---
_id: '3276'
abstract:
- lang: eng
text: 'We present an algorithm to identify individual neural spikes observed on
high-density multi-electrode arrays (MEAs). Our method can distinguish large numbers
of distinct neural units, even when spikes overlap, and accounts for intrinsic
variability of spikes from each unit. As MEAs grow larger, it is important to
find spike-identification methods that are scalable, that is, the computational
cost of spike fitting should scale well with the number of units observed. Our
algorithm accomplishes this goal, and is fast, because it exploits the spatial
locality of each unit and the basic biophysics of extracellular signal propagation.
Human interaction plays a key role in our method; but effort is minimized and
streamlined via a graphical interface. We illustrate our method on data from guinea
pig retinal ganglion cells and document its performance on simulated data consisting
of spikes added to experimentally measured background noise. We present several
tests demonstrating that the algorithm is highly accurate: it exhibits low error
rates on fits to synthetic data, low refractory violation rates, good receptive
field coverage, and consistency across users.'
acknowledgement: |+
This work was supported by National Science Foundation (NSF) grants IBN-0344678, EF-0928048, National Institutes of Health (NIH) grant RO1 EY08124, NIH training grant T32-07035, and NIH training grant 5T90DA022763-04.
Michael Berry and Olivier Marre have developed an algorithm similar to, but different from, ours (manuscript in preparation). We thank them for discussions of their work, and specifically thank Olivier Marre for suggesting to us that the most complete subtraction of a spike can be obtained by refitting the spike without a prior.
author:
- first_name: Jason
full_name: Prentice, Jason S
last_name: Prentice
- first_name: Jan
full_name: Homann, Jan
last_name: Homann
- first_name: Kristina
full_name: Simmons, Kristina D
last_name: Simmons
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Vijay
full_name: Balasubramanian, Vijay
last_name: Balasubramanian
- first_name: Philip
full_name: Nelson, Philip C
last_name: Nelson
citation:
ama: Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. Fast,
scalable, Bayesian spike identification for multi-electrode arrays. PLoS One.
2011;6(7). doi:10.1371/journal.pone.0019884
apa: Prentice, J., Homann, J., Simmons, K., Tkačik, G., Balasubramanian, V., &
Nelson, P. (2011). Fast, scalable, Bayesian spike identification for multi-electrode
arrays. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0019884
chicago: Prentice, Jason, Jan Homann, Kristina Simmons, Gašper Tkačik, Vijay Balasubramanian,
and Philip Nelson. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode
Arrays.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0019884.
ieee: J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, and P.
Nelson, “Fast, scalable, Bayesian spike identification for multi-electrode arrays,”
PLoS One, vol. 6, no. 7. Public Library of Science, 2011.
ista: Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. 2011.
Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS
One. 6(7).
mla: Prentice, Jason, et al. “Fast, Scalable, Bayesian Spike Identification for
Multi-Electrode Arrays.” PLoS One, vol. 6, no. 7, Public Library of Science,
2011, doi:10.1371/journal.pone.0019884.
short: J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, P. Nelson,
PLoS One 6 (2011).
date_created: 2018-12-11T12:02:24Z
date_published: 2011-07-20T00:00:00Z
date_updated: 2021-01-12T07:42:19Z
day: '20'
doi: 10.1371/journal.pone.0019884
extern: 1
file:
- access_level: open_access
checksum: 654464e99683b55a699734213d5356f1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:38Z
date_updated: 2020-07-14T12:46:06Z
file_id: '4894'
file_name: IST-2015-381-v1+1_journal.pone.0019884.pdf
file_size: 885464
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
fulldoi: https://doi.org/10.1371/journal.pone.0019884
intvolume: ' 6'
issue: '7'
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3370'
pubrep_id: '381'
quality_controlled: 0
status: public
title: Fast, scalable, Bayesian spike identification for multi-electrode arrays
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: 6
year: '2011'
...
...
---
_id: '3278'
abstract:
- lang: eng
text: |-
Despite much research on the socially parasitic large blue butterflies (genus Maculinea) in the past 40 years, their relationship to their closest relatives, Phengaris, is controversial and the relationships among the remaining genera in the Glaucopsyche section are largely unresolved. The evolutionary history of this butterfly section is particularly important to understand the evolution of life history diversity con- nected to food-plant and host-ant associations in the larval stage. In the present study, we use a combi- nation of four nuclear and two mitochondrial genes to reconstruct the phylogeny of the Glaucopsyche section, and in particular, to study the relationships among and within the Phengaris–Maculinea species.
We find a clear pattern between the clades recovered in the Glaucopsyche section phylogeny and their food-plant associations, with only the Phengaris–Maculinea clade utilising more than one plant family. Maculinea is, for the first time, recovered with strong support as a monophyletic group nested within Phengaris, with the closest relative being the rare genus Caerulea. The genus Glaucopsyche is polyphyletic, including the genera Sinia and Iolana. Interestingly, we find evidence for additional potential cryptic spe- cies within the highly endangered Maculinea, which has long been suspected from morphological, ecolog- ical and molecular studies.
author:
- first_name: Roger
full_name: Vila, Roger
last_name: Vila
- first_name: Naomi
full_name: Pierce, Naomi E
last_name: Pierce
- first_name: David
full_name: Nash, David R
last_name: Nash
- first_name: Line V
full_name: Line Ugelvig
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
citation:
ama: 'Vila R, Pierce N, Nash D, Ugelvig LV. A phylogenetic revision of the Glaucopsyche
section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea
clade. Molecular Phylogenetics and Evolution. 2011;61(1):237-243. doi:10.1016/j.ympev.2011.05.016'
apa: 'Vila, R., Pierce, N., Nash, D., & Ugelvig, L. V. (2011). A phylogenetic
revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus
on the Phengaris-Maculinea clade. Molecular Phylogenetics and Evolution.
Elsevier. https://doi.org/10.1016/j.ympev.2011.05.016'
chicago: 'Vila, Roger, Naomi Pierce, David Nash, and Line V Ugelvig. “A Phylogenetic
Revision of the Glaucopsyche Section (Lepidoptera: Lycaenidae), with Special Focus
on the Phengaris-Maculinea Clade.” Molecular Phylogenetics and Evolution.
Elsevier, 2011. https://doi.org/10.1016/j.ympev.2011.05.016.'
ieee: 'R. Vila, N. Pierce, D. Nash, and L. V. Ugelvig, “A phylogenetic revision
of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the
Phengaris-Maculinea clade,” Molecular Phylogenetics and Evolution, vol.
61, no. 1. Elsevier, pp. 237–243, 2011.'
ista: 'Vila R, Pierce N, Nash D, Ugelvig LV. 2011. A phylogenetic revision of the
Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea
clade. Molecular Phylogenetics and Evolution. 61(1), 237–243.'
mla: 'Vila, Roger, et al. “A Phylogenetic Revision of the Glaucopsyche Section (Lepidoptera:
Lycaenidae), with Special Focus on the Phengaris-Maculinea Clade.” Molecular
Phylogenetics and Evolution, vol. 61, no. 1, Elsevier, 2011, pp. 237–43, doi:10.1016/j.ympev.2011.05.016.'
short: R. Vila, N. Pierce, D. Nash, L.V. Ugelvig, Molecular Phylogenetics and Evolution
61 (2011) 237–243.
date_created: 2018-12-11T12:02:25Z
date_published: 2011-10-01T00:00:00Z
date_updated: 2021-01-12T07:42:20Z
day: '01'
doi: 10.1016/j.ympev.2011.05.016
extern: 1
fulldoi: https://doi.org/10.1016/j.ympev.2011.05.016
intvolume: ' 61'
issue: '1'
month: '10'
page: 237 - 243
publication: Molecular Phylogenetics and Evolution
publication_status: published
publisher: Elsevier
publist_id: '3368'
quality_controlled: 0
status: public
title: 'A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae),
with special focus on the Phengaris-Maculinea clade'
type: journal_article
volume: 61
year: '2011'
...
---
_id: '3285'
abstract:
- lang: eng
text: Resolving the dynamical interplay of proteins and lipids in the live-cell
plasma membrane represents a central goal in current cell biology. Superresolution
concepts have introduced a means of capturing spatial heterogeneity at a nanoscopic
length scale. Similar concepts for detecting dynamical transitions (superresolution
chronoscopy) are still lacking. Here, we show that recently introduced spot-variation
fluorescence correlation spectroscopy allows for sensing transient confinement
times of membrane constituents at dramatically improved resolution. Using standard
diffraction-limited optics, spot-variation fluorescence correlation spectroscopy
captures signatures of single retardation events far below the transit time of
the tracer through the focal spot. We provide an analytical description of special
cases of transient binding of a tracer to pointlike traps, or association of a
tracer with nanodomains. The influence of trap mobility and the underlying binding
kinetics are quantified. Experimental approaches are suggested that allow for
gaining quantitative mechanistic insights into the interaction processes of membrane
constituents.
acknowledgement: Y 250-B03/Austrian Science Fund FWF/Austria
author:
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Didier
full_name: Marguet, Didier
last_name: Marguet
- first_name: Gerhard
full_name: Schuetz, Gerhard
last_name: Schuetz
citation:
ama: Ruprecht V, Wieser S, Marguet D, Schuetz G. Spot variation fluorescence correlation
spectroscopy allows for superresolution chronoscopy of confinement times in membranes.
Biophysical Journal. 2011;100(11):2839-2845. doi:10.1016/j.bpj.2011.04.035
apa: Ruprecht, V., Wieser, S., Marguet, D., & Schuetz, G. (2011). Spot variation
fluorescence correlation spectroscopy allows for superresolution chronoscopy of
confinement times in membranes. Biophysical Journal. Biophysical Society.
https://doi.org/10.1016/j.bpj.2011.04.035
chicago: Ruprecht, Verena, Stefan Wieser, Didier Marguet, and Gerhard Schuetz. “Spot
Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy
of Confinement Times in Membranes.” Biophysical Journal. Biophysical Society,
2011. https://doi.org/10.1016/j.bpj.2011.04.035.
ieee: V. Ruprecht, S. Wieser, D. Marguet, and G. Schuetz, “Spot variation fluorescence
correlation spectroscopy allows for superresolution chronoscopy of confinement
times in membranes,” Biophysical Journal, vol. 100, no. 11. Biophysical
Society, pp. 2839–2845, 2011.
ista: Ruprecht V, Wieser S, Marguet D, Schuetz G. 2011. Spot variation fluorescence
correlation spectroscopy allows for superresolution chronoscopy of confinement
times in membranes. Biophysical Journal. 100(11), 2839–2845.
mla: Ruprecht, Verena, et al. “Spot Variation Fluorescence Correlation Spectroscopy
Allows for Superresolution Chronoscopy of Confinement Times in Membranes.” Biophysical
Journal, vol. 100, no. 11, Biophysical Society, 2011, pp. 2839–45, doi:10.1016/j.bpj.2011.04.035.
short: V. Ruprecht, S. Wieser, D. Marguet, G. Schuetz, Biophysical Journal 100 (2011)
2839–2845.
date_created: 2018-12-11T12:02:27Z
date_published: 2011-06-08T00:00:00Z
date_updated: 2021-01-12T07:42:23Z
day: '08'
doi: 10.1016/j.bpj.2011.04.035
extern: '1'
fulldoi: https://doi.org/10.1016/j.bpj.2011.04.035
intvolume: ' 100'
issue: '11'
language:
- iso: eng
month: '06'
oa_version: None
page: 2839 - 2845
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '3360'
status: public
title: Spot variation fluorescence correlation spectroscopy allows for superresolution
chronoscopy of confinement times in membranes
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2011'
...
---
_id: '3286'
abstract:
- lang: eng
text: Cationic antimicrobial peptides (CAMPs) selectively target bacterial membranes
by electrostatic interactions with negatively charged lipids. It turned out that
for inhibition of microbial growth a high CAMP membrane concentration is required,
which can be realized by the incorporation of hydrophobic groups within the peptide.
Increasing hydrophobicity, however, reduces the CAMP selectivity for bacterial
over eukaryotic host membranes, thereby causing the risk of detrimental side-effects.
In this study we addressed how cationic amphipathic peptides—in particular a CAMP
with Lysine–Leucine–Lysine repeats (termed KLK)—affect the localization and dynamics
of molecules in eukaryotic membranes. We found KLK to selectively inhibit the
endocytosis of a subgroup of membrane proteins and lipids by electrostatically
interacting with negatively charged sialic acid moieties. Ultrastructural characterization
revealed the formation of membrane invaginations representing fission or fusion
intermediates, in which the sialylated proteins and lipids were immobilized. Experiments
on structurally different cationic amphipathic peptides (KLK, 6-MO-LF11-322 and
NK14-2) indicated a cooperation of electrostatic and hydrophobic forces that selectively
arrest sialylated membrane constituents.
acknowledgement: "This work was funded by the GEN-AU project of the Austrian Research
Promotion Agency, the Austrian Science Fund (FWF; project Y250-B03) and Intercell
AG.\nWe thank the following colleagues for providing plasmids and cells: Daniel
Legler (University of Konstanz, Switzerland), Jennifer Lippincott-Schwartz (NIH,
Bethesda, USA), Hannes Stockinger (Medical University Vienna, Austria), Katharina
Strub (University of Geneva, Switzerland), Lawrence Rajendran (ETH Zurich, Switzerland),
Eileen M. Lafer (UTHSC San Antonio, Texas, USA), Mark McNiven (Mayo Clinic, Minnesota,
USA), John Silvius (McGill University, Montreal, Canada), Christoph Romanin (JKU
Linz, Austria), Herbert Stangl (Medical University Vienna, Austria) and Anton van
der Merwe (Oxford University, Oxford, UK). We thank Harald Kotisch (MFPL, Vienna)
for excellent technical assistance in the processing of samples for electron microscopy
and Sergio Grinstein (Hospital for Sick Children Research Institute, Toronto) for
fruitful discussions. "
author:
- first_name: Julian
full_name: Weghuber, Julian
last_name: Weghuber
- first_name: Michael
full_name: Aichinger, Michael C.
last_name: Aichinger
- first_name: Mario
full_name: Brameshuber, Mario
last_name: Brameshuber
- first_name: Stefan
full_name: Stefan Wieser
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Verena
full_name: Verena Ruprecht
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Birgit
full_name: Plochberger, Birgit
last_name: Plochberger
- first_name: Josef
full_name: Madl, Josef
last_name: Madl
- first_name: Andreas
full_name: Horner, Andreas
last_name: Horner
- first_name: Siegfried
full_name: Reipert, Siegfried
last_name: Reipert
- first_name: Karl
full_name: Lohner, Karl
last_name: Lohner
- first_name: Tamas
full_name: Henics, Tamas
last_name: Henics
- first_name: Gerhard
full_name: Schuetz, Gerhard J
last_name: Schuetz
citation:
ama: Weghuber J, Aichinger M, Brameshuber M, et al. Cationic amphipathic peptides
accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic
host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2011;1808(10):2581-2590.
doi:10.1016/j.bbamem.2011.06.007
apa: Weghuber, J., Aichinger, M., Brameshuber, M., Wieser, S., Ruprecht, V., Plochberger,
B., … Schuetz, G. (2011). Cationic amphipathic peptides accumulate sialylated
proteins and lipids in the plasma membrane of eukaryotic host cells. Biochimica
et Biophysica Acta (BBA) - Biomembranes. Elsevier. https://doi.org/10.1016/j.bbamem.2011.06.007
chicago: Weghuber, Julian, Michael Aichinger, Mario Brameshuber, Stefan Wieser,
Verena Ruprecht, Birgit Plochberger, Josef Madl, et al. “Cationic Amphipathic
Peptides Accumulate Sialylated Proteins and Lipids in the Plasma Membrane of Eukaryotic
Host Cells.” Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier,
2011. https://doi.org/10.1016/j.bbamem.2011.06.007.
ieee: J. Weghuber et al., “Cationic amphipathic peptides accumulate sialylated
proteins and lipids in the plasma membrane of eukaryotic host cells,” Biochimica
et Biophysica Acta (BBA) - Biomembranes, vol. 1808, no. 10. Elsevier, pp.
2581–2590, 2011.
ista: Weghuber J, Aichinger M, Brameshuber M, Wieser S, Ruprecht V, Plochberger
B, Madl J, Horner A, Reipert S, Lohner K, Henics T, Schuetz G. 2011. Cationic
amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane
of eukaryotic host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes.
1808(10), 2581–2590.
mla: Weghuber, Julian, et al. “Cationic Amphipathic Peptides Accumulate Sialylated
Proteins and Lipids in the Plasma Membrane of Eukaryotic Host Cells.” Biochimica
et Biophysica Acta (BBA) - Biomembranes, vol. 1808, no. 10, Elsevier, 2011,
pp. 2581–90, doi:10.1016/j.bbamem.2011.06.007.
short: J. Weghuber, M. Aichinger, M. Brameshuber, S. Wieser, V. Ruprecht, B. Plochberger,
J. Madl, A. Horner, S. Reipert, K. Lohner, T. Henics, G. Schuetz, Biochimica et
Biophysica Acta (BBA) - Biomembranes 1808 (2011) 2581–2590.
date_created: 2018-12-11T12:02:28Z
date_published: 2011-10-01T00:00:00Z
date_updated: 2021-01-12T07:42:24Z
day: '01'
doi: 10.1016/j.bbamem.2011.06.007
extern: 1
fulldoi: https://doi.org/10.1016/j.bbamem.2011.06.007
intvolume: ' 1808'
issue: '10'
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
page: 2581 - 2590
publication: Biochimica et Biophysica Acta (BBA) - Biomembranes
publication_status: published
publisher: Elsevier
publist_id: '3359'
quality_controlled: 0
status: public
title: Cationic amphipathic peptides accumulate sialylated proteins and lipids in
the plasma membrane of eukaryotic host cells
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
volume: 1808
year: '2011'
...
---
_id: '3287'
abstract:
- lang: eng
text: 'Diffusing membrane constituents are constantly exposed to a variety of forces
that influence their stochastic path. Single molecule experiments allow for resolving
trajectories at extremely high spatial and temporal accuracy, thereby offering
insights into en route interactions of the tracer. In this review we discuss approaches
to derive information about the underlying processes, based on single molecule
tracking experiments. In particular, we focus on a new versatile way to analyze
single molecule diffusion in the absence of a full analytical treatment. The method
is based on comprehensive comparison of an experimental data set against the hypothetical
outcome of multiple experiments performed on the computer. Since Monte Carlo simulations
can be easily and rapidly performed even on state-of-the-art PCs, our method provides
a simple way for testing various - even complicated - diffusion models. We describe
the new method in detail, and show the applicability on two specific examples:
firstly, kinetic rate constants can be derived for the transient interaction of
mobile membrane proteins; secondly, residence time and corral size can be extracted
for confined diffusion.'
article_processing_charge: No
author:
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Markus
full_name: Axmann, Markus
last_name: Axmann
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Gerhard
full_name: Schuetz, Gerhard
last_name: Schuetz
citation:
ama: Ruprecht V, Axmann M, Wieser S, Schuetz G. What can we learn from single molecule
trajectories? Current Protein & Peptide Science. 2011;12(8):714-724.
doi:10.2174/138920311798841753
apa: Ruprecht, V., Axmann, M., Wieser, S., & Schuetz, G. (2011). What can we
learn from single molecule trajectories? Current Protein & Peptide Science.
Bentham Science Publishers. https://doi.org/10.2174/138920311798841753
chicago: Ruprecht, Verena, Markus Axmann, Stefan Wieser, and Gerhard Schuetz. “What
Can We Learn from Single Molecule Trajectories?” Current Protein & Peptide
Science. Bentham Science Publishers, 2011. https://doi.org/10.2174/138920311798841753.
ieee: V. Ruprecht, M. Axmann, S. Wieser, and G. Schuetz, “What can we learn from
single molecule trajectories?,” Current Protein & Peptide Science,
vol. 12, no. 8. Bentham Science Publishers, pp. 714–724, 2011.
ista: Ruprecht V, Axmann M, Wieser S, Schuetz G. 2011. What can we learn from single
molecule trajectories? Current Protein & Peptide Science. 12(8), 714–724.
mla: Ruprecht, Verena, et al. “What Can We Learn from Single Molecule Trajectories?”
Current Protein & Peptide Science, vol. 12, no. 8, Bentham Science
Publishers, 2011, pp. 714–24, doi:10.2174/138920311798841753.
short: V. Ruprecht, M. Axmann, S. Wieser, G. Schuetz, Current Protein & Peptide
Science 12 (2011) 714–724.
date_created: 2018-12-11T12:02:28Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2025-09-30T09:21:31Z
day: '01'
department:
- _id: CaHe
- _id: MiSi
doi: 10.2174/138920311798841753
external_id:
isi:
- '000299672600005'
fulldoi: https://doi.org/10.2174/138920311798841753
intvolume: ' 12'
isi: 1
issue: '8'
language:
- iso: eng
month: '12'
oa_version: None
page: 714 - 724
publication: Current Protein & Peptide Science
publication_status: published
publisher: Bentham Science Publishers
publist_id: '3358'
quality_controlled: '1'
scopus_import: '1'
status: public
title: What can we learn from single molecule trajectories?
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 12
year: '2011'
...
---
_id: '3288'
abstract:
- lang: eng
text: 'The zonula adherens (ZA) of epithelial cells is a site of cell-cell adhesion
where cellular forces are exerted and resisted. Increasing evidence indicates
that E-cadherin adhesion molecules at the ZA serve to sense force applied on the
junctions and coordinate cytoskeletal responses to those forces. Efforts to understand
the role that cadherins play in mechanotransduction have been limited by the lack
of assays to measure the impact of forces on the ZA. In this study we used 4D
imaging of GFP-tagged E-cadherin to analyse the movement of the ZA. Junctions
in confluent epithelial monolayers displayed prominent movements oriented orthogonal
(perpendicular) to the ZA itself. Two components were identified in these movements:
a relatively slow unidirectional (translational) component that could be readily
fitted by least-squares regression analysis, upon which were superimposed more
rapid oscillatory movements. Myosin IIB was a dominant factor responsible for
driving the unilateral translational movements. In contrast, frequency spectrum
analysis revealed that depletion of Myosin IIA increased the power of the oscillatory
movements. This implies that Myosin IIA may serve to dampen oscillatory movements
of the ZA. This extends our recent analysis of Myosin II at the ZA to demonstrate
that Myosin IIA and Myosin IIB make distinct contributions to junctional movement
at the ZA.'
acknowledgement: his work was funded by the National Health and Medical Research Council
(NHMRC) of Australia. M.S. was an Erwin Schroedinger postdoctoral fellow of the
Austrian Science Fund (FWF), S.K.W. is supported by a UQ International Research
Tuition Award and Research Scholarship, S.M .by an ANZ Trustees PhD Scholarship.
A.S.Y. is a Research Fellow of the NHMRC. Confocal imaging was performed at the
Australian Cancer Research Foundation (ACRF) Cancer Biology Imaging Centre at the
Institute for Molecular Bioscience, established with the generous support of the
ACRF.
article_processing_charge: No
author:
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Selwin
full_name: Wu, Selwin
last_name: Wu
- first_name: Guillermo
full_name: Gomez, Guillermo
last_name: Gomez
- first_name: Sabine
full_name: Mangold, Sabine
last_name: Mangold
- first_name: Alpha
full_name: Yap, Alpha
last_name: Yap
- first_name: Nicholas
full_name: Hamilton, Nicholas
last_name: Hamilton
citation:
ama: Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. Multicomponent analysis
of junctional movements regulated by Myosin II isoforms at the epithelial zonula
adherens. PLoS One. 2011;6(7). doi:10.1371/journal.pone.0022458
apa: Smutny, M., Wu, S., Gomez, G., Mangold, S., Yap, A., & Hamilton, N. (2011).
Multicomponent analysis of junctional movements regulated by Myosin II isoforms
at the epithelial zonula adherens. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0022458
chicago: Smutny, Michael, Selwin Wu, Guillermo Gomez, Sabine Mangold, Alpha Yap,
and Nicholas Hamilton. “Multicomponent Analysis of Junctional Movements Regulated
by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One. Public
Library of Science, 2011. https://doi.org/10.1371/journal.pone.0022458.
ieee: M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, and N. Hamilton, “Multicomponent
analysis of junctional movements regulated by Myosin II isoforms at the epithelial
zonula adherens,” PLoS One, vol. 6, no. 7. Public Library of Science, 2011.
ista: Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. 2011. Multicomponent
analysis of junctional movements regulated by Myosin II isoforms at the epithelial
zonula adherens. PLoS One. 6(7).
mla: Smutny, Michael, et al. “Multicomponent Analysis of Junctional Movements Regulated
by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One, vol.
6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0022458.
short: M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, N. Hamilton, PLoS One 6 (2011).
date_created: 2018-12-11T12:02:28Z
date_published: 2011-07-22T00:00:00Z
date_updated: 2025-09-30T09:26:01Z
day: '22'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1371/journal.pone.0022458
external_id:
isi:
- '000293097300049'
file:
- access_level: open_access
checksum: 57a5eb11dd05241c48c44f492b3ec3ac
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T10:51:43Z
date_updated: 2020-07-14T12:46:06Z
file_id: '6399'
file_name: 2011_PLOS_Smutny.PDF
file_size: 1984567
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
fulldoi: https://doi.org/10.1371/journal.pone.0022458
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3357'
quality_controlled: '1'
status: public
title: Multicomponent analysis of junctional movements regulated by Myosin II isoforms
at the epithelial zonula adherens
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2011'
...
---
_id: '3290'
abstract:
- lang: eng
text: 'Analysis of genomic data requires an efficient way to calculate likelihoods
across very large numbers of loci. We describe a general method for finding the
distribution of genealogies: we allow migration between demes, splitting of demes
[as in the isolation-with-migration (IM) model], and recombination between linked
loci. These processes are described by a set of linear recursions for the generating
function of branch lengths. Under the infinite-sites model, the probability of
any configuration of mutations can be found by differentiating this generating
function. Such calculations are feasible for small numbers of sampled genomes:
as an example, we show how the generating function can be derived explicitly for
three genes under the two-deme IM model. This derivation is done automatically,
using Mathematica. Given data from a large number of unlinked and nonrecombining
blocks of sequence, these results can be used to find maximum-likelihood estimates
of model parameters by tabulating the probabilities of all relevant mutational
configurations and then multiplying across loci. The feasibility of the method
is demonstrated by applying it to simulated data and to a data set previously
analyzed by Wang and Hey (2010) consisting of 26,141 loci sampled from Drosophila
simulans and D. melanogaster. Our results suggest that such likelihood calculations
are scalable to genomic data as long as the numbers of sampled individuals and
mutations per sequence block are small.'
article_processing_charge: No
author:
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Richard
full_name: Harrison, Richard
last_name: Harrison
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Lohse K, Harrison R, Barton NH. A general method for calculating likelihoods
under the coalescent process. Genetics. 2011;189(3):977-987. doi:10.1534/genetics.111.129569
apa: Lohse, K., Harrison, R., & Barton, N. H. (2011). A general method for calculating
likelihoods under the coalescent process. Genetics. Genetics Society of
America. https://doi.org/10.1534/genetics.111.129569
chicago: Lohse, Konrad, Richard Harrison, and Nicholas H Barton. “A General Method
for Calculating Likelihoods under the Coalescent Process.” Genetics. Genetics
Society of America, 2011. https://doi.org/10.1534/genetics.111.129569.
ieee: K. Lohse, R. Harrison, and N. H. Barton, “A general method for calculating
likelihoods under the coalescent process,” Genetics, vol. 189, no. 3. Genetics
Society of America, pp. 977–987, 2011.
ista: Lohse K, Harrison R, Barton NH. 2011. A general method for calculating likelihoods
under the coalescent process. Genetics. 189(3), 977–987.
mla: Lohse, Konrad, et al. “A General Method for Calculating Likelihoods under the
Coalescent Process.” Genetics, vol. 189, no. 3, Genetics Society of America,
2011, pp. 977–87, doi:10.1534/genetics.111.129569.
short: K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 977–987.
date_created: 2018-12-11T12:02:29Z
date_published: 2011-11-01T00:00:00Z
date_updated: 2025-09-30T09:21:06Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.111.129569
ec_funded: 1
external_id:
isi:
- '000297020800022'
fulldoi: https://doi.org/10.1534/genetics.111.129569
intvolume: ' 189'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/
month: '11'
oa: 1
oa_version: Submitted Version
page: 977 - 987
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3355'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A general method for calculating likelihoods under the coalescent process
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 189
year: '2011'
...
---
_id: '3297'
abstract:
- lang: eng
text: "Animating detailed liquid surfaces has always been a challenge for computer
graphics researchers and visual effects artists. Over the past few years, researchers
in this field have focused on mesh-based surface tracking to synthesize extremely
detailed liquid surfaces as efficiently as possible. This course provides a solid
understanding of the steps required to create a fluid simulator with a mesh-based
liquid surface.\r\n\r\nThe course begins with an overview of several existing
liquid-surface-tracking techniques and the pros and cons of each method. Then
it explains how to embed a triangle mesh into a finite-difference-based fluid
simulator and describes several methods for allowing the liquid surface to merge
together or break apart. The final section showcases the benefits and further
applications of a mesh-based liquid surface, highlighting state-of-the-art methods
for tracking colors and textures, maintaining liquid volume, preserving small
surface features, and simulating realistic surface-tension waves."
article_number: '8'
author:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Matthias
full_name: Müller Fischer, Matthias
last_name: Müller Fischer
- first_name: Tyson
full_name: Brochu, Tyson
last_name: Brochu
citation:
ama: 'Wojtan C, Müller Fischer M, Brochu T. Liquid simulation with mesh-based surface
tracking. In: ACM; 2011. doi:10.1145/2037636.2037644'
apa: 'Wojtan, C., Müller Fischer, M., & Brochu, T. (2011). Liquid simulation
with mesh-based surface tracking. Presented at the SIGGRAPH: Special Interest
Group on Computer Graphics and Interactive Techniques, Vancouver, BC, Canada:
ACM. https://doi.org/10.1145/2037636.2037644'
chicago: Wojtan, Chris, Matthias Müller Fischer, and Tyson Brochu. “Liquid Simulation
with Mesh-Based Surface Tracking.” ACM, 2011. https://doi.org/10.1145/2037636.2037644.
ieee: 'C. Wojtan, M. Müller Fischer, and T. Brochu, “Liquid simulation with mesh-based
surface tracking,” presented at the SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques, Vancouver, BC, Canada, 2011.'
ista: 'Wojtan C, Müller Fischer M, Brochu T. 2011. Liquid simulation with mesh-based
surface tracking. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques, 8.'
mla: Wojtan, Chris, et al. Liquid Simulation with Mesh-Based Surface Tracking.
8, ACM, 2011, doi:10.1145/2037636.2037644.
short: C. Wojtan, M. Müller Fischer, T. Brochu, in:, ACM, 2011.
conference:
end_date: 2011-08-11
location: Vancouver, BC, Canada
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2011-08-07
corr_author: '1'
date_created: 2018-12-11T12:02:31Z
date_published: 2011-08-07T00:00:00Z
date_updated: 2024-10-09T20:54:35Z
day: '07'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2037636.2037644
file:
- access_level: open_access
checksum: 8d508ad7c82f50978acbaa4170ee0a75
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:34Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5018'
file_name: IST-2016-599-v1+1_meshyFluidsCourseSIGGRAPH2011.pdf
file_size: 34672096
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
fulldoi: https://doi.org/10.1145/2037636.2037644
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication_status: published
publisher: ACM
publist_id: '3344'
pubrep_id: '599'
quality_controlled: '1'
scopus_import: 1
status: public
title: Liquid simulation with mesh-based surface tracking
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3298'
abstract:
- lang: eng
text: We present a new algorithm for enforcing incompressibility for Smoothed Particle
Hydrodynamics (SPH) by preserving uniform density across the domain. We propose
a hybrid method that uses a Poisson solve on a coarse grid to enforce a divergence
free velocity field, followed by a local density correction of the particles. This
avoids typical grid artifacts and maintains the Lagrangian nature of SPH by directly
transferring pressures onto particles. Our method can be easily integrated with
existing SPH techniques such as the incompressible PCISPH method as well as weakly
compressible SPH by adding an additional force term. We show that this hybrid
method accelerates convergence towards uniform density and permits a significantly
larger time step compared to earlier approaches while producing similar results.
We demonstrate our approach in a variety of scenarios with significant pressure
gradients such as splashing liquids.
author:
- first_name: Karthik
full_name: Raveendran, Karthik
last_name: Raveendran
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
citation:
ama: 'Raveendran K, Wojtan C, Turk G. Hybrid smoothed particle hydrodynamics. In:
Spencer S, ed. ACM; 2011:33-42. doi:10.1145/2019406.2019411'
apa: 'Raveendran, K., Wojtan, C., & Turk, G. (2011). Hybrid smoothed particle
hydrodynamics. In S. Spencer (Ed.) (pp. 33–42). Presented at the SCA: ACM SIGGRAPH/Eurographics
Symposium on Computer animation, Vancouver, Canada: ACM. https://doi.org/10.1145/2019406.2019411'
chicago: Raveendran, Karthik, Chris Wojtan, and Greg Turk. “Hybrid Smoothed Particle
Hydrodynamics.” edited by Stephen Spencer, 33–42. ACM, 2011. https://doi.org/10.1145/2019406.2019411.
ieee: 'K. Raveendran, C. Wojtan, and G. Turk, “Hybrid smoothed particle hydrodynamics,”
presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation,
Vancouver, Canada, 2011, pp. 33–42.'
ista: 'Raveendran K, Wojtan C, Turk G. 2011. Hybrid smoothed particle hydrodynamics.
SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 33–42.'
mla: Raveendran, Karthik, et al. Hybrid Smoothed Particle Hydrodynamics.
Edited by Stephen Spencer, ACM, 2011, pp. 33–42, doi:10.1145/2019406.2019411.
short: K. Raveendran, C. Wojtan, G. Turk, in:, S. Spencer (Ed.), ACM, 2011, pp.
33–42.
conference:
end_date: 2011-08-07
location: Vancouver, Canada
name: 'SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation'
start_date: 2011-08-05
date_created: 2018-12-11T12:02:32Z
date_published: 2011-08-05T00:00:00Z
date_updated: 2023-02-23T11:21:05Z
day: '05'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2019406.2019411
editor:
- first_name: Stephen
full_name: Spencer, Stephen
last_name: Spencer
file:
- access_level: open_access
checksum: 6579d27709946e0eefbfa60a456b4913
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:44Z
date_updated: 2020-07-14T12:46:06Z
file_id: '4769'
file_name: IST-2016-598-v1+1_HybridSPH_Preprint.pdf
file_size: 2536216
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
fulldoi: https://doi.org/10.1145/2019406.2019411
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 33 - 42
publication_status: published
publisher: ACM
publist_id: '3343'
pubrep_id: '598'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hybrid smoothed particle hydrodynamics
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3299'
abstract:
- lang: eng
text: 'We introduce propagation models, a formalism designed to support general
and efficient data structures for the transient analysis of biochemical reaction
networks. We give two use cases for propagation abstract data types: the uniformization
method and numerical integration. We also sketch an implementation of a propagation
abstract data type, which uses abstraction to approximate states.'
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Maria
full_name: Mateescu, Maria
last_name: Mateescu
citation:
ama: 'Henzinger TA, Mateescu M. Propagation models for computing biochemical reaction
networks. In: Springer; 2011:1-3. doi:10.1145/2037509.2037510'
apa: 'Henzinger, T. A., & Mateescu, M. (2011). Propagation models for computing
biochemical reaction networks (pp. 1–3). Presented at the CMSB: Computational
Methods in Systems Biology, Paris, France: Springer. https://doi.org/10.1145/2037509.2037510'
chicago: Henzinger, Thomas A, and Maria Mateescu. “Propagation Models for Computing
Biochemical Reaction Networks,” 1–3. Springer, 2011. https://doi.org/10.1145/2037509.2037510.
ieee: 'T. A. Henzinger and M. Mateescu, “Propagation models for computing biochemical
reaction networks,” presented at the CMSB: Computational Methods in Systems Biology,
Paris, France, 2011, pp. 1–3.'
ista: 'Henzinger TA, Mateescu M. 2011. Propagation models for computing biochemical
reaction networks. CMSB: Computational Methods in Systems Biology, 1–3.'
mla: Henzinger, Thomas A., and Maria Mateescu. Propagation Models for Computing
Biochemical Reaction Networks. Springer, 2011, pp. 1–3, doi:10.1145/2037509.2037510.
short: T.A. Henzinger, M. Mateescu, in:, Springer, 2011, pp. 1–3.
conference:
end_date: 2011-09-23
location: Paris, France
name: 'CMSB: Computational Methods in Systems Biology'
start_date: 2011-09-21
corr_author: '1'
date_created: 2018-12-11T12:02:32Z
date_published: 2011-09-21T00:00:00Z
date_updated: 2024-10-09T20:54:34Z
day: '21'
ddc:
- '000'
- '004'
department:
- _id: ToHe
doi: 10.1145/2037509.2037510
file:
- access_level: open_access
checksum: 7f5c65509db1a9fb049abedd9663ed06
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:50Z
date_updated: 2020-07-14T12:46:06Z
file_id: '4649'
file_name: IST-2012-92-v1+1_Propagation_models_for_computing_biochemical_reaction_networks.pdf
file_size: 255780
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
fulldoi: https://doi.org/10.1145/2037509.2037510
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 1 - 3
publication_status: published
publisher: Springer
publist_id: '3341'
pubrep_id: '92'
quality_controlled: '1'
scopus_import: 1
status: public
title: Propagation models for computing biochemical reaction networks
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3301'
abstract:
- lang: eng
text: The chemical master equation is a differential equation describing the time
evolution of the probability distribution over the possible “states” of a biochemical
system. The solution of this equation is of interest within the systems biology
field ever since the importance of the molec- ular noise has been acknowledged.
Unfortunately, most of the systems do not have analytical solutions, and numerical
solutions suffer from the course of dimensionality and therefore need to be approximated.
Here, we introduce the concept of tail approximation, which retrieves an approximation
of the probabilities in the tail of a distribution from the total probability
of the tail and its conditional expectation. This approximation method can then
be used to numerically compute the solution of the chemical master equation on
a subset of the state space, thus fighting the explosion of the state space, for
which this problem is renowned.
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Maria
full_name: Mateescu, Maria
last_name: Mateescu
citation:
ama: 'Henzinger TA, Mateescu M. Tail approximation for the chemical master equation.
In: Tampere International Center for Signal Processing; 2011.'
apa: 'Henzinger, T. A., & Mateescu, M. (2011). Tail approximation for the chemical
master equation. Presented at the WCSB: Workshop on Computational Systems Biology
(TICSP), Tampere International Center for Signal Processing.'
chicago: Henzinger, Thomas A, and Maria Mateescu. “Tail Approximation for the Chemical
Master Equation.” Tampere International Center for Signal Processing, 2011.
ieee: 'T. A. Henzinger and M. Mateescu, “Tail approximation for the chemical master
equation,” presented at the WCSB: Workshop on Computational Systems Biology (TICSP),
2011.'
ista: 'Henzinger TA, Mateescu M. 2011. Tail approximation for the chemical master
equation. WCSB: Workshop on Computational Systems Biology (TICSP).'
mla: Henzinger, Thomas A., and Maria Mateescu. Tail Approximation for the Chemical
Master Equation. Tampere International Center for Signal Processing, 2011.
short: T.A. Henzinger, M. Mateescu, in:, Tampere International Center for Signal
Processing, 2011.
conference:
name: 'WCSB: Workshop on Computational Systems Biology (TICSP)'
corr_author: '1'
date_created: 2018-12-11T12:02:33Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2024-10-09T20:54:34Z
day: '01'
ddc:
- '005'
- '570'
department:
- _id: ToHe
file:
- access_level: open_access
checksum: aa4d7a832a5419e6c0090650ebff2b9a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:12Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5331'
file_name: IST-2012-91-v1+1_Tail_approximation_for_the_chemical_master_equation.pdf
file_size: 240820
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
publication_status: published
publisher: Tampere International Center for Signal Processing
publist_id: '3339'
pubrep_id: '91'
quality_controlled: '1'
status: public
title: Tail approximation for the chemical master equation
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3311'
abstract:
- lang: eng
text: Alpha shapes have been conceived in 1981 as an attempt to define the shape
of a finite set of point in the plane. Since then, connections to diverse areas
in the sciences and engineering have developed, including to pattern recognition,
digital shape sampling and processing, and structural molecular biology. This
survey begins with a historical account and discusses geometric, algorithmic,
topological, and combinatorial aspects of alpha shapes in this sequence.
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. Alpha shapes - a survey. In: van de Weygaert R, Vegter G,
Ritzerveld J, Icke V, eds. Tessellations in the Sciences: Virtues, Techniques
and Applications of Geometric Tilings. Springer.'
apa: 'Edelsbrunner, H. (n.d.). Alpha shapes - a survey. In R. van de Weygaert, G.
Vegter, J. Ritzerveld, & V. Icke (Eds.), Tessellations in the Sciences:
Virtues, Techniques and Applications of Geometric Tilings. Springer.'
chicago: 'Edelsbrunner, Herbert. “Alpha Shapes - a Survey.” In Tessellations
in the Sciences: Virtues, Techniques and Applications of Geometric Tilings,
edited by R van de Weygaert, G Vegter, J Ritzerveld, and V Icke. Springer, n.d.'
ieee: 'H. Edelsbrunner, “Alpha shapes - a survey,” in Tessellations in the Sciences:
Virtues, Techniques and Applications of Geometric Tilings, R. van de Weygaert,
G. Vegter, J. Ritzerveld, and V. Icke, Eds. Springer.'
ista: 'Edelsbrunner H.Alpha shapes - a survey. In: Tessellations in the Sciences:
Virtues, Techniques and Applications of Geometric Tilings. .'
mla: 'Edelsbrunner, Herbert. “Alpha Shapes - a Survey.” Tessellations in the
Sciences: Virtues, Techniques and Applications of Geometric Tilings, edited
by R van de Weygaert et al., Springer.'
short: 'H. Edelsbrunner, in:, R. van de Weygaert, G. Vegter, J. Ritzerveld, V. Icke
(Eds.), Tessellations in the Sciences: Virtues, Techniques and Applications of
Geometric Tilings, Springer, n.d.'
corr_author: '1'
date_created: 2018-12-11T12:02:36Z
date_published: 2011-12-31T00:00:00Z
date_updated: 2024-10-09T20:54:33Z
day: '31'
ddc:
- '510'
department:
- _id: HeEd
editor:
- first_name: R
full_name: van de Weygaert, R
last_name: van de Weygaert
- first_name: G
full_name: Vegter, G
last_name: Vegter
- first_name: J
full_name: Ritzerveld, J
last_name: Ritzerveld
- first_name: V
full_name: Icke, V
last_name: Icke
file:
- access_level: open_access
checksum: a592ea438351e7280eea993a7713ab8f
content_type: application/pdf
creator: dernst
date_created: 2022-05-24T07:55:05Z
date_updated: 2022-05-24T07:55:05Z
file_id: '11408'
file_name: 2010_AlphaShapes.pdf
file_size: 475254
relation: main_file
success: 1
file_date_updated: 2022-05-24T07:55:05Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
publication: 'Tessellations in the Sciences: Virtues, Techniques and Applications
of Geometric Tilings'
publication_status: inpress
publisher: Springer
publist_id: '3329'
quality_controlled: '1'
status: public
title: Alpha shapes - a survey
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3312'
abstract:
- lang: eng
text: We study the 3D reconstruction of plant roots from multiple 2D images. To
meet the challenge caused by the delicate nature of thin branches, we make three
innovations to cope with the sensitivity to image quality and calibration. First,
we model the background as a harmonic function to improve the segmentation of
the root in each 2D image. Second, we develop the concept of the regularized visual
hull which reduces the effect of jittering and refraction by ensuring consistency
with one 2D image. Third, we guarantee connectedness through adjustments to the
3D reconstruction that minimize global error. Our software is part of a biological
phenotype/genotype study of agricultural root systems. It has been tested on more
than 40 plant roots and results are promising in terms of reconstruction quality
and efficiency.
acknowledgement: This research is supported by the National Science Foundation (NSF)
under grant DBI-0820624.
article_number: '6126475'
article_processing_charge: No
author:
- first_name: Ying
full_name: Zheng, Ying
last_name: Zheng
- first_name: Steve
full_name: Gu, Steve
last_name: Gu
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Carlo
full_name: Tomasi, Carlo
last_name: Tomasi
- first_name: Philip
full_name: Benfey, Philip
last_name: Benfey
citation:
ama: Zheng Y, Gu S, Edelsbrunner H, Tomasi C, Benfey P. Detailed Reconstruction
of 3D Plant Root Shape. IEEE; 2011. doi:10.1109/ICCV.2011.6126475
apa: 'Zheng, Y., Gu, S., Edelsbrunner, H., Tomasi, C., & Benfey, P. (2011).
Detailed reconstruction of 3D plant root shape. Proceedings of the IEEE
International Conference on Computer Vision. Barcelona, Spain: IEEE. https://doi.org/10.1109/ICCV.2011.6126475'
chicago: Zheng, Ying, Steve Gu, Herbert Edelsbrunner, Carlo Tomasi, and Philip Benfey.
Detailed Reconstruction of 3D Plant Root Shape. Proceedings of the IEEE
International Conference on Computer Vision. IEEE, 2011. https://doi.org/10.1109/ICCV.2011.6126475.
ieee: Y. Zheng, S. Gu, H. Edelsbrunner, C. Tomasi, and P. Benfey, Detailed reconstruction
of 3D plant root shape. IEEE, 2011.
ista: Zheng Y, Gu S, Edelsbrunner H, Tomasi C, Benfey P. 2011. Detailed reconstruction
of 3D plant root shape, IEEE,p.
mla: Zheng, Ying, et al. “Detailed Reconstruction of 3D Plant Root Shape.” Proceedings
of the IEEE International Conference on Computer Vision, 6126475, IEEE, 2011,
doi:10.1109/ICCV.2011.6126475.
short: Y. Zheng, S. Gu, H. Edelsbrunner, C. Tomasi, P. Benfey, Detailed Reconstruction
of 3D Plant Root Shape, IEEE, 2011.
conference:
end_date: 2011-11-13
location: Barcelona, Spain
name: 'ICCV: International Conference on Computer Vision'
start_date: 2011-11-06
date_created: 2018-12-11T12:02:36Z
date_published: 2011-12-31T00:00:00Z
date_updated: 2024-10-21T06:03:02Z
day: '31'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1109/ICCV.2011.6126475
file:
- access_level: open_access
checksum: 30a33564b7b45a7ee31610898267fd0e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:04Z
date_updated: 2020-07-14T12:46:07Z
file_id: '4727'
file_name: IST-2016-541-v1+1_2011-P-07-RootReconstruction.pdf
file_size: 5622728
relation: main_file
file_date_updated: 2020-07-14T12:46:07Z
fulldoi: https://doi.org/10.1109/ICCV.2011.6126475
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
publication: Proceedings of the IEEE International Conference on Computer Vision
publication_status: published
publisher: IEEE
publist_id: '3328'
pubrep_id: '541'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Detailed reconstruction of 3D plant root shape
type: conference_poster
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3313'
abstract:
- lang: eng
text: Interpreting an image as a function on a compact sub- set of the Euclidean
plane, we get its scale-space by diffu- sion, spreading the image over the entire
plane. This gener- ates a 1-parameter family of functions alternatively defined
as convolutions with a progressively wider Gaussian ker- nel. We prove that the
corresponding 1-parameter family of persistence diagrams have norms that go rapidly
to zero as time goes to infinity. This result rationalizes experimental observations
about scale-space. We hope this will lead to targeted improvements of related
computer vision methods.
article_number: '6126271'
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Chen C, Edelsbrunner H. Diffusion runs low on persistence fast. In: Proceedings
of the IEEE International Conference on Computer Vision. IEEE; 2011. doi:10.1109/ICCV.2011.6126271'
apa: 'Chen, C., & Edelsbrunner, H. (2011). Diffusion runs low on persistence
fast. In Proceedings of the IEEE International Conference on Computer Vision.
Barcelona, Spain: IEEE. https://doi.org/10.1109/ICCV.2011.6126271'
chicago: Chen, Chao, and Herbert Edelsbrunner. “Diffusion Runs Low on Persistence
Fast.” In Proceedings of the IEEE International Conference on Computer Vision.
IEEE, 2011. https://doi.org/10.1109/ICCV.2011.6126271.
ieee: C. Chen and H. Edelsbrunner, “Diffusion runs low on persistence fast,” in
Proceedings of the IEEE International Conference on Computer Vision, Barcelona,
Spain, 2011.
ista: 'Chen C, Edelsbrunner H. 2011. Diffusion runs low on persistence fast. Proceedings
of the IEEE International Conference on Computer Vision. ICCV: International Conference
on Computer Vision, 6126271.'
mla: Chen, Chao, and Herbert Edelsbrunner. “Diffusion Runs Low on Persistence Fast.”
Proceedings of the IEEE International Conference on Computer Vision, 6126271,
IEEE, 2011, doi:10.1109/ICCV.2011.6126271.
short: C. Chen, H. Edelsbrunner, in:, Proceedings of the IEEE International Conference
on Computer Vision, IEEE, 2011.
conference:
end_date: 2011-11-13
location: Barcelona, Spain
name: 'ICCV: International Conference on Computer Vision'
start_date: 2011-11-06
corr_author: '1'
date_created: 2018-12-11T12:02:37Z
date_published: 2011-11-06T00:00:00Z
date_updated: 2024-10-09T20:54:33Z
day: '06'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1109/ICCV.2011.6126271
file:
- access_level: open_access
checksum: 6984684081ba123808b344f9f2e64a8f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:28Z
date_updated: 2020-07-14T12:46:07Z
file_id: '5282'
file_name: IST-2016-540-v1+1_2011-P-08-RunEmpty.pdf
file_size: 614050
relation: main_file
file_date_updated: 2020-07-14T12:46:07Z
fulldoi: https://doi.org/10.1109/ICCV.2011.6126271
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
publication: Proceedings of the IEEE International Conference on Computer Vision
publication_status: published
publisher: IEEE
publist_id: '3327'
pubrep_id: '540'
quality_controlled: '1'
scopus_import: 1
status: public
title: Diffusion runs low on persistence fast
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3316'
abstract:
- lang: eng
text: In addition to being correct, a system should be robust, that is, it should
behave reasonably even after receiving unexpected inputs. In this paper, we summarize
two formal notions of robustness that we have introduced previously for reactive
systems. One of the notions is based on assigning costs for failures on a user-provided
notion of incorrect transitions in a specification. Here, we define a system to
be robust if a finite number of incorrect inputs does not lead to an infinite
number of incorrect outputs. We also give a more refined notion of robustness
that aims to minimize the ratio of output failures to input failures. The second
notion is aimed at liveness. In contrast to the previous notion, it has no concept
of recovery from an error. Instead, it compares the ratio of the number of liveness
constraints that the system violates to the number of liveness constraints that
the environment violates.
article_processing_charge: No
author:
- first_name: Roderick
full_name: Bloem, Roderick
last_name: Bloem
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Karin
full_name: Greimel, Karin
last_name: Greimel
- 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: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
citation:
ama: 'Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. Specification-centered
robustness. In: 6th IEEE International Symposium on Industrial and Embedded
Systems. IEEE; 2011:176-185. doi:10.1109/SIES.2011.5953660'
apa: 'Bloem, R., Chatterjee, K., Greimel, K., Henzinger, T. A., & Jobstmann,
B. (2011). Specification-centered robustness. In 6th IEEE International Symposium
on Industrial and Embedded Systems (pp. 176–185). Vasteras, Sweden: IEEE.
https://doi.org/10.1109/SIES.2011.5953660'
chicago: Bloem, Roderick, Krishnendu Chatterjee, Karin Greimel, Thomas A Henzinger,
and Barbara Jobstmann. “Specification-Centered Robustness.” In 6th IEEE International
Symposium on Industrial and Embedded Systems, 176–85. IEEE, 2011. https://doi.org/10.1109/SIES.2011.5953660.
ieee: R. Bloem, K. Chatterjee, K. Greimel, T. A. Henzinger, and B. Jobstmann, “Specification-centered
robustness,” in 6th IEEE International Symposium on Industrial and Embedded
Systems, Vasteras, Sweden, 2011, pp. 176–185.
ista: 'Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. 2011. Specification-centered
robustness. 6th IEEE International Symposium on Industrial and Embedded Systems.
SIES: International Symposium on Industrial Embedded Systems, 176–185.'
mla: Bloem, Roderick, et al. “Specification-Centered Robustness.” 6th IEEE International
Symposium on Industrial and Embedded Systems, IEEE, 2011, pp. 176–85, doi:10.1109/SIES.2011.5953660.
short: R. Bloem, K. Chatterjee, K. Greimel, T.A. Henzinger, B. Jobstmann, in:, 6th
IEEE International Symposium on Industrial and Embedded Systems, IEEE, 2011, pp.
176–185.
conference:
end_date: 2011-06-17
location: Vasteras, Sweden
name: 'SIES: International Symposium on Industrial Embedded Systems'
start_date: 2011-06-15
date_created: 2018-12-11T12:02:38Z
date_published: 2011-07-14T00:00:00Z
date_updated: 2026-06-18T18:43:15Z
day: '14'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1109/SIES.2011.5953660
ec_funded: 1
fulldoi: https://doi.org/10.1109/SIES.2011.5953660
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://openlib.tugraz.at/download.php?id=5cb57c8a49344&location=browse
month: '07'
oa: 1
oa_version: Published Version
page: 176 - 185
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: 6th IEEE International Symposium on Industrial and Embedded Systems
publication_status: published
publisher: IEEE
publist_id: '3323'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Specification-centered robustness
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3318'
abstract:
- lang: eng
text: Parvalbumin is thought to act in a manner similar to EGTA, but how a slow
Ca2+ buffer affects nanodomain-coupling regimes at GABAergic synapses is unclear.
Direct measurements of parvalbumin concentration and paired recordings in rodent
hippocampus and cerebellum revealed that parvalbumin affects synaptic dynamics
only when expressed at high levels. Modeling suggests that, in high concentrations,
parvalbumin may exert BAPTA-like effects, modulating nanodomain coupling via competition
with local saturation of endogenous fixed buffers.
article_processing_charge: No
author:
- first_name: Emmanuel
full_name: Eggermann, Emmanuel
last_name: Eggermann
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Eggermann E, Jonas PM. How the “slow” Ca(2+) buffer parvalbumin affects transmitter
release in nanodomain coupling regimes at GABAergic synapses. Nature Neuroscience.
2011;15:20-22. doi:10.1038/nn.3002
apa: Eggermann, E., & Jonas, P. M. (2011). How the “slow” Ca(2+) buffer parvalbumin
affects transmitter release in nanodomain coupling regimes at GABAergic synapses.
Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3002
chicago: Eggermann, Emmanuel, and Peter M Jonas. “How the ‘Slow’ Ca(2+) Buffer Parvalbumin
Affects Transmitter Release in Nanodomain Coupling Regimes at GABAergic Synapses.”
Nature Neuroscience. Nature Publishing Group, 2011. https://doi.org/10.1038/nn.3002.
ieee: E. Eggermann and P. M. Jonas, “How the ‘slow’ Ca(2+) buffer parvalbumin affects
transmitter release in nanodomain coupling regimes at GABAergic synapses,” Nature
Neuroscience, vol. 15. Nature Publishing Group, pp. 20–22, 2011.
ista: Eggermann E, Jonas PM. 2011. How the “slow” Ca(2+) buffer parvalbumin affects
transmitter release in nanodomain coupling regimes at GABAergic synapses. Nature
Neuroscience. 15, 20–22.
mla: Eggermann, Emmanuel, and Peter M. Jonas. “How the ‘Slow’ Ca(2+) Buffer Parvalbumin
Affects Transmitter Release in Nanodomain Coupling Regimes at GABAergic Synapses.”
Nature Neuroscience, vol. 15, Nature Publishing Group, 2011, pp. 20–22,
doi:10.1038/nn.3002.
short: E. Eggermann, P.M. Jonas, Nature Neuroscience 15 (2011) 20–22.
corr_author: '1'
date_created: 2018-12-11T12:02:38Z
date_published: 2011-12-04T00:00:00Z
date_updated: 2025-09-30T09:20:05Z
day: '04'
department:
- _id: PeJo
doi: 10.1038/nn.3002
external_id:
isi:
- '000298414400008'
fulldoi: https://doi.org/10.1038/nn.3002
intvolume: ' 15'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631701/
month: '12'
oa: 1
oa_version: Submitted Version
page: 20 - 22
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '3321'
quality_controlled: '1'
scopus_import: '1'
status: public
title: How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain
coupling regimes at GABAergic synapses
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2011'
...
---
_id: '3319'
abstract:
- lang: eng
text: We address the problem of metric learning for multi-view data, namely the
construction of embedding projections from data in different representations into
a shared feature space, such that the Euclidean distance in this space provides
a meaningful within-view as well as between-view similarity. Our motivation stems
from the problem of cross-media retrieval tasks, where the availability of a joint
Euclidean distance function is a pre-requisite to allow fast, in particular hashing-based,
nearest neighbor queries. We formulate an objective function that expresses the
intuitive concept that matching samples are mapped closely together in the output
space, whereas non-matching samples are pushed apart, no matter in which view
they are available. The resulting optimization problem is not convex, but it can
be decomposed explicitly into a convex and a concave part, thereby allowing efficient
optimization using the convex-concave procedure. Experiments on an image retrieval
task show that nearest-neighbor based cross-view retrieval is indeed possible,
and the proposed technique improves the retrieval accuracy over baseline techniques.
article_processing_charge: No
author:
- first_name: Novi
full_name: Quadrianto, Novi
last_name: Quadrianto
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Quadrianto N, Lampert C. Learning multi-view neighborhood preserving projections.
In: ML Research Press; 2011:425-432.'
apa: 'Quadrianto, N., & Lampert, C. (2011). Learning multi-view neighborhood
preserving projections (pp. 425–432). Presented at the ICML: International Conference
on Machine Learning, Bellevue, United States: ML Research Press.'
chicago: Quadrianto, Novi, and Christoph Lampert. “Learning Multi-View Neighborhood
Preserving Projections,” 425–32. ML Research Press, 2011.
ieee: 'N. Quadrianto and C. Lampert, “Learning multi-view neighborhood preserving
projections,” presented at the ICML: International Conference on Machine Learning,
Bellevue, United States, 2011, pp. 425–432.'
ista: 'Quadrianto N, Lampert C. 2011. Learning multi-view neighborhood preserving
projections. ICML: International Conference on Machine Learning, 425–432.'
mla: Quadrianto, Novi, and Christoph Lampert. Learning Multi-View Neighborhood
Preserving Projections. ML Research Press, 2011, pp. 425–32.
short: N. Quadrianto, C. Lampert, in:, ML Research Press, 2011, pp. 425–432.
conference:
end_date: 2011-07-02
location: Bellevue, United States
name: 'ICML: International Conference on Machine Learning'
start_date: 2011-06-28
corr_author: '1'
date_created: 2018-12-11T12:02:39Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2024-10-09T20:54:32Z
day: '01'
department:
- _id: ChLa
language:
- iso: eng
month: '01'
oa_version: None
page: 425 - 432
publication_status: published
publisher: ML Research Press
publist_id: '3316'
scopus_import: '1'
status: public
title: Learning multi-view neighborhood preserving projections
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3320'
abstract:
- lang: eng
text: Powerful statistical models that can be learned efficiently from large amounts
of data are currently revolutionizing computer vision. These models possess a
rich internal structure reflecting task-specific relations and constraints. This
monograph introduces the reader to the most popular classes of structured models
in computer vision. Our focus is discrete undirected graphical models which we
cover in detail together with a description of algorithms for both probabilistic
inference and maximum a posteriori inference. We discuss separately recently successful
techniques for prediction in general structured models. In the second part of
this monograph we describe methods for parameter learning where we distinguish
the classic maximum likelihood based methods from the more recent prediction-based
parameter learning methods. We highlight developments to enhance current models
and discuss kernelized models and latent variable models. To make the monograph
more practical and to provide links to further study we provide examples of successful
application of many methods in the computer vision literature.
article_processing_charge: No
article_type: original
author:
- first_name: Sebastian
full_name: Nowozin, Sebastian
last_name: Nowozin
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Nowozin S, Lampert C. Structured learning and prediction in computer vision.
Foundations and Trends in Computer Graphics and Vision. 2011;6(3-4):185-365.
doi:10.1561/0600000033
apa: Nowozin, S., & Lampert, C. (2011). Structured learning and prediction in
computer vision. Foundations and Trends in Computer Graphics and Vision.
Now Publishers. https://doi.org/10.1561/0600000033
chicago: Nowozin, Sebastian, and Christoph Lampert. “Structured Learning and Prediction
in Computer Vision.” Foundations and Trends in Computer Graphics and Vision.
Now Publishers, 2011. https://doi.org/10.1561/0600000033.
ieee: S. Nowozin and C. Lampert, “Structured learning and prediction in computer
vision,” Foundations and Trends in Computer Graphics and Vision, vol. 6,
no. 3–4. Now Publishers, pp. 185–365, 2011.
ista: Nowozin S, Lampert C. 2011. Structured learning and prediction in computer
vision. Foundations and Trends in Computer Graphics and Vision. 6(3–4), 185–365.
mla: Nowozin, Sebastian, and Christoph Lampert. “Structured Learning and Prediction
in Computer Vision.” Foundations and Trends in Computer Graphics and Vision,
vol. 6, no. 3–4, Now Publishers, 2011, pp. 185–365, doi:10.1561/0600000033.
short: S. Nowozin, C. Lampert, Foundations and Trends in Computer Graphics and Vision
6 (2011) 185–365.
corr_author: '1'
date_created: 2018-12-11T12:02:39Z
date_published: 2011-05-23T00:00:00Z
date_updated: 2024-10-09T20:54:32Z
day: '23'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.1561/0600000033
file:
- access_level: open_access
checksum: f1043ef389f1558e2a226bb51568511f
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T14:34:47Z
date_updated: 2020-07-14T12:46:07Z
file_id: '7837'
file_name: 2011_CompGraphicsVision_Nowozin.pdf
file_size: 3745064
relation: main_file
file_date_updated: 2020-07-14T12:46:07Z
fulldoi: https://doi.org/10.1561/0600000033
has_accepted_license: '1'
intvolume: ' 6'
issue: 3-4
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 185 - 365
publication: Foundations and Trends in Computer Graphics and Vision
publication_status: published
publisher: Now Publishers
publist_id: '3315'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structured learning and prediction in computer vision
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2011'
...
---
_id: '3322'
abstract:
- lang: eng
text: We study multi-label prediction for structured output spaces, a problem that
occurs, for example, in object detection in images, secondary structure prediction
in computational biology, and graph matching with symmetries. Conventional multi-label
classification techniques are typically not applicable in this situation, because
they require explicit enumeration of the label space, which is infeasible in case
of structured outputs. Relying on techniques originally designed for single- label
structured prediction, in particular structured support vector machines, results
in reduced prediction accuracy, or leads to infeasible optimization problems.
In this work we derive a maximum-margin training formulation for multi-label structured
prediction that remains computationally tractable while achieving high prediction
accuracy. It also shares most beneficial properties with single-label maximum-margin
approaches, in particular a formulation as a convex optimization problem, efficient
working set training, and PAC-Bayesian generalization bounds.
article_processing_charge: No
author:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Lampert C. Maximum Margin Multi Label Structured Prediction. Neural
Information Processing Systems Foundation; 2011.
apa: 'Lampert, C. (2011). Maximum margin multi label structured prediction.
NIPS: Neural Information Processing Systems. Neural Information Processing
Systems Foundation.'
chicago: 'Lampert, Christoph. Maximum Margin Multi Label Structured Prediction.
NIPS: Neural Information Processing Systems. Neural Information Processing
Systems Foundation, 2011.'
ieee: C. Lampert, Maximum margin multi label structured prediction. Neural
Information Processing Systems Foundation, 2011.
ista: Lampert C. 2011. Maximum margin multi label structured prediction, Neural
Information Processing Systems Foundation,p.
mla: 'Lampert, Christoph. “Maximum Margin Multi Label Structured Prediction.” NIPS:
Neural Information Processing Systems, Neural Information Processing Systems
Foundation, 2011.'
short: C. Lampert, Maximum Margin Multi Label Structured Prediction, Neural Information
Processing Systems Foundation, 2011.
date_created: 2018-12-11T12:02:40Z
date_published: 2011-12-13T00:00:00Z
date_updated: 2025-06-03T11:47:47Z
day: '13'
department:
- _id: ChLa
language:
- iso: eng
month: '12'
oa_version: None
publication: 'NIPS: Neural Information Processing Systems'
publication_status: published
publisher: Neural Information Processing Systems Foundation
publist_id: '3313'
related_material:
record:
- id: '3163'
relation: earlier_version
status: public
status: public
title: Maximum margin multi label structured prediction
type: conference_poster
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3323'
abstract:
- lang: eng
text: We present a new decidable logic called TREX for expressing constraints about
imperative tree data structures. In particular, TREX supports a transitive closure
operator that can express reachability constraints, which often appear in data
structure invariants. We show that our logic is closed under weakest precondition
computation, which enables its use for automated software verification. We further
show that satisfiability of formulas in TREX is decidable in NP. The low complexity
makes it an attractive alternative to more expensive logics such as monadic second-order
logic (MSOL) over trees, which have been traditionally used for reasoning about
tree data structures.
alternative_title:
- 'LNAI '
author:
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
- first_name: Marco
full_name: Muñiz, Marco
last_name: Muñiz
- first_name: Viktor
full_name: Kuncak, Viktor
last_name: Kuncak
citation:
ama: 'Wies T, Muñiz M, Kuncak V. An efficient decision procedure for imperative
tree data structures. In: Vol 6803. Springer; 2011:476-491. doi:10.1007/978-3-642-22438-6_36'
apa: 'Wies, T., Muñiz, M., & Kuncak, V. (2011). An efficient decision procedure
for imperative tree data structures (Vol. 6803, pp. 476–491). Presented at the
CADE 23: Automated Deduction , Wrocław, Poland: Springer. https://doi.org/10.1007/978-3-642-22438-6_36'
chicago: Wies, Thomas, Marco Muñiz, and Viktor Kuncak. “An Efficient Decision Procedure
for Imperative Tree Data Structures,” 6803:476–91. Springer, 2011. https://doi.org/10.1007/978-3-642-22438-6_36.
ieee: 'T. Wies, M. Muñiz, and V. Kuncak, “An efficient decision procedure for imperative
tree data structures,” presented at the CADE 23: Automated Deduction , Wrocław,
Poland, 2011, vol. 6803, pp. 476–491.'
ista: 'Wies T, Muñiz M, Kuncak V. 2011. An efficient decision procedure for imperative
tree data structures. CADE 23: Automated Deduction , LNAI , vol. 6803, 476–491.'
mla: Wies, Thomas, et al. An Efficient Decision Procedure for Imperative Tree
Data Structures. Vol. 6803, Springer, 2011, pp. 476–91, doi:10.1007/978-3-642-22438-6_36.
short: T. Wies, M. Muñiz, V. Kuncak, in:, Springer, 2011, pp. 476–491.
conference:
end_date: 2011-08-05
location: Wrocław, Poland
name: 'CADE 23: Automated Deduction '
start_date: 2011-07-31
corr_author: '1'
date_created: 2018-12-11T12:02:40Z
date_published: 2011-07-19T00:00:00Z
date_updated: 2024-10-09T20:54:31Z
day: '19'
department:
- _id: ToHe
doi: 10.1007/978-3-642-22438-6_36
fulldoi: https://doi.org/10.1007/978-3-642-22438-6_36
intvolume: ' 6803'
language:
- iso: eng
month: '07'
oa_version: None
page: 476 - 491
publication_status: published
publisher: Springer
publist_id: '3312'
quality_controlled: '1'
related_material:
record:
- id: '5383'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: An efficient decision procedure for imperative tree data structures
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6803
year: '2011'
...