---
OA_place: repository
OA_type: green
_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.
acknowledgement: We thank David Grunwald for providing the spadetail-myc fusion construct.
This work was supported by an NIH grant (GM079203) to D.K. and grants from the Austrian
Academy of Sciences to P.S., and from the DFG, MPG and IST Austria to C.-P.H. R.R.
was supported by a Developmental Biology Predoctoral Training Grant, T32HD007183,
from the National Institute of Child Health and Human Development. B.L.M. was supported
by an American Cancer Society fellowship (PF-07-048-01-DDC).
article_processing_charge: No
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.
das_tickbox: '1'
date_created: 2018-12-11T12:03:00Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2026-07-28T08:31:27Z
day: '01'
department:
- _id: CaHe
doi: 10.1016/j.ydbio.2011.03.025
external_id:
isi:
- '000290550500010'
pmid:
- '21463614'
fulldoi: https://doi.org/10.1016/j.ydbio.2011.03.025
intvolume: ' 354'
isi: 1
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'
...
---
OA_type: closed access
_id: '3781'
abstract:
- lang: eng
text: We bound the difference in length of two curves in terms of their total curvatures
and the Fréchet distance. The bound is independent of the dimension of the ambient
Euclidean space, it improves upon a bound by Cohen-Steiner and Edelsbrunner, and
it generalizes a result by Fáry and Chakerian.
acknowledgement: Funded by Graduate Aid in Areas of National Need (GAANN) Fellowship.
The author would like to thank Herbert Edelsbrunner for his discussions and guidance.
article_processing_charge: No
article_type: original
author:
- first_name: Brittany Terese
full_name: Fasy, Brittany Terese
id: F65D502E-E68D-11E9-9252-C644099818F6
last_name: Fasy
citation:
ama: Fasy BT. The difference in length of curves in R^n. Acta Scientiarum Mathematicarum.
2011;77(1-2):359-367. doi:10.1007/BF03651375
apa: Fasy, B. T. (2011). The difference in length of curves in R^n. Acta Scientiarum
Mathematicarum. Springer Nature. https://doi.org/10.1007/BF03651375
chicago: Fasy, Brittany Terese. “The Difference in Length of Curves in R^n.” Acta
Scientiarum Mathematicarum. Springer Nature, 2011. https://doi.org/10.1007/BF03651375.
ieee: B. T. Fasy, “The difference in length of curves in R^n,” Acta Scientiarum
Mathematicarum, vol. 77, no. 1–2. Springer Nature, pp. 359–367, 2011.
ista: Fasy BT. 2011. The difference in length of curves in R^n. Acta Scientiarum
Mathematicarum. 77(1–2), 359–367.
mla: Fasy, Brittany Terese. “The Difference in Length of Curves in R^n.” Acta
Scientiarum Mathematicarum, vol. 77, no. 1–2, Springer Nature, 2011, pp. 359–67,
doi:10.1007/BF03651375.
short: B.T. Fasy, Acta Scientiarum Mathematicarum 77 (2011) 359–367.
corr_author: '1'
das_tickbox: '1'
date_created: 2018-12-11T12:05:08Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2026-07-28T08:11:07Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/BF03651375
fulldoi: https://doi.org/10.1007/BF03651375
intvolume: ' 77'
issue: 1-2
language:
- iso: eng
month: '06'
oa_version: None
page: 359 - 367
publication: Acta Scientiarum Mathematicarum
publication_identifier:
eissn:
- 2064-8316
issn:
- 0001-6969
publication_status: published
publisher: Springer Nature
publist_id: '2446'
quality_controlled: '1'
status: public
title: The difference in length of curves in R^n
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2011'
...
---
OA_place: publisher
OA_type: free access
_id: '3383'
article_processing_charge: No
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. In: The FEBS Journal.
Vol 278. Wiley; 2011:24-24. doi:10.1111/j.1742-4658.2011.08136.x'
apa: 'Heisenberg, C.-P. J. (2011). Invited Lectures ‐ Symposia Area. In The FEBS
Journal (Vol. 278, pp. 24–24). Torino, Italy: Wiley. https://doi.org/10.1111/j.1742-4658.2011.08136.x'
chicago: Heisenberg, Carl-Philipp J. “Invited Lectures ‐ Symposia Area.” In The
FEBS Journal, 278:24–24. Wiley, 2011. https://doi.org/10.1111/j.1742-4658.2011.08136.x.
ieee: C.-P. J. Heisenberg, “Invited Lectures ‐ Symposia Area,” in The FEBS Journal,
Torino, Italy, 2011, vol. 278, no. S1, pp. 24–24.
ista: Heisenberg C-PJ. 2011. Invited Lectures ‐ Symposia Area. The FEBS Journal.
FEBS Congress on Biochemistry for Tomorrow’s Medicine vol. 278, 24–24.
mla: Heisenberg, Carl-Philipp J. “Invited Lectures ‐ Symposia Area.” The FEBS
Journal, vol. 278, no. S1, Wiley, 2011, pp. 24–24, doi:10.1111/j.1742-4658.2011.08136.x.
short: C.-P.J. Heisenberg, in:, The FEBS Journal, Wiley, 2011, pp. 24–24.
conference:
end_date: 2011-06-30
location: Torino, Italy
name: FEBS Congress on Biochemistry for Tomorrow's Medicine
start_date: 2011-06-25
corr_author: '1'
date_created: 2018-12-11T12:03:01Z
date_published: 2011-07-01T00:00:00Z
date_updated: 2026-07-28T08:27:55Z
day: '01'
department:
- _id: CaHe
doi: 10.1111/j.1742-4658.2011.08136.x
fulldoi: https://doi.org/10.1111/j.1742-4658.2011.08136.x
intvolume: ' 278'
issue: S1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/j.1742-4658.2011.08136.x
month: '07'
oa: 1
oa_version: Published Version
page: 24 - 24
publication: The FEBS Journal
publication_status: published
publisher: Wiley
publist_id: '3224'
quality_controlled: '1'
status: public
title: Invited Lectures ‐ Symposia Area
type: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 278
year: '2011'
...
---
_id: '3368'
abstract:
- lang: eng
text: Tissue surface tension (TST) is an important mechanical property influencing
cell sorting and tissue envelopment. The study by Manning et al. (1) reported
on a mathematical model describing TST on the basis of the balance between adhesive
and tensile properties of the constituent cells. The model predicts that, in high-adhesion
cell aggregates, surface cells will be stretched to maintain the same area of
cell–cell contact as interior bulk cells, resulting in an elongated and flattened
cell shape. The authors (1) observed flat and elongated cells at the surface of
high-adhesion zebrafish germ-layer explants, which they argue are undifferentiated
stretched germ-layer progenitor cells, and they use this observation as a validation
of their model.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Stephanie
full_name: Möllmert, Stephanie
id: 260FD49C-E911-11E9-B5EA-D9538404589B
last_name: Möllmert
- 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: Krens G, Möllmert S, Heisenberg C-PJ. Enveloping cell layer differentiation
at the surface of zebrafish germ layer tissue explants. PNAS. 2011;108(3):E9-E10.
doi:10.1073/pnas.1010767108
apa: Krens, G., Möllmert, S., & Heisenberg, C.-P. J. (2011). Enveloping cell
layer differentiation at the surface of zebrafish germ layer tissue explants.
PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1010767108
chicago: Krens, Gabriel, Stephanie Möllmert, and Carl-Philipp J Heisenberg. “Enveloping
Cell Layer Differentiation at the Surface of Zebrafish Germ Layer Tissue Explants.”
PNAS. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1010767108.
ieee: G. Krens, S. Möllmert, and C.-P. J. Heisenberg, “Enveloping cell layer differentiation
at the surface of zebrafish germ layer tissue explants,” PNAS, vol. 108,
no. 3. National Academy of Sciences, pp. E9–E10, 2011.
ista: Krens G, Möllmert S, Heisenberg C-PJ. 2011. Enveloping cell layer differentiation
at the surface of zebrafish germ layer tissue explants. PNAS. 108(3), E9–E10.
mla: Krens, Gabriel, et al. “Enveloping Cell Layer Differentiation at the Surface
of Zebrafish Germ Layer Tissue Explants.” PNAS, vol. 108, no. 3, National
Academy of Sciences, 2011, pp. E9–10, doi:10.1073/pnas.1010767108.
short: G. Krens, S. Möllmert, C.-P.J. Heisenberg, PNAS 108 (2011) E9–E10.
corr_author: '1'
das_tickbox: '1'
date_created: 2018-12-11T12:02:56Z
date_published: 2011-01-18T00:00:00Z
date_updated: 2026-07-28T09:03:18Z
day: '18'
department:
- _id: CaHe
doi: 10.1073/pnas.1010767108
external_id:
isi:
- '000286310300003'
pmid:
- '21212360'
fulldoi: https://doi.org/10.1073/pnas.1010767108
intvolume: ' 108'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024655
month: '01'
oa: 1
oa_version: Submitted Version
page: E9 - E10
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3244'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Enveloping cell layer differentiation at the surface of zebrafish germ layer
tissue explants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2011'
...
---
_id: '3373'
abstract:
- lang: eng
text: The use of optical traps to measure or apply forces on the molecular level
requires a precise knowledge of the trapping force field. Close to the trap center,
this field is typically approximated as linear in the displacement of the trapped
microsphere. However, applications demanding high forces at low laser intensities
can probe the light-microsphere interaction beyond the linear regime. Here, we
measured the full nonlinear force and displacement response of an optical trap
in two dimensions using a dual-beam optical trap setup with back-focal-plane photodetection.
We observed a substantial stiffening of the trap beyond the linear regime that
depends on microsphere size, in agreement with Mie theory calculations. Surprisingly,
we found that the linear detection range for forces exceeds the one for displacement
by far. Our approach allows for a complete calibration of an optical trap.
article_processing_charge: No
author:
- first_name: Marcus
full_name: Jahnel, Marcus
last_name: Jahnel
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Anita
full_name: Jannasch, Anita
last_name: Jannasch
- first_name: Erik
full_name: Schaeffer, Erik
last_name: Schaeffer
- first_name: Stephan
full_name: Grill, Stephan
last_name: Grill
citation:
ama: Jahnel M, Behrndt M, Jannasch A, Schaeffer E, Grill S. Measuring the complete
force field of an optical trap. Optics Letters. 2011;36(7):1260-1262. doi:10.1364/OL.36.001260
apa: Jahnel, M., Behrndt, M., Jannasch, A., Schaeffer, E., & Grill, S. (2011).
Measuring the complete force field of an optical trap. Optics Letters.
Optica Publishing Group. https://doi.org/10.1364/OL.36.001260
chicago: Jahnel, Marcus, Martin Behrndt, Anita Jannasch, Erik Schaeffer, and Stephan
Grill. “Measuring the Complete Force Field of an Optical Trap.” Optics Letters.
Optica Publishing Group, 2011. https://doi.org/10.1364/OL.36.001260.
ieee: M. Jahnel, M. Behrndt, A. Jannasch, E. Schaeffer, and S. Grill, “Measuring
the complete force field of an optical trap,” Optics Letters, vol. 36,
no. 7. Optica Publishing Group, pp. 1260–1262, 2011.
ista: Jahnel M, Behrndt M, Jannasch A, Schaeffer E, Grill S. 2011. Measuring the
complete force field of an optical trap. Optics Letters. 36(7), 1260–1262.
mla: Jahnel, Marcus, et al. “Measuring the Complete Force Field of an Optical Trap.”
Optics Letters, vol. 36, no. 7, Optica Publishing Group, 2011, pp. 1260–62,
doi:10.1364/OL.36.001260.
short: M. Jahnel, M. Behrndt, A. Jannasch, E. Schaeffer, S. Grill, Optics Letters
36 (2011) 1260–1262.
date_created: 2018-12-11T12:02:58Z
date_published: 2011-03-30T00:00:00Z
date_updated: 2026-07-29T10:07:18Z
day: '30'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1364/OL.36.001260
external_id:
isi:
- '000289251000080'
fulldoi: https://doi.org/10.1364/OL.36.001260
intvolume: ' 36'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.osapublishing.org/ol/abstract.cfm?uri=ol-36-7-1260
month: '03'
oa: 1
oa_version: Published Version
page: 1260 - 1262
publication: Optics Letters
publication_status: published
publisher: Optica Publishing Group
publist_id: '3234'
quality_controlled: '1'
related_material:
record:
- id: '1403'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Measuring the complete force field of an optical trap
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2011'
...
---
_id: '3393'
abstract:
- lang: eng
text: 'Unlike unconditionally advantageous “Fisherian” variants that tend to spread
throughout a species range once introduced anywhere, “bistable” variants, such
as chromosome translocations, have two alternative stable frequencies, absence
and (near) fixation. Analogous to populations with Allee effects, bistable variants
tend to increase locally only once they become sufficiently common, and their
spread depends on their rate of increase averaged over all frequencies. Several
proposed manipulations of insect populations, such as using Wolbachia or “engineered
underdominance” to suppress vector-borne diseases, produce bistable rather than
Fisherian dynamics. We synthesize and extend theoretical analyses concerning three
features of their spatial behavior: rate of spread, conditions to initiate spread
from a localized introduction, and wave stopping caused by variation in population
densities or dispersal rates. Unlike Fisherian variants, bistable variants tend
to spread spatially only for particular parameter combinations and initial conditions.
Wave initiation requires introduction over an extended region, while subsequent
spatial spread is slower than for Fisherian waves and can easily be halted by
local spatial inhomogeneities. We present several new results, including robust
sufficient conditions to initiate (and stop) spread, using a one-parameter cubic
approximation applicable to several models. The results have both basic and applied
implications.'
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: 'Barton NH, Turelli M. Spatial waves of advance with bistable dynamics: Cytoplasmic
and genetic analogues of Allee effects. American Naturalist. 2011;178(3):E48-E75.
doi:10.1086/661246'
apa: 'Barton, N. H., & Turelli, M. (2011). Spatial waves of advance with bistable
dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist.
University of Chicago Press. https://doi.org/10.1086/661246'
chicago: 'Barton, Nicholas H, and Michael Turelli. “Spatial Waves of Advance with
Bistable Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” American
Naturalist. University of Chicago Press, 2011. https://doi.org/10.1086/661246.'
ieee: 'N. H. Barton and M. Turelli, “Spatial waves of advance with bistable dynamics:
Cytoplasmic and genetic analogues of Allee effects,” American Naturalist,
vol. 178, no. 3. University of Chicago Press, pp. E48–E75, 2011.'
ista: 'Barton NH, Turelli M. 2011. Spatial waves of advance with bistable dynamics:
Cytoplasmic and genetic analogues of Allee effects. American Naturalist. 178(3),
E48–E75.'
mla: 'Barton, Nicholas H., and Michael Turelli. “Spatial Waves of Advance with Bistable
Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” American Naturalist,
vol. 178, no. 3, University of Chicago Press, 2011, pp. E48–75, doi:10.1086/661246.'
short: N.H. Barton, M. Turelli, American Naturalist 178 (2011) E48–E75.
date_created: 2018-12-11T12:03:05Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2026-08-04T09:17:38Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1086/661246
external_id:
isi:
- '000294256800001'
file:
- access_level: open_access
checksum: 7fd22a2ef3321a6fca6a439b3be5d8f4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:31Z
date_updated: 2020-07-14T12:46:11Z
file_id: '4692'
file_name: IST-2016-554-v1+1_BartonTurelli2011_copy.pdf
file_size: 629130
relation: main_file
file_date_updated: 2020-07-14T12:46:11Z
fulldoi: https://doi.org/10.1086/661246
has_accepted_license: '1'
intvolume: ' 178'
isi: 1
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: E48 - E75
publication: American Naturalist
publication_identifier:
eissn:
- 1537-5323
issn:
- 0003-0147
publication_status: published
publisher: University of Chicago Press
publist_id: '3214'
pubrep_id: '554'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues
of Allee effects'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 178
year: '2011'
...
---
_id: '3375'
abstract:
- lang: eng
text: 'By exploiting an analogy between population genetics and statistical mechanics,
we study the evolution of a polygenic trait under stabilizing selection, mutation
and genetic drift. This requires us to track only four macroscopic variables,
instead of the distribution of all the allele frequencies that influence the trait.
These macroscopic variables are the expectations of: the trait mean and its square,
the genetic variance, and of a measure of heterozygosity, and are derived from
a generating function that is in turn derived by maximizing an entropy measure.
These four macroscopics are enough to accurately describe the dynamics of the
trait mean and of its genetic variance (and in principle of any other quantity).
Unlike previous approaches that were based on an infinite series of moments or
cumulants, which had to be truncated arbitrarily, our calculations provide a well-defined
approximation procedure. We apply the framework to abrupt and gradual changes
in the optimum, as well as to changes in the strength of stabilizing selection.
Our approximations are surprisingly accurate, even for systems with as few as
five loci. We find that when the effects of drift are included, the expected genetic
variance is hardly altered by directional selection, even though it fluctuates
in any particular instance. We also find hysteresis, showing that even after averaging
over the microscopic variables, the macroscopic trajectories retain a memory of
the underlying genetic states.'
article_processing_charge: No
article_type: original
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- 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: de Vladar H, Barton NH. The statistical mechanics of a polygenic character
under stabilizing selection mutation and drift. Journal of the Royal Society
Interface. 2011;8(58):720-739. doi:10.1098/rsif.2010.0438
apa: de Vladar, H., & Barton, N. H. (2011). The statistical mechanics of a polygenic
character under stabilizing selection mutation and drift. Journal of the Royal
Society Interface. Royal Society. https://doi.org/10.1098/rsif.2010.0438
chicago: Vladar, Harold de, and Nicholas H Barton. “The Statistical Mechanics of
a Polygenic Character under Stabilizing Selection Mutation and Drift.” Journal
of the Royal Society Interface. Royal Society, 2011. https://doi.org/10.1098/rsif.2010.0438.
ieee: H. de Vladar and N. H. Barton, “The statistical mechanics of a polygenic character
under stabilizing selection mutation and drift,” Journal of the Royal Society
Interface, vol. 8, no. 58. Royal Society, pp. 720–739, 2011.
ista: de Vladar H, Barton NH. 2011. The statistical mechanics of a polygenic character
under stabilizing selection mutation and drift. Journal of the Royal Society Interface.
8(58), 720–739.
mla: de Vladar, Harold, and Nicholas H. Barton. “The Statistical Mechanics of a
Polygenic Character under Stabilizing Selection Mutation and Drift.” Journal
of the Royal Society Interface, vol. 8, no. 58, Royal Society, 2011, pp. 720–39,
doi:10.1098/rsif.2010.0438.
short: H. de Vladar, N.H. Barton, Journal of the Royal Society Interface 8 (2011)
720–739.
corr_author: '1'
date_created: 2018-12-11T12:02:58Z
date_published: 2011-05-01T00:00:00Z
date_updated: 2026-08-12T14:07:44Z
day: '01'
department:
- _id: NiBa
doi: 10.1098/rsif.2010.0438
ec_funded: 1
external_id:
isi:
- '000289671700011'
pmid:
- '21084341'
fulldoi: https://doi.org/10.1098/rsif.2010.0438
intvolume: ' 8'
isi: 1
issue: '58'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061091/
month: '05'
oa: 1
oa_version: Submitted Version
page: 720 - 739
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Journal of the Royal Society Interface
publication_status: published
publisher: Royal Society
publist_id: '3232'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The statistical mechanics of a polygenic character under stabilizing selection
mutation and drift
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2011'
...
---
_id: '10908'
abstract:
- lang: eng
text: We present ABC, a software tool for automatically computing symbolic upper
bounds on the number of iterations of nested program loops. The system combines
static analysis of programs with symbolic summation techniques to derive loop
invariant relations between program variables. Iteration bounds are obtained from
the inferred invariants, by replacing variables with bounds on their greatest
values. We have successfully applied ABC to a large number of examples. The derived
symbolic bounds express non-trivial polynomial relations over loop variables.
We also report on results to automatically infer symbolic expressions over harmonic
numbers as upper bounds on loop iteration counts.
acknowledgement: This work was supported in part by the Swiss NSF. The fourth author
is supported by an FWF Hertha Firnberg Research grant (T425-N23).
article_processing_charge: No
author:
- first_name: Régis
full_name: Blanc, Régis
last_name: Blanc
- 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: Thibaud
full_name: Hottelier, Thibaud
last_name: Hottelier
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
citation:
ama: 'Blanc R, Henzinger TA, Hottelier T, Kovács L. ABC: Algebraic Bound Computation
for loops. In: Clarke EM, Voronkov A, eds. Logic for Programming, Artificial
Intelligence, and Reasoning. Vol 6355. LNCS. Berlin, Heidelberg: Springer
Nature; 2010:103-118. doi:10.1007/978-3-642-17511-4_7'
apa: 'Blanc, R., Henzinger, T. A., Hottelier, T., & Kovács, L. (2010). ABC:
Algebraic Bound Computation for loops. In E. M. Clarke & A. Voronkov (Eds.),
Logic for Programming, Artificial Intelligence, and Reasoning (Vol. 6355,
pp. 103–118). Berlin, Heidelberg: Springer Nature. https://doi.org/10.1007/978-3-642-17511-4_7'
chicago: 'Blanc, Régis, Thomas A Henzinger, Thibaud Hottelier, and Laura Kovács.
“ABC: Algebraic Bound Computation for Loops.” In Logic for Programming, Artificial
Intelligence, and Reasoning, edited by Edmund M Clarke and Andrei Voronkov,
6355:103–18. LNCS. Berlin, Heidelberg: Springer Nature, 2010. https://doi.org/10.1007/978-3-642-17511-4_7.'
ieee: 'R. Blanc, T. A. Henzinger, T. Hottelier, and L. Kovács, “ABC: Algebraic Bound
Computation for loops,” in Logic for Programming, Artificial Intelligence,
and Reasoning, Dakar, Senegal, 2010, vol. 6355, pp. 103–118.'
ista: 'Blanc R, Henzinger TA, Hottelier T, Kovács L. 2010. ABC: Algebraic Bound
Computation for loops. Logic for Programming, Artificial Intelligence, and Reasoning.
LPAR: Logic for Programming, Artificial Intelligence and ReasoningLNCS vol. 6355,
103–118.'
mla: 'Blanc, Régis, et al. “ABC: Algebraic Bound Computation for Loops.” Logic
for Programming, Artificial Intelligence, and Reasoning, edited by Edmund
M Clarke and Andrei Voronkov, vol. 6355, Springer Nature, 2010, pp. 103–18, doi:10.1007/978-3-642-17511-4_7.'
short: R. Blanc, T.A. Henzinger, T. Hottelier, L. Kovács, in:, E.M. Clarke, A. Voronkov
(Eds.), Logic for Programming, Artificial Intelligence, and Reasoning, Springer
Nature, Berlin, Heidelberg, 2010, pp. 103–118.
conference:
end_date: 2010-05-01
location: Dakar, Senegal
name: 'LPAR: Logic for Programming, Artificial Intelligence and Reasoning'
start_date: 2010-04-25
corr_author: '1'
date_created: 2022-03-21T08:14:35Z
date_published: 2010-05-01T00:00:00Z
date_updated: 2025-09-30T09:51:13Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-642-17511-4_7
editor:
- first_name: Edmund M
full_name: Clarke, Edmund M
last_name: Clarke
- first_name: Andrei
full_name: Voronkov, Andrei
last_name: Voronkov
external_id:
isi:
- '000309668000007'
fulldoi: https://doi.org/10.1007/978-3-642-17511-4_7
intvolume: ' 6355'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://infoscience.epfl.ch/record/186096
month: '05'
oa: 1
oa_version: Submitted Version
page: 103-118
place: Berlin, Heidelberg
publication: Logic for Programming, Artificial Intelligence, and Reasoning
publication_identifier:
eisbn:
- '9783642175114'
eissn:
- 1611-3349
isbn:
- '9783642175107'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: 'ABC: Algebraic Bound Computation for loops'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6355
year: '2010'
...
---
_id: '10909'
abstract:
- lang: eng
text: We address the problem of localizing homology classes, namely, finding the
cycle representing a given class with the most concise geometric measure. We focus
on the volume measure, that is, the 1-norm of a cycle. Two main results are presented.
First, we prove the problem is NP-hard to approximate within any constant factor.
Second, we prove that for homology of dimension two or higher, the problem is
NP-hard to approximate even when the Betti number is O(1). A side effect is the
inapproximability of the problem of computing the nonbounding cycle with the smallest
volume, and computing cycles representing a homology basis with the minimal total
volume. We also discuss other geometric measures (diameter and radius) and show
their disadvantages in homology localization. Our work is restricted to homology
over the ℤ2 field.
acknowledgement: Partially supported by the Austrian Science Fund under grantFSP-S9103-N04
and P20134-N13.
article_processing_charge: No
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Daniel
full_name: Freedman, Daniel
last_name: Freedman
citation:
ama: 'Chen C, Freedman D. Hardness results for homology localization. In: Proceedings
of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for
Industrial and Applied Mathematics; 2010:1594-1604. doi:10.1137/1.9781611973075.129'
apa: 'Chen, C., & Freedman, D. (2010). Hardness results for homology localization.
In Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms
(pp. 1594–1604). Austin, TX, United States: Society for Industrial and Applied
Mathematics. https://doi.org/10.1137/1.9781611973075.129'
chicago: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.”
In Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms,
1594–1604. Society for Industrial and Applied Mathematics, 2010. https://doi.org/10.1137/1.9781611973075.129.
ieee: C. Chen and D. Freedman, “Hardness results for homology localization,” in
Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms,
Austin, TX, United States, 2010, pp. 1594–1604.
ista: 'Chen C, Freedman D. 2010. Hardness results for homology localization. Proceedings
of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium
on Discrete Algorithms, 1594–1604.'
mla: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.”
Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms,
Society for Industrial and Applied Mathematics, 2010, pp. 1594–604, doi:10.1137/1.9781611973075.129.
short: C. Chen, D. Freedman, in:, Proceedings of the 2010 Annual ACM-SIAM Symposium
on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2010,
pp. 1594–1604.
conference:
end_date: 2010-01-19
location: Austin, TX, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2010-01-17
corr_author: '1'
date_created: 2022-03-21T08:24:07Z
date_published: 2010-02-01T00:00:00Z
date_updated: 2025-09-30T09:22:32Z
day: '01'
department:
- _id: HeEd
doi: 10.1137/1.9781611973075.129
fulldoi: https://doi.org/10.1137/1.9781611973075.129
language:
- iso: eng
month: '02'
oa_version: None
page: 1594-1604
publication: Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
eisbn:
- '9781611973075'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
record:
- id: '3267'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Hardness results for homology localization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '2409'
abstract:
- lang: eng
text: "Background: The availability of many gene alignments with overlapping taxon
sets raises the question of which strategy is the best to infer species phylogenies
from multiple gene information. Methods and programs abound that use the gene
alignment in different ways to reconstruct the species tree. In particular, different
methods combine the original data at different points along the way from the underlying
sequences to the final tree. Accordingly, they are classified into superalignment,
supertree and medium-level approaches. Here, we present a simulation study to
compare different methods from each of these three approaches.\r\n\r\nResults:
We observe that superalignment methods usually outperform the other approaches
over a wide range of parameters including sparse data and gene-specific evolutionary
parameters. In the presence of high incongruency among gene trees, however, other
combination methods show better performance than the superalignment approach.
Surprisingly, some supertree and medium-level methods exhibit, on average, worse
results than a single gene phylogeny with complete taxon information.\r\n\r\nConclusions:
For some methods, using the reconstructed gene tree as an estimation of the species
tree is superior to the combination of incomplete information. Superalignment
usually performs best since it is less susceptible to stochastic error. Supertree
methods can outperform superalignment in the presence of gene-tree conflict."
acknowledgement: Financial support from the Wiener Wissenschafts-, Forschungs- and
Technologiefonds (WWTF) is greatly appreciated. A.v.H. acknowledges support from
the German Research Foundation (DFG, SPP-1174).
article_number: '37'
article_processing_charge: No
author:
- first_name: Anne
full_name: Kupczok, Anne
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Heiko
full_name: Schmidt, Heiko
last_name: Schmidt
- first_name: Arndt
full_name: Von Haeseler, Arndt
last_name: Von Haeseler
citation:
ama: Kupczok A, Schmidt H, Von Haeseler A. Accuracy of phylogeny reconstruction
methods combining overlapping gene data sets. Algorithms for Molecular Biology.
2010;5(1). doi:10.1186/1748-7188-5-37
apa: Kupczok, A., Schmidt, H., & Von Haeseler, A. (2010). Accuracy of phylogeny
reconstruction methods combining overlapping gene data sets. Algorithms for
Molecular Biology. BioMed Central. https://doi.org/10.1186/1748-7188-5-37
chicago: Kupczok, Anne, Heiko Schmidt, and Arndt Von Haeseler. “Accuracy of Phylogeny
Reconstruction Methods Combining Overlapping Gene Data Sets.” Algorithms for
Molecular Biology. BioMed Central, 2010. https://doi.org/10.1186/1748-7188-5-37.
ieee: A. Kupczok, H. Schmidt, and A. Von Haeseler, “Accuracy of phylogeny reconstruction
methods combining overlapping gene data sets,” Algorithms for Molecular Biology,
vol. 5, no. 1. BioMed Central, 2010.
ista: Kupczok A, Schmidt H, Von Haeseler A. 2010. Accuracy of phylogeny reconstruction
methods combining overlapping gene data sets. Algorithms for Molecular Biology.
5(1), 37.
mla: Kupczok, Anne, et al. “Accuracy of Phylogeny Reconstruction Methods Combining
Overlapping Gene Data Sets.” Algorithms for Molecular Biology, vol. 5,
no. 1, 37, BioMed Central, 2010, doi:10.1186/1748-7188-5-37.
short: A. Kupczok, H. Schmidt, A. Von Haeseler, Algorithms for Molecular Biology
5 (2010).
date_created: 2018-12-11T11:57:30Z
date_published: 2010-12-06T00:00:00Z
date_updated: 2025-09-30T09:48:29Z
day: '06'
ddc:
- '576'
department:
- _id: JoBo
doi: 10.1186/1748-7188-5-37
external_id:
isi:
- '000286183400001'
file:
- access_level: open_access
checksum: e2497285388bc4da629bafb46662eb43
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:16Z
date_updated: 2020-07-14T12:45:40Z
file_id: '4739'
file_name: IST-2018-939-v1+1_2010_Kupczok_Accuracy_of.pdf
file_size: 723929
relation: main_file
file_date_updated: 2020-07-14T12:45:40Z
fulldoi: https://doi.org/10.1186/1748-7188-5-37
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Algorithms for Molecular Biology
publication_status: published
publisher: BioMed Central
publist_id: '4517'
pubrep_id: '939'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Accuracy of phylogeny reconstruction methods combining overlapping gene data
sets
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5
year: '2010'
...
---
_id: '12199'
abstract:
- lang: eng
text: The four microsporangia of the flowering plant anther develop from archesporial
cells in the L2 of the primordium. Within each microsporangium, developing microsporocytes
are surrounded by concentric monolayers of tapetal, middle layer and endothecial
cells. How this intricate array of tissues, each containing relatively few cells,
is established in an organ possessing no formal meristems is poorly understood.
We describe here the pivotal role of the LRR receptor kinase EXCESS MICROSPOROCYTES
1 (EMS1) in forming the monolayer of tapetal nurse cells in Arabidopsis. Unusually
for plants, tapetal cells are specified very early in development, and are subsequently
stimulated to proliferate by a receptor-like kinase (RLK) complex that includes
EMS1. Mutations in members of this EMS1 signalling complex and its putative ligand
result in male-sterile plants in which tapetal initials fail to proliferate. Surprisingly,
these cells continue to develop, isolated at the locular periphery. Mutant and
wild-type microsporangia expand at similar rates and the ‘tapetal’ space at the
periphery of mutant locules becomes occupied by microsporocytes. However, induction
of late expression of EMS1 in the few tapetal initials in ems1 plants results
in their proliferation to generate a functional tapetum, and this proliferation
suppresses microsporocyte number. Our experiments also show that integrity of
the tapetal monolayer is crucial for the maintenance of the polarity of divisions
within it. This unexpected autonomy of the tapetal ‘lineage’ is discussed in the
context of tissue development in complex plant organs, where constancy in size,
shape and cell number is crucial.
acknowledgement: 'We thank the following for providing mutant lines and reagents:
Hong Ma, De Ye, Sacco De Vries, and Rod Scott for providing the pA9::Barnase lines
and information on A9 expression patterns. Carla Galinha and Paolo Piazza gave valuable
help with in situ hybridisation and qRT-PCR, respectively, and we acknowledge Qing
Zhang, Helen Prescott and Matthew Dicks for providing excellent technical assistance.
We are indebted to Miltos Tsiantis and Angela Hay for helpful discussion, and the
research was funded by Oxford University through a Clarendon Scholarship to X.F.,
with additional financial support from Magdalen College (Oxford).'
article_processing_charge: No
article_type: original
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Hugh G.
full_name: Dickinson, Hugh G.
last_name: Dickinson
citation:
ama: Feng X, Dickinson HG. Tapetal cell fate, lineage and proliferation in the Arabidopsis
anther. Development. 2010;137(14):2409-2416. doi:10.1242/dev.049320
apa: Feng, X., & Dickinson, H. G. (2010). Tapetal cell fate, lineage and proliferation
in the Arabidopsis anther. Development. The Company of Biologists. https://doi.org/10.1242/dev.049320
chicago: Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation
in the Arabidopsis Anther.” Development. The Company of Biologists, 2010.
https://doi.org/10.1242/dev.049320.
ieee: X. Feng and H. G. Dickinson, “Tapetal cell fate, lineage and proliferation
in the Arabidopsis anther,” Development, vol. 137, no. 14. The Company
of Biologists, pp. 2409–2416, 2010.
ista: Feng X, Dickinson HG. 2010. Tapetal cell fate, lineage and proliferation in
the Arabidopsis anther. Development. 137(14), 2409–2416.
mla: Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation
in the Arabidopsis Anther.” Development, vol. 137, no. 14, The Company
of Biologists, 2010, pp. 2409–16, doi:10.1242/dev.049320.
short: X. Feng, H.G. Dickinson, Development 137 (2010) 2409–2416.
date_created: 2023-01-16T09:21:54Z
date_published: 2010-07-15T00:00:00Z
date_updated: 2023-05-08T10:57:11Z
day: '15'
department:
- _id: XiFe
doi: 10.1242/dev.049320
extern: '1'
external_id:
pmid:
- '20570940'
fulldoi: https://doi.org/10.1242/dev.049320
intvolume: ' 137'
issue: '14'
keyword:
- Developmental Biology
- Molecular Biology
- Anther Tapetum
- Arabidopsis
- Cell Fate Establishment
- EMS1
- Reproductive Cell Lineage
language:
- iso: eng
month: '07'
oa_version: None
page: 2409-2416
pmid: 1
publication: Development
publication_identifier:
issn:
- 1477-9129
- 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tapetal cell fate, lineage and proliferation in the Arabidopsis anther
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 137
year: '2010'
...
---
_id: '12200'
abstract:
- lang: eng
text: Key steps in the evolution of the angiosperm anther include the patterning
of the concentrically organized microsporangium and the incorporation of four
such microsporangia into a leaf-like structure. Mutant studies in the model plant
Arabidopsis thaliana are leading to an increasingly accurate picture of (i) the
cell lineages culminating in the different cell types present in the microsporangium
(the microsporocytes, the tapetum, and the middle and endothecial layers), and
(ii) some of the genes responsible for specifying their fates. However, the processes
that confer polarity on the developing anther and position the microsporangia
within it remain unclear. Certainly, data from a range of experimental strategies
suggest that hormones play a central role in establishing polarity and the patterning
of the anther initial, and may be responsible for locating the microsporangia.
But the fact that microsporangia were originally positioned externally suggests
that their development is likely to be autonomous, perhaps with the reproductive
cells generating signals controlling the growth and division of the investing
anther epidermis. These possibilities are discussed in the context of the expression
of genes which initiate and maintain male and female reproductive development,
and in the perspective of our current views of anther evolution.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Hugh G.
full_name: Dickinson, Hugh G.
last_name: Dickinson
citation:
ama: Feng X, Dickinson HG. Cell–cell interactions during patterning of the Arabidopsis
anther. Biochemical Society Transactions. 2010;38(2):571-576. doi:10.1042/bst0380571
apa: Feng, X., & Dickinson, H. G. (2010). Cell–cell interactions during patterning
of the Arabidopsis anther. Biochemical Society Transactions. Portland
Press Ltd. https://doi.org/10.1042/bst0380571
chicago: Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning
of the Arabidopsis Anther.” Biochemical Society Transactions. Portland
Press Ltd., 2010. https://doi.org/10.1042/bst0380571.
ieee: X. Feng and H. G. Dickinson, “Cell–cell interactions during patterning of
the Arabidopsis anther,” Biochemical Society Transactions, vol.
38, no. 2. Portland Press Ltd., pp. 571–576, 2010.
ista: Feng X, Dickinson HG. 2010. Cell–cell interactions during patterning of the
Arabidopsis anther. Biochemical Society Transactions. 38(2), 571–576.
mla: Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning
of the Arabidopsis Anther.” Biochemical Society Transactions, vol.
38, no. 2, Portland Press Ltd., 2010, pp. 571–76, doi:10.1042/bst0380571.
short: X. Feng, H.G. Dickinson, Biochemical Society Transactions 38 (2010) 571–576.
date_created: 2023-01-16T09:22:18Z
date_published: 2010-03-22T00:00:00Z
date_updated: 2023-05-08T10:57:59Z
day: '22'
department:
- _id: XiFe
doi: 10.1042/bst0380571
extern: '1'
external_id:
pmid:
- '20298223'
fulldoi: https://doi.org/10.1042/bst0380571
intvolume: ' 38'
issue: '2'
keyword:
- Biochemistry
- Anther Development
- Arabidopsis
- Cell Fate
- Microsporangium
- Polarity
- Receptor Kinase
language:
- iso: eng
month: '03'
oa_version: None
page: 571-576
pmid: 1
publication: Biochemical Society Transactions
publication_identifier:
issn:
- 0300-5127
- 1470-8752
publication_status: published
publisher: Portland Press Ltd.
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell–cell interactions during patterning of the Arabidopsis anther
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2010'
...
---
_id: '14983'
abstract:
- lang: eng
text: 'This chapter tackles a difficult challenge: presenting signal processing
material to non-experts. This chapter is meant to be comprehensible to people
who have some math background, including a course in linear algebra and basic
statistics, but do not specialize in mathematics, engineering, or related fields.
Some formulas assume the reader is familiar with matrices and basic matrix operations,
but not more advanced material. Furthermore, we tried to make the chapter readable
even if you skip the formulas. Nevertheless, we include some simple methods to
demonstrate the basics of adaptive data processing, then we proceed with some
advanced methods that are fundamental in adaptive signal processing, and are likely
to be useful in a variety of applications. The advanced algorithms are also online
available [30]. In the second part, these techniques are applied to some real-world
BCI data.'
acknowledgement: This work was supported by the EU grants “BrainCom” (FP6-2004-Mobility-5
Grant No 024259) and “Multi-adaptive BCI” (MEIF-CT-2006 Grant No 040666). Furthermore,
we thank Matthias Krauledat for fruitful discussions and tools for generating Fig.
5.
alternative_title:
- The Frontiers Collection
article_processing_charge: No
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Carmen
full_name: Vidaurre, Carmen
last_name: Vidaurre
- first_name: Klaus-Robert
full_name: Müller, Klaus-Robert
last_name: Müller
citation:
ama: 'Schlögl A, Vidaurre C, Müller K-R. Adaptive Methods in BCI Research - An Introductory
Tutorial. In: Graimann B, Pfurtscheller G, Allison B, eds. Brain-Computer Interfaces.
1st ed. FRONTCOLL. Berlin, Heidelberg: Springer; 2010:331-355. doi:10.1007/978-3-642-02091-9_18'
apa: 'Schlögl, A., Vidaurre, C., & Müller, K.-R. (2010). Adaptive Methods in
BCI Research - An Introductory Tutorial. In B. Graimann, G. Pfurtscheller, &
B. Allison (Eds.), Brain-Computer Interfaces (1st ed., pp. 331–355). Berlin,
Heidelberg: Springer. https://doi.org/10.1007/978-3-642-02091-9_18'
chicago: 'Schlögl, Alois, Carmen Vidaurre, and Klaus-Robert Müller. “Adaptive Methods
in BCI Research - An Introductory Tutorial.” In Brain-Computer Interfaces,
edited by Bernhard Graimann, Gert Pfurtscheller, and Brendan Allison, 1st ed.,
331–55. FRONTCOLL. Berlin, Heidelberg: Springer, 2010. https://doi.org/10.1007/978-3-642-02091-9_18.'
ieee: 'A. Schlögl, C. Vidaurre, and K.-R. Müller, “Adaptive Methods in BCI Research
- An Introductory Tutorial,” in Brain-Computer Interfaces, 1st ed., B.
Graimann, G. Pfurtscheller, and B. Allison, Eds. Berlin, Heidelberg: Springer,
2010, pp. 331–355.'
ista: 'Schlögl A, Vidaurre C, Müller K-R. 2010.Adaptive Methods in BCI Research
- An Introductory Tutorial. In: Brain-Computer Interfaces. The Frontiers Collection,
, 331–355.'
mla: Schlögl, Alois, et al. “Adaptive Methods in BCI Research - An Introductory
Tutorial.” Brain-Computer Interfaces, edited by Bernhard Graimann et al.,
1st ed., Springer, 2010, pp. 331–55, doi:10.1007/978-3-642-02091-9_18.
short: A. Schlögl, C. Vidaurre, K.-R. Müller, in:, B. Graimann, G. Pfurtscheller,
B. Allison (Eds.), Brain-Computer Interfaces, 1st ed., Springer, Berlin, Heidelberg,
2010, pp. 331–355.
corr_author: '1'
date_created: 2024-02-14T09:56:00Z
date_published: 2010-09-06T00:00:00Z
date_updated: 2024-10-21T06:03:06Z
day: '06'
department:
- _id: ScienComp
doi: 10.1007/978-3-642-02091-9_18
edition: '1'
editor:
- first_name: Bernhard
full_name: Graimann, Bernhard
last_name: Graimann
- first_name: Gert
full_name: Pfurtscheller, Gert
last_name: Pfurtscheller
- first_name: Brendan
full_name: Allison, Brendan
last_name: Allison
fulldoi: https://doi.org/10.1007/978-3-642-02091-9_18
language:
- iso: eng
month: '09'
oa_version: None
page: 331-355
place: Berlin, Heidelberg
publication: Brain-Computer Interfaces
publication_identifier:
eisbn:
- '9783642020919'
isbn:
- '9783642020902'
issn:
- 1612-3018
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
series_title: FRONTCOLL
status: public
title: Adaptive Methods in BCI Research - An Introductory Tutorial
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '4361'
abstract:
- lang: eng
text: Depth-bounded processes form the most expressive known fragment of the π-calculus
for which interesting verification problems are still decidable. In this paper
we develop an adequate domain of limits for the well-structured transition systems
that are induced by depth-bounded processes. An immediate consequence of our result
is that there exists a forward algorithm that decides the covering problem for
this class. Unlike backward algorithms, the forward algorithm terminates even
if the depth of the process is not known a priori. More importantly, our result
suggests a whole spectrum of forward algorithms that enable the effective verification
of a large class of mobile systems.
alternative_title:
- LNCS
author:
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Wies T, Zufferey D, Henzinger TA. Forward analysis of depth-bounded processes.
In: Ong L, ed. Vol 6014. Springer; 2010:94-108. doi:10.1007/978-3-642-12032-9_8'
apa: 'Wies, T., Zufferey, D., & Henzinger, T. A. (2010). Forward analysis of
depth-bounded processes. In L. Ong (Ed.) (Vol. 6014, pp. 94–108). Presented at
the FoSSaCS: Foundations of Software Science and Computation Structures, Paphos,
Cyprus: Springer. https://doi.org/10.1007/978-3-642-12032-9_8'
chicago: Wies, Thomas, Damien Zufferey, and Thomas A Henzinger. “Forward Analysis
of Depth-Bounded Processes.” edited by Luke Ong, 6014:94–108. Springer, 2010.
https://doi.org/10.1007/978-3-642-12032-9_8.
ieee: 'T. Wies, D. Zufferey, and T. A. Henzinger, “Forward analysis of depth-bounded
processes,” presented at the FoSSaCS: Foundations of Software Science and Computation
Structures, Paphos, Cyprus, 2010, vol. 6014, pp. 94–108.'
ista: 'Wies T, Zufferey D, Henzinger TA. 2010. Forward analysis of depth-bounded
processes. FoSSaCS: Foundations of Software Science and Computation Structures,
LNCS, vol. 6014, 94–108.'
mla: Wies, Thomas, et al. Forward Analysis of Depth-Bounded Processes. Edited
by Luke Ong, vol. 6014, Springer, 2010, pp. 94–108, doi:10.1007/978-3-642-12032-9_8.
short: T. Wies, D. Zufferey, T.A. Henzinger, in:, L. Ong (Ed.), Springer, 2010,
pp. 94–108.
conference:
end_date: 2010-03-28
location: Paphos, Cyprus
name: 'FoSSaCS: Foundations of Software Science and Computation Structures'
start_date: 2010-03-20
corr_author: '1'
date_created: 2018-12-11T12:08:27Z
date_published: 2010-03-01T00:00:00Z
date_updated: 2026-04-09T14:35:23Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1007/978-3-642-12032-9_8
editor:
- first_name: Luke
full_name: Ong, Luke
last_name: Ong
file:
- access_level: open_access
checksum: 3e610de84937d821316362658239134a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:17Z
date_updated: 2020-07-14T12:46:27Z
file_id: '4677'
file_name: IST-2012-50-v1+1_Forward_analysis_of_depth-bounded_processes.pdf
file_size: 240766
relation: main_file
file_date_updated: 2020-07-14T12:46:27Z
fulldoi: https://doi.org/10.1007/978-3-642-12032-9_8
has_accepted_license: '1'
intvolume: ' 6014'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 94 - 108
publication_status: published
publisher: Springer
publist_id: '1099'
pubrep_id: '50'
quality_controlled: '1'
related_material:
record:
- id: '1405'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Forward analysis of depth-bounded processes
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6014
year: '2010'
...
---
_id: '4362'
abstract:
- lang: eng
text: Software transactional memories (STMs) promise simple and efficient concurrent
programming. Several correctness properties have been proposed for STMs. Based
on a bounded conflict graph algorithm for verifying correctness of STMs, we develop
TRACER, a tool for runtime verification of STM implementations. The novelty of
TRACER lies in the way it combines coarse and precise runtime analyses to guarantee
sound and complete verification in an efficient manner. We implement TRACER in
the TL2 STM implementation. We evaluate the performance of TRACER on STAMP benchmarks.
While a precise runtime verification technique based on conflict graphs results
in an average slowdown of 60x, the two-level approach of TRACER performs complete
verification with an average slowdown of around 25x across different benchmarks.
alternative_title:
- LNCS
author:
- first_name: Vasu
full_name: Singh, Vasu
id: 4DAE2708-F248-11E8-B48F-1D18A9856A87
last_name: Singh
citation:
ama: 'Singh V. Runtime verification for software transactional memories. In: Sokolsky
O, Rosu G, Tilmann N, et al., eds. Vol 6418. Springer; 2010:421-435. doi:10.1007/978-3-642-16612-9_32'
apa: 'Singh, V. (2010). Runtime verification for software transactional memories.
In O. Sokolsky, G. Rosu, N. Tilmann, H. Barringer, Y. Falcone, B. Finkbeiner,
… G. Pace (Eds.) (Vol. 6418, pp. 421–435). Presented at the RV: International
Conference on Runtime Verification, St. Julians, Malta: Springer. https://doi.org/10.1007/978-3-642-16612-9_32'
chicago: Singh, Vasu. “Runtime Verification for Software Transactional Memories.”
edited by Oleg Sokolsky, Grigore Rosu, Nikolai Tilmann, Howard Barringer, Ylies
Falcone, Bernd Finkbeiner, Klaus Havelund, Insup Lee, and Gordon Pace, 6418:421–35.
Springer, 2010. https://doi.org/10.1007/978-3-642-16612-9_32.
ieee: 'V. Singh, “Runtime verification for software transactional memories,” presented
at the RV: International Conference on Runtime Verification, St. Julians, Malta,
2010, vol. 6418, pp. 421–435.'
ista: 'Singh V. 2010. Runtime verification for software transactional memories.
RV: International Conference on Runtime Verification, LNCS, vol. 6418, 421–435.'
mla: Singh, Vasu. Runtime Verification for Software Transactional Memories.
Edited by Oleg Sokolsky et al., vol. 6418, Springer, 2010, pp. 421–35, doi:10.1007/978-3-642-16612-9_32.
short: V. Singh, in:, O. Sokolsky, G. Rosu, N. Tilmann, H. Barringer, Y. Falcone,
B. Finkbeiner, K. Havelund, I. Lee, G. Pace (Eds.), Springer, 2010, pp. 421–435.
conference:
end_date: 2010-11-04
location: St. Julians, Malta
name: 'RV: International Conference on Runtime Verification'
start_date: 2010-11-01
corr_author: '1'
date_created: 2018-12-11T12:08:28Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2024-10-09T20:54:01Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-642-16612-9_32
editor:
- first_name: Oleg
full_name: Sokolsky, Oleg
last_name: Sokolsky
- first_name: Grigore
full_name: Rosu, Grigore
last_name: Rosu
- first_name: Nikolai
full_name: Tilmann, Nikolai
last_name: Tilmann
- first_name: Howard
full_name: Barringer, Howard
last_name: Barringer
- first_name: Ylies
full_name: Falcone, Ylies
last_name: Falcone
- first_name: Bernd
full_name: Finkbeiner, Bernd
last_name: Finkbeiner
- first_name: Klaus
full_name: Havelund, Klaus
last_name: Havelund
- first_name: Insup
full_name: Lee, Insup
last_name: Lee
- first_name: Gordon
full_name: Pace, Gordon
last_name: Pace
fulldoi: https://doi.org/10.1007/978-3-642-16612-9_32
intvolume: ' 6418'
language:
- iso: eng
month: '01'
oa_version: None
page: 421 - 435
publication_status: published
publisher: Springer
publist_id: '1096'
quality_controlled: '1'
scopus_import: 1
status: public
title: Runtime verification for software transactional memories
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6418
year: '2010'
...
---
_id: '4369'
abstract:
- lang: eng
text: In this paper we propose a novel technique for constructing timed automata
from properties expressed in the logic mtl, under bounded-variability assumptions.
We handle full mtl and include all future operators. Our construction is based
on separation of the continuous time monitoring of the input sequence and discrete
predictions regarding the future. The separation of the continuous from the discrete
allows us to determinize our automata in an exponential construction that does
not increase the number of clocks. This leads to a doubly exponential construction
from mtl to deterministic timed automata, compared with triply exponential using
existing approaches. We offer an alternative to the existing approach to linear
real-time model checking, which has never been implemented. It further offers
a unified framework for model checking, runtime monitoring, and synthesis, in
an approach that can reuse tools, implementations, and insights from the discrete
setting.
alternative_title:
- LNCS
author:
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Nir
full_name: Piterman, Nir
last_name: Piterman
citation:
ama: 'Nickovic D, Piterman N. From MTL to deterministic timed automata. In: Henzinger
TA, Chatterjee K, eds. Vol 6246. Springer; 2010:152-167. doi:10.1007/978-3-642-15297-9_13'
apa: 'Nickovic, D., & Piterman, N. (2010). From MTL to deterministic timed automata.
In T. A. Henzinger & K. Chatterjee (Eds.) (Vol. 6246, pp. 152–167). Presented
at the FORMATS: Formal Modeling and Analysis of Timed Systems, Klosterneuburg,
Austria: Springer. https://doi.org/10.1007/978-3-642-15297-9_13'
chicago: Nickovic, Dejan, and Nir Piterman. “From MTL to Deterministic Timed Automata.”
edited by Thomas A. Henzinger and Krishnendu Chatterjee, 6246:152–67. Springer,
2010. https://doi.org/10.1007/978-3-642-15297-9_13.
ieee: 'D. Nickovic and N. Piterman, “From MTL to deterministic timed automata,”
presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Klosterneuburg,
Austria, 2010, vol. 6246, pp. 152–167.'
ista: 'Nickovic D, Piterman N. 2010. From MTL to deterministic timed automata. FORMATS:
Formal Modeling and Analysis of Timed Systems, LNCS, vol. 6246, 152–167.'
mla: Nickovic, Dejan, and Nir Piterman. From MTL to Deterministic Timed Automata.
Edited by Thomas A. Henzinger and Krishnendu Chatterjee, vol. 6246, Springer,
2010, pp. 152–67, doi:10.1007/978-3-642-15297-9_13.
short: D. Nickovic, N. Piterman, in:, T.A. Henzinger, K. Chatterjee (Eds.), Springer,
2010, pp. 152–167.
conference:
end_date: 2010-09-10
location: Klosterneuburg, Austria
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
start_date: 2010-09-08
corr_author: '1'
date_created: 2018-12-11T12:08:30Z
date_published: 2010-09-08T00:00:00Z
date_updated: 2024-10-09T20:54:01Z
day: '08'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1007/978-3-642-15297-9_13
ec_funded: 1
editor:
- first_name: Thomas A.
full_name: Henzinger, Thomas A.
last_name: Henzinger
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
last_name: Chatterjee
file:
- access_level: open_access
checksum: b0ca5f5fbe8a3d20ccbc6f51a344a459
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:43Z
date_updated: 2020-07-14T12:46:27Z
file_id: '5028'
file_name: IST-2012-49-v1+1_From_MTL_to_deterministic_timed_automata.pdf
file_size: 249789
relation: main_file
file_date_updated: 2020-07-14T12:46:27Z
fulldoi: https://doi.org/10.1007/978-3-642-15297-9_13
has_accepted_license: '1'
intvolume: ' 6246'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 152 - 167
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
publication_status: published
publisher: Springer
publist_id: '1090'
pubrep_id: '49'
quality_controlled: '1'
scopus_import: 1
status: public
title: From MTL to deterministic timed automata
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6246
year: '2010'
...
---
_id: '4378'
abstract:
- lang: eng
text: 'Techniques such as verification condition generation, predicate abstraction,
and expressive type systems reduce software verification to proving formulas in
expressive logics. Programs and their specifications often make use of data structures
such as sets, multisets, algebraic data types, or graphs. Consequently, formulas
generated from verification also involve such data structures. To automate the
proofs of such formulas we propose a logic (a “calculus”) of such data structures.
We build the calculus by starting from decidable logics of individual data structures,
and connecting them through functions and sets, in ways that go beyond the frameworks
such as Nelson-Oppen. The result are new decidable logics that can simultaneously
specify properties of different kinds of data structures and overcome the limitations
of the individual logics. Several of our decidable logics include abstraction
functions that map a data structure into its more abstract view (a tree into a
multiset, a multiset into a set), into a numerical quantity (the size or the height),
or into the truth value of a candidate data structure invariant (sortedness, or
the heap property). For algebraic data types, we identify an asymptotic many-to-one
condition on the abstraction function that guarantees the existence of a decision
procedure. In addition to the combination based on abstraction functions, we can
combine multiple data structure theories if they all reduce to the same data structure
logic. As an instance of this approach, we describe a decidable logic whose formulas
are propositional combinations of formulas in: weak monadic second-order logic
of two successors, two-variable logic with counting, multiset algebra with Presburger
arithmetic, the Bernays-Schönfinkel-Ramsey class of first-order logic, and the
logic of algebraic data types with the set content function. The subformulas in
this combination can share common variables that refer to sets of objects along
with the common set algebra operations. Such sound and complete combination is
possible because the relations on sets definable in the component logics are all
expressible in Boolean Algebra with Presburger Arithmetic. Presburger arithmetic
and its new extensions play an important role in our decidability results. In
several cases, when we combine logics that belong to NP, we can prove the satisfiability
for the combined logic is still in NP.'
alternative_title:
- LNCS
author:
- first_name: Viktor
full_name: Kuncak, Viktor
last_name: Kuncak
- first_name: Ruzica
full_name: Piskac, Ruzica
last_name: Piskac
- first_name: Philippe
full_name: Suter, Philippe
last_name: Suter
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
citation:
ama: 'Kuncak V, Piskac R, Suter P, Wies T. Building a calculus of data structures.
In: Barthe G, Hermenegildo M, eds. Vol 5944. Springer; 2010:26-44. doi:10.1007/978-3-642-11319-2_6'
apa: 'Kuncak, V., Piskac, R., Suter, P., & Wies, T. (2010). Building a calculus
of data structures. In G. Barthe & M. Hermenegildo (Eds.) (Vol. 5944, pp.
26–44). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation,
Madrid, Spain: Springer. https://doi.org/10.1007/978-3-642-11319-2_6'
chicago: Kuncak, Viktor, Ruzica Piskac, Philippe Suter, and Thomas Wies. “Building
a Calculus of Data Structures.” edited by Gilles Barthe and Manuel Hermenegildo,
5944:26–44. Springer, 2010. https://doi.org/10.1007/978-3-642-11319-2_6.
ieee: 'V. Kuncak, R. Piskac, P. Suter, and T. Wies, “Building a calculus of data
structures,” presented at the VMCAI: Verification, Model Checking and Abstract
Interpretation, Madrid, Spain, 2010, vol. 5944, pp. 26–44.'
ista: 'Kuncak V, Piskac R, Suter P, Wies T. 2010. Building a calculus of data structures.
VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 5944,
26–44.'
mla: Kuncak, Viktor, et al. Building a Calculus of Data Structures. Edited
by Gilles Barthe and Manuel Hermenegildo, vol. 5944, Springer, 2010, pp. 26–44,
doi:10.1007/978-3-642-11319-2_6.
short: V. Kuncak, R. Piskac, P. Suter, T. Wies, in:, G. Barthe, M. Hermenegildo
(Eds.), Springer, 2010, pp. 26–44.
conference:
end_date: 2010-01-19
location: Madrid, Spain
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2010-01-17
date_created: 2018-12-11T12:08:33Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:31Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-642-11319-2_6
editor:
- first_name: Gilles
full_name: Barthe, Gilles
last_name: Barthe
- first_name: Manuel
full_name: Hermenegildo, Manuel
last_name: Hermenegildo
fulldoi: https://doi.org/10.1007/978-3-642-11319-2_6
intvolume: ' 5944'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://infoscience.epfl.ch/record/161290/
month: '01'
oa: 1
oa_version: Submitted Version
page: 26 - 44
publication_status: published
publisher: Springer
publist_id: '1081'
quality_controlled: '1'
scopus_import: 1
status: public
title: Building a calculus of data structures
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 5944
year: '2010'
...
---
_id: '4380'
abstract:
- lang: eng
text: Cloud computing is an emerging paradigm aimed to offer users pay-per-use computing
resources, while leaving the burden of managing the computing infrastructure to
the cloud provider. We present a new programming and pricing model that gives
the cloud user the flexibility of trading execution speed and price on a per-job
basis. We discuss the scheduling and resource management challenges for the cloud
provider that arise in the implementation of this model. We argue that techniques
from real-time and embedded software can be useful in this context.
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: Anmol
full_name: Tomar, Anmol
id: 3D8D36B6-F248-11E8-B48F-1D18A9856A87
last_name: Tomar
- 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, Tomar A, Singh V, Wies T, Zufferey D. A marketplace for cloud
resources. In: ACM; 2010:1-8. doi:10.1145/1879021.1879022'
apa: 'Henzinger, T. A., Tomar, A., Singh, V., Wies, T., & Zufferey, D. (2010).
A marketplace for cloud resources (pp. 1–8). Presented at the EMSOFT: Embedded
Software , Arizona, USA: ACM. https://doi.org/10.1145/1879021.1879022'
chicago: Henzinger, Thomas A, Anmol Tomar, Vasu Singh, Thomas Wies, and Damien Zufferey.
“A Marketplace for Cloud Resources,” 1–8. ACM, 2010. https://doi.org/10.1145/1879021.1879022.
ieee: 'T. A. Henzinger, A. Tomar, V. Singh, T. Wies, and D. Zufferey, “A marketplace
for cloud resources,” presented at the EMSOFT: Embedded Software , Arizona, USA,
2010, pp. 1–8.'
ista: 'Henzinger TA, Tomar A, Singh V, Wies T, Zufferey D. 2010. A marketplace for
cloud resources. EMSOFT: Embedded Software , 1–8.'
mla: Henzinger, Thomas A., et al. A Marketplace for Cloud Resources. ACM,
2010, pp. 1–8, doi:10.1145/1879021.1879022.
short: T.A. Henzinger, A. Tomar, V. Singh, T. Wies, D. Zufferey, in:, ACM, 2010,
pp. 1–8.
conference:
end_date: 2010-10-29
location: Arizona, USA
name: 'EMSOFT: Embedded Software '
start_date: 2010-10-24
corr_author: '1'
date_created: 2018-12-11T12:08:33Z
date_published: 2010-10-24T00:00:00Z
date_updated: 2024-10-09T20:54:01Z
day: '24'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1145/1879021.1879022
file:
- access_level: open_access
checksum: 7680dd24016810710f7c977bc94f85e9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:42Z
date_updated: 2020-07-14T12:46:28Z
file_id: '4767'
file_name: IST-2012-48-v1+1_A_marketplace_for_cloud_resources.pdf
file_size: 222626
relation: main_file
file_date_updated: 2020-07-14T12:46:28Z
fulldoi: https://doi.org/10.1145/1879021.1879022
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 1 - 8
publication_status: published
publisher: ACM
publist_id: '1078'
pubrep_id: '48'
quality_controlled: '1'
scopus_import: 1
status: public
title: A marketplace for cloud resources
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '4381'
abstract:
- lang: eng
text: Cloud computing aims to give users virtually unlimited pay-per-use computing
resources without the burden of managing the underlying infrastructure. We claim
that, in order to realize the full potential of cloud computing, the user must
be presented with a pricing model that offers flexibility at the requirements
level, such as a choice between different degrees of execution speed and the cloud
provider must be presented with a programming model that offers flexibility at
the execution level, such as a choice between different scheduling policies. In
such a flexible framework, with each job, the user purchases a virtual computer
with the desired speed and cost characteristics, and the cloud provider can optimize
the utilization of resources across a stream of jobs from different users. We
designed a flexible framework to test our hypothesis, which is called FlexPRICE
(Flexible Provisioning of Resources in a Cloud Environment) and works as follows.
A user presents a job to the cloud. The cloud finds different schedules to execute
the job and presents a set of quotes to the user in terms of price and duration
for the execution. The user then chooses a particular quote and the cloud is obliged
to execute the job according to the chosen quote. FlexPRICE thus hides the complexity
of the actual scheduling decisions from the user, but still provides enough flexibility
to meet the users actual demands. We implemented FlexPRICE in a simulator called
PRICES that allows us to experiment with our framework. We observe that FlexPRICE
provides a wide range of execution options-from fast and expensive to slow and
cheap-- for the whole spectrum of data-intensive and computation-intensive jobs.
We also observe that the set of quotes computed by FlexPRICE do not vary as the
number of simultaneous jobs increases.
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: Anmol
full_name: Tomar, Anmol
id: 3D8D36B6-F248-11E8-B48F-1D18A9856A87
last_name: Tomar
- 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, Tomar A, Singh V, Wies T, Zufferey D. FlexPRICE: Flexible provisioning
of resources in a cloud environment. In: IEEE; 2010:83-90. doi:10.1109/CLOUD.2010.71'
apa: 'Henzinger, T. A., Tomar, A., Singh, V., Wies, T., & Zufferey, D. (2010).
FlexPRICE: Flexible provisioning of resources in a cloud environment (pp. 83–90).
Presented at the CLOUD: Cloud Computing, Miami, USA: IEEE. https://doi.org/10.1109/CLOUD.2010.71'
chicago: 'Henzinger, Thomas A, Anmol Tomar, Vasu Singh, Thomas Wies, and Damien
Zufferey. “FlexPRICE: Flexible Provisioning of Resources in a Cloud Environment,”
83–90. IEEE, 2010. https://doi.org/10.1109/CLOUD.2010.71.'
ieee: 'T. A. Henzinger, A. Tomar, V. Singh, T. Wies, and D. Zufferey, “FlexPRICE:
Flexible provisioning of resources in a cloud environment,” presented at the CLOUD:
Cloud Computing, Miami, USA, 2010, pp. 83–90.'
ista: 'Henzinger TA, Tomar A, Singh V, Wies T, Zufferey D. 2010. FlexPRICE: Flexible
provisioning of resources in a cloud environment. CLOUD: Cloud Computing, 83–90.'
mla: 'Henzinger, Thomas A., et al. FlexPRICE: Flexible Provisioning of Resources
in a Cloud Environment. IEEE, 2010, pp. 83–90, doi:10.1109/CLOUD.2010.71.'
short: T.A. Henzinger, A. Tomar, V. Singh, T. Wies, D. Zufferey, in:, IEEE, 2010,
pp. 83–90.
conference:
end_date: 2010-07-10
location: Miami, USA
name: 'CLOUD: Cloud Computing'
start_date: 2010-07-05
corr_author: '1'
date_created: 2018-12-11T12:08:33Z
date_published: 2010-08-26T00:00:00Z
date_updated: 2024-10-09T20:54:00Z
day: '26'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1109/CLOUD.2010.71
file:
- access_level: open_access
checksum: 98e534675339a8e2beca08890d048145
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:03Z
date_updated: 2020-07-14T12:46:28Z
file_id: '5188'
file_name: IST-2012-47-v1+1_FlexPRICE-_Flexible_provisioning_of_resources_in_a_cloud_environment.pdf
file_size: 467436
relation: main_file
file_date_updated: 2020-07-14T12:46:28Z
fulldoi: https://doi.org/10.1109/CLOUD.2010.71
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 83 - 90
publication_status: published
publisher: IEEE
publist_id: '1077'
pubrep_id: '47'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'FlexPRICE: Flexible provisioning of resources in a cloud environment'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '4382'
abstract:
- lang: eng
text: 'Transactional memory (TM) has shown potential to simplify the task of writing
concurrent programs. Inspired by classical work on databases, formal definitions
of the semantics of TM executions have been proposed. Many of these definitions
assumed that accesses to shared data are solely performed through transactions.
In practice, due to legacy code and concurrency libraries, transactions in a TM
have to share data with non-transactional operations. The semantics of such interaction,
while widely discussed by practitioners, lacks a clear formal specification. Those
interactions can vary, sometimes in subtle ways, between TM implementations and
underlying memory models. We propose a correctness condition for TMs, parametrized
opacity, to formally capture the now folklore notion of strong atomicity by stipulating
the two following intuitive requirements: first, every transaction appears as
if it is executed instantaneously with respect to other transactions and non-transactional
operations, and second, non-transactional operations conform to the given underlying
memory model. We investigate the inherent cost of implementing parametrized opacity.
We first prove that parametrized opacity requires either instrumenting non-transactional
operations (for most memory models) or writing to memory by transactions using
potentially expensive read-modify-write instructions (such as compare-and-swap).
Then, we show that for a class of practical relaxed memory models, parametrized
opacity can indeed be implemented with constant-time instrumentation of non-transactional
writes and no instrumentation of non-transactional reads. We show that, in practice,
parametrizing the notion of correctness allows developing more efficient TM implementations.'
author:
- first_name: Rachid
full_name: Guerraoui, Rachid
last_name: Guerraoui
- 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: Michal
full_name: Kapalka, Michal
last_name: Kapalka
- first_name: Vasu
full_name: Singh, Vasu
id: 4DAE2708-F248-11E8-B48F-1D18A9856A87
last_name: Singh
citation:
ama: 'Guerraoui R, Henzinger TA, Kapalka M, Singh V. Transactions in the jungle.
In: ACM; 2010:263-272. doi:10.1145/1810479.1810529'
apa: 'Guerraoui, R., Henzinger, T. A., Kapalka, M., & Singh, V. (2010). Transactions
in the jungle (pp. 263–272). Presented at the SPAA: ACM Symposium on Parallel
Algorithms and Architectures, Santorini, Greece: ACM. https://doi.org/10.1145/1810479.1810529'
chicago: Guerraoui, Rachid, Thomas A Henzinger, Michal Kapalka, and Vasu Singh.
“Transactions in the Jungle,” 263–72. ACM, 2010. https://doi.org/10.1145/1810479.1810529.
ieee: 'R. Guerraoui, T. A. Henzinger, M. Kapalka, and V. Singh, “Transactions in
the jungle,” presented at the SPAA: ACM Symposium on Parallel Algorithms and Architectures,
Santorini, Greece, 2010, pp. 263–272.'
ista: 'Guerraoui R, Henzinger TA, Kapalka M, Singh V. 2010. Transactions in the
jungle. SPAA: ACM Symposium on Parallel Algorithms and Architectures, 263–272.'
mla: Guerraoui, Rachid, et al. Transactions in the Jungle. ACM, 2010, pp.
263–72, doi:10.1145/1810479.1810529.
short: R. Guerraoui, T.A. Henzinger, M. Kapalka, V. Singh, in:, ACM, 2010, pp. 263–272.
conference:
end_date: 2010-06-15
location: Santorini, Greece
name: 'SPAA: ACM Symposium on Parallel Algorithms and Architectures'
start_date: 2010-06-13
date_created: 2018-12-11T12:08:34Z
date_published: 2010-06-13T00:00:00Z
date_updated: 2024-10-21T06:03:05Z
day: '13'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1145/1810479.1810529
file:
- access_level: open_access
checksum: f2ad6c00a6304da34bf21bcdcfd36c4b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:28Z
date_updated: 2020-07-14T12:46:28Z
file_id: '5080'
file_name: IST-2012-46-v1+1_Transactions_in_the_jungle.pdf
file_size: 246409
relation: main_file
file_date_updated: 2020-07-14T12:46:28Z
fulldoi: https://doi.org/10.1145/1810479.1810529
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 263 - 272
publication_status: published
publisher: ACM
publist_id: '1076'
pubrep_id: '46'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transactions in the jungle
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2010'
...