---
_id: '910'
abstract:
- lang: eng
text: "Frequency-independent selection is generally considered as a force that acts
to reduce the genetic variation in evolving populations, yet rigorous arguments
for this idea are scarce. When selection fluctuates in time, it is unclear whether
frequency-independent selection may maintain genetic polymorphism without invoking
additional mechanisms. We show that constant frequency-independent selection with
arbitrary epistasis on a well-mixed haploid population eliminates genetic variation
if we assume linkage equilibrium between alleles. To this end, we introduce the
notion of frequency-independent selection at the level of alleles, which is sufficient
to prove our claim and contains the notion of frequency-independent selection
on haploids. When selection and recombination are weak but of the same order,
there may be strong linkage disequilibrium; numerical calculations show that stable
equilibria are highly unlikely. Using the example of a diallelic two-locus model,
we then demonstrate that frequency-independent selection that fluctuates in time
can maintain stable polymorphism if linkage disequilibrium changes its sign periodically.
We put our findings in the context of results from the existing literature and
point out those scenarios in which the possible role of frequency-independent
selection in maintaining genetic variation remains unclear.\r\n"
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Novak S, Barton NH. When does frequency-independent selection maintain genetic
variation? Genetics. 2017;207(2):653-668. doi:10.1534/genetics.117.300129
apa: Novak, S., & Barton, N. H. (2017). When does frequency-independent selection
maintain genetic variation? Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300129
chicago: Novak, Sebastian, and Nicholas H Barton. “When Does Frequency-Independent
Selection Maintain Genetic Variation?” Genetics. Genetics Society of America,
2017. https://doi.org/10.1534/genetics.117.300129.
ieee: S. Novak and N. H. Barton, “When does frequency-independent selection maintain
genetic variation?,” Genetics, vol. 207, no. 2. Genetics Society of America,
pp. 653–668, 2017.
ista: Novak S, Barton NH. 2017. When does frequency-independent selection maintain
genetic variation? Genetics. 207(2), 653–668.
mla: Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent
Selection Maintain Genetic Variation?” Genetics, vol. 207, no. 2, Genetics
Society of America, 2017, pp. 653–68, doi:10.1534/genetics.117.300129.
short: S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.
corr_author: '1'
date_created: 2018-12-11T11:49:09Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2025-04-15T08:22:21Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1534/genetics.117.300129
ec_funded: 1
external_id:
isi:
- '000412232600019'
file:
- access_level: open_access
checksum: f7c32dabf52e6d9e709d9203761e39fd
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:12Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5264'
file_name: IST-2018-974-v1+1_manuscript.pdf
file_size: 494268
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 207'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 653 - 668
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '6533'
pubrep_id: '974'
quality_controlled: '1'
scopus_import: '1'
status: public
title: When does frequency-independent selection maintain genetic variation?
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 207
year: '2017'
...
---
_id: '912'
abstract:
- lang: eng
text: "We consider a many-body system of fermionic atoms interacting via a local
pair potential and subject to an external potential within the framework of Bardeen-Cooper-Schrieffer
(BCS) theory. We measure the free energy of the whole sample with respect to the
free energy of a reference state which allows us to define a BCS functional with
boundary conditions at infinity. Our main result is a lower bound for this energy
functional in terms of expressions that typically appear in Ginzburg-Landau functionals.\r\n"
article_number: '081901'
article_processing_charge: No
arxiv: 1
author:
- first_name: Andreas
full_name: Deuchert, Andreas
id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87
last_name: Deuchert
orcid: 0000-0003-3146-6746
citation:
ama: Deuchert A. A lower bound for the BCS functional with boundary conditions at
infinity. Journal of Mathematical Physics. 2017;58(8). doi:10.1063/1.4996580
apa: Deuchert, A. (2017). A lower bound for the BCS functional with boundary conditions
at infinity. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.4996580
chicago: Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary
Conditions at Infinity.” Journal of Mathematical Physics. AIP Publishing,
2017. https://doi.org/10.1063/1.4996580.
ieee: A. Deuchert, “A lower bound for the BCS functional with boundary conditions
at infinity,” Journal of Mathematical Physics, vol. 58, no. 8. AIP Publishing,
2017.
ista: Deuchert A. 2017. A lower bound for the BCS functional with boundary conditions
at infinity. Journal of Mathematical Physics. 58(8), 081901.
mla: Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions
at Infinity.” Journal of Mathematical Physics, vol. 58, no. 8, 081901,
AIP Publishing, 2017, doi:10.1063/1.4996580.
short: A. Deuchert, Journal of Mathematical Physics 58 (2017).
corr_author: '1'
date_created: 2018-12-11T11:49:10Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2025-06-04T08:19:58Z
day: '01'
department:
- _id: RoSe
doi: 10.1063/1.4996580
ec_funded: 1
external_id:
arxiv:
- '1703.04616'
isi:
- '000409197200015'
intvolume: ' 58'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.04616
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: ' Journal of Mathematical Physics'
publication_identifier:
issn:
- 0022-2488
publication_status: published
publisher: AIP Publishing
publist_id: '6531'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A lower bound for the BCS functional with boundary conditions at infinity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2017'
...
---
_id: '914'
abstract:
- lang: eng
text: Infections with potentially lethal pathogens may negatively affect an individual’s
lifespan and decrease its reproductive value. The terminal investment hypothesis
predicts that individuals faced with a reduced survival should invest more into
reproduction instead of maintenance and growth. Several studies suggest that individuals
are indeed able to estimate their body condition and to increase their reproductive
effort with approaching death, while other studies gave ambiguous results. We
investigate whether queens of a perennial social insect (ant) are able to boost
their reproduction following infection with an obligate killing pathogen. Social
insect queens are special with regard to reproduction and aging, as they outlive
conspecific non-reproductive workers. Moreover, in the ant Cardiocondyla obscurior,
fecundity increases with queen age. However, it remained unclear whether this
reflects negative reproductive senescence or terminal investment in response to
approaching death. Here, we test whether queens of C. obscurior react to infection
with the entomopathogenic fungus Metarhizium brunneum by an increased egg-laying
rate. We show that a fungal infection triggers a reinforced investment in reproduction
in queens. This adjustment of the reproductive rate by ant queens is consistent
with predictions of the terminal investment hypothesis and is reported for the
first time in a social insect.
acknowledgement: We thank two anonymous reviewers for helpful suggestions on the manuscript.
article_number: '170547'
article_processing_charge: No
author:
- first_name: Julia
full_name: Giehr, Julia
last_name: Giehr
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
citation:
ama: Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. Ant queens increase their
reproductive efforts after pathogen infection. Royal Society Open Science.
2017;4(7). doi:10.1098/rsos.170547
apa: Giehr, J., Grasse, A. V., Cremer, S., Heinze, J., & Schrempf, A. (2017).
Ant queens increase their reproductive efforts after pathogen infection. Royal
Society Open Science. Royal Society, The. https://doi.org/10.1098/rsos.170547
chicago: Giehr, Julia, Anna V Grasse, Sylvia Cremer, Jürgen Heinze, and Alexandra
Schrempf. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.”
Royal Society Open Science. Royal Society, The, 2017. https://doi.org/10.1098/rsos.170547.
ieee: J. Giehr, A. V. Grasse, S. Cremer, J. Heinze, and A. Schrempf, “Ant queens
increase their reproductive efforts after pathogen infection,” Royal Society
Open Science, vol. 4, no. 7. Royal Society, The, 2017.
ista: Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. 2017. Ant queens increase
their reproductive efforts after pathogen infection. Royal Society Open Science.
4(7), 170547.
mla: Giehr, Julia, et al. “Ant Queens Increase Their Reproductive Efforts after
Pathogen Infection.” Royal Society Open Science, vol. 4, no. 7, 170547,
Royal Society, The, 2017, doi:10.1098/rsos.170547.
short: J. Giehr, A.V. Grasse, S. Cremer, J. Heinze, A. Schrempf, Royal Society Open
Science 4 (2017).
date_created: 2018-12-11T11:49:10Z
date_published: 2017-07-05T00:00:00Z
date_updated: 2025-07-10T12:01:39Z
day: '05'
ddc:
- '576'
- '592'
department:
- _id: SyCr
doi: 10.1098/rsos.170547
external_id:
isi:
- '000406670000025'
file:
- access_level: open_access
checksum: 351ae5e7a37e6e7d9295cd41146c4190
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:24Z
date_updated: 2020-07-14T12:48:15Z
file_id: '4684'
file_name: IST-2017-849-v1+1_2017_Grasse_Cremer_AntQueens.pdf
file_size: 530412
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
publication: Royal Society Open Science
publication_identifier:
issn:
- 2054-5703
publication_status: published
publisher: Royal Society, The
publist_id: '6527'
pubrep_id: '849'
quality_controlled: '1'
related_material:
record:
- id: '9853'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Ant queens increase their reproductive efforts after pathogen infection
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: 4
year: '2017'
...
---
_id: '915'
abstract:
- lang: eng
text: We propose a dual decomposition and linear program relaxation of the NP-hard
minimum cost multicut problem. Unlike other polyhedral relaxations of the multicut
polytope, it is amenable to efficient optimization by message passing. Like other
polyhedral relaxations, it can be tightened efficiently by cutting planes. We
define an algorithm that alternates between message passing and efficient separation
of cycle- and odd-wheel inequalities. This algorithm is more efficient than state-of-the-art
algorithms based on linear programming, including algorithms written in the framework
of leading commercial software, as we show in experiments with large instances
of the problem from applications in computer vision, biomedical image analysis
and data mining.
article_processing_charge: No
author:
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
- first_name: Bjoern
full_name: Andres, Bjoern
last_name: Andres
citation:
ama: 'Swoboda P, Andres B. A message passing algorithm for the minimum cost multicut
problem. In: Vol 2017. IEEE; 2017:4990-4999. doi:10.1109/CVPR.2017.530'
apa: 'Swoboda, P., & Andres, B. (2017). A message passing algorithm for the
minimum cost multicut problem (Vol. 2017, pp. 4990–4999). Presented at the CVPR:
Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.530'
chicago: Swoboda, Paul, and Bjoern Andres. “A Message Passing Algorithm for the
Minimum Cost Multicut Problem,” 2017:4990–99. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.530.
ieee: 'P. Swoboda and B. Andres, “A message passing algorithm for the minimum cost
multicut problem,” presented at the CVPR: Computer Vision and Pattern Recognition,
Honolulu, HA, United States, 2017, vol. 2017, pp. 4990–4999.'
ista: 'Swoboda P, Andres B. 2017. A message passing algorithm for the minimum cost
multicut problem. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4990–4999.'
mla: Swoboda, Paul, and Bjoern Andres. A Message Passing Algorithm for the Minimum
Cost Multicut Problem. Vol. 2017, IEEE, 2017, pp. 4990–99, doi:10.1109/CVPR.2017.530.
short: P. Swoboda, B. Andres, in:, IEEE, 2017, pp. 4990–4999.
conference:
end_date: 2017-07-26
location: Honolulu, HA, United States
name: 'CVPR: Computer Vision and Pattern Recognition'
start_date: 2017-07-21
corr_author: '1'
date_created: 2018-12-11T11:49:11Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2024-11-04T13:52:34Z
day: '01'
ddc:
- '000'
department:
- _id: VlKo
doi: 10.1109/CVPR.2017.530
ec_funded: 1
external_id:
isi:
- '000418371405009'
file:
- access_level: open_access
checksum: 7e51dacefa693574581a32da3eff63dc
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T12:52:46Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5849'
file_name: Swoboda_A_Message_Passing_CVPR_2017_paper.pdf
file_size: 883264
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 2017'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 4990-4999
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_identifier:
isbn:
- 978-153860457-1
publication_status: published
publisher: IEEE
publist_id: '6526'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A message passing algorithm for the minimum cost multicut problem
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '916'
abstract:
- lang: eng
text: We study the quadratic assignment problem, in computer vision also known as
graph matching. Two leading solvers for this problem optimize the Lagrange decomposition
duals with sub-gradient and dual ascent (also known as message passing) updates.
We explore this direction further and propose several additional Lagrangean relaxations
of the graph matching problem along with corresponding algorithms, which are all
based on a common dual ascent framework. Our extensive empirical evaluation gives
several theoretical insights and suggests a new state-of-the-art anytime solver
for the considered problem. Our improvement over state-of-the-art is particularly
visible on a new dataset with large-scale sparse problem instances containing
more than 500 graph nodes each.
article_processing_charge: No
author:
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Carsten
full_name: Abu Alhaija, Carsten
last_name: Abu Alhaija
- first_name: Dagmar
full_name: Kainmueller, Dagmar
last_name: Kainmueller
- first_name: Bogdan
full_name: Savchynskyy, Bogdan
last_name: Savchynskyy
citation:
ama: 'Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. A study
of lagrangean decompositions and dual ascent solvers for graph matching. In: Vol
2017. IEEE; 2017:7062-7071. doi:10.1109/CVPR.2017.747'
apa: 'Swoboda, P., Rother, C., Abu Alhaija, C., Kainmueller, D., & Savchynskyy,
B. (2017). A study of lagrangean decompositions and dual ascent solvers for graph
matching (Vol. 2017, pp. 7062–7071). Presented at the CVPR: Computer Vision and
Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.747'
chicago: Swoboda, Paul, Carsten Rother, Carsten Abu Alhaija, Dagmar Kainmueller,
and Bogdan Savchynskyy. “A Study of Lagrangean Decompositions and Dual Ascent
Solvers for Graph Matching,” 2017:7062–71. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.747.
ieee: 'P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, and B. Savchynskyy,
“A study of lagrangean decompositions and dual ascent solvers for graph matching,”
presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA,
United States, 2017, vol. 2017, pp. 7062–7071.'
ista: 'Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. 2017. A
study of lagrangean decompositions and dual ascent solvers for graph matching.
CVPR: Computer Vision and Pattern Recognition vol. 2017, 7062–7071.'
mla: Swoboda, Paul, et al. A Study of Lagrangean Decompositions and Dual Ascent
Solvers for Graph Matching. Vol. 2017, IEEE, 2017, pp. 7062–71, doi:10.1109/CVPR.2017.747.
short: P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, B. Savchynskyy, in:,
IEEE, 2017, pp. 7062–7071.
conference:
end_date: 2017-07-26
location: Honolulu, HA, United States
name: 'CVPR: Computer Vision and Pattern Recognition'
start_date: 2017-07-21
corr_author: '1'
date_created: 2018-12-11T11:49:11Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2024-11-04T13:52:34Z
day: '01'
ddc:
- '000'
department:
- _id: VlKo
doi: 10.1109/CVPR.2017.747
ec_funded: 1
external_id:
isi:
- '000418371407018'
file:
- access_level: open_access
checksum: e38a2740daad1ea178465843b5072906
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T12:49:38Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5848'
file_name: 2017_CVPR_Swoboda2.pdf
file_size: 944332
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 2017'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 7062-7071
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_identifier:
isbn:
- 978-153860457-1
publication_status: published
publisher: IEEE
publist_id: '6525'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A study of lagrangean decompositions and dual ascent solvers for graph matching
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '917'
abstract:
- lang: eng
text: We propose a general dual ascent framework for Lagrangean decomposition
of combinatorial problems. Although methods of this type have shown their efficiency
for a number of problems, so far there was no general algorithm applicable to
multiple problem types. In this work, we propose such a general algorithm. It
depends on several parameters, which can be used to optimize its performance in
each particular setting. We demonstrate efficacy of our method on graph matching
and multicut problems, where it outperforms state-of-the-art solvers including
those based on subgradient optimization and off-the-shelf linear programming solvers.
article_processing_charge: No
author:
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
- first_name: Jan
full_name: Kuske, Jan
last_name: Kuske
- first_name: Bogdan
full_name: Savchynskyy, Bogdan
last_name: Savchynskyy
citation:
ama: 'Swoboda P, Kuske J, Savchynskyy B. A dual ascent framework for Lagrangean
decomposition of combinatorial problems. In: Vol 2017. IEEE; 2017:4950-4960. doi:10.1109/CVPR.2017.526'
apa: 'Swoboda, P., Kuske, J., & Savchynskyy, B. (2017). A dual ascent framework
for Lagrangean decomposition of combinatorial problems (Vol. 2017, pp. 4950–4960).
Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA,
United States: IEEE. https://doi.org/10.1109/CVPR.2017.526'
chicago: Swoboda, Paul, Jan Kuske, and Bogdan Savchynskyy. “A Dual Ascent Framework
for Lagrangean Decomposition of Combinatorial Problems,” 2017:4950–60. IEEE, 2017.
https://doi.org/10.1109/CVPR.2017.526.
ieee: 'P. Swoboda, J. Kuske, and B. Savchynskyy, “A dual ascent framework for Lagrangean
decomposition of combinatorial problems,” presented at the CVPR: Computer Vision
and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4950–4960.'
ista: 'Swoboda P, Kuske J, Savchynskyy B. 2017. A dual ascent framework for Lagrangean
decomposition of combinatorial problems. CVPR: Computer Vision and Pattern Recognition
vol. 2017, 4950–4960.'
mla: Swoboda, Paul, et al. A Dual Ascent Framework for Lagrangean Decomposition
of Combinatorial Problems. Vol. 2017, IEEE, 2017, pp. 4950–60, doi:10.1109/CVPR.2017.526.
short: P. Swoboda, J. Kuske, B. Savchynskyy, in:, IEEE, 2017, pp. 4950–4960.
conference:
end_date: 2017-07-26
location: Honolulu, HA, United States
name: 'CVPR: Computer Vision and Pattern Recognition'
start_date: 2017-07-21
corr_author: '1'
date_created: 2018-12-11T11:49:11Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2024-11-04T13:52:34Z
day: '01'
ddc:
- '000'
department:
- _id: VlKo
doi: 10.1109/CVPR.2017.526
ec_funded: 1
external_id:
isi:
- '000418371405005'
file:
- access_level: open_access
checksum: 72fd291046bd8e5717961bd68f6b6f03
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T12:45:55Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5847'
file_name: 2017_CVPR_Swoboda.pdf
file_size: 898652
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 2017'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 4950-4960
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_identifier:
isbn:
- 978-153860457-1
publication_status: published
publisher: IEEE
publist_id: '6524'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A dual ascent framework for Lagrangean decomposition of combinatorial problems
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '939'
abstract:
- lang: eng
text: We reveal the existence of continuous families of guided single-mode solitons
in planar waveguides with weakly nonlinear active core and absorbing boundaries.
Stable propagation of TE and TM-polarized solitons is accompanied by attenuation
of all other modes, i.e., the waveguide features properties of conservative and
dissipative systems. If the linear spectrum of the waveguide possesses exceptional
points, which occurs in the case of TM polarization, an originally focusing (defocusing)
material nonlinearity may become effectively defocusing (focusing). This occurs
due to the geometric phase of the carried eigenmode when the surface impedance
encircles the exceptional point. In its turn, the change of the effective nonlinearity
ensures the existence of dark (bright) solitons in spite of focusing (defocusing)
Kerr nonlinearity of the core. The existence of an exceptional point can also
result in anomalous enhancement of the effective nonlinearity. In terms of practical
applications, the nonlinearity of the reported waveguide can be manipulated by
controlling the properties of the absorbing cladding.
article_number: '033905'
article_processing_charge: No
arxiv: 1
author:
- first_name: Bikashkali
full_name: Midya, Bikashkali
id: 456187FC-F248-11E8-B48F-1D18A9856A87
last_name: Midya
- first_name: Vladimir
full_name: Konotop, Vladimir
last_name: Konotop
citation:
ama: 'Midya B, Konotop V. Waveguides with absorbing boundaries: Nonlinearity controlled
by an exceptional point and solitons. Physical Review Letters. 2017;119(3).
doi:10.1103/PhysRevLett.119.033905'
apa: 'Midya, B., & Konotop, V. (2017). Waveguides with absorbing boundaries:
Nonlinearity controlled by an exceptional point and solitons. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.033905'
chicago: 'Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries:
Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review
Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.033905.'
ieee: 'B. Midya and V. Konotop, “Waveguides with absorbing boundaries: Nonlinearity
controlled by an exceptional point and solitons,” Physical Review Letters,
vol. 119, no. 3. American Physical Society, 2017.'
ista: 'Midya B, Konotop V. 2017. Waveguides with absorbing boundaries: Nonlinearity
controlled by an exceptional point and solitons. Physical Review Letters. 119(3),
033905.'
mla: 'Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries:
Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review
Letters, vol. 119, no. 3, 033905, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.033905.'
short: B. Midya, V. Konotop, Physical Review Letters 119 (2017).
corr_author: '1'
date_created: 2018-12-11T11:49:18Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2025-06-04T08:20:23Z
day: '18'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.119.033905
ec_funded: 1
external_id:
arxiv:
- '1706.04085 '
isi:
- '000405718200012'
intvolume: ' 119'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://arxiv.org/abs/1706.04085 '
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review Letters
publication_identifier:
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
publist_id: '6481'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional
point and solitons'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2017'
...
---
_id: '941'
abstract:
- lang: eng
text: 'Recently there has been a proliferation of automated program repair (APR)
techniques, targeting various programming languages. Such techniques can be generally
classified into two families: syntactic- and semantics-based. Semantics-based
APR, on which we focus, typically uses symbolic execution to infer semantic constraints
and then program synthesis to construct repairs conforming to them. While syntactic-based
APR techniques have been shown successful on bugs in real-world programs written
in both C and Java, semantics-based APR techniques mostly target C programs. This
leaves empirical comparisons of the APR families not fully explored, and developers
without a Java-based semantics APR technique. We present JFix, a semantics-based
APR framework that targets Java, and an associated Eclipse plugin. JFix is implemented
atop Symbolic PathFinder, a well-known symbolic execution engine for Java programs.
It extends one particular APR technique (Angelix), and is designed to be sufficiently
generic to support a variety of such techniques. We demonstrate that semantics-based
APR can indeed efficiently and effectively repair a variety of classes of bugs
in large real-world Java programs. This supports our claim that the framework
can both support developers seeking semantics-based repair of bugs in Java programs,
as well as enable larger scale empirical studies comparing syntactic- and semantics-based
APR targeting Java. The demonstration of our tool is available via the project
website at: https://xuanbachle.github.io/semanticsrepair/ '
acknowledgement: We thank Vu Le (Microsoft Research, Redmond), and anonymous reviewers
for their comments. Duc-Hiep Chu was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).
article_processing_charge: No
author:
- first_name: Xuan
full_name: Le, Xuan
last_name: Le
- first_name: Duc Hiep
full_name: Chu, Duc Hiep
id: 3598E630-F248-11E8-B48F-1D18A9856A87
last_name: Chu
- first_name: David
full_name: Lo, David
last_name: Lo
- first_name: Claire
full_name: Le Goues, Claire
last_name: Le Goues
- first_name: Willem
full_name: Visser, Willem
last_name: Visser
citation:
ama: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. JFIX: Semantics-based repair of
Java programs via symbolic PathFinder. In: Proceedings of the 26th ACM SIGSOFT
International Symposium on Software Testing and Analysis. ACM; 2017:376-379.
doi:10.1145/3092703.3098225'
apa: 'Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). JFIX: Semantics-based
repair of Java programs via symbolic PathFinder. In Proceedings of the 26th
ACM SIGSOFT International Symposium on Software Testing and Analysis (pp.
376–379). Santa Barbara, CA, United States: ACM. https://doi.org/10.1145/3092703.3098225'
chicago: 'Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser.
“JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” In Proceedings
of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis,
376–79. ACM, 2017. https://doi.org/10.1145/3092703.3098225.'
ieee: 'X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “JFIX: Semantics-based
repair of Java programs via symbolic PathFinder,” in Proceedings of the 26th
ACM SIGSOFT International Symposium on Software Testing and Analysis, Santa
Barbara, CA, United States, 2017, pp. 376–379.'
ista: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. JFIX: Semantics-based repair
of Java programs via symbolic PathFinder. Proceedings of the 26th ACM SIGSOFT
International Symposium on Software Testing and Analysis. ISSTA: International
Symposium on Software Testing and Analysis, 376–379.'
mla: 'Le, Xuan, et al. “JFIX: Semantics-Based Repair of Java Programs via Symbolic
PathFinder.” Proceedings of the 26th ACM SIGSOFT International Symposium on
Software Testing and Analysis, ACM, 2017, pp. 376–79, doi:10.1145/3092703.3098225.'
short: X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, Proceedings of the 26th
ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017,
pp. 376–379.
conference:
end_date: 2017-07-14
location: Santa Barbara, CA, United States
name: 'ISSTA: International Symposium on Software Testing and Analysis'
start_date: 2017-07-10
corr_author: '1'
date_created: 2018-12-11T11:49:19Z
date_published: 2017-07-10T00:00:00Z
date_updated: 2025-09-18T10:39:32Z
day: '10'
department:
- _id: ToHe
doi: 10.1145/3092703.3098225
external_id:
isi:
- '000462903600038'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://core.ac.uk/download/pdf/111759662.pdf
month: '07'
oa: 1
oa_version: Published Version
page: '376 - 379 '
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: Proceedings of the 26th ACM SIGSOFT International Symposium on Software
Testing and Analysis
publication_status: published
publisher: ACM
publist_id: '6478'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'JFIX: Semantics-based repair of Java programs via symbolic PathFinder'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2017'
...
---
_id: '942'
abstract:
- lang: eng
text: 'A notable class of techniques for automatic program repair is known as semantics-based.
Such techniques, e.g., Angelix, infer semantic specifications via symbolic execution,
and then use program synthesis to construct new code that satisfies those inferred
specifications. However, the obtained specifications are naturally incomplete,
leaving the synthesis engine with a difficult task of synthesizing a general solution
from a sparse space of many possible solutions that are consistent with the provided
specifications but that do not necessarily generalize. We present S3, a new repair
synthesis engine that leverages programming-by-examples methodology to synthesize
high-quality bug repairs. The novelty in S3 that allows it to tackle the sparse
search space to create more general repairs is three-fold: (1) A systematic way
to customize and constrain the syntactic search space via a domain-specific language,
(2) An efficient enumeration-based search strategy over the constrained search
space, and (3) A number of ranking features based on measures of the syntactic
and semantic distances between candidate solutions and the original buggy program.
We compare S3’s repair effectiveness with state-of-the-art synthesis engines Angelix,
Enumerative, and CVC4. S3 can successfully and correctly fix at least three times
more bugs than the best baseline on datasets of 52 bugs in small programs, and
100 bugs in real-world large programs. '
article_processing_charge: No
author:
- first_name: Xuan
full_name: Le, Xuan
last_name: Le
- first_name: Duc Hiep
full_name: Chu, Duc Hiep
id: 3598E630-F248-11E8-B48F-1D18A9856A87
last_name: Chu
- first_name: David
full_name: Lo, David
last_name: Lo
- first_name: Claire
full_name: Le Goues, Claire
last_name: Le Goues
- first_name: Willem
full_name: Visser, Willem
last_name: Visser
citation:
ama: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. S3: Syntax- and semantic-guided
repair synthesis via programming by examples. In: Vol F130154. ACM; 2017:593-604.
doi:10.1145/3106237.3106309'
apa: 'Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). S3: Syntax-
and semantic-guided repair synthesis via programming by examples (Vol. F130154,
pp. 593–604). Presented at the FSE: Foundations of Software Engineering, Paderborn,
Germany: ACM. https://doi.org/10.1145/3106237.3106309'
chicago: 'Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser.
“S3: Syntax- and Semantic-Guided Repair Synthesis via Programming by Examples,”
F130154:593–604. ACM, 2017. https://doi.org/10.1145/3106237.3106309.'
ieee: 'X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “S3: Syntax- and semantic-guided
repair synthesis via programming by examples,” presented at the FSE: Foundations
of Software Engineering, Paderborn, Germany, 2017, vol. F130154, pp. 593–604.'
ista: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. S3: Syntax- and semantic-guided
repair synthesis via programming by examples. FSE: Foundations of Software Engineering
vol. F130154, 593–604.'
mla: 'Le, Xuan, et al. S3: Syntax- and Semantic-Guided Repair Synthesis via Programming
by Examples. Vol. F130154, ACM, 2017, pp. 593–604, doi:10.1145/3106237.3106309.'
short: X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, ACM, 2017, pp. 593–604.
conference:
end_date: 2017-09-08
location: Paderborn, Germany
name: 'FSE: Foundations of Software Engineering'
start_date: 2017-09-04
date_created: 2018-12-11T11:49:19Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2025-04-15T06:25:57Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/3106237.3106309
external_id:
isi:
- '000414279300055'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
page: 593 - 604
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication_identifier:
isbn:
- 978-145035105-8
publication_status: published
publisher: ACM
publist_id: '6477'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'S3: Syntax- and semantic-guided repair synthesis via programming by examples'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: F130154
year: '2017'
...
---
_id: '943'
abstract:
- lang: eng
text: Like many developing tissues, the vertebrate neural tube is patterned by antiparallel
morphogen gradients. To understand how these inputs are interpreted, we measured
morphogen signaling and target gene expression in mouse embryos and chick ex vivo
assays. From these data, we derived and validated a characteristic decoding map
that relates morphogen input to the positional identity of neural progenitors.
Analysis of the observed responses indicates that the underlying interpretation
strategy minimizes patterning errors in response to the joint input of noisy opposing
gradients. We reverse-engineered a transcriptional network that provides a mechanistic
basis for the observed cell fate decisions and accounts for the precision and
dynamics of pattern formation. Together, our data link opposing gradient dynamics
in a growing tissue to precise pattern formation.
article_processing_charge: No
author:
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Yoji
full_name: Tabata, Yoji
last_name: Tabata
- first_name: Nathalie
full_name: Brandenberg, Nathalie
last_name: Brandenberg
- first_name: Matthias
full_name: Lutolf, Matthias
last_name: Lutolf
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Tobias
full_name: Bollenbach, Tobias
last_name: Bollenbach
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing
neural tube from antiparallel morphogen gradients. Science. 2017;356(6345):1379-1383.
doi:10.1126/science.aam5887
apa: Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach,
T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from
antiparallel morphogen gradients. Science. American Association for the
Advancement of Science. https://doi.org/10.1126/science.aam5887
chicago: Zagórski, Marcin P, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf,
Gašper Tkačik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of
Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.”
Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam5887.
ieee: M. P. Zagórski et al., “Decoding of position in the developing neural
tube from antiparallel morphogen gradients,” Science, vol. 356, no. 6345.
American Association for the Advancement of Science, pp. 1379–1383, 2017.
ista: Zagórski MP, Tabata Y, Brandenberg N, Lutolf M, Tkačik G, Bollenbach T, Briscoe
J, Kicheva A. 2017. Decoding of position in the developing neural tube from antiparallel
morphogen gradients. Science. 356(6345), 1379–1383.
mla: Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural
Tube from Antiparallel Morphogen Gradients.” Science, vol. 356, no. 6345,
American Association for the Advancement of Science, 2017, pp. 1379–83, doi:10.1126/science.aam5887.
short: M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach,
J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.
corr_author: '1'
date_created: 2018-12-11T11:49:20Z
date_published: 2017-06-30T00:00:00Z
date_updated: 2025-07-10T12:01:45Z
day: '30'
department:
- _id: AnKi
- _id: GaTk
doi: 10.1126/science.aam5887
ec_funded: 1
external_id:
isi:
- '000404351500036'
pmid:
- '28663499'
intvolume: ' 356'
isi: 1
issue: '6345'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568706/
month: '06'
oa: 1
oa_version: Submitted Version
page: 1379 - 1383
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2524F500-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '201439'
name: Developing High-Throughput Bioassays for Human Cancers in Zebrafish
publication: Science
publication_identifier:
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6474'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Decoding of position in the developing neural tube from antiparallel morphogen
gradients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 356
year: '2017'
...
---
_id: '9445'
abstract:
- lang: eng
text: Cytosine methylation regulates essential genome functions across eukaryotes,
but the fundamental question of whether nucleosomal or naked DNA is the preferred
substrate of plant and animal methyltransferases remains unresolved. Here, we
show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler
biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana
and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome,
suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases
in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone
H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of
species that diverged from flowering plants and animals over a billion years ago.
Our results indicate that in the absence of remodeling, nucleosomes are strong
barriers to DNA methyltransferases. Linker-specific methylation can evolve simply
by breaking the connection between nucleosome remodeling and DNA methylation.
article_number: e30674
article_processing_charge: No
article_type: original
author:
- first_name: David B
full_name: Lyons, David B
last_name: Lyons
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped
in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674
apa: Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation
of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674
chicago: Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation
of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017.
https://doi.org/10.7554/elife.30674.
ieee: D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of
DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications,
2017.
ista: Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of
DNA wrapped in nucleosomes. eLife. 6, e30674.
mla: Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation
of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications,
2017, doi:10.7554/elife.30674.
short: D.B. Lyons, D. Zilberman, ELife 6 (2017).
date_created: 2021-06-02T14:28:58Z
date_published: 2017-11-15T00:00:00Z
date_updated: 2021-12-14T07:54:36Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.7554/elife.30674
extern: '1'
external_id:
pmid:
- '29140247'
file:
- access_level: open_access
checksum: 4cfcdd67511ae4aed3d993550e46e146
content_type: application/pdf
creator: cziletti
date_created: 2021-06-02T14:33:36Z
date_updated: 2021-06-02T14:33:36Z
file_id: '9446'
file_name: 2017_eLife_Lyons.pdf
file_size: 1603102
relation: main_file
success: 1
file_date_updated: 2021-06-02T14:33:36Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2017'
...
---
_id: '946'
abstract:
- lang: eng
text: Roots navigate through soil integrating environmental signals to orient their
growth. The Arabidopsis root is a widely used model for developmental, physiological
and cell biological studies. Live imaging greatly aids these efforts, but the
horizontal sample position and continuous root tip displacement present significant
difficulties. Here, we develop a confocal microscope setup for vertical sample
mounting and integrated directional illumination. We present TipTracker – a custom
software for automatic tracking of diverse moving objects usable on various microscope
setups. Combined, this enables observation of root tips growing along the natural
gravity vector over prolonged periods of time, as well as the ability to induce
rapid gravity or light stimulation. We also track migrating cells in the developing
zebrafish embryo, demonstrating the utility of this system in the acquisition
of high-resolution data sets of dynamic samples. We provide detailed descriptions
of the tools enabling the easy implementation on other microscopes.
acknowledged_ssus:
- _id: M-Shop
- _id: Bio
acknowledgement: "Funding: Marie Curie Actions (FP7/2007-2013 no 291734) to Daniel
von Wangenheim; Austrian Science Fund (M 2128-B21) to Matyáš Fendrych; Austrian
Science Fund (FWF01_I1774S) to Eva Benková; European Research Council (FP7/2007-2013
no 282300) to Jiří Friml. \r\nThe authors are grateful to the Miba Machine Shop
at IST Austria for their contribution to the microscope setup and to Yvonne Kemper
for reading, understanding and correcting the manuscript.\r\n#BioimagingFacility"
article_number: e26792
article_processing_charge: Yes
author:
- first_name: Daniel
full_name: Von Wangenheim, Daniel
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. Live
tracking of moving samples in confocal microscopy for vertically grown roots.
eLife. 2017;6. doi:10.7554/eLife.26792
apa: von Wangenheim, D., Hauschild, R., Fendrych, M., Barone, V., Benková, E., &
Friml, J. (2017). Live tracking of moving samples in confocal microscopy for vertically
grown roots. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.26792
chicago: Wangenheim, Daniel von, Robert Hauschild, Matyas Fendrych, Vanessa Barone,
Eva Benková, and Jiří Friml. “Live Tracking of Moving Samples in Confocal Microscopy
for Vertically Grown Roots.” ELife. eLife Sciences Publications, 2017.
https://doi.org/10.7554/eLife.26792.
ieee: D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, and J.
Friml, “Live tracking of moving samples in confocal microscopy for vertically
grown roots,” eLife, vol. 6. eLife Sciences Publications, 2017.
ista: von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. 2017.
Live tracking of moving samples in confocal microscopy for vertically grown roots.
eLife. 6, e26792.
mla: von Wangenheim, Daniel, et al. “Live Tracking of Moving Samples in Confocal
Microscopy for Vertically Grown Roots.” ELife, vol. 6, e26792, eLife Sciences
Publications, 2017, doi:10.7554/eLife.26792.
short: D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, J. Friml,
ELife 6 (2017).
date_created: 2018-12-11T11:49:21Z
date_published: 2017-06-19T00:00:00Z
date_updated: 2025-04-15T06:37:26Z
day: '19'
ddc:
- '570'
department:
- _id: JiFr
- _id: Bio
- _id: CaHe
- _id: EvBe
doi: 10.7554/eLife.26792
ec_funded: 1
external_id:
isi:
- '000404728300001'
file:
- access_level: open_access
checksum: 9af3398cb0d81f99d79016a616df22e9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:57Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5315'
file_name: IST-2017-847-v1+1_elife-26792-v2.pdf
file_size: 19581847
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2572ED28-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02128
name: Molecular basis of root growth inhibition by auxin
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6471'
pubrep_id: '847'
quality_controlled: '1'
related_material:
record:
- id: '5566'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Live tracking of moving samples in confocal microscopy for vertically grown
roots
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 6
year: '2017'
...
---
_id: '947'
abstract:
- lang: eng
text: Viewing the ways a living cell can organize its metabolism as the phase space
of a physical system, regulation can be seen as the ability to reduce the entropy
of that space by selecting specific cellular configurations that are, in some
sense, optimal. Here we quantify the amount of regulation required to control
a cell's growth rate by a maximum-entropy approach to the space of underlying
metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern
as described by genome-scale models. We link the mean growth rate achieved by
a population of cells to the minimal amount of metabolic regulation needed to
achieve it through a phase diagram that highlights how growth suppression can
be as costly (in regulatory terms) as growth enhancement. Moreover, we provide
an interpretation of the inverse temperature β controlling maximum-entropy distributions
based on the underlying growth dynamics. Specifically, we show that the asymptotic
value of β for a cell population can be expected to depend on (i) the carrying
capacity of the environment, (ii) the initial size of the colony, and (iii) the
probability distribution from which the inoculum was sampled. Results obtained
for E. coli and human cells are found to be remarkably consistent with empirical
evidence.
article_number: '010401'
article_processing_charge: No
arxiv: 1
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Fabrizio
full_name: Capuani, Fabrizio
last_name: Capuani
- first_name: Andrea
full_name: De Martino, Andrea
last_name: De Martino
citation:
ama: De Martino D, Capuani F, De Martino A. Quantifying the entropic cost of cellular
growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics
. 2017;96(1). doi:10.1103/PhysRevE.96.010401
apa: De Martino, D., Capuani, F., & De Martino, A. (2017). Quantifying the entropic
cost of cellular growth control. Physical Review E Statistical Nonlinear and
Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.010401
chicago: De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying
the Entropic Cost of Cellular Growth Control.” Physical Review E Statistical
Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.010401.
ieee: D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost
of cellular growth control,” Physical Review E Statistical Nonlinear and Soft
Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017.
ista: De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost
of cellular growth control. Physical Review E Statistical Nonlinear and Soft
Matter Physics . 96(1), 010401.
mla: De Martino, Daniele, et al. “Quantifying the Entropic Cost of Cellular Growth
Control.” Physical Review E Statistical Nonlinear and Soft Matter Physics
, vol. 96, no. 1, 010401, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.010401.
short: D. De Martino, F. Capuani, A. De Martino, Physical Review E Statistical
Nonlinear and Soft Matter Physics 96 (2017).
date_created: 2018-12-11T11:49:21Z
date_published: 2017-07-10T00:00:00Z
date_updated: 2025-06-04T08:12:18Z
day: '10'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.96.010401
ec_funded: 1
external_id:
arxiv:
- '1703.00219'
isi:
- '000405194200002'
intvolume: ' 96'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.00219
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Physical Review E Statistical Nonlinear and Soft Matter Physics '
publication_identifier:
issn:
- 2470-0045
publication_status: published
publisher: American Institute of Physics
publist_id: '6470'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantifying the entropic cost of cellular growth control
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 96
year: '2017'
...
---
_id: '950'
abstract:
- lang: eng
text: "Two-player games on graphs are widely studied in formal methods as they model
the interaction between a system and its environment. The game is played by moving
a token throughout a graph to produce an infinite path. There are several common
modes to determine how the players move the token through the graph; e.g., in
turn-based games the players alternate turns in moving the token. We study the
bidding mode of moving the token, which, to the best of our knowledge, has never
been studied in infinite-duration games. Both players have separate budgets, which
sum up to $1$. In each turn, a bidding takes place. Both players submit bids simultaneously,
and a bid is legal if it does not exceed the available budget. The winner of the
bidding pays his bid to the other player and moves the token. For reachability
objectives, repeated bidding games have been studied and are called Richman games.
There, a central question is the existence and computation of threshold budgets;
namely, a value t\\in [0,1] such that if\\PO's budget exceeds $t$, he can win
the game, and if\\PT's budget exceeds 1-t, he can win the game. We focus on parity
games and mean-payoff games. We show the existence of threshold budgets in these
games, and reduce the problem of finding them to Richman games. We also determine
the strategy-complexity of an optimal strategy. Our most interesting result shows
that memoryless strategies suffice for mean-payoff bidding games. \r\n"
alternative_title:
- LIPIcs
article_number: '17'
arxiv: 1
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- 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: Ventsislav K
full_name: Chonev, Ventsislav K
id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87
last_name: Chonev
citation:
ama: 'Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. In: Vol
85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.21'
apa: 'Avni, G., Henzinger, T. A., & Chonev, V. K. (2017). Infinite-duration
bidding games (Vol. 85). Presented at the CONCUR: Concurrency Theory, Berlin,
Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21'
chicago: Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration
Bidding Games,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.
https://doi.org/10.4230/LIPIcs.CONCUR.2017.21.
ieee: 'G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,”
presented at the CONCUR: Concurrency Theory, Berlin, Germany, 2017, vol. 85.'
ista: 'Avni G, Henzinger TA, Chonev VK. 2017. Infinite-duration bidding games. CONCUR:
Concurrency Theory, LIPIcs, vol. 85, 17.'
mla: Avni, Guy, et al. Infinite-Duration Bidding Games. Vol. 85, 17, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.21.
short: G. Avni, T.A. Henzinger, V.K. Chonev, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2017.
conference:
end_date: 2017-09-07
location: Berlin, Germany
name: 'CONCUR: Concurrency Theory'
start_date: 2017-09-05
date_created: 2018-12-11T11:49:22Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2025-07-10T11:53:48Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.4230/LIPIcs.CONCUR.2017.21
external_id:
arxiv:
- '1705.01433'
file:
- access_level: open_access
checksum: 6d5cccf755207b91ccbef95d8275b013
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:00Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5318'
file_name: IST-2017-844-v1+1_concur-cr.pdf
file_size: 335170
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 85'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication_identifier:
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6466'
pubrep_id: '844'
quality_controlled: '1'
related_material:
record:
- id: '6752'
relation: later_version
status: public
scopus_import: 1
status: public
title: Infinite-duration bidding games
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 85
year: '2017'
...
---
_id: '9506'
abstract:
- lang: eng
text: Methylation in the bodies of active genes is common in animals and vascular
plants. Evolutionary patterns indicate homeostatic functions for this type of
methylation.
article_number: '87'
article_processing_charge: No
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zilberman D. An evolutionary case for functional gene body methylation in plants
and animals. Genome Biology. 2017;18(1). doi:10.1186/s13059-017-1230-2
apa: Zilberman, D. (2017). An evolutionary case for functional gene body methylation
in plants and animals. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-017-1230-2
chicago: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation
in Plants and Animals.” Genome Biology. Springer Nature, 2017. https://doi.org/10.1186/s13059-017-1230-2.
ieee: D. Zilberman, “An evolutionary case for functional gene body methylation in
plants and animals,” Genome Biology, vol. 18, no. 1. Springer Nature, 2017.
ista: Zilberman D. 2017. An evolutionary case for functional gene body methylation
in plants and animals. Genome Biology. 18(1), 87.
mla: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation
in Plants and Animals.” Genome Biology, vol. 18, no. 1, 87, Springer Nature,
2017, doi:10.1186/s13059-017-1230-2.
short: D. Zilberman, Genome Biology 18 (2017).
date_created: 2021-06-07T12:27:39Z
date_published: 2017-05-09T00:00:00Z
date_updated: 2021-12-14T07:55:02Z
day: '09'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1186/s13059-017-1230-2
extern: '1'
external_id:
pmid:
- '28486944'
file:
- access_level: open_access
checksum: 5a455ad914e7d225b1baa4ab07fd925e
content_type: application/pdf
creator: asandaue
date_created: 2021-06-07T12:31:36Z
date_updated: 2021-06-07T12:31:36Z
file_id: '9507'
file_name: 2017_GenomeBiology_Zilberman.pdf
file_size: 278183
relation: main_file
success: 1
file_date_updated: 2021-06-07T12:31:36Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
eissn:
- 1465-6906
issn:
- 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An evolutionary case for functional gene body methylation in plants and animals
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 18
year: '2017'
...
---
_id: '951'
abstract:
- lang: eng
text: Dengue-suppressing Wolbachia strains are promising tools for arbovirus control,
particularly as they have the potential to self-spread following local introductions.
To test this, we followed the frequency of the transinfected Wolbachia strain
wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated
locations within the city in early 2013. Spatial spread was analysed graphically
using interpolation and by fitting a statistical model describing the position
and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and
0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per
year, roughly consistent with theoretical predictions. In contrast, the smallest
release (0.11 km2) produced erratic temporal and spatial dynamics, with little
evidence of spread after 2 years. This is consistent with the prediction concerning
fitness-decreasing Wolbachia transinfections that a minimum release area is needed
to achieve stable local establishment and spread in continuous habitats. Our graphical
and likelihood analyses produced broadly consistent estimates of wave speed and
wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental
heterogeneity will affect large-scale Wolbachia transformations of urban mosquito
populations. The persistence and spread of Wolbachia in release areas meeting
minimum area requirements indicates the promise of successful large-scale population
transfo
article_number: e2001894
article_processing_charge: No
author:
- first_name: Tom
full_name: Schmidt, Tom
last_name: Schmidt
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gordana
full_name: Rasic, Gordana
last_name: Rasic
- first_name: Andrew
full_name: Turley, Andrew
last_name: Turley
- first_name: Brian
full_name: Montgomery, Brian
last_name: Montgomery
- first_name: Inaki
full_name: Iturbe Ormaetxe, Inaki
last_name: Iturbe Ormaetxe
- first_name: Peter
full_name: Cook, Peter
last_name: Cook
- first_name: Peter
full_name: Ryan, Peter
last_name: Ryan
- first_name: Scott
full_name: Ritchie, Scott
last_name: Ritchie
- first_name: Ary
full_name: Hoffmann, Ary
last_name: Hoffmann
- first_name: Scott
full_name: O’Neill, Scott
last_name: O’Neill
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: Schmidt T, Barton NH, Rasic G, et al. Local introduction and heterogeneous
spatial spread of dengue-suppressing Wolbachia through an urban population of
Aedes Aegypti. PLoS Biology. 2017;15(5). doi:10.1371/journal.pbio.2001894
apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe,
I., … Turelli, M. (2017). Local introduction and heterogeneous spatial spread
of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894
chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery,
Inaki Iturbe Ormaetxe, Peter Cook, et al. “Local Introduction and Heterogeneous
Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of
Aedes Aegypti.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.
ieee: T. Schmidt et al., “Local introduction and heterogeneous spatial spread
of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti,”
PLoS Biology, vol. 15, no. 5. Public Library of Science, 2017.
ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I,
Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Local introduction
and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban
population of Aedes Aegypti. PLoS Biology. 15(5), e2001894.
mla: Schmidt, Tom, et al. “Local Introduction and Heterogeneous Spatial Spread of
Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS
Biology, vol. 15, no. 5, e2001894, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.
short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe,
P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, PLoS Biology
15 (2017).
date_created: 2018-12-11T11:49:22Z
date_published: 2017-05-30T00:00:00Z
date_updated: 2025-07-10T12:01:48Z
day: '30'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2001894
external_id:
isi:
- '000402520000012'
file:
- access_level: open_access
checksum: 107d290bd1159ec77b734eb2824b01c8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:30Z
date_updated: 2020-07-14T12:48:16Z
file_id: '4691'
file_name: IST-2017-843-v1+1_journal.pbio.2001894.pdf
file_size: 5541206
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_identifier:
issn:
- 1544-9173
publication_status: published
publisher: Public Library of Science
publist_id: '6464'
pubrep_id: '843'
quality_controlled: '1'
related_material:
record:
- id: '9856'
relation: research_data
status: public
- id: '9857'
relation: research_data
status: public
- id: '9858'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia
through an urban population of Aedes Aegypti
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: 15
year: '2017'
...
---
_id: '952'
abstract:
- lang: eng
text: A novel strategy for controlling the spread of arboviral diseases such as
dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing
Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness
costs through lower viability or fecundity. These maternally inherited bacteria
also produce a frequency-dependent advantage for infected females by inducing
cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected
females mated to infected males. These competing effects, a frequency-dependent
advantage and frequency-independent costs, produce bistable Wolbachia frequency
dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing
Wolbachia transinfections through local populations; but below pˆ, infection frequencies
tend to decline to zero. If pˆ is not too high, CI also drives spatial spread
once infections become established over sufficiently large areas. We illustrate
how simple models provide testable predictions concerning the spatial and temporal
dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape
of spreading waves, and the conditions for initiating spread from local introductions.
First, we consider the robustness of diffusion-based predictions to incorporating
two important features of wMel-Aedes aegypti biology that may be inconsistent
with the diffusion approximations, namely fast local dynamics induced by complete
CI (i.e., all embryos produced from incompatible crosses die) and long-tailed,
non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed
dispersal changes wave-width predictions only slightly; but it can significantly
reduce wave speed relative to the diffusion prediction; it also allows smaller
local introductions to initiate spatial spread. Second, we use approximations
for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected
Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti
populations near Cairns, Australia that demonstrate long-distance dispersal and
provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally,
we apply our analyses to produce operational guidelines for efficient transformation
of vector populations over large areas. We demonstrate that even very slow spatial
spread, on the order of 10-20 m/month (as predicted), can produce area-wide population
transformation within a few years following initial releases covering about 20-30%
of the target area.
article_processing_charge: No
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Turelli M, Barton NH. Deploying dengue-suppressing Wolbachia: Robust models
predict slow but effective spatial spread in Aedes aegypti. Theoretical Population
Biology. 2017;115:45-60. doi:10.1016/j.tpb.2017.03.003'
apa: 'Turelli, M., & Barton, N. H. (2017). Deploying dengue-suppressing Wolbachia:
Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical
Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2017.03.003'
chicago: 'Turelli, Michael, and Nicholas H Barton. “Deploying Dengue-Suppressing
Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.”
Theoretical Population Biology. Elsevier, 2017. https://doi.org/10.1016/j.tpb.2017.03.003.'
ieee: 'M. Turelli and N. H. Barton, “Deploying dengue-suppressing Wolbachia: Robust
models predict slow but effective spatial spread in Aedes aegypti,” Theoretical
Population Biology, vol. 115. Elsevier, pp. 45–60, 2017.'
ista: 'Turelli M, Barton NH. 2017. Deploying dengue-suppressing Wolbachia: Robust
models predict slow but effective spatial spread in Aedes aegypti. Theoretical
Population Biology. 115, 45–60.'
mla: 'Turelli, Michael, and Nicholas H. Barton. “Deploying Dengue-Suppressing Wolbachia:
Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical
Population Biology, vol. 115, Elsevier, 2017, pp. 45–60, doi:10.1016/j.tpb.2017.03.003.'
short: M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60.
date_created: 2018-12-11T11:49:22Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2025-07-10T12:01:49Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2017.03.003
external_id:
pmid:
- '28411063'
file:
- access_level: open_access
checksum: 9aeff86fa7de69f7a15cf4fc60d57d01
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T06:39:45Z
date_updated: 2020-07-14T12:48:16Z
file_id: '6327'
file_name: 2017_TheoreticalPopulationBio_Turelli.pdf
file_size: 2073856
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 115'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '06'
oa: 1
oa_version: Submitted Version
page: 45 - 60
pmid: 1
publication: Theoretical Population Biology
publication_identifier:
issn:
- 0040-5809
publication_status: published
publisher: Elsevier
publist_id: '6463'
pubrep_id: '972'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective
spatial spread in Aedes aegypti'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2017'
...
---
_id: '953'
abstract:
- lang: eng
text: 'The role of natural selection in the evolution of adaptive phenotypes has
undergone constant probing by evolutionary biologists, employing both theoretical
and empirical approaches. As Darwin noted, natural selection can act together
with other processes, including random changes in the frequencies of phenotypic
differences that are not under strong selection, and changes in the environment,
which may reflect evolutionary changes in the organisms themselves. As understanding
of genetics developed after 1900, the new genetic discoveries were incorporated
into evolutionary biology. The resulting general principles were summarized by
Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine
how recent advances in genetics, developmental biology and molecular biology,
including epigenetics, relate to today''s understanding of the evolution of adaptations.
We illustrate how careful genetic studies have repeatedly shown that apparently
puzzling results in a wide diversity of organisms involve processes that are consistent
with neo-Darwinism. They do not support important roles in adaptation for processes
such as directed mutation or the inheritance of acquired characters, and therefore
no radical revision of our understanding of the mechanism of adaptive evolution
is needed.'
article_number: '20162864'
article_processing_charge: No
author:
- first_name: Deborah
full_name: Charlesworth, Deborah
last_name: Charlesworth
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
citation:
ama: Charlesworth D, Barton NH, Charlesworth B. The sources of adaptive evolution.
Proceedings of the Royal Society of London Series B Biological Sciences.
2017;284(1855). doi:10.1098/rspb.2016.2864
apa: Charlesworth, D., Barton, N. H., & Charlesworth, B. (2017). The sources
of adaptive evolution. Proceedings of the Royal Society of London Series B
Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.2864
chicago: Charlesworth, Deborah, Nicholas H Barton, and Brian Charlesworth. “The
Sources of Adaptive Evolution.” Proceedings of the Royal Society of London
Series B Biological Sciences. Royal Society, The, 2017. https://doi.org/10.1098/rspb.2016.2864.
ieee: D. Charlesworth, N. H. Barton, and B. Charlesworth, “The sources of adaptive
evolution,” Proceedings of the Royal Society of London Series B Biological
Sciences, vol. 284, no. 1855. Royal Society, The, 2017.
ista: Charlesworth D, Barton NH, Charlesworth B. 2017. The sources of adaptive evolution.
Proceedings of the Royal Society of London Series B Biological Sciences. 284(1855),
20162864.
mla: Charlesworth, Deborah, et al. “The Sources of Adaptive Evolution.” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 284, no.
1855, 20162864, Royal Society, The, 2017, doi:10.1098/rspb.2016.2864.
short: D. Charlesworth, N.H. Barton, B. Charlesworth, Proceedings of the Royal Society
of London Series B Biological Sciences 284 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-05-31T00:00:00Z
date_updated: 2023-09-22T10:01:48Z
day: '31'
department:
- _id: NiBa
doi: 10.1098/rspb.2016.2864
external_id:
isi:
- '000405148800021'
pmid:
- '28566483'
intvolume: ' 284'
isi: 1
issue: '1855'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454256/
month: '05'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '6462'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The sources of adaptive evolution
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 284
year: '2017'
...
---
_id: '954'
abstract:
- lang: eng
text: Understanding the relation between genotype and phenotype remains a major
challenge. The difficulty of predicting individual mutation effects, and particularly
the interactions between them, has prevented the development of a comprehensive
theory that links genotypic changes to their phenotypic effects. We show that
a general thermodynamic framework for gene regulation, based on a biophysical
understanding of protein-DNA binding, accurately predicts the sign of epistasis
in a canonical cis-regulatory element consisting of overlapping RNA polymerase
and repressor binding sites. Sign and magnitude of individual mutation effects
are sufficient to predict the sign of epistasis and its environmental dependence.
Thus, the thermodynamic model offers the correct null prediction for epistasis
between mutations across DNA-binding sites. Our results indicate that a predictive
theory for the effects of cis-regulatory mutations is possible from first principles,
as long as the essential molecular mechanisms and the constraints these impose
on a biological system are accounted for.
article_number: e25192
article_processing_charge: Yes
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature
of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192
apa: Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C.
(2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element.
ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192
chicago: Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and
Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory
Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192.
ieee: M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the
mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife,
vol. 6. eLife Sciences Publications, 2017.
ista: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic
nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192.
mla: Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical
Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications,
2017, doi:10.7554/eLife.25192.
short: M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-05-18T00:00:00Z
date_updated: 2025-07-10T12:01:50Z
day: '18'
ddc:
- '576'
department:
- _id: CaGu
- _id: NiBa
- _id: JoBo
doi: 10.7554/eLife.25192
ec_funded: 1
external_id:
isi:
- '000404024800001'
file:
- access_level: open_access
checksum: 59cdd4400fb41280122d414fea971546
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:49Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5306'
file_name: IST-2017-841-v1+1_elife-25192-v2.pdf
file_size: 2441529
relation: main_file
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checksum: b69024880558b858eb8c5d47a92b6377
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:50Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5307'
file_name: IST-2017-841-v1+2_elife-25192-figures-v2.pdf
file_size: 3752660
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6460'
pubrep_id: '841'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the mechanistic nature of epistasis in a canonical cis-regulatory element
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: 6
year: '2017'
...
---
_id: '956'
abstract:
- lang: eng
text: We study a class of ergodic quantum Markov semigroups on finite-dimensional
unital C⁎-algebras. These semigroups have a unique stationary state σ, and we
are concerned with those that satisfy a quantum detailed balance condition with
respect to σ. We show that the evolution on the set of states that is given by
such a quantum Markov semigroup is gradient flow for the relative entropy with
respect to σ in a particular Riemannian metric on the set of states. This metric
is a non-commutative analog of the 2-Wasserstein metric, and in several interesting
cases we are able to show, in analogy with work of Otto on gradient flows with
respect to the classical 2-Wasserstein metric, that the relative entropy is strictly
and uniformly convex with respect to the Riemannian metric introduced here. As
a consequence, we obtain a number of new inequalities for the decay of relative
entropy for ergodic quantum Markov semigroups with detailed balance.
article_processing_charge: No
arxiv: 1
author:
- first_name: Eric
full_name: Carlen, Eric
last_name: Carlen
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
citation:
ama: Carlen E, Maas J. Gradient flow and entropy inequalities for quantum Markov
semigroups with detailed balance. Journal of Functional Analysis. 2017;273(5):1810-1869.
doi:10.1016/j.jfa.2017.05.003
apa: Carlen, E., & Maas, J. (2017). Gradient flow and entropy inequalities for
quantum Markov semigroups with detailed balance. Journal of Functional Analysis.
Academic Press. https://doi.org/10.1016/j.jfa.2017.05.003
chicago: Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for
Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis.
Academic Press, 2017. https://doi.org/10.1016/j.jfa.2017.05.003.
ieee: E. Carlen and J. Maas, “Gradient flow and entropy inequalities for quantum
Markov semigroups with detailed balance,” Journal of Functional Analysis,
vol. 273, no. 5. Academic Press, pp. 1810–1869, 2017.
ista: Carlen E, Maas J. 2017. Gradient flow and entropy inequalities for quantum
Markov semigroups with detailed balance. Journal of Functional Analysis. 273(5),
1810–1869.
mla: Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum
Markov Semigroups with Detailed Balance.” Journal of Functional Analysis,
vol. 273, no. 5, Academic Press, 2017, pp. 1810–69, doi:10.1016/j.jfa.2017.05.003.
short: E. Carlen, J. Maas, Journal of Functional Analysis 273 (2017) 1810–1869.
date_created: 2018-12-11T11:49:24Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2025-06-04T08:14:53Z
day: '01'
department:
- _id: JaMa
doi: 10.1016/j.jfa.2017.05.003
external_id:
arxiv:
- '1609.01254'
isi:
- '000406082300005'
intvolume: ' 273'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.01254
month: '09'
oa: 1
oa_version: Submitted Version
page: 1810 - 1869
publication: Journal of Functional Analysis
publication_identifier:
issn:
- 0022-1236
publication_status: published
publisher: Academic Press
publist_id: '6452'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gradient flow and entropy inequalities for quantum Markov semigroups with detailed
balance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 273
year: '2017'
...