---
_id: '3914'
abstract:
- lang: eng
text: We compare the performances of established means of character selection for
discriminant analysis in species distinction with a combination procedure for
finding the optimal character combination (minimum classification error, minimum
number of required characters), using morphometric data sets from the ant genera
Cardiocondyla, Lasius and Tetramorium. The established methods are empirical character
selection as well as forward selection, backward elimination and stepwise selection
of discriminant analysis. The combination procedure is clearly superior to the
established methods of character selection, and is widely applicable.
author:
- first_name: Karl
full_name: Moder, Karl
last_name: Moder
- first_name: Birgit
full_name: Schlick Steiner, Birgit
last_name: Schlick Steiner
- first_name: Florian
full_name: Steiner, Florian
last_name: Steiner
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Erhard
full_name: Christian, Erhard
last_name: Christian
- first_name: Bernhard
full_name: Seifert, Bernhard
last_name: Seifert
citation:
ama: 'Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B. Optimal
species distinction by discriminant analysis: comparing established methods of
character selection with a combination procedure using ant morphometrics as a
case study. Journal of Zoological Systematics and Evolutionary Research.
2006;45(1):82-87. doi:10.1111/j.1439-0469.2006.00372.x'
apa: 'Moder, K., Schlick Steiner, B., Steiner, F., Cremer, S., Christian, E., &
Seifert, B. (2006). Optimal species distinction by discriminant analysis: comparing
established methods of character selection with a combination procedure using
ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary
Research. Wiley-Blackwell. https://doi.org/10.1111/j.1439-0469.2006.00372.x'
chicago: 'Moder, Karl, Birgit Schlick Steiner, Florian Steiner, Sylvia Cremer, Erhard
Christian, and Bernhard Seifert. “Optimal Species Distinction by Discriminant
Analysis: Comparing Established Methods of Character Selection with a Combination
Procedure Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics
and Evolutionary Research. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.1439-0469.2006.00372.x.'
ieee: 'K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, and B.
Seifert, “Optimal species distinction by discriminant analysis: comparing established
methods of character selection with a combination procedure using ant morphometrics
as a case study,” Journal of Zoological Systematics and Evolutionary Research,
vol. 45, no. 1. Wiley-Blackwell, pp. 82–87, 2006.'
ista: 'Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B.
2006. Optimal species distinction by discriminant analysis: comparing established
methods of character selection with a combination procedure using ant morphometrics
as a case study. Journal of Zoological Systematics and Evolutionary Research.
45(1), 82–87.'
mla: 'Moder, Karl, et al. “Optimal Species Distinction by Discriminant Analysis:
Comparing Established Methods of Character Selection with a Combination Procedure
Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics
and Evolutionary Research, vol. 45, no. 1, Wiley-Blackwell, 2006, pp. 82–87,
doi:10.1111/j.1439-0469.2006.00372.x.'
short: K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, B. Seifert,
Journal of Zoological Systematics and Evolutionary Research 45 (2006) 82–87.
date_created: 2018-12-11T12:05:52Z
date_published: 2006-08-29T00:00:00Z
date_updated: 2021-01-12T07:53:10Z
day: '29'
doi: 10.1111/j.1439-0469.2006.00372.x
extern: '1'
intvolume: ' 45'
issue: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 82 - 87
publication: Journal of Zoological Systematics and Evolutionary Research
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2241'
status: public
title: 'Optimal species distinction by discriminant analysis: comparing established
methods of character selection with a combination procedure using ant morphometrics
as a case study'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2006'
...
---
_id: '3913'
abstract:
- lang: eng
text: Many invasive ant species, such as the Argentine ant or the red imported fire
ant, have huge colonies with thousands of mass-foraging workers, which quickly
monopolise resources and therefore represent a considerable threat to the native
ant fauna. Cardiocondyla obscurior and several other species of this myrmicine
genus have similarly been transferred throughout the tropics by human activities.
However, because their colonies are tiny and workers forage solitarily, Cardiocondyla
are often not recognized as successful invaders. Here, we document that the life
history of Cardiocondyla closely resembles that of the more conspicuous tramp
species, with polygyny, intranidal mating, budding, worker sterility, low genetic
variability, and possibly also unicoloniality. Given that introduced Cardiocondyla
may locally reach a very high population density, the effects of these stealthy
invaders on the native arthropod fauna should receive more attention.
author:
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Norbert
full_name: Eckl, Norbert
last_name: Eckl
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
citation:
ama: 'Heinze J, Cremer S, Eckl N, Schrempf A. Stealthy invaders: the biology of
Cardiocondyla tramp ants. Insectes Sociaux. 2006;53(1):1-7. doi:10.1007/s00040-005-0847-4'
apa: 'Heinze, J., Cremer, S., Eckl, N., & Schrempf, A. (2006). Stealthy invaders:
the biology of Cardiocondyla tramp ants. Insectes Sociaux. Springer. https://doi.org/10.1007/s00040-005-0847-4'
chicago: 'Heinze, Jürgen, Sylvia Cremer, Norbert Eckl, and Alexandra Schrempf. “Stealthy
Invaders: The Biology of Cardiocondyla Tramp Ants.” Insectes Sociaux. Springer,
2006. https://doi.org/10.1007/s00040-005-0847-4.'
ieee: 'J. Heinze, S. Cremer, N. Eckl, and A. Schrempf, “Stealthy invaders: the biology
of Cardiocondyla tramp ants,” Insectes Sociaux, vol. 53, no. 1. Springer,
pp. 1–7, 2006.'
ista: 'Heinze J, Cremer S, Eckl N, Schrempf A. 2006. Stealthy invaders: the biology
of Cardiocondyla tramp ants. Insectes Sociaux. 53(1), 1–7.'
mla: 'Heinze, Jürgen, et al. “Stealthy Invaders: The Biology of Cardiocondyla Tramp
Ants.” Insectes Sociaux, vol. 53, no. 1, Springer, 2006, pp. 1–7, doi:10.1007/s00040-005-0847-4.'
short: J. Heinze, S. Cremer, N. Eckl, A. Schrempf, Insectes Sociaux 53 (2006) 1–7.
date_created: 2018-12-11T12:05:51Z
date_published: 2006-02-01T00:00:00Z
date_updated: 2021-01-12T07:53:09Z
day: '01'
doi: 10.1007/s00040-005-0847-4
extern: '1'
intvolume: ' 53'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 1 - 7
publication: Insectes Sociaux
publication_status: published
publisher: Springer
publist_id: '2240'
status: public
title: 'Stealthy invaders: the biology of Cardiocondyla tramp ants'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2006'
...
---
_id: '3932'
abstract:
- lang: eng
text: 'OBJECTIVES: The EGFR is expressed in malignant ovarian tumor tissue, and
tissue content of EGFR has been directly associated with poor prognosis in patients
with ovarian cancer. The uPA system plays a role in pericellular proteolysis,
cell migration, invasion, and is over-expressed in ovarian cancer. This study
explored the effects of EGF on uPAR expression in the ovarian cancer cell line
OVCAR-3. METHODS: We used OVCAR-3 cells and the following methods: cell migration
assay, time-lapse video microscopy, real-time PCR, assays for cellular binding
of 125I-uPA and cellular degradation of 125I-uPA:PAI-1 complex, biosynthetic labeling
using 35S-methionin, Western blot, Northern blot, and ELISAs for uPA, PAI-1, and
uPAR. RESULTS: EGF up-regulates both protein and mRNA not only for uPAR, but also
for the ligand uPA and its inhibitor PAI-1. Cell surface uPAR, in control as well
as EGF-stimulated cells, is present only in the intact, not the cleaved, form.
Ligand binding experiments showed an increase of endogenously occupied uPAR, whereas
non-occupied receptor sites were not increased. In addition, EGF treatment resulted
in decreased degradation of radiolabeled uPA:PAI-1 complex. This suggests decreased
internalization of uPAR, since the complex is internalized together with uPAR.
Like EGF, colchicine, which inhibits endocytosis, increased cell surface expression
of uPAR. In addition, we found an immediate increase of uPAR after exposing the
cells to EGF and this was accompanied by a transient increase of cell migration.
The increase of cell surface uPAR in response to EGF is accompanied by increased
release of the soluble form of uPAR (suPAR) to the medium as well as by increased
cell migration. Both uPAR and suPAR increased in cells treated with the endocytosis
inhibitor colchicine even though cell migration was inhibited, suggesting that
the mechanism of uPAR shedding is not related to cell migration. CONCLUSION: Increased
cell surface uPAR in response to EGF stimulation results from mobilization of
uPAR from detergent-resistant domains, increased expression of uPAR mRNA, and
decreased internalization and degradation of uPAR. Both the anti-uPAR antibody
R3, which inhibits binding of uPA, and the EGFR phosphorylation inhibitor Iressa
inhibited cell migration in response to uPA as well as to EGF, suggesting that
EGFR and uPAR are engaged in the same multiprotein assembly on the cell surface.'
author:
- first_name: Emir
full_name: Henic, Emir
last_name: Henic
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Stefan
full_name: Hansson, Stefan
last_name: Hansson
- first_name: Gunilla
full_name: Høyer-Hansen, Gunilla
last_name: Høyer Hansen
- first_name: Bertil
full_name: Casslén, Bertil
last_name: Casslén
citation:
ama: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. EGF-stimulated migration
in ovarian cancer cells is associated with decreased internalization, increased
surface expression, and increased shedding of the urokinase plasminogen activator
receptor. Gynecologic Oncology. 2006;101(1):28-39. doi:10.1016/j.ygyno.2005.09.038
apa: Henic, E., Sixt, M. K., Hansson, S., Høyer Hansen, G., & Casslén, B. (2006).
EGF-stimulated migration in ovarian cancer cells is associated with decreased
internalization, increased surface expression, and increased shedding of the urokinase
plasminogen activator receptor. Gynecologic Oncology. Elsevier. https://doi.org/10.1016/j.ygyno.2005.09.038
chicago: Henic, Emir, Michael K Sixt, Stefan Hansson, Gunilla Høyer Hansen, and
Bertil Casslén. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated
with Decreased Internalization, Increased Surface Expression, and Increased Shedding
of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology.
Elsevier, 2006. https://doi.org/10.1016/j.ygyno.2005.09.038.
ieee: E. Henic, M. K. Sixt, S. Hansson, G. Høyer Hansen, and B. Casslén, “EGF-stimulated
migration in ovarian cancer cells is associated with decreased internalization,
increased surface expression, and increased shedding of the urokinase plasminogen
activator receptor,” Gynecologic Oncology, vol. 101, no. 1. Elsevier, pp.
28–39, 2006.
ista: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. 2006. EGF-stimulated
migration in ovarian cancer cells is associated with decreased internalization,
increased surface expression, and increased shedding of the urokinase plasminogen
activator receptor. Gynecologic Oncology. 101(1), 28–39.
mla: Henic, Emir, et al. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated
with Decreased Internalization, Increased Surface Expression, and Increased Shedding
of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology,
vol. 101, no. 1, Elsevier, 2006, pp. 28–39, doi:10.1016/j.ygyno.2005.09.038.
short: E. Henic, M.K. Sixt, S. Hansson, G. Høyer Hansen, B. Casslén, Gynecologic
Oncology 101 (2006) 28–39.
date_created: 2018-12-11T12:05:57Z
date_published: 2006-04-01T00:00:00Z
date_updated: 2021-01-12T07:53:17Z
day: '01'
doi: 10.1016/j.ygyno.2005.09.038
extern: 1
intvolume: ' 101'
issue: '1'
month: '04'
page: 28 - 39
publication: Gynecologic Oncology
publication_status: published
publisher: Elsevier
publist_id: '2194'
quality_controlled: 0
status: public
title: EGF-stimulated migration in ovarian cancer cells is associated with decreased
internalization, increased surface expression, and increased shedding of the urokinase
plasminogen activator receptor
type: journal_article
volume: 101
year: '2006'
...
---
_id: '3978'
abstract:
- lang: eng
text: Evaluating the quality of experimentally determined protein structural models
is an essential step toward identifying potential errors and guiding further structural
refinement. Herein, we report the use of proton local density as a sensitive measure
to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256
high-resolution crystal structures with protons added and optimized, we show that
the local density of different proton types display distinct distributions. These
distributions can be characterized by statistical moments and are used to establish
local density Z-scores for evaluating both global and local packing for individual
protons. Analysis of 546 crystal structures at various resolutions shows that
the local density Z-scores increase as the structural resolution decreases and
correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733)
generated by all atom contact analysis. Local density Z-scores for NMR structures
exhibit a significantly wider range of values than for X-ray structures and demonstrate
a combination of potentially problematic inflation and compression. Water-refined
NMR structures show improved packing quality. Our analysis of a high-quality structural
ensemble of ubiquitin refined against order parameters shows proton density distributions
that correlate nearly perfectly with our standards derived from crystal structures,
further validating our approach. We present an automated analysis and visualization
tool for proton packing to evaluate the quality of NMR structures.
author:
- first_name: Yih
full_name: Ban, Yih-En Andrew
last_name: Ban
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
- first_name: Pei
full_name: Zhou, Pei
last_name: Zhou
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. Evaluating the quality of NMR structures
by local density of protons. Proteins: Structure, Function and Bioinformatics.
2006;62(4):852-864. doi:10.1002/prot.20811'
apa: 'Ban, Y., Rudolph, J., Zhou, P., & Edelsbrunner, H. (2006). Evaluating
the quality of NMR structures by local density of protons. Proteins: Structure,
Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.20811'
chicago: 'Ban, Yih, Johannes Rudolph, Pei Zhou, and Herbert Edelsbrunner. “Evaluating
the Quality of NMR Structures by Local Density of Protons.” Proteins: Structure,
Function and Bioinformatics. Wiley-Blackwell, 2006. https://doi.org/10.1002/prot.20811.'
ieee: 'Y. Ban, J. Rudolph, P. Zhou, and H. Edelsbrunner, “Evaluating the quality
of NMR structures by local density of protons,” Proteins: Structure, Function
and Bioinformatics, vol. 62, no. 4. Wiley-Blackwell, pp. 852–864, 2006.'
ista: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. 2006. Evaluating the quality of
NMR structures by local density of protons. Proteins: Structure, Function and
Bioinformatics. 62(4), 852–864.'
mla: 'Ban, Yih, et al. “Evaluating the Quality of NMR Structures by Local Density
of Protons.” Proteins: Structure, Function and Bioinformatics, vol. 62,
no. 4, Wiley-Blackwell, 2006, pp. 852–64, doi:10.1002/prot.20811.'
short: 'Y. Ban, J. Rudolph, P. Zhou, H. Edelsbrunner, Proteins: Structure, Function
and Bioinformatics 62 (2006) 852–864.'
date_created: 2018-12-11T12:06:14Z
date_published: 2006-03-01T00:00:00Z
date_updated: 2021-01-12T07:53:36Z
day: '01'
doi: 10.1002/prot.20811
extern: 1
intvolume: ' 62'
issue: '4'
month: '03'
page: 852 - 864
publication: 'Proteins: Structure, Function and Bioinformatics'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2146'
quality_controlled: 0
status: public
title: Evaluating the quality of NMR structures by local density of protons
type: journal_article
volume: 62
year: '2006'
...
---
_id: '3979'
abstract:
- lang: eng
text: Protein-protein interactions, which form the basis for most cellular processes,
result in the formation of protein interfaces. Believing that the local shape
of proteins is crucial, we take a geometric approach and present a definition
of an interface surface formed by two or more proteins as a subset of their Voronoi
diagram. The definition deals with the difficult and important problem of specifying
interface boundaries by invoking methods used in the alpha shape representation
of molecules, the discrete flow on Delaunay simplices to define pockets and reconstruct
surfaces, and the assessment of the importance of topological features. We present
an algorithm to construct the surface and define a hierarchy that distinguishes
core and peripheral regions. This hierarchy is shown to have correlation with
hot-spots in protein-protein interactions. Finally, we study the geometric and
topological properties of interface surfaces and show their high degree of contortion.
author:
- first_name: Yih
full_name: Ban, Yih-En Andrew
last_name: Ban
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
citation:
ama: Ban Y, Edelsbrunner H, Rudolph J. Interface surfaces for protein-protein complexes.
Journal of the ACM. 2006;53(3):361-378. doi:10.1145/1147954.1147957
apa: Ban, Y., Edelsbrunner, H., & Rudolph, J. (2006). Interface surfaces for
protein-protein complexes. Journal of the ACM. ACM. https://doi.org/10.1145/1147954.1147957
chicago: Ban, Yih, Herbert Edelsbrunner, and Johannes Rudolph. “Interface Surfaces
for Protein-Protein Complexes.” Journal of the ACM. ACM, 2006. https://doi.org/10.1145/1147954.1147957.
ieee: Y. Ban, H. Edelsbrunner, and J. Rudolph, “Interface surfaces for protein-protein
complexes,” Journal of the ACM, vol. 53, no. 3. ACM, pp. 361–378, 2006.
ista: Ban Y, Edelsbrunner H, Rudolph J. 2006. Interface surfaces for protein-protein
complexes. Journal of the ACM. 53(3), 361–378.
mla: Ban, Yih, et al. “Interface Surfaces for Protein-Protein Complexes.” Journal
of the ACM, vol. 53, no. 3, ACM, 2006, pp. 361–78, doi:10.1145/1147954.1147957.
short: Y. Ban, H. Edelsbrunner, J. Rudolph, Journal of the ACM 53 (2006) 361–378.
date_created: 2018-12-11T12:06:14Z
date_published: 2006-05-01T00:00:00Z
date_updated: 2021-01-12T07:53:37Z
day: '01'
doi: 10.1145/1147954.1147957
extern: 1
intvolume: ' 53'
issue: '3'
month: '05'
page: 361 - 378
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '2147'
quality_controlled: 0
status: public
title: Interface surfaces for protein-protein complexes
type: journal_article
volume: 53
year: '2006'
...
---
_id: '3980'
abstract:
- lang: eng
text: Given a smoothly embedded 2-manifold in R-3, we define the elevation of a
point as the height difference to a canonically defined second point on the same
manifold. Our definition is invariant under rigid motions and can be used to define
features such as lines of discontinuous or continuous but non-smooth elevation.
We give an algorithm for finding points of locally maximum elevation, which we
suggest mark cavities and protrusions and are useful in matching shapes as for
example in protein docking.
author:
- first_name: Pankaj
full_name: Agarwal, Pankaj K
last_name: Agarwal
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Yusu
full_name: Wang, Yusu
last_name: Wang
citation:
ama: Agarwal P, Edelsbrunner H, Harer J, Wang Y. Extreme elevation on a 2-manifold.
Discrete & Computational Geometry. 2006;36(4):553-572. doi:10.1007/s00454-006-1265-8
apa: Agarwal, P., Edelsbrunner, H., Harer, J., & Wang, Y. (2006). Extreme elevation
on a 2-manifold. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-006-1265-8
chicago: Agarwal, Pankaj, Herbert Edelsbrunner, John Harer, and Yusu Wang. “Extreme
Elevation on a 2-Manifold.” Discrete & Computational Geometry. Springer,
2006. https://doi.org/10.1007/s00454-006-1265-8.
ieee: P. Agarwal, H. Edelsbrunner, J. Harer, and Y. Wang, “Extreme elevation on
a 2-manifold,” Discrete & Computational Geometry, vol. 36, no. 4. Springer,
pp. 553–572, 2006.
ista: Agarwal P, Edelsbrunner H, Harer J, Wang Y. 2006. Extreme elevation on a 2-manifold.
Discrete & Computational Geometry. 36(4), 553–572.
mla: Agarwal, Pankaj, et al. “Extreme Elevation on a 2-Manifold.” Discrete &
Computational Geometry, vol. 36, no. 4, Springer, 2006, pp. 553–72, doi:10.1007/s00454-006-1265-8.
short: P. Agarwal, H. Edelsbrunner, J. Harer, Y. Wang, Discrete & Computational
Geometry 36 (2006) 553–572.
date_created: 2018-12-11T12:06:15Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2021-01-12T07:53:38Z
day: '01'
doi: 10.1007/s00454-006-1265-8
extern: 1
intvolume: ' 36'
issue: '4'
month: '12'
page: 553 - 572
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2148'
quality_controlled: 0
status: public
title: Extreme elevation on a 2-manifold
type: journal_article
volume: 36
year: '2006'
...
---
_id: '4345'
abstract:
- lang: eng
text: Der Artikel beschäftigt sich mit dem Konzept der Bibliothek 2.0 (bzw. Library
2.0). Er skizziert anhand einiger Beispiele die Entwicklung zum Web 2.0 und beschreibt,
wie Web 2.0-Technologien und -Anwendungen in Bibliotheken eingesetzt werden. Im
Mittelpunkt stehen Social-Tagging-Systeme, benutzerorientierte Erweiterungen von
Bibliothekskatalogen und Dokumentenservern sowie der Einsatz von Weblogs an Bibliotheken.
Ferner werden neue Anforderungen an Bibliothekare diskutiert.
author:
- first_name: Patrick
full_name: Patrick Danowski
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
- first_name: Lambert
full_name: Heller,Lambert
last_name: Heller
citation:
ama: Danowski P, Heller L. Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst.
2006;40(11):1250-1271. doi:424
apa: Danowski, P., & Heller, L. (2006). Bibliothek 2.0 - Die Bibliothek der
Zukunft? Bibliotheksdienst. Zentral- und Landesbibliothek Berlin. https://doi.org/424
chicago: Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 - Die Bibliothek
Der Zukunft?” Bibliotheksdienst. Zentral- und Landesbibliothek Berlin,
2006. https://doi.org/424.
ieee: P. Danowski and L. Heller, “Bibliothek 2.0 - Die Bibliothek der Zukunft?,”
Bibliotheksdienst, vol. 40, no. 11. Zentral- und Landesbibliothek Berlin,
pp. 1250–1271, 2006.
ista: Danowski P, Heller L. 2006. Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst.
40(11), 1250–1271.
mla: Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 - Die Bibliothek Der
Zukunft?” Bibliotheksdienst, vol. 40, no. 11, Zentral- und Landesbibliothek
Berlin, 2006, pp. 1250–71, doi:424.
short: P. Danowski, L. Heller, Bibliotheksdienst 40 (2006) 1250–1271.
date_created: 2018-12-11T12:08:23Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:17Z
day: '01'
doi: '424'
extern: 1
intvolume: ' 40'
issue: '11'
main_file_link:
- open_access: '0'
url: http://www.zlb.de/aktivitaeten/bd_neu/heftinhalte2006/DigitaleBib011106.pdf
month: '01'
page: 1250 - 1271
publication: Bibliotheksdienst
publication_status: published
publisher: Zentral- und Landesbibliothek Berlin
publist_id: '1229'
quality_controlled: 0
status: public
title: Bibliothek 2.0 - Die Bibliothek der Zukunft?
type: journal_article
volume: 40
year: '2006'
...
---
_id: '4352'
abstract:
- lang: eng
text: 'Anopheles darlingi is the primary malaria vector in Latin America, and is
especially important in Amazonian Brazil. Historically, control efforts have been
focused on indoor house spraying using a variety of insecticides, but since the
mid-1990s there has been a shift to patient treatment and focal insecticide fogging.
Anopheles darlingi was believed to have been significantly reduced in a gold-mining
community, Peixoto de Azevedo (in Mato Grosso State), in the early 1990s by insecticide
use during a severe malaria epidemic. In contrast, although An. darlingi was eradicated
from some districts of the city of Belem (the capital of Para State) in 1968 to
reduce malaria, populations around the water protection area in the eastern district
were treated only briefly. To investigate the population structure of An. darlingi
including evidence for a population bottleneck in Peixoto, we analyzed eight microsatellite
loci of 256 individuals from seven locations in Brazil: three in Amapa State,
three in Para State, and one in Mato Grosso State. Allelic diversity and mean
expected heterozygosity were high for all populations (mean number alleles/locus
and H(E) were 13.5 and 0.834, respectively) and did not differ significantly between
locations. Significant heterozygote deficits were associated with linkage disequilibrium,
most likely due to either the Wahlund effect or selection. We found no evidence
for a population bottleneck in Peixoto, possibly because the reduction was not
extreme enough to be detected. Overall estimates of long-term N(e) varied from
92.4 individuals under the linkage disequilibrium model to infinity under the
heterozygote excess model. Fixation indices and analysis of molecular variance
demonstrated significant differentiation between locations north and south of
the Amazon River, suggesting a degree of genetic isolation between them, attributed
to isolation by distance.'
author:
- first_name: Jan
full_name: Conn, Jan E
last_name: Conn
- first_name: Joseph
full_name: Vineis, Joseph H
last_name: Vineis
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: David
full_name: Onyabe, David Y
last_name: Onyabe
- first_name: Richard
full_name: Wilkerson, Richard C
last_name: Wilkerson
- first_name: Marinete
full_name: Povoa, Marinete M
last_name: Povoa
citation:
ama: Conn J, Vineis J, Bollback JP, Onyabe D, Wilkerson R, Povoa M. Population structure
of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern
Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene.
2006;74(5):798-806.
apa: Conn, J., Vineis, J., Bollback, J. P., Onyabe, D., Wilkerson, R., & Povoa,
M. (2006). Population structure of the malaria vector Anopheles darlingi in a
malaria-endemic region of eastern Amazonian Brazil. The American Journal of
Tropical Medicine and Hygiene. American Society of Tropical Medicine and Hygiene.
chicago: Conn, Jan, Joseph Vineis, Jonathan P Bollback, David Onyabe, Richard Wilkerson,
and Marinete Povoa. “Population Structure of the Malaria Vector Anopheles Darlingi
in a Malaria-Endemic Region of Eastern Amazonian Brazil.” The American Journal
of Tropical Medicine and Hygiene. American Society of Tropical Medicine and
Hygiene, 2006.
ieee: J. Conn, J. Vineis, J. P. Bollback, D. Onyabe, R. Wilkerson, and M. Povoa,
“Population structure of the malaria vector Anopheles darlingi in a malaria-endemic
region of eastern Amazonian Brazil,” The American Journal of Tropical Medicine
and Hygiene, vol. 74, no. 5. American Society of Tropical Medicine and Hygiene,
pp. 798–806, 2006.
ista: Conn J, Vineis J, Bollback JP, Onyabe D, Wilkerson R, Povoa M. 2006. Population
structure of the malaria vector Anopheles darlingi in a malaria-endemic region
of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene.
74(5), 798–806.
mla: Conn, Jan, et al. “Population Structure of the Malaria Vector Anopheles Darlingi
in a Malaria-Endemic Region of Eastern Amazonian Brazil.” The American Journal
of Tropical Medicine and Hygiene, vol. 74, no. 5, American Society of Tropical
Medicine and Hygiene, 2006, pp. 798–806.
short: J. Conn, J. Vineis, J.P. Bollback, D. Onyabe, R. Wilkerson, M. Povoa, The
American Journal of Tropical Medicine and Hygiene 74 (2006) 798–806.
date_created: 2018-12-11T12:08:25Z
date_published: 2006-05-01T00:00:00Z
date_updated: 2021-01-12T07:56:20Z
day: '01'
extern: 1
intvolume: ' 74'
issue: '5'
main_file_link:
- open_access: '0'
url: http://www.ajtmh.org/content/74/5/798.full
month: '05'
page: 798 - 806
publication: The American Journal of Tropical Medicine and Hygiene
publication_status: published
publisher: American Society of Tropical Medicine and Hygiene
publist_id: '1108'
quality_controlled: 0
status: public
title: Population structure of the malaria vector Anopheles darlingi in a malaria-endemic
region of eastern Amazonian Brazil
type: journal_article
volume: 74
year: '2006'
...
---
_id: '4351'
abstract:
- lang: eng
text: 'BACKGROUND: Character mapping on phylogenies has played an important, if
not critical role, in our understanding of molecular, morphological, and behavioral
evolution. Until very recently we have relied on parsimony to infer character
changes. Parsimony has a number of serious limitations that are drawbacks to our
understanding. Recent statistical methods have been developed that free us from
these limitations enabling us to overcome the problems of parsimony by accommodating
uncertainty in evolutionary time, ancestral states, and the phylogeny. RESULTS:
SIMMAP has been developed to implement stochastic character mapping that is useful
to both molecular evolutionists, systematists, and bioinformaticians. Researchers
can address questions about positive selection, patterns of amino acid substitution,
character association, and patterns of morphological evolution. CONCLUSION: Stochastic
character mapping, as implemented in the SIMMAP software, enables users to address
questions that require mapping characters onto phylogenies using a probabilistic
approach that does not rely on parsimony. Analyses can be performed using a fully
Bayesian approach that is not reliant on considering a single topology, set of
substitution model parameters, or reconstruction of ancestral states. Uncertainty
in these quantities is accommodated by using MCMC samples from their respective
posterior distributions.'
author:
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: 'Bollback JP. SIMMAP: stochastic character mapping of discrete traits on phylogenies.
BMC Bioinformatics. 2006;7. doi:10.1186/1471-2105-7-88'
apa: 'Bollback, J. P. (2006). SIMMAP: stochastic character mapping of discrete traits
on phylogenies. BMC Bioinformatics. BioMed Central. https://doi.org/10.1186/1471-2105-7-88'
chicago: 'Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete
Traits on Phylogenies.” BMC Bioinformatics. BioMed Central, 2006. https://doi.org/10.1186/1471-2105-7-88.'
ieee: 'J. P. Bollback, “SIMMAP: stochastic character mapping of discrete traits
on phylogenies,” BMC Bioinformatics, vol. 7. BioMed Central, 2006.'
ista: 'Bollback JP. 2006. SIMMAP: stochastic character mapping of discrete traits
on phylogenies. BMC Bioinformatics. 7.'
mla: 'Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete Traits
on Phylogenies.” BMC Bioinformatics, vol. 7, BioMed Central, 2006, doi:10.1186/1471-2105-7-88.'
short: J.P. Bollback, BMC Bioinformatics 7 (2006).
date_created: 2018-12-11T12:08:25Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:20Z
day: '01'
doi: 10.1186/1471-2105-7-88
extern: 1
intvolume: ' 7'
license: https://creativecommons.org/licenses/by/4.0/
month: '01'
publication: BMC Bioinformatics
publication_status: published
publisher: BioMed Central
publist_id: '1109'
quality_controlled: 0
status: public
title: 'SIMMAP: stochastic character mapping of discrete traits on phylogenies'
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: 7
year: '2006'
...
---
_id: '3180'
abstract:
- lang: eng
text: 'One of the most exciting advances in early vision has been the development
of efficient energy minimization algorithms. Many early vision tasks require labeling
each pixel with some quantity such as depth or texture. While many such problems
can be elegantly expressed in the language of Markov Random Fields (MRF''s), the
resulting energy minimization problems were widely viewed as intractable. Recently,
algorithms such as graph cuts and loopy belief propagation (LBP) have proven to
be very powerful: for example, such methods form the basis for almost all the
top-performing stereo methods. Unfortunately, most papers define their own energy
function, which is minimized with a specific algorithm of their choice. As a result,
the tradeoffs among different energy minimization algorithms are not well understood.
In this paper we describe a set of energy minimization benchmarks, which we use
to compare the solution quality and running time of several common energy minimization
algorithms. We investigate three promising recent methods - graph cuts, LBP, and
tree-reweighted message passing - as well as the well-known older iterated conditional
modes (ICM) algorithm. Our benchmark problems are drawn from published energy
functions used for stereo, image stitching and interactive segmentation. We also
provide a general-purpose software interface that allows vision researchers to
easily switch between optimization methods with minimal overhead. We expect that
the availability of our benchmarks and interface will make it significantly easier
for vision researchers to adopt the best method for their specific problems. Benchmarks,
code, results and images are available at http://vision.middlebury.edu/MRF.'
author:
- first_name: Richard
full_name: Szeliski, Richard S
last_name: Szeliski
- first_name: Ramin
full_name: Zabih, Ramin
last_name: Zabih
- first_name: Daniel
full_name: Scharstein, Daniel
last_name: Scharstein
- first_name: Olga
full_name: Veksler, Olga
last_name: Veksler
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Aseem
full_name: Agarwala, Aseem
last_name: Agarwala
- first_name: Marshall
full_name: Tappen, Marshall F
last_name: Tappen
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: 'Szeliski R, Zabih R, Scharstein D, et al. A comparative study of energy minimization
methods for Markov random fields. In: Vol 3952. Springer; 2006:16-29. doi:10.1007/11744047_2'
apa: 'Szeliski, R., Zabih, R., Scharstein, D., Veksler, O., Kolmogorov, V., Agarwala,
A., … Rother, C. (2006). A comparative study of energy minimization methods for
Markov random fields (Vol. 3952, pp. 16–29). Presented at the ECCV: European Conference
on Computer Vision, Springer. https://doi.org/10.1007/11744047_2'
chicago: Szeliski, Richard, Ramin Zabih, Daniel Scharstein, Olga Veksler, Vladimir
Kolmogorov, Aseem Agarwala, Marshall Tappen, and Carsten Rother. “A Comparative
Study of Energy Minimization Methods for Markov Random Fields,” 3952:16–29. Springer,
2006. https://doi.org/10.1007/11744047_2.
ieee: 'R. Szeliski et al., “A comparative study of energy minimization methods
for Markov random fields,” presented at the ECCV: European Conference on Computer
Vision, 2006, vol. 3952, pp. 16–29.'
ista: 'Szeliski R, Zabih R, Scharstein D, Veksler O, Kolmogorov V, Agarwala A, Tappen
M, Rother C. 2006. A comparative study of energy minimization methods for Markov
random fields. ECCV: European Conference on Computer Vision vol. 3952, 16–29.'
mla: Szeliski, Richard, et al. A Comparative Study of Energy Minimization Methods
for Markov Random Fields. Vol. 3952, Springer, 2006, pp. 16–29, doi:10.1007/11744047_2.
short: R. Szeliski, R. Zabih, D. Scharstein, O. Veksler, V. Kolmogorov, A. Agarwala,
M. Tappen, C. Rother, in:, Springer, 2006, pp. 16–29.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:01:51Z
date_published: 2006-05-03T00:00:00Z
date_updated: 2021-01-12T07:41:37Z
day: '03'
doi: 10.1007/11744047_2
extern: 1
intvolume: ' 3952'
main_file_link:
- open_access: '0'
url: http://research-srv.microsoft.com/pubs/67896/szsvkatr-eccv06.pdf
month: '05'
page: 16 - 29
publication_status: published
publisher: Springer
publist_id: '3499'
quality_controlled: 0
status: public
title: A comparative study of energy minimization methods for Markov random fields
type: conference
volume: 3952
year: '2006'
...
---
_id: '3184'
abstract:
- lang: eng
text: 'Algorithms for discrete energy minimization play a fundamental role for low-level
vision. Known techniques include graph cuts, belief propagation (BP) and recently
introduced tree-reweighted message passing (TRW). So far, the standard benchmark
for their comparison has been a 4-connected grid-graph arising in pixel-labelling
stereo. This minimization problem, however, has been largely solved: recent work
shows that for many scenes TRW finds the global optimum. Furthermore, it is known
that a 4-connecled grid-graph is a poor stereo model since it does not take occlusions
into account. We propose the problem of stereo with occlusions as a new test bed
for minimization algorithms. This is a more challenging graph since it has much
larger connectivity, and it also serves as a better stereo model. An attractive
feature of this problem is that increased connectivity does not result in increased
complexity of message passing algorithms. Indeed, one contribution of this paper
is to show that sophisticated implementations of BP and TRW have the same time
and memory complexity as that of 4-connecled grid-graph stereo. The main conclusion
of our experimental study is that for our problem graph cut outperforms both TRW
and BP considerably. TRW achieves consistently a lower energy than BP. However,
as connectivity increases the speed of convergence of TRW becomes slower. Unlike
4-connected grids, the difference between the energy of the best optimization
method and the lower bound of TRW appears significant. This shows the hardness
of the problem and motivates future research.'
alternative_title:
- LNCS
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: 'Kolmogorov V, Rother C. Comparison of energy minimization algorithms for highly
connected graphs. In: Vol 3952 LNCS. Springer; 2006:1-15. doi:10.1007/11744047_1'
apa: 'Kolmogorov, V., & Rother, C. (2006). Comparison of energy minimization
algorithms for highly connected graphs (Vol. 3952 LNCS, pp. 1–15). Presented at
the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744047_1'
chicago: Kolmogorov, Vladimir, and Carsten Rother. “Comparison of Energy Minimization
Algorithms for Highly Connected Graphs,” 3952 LNCS:1–15. Springer, 2006. https://doi.org/10.1007/11744047_1.
ieee: 'V. Kolmogorov and C. Rother, “Comparison of energy minimization algorithms
for highly connected graphs,” presented at the ECCV: European Conference on Computer
Vision, 2006, vol. 3952 LNCS, pp. 1–15.'
ista: 'Kolmogorov V, Rother C. 2006. Comparison of energy minimization algorithms
for highly connected graphs. ECCV: European Conference on Computer Vision, LNCS,
vol. 3952 LNCS, 1–15.'
mla: Kolmogorov, Vladimir, and Carsten Rother. Comparison of Energy Minimization
Algorithms for Highly Connected Graphs. Vol. 3952 LNCS, Springer, 2006, pp.
1–15, doi:10.1007/11744047_1.
short: V. Kolmogorov, C. Rother, in:, Springer, 2006, pp. 1–15.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:01:52Z
date_published: 2006-05-03T00:00:00Z
date_updated: 2021-01-12T07:41:39Z
day: '03'
doi: 10.1007/11744047_1
extern: 1
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67889/paper_eccv06-trw.pdf
month: '05'
page: 1 - 15
publication_status: published
publisher: Springer
publist_id: '3498'
quality_controlled: 0
status: public
title: Comparison of energy minimization algorithms for highly connected graphs
type: conference
volume: 3952 LNCS
year: '2006'
...
---
_id: '3185'
abstract:
- lang: eng
text: This paper describes models and algorithms for the real-time segmentation
of foreground from background layers in stereo video sequences. Automatic separation
of layers from color/contrast or from stereo alone is known to be error-prone.
Here, color, contrast, and stereo matching information are fused to infer layers
accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP),
solves stereo in an extended six-state space that represents both foreground/background
layers and occluded regions. The stereo-match likelihood is then fused with a
contrast-sensitive color model that is learned on-the-fly and stereo disparities
are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC),
does not directly solve stereo. Instead, the stereo match likelihood is marginalized
over disparities to evaluate foreground and background hypotheses and then fused
with a contrast-sensitive color model like the one used in LDP. Segmentation is
solved efficiently by ternary graph cut. Both algorithms are evaluated with respect
to ground truth data and found to have similar performance, substantially better
than either stereo or color/contrast alone. However, their characteristics with
respect to computational efficiency are rather different. The algorithms are demonstrated
in the application of background substitution and shown to give good quality composite
video output.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Antonio
full_name: Criminisi, Antonio
last_name: Criminisi
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Geoffrey
full_name: Cross, Geoffrey
last_name: Cross
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Probabilistic fusion
of stereo with color and contrast for bilayer segmentation. IEEE Transactions
on Pattern Analysis and Machine Intelligence. 2006;28(9):1480-1492. doi:10.1109/TPAMI.2006.193
apa: Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2006).
Probabilistic fusion of stereo with color and contrast for bilayer segmentation.
IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2006.193
chicago: Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross,
and Carsten Rother. “Probabilistic Fusion of Stereo with Color and Contrast for
Bilayer Segmentation.” IEEE Transactions on Pattern Analysis and Machine Intelligence.
IEEE, 2006. https://doi.org/10.1109/TPAMI.2006.193.
ieee: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Probabilistic
fusion of stereo with color and contrast for bilayer segmentation,” IEEE Transactions
on Pattern Analysis and Machine Intelligence, vol. 28, no. 9. IEEE, pp. 1480–1492,
2006.
ista: Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2006. Probabilistic
fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions
on Pattern Analysis and Machine Intelligence. 28(9), 1480–1492.
mla: Kolmogorov, Vladimir, et al. “Probabilistic Fusion of Stereo with Color and
Contrast for Bilayer Segmentation.” IEEE Transactions on Pattern Analysis and
Machine Intelligence, vol. 28, no. 9, IEEE, 2006, pp. 1480–92, doi:10.1109/TPAMI.2006.193.
short: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, IEEE Transactions
on Pattern Analysis and Machine Intelligence 28 (2006) 1480–1492.
date_created: 2018-12-11T12:01:53Z
date_published: 2006-09-01T00:00:00Z
date_updated: 2021-01-12T07:41:39Z
day: '01'
doi: 10.1109/TPAMI.2006.193
extern: 1
intvolume: ' 28'
issue: '9'
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67414/criminisi_pami2006.pdf
month: '09'
page: 1480 - 1492
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3496'
quality_controlled: 0
status: public
title: Probabilistic fusion of stereo with color and contrast for bilayer segmentation
type: journal_article
volume: 28
year: '2006'
...
---
_id: '3186'
abstract:
- lang: eng
text: We introduce a new approach to modelling gradient flows of contours and surfaces.
While standard variational methods (e.g. level sets) compute local interface motion
in a differential fashion by estimating local contour velocity via energy derivatives,
we propose to solve surface evolution PDEs by explicitly estimating integral motion
of the whole surface. We formulate an optimization problem directly based on an
integral characterization of gradient flow as an infinitesimal move of the (whole)
surface giving the largest energy decrease among all moves of equal size. We show
that this problem can be efficiently solved using recent advances in algorithms
for global hypersurface optimization [4, 2, 11]. In particular, we employ the
geo-cuts method [4] that uses ideas from integral geometry to represent continuous
surfaces as cuts on discrete graphs. The resulting interface evolution algorithm
is validated on some 2D and 3D examples similar to typical demonstrations of level-set
methods. Our method can compute gradient flows of hypersurfaces with respect to
a fairly general class of continuous functional and it is flexible with respect
to distance metrics on the space of contours/surfaces. Preliminary tests for standard
L2 distance metric demonstrate numerical stability, topological changes and an
absence of any oscillatory motion.
alternative_title:
- LNCS
author:
- first_name: Yuri
full_name: Boykov, Yuri
last_name: Boykov
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Daniel
full_name: Cremers, Daniel
last_name: Cremers
- first_name: Andrew
full_name: Delong, Andrew
last_name: Delong
citation:
ama: 'Boykov Y, Kolmogorov V, Cremers D, Delong A. An integral solution to surface
evolution PDEs via geo cuts. In: Vol 3953. Springer; 2006:409-422. doi:10.1007/11744078_32'
apa: 'Boykov, Y., Kolmogorov, V., Cremers, D., & Delong, A. (2006). An integral
solution to surface evolution PDEs via geo cuts (Vol. 3953, pp. 409–422). Presented
at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744078_32'
chicago: Boykov, Yuri, Vladimir Kolmogorov, Daniel Cremers, and Andrew Delong. “An
Integral Solution to Surface Evolution PDEs via Geo Cuts,” 3953:409–22. Springer,
2006. https://doi.org/10.1007/11744078_32.
ieee: 'Y. Boykov, V. Kolmogorov, D. Cremers, and A. Delong, “An integral solution
to surface evolution PDEs via geo cuts,” presented at the ECCV: European Conference
on Computer Vision, 2006, vol. 3953, pp. 409–422.'
ista: 'Boykov Y, Kolmogorov V, Cremers D, Delong A. 2006. An integral solution to
surface evolution PDEs via geo cuts. ECCV: European Conference on Computer Vision,
LNCS, vol. 3953, 409–422.'
mla: Boykov, Yuri, et al. An Integral Solution to Surface Evolution PDEs via
Geo Cuts. Vol. 3953, Springer, 2006, pp. 409–22, doi:10.1007/11744078_32.
short: Y. Boykov, V. Kolmogorov, D. Cremers, A. Delong, in:, Springer, 2006, pp.
409–422.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:01:53Z
date_published: 2006-04-28T00:00:00Z
date_updated: 2021-01-12T07:41:39Z
day: '28'
doi: 10.1007/11744078_32
extern: 1
intvolume: ' 3953'
month: '04'
page: 409 - 422
publication_status: published
publisher: Springer
publist_id: '3497'
quality_controlled: 0
status: public
title: An integral solution to surface evolution PDEs via geo cuts
type: conference
volume: 3953
year: '2006'
...
---
_id: '3404'
alternative_title:
- Manuals in Biomedical Research
author:
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Ravi
full_name: Sawhney, Ravi K
last_name: Sawhney
- first_name: Martin
full_name: Stark, Martin
last_name: Stark
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: 'Janovjak HL, Sawhney R, Stark M, Mueller D. Atomic force microscopy. In: Techniques
in Microscopy for Biomedical Applications. Vol 2. World Scientific Publishing;
2006:213-284.'
apa: Janovjak, H. L., Sawhney, R., Stark, M., & Mueller, D. (2006). Atomic force
microscopy. In Techniques in Microscopy for Biomedical Applications (Vol.
2, pp. 213–284). World Scientific Publishing.
chicago: Janovjak, Harald L, Ravi Sawhney, Martin Stark, and Daniel Mueller. “Atomic
Force Microscopy.” In Techniques in Microscopy for Biomedical Applications,
2:213–84. World Scientific Publishing, 2006.
ieee: H. L. Janovjak, R. Sawhney, M. Stark, and D. Mueller, “Atomic force microscopy,”
in Techniques in Microscopy for Biomedical Applications, vol. 2, World
Scientific Publishing, 2006, pp. 213–284.
ista: 'Janovjak HL, Sawhney R, Stark M, Mueller D. 2006.Atomic force microscopy.
In: Techniques in Microscopy for Biomedical Applications. Manuals in Biomedical
Research, vol. 2, 213–284.'
mla: Janovjak, Harald L., et al. “Atomic Force Microscopy.” Techniques in Microscopy
for Biomedical Applications, vol. 2, World Scientific Publishing, 2006, pp.
213–84.
short: H.L. Janovjak, R. Sawhney, M. Stark, D. Mueller, in:, Techniques in Microscopy
for Biomedical Applications, World Scientific Publishing, 2006, pp. 213–284.
date_created: 2018-12-11T12:03:09Z
date_published: 2006-09-28T00:00:00Z
date_updated: 2021-01-12T07:43:15Z
day: '28'
extern: 1
intvolume: ' 2'
month: '09'
page: 213 - 284
publication: Techniques in Microscopy for Biomedical Applications
publication_status: published
publisher: World Scientific Publishing
publist_id: '2998'
quality_controlled: 0
status: public
title: Atomic force microscopy
type: book_chapter
volume: 2
year: '2006'
...
---
_id: '3413'
abstract:
- lang: eng
text: |-
Despite their crucial importance for cellular function, little is known about the folding mechanisms of membrane proteins. Recently details of the folding energy landscape were elucidated by atomic force microscope (AFM)-based single molecule force spectroscopy. Upon unfolding and extraction of individual membrane proteins energy barriers in structural elements such as loops and helices were mapped and quantified with the precision of a few amino acids.
Here we report on the next logical step: controlled refolding of single proteins into the membrane. First individual bacteriorhodopsin monomers were partially unfolded and extracted from the purple membrane by pulling at the C-terminal end with an AFM tip. Then by gradually lowering the tip, the protein was allowed to refold into the membrane while the folding force was recorded.
We discovered that upon refolding certain helices are pulled into the membraneagainst a sizable externalforce of several tens of picoNewton. From the mechanical work, which the helix performs on the AFM cantilever, we derive an upper limit for the Gibbs free folding energy. Subsequent unfolding allowed us to analyze the pattern of unfolding barriers and corroborate that the protein had refolded into the native state.
author:
- first_name: Max
full_name: Kessler, Max
last_name: Kessler
- first_name: Kay
full_name: Gottschalk, Kay E
last_name: Gottschalk
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
- first_name: Hermann
full_name: Gaub, Hermann
last_name: Gaub
citation:
ama: Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. Bacteriorhodopsin
folds into the membrane against an external force. Journal of Molecular Biology.
2006;357(2):644-654. doi:10.1016/j.jmb.2005.12.065
apa: Kessler, M., Gottschalk, K., Janovjak, H. L., Mueller, D., & Gaub, H. (2006).
Bacteriorhodopsin folds into the membrane against an external force. Journal
of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2005.12.065
chicago: Kessler, Max, Kay Gottschalk, Harald L Janovjak, Daniel Mueller, and Hermann
Gaub. “Bacteriorhodopsin Folds into the Membrane against an External Force.” Journal
of Molecular Biology. Elsevier, 2006. https://doi.org/10.1016/j.jmb.2005.12.065.
ieee: M. Kessler, K. Gottschalk, H. L. Janovjak, D. Mueller, and H. Gaub, “Bacteriorhodopsin
folds into the membrane against an external force,” Journal of Molecular Biology,
vol. 357, no. 2. Elsevier, pp. 644–654, 2006.
ista: Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. 2006. Bacteriorhodopsin
folds into the membrane against an external force. Journal of Molecular Biology.
357(2), 644–654.
mla: Kessler, Max, et al. “Bacteriorhodopsin Folds into the Membrane against an
External Force.” Journal of Molecular Biology, vol. 357, no. 2, Elsevier,
2006, pp. 644–54, doi:10.1016/j.jmb.2005.12.065.
short: M. Kessler, K. Gottschalk, H.L. Janovjak, D. Mueller, H. Gaub, Journal of
Molecular Biology 357 (2006) 644–654.
date_created: 2018-12-11T12:03:12Z
date_published: 2006-03-24T00:00:00Z
date_updated: 2021-01-12T07:43:18Z
day: '24'
doi: 10.1016/j.jmb.2005.12.065
extern: 1
intvolume: ' 357'
issue: '2'
month: '03'
page: 644 - 654
publication: Journal of Molecular Biology
publication_status: published
publisher: Elsevier
publist_id: '2988'
quality_controlled: 0
status: public
title: Bacteriorhodopsin folds into the membrane against an external force
type: journal_article
volume: 357
year: '2006'
...
---
_id: '3414'
abstract:
- lang: eng
text: Mechanisms of folding and misfolding of membrane proteins are of interest
in cell biology. Recently, we have established single-molecule force spectroscopy
to observe directly the stepwise folding of the Na+/H+antiporter NhaA from Escherichia
coli in vitro. Here, we improved this approach significantly to track the folding
intermediates of asingle NhaA polypeptide forming structural segments such as
the Na+-binding site, transmembrane α-helices, and helical pairs. The folding
rates of structural segments ranged from 0.31 s−1 to 47 s−1, providing detailed
insight into a distinct folding hierarchy of an unfolded polypeptide into the
native membrane protein structure. In some cases, however, the folding chain formed
stable and kinetically trapped non-native structures, which could be assigned
to misfolding events of the antiporter.
author:
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Christine
full_name: Ziegler, Christine
last_name: Ziegler
- first_name: Werner
full_name: Kühlbrandt, Werner
last_name: Kühlbrandt
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. Observing folding
pathways and kinetics of a single sodium-proton antiporter from Escherichia coli.
Journal of Molecular Biology. 2006;355(1):2-8. doi:10.1016/j.jmb.2005.10.028
apa: Kedrov, A., Janovjak, H. L., Ziegler, C., Kühlbrandt, W., & Mueller, D.
(2006). Observing folding pathways and kinetics of a single sodium-proton antiporter
from Escherichia coli. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2005.10.028
chicago: Kedrov, Alexej, Harald L Janovjak, Christine Ziegler, Werner Kühlbrandt,
and Daniel Mueller. “Observing Folding Pathways and Kinetics of a Single Sodium-Proton
Antiporter from Escherichia Coli.” Journal of Molecular Biology. Elsevier,
2006. https://doi.org/10.1016/j.jmb.2005.10.028.
ieee: A. Kedrov, H. L. Janovjak, C. Ziegler, W. Kühlbrandt, and D. Mueller, “Observing
folding pathways and kinetics of a single sodium-proton antiporter from Escherichia
coli,” Journal of Molecular Biology, vol. 355, no. 1. Elsevier, pp. 2–8,
2006.
ista: Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. 2006. Observing
folding pathways and kinetics of a single sodium-proton antiporter from Escherichia
coli. Journal of Molecular Biology. 355(1), 2–8.
mla: Kedrov, Alexej, et al. “Observing Folding Pathways and Kinetics of a Single
Sodium-Proton Antiporter from Escherichia Coli.” Journal of Molecular Biology,
vol. 355, no. 1, Elsevier, 2006, pp. 2–8, doi:10.1016/j.jmb.2005.10.028.
short: A. Kedrov, H.L. Janovjak, C. Ziegler, W. Kühlbrandt, D. Mueller, Journal
of Molecular Biology 355 (2006) 2–8.
date_created: 2018-12-11T12:03:12Z
date_published: 2006-01-06T00:00:00Z
date_updated: 2021-01-12T07:43:19Z
day: '06'
doi: 10.1016/j.jmb.2005.10.028
extern: 1
intvolume: ' 355'
issue: '1'
month: '01'
page: 2 - 8
publication: Journal of Molecular Biology
publication_status: published
publisher: Elsevier
publist_id: '2987'
quality_controlled: 0
status: public
title: Observing folding pathways and kinetics of a single sodium-proton antiporter
from Escherichia coli
type: journal_article
volume: 355
year: '2006'
...
---
_id: '3415'
author:
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: David
full_name: Cisneros, David
last_name: Cisneros
- first_name: Tanuj
full_name: Sapra, Tanuj K
last_name: Sapra
- first_name: Jens
full_name: Struckmeier, Jens
last_name: Struckmeier
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. Imaging
and detecting molecular interactions of single membrane proteins. Neurobiology
of Aging. 2006;27:546-561. doi:10.1016/j.neurobiolaging.2005.03.031
apa: Janovjak, H. L., Kedrov, A., Cisneros, D., Sapra, T., Struckmeier, J., &
Mueller, D. (2006). Imaging and detecting molecular interactions of single membrane
proteins. Neurobiology of Aging. Elsevier. https://doi.org/10.1016/j.neurobiolaging.2005.03.031
chicago: Janovjak, Harald L, Alexej Kedrov, David Cisneros, Tanuj Sapra, Jens Struckmeier,
and Daniel Mueller. “Imaging and Detecting Molecular Interactions of Single Membrane
Proteins.” Neurobiology of Aging. Elsevier, 2006. https://doi.org/10.1016/j.neurobiolaging.2005.03.031.
ieee: H. L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, and D. Mueller,
“Imaging and detecting molecular interactions of single membrane proteins,” Neurobiology
of Aging, vol. 27. Elsevier, pp. 546–561, 2006.
ista: Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. 2006.
Imaging and detecting molecular interactions of single membrane proteins. Neurobiology
of Aging. 27, 546–561.
mla: Janovjak, Harald L., et al. “Imaging and Detecting Molecular Interactions of
Single Membrane Proteins.” Neurobiology of Aging, vol. 27, Elsevier, 2006,
pp. 546–61, doi:10.1016/j.neurobiolaging.2005.03.031.
short: H.L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, D. Mueller,
Neurobiology of Aging 27 (2006) 546–561.
date_created: 2018-12-11T12:03:12Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2019-04-26T07:22:27Z
day: '01'
doi: 10.1016/j.neurobiolaging.2005.03.031
extern: 1
intvolume: ' 27'
month: '01'
page: 546 - 561
publication: Neurobiology of Aging
publication_status: published
publisher: Elsevier
publist_id: '2986'
quality_controlled: 0
status: public
title: Imaging and detecting molecular interactions of single membrane proteins
type: review
volume: 27
year: '2006'
...
---
_id: '3437'
abstract:
- lang: eng
text: The mutational landscape model is a theoretical model describing sequence
evolution in natural populations. However, recent experimental work has begun
to test its predictions in laboratory populations of microbes. Several of these
studies have focused on testing the prediction that the effects of beneficial
mutations should be roughly exponentially distributed. The prediction appears
to be borne out by most of these studies, at least qualitatively. Another study
showed that a modified version of the model was able to predict, with reasonable
accuracy, which of a ranked set of beneficial alleles will be fixed next. Although
it remains to be seen whether the mutational landscape model adequately describes
adaptation in organisms other than microbes, together these studies suggest that
adaptive evolution has surprisingly general properties that can be successfully
captured by theoretical models.
author:
- first_name: Andrea
full_name: Betancourt, Andrea J
last_name: Betancourt
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: 'Betancourt A, Bollback JP. Fitness effects of beneficial mutations: the mutational
landscape model in experimental evolution. Current Opinion in Genetics &
Development. 2006;16(6):618-623. doi:10.1016/j.gde.2006.10.006'
apa: 'Betancourt, A., & Bollback, J. P. (2006). Fitness effects of beneficial
mutations: the mutational landscape model in experimental evolution. Current
Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2006.10.006'
chicago: 'Betancourt, Andrea, and Jonathan P Bollback. “Fitness Effects of Beneficial
Mutations: The Mutational Landscape Model in Experimental Evolution.” Current
Opinion in Genetics & Development. Elsevier, 2006. https://doi.org/10.1016/j.gde.2006.10.006.'
ieee: 'A. Betancourt and J. P. Bollback, “Fitness effects of beneficial mutations:
the mutational landscape model in experimental evolution,” Current Opinion
in Genetics & Development, vol. 16, no. 6. Elsevier, pp. 618–623, 2006.'
ista: 'Betancourt A, Bollback JP. 2006. Fitness effects of beneficial mutations:
the mutational landscape model in experimental evolution. Current Opinion in Genetics
& Development. 16(6), 618–623.'
mla: 'Betancourt, Andrea, and Jonathan P. Bollback. “Fitness Effects of Beneficial
Mutations: The Mutational Landscape Model in Experimental Evolution.” Current
Opinion in Genetics & Development, vol. 16, no. 6, Elsevier, 2006, pp.
618–23, doi:10.1016/j.gde.2006.10.006.'
short: A. Betancourt, J.P. Bollback, Current Opinion in Genetics & Development
16 (2006) 618–623.
date_created: 2018-12-11T12:03:19Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2021-01-12T07:43:27Z
day: '01'
doi: 10.1016/j.gde.2006.10.006
extern: 1
intvolume: ' 16'
issue: '6'
month: '12'
page: 618 - 623
publication: Current Opinion in Genetics & Development
publication_status: published
publisher: Elsevier
publist_id: '2963'
quality_controlled: 0
status: public
title: 'Fitness effects of beneficial mutations: the mutational landscape model in
experimental evolution'
type: journal_article
volume: 16
year: '2006'
...
---
_id: '3431'
abstract:
- lang: eng
text: Ising models with pairwise interactions are the least structured, or maximum-entropy,
probability distributions that exactly reproduce measured pairwise correlations
between spins. Here we use this equivalence to construct Ising models that describe
the correlated spiking activity of populations of 40 neurons in the retina, and
show that pairwise interactions account for observed higher-order correlations.
By first finding a representative ensemble for observed networks we can create
synthetic networks of 120 neurons, and find that with increasing size the networks
operate closer to a critical point and start exhibiting collective behaviors reminiscent
of spin glasses.
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: E.
full_name: Schneidman, E.
last_name: Schneidman
- first_name: M.
full_name: Berry, M. J.
last_name: Berry
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Tkačik G, Schneidman E, Berry M, Bialek W. Ising models for networks of real
neurons. ArXiv. 2006:1-4.
apa: Tkačik, G., Schneidman, E., Berry, M., & Bialek, W. (2006). Ising models
for networks of real neurons. ArXiv. ArXiv.
chicago: Tkačik, Gašper, E. Schneidman, M. Berry, and William Bialek. “Ising Models
for Networks of Real Neurons.” ArXiv. ArXiv, 2006.
ieee: G. Tkačik, E. Schneidman, M. Berry, and W. Bialek, “Ising models for networks
of real neurons,” ArXiv. ArXiv, pp. 1–4, 2006.
ista: Tkačik G, Schneidman E, Berry M, Bialek W. 2006. Ising models for networks
of real neurons. ArXiv, 1–4, .
mla: Tkačik, Gašper, et al. “Ising Models for Networks of Real Neurons.” ArXiv,
ArXiv, 2006, pp. 1–4.
short: G. Tkačik, E. Schneidman, M. Berry, W. Bialek, ArXiv (2006) 1–4.
date_created: 2018-12-11T12:03:18Z
date_published: 2006-11-22T00:00:00Z
date_updated: 2021-01-12T07:43:25Z
day: '22'
extern: 1
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/q-bio/0611072
month: '11'
oa: 1
page: 1 - 4
publication: ArXiv
publication_status: published
publisher: ArXiv
publist_id: '2969'
quality_controlled: 0
status: public
title: Ising models for networks of real neurons
type: preprint
year: '2006'
...
---
_id: '3449'
abstract:
- lang: eng
text: We argue that games are expressive enough to encompass (history-based) access
control, (resource) usage control (e.g., dynamic adaptive access control of reputation
systems), accountability based controls (e.g., insurance), controls derived from
rationality assumptions on participants (e.g., network mechanisms), and their
composition. Building on the extensive research into games, we demonstrate that
this expressive power coexists with a formal analysis framework comparable to
that available for access control.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rhada
full_name: Jagadeesan, Rhada
last_name: Jagadeesan
- first_name: Corin
full_name: Pitcher, Corin
last_name: Pitcher
citation:
ama: 'Chatterjee K, Jagadeesan R, Pitcher C. Games for controls. In: IEEE; 2006:70-82.
doi:10.1109/CSFW.2006.14'
apa: 'Chatterjee, K., Jagadeesan, R., & Pitcher, C. (2006). Games for controls
(pp. 70–82). Presented at the CSF: Computer Security Foundations, IEEE. https://doi.org/10.1109/CSFW.2006.14'
chicago: Chatterjee, Krishnendu, Rhada Jagadeesan, and Corin Pitcher. “Games for
Controls,” 70–82. IEEE, 2006. https://doi.org/10.1109/CSFW.2006.14.
ieee: 'K. Chatterjee, R. Jagadeesan, and C. Pitcher, “Games for controls,” presented
at the CSF: Computer Security Foundations, 2006, pp. 70–82.'
ista: 'Chatterjee K, Jagadeesan R, Pitcher C. 2006. Games for controls. CSF: Computer
Security Foundations, 70–82.'
mla: Chatterjee, Krishnendu, et al. Games for Controls. IEEE, 2006, pp. 70–82,
doi:10.1109/CSFW.2006.14.
short: K. Chatterjee, R. Jagadeesan, C. Pitcher, in:, IEEE, 2006, pp. 70–82.
conference:
name: 'CSF: Computer Security Foundations'
date_created: 2018-12-11T12:03:23Z
date_published: 2006-07-31T00:00:00Z
date_updated: 2021-01-12T07:43:32Z
day: '31'
doi: 10.1109/CSFW.2006.14
extern: 1
month: '07'
page: 70 - 82
publication_status: published
publisher: IEEE
publist_id: '2938'
quality_controlled: 0
status: public
title: Games for controls
type: conference
year: '2006'
...