---
_id: '12643'
abstract:
- lang: eng
text: Parameterizations of incoming longwave radiation are increasingly receiving
attention for both low and high elevation glacierized sites. In this paper, we
test 13 clear-sky parameterizations combined with seven cloud corrections for
all-sky atmospheric emissivity at one location on Haut Glacier d'Arolla. We also
analyze the four seasons separately and conduct a cross-validation to test the
parameters’ robustness. The best parameterization is the one by Dilley and O'Brien,
B for clear-sky conditions combined with Unsworth and Monteith cloud correction.
This model is also the most robust when tested in cross-validation. When validated
at different sites in the southern Alps of Switzerland and north-western Italian
Alps, all parameterizations show a substantial decrease in performance, except
for one site, thus suggesting that it is important to recalibrate parameterizations
of incoming longwave radiation for different locations. We argue that this is
due to differences in the structure of the atmosphere at the sites. We also quantify
the effect that the incoming longwave radiation parameterizations have on energy-balance
melt modeling, and show that recalibration of model parameters is needed. Using
parameters from other sites leads to a significant underestimation of melt and
to an error that is larger than that associated with using different parameterizations.
Once recalibrated, however, the parameters of most models seem to be stable over
seasons and years at the location on Haut Glacier d'Arolla.
article_processing_charge: No
article_type: original
author:
- first_name: I.
full_name: Juszak, I.
last_name: Juszak
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: 'Juszak I, Pellicciotti F. A comparison of parameterizations of incoming longwave
radiation over melting glaciers: Model robustness and seasonal variability. Journal
of Geophysical Research: Atmospheres. 2013;118(8):3066-3084. doi:10.1002/jgrd.50277'
apa: 'Juszak, I., & Pellicciotti, F. (2013). A comparison of parameterizations
of incoming longwave radiation over melting glaciers: Model robustness and seasonal
variability. Journal of Geophysical Research: Atmospheres. American Geophysical
Union. https://doi.org/10.1002/jgrd.50277'
chicago: 'Juszak, I., and Francesca Pellicciotti. “A Comparison of Parameterizations
of Incoming Longwave Radiation over Melting Glaciers: Model Robustness and Seasonal
Variability.” Journal of Geophysical Research: Atmospheres. American Geophysical
Union, 2013. https://doi.org/10.1002/jgrd.50277.'
ieee: 'I. Juszak and F. Pellicciotti, “A comparison of parameterizations of incoming
longwave radiation over melting glaciers: Model robustness and seasonal variability,”
Journal of Geophysical Research: Atmospheres, vol. 118, no. 8. American
Geophysical Union, pp. 3066–3084, 2013.'
ista: 'Juszak I, Pellicciotti F. 2013. A comparison of parameterizations of incoming
longwave radiation over melting glaciers: Model robustness and seasonal variability.
Journal of Geophysical Research: Atmospheres. 118(8), 3066–3084.'
mla: 'Juszak, I., and Francesca Pellicciotti. “A Comparison of Parameterizations
of Incoming Longwave Radiation over Melting Glaciers: Model Robustness and Seasonal
Variability.” Journal of Geophysical Research: Atmospheres, vol. 118, no.
8, American Geophysical Union, 2013, pp. 3066–84, doi:10.1002/jgrd.50277.'
short: 'I. Juszak, F. Pellicciotti, Journal of Geophysical Research: Atmospheres
118 (2013) 3066–3084.'
date_created: 2023-02-20T08:17:34Z
date_published: 2013-04-27T00:00:00Z
date_updated: 2023-02-21T10:10:46Z
day: '27'
doi: 10.1002/jgrd.50277
extern: '1'
intvolume: ' 118'
issue: '8'
keyword:
- Space and Planetary Science
- Earth and Planetary Sciences (miscellaneous)
- Atmospheric Science
- Geophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/jgrd.50277
month: '04'
oa: 1
oa_version: Published Version
page: 3066-3084
publication: 'Journal of Geophysical Research: Atmospheres'
publication_identifier:
issn:
- 2169-897X
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A comparison of parameterizations of incoming longwave radiation over melting
glaciers: Model robustness and seasonal variability'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2013'
...
---
_id: '1304'
abstract:
- lang: eng
text: When confronted with a large-field stimulus rotating around the vertical body
axis, flies display a following behavior called "optomotor response."
As neural control elements, the large tangential horizontal system (HS) cells
of the lobula plate have been prime candidates for long. Here, we applied optogenetic
stimulation of HS cells to evaluate their behavioral role in Drosophila. To minimize
interference of the optical activation of channelrhodopsin-2 with the visual perception
of the flies, we used a bistable variant called ChR2-C128S. By applying pulses
of blue and yellow light, we first demonstrate electrophysiologically that lobula
plate tangential cells can be activated and deactivated repeatedly with no evident
change in depolarization strength over trials. We next show that selective optogenetic
activation of HS cells elicits robust yaw head movements and yaw turning responses
in fixed and tethered flying flies, respectively.
acknowledgement: 'This work was supported by the Max Planck Society. '
author:
- first_name: Väinö
full_name: Haikala, Väinö
last_name: Haikala
- first_name: Maximilian A
full_name: Maximilian Jösch
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Alexander
full_name: Borst, Alexander
last_name: Borst
- first_name: Alex
full_name: Mauss, Alex S
last_name: Mauss
citation:
ama: Haikala V, Jösch MA, Borst A, Mauss A. Optogenetic control of fly optomotor
responses. Journal of Neuroscience. 2013;33(34):13927-13934. doi:10.1523/JNEUROSCI.0340-13.2013
apa: Haikala, V., Jösch, M. A., Borst, A., & Mauss, A. (2013). Optogenetic control
of fly optomotor responses. Journal of Neuroscience. Society for Neuroscience.
https://doi.org/10.1523/JNEUROSCI.0340-13.2013
chicago: Haikala, Väinö, Maximilian A Jösch, Alexander Borst, and Alex Mauss. “Optogenetic
Control of Fly Optomotor Responses.” Journal of Neuroscience. Society for
Neuroscience, 2013. https://doi.org/10.1523/JNEUROSCI.0340-13.2013.
ieee: V. Haikala, M. A. Jösch, A. Borst, and A. Mauss, “Optogenetic control of fly
optomotor responses,” Journal of Neuroscience, vol. 33, no. 34. Society
for Neuroscience, pp. 13927–13934, 2013.
ista: Haikala V, Jösch MA, Borst A, Mauss A. 2013. Optogenetic control of fly optomotor
responses. Journal of Neuroscience. 33(34), 13927–13934.
mla: Haikala, Väinö, et al. “Optogenetic Control of Fly Optomotor Responses.” Journal
of Neuroscience, vol. 33, no. 34, Society for Neuroscience, 2013, pp. 13927–34,
doi:10.1523/JNEUROSCI.0340-13.2013.
short: V. Haikala, M.A. Jösch, A. Borst, A. Mauss, Journal of Neuroscience 33 (2013)
13927–13934.
date_created: 2018-12-11T11:51:16Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:45Z
day: '01'
doi: 10.1523/JNEUROSCI.0340-13.2013
extern: 1
intvolume: ' 33'
issue: '34'
month: '01'
page: 13927 - 13934
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '5967'
quality_controlled: 0
status: public
title: Optogenetic control of fly optomotor responses
type: journal_article
volume: 33
year: '2013'
...
---
_id: '1305'
abstract:
- lang: eng
text: In the fly Drosophila melanogaster, photoreceptor input to motion vision is
split into two parallel pathways as represented by first-order interneurons L1
and L2 (Rister et al., 2007; Joesch et al., 2010). However, how these pathways
are functionally specialized remains controversial. One study (Eichner et al.,
2011) proposed that the L1-pathway evaluates only sequences of brightness increments
(ON-ON), while the L2-pathway processes exclusively brightness decrements (OFF-OFF).
Another study (Clark et al., 2011) proposed that each of the two pathways evaluates
both ON-ON and OFF-OFF sequences. To decide between these alternatives, we recorded
from motionsensitive neurons in flies in which the output from either L1 or L2
was genetically blocked. We found that blocking L1 abolishes ON-ON responses but
leaves OFF-OFF responses intact. The opposite was true, when the output from L2
was blocked. We conclude that the L1 and L2 pathways are functionally specialized
to detect ON-ON and OFF-OFF sequences, respectively.
acknowledgement: This work was supported by the Max-Planck-Society and the SFB 870
of the Deutsche Forschungsgemeinschaft.
author:
- first_name: Maximilian A
full_name: Maximilian Jösch
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Franz
full_name: Weber, Franz
last_name: Weber
- first_name: Hubert
full_name: Eichner, Hubert
last_name: Eichner
- first_name: Alexander
full_name: Borst, Alexander
last_name: Borst
citation:
ama: Jösch MA, Weber F, Eichner H, Borst A. Functional specialization of parallel
motion detection circuits in the fly. Journal of Neuroscience. 2013;33(3):902-905.
doi:10.1523/JNEUROSCI.3374-12.2013
apa: Jösch, M. A., Weber, F., Eichner, H., & Borst, A. (2013). Functional specialization
of parallel motion detection circuits in the fly. Journal of Neuroscience.
Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.3374-12.2013
chicago: Jösch, Maximilian A, Franz Weber, Hubert Eichner, and Alexander Borst.
“Functional Specialization of Parallel Motion Detection Circuits in the Fly.”
Journal of Neuroscience. Society for Neuroscience, 2013. https://doi.org/10.1523/JNEUROSCI.3374-12.2013.
ieee: M. A. Jösch, F. Weber, H. Eichner, and A. Borst, “Functional specialization
of parallel motion detection circuits in the fly,” Journal of Neuroscience,
vol. 33, no. 3. Society for Neuroscience, pp. 902–905, 2013.
ista: Jösch MA, Weber F, Eichner H, Borst A. 2013. Functional specialization of
parallel motion detection circuits in the fly. Journal of Neuroscience. 33(3),
902–905.
mla: Jösch, Maximilian A., et al. “Functional Specialization of Parallel Motion
Detection Circuits in the Fly.” Journal of Neuroscience, vol. 33, no. 3,
Society for Neuroscience, 2013, pp. 902–05, doi:10.1523/JNEUROSCI.3374-12.2013.
short: M.A. Jösch, F. Weber, H. Eichner, A. Borst, Journal of Neuroscience 33 (2013)
902–905.
date_created: 2018-12-11T11:51:16Z
date_published: 2013-01-16T00:00:00Z
date_updated: 2021-01-12T06:49:45Z
day: '16'
doi: 10.1523/JNEUROSCI.3374-12.2013
extern: 1
intvolume: ' 33'
issue: '3'
month: '01'
page: 902 - 905
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '5968'
quality_controlled: 0
status: public
title: Functional specialization of parallel motion detection circuits in the fly
type: journal_article
volume: 33
year: '2013'
...
---
_id: '1307'
abstract:
- lang: eng
text: We prove uniqueness of solutions of the DLSS equation in a class of sufficiently
regular functions. The global weak solutions of the DLSS equation constructed
by Jüngel and Matthes belong to this class of uniqueness. We also show uniqueness
of solutions for the quantum drift-diffusion equation, which contains additional
drift and second-order diffusion terms. The results hold in case of periodic or
Dirichlet-Neumann boundary conditions. Our proof is based on a monotonicity property
of the DLSS operator and sophisticated approximation arguments; we derive a PDE
satisfied by the pointwise square root of the solution, which enables us to exploit
the monotonicity property of the operator.
author:
- first_name: Julian L
full_name: Julian Fischer
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: Fischer JL. Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation
and quantum drift diffusion models. Communications in Partial Differential
Equations. 2013;38(11):2004-2047. doi:10.1080/03605302.2013.823548
apa: Fischer, J. L. (2013). Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift diffusion models. Communications in Partial Differential
Equations. Taylor & Francis. https://doi.org/10.1080/03605302.2013.823548
chicago: Fischer, Julian L. “Uniqueness of Solutions of the Derrida-Lebowitz-Speer-Spohn
Equation and Quantum Drift Diffusion Models.” Communications in Partial Differential
Equations. Taylor & Francis, 2013. https://doi.org/10.1080/03605302.2013.823548.
ieee: J. L. Fischer, “Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift diffusion models,” Communications in Partial Differential
Equations, vol. 38, no. 11. Taylor & Francis, pp. 2004–2047, 2013.
ista: Fischer JL. 2013. Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift diffusion models. Communications in Partial Differential
Equations. 38(11), 2004–2047.
mla: Fischer, Julian L. “Uniqueness of Solutions of the Derrida-Lebowitz-Speer-Spohn
Equation and Quantum Drift Diffusion Models.” Communications in Partial Differential
Equations, vol. 38, no. 11, Taylor & Francis, 2013, pp. 2004–47, doi:10.1080/03605302.2013.823548.
short: J.L. Fischer, Communications in Partial Differential Equations 38 (2013)
2004–2047.
date_created: 2018-12-11T11:51:17Z
date_published: 2013-11-01T00:00:00Z
date_updated: 2021-01-12T06:49:46Z
day: '01'
doi: 10.1080/03605302.2013.823548
extern: 1
intvolume: ' 38'
issue: '11'
month: '11'
page: 2004 - 2047
publication: Communications in Partial Differential Equations
publication_status: published
publisher: Taylor & Francis
publist_id: '5962'
quality_controlled: 0
status: public
title: Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum
drift diffusion models
type: journal_article
volume: 38
year: '2013'
...
---
_id: '1308'
abstract:
- lang: eng
text: We derive sufficient conditions for advection-driven backward motion of the
free boundary in a chemotaxis model with degenerate mobility. In this model, a
porous-medium-type diffusive term and an advection term are in competition. The
former induces forward motion, the latter may induce backward motion of the free
boundary depending on the direction of advection. We deduce conditions on the
growth of the initial data at the free boundary which ensure that at least initially
the advection term is dominant. This implies local backward motion of the free
boundary provided the advection is (locally) directed appropriately. Our result
is based on a new class of moving test functions and Stampacchia's lemma. As a
by-product of our estimates, we obtain quantitative bounds on the spreading of
the support of solutions for the chemotaxis model and provide a proof for the
finite speed of the support propagation property of solutions.
author:
- first_name: Julian L
full_name: Julian Fischer
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: Fischer JL. Advection-driven support shrinking in a chemotaxis model with degenerate
mobility. SIAM Journal on Mathematical Analysis. 2013;45(3):1585-1615.
doi:10.1137/120874291
apa: Fischer, J. L. (2013). Advection-driven support shrinking in a chemotaxis model
with degenerate mobility. SIAM Journal on Mathematical Analysis. Society
for Industrial and Applied Mathematics . https://doi.org/10.1137/120874291
chicago: Fischer, Julian L. “Advection-Driven Support Shrinking in a Chemotaxis
Model with Degenerate Mobility.” SIAM Journal on Mathematical Analysis.
Society for Industrial and Applied Mathematics , 2013. https://doi.org/10.1137/120874291.
ieee: J. L. Fischer, “Advection-driven support shrinking in a chemotaxis model with
degenerate mobility,” SIAM Journal on Mathematical Analysis, vol. 45, no.
3. Society for Industrial and Applied Mathematics , pp. 1585–1615, 2013.
ista: Fischer JL. 2013. Advection-driven support shrinking in a chemotaxis model
with degenerate mobility. SIAM Journal on Mathematical Analysis. 45(3), 1585–1615.
mla: Fischer, Julian L. “Advection-Driven Support Shrinking in a Chemotaxis Model
with Degenerate Mobility.” SIAM Journal on Mathematical Analysis, vol.
45, no. 3, Society for Industrial and Applied Mathematics , 2013, pp. 1585–615,
doi:10.1137/120874291.
short: J.L. Fischer, SIAM Journal on Mathematical Analysis 45 (2013) 1585–1615.
date_created: 2018-12-11T11:51:17Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:46Z
day: '01'
doi: 10.1137/120874291
extern: 1
intvolume: ' 45'
issue: '3'
month: '01'
page: 1585 - 1615
publication: SIAM Journal on Mathematical Analysis
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '5963'
quality_controlled: 0
status: public
title: Advection-driven support shrinking in a chemotaxis model with degenerate mobility
type: journal_article
volume: 45
year: '2013'
...
---
_id: '1310'
abstract:
- lang: eng
text: We derive lower bounds on asymptotic support propagation rates for strong
solutions of the Cauchy problem for the thin-film equation. The bounds coincide
up to a constant factor with the previously known upper bounds and thus are sharp.
Our results hold in case of at most three spatial dimensions and n∈. (1, 2.92).
The result is established using weighted backward entropy inequalities with singular
weight functions to yield a differential inequality; combined with some entropy
production estimates, the optimal rate of propagation is obtained. To the best
of our knowledge, these are the first lower bounds on asymptotic support propagation
rates for higher-order nonnegativity-preserving parabolic equations.
author:
- first_name: Julian L
full_name: Julian Fischer
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: Fischer JL. Optimal lower bounds on asymptotic support propagation rates for
the thin-film equation. Journal of Differential Equations. 2013;255(10):3127-3149.
doi:10.1016/j.jde.2013.07.028
apa: Fischer, J. L. (2013). Optimal lower bounds on asymptotic support propagation
rates for the thin-film equation. Journal of Differential Equations. Academic
Press. https://doi.org/10.1016/j.jde.2013.07.028
chicago: Fischer, Julian L. “Optimal Lower Bounds on Asymptotic Support Propagation
Rates for the Thin-Film Equation.” Journal of Differential Equations. Academic
Press, 2013. https://doi.org/10.1016/j.jde.2013.07.028.
ieee: J. L. Fischer, “Optimal lower bounds on asymptotic support propagation rates
for the thin-film equation,” Journal of Differential Equations, vol. 255,
no. 10. Academic Press, pp. 3127–3149, 2013.
ista: Fischer JL. 2013. Optimal lower bounds on asymptotic support propagation rates
for the thin-film equation. Journal of Differential Equations. 255(10), 3127–3149.
mla: Fischer, Julian L. “Optimal Lower Bounds on Asymptotic Support Propagation
Rates for the Thin-Film Equation.” Journal of Differential Equations, vol.
255, no. 10, Academic Press, 2013, pp. 3127–49, doi:10.1016/j.jde.2013.07.028.
short: J.L. Fischer, Journal of Differential Equations 255 (2013) 3127–3149.
date_created: 2018-12-11T11:51:18Z
date_published: 2013-11-15T00:00:00Z
date_updated: 2021-01-12T06:49:47Z
day: '15'
doi: 10.1016/j.jde.2013.07.028
extern: 1
intvolume: ' 255'
issue: '10'
month: '11'
page: 3127 - 3149
publication: Journal of Differential Equations
publication_status: published
publisher: Academic Press
publist_id: '5961'
quality_controlled: 0
status: public
title: Optimal lower bounds on asymptotic support propagation rates for the thin-film
equation
type: journal_article
volume: 255
year: '2013'
...
---
_id: '1978'
abstract:
- lang: eng
text: Complex I is the first and largest enzyme of the respiratory chain and has
a central role in cellular energy production through the coupling of NADH:ubiquinone
electron transfer to proton translocation. It is also implicated in many common
human neurodegenerative diseases. Here, we report the first crystal structure
of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution.
The structure of the 536-kDa complex comprises 16 different subunits, with a total
of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit
Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like
subunits. Small subunits nearby form a linked second half-channel, which completes
the fourth proton-translocation pathway (present in addition to the channels in
three antiporter-like subunits). The quinone-binding site is unusually long, narrow
and enclosed. The quinone headgroup binds at the deep end of this chamber, near
iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel
by a 'funnel' of charged residues. The link continues over the entire membrane
domain as a flexible central axis of charged and polar residues, and probably
has a leading role in the propagation of conformational changes, aided by coupling
elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction
chamber enables the redox energy to drive concerted long-range conformational
changes in the four antiporter-like domains, resulting in translocation of four
protons per cycle.
acknowledgement: This work was funded by the Medical Research Council.
author:
- first_name: Rozbeh
full_name: 'Baradaran, Rozbeh '
last_name: Baradaran
- first_name: John
full_name: Berrisford, John M
last_name: Berrisford
- first_name: Gurdeep
full_name: Minhas, Gurdeep S
last_name: Minhas
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Baradaran R, Berrisford J, Minhas G, Sazanov LA. Crystal structure of the entire
respiratory complex i. Nature. 2013;494(7438):443-448. doi:10.1038/nature11871
apa: Baradaran, R., Berrisford, J., Minhas, G., & Sazanov, L. A. (2013). Crystal
structure of the entire respiratory complex i. Nature. Nature Publishing
Group. https://doi.org/10.1038/nature11871
chicago: Baradaran, Rozbeh, John Berrisford, Gurdeep Minhas, and Leonid A Sazanov.
“Crystal Structure of the Entire Respiratory Complex I.” Nature. Nature
Publishing Group, 2013. https://doi.org/10.1038/nature11871.
ieee: R. Baradaran, J. Berrisford, G. Minhas, and L. A. Sazanov, “Crystal structure
of the entire respiratory complex i,” Nature, vol. 494, no. 7438. Nature
Publishing Group, pp. 443–448, 2013.
ista: Baradaran R, Berrisford J, Minhas G, Sazanov LA. 2013. Crystal structure of
the entire respiratory complex i. Nature. 494(7438), 443–448.
mla: Baradaran, Rozbeh, et al. “Crystal Structure of the Entire Respiratory Complex
I.” Nature, vol. 494, no. 7438, Nature Publishing Group, 2013, pp. 443–48,
doi:10.1038/nature11871.
short: R. Baradaran, J. Berrisford, G. Minhas, L.A. Sazanov, Nature 494 (2013) 443–448.
date_created: 2018-12-11T11:55:01Z
date_published: 2013-02-28T00:00:00Z
date_updated: 2021-01-12T06:54:28Z
day: '28'
doi: 10.1038/nature11871
extern: 1
intvolume: ' 494'
issue: '7438'
month: '02'
page: 443 - 448
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5107'
quality_controlled: 0
status: public
title: Crystal structure of the entire respiratory complex i
type: journal_article
volume: 494
year: '2013'
...
---
_id: '1988'
abstract:
- lang: eng
text: The rod-shaped bacterium Escherichia coli selects the cell center as site
of division with the help of the proteins MinC, MinD, and MinE. This protein system
collectively oscillates between the two cell poles by alternately binding to the
membrane in one of the two cell halves. This dynamic behavior, which emerges from
the interaction of the ATPase MinD and its activator MinE on the cell membrane,
has become a paradigm for protein self-organization. Recently, it has been found
that not only the binding of MinD to the membrane, but also interactions of MinE
with the membrane contribute to Min-protein self-organization. Here, we show that
by accounting for this finding in a computational model, we can comprehensively
describe all observed Min-protein patterns in vivo and in vitro. Furthermore,
by varying the system's geometry, our computations predict patterns that have
not yet been reported. We confirm these predictions experimentally.
author:
- first_name: Mike
full_name: 'Bonny, Mike '
last_name: Bonny
- first_name: Elisabeth
full_name: Fischer-Friedrich, Elisabeth
last_name: Fischer Friedrich
- first_name: Martin
full_name: Martin Loose
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Petra
full_name: 'Schwille, Petra '
last_name: Schwille
- first_name: Karsten
full_name: Kruse, Karsten
last_name: Kruse
citation:
ama: Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. Membrane binding
of MinE allows for a comprehensive description of Min-protein pattern formation.
PLoS Computational Biology. 2013;9(12). doi:10.1371/journal.pcbi.1003347
apa: Bonny, M., Fischer Friedrich, E., Loose, M., Schwille, P., & Kruse, K.
(2013). Membrane binding of MinE allows for a comprehensive description of Min-protein
pattern formation. PLoS Computational Biology. Public Library of Science.
https://doi.org/10.1371/journal.pcbi.1003347
chicago: Bonny, Mike, Elisabeth Fischer Friedrich, Martin Loose, Petra Schwille,
and Karsten Kruse. “Membrane Binding of MinE Allows for a Comprehensive Description
of Min-Protein Pattern Formation.” PLoS Computational Biology. Public Library
of Science, 2013. https://doi.org/10.1371/journal.pcbi.1003347.
ieee: M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, and K. Kruse, “Membrane
binding of MinE allows for a comprehensive description of Min-protein pattern
formation,” PLoS Computational Biology, vol. 9, no. 12. Public Library
of Science, 2013.
ista: Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. 2013. Membrane
binding of MinE allows for a comprehensive description of Min-protein pattern
formation. PLoS Computational Biology. 9(12).
mla: Bonny, Mike, et al. “Membrane Binding of MinE Allows for a Comprehensive Description
of Min-Protein Pattern Formation.” PLoS Computational Biology, vol. 9,
no. 12, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1003347.
short: M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, K. Kruse, PLoS Computational
Biology 9 (2013).
date_created: 2018-12-11T11:55:04Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2021-01-12T06:54:32Z
day: '01'
doi: 10.1371/journal.pcbi.1003347
extern: 1
intvolume: ' 9'
issue: '12'
month: '12'
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5095'
quality_controlled: 0
status: public
title: Membrane binding of MinE allows for a comprehensive description of Min-protein
pattern formation
type: journal_article
volume: 9
year: '2013'
...
---
_id: '1991'
abstract:
- lang: eng
text: Although transitions of sex-determination mechanisms are frequent in species
with homomorphic sex chromosomes, heteromorphic sex chromosomes are thought to
represent a terminal evolutionary stage owing to chromosome-specific adaptations
such as dosage compensation or an accumulation of sex-specific mutations. Here
we show that an autosome of Drosophila, the dot chromosome, was ancestrally a
differentiated X chromosome. We analyse the whole genome of true fruitflies (Tephritidae),
flesh flies (Sarcophagidae) and soldier flies (Stratiomyidae) to show that genes
located on the dot chromosome of Drosophila are X-linked in outgroup species,
whereas Drosophila X-linked genes are autosomal. We date this chromosomal transition
to early drosophilid evolution by sequencing the genome of other Drosophilidae.
Our results reveal several puzzling aspects of Drosophila dot chromosome biology
to be possible remnants of its former life as a sex chromosome, such as its minor
feminizing role in sex determination or its targeting by a chromosome-specific
regulatory mechanism. We also show that patterns of biased gene expression of
the dot chromosome during early embryogenesis, oogenesis and spermatogenesis resemble
that of the current X chromosome. Thus, although sex chromosomes are not necessarily
evolutionary end points and can revert back to an autosomal inheritance, the highly
specialized genome architecture of this former X chromosome suggests that severe
fitness costs must be overcome for such a turnover to occur.
acknowledgement: Funded by National Institutes of Health grants (R01GM076007 and R01GM093182)
and a Packard Fellowship to D.B.
author:
- first_name: Beatriz
full_name: Beatriz Vicoso
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Doris
full_name: Bachtrog, Doris
last_name: Bachtrog
citation:
ama: Vicoso B, Bachtrog D. Reversal of an ancient sex chromosome to an autosome
in Drosophila. Nature. 2013;499(7458):332-335. doi:10.1038/nature12235
apa: Vicoso, B., & Bachtrog, D. (2013). Reversal of an ancient sex chromosome
to an autosome in Drosophila. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12235
chicago: Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome
to an Autosome in Drosophila.” Nature. Nature Publishing Group, 2013. https://doi.org/10.1038/nature12235.
ieee: B. Vicoso and D. Bachtrog, “Reversal of an ancient sex chromosome to an autosome
in Drosophila,” Nature, vol. 499, no. 7458. Nature Publishing Group, pp.
332–335, 2013.
ista: Vicoso B, Bachtrog D. 2013. Reversal of an ancient sex chromosome to an autosome
in Drosophila. Nature. 499(7458), 332–335.
mla: Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome
to an Autosome in Drosophila.” Nature, vol. 499, no. 7458, Nature Publishing
Group, 2013, pp. 332–35, doi:10.1038/nature12235.
short: B. Vicoso, D. Bachtrog, Nature 499 (2013) 332–335.
date_created: 2018-12-11T11:55:05Z
date_published: 2013-07-18T00:00:00Z
date_updated: 2021-01-12T06:54:33Z
day: '18'
doi: 10.1038/nature12235
extern: 1
intvolume: ' 499'
issue: '7458'
month: '07'
page: 332 - 335
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5092'
quality_controlled: 0
status: public
title: Reversal of an ancient sex chromosome to an autosome in Drosophila
type: journal_article
volume: 499
year: '2013'
...
---
OA_place: repository
OA_type: green
_id: '19995'
abstract:
- lang: eng
text: Markov decision processes (MDPs) and simple stochastic games (SSGs) provide
a rich mathematical framework to study many important problems related to probabilistic
systems. MDPs and SSGs with finite-horizon objectives, where the goal is to maximize
the probability to reach a target state in a given finite time, is a classical
and well-studied problem. In this work we consider the strategy complexity of
finite-horizon MDPs and SSGs. We show that for all ε > 0, the natural class of
counter-based strategies require at most log log/(1/ε) + n + 1 memory states,
and memory of size Omega(log log(1/ε) + n) is required, for ε-optimality, where
n is the number of states of the MDP (resp. SSG). Thus our bounds are asymptotically
optimal. We then study the periodic property of optimal strategies, and show a
sub-exponential lower bound on the period for optimal strategies.
acknowledgement: 'Work of the second author supported by the Sino-Danish Center for
the Theory of Interactive Computation, funded by the Danish National Research Foundation
and the National Science Foundation of China (under the grant 61061130540). The
second author acknowledge support from the Center for research in the Foundations
of Electronic Markets (CFEM), supported by the Danish Strategic Research Council.
The first author was supported by FWF Grant No P 23499-N23, FWF NFN Grant No S11407-N23
(RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.'
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Chatterjee K, Ibsen-Jensen R. Strategy complexity of finite-horizon Markov
decision processes and simple stochastic games. In: Mathematical and Engineering
Methods in Computer Science. Vol 7721. Springer Nature; 2013:106-117. doi:10.1007/978-3-642-36046-6_11'
apa: 'Chatterjee, K., & Ibsen-Jensen, R. (2013). Strategy complexity of finite-horizon
Markov decision processes and simple stochastic games. In Mathematical and
Engineering Methods in Computer Science (Vol. 7721, pp. 106–117). Znojmo,
Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-642-36046-6_11'
chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Strategy Complexity of
Finite-Horizon Markov Decision Processes and Simple Stochastic Games.” In Mathematical
and Engineering Methods in Computer Science, 7721:106–17. Springer Nature,
2013. https://doi.org/10.1007/978-3-642-36046-6_11.
ieee: K. Chatterjee and R. Ibsen-Jensen, “Strategy complexity of finite-horizon
Markov decision processes and simple stochastic games,” in Mathematical and
Engineering Methods in Computer Science, Znojmo, Czech Republic, 2013, vol.
7721, pp. 106–117.
ista: 'Chatterjee K, Ibsen-Jensen R. 2013. Strategy complexity of finite-horizon
Markov decision processes and simple stochastic games. Mathematical and Engineering
Methods in Computer Science. MEMICS: Mathematical and Engineering Methods in Computer
Science, LNCS, vol. 7721, 106–117.'
mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Strategy Complexity of Finite-Horizon
Markov Decision Processes and Simple Stochastic Games.” Mathematical and Engineering
Methods in Computer Science, vol. 7721, Springer Nature, 2013, pp. 106–17,
doi:10.1007/978-3-642-36046-6_11.
short: K. Chatterjee, R. Ibsen-Jensen, in:, Mathematical and Engineering Methods
in Computer Science, Springer Nature, 2013, pp. 106–117.
conference:
end_date: 2012-10-28
location: Znojmo, Czech Republic
name: 'MEMICS: Mathematical and Engineering Methods in Computer Science'
start_date: 2012-10-25
corr_author: '1'
date_created: 2025-07-10T14:08:49Z
date_published: 2013-01-17T00:00:00Z
date_updated: 2025-09-23T09:24:13Z
day: '17'
department:
- _id: KrCh
doi: 10.1007/978-3-642-36046-6_11
ec_funded: 1
external_id:
arxiv:
- '1209.3617'
intvolume: ' 7721'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1209.3617
month: '01'
oa: 1
oa_version: Preprint
page: 106-117
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Mathematical and Engineering Methods in Computer Science
publication_identifier:
eisbn:
- '9783642360466'
eissn:
- 1611-3349
isbn:
- '9783642360442'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strategy complexity of finite-horizon Markov decision processes and simple
stochastic games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7721
year: '2013'
...
---
_id: '2009'
abstract:
- lang: eng
text: Traditional statistical methods for confidentiality protection of statistical
databases do not scale well to deal with GWAS databases especially in terms of
guarantees regarding protection from linkage to external information. The more
recent concept of differential privacy, introduced by the cryptographic community,
is an approach which provides a rigorous definition of privacy with meaningful
privacy guarantees in the presence of arbitrary external information, although
the guarantees may come at a serious price in terms of data utility. Building
on such notions, we propose new methods to release aggregate GWAS data without
compromising an individual’s privacy. We present methods for releasing differentially
private minor allele frequencies, chi-square statistics and p-values. We compare
these approaches on simulated data and on a GWAS study of canine hair length involving
685 dogs. We also propose a privacy-preserving method for finding genome-wide
associations based on a differentially-private approach to penalized logistic
regression.
article_processing_charge: No
author:
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Aleksandra
full_name: Slavkovic, Aleksandra
last_name: Slavkovic
- first_name: Stephen
full_name: Fienberg, Stephen
last_name: Fienberg
citation:
ama: Uhler C, Slavkovic A, Fienberg S. Privacy-preserving data sharing for genome-wide
association studies. Journal of Privacy and Confidentiality . 2013;5(1):137-166.
doi:10.29012/jpc.v5i1.629
apa: Uhler, C., Slavkovic, A., & Fienberg, S. (2013). Privacy-preserving data
sharing for genome-wide association studies. Journal of Privacy and Confidentiality
. Carnegie Mellon University. https://doi.org/10.29012/jpc.v5i1.629
chicago: Uhler, Caroline, Aleksandra Slavkovic, and Stephen Fienberg. “Privacy-Preserving
Data Sharing for Genome-Wide Association Studies.” Journal of Privacy and Confidentiality
. Carnegie Mellon University, 2013. https://doi.org/10.29012/jpc.v5i1.629.
ieee: C. Uhler, A. Slavkovic, and S. Fienberg, “Privacy-preserving data sharing
for genome-wide association studies,” Journal of Privacy and Confidentiality
, vol. 5, no. 1. Carnegie Mellon University, pp. 137–166, 2013.
ista: Uhler C, Slavkovic A, Fienberg S. 2013. Privacy-preserving data sharing for
genome-wide association studies. Journal of Privacy and Confidentiality . 5(1),
137–166.
mla: Uhler, Caroline, et al. “Privacy-Preserving Data Sharing for Genome-Wide Association
Studies.” Journal of Privacy and Confidentiality , vol. 5, no. 1, Carnegie
Mellon University, 2013, pp. 137–66, doi:10.29012/jpc.v5i1.629.
short: C. Uhler, A. Slavkovic, S. Fienberg, Journal of Privacy and Confidentiality 5
(2013) 137–166.
date_created: 2018-12-11T11:55:11Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T06:54:41Z
day: '01'
department:
- _id: CaUh
doi: 10.29012/jpc.v5i1.629
intvolume: ' 5'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://repository.cmu.edu/jpc/vol5/iss1/6
month: '08'
oa: 1
oa_version: Published Version
page: 137 - 166
publication: 'Journal of Privacy and Confidentiality '
publication_status: published
publisher: Carnegie Mellon University
publist_id: '5067'
quality_controlled: '1'
status: public
title: Privacy-preserving data sharing for genome-wide association studies
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2013'
...
---
_id: '2010'
abstract:
- lang: eng
text: Many algorithms for inferring causality rely heavily on the faithfulness assumption.
The main justification for imposing this assumption is that the set of unfaithful
distributions has Lebesgue measure zero, since it can be seen as a collection
of hypersurfaces in a hypercube. However, due to sampling error the faithfulness
condition alone is not sufficient for statistical estimation, and strong-faithfulness
has been proposed and assumed to achieve uniform or high-dimensional consistency.
In contrast to the plain faithfulness assumption, the set of distributions that
is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly
large as we show in this paper. We study the strong-faithfulness condition from
a geometric and combinatorial point of view and give upper and lower bounds on
the Lebesgue measure of strong-faithful distributions for various classes of directed
acyclic graphs. Our results imply fundamental limitations for the PC-algorithm
and potentially also for other algorithms based on partial correlation testing
in the Gaussian case.
article_processing_charge: No
arxiv: 1
author:
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Garvesh
full_name: Raskutti, Garvesh
last_name: Raskutti
- first_name: Peter
full_name: Bühlmann, Peter
last_name: Bühlmann
- first_name: Bin
full_name: Yu, Bin
last_name: Yu
citation:
ama: Uhler C, Raskutti G, Bühlmann P, Yu B. Geometry of the faithfulness assumption
in causal inference. The Annals of Statistics. 2013;41(2):436-463. doi:10.1214/12-AOS1080
apa: Uhler, C., Raskutti, G., Bühlmann, P., & Yu, B. (2013). Geometry of the
faithfulness assumption in causal inference. The Annals of Statistics.
Institute of Mathematical Statistics. https://doi.org/10.1214/12-AOS1080
chicago: Uhler, Caroline, Garvesh Raskutti, Peter Bühlmann, and Bin Yu. “Geometry
of the Faithfulness Assumption in Causal Inference.” The Annals of Statistics.
Institute of Mathematical Statistics, 2013. https://doi.org/10.1214/12-AOS1080.
ieee: C. Uhler, G. Raskutti, P. Bühlmann, and B. Yu, “Geometry of the faithfulness
assumption in causal inference,” The Annals of Statistics, vol. 41, no.
2. Institute of Mathematical Statistics, pp. 436–463, 2013.
ista: Uhler C, Raskutti G, Bühlmann P, Yu B. 2013. Geometry of the faithfulness
assumption in causal inference. The Annals of Statistics. 41(2), 436–463.
mla: Uhler, Caroline, et al. “Geometry of the Faithfulness Assumption in Causal
Inference.” The Annals of Statistics, vol. 41, no. 2, Institute of Mathematical
Statistics, 2013, pp. 436–63, doi:10.1214/12-AOS1080.
short: C. Uhler, G. Raskutti, P. Bühlmann, B. Yu, The Annals of Statistics 41 (2013)
436–463.
date_created: 2018-12-11T11:55:11Z
date_published: 2013-04-01T00:00:00Z
date_updated: 2025-09-29T14:31:39Z
day: '01'
department:
- _id: CaUh
doi: 10.1214/12-AOS1080
external_id:
arxiv:
- '1207.0547'
isi:
- '000320488200002'
intvolume: ' 41'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: www.doi.org/10.1214/12-AOS1080
month: '04'
oa: 1
oa_version: Published Version
page: 436 - 463
publication: The Annals of Statistics
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '5066'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometry of the faithfulness assumption in causal inference
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 41
year: '2013'
...
---
_id: '2074'
abstract:
- lang: eng
text: 'Sex chromosomes originate from autosomes. The accumulation of sexually antagonistic
mutations on protosex chromosomes selects for a loss of recombination and sets
in motion the evolutionary processes generating heteromorphic sex chromosomes.
Recombination suppression and differentiation are generally viewed as the default
path of sex chromosome evolution, and the occurrence of old, homomorphic sex chromosomes,
such as those of ratite birds, has remained a mystery. Here, we analyze the genome
and transcriptome of emu (Dromaius novaehollandiae) and confirm that most genes
on the sex chromosome are shared between the Z and W. Surprisingly, however, levels
of gene expression are generally sex-biased for all sex-linked genes relative
to autosomes, including those in the pseudoautosomal region, and the male-bias
increases after gonad formation. This expression bias suggests that the emu sex
chromosomes have become masculinized, even in the absence of ZW differentiation.
Thus, birds may have taken different evolutionary solutions to minimize the deleterious
effects imposed by sexually antagonistic mutations: some lineages eliminate recombination
along the protosex chromosomes to physically restrict sexually antagonistic alleles
to one sex, whereas ratites evolved sex-biased expression to confine the product
of a sexually antagonistic allele to the sex it benefits. This difference in conflict
resolution may explain the preservation of recombining, homomorphic sex chromosomes
in other lineages and illustrates the importance of sexually antagonistic mutations
driving the evolution of sex chromosomes. '
author:
- first_name: Beatriz
full_name: Beatriz Vicoso
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Vera
full_name: Kaiser, Vera B
last_name: Kaiser
- first_name: Doris
full_name: Bachtrog, Doris
last_name: Bachtrog
citation:
ama: Vicoso B, Kaiser V, Bachtrog D. Sex biased gene expression at homomorphic sex
chromosomes in emus and its implication for sex chromosome evolution. PNAS.
2013;110(16):6453-6458. doi:10.1073/pnas.1217027110
apa: Vicoso, B., Kaiser, V., & Bachtrog, D. (2013). Sex biased gene expression
at homomorphic sex chromosomes in emus and its implication for sex chromosome
evolution. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1217027110
chicago: Vicoso, Beatriz, Vera Kaiser, and Doris Bachtrog. “Sex Biased Gene Expression
at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome
Evolution.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1217027110.
ieee: B. Vicoso, V. Kaiser, and D. Bachtrog, “Sex biased gene expression at homomorphic
sex chromosomes in emus and its implication for sex chromosome evolution,” PNAS,
vol. 110, no. 16. National Academy of Sciences, pp. 6453–6458, 2013.
ista: Vicoso B, Kaiser V, Bachtrog D. 2013. Sex biased gene expression at homomorphic
sex chromosomes in emus and its implication for sex chromosome evolution. PNAS.
110(16), 6453–6458.
mla: Vicoso, Beatriz, et al. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes
in Emus and Its Implication for Sex Chromosome Evolution.” PNAS, vol. 110,
no. 16, National Academy of Sciences, 2013, pp. 6453–58, doi:10.1073/pnas.1217027110.
short: B. Vicoso, V. Kaiser, D. Bachtrog, PNAS 110 (2013) 6453–6458.
date_created: 2018-12-11T11:55:33Z
date_published: 2013-04-16T00:00:00Z
date_updated: 2021-01-12T06:55:08Z
day: '16'
doi: 10.1073/pnas.1217027110
extern: 1
intvolume: ' 110'
issue: '16'
month: '04'
page: 6453 - 6458
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '4964'
quality_controlled: 0
status: public
title: Sex biased gene expression at homomorphic sex chromosomes in emus and its implication
for sex chromosome evolution
type: journal_article
volume: 110
year: '2013'
...
---
_id: '2076'
abstract:
- lang: eng
text: |
Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes evolution.
acknowledgement: Funded by NIH grants (R01GM076007 and R01GM093182) and a Packard
Fellowship to DB.
author:
- first_name: Beatriz
full_name: Beatriz Vicoso
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Jr
full_name: Emerson, Jr J.
last_name: Emerson
- first_name: Yulia
full_name: Zektser, Yulia
last_name: Zektser
- first_name: Shivani
full_name: Mahajan, Shivani
last_name: Mahajan
- first_name: Doris
full_name: Bachtrog, Doris
last_name: Bachtrog
citation:
ama: 'Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. Comparative sex chromosome
genomics in snakes: Differentiation evolutionary strata and lack of global dosage
compensation. PLoS Biology. 2013;11(8). doi:10.1371/journal.pbio.1001643'
apa: 'Vicoso, B., Emerson, J., Zektser, Y., Mahajan, S., & Bachtrog, D. (2013).
Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata
and lack of global dosage compensation. PLoS Biology. Public Library of
Science. https://doi.org/10.1371/journal.pbio.1001643'
chicago: 'Vicoso, Beatriz, Jr Emerson, Yulia Zektser, Shivani Mahajan, and Doris
Bachtrog. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary
Strata and Lack of Global Dosage Compensation.” PLoS Biology. Public Library
of Science, 2013. https://doi.org/10.1371/journal.pbio.1001643.'
ieee: 'B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, and D. Bachtrog, “Comparative
sex chromosome genomics in snakes: Differentiation evolutionary strata and lack
of global dosage compensation,” PLoS Biology, vol. 11, no. 8. Public Library
of Science, 2013.'
ista: 'Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. 2013. Comparative
sex chromosome genomics in snakes: Differentiation evolutionary strata and lack
of global dosage compensation. PLoS Biology. 11(8).'
mla: 'Vicoso, Beatriz, et al. “Comparative Sex Chromosome Genomics in Snakes: Differentiation
Evolutionary Strata and Lack of Global Dosage Compensation.” PLoS Biology,
vol. 11, no. 8, Public Library of Science, 2013, doi:10.1371/journal.pbio.1001643.'
short: B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, D. Bachtrog, PLoS Biology
11 (2013).
date_created: 2018-12-11T11:55:34Z
date_published: 2013-08-27T00:00:00Z
date_updated: 2021-01-12T06:55:09Z
day: '27'
doi: 10.1371/journal.pbio.1001643
extern: 1
intvolume: ' 11'
issue: '8'
month: '08'
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '4962'
quality_controlled: 0
status: public
title: 'Comparative sex chromosome genomics in snakes: Differentiation evolutionary
strata and lack of global dosage compensation'
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
volume: 11
year: '2013'
...
---
_id: '1977'
abstract:
- lang: eng
text: Complex I (NADH:ubiquinone oxidoreductase) is central to cellular energy production,
being the first and largest enzyme of the respiratory chain in mitochondria. It
couples electron transfer from NADH to ubiquinone with proton translocation across
the inner mitochondrial membrane and is involved in a wide range of human neurodegenerative
disorders. Mammalian complex I is composed of 44 different subunits, whereas the
'minimal' bacterial version contains 14 highly conserved 'core' subunits. The
L-shaped assembly consists of hydrophilic and membrane domains. We have determined
all known atomic structures of complex I, starting from the hydrophilic domain
of Thermus thermophilus enzyme (eight subunits, nine Fe-S clusters), followed
by the membrane domains of the Escherichia coli (six subunits, 55 transmembrane
helices) and T. thermophilus (seven subunits, 64 transmembrane helices) enzymes,
and finally culminating in a recent crystal structure of the entire intact complex
I from T. thermophilus (536 kDa, 16 subunits, nine Fe-S clusters, 64 transmembrane
helices). The structure suggests an unusual and unique coupling mechanism via
longrange conformational changes. Determination of the structure of the entire
complex was possible only through this step-by-step approach, building on from
smaller subcomplexes towards the entire assembly. Large membrane proteins are
notoriously difficult to crystallize, and so various non-standard and sometimes
counterintuitive approaches were employed in order to achieve crystal diffraction
to high resolution and solve the structures. These steps, as well as the implications
from the final structure, are discussed in the present review.
acknowledgement: This work was funded by the Medical Research Council.
author:
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Rozbeh
full_name: 'Baradaran, Rozbeh '
last_name: Baradaran
- first_name: Rouslan
full_name: Efremov, Rouslan G
last_name: Efremov
- first_name: John
full_name: Berrisford, John M
last_name: Berrisford
- first_name: Gurdeep
full_name: Minhas, Gurdeep S
last_name: Minhas
citation:
ama: Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. A long road towards
the structure of respiratory complex I, a giant molecular proton pump. Biochemical
Society Transactions. 2013;41(5):1265-1271. doi:10.1042/BST20130193
apa: Sazanov, L. A., Baradaran, R., Efremov, R., Berrisford, J., & Minhas, G.
(2013). A long road towards the structure of respiratory complex I, a giant molecular
proton pump. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/BST20130193
chicago: Sazanov, Leonid A, Rozbeh Baradaran, Rouslan Efremov, John Berrisford,
and Gurdeep Minhas. “A Long Road towards the Structure of Respiratory Complex
I, a Giant Molecular Proton Pump.” Biochemical Society Transactions. Portland
Press, 2013. https://doi.org/10.1042/BST20130193.
ieee: L. A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, and G. Minhas, “A
long road towards the structure of respiratory complex I, a giant molecular proton
pump,” Biochemical Society Transactions, vol. 41, no. 5. Portland Press,
pp. 1265–1271, 2013.
ista: Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. 2013. A long road
towards the structure of respiratory complex I, a giant molecular proton pump.
Biochemical Society Transactions. 41(5), 1265–1271.
mla: Sazanov, Leonid A., et al. “A Long Road towards the Structure of Respiratory
Complex I, a Giant Molecular Proton Pump.” Biochemical Society Transactions,
vol. 41, no. 5, Portland Press, 2013, pp. 1265–71, doi:10.1042/BST20130193.
short: L.A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, G. Minhas, Biochemical
Society Transactions 41 (2013) 1265–1271.
date_created: 2018-12-11T11:55:00Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2021-01-12T06:54:28Z
day: '01'
doi: 10.1042/BST20130193
extern: 1
intvolume: ' 41'
issue: '5'
month: '10'
page: 1265 - 1271
publication: Biochemical Society Transactions
publication_status: published
publisher: Portland Press
publist_id: '5106'
quality_controlled: 0
status: public
title: A long road towards the structure of respiratory complex I, a giant molecular
proton pump
type: journal_article
volume: 41
year: '2013'
...
---
_id: '15162'
abstract:
- lang: eng
text: Cytological profiling (CP) is an unbiased image-based screening technique
that uses automated microscopy and image analysis to profile compounds based on
numerous quantifiable phenotypic features. We used CP to evaluate a library of
nearly 500 compounds with documented mechanisms of action (MOAs) spanning a wide
range of biological pathways. We developed informatics techniques for generating
dosage-independent phenotypic “fingerprints” for each compound, and for quantifying
the likelihood that a compound's CP fingerprint corresponds to its annotated MOA.
We identified groups of features that distinguish classes with closely related
phenotypes, such as microtubule poisons vs. HSP90 inhibitors, and DNA synthesis
vs. proteasome inhibitors. We tested several cases in which cytological profiles
indicated novel mechanisms, including a tyrphostin kinase inhibitor involved in
mitochondrial uncoupling, novel microtubule poisons, and a nominal PPAR-gamma
ligand that acts as a proteasome inhibitor, using independent biochemical assays
to confirm the MOAs predicted by the CP signatures. We also applied maximal-information
statistics to identify correlations between cytological features and kinase inhibitory
activities by combining the CP fingerprints of 24 kinase inhibitors with published
data on their specificities against a diverse panel of kinases. The resulting
analysis suggests a strategy for probing the biological functions of specific
kinases by compiling cytological data from inhibitors of varying specificities.
article_number: '2604'
article_processing_charge: No
article_type: original
author:
- first_name: Marcos H.
full_name: Woehrmann, Marcos H.
last_name: Woehrmann
- first_name: Walter M.
full_name: Bray, Walter M.
last_name: Bray
- first_name: James K.
full_name: Durbin, James K.
last_name: Durbin
- first_name: Sean C.
full_name: Nisam, Sean C.
last_name: Nisam
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Emerson
full_name: Glassey, Emerson
last_name: Glassey
- first_name: Joshua M.
full_name: Stuart, Joshua M.
last_name: Stuart
- first_name: R. Scott
full_name: Lokey, R. Scott
last_name: Lokey
citation:
ama: Woehrmann MH, Bray WM, Durbin JK, et al. Large-scale cytological profiling
for functional analysis of bioactive compounds. Molecular BioSystems. 2013;9(11).
doi:10.1039/c3mb70245f
apa: Woehrmann, M. H., Bray, W. M., Durbin, J. K., Nisam, S. C., Michael, A. K.,
Glassey, E., … Lokey, R. S. (2013). Large-scale cytological profiling for functional
analysis of bioactive compounds. Molecular BioSystems. Royal Society of
Chemistry. https://doi.org/10.1039/c3mb70245f
chicago: Woehrmann, Marcos H., Walter M. Bray, James K. Durbin, Sean C. Nisam, Alicia
K. Michael, Emerson Glassey, Joshua M. Stuart, and R. Scott Lokey. “Large-Scale
Cytological Profiling for Functional Analysis of Bioactive Compounds.” Molecular
BioSystems. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3mb70245f.
ieee: M. H. Woehrmann et al., “Large-scale cytological profiling for functional
analysis of bioactive compounds,” Molecular BioSystems, vol. 9, no. 11.
Royal Society of Chemistry, 2013.
ista: Woehrmann MH, Bray WM, Durbin JK, Nisam SC, Michael AK, Glassey E, Stuart
JM, Lokey RS. 2013. Large-scale cytological profiling for functional analysis
of bioactive compounds. Molecular BioSystems. 9(11), 2604.
mla: Woehrmann, Marcos H., et al. “Large-Scale Cytological Profiling for Functional
Analysis of Bioactive Compounds.” Molecular BioSystems, vol. 9, no. 11,
2604, Royal Society of Chemistry, 2013, doi:10.1039/c3mb70245f.
short: M.H. Woehrmann, W.M. Bray, J.K. Durbin, S.C. Nisam, A.K. Michael, E. Glassey,
J.M. Stuart, R.S. Lokey, Molecular BioSystems 9 (2013).
date_created: 2024-03-21T07:58:57Z
date_published: 2013-08-20T00:00:00Z
date_updated: 2024-03-25T11:45:46Z
day: '20'
doi: 10.1039/c3mb70245f
extern: '1'
intvolume: ' 9'
issue: '11'
keyword:
- Molecular Biology
- Biotechnology
language:
- iso: eng
month: '08'
oa_version: None
publication: Molecular BioSystems
publication_identifier:
eissn:
- 1742-2051
issn:
- 1742-206X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Large-scale cytological profiling for functional analysis of bioactive compounds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '10749'
abstract:
- lang: eng
text: Fluxoid quantization provides a direct means to study phase coherence. In
cuprate superconductors, there have been observations which suggest that phase
coherent superconducting fluctuations may persist at temperatures significantly
above Tc. The focus of this work is to study the vortex states in mesoscopic cuprate
superconducting samples to directly probe phase coherence over a wide range of
temperatures. We present cantilever torque susceptometry measurements of micron
and sub-micron size Bi2212 rings and disks. The high sensitivity of this technique
allowed observation of transitions between different fluxoid states of a single
ring, and the discrete vortex states of micron size disks. The dependence of magnetic
susceptibility on diameter and wall thickness of the ring was investigated. Measurements
were made at different values of the in-plane magnetic field, and over a wide
range of temperatures.
acknowledgement: This work was supported by the Center for Emergent Superconductivity,
an Energy Frontier Research Center funded by the US DOE, Office of Science.
alternative_title:
- Bulletin of the American Physical Society
article_number: N36.00001
article_processing_charge: No
author:
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: Raffi
full_name: Budakian, Raffi
last_name: Budakian
- first_name: Genda
full_name: Gu, Genda
last_name: Gu
citation:
ama: 'Polshyn H, Budakian R, Gu G. Cantilever micro-susceptometry of mesoscopic
Bi2212 samples. In: APS March Meeting 2013. Vol 58. American Physical Society;
2013.'
apa: 'Polshyn, H., Budakian, R., & Gu, G. (2013). Cantilever micro-susceptometry
of mesoscopic Bi2212 samples. In APS March Meeting 2013 (Vol. 58). Baltimore,
MD, United States: American Physical Society.'
chicago: Polshyn, Hryhoriy, Raffi Budakian, and Genda Gu. “Cantilever Micro-Susceptometry
of Mesoscopic Bi2212 Samples.” In APS March Meeting 2013, Vol. 58. American
Physical Society, 2013.
ieee: H. Polshyn, R. Budakian, and G. Gu, “Cantilever micro-susceptometry of mesoscopic
Bi2212 samples,” in APS March Meeting 2013, Baltimore, MD, United States,
2013, vol. 58, no. 1.
ista: 'Polshyn H, Budakian R, Gu G. 2013. Cantilever micro-susceptometry of mesoscopic
Bi2212 samples. APS March Meeting 2013. APS: American Physical Society, Bulletin
of the American Physical Society, vol. 58, N36.00001.'
mla: Polshyn, Hryhoriy, et al. “Cantilever Micro-Susceptometry of Mesoscopic Bi2212
Samples.” APS March Meeting 2013, vol. 58, no. 1, N36.00001, American Physical
Society, 2013.
short: H. Polshyn, R. Budakian, G. Gu, in:, APS March Meeting 2013, American Physical
Society, 2013.
conference:
end_date: 2013-03-22
location: Baltimore, MD, United States
name: 'APS: American Physical Society'
start_date: 2013-03-18
date_created: 2022-02-08T10:34:29Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2022-02-08T10:48:06Z
day: '01'
extern: '1'
intvolume: ' 58'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://meetings.aps.org/Meeting/MAR13/Event/186873
month: '03'
oa: 1
oa_version: Published Version
publication: APS March Meeting 2013
publication_identifier:
issn:
- 0003-0503
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Cantilever micro-susceptometry of mesoscopic Bi2212 samples
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 58
year: '2013'
...
---
_id: '10895'
abstract:
- lang: eng
text: 'Due to their sessile lifestyles, plants need to deal with the limitations
and stresses imposed by the changing environment. Plants cope with these by a
remarkable developmental flexibility, which is embedded in their strategy to survive.
Plants can adjust their size, shape and number of organs, bend according to gravity
and light, and regenerate tissues that were damaged, utilizing a coordinating,
intercellular signal, the plant hormone, auxin. Another versatile signal is the
cation, Ca2+, which is a crucial second messenger for many rapid cellular processes
during responses to a wide range of endogenous and environmental signals, such
as hormones, light, drought stress and others. Auxin is a good candidate for one
of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling
is poorly understood. Here, we will provide an overview of possible developmental
and physiological roles, as well as mechanisms underlying the interconnection
of Ca2+ and auxin signaling. '
article_processing_charge: No
article_type: original
author:
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Vanneste S, Friml J. Calcium: The missing link in auxin action. Plants.
2013;2(4):650-675. doi:10.3390/plants2040650'
apa: 'Vanneste, S., & Friml, J. (2013). Calcium: The missing link in auxin action.
Plants. MDPI. https://doi.org/10.3390/plants2040650'
chicago: 'Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin
Action.” Plants. MDPI, 2013. https://doi.org/10.3390/plants2040650.'
ieee: 'S. Vanneste and J. Friml, “Calcium: The missing link in auxin action,” Plants,
vol. 2, no. 4. MDPI, pp. 650–675, 2013.'
ista: 'Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants.
2(4), 650–675.'
mla: 'Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.”
Plants, vol. 2, no. 4, MDPI, 2013, pp. 650–75, doi:10.3390/plants2040650.'
short: S. Vanneste, J. Friml, Plants 2 (2013) 650–675.
corr_author: '1'
date_created: 2022-03-21T07:13:49Z
date_published: 2013-10-21T00:00:00Z
date_updated: 2024-10-09T21:01:52Z
day: '21'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3390/plants2040650
external_id:
pmid:
- '27137397'
file:
- access_level: open_access
checksum: fb4ff2e820e344e253c9197544610be6
content_type: application/pdf
creator: dernst
date_created: 2022-03-21T12:12:56Z
date_updated: 2022-03-21T12:12:56Z
file_id: '10916'
file_name: 2013_Plants_Vanneste.pdf
file_size: 670188
relation: main_file
success: 1
file_date_updated: 2022-03-21T12:12:56Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '4'
keyword:
- Plant Science
- Ecology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '10'
oa: 1
oa_version: Published Version
page: 650-675
pmid: 1
publication: Plants
publication_identifier:
issn:
- 2223-7747
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Calcium: The missing link in auxin action'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2013'
...
---
_id: '10897'
abstract:
- lang: eng
text: Taking images is an efficient way to collect data about the physical world.
It can be done fast and in exquisite detail. By definition, image processing is
the field that concerns itself with the computation aimed at harnessing the information
contained in images [10]. This talk is concerned with topological information.
Our main thesis is that persistent homology [5] is a useful method to quantify
and summarize topological information, building a bridge that connects algebraic
topology with applications. We provide supporting evidence for this thesis by
touching upon four technical developments in the overlap between persistent homology
and image processing.
acknowledgement: This research is partially supported by the European Science Foundation
(ESF) under the Research Network Programme, the European Union under the Toposys
Project FP7-ICT-318493-STREP, the Russian Government under the Mega Project 11.G34.31.0053.
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Edelsbrunner H. Persistent homology in image processing. In: Graph-Based
Representations in Pattern Recognition. Vol 7877. LNCS. Berlin, Heidelberg:
Springer Nature; 2013:182-183. doi:10.1007/978-3-642-38221-5_19'
apa: 'Edelsbrunner, H. (2013). Persistent homology in image processing. In Graph-Based
Representations in Pattern Recognition (Vol. 7877, pp. 182–183). Berlin, Heidelberg:
Springer Nature. https://doi.org/10.1007/978-3-642-38221-5_19'
chicago: 'Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” In Graph-Based
Representations in Pattern Recognition, 7877:182–83. LNCS. Berlin, Heidelberg:
Springer Nature, 2013. https://doi.org/10.1007/978-3-642-38221-5_19.'
ieee: H. Edelsbrunner, “Persistent homology in image processing,” in Graph-Based
Representations in Pattern Recognition, Vienna, Austria, 2013, vol. 7877,
pp. 182–183.
ista: 'Edelsbrunner H. 2013. Persistent homology in image processing. Graph-Based
Representations in Pattern Recognition. GbRPR: Graph-based Representations in
Pattern RecognitionLNCS vol. 7877, 182–183.'
mla: Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” Graph-Based
Representations in Pattern Recognition, vol. 7877, Springer Nature, 2013,
pp. 182–83, doi:10.1007/978-3-642-38221-5_19.
short: H. Edelsbrunner, in:, Graph-Based Representations in Pattern Recognition,
Springer Nature, Berlin, Heidelberg, 2013, pp. 182–183.
conference:
end_date: 2013-05-17
location: Vienna, Austria
name: 'GbRPR: Graph-based Representations in Pattern Recognition'
start_date: 2013-05-15
corr_author: '1'
date_created: 2022-03-21T07:30:33Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2025-04-15T08:37:54Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-642-38221-5_19
ec_funded: 1
intvolume: ' 7877'
language:
- iso: eng
month: '06'
oa_version: None
page: 182-183
place: Berlin, Heidelberg
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Graph-Based Representations in Pattern Recognition
publication_identifier:
eisbn:
- '9783642382215'
eissn:
- 1611-3349
isbn:
- '9783642382208'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: Persistent homology in image processing
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7877
year: '2013'
...
---
_id: '10898'
abstract:
- lang: eng
text: A prominent remedy to multicore scalability issues in concurrent data structure
implementations is to relax the sequential specification of the data structure.
We present distributed queues (DQ), a new family of relaxed concurrent queue implementations.
DQs implement relaxed queues with linearizable emptiness check and either configurable
or bounded out-of-order behavior or pool behavior. Our experiments show that DQs
outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue
as well as pool implementations that we considered.
acknowledgement: This work has been supported by the European Research Council advanced
grant on Quantitative Reactive Modeling (QUAREM) and the National Research Network
RiSE on Rigorous Systems Engineering (Austrian Science Fund S11402-N23 and S11404-N23).
article_number: '17'
article_processing_charge: No
author:
- first_name: Andreas
full_name: Haas, Andreas
last_name: Haas
- first_name: Michael
full_name: Lippautz, Michael
last_name: Lippautz
- 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: Hannes
full_name: Payer, Hannes
last_name: Payer
- first_name: Ana
full_name: Sokolova, Ana
last_name: Sokolova
- first_name: Christoph M.
full_name: Kirsch, Christoph M.
last_name: Kirsch
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
citation:
ama: 'Haas A, Lippautz M, Henzinger TA, et al. Distributed queues in shared memory:
Multicore performance and scalability through quantitative relaxation. In: Proceedings
of the ACM International Conference on Computing Frontiers - CF ’13. ACM;
2013. doi:10.1145/2482767.2482789'
apa: 'Haas, A., Lippautz, M., Henzinger, T. A., Payer, H., Sokolova, A., Kirsch,
C. M., & Sezgin, A. (2013). Distributed queues in shared memory: Multicore
performance and scalability through quantitative relaxation. In Proceedings
of the ACM International Conference on Computing Frontiers - CF ’13. Ischia,
Italy: ACM. https://doi.org/10.1145/2482767.2482789'
chicago: 'Haas, Andreas, Michael Lippautz, Thomas A Henzinger, Hannes Payer, Ana
Sokolova, Christoph M. Kirsch, and Ali Sezgin. “Distributed Queues in Shared Memory:
Multicore Performance and Scalability through Quantitative Relaxation.” In Proceedings
of the ACM International Conference on Computing Frontiers - CF ’13. ACM,
2013. https://doi.org/10.1145/2482767.2482789.'
ieee: 'A. Haas et al., “Distributed queues in shared memory: Multicore performance
and scalability through quantitative relaxation,” in Proceedings of the ACM
International Conference on Computing Frontiers - CF ’13, Ischia, Italy, 2013,
no. 5.'
ista: 'Haas A, Lippautz M, Henzinger TA, Payer H, Sokolova A, Kirsch CM, Sezgin
A. 2013. Distributed queues in shared memory: Multicore performance and scalability
through quantitative relaxation. Proceedings of the ACM International Conference
on Computing Frontiers - CF ’13. CF: Conference on Computing Frontiers, 17.'
mla: 'Haas, Andreas, et al. “Distributed Queues in Shared Memory: Multicore Performance
and Scalability through Quantitative Relaxation.” Proceedings of the ACM International
Conference on Computing Frontiers - CF ’13, no. 5, 17, ACM, 2013, doi:10.1145/2482767.2482789.'
short: A. Haas, M. Lippautz, T.A. Henzinger, H. Payer, A. Sokolova, C.M. Kirsch,
A. Sezgin, in:, Proceedings of the ACM International Conference on Computing Frontiers
- CF ’13, ACM, 2013.
conference:
end_date: 2013-05-16
location: Ischia, Italy
name: 'CF: Conference on Computing Frontiers'
start_date: 2013-05-14
date_created: 2022-03-21T07:33:22Z
date_published: 2013-05-14T00:00:00Z
date_updated: 2025-05-14T11:23:58Z
day: '14'
department:
- _id: ToHe
doi: 10.1145/2482767.2482789
ec_funded: 1
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: Proceedings of the ACM International Conference on Computing Frontiers
- CF '13
publication_identifier:
isbn:
- 978-145032053-5
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Distributed queues in shared memory: Multicore performance and scalability
through quantitative relaxation'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...