---
_id: '3292'
abstract:
- lang: eng
text: Galactofuranose (Galf) containing molecules have been described at the cell
surface of several eukaryotes and shown to contribute to the virulence of the
parasite Leishmania major and the fungus Aspergillus fumigatus. It is anticipated
that a number of the surface glycoconjugates such as N-glycans or glycolipids
are galactofuranosylated in the Golgi apparatus. This raises the question of how
the substrate for galactofuranosylation reactions, UDP-Galf, which is synthesized
in the cytosol, translocates into the organelles of the secretory pathway. Here
we report the first identification of a Golgi-localized nucleotide sugar transporter,
named GlfB, with specificity for a UDP-Galf. In vitro transport assays established
binding of UDP-Galf to GlfB and excluded transport of several other nucleotide
sugars. Furthermore, the implication of glfB in the galactofuranosylation of A.
fumigatus glycoconjugates and galactomannan was demonstrated by a targeted gene
deletion approach. Our data reveal a direct connection between galactomannan and
the organelles of the secretory pathway that strongly suggests that the cell wall-bound
polysaccharide originates from its glycosylphosphatidylinositol-anchored form.
author:
- first_name: Jakob
full_name: Engel, Jakob
last_name: Engel
- first_name: Philipp S
full_name: Schmalhorst, Philipp S
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Thilo
full_name: Dörk Bousset, Thilo
last_name: Dörk Bousset
- first_name: Vincent
full_name: Ferrières, Vincent
last_name: Ferrières
- first_name: Françoise
full_name: Routier, Françoise
last_name: Routier
citation:
ama: Engel J, Schmalhorst PS, Dörk Bousset T, Ferrières V, Routier F. A single UDP
galactofuranose transporter is required for galactofuranosylation in Aspergillus
fumigatus. Journal of Biological Chemistry. 2009;284(49):33859-33868. doi:10.1074/jbc.M109.070219
apa: Engel, J., Schmalhorst, P. S., Dörk Bousset, T., Ferrières, V., & Routier,
F. (2009). A single UDP galactofuranose transporter is required for galactofuranosylation
in Aspergillus fumigatus. Journal of Biological Chemistry. American Society
for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M109.070219
chicago: Engel, Jakob, Philipp S Schmalhorst, Thilo Dörk Bousset, Vincent Ferrières,
and Françoise Routier. “A Single UDP Galactofuranose Transporter Is Required for
Galactofuranosylation in Aspergillus Fumigatus.” Journal of Biological Chemistry.
American Society for Biochemistry and Molecular Biology, 2009. https://doi.org/10.1074/jbc.M109.070219 .
ieee: J. Engel, P. S. Schmalhorst, T. Dörk Bousset, V. Ferrières, and F. Routier,
“A single UDP galactofuranose transporter is required for galactofuranosylation
in Aspergillus fumigatus,” Journal of Biological Chemistry, vol. 284, no.
49. American Society for Biochemistry and Molecular Biology, pp. 33859–33868,
2009.
ista: Engel J, Schmalhorst PS, Dörk Bousset T, Ferrières V, Routier F. 2009. A single
UDP galactofuranose transporter is required for galactofuranosylation in Aspergillus
fumigatus. Journal of Biological Chemistry. 284(49), 33859–33868.
mla: Engel, Jakob, et al. “A Single UDP Galactofuranose Transporter Is Required
for Galactofuranosylation in Aspergillus Fumigatus.” Journal of Biological
Chemistry, vol. 284, no. 49, American Society for Biochemistry and Molecular
Biology, 2009, pp. 33859–68, doi:10.1074/jbc.M109.070219 .
short: J. Engel, P.S. Schmalhorst, T. Dörk Bousset, V. Ferrières, F. Routier, Journal
of Biological Chemistry 284 (2009) 33859–33868.
date_created: 2018-12-11T12:02:30Z
date_published: 2009-12-04T00:00:00Z
date_updated: 2021-01-12T07:42:26Z
day: '04'
doi: '10.1074/jbc.M109.070219 '
extern: '1'
intvolume: ' 284'
issue: '49'
language:
- iso: eng
month: '12'
oa_version: None
page: 33859 - 33868
publication: Journal of Biological Chemistry
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '3353'
quality_controlled: '1'
status: public
title: A single UDP galactofuranose transporter is required for galactofuranosylation
in Aspergillus fumigatus
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 284
year: '2009'
...
---
_id: '3293'
abstract:
- lang: eng
text: Chemotactic responses of Drosophila to certain esters and alcohols are experience
dependent. When the flies are exposed after eclosion to these chemicals, the odorants
become strongly attractive. We show that behavioral conditioning is accompanied
by an increase in the electrophysiological responses of single neurons in sensilla
basiconica. Sensitization involves odorants that act on a common olfactory receptor.
The possible mechanism of imaginal conditioning and its ecological and evolutionary
significance are discussed.
author:
- first_name: Subhra
full_name: Chakraborty Tuhin, Subhra
last_name: Chakraborty Tuhin
- first_name: Sarit
full_name: Sarit Goswami
id: 3A578F32-F248-11E8-B48F-1D18A9856A87
last_name: Goswami
- first_name: Obaid
full_name: Siddiqi, Obaid
last_name: Siddiqi
citation:
ama: Chakraborty Tuhin S, Goswami S, Siddiqi O. Sensory correlates of imaginal conditioning
in Drosophila melanogaster. Journal of Neurogenetics. 2009;23(1-2):210-219.
doi:10.1080/01677060802491559
apa: Chakraborty Tuhin, S., Goswami, S., & Siddiqi, O. (2009). Sensory correlates
of imaginal conditioning in Drosophila melanogaster. Journal of Neurogenetics.
Informa Healthcare. https://doi.org/10.1080/01677060802491559
chicago: Chakraborty Tuhin, Subhra, Sarit Goswami, and Obaid Siddiqi. “Sensory Correlates
of Imaginal Conditioning in Drosophila Melanogaster.” Journal of Neurogenetics.
Informa Healthcare, 2009. https://doi.org/10.1080/01677060802491559
.
ieee: S. Chakraborty Tuhin, S. Goswami, and O. Siddiqi, “Sensory correlates of imaginal
conditioning in Drosophila melanogaster,” Journal of Neurogenetics, vol.
23, no. 1–2. Informa Healthcare, pp. 210–9, 2009.
ista: Chakraborty Tuhin S, Goswami S, Siddiqi O. 2009. Sensory correlates of imaginal
conditioning in Drosophila melanogaster. Journal of Neurogenetics. 23(1–2), 210–9.
mla: Chakraborty Tuhin, Subhra, et al. “Sensory Correlates of Imaginal Conditioning
in Drosophila Melanogaster.” Journal of Neurogenetics, vol. 23, no. 1–2,
Informa Healthcare, 2009, pp. 210–19, doi:10.1080/01677060802491559 .
short: S. Chakraborty Tuhin, S. Goswami, O. Siddiqi, Journal of Neurogenetics 23
(2009) 210–9.
date_created: 2018-12-11T12:02:30Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:27Z
day: '01'
doi: '10.1080/01677060802491559 '
extern: 1
intvolume: ' 23'
issue: 1-2
month: '01'
page: 210 - 9
publication: Journal of Neurogenetics
publication_status: published
publisher: Informa Healthcare
publist_id: '3348'
quality_controlled: 0
status: public
title: Sensory correlates of imaginal conditioning in Drosophila melanogaster
type: journal_article
volume: 23
year: '2009'
...
---
_id: '3304'
abstract:
- lang: eng
text: Complex traits often involve interactions between different genetic loci.
This can lead to sign epistasis, whereby mutations that are individually deleterious
or neutral combine to confer a fitness benefit. In order to acquire the beneficial
genotype, an asexual population must cross a fitness valley or plateau by first
acquiring the deleterious or neutral intermediates. Here, we present a complete,
intuitive theoretical description of the valley-crossing process across the full
spectrum of possible parameter regimes. We calculate the rate at which a population
crosses a fitness valley or plateau of arbitrary width, as a function of the mutation
rates, the population size, and the fitnesses of the intermediates. We find that
when intermediates are close to neutral, a large population can cross even wide
fitness valleys remarkably quickly, so that valley-crossing dynamics may be common
even when mutations that directly increase fitness are also possible. Thus the
evolutionary dynamics of large populations can be sensitive to the structure of
an extended region of the fitness landscape — the population may not take directly
uphill paths in favor of paths across valleys and plateaus that lead eventually
to fitter genotypes. In smaller populations, we find that below a threshold size,
which depends on the width of the fitness valley and the strength of selection
against intermediate genotypes, valley-crossing is much less likely and hence
the evolutionary dynamics are less influenced by distant regions of the fitness
landscape.
author:
- first_name: Daniel
full_name: Daniel Weissman
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Michael
full_name: Desai, Michael M
last_name: Desai
- first_name: Daniel
full_name: Fisher, Daniel S
last_name: Fisher
- first_name: Marcus
full_name: Feldman, Marcus W
last_name: Feldman
citation:
ama: Weissman D, Desai M, Fisher D, Feldman M. The rate at which asexual populations
cross fitness valleys. Theoretical Population Biology. 2009;75(4):286-300.
doi:10.1016/j.tpb.2009.02.006
apa: Weissman, D., Desai, M., Fisher, D., & Feldman, M. (2009). The rate at
which asexual populations cross fitness valleys. Theoretical Population Biology.
Academic Press. https://doi.org/10.1016/j.tpb.2009.02.006
chicago: Weissman, Daniel, Michael Desai, Daniel Fisher, and Marcus Feldman. “The
Rate at Which Asexual Populations Cross Fitness Valleys.” Theoretical Population
Biology. Academic Press, 2009. https://doi.org/10.1016/j.tpb.2009.02.006.
ieee: D. Weissman, M. Desai, D. Fisher, and M. Feldman, “The rate at which asexual
populations cross fitness valleys,” Theoretical Population Biology, vol.
75, no. 4. Academic Press, pp. 286–300, 2009.
ista: Weissman D, Desai M, Fisher D, Feldman M. 2009. The rate at which asexual
populations cross fitness valleys. Theoretical Population Biology. 75(4), 286–300.
mla: Weissman, Daniel, et al. “The Rate at Which Asexual Populations Cross Fitness
Valleys.” Theoretical Population Biology, vol. 75, no. 4, Academic Press,
2009, pp. 286–300, doi:10.1016/j.tpb.2009.02.006.
short: D. Weissman, M. Desai, D. Fisher, M. Feldman, Theoretical Population Biology
75 (2009) 286–300.
date_created: 2018-12-11T12:02:34Z
date_published: 2009-06-01T00:00:00Z
date_updated: 2021-01-12T07:42:31Z
day: '01'
doi: 10.1016/j.tpb.2009.02.006
extern: 1
intvolume: ' 75'
issue: '4'
month: '06'
page: 286 - 300
publication: Theoretical Population Biology
publication_status: published
publisher: Academic Press
publist_id: '3336'
quality_controlled: 0
status: public
title: The rate at which asexual populations cross fitness valleys
type: journal_article
volume: 75
year: '2009'
...
---
_id: '3309'
abstract:
- lang: eng
text: |2-
Mastitis, a worldwide endemic disease of dairy cows, is an important cause of decreased efficiency in milk production. Early medical treatment can reduce the nonreversible losses in milk production caused by this infection. Various diagnostic tests for mastitis are available, including a test measuring the electrical conductivity of milk (MEC test), the industry standard of somatic cell counting (SCC test), a bacteriological test, and a recently developed test measuring mammary associated amyloid A (MAA test). None of these tests is considered a gold standard, however. The aim of the present study was to determine which of these tests provides the best results, and at what cost, to improve the efficiency of milk production. For this study, 25 cows were tested at all four quarters of the udder with each of the aforementioned mastitis diagnostic tests. Based on the data, the disease prevalence as well as the sensitivity and the specificity of the four tests were estimated with a Bayesian approach by extending the Hui and Walter model with two independent tests and two populations to a model with four partially dependent tests and one population. This model was further combined with a receiver operating characteristics analysis to estimate the overall test accuracy.
author:
- first_name: Caroline
full_name: Caroline Uhler
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: 'Uhler C. Mastitis in dairy production: Estimation of sensitivity, specificity
and disease prevalence in the absence of a gold standard. Journal of Agricultural
Biological and Environmental Statistics. 2009;14(1):79-98. doi:10.1198/jabes.2009.0005'
apa: 'Uhler, C. (2009). Mastitis in dairy production: Estimation of sensitivity,
specificity and disease prevalence in the absence of a gold standard. Journal
of Agricultural Biological and Environmental Statistics. Springer. https://doi.org/10.1198/jabes.2009.0005'
chicago: 'Uhler, Caroline. “Mastitis in Dairy Production: Estimation of Sensitivity,
Specificity and Disease Prevalence in the Absence of a Gold Standard.” Journal
of Agricultural Biological and Environmental Statistics. Springer, 2009. https://doi.org/10.1198/jabes.2009.0005.'
ieee: 'C. Uhler, “Mastitis in dairy production: Estimation of sensitivity, specificity
and disease prevalence in the absence of a gold standard,” Journal of Agricultural
Biological and Environmental Statistics, vol. 14, no. 1. Springer, pp. 79–98,
2009.'
ista: 'Uhler C. 2009. Mastitis in dairy production: Estimation of sensitivity, specificity
and disease prevalence in the absence of a gold standard. Journal of Agricultural
Biological and Environmental Statistics. 14(1), 79–98.'
mla: 'Uhler, Caroline. “Mastitis in Dairy Production: Estimation of Sensitivity,
Specificity and Disease Prevalence in the Absence of a Gold Standard.” Journal
of Agricultural Biological and Environmental Statistics, vol. 14, no. 1, Springer,
2009, pp. 79–98, doi:10.1198/jabes.2009.0005.'
short: C. Uhler, Journal of Agricultural Biological and Environmental Statistics
14 (2009) 79–98.
date_created: 2018-12-11T12:02:35Z
date_published: 2009-03-01T00:00:00Z
date_updated: 2021-01-12T07:42:33Z
day: '01'
doi: 10.1198/jabes.2009.0005
extern: 1
intvolume: ' 14'
issue: '1'
month: '03'
page: 79 - 98
publication: Journal of Agricultural Biological and Environmental Statistics
publication_status: published
publisher: Springer
publist_id: '3331'
quality_controlled: 0
status: public
title: 'Mastitis in dairy production: Estimation of sensitivity, specificity and disease
prevalence in the absence of a gold standard'
type: journal_article
volume: 14
year: '2009'
...
---
_id: '337'
abstract:
- lang: eng
text: 'The formation of hollow vs solid particles by means of the oxidation reaction
of solid metal particles depends on the differential self-diffusivities of the
reactants through the composite shell, the reaction probabilities at each interface,
and the concentration and diffusivity of the element in solution. By means of
a kinetic model of the oxidation process, we determine the phase diagrams for
the geometry of the oxidized particles and propose four shell growth regimes.
We experimentally illustrate the different growth scenarios by changing the conditions
of oxidation of cadmium spherical crystals using different chalcogen precursors. '
article_processing_charge: No
article_type: original
author:
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Pablo
full_name: Guardia, Pablo
last_name: Guardia
- first_name: Paul
full_name: Alivisatos, Paul
last_name: Alivisatos
citation:
ama: Cabot A, Ibáñez M, Guardia P, Alivisatos P. Reaction regimes on the synthesis
of hollow particles by the Kirkendall effect. Journal of the American Chemical
Society. 2009;131(32):11326-11328. doi:10.1021/ja903751p
apa: Cabot, A., Ibáñez, M., Guardia, P., & Alivisatos, P. (2009). Reaction regimes
on the synthesis of hollow particles by the Kirkendall effect. Journal of the
American Chemical Society. ACS. https://doi.org/10.1021/ja903751p
chicago: Cabot, Andreu, Maria Ibáñez, Pablo Guardia, and Paul Alivisatos. “Reaction
Regimes on the Synthesis of Hollow Particles by the Kirkendall Effect.” Journal
of the American Chemical Society. ACS, 2009. https://doi.org/10.1021/ja903751p.
ieee: A. Cabot, M. Ibáñez, P. Guardia, and P. Alivisatos, “Reaction regimes on the
synthesis of hollow particles by the Kirkendall effect,” Journal of the American
Chemical Society, vol. 131, no. 32. ACS, pp. 11326–11328, 2009.
ista: Cabot A, Ibáñez M, Guardia P, Alivisatos P. 2009. Reaction regimes on the
synthesis of hollow particles by the Kirkendall effect. Journal of the American
Chemical Society. 131(32), 11326–11328.
mla: Cabot, Andreu, et al. “Reaction Regimes on the Synthesis of Hollow Particles
by the Kirkendall Effect.” Journal of the American Chemical Society, vol.
131, no. 32, ACS, 2009, pp. 11326–28, doi:10.1021/ja903751p.
short: A. Cabot, M. Ibáñez, P. Guardia, P. Alivisatos, Journal of the American Chemical
Society 131 (2009) 11326–11328.
date_created: 2018-12-11T11:45:53Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:00Z
day: '01'
doi: 10.1021/ja903751p
extern: '1'
intvolume: ' 131'
issue: '32'
language:
- iso: eng
month: '01'
oa_version: None
page: 11326 - 11328
publication: Journal of the American Chemical Society
publication_status: published
publisher: ACS
publist_id: '7494'
quality_controlled: '1'
status: public
title: Reaction regimes on the synthesis of hollow particles by the Kirkendall effect
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2009'
...
---
_id: '3398'
abstract:
- lang: eng
text: Why is a particular architecture for a pathway chosen over seemingly equivalent
alternatives? Çağatay et al. (2009) use a synthetic biology approach to show that
fluctuations—or noise—in protein levels may play a key role in determining which
network design is selected during evolution.
article_processing_charge: No
author:
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Bollenbach MT, Kishony R. Quiet gene circuit more fragile than its noisy peer.
Cell. 2009;139(3):460-461. doi:10.1016/j.cell.2009.10.005
apa: Bollenbach, M. T., & Kishony, R. (2009). Quiet gene circuit more fragile
than its noisy peer. Cell. Cell Press. https://doi.org/10.1016/j.cell.2009.10.005
chicago: Bollenbach, Mark Tobias, and Roy Kishony. “Quiet Gene Circuit More Fragile
than Its Noisy Peer.” Cell. Cell Press, 2009. https://doi.org/10.1016/j.cell.2009.10.005.
ieee: M. T. Bollenbach and R. Kishony, “Quiet gene circuit more fragile than its
noisy peer,” Cell, vol. 139, no. 3. Cell Press, pp. 460–461, 2009.
ista: Bollenbach MT, Kishony R. 2009. Quiet gene circuit more fragile than its noisy
peer. Cell. 139(3), 460–461.
mla: Bollenbach, Mark Tobias, and Roy Kishony. “Quiet Gene Circuit More Fragile
than Its Noisy Peer.” Cell, vol. 139, no. 3, Cell Press, 2009, pp. 460–61,
doi:10.1016/j.cell.2009.10.005.
short: M.T. Bollenbach, R. Kishony, Cell 139 (2009) 460–461.
date_created: 2018-12-11T12:03:07Z
date_published: 2009-10-30T00:00:00Z
date_updated: 2021-01-12T07:43:12Z
day: '30'
doi: 10.1016/j.cell.2009.10.005
extern: '1'
intvolume: ' 139'
issue: '3'
language:
- iso: eng
month: '10'
oa_version: None
page: 460 - 461
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3061'
status: public
title: Quiet gene circuit more fragile than its noisy peer
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 139
year: '2009'
...
---
_id: '3400'
abstract:
- lang: eng
text: |-
Invasive fungal infections pose a serious threat to immunocompromised people. Most of these infections are caused by either Candida or Aspergillus species, with A. fumigatus being the predominant causative agent of Invasive Aspergillosis. Affected people comprise mainly haematopoietic stem cell or solid organ transplant patients who receive either high-dose corticosteroids or immunosuppressants. These risk factors predispose to the development of Invasive
Aspergillosis which is lethal in 20 to 80 % of the cases, largely due to insufficient efficacy of current antifungal therapy. Thus one major aim in current mycological research is the identification of new drug targets.
The polysaccharide-based fungal cell wall is both essential to fungi and absent from human cells which makes it appear an attractive new target. Notably, many components of the A. fumigatus cell wall, including the polysaccharide galactomannan, glycoproteins, and glycolipids, contain the unusual sugar galactofuranose (Galf). In contrast to the other cell wall monosaccharides, Galf does not occur on human cells but is known as component of cell surface molecules of many pathogenic bacteria and protozoa, such as Mycobacterium tuberculosis or Leishmania major. These molecules are often essential for virulence or viability of these organisms which suggested a possible role of Galf in the pathogenicity of A. fumigatus.
To address the importance of Galf in A. fumigatus, the key biosynthesis gene glfA, encoding UDPgalactopyranose mutase (UGM), was deleted. In different experimental approaches it was demonstrated that the absence of the glfA gene led to a complete loss of Galf-containing glycans.
Analysis of the DeltaglfA phenotype revealed growth and sporulation defects, reduced thermotolerance and an increased susceptibility to antifungal drugs. Electron Microscopy indicated a cell wall defect as a likely cause for the observed impairments. Furthermore, the virulence of the DeltaglfA mutant was found to be severely attenuated in a murine model of Invasive Aspergillosis.
The second focus of this study was laid on further elucidation of the galactofuranosylation pathway in A. fumigatus. In eukaryotes, a UDP-Galf transporter is likely required to transport UDP-Galf from the
cytosol into the organelles of the secretory pathway, but no such activity had been described. Sixteen candidate genes were identified in the A. fumigatus genome of which one, glfB, was found in close proximity to the glfA gene. In vitro transport assays revealed specificity of GlfB for UDP-Galf suggesting that glfB encoded indeed a UDP-Galf transporter. The influence of glfB on
galactofuranosylation was determined by a DeltaglfB deletion mutant, which closely recapitulated the DeltaglfA phenotype and was likewise found to be completely devoid of Galf. It could be concluded that all galactofuranosylation processes in A. fumigatus occur in the secretory pathway, including the biosynthesis of the cell wall polysaccharide galactomannan whose subcellular origin was previously disputed.
Thus in the course of this study the first UDP-Galf specific nucleotide sugar transporter was identified and its requirement for galactofuranosylation in A. fumigatus demonstrated. Moreover, it was shown that blocking the galactofuranosylation pathway impaired virulence of A. fumigatus which suggests the UDP-Galf biosynthesis enzyme UGM as a target for new antifungal drugs.
author:
- first_name: Philipp S
full_name: Philipp Schmalhorst
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
citation:
ama: Schmalhorst PS. Biosynthesis of Galactofuranose Containing Glycans and Their
Relevance for the Pathogenic Fungus Aspergillus fumigatus. 2009:1-72.
apa: Schmalhorst, P. S. (2009). Biosynthesis of Galactofuranose Containing Glycans
and Their Relevance for the Pathogenic Fungus Aspergillus fumigatus. Gottfried
Wilhelm Leibniz Universität Hannover.
chicago: Schmalhorst, Philipp S. “Biosynthesis of Galactofuranose Containing Glycans
and Their Relevance for the Pathogenic Fungus Aspergillus Fumigatus.” Gottfried
Wilhelm Leibniz Universität Hannover, 2009.
ieee: P. S. Schmalhorst, “Biosynthesis of Galactofuranose Containing Glycans and
Their Relevance for the Pathogenic Fungus Aspergillus fumigatus,” Gottfried Wilhelm
Leibniz Universität Hannover, 2009.
ista: Schmalhorst PS. 2009. Biosynthesis of Galactofuranose Containing Glycans and
Their Relevance for the Pathogenic Fungus Aspergillus fumigatus. Gottfried Wilhelm
Leibniz Universität Hannover.
mla: Schmalhorst, Philipp S. Biosynthesis of Galactofuranose Containing Glycans
and Their Relevance for the Pathogenic Fungus Aspergillus Fumigatus. Gottfried
Wilhelm Leibniz Universität Hannover, 2009, pp. 1–72.
short: P.S. Schmalhorst, Biosynthesis of Galactofuranose Containing Glycans and
Their Relevance for the Pathogenic Fungus Aspergillus Fumigatus, Gottfried Wilhelm
Leibniz Universität Hannover, 2009.
date_created: 2018-12-11T12:03:07Z
date_published: 2009-08-13T00:00:00Z
date_updated: 2021-01-12T07:43:13Z
day: '13'
extern: 1
main_file_link:
- open_access: '0'
url: http://edok01.tib.uni-hannover.de/edoks/e01dh09/609861891.pdf
month: '08'
page: 1 - 72
publication_status: published
publisher: Gottfried Wilhelm Leibniz Universität Hannover
publist_id: '3058'
quality_controlled: 0
status: public
title: Biosynthesis of Galactofuranose Containing Glycans and Their Relevance for
the Pathogenic Fungus Aspergillus fumigatus
type: dissertation
year: '2009'
...
---
_id: '3408'
abstract:
- lang: eng
text: Mechanical forces govern physiological processes in all living organisms.
Many cellular forces, for example, those generated in cyclic conformational changes
of biological machines, have repetitive components. In apparent contrast, little
is known about how dynamic protein structures respond to periodic mechanical information.
Ubiquitin is a small protein found in all eukaryotes. We developed molecular dynamics
simulations to unfold single and multimeric ubiquitins with periodic forces. By
using a coarse-grained representation, we were able to model forces with periods
about 2 orders of magnitude longer than the protein's relaxation time. We found
that even a moderate periodic force weakened the protein and shifted its unfolding
pathways in a frequency- and amplitude-dependent manner. A complex dynamic response
with secondary structure refolding and an increasing importance of local interactions
was revealed. Importantly, repetitive forces with broadly distributed frequencies
elicited very similar molecular responses compared to fixed-frequency forces.
When testing the influence of pulling geometry on ubiquitin's mechanical stability,
it was found that the linkage involved in the mechanical degradation of cellular
proteins renders the protein remarkably insensitive to periodic forces. We also
devised a complementary kinetic energy landscape model that traces these observations
and explains periodic-force, single-molecule measurements. In turn, this analytical
model is capable of predicting dynamic protein responses. These results provide
new insights into ubiquitin mechanics and a potential mechanical role during protein
degradation, as well as first frameworks for dynamic protein stability and the
modeling of repetitive mechanical processes.
author:
- first_name: Piotr
full_name: Szymczak, Piotr
last_name: Szymczak
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Szymczak P, Janovjak HL. Periodic forces trigger a complex mechanical response
in ubiquitin. Journal of Molecular Biology. 2009;390(3):443-456. doi:10.1016/j.jmb.2009.04.071
apa: Szymczak, P., & Janovjak, H. L. (2009). Periodic forces trigger a complex
mechanical response in ubiquitin. Journal of Molecular Biology. Elsevier.
https://doi.org/10.1016/j.jmb.2009.04.071
chicago: Szymczak, Piotr, and Harald L Janovjak. “Periodic Forces Trigger a Complex
Mechanical Response in Ubiquitin.” Journal of Molecular Biology. Elsevier,
2009. https://doi.org/10.1016/j.jmb.2009.04.071.
ieee: P. Szymczak and H. L. Janovjak, “Periodic forces trigger a complex mechanical
response in ubiquitin,” Journal of Molecular Biology, vol. 390, no. 3.
Elsevier, pp. 443–456, 2009.
ista: Szymczak P, Janovjak HL. 2009. Periodic forces trigger a complex mechanical
response in ubiquitin. Journal of Molecular Biology. 390(3), 443–456.
mla: Szymczak, Piotr, and Harald L. Janovjak. “Periodic Forces Trigger a Complex
Mechanical Response in Ubiquitin.” Journal of Molecular Biology, vol. 390,
no. 3, Elsevier, 2009, pp. 443–56, doi:10.1016/j.jmb.2009.04.071.
short: P. Szymczak, H.L. Janovjak, Journal of Molecular Biology 390 (2009) 443–456.
date_created: 2018-12-11T12:03:10Z
date_published: 2009-07-17T00:00:00Z
date_updated: 2021-01-12T07:43:16Z
day: '17'
doi: 10.1016/j.jmb.2009.04.071
extern: 1
intvolume: ' 390'
issue: '3'
month: '07'
page: 443 - 456
publication: Journal of Molecular Biology
publication_status: published
publisher: Elsevier
publist_id: '2994'
quality_controlled: 0
status: public
title: Periodic forces trigger a complex mechanical response in ubiquitin
type: journal_article
volume: 390
year: '2009'
...
---
_id: '3428'
abstract:
- lang: eng
text: In this issue of Molecular Cell, Davies et al. (2009) work out a sequence
of active cellular events that lead to the death of Escherichia coli in the presence
of the drug hydroxyurea.
article_processing_charge: No
author:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Bollenbach MT, Kishony R. Hydroxyurea triggers cellular responses that actively
cause bacterial cell death. Molecular Cell. 2009;36(5):728-729. doi:10.1016/j.molcel.2009.11.027
apa: Bollenbach, M. T., & Kishony, R. (2009). Hydroxyurea triggers cellular
responses that actively cause bacterial cell death. Molecular Cell. Cell
Press. https://doi.org/10.1016/j.molcel.2009.11.027
chicago: Bollenbach, Mark Tobias, and Roy Kishony. “Hydroxyurea Triggers Cellular
Responses That Actively Cause Bacterial Cell Death.” Molecular Cell. Cell
Press, 2009. https://doi.org/10.1016/j.molcel.2009.11.027.
ieee: M. T. Bollenbach and R. Kishony, “Hydroxyurea triggers cellular responses
that actively cause bacterial cell death,” Molecular Cell, vol. 36, no.
5. Cell Press, pp. 728–729, 2009.
ista: Bollenbach MT, Kishony R. 2009. Hydroxyurea triggers cellular responses that
actively cause bacterial cell death. Molecular Cell. 36(5), 728–729.
mla: Bollenbach, Mark Tobias, and Roy Kishony. “Hydroxyurea Triggers Cellular Responses
That Actively Cause Bacterial Cell Death.” Molecular Cell, vol. 36, no.
5, Cell Press, 2009, pp. 728–29, doi:10.1016/j.molcel.2009.11.027.
short: M.T. Bollenbach, R. Kishony, Molecular Cell 36 (2009) 728–729.
date_created: 2018-12-11T12:03:17Z
date_published: 2009-12-11T00:00:00Z
date_updated: 2021-01-12T07:43:24Z
day: '11'
doi: 10.1016/j.molcel.2009.11.027
extern: '1'
intvolume: ' 36'
issue: '5'
language:
- iso: eng
month: '12'
oa_version: None
page: 728 - 729
publication: Molecular Cell
publication_status: published
publisher: Cell Press
publist_id: '2972'
status: public
title: Hydroxyurea triggers cellular responses that actively cause bacterial cell
death
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2009'
...
---
_id: '3503'
abstract:
- lang: eng
text: 'We give polynomial-time algorithms for computing the values of Markov decision
processes (MDPs) with limsup and liminf objectives. A real-valued reward is assigned
to each state, and the value of an infinite path in the MDP is the limsup (resp.
liminf) of all rewards along the path. The value of an MDP is the maximal expected
value of an infinite path that can be achieved by resolving the decisions of the
MDP. Using our result on MDPs, we show that turn-based stochastic games with limsup
and liminf objectives can be solved in NP ∩ coNP. '
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, Henzinger TA. Probabilistic systems with limsup and liminf objectives.
In: Vol 5489. Springer; 2009:32-45. doi:10.1007/978-3-642-03092-5_4'
apa: 'Chatterjee, K., & Henzinger, T. A. (2009). Probabilistic systems with
limsup and liminf objectives (Vol. 5489, pp. 32–45). Presented at the ILC: Infinity
in Logic and Computation, Springer. https://doi.org/10.1007/978-3-642-03092-5_4'
chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Probabilistic Systems
with Limsup and Liminf Objectives,” 5489:32–45. Springer, 2009. https://doi.org/10.1007/978-3-642-03092-5_4.
ieee: 'K. Chatterjee and T. A. Henzinger, “Probabilistic systems with limsup and
liminf objectives,” presented at the ILC: Infinity in Logic and Computation, 2009,
vol. 5489, pp. 32–45.'
ista: 'Chatterjee K, Henzinger TA. 2009. Probabilistic systems with limsup and liminf
objectives. ILC: Infinity in Logic and Computation, LNCS, vol. 5489, 32–45.'
mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. Probabilistic Systems with
Limsup and Liminf Objectives. Vol. 5489, Springer, 2009, pp. 32–45, doi:10.1007/978-3-642-03092-5_4.
short: K. Chatterjee, T.A. Henzinger, in:, Springer, 2009, pp. 32–45.
conference:
name: 'ILC: Infinity in Logic and Computation'
date_created: 2018-12-11T12:03:40Z
date_published: 2009-12-15T00:00:00Z
date_updated: 2021-01-12T07:43:54Z
day: '15'
doi: 10.1007/978-3-642-03092-5_4
extern: 1
intvolume: ' 5489'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0809.1465
month: '12'
oa: 1
page: 32 - 45
publication_status: published
publisher: Springer
publist_id: '2884'
quality_controlled: 0
status: public
title: Probabilistic systems with limsup and liminf objectives
type: conference
volume: 5489
year: '2009'
...
---
_id: '3547'
abstract:
- lang: eng
text: Neurons possess elaborate dendritic arbors which receive and integrate excitatory
synaptic signals. Individual dendritic subbranches exhibit local membrane potential
supralinearities, termed dendritic spikes, which control transfer of local synaptic
input to the soma. Here, we show that dendritic spikes in CA1 pyramidal cells
are strongly regulated by specific types of prior input. While input in the linear
range is without effect, supralinear input inhibits subsequent spikes, causing
them to attenuate and ultimately fail due to dendritic Na+ channel inactivation.
This mechanism acts locally within the boundaries of the input branch. If an input
is sufficiently strong to trigger axonal action potentials, their back-propagation
into the dendritic tree causes a widespread global reduction in dendritic excitability
which is prominent after firing patterns occurring in vivo. Together, these mechanisms
control the capability of individual dendritic branches to trigger somatic action
potential output. They are invoked at frequencies encountered during learning,
and impose limits on the storage and retrieval rates of information encoded as
branch excitability.
author:
- first_name: Stefan
full_name: Remy,Stefan
last_name: Remy
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Heinz
full_name: Beck,Heinz
last_name: Beck
citation:
ama: Remy S, Csicsvari JL, Beck H. Activity-dependent control of neuronal output
by local and global dendritic spike attenuation. Neuron. 2009;61(6):906-916.
doi:10.1016/j.neuron.2009.01.032
apa: Remy, S., Csicsvari, J. L., & Beck, H. (2009). Activity-dependent control
of neuronal output by local and global dendritic spike attenuation. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2009.01.032
chicago: Remy, Stefan, Jozsef L Csicsvari, and Heinz Beck. “Activity-Dependent Control
of Neuronal Output by Local and Global Dendritic Spike Attenuation.” Neuron.
Elsevier, 2009. https://doi.org/10.1016/j.neuron.2009.01.032.
ieee: S. Remy, J. L. Csicsvari, and H. Beck, “Activity-dependent control of neuronal
output by local and global dendritic spike attenuation,” Neuron, vol. 61,
no. 6. Elsevier, pp. 906–916, 2009.
ista: Remy S, Csicsvari JL, Beck H. 2009. Activity-dependent control of neuronal
output by local and global dendritic spike attenuation. Neuron. 61(6), 906–916.
mla: Remy, Stefan, et al. “Activity-Dependent Control of Neuronal Output by Local
and Global Dendritic Spike Attenuation.” Neuron, vol. 61, no. 6, Elsevier,
2009, pp. 906–16, doi:10.1016/j.neuron.2009.01.032.
short: S. Remy, J.L. Csicsvari, H. Beck, Neuron 61 (2009) 906–916.
date_created: 2018-12-11T12:03:54Z
date_published: 2009-03-26T00:00:00Z
date_updated: 2021-01-12T07:44:13Z
day: '26'
doi: 10.1016/j.neuron.2009.01.032
extern: 1
intvolume: ' 61'
issue: '6'
month: '03'
page: 906 - 916
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2838'
quality_controlled: 0
status: public
title: Activity-dependent control of neuronal output by local and global dendritic
spike attenuation
type: journal_article
volume: 61
year: '2009'
...
---
_id: '3578'
abstract:
- lang: eng
text: The medial axis of a geometric shape captures its connectivity. In spite of
its inherent instability, it has found applications in a number of areas that
deal with shapes. In this survey paper, we focus on results that shed light on
this instability and use the new insights to generate simplified and stable modifications
of the medial axis.
alternative_title:
- Mathematics and Visualization
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: Jean
full_name: Boissonnat, Jean-Daniel
last_name: Boissonnat
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Attali D, Boissonnat J, Edelsbrunner H. Stability and computation of medial
axes: a state-of-the-art report. In: Mathematical Foundations of Scientific
Visualization, Computer Graphics, and Massive Data Exploration. Springer;
2009:109-125. doi:10.1007/b106657_6'
apa: 'Attali, D., Boissonnat, J., & Edelsbrunner, H. (2009). Stability and computation
of medial axes: a state-of-the-art report. In Mathematical Foundations of Scientific
Visualization, Computer Graphics, and Massive Data Exploration (pp. 109–125).
Springer. https://doi.org/10.1007/b106657_6'
chicago: 'Attali, Dominique, Jean Boissonnat, and Herbert Edelsbrunner. “Stability
and Computation of Medial Axes: A State-of-the-Art Report.” In Mathematical
Foundations of Scientific Visualization, Computer Graphics, and Massive Data Exploration,
109–25. Springer, 2009. https://doi.org/10.1007/b106657_6.'
ieee: 'D. Attali, J. Boissonnat, and H. Edelsbrunner, “Stability and computation
of medial axes: a state-of-the-art report,” in Mathematical Foundations of
Scientific Visualization, Computer Graphics, and Massive Data Exploration,
Springer, 2009, pp. 109–125.'
ista: 'Attali D, Boissonnat J, Edelsbrunner H. 2009.Stability and computation of
medial axes: a state-of-the-art report. In: Mathematical Foundations of Scientific
Visualization, Computer Graphics, and Massive Data Exploration. Mathematics and
Visualization, , 109–125.'
mla: 'Attali, Dominique, et al. “Stability and Computation of Medial Axes: A State-of-the-Art
Report.” Mathematical Foundations of Scientific Visualization, Computer Graphics,
and Massive Data Exploration, Springer, 2009, pp. 109–25, doi:10.1007/b106657_6.'
short: D. Attali, J. Boissonnat, H. Edelsbrunner, in:, Mathematical Foundations
of Scientific Visualization, Computer Graphics, and Massive Data Exploration,
Springer, 2009, pp. 109–125.
date_created: 2018-12-11T12:04:03Z
date_published: 2009-06-22T00:00:00Z
date_updated: 2021-01-12T07:44:25Z
day: '22'
doi: 10.1007/b106657_6
extern: 1
main_file_link:
- open_access: '0'
url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.103.9122
month: '06'
page: 109 - 125
publication: Mathematical Foundations of Scientific Visualization, Computer Graphics,
and Massive Data Exploration
publication_status: published
publisher: Springer
publist_id: '2807'
quality_controlled: 0
status: public
title: 'Stability and computation of medial axes: a state-of-the-art report'
type: book_chapter
year: '2009'
...
---
_id: '3675'
abstract:
- lang: eng
text: "Sex and recombination have long been seen as adaptations that facilitate
natural selection by generating favorable variations. If recombination is to aid
selection, there must be negative linkage disequilibria—favorable alleles must
be found together less often than expected by chance. These negative linkage disequilibria
can be generated directly by selection, but this must involve negative epistasis
of just the right strength, which is not expected, from either experiment or theory.
Random drift provides a more general source of negative associations: Favorable
mutations almost always arise on different genomes, and negative associations
tend to persist, precisely because they shield variation from selection.\r\n\r\nWe
can understand how recombination aids adaptation by determining the maximum possible
rate of adaptation. With unlinked loci, this rate increases only logarithmically
with the influx of favorable mutations. With a linear genome, a scaling argument
shows that in a large population, the rate of adaptive substitution depends only
on the expected rate in the absence of interference, divided by the total rate
of recombination. A two-locus approximation predicts an upper bound on the rate
of substitution, proportional to recombination rate.\r\n\r\nIf associations between
linked loci do impede adaptation, there can be substantial selection for modifiers
that increase recombination. Whether this can account for the maintenance of high
rates of sex and recombination depends on the extent of selection. It is clear
that the rate of species-wide substitutions is typically far too low to generate
appreciable selection for recombination. However, local sweeps within a subdivided
population may be effective."
acknowledgement: Royal Society and the Engineering and Physical Sciences for support
(GR/ T11753/01)
author:
- 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: 'Barton NH. Why sex and recombination? . In: Cold Spring Harbor Symposia
on Quantitative Biology. Vol 74. Cold Spring Harbor Laboratory Press; 2009:187-195.
doi:10.1101/sqb.2009.74.030'
apa: Barton, N. H. (2009). Why sex and recombination? . In Cold Spring Harbor
Symposia on Quantitative Biology (Vol. 74, pp. 187–195). Cold Spring Harbor
Laboratory Press. https://doi.org/10.1101/sqb.2009.74.030
chicago: Barton, Nicholas H. “Why Sex and Recombination? .” In Cold Spring Harbor
Symposia on Quantitative Biology, 74:187–95. Cold Spring Harbor Laboratory
Press, 2009. https://doi.org/10.1101/sqb.2009.74.030.
ieee: N. H. Barton, “Why sex and recombination? ,” in Cold Spring Harbor Symposia
on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009,
pp. 187–195.
ista: 'Barton NH. 2009.Why sex and recombination? . In: Cold Spring Harbor Symposia
on Quantitative Biology. vol. 74, 187–195.'
mla: Barton, Nicholas H. “Why Sex and Recombination? .” Cold Spring Harbor Symposia
on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009,
pp. 187–95, doi:10.1101/sqb.2009.74.030.
short: N.H. Barton, in:, Cold Spring Harbor Symposia on Quantitative Biology, Cold
Spring Harbor Laboratory Press, 2009, pp. 187–195.
date_created: 2018-12-11T12:04:33Z
date_published: 2009-11-10T00:00:00Z
date_updated: 2021-01-12T07:45:04Z
day: '10'
department:
- _id: NiBa
doi: 10.1101/sqb.2009.74.030
intvolume: ' 74'
language:
- iso: eng
month: '11'
oa_version: None
page: 187 - 195
publication: Cold Spring Harbor Symposia on Quantitative Biology
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '2708'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Why sex and recombination? '
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2009'
...
---
_id: '3690'
abstract:
- lang: eng
text: An important cue to high level scene understanding is to analyze the objects
in the scene and their behavior and interactions. In this paper, we study the
problem of classification of activities in videos, as this is an integral component
of any scene understanding system, and present a novel approach for recognizing
human action categories in videos by combining information from appearance and
motion of human body parts. Our approach is based on tracking human body parts
by using mixture particle filters and then clustering the particles using local
non - parametric clustering, hence associating a local set of particles to each
cluster mode. The trajectory of these cluster modes provides the "motion"
information and the "appearance" information is provided by the statistical
information about the relative motion of these local set of particles over a number
of frames. Later we use a "Bag of Words" model to build one histogram
per video sequence from the set of these robust appearance and motion descriptors.
These histograms provide us characteristic information which helps us to discriminate
among various human actions which ultimately helps us in better understanding
of the complete scene. We tested our approach on the standard KTH and Weizmann
human action dataseis and the results were comparable to the state of the art
methods. Additionally our approach is able to distinguish between activities that
involve the motion of complete body from those in which only certain body parts
move. In other words, our method discriminates well between activities with "global
body motion" like running, jogging etc. and "local motion" like
waving, boxing etc.
author:
- first_name: Paramveer
full_name: Dhillon, Paramveer S
last_name: Dhillon
- first_name: Sebastian
full_name: Nowozin, Sebastian
last_name: Nowozin
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Dhillon P, Nowozin S, Lampert C. Combining appearance and motion for human
action classification in videos. In: IEEE; 2009:22-29. doi:10.1109/CVPRW.2009.5204237'
apa: 'Dhillon, P., Nowozin, S., & Lampert, C. (2009). Combining appearance and
motion for human action classification in videos (pp. 22–29). Presented at the
CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPRW.2009.5204237'
chicago: Dhillon, Paramveer, Sebastian Nowozin, and Christoph Lampert. “Combining
Appearance and Motion for Human Action Classification in Videos,” 22–29. IEEE,
2009. https://doi.org/10.1109/CVPRW.2009.5204237.
ieee: 'P. Dhillon, S. Nowozin, and C. Lampert, “Combining appearance and motion
for human action classification in videos,” presented at the CVPR: Computer Vision
and Pattern Recognition, 2009, no. 174, pp. 22–29.'
ista: 'Dhillon P, Nowozin S, Lampert C. 2009. Combining appearance and motion for
human action classification in videos. CVPR: Computer Vision and Pattern Recognition,
22–29.'
mla: Dhillon, Paramveer, et al. Combining Appearance and Motion for Human Action
Classification in Videos. no. 174, IEEE, 2009, pp. 22–29, doi:10.1109/CVPRW.2009.5204237.
short: P. Dhillon, S. Nowozin, C. Lampert, in:, IEEE, 2009, pp. 22–29.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:04:38Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:48:59Z
day: '01'
doi: 10.1109/CVPRW.2009.5204237
extern: 1
issue: '174'
month: '01'
page: 22 - 29
publication_status: published
publisher: IEEE
publist_id: '2675'
quality_controlled: 0
status: public
title: Combining appearance and motion for human action classification in videos
type: conference
year: '2009'
...
---
_id: '3696'
abstract:
- lang: eng
text: Discriminative techniques, such as conditional random fields (CRFs) or structure
aware maximum-margin techniques (maximum margin Markov networks (M3N), structured
output support vector machines (S-SVM)), are state-of-the-art in the prediction
of structured data. However, to achieve good results these techniques require
complete and reliable ground truth, which is not always available in realistic
problems. Furthermore, training either CRFs or margin-based techniques is computationally
costly, because the runtime of current training methods depends not only on the
size of the training set but also on properties of the output space to which the
training samples are assigned. We propose an alternative model for structured
output prediction, Joint Kernel Support Estimation (JKSE), which is rather generative
in nature as it relies on estimating the joint probability density of samples
and labels in the training set. This makes it tolerant against incomplete or incorrect
labels and also opens the possibility of learning in situations where more than
one output label can be considered correct. At the same time, we avoid typical
problems of generative models as we do not attempt to learn the full joint probability
distribution, but we model only its support in a joint reproducing kernel Hilbert
space. As a consequence, JKSE training is possible by an adaption of the classical
one-class SVM procedure. The resulting optimization problem is convex and efficiently
solvable even with tens of thousands of training examples. A particular advantage
of JKSE is that the training speed depends only on the size of the training set,
and not on the total size of the label space. No inference step during training
is required (as M3N and S-SVM would) nor do we have calculate a partition function
(as CRFs do). Experiments on realistic data show that, for suitable kernel functions,
our method works efficiently and robustly in situations that discriminative techniques
have problems with or that are computationally infeasible for them.
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
citation:
ama: Lampert C, Blaschko M. Structured prediction by joint kernel support estimation.
Machine Learning. 2009;77(2-3):249-269. doi:10.1007/s10994-009-5111-0
apa: Lampert, C., & Blaschko, M. (2009). Structured prediction by joint kernel
support estimation. Machine Learning. Springer. https://doi.org/10.1007/s10994-009-5111-0
chicago: Lampert, Christoph, and Matthew Blaschko. “Structured Prediction by Joint
Kernel Support Estimation.” Machine Learning. Springer, 2009. https://doi.org/10.1007/s10994-009-5111-0.
ieee: C. Lampert and M. Blaschko, “Structured prediction by joint kernel support
estimation,” Machine Learning, vol. 77, no. 2–3. Springer, pp. 249–269,
2009.
ista: Lampert C, Blaschko M. 2009. Structured prediction by joint kernel support
estimation. Machine Learning. 77(2–3), 249–269.
mla: Lampert, Christoph, and Matthew Blaschko. “Structured Prediction by Joint Kernel
Support Estimation.” Machine Learning, vol. 77, no. 2–3, Springer, 2009,
pp. 249–69, doi:10.1007/s10994-009-5111-0.
short: C. Lampert, M. Blaschko, Machine Learning 77 (2009) 249–269.
date_created: 2018-12-11T12:04:40Z
date_published: 2009-04-07T00:00:00Z
date_updated: 2021-01-12T07:49:01Z
day: '07'
doi: 10.1007/s10994-009-5111-0
extern: 1
intvolume: ' 77'
issue: 2-3
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '04'
page: 249 - 269
publication: Machine Learning
publication_status: published
publisher: Springer
publist_id: '2663'
quality_controlled: 0
status: public
title: Structured prediction by joint kernel support estimation
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
volume: 77
year: '2009'
...
---
_id: '3699'
abstract:
- lang: eng
text: Kernel Canonical Correlation Analysis (KCCA) is a general technique for subspace
learning that incorporates principal components analysis (PCA) and Fisher linear
discriminant analysis (LDA) as special cases. By finding directions that maximize
correlation, CCA learns representations tied more closely to underlying process
generating the the data and can ignore high-variance noise directions. However,
for data where acquisition in a given modality is expensive or otherwise limited,
CCA may suffer from small sample effects. We propose to use semisupervised Laplacian
regularization to utilize data that are present in only one modality. This approach
is able to find highly correlated directions that also lie along the data manifold,
resulting in a more robust estimate of correlated subspaces. Functional magnetic
resonance imaging (fMRI) acquired data are naturally amenable to subspace techniques
as data are well aligned. fMRI data of the human brain are a particularly interesting
candidate. In this study we implemented various supervised and semi-supervised
versions of CCA on human fMRI data, with regression to single and multivariate
labels (corresponding to video content subjects viewed during the image acquisition).
In each variate condition, the semi-supervised variants of CCA performed better
than the supervised variants, including a supervised variant with Laplacian regularization.
We additionally analyze the weights learned by the regression in order to infer
brain regions that are important to different types of visual processing.
author:
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Andreas
full_name: Bartels, Andreas
last_name: Bartels
citation:
ama: Blaschko M, Lampert C, Bartels A. Semi-Supervised Analysis of Human FMRI
Data. Berlin Institute of Technology; 2009.
apa: 'Blaschko, M., Lampert, C., & Bartels, A. (2009). Semi-supervised analysis
of human fMRI data. BBCI: Berlin Brain-Computer Interface Workshop - Advances
in Neurotechnology. Berlin Institute of Technology.'
chicago: 'Blaschko, Matthew, Christoph Lampert, and Andreas Bartels. Semi-Supervised
Analysis of Human FMRI Data. BBCI: Berlin Brain-Computer Interface Workshop
- Advances in Neurotechnology. Berlin Institute of Technology, 2009.'
ieee: M. Blaschko, C. Lampert, and A. Bartels, Semi-supervised analysis of human
fMRI data. Berlin Institute of Technology, 2009.
ista: Blaschko M, Lampert C, Bartels A. 2009. Semi-supervised analysis of human
fMRI data, Berlin Institute of Technology,p.
mla: 'Blaschko, Matthew, et al. “Semi-Supervised Analysis of Human FMRI Data.” BBCI:
Berlin Brain-Computer Interface Workshop - Advances in Neurotechnology, Berlin
Institute of Technology, 2009.'
short: M. Blaschko, C. Lampert, A. Bartels, Semi-Supervised Analysis of Human FMRI
Data, Berlin Institute of Technology, 2009.
date_created: 2018-12-11T12:04:41Z
date_published: 2009-07-10T00:00:00Z
date_updated: 2019-04-26T07:22:33Z
day: '10'
extern: 1
main_file_link:
- open_access: '0'
url: http://pubman.mpdl.mpg.de/pubman/faces/viewItemOverviewPage.jsp?itemId=escidoc:1789281
month: '07'
publication: 'BBCI: Berlin Brain-Computer Interface Workshop - Advances in Neurotechnology'
publication_status: published
publisher: Berlin Institute of Technology
publist_id: '2661'
quality_controlled: 0
status: public
title: Semi-supervised analysis of human fMRI data
type: conference_poster
year: '2009'
...
---
_id: '3703'
abstract:
- lang: eng
text: Recent research has shown that the use of contextual cues significantly improves
performance in sliding window type localization systems. In this work, we propose
a method that incorporates both global and local context information through appropriately
defined kernel functions. In particular, we make use of a weighted combination
of kernels defined over local spatial regions, as well as a global context kernel.
The relative importance of the context contributions is learned automatically,
and the resulting discriminant function is of a form such that localization at
test time can be solved efficiently using a branch and bound optimization scheme.
By specifying context directly with a kernel learning approach, we achieve high
localization accuracy with a simple and efficient representation. This is in contrast
to other systems that incorporate context for which expensive inference needs
to be done at test time. We show experimentally on the PASCAL VOC datasets that
the inclusion of context can significantly improve localization performance, provided
the relative contributions of context cues are learned appropriately.
acknowledgement: The research leading to these results has received funding from the
European Research Council under the European Community’s Seventh Framework Programme
(FP7/2007- 2013) / ERC grant agreement no. 228180. This work was funded in part
by the EC project CLASS, IST 027978, and the PASCAL2 network of excellence. The
first author is supported by the Royal Academy of Engineering through a Newton International
Fellowship.
alternative_title:
- Proceedings of the BMVC
author:
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Blaschko M, Lampert C. Object localization with global and local context kernels.
In: BMVA Press; 2009:1-11. doi:10.5244/C.23.63'
apa: 'Blaschko, M., & Lampert, C. (2009). Object localization with global and
local context kernels (pp. 1–11). Presented at the BMVC: British Machine Vision
Conference, BMVA Press. https://doi.org/10.5244/C.23.63'
chicago: Blaschko, Matthew, and Christoph Lampert. “Object Localization with Global
and Local Context Kernels,” 1–11. BMVA Press, 2009. https://doi.org/10.5244/C.23.63.
ieee: 'M. Blaschko and C. Lampert, “Object localization with global and local context
kernels,” presented at the BMVC: British Machine Vision Conference, 2009, pp.
1–11.'
ista: 'Blaschko M, Lampert C. 2009. Object localization with global and local context
kernels. BMVC: British Machine Vision Conference, Proceedings of the BMVC, , 1–11.'
mla: Blaschko, Matthew, and Christoph Lampert. Object Localization with Global
and Local Context Kernels. BMVA Press, 2009, pp. 1–11, doi:10.5244/C.23.63.
short: M. Blaschko, C. Lampert, in:, BMVA Press, 2009, pp. 1–11.
conference:
name: 'BMVC: British Machine Vision Conference'
date_created: 2018-12-11T12:04:42Z
date_published: 2009-09-10T00:00:00Z
date_updated: 2021-01-12T07:51:36Z
day: '10'
doi: 10.5244/C.23.63
extern: 1
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '0'
url: http://www.bmva.org/bmvc/2009/Papers/Paper228/Paper228.pdf
month: '09'
page: 1 - 11
publication_status: published
publisher: BMVA Press
publist_id: '2655'
quality_controlled: 0
status: public
title: Object localization with global and local context kernels
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: conference
year: '2009'
...
---
_id: '3704'
abstract:
- lang: eng
text: We study the problem of object classification when training and test classes
are disjoint, i.e. no training examples of the target classes are available. This
setup has hardly been studied in computer vision research, but it is the rule
rather than the exception, because the world contains tens of thousands of different
object classes and for only a very few of them image, collections have been formed
and annotated with suitable class labels. In this paper, we tackle the problem
by introducing attribute-based classification. It performs object detection based
on a human-specified high-level description of the target objects instead of training
images. The description consists of arbitrary semantic attributes, like shape,
color or even geographic information. Because such properties transcend the specific
learning task at hand, they can be pre-learned, e.g. from image datasets unrelated
to the current task. Afterwards, new classes can be detected based on their attribute
representation, without the need for a new training phase. In order to evaluate
our method and to facilitate research in this area, we have assembled a new large-scale
dataset, ldquoAnimals with Attributesrdquo, of over 30,000 animal images that
match the 50 classes in Osherson‘s classic table of how strongly humans associate
85 semantic attributes with animal classes. Our experiments show that by using
an attribute layer it is indeed possible to build a learning object detection
system that does not require any training images of the target classes.
acknowledgement: This work was funded in part by the EC project CLASS, IST 027978,
and the PASCAL2 network of excellence.
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Hannes
full_name: Nickisch,Hannes
last_name: Nickisch
- first_name: Stefan
full_name: Harmeling,Stefan
last_name: Harmeling
citation:
ama: 'Lampert C, Nickisch H, Harmeling S. Learning to detect unseen object classes
by between-class attribute transfer. In: IEEE; 2009:951-958. doi:10.1109/CVPR.2009.5206594'
apa: 'Lampert, C., Nickisch, H., & Harmeling, S. (2009). Learning to detect
unseen object classes by between-class attribute transfer (pp. 951–958). Presented
at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2009.5206594'
chicago: Lampert, Christoph, Hannes Nickisch, and Stefan Harmeling. “Learning to
Detect Unseen Object Classes by Between-Class Attribute Transfer,” 951–58. IEEE,
2009. https://doi.org/10.1109/CVPR.2009.5206594.
ieee: 'C. Lampert, H. Nickisch, and S. Harmeling, “Learning to detect unseen object
classes by between-class attribute transfer,” presented at the CVPR: Computer
Vision and Pattern Recognition, 2009, pp. 951–958.'
ista: 'Lampert C, Nickisch H, Harmeling S. 2009. Learning to detect unseen object
classes by between-class attribute transfer. CVPR: Computer Vision and Pattern
Recognition, 951–958.'
mla: Lampert, Christoph, et al. Learning to Detect Unseen Object Classes by Between-Class
Attribute Transfer. IEEE, 2009, pp. 951–58, doi:10.1109/CVPR.2009.5206594.
short: C. Lampert, H. Nickisch, S. Harmeling, in:, IEEE, 2009, pp. 951–958.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:04:43Z
date_published: 2009-06-20T00:00:00Z
date_updated: 2021-01-12T07:51:36Z
day: '20'
doi: 10.1109/CVPR.2009.5206594
extern: 1
month: '06'
page: 951 - 958
publication_status: published
publisher: IEEE
publist_id: '2652'
quality_controlled: 0
status: public
title: Learning to detect unseen object classes by between-class attribute transfer
type: conference
year: '2009'
...
---
_id: '3707'
abstract:
- lang: eng
text: Over the last years, kernel methods have established themselves as powerful
tools for computer vision researchers as well as for practitioners. In this tutorial,
we give an introduction to kernel methods in computer vision from a geometric
perspective, introducing not only the ubiquitous support vector machines, but
also less known techniques for regression, dimensionality reduction, outlier detection
and clustering. Additionally, we give an outlook on very recent, non-classical
techniques for the prediction of structure data, for the estimation of statistical
dependency and for learning the kernel function itself. All methods are illustrated
with examples of successful application from the recent computer vision research
literature.
alternative_title:
- Foundations and Trends® in Computer Graphics and Vision
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. Kernel Methods in Computer Vision. Vol 4. now publishers;
2009. doi:10.1561/0600000027
apa: Lampert, C. (2009). Kernel Methods in Computer Vision (Vol. 4). now
publishers. https://doi.org/10.1561/0600000027
chicago: Lampert, Christoph. Kernel Methods in Computer Vision. Vol. 4. now
publishers, 2009. https://doi.org/10.1561/0600000027.
ieee: C. Lampert, Kernel Methods in Computer Vision, vol. 4. now publishers,
2009.
ista: Lampert C. 2009. Kernel Methods in Computer Vision, now publishers, 112p.
mla: Lampert, Christoph. Kernel Methods in Computer Vision. Vol. 4, now publishers,
2009, doi:10.1561/0600000027.
short: C. Lampert, Kernel Methods in Computer Vision, now publishers, 2009.
date_created: 2018-12-11T12:04:44Z
date_published: 2009-09-03T00:00:00Z
date_updated: 2021-12-21T15:38:43Z
day: '03'
doi: 10.1561/0600000027
extern: '1'
intvolume: ' 4'
language:
- iso: eng
month: '09'
oa_version: None
page: '112'
publication_identifier:
eisbn:
- 978-1-60198-269-8
isbn:
- 978-1-60198-268-1
publication_status: published
publisher: now publishers
publist_id: '2651'
quality_controlled: '1'
status: public
title: Kernel Methods in Computer Vision
type: book
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 4
year: '2009'
...
---
_id: '3708'
abstract:
- lang: eng
text: Markov random field (MRF, CRF) models are popular in computer vision. However,
in order to be computationally tractable they are limited to incorporate only
local interactions and cannot model global properties, such as connectedness,
which is a potentially useful high-level prior for object segmentation. In this
work, we overcome this limitation by deriving a potential function that enforces
the output labeling to be connected and that can naturally be used in the framework
of recent MAP-MRF LP relaxations. Using techniques from polyhedral combinatorics,
we show that a provably tight approximation to the MAP solution of the resulting
MRF can still be found efficiently by solving a sequence of max-flow problems.
The efficiency of the inference procedure also allows us to learn the parameters
of a MRF with global connectivity potentials by means of a cutting plane algorithm.
We experimentally evaluate our algorithm on both synthetic data and on the challenging
segmentation task of the PASCAL VOC 2008 data set. We show that in both cases
the addition of a connectedness prior significantly reduces the segmentation error.
acknowledgement: |-
Conference Information URL:
http://www.cvpr2009.org/
author:
- first_name: Sebastian
full_name: Nowozin, Sebastian
last_name: Nowozin
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Nowozin S, Lampert C. Global connectivity potentials for random field models.
In: IEEE; 2009:818-825. doi:10.1109/CVPR.2009.5206567'
apa: 'Nowozin, S., & Lampert, C. (2009). Global connectivity potentials for
random field models (pp. 818–825). Presented at the CVPR: Computer Vision and
Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2009.5206567'
chicago: Nowozin, Sebastian, and Christoph Lampert. “Global Connectivity Potentials
for Random Field Models,” 818–25. IEEE, 2009. https://doi.org/10.1109/CVPR.2009.5206567.
ieee: 'S. Nowozin and C. Lampert, “Global connectivity potentials for random field
models,” presented at the CVPR: Computer Vision and Pattern Recognition, 2009,
pp. 818–825.'
ista: 'Nowozin S, Lampert C. 2009. Global connectivity potentials for random field
models. CVPR: Computer Vision and Pattern Recognition, 818–825.'
mla: Nowozin, Sebastian, and Christoph Lampert. Global Connectivity Potentials
for Random Field Models. IEEE, 2009, pp. 818–25, doi:10.1109/CVPR.2009.5206567.
short: S. Nowozin, C. Lampert, in:, IEEE, 2009, pp. 818–825.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:04:44Z
date_published: 2009-06-20T00:00:00Z
date_updated: 2021-01-12T07:51:38Z
day: '20'
doi: 10.1109/CVPR.2009.5206567
extern: 1
month: '06'
page: 818 - 825
publication_status: published
publisher: IEEE
publist_id: '2649'
quality_controlled: 0
status: public
title: Global connectivity potentials for random field models
type: conference
year: '2009'
...