by the scattering of
surface-state electrons. We discover that the intensity and energy dependences
of the Fourier transforms show distinct characteristics, which can be directly
attributed to orbital effects. Our experiments reveal a complex band topology
involving two Lifshitz transitions and establish the orbital nature of the Dirac
bands, which could provide an alternative pathway towards future quantum applications.
acknowledgement: V.M. gratefully acknowledges funding from the US Department of Energy,
Scanned Probe Division under Award Number DE-FG02-12ER46880 for the primary support
of I.Z. and Y.O. (experiments, data analysis and writing the paper) and NSF-ECCS-1232105
for the partial support of W.Z. and D.W. (data acquisition). Work at Massachusetts
Institute of Technology is supported by US Department of Energy, Office of Basic
Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526
(L.F.), and NSF DMR 1104498 (M.S.). H.L. acknowledges the Singapore National Research
Foundation for support under NRF Award No. NRF-NRFF2013-03. The work at Northeastern
University is supported by the US Department of Energy grant number DE-FG02-07ER46352,
and benefited from Northeastern University’s Advanced Scientific Computation Center
(ASCC), theory support at the Advanced Light Source, Berkeley and the allocation
of time at the NERSC supercomputing centre through DOE grant number DE-AC02-05CH11231.
W-F.T. and C-Y.H. were supported by the NSC in Taiwan under Grant No. 102-2112-M-110-009.
W-F.T. also thanks C. Fang for useful discussions. Work at Princeton University
is supported by the US National Science Foundation Grant, NSF-DMR-1006492. F.C.
acknowledges the support provided by MOST-Taiwan under project number NSC-102-2119-M-002-004.
author:
- first_name: Ilija
full_name: Zeljkovic, Ilija
last_name: Zeljkovic
- first_name: Yoshinori
full_name: Okada, Yoshinori
last_name: Okada
- first_name: Chengyi
full_name: Huang, Chengyi
last_name: Huang
- first_name: Raman
full_name: Sankar, Raman
last_name: Sankar
- first_name: Daniel
full_name: Walkup, Daniel
last_name: Walkup
- first_name: Wenwen
full_name: Zhou, Wenwen
last_name: Zhou
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Fangcheng
full_name: Chou, Fangcheng
last_name: Chou
- first_name: Wei
full_name: Tsai, Wei-Feng
last_name: Tsai
- first_name: Hsin
full_name: Lin, Hsin
last_name: Lin
- first_name: Arun
full_name: Bansil, Arun
last_name: Bansil
- first_name: Liang
full_name: Fu, Liang
last_name: Fu
- first_name: Md
full_name: Hasan, Md Z
last_name: Hasan
- first_name: Vidya
full_name: Madhavan, Vidya
last_name: Madhavan
citation:
ama: Zeljkovic I, Okada Y, Huang C, et al. Mapping the unconventional orbital texture
in topological crystalline insulators. Nature Physics. 2014;10(8):572-577.
doi:10.1038/nphys3012
apa: Zeljkovic, I., Okada, Y., Huang, C., Sankar, R., Walkup, D., Zhou, W., … Madhavan,
V. (2014). Mapping the unconventional orbital texture in topological crystalline
insulators. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3012
chicago: Zeljkovic, Ilija, Yoshinori Okada, Chengyi Huang, Raman Sankar, Daniel
Walkup, Wenwen Zhou, Maksym Serbyn, et al. “Mapping the Unconventional Orbital
Texture in Topological Crystalline Insulators.” Nature Physics. Nature
Publishing Group, 2014. https://doi.org/10.1038/nphys3012.
ieee: I. Zeljkovic et al., “Mapping the unconventional orbital texture in
topological crystalline insulators,” Nature Physics, vol. 10, no. 8. Nature
Publishing Group, pp. 572–577, 2014.
ista: Zeljkovic I, Okada Y, Huang C, Sankar R, Walkup D, Zhou W, Serbyn M, Chou
F, Tsai W, Lin H, Bansil A, Fu L, Hasan M, Madhavan V. 2014. Mapping the unconventional
orbital texture in topological crystalline insulators. Nature Physics. 10(8),
572–577.
mla: Zeljkovic, Ilija, et al. “Mapping the Unconventional Orbital Texture in Topological
Crystalline Insulators.” Nature Physics, vol. 10, no. 8, Nature Publishing
Group, 2014, pp. 572–77, doi:10.1038/nphys3012.
short: I. Zeljkovic, Y. Okada, C. Huang, R. Sankar, D. Walkup, W. Zhou, M. Serbyn,
F. Chou, W. Tsai, H. Lin, A. Bansil, L. Fu, M. Hasan, V. Madhavan, Nature Physics
10 (2014) 572–577.
date_created: 2018-12-11T11:49:30Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:22:23Z
day: '01'
doi: 10.1038/nphys3012
extern: 1
intvolume: ' 10'
issue: '8'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1312.0164
month: '08'
oa: 1
page: 572 - 577
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6423'
quality_controlled: 0
status: public
title: Mapping the unconventional orbital texture in topological crystalline insulators
type: journal_article
volume: 10
year: '2014'
...
---
_id: '979'
abstract:
- lang: eng
text: In the recently discovered topological crystalline insulators SnTe and Pb1-xSnx(Te,
Se), crystal symmetry and electronic topology intertwine to create topological
surface states with many interesting features including Lifshitz transition, Van-Hove
singularity, and fermion mass generation. These surface states are protected by
mirror symmetry with respect to the (110) plane. In this work we present a comprehensive
study of the effects of different mirror-symmetry-breaking perturbations on the
(001) surface band structure. Pristine (001) surface states have four branches
of Dirac fermions at low energy. We show that ferroelectric-type structural distortion
generates a mass and gaps out some or all of these Dirac points, while strain
shifts Dirac points in the Brillouin zone. An in-plane magnetic field leaves the
surface state gapless, but introduces asymmetry between Dirac points. Finally,
an out-of-plane magnetic field leads to discrete Landau levels. We show that the
Landau level spectrum has an unusual pattern of degeneracy and interesting features
due to the unique underlying band structure. This suggests that Landau level spectroscopy
can detect and distinguish between different mechanisms of symmetry breaking in
topological crystalline insulators.
acknowledgement: We thank V. Madhavan and Y. Okada for related collaborations, and
P. A. Lee for discussions. M.S. was supported by P. A. Lee via Grant No. NSF DMR
1104498. L.F. is supported by the DOE Office of Basic Energy Sciences, Division
of Materials Sciences and Engineering under award DE-SC0010526.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Liang
full_name: Fu, Liang
last_name: Fu
citation:
ama: Serbyn M, Fu L. Symmetry breaking and Landau quantization in topological crystalline
insulators. Physical Review B - Condensed Matter and Materials Physics.
2014;90(3). doi:10.1103/PhysRevB.90.035402
apa: Serbyn, M., & Fu, L. (2014). Symmetry breaking and Landau quantization
in topological crystalline insulators. Physical Review B - Condensed Matter
and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.90.035402
chicago: Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization
in Topological Crystalline Insulators.” Physical Review B - Condensed Matter
and Materials Physics. American Physical Society, 2014. https://doi.org/10.1103/PhysRevB.90.035402.
ieee: M. Serbyn and L. Fu, “Symmetry breaking and Landau quantization in topological
crystalline insulators,” Physical Review B - Condensed Matter and Materials
Physics, vol. 90, no. 3. American Physical Society, 2014.
ista: Serbyn M, Fu L. 2014. Symmetry breaking and Landau quantization in topological
crystalline insulators. Physical Review B - Condensed Matter and Materials Physics.
90(3).
mla: Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization in
Topological Crystalline Insulators.” Physical Review B - Condensed Matter and
Materials Physics, vol. 90, no. 3, American Physical Society, 2014, doi:10.1103/PhysRevB.90.035402.
short: M. Serbyn, L. Fu, Physical Review B - Condensed Matter and Materials Physics
90 (2014).
date_created: 2018-12-11T11:49:31Z
date_published: 2014-07-03T00:00:00Z
date_updated: 2021-01-12T08:22:23Z
day: '03'
doi: 10.1103/PhysRevB.90.035402
extern: 1
intvolume: ' 90'
issue: '3'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.8153
month: '07'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6422'
quality_controlled: 0
status: public
title: Symmetry breaking and Landau quantization in topological crystalline insulators
type: journal_article
volume: 90
year: '2014'
...
---
_id: '98'
abstract:
- lang: eng
text: Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si
nanowire double quantum dot using a fast pulsed-gate method and dispersive readout.
An inhomogeneous dephasing time T2* ∼ 0.18 μs exceeds corresponding measurements
in III-V semiconductors by more than an order of magnitude, as expected for predominately
nuclear-spin-free materials. Dephasing is observed to be exponential in time,
indicating the presence of a broadband noise source, rather than Gaussian, previously
seen in systems with nuclear-spin-dominated dephasing.
acknowledgement: Funding from the Department of Energy, Office of Science & SCGF,
the EC FP7-ICT project SiSPIN no. 323841, and the Danish National Research Foundation
is acknowledged.
arxiv: 1
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Thorvald
full_name: Larsen, Thorvald
last_name: Larsen
- first_name: Jun
full_name: Yao, Jun
last_name: Yao
- first_name: Hao
full_name: Yan, Hao
last_name: Yan
- first_name: Charles
full_name: Lieber, Charles
last_name: Lieber
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
- first_name: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
citation:
ama: Higginbotham AP, Larsen T, Yao J, et al. Hole spin coherence in a Ge/Si heterostructure
nanowire. Nano Letters. 2014;14(6):3582-3586. doi:10.1021/nl501242b
apa: Higginbotham, A. P., Larsen, T., Yao, J., Yan, H., Lieber, C., Marcus, C.,
& Kuemmeth, F. (2014). Hole spin coherence in a Ge/Si heterostructure nanowire.
Nano Letters. American Chemical Society. https://doi.org/10.1021/nl501242b
chicago: Higginbotham, Andrew P, Thorvald Larsen, Jun Yao, Hao Yan, Charles Lieber,
Charles Marcus, and Ferdinand Kuemmeth. “Hole Spin Coherence in a Ge/Si Heterostructure
Nanowire.” Nano Letters. American Chemical Society, 2014. https://doi.org/10.1021/nl501242b.
ieee: A. P. Higginbotham et al., “Hole spin coherence in a Ge/Si heterostructure
nanowire,” Nano Letters, vol. 14, no. 6. American Chemical Society, pp.
3582–3586, 2014.
ista: Higginbotham AP, Larsen T, Yao J, Yan H, Lieber C, Marcus C, Kuemmeth F. 2014.
Hole spin coherence in a Ge/Si heterostructure nanowire. Nano Letters. 14(6),
3582–3586.
mla: Higginbotham, Andrew P., et al. “Hole Spin Coherence in a Ge/Si Heterostructure
Nanowire.” Nano Letters, vol. 14, no. 6, American Chemical Society, 2014,
pp. 3582–86, doi:10.1021/nl501242b.
short: A.P. Higginbotham, T. Larsen, J. Yao, H. Yan, C. Lieber, C. Marcus, F. Kuemmeth,
Nano Letters 14 (2014) 3582–3586.
date_created: 2018-12-11T11:44:37Z
date_published: 2014-05-05T00:00:00Z
date_updated: 2021-01-12T08:22:24Z
day: '05'
doi: 10.1021/nl501242b
extern: '1'
external_id:
arxiv:
- '1403.2093'
intvolume: ' 14'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.2093
month: '05'
oa: 1
oa_version: Preprint
page: 3582 - 3586
publication: Nano Letters
publication_status: published
publisher: American Chemical Society
publist_id: '7956'
quality_controlled: '1'
status: public
title: Hole spin coherence in a Ge/Si heterostructure nanowire
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2014'
...
---
_id: '980'
abstract:
- lang: eng
text: Many-body localized (MBL) systems are characterized by the absence of transport
and thermalization and, therefore, cannot be described by conventional statistical
mechanics. In this paper, using analytic arguments and numerical simulations,
we study the behavior of local observables in an isolated MBL system following
a quantum quench. For the case of a global quench, we find that the local observables
reach stationary, highly nonthermal values at long times as a result of slow dephasing
characteristic of the MBL phase. These stationary values retain the local memory
of the initial state due to the existence of local integrals of motion in the
MBL phase. The temporal fluctuations around stationary values exhibit universal
power-law decay in time, with an exponent set by the localization length and the
diagonal entropy of the initial state. Such a power-law decay holds for any local
observable and is related to the logarithmic in time growth of entanglement in
the MBL phase. This behavior distinguishes the MBL phase from both the Anderson
insulator (where no stationary state is reached) and from the ergodic phase (where
relaxation is expected to be exponential). For the case of a local quench, we
also find a power-law approach of local observables to their stationary values
when the system is prepared in a mixed state. Quench protocols considered in this
paper can be naturally implemented in systems of ultracold atoms in disordered
optical lattices, and the behavior of local observables provides a direct experimental
signature of many-body localization.
acknowledgement: Research at Perimeter Institute is supported by the Government of
Canada through Industry Canada and by the Province of Ontario through the Ministry
of Economic Development & Innovation. We acknowledge support by NSERC Discovery
Grant (D.A.).
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
citation:
ama: Serbyn M, Papić Z, Abanin D. Quantum quenches in the many-body localized phase.
Physical Review B - Condensed Matter and Materials Physics. 2014;90(17).
doi:10.1103/PhysRevB.90.174302
apa: Serbyn, M., Papić, Z., & Abanin, D. (2014). Quantum quenches in the many-body
localized phase. Physical Review B - Condensed Matter and Materials Physics.
American Physical Society. https://doi.org/10.1103/PhysRevB.90.174302
chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Quantum Quenches in the
Many-Body Localized Phase.” Physical Review B - Condensed Matter and Materials
Physics. American Physical Society, 2014. https://doi.org/10.1103/PhysRevB.90.174302.
ieee: M. Serbyn, Z. Papić, and D. Abanin, “Quantum quenches in the many-body localized
phase,” Physical Review B - Condensed Matter and Materials Physics, vol.
90, no. 17. American Physical Society, 2014.
ista: Serbyn M, Papić Z, Abanin D. 2014. Quantum quenches in the many-body localized
phase. Physical Review B - Condensed Matter and Materials Physics. 90(17).
mla: Serbyn, Maksym, et al. “Quantum Quenches in the Many-Body Localized Phase.”
Physical Review B - Condensed Matter and Materials Physics, vol. 90, no.
17, American Physical Society, 2014, doi:10.1103/PhysRevB.90.174302.
short: M. Serbyn, Z. Papić, D. Abanin, Physical Review B - Condensed Matter and
Materials Physics 90 (2014).
date_created: 2018-12-11T11:49:31Z
date_published: 2014-11-06T00:00:00Z
date_updated: 2021-01-12T08:22:24Z
day: '06'
doi: 10.1103/PhysRevB.90.174302
extern: 1
intvolume: ' 90'
issue: '17'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1408.4105
month: '11'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6420'
quality_controlled: 0
status: public
title: Quantum quenches in the many-body localized phase
type: journal_article
volume: 90
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: '10817'
abstract:
- lang: eng
text: The Morse-Smale complex can be either explicitly or implicitly represented.
Depending on the type of representation, the simplification of the Morse-Smale
complex works differently. In the explicit representation, the Morse-Smale complex
is directly simplified by explicitly reconnecting the critical points during the
simplification. In the implicit representation, on the other hand, the Morse-Smale
complex is given by a combinatorial gradient field. In this setting, the simplification
changes the combinatorial flow, which yields an indirect simplification of the
Morse-Smale complex. The topological complexity of the Morse-Smale complex is
reduced in both representations. However, the simplifications generally yield
different results. In this chapter, we emphasize properties of the two representations
that cause these differences. We also provide a complexity analysis of the two
schemes with respect to running time and memory consumption.
acknowledgement: This research is supported and funded by the Digiteo unTopoVis project,
the TOPOSYS project FP7-ICT-318493-STREP, and MPC-VCC.
article_processing_charge: No
author:
- first_name: David
full_name: Günther, David
last_name: Günther
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Hans-Peter
full_name: Seidel, Hans-Peter
last_name: Seidel
- first_name: Tino
full_name: Weinkauf, Tino
last_name: Weinkauf
citation:
ama: 'Günther D, Reininghaus J, Seidel H-P, Weinkauf T. Notes on the simplification
of the Morse-Smale complex. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds.
Topological Methods in Data Analysis and Visualization III. Mathematics
and Visualization. Cham: Springer Nature; 2014:135-150. doi:10.1007/978-3-319-04099-8_9'
apa: 'Günther, D., Reininghaus, J., Seidel, H.-P., & Weinkauf, T. (2014). Notes
on the simplification of the Morse-Smale complex. In P.-T. Bremer, I. Hotz, V.
Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and
Visualization III. (pp. 135–150). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-04099-8_9'
chicago: 'Günther, David, Jan Reininghaus, Hans-Peter Seidel, and Tino Weinkauf.
“Notes on the Simplification of the Morse-Smale Complex.” In Topological Methods
in Data Analysis and Visualization III., edited by Peer-Timo Bremer, Ingrid
Hotz, Valerio Pascucci, and Ronald Peikert, 135–50. Mathematics and Visualization.
Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-319-04099-8_9.'
ieee: 'D. Günther, J. Reininghaus, H.-P. Seidel, and T. Weinkauf, “Notes on the
simplification of the Morse-Smale complex,” in Topological Methods in Data
Analysis and Visualization III., P.-T. Bremer, I. Hotz, V. Pascucci, and R.
Peikert, Eds. Cham: Springer Nature, 2014, pp. 135–150.'
ista: 'Günther D, Reininghaus J, Seidel H-P, Weinkauf T. 2014.Notes on the simplification
of the Morse-Smale complex. In: Topological Methods in Data Analysis and Visualization
III. , 135–150.'
mla: Günther, David, et al. “Notes on the Simplification of the Morse-Smale Complex.”
Topological Methods in Data Analysis and Visualization III., edited by
Peer-Timo Bremer et al., Springer Nature, 2014, pp. 135–50, doi:10.1007/978-3-319-04099-8_9.
short: D. Günther, J. Reininghaus, H.-P. Seidel, T. Weinkauf, in:, P.-T. Bremer,
I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis
and Visualization III., Springer Nature, Cham, 2014, pp. 135–150.
date_created: 2022-03-04T08:33:57Z
date_published: 2014-03-19T00:00:00Z
date_updated: 2023-09-05T15:33:45Z
day: '19'
department:
- _id: HeEd
doi: 10.1007/978-3-319-04099-8_9
ec_funded: 1
editor:
- first_name: Peer-Timo
full_name: Bremer, Peer-Timo
last_name: Bremer
- first_name: Ingrid
full_name: Hotz, Ingrid
last_name: Hotz
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
- first_name: Ronald
full_name: Peikert, Ronald
last_name: Peikert
language:
- iso: eng
month: '03'
oa_version: None
page: 135-150
place: Cham
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Topological Methods in Data Analysis and Visualization III.
publication_identifier:
eisbn:
- '9783319040998'
eissn:
- 2197-666X
isbn:
- '9783319040981'
issn:
- 1612-3786
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: Mathematics and Visualization
status: public
title: Notes on the simplification of the Morse-Smale complex
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2014'
...
---
_id: '10884'
abstract:
- lang: eng
text: "We revisit the parameterized model checking problem for token-passing systems
and specifications in indexed CTL ∗ \\X. Emerson and Namjoshi (1995, 2003) have
shown that parameterized model checking of indexed CTL ∗ \\X in uni-directional
token rings can be reduced to checking rings up to some cutoff size. Clarke et
al. (2004) have shown a similar result for general topologies and indexed LTL
\\X, provided processes cannot choose the directions for sending or receiving
the token.\r\nWe unify and substantially extend these results by systematically
exploring fragments of indexed CTL ∗ \\X with respect to general topologies.
For each fragment we establish whether a cutoff exists, and for some concrete
topologies, such as rings, cliques and stars, we infer small cutoffs. Finally,
we show that the problem becomes undecidable, and thus no cutoffs exist, if processes
are allowed to choose the directions in which they send or from which they receive
the token."
acknowledgement: "This work was supported by the Austrian Science Fund through grant
P23499-N23\r\nand through the RiSE network (S11403, S11405, S11406, S11407-N23);
ERC Starting Grant (279307: Graph Games); Vienna Science and Technology Fund (WWTF)\r\ngrants
PROSEED, ICT12-059, and VRG11-005."
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Benjamin
full_name: Aminof, Benjamin
id: 4A55BD00-F248-11E8-B48F-1D18A9856A87
last_name: Aminof
- first_name: Swen
full_name: Jacobs, Swen
last_name: Jacobs
- first_name: Ayrat
full_name: Khalimov, Ayrat
last_name: Khalimov
- first_name: Sasha
full_name: Rubin, Sasha
id: 2EC51194-F248-11E8-B48F-1D18A9856A87
last_name: Rubin
citation:
ama: 'Aminof B, Jacobs S, Khalimov A, Rubin S. Parameterized model checking of token-passing
systems. In: Verification, Model Checking, and Abstract Interpretation.
Vol 8318. Springer Nature; 2014:262-281. doi:10.1007/978-3-642-54013-4_15'
apa: 'Aminof, B., Jacobs, S., Khalimov, A., & Rubin, S. (2014). Parameterized
model checking of token-passing systems. In Verification, Model Checking, and
Abstract Interpretation (Vol. 8318, pp. 262–281). San Diego, CA, United States:
Springer Nature. https://doi.org/10.1007/978-3-642-54013-4_15'
chicago: Aminof, Benjamin, Swen Jacobs, Ayrat Khalimov, and Sasha Rubin. “Parameterized
Model Checking of Token-Passing Systems.” In Verification, Model Checking,
and Abstract Interpretation, 8318:262–81. Springer Nature, 2014. https://doi.org/10.1007/978-3-642-54013-4_15.
ieee: B. Aminof, S. Jacobs, A. Khalimov, and S. Rubin, “Parameterized model checking
of token-passing systems,” in Verification, Model Checking, and Abstract Interpretation,
San Diego, CA, United States, 2014, vol. 8318, pp. 262–281.
ista: 'Aminof B, Jacobs S, Khalimov A, Rubin S. 2014. Parameterized model checking
of token-passing systems. Verification, Model Checking, and Abstract Interpretation.
VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318,
262–281.'
mla: Aminof, Benjamin, et al. “Parameterized Model Checking of Token-Passing Systems.”
Verification, Model Checking, and Abstract Interpretation, vol. 8318, Springer
Nature, 2014, pp. 262–81, doi:10.1007/978-3-642-54013-4_15.
short: B. Aminof, S. Jacobs, A. Khalimov, S. Rubin, in:, Verification, Model Checking,
and Abstract Interpretation, Springer Nature, 2014, pp. 262–281.
conference:
end_date: 2014-01-21
location: San Diego, CA, United States
name: 'VMCAI: Verifcation, Model Checking, and Abstract Interpretation'
start_date: 2014-01-19
date_created: 2022-03-18T13:01:22Z
date_published: 2014-01-30T00:00:00Z
date_updated: 2022-05-17T08:36:01Z
day: '30'
department:
- _id: KrCh
doi: 10.1007/978-3-642-54013-4_15
ec_funded: 1
external_id:
arxiv:
- '1311.4425'
intvolume: ' 8318'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1311.4425'
month: '01'
oa: 1
oa_version: Preprint
page: 262-281
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'
publication: Verification, Model Checking, and Abstract Interpretation
publication_identifier:
eisbn:
- '9783642540134'
eissn:
- 1611-3349
isbn:
- '9783642540127'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Parameterized model checking of token-passing systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8318
year: '2014'
...
---
_id: '10885'
abstract:
- lang: eng
text: "Two-player games on graphs provide the theoretical framework for many important
problems such as reactive synthesis. While the traditional study of two-player
zero-sum games has been extended to multi-player games with several notions of
equilibria, they are decidable only for perfect-information games, whereas several
applications require imperfect-information games.\r\nIn this paper we propose
a new notion of equilibria, called doomsday equilibria, which is a strategy profile
such that all players satisfy their own objective, and if any coalition of players
deviates and violates even one of the players objective, then the objective of
every player is violated.\r\nWe present algorithms and complexity results for
deciding the existence of doomsday equilibria for various classes of ω-regular
objectives, both for imperfect-information games, and for perfect-information
games.We provide optimal complexity bounds for imperfect-information games, and
in most cases for perfect-information games."
acknowledgement: " Supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF
NFN Grant No\r\nS11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft
faculty fellows award."
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Emmanuel
full_name: Filiot, Emmanuel
last_name: Filiot
- first_name: Jean-François
full_name: Raskin, Jean-François
last_name: Raskin
citation:
ama: 'Chatterjee K, Doyen L, Filiot E, Raskin J-F. Doomsday equilibria for omega-regular
games. In: VMCAI 2014: Verification, Model Checking, and Abstract Interpretation.
Vol 8318. Springer Nature; 2014:78-97. doi:10.1007/978-3-642-54013-4_5'
apa: 'Chatterjee, K., Doyen, L., Filiot, E., & Raskin, J.-F. (2014). Doomsday
equilibria for omega-regular games. In VMCAI 2014: Verification, Model Checking,
and Abstract Interpretation (Vol. 8318, pp. 78–97). San Diego, CA, United
States: Springer Nature. https://doi.org/10.1007/978-3-642-54013-4_5'
chicago: 'Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean-François
Raskin. “Doomsday Equilibria for Omega-Regular Games.” In VMCAI 2014: Verification,
Model Checking, and Abstract Interpretation, 8318:78–97. Springer Nature,
2014. https://doi.org/10.1007/978-3-642-54013-4_5.'
ieee: 'K. Chatterjee, L. Doyen, E. Filiot, and J.-F. Raskin, “Doomsday equilibria
for omega-regular games,” in VMCAI 2014: Verification, Model Checking, and
Abstract Interpretation, San Diego, CA, United States, 2014, vol. 8318, pp.
78–97.'
ista: 'Chatterjee K, Doyen L, Filiot E, Raskin J-F. 2014. Doomsday equilibria for
omega-regular games. VMCAI 2014: Verification, Model Checking, and Abstract Interpretation.
VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318,
78–97.'
mla: 'Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.”
VMCAI 2014: Verification, Model Checking, and Abstract Interpretation,
vol. 8318, Springer Nature, 2014, pp. 78–97, doi:10.1007/978-3-642-54013-4_5.'
short: 'K. Chatterjee, L. Doyen, E. Filiot, J.-F. Raskin, in:, VMCAI 2014: Verification,
Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 78–97.'
conference:
end_date: 2014-01-21
location: San Diego, CA, United States
name: 'VMCAI: Verifcation, Model Checking, and Abstract Interpretation'
start_date: 2014-01-19
date_created: 2022-03-18T13:03:15Z
date_published: 2014-01-30T00:00:00Z
date_updated: 2023-02-23T12:52:24Z
day: '30'
department:
- _id: KrCh
doi: 10.1007/978-3-642-54013-4_5
ec_funded: 1
external_id:
arxiv:
- '1311.3238'
intvolume: ' 8318'
language:
- iso: eng
month: '01'
oa_version: Preprint
page: 78-97
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: 'VMCAI 2014: Verification, Model Checking, and Abstract Interpretation'
publication_identifier:
eisbn:
- '9783642540134'
eissn:
- 1611-3349
isbn:
- '9783642540127'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '681'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Doomsday equilibria for omega-regular games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8318
year: '2014'
...
---
_id: '10886'
abstract:
- lang: eng
text: We propose a method for visualizing two-dimensional symmetric positive definite
tensor fields using the Heat Kernel Signature (HKS). The HKS is derived from the
heat kernel and was originally introduced as an isometry invariant shape signature.
Each positive definite tensor field defines a Riemannian manifold by considering
the tensor field as a Riemannian metric. On this Riemmanian manifold we can apply
the definition of the HKS. The resulting scalar quantity is used for the visualization
of tensor fields. The HKS is closely related to the Gaussian curvature of the
Riemannian manifold and the time parameter of the heat kernel allows a multiscale
analysis in a natural way. In this way, the HKS represents field related scale
space properties, enabling a level of detail analysis of tensor fields. This makes
the HKS an interesting new scalar quantity for tensor fields, which differs significantly
from usual tensor invariants like the trace or the determinant. A method for visualization
and a numerical realization of the HKS for tensor fields is proposed in this chapter.
To validate the approach we apply it to some illustrating simple examples as isolated
critical points and to a medical diffusion tensor data set.
acknowledgement: This research is partially supported by the TOPOSYS project FP7-ICT-318493-STREP.
alternative_title:
- Mathematics and Visualization
article_processing_charge: No
author:
- first_name: Valentin
full_name: Zobel, Valentin
last_name: Zobel
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Ingrid
full_name: Hotz, Ingrid
last_name: Hotz
citation:
ama: 'Zobel V, Reininghaus J, Hotz I. Visualization of two-dimensional symmetric
positive definite tensor fields using the heat kernel signature. In: Topological
Methods in Data Analysis and Visualization III . Springer; 2014:249-262. doi:10.1007/978-3-319-04099-8_16'
apa: Zobel, V., Reininghaus, J., & Hotz, I. (2014). Visualization of two-dimensional
symmetric positive definite tensor fields using the heat kernel signature. In
Topological Methods in Data Analysis and Visualization III (pp. 249–262).
Springer. https://doi.org/10.1007/978-3-319-04099-8_16
chicago: Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualization of Two-Dimensional
Symmetric Positive Definite Tensor Fields Using the Heat Kernel Signature.” In
Topological Methods in Data Analysis and Visualization III , 249–62. Springer,
2014. https://doi.org/10.1007/978-3-319-04099-8_16.
ieee: V. Zobel, J. Reininghaus, and I. Hotz, “Visualization of two-dimensional symmetric
positive definite tensor fields using the heat kernel signature,” in Topological
Methods in Data Analysis and Visualization III , 2014, pp. 249–262.
ista: Zobel V, Reininghaus J, Hotz I. 2014. Visualization of two-dimensional symmetric
positive definite tensor fields using the heat kernel signature. Topological Methods
in Data Analysis and Visualization III . , Mathematics and Visualization, , 249–262.
mla: Zobel, Valentin, et al. “Visualization of Two-Dimensional Symmetric Positive
Definite Tensor Fields Using the Heat Kernel Signature.” Topological Methods
in Data Analysis and Visualization III , Springer, 2014, pp. 249–62, doi:10.1007/978-3-319-04099-8_16.
short: V. Zobel, J. Reininghaus, I. Hotz, in:, Topological Methods in Data Analysis
and Visualization III , Springer, 2014, pp. 249–262.
date_created: 2022-03-18T13:05:39Z
date_published: 2014-03-19T00:00:00Z
date_updated: 2023-09-05T14:13:16Z
day: '19'
department:
- _id: HeEd
doi: 10.1007/978-3-319-04099-8_16
language:
- iso: eng
month: '03'
oa_version: None
page: 249-262
publication: 'Topological Methods in Data Analysis and Visualization III '
publication_identifier:
eisbn:
- '9783319040998'
eissn:
- 2197-666X
isbn:
- '9783319040981'
issn:
- 1612-3786
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Visualization of two-dimensional symmetric positive definite tensor fields
using the heat kernel signature
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2014'
...
---
_id: '10892'
abstract:
- lang: eng
text: "In this paper, we introduce planar matchings on directed pseudo-line arrangements,
which yield a planar set of pseudo-line segments such that only matching-partners
are adjacent. By translating the planar matching problem into a corresponding
stable roommates problem we show that such matchings always exist.\r\nUsing our
new framework, we establish, for the first time, a complete, rigorous definition
of weighted straight skeletons, which are based on a so-called wavefront propagation
process. We present a generalized and unified approach to treat structural changes
in the wavefront that focuses on the restoration of weak planarity by finding
planar matchings."
acknowledgement: 'T. Biedl was supported by NSERC and the Ross and Muriel Cheriton
Fellowship. P. Palfrader was supported by Austrian Science Fund (FWF): P25816-N15.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Therese
full_name: Biedl, Therese
last_name: Biedl
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Peter
full_name: Palfrader, Peter
last_name: Palfrader
citation:
ama: 'Biedl T, Huber S, Palfrader P. Planar matchings for weighted straight skeletons.
In: 25th International Symposium, ISAAC 2014. Vol 8889. Springer Nature;
2014:117-127. doi:10.1007/978-3-319-13075-0_10'
apa: 'Biedl, T., Huber, S., & Palfrader, P. (2014). Planar matchings for weighted
straight skeletons. In 25th International Symposium, ISAAC 2014 (Vol. 8889,
pp. 117–127). Jeonju, Korea: Springer Nature. https://doi.org/10.1007/978-3-319-13075-0_10'
chicago: Biedl, Therese, Stefan Huber, and Peter Palfrader. “Planar Matchings for
Weighted Straight Skeletons.” In 25th International Symposium, ISAAC 2014,
8889:117–27. Springer Nature, 2014. https://doi.org/10.1007/978-3-319-13075-0_10.
ieee: T. Biedl, S. Huber, and P. Palfrader, “Planar matchings for weighted straight
skeletons,” in 25th International Symposium, ISAAC 2014, Jeonju, Korea,
2014, vol. 8889, pp. 117–127.
ista: 'Biedl T, Huber S, Palfrader P. 2014. Planar matchings for weighted straight
skeletons. 25th International Symposium, ISAAC 2014. ISAAC: International Symposium
on Algorithms and Computation, LNCS, vol. 8889, 117–127.'
mla: Biedl, Therese, et al. “Planar Matchings for Weighted Straight Skeletons.”
25th International Symposium, ISAAC 2014, vol. 8889, Springer Nature, 2014,
pp. 117–27, doi:10.1007/978-3-319-13075-0_10.
short: T. Biedl, S. Huber, P. Palfrader, in:, 25th International Symposium, ISAAC
2014, Springer Nature, 2014, pp. 117–127.
conference:
end_date: 2014-12-17
location: Jeonju, Korea
name: 'ISAAC: International Symposium on Algorithms and Computation'
start_date: 2014-12-15
date_created: 2022-03-21T07:09:03Z
date_published: 2014-11-08T00:00:00Z
date_updated: 2023-02-23T12:20:55Z
day: '08'
department:
- _id: HeEd
doi: 10.1007/978-3-319-13075-0_10
intvolume: ' 8889'
language:
- iso: eng
month: '11'
oa_version: None
page: 117-127
publication: 25th International Symposium, ISAAC 2014
publication_identifier:
eisbn:
- '9783319130750'
eissn:
- 1611-3349
isbn:
- '9783319130743'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '481'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Planar matchings for weighted straight skeletons
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8889
year: '2014'
...