---
_id: '3361'
abstract:
- lang: eng
text: In this paper, we investigate the computational complexity of quantitative
information flow (QIF) problems. Information-theoretic quantitative relaxations
of noninterference (based on Shannon entropy)have been introduced to enable more
fine-grained reasoning about programs in situations where limited information
flow is acceptable. The QIF bounding problem asks whether the information flow
in a given program is bounded by a constant $d$. Our first result is that the
QIF bounding problem is PSPACE-complete. The QIF memoryless synthesis problem
asks whether it is possible to resolve nondeterministic choices in a given partial
program in such a way that in the resulting deterministic program, the quantitative
information flow is bounded by a given constant $d$. Our second result is that
the QIF memoryless synthesis problem is also EXPTIME-complete. The QIF memoryless
synthesis problem generalizes to QIF general synthesis problem which does not
impose the memoryless requirement (that is, by allowing the synthesized program
to have more variables then the original partial program). Our third result is
that the QIF general synthesis problem is EXPTIME-hard.
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Cerny P, Chatterjee K, Henzinger TA. The complexity of quantitative information
flow problems. In: IEEE; 2011:205-217. doi:10.1109/CSF.2011.21'
apa: 'Cerny, P., Chatterjee, K., & Henzinger, T. A. (2011). The complexity of
quantitative information flow problems (pp. 205–217). Presented at the CSF: Computer
Security Foundations, Cernay-la-Ville, France: IEEE. https://doi.org/10.1109/CSF.2011.21'
chicago: Cerny, Pavol, Krishnendu Chatterjee, and Thomas A Henzinger. “The Complexity
of Quantitative Information Flow Problems,” 205–17. IEEE, 2011. https://doi.org/10.1109/CSF.2011.21.
ieee: 'P. Cerny, K. Chatterjee, and T. A. Henzinger, “The complexity of quantitative
information flow problems,” presented at the CSF: Computer Security Foundations,
Cernay-la-Ville, France, 2011, pp. 205–217.'
ista: 'Cerny P, Chatterjee K, Henzinger TA. 2011. The complexity of quantitative
information flow problems. CSF: Computer Security Foundations, 205–217.'
mla: Cerny, Pavol, et al. The Complexity of Quantitative Information Flow Problems.
IEEE, 2011, pp. 205–17, doi:10.1109/CSF.2011.21.
short: P. Cerny, K. Chatterjee, T.A. Henzinger, in:, IEEE, 2011, pp. 205–217.
conference:
end_date: 2011-06-29
location: Cernay-la-Ville, France
name: 'CSF: Computer Security Foundations'
start_date: 2011-06-27
date_created: 2018-12-11T12:02:54Z
date_published: 2011-06-27T00:00:00Z
date_updated: 2021-01-12T07:42:56Z
day: '27'
ddc:
- '000'
- '005'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1109/CSF.2011.21
ec_funded: 1
file:
- access_level: open_access
checksum: 1a25be0c62459fc7640db88af08ff63a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:07Z
date_updated: 2020-07-14T12:46:10Z
file_id: '4792'
file_name: IST-2012-81-v1+1_The_complexity_of_quantitative_information_flow_problems.pdf
file_size: 299069
relation: main_file
file_date_updated: 2020-07-14T12:46:10Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 205 - 217
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: IEEE
publist_id: '3254'
pubrep_id: '81'
quality_controlled: '1'
scopus_import: 1
status: public
title: The complexity of quantitative information flow problems
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3358'
abstract:
- lang: eng
text: The static scheduling problem often arises as a fundamental problem in real-time
systems and grid computing. We consider the problem of statically scheduling a
large job expressed as a task graph on a large number of computing nodes, such
as a data center. This paper solves the large-scale static scheduling problem
using abstraction refinement, a technique commonly used in formal verification
to efficiently solve computationally hard problems. A scheduler based on abstraction
refinement first attempts to solve the scheduling problem with abstract representations
of the job and the computing resources. As abstract representations are generally
small, the scheduling can be done reasonably fast. If the obtained schedule does
not meet specified quality conditions (like data center utilization or schedule
makespan) then the scheduler refines the job and data center abstractions and,
again solves the scheduling problem. We develop different schedulers based on
abstraction refinement. We implemented these schedulers and used them to schedule
task graphs from various computing domains on simulated data centers with realistic
topologies. We compared the speed of scheduling and the quality of the produced
schedules with our abstraction refinement schedulers against a baseline scheduler
that does not use any abstraction. We conclude that abstraction refinement techniques
give a significant speed-up compared to traditional static scheduling heuristics,
at a reasonable cost in the quality of the produced schedules. We further used
our static schedulers in an actual system that we deployed on Amazon EC2 and compared
it against the Hadoop dynamic scheduler for large MapReduce jobs. Our experiments
indicate that there is great potential for static scheduling techniques.
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Vasu
full_name: Singh, Vasu
id: 4DAE2708-F248-11E8-B48F-1D18A9856A87
last_name: Singh
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: 'Henzinger TA, Singh V, Wies T, Zufferey D. Scheduling large jobs by abstraction
refinement. In: ACM; 2011:329-342. doi:10.1145/1966445.1966476'
apa: 'Henzinger, T. A., Singh, V., Wies, T., & Zufferey, D. (2011). Scheduling
large jobs by abstraction refinement (pp. 329–342). Presented at the EuroSys,
Salzburg, Austria: ACM. https://doi.org/10.1145/1966445.1966476'
chicago: Henzinger, Thomas A, Vasu Singh, Thomas Wies, and Damien Zufferey. “Scheduling
Large Jobs by Abstraction Refinement,” 329–42. ACM, 2011. https://doi.org/10.1145/1966445.1966476.
ieee: T. A. Henzinger, V. Singh, T. Wies, and D. Zufferey, “Scheduling large jobs
by abstraction refinement,” presented at the EuroSys, Salzburg, Austria, 2011,
pp. 329–342.
ista: Henzinger TA, Singh V, Wies T, Zufferey D. 2011. Scheduling large jobs by
abstraction refinement. EuroSys, 329–342.
mla: Henzinger, Thomas A., et al. Scheduling Large Jobs by Abstraction Refinement.
ACM, 2011, pp. 329–42, doi:10.1145/1966445.1966476.
short: T.A. Henzinger, V. Singh, T. Wies, D. Zufferey, in:, ACM, 2011, pp. 329–342.
conference:
end_date: 2011-04-13
location: Salzburg, Austria
name: EuroSys
start_date: 2011-04-10
date_created: 2018-12-11T12:02:53Z
date_published: 2011-04-10T00:00:00Z
date_updated: 2021-01-12T07:42:55Z
day: '10'
department:
- _id: ToHe
doi: 10.1145/1966445.1966476
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://cs.nyu.edu/wies/publ/scheduling_large_jobs_by_abstraction_refinement.pdf
month: '04'
oa: 1
oa_version: Published Version
page: 329 - 342
publication_status: published
publisher: ACM
publist_id: '3257'
quality_controlled: '1'
scopus_import: 1
status: public
title: Scheduling large jobs by abstraction refinement
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3359'
abstract:
- lang: eng
text: "Motivated by improvements in constraint-solving technology and by the increase
of routinely available computational power, partial-program synthesis is emerging
as an effective approach for increasing programmer productivity. The goal of the
approach is to allow the programmer to specify a part of her intent imperatively
(that is, give a partial program) and a part of her intent declaratively, by specifying
which conditions need to be achieved or maintained. The task of the synthesizer
is to construct a program that satisfies the specification. As an example, consider
a partial program where threads access shared data without using any synchronization
mechanism, and a declarative specification that excludes data races and deadlocks.
The task of the synthesizer is then to place locks into the program code in order
for the program to meet the specification.\r\n\r\nIn this paper, we argue that
quantitative objectives are needed in partial-program synthesis in order to produce
higher-quality programs, while enabling simpler specifications. Returning to the
example, the synthesizer could construct a naive solution that uses one global
lock for shared data. This can be prevented either by constraining the solution
space further (which is error-prone and partly defeats the point of synthesis),
or by optimizing a quantitative objective that models performance. Other quantitative
notions useful in synthesis include fault tolerance, robustness, resource (memory,
power) consumption, and information flow."
acknowledgement: This work was partially supported by the ERC Advanced Grant QUAREM,
the FWF NFN Grant S11402-N23 (RiSE), and the EU NOE Grant ArtistDesign.
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Cerny P, Henzinger TA. From boolean to quantitative synthesis. In: ACM; 2011:149-154.
doi:10.1145/2038642.2038666'
apa: 'Cerny, P., & Henzinger, T. A. (2011). From boolean to quantitative synthesis
(pp. 149–154). Presented at the EMSOFT: Embedded Software , Taipei; Taiwan: ACM.
https://doi.org/10.1145/2038642.2038666'
chicago: Cerny, Pavol, and Thomas A Henzinger. “From Boolean to Quantitative Synthesis,”
149–54. ACM, 2011. https://doi.org/10.1145/2038642.2038666.
ieee: 'P. Cerny and T. A. Henzinger, “From boolean to quantitative synthesis,” presented
at the EMSOFT: Embedded Software , Taipei; Taiwan, 2011, pp. 149–154.'
ista: 'Cerny P, Henzinger TA. 2011. From boolean to quantitative synthesis. EMSOFT:
Embedded Software , 149–154.'
mla: Cerny, Pavol, and Thomas A. Henzinger. From Boolean to Quantitative Synthesis.
ACM, 2011, pp. 149–54, doi:10.1145/2038642.2038666.
short: P. Cerny, T.A. Henzinger, in:, ACM, 2011, pp. 149–154.
conference:
end_date: 2011-10-14
location: Taipei; Taiwan
name: 'EMSOFT: Embedded Software '
start_date: 2011-10-09
date_created: 2018-12-11T12:02:53Z
date_published: 2011-10-09T00:00:00Z
date_updated: 2021-01-12T07:42:55Z
day: '09'
department:
- _id: ToHe
doi: 10.1145/2038642.2038666
ec_funded: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 149 - 154
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
publication_status: published
publisher: ACM
publist_id: '3256'
quality_controlled: '1'
status: public
title: From boolean to quantitative synthesis
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3357'
abstract:
- lang: eng
text: We consider two-player graph games whose objectives are request-response condition,
i.e conjunctions of conditions of the form "if a state with property Rq is visited,
then later a state with property Rp is visited". The winner of such games can
be decided in EXPTIME and the problem is known to be NP-hard. In this paper, we
close this gap by showing that this problem is, in fact, EXPTIME-complete. We
show that the problem becomes PSPACE-complete if we only consider games played
on DAGs, and NP-complete or PTIME-complete if there is only one player (depending
on whether he wants to enforce or spoil the request-response condition). We also
present near-optimal bounds on the memory needed to design winning strategies
for each player, in each case.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Florian
full_name: Horn, Florian
id: 37327ACE-F248-11E8-B48F-1D18A9856A87
last_name: Horn
citation:
ama: 'Chatterjee K, Henzinger TA, Horn F. The complexity of request-response games.
In: Dediu A-H, Inenaga S, Martín-Vide C, eds. Vol 6638. Springer; 2011:227-237.
doi:10.1007/978-3-642-21254-3_17'
apa: 'Chatterjee, K., Henzinger, T. A., & Horn, F. (2011). The complexity of
request-response games. In A.-H. Dediu, S. Inenaga, & C. Martín-Vide (Eds.)
(Vol. 6638, pp. 227–237). Presented at the LATA: Language and Automata Theory
and Applications, Tarragona, Spain: Springer. https://doi.org/10.1007/978-3-642-21254-3_17'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “The Complexity
of Request-Response Games.” edited by Adrian-Horia Dediu, Shunsuke Inenaga, and
Carlos Martín-Vide, 6638:227–37. Springer, 2011. https://doi.org/10.1007/978-3-642-21254-3_17.
ieee: 'K. Chatterjee, T. A. Henzinger, and F. Horn, “The complexity of request-response
games,” presented at the LATA: Language and Automata Theory and Applications,
Tarragona, Spain, 2011, vol. 6638, pp. 227–237.'
ista: 'Chatterjee K, Henzinger TA, Horn F. 2011. The complexity of request-response
games. LATA: Language and Automata Theory and Applications, LNCS, vol. 6638, 227–237.'
mla: Chatterjee, Krishnendu, et al. The Complexity of Request-Response Games.
Edited by Adrian-Horia Dediu et al., vol. 6638, Springer, 2011, pp. 227–37, doi:10.1007/978-3-642-21254-3_17.
short: K. Chatterjee, T.A. Henzinger, F. Horn, in:, A.-H. Dediu, S. Inenaga, C.
Martín-Vide (Eds.), Springer, 2011, pp. 227–237.
conference:
end_date: 2011-05-31
location: Tarragona, Spain
name: 'LATA: Language and Automata Theory and Applications'
start_date: 2011-05-26
date_created: 2018-12-11T12:02:52Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:54Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-642-21254-3_17
editor:
- first_name: Adrian-Horia
full_name: Dediu, Adrian-Horia
last_name: Dediu
- first_name: Shunsuke
full_name: Inenaga, Shunsuke
last_name: Inenaga
- first_name: Carlos
full_name: Martín-Vide, Carlos
last_name: Martín-Vide
intvolume: ' 6638'
language:
- iso: eng
month: '01'
oa_version: None
page: 227 - 237
publication_status: published
publisher: Springer
publist_id: '3258'
quality_controlled: '1'
scopus_import: 1
status: public
title: The complexity of request-response games
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6638
year: '2011'
...
---
_id: '336'
abstract:
- lang: eng
text: 'The growth kinetics of colloidal Bi2S3 nanorods was investigated. After nucleation,
the length distribution of the growing Bi 2S3 nanorods narrows with the reaction
time until a bimodal length distribution appears. From this critical reaction
time on, the smallest nanorods of the ensemble dissolve, feeding with monomer
the growth of the largest ones. A comprehensive characterization of the size-distribution
evolution of Bi2S3 nanorods is used here to illustrate the dependences of the
anisotropic growth rates of cylindrical nanoparticles on the nanoparticle dimensions
and the monomer concentration in solution. With this goal in mind, a diffusion-reaction
model is presented to explain the origin of the experimentally obtained length
distribution focusing mechanism. The model is able to reproduce the decrease of
the growth rate in the nanorod axial direction with both its thickness and length.
On the other hand, low lateral reaction rates prevent the nanorod thickness distribution
to be focused. In both crystallographic growth directions, a concentration-dependent
critical thickness exists, which discriminates between nanorods with positive
growth rates and those dissolving in the reaction solution. '
acknowledgement: This work was supported by the Spanish MICINN Projects MAT2008-05779,
MAT2008-03400-E/MAT, and ENE2008-03277-E/CON. Maria Ibáñez thanks the Ph.D. grant
from the Spanish MICINN.
article_processing_charge: No
article_type: original
author:
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Pablo
full_name: Guardia, Pablo
last_name: Guardia
- first_name: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Joan
full_name: Morante, Joan
last_name: Morante
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: 'Ibáñez M, Guardia P, Shavel A, et al. Growth kinetics of asymmetric Bi2S3
nanocrystals: Size distribution focusing in nanorods. Journal of Physical Chemistry
C. 2011;115(16):7947-7955. doi:10.1021/jp2002904'
apa: 'Ibáñez, M., Guardia, P., Shavel, A., Cadavid, D., Arbiol, J., Morante, J.,
& Cabot, A. (2011). Growth kinetics of asymmetric Bi2S3 nanocrystals: Size
distribution focusing in nanorods. Journal of Physical Chemistry C. American
Chemical Society. https://doi.org/10.1021/jp2002904'
chicago: 'Ibáñez, Maria, Pablo Guardia, Alexey Shavel, Doris Cadavid, Jordi Arbiol,
Joan Morante, and Andreu Cabot. “Growth Kinetics of Asymmetric Bi2S3 Nanocrystals:
Size Distribution Focusing in Nanorods.” Journal of Physical Chemistry C.
American Chemical Society, 2011. https://doi.org/10.1021/jp2002904.'
ieee: 'M. Ibáñez et al., “Growth kinetics of asymmetric Bi2S3 nanocrystals:
Size distribution focusing in nanorods,” Journal of Physical Chemistry C,
vol. 115, no. 16. American Chemical Society, pp. 7947–7955, 2011.'
ista: 'Ibáñez M, Guardia P, Shavel A, Cadavid D, Arbiol J, Morante J, Cabot A. 2011.
Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in
nanorods. Journal of Physical Chemistry C. 115(16), 7947–7955.'
mla: 'Ibáñez, Maria, et al. “Growth Kinetics of Asymmetric Bi2S3 Nanocrystals: Size
Distribution Focusing in Nanorods.” Journal of Physical Chemistry C, vol.
115, no. 16, American Chemical Society, 2011, pp. 7947–55, doi:10.1021/jp2002904.'
short: M. Ibáñez, P. Guardia, A. Shavel, D. Cadavid, J. Arbiol, J. Morante, A. Cabot,
Journal of Physical Chemistry C 115 (2011) 7947–7955.
date_created: 2018-12-11T11:45:53Z
date_published: 2011-04-28T00:00:00Z
date_updated: 2021-01-12T07:42:56Z
day: '28'
doi: 10.1021/jp2002904
extern: '1'
intvolume: ' 115'
issue: '16'
language:
- iso: eng
month: '04'
oa_version: None
page: 7947 - 7955
publication: Journal of Physical Chemistry C
publication_status: published
publisher: American Chemical Society
publist_id: '7493'
quality_controlled: '1'
status: public
title: 'Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing
in nanorods'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2011'
...
---
_id: '3379'
abstract:
- lang: eng
text: The process of gastrulation is highly conserved across vertebrates on both
the genetic and morphological levels, despite great variety in embryonic shape
and speed of development. This mechanism spatially separates the germ layers and
establishes the organizational foundation for future development. Mesodermal identity
is specified in a superficial layer of cells, the epiblast, where cells maintain
an epithelioid morphology. These cells involute to join the deeper hypoblast layer
where they adopt a migratory, mesenchymal morphology. Expression of a cascade
of related transcription factors orchestrates the parallel genetic transition
from primitive to mature mesoderm. Although the early and late stages of this
process are increasingly well understood, the transition between them has remained
largely mysterious. We present here the first high resolution in vivo observations
of the blebby transitional morphology of involuting mesodermal cells in a vertebrate
embryo. We further demonstrate that the zebrafish spadetail mutation creates a
reversible block in the maturation program, stalling cells in the transition state.
This mutation creates an ideal system for dissecting the specific properties of
cells undergoing the morphological transition of maturing mesoderm, as we demonstrate
with a direct measurement of cell–cell adhesion.
article_type: original
author:
- first_name: Richard
full_name: Row, Richard
last_name: Row
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
- first_name: Benjamin
full_name: Martin, Benjamin
last_name: Martin
- first_name: Petra
full_name: Stockinger, Petra
id: 261CB030-E90D-11E9-B182-F697D44B663C
last_name: Stockinger
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: David
full_name: Kimelman, David
last_name: Kimelman
citation:
ama: Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. Completion
of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail.
Developmental Biology. 2011;354(1):102-110. doi:10.1016/j.ydbio.2011.03.025
apa: Row, R., Maître, J.-L., Martin, B., Stockinger, P., Heisenberg, C.-P. J., &
Kimelman, D. (2011). Completion of the epithelial to mesenchymal transition in
zebrafish mesoderm requires Spadetail. Developmental Biology. Elsevier.
https://doi.org/10.1016/j.ydbio.2011.03.025
chicago: Row, Richard, Jean-Léon Maître, Benjamin Martin, Petra Stockinger, Carl-Philipp
J Heisenberg, and David Kimelman. “Completion of the Epithelial to Mesenchymal
Transition in Zebrafish Mesoderm Requires Spadetail.” Developmental Biology.
Elsevier, 2011. https://doi.org/10.1016/j.ydbio.2011.03.025.
ieee: R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P. J. Heisenberg, and D.
Kimelman, “Completion of the epithelial to mesenchymal transition in zebrafish
mesoderm requires Spadetail,” Developmental Biology, vol. 354, no. 1. Elsevier,
pp. 102–110, 2011.
ista: Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. 2011.
Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires
Spadetail. Developmental Biology. 354(1), 102–110.
mla: Row, Richard, et al. “Completion of the Epithelial to Mesenchymal Transition
in Zebrafish Mesoderm Requires Spadetail.” Developmental Biology, vol.
354, no. 1, Elsevier, 2011, pp. 102–10, doi:10.1016/j.ydbio.2011.03.025.
short: R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P.J. Heisenberg, D. Kimelman,
Developmental Biology 354 (2011) 102–110.
date_created: 2018-12-11T12:03:00Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2021-01-12T07:43:04Z
day: '01'
department:
- _id: CaHe
doi: 10.1016/j.ydbio.2011.03.025
external_id:
pmid:
- '1463614'
intvolume: ' 354'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090540/
month: '06'
oa: 1
oa_version: Submitted Version
page: 102 - 110
pmid: 1
publication: Developmental Biology
publication_status: published
publisher: Elsevier
publist_id: '3228'
quality_controlled: '1'
scopus_import: 1
status: public
title: Completion of the epithelial to mesenchymal transition in zebrafish mesoderm
requires Spadetail
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 354
year: '2011'
...
---
_id: '3376'
abstract:
- lang: eng
text: Regulatory conflicts occur when two signals that individually trigger opposite
cellular responses are present simultaneously. Here, we investigate regulatory
conflicts in the bacterial response to antibiotic combinations. We use an Escherichia
coli promoter-GFP library to study the transcriptional response of many promoters
to either additive or antagonistic drug pairs at fine two-dimensional (2D) resolution
of drug concentration. Surprisingly, we find that this data set can be characterized
as a linear sum of only two principal components. Component one, accounting for
over 70% of the response, represents the response to growth inhibition by the
drugs. Component two describes how regulatory conflicts are resolved. For the
additive drug pair, conflicts are resolved by linearly interpolating the single
drug responses, while for the antagonistic drug pair, the growth-limiting drug
dominates the response. Importantly, for a given drug pair, the same conflict
resolution strategy applies to almost all genes. These results provide a recipe
for predicting gene expression responses to antibiotic combinations.
acknowledgement: This work was supported by a Feodor Lynen Fellowship of the Alexander
von Humboldt Foundation (to T.B.).
author:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Bollenbach MT, Kishony R. Resolution of gene regulatory conflicts caused by
combinations of antibiotics. Molecular Cell. 2011;42(4):413-425. doi:10.1016/j.molcel.2011.04.016
apa: Bollenbach, M. T., & Kishony, R. (2011). Resolution of gene regulatory
conflicts caused by combinations of antibiotics. Molecular Cell. Cell Press.
https://doi.org/10.1016/j.molcel.2011.04.016
chicago: Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory
Conflicts Caused by Combinations of Antibiotics.” Molecular Cell. Cell
Press, 2011. https://doi.org/10.1016/j.molcel.2011.04.016.
ieee: M. T. Bollenbach and R. Kishony, “Resolution of gene regulatory conflicts
caused by combinations of antibiotics,” Molecular Cell, vol. 42, no. 4.
Cell Press, pp. 413–425, 2011.
ista: Bollenbach MT, Kishony R. 2011. Resolution of gene regulatory conflicts caused
by combinations of antibiotics. Molecular Cell. 42(4), 413–425.
mla: Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts
Caused by Combinations of Antibiotics.” Molecular Cell, vol. 42, no. 4,
Cell Press, 2011, pp. 413–25, doi:10.1016/j.molcel.2011.04.016.
short: M.T. Bollenbach, R. Kishony, Molecular Cell 42 (2011) 413–425.
date_created: 2018-12-11T12:02:59Z
date_published: 2011-05-20T00:00:00Z
date_updated: 2021-01-12T07:43:03Z
day: '20'
department:
- _id: ToBo
doi: 10.1016/j.molcel.2011.04.016
intvolume: ' 42'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143497/
month: '05'
oa: 1
oa_version: Submitted Version
page: 413 - 425
publication: Molecular Cell
publication_status: published
publisher: Cell Press
publist_id: '3231'
quality_controlled: '1'
scopus_import: 1
status: public
title: Resolution of gene regulatory conflicts caused by combinations of antibiotics
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2011'
...
---
_id: '3380'
abstract:
- lang: eng
text: Linkage between markers and genes that affect a phenotype of interest may
be determined by examining differences in marker allele frequency in the extreme
progeny of a cross between two inbred lines. This strategy is usually employed
when pooling is used to reduce genotyping costs. When the cross progeny are asexual,
the extreme progeny may be selected by multiple generations of asexual reproduction
and selection. We analyse this method of measuring phenotype in asexual progeny
and examine the changes in marker allele frequency due to selection over many
generations. Stochasticity in marker frequency in the selected population arises
due to the finite initial population size. We derive the distribution of marker
frequency as a result of selection at a single major locus, and show that in order
to avoid spurious changes in marker allele frequency in the selected population,
the initial population size should be in the low to mid hundreds.
article_processing_charge: No
article_type: original
author:
- first_name: Sayanthan
full_name: Logeswaran, Sayanthan
last_name: Logeswaran
- 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: Logeswaran S, Barton NH. Mapping Mendelian traits in asexual progeny using
changes in marker allele frequency. Genetical Research. 2011;93(3):221-232.
doi:10.1017/S0016672311000115
apa: Logeswaran, S., & Barton, N. H. (2011). Mapping Mendelian traits in asexual
progeny using changes in marker allele frequency. Genetical Research. Cambridge
University Press. https://doi.org/10.1017/S0016672311000115
chicago: Logeswaran, Sayanthan, and Nicholas H Barton. “Mapping Mendelian Traits
in Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research.
Cambridge University Press, 2011. https://doi.org/10.1017/S0016672311000115.
ieee: S. Logeswaran and N. H. Barton, “Mapping Mendelian traits in asexual progeny
using changes in marker allele frequency,” Genetical Research, vol. 93,
no. 3. Cambridge University Press, pp. 221–232, 2011.
ista: Logeswaran S, Barton NH. 2011. Mapping Mendelian traits in asexual progeny
using changes in marker allele frequency. Genetical Research. 93(3), 221–232.
mla: Logeswaran, Sayanthan, and Nicholas H. Barton. “Mapping Mendelian Traits in
Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research,
vol. 93, no. 3, Cambridge University Press, 2011, pp. 221–32, doi:10.1017/S0016672311000115.
short: S. Logeswaran, N.H. Barton, Genetical Research 93 (2011) 221–232.
date_created: 2018-12-11T12:03:00Z
date_published: 2011-05-18T00:00:00Z
date_updated: 2021-01-12T07:43:05Z
day: '18'
department:
- _id: NiBa
doi: 10.1017/S0016672311000115
intvolume: ' 93'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pure.ed.ac.uk/ws/files/8144621/GR_2011_Barton.pdf
month: '05'
oa: 1
oa_version: Published Version
page: 221 - 232
publication: Genetical Research
publication_status: published
publisher: Cambridge University Press
publist_id: '3227'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mapping Mendelian traits in asexual progeny using changes in marker allele
frequency
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2011'
...
---
_id: '3377'
abstract:
- lang: eng
text: By definition, transverse intersections are stable under in- finitesimal perturbations.
Using persistent homology, we ex- tend this notion to sizeable perturbations.
Specifically, we assign to each homology class of the intersection its robust-
ness, the magnitude of a perturbation necessary to kill it, and prove that robustness
is stable. Among the applications of this result is a stable notion of robustness
for fixed points of continuous mappings and a statement of stability for con-
tours of smooth mappings.
acknowledgement: This research is partially supported by the Defense Advanced Research
Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Dmitriy
full_name: Morozov, Dmitriy
last_name: Morozov
- first_name: Amit
full_name: Patel, Amit
id: 34A254A0-F248-11E8-B48F-1D18A9856A87
last_name: Patel
citation:
ama: Edelsbrunner H, Morozov D, Patel A. Quantifying transversality by measuring
the robustness of intersections. Foundations of Computational Mathematics.
2011;11(3):345-361. doi:10.1007/s10208-011-9090-8
apa: Edelsbrunner, H., Morozov, D., & Patel, A. (2011). Quantifying transversality
by measuring the robustness of intersections. Foundations of Computational
Mathematics. Springer. https://doi.org/10.1007/s10208-011-9090-8
chicago: Edelsbrunner, Herbert, Dmitriy Morozov, and Amit Patel. “Quantifying Transversality
by Measuring the Robustness of Intersections.” Foundations of Computational
Mathematics. Springer, 2011. https://doi.org/10.1007/s10208-011-9090-8.
ieee: H. Edelsbrunner, D. Morozov, and A. Patel, “Quantifying transversality by
measuring the robustness of intersections,” Foundations of Computational Mathematics,
vol. 11, no. 3. Springer, pp. 345–361, 2011.
ista: Edelsbrunner H, Morozov D, Patel A. 2011. Quantifying transversality by measuring
the robustness of intersections. Foundations of Computational Mathematics. 11(3),
345–361.
mla: Edelsbrunner, Herbert, et al. “Quantifying Transversality by Measuring the
Robustness of Intersections.” Foundations of Computational Mathematics,
vol. 11, no. 3, Springer, 2011, pp. 345–61, doi:10.1007/s10208-011-9090-8.
short: H. Edelsbrunner, D. Morozov, A. Patel, Foundations of Computational Mathematics
11 (2011) 345–361.
date_created: 2018-12-11T12:02:59Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2021-01-12T07:43:04Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s10208-011-9090-8
intvolume: ' 11'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0911.2142
month: '06'
oa: 1
oa_version: Submitted Version
page: 345 - 361
publication: Foundations of Computational Mathematics
publication_status: published
publisher: Springer
publist_id: '3230'
quality_controlled: '1'
scopus_import: 1
status: public
title: Quantifying transversality by measuring the robustness of intersections
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2011'
...
---
_id: '3378'
abstract:
- lang: eng
text: The theory of intersection homology was developed to study the singularities
of a topologically stratified space. This paper in- corporates this theory into
the already developed framework of persistent homology. We demonstrate that persistent
intersec- tion homology gives useful information about the relationship between
an embedded stratified space and its singularities. We give, and prove the correctness
of, an algorithm for the computa- tion of the persistent intersection homology
groups of a filtered simplicial complex equipped with a stratification by subcom-
plexes. We also derive, from Poincare ́ Duality, some structural results about
persistent intersection homology.
acknowledgement: This research was partially supported by the Defense Advanced Research
Projects Agency (DARPA) under grant HR0011-05-1-0007.
author:
- first_name: Paul
full_name: Bendich, Paul
id: 43F6EC54-F248-11E8-B48F-1D18A9856A87
last_name: Bendich
- first_name: John
full_name: Harer, John
last_name: Harer
citation:
ama: Bendich P, Harer J. Persistent intersection homology. Foundations of Computational
Mathematics. 2011;11(3):305-336. doi:10.1007/s10208-010-9081-1
apa: Bendich, P., & Harer, J. (2011). Persistent intersection homology. Foundations
of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-010-9081-1
chicago: Bendich, Paul, and John Harer. “Persistent Intersection Homology.” Foundations
of Computational Mathematics. Springer, 2011. https://doi.org/10.1007/s10208-010-9081-1.
ieee: P. Bendich and J. Harer, “Persistent intersection homology,” Foundations
of Computational Mathematics, vol. 11, no. 3. Springer, pp. 305–336, 2011.
ista: Bendich P, Harer J. 2011. Persistent intersection homology. Foundations of
Computational Mathematics. 11(3), 305–336.
mla: Bendich, Paul, and John Harer. “Persistent Intersection Homology.” Foundations
of Computational Mathematics, vol. 11, no. 3, Springer, 2011, pp. 305–36,
doi:10.1007/s10208-010-9081-1.
short: P. Bendich, J. Harer, Foundations of Computational Mathematics 11 (2011)
305–336.
date_created: 2018-12-11T12:02:59Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2021-01-12T07:43:04Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s10208-010-9081-1
intvolume: ' 11'
issue: '3'
language:
- iso: eng
month: '06'
oa_version: None
page: 305 - 336
publication: Foundations of Computational Mathematics
publication_status: published
publisher: Springer
publist_id: '3229'
quality_controlled: '1'
scopus_import: 1
status: public
title: Persistent intersection homology
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2011'
...
---
_id: '3388'
abstract:
- lang: eng
text: 'Background: Fragmentation of terrestrial ecosystems has had detrimental effects
on metapopulations of habitat specialists. Maculinea butterflies have been particularly
affected because of their specialized lifecycles, requiring both specific food-plants
and host-ants. However, the interaction between dispersal, effective population
size, and long-term genetic erosion of these endangered butterflies remains unknown.
Using non-destructive sampling, we investigated the genetic diversity of the last
extant population of M. arion in Denmark, which experienced critically low numbers
in the 1980s. Results: Using nine microsatellite markers, we show that the population
is genetically impoverished compared to nearby populations in Sweden, but less
so than monitoring programs suggested. Ten additional short repeat microsatellites
were used to reconstruct changes in genetic diversity and population structure
over the last 77 years from museum specimens. We also tested amplification efficiency
in such historical samples as a function of repeat length and sample age. Low
population numbers in the 1980s did not affect genetic diversity, but considerable
turnover of alleles has characterized this population throughout the time-span
of our analysis. Conclusions: Our results suggest that M. arion is less sensitive
to genetic erosion via population bottlenecks than previously thought, and that
managing clusters of high quality habitat may be key for long-term conservation.'
article_number: '201'
author:
- 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: Per
full_name: Nielsen, Per
last_name: Nielsen
- first_name: Jacobus
full_name: Boomsma, Jacobus
last_name: Boomsma
- first_name: David
full_name: Nash, David
last_name: Nash
citation:
ama: Ugelvig LV, Nielsen P, Boomsma J, Nash D. Reconstructing eight decades of genetic
variation in an isolated Danish population of the large blue butterfly Maculinea
arion. BMC Evolutionary Biology. 2011;11(201). doi:10.1186/1471-2148-11-201
apa: Ugelvig, L. V., Nielsen, P., Boomsma, J., & Nash, D. (2011). Reconstructing
eight decades of genetic variation in an isolated Danish population of the large
blue butterfly Maculinea arion. BMC Evolutionary Biology. BioMed Central.
https://doi.org/10.1186/1471-2148-11-201
chicago: Ugelvig, Line V, Per Nielsen, Jacobus Boomsma, and David Nash. “Reconstructing
Eight Decades of Genetic Variation in an Isolated Danish Population of the Large
Blue Butterfly Maculinea Arion.” BMC Evolutionary Biology. BioMed Central,
2011. https://doi.org/10.1186/1471-2148-11-201.
ieee: L. V. Ugelvig, P. Nielsen, J. Boomsma, and D. Nash, “Reconstructing eight
decades of genetic variation in an isolated Danish population of the large blue
butterfly Maculinea arion,” BMC Evolutionary Biology, vol. 11, no. 201.
BioMed Central, 2011.
ista: Ugelvig LV, Nielsen P, Boomsma J, Nash D. 2011. Reconstructing eight decades
of genetic variation in an isolated Danish population of the large blue butterfly
Maculinea arion. BMC Evolutionary Biology. 11(201), 201.
mla: Ugelvig, Line V., et al. “Reconstructing Eight Decades of Genetic Variation
in an Isolated Danish Population of the Large Blue Butterfly Maculinea Arion.”
BMC Evolutionary Biology, vol. 11, no. 201, 201, BioMed Central, 2011,
doi:10.1186/1471-2148-11-201.
short: L.V. Ugelvig, P. Nielsen, J. Boomsma, D. Nash, BMC Evolutionary Biology 11
(2011).
date_created: 2018-12-11T12:03:03Z
date_published: 2011-07-11T00:00:00Z
date_updated: 2021-01-12T07:43:08Z
day: '11'
ddc:
- '576'
department:
- _id: SyCr
doi: 10.1186/1471-2148-11-201
file:
- access_level: open_access
checksum: 9ebfed0740f1fa071d02ec32c2b8c17f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:18Z
date_updated: 2020-07-14T12:46:11Z
file_id: '5069'
file_name: IST-2015-371-v1+1_1471-2148-11-201.pdf
file_size: 2166556
relation: main_file
file_date_updated: 2020-07-14T12:46:11Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '201'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: BMC Evolutionary Biology
publication_status: published
publisher: BioMed Central
publist_id: '3220'
pubrep_id: '371'
quality_controlled: '1'
scopus_import: 1
status: public
title: Reconstructing eight decades of genetic variation in an isolated Danish population
of the large blue butterfly Maculinea arion
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2011'
...
---
_id: '3384'
abstract:
- lang: eng
text: Here we introduce a database of calibrated natural images publicly available
through an easy-to-use web interface. Using a Nikon D70 digital SLR camera, we
acquired about six-megapixel images of Okavango Delta of Botswana, a tropical
savanna habitat similar to where the human eye is thought to have evolved. Some
sequences of images were captured unsystematically while following a baboon troop,
while others were designed to vary a single parameter such as aperture, object
distance, time of day or position on the horizon. Images are available in the
raw RGB format and in grayscale. Images are also available in units relevant to
the physiology of human cone photoreceptors, where pixel values represent the
expected number of photoisomerizations per second for cones sensitive to long
(L), medium (M) and short (S) wavelengths. This database is distributed under
a Creative Commons Attribution-Noncommercial Unported license to facilitate research
in computer vision, psychophysics of perception, and visual neuroscience.
article_number: e20409
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Patrick
full_name: Garrigan, Patrick
last_name: Garrigan
- first_name: Charles
full_name: Ratliff, Charles
last_name: Ratliff
- first_name: Grega
full_name: Milcinski, Grega
last_name: Milcinski
- first_name: Jennifer
full_name: Klein, Jennifer
last_name: Klein
- first_name: Lucia
full_name: Seyfarth, Lucia
last_name: Seyfarth
- first_name: Peter
full_name: Sterling, Peter
last_name: Sterling
- first_name: David
full_name: Brainard, David
last_name: Brainard
- first_name: Vijay
full_name: Balasubramanian, Vijay
last_name: Balasubramanian
citation:
ama: Tkačik G, Garrigan P, Ratliff C, et al. Natural images from the birthplace
of the human eye. PLoS One. 2011;6(6). doi:10.1371/journal.pone.0020409
apa: Tkačik, G., Garrigan, P., Ratliff, C., Milcinski, G., Klein, J., Seyfarth,
L., … Balasubramanian, V. (2011). Natural images from the birthplace of the human
eye. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0020409
chicago: Tkačik, Gašper, Patrick Garrigan, Charles Ratliff, Grega Milcinski, Jennifer
Klein, Lucia Seyfarth, Peter Sterling, David Brainard, and Vijay Balasubramanian.
“Natural Images from the Birthplace of the Human Eye.” PLoS One. Public
Library of Science, 2011. https://doi.org/10.1371/journal.pone.0020409.
ieee: G. Tkačik et al., “Natural images from the birthplace of the human
eye,” PLoS One, vol. 6, no. 6. Public Library of Science, 2011.
ista: Tkačik G, Garrigan P, Ratliff C, Milcinski G, Klein J, Seyfarth L, Sterling
P, Brainard D, Balasubramanian V. 2011. Natural images from the birthplace of
the human eye. PLoS One. 6(6), e20409.
mla: Tkačik, Gašper, et al. “Natural Images from the Birthplace of the Human Eye.”
PLoS One, vol. 6, no. 6, e20409, Public Library of Science, 2011, doi:10.1371/journal.pone.0020409.
short: G. Tkačik, P. Garrigan, C. Ratliff, G. Milcinski, J. Klein, L. Seyfarth,
P. Sterling, D. Brainard, V. Balasubramanian, PLoS One 6 (2011).
date_created: 2018-12-11T12:03:01Z
date_published: 2011-06-16T00:00:00Z
date_updated: 2021-01-12T07:43:07Z
day: '16'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0020409
file:
- access_level: open_access
checksum: 307d4356916471306e3705ac65b82fa1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:25Z
date_updated: 2020-07-14T12:46:11Z
file_id: '4749'
file_name: IST-2015-379-v1+1_journal.pone.0020409.pdf
file_size: 1424768
relation: main_file
file_date_updated: 2020-07-14T12:46:11Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3223'
pubrep_id: '379'
quality_controlled: '1'
scopus_import: 1
status: public
title: Natural images from the birthplace of the human eye
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2011'
...
---
_id: '3387'
abstract:
- lang: eng
text: 'Background: Supertree methods combine overlapping input trees into a larger
supertree. Here, I consider split-based supertree methods that first extract the
split information of the input trees and subsequently combine this split information
into a phylogeny. Well known split-based supertree methods are matrix representation
with parsimony and matrix representation with compatibility. Combining input trees
on the same taxon set, as in the consensus setting, is a well-studied task and
it is thus desirable to generalize consensus methods to supertree methods. Results:
Here, three variants of majority-rule (MR) supertrees that generalize majority-rule
consensus trees are investigated. I provide simple formulas for computing the
respective score for bifurcating input- and supertrees. These score computations,
together with a heuristic tree search minmizing the scores, were implemented in
the python program PluMiST (Plus- and Minus SuperTrees) available from http://www.cibiv.at/software/
plumist. The different MR methods were tested by simulation and on real data sets.
The search heuristic was successful in combining compatible input trees. When
combining incompatible input trees, especially one variant, MR(-) supertrees,
performed well. Conclusions: The presented framework allows for an efficient score
computation of three majority-rule supertree variants and input trees. I combined
the score computation with a heuristic search over the supertree space. The implementation
was tested by simulation and on real data sets and showed promising results. Especially
the MR(-) variant seems to be a reasonable score for supertree reconstruction.
Generalizing these computations to multifurcating trees is an open problem, which
may be tackled using this framework.'
article_number: '205'
author:
- first_name: Anne
full_name: Kupczok, Anne
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
citation:
ama: Kupczok A. Split based computation of majority rule supertrees. BMC Evolutionary
Biology. 2011;11(205). doi:10.1186/1471-2148-11-205
apa: Kupczok, A. (2011). Split based computation of majority rule supertrees. BMC
Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-11-205
chicago: Kupczok, Anne. “Split Based Computation of Majority Rule Supertrees.” BMC
Evolutionary Biology. BioMed Central, 2011. https://doi.org/10.1186/1471-2148-11-205.
ieee: A. Kupczok, “Split based computation of majority rule supertrees,” BMC
Evolutionary Biology, vol. 11, no. 205. BioMed Central, 2011.
ista: Kupczok A. 2011. Split based computation of majority rule supertrees. BMC
Evolutionary Biology. 11(205), 205.
mla: Kupczok, Anne. “Split Based Computation of Majority Rule Supertrees.” BMC
Evolutionary Biology, vol. 11, no. 205, 205, BioMed Central, 2011, doi:10.1186/1471-2148-11-205.
short: A. Kupczok, BMC Evolutionary Biology 11 (2011).
date_created: 2018-12-11T12:03:03Z
date_published: 2011-07-13T00:00:00Z
date_updated: 2021-01-12T07:43:08Z
day: '13'
ddc:
- '576'
department:
- _id: JoBo
doi: 10.1186/1471-2148-11-205
file:
- access_level: open_access
checksum: 68da8d04af1b97b4cbe8606e2f92ddd8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:09Z
date_updated: 2020-07-14T12:46:11Z
file_id: '5058'
file_name: IST-2015-372-v1+1_1471-2148-11-205.pdf
file_size: 465042
relation: main_file
file_date_updated: 2020-07-14T12:46:11Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '205'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: BMC Evolutionary Biology
publication_status: published
publisher: BioMed Central
publist_id: '3219'
pubrep_id: '372'
quality_controlled: '1'
scopus_import: 1
status: public
title: Split based computation of majority rule supertrees
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2011'
...
---
_id: '3389'
abstract:
- lang: eng
text: Kernel canonical correlation analysis (KCCA) is a general technique for subspace
learning that incorporates principal components analysis (PCA) and Fisher linear
discriminant analysis (LDA) as special cases. By finding directions that maximize
correlation, KCCA learns representations that are more closely tied to the underlying
process that generates the data and can ignore high-variance noise directions.
However, for data where acquisition in one or more modalities is expensive or
otherwise limited, KCCA may suffer from small sample effects. We propose to use
semi-supervised Laplacian regularization to utilize data that are present in only
one modality. This approach is able to find highly correlated directions that
also lie along the data manifold, resulting in a more robust estimate of correlated
subspaces. Functional magnetic resonance imaging (fMRI) acquired data are naturally
amenable to subspace techniques as data are well aligned. fMRI data of the human
brain are a particularly interesting candidate. In this study we implemented various
supervised and semi-supervised versions of KCCA on human fMRI data, with regression
to single and multi-variate labels (corresponding to video content subjects viewed
during the image acquisition). In each variate condition, the semi-supervised
variants of KCCA performed better than the supervised variants, including a supervised
variant with Laplacian regularization. We additionally analyze the weights learned
by the regression in order to infer brain regions that are important to different
types of visual processing.
acknowledgement: The research leading to these results has received funding from the
European Research Council under the European Community’s Seventh Framework Programme
(FP7/2007-2013)/ERC Grant Agreement No. 228180. This work was funded in part by
the EC project CLASS, IST 027978, and the PASCAL2 network of excellence, IST 2002-506778.
author:
- first_name: Matthew
full_name: Blaschko, Matthew
last_name: Blaschko
- first_name: Jacquelyn
full_name: Shelton, Jacquelyn
last_name: Shelton
- first_name: Andreas
full_name: Bartels, Andreas
last_name: Bartels
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Arthur
full_name: Gretton, Arthur
last_name: Gretton
citation:
ama: Blaschko M, Shelton J, Bartels A, Lampert C, Gretton A. Semi supervised kernel
canonical correlation analysis with application to human fMRI. Pattern Recognition
Letters. 2011;32(11):1572-1583. doi:10.1016/j.patrec.2011.02.011
apa: Blaschko, M., Shelton, J., Bartels, A., Lampert, C., & Gretton, A. (2011).
Semi supervised kernel canonical correlation analysis with application to human
fMRI. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2011.02.011
chicago: Blaschko, Matthew, Jacquelyn Shelton, Andreas Bartels, Christoph Lampert,
and Arthur Gretton. “Semi Supervised Kernel Canonical Correlation Analysis with
Application to Human FMRI.” Pattern Recognition Letters. Elsevier, 2011.
https://doi.org/10.1016/j.patrec.2011.02.011.
ieee: M. Blaschko, J. Shelton, A. Bartels, C. Lampert, and A. Gretton, “Semi supervised
kernel canonical correlation analysis with application to human fMRI,” Pattern
Recognition Letters, vol. 32, no. 11. Elsevier, pp. 1572–1583, 2011.
ista: Blaschko M, Shelton J, Bartels A, Lampert C, Gretton A. 2011. Semi supervised
kernel canonical correlation analysis with application to human fMRI. Pattern
Recognition Letters. 32(11), 1572–1583.
mla: Blaschko, Matthew, et al. “Semi Supervised Kernel Canonical Correlation Analysis
with Application to Human FMRI.” Pattern Recognition Letters, vol. 32,
no. 11, Elsevier, 2011, pp. 1572–83, doi:10.1016/j.patrec.2011.02.011.
short: M. Blaschko, J. Shelton, A. Bartels, C. Lampert, A. Gretton, Pattern Recognition
Letters 32 (2011) 1572–1583.
date_created: 2018-12-11T12:03:03Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2021-01-12T07:43:09Z
day: '01'
department:
- _id: ChLa
doi: 10.1016/j.patrec.2011.02.011
intvolume: ' 32'
issue: '11'
language:
- iso: eng
month: '08'
oa_version: None
page: 1572 - 1583
publication: Pattern Recognition Letters
publication_status: published
publisher: Elsevier
publist_id: '3218'
quality_controlled: '1'
scopus_import: 1
status: public
title: Semi supervised kernel canonical correlation analysis with application to human
fMRI
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2011'
...
---
_id: '3382'
abstract:
- lang: eng
text: Dynamic tactile sensing is a fundamental ability to recognize materials and
objects. However, while humans are born with partially developed dynamic tactile
sensing and quickly master this skill, today's robots remain in their infancy.
The development of such a sense requires not only better sensors but the right
algorithms to deal with these sensors' data as well. For example, when classifying
a material based on touch, the data are noisy, high-dimensional, and contain irrelevant
signals as well as essential ones. Few classification methods from machine learning
can deal with such problems. In this paper, we propose an efficient approach to
infer suitable lower dimensional representations of the tactile data. In order
to classify materials based on only the sense of touch, these representations
are autonomously discovered using visual information of the surfaces during training.
However, accurately pairing vision and tactile samples in real-robot applications
is a difficult problem. The proposed approach, therefore, works with weak pairings
between the modalities. Experiments show that the resulting approach is very robust
and yields significantly higher classification performance based on only dynamic
tactile sensing.
author:
- first_name: Oliver
full_name: Kroemer, Oliver
last_name: Kroemer
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Jan
full_name: Peters, Jan
last_name: Peters
citation:
ama: Kroemer O, Lampert C, Peters J. Learning dynamic tactile sensing with robust
vision based training. IEEE Transactions on Robotics. 2011;27(3):545-557.
doi:10.1109/TRO.2011.2121130
apa: Kroemer, O., Lampert, C., & Peters, J. (2011). Learning dynamic tactile
sensing with robust vision based training. IEEE Transactions on Robotics.
IEEE. https://doi.org/10.1109/TRO.2011.2121130
chicago: Kroemer, Oliver, Christoph Lampert, and Jan Peters. “Learning Dynamic Tactile
Sensing with Robust Vision Based Training.” IEEE Transactions on Robotics.
IEEE, 2011. https://doi.org/10.1109/TRO.2011.2121130.
ieee: O. Kroemer, C. Lampert, and J. Peters, “Learning dynamic tactile sensing with
robust vision based training,” IEEE Transactions on Robotics, vol. 27,
no. 3. IEEE, pp. 545–557, 2011.
ista: Kroemer O, Lampert C, Peters J. 2011. Learning dynamic tactile sensing with
robust vision based training. IEEE Transactions on Robotics. 27(3), 545–557.
mla: Kroemer, Oliver, et al. “Learning Dynamic Tactile Sensing with Robust Vision
Based Training.” IEEE Transactions on Robotics, vol. 27, no. 3, IEEE, 2011,
pp. 545–57, doi:10.1109/TRO.2011.2121130.
short: O. Kroemer, C. Lampert, J. Peters, IEEE Transactions on Robotics 27 (2011)
545–557.
date_created: 2018-12-11T12:03:01Z
date_published: 2011-05-21T00:00:00Z
date_updated: 2021-01-12T07:43:06Z
day: '21'
department:
- _id: ChLa
doi: 10.1109/TRO.2011.2121130
intvolume: ' 27'
issue: '3'
language:
- iso: eng
month: '05'
oa_version: None
page: 545 - 557
publication: IEEE Transactions on Robotics
publication_status: published
publisher: IEEE
publist_id: '3225'
quality_controlled: '1'
scopus_import: 1
status: public
title: Learning dynamic tactile sensing with robust vision based training
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2011'
...
---
_id: '3386'
abstract:
- lang: eng
text: 'Evolutionary theories of ageing predict that life span increases with decreasing
extrinsic mortality, and life span variation among queens in ant species seems
to corroborate this prediction: queens, which are the only reproductive in a colony,
live much longer than queens in multi-queen colonies. The latter often inhabit
ephemeral nest sites and accordingly are assumed to experience a higher mortality
risk. Yet, all prior studies compared queens from different single- and multi-queen
species. Here, we demonstrate an effect of queen number on longevity and fecundity
within a single, socially plastic species, where queens experience the similar
level of extrinsic mortality. Queens from single- and two-queen colonies had significantly
longer lifespan and higher fecundity than queens living in associations of eight
queens. As queens also differ neither in morphology nor the mode of colony foundation,
our study shows that the social environment itself strongly affects ageing rate.'
author:
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
- 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
citation:
ama: Schrempf A, Cremer S, Heinze J. Social influence on age and reproduction reduced
lifespan and fecundity in multi queen ant colonies. Journal of Evolutionary
Biology. 2011;24(7):1455-1461. doi:10.1111/j.1420-9101.2011.02278.x
apa: Schrempf, A., Cremer, S., & Heinze, J. (2011). Social influence on age
and reproduction reduced lifespan and fecundity in multi queen ant colonies. Journal
of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/j.1420-9101.2011.02278.x
chicago: Schrempf, Alexandra, Sylvia Cremer, and Jürgen Heinze. “Social Influence
on Age and Reproduction Reduced Lifespan and Fecundity in Multi Queen Ant Colonies.”
Journal of Evolutionary Biology. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1420-9101.2011.02278.x.
ieee: A. Schrempf, S. Cremer, and J. Heinze, “Social influence on age and reproduction
reduced lifespan and fecundity in multi queen ant colonies,” Journal of Evolutionary
Biology, vol. 24, no. 7. Wiley-Blackwell, pp. 1455–1461, 2011.
ista: Schrempf A, Cremer S, Heinze J. 2011. Social influence on age and reproduction
reduced lifespan and fecundity in multi queen ant colonies. Journal of Evolutionary
Biology. 24(7), 1455–1461.
mla: Schrempf, Alexandra, et al. “Social Influence on Age and Reproduction Reduced
Lifespan and Fecundity in Multi Queen Ant Colonies.” Journal of Evolutionary
Biology, vol. 24, no. 7, Wiley-Blackwell, 2011, pp. 1455–61, doi:10.1111/j.1420-9101.2011.02278.x.
short: A. Schrempf, S. Cremer, J. Heinze, Journal of Evolutionary Biology 24 (2011)
1455–1461.
date_created: 2018-12-11T12:03:02Z
date_published: 2011-04-21T00:00:00Z
date_updated: 2021-01-12T07:43:08Z
day: '21'
department:
- _id: SyCr
doi: 10.1111/j.1420-9101.2011.02278.x
intvolume: ' 24'
issue: '7'
language:
- iso: eng
month: '04'
oa_version: None
page: 1455 - 1461
publication: Journal of Evolutionary Biology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3221'
quality_controlled: '1'
scopus_import: 1
status: public
title: Social influence on age and reproduction reduced lifespan and fecundity in
multi queen ant colonies
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2011'
...
---
_id: '3385'
article_type: review
author:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Sixt MK. Interstitial locomotion of leukocytes. Immunology Letters.
2011;138(1):32-34. doi:10.1016/j.imlet.2011.02.013
apa: Sixt, M. K. (2011). Interstitial locomotion of leukocytes. Immunology Letters.
Elsevier. https://doi.org/10.1016/j.imlet.2011.02.013
chicago: Sixt, Michael K. “Interstitial Locomotion of Leukocytes.” Immunology
Letters. Elsevier, 2011. https://doi.org/10.1016/j.imlet.2011.02.013.
ieee: M. K. Sixt, “Interstitial locomotion of leukocytes,” Immunology Letters,
vol. 138, no. 1. Elsevier, pp. 32–34, 2011.
ista: Sixt MK. 2011. Interstitial locomotion of leukocytes. Immunology Letters.
138(1), 32–34.
mla: Sixt, Michael K. “Interstitial Locomotion of Leukocytes.” Immunology Letters,
vol. 138, no. 1, Elsevier, 2011, pp. 32–34, doi:10.1016/j.imlet.2011.02.013.
short: M.K. Sixt, Immunology Letters 138 (2011) 32–34.
date_created: 2018-12-11T12:03:02Z
date_published: 2011-07-01T00:00:00Z
date_updated: 2021-01-12T07:43:07Z
day: '01'
department:
- _id: MiSi
doi: 10.1016/j.imlet.2011.02.013
intvolume: ' 138'
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 32 - 34
publication: Immunology Letters
publication_status: published
publisher: Elsevier
publist_id: '3222'
quality_controlled: '1'
scopus_import: 1
status: public
title: Interstitial locomotion of leukocytes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 138
year: '2011'
...
---
_id: '3383'
author:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Heisenberg C-PJ. Invited Lectures ‐ Symposia Area. FEBS Journal. 2011;278(S1):24-24.
doi:10.1111/j.1742-4658.2011.08136.x
apa: Heisenberg, C.-P. J. (2011). Invited Lectures ‐ Symposia Area. FEBS Journal.
Wiley-Blackwell. https://doi.org/10.1111/j.1742-4658.2011.08136.x
chicago: Heisenberg, Carl-Philipp J. “Invited Lectures ‐ Symposia Area.” FEBS
Journal. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1742-4658.2011.08136.x.
ieee: C.-P. J. Heisenberg, “Invited Lectures ‐ Symposia Area,” FEBS Journal,
vol. 278, no. S1. Wiley-Blackwell, pp. 24–24, 2011.
ista: Heisenberg C-PJ. 2011. Invited Lectures ‐ Symposia Area. FEBS Journal. 278(S1),
24–24.
mla: Heisenberg, Carl-Philipp J. “Invited Lectures ‐ Symposia Area.” FEBS Journal,
vol. 278, no. S1, Wiley-Blackwell, 2011, pp. 24–24, doi:10.1111/j.1742-4658.2011.08136.x.
short: C.-P.J. Heisenberg, FEBS Journal 278 (2011) 24–24.
date_created: 2018-12-11T12:03:01Z
date_published: 2011-07-01T00:00:00Z
date_updated: 2021-01-12T07:43:06Z
day: '01'
department:
- _id: CaHe
doi: 10.1111/j.1742-4658.2011.08136.x
intvolume: ' 278'
issue: S1
language:
- iso: eng
month: '07'
oa_version: None
page: 24 - 24
publication: FEBS Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3224'
status: public
title: Invited Lectures ‐ Symposia Area
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 278
year: '2011'
...
---
_id: '3399'
abstract:
- lang: eng
text: Context-dependent adjustment of mating tactics can drastically increase the
mating success of behaviourally flexible animals. We used the ant Cardiocondyla
obscurior as a model system to study adaptive adjustment of male mating tactics.
This species shows a male diphenism of wingless fighter males and peaceful winged
males. Whereas the wingless males stay and exclusively mate in the maternal colony,
the mating behaviour of winged males is plastic. They copulate with female sexuals
in their natal nests early in life but later disperse in search for sexuals outside.
In this study, we observed the nest-leaving behaviour of winged males under different
conditions and found that they adaptively adjust the timing of their dispersal
to the availability of mating partners, as well as the presence, and even the
type of competitors in their natal nests. In colonies with virgin female queens
winged males stayed longest when they were the only male in the nest. They left
earlier when mating partners were not available or when other males were present.
In the presence of wingless, locally mating fighter males, winged males dispersed
earlier than in the presence of docile, winged competitors. This suggests that
C. obscurior males are capable of estimating their local breeding chances and
adaptively adjust their dispersal behaviour in both an opportunistic and a risk-sensitive
way, thus showing hitherto unknown behavioural plasticity in social insect males.
acknowledgement: This work was supported by the German Science Foundation (www.dfg.de,
He 1623/23).
article_number: e17323
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
citation:
ama: Cremer S, Schrempf A, Heinze J. Competition and opportunity shape the reproductive
tactics of males in the ant Cardiocondyla obscurior. PLoS One. 2011;6(3).
doi:10.1371/journal.pone.0017323
apa: Cremer, S., Schrempf, A., & Heinze, J. (2011). Competition and opportunity
shape the reproductive tactics of males in the ant Cardiocondyla obscurior. PLoS
One. Public Library of Science. https://doi.org/10.1371/journal.pone.0017323
chicago: Cremer, Sylvia, Alexandra Schrempf, and Jürgen Heinze. “Competition and
Opportunity Shape the Reproductive Tactics of Males in the Ant Cardiocondyla Obscurior.”
PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0017323.
ieee: S. Cremer, A. Schrempf, and J. Heinze, “Competition and opportunity shape
the reproductive tactics of males in the ant Cardiocondyla obscurior,” PLoS
One, vol. 6, no. 3. Public Library of Science, 2011.
ista: Cremer S, Schrempf A, Heinze J. 2011. Competition and opportunity shape the
reproductive tactics of males in the ant Cardiocondyla obscurior. PLoS One. 6(3),
e17323.
mla: Cremer, Sylvia, et al. “Competition and Opportunity Shape the Reproductive
Tactics of Males in the Ant Cardiocondyla Obscurior.” PLoS One, vol. 6,
no. 3, e17323, Public Library of Science, 2011, doi:10.1371/journal.pone.0017323.
short: S. Cremer, A. Schrempf, J. Heinze, PLoS One 6 (2011).
date_created: 2018-12-11T12:03:07Z
date_published: 2011-03-29T00:00:00Z
date_updated: 2021-01-12T07:43:12Z
day: '29'
ddc:
- '576'
department:
- _id: SyCr
doi: 10.1371/journal.pone.0017323
file:
- access_level: open_access
checksum: 46f8cbde61f06fcacf8fa297cacfa0e5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:40Z
date_updated: 2020-07-14T12:46:12Z
file_id: '5162'
file_name: IST-2015-377-v1+1_journal.pone.0017323.pdf
file_size: 147367
relation: main_file
file_date_updated: 2020-07-14T12:46:12Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3059'
pubrep_id: '377'
quality_controlled: '1'
scopus_import: 1
status: public
title: Competition and opportunity shape the reproductive tactics of males in the
ant Cardiocondyla obscurior
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: '2011'
...
---
_id: '3401'
abstract:
- lang: eng
text: The Bicoid morphogen gradient directs the patterning of cell fates along the
anterior-posterior axis of the syncytial Drosophila embryo and serves as a paradigm
of morphogen-mediated patterning. The simplest models of gradient formation rely
on constant protein synthesis and diffusion from anteriorly localized source mRNA,
coupled with uniform protein degradation. However, currently such models cannot
account for all known gradient characteristics. Recent work has proposed that
bicoid mRNA spatial distribution is sufficient to produce the observed protein
gradient, minimizing the role of protein transport. Here, we adapt a novel method
of fluorescent in situ hybridization to quantify the global spatio-temporal dynamics
of bicoid mRNA particles. We determine that >90% of all bicoid mRNA is continuously
present within the anterior 20% of the embryo. bicoid mRNA distribution along
the body axis remains nearly unchanged despite dynamic mRNA translocation from
the embryo core to the cortex. To evaluate the impact of mRNA distribution on
protein gradient dynamics, we provide detailed quantitative measurements of nuclear
Bicoid levels during the formation of the protein gradient. We find that gradient
establishment begins 45 minutes after fertilization and that the gradient requires
about 50 minutes to reach peak levels. In numerical simulations of gradient formation,
we find that incorporating the actual bicoid mRNA distribution yields a closer
prediction of the observed protein dynamics compared to modeling protein production
from a point source at the anterior pole. We conclude that the spatial distribution
of bicoid mRNA contributes to, but cannot account for, protein gradient formation,
and therefore that protein movement, either active or passive, is required for
gradient formation.
article_number: e1000596
article_type: original
author:
- first_name: Shawn
full_name: Little, Shawn
last_name: Little
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Thomas
full_name: Kneeland, Thomas
last_name: Kneeland
- first_name: Eric
full_name: Wieschaus, Eric
last_name: Wieschaus
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
citation:
ama: Little S, Tkačik G, Kneeland T, Wieschaus E, Gregor T. The formation of the
Bicoid morphogen gradient requires protein movement from anteriorly localized
source. PLoS Biology. 2011;9(3). doi:10.1371/journal.pbio.1000596
apa: Little, S., Tkačik, G., Kneeland, T., Wieschaus, E., & Gregor, T. (2011).
The formation of the Bicoid morphogen gradient requires protein movement from
anteriorly localized source. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000596
chicago: Little, Shawn, Gašper Tkačik, Thomas Kneeland, Eric Wieschaus, and Thomas
Gregor. “The Formation of the Bicoid Morphogen Gradient Requires Protein Movement
from Anteriorly Localized Source.” PLoS Biology. Public Library of Science,
2011. https://doi.org/10.1371/journal.pbio.1000596.
ieee: S. Little, G. Tkačik, T. Kneeland, E. Wieschaus, and T. Gregor, “The formation
of the Bicoid morphogen gradient requires protein movement from anteriorly localized
source,” PLoS Biology, vol. 9, no. 3. Public Library of Science, 2011.
ista: Little S, Tkačik G, Kneeland T, Wieschaus E, Gregor T. 2011. The formation
of the Bicoid morphogen gradient requires protein movement from anteriorly localized
source. PLoS Biology. 9(3), e1000596.
mla: Little, Shawn, et al. “The Formation of the Bicoid Morphogen Gradient Requires
Protein Movement from Anteriorly Localized Source.” PLoS Biology, vol.
9, no. 3, e1000596, Public Library of Science, 2011, doi:10.1371/journal.pbio.1000596.
short: S. Little, G. Tkačik, T. Kneeland, E. Wieschaus, T. Gregor, PLoS Biology
9 (2011).
date_created: 2018-12-11T12:03:08Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2021-01-12T07:43:14Z
day: '01'
doi: 10.1371/journal.pbio.1000596
extern: '1'
intvolume: ' 9'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '3057'
quality_controlled: '1'
status: public
title: The formation of the Bicoid morphogen gradient requires protein movement from
anteriorly localized source
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2011'
...