---
_id: '3574'
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Edelsbrunner H. Biological applications of computational topology. In: Handbook
of Discrete and Computational Geometry. CRC Press; 2004:1395-1412.'
apa: Edelsbrunner, H. (2004). Biological applications of computational topology.
In Handbook of Discrete and Computational Geometry (pp. 1395–1412). CRC
Press.
chicago: Edelsbrunner, Herbert. “Biological Applications of Computational Topology.”
In Handbook of Discrete and Computational Geometry, 1395–1412. CRC Press,
2004.
ieee: H. Edelsbrunner, “Biological applications of computational topology,” in Handbook
of Discrete and Computational Geometry, CRC Press, 2004, pp. 1395–1412.
ista: 'Edelsbrunner H. 2004.Biological applications of computational topology. In:
Handbook of Discrete and Computational Geometry. , 1395–1412.'
mla: Edelsbrunner, Herbert. “Biological Applications of Computational Topology.”
Handbook of Discrete and Computational Geometry, CRC Press, 2004, pp. 1395–412.
short: H. Edelsbrunner, in:, Handbook of Discrete and Computational Geometry, CRC
Press, 2004, pp. 1395–1412.
date_created: 2018-12-11T12:04:02Z
date_published: 2004-04-15T00:00:00Z
date_updated: 2021-01-12T07:44:24Z
day: '15'
extern: 1
main_file_link:
- open_access: '0'
url: http://www.cs.duke.edu/~edels/Papers/2004-B-01-BiologicalApplicationsTopology.pdf
month: '04'
page: 1395 - 1412
publication: Handbook of Discrete and Computational Geometry
publication_status: published
publisher: CRC Press
publist_id: '2811'
quality_controlled: 0
status: public
title: Biological applications of computational topology
type: book_chapter
year: '2004'
...
---
_id: '3595'
abstract:
- lang: eng
text: Genome sizes vary enormously. This variation in DNA content correlates with
effective population size, suggesting that deleterious additions to the genome
can accumulate in small populations. On this view, the increased complexity of
biological functions associated with large genomes partly reflects evolutionary
degeneration.
author:
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Charlesworth B, Barton NH. Genome size: Does bigger mean worse? Current
Biology. 2004;14(6):R233-R235. doi:10.1016/j.cub.2004.02.054'
apa: 'Charlesworth, B., & Barton, N. H. (2004). Genome size: Does bigger mean
worse? Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2004.02.054'
chicago: 'Charlesworth, Brian, and Nicholas H Barton. “Genome Size: Does Bigger
Mean Worse?” Current Biology. Cell Press, 2004. https://doi.org/10.1016/j.cub.2004.02.054.'
ieee: 'B. Charlesworth and N. H. Barton, “Genome size: Does bigger mean worse?,”
Current Biology, vol. 14, no. 6. Cell Press, pp. R233–R235, 2004.'
ista: 'Charlesworth B, Barton NH. 2004. Genome size: Does bigger mean worse? Current
Biology. 14(6), R233–R235.'
mla: 'Charlesworth, Brian, and Nicholas H. Barton. “Genome Size: Does Bigger Mean
Worse?” Current Biology, vol. 14, no. 6, Cell Press, 2004, pp. R233–35,
doi:10.1016/j.cub.2004.02.054.'
short: B. Charlesworth, N.H. Barton, Current Biology 14 (2004) R233–R235.
date_created: 2018-12-11T12:04:09Z
date_published: 2004-03-01T00:00:00Z
date_updated: 2019-04-26T07:22:31Z
day: '01'
doi: 10.1016/j.cub.2004.02.054
extern: 1
intvolume: ' 14'
issue: '6'
month: '03'
page: R233 - R235
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '2788'
quality_controlled: 0
status: public
title: 'Genome size: Does bigger mean worse?'
type: review
volume: 14
year: '2004'
...
---
_id: '3614'
abstract:
- lang: eng
text: 'We analyze the changes in the mean and variance components of a quantitative
trait caused by changes in allele frequencies, concentrating on the effects of
genetic drift. We use a general representation of epistasis and dominance that
allows an arbitrary relation between genotype and phenotype for any number of
diallelic loci. We assume initial and final Hardy-Weinberg and linkage equilibrium
in our analyses of drift-induced changes. Random drift generates transient linkage
disequilibria that cause correlations between allele frequency fluctuations at
different loci. However, we show that these have negligible effects, at least
for interactions among small numbers of loci. Our analyses are based on diffusion
approximations that summarize the effects of drift in terms of F, the inbreeding
coefficient, interpreted as the expected proportional decrease in heterozygosity
at each locus. For haploids, the variance of the trait mean after a population
bottleneck is var(Δz̄) =inline imagewhere n is the number of loci contributing
to the trait variance, VA(1)=VA is the additive genetic variance, and VA(k) is
the kth-order additive epistatic variance. The expected additive genetic variance
after the bottleneck, denoted (V*A), is closely related to var(Δz̄);
(V*A) (1 –F)inline imageThus, epistasis inflates the expected additive variance
above VA(1 –F), the expectation under additivity. For haploids (and diploids without
dominance), the expected value of every variance component is inflated by the
existence of higher order interactions (e.g., third-order epistasis inflates (V*AA)).
This is not true in general with diploidy, because dominance alone can reduce
(V*A) below VA(1 –F) (e.g., when dominant alleles are rare). Without dominance,
diploidy produces simple expressions: var(Δz̄)=inline image=1 (2F)
kVA(k) and (V*A) = (1 –F)inline imagek(2F)k-1VA(k) With dominance (and even without
epistasis), var(Δz̄)and (V*A) no longer depend solely on the variance
components in the base population. For small F, the expected additive variance
simplifies to (V*A)(1 –F) VA+ 4FVAA+2FVD+2FCAD, where CAD is a sum of two terms
describing covariances between additive effects and dominance and additive × dominance
interactions. Whether population bottlenecks lead to expected increases in additive
variance depends primarily on the ratio of nonadditive to additive genetic variance
in the base population, but dominance precludes simple predictions based solely
on variance components. We illustrate these results using a model in which genotypic
values are drawn at random, allowing extreme and erratic epistatic interactions.
Although our analyses clarify the conditions under which drift is expected to
increase VA, we question the evolutionary importance of such increases.'
author:
- first_name: Nicholas H
full_name: Nicholas Barton
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. Effects of allele frequency changes on variance components
under a general model of epistasis. Evolution; International Journal of Organic
Evolution. 2004;58(10):2111-2132. doi:10.1111/j.0014-3820.2004.tb01591.x
apa: Barton, N. H., & Turelli, M. (2004). Effects of allele frequency changes
on variance components under a general model of epistasis. Evolution; International
Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2004.tb01591.x
chicago: Barton, Nicholas H, and Michael Turelli. “Effects of Allele Frequency Changes
on Variance Components under a General Model of Epistasis.” Evolution; International
Journal of Organic Evolution. Wiley-Blackwell, 2004. https://doi.org/10.1111/j.0014-3820.2004.tb01591.x.
ieee: N. H. Barton and M. Turelli, “Effects of allele frequency changes on variance
components under a general model of epistasis,” Evolution; International Journal
of Organic Evolution, vol. 58, no. 10. Wiley-Blackwell, pp. 2111–2132, 2004.
ista: Barton NH, Turelli M. 2004. Effects of allele frequency changes on variance
components under a general model of epistasis. Evolution; International Journal
of Organic Evolution. 58(10), 2111–2132.
mla: Barton, Nicholas H., and Michael Turelli. “Effects of Allele Frequency Changes
on Variance Components under a General Model of Epistasis.” Evolution; International
Journal of Organic Evolution, vol. 58, no. 10, Wiley-Blackwell, 2004, pp.
2111–32, doi:10.1111/j.0014-3820.2004.tb01591.x.
short: N.H. Barton, M. Turelli, Evolution; International Journal of Organic Evolution
58 (2004) 2111–2132.
date_created: 2018-12-11T12:04:15Z
date_published: 2004-10-01T00:00:00Z
date_updated: 2021-01-12T07:44:40Z
day: '01'
doi: 10.1111/j.0014-3820.2004.tb01591.x
extern: 1
intvolume: ' 58'
issue: '10'
month: '10'
page: 2111 - 2132
publication: Evolution; International Journal of Organic Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2769'
quality_controlled: 0
status: public
title: Effects of allele frequency changes on variance components under a general
model of epistasis
type: journal_article
volume: 58
year: '2004'
...
---
_id: '3615'
abstract:
- lang: eng
text: 'We investigate three alternative selection-based scenarios proposed to maintain
polygenic variation: pleiotropic balancing selection, G x E interactions (with
spatial or temporal variation in allelic effects), and sex-dependent allelic effects.
Each analysis assumes an additive polygenic trait with n diallelic loci under
stabilizing selection. We allow loci to have different effects and consider equilibria
at which the population mean departs from the stabilizing-selection optimum. Under
weak selection, each model produces essentially identical, approximate allele-frequency
dynamics. Variation is maintained under pleiotropic balancing selection only at
loci for which the strength of balancing selection exceeds the effective strength
of stabilizing selection. In addition, for all models, polymorphism requires that
the population mean be close enough to the optimum that directional selection
does not overwhelm balancing selection. This balance allows many simultaneously
stable equilibria, and we explore their properties numerically. Both spatial and
temporal G x E can maintain variation at loci for which the coefficient of variation
(across environments) of the effect of a substitution exceeds a critical value
greater than one. The critical value depends on the correlation between substitution
effects at different loci. For large positive correlations (e.g., ρ2ij > 3/4),
even extreme fluctuations in allelic effects cannot maintain variation. Surprisingly,
this constraint on correlations implies that sex-dependent allelic effects cannot
maintain polygenic variation. We present numerical results that support our analytical
approximations and discuss our results in connection to relevant data and alternative
variance-maintaining mechanisms.'
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Turelli M, Barton NH. Polygenic variation maintained by balancing selection:
pleiotropy, sex-dependent allelic effects and GxE interactions. Genetics.
2004;166(2):1053-1079. doi:10.1534/genetics.166.2.1053'
apa: 'Turelli, M., & Barton, N. H. (2004). Polygenic variation maintained by
balancing selection: pleiotropy, sex-dependent allelic effects and GxE interactions.
Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.166.2.1053'
chicago: 'Turelli, Michael, and Nicholas H Barton. “Polygenic Variation Maintained
by Balancing Selection: Pleiotropy, Sex-Dependent Allelic Effects and GxE Interactions.”
Genetics. Genetics Society of America, 2004. https://doi.org/10.1534/genetics.166.2.1053.'
ieee: 'M. Turelli and N. H. Barton, “Polygenic variation maintained by balancing
selection: pleiotropy, sex-dependent allelic effects and GxE interactions,” Genetics,
vol. 166, no. 2. Genetics Society of America, pp. 1053–1079, 2004.'
ista: 'Turelli M, Barton NH. 2004. Polygenic variation maintained by balancing selection:
pleiotropy, sex-dependent allelic effects and GxE interactions. Genetics. 166(2),
1053–1079.'
mla: 'Turelli, Michael, and Nicholas H. Barton. “Polygenic Variation Maintained
by Balancing Selection: Pleiotropy, Sex-Dependent Allelic Effects and GxE Interactions.”
Genetics, vol. 166, no. 2, Genetics Society of America, 2004, pp. 1053–79,
doi:10.1534/genetics.166.2.1053.'
short: M. Turelli, N.H. Barton, Genetics 166 (2004) 1053–1079.
date_created: 2018-12-11T12:04:15Z
date_published: 2004-02-01T00:00:00Z
date_updated: 2021-01-12T07:44:41Z
day: '01'
doi: 10.1534/genetics.166.2.1053
extern: 1
intvolume: ' 166'
issue: '2'
month: '02'
page: 1053 - 1079
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '2768'
quality_controlled: 0
status: public
title: 'Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent
allelic effects and GxE interactions'
type: journal_article
volume: 166
year: '2004'
...
---
_id: '3807'
abstract:
- lang: eng
text: The time course of Mg(2+) block and unblock of NMDA receptors (NMDARs) determines
the extent they are activated by depolarization. Here, we directly measure the
rate of NMDAR channel opening in response to depolarizations at different times
after brief (1 ms) and sustained (4.6 s) applications of glutamate to nucleated
patches from neocortical pyramidal neurons. The kinetics of Mg(2+) unblock were
found to be non-instantaneous and complex, consisting of a prominent fast component
(time constant approximately 100 micros) and slower components (time constants
4 and approximately 300 ms), the relative amplitudes of which depended on the
timing of the depolarizing pulse. Fitting a kinetic model to these data indicated
that Mg(2+) not only blocks the NMDAR channel, but reduces both the open probability
and affinity for glutamate, while enhancing desensitization. These effects slow
the rate of NMDAR channel opening in response to depolarization in a time-dependent
manner such that the slower components of Mg(2+) unblock are enhanced during depolarizations
at later times after glutamate application. One physiological consequence of this
is that brief depolarizations occurring earlier in time after glutamate application
are better able to open NMDAR channels. This finding has important implications
for spike-timing-dependent synaptic plasticity (STDP), where the precise (millisecond)
timing of action potentials relative to synaptic inputs determines the magnitude
and sign of changes in synaptic strength. Indeed, we find that STDP timing curves
of NMDAR channel activation elicited by realistic dendritic action potential waveforms
are narrower than expected assuming instantaneous Mg(2+) unblock, indicating that
slow Mg(2+) unblock of NMDAR channels makes the STDP timing window more precise.
author:
- first_name: Bjorn
full_name: Kampa, Bjorn M
last_name: Kampa
- first_name: John
full_name: Clements, John
last_name: Clements
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Greg
full_name: Stuart, Greg J
last_name: Stuart
citation:
ama: 'Kampa B, Clements J, Jonas PM, Stuart G. Kinetics of Mg(2+) unblock of NMDA
receptors: implications for spike-timing dependent synaptic plasticity. Journal
of Physiology. 2004;556(Pt 2):337-345. doi:10.1113/jphysiol.2003.058842 '
apa: 'Kampa, B., Clements, J., Jonas, P. M., & Stuart, G. (2004). Kinetics of
Mg(2+) unblock of NMDA receptors: implications for spike-timing dependent synaptic
plasticity. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2003.058842 '
chicago: 'Kampa, Bjorn, John Clements, Peter M Jonas, and Greg Stuart. “Kinetics
of Mg(2+) Unblock of NMDA Receptors: Implications for Spike-Timing Dependent Synaptic
Plasticity.” Journal of Physiology. Wiley-Blackwell, 2004. https://doi.org/10.1113/jphysiol.2003.058842 .'
ieee: 'B. Kampa, J. Clements, P. M. Jonas, and G. Stuart, “Kinetics of Mg(2+) unblock
of NMDA receptors: implications for spike-timing dependent synaptic plasticity,”
Journal of Physiology, vol. 556, no. Pt 2. Wiley-Blackwell, pp. 337–45,
2004.'
ista: 'Kampa B, Clements J, Jonas PM, Stuart G. 2004. Kinetics of Mg(2+) unblock
of NMDA receptors: implications for spike-timing dependent synaptic plasticity.
Journal of Physiology. 556(Pt 2), 337–45.'
mla: 'Kampa, Bjorn, et al. “Kinetics of Mg(2+) Unblock of NMDA Receptors: Implications
for Spike-Timing Dependent Synaptic Plasticity.” Journal of Physiology,
vol. 556, no. Pt 2, Wiley-Blackwell, 2004, pp. 337–45, doi:10.1113/jphysiol.2003.058842 .'
short: B. Kampa, J. Clements, P.M. Jonas, G. Stuart, Journal of Physiology 556 (2004)
337–45.
date_created: 2018-12-11T12:05:17Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:20Z
day: '01'
doi: '10.1113/jphysiol.2003.058842 '
extern: 1
intvolume: ' 556'
issue: Pt 2
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664940/
month: '01'
oa: 1
page: 337 - 45
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2403'
quality_controlled: 0
status: public
title: 'Kinetics of Mg(2+) unblock of NMDA receptors: implications for spike-timing
dependent synaptic plasticity'
type: journal_article
volume: 556
year: '2004'
...
---
_id: '3809'
abstract:
- lang: eng
text: Neural stem cells in various regions of the vertebrate brain continuously
generate neurons throughout life. In the mammalian hippocampus, a region important
for spatial and episodic memory, thousands of new granule cells are produced per
day, with the exact number depending on environmental conditions and physical
exercise. The survival of these neurons is improved by learning and conversely
learning may be promoted by neurogenesis. Although it has been suggested that
newly generated neurons may have specific properties to facilitate learning, the
cellular and synaptic mechanisms of plasticity in these neurons are largely unknown.
Here we show that young granule cells in the adult hippocampus differ substantially
from mature granule cells in both active and passive membrane properties. In young
neurons, T-type Ca2+ channels can generate isolated Ca2+ spikes and boost fast
Na+ action potentials, contributing to the induction of synaptic plasticity. Associative
long-term potentiation can be induced more easily in young neurons than in mature
neurons under identical conditions. Thus, newly generated neurons express unique
mechanisms to facilitate synaptic plasticity, which may be important for the formation
of new memories.
author:
- first_name: Christoph
full_name: Schmidt-Hieber, Christoph
last_name: Schmidt Hieber
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
citation:
ama: Schmidt Hieber C, Jonas PM, Bischofberger J. Enhanced synaptic plasticity in
newly generated granule cells of the adult hippocampus. Nature. 2004;429(6988):184-187.
doi:10.1038/nature02553
apa: Schmidt Hieber, C., Jonas, P. M., & Bischofberger, J. (2004). Enhanced
synaptic plasticity in newly generated granule cells of the adult hippocampus.
Nature. Nature Publishing Group. https://doi.org/10.1038/nature02553
chicago: Schmidt Hieber, Christoph, Peter M Jonas, and Josef Bischofberger. “Enhanced
Synaptic Plasticity in Newly Generated Granule Cells of the Adult Hippocampus.”
Nature. Nature Publishing Group, 2004. https://doi.org/10.1038/nature02553.
ieee: C. Schmidt Hieber, P. M. Jonas, and J. Bischofberger, “Enhanced synaptic plasticity
in newly generated granule cells of the adult hippocampus,” Nature, vol.
429, no. 6988. Nature Publishing Group, pp. 184–7, 2004.
ista: Schmidt Hieber C, Jonas PM, Bischofberger J. 2004. Enhanced synaptic plasticity
in newly generated granule cells of the adult hippocampus. Nature. 429(6988),
184–7.
mla: Schmidt Hieber, Christoph, et al. “Enhanced Synaptic Plasticity in Newly Generated
Granule Cells of the Adult Hippocampus.” Nature, vol. 429, no. 6988, Nature
Publishing Group, 2004, pp. 184–87, doi:10.1038/nature02553.
short: C. Schmidt Hieber, P.M. Jonas, J. Bischofberger, Nature 429 (2004) 184–7.
date_created: 2018-12-11T12:05:17Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:21Z
day: '01'
doi: 10.1038/nature02553
extern: 1
intvolume: ' 429'
issue: '6988'
month: '01'
page: 184 - 7
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '2401'
quality_controlled: 0
status: public
title: Enhanced synaptic plasticity in newly generated granule cells of the adult
hippocampus
type: journal_article
volume: 429
year: '2004'
...
---
_id: '3805'
abstract:
- lang: eng
text: The operation of neuronal networks crucially depends on a fast time course
of signaling in inhibitory interneurons. Synapses that excite interneurons generate
fast currents, owing to the expression of glutamate receptors of specific subunit
composition. Interneurons generate brief action potentials in response to transient
synaptic activation and discharge repetitively at very high frequencies during
sustained stimulation. The ability to generate short-duration action potentials
at high frequencies depends on the expression of specific voltage-gated K+ channels.
Factors facilitating fast action potential initiation following synaptic excitation
include depolarized interneuron resting potential, subthreshold conductances and
active dendrites. Finally, GABA release at interneuron output synapses is rapid
and highly synchronized, leading to a faster inhibition in postsynaptic interneurons
than in principal cells. Thus, the expression of distinct transmitter receptors
and voltage-gated ion channels ensures that interneurons operate with high speed
and temporal precision.
author:
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
- first_name: Desdemona
full_name: Fricker, Desdemona
last_name: Fricker
- first_name: Richard
full_name: Miles, Richard
last_name: Miles
citation:
ama: 'Jonas PM, Bischofberger J, Fricker D, Miles R. Interneuron Diversity series:
Fast in, fast out--temporal and spatial signal processing in hippocampal interneurons.
Trends in Neurosciences. 2004;27(1):30-40. doi:doi:10.1016/j.tins.2003.10.010'
apa: 'Jonas, P. M., Bischofberger, J., Fricker, D., & Miles, R. (2004). Interneuron
Diversity series: Fast in, fast out--temporal and spatial signal processing in
hippocampal interneurons. Trends in Neurosciences. Elsevier. https://doi.org/doi:10.1016/j.tins.2003.10.010'
chicago: 'Jonas, Peter M, Josef Bischofberger, Desdemona Fricker, and Richard Miles.
“Interneuron Diversity Series: Fast in, Fast out--Temporal and Spatial Signal
Processing in Hippocampal Interneurons.” Trends in Neurosciences. Elsevier,
2004. https://doi.org/doi:10.1016/j.tins.2003.10.010.'
ieee: 'P. M. Jonas, J. Bischofberger, D. Fricker, and R. Miles, “Interneuron Diversity
series: Fast in, fast out--temporal and spatial signal processing in hippocampal
interneurons,” Trends in Neurosciences, vol. 27, no. 1. Elsevier, pp. 30–40,
2004.'
ista: 'Jonas PM, Bischofberger J, Fricker D, Miles R. 2004. Interneuron Diversity
series: Fast in, fast out--temporal and spatial signal processing in hippocampal
interneurons. Trends in Neurosciences. 27(1), 30–40.'
mla: 'Jonas, Peter M., et al. “Interneuron Diversity Series: Fast in, Fast out--Temporal
and Spatial Signal Processing in Hippocampal Interneurons.” Trends in Neurosciences,
vol. 27, no. 1, Elsevier, 2004, pp. 30–40, doi:doi:10.1016/j.tins.2003.10.010.'
short: P.M. Jonas, J. Bischofberger, D. Fricker, R. Miles, Trends in Neurosciences
27 (2004) 30–40.
date_created: 2018-12-11T12:05:16Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:19Z
day: '01'
doi: doi:10.1016/j.tins.2003.10.010
extern: 1
intvolume: ' 27'
issue: '1'
month: '01'
page: 30 - 40
publication: Trends in Neurosciences
publication_status: published
publisher: Elsevier
publist_id: '2404'
quality_controlled: 0
status: public
title: 'Interneuron Diversity series: Fast in, fast out--temporal and spatial signal
processing in hippocampal interneurons'
type: journal_article
volume: 27
year: '2004'
...
---
_id: '3918'
abstract:
- lang: eng
text: Wingless (ergatoid) males of the tramp ant Cardiocondyla minutior attack and
kill their young ergatoid rivals and thus attempt to monopolize mating with female
sexuals reared in the colony. Because of the different strength of local mate
competition in colonies with one or several reproductive queens, we expected the
production of new ergatoid males to vary with queen number. Sex ratios were mostly
female-biased, but in contrast to the sympatric species C. obscurior (Cremer and
Heinze, 2002) neither the percentage of ergatoid males nor of female sexuals among
the first 20 sexuals produced varied considerably with queen number. As in C.
obscurior, experimental colony fragmentation led to the production of winged males,
whereas in unfragmented control colonies only ergatoid males eclosed.
author:
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: A.
full_name: Böttcher, A.
last_name: Böttcher
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Heinze J, Böttcher A, Cremer S. Production of winged and wingless males in
the ant, Cardiocondyla minutior. Insectes Sociaux. 2004;51(3):275-278.
doi:10.1007/s00040-004-0740-6
apa: Heinze, J., Böttcher, A., & Cremer, S. (2004). Production of winged and
wingless males in the ant, Cardiocondyla minutior. Insectes Sociaux. Springer.
https://doi.org/10.1007/s00040-004-0740-6
chicago: Heinze, Jürgen, A. Böttcher, and Sylvia Cremer. “Production of Winged and
Wingless Males in the Ant, Cardiocondyla Minutior.” Insectes Sociaux. Springer,
2004. https://doi.org/10.1007/s00040-004-0740-6.
ieee: J. Heinze, A. Böttcher, and S. Cremer, “Production of winged and wingless
males in the ant, Cardiocondyla minutior,” Insectes Sociaux, vol. 51, no.
3. Springer, pp. 275–278, 2004.
ista: Heinze J, Böttcher A, Cremer S. 2004. Production of winged and wingless males
in the ant, Cardiocondyla minutior. Insectes Sociaux. 51(3), 275–278.
mla: Heinze, Jürgen, et al. “Production of Winged and Wingless Males in the Ant,
Cardiocondyla Minutior.” Insectes Sociaux, vol. 51, no. 3, Springer, 2004,
pp. 275–78, doi:10.1007/s00040-004-0740-6.
short: J. Heinze, A. Böttcher, S. Cremer, Insectes Sociaux 51 (2004) 275–278.
date_created: 2018-12-11T12:05:53Z
date_published: 2004-08-19T00:00:00Z
date_updated: 2021-01-12T07:53:11Z
day: '19'
doi: 10.1007/s00040-004-0740-6
extern: '1'
intvolume: ' 51'
issue: '3'
language:
- iso: eng
month: '08'
oa_version: None
page: 275 - 278
publication: Insectes Sociaux
publication_status: published
publisher: Springer
publist_id: '2236'
status: public
title: Production of winged and wingless males in the ant, Cardiocondyla minutior
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2004'
...
---
_id: '3988'
abstract:
- lang: eng
text: We give an algorithm that locally improves the fit between two proteins modeled
as space-filling diagrams. The algorithm defines the fit in purely geometric terms
and improves by applying a rigid motion to one of the two proteins. Our implementation
of the algorithm takes between three and ten seconds and converges with high likelihood
to the correct docked configuration, provided it starts at a position away from
the correct one by at most 18 degrees of rotation and at most 3.0Angstrom of translation.
The speed and convergence radius make this an attractive algorithm to use in combination
with a coarse sampling of the six-dimensional space of rigid motions.
acknowledgement: Supported by NSF under grant CCR-00-86013, BGT Postdoc Program from
Duke University and NIH under grant R01 GM61822-01.
alternative_title:
- LNCS
author:
- first_name: Vicky
full_name: Choi, Vicky
last_name: Choi
- first_name: Pankaj
full_name: Agarwal, Pankaj K
last_name: Agarwal
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
citation:
ama: 'Choi V, Agarwal P, Edelsbrunner H, Rudolph J. Local search heuristic for rigid
protein docking. In: Vol 3240. Springer; 2004:218-229. doi:10.1007/978-3-540-30219-3_19'
apa: 'Choi, V., Agarwal, P., Edelsbrunner, H., & Rudolph, J. (2004). Local search
heuristic for rigid protein docking (Vol. 3240, pp. 218–229). Presented at the
WABI: 4th International Workshop on Algorithms in Bioinformatics, Springer. https://doi.org/10.1007/978-3-540-30219-3_19'
chicago: Choi, Vicky, Pankaj Agarwal, Herbert Edelsbrunner, and Johannes Rudolph.
“Local Search Heuristic for Rigid Protein Docking,” 3240:218–29. Springer, 2004.
https://doi.org/10.1007/978-3-540-30219-3_19.
ieee: 'V. Choi, P. Agarwal, H. Edelsbrunner, and J. Rudolph, “Local search heuristic
for rigid protein docking,” presented at the WABI: 4th International Workshop
on Algorithms in Bioinformatics, 2004, vol. 3240, pp. 218–229.'
ista: 'Choi V, Agarwal P, Edelsbrunner H, Rudolph J. 2004. Local search heuristic
for rigid protein docking. WABI: 4th International Workshop on Algorithms in Bioinformatics,
LNCS, vol. 3240, 218–229.'
mla: Choi, Vicky, et al. Local Search Heuristic for Rigid Protein Docking.
Vol. 3240, Springer, 2004, pp. 218–29, doi:10.1007/978-3-540-30219-3_19.
short: V. Choi, P. Agarwal, H. Edelsbrunner, J. Rudolph, in:, Springer, 2004, pp.
218–229.
conference:
name: 'WABI: 4th International Workshop on Algorithms in Bioinformatics'
date_created: 2018-12-11T12:06:17Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:41Z
day: '01'
doi: 10.1007/978-3-540-30219-3_19
extern: 1
intvolume: ' 3240'
month: '01'
page: 218 - 229
publication_status: published
publisher: Springer
publist_id: '2136'
quality_controlled: 0
status: public
title: Local search heuristic for rigid protein docking
type: conference
volume: 3240
year: '2004'
...
---
_id: '3986'
abstract:
- lang: eng
text: The motion of a biomolecule greatly depends on the engulfing solution, which
is mostly water. Instead of representing individual water molecules, it is desirable
to develop implicit solvent models that nevertheless accurately represent the
contribution of the solvent interaction to the motion. In such models, hydrophobicity
is expressed as a weighted sum of atomic surface areas. The derivatives of these
weighted areas contribute to the force that drives the motion. In this paper we
give formulas for the weighted and unweighted area derivatives of a molecule modeled
as a space-filling diagram made up of balls in motion. Other than the radii and
the centers of the balls, the formulas are given in terms of the sizes of circular
arcs of the boundary and edges of the power diagram. We also give inclusion-exclusion
formulas for these sizes.
acknowledgement: Partially supported by NSF under grant CCR-00-86013 and NSF under
grant CCR-97-12088.
author:
- first_name: Robert
full_name: Bryant, Robert
last_name: Bryant
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Patrice
full_name: Koehl, Patrice
last_name: Koehl
- first_name: Michael
full_name: Levitt, Michael
last_name: Levitt
citation:
ama: Bryant R, Edelsbrunner H, Koehl P, Levitt M. The area derivative of a space-filling
diagram. Discrete & Computational Geometry. 2004;32(3):293-308. doi:10.1007/s00454-004-1099-1
apa: Bryant, R., Edelsbrunner, H., Koehl, P., & Levitt, M. (2004). The area
derivative of a space-filling diagram. Discrete & Computational Geometry.
Springer. https://doi.org/10.1007/s00454-004-1099-1
chicago: Bryant, Robert, Herbert Edelsbrunner, Patrice Koehl, and Michael Levitt.
“The Area Derivative of a Space-Filling Diagram.” Discrete & Computational
Geometry. Springer, 2004. https://doi.org/10.1007/s00454-004-1099-1.
ieee: R. Bryant, H. Edelsbrunner, P. Koehl, and M. Levitt, “The area derivative
of a space-filling diagram,” Discrete & Computational Geometry, vol.
32, no. 3. Springer, pp. 293–308, 2004.
ista: Bryant R, Edelsbrunner H, Koehl P, Levitt M. 2004. The area derivative of
a space-filling diagram. Discrete & Computational Geometry. 32(3), 293–308.
mla: Bryant, Robert, et al. “The Area Derivative of a Space-Filling Diagram.” Discrete
& Computational Geometry, vol. 32, no. 3, Springer, 2004, pp. 293–308,
doi:10.1007/s00454-004-1099-1.
short: R. Bryant, H. Edelsbrunner, P. Koehl, M. Levitt, Discrete & Computational
Geometry 32 (2004) 293–308.
date_created: 2018-12-11T12:06:17Z
date_published: 2004-09-01T00:00:00Z
date_updated: 2021-01-12T07:53:40Z
day: '01'
doi: 10.1007/s00454-004-1099-1
extern: 1
intvolume: ' 32'
issue: '3'
month: '09'
page: 293 - 308
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2141'
quality_controlled: 0
status: public
title: The area derivative of a space-filling diagram
type: journal_article
volume: 32
year: '2004'
...
---
_id: '3984'
abstract:
- lang: eng
text: We combine topological and geometric methods to construct a multiresolution
representation for a function over a two-dimensional domain. In a preprocessing
stage, we create the Morse-Smale complex of the function and progressively simplify
its topology by cancelling pairs of critical points. Based on a simple notion
of dependency among these cancellations, we construct a hierarchical data structure
supporting traversal and reconstruction operations similarly to traditional geometry-based
representations. We use this data structure to extract topologically valid approximations
that satisfy error bounds provided at runtime.
author:
- first_name: Peer
full_name: Bremer, Peer-Timo
last_name: Bremer
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Bernd
full_name: Hamann, Bernd
last_name: Hamann
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
citation:
ama: Bremer P, Edelsbrunner H, Hamann B, Pascucci V. A topological hierarchy for
functions on triangulated surfaces. IEEE Transactions on Visualization and
Computer Graphics. 2004;10(4):385-396. doi:10.1109/TVCG.2004.3
apa: Bremer, P., Edelsbrunner, H., Hamann, B., & Pascucci, V. (2004). A topological
hierarchy for functions on triangulated surfaces. IEEE Transactions on Visualization
and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2004.3
chicago: Bremer, Peer, Herbert Edelsbrunner, Bernd Hamann, and Valerio Pascucci.
“A Topological Hierarchy for Functions on Triangulated Surfaces.” IEEE Transactions
on Visualization and Computer Graphics. IEEE, 2004. https://doi.org/10.1109/TVCG.2004.3.
ieee: P. Bremer, H. Edelsbrunner, B. Hamann, and V. Pascucci, “A topological hierarchy
for functions on triangulated surfaces,” IEEE Transactions on Visualization
and Computer Graphics, vol. 10, no. 4. IEEE, pp. 385–396, 2004.
ista: Bremer P, Edelsbrunner H, Hamann B, Pascucci V. 2004. A topological hierarchy
for functions on triangulated surfaces. IEEE Transactions on Visualization and
Computer Graphics. 10(4), 385–396.
mla: Bremer, Peer, et al. “A Topological Hierarchy for Functions on Triangulated
Surfaces.” IEEE Transactions on Visualization and Computer Graphics, vol.
10, no. 4, IEEE, 2004, pp. 385–96, doi:10.1109/TVCG.2004.3.
short: P. Bremer, H. Edelsbrunner, B. Hamann, V. Pascucci, IEEE Transactions on
Visualization and Computer Graphics 10 (2004) 385–396.
date_created: 2018-12-11T12:06:16Z
date_published: 2004-07-01T00:00:00Z
date_updated: 2021-01-12T07:53:39Z
day: '01'
doi: 10.1109/TVCG.2004.3
extern: 1
intvolume: ' 10'
issue: '4'
month: '07'
page: 385 - 396
publication: IEEE Transactions on Visualization and Computer Graphics
publication_status: published
publisher: IEEE
publist_id: '2139'
quality_controlled: 0
status: public
title: A topological hierarchy for functions on triangulated surfaces
type: journal_article
volume: 10
year: '2004'
...
---
_id: '3987'
abstract:
- lang: eng
text: 'We consider scientific data sets that describe density functions over three-dimensional
geometric domains. Such data sets are often large and coarsened representations
are needed for visualization and analysis. Assuming a tetrahedral mesh representation,
we construct such representations with a simplification algorithm that combines
three goals: the approximation of the function, the preservation of the mesh topology,
and the improvement of the mesh quality. The third goal is achieved with a novel
extension of the well-known quadric error metric. We perform a number of computational
experiments to understand the effect of mesh quality improvement on the density
map approximation. In addition, we study the effect of geometric simplification
on the topological features of the function by monitoring its critical points.'
author:
- first_name: Vijay
full_name: Natarajan, Vijay
last_name: Natarajan
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Natarajan V, Edelsbrunner H. Simplification of three-dimensional density maps.
IEEE Transactions on Visualization and Computer Graphics. 2004;10(5):587-597.
doi:10.1109/TVCG.2004.32
apa: Natarajan, V., & Edelsbrunner, H. (2004). Simplification of three-dimensional
density maps. IEEE Transactions on Visualization and Computer Graphics.
IEEE. https://doi.org/10.1109/TVCG.2004.32
chicago: Natarajan, Vijay, and Herbert Edelsbrunner. “Simplification of Three-Dimensional
Density Maps.” IEEE Transactions on Visualization and Computer Graphics.
IEEE, 2004. https://doi.org/10.1109/TVCG.2004.32.
ieee: V. Natarajan and H. Edelsbrunner, “Simplification of three-dimensional density
maps,” IEEE Transactions on Visualization and Computer Graphics, vol. 10,
no. 5. IEEE, pp. 587–597, 2004.
ista: Natarajan V, Edelsbrunner H. 2004. Simplification of three-dimensional density
maps. IEEE Transactions on Visualization and Computer Graphics. 10(5), 587–597.
mla: Natarajan, Vijay, and Herbert Edelsbrunner. “Simplification of Three-Dimensional
Density Maps.” IEEE Transactions on Visualization and Computer Graphics,
vol. 10, no. 5, IEEE, 2004, pp. 587–97, doi:10.1109/TVCG.2004.32.
short: V. Natarajan, H. Edelsbrunner, IEEE Transactions on Visualization and Computer
Graphics 10 (2004) 587–597.
date_created: 2018-12-11T12:06:17Z
date_published: 2004-07-12T00:00:00Z
date_updated: 2021-01-12T07:53:40Z
day: '12'
doi: 10.1109/TVCG.2004.32
extern: 1
intvolume: ' 10'
issue: '5'
month: '07'
page: 587 - 597
publication: IEEE Transactions on Visualization and Computer Graphics
publication_status: published
publisher: IEEE
publist_id: '2142'
quality_controlled: 0
status: public
title: Simplification of three-dimensional density maps
type: journal_article
volume: 10
year: '2004'
...
---
_id: '3985'
abstract:
- lang: eng
text: Given a Morse function f over a 2-manifold with or without boundary, the Reeb
graph is obtained by contracting the connected components of the level sets to
points. We prove tight upper and lower bounds on the number of loops in the Reeb
graph that depend on the genus, the number of boundary components, and whether
or not the 2-manifold is orientable. We also give an algorithm that constructs
the Reeb graph in time O(n log n), where n is the number of edges in the triangulation
used to represent the 2-manifold and the Morse function.
acknowledgement: Partially supported by NSF under Grants EIA-99-72879 and CCR-00-86013.
author:
- first_name: Kree
full_name: Cole-McLaughlin, Kree
last_name: Cole Mclaughlin
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Vijay
full_name: Natarajan, Vijay
last_name: Natarajan
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
citation:
ama: Cole Mclaughlin K, Edelsbrunner H, Harer J, Natarajan V, Pascucci V. Loops
in Reeb graphs of 2-manifolds. Discrete & Computational Geometry. 2004;32(2):231-244.
doi:10.1007/s00454-004-1122-6
apa: Cole Mclaughlin, K., Edelsbrunner, H., Harer, J., Natarajan, V., & Pascucci,
V. (2004). Loops in Reeb graphs of 2-manifolds. Discrete & Computational
Geometry. Springer. https://doi.org/10.1007/s00454-004-1122-6
chicago: Cole Mclaughlin, Kree, Herbert Edelsbrunner, John Harer, Vijay Natarajan,
and Valerio Pascucci. “Loops in Reeb Graphs of 2-Manifolds.” Discrete &
Computational Geometry. Springer, 2004. https://doi.org/10.1007/s00454-004-1122-6.
ieee: K. Cole Mclaughlin, H. Edelsbrunner, J. Harer, V. Natarajan, and V. Pascucci,
“Loops in Reeb graphs of 2-manifolds,” Discrete & Computational Geometry,
vol. 32, no. 2. Springer, pp. 231–244, 2004.
ista: Cole Mclaughlin K, Edelsbrunner H, Harer J, Natarajan V, Pascucci V. 2004.
Loops in Reeb graphs of 2-manifolds. Discrete & Computational Geometry. 32(2),
231–244.
mla: Cole Mclaughlin, Kree, et al. “Loops in Reeb Graphs of 2-Manifolds.” Discrete
& Computational Geometry, vol. 32, no. 2, Springer, 2004, pp. 231–44,
doi:10.1007/s00454-004-1122-6.
short: K. Cole Mclaughlin, H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci,
Discrete & Computational Geometry 32 (2004) 231–244.
date_created: 2018-12-11T12:06:16Z
date_published: 2004-07-01T00:00:00Z
date_updated: 2021-01-12T07:53:39Z
day: '01'
doi: 10.1007/s00454-004-1122-6
extern: 1
intvolume: ' 32'
issue: '2'
month: '07'
page: 231 - 244
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2140'
quality_controlled: 0
status: public
title: Loops in Reeb graphs of 2-manifolds
type: journal_article
volume: 32
year: '2004'
...
---
_id: '3989'
abstract:
- lang: eng
text: We introduce local and global comparison measures for a collection of k less
than or equal to d real-valued smooth functions on a common d-dimensional Riemannian
manifold. For k = d = 2 we relate the measures to the set of critical points of
one function restricted to the level sets of the other. The definition of the
measures extends to piecewise linear functions for which they ace easy to compute.
The computation of the measures forms the centerpiece of a software tool which
we use to study scientific datasets.
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Vijay
full_name: Natarajan, Vijay
last_name: Natarajan
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
citation:
ama: 'Edelsbrunner H, Harer J, Natarajan V, Pascucci V. Local and global comparison
of continuous functions. In: IEEE; 2004:275-280. doi:10.1109/VISUAL.2004.68'
apa: 'Edelsbrunner, H., Harer, J., Natarajan, V., & Pascucci, V. (2004). Local
and global comparison of continuous functions (pp. 275–280). Presented at the
VIS: IEEE Visualization, IEEE. https://doi.org/10.1109/VISUAL.2004.68'
chicago: Edelsbrunner, Herbert, John Harer, Vijay Natarajan, and Valerio Pascucci.
“Local and Global Comparison of Continuous Functions,” 275–80. IEEE, 2004. https://doi.org/10.1109/VISUAL.2004.68.
ieee: 'H. Edelsbrunner, J. Harer, V. Natarajan, and V. Pascucci, “Local and global
comparison of continuous functions,” presented at the VIS: IEEE Visualization,
2004, pp. 275–280.'
ista: 'Edelsbrunner H, Harer J, Natarajan V, Pascucci V. 2004. Local and global
comparison of continuous functions. VIS: IEEE Visualization, 275–280.'
mla: Edelsbrunner, Herbert, et al. Local and Global Comparison of Continuous
Functions. IEEE, 2004, pp. 275–80, doi:10.1109/VISUAL.2004.68.
short: H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci, in:, IEEE, 2004, pp.
275–280.
conference:
name: 'VIS: IEEE Visualization'
date_created: 2018-12-11T12:06:18Z
date_published: 2004-10-01T00:00:00Z
date_updated: 2021-01-12T07:53:41Z
day: '01'
doi: 10.1109/VISUAL.2004.68
extern: 1
month: '10'
page: 275 - 280
publication_status: published
publisher: IEEE
publist_id: '2137'
quality_controlled: 0
status: public
title: Local and global comparison of continuous functions
type: conference
year: '2004'
...
---
_id: '4172'
abstract:
- lang: eng
text: 'During vertebrate gastrulation, a relatively limited number of blastodermal
cells undergoes a stereotypical set of cellular movements that leads to formation
of the three germ layers: ectoderm, mesoderm and endoderm. Gastrulation, therefore,
provides a unique developmental system in which to study cell movements in vivo
in a fairly simple cellular context. Recent advances have been made in elucidating
the cellular and molecular mechanisms that underlie cell movements during zebrafish
gastrulation. These findings can be compared with observations made in other model
systems to identify potential general mechanisms of cell migration during development.'
article_processing_charge: No
author:
- first_name: Juan
full_name: Montero, Juan
last_name: Montero
- 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: 'Montero J, Heisenberg C-PJ. Gastrulation dynamics: cells move into focus.
Trends in Cell Biology. 2004;14(11):620-627. doi:10.1016/j.tcb.2004.09.008'
apa: 'Montero, J., & Heisenberg, C.-P. J. (2004). Gastrulation dynamics: cells
move into focus. Trends in Cell Biology. Cell Press. https://doi.org/10.1016/j.tcb.2004.09.008'
chicago: 'Montero, Juan, and Carl-Philipp J Heisenberg. “Gastrulation Dynamics:
Cells Move into Focus.” Trends in Cell Biology. Cell Press, 2004. https://doi.org/10.1016/j.tcb.2004.09.008.'
ieee: 'J. Montero and C.-P. J. Heisenberg, “Gastrulation dynamics: cells move into
focus,” Trends in Cell Biology, vol. 14, no. 11. Cell Press, pp. 620–627,
2004.'
ista: 'Montero J, Heisenberg C-PJ. 2004. Gastrulation dynamics: cells move into
focus. Trends in Cell Biology. 14(11), 620–627.'
mla: 'Montero, Juan, and Carl-Philipp J. Heisenberg. “Gastrulation Dynamics: Cells
Move into Focus.” Trends in Cell Biology, vol. 14, no. 11, Cell Press,
2004, pp. 620–27, doi:10.1016/j.tcb.2004.09.008.'
short: J. Montero, C.-P.J. Heisenberg, Trends in Cell Biology 14 (2004) 620–627.
date_created: 2018-12-11T12:07:23Z
date_published: 2004-11-01T00:00:00Z
date_updated: 2021-01-12T07:55:02Z
day: '01'
doi: 10.1016/j.tcb.2004.09.008
extern: '1'
intvolume: ' 14'
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 620 - 627
publication: Trends in Cell Biology
publication_status: published
publisher: Cell Press
publist_id: '1948'
status: public
title: 'Gastrulation dynamics: cells move into focus'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2004'
...
---
_id: '4238'
abstract:
- lang: eng
text: The dynamical basis of tumoral growth has been controversial. Many models
have been proposed to explain cancer development. The descriptions employ exponential,
potential, logistic or Gompertzian growth laws. Some of these models are concerned
with the interaction between cancer and the immunological, system. Among other
properties, these models are concerned with the microscopic behavior of tumors
and the emergence of cancer. We propose a modification of a previous model by
Stepanova, which describes the specific immunological response against cancer.
The modification consists of the substitution of a Gompertian law for the exponential
rate used for tumoral growth. This modification is motivated by the numerous works
confirming that Gompertz's equation correctly describes solid tumor growth. The
modified model predicts that near zero, tumors always tend to grow. Immunological
contraposition never suffices to induce a complete regression of the tumor. Instead,
a stable microscopic equilibrium between cancer and immunological activity can
be attained. In other words, our model predicts that the theory of immune surveillance
is plausible. A macroscopic equilibrium in which the system develops cancer is
also possible. In this case, immunological activity is depleted. This is consistent
with the phenomena of cancer tolerance. Both equilibrium points can coexist or
can exist without the other. In all cases the fixed point at zero tumor size is
unstable. Since immunity cannot induce a complete tumor regression, a therapy
is required. We include constant-dose therapies and show that they are insufficient.
Final levels of immunocompetent cells and tumoral cells are finite, thus post-treatment
regrowth of the tumor is certain. We also evaluate late-intensification therapies
which are successful. They induce an asymptotic regression to zero tumor size.
Immune response is also suppressed by the therapy, and thus plays a negligible
role in the remission. We conclude that treatment evaluation should be successful
without taking into account immunological effects. (C) 2003 Elsevier Ltd. All
rights reserved.
article_processing_charge: No
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: J.
full_name: González, J.
last_name: González
citation:
ama: de Vladar H, González J. Dynamic response of cancer under the influence of
immunological activity and therapy. Journal of Theoretical Biology. 2004;227(3):335-348.
doi:3801
apa: de Vladar, H., & González, J. (2004). Dynamic response of cancer under
the influence of immunological activity and therapy. Journal of Theoretical
Biology. Elsevier. https://doi.org/3801
chicago: Vladar, Harold de, and J. González. “Dynamic Response of Cancer under the
Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology.
Elsevier, 2004. https://doi.org/3801.
ieee: H. de Vladar and J. González, “Dynamic response of cancer under the influence
of immunological activity and therapy,” Journal of Theoretical Biology,
vol. 227, no. 3. Elsevier, pp. 335–348, 2004.
ista: de Vladar H, González J. 2004. Dynamic response of cancer under the influence
of immunological activity and therapy. Journal of Theoretical Biology. 227(3),
335–348.
mla: de Vladar, Harold, and J. González. “Dynamic Response of Cancer under the Influence
of Immunological Activity and Therapy.” Journal of Theoretical Biology,
vol. 227, no. 3, Elsevier, 2004, pp. 335–48, doi:3801.
short: H. de Vladar, J. González, Journal of Theoretical Biology 227 (2004) 335–348.
date_created: 2018-12-11T12:07:46Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:31Z
day: '01'
doi: '3801'
extern: '1'
intvolume: ' 227'
issue: '3'
language:
- iso: eng
month: '01'
oa_version: None
page: 335 - 348
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '1876'
status: public
title: Dynamic response of cancer under the influence of immunological activity and
therapy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 227
year: '2004'
...
---
_id: '4230'
alternative_title:
- Cellular Origin and Life in Extreme Habitats and Astrobiology
author:
- first_name: Harold
full_name: Harold Vladar
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
- first_name: Roberto
full_name: Cipriani, Roberto
last_name: Cipriani
- first_name: Benjamin
full_name: Scharifker, Benjamin
last_name: Scharifker
- first_name: Jose
full_name: Bubis, Jose
last_name: Bubis
citation:
ama: 'de Vladar H, Cipriani R, Scharifker B, Bubis J. A mechanism for the prebiotic
emergence of proteins. In: Hanslmeier A, Kempe S, Seckbach J, eds. Life in
the Universe From the Miller Experiment to the Search for Life on Other Worlds.
Springer; 2004:83-87.'
apa: de Vladar, H., Cipriani, R., Scharifker, B., & Bubis, J. (2004). A mechanism
for the prebiotic emergence of proteins. In A. Hanslmeier, S. Kempe, & J.
Seckbach (Eds.), Life in the Universe From the Miller Experiment to the Search
for Life on Other Worlds (pp. 83–87). Springer.
chicago: Vladar, Harold de, Roberto Cipriani, Benjamin Scharifker, and Jose Bubis.
“A Mechanism for the Prebiotic Emergence of Proteins.” In Life in the Universe
From the Miller Experiment to the Search for Life on Other Worlds, edited
by A. Hanslmeier, S. Kempe, and J. Seckbach, 83–87. Springer, 2004.
ieee: H. de Vladar, R. Cipriani, B. Scharifker, and J. Bubis, “A mechanism for the
prebiotic emergence of proteins,” in Life in the Universe From the Miller Experiment
to the Search for Life on Other Worlds, A. Hanslmeier, S. Kempe, and J. Seckbach,
Eds. Springer, 2004, pp. 83–87.
ista: 'de Vladar H, Cipriani R, Scharifker B, Bubis J. 2004.A mechanism for the
prebiotic emergence of proteins. In: Life in the Universe From the Miller Experiment
to the Search for Life on Other Worlds. Cellular Origin and Life in Extreme Habitats
and Astrobiology, , 83–87.'
mla: de Vladar, Harold, et al. “A Mechanism for the Prebiotic Emergence of Proteins.”
Life in the Universe From the Miller Experiment to the Search for Life on Other
Worlds, edited by A. Hanslmeier et al., Springer, 2004, pp. 83–87.
short: H. de Vladar, R. Cipriani, B. Scharifker, J. Bubis, in:, A. Hanslmeier, S.
Kempe, J. Seckbach (Eds.), Life in the Universe From the Miller Experiment to
the Search for Life on Other Worlds, Springer, 2004, pp. 83–87.
date_created: 2018-12-11T12:07:44Z
date_published: 2004-12-31T00:00:00Z
date_updated: 2021-01-12T07:55:28Z
day: '31'
editor:
- first_name: A.
full_name: Hanslmeier,A.
last_name: Hanslmeier
- first_name: S.
full_name: Kempe,S.
last_name: Kempe
- first_name: J.
full_name: Seckbach,J.
last_name: Seckbach
extern: 1
month: '12'
page: 83 - 87
publication: Life in the Universe From the Miller Experiment to the Search for Life
on Other Worlds
publication_status: published
publisher: Springer
publist_id: '1884'
quality_controlled: 0
status: public
title: A mechanism for the prebiotic emergence of proteins
type: book_chapter
year: '2004'
...
---
_id: '4236'
article_processing_charge: No
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
citation:
ama: de Vladar H. Métodos no lineales y sus aplicaciones en dinámicas aleatorias
de poblaciones celulares. 2004. doi:3810
apa: de Vladar, H. (2004). Métodos no lineales y sus aplicaciones en dinámicas
aleatorias de poblaciones celulares. Centro de estudios avazados, IVIC. https://doi.org/3810
chicago: Vladar, Harold de. “Métodos No Lineales y Sus Aplicaciones En Dinámicas
Aleatorias de Poblaciones Celulares.” Centro de estudios avazados, IVIC, 2004.
https://doi.org/3810.
ieee: H. de Vladar, “Métodos no lineales y sus aplicaciones en dinámicas aleatorias
de poblaciones celulares,” Centro de estudios avazados, IVIC, 2004.
ista: de Vladar H. 2004. Métodos no lineales y sus aplicaciones en dinámicas aleatorias
de poblaciones celulares. Centro de estudios avazados, IVIC.
mla: de Vladar, Harold. Métodos No Lineales y Sus Aplicaciones En Dinámicas Aleatorias
de Poblaciones Celulares. Centro de estudios avazados, IVIC, 2004, doi:3810.
short: H. de Vladar, Métodos No Lineales y Sus Aplicaciones En Dinámicas Aleatorias
de Poblaciones Celulares, Centro de estudios avazados, IVIC, 2004.
date_created: 2018-12-11T12:07:46Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:30Z
day: '01'
doi: '3810'
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication_status: published
publisher: Centro de estudios avazados, IVIC
publist_id: '1877'
status: public
title: Métodos no lineales y sus aplicaciones en dinámicas aleatorias de poblaciones
celulares
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2004'
...
---
_id: '4372'
alternative_title:
- LNCS
author:
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Dejan Nickovic
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
citation:
ama: 'Maler O, Nickovic D. Monitoring Temporal Properties of Continuous Signals.
In: Springer; 2004:152-166. doi:1572'
apa: 'Maler, O., & Nickovic, D. (2004). Monitoring Temporal Properties of Continuous
Signals (pp. 152–166). Presented at the FORMATS: Formal Modeling and Analysis
of Timed Systems, Springer. https://doi.org/1572'
chicago: Maler, Oded, and Dejan Nickovic. “Monitoring Temporal Properties of Continuous
Signals,” 152–66. Springer, 2004. https://doi.org/1572.
ieee: 'O. Maler and D. Nickovic, “Monitoring Temporal Properties of Continuous Signals,”
presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2004,
pp. 152–166.'
ista: 'Maler O, Nickovic D. 2004. Monitoring Temporal Properties of Continuous Signals.
FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, , 152–166.'
mla: Maler, Oded, and Dejan Nickovic. Monitoring Temporal Properties of Continuous
Signals. Springer, 2004, pp. 152–66, doi:1572.
short: O. Maler, D. Nickovic, in:, Springer, 2004, pp. 152–166.
conference:
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
date_created: 2018-12-11T12:08:31Z
date_published: 2004-12-14T00:00:00Z
date_updated: 2021-01-12T07:56:29Z
day: '14'
doi: '1572'
extern: 1
month: '12'
page: 152 - 166
publication_status: published
publisher: Springer
publist_id: '1088'
quality_controlled: 0
status: public
title: Monitoring Temporal Properties of Continuous Signals
type: conference
year: '2004'
...
---
_id: '4424'
abstract:
- lang: eng
text: "The enormous cost and ubiquity of software errors necessitates the need for
techniques and tools that can precisely analyze large systems and prove that they
meet given specifications, or if they don't, return counterexample behaviors showing
how the system fails. Recent advances in model checking, decision procedures,
program analysis and type systems, and a shift of focus to partial specifications
common to several systems (e.g., memory safety and race freedom) have resulted
in several practical verification methods. However, these methods are either precise
or they are scalable, depending on whether they track the values of variables
or only a fixed small set of dataflow facts (e.g., types), and are usually insufficient
for precisely verifying large programs.\r\n\r\nWe describe a new technique called
Lazy Abstraction (LA) which achieves both precision and scalability by localizing
the use of precise information. LA automatically builds, explores and refines
a single abstract model of the program in a way that different parts of the model
exhibit different degrees of precision, namely just enough to verify the desired
property. The algorithm automatically mines the information required by partitioning
mechanical proofs of unsatisfiability of spurious counterexamples into Craig Interpolants.
For multithreaded systems, we give a new technique based on analyzing the behavior
of a single thread executing in a context which is an abstraction of the other
(arbitrarily many) threads. We define novel context models and show how to automatically
infer them and analyze the full system (thread + context) using LA.\r\n\r\nLA
is implemented in BLAST. We have run BLAST on Windows and Linux Device Drivers
to verify API conformance properties, and have used it to find (or guarantee the
absence of) data races in multithreaded Networked Embedded Systems (NESC) applications.
BLAST is able to prove the absence of races in several cases where earlier methods,
which depend on lock-based synchronization, fail."
article_processing_charge: No
author:
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
citation:
ama: Jhala R. Program verification by lazy abstraction. 2004:1-165.
apa: Jhala, R. (2004). Program verification by lazy abstraction. University
of California, Berkeley.
chicago: Jhala, Ranjit. “Program Verification by Lazy Abstraction.” University of
California, Berkeley, 2004.
ieee: R. Jhala, “Program verification by lazy abstraction,” University of California,
Berkeley, 2004.
ista: Jhala R. 2004. Program verification by lazy abstraction. University of California,
Berkeley.
mla: Jhala, Ranjit. Program Verification by Lazy Abstraction. University
of California, Berkeley, 2004, pp. 1–165.
short: R. Jhala, Program Verification by Lazy Abstraction, University of California,
Berkeley, 2004.
date_created: 2018-12-11T12:08:47Z
date_published: 2004-12-01T00:00:00Z
date_updated: 2021-01-12T07:56:52Z
day: '01'
extern: '1'
language:
- iso: eng
month: '12'
oa_version: None
page: 1 - 165
publication_status: published
publisher: University of California, Berkeley
publist_id: '307'
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
title: Program verification by lazy abstraction
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2004'
...