---
_id: '11762'
abstract:
- lang: eng
text: 'In this paper, we describe six algorithmic problems that arise in web search
engines and that are not or only partially solved: (1) Uniformly sampling of web
pages; (2) modeling the web graph; (3) finding duplicate hosts; (4) finding top
gainers and losers in data streams; (5) finding large dense bipartite graphs; and
(6) understanding how eigenvectors partition the web.'
article_processing_charge: No
article_type: original
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: Henzinger MH. Algorithmic challenges in web search engines. Internet Mathematics.
2004;1(1):115-123. doi:10.1080/15427951.2004.10129079
apa: Henzinger, M. H. (2004). Algorithmic challenges in web search engines. Internet
Mathematics. Internet Mathematics. https://doi.org/10.1080/15427951.2004.10129079
chicago: Henzinger, Monika H. “Algorithmic Challenges in Web Search Engines.” Internet
Mathematics. Internet Mathematics, 2004. https://doi.org/10.1080/15427951.2004.10129079.
ieee: M. H. Henzinger, “Algorithmic challenges in web search engines,” Internet
Mathematics, vol. 1, no. 1. Internet Mathematics, pp. 115–123, 2004.
ista: Henzinger MH. 2004. Algorithmic challenges in web search engines. Internet
Mathematics. 1(1), 115–123.
mla: Henzinger, Monika H. “Algorithmic Challenges in Web Search Engines.” Internet
Mathematics, vol. 1, no. 1, Internet Mathematics, 2004, pp. 115–23, doi:10.1080/15427951.2004.10129079.
short: M.H. Henzinger, Internet Mathematics 1 (2004) 115–123.
date_created: 2022-08-08T11:55:53Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2023-02-10T07:47:21Z
day: '01'
doi: 10.1080/15427951.2004.10129079
extern: '1'
intvolume: ' 1'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1080/15427951.2004.10129079
month: '01'
oa: 1
oa_version: Published Version
page: 115-123
publication: Internet Mathematics
publication_identifier:
eissn:
- 1944-9488
issn:
- 1542-7951
publication_status: published
publisher: Internet Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Algorithmic challenges in web search engines
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2004'
...
---
_id: '11801'
abstract:
- lang: eng
text: "Web search engines have emerged as one of the central applications on the
internet. In fact, search has become one of the most important activities that
people engage in on the Internet. Even beyond becoming the number one source of
information, a growing number of businesses are depending on web search engines
for customer acquisition. In this talk I will brief review the history of web
search engines: The first generation of web search engines used text-only retrieval
techniques. Google revolutionized the field by deploying the PageRank technology
– an eigenvector-based analysis of the hyperlink structure- to analyze the web
in order to produce relevant results. Moving forward, our goal is to achieve a
better understanding of a page with a view towards producing even more relevant
results.\r\n\r\nGoogle is powered by a large number of PCs. Using this infrastructure
and striving to be as efficient as possible poses challenging systems problems
but also various algorithmic challenges. I will discuss some of them in my talk."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: 'Henzinger MH. Algorithmic aspects of web search engines. In: 2th Annual
European Symposium on Algorithms. Vol 3221. Springer Nature; 2004:3. doi:10.1007/978-3-540-30140-0_2'
apa: 'Henzinger, M. H. (2004). Algorithmic aspects of web search engines. In 2th
Annual European Symposium on Algorithms (Vol. 3221, p. 3). Bergen, Norway:
Springer Nature. https://doi.org/10.1007/978-3-540-30140-0_2'
chicago: Henzinger, Monika H. “Algorithmic Aspects of Web Search Engines.” In 2th
Annual European Symposium on Algorithms, 3221:3. Springer Nature, 2004. https://doi.org/10.1007/978-3-540-30140-0_2.
ieee: M. H. Henzinger, “Algorithmic aspects of web search engines,” in 2th Annual
European Symposium on Algorithms, Bergen, Norway, 2004, vol. 3221, p. 3.
ista: 'Henzinger MH. 2004. Algorithmic aspects of web search engines. 2th Annual
European Symposium on Algorithms. ESA: European Symposium on Algorithms, LNCS,
vol. 3221, 3.'
mla: Henzinger, Monika H. “Algorithmic Aspects of Web Search Engines.” 2th Annual
European Symposium on Algorithms, vol. 3221, Springer Nature, 2004, p. 3,
doi:10.1007/978-3-540-30140-0_2.
short: M.H. Henzinger, in:, 2th Annual European Symposium on Algorithms, Springer
Nature, 2004, p. 3.
conference:
end_date: 2004-09-17
location: Bergen, Norway
name: 'ESA: European Symposium on Algorithms'
start_date: 2004-09-14
date_created: 2022-08-11T13:18:05Z
date_published: 2004-09-01T00:00:00Z
date_updated: 2023-02-13T11:47:26Z
day: '01'
doi: 10.1007/978-3-540-30140-0_2
extern: '1'
intvolume: ' 3221'
language:
- iso: eng
month: '09'
oa_version: None
page: '3'
publication: 2th Annual European Symposium on Algorithms
publication_identifier:
eissn:
- 1611-3349
isbn:
- ' 3540230254'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Algorithmic aspects of web search engines
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3221
year: '2004'
...
---
_id: '11800'
abstract:
- lang: eng
text: "Web search engines have emerged as one of the central applications on the
Internet. In fact, search has become one of the most important activities that
people engage in on the the Internet. Even beyond becoming the number one source
of information, a growing number of businesses are depending on web search engines
for customer acquisition.\r\n\r\nThe first generation of web search engines used
text-only retrieval techniques. Google revolutionized the field by deploying the
PageRank technology – an eigenvector-based analysis of the hyperlink structure
– to analyze the web in order to produce relevant results. Moving forward, our
goal is to achieve a better understanding of a page with a view towards producing
even more relevant results."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: 'Henzinger MH. The past, present, and future of web search engines. In: 31st
International Colloquium on Automata, Languages and Programming. Vol 3142.
Springer Nature; 2004:3. doi:10.1007/978-3-540-27836-8_2'
apa: 'Henzinger, M. H. (2004). The past, present, and future of web search engines.
In 31st International Colloquium on Automata, Languages and Programming
(Vol. 3142, p. 3). Turku, Finland: Springer Nature. https://doi.org/10.1007/978-3-540-27836-8_2'
chicago: Henzinger, Monika H. “The Past, Present, and Future of Web Search Engines.”
In 31st International Colloquium on Automata, Languages and Programming,
3142:3. Springer Nature, 2004. https://doi.org/10.1007/978-3-540-27836-8_2.
ieee: M. H. Henzinger, “The past, present, and future of web search engines,” in
31st International Colloquium on Automata, Languages and Programming, Turku,
Finland, 2004, vol. 3142, p. 3.
ista: 'Henzinger MH. 2004. The past, present, and future of web search engines.
31st International Colloquium on Automata, Languages and Programming. ICALP: International
Colloquium on Automata, Languages, and Programming, LNCS, vol. 3142, 3.'
mla: Henzinger, Monika H. “The Past, Present, and Future of Web Search Engines.”
31st International Colloquium on Automata, Languages and Programming, vol.
3142, Springer Nature, 2004, p. 3, doi:10.1007/978-3-540-27836-8_2.
short: M.H. Henzinger, in:, 31st International Colloquium on Automata, Languages
and Programming, Springer Nature, 2004, p. 3.
conference:
end_date: 2004-07-16
location: Turku, Finland
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2004-07-12
date_created: 2022-08-11T12:38:58Z
date_published: 2004-07-01T00:00:00Z
date_updated: 2023-02-13T11:45:25Z
day: '01'
doi: 10.1007/978-3-540-27836-8_2
extern: '1'
intvolume: ' 3142'
language:
- iso: eng
month: '07'
oa_version: None
page: '3'
publication: 31st International Colloquium on Automata, Languages and Programming
publication_identifier:
eissn:
- 1611-3349
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The past, present, and future of web search engines
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3142
year: '2004'
...
---
_id: '11859'
abstract:
- lang: eng
text: In this article we describe the approach taken by the first web search engines,
discuss the state of the art, and present some of the challenges for the future.
article_processing_charge: No
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: 'Henzinger MH. The past, present, and future of web information retrieval.
In: SPIE Proceedings. Vol 5296. Society of Photo-Optical Instrumentation
Engineers; 2004:23-26. doi:10.1117/12.537534'
apa: 'Henzinger, M. H. (2004). The past, present, and future of web information
retrieval. In SPIE Proceedings (Vol. 5296, pp. 23–26). San Jose, CA, United
States: Society of Photo-Optical Instrumentation Engineers. https://doi.org/10.1117/12.537534'
chicago: Henzinger, Monika H. “The Past, Present, and Future of Web Information
Retrieval.” In SPIE Proceedings, 5296:23–26. Society of Photo-Optical Instrumentation
Engineers, 2004. https://doi.org/10.1117/12.537534.
ieee: M. H. Henzinger, “The past, present, and future of web information retrieval,”
in SPIE Proceedings, San Jose, CA, United States, 2004, vol. 5296, pp.
23–26.
ista: Henzinger MH. 2004. The past, present, and future of web information retrieval.
SPIE Proceedings. Document Recognition and Retrieval XI vol. 5296, 23–26.
mla: Henzinger, Monika H. “The Past, Present, and Future of Web Information Retrieval.”
SPIE Proceedings, vol. 5296, Society of Photo-Optical Instrumentation Engineers,
2004, pp. 23–26, doi:10.1117/12.537534.
short: M.H. Henzinger, in:, SPIE Proceedings, Society of Photo-Optical Instrumentation
Engineers, 2004, pp. 23–26.
conference:
end_date: 2004-01-22
location: San Jose, CA, United States
name: Document Recognition and Retrieval XI
start_date: 2004-01-21
date_created: 2022-08-16T08:46:41Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2023-02-17T10:05:19Z
day: '01'
doi: 10.1117/12.537534
extern: '1'
intvolume: ' 5296'
language:
- iso: eng
month: '01'
oa_version: None
page: 23 - 26
publication: SPIE Proceedings
publication_identifier:
issn:
- 0277-786X
publication_status: published
publisher: Society of Photo-Optical Instrumentation Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: The past, present, and future of web information retrieval
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5296
year: '2004'
...
---
_id: '11877'
abstract:
- lang: eng
text: The World Wide Web provides a unprecedented opportunity to automatically analyze
a large sample of interests and activity in the world. We discuss methods for
extracting knowledge from the web by randomly sampling and analyzing hosts and
pages, and by analyzing the link structure of the web and how links accumulate
over time. A variety of interesting and valuable information can be extracted,
such as the distribution of web pages over domains, the distribution of interest
in different areas, communities related to different topics, the nature of competition
in different categories of sites, and the degree of communication between different
communities or countries.
article_processing_charge: No
article_type: original
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Steve
full_name: Lawrence, Steve
last_name: Lawrence
citation:
ama: Henzinger MH, Lawrence S. Extracting knowledge from the World Wide Web. Proceedings
of the National Academy of Sciences. 2004;101(suppl_1):5186-5191. doi:10.1073/pnas.0307528100
apa: Henzinger, M. H., & Lawrence, S. (2004). Extracting knowledge from the
World Wide Web. Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.0307528100
chicago: Henzinger, Monika H, and Steve Lawrence. “Extracting Knowledge from the
World Wide Web.” Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences, 2004. https://doi.org/10.1073/pnas.0307528100.
ieee: M. H. Henzinger and S. Lawrence, “Extracting knowledge from the World Wide
Web,” Proceedings of the National Academy of Sciences, vol. 101, no. suppl_1.
Proceedings of the National Academy of Sciences, pp. 5186–5191, 2004.
ista: Henzinger MH, Lawrence S. 2004. Extracting knowledge from the World Wide Web.
Proceedings of the National Academy of Sciences. 101(suppl_1), 5186–5191.
mla: Henzinger, Monika H., and Steve Lawrence. “Extracting Knowledge from the World
Wide Web.” Proceedings of the National Academy of Sciences, vol. 101, no.
suppl_1, Proceedings of the National Academy of Sciences, 2004, pp. 5186–91, doi:10.1073/pnas.0307528100.
short: M.H. Henzinger, S. Lawrence, Proceedings of the National Academy of Sciences
101 (2004) 5186–5191.
date_created: 2022-08-16T13:06:10Z
date_published: 2004-04-06T00:00:00Z
date_updated: 2023-02-17T12:21:43Z
day: '06'
doi: 10.1073/pnas.0307528100
extern: '1'
external_id:
pmid:
- '14745041'
intvolume: ' 101'
issue: suppl_1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC387294/
month: '04'
oa: 1
oa_version: Published Version
page: 5186-5191
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extracting knowledge from the World Wide Web
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 101
year: '2004'
...
---
_id: '12658'
abstract:
- lang: eng
text: '[1] During the ablation period 2001 a glaciometeorological experiment was
carried out on Haut Glacier d''Arolla, Switzerland. Five meteorological stations
were installed on the glacier, and one permanent automatic weather station in
the glacier foreland. The altitudes of the stations ranged between 2500 and 3000
m a.s.l., and they were in operation from end of May to beginning of September
2001. The spatial arrangement of the stations and temporal duration of the measurements
generated a unique data set enabling the analysis of the spatial and temporal
variability of the meteorological variables across an alpine glacier. All measurements
were taken at a nominal height of 2 m, and hourly averages were derived for the
analysis. The wind regime was dominated by the glacier wind (mean value 2.8 m
s−1) but due to erosion by the synoptic gradient wind, occasionally the wind would
blow up the valley. A slight decrease in mean 2 m air temperatures with altitude
was found, however the 2 m air temperature gradient varied greatly and frequently
changed its sign. Mean relative humidity was 71% and exhibited limited spatial
variation. Mean incoming shortwave radiation and albedo both generally increased
with elevation. The different components of shortwave radiation are quantified
with a parameterization scheme. Resulting spatial variations are mainly due to
horizon obstruction and reflections from surrounding slopes, i.e., topography.
The effect of clouds accounts for a loss of 30% of the extraterrestrial flux.
Albedos derived from a Landsat TM image of 30 July show remarkably constant values,
in the range 0.49 to 0.50, across snow covered parts of the glacier, while albedo
is highly spatially variable below the zone of continuous snow cover. These results
are verified with ground measurements and compared with parameterized albedo.
Mean longwave radiative fluxes decreased with elevation due to lower air temperatures
and the effect of upper hemisphere slopes. It is shown through parameterization
that this effect would even be more pronounced without the effect of clouds. Results
are discussed with respect to a similar study which has been carried out on Pasterze
Glacier (Austria). The presented algorithms for interpolating, parameterizing
and simulating variables and parameters in alpine regions are integrated in the
software package AMUNDSEN which is freely available to be adapted and further
developed by the community.'
article_number: D03103
article_processing_charge: No
article_type: original
author:
- first_name: Ulrich
full_name: Strasser, Ulrich
last_name: Strasser
- first_name: Javier
full_name: Corripio, Javier
last_name: Corripio
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Paolo
full_name: Burlando, Paolo
last_name: Burlando
- first_name: Ben
full_name: Brock, Ben
last_name: Brock
- first_name: Martin
full_name: Funk, Martin
last_name: Funk
citation:
ama: 'Strasser U, Corripio J, Pellicciotti F, Burlando P, Brock B, Funk M. Spatial
and temporal variability of meteorological variables at Haut Glacier d’Arolla
(Switzerland) during the ablation season 2001: Measurements and simulations. Journal
of Geophysical Research: Atmospheres. 2004;109(D3). doi:10.1029/2003jd003973'
apa: 'Strasser, U., Corripio, J., Pellicciotti, F., Burlando, P., Brock, B., &
Funk, M. (2004). Spatial and temporal variability of meteorological variables
at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements
and simulations. Journal of Geophysical Research: Atmospheres. American
Geophysical Union. https://doi.org/10.1029/2003jd003973'
chicago: 'Strasser, Ulrich, Javier Corripio, Francesca Pellicciotti, Paolo Burlando,
Ben Brock, and Martin Funk. “Spatial and Temporal Variability of Meteorological
Variables at Haut Glacier d’Arolla (Switzerland) during the Ablation Season 2001:
Measurements and Simulations.” Journal of Geophysical Research: Atmospheres.
American Geophysical Union, 2004. https://doi.org/10.1029/2003jd003973.'
ieee: 'U. Strasser, J. Corripio, F. Pellicciotti, P. Burlando, B. Brock, and M.
Funk, “Spatial and temporal variability of meteorological variables at Haut Glacier
d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations,”
Journal of Geophysical Research: Atmospheres, vol. 109, no. D3. American
Geophysical Union, 2004.'
ista: 'Strasser U, Corripio J, Pellicciotti F, Burlando P, Brock B, Funk M. 2004.
Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla
(Switzerland) during the ablation season 2001: Measurements and simulations. Journal
of Geophysical Research: Atmospheres. 109(D3), D03103.'
mla: 'Strasser, Ulrich, et al. “Spatial and Temporal Variability of Meteorological
Variables at Haut Glacier d’Arolla (Switzerland) during the Ablation Season 2001:
Measurements and Simulations.” Journal of Geophysical Research: Atmospheres,
vol. 109, no. D3, D03103, American Geophysical Union, 2004, doi:10.1029/2003jd003973.'
short: 'U. Strasser, J. Corripio, F. Pellicciotti, P. Burlando, B. Brock, M. Funk,
Journal of Geophysical Research: Atmospheres 109 (2004).'
date_created: 2023-02-20T08:18:57Z
date_published: 2004-02-16T00:00:00Z
date_updated: 2023-02-20T08:40:21Z
day: '16'
doi: 10.1029/2003jd003973
extern: '1'
intvolume: ' 109'
issue: D3
keyword:
- Paleontology
- Space and Planetary Science
- Earth and Planetary Sciences (miscellaneous)
- Atmospheric Science
- Earth-Surface Processes
- Geochemistry and Petrology
- Soil Science
- Water Science and Technology
- Ecology
- Aquatic Science
- Forestry
- Oceanography
- Geophysics
language:
- iso: eng
month: '02'
oa_version: None
publication: 'Journal of Geophysical Research: Atmospheres'
publication_identifier:
issn:
- 0148-0227
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Spatial and temporal variability of meteorological variables at Haut Glacier
d''Arolla (Switzerland) during the ablation season 2001: Measurements and simulations'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 109
year: '2004'
...
---
_id: '1456'
abstract:
- lang: eng
text: We study the space of L2 harmonic forms on complete manifolds with metrics
of fibred boundary or fibred cusp type. These metrics generalize the geometric
structures at infinity of several different well-known classes of metrics, including
asymptotically locally Euclidean manifolds, the (known types of) gravitational
instantons, and also Poincaré metrics on ℚ-rank 1 ends of locally symmetric spaces
and on the complements of smooth divisors in Kähler manifolds. The answer in all
cases is given in terms of intersection cohomology of a stratified compactification
of the manifold. The L2 signature formula implied by our result is closely related
to the one proved by Dai and more generally by Vaillant and identifies Dai's τ-invariant
directly in terms of intersection cohomology of differing perversities. This work
is also closely related to a recent paper of Carron and the forthcoming paper
of Cheeger and Dai. We apply our results to a number of examples, gravitational
instantons among them, arising in predictions about L2 harmonic forms in duality
theories in string theory.
acknowledgement: |-
Hausel’s work supported by a Miller Research Fellowship at the University of California, Berkeley.
Hunsicker’s work partially supported by Stanford University.
Mazzeo’s work supported by National Science Foundation grant numbers DMS-991975 and DMS-0204730 and
by the Mathematical Sciences Research Institute.
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Eugénie
full_name: Hunsicker, Eugénie
last_name: Hunsicker
- first_name: Rafe
full_name: Mazzeo, Rafe R
last_name: Mazzeo
citation:
ama: Hausel T, Hunsicker E, Mazzeo R. Hodge cohomology of gravitational instantons.
Duke Mathematical Journal. 2004;122(3):485-548. doi:10.1215/S0012-7094-04-12233-X
apa: Hausel, T., Hunsicker, E., & Mazzeo, R. (2004). Hodge cohomology of gravitational
instantons. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/S0012-7094-04-12233-X
chicago: Hausel, Tamás, Eugénie Hunsicker, and Rafe Mazzeo. “Hodge Cohomology of
Gravitational Instantons.” Duke Mathematical Journal. Duke University Press,
2004. https://doi.org/10.1215/S0012-7094-04-12233-X.
ieee: T. Hausel, E. Hunsicker, and R. Mazzeo, “Hodge cohomology of gravitational
instantons,” Duke Mathematical Journal, vol. 122, no. 3. Duke University
Press, pp. 485–548, 2004.
ista: Hausel T, Hunsicker E, Mazzeo R. 2004. Hodge cohomology of gravitational instantons.
Duke Mathematical Journal. 122(3), 485–548.
mla: Hausel, Tamás, et al. “Hodge Cohomology of Gravitational Instantons.” Duke
Mathematical Journal, vol. 122, no. 3, Duke University Press, 2004, pp. 485–548,
doi:10.1215/S0012-7094-04-12233-X.
short: T. Hausel, E. Hunsicker, R. Mazzeo, Duke Mathematical Journal 122 (2004)
485–548.
date_created: 2018-12-11T11:52:08Z
date_published: 2004-04-15T00:00:00Z
date_updated: 2021-01-12T06:50:52Z
day: '15'
doi: 10.1215/S0012-7094-04-12233-X
extern: 1
intvolume: ' 122'
issue: '3'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math/0207169
month: '04'
oa: 1
page: 485 - 548
publication: Duke Mathematical Journal
publication_status: published
publisher: Duke University Press
publist_id: '5737'
quality_controlled: 0
status: public
title: Hodge cohomology of gravitational instantons
type: journal_article
volume: 122
year: '2004'
...
---
_id: '1464'
abstract:
- lang: eng
text: "The moduli space of stable vector bundles on a Riemann surface is smooth
when the rank and degree are coprime, and is diffeomorphic to the space of unitary
connections of central constant curvature. A classic result of Newstead and Atiyah
and Bott asserts that its rational cohomology ring is generated by the universal
classes, that is, by the Kunneth components of the Chern classes of the universal
bundle.\n\nThis paper studies the larger, non-compact moduli space of Higgs bundles,
as introduced by Hitchin and Simpson, with values in the canonical bundle K. This
is diffeomorphic to the space of all connections of central constant curvature,
whether unitary or not. The main result of the paper is that, in the rank 2 case,
the rational cohomology ring of this space is again generated by universal classes.\n\nThe
spaces of Higgs bundles with values in K(n) for n > 0 turn out to be essential
to the story. Indeed, we show that their direct limit has the homotopy type of
the classifying space of the gauge group, and hence has cohomology generated by
universal classes. 2000 Mathematics Subject Classification 14H60 (primary), 14D20,
14H81, 32Q55, 58D27 (secondary). "
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Michael
full_name: Thaddeus, Michael
last_name: Thaddeus
citation:
ama: Hausel T, Thaddeus M. Generators for the cohomology ring of the moduli space
of rank 2 higgs bundles. Proceedings of the London Mathematical Society.
2004;88(3):632-658. doi:10.1112/S0024611503014618
apa: Hausel, T., & Thaddeus, M. (2004). Generators for the cohomology ring of
the moduli space of rank 2 higgs bundles. Proceedings of the London Mathematical
Society. Oxford University Press. https://doi.org/10.1112/S0024611503014618
chicago: Hausel, Tamás, and Michael Thaddeus. “Generators for the Cohomology Ring
of the Moduli Space of Rank 2 Higgs Bundles.” Proceedings of the London Mathematical
Society. Oxford University Press, 2004. https://doi.org/10.1112/S0024611503014618.
ieee: T. Hausel and M. Thaddeus, “Generators for the cohomology ring of the moduli
space of rank 2 higgs bundles,” Proceedings of the London Mathematical Society,
vol. 88, no. 3. Oxford University Press, pp. 632–658, 2004.
ista: Hausel T, Thaddeus M. 2004. Generators for the cohomology ring of the moduli
space of rank 2 higgs bundles. Proceedings of the London Mathematical Society.
88(3), 632–658.
mla: Hausel, Tamás, and Michael Thaddeus. “Generators for the Cohomology Ring of
the Moduli Space of Rank 2 Higgs Bundles.” Proceedings of the London Mathematical
Society, vol. 88, no. 3, Oxford University Press, 2004, pp. 632–58, doi:10.1112/S0024611503014618.
short: T. Hausel, M. Thaddeus, Proceedings of the London Mathematical Society 88
(2004) 632–658.
date_created: 2018-12-11T11:52:10Z
date_published: 2004-05-01T00:00:00Z
date_updated: 2021-01-12T06:50:55Z
day: '01'
doi: 10.1112/S0024611503014618
extern: 1
intvolume: ' 88'
issue: '3'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math/0003093
month: '05'
oa: 1
page: 632 - 658
publication: Proceedings of the London Mathematical Society
publication_status: published
publisher: Oxford University Press
publist_id: '5736'
quality_controlled: 0
status: public
title: Generators for the cohomology ring of the moduli space of rank 2 higgs bundles
type: journal_article
volume: 88
year: '2004'
...
---
_id: '1963'
abstract:
- lang: eng
text: The mechanism coupling electron transfer and proton pumping in respiratory
complex I (NADH-ubiquinone oxidoreductase) has not been established, but it has
been suggested that it involves conformational changes. Here, the influence of
substrates on the conformation of purified complex I from Escherichia coli was
studied by cross-linking and electron microscopy. When a zero-length cross-linking
reagent was used, the presence of NAD(P)H, in contrast to that of NAD+, prevented
the formation of cross-links between the hydrophilic subunits of the complex,
including NuoB, NuoI, and NuoCD. Comparisons using different cross-linkers suggested
that NuoB, which is likely to coordinate the key iron-sulfur cluster N2, is the
most mobile subunit. The presence of NAD(P)H led also to enhanced proteolysis
of subunit NuoG. These data indicate that upon NAD(P)H binding, the peripheral
arm of the complex adopts a more open conformation, with increased distances between
subunits. Single particle analysis showed the nature of this conformational change.
The enzyme retains its L-shape in the presence of NADH, but exhibits a significantly
more open or expanded structure both in the peripheral arm and, unexpectedly,
in the membrane domain also.
acknowledgement: This work was supported by the Medical Research Council and by a
Royal Society/North Atlantic Treaty Organization postdoctoral fellowship (to A.
A. M.)
author:
- first_name: Aygun
full_name: Mamedova, Aygun A
last_name: Mamedova
- first_name: Peter
full_name: Holt, Peter J
last_name: Holt
- first_name: Joe
full_name: Carroll, Joe D
last_name: Carroll
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Mamedova A, Holt P, Carroll J, Sazanov LA. Substrate-induced conformational
change in bacterial complex I. Journal of Biological Chemistry. 2004;279(22):23830-23836.
doi:10.1074/jbc.M401539200
apa: Mamedova, A., Holt, P., Carroll, J., & Sazanov, L. A. (2004). Substrate-induced
conformational change in bacterial complex I. Journal of Biological Chemistry.
American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M401539200
chicago: Mamedova, Aygun, Peter Holt, Joe Carroll, and Leonid A Sazanov. “Substrate-Induced
Conformational Change in Bacterial Complex I.” Journal of Biological Chemistry.
American Society for Biochemistry and Molecular Biology, 2004. https://doi.org/10.1074/jbc.M401539200.
ieee: A. Mamedova, P. Holt, J. Carroll, and L. A. Sazanov, “Substrate-induced conformational
change in bacterial complex I,” Journal of Biological Chemistry, vol. 279,
no. 22. American Society for Biochemistry and Molecular Biology, pp. 23830–23836,
2004.
ista: Mamedova A, Holt P, Carroll J, Sazanov LA. 2004. Substrate-induced conformational
change in bacterial complex I. Journal of Biological Chemistry. 279(22), 23830–23836.
mla: Mamedova, Aygun, et al. “Substrate-Induced Conformational Change in Bacterial
Complex I.” Journal of Biological Chemistry, vol. 279, no. 22, American
Society for Biochemistry and Molecular Biology, 2004, pp. 23830–36, doi:10.1074/jbc.M401539200.
short: A. Mamedova, P. Holt, J. Carroll, L.A. Sazanov, Journal of Biological Chemistry
279 (2004) 23830–23836.
date_created: 2018-12-11T11:54:56Z
date_published: 2004-05-28T00:00:00Z
date_updated: 2021-01-12T06:54:22Z
day: '28'
doi: 10.1074/jbc.M401539200
extern: 1
intvolume: ' 279'
issue: '22'
month: '05'
page: 23830 - 23836
publication: Journal of Biological Chemistry
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '5123'
quality_controlled: 0
status: public
title: Substrate-induced conformational change in bacterial complex I
type: journal_article
volume: 279
year: '2004'
...
---
_id: '209'
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Roger
full_name: Heath-Brown, Roger
last_name: Heath Brown
citation:
ama: Browning TD, Heath Brown R. Equal sums of three powers. Inventiones Mathematicae.
2004;157(3):553-573. doi:10.1007/s00222-004-0360-9
apa: Browning, T. D., & Heath Brown, R. (2004). Equal sums of three powers.
Inventiones Mathematicae. Unknown. https://doi.org/10.1007/s00222-004-0360-9
chicago: Browning, Timothy D, and Roger Heath Brown. “Equal Sums of Three Powers.”
Inventiones Mathematicae. Unknown, 2004. https://doi.org/10.1007/s00222-004-0360-9.
ieee: T. D. Browning and R. Heath Brown, “Equal sums of three powers,” Inventiones
Mathematicae, vol. 157, no. 3. Unknown, pp. 553–573, 2004.
ista: Browning TD, Heath Brown R. 2004. Equal sums of three powers. Inventiones
Mathematicae. 157(3), 553–573.
mla: Browning, Timothy D., and Roger Heath Brown. “Equal Sums of Three Powers.”
Inventiones Mathematicae, vol. 157, no. 3, Unknown, 2004, pp. 553–73, doi:10.1007/s00222-004-0360-9.
short: T.D. Browning, R. Heath Brown, Inventiones Mathematicae 157 (2004) 553–573.
date_created: 2018-12-11T11:45:13Z
date_published: 2004-03-17T00:00:00Z
date_updated: 2021-01-12T06:55:14Z
day: '17'
doi: 10.1007/s00222-004-0360-9
extern: 1
intvolume: ' 157'
issue: '3'
month: '03'
page: 553 - 573
publication: Inventiones Mathematicae
publication_status: published
publisher: Unknown
publist_id: '7703'
quality_controlled: 0
status: public
title: Equal sums of three powers
type: journal_article
volume: 157
year: '2004'
...
---
_id: '2308'
abstract:
- lang: eng
text: It is widely believed that the inflammatory events mediated by microglial
activation contribute to several neurodegenerative processes. Alzheimer's disease,
for example, is characterized by an accumulation of β-amyloid protein (Aβ) in
neuritic plaques that are infiltrated by reactive microglia and astrocytes. Although
Aβ and its fragment 25-35 exert a direct toxic effect on neurons, they also activate
microglia. Microglial activation is accompanied by morphological changes, cell
proliferation, and release of various cytokines and growth factors. A number of
scientific reports suggest that the increased proliferation of microglial cells
is dependent on ionic membrane currents and in particular on chloride conductances.
An unusual chloride ion channel known to be associated with macrophage activation
is the chloride intracellular channel-1 (CLIC1). Here we show that Aβ stimulation
of neonatal rat microglia specifically leads to the increase in CLIC1 protein
and to the functional expression of CLIC1 chloride conductance, both barely detectable
on the plasma membrane of quiescent cells. CLIC1 protein expression in microglia
increases after 24 hr of incubation with Aβ, simultaneously with the production
of reactive nitrogen intermediates and of tumor necrosis factor-α (TNF-α). We
demonstrate that reducing CLIC1 chloride conductance by a specific blocker [IAA-94
(R(+)-[(6,7-dichloro-2-cyclopentyl-2,3-dihydro-2-methyl-1-oxo-1H-inden-5yl)-oxy]
acetic acid)] prevents neuronal apoptosis in neurons cocultured with Aβ-treated
microglia. Furthermore, we show that small interfering RNAs used to knock down
CLIC1 expression prevent TNF-α release induced by Aβ stimulation. These results
provide a direct link between Aβ-induced microglial activation and CLIC1 functional
expression.
author:
- first_name: Gaia
full_name: Gaia Novarino
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Cinzia
full_name: Fabrizi, Cinzia
last_name: Fabrizi
- first_name: Raffaella
full_name: Tonini, Raffaella
last_name: Tonini
- first_name: Michela
full_name: Denti, Michela A
last_name: Denti
- first_name: Albedi
full_name: Malchiodi, Albedi F
last_name: Malchiodi
- first_name: Giuliana
full_name: Lauro, Giuliana M
last_name: Lauro
- first_name: Benedetto
full_name: Sacchetti, Benedetto
last_name: Sacchetti
- first_name: Silvia
full_name: Paradisi, Silvia
last_name: Paradisi
- first_name: Arnaldo
full_name: Ferroni, Arnaldo
last_name: Ferroni
- first_name: Paul
full_name: Curmi, Paul M G
last_name: Curmi
- first_name: Samuel
full_name: Breit, Samuel N
last_name: Breit
- first_name: Michele
full_name: Mazzanti, Michele
last_name: Mazzanti
citation:
ama: Novarino G, Fabrizi C, Tonini R, et al. Involvement of the intracellular ion
channel CLIC1 in microglia-mediated β-amyloid-induced neurotoxicity. Journal
of Neuroscience. 2004;24(23):5322-5330. doi:10.1523/JNEUROSCI.1170-04.2004
apa: Novarino, G., Fabrizi, C., Tonini, R., Denti, M., Malchiodi, A., Lauro, G.,
… Mazzanti, M. (2004). Involvement of the intracellular ion channel CLIC1 in microglia-mediated
β-amyloid-induced neurotoxicity. Journal of Neuroscience. Society for Neuroscience.
https://doi.org/10.1523/JNEUROSCI.1170-04.2004
chicago: Novarino, Gaia, Cinzia Fabrizi, Raffaella Tonini, Michela Denti, Albedi
Malchiodi, Giuliana Lauro, Benedetto Sacchetti, et al. “Involvement of the Intracellular
Ion Channel CLIC1 in Microglia-Mediated β-Amyloid-Induced Neurotoxicity.” Journal
of Neuroscience. Society for Neuroscience, 2004. https://doi.org/10.1523/JNEUROSCI.1170-04.2004.
ieee: G. Novarino et al., “Involvement of the intracellular ion channel CLIC1
in microglia-mediated β-amyloid-induced neurotoxicity,” Journal of Neuroscience,
vol. 24, no. 23. Society for Neuroscience, pp. 5322–5330, 2004.
ista: Novarino G, Fabrizi C, Tonini R, Denti M, Malchiodi A, Lauro G, Sacchetti
B, Paradisi S, Ferroni A, Curmi P, Breit S, Mazzanti M. 2004. Involvement of the
intracellular ion channel CLIC1 in microglia-mediated β-amyloid-induced neurotoxicity.
Journal of Neuroscience. 24(23), 5322–5330.
mla: Novarino, Gaia, et al. “Involvement of the Intracellular Ion Channel CLIC1
in Microglia-Mediated β-Amyloid-Induced Neurotoxicity.” Journal of Neuroscience,
vol. 24, no. 23, Society for Neuroscience, 2004, pp. 5322–30, doi:10.1523/JNEUROSCI.1170-04.2004.
short: G. Novarino, C. Fabrizi, R. Tonini, M. Denti, A. Malchiodi, G. Lauro, B.
Sacchetti, S. Paradisi, A. Ferroni, P. Curmi, S. Breit, M. Mazzanti, Journal of
Neuroscience 24 (2004) 5322–5330.
date_created: 2018-12-11T11:56:54Z
date_published: 2004-06-09T00:00:00Z
date_updated: 2021-01-12T06:56:41Z
day: '09'
doi: 10.1523/JNEUROSCI.1170-04.2004
extern: 1
intvolume: ' 24'
issue: '23'
month: '06'
page: 5322 - 5330
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '4620'
quality_controlled: 0
status: public
title: Involvement of the intracellular ion channel CLIC1 in microglia-mediated β-amyloid-induced
neurotoxicity
type: journal_article
volume: 24
year: '2004'
...
---
_id: '2356'
abstract:
- lang: eng
text: 'Recent experimental and theoretical work has shown that there are conditions
in which a trapped, low-density Bose gas behaves like the one-dimensional delta-function
Bose gas solved years ago by Lieb and Liniger. This is an intrinsically quantum-mechanical
phenomenon because it is not necessary to have a trap width that is the size of
an atom - as might have been supposed - but it suffices merely to have a trap
width such that the energy gap for motion in the transverse direction is large
compared to the energy associated with the motion along the trap. Up to now the
theoretical arguments have been based on variational - perturbative ideas or numerical
investigations. In contrast, this paper gives a rigorous proof of the one-dimensional
behavior as far as the ground state energy and particle density are concerned.
There are four parameters involved: the particle number, N, transverse and longitudinal
dimensions of the trap, r and L, and the scattering length a of the interaction
potential. Our main result is that if r/L → 0 and N → ∞ the ground state energy
and density can be obtained by minimizing a one-dimensional density functional
involving the Lieb-Liniger energy density with coupling constant ∼ a/r 2. This
density functional simplifies in various limiting cases and we identify five asymptotic
parameter regions altogether. Three of these, corresponding to the weak coupling
regime, can also be obtained as limits of a three-dimensional Gross-Pitaevskii
theory. We also show that Bose-Einstein condensation in the ground state persists
in a part of this regime. In the strong coupling regime the longitudinal motion
of the particles is strongly correlated. The Gross-Pitaevskii description is not
valid in this regime and new mathematical methods come into play.'
author:
- first_name: Élliott
full_name: Lieb, Élliott H
last_name: Lieb
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jakob
full_name: Yngvason, Jakob
last_name: Yngvason
citation:
ama: Lieb É, Seiringer R, Yngvason J. One-dimensional behavior of dilute, trapped
Bose gases. Communications in Mathematical Physics. 2004;244(2):347-393.
doi:10.1007/s00220-003-0993-3
apa: Lieb, É., Seiringer, R., & Yngvason, J. (2004). One-dimensional behavior
of dilute, trapped Bose gases. Communications in Mathematical Physics.
Springer. https://doi.org/10.1007/s00220-003-0993-3
chicago: Lieb, Élliott, Robert Seiringer, and Jakob Yngvason. “One-Dimensional Behavior
of Dilute, Trapped Bose Gases.” Communications in Mathematical Physics.
Springer, 2004. https://doi.org/10.1007/s00220-003-0993-3.
ieee: É. Lieb, R. Seiringer, and J. Yngvason, “One-dimensional behavior of dilute,
trapped Bose gases,” Communications in Mathematical Physics, vol. 244,
no. 2. Springer, pp. 347–393, 2004.
ista: Lieb É, Seiringer R, Yngvason J. 2004. One-dimensional behavior of dilute,
trapped Bose gases. Communications in Mathematical Physics. 244(2), 347–393.
mla: Lieb, Élliott, et al. “One-Dimensional Behavior of Dilute, Trapped Bose Gases.”
Communications in Mathematical Physics, vol. 244, no. 2, Springer, 2004,
pp. 347–93, doi:10.1007/s00220-003-0993-3.
short: É. Lieb, R. Seiringer, J. Yngvason, Communications in Mathematical Physics
244 (2004) 347–393.
date_created: 2018-12-11T11:57:11Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:59Z
day: '01'
doi: 10.1007/s00220-003-0993-3
extern: 1
intvolume: ' 244'
issue: '2'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math-ph/0305025
month: '01'
oa: 1
page: 347 - 393
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4569'
quality_controlled: 0
status: public
title: One-dimensional behavior of dilute, trapped Bose gases
type: journal_article
volume: 244
year: '2004'
...
---
_id: '2355'
abstract:
- lang: eng
text: 'The BMV conjecture for traces, which states that Tr exp(A - λB) is the Laplace
transform of a positive measure, is shown to be equivalent to two other statements:
(i) The polynomial λ → Tr(A + λB) p has only non-negative coefficients for all
A, B ≥ 0, p ∈ ℕ and (ii) λ → Tr(A + λB)-p is the Laplace transform of a positive
measure for A, B ≥ 0, p > 0.'
author:
- first_name: Élliott
full_name: Lieb, Élliott H
last_name: Lieb
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Lieb É, Seiringer R. Equivalent forms of the Bessis-Moussa-Villani conjecture.
Journal of Statistical Physics. 2004;115(1-2):185-190. doi:10.1023/B:JOSS.0000019811.15510.27
apa: Lieb, É., & Seiringer, R. (2004). Equivalent forms of the Bessis-Moussa-Villani
conjecture. Journal of Statistical Physics. Springer. https://doi.org/10.1023/B:JOSS.0000019811.15510.27
chicago: Lieb, Élliott, and Robert Seiringer. “ Equivalent Forms of the Bessis-Moussa-Villani
Conjecture.” Journal of Statistical Physics. Springer, 2004. https://doi.org/10.1023/B:JOSS.0000019811.15510.27.
ieee: É. Lieb and R. Seiringer, “ Equivalent forms of the Bessis-Moussa-Villani
conjecture,” Journal of Statistical Physics, vol. 115, no. 1–2. Springer,
pp. 185–190, 2004.
ista: Lieb É, Seiringer R. 2004. Equivalent forms of the Bessis-Moussa-Villani
conjecture. Journal of Statistical Physics. 115(1–2), 185–190.
mla: Lieb, Élliott, and Robert Seiringer. “ Equivalent Forms of the Bessis-Moussa-Villani
Conjecture.” Journal of Statistical Physics, vol. 115, no. 1–2, Springer,
2004, pp. 185–90, doi:10.1023/B:JOSS.0000019811.15510.27.
short: É. Lieb, R. Seiringer, Journal of Statistical Physics 115 (2004) 185–190.
date_created: 2018-12-11T11:57:11Z
date_published: 2004-04-01T00:00:00Z
date_updated: 2021-01-12T06:56:59Z
day: '01'
doi: 10.1023/B:JOSS.0000019811.15510.27
extern: 1
intvolume: ' 115'
issue: 1-2
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math-ph/0210027
month: '04'
oa: 1
page: 185 - 190
publication: Journal of Statistical Physics
publication_status: published
publisher: Springer
publist_id: '4568'
quality_controlled: 0
status: public
title: ' Equivalent forms of the Bessis-Moussa-Villani conjecture'
type: journal_article
volume: 115
year: '2004'
...
---
_id: '2360'
abstract:
- lang: eng
text: An optical lattice model developed that is similar to the Bose-Hubbard model
to describe the transition between Bose-Einstein condensation (BEC) and a Mott
insulator state was analyzed. It was found that the system was a hard core lattice
gas at half of the maximum density and the optical lattice was modeled by a periodic
potential of strength λ. It was also observed that the interparticle interaction
was essential for this transition that occurred even in the ground state. The
results show that all the essential features could be proved rigorously such as
the existence of BEC for small λ and its suppression for a large λ.
author:
- first_name: Michael
full_name: Aizenman, Michael
last_name: Aizenman
- first_name: Élliott
full_name: Lieb, Élliott H
last_name: Lieb
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jan
full_name: Solovej, Jan P
last_name: Solovej
- first_name: Jakob
full_name: Yngvason, Jakob
last_name: Yngvason
citation:
ama: Aizenman M, Lieb É, Seiringer R, Solovej J, Yngvason J. Bose-Einstein quantum
phase transition in an optical lattice model. Physical Review A - Atomic, Molecular,
and Optical Physics. 2004;70(2):023612-1-0236121-2. doi:10.1103/PhysRevA.70.023612
apa: Aizenman, M., Lieb, É., Seiringer, R., Solovej, J., & Yngvason, J. (2004).
Bose-Einstein quantum phase transition in an optical lattice model. Physical
Review A - Atomic, Molecular, and Optical Physics. American Physical Society.
https://doi.org/10.1103/PhysRevA.70.023612
chicago: Aizenman, Michael, Élliott Lieb, Robert Seiringer, Jan Solovej, and Jakob
Yngvason. “Bose-Einstein Quantum Phase Transition in an Optical Lattice Model.”
Physical Review A - Atomic, Molecular, and Optical Physics. American Physical
Society, 2004. https://doi.org/10.1103/PhysRevA.70.023612.
ieee: M. Aizenman, É. Lieb, R. Seiringer, J. Solovej, and J. Yngvason, “Bose-Einstein
quantum phase transition in an optical lattice model,” Physical Review A -
Atomic, Molecular, and Optical Physics, vol. 70, no. 2. American Physical
Society, pp. 023612-1-0236121-2, 2004.
ista: Aizenman M, Lieb É, Seiringer R, Solovej J, Yngvason J. 2004. Bose-Einstein
quantum phase transition in an optical lattice model. Physical Review A - Atomic,
Molecular, and Optical Physics. 70(2), 023612-1-0236121-2.
mla: Aizenman, Michael, et al. “Bose-Einstein Quantum Phase Transition in an Optical
Lattice Model.” Physical Review A - Atomic, Molecular, and Optical Physics,
vol. 70, no. 2, American Physical Society, 2004, pp. 023612-1-0236121-2, doi:10.1103/PhysRevA.70.023612.
short: M. Aizenman, É. Lieb, R. Seiringer, J. Solovej, J. Yngvason, Physical Review
A - Atomic, Molecular, and Optical Physics 70 (2004) 023612-1-0236121-2.
date_created: 2018-12-11T11:57:12Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2021-01-12T06:57:01Z
day: '01'
doi: 10.1103/PhysRevA.70.023612
extern: 1
intvolume: ' 70'
issue: '2'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/cond-mat/0403240
month: '08'
oa: 1
page: 023612 - 1-0236121-2
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '4567'
quality_controlled: 0
status: public
title: Bose-Einstein quantum phase transition in an optical lattice model
type: journal_article
volume: 70
year: '2004'
...
---
_id: '2417'
alternative_title:
- 'Contemporary Mathematics '
author:
- first_name: László
full_name: Lovász, László
last_name: Lovász
- first_name: Katalin
full_name: Vesztergombi, Katalin
last_name: Vesztergombi
- first_name: Uli
full_name: Uli Wagner
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
- first_name: Emo
full_name: Welzl, Emo
last_name: Welzl
citation:
ama: 'Lovász L, Vesztergombi K, Wagner U, Welzl E. Convex quadrilaterals and k-sets
. In: Pach J, ed. Towards a Theory of Geometric Graphs. Vol 342. American
Mathematical Society; 2004:139-148. doi:10.1090/conm/342'
apa: Lovász, L., Vesztergombi, K., Wagner, U., & Welzl, E. (2004). Convex quadrilaterals
and k-sets . In J. Pach (Ed.), Towards a Theory of Geometric Graphs (Vol.
342, pp. 139–148). American Mathematical Society. https://doi.org/10.1090/conm/342
chicago: Lovász, László, Katalin Vesztergombi, Uli Wagner, and Emo Welzl. “Convex
Quadrilaterals and K-Sets .” In Towards a Theory of Geometric Graphs, edited
by János Pach, 342:139–48. American Mathematical Society, 2004. https://doi.org/10.1090/conm/342.
ieee: L. Lovász, K. Vesztergombi, U. Wagner, and E. Welzl, “Convex quadrilaterals
and k-sets ,” in Towards a Theory of Geometric Graphs, vol. 342, J. Pach,
Ed. American Mathematical Society, 2004, pp. 139–148.
ista: 'Lovász L, Vesztergombi K, Wagner U, Welzl E. 2004.Convex quadrilaterals and
k-sets . In: Towards a Theory of Geometric Graphs. Contemporary Mathematics ,
vol. 342, 139–148.'
mla: Lovász, László, et al. “Convex Quadrilaterals and K-Sets .” Towards a Theory
of Geometric Graphs, edited by János Pach, vol. 342, American Mathematical
Society, 2004, pp. 139–48, doi:10.1090/conm/342.
short: L. Lovász, K. Vesztergombi, U. Wagner, E. Welzl, in:, J. Pach (Ed.), Towards
a Theory of Geometric Graphs, American Mathematical Society, 2004, pp. 139–148.
date_created: 2018-12-11T11:57:32Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T06:57:21Z
day: '01'
doi: 10.1090/conm/342
editor:
- first_name: János
full_name: Pach, János
last_name: Pach
extern: 1
intvolume: ' 342'
month: '01'
page: 139 - 148
publication: Towards a Theory of Geometric Graphs
publication_status: published
publisher: American Mathematical Society
publist_id: '4508'
quality_controlled: 0
status: public
title: 'Convex quadrilaterals and k-sets '
type: book_chapter
volume: 342
year: '2004'
...
---
_id: '2426'
abstract:
- lang: eng
text: We introduce the adaptive neighborhood graph as a data structure for modeling
a smooth manifold M embedded in some Euclidean space ℝ d. We assume that M is
known to us only through a finite sample P ⊂ M, as is often the case in applications.
The adaptive neighborhood graph is a geometric graph on P. Its complexity is at
most min{2O(k)n, n2}, where n = P and k = dim M, as opposed to the n[d/2] complexity
of the Delaunay triangulation, which is often used to model manifolds. We prove
that we can correctly infer the connected components and the dimension of M from
the adaptive neighborhood graph provided a certain standard sampling condition
is fulfilled. The running time of the dimension detection algorithm is d20(k7
log k) for each connected component of M. If the dimension is considered constant,
this is a constant-time operation, and the adaptive neighborhood graph is of linear
size. Moreover, the exponential dependence of the constants is only on the intrinsic
dimension k, not on the ambient dimension d. This is of particular interest if
the co-dimension is high, i.e., if k is much smaller than d, as is the case in
many applications. The adaptive neighborhood graph also allows us to approximate
the geodesic distances between the points in P.
author:
- first_name: Joachim
full_name: Giesen, Joachim
last_name: Giesen
- first_name: Uli
full_name: Uli Wagner
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Giesen J, Wagner U. Shape dimension and intrinsic metric from samples of manifolds.
Discrete & Computational Geometry. 2004;32(2):245-267. doi:10.1007/s00454-004-1120-8
apa: Giesen, J., & Wagner, U. (2004). Shape dimension and intrinsic metric from
samples of manifolds. Discrete & Computational Geometry. Springer.
https://doi.org/10.1007/s00454-004-1120-8
chicago: Giesen, Joachim, and Uli Wagner. “Shape Dimension and Intrinsic Metric
from Samples of Manifolds.” Discrete & Computational Geometry. Springer,
2004. https://doi.org/10.1007/s00454-004-1120-8.
ieee: J. Giesen and U. Wagner, “Shape dimension and intrinsic metric from samples
of manifolds,” Discrete & Computational Geometry, vol. 32, no. 2. Springer,
pp. 245–267, 2004.
ista: Giesen J, Wagner U. 2004. Shape dimension and intrinsic metric from samples
of manifolds. Discrete & Computational Geometry. 32(2), 245–267.
mla: Giesen, Joachim, and Uli Wagner. “Shape Dimension and Intrinsic Metric from
Samples of Manifolds.” Discrete & Computational Geometry, vol. 32,
no. 2, Springer, 2004, pp. 245–67, doi:10.1007/s00454-004-1120-8.
short: J. Giesen, U. Wagner, Discrete & Computational Geometry 32 (2004) 245–267.
date_created: 2018-12-11T11:57:35Z
date_published: 2004-09-01T00:00:00Z
date_updated: 2021-01-12T06:57:25Z
day: '01'
doi: 10.1007/s00454-004-1120-8
extern: 1
intvolume: ' 32'
issue: '2'
month: '09'
page: 245 - 267
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '4499'
quality_controlled: 0
status: public
title: Shape dimension and intrinsic metric from samples of manifolds
type: journal_article
volume: 32
year: '2004'
...
---
_id: '2425'
abstract:
- lang: eng
text: A finite set N ⊂ Rd is a weak ε-net for an n-point set X ⊂ Rd (with respect
to convex sets) if N intersects every convex set K with |K ∩ X| ≥ εn. We give
an alternative, and arguably simpler, proof of the fact, first shown by Chazelle
et al., that every point set X in Rd admits a weak ε-net of cardinality O(ε-dpolylog(1/ε)).
Moreover, for a number of special point sets (e.g., for points on the moment curve),
our method gives substantially better bounds. The construction yields an algorithm
to construct such weak ε-nets in time O(n ln(1/ε)).
author:
- first_name: Jiří
full_name: Matoušek, Jiří
last_name: Matoušek
- first_name: Uli
full_name: Uli Wagner
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Matoušek J, Wagner U. New constructions of weak ε-nets. Discrete & Computational
Geometry. 2004;32(2):195-206. doi:10.1007/s00454-004-1116-4
apa: Matoušek, J., & Wagner, U. (2004). New constructions of weak ε-nets. Discrete
& Computational Geometry. Springer. https://doi.org/10.1007/s00454-004-1116-4
chicago: Matoušek, Jiří, and Uli Wagner. “New Constructions of Weak ε-Nets.” Discrete
& Computational Geometry. Springer, 2004. https://doi.org/10.1007/s00454-004-1116-4.
ieee: J. Matoušek and U. Wagner, “New constructions of weak ε-nets,” Discrete
& Computational Geometry, vol. 32, no. 2. Springer, pp. 195–206, 2004.
ista: Matoušek J, Wagner U. 2004. New constructions of weak ε-nets. Discrete &
Computational Geometry. 32(2), 195–206.
mla: Matoušek, Jiří, and Uli Wagner. “New Constructions of Weak ε-Nets.” Discrete
& Computational Geometry, vol. 32, no. 2, Springer, 2004, pp. 195–206,
doi:10.1007/s00454-004-1116-4.
short: J. Matoušek, U. Wagner, Discrete & Computational Geometry 32 (2004) 195–206.
date_created: 2018-12-11T11:57:35Z
date_published: 2004-07-01T00:00:00Z
date_updated: 2021-01-12T06:57:24Z
day: '01'
doi: 10.1007/s00454-004-1116-4
extern: 1
intvolume: ' 32'
issue: '2'
month: '07'
page: 195 - 206
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '4500'
quality_controlled: 0
status: public
title: New constructions of weak ε-nets
type: journal_article
volume: 32
year: '2004'
...
---
_id: '2461'
author:
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Sauer M, Friml J. The Matryoshka dolls of plant polarity. Development.
2004;131(23):5774-5775. doi:10.1242/dev.01463
apa: Sauer, M., & Friml, J. (2004). The Matryoshka dolls of plant polarity.
Development. Company of Biologists. https://doi.org/10.1242/dev.01463
chicago: Sauer, Michael, and Jiří Friml. “The Matryoshka Dolls of Plant Polarity.”
Development. Company of Biologists, 2004. https://doi.org/10.1242/dev.01463.
ieee: M. Sauer and J. Friml, “The Matryoshka dolls of plant polarity,” Development,
vol. 131, no. 23. Company of Biologists, pp. 5774–5775, 2004.
ista: Sauer M, Friml J. 2004. The Matryoshka dolls of plant polarity. Development.
131(23), 5774–5775.
mla: Sauer, Michael, and Jiří Friml. “The Matryoshka Dolls of Plant Polarity.” Development,
vol. 131, no. 23, Company of Biologists, 2004, pp. 5774–75, doi:10.1242/dev.01463.
short: M. Sauer, J. Friml, Development 131 (2004) 5774–5775.
date_created: 2018-12-11T11:57:48Z
date_published: 2004-12-01T00:00:00Z
date_updated: 2021-01-12T06:57:37Z
day: '01'
doi: 10.1242/dev.01463
extern: '1'
intvolume: ' 131'
issue: '23'
language:
- iso: eng
month: '12'
oa_version: None
page: 5774 - 5775
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '4442'
quality_controlled: '1'
status: public
title: The Matryoshka dolls of plant polarity
type: review
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2004'
...
---
_id: '2642'
abstract:
- lang: eng
text: In the hippocampal CA1 region, metabotropic glutamate subtype 1 (mGluR1) receptors
have been implicated in a variety of physiological responses to glutamate, which
include modulation of synaptic transmission and plasticity, as well as neuronal
excitability and synchronization. The mGluR1α isoform is characteristically expressed
only by nonprincipal cells, and it is particularly enriched in somatostatin (SS
-containing interneurons in stratum oriens-alveus. Anatomical and physiological
data have indicated the presence of mGluR1α in several distinct classes of interneurons
with their somata located also in strata pyramidale, radiatum, and lacunosum moleculare.
Each different interneuron subtype, as defined by functionally relevant criteria,
including input/output characteristics and expression of selective molecular markers,
subserves distinct functions in local hippocampal circuits. We have investigated
which of the different CA1 interneuron classes express mGluR1α by immunofluorescent
labeling, combining antibodies to mGluR1α, calcium-binding proteins, and neuropeptides,
and by intracellular labeling in vitro. Several types of interneuron that are
immunopositive for mGluR1α each targeted different domains of pyramidal cells
and included (1) O-LM interneurons, found to coexpress both SS and parvalbumin
(PV); (2) interneurons with target selectivity for other interneurons, expressing
vasoactive intestinal polypeptide (VIP) and/or the calcium-binding protein calretinin;
(3) procholecystokinin-immunopositive interneurons probably non-basket and dendrite-targeting;
and (4) an as-yet unidentified SS-immunoreactive but PV-immunonegative interneuron
class, possibly corresponding to oriensbistratified cells. Estimation of the relative
proportion of mGluR1α-positive interneurons showed 43%, 46%, and 30% co-labeling
with SS, VIP, or PV, respectively. The identification of the specific subclasses
of CA1 interneurons expressing mGluR1α provides the network basis for assessing
the contribution of this receptor to the excitability of the hippocampus.
author:
- first_name: Francesco
full_name: Ferraguti, Francesco
last_name: Ferraguti
- first_name: Philip
full_name: Cobden, Philip M
last_name: Cobden
- first_name: Marie
full_name: Pollard, Marie
last_name: Pollard
- first_name: David
full_name: Cope, David W
last_name: Cope
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Masahiko
full_name: Watanabe, Masahiko
last_name: Watanabe
- first_name: Péter
full_name: Somogyi, Péter
last_name: Somogyi
citation:
ama: Ferraguti F, Cobden P, Pollard M, et al. Immunolocalization of metabotropic
glutamate receptor 1α (mGluR1α) in distinct classes of interneuron in the CA1
region of the rat hippocampus. Hippocampus. 2004;14(2):193-215. doi:10.1002/hipo.10163
apa: Ferraguti, F., Cobden, P., Pollard, M., Cope, D., Shigemoto, R., Watanabe,
M., & Somogyi, P. (2004). Immunolocalization of metabotropic glutamate receptor
1α (mGluR1α) in distinct classes of interneuron in the CA1 region of the rat hippocampus.
Hippocampus. Wiley-Blackwell. https://doi.org/10.1002/hipo.10163
chicago: Ferraguti, Francesco, Philip Cobden, Marie Pollard, David Cope, Ryuichi
Shigemoto, Masahiko Watanabe, and Péter Somogyi. “Immunolocalization of Metabotropic
Glutamate Receptor 1α (MGluR1α) in Distinct Classes of Interneuron in the CA1
Region of the Rat Hippocampus.” Hippocampus. Wiley-Blackwell, 2004. https://doi.org/10.1002/hipo.10163.
ieee: F. Ferraguti et al., “Immunolocalization of metabotropic glutamate
receptor 1α (mGluR1α) in distinct classes of interneuron in the CA1 region of
the rat hippocampus,” Hippocampus, vol. 14, no. 2. Wiley-Blackwell, pp.
193–215, 2004.
ista: Ferraguti F, Cobden P, Pollard M, Cope D, Shigemoto R, Watanabe M, Somogyi
P. 2004. Immunolocalization of metabotropic glutamate receptor 1α (mGluR1α) in
distinct classes of interneuron in the CA1 region of the rat hippocampus. Hippocampus.
14(2), 193–215.
mla: Ferraguti, Francesco, et al. “Immunolocalization of Metabotropic Glutamate
Receptor 1α (MGluR1α) in Distinct Classes of Interneuron in the CA1 Region of
the Rat Hippocampus.” Hippocampus, vol. 14, no. 2, Wiley-Blackwell, 2004,
pp. 193–215, doi:10.1002/hipo.10163.
short: F. Ferraguti, P. Cobden, M. Pollard, D. Cope, R. Shigemoto, M. Watanabe,
P. Somogyi, Hippocampus 14 (2004) 193–215.
date_created: 2018-12-11T11:58:50Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T06:58:46Z
day: '01'
doi: 10.1002/hipo.10163
extern: 1
intvolume: ' 14'
issue: '2'
month: '01'
page: 193 - 215
publication: Hippocampus
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4256'
quality_controlled: 0
status: public
title: Immunolocalization of metabotropic glutamate receptor 1α (mGluR1α) in distinct
classes of interneuron in the CA1 region of the rat hippocampus
type: journal_article
volume: 14
year: '2004'
...
---
_id: '2639'
abstract:
- lang: eng
text: Vesicular glutamate transporter type 3 (VGLUT3) containing neuronal elements
were characterized using antibodies to VGLUT3 and molecular cell markers. All
VGLUT3-positive somata were immunoreactive for CCK, and very rarely, also for
calbindin; none was positive for parvalbumin, calretinin, VIP or somatostatin.
In the CA1 area, 26.8 ± 0.7% of CCK-positive interneuron somata were VGLUT3-positive,
a nonoverlapping 22.8 ± 1.9% were calbindin-positive, 10.7 ± 2.5% VIP-positive
and the rest were only CCK-positive. The patterns of coexpression were similar
in the CA3 area, the dentate gyrus and the isocortex. Immunoreactivity for VGLUT3
was undetectable in pyramidal and dentate granule cells. Boutons colabelled for
VGLUT3, CCK and GAD were most abundant in the cellular layers of the hippocampus
and in layers II-III of the isocortex. Large VGLUT3-labelled boutons at the border
of strata radiatum and lacunosum-moleculare in the CA1 area were negative for
GAD, but were labelled for vesicular monoamine transporter type 2, plasmalemmal
serotonin transporter or serotonin. No colocalization was found in terminals between
VGLUT3 and parvalbumin, vesicular acetylcholine transporter and group III (mGluR7a,b;
mGluR8a,b) metabotropic glutamate receptors. In stratum radiatum and the isocortex,
VGLUT3-positive but GAD-negative boutons heavily innervated the soma and proximal
dendrites of some VGLUT3- or calbindin-positive interneurons. The results suggest
that boutons coexpressing VGLUT3, CCK and GAD originate from CCK-positive basket
cells, which are VIP-immunonegative. Other VGLUT3-positive boutons immunopositive
for serotonergic markers but negative for GAD probably originate from the median
raphe nucleus and innervate select interneurons. The presumed amino acid substrate
of VGLUT3 may act on presynaptic kainate or group II metabotropic glutamate receptors.
author:
- first_name: Jozsef
full_name: Somogyi, Jozsef
last_name: Somogyi
- first_name: Agnès
full_name: Baude, Agnès
last_name: Baude
- first_name: Yuko
full_name: Omori, Yuko
last_name: Omori
- first_name: Hidemi
full_name: Shimizu, Hidemi
last_name: Shimizu
- first_name: Salah
full_name: El-Mestikawy, Salah
last_name: El Mestikawy
- first_name: Masahiro
full_name: Fukaya, Masahiro
last_name: Fukaya
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Masahiko
full_name: Watanabe, Masahiko
last_name: Watanabe
- first_name: Péter
full_name: Somogyi, Péter
last_name: Somogyi
citation:
ama: Somogyi J, Baude A, Omori Y, et al. GABAergic basket cells expressing cholecystokinin
contain vesicular glutamate transporter type 3 (VGLUT3) in their synaptic terminals
in hippocampus and isocortex of the rat. European Journal of Neuroscience.
2004;19(3):552-569. doi:10.1111/j.0953-816X.2003.03091.x
apa: Somogyi, J., Baude, A., Omori, Y., Shimizu, H., El Mestikawy, S., Fukaya, M.,
… Somogyi, P. (2004). GABAergic basket cells expressing cholecystokinin contain
vesicular glutamate transporter type 3 (VGLUT3) in their synaptic terminals in
hippocampus and isocortex of the rat. European Journal of Neuroscience.
Wiley-Blackwell. https://doi.org/10.1111/j.0953-816X.2003.03091.x
chicago: Somogyi, Jozsef, Agnès Baude, Yuko Omori, Hidemi Shimizu, Salah El Mestikawy,
Masahiro Fukaya, Ryuichi Shigemoto, Masahiko Watanabe, and Péter Somogyi. “GABAergic
Basket Cells Expressing Cholecystokinin Contain Vesicular Glutamate Transporter
Type 3 (VGLUT3) in Their Synaptic Terminals in Hippocampus and Isocortex of the
Rat.” European Journal of Neuroscience. Wiley-Blackwell, 2004. https://doi.org/10.1111/j.0953-816X.2003.03091.x.
ieee: J. Somogyi et al., “GABAergic basket cells expressing cholecystokinin
contain vesicular glutamate transporter type 3 (VGLUT3) in their synaptic terminals
in hippocampus and isocortex of the rat,” European Journal of Neuroscience,
vol. 19, no. 3. Wiley-Blackwell, pp. 552–569, 2004.
ista: Somogyi J, Baude A, Omori Y, Shimizu H, El Mestikawy S, Fukaya M, Shigemoto
R, Watanabe M, Somogyi P. 2004. GABAergic basket cells expressing cholecystokinin
contain vesicular glutamate transporter type 3 (VGLUT3) in their synaptic terminals
in hippocampus and isocortex of the rat. European Journal of Neuroscience. 19(3),
552–569.
mla: Somogyi, Jozsef, et al. “GABAergic Basket Cells Expressing Cholecystokinin
Contain Vesicular Glutamate Transporter Type 3 (VGLUT3) in Their Synaptic Terminals
in Hippocampus and Isocortex of the Rat.” European Journal of Neuroscience,
vol. 19, no. 3, Wiley-Blackwell, 2004, pp. 552–69, doi:10.1111/j.0953-816X.2003.03091.x.
short: J. Somogyi, A. Baude, Y. Omori, H. Shimizu, S. El Mestikawy, M. Fukaya, R.
Shigemoto, M. Watanabe, P. Somogyi, European Journal of Neuroscience 19 (2004)
552–569.
date_created: 2018-12-11T11:58:49Z
date_published: 2004-02-01T00:00:00Z
date_updated: 2021-01-12T06:58:44Z
day: '01'
doi: 10.1111/j.0953-816X.2003.03091.x
extern: 1
intvolume: ' 19'
issue: '3'
month: '02'
page: 552 - 569
publication: European Journal of Neuroscience
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4260'
quality_controlled: 0
status: public
title: GABAergic basket cells expressing cholecystokinin contain vesicular glutamate
transporter type 3 (VGLUT3) in their synaptic terminals in hippocampus and isocortex
of the rat
type: journal_article
volume: 19
year: '2004'
...
---
_id: '2643'
abstract:
- lang: eng
text: Metabotropic γ-aminobutyric acid receptors (GABAB) are involved in pre- and
postsynaptic inhibitory effects upon auditory neurons and have been implicated
in different aspects of acoustic information processing. To understand better
the mechanisms by which GABAB receptors mediate their inhibitory effects, we used
pre-embedding immunocytochemical techniques combined with quantification of immunogold
particles to reveal the precise subcellular distribution of the GABAB1 subunit
in the rat dorsal cochlear nucleus. At the light microscopic level, GABAB1 was
detected in all divisions of the cochlear complex. The most intense immunoreactivity
for GABAB1 was found in the dorsal cochlear nucleus, whereas immunoreactivity
in the anteroventral and posteroventral cochlear nuclei was very low. In the dorsal
cochlear nucleus, a punctate labeling was observed in the superficial (molecular
and fusiform cell) layers. At the electron microscopic level, GABAB1 was found
at both post- and presynaptic locations. Postsynaptically, GABAB1 was localized
mainly in the dendritic spines of presumed fusiform cells. Quantitative immunogold
immunocytochemistry revealed that the highest concentration of GABA B1 in the
plasma membrane was in dendritic spines, followed by dendritic shafts and somata.
Thus, the most intense immunoreactivity for GABAB1 was observed in dendritic spines
with a high density of immunogold particles at extrasynaptic sites, peaking around
300 nm from glutamatergic synapses. This is in contrast to GABAergic synapses,
in which GABAB1 was only occasionally found. Presynaptically, receptor immunoreactivity
was detected primarily in axospinous endings, probably from granule cells, in
both the active zone and extrasynaptic sites. The localization of GABAB1 relative
to synaptic sites in the DCN suggests a role for the receptor in the regulation
of dendritic excitability and excitatory inputs.
author:
- first_name: Rafael
full_name: Luján, Rafael
last_name: Luján
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Ákos
full_name: Kulik, Ákos
last_name: Kulik
- first_name: José
full_name: Juíz, José M
last_name: Juíz
citation:
ama: Luján R, Shigemoto R, Kulik Á, Juíz J. Localization of the GABAB receptor 1a/b
subunit relative to glutamatergic synapses in the dorsal cochlear nucleus of the
rat. Journal of Comparative Neurology. 2004;475(1):36-46. doi:10.1002/cne.20160
apa: Luján, R., Shigemoto, R., Kulik, Á., & Juíz, J. (2004). Localization of
the GABAB receptor 1a/b subunit relative to glutamatergic synapses in the dorsal
cochlear nucleus of the rat. Journal of Comparative Neurology. Wiley-Blackwell.
https://doi.org/10.1002/cne.20160
chicago: Luján, Rafael, Ryuichi Shigemoto, Ákos Kulik, and José Juíz. “Localization
of the GABAB Receptor 1a/b Subunit Relative to Glutamatergic Synapses in the Dorsal
Cochlear Nucleus of the Rat.” Journal of Comparative Neurology. Wiley-Blackwell,
2004. https://doi.org/10.1002/cne.20160.
ieee: R. Luján, R. Shigemoto, Á. Kulik, and J. Juíz, “Localization of the GABAB
receptor 1a/b subunit relative to glutamatergic synapses in the dorsal cochlear
nucleus of the rat,” Journal of Comparative Neurology, vol. 475, no. 1.
Wiley-Blackwell, pp. 36–46, 2004.
ista: Luján R, Shigemoto R, Kulik Á, Juíz J. 2004. Localization of the GABAB receptor
1a/b subunit relative to glutamatergic synapses in the dorsal cochlear nucleus
of the rat. Journal of Comparative Neurology. 475(1), 36–46.
mla: Luján, Rafael, et al. “Localization of the GABAB Receptor 1a/b Subunit Relative
to Glutamatergic Synapses in the Dorsal Cochlear Nucleus of the Rat.” Journal
of Comparative Neurology, vol. 475, no. 1, Wiley-Blackwell, 2004, pp. 36–46,
doi:10.1002/cne.20160.
short: R. Luján, R. Shigemoto, Á. Kulik, J. Juíz, Journal of Comparative Neurology
475 (2004) 36–46.
date_created: 2018-12-11T11:58:50Z
date_published: 2004-07-12T00:00:00Z
date_updated: 2021-01-12T06:58:46Z
day: '12'
doi: 10.1002/cne.20160
extern: 1
intvolume: ' 475'
issue: '1'
month: '07'
page: 36 - 46
publication: Journal of Comparative Neurology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4254'
quality_controlled: 0
status: public
title: Localization of the GABAB receptor 1a/b subunit relative to glutamatergic synapses
in the dorsal cochlear nucleus of the rat
type: journal_article
volume: 475
year: '2004'
...
---
_id: '2638'
abstract:
- lang: eng
text: Among various types of low- and high-threshold calcium channels, the high
voltage-activated P/Q-type channel is the most abundant in the cerebellum. These
P/Q-type channels are involved in the regulation of neurotransmitter release and
in the integration of dendritic inputs. We used an antibody specific for the α1A
subunit of the P/Q-type channel in quantitative pre-embedding immunogold labelling
combined with three-dimensional reconstruction to reveal the subcellular distribution
of pre- and postsynaptic P/Q-type channels in the rat cerebellum. At the light
microscopic level, immunoreactivity for the α1A protein was prevalent in the molecular
layer, whereas immunostaining was moderate in the somata of Purkinje cells and
weak in the granule cell layer. At the electron microscopic level, the most intense
Immunoreactivity for the α1A subunit was found in the presynaptic active zone
of parallel fibre varicosities. The dendritic spines of Purkinje cells were also
strongly labelled with the highest density of immunoparticles detected within
180 nm from the edge of the asymmetrical parallel fibre-Purkinje cell synapses.
By contrast, the immunolabelling was sparse in climbing fibre varicosities and
axon terminals of GABAergic cells, and weak and diffuse in dendritic shafts of
Purkinje cells. The association of the α1A subunit with the glutamatergic parallel
fibre-Purkinje cell synapses suggests that presynaptic channels have a major role
in the mediation of excitatory neurotransmission, whereas postsynaptic channels
are likely to be involved in depolarization-induced generation of local calcium
transients in Purkinje cells.
author:
- first_name: Ákos
full_name: Kulik, Ákos
last_name: Kulik
- first_name: Kazuhiko
full_name: Nakadate, Kazuhiko
last_name: Nakadate
- first_name: Akari
full_name: Hagiwara, Akari
last_name: Hagiwara
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
- first_name: Rafael
full_name: Luján, Rafael
last_name: Luján
- first_name: Hiromitsu
full_name: Saito, Hiromitsu
last_name: Saito
- first_name: Noboru
full_name: Suzuki, Noboru
last_name: Suzuki
- first_name: Akira
full_name: Futatsugi, Akira
last_name: Futatsugi
- first_name: Katsuhiko
full_name: Mikoshiba, Katsuhiko
last_name: Mikoshiba
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Kulik Á, Nakadate K, Hagiwara A, et al. Immunocytochemical localization of
the α1A subunit of the P/Q-type calcium channel in the rat cerebellum. European
Journal of Neuroscience. 2004;19(8):2169-2178. doi:10.1111/j.0953-816X.2004.03319.x
apa: Kulik, Á., Nakadate, K., Hagiwara, A., Fukazawa, Y., Luján, R., Saito, H.,
… Shigemoto, R. (2004). Immunocytochemical localization of the α1A subunit of
the P/Q-type calcium channel in the rat cerebellum. European Journal of Neuroscience.
Wiley-Blackwell. https://doi.org/10.1111/j.0953-816X.2004.03319.x
chicago: Kulik, Ákos, Kazuhiko Nakadate, Akari Hagiwara, Yugo Fukazawa, Rafael Luján,
Hiromitsu Saito, Noboru Suzuki, et al. “Immunocytochemical Localization of the
Α1A Subunit of the P/Q-Type Calcium Channel in the Rat Cerebellum.” European
Journal of Neuroscience. Wiley-Blackwell, 2004. https://doi.org/10.1111/j.0953-816X.2004.03319.x.
ieee: Á. Kulik et al., “Immunocytochemical localization of the α1A subunit
of the P/Q-type calcium channel in the rat cerebellum,” European Journal of
Neuroscience, vol. 19, no. 8. Wiley-Blackwell, pp. 2169–2178, 2004.
ista: Kulik Á, Nakadate K, Hagiwara A, Fukazawa Y, Luján R, Saito H, Suzuki N, Futatsugi
A, Mikoshiba K, Frotscher M, Shigemoto R. 2004. Immunocytochemical localization
of the α1A subunit of the P/Q-type calcium channel in the rat cerebellum. European
Journal of Neuroscience. 19(8), 2169–2178.
mla: Kulik, Ákos, et al. “Immunocytochemical Localization of the Α1A Subunit of
the P/Q-Type Calcium Channel in the Rat Cerebellum.” European Journal of Neuroscience,
vol. 19, no. 8, Wiley-Blackwell, 2004, pp. 2169–78, doi:10.1111/j.0953-816X.2004.03319.x.
short: Á. Kulik, K. Nakadate, A. Hagiwara, Y. Fukazawa, R. Luján, H. Saito, N. Suzuki,
A. Futatsugi, K. Mikoshiba, M. Frotscher, R. Shigemoto, European Journal of Neuroscience
19 (2004) 2169–2178.
date_created: 2018-12-11T11:58:48Z
date_published: 2004-04-01T00:00:00Z
date_updated: 2021-01-12T06:58:44Z
day: '01'
doi: 10.1111/j.0953-816X.2004.03319.x
extern: 1
intvolume: ' 19'
issue: '8'
month: '04'
page: 2169 - 2178
publication: European Journal of Neuroscience
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4259'
quality_controlled: 0
status: public
title: Immunocytochemical localization of the α1A subunit of the P/Q-type calcium
channel in the rat cerebellum
type: journal_article
volume: 19
year: '2004'
...
---
_id: '2640'
abstract:
- lang: eng
text: Hyperpolarization-activated cation currents (Ih) contribute to various physiological
properties and functions in the brain, including neuronal pacemaker activity,
setting of resting membrane potential, and dendritic integration of synaptic input.
Four subunits of the Hyperpolarization-activated and Cyclic-Nucleotide-gated nonselective
cation channels (HCN1-4), which generate Ih, have been cloned recently. To better
understand the functional diversity of Ih in the brain, we examined precise immunohistochemical
localization of four HCNs in the rat brain. Immunoreactivity for HCN1 showed predominantly
cortical distribution, being intense in the neocortex, hippocampus, superior colliculus,
and cerebellum, whereas those for HCN3 and HCN4 exhibited subcortical distribution
mainly concentrated in the hypothalamus and thalamus, respectively. Immunoreactivity
for HCN2 had a widespread distribution throughout the brain. Double immunofluorescence
revealed colocalization of immunoreactivity for HCN1 and HCN2 in distal dendrites
of pyramidal cells in the hippocampus and neocortex. At the electron microscopic
level, immunogold particles for HCN1 and HCN2 had similar distribution patterns
along plasma membrane of dendritic shafts in layer I of the neocortex and stratum
lacunosum moleculare of the hippocampal CA1 area, suggesting that these subunits
could form heteromeric channels. Our results further indicate that HCNs are localized
not only in somato-dendritic compartments but also in axonal compartments of neurons.
Immunoreactivity for HCNs often occurred in preterminal rather than terminal portions
of axons and in specific populations of myelinated axons. We also found HCN2-immunopositive
oligodendrocytes including perineuronal oligodendrocytes throughout the brain.
These results support previous electrophysiological findings and further suggest
unexpected roles of Ih channels in the brain.
author:
- first_name: Takuya
full_name: Notomi, Takuya
last_name: Notomi
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Notomi T, Shigemoto R. Immunohistochemical localization of Ih channel subunits,
HCN1-4, in the rat brain. Journal of Comparative Neurology. 2004;471(3):241-276.
doi:10.1002/cne.11039
apa: Notomi, T., & Shigemoto, R. (2004). Immunohistochemical localization of
Ih channel subunits, HCN1-4, in the rat brain. Journal of Comparative Neurology.
Wiley-Blackwell. https://doi.org/10.1002/cne.11039
chicago: Notomi, Takuya, and Ryuichi Shigemoto. “Immunohistochemical Localization
of Ih Channel Subunits, HCN1-4, in the Rat Brain.” Journal of Comparative Neurology.
Wiley-Blackwell, 2004. https://doi.org/10.1002/cne.11039.
ieee: T. Notomi and R. Shigemoto, “Immunohistochemical localization of Ih channel
subunits, HCN1-4, in the rat brain,” Journal of Comparative Neurology,
vol. 471, no. 3. Wiley-Blackwell, pp. 241–276, 2004.
ista: Notomi T, Shigemoto R. 2004. Immunohistochemical localization of Ih channel
subunits, HCN1-4, in the rat brain. Journal of Comparative Neurology. 471(3),
241–276.
mla: Notomi, Takuya, and Ryuichi Shigemoto. “Immunohistochemical Localization of
Ih Channel Subunits, HCN1-4, in the Rat Brain.” Journal of Comparative Neurology,
vol. 471, no. 3, Wiley-Blackwell, 2004, pp. 241–76, doi:10.1002/cne.11039.
short: T. Notomi, R. Shigemoto, Journal of Comparative Neurology 471 (2004) 241–276.
date_created: 2018-12-11T11:58:49Z
date_published: 2004-04-05T00:00:00Z
date_updated: 2021-01-12T06:58:45Z
day: '05'
doi: 10.1002/cne.11039
extern: 1
intvolume: ' 471'
issue: '3'
month: '04'
page: 241 - 276
publication: Journal of Comparative Neurology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4258'
quality_controlled: 0
status: public
title: Immunohistochemical localization of Ih channel subunits, HCN1-4, in the rat
brain
type: journal_article
volume: 471
year: '2004'
...
---
_id: '2641'
abstract:
- lang: eng
text: The Na+-K+ pump current (Ip) and the h-current (Ih) flowing through hyperpolarization-activated
channels (h-channels) participate in generating the resting potential. These two
currents are thought to be produced independently. We show here bidirectional
interactions between Na+-K+ pumps and h-channels in mesencephalic trigeminal neurons.
Activation of Ih leads to the generation of two types of ouabain-sensitive Ip
with temporal profiles similar to those of instantaneous and slow components of
I h, presumably reflecting Na+ transients in a restricted cellular space. Moreover,
the Ip activated by instantaneous I h can facilitate the subsequent activation
of slow Ih. Such counteractive and cooperative interactions were also disclosed
by replacing extracellular Na+ with Li+, which is permeant through h-channels
but does not stimulate the Na+-K+ pump as strongly as Na+ ions. These observations
indicate that the interactions are bidirectional and mediated by Na+ ions. Also
after substitution of extracellular Na+ with Li+, the tail Ih was reduced markedly
despite an enhancement of Ih itself, attributable to a negative shift of the reversal
potential for I h presumably caused by intracellular accumulation of Li+ ions.
This suggests the presence of a microdomain where the interactions can take place.
Thus, the bidirectional interactions between Na+-K + pumps and h-channels are
likely to be mediated by Na+ microdomain. Consistent with these findings, hyperpolarization-activated
and cyclic nucleotide-modulated subunits (HCN1/2) and the Na+-K + pump α3 isoform
were colocalized in plasma membrane of mesencephalic trigeminal neurons having
numerous spines.
author:
- first_name: Youngnam
full_name: Kang, Youngnam
last_name: Kang
- first_name: Takuya
full_name: Notomi, Takuya
last_name: Notomi
- first_name: Mitsuru
full_name: Saito, Mitsuru
last_name: Saito
- first_name: Wei
full_name: Zhang, Wei
last_name: Zhang
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Kang Y, Notomi T, Saito M, Zhang W, Shigemoto R. Bidirectional interactions
between H-channels and Na+-K + pumps in mesencephalic trigeminal neurons. Journal
of Neuroscience. 2004;24(14):3694-3702. doi:10.1523/JNEUROSCI.5641-03.2004
apa: Kang, Y., Notomi, T., Saito, M., Zhang, W., & Shigemoto, R. (2004). Bidirectional
interactions between H-channels and Na+-K + pumps in mesencephalic trigeminal
neurons. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.5641-03.2004
chicago: Kang, Youngnam, Takuya Notomi, Mitsuru Saito, Wei Zhang, and Ryuichi Shigemoto.
“Bidirectional Interactions between H-Channels and Na+-K + Pumps in Mesencephalic
Trigeminal Neurons.” Journal of Neuroscience. Society for Neuroscience,
2004. https://doi.org/10.1523/JNEUROSCI.5641-03.2004.
ieee: Y. Kang, T. Notomi, M. Saito, W. Zhang, and R. Shigemoto, “Bidirectional interactions
between H-channels and Na+-K + pumps in mesencephalic trigeminal neurons,” Journal
of Neuroscience, vol. 24, no. 14. Society for Neuroscience, pp. 3694–3702,
2004.
ista: Kang Y, Notomi T, Saito M, Zhang W, Shigemoto R. 2004. Bidirectional interactions
between H-channels and Na+-K + pumps in mesencephalic trigeminal neurons. Journal
of Neuroscience. 24(14), 3694–3702.
mla: Kang, Youngnam, et al. “Bidirectional Interactions between H-Channels and Na+-K
+ Pumps in Mesencephalic Trigeminal Neurons.” Journal of Neuroscience,
vol. 24, no. 14, Society for Neuroscience, 2004, pp. 3694–702, doi:10.1523/JNEUROSCI.5641-03.2004.
short: Y. Kang, T. Notomi, M. Saito, W. Zhang, R. Shigemoto, Journal of Neuroscience
24 (2004) 3694–3702.
date_created: 2018-12-11T11:58:49Z
date_published: 2004-04-07T00:00:00Z
date_updated: 2021-01-12T06:58:45Z
day: '07'
doi: 10.1523/JNEUROSCI.5641-03.2004
extern: 1
intvolume: ' 24'
issue: '14'
month: '04'
page: 3694 - 3702
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '4257'
quality_controlled: 0
status: public
title: Bidirectional interactions between H-channels and Na+-K + pumps in mesencephalic
trigeminal neurons
type: journal_article
volume: 24
year: '2004'
...
---
_id: '2636'
author:
- first_name: Akiko
full_name: Momiyama, Akiko
last_name: Momiyama
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Momiyama A, Shigemoto R. Function and distribution of glutamate receptors in
the central synapses. Tanpakushitsu kakusan koso Protein nucleic acid enzyme.
2004;49(3 Suppl):287-294.
apa: Momiyama, A., & Shigemoto, R. (2004). Function and distribution of glutamate
receptors in the central synapses. Tanpakushitsu Kakusan Koso Protein Nucleic
Acid Enzyme. Kyoritsu Shuppan.
chicago: Momiyama, Akiko, and Ryuichi Shigemoto. “Function and Distribution of Glutamate
Receptors in the Central Synapses.” Tanpakushitsu Kakusan Koso Protein Nucleic
Acid Enzyme. Kyoritsu Shuppan, 2004.
ieee: A. Momiyama and R. Shigemoto, “Function and distribution of glutamate receptors
in the central synapses,” Tanpakushitsu kakusan koso Protein nucleic acid enzyme,
vol. 49, no. 3 Suppl. Kyoritsu Shuppan, pp. 287–294, 2004.
ista: Momiyama A, Shigemoto R. 2004. Function and distribution of glutamate receptors
in the central synapses. Tanpakushitsu kakusan koso Protein nucleic acid enzyme.
49(3 Suppl), 287–294.
mla: Momiyama, Akiko, and Ryuichi Shigemoto. “Function and Distribution of Glutamate
Receptors in the Central Synapses.” Tanpakushitsu Kakusan Koso Protein Nucleic
Acid Enzyme, vol. 49, no. 3 Suppl, Kyoritsu Shuppan, 2004, pp. 287–94.
short: A. Momiyama, R. Shigemoto, Tanpakushitsu Kakusan Koso Protein Nucleic Acid
Enzyme 49 (2004) 287–294.
date_created: 2018-12-11T11:58:48Z
date_published: 2004-02-01T00:00:00Z
date_updated: 2020-07-14T12:45:44Z
day: '01'
extern: 1
intvolume: ' 49'
issue: 3 Suppl
month: '02'
page: 287 - 294
publication: Tanpakushitsu kakusan koso Protein nucleic acid enzyme
publication_status: published
publisher: Kyoritsu Shuppan
publist_id: '4261'
quality_controlled: 0
status: public
title: Function and distribution of glutamate receptors in the central synapses
type: review
volume: 49
year: '2004'
...
---
_id: '2645'
abstract:
- lang: eng
text: 'The globus pallidus (GP) is a critical component of the basal ganglia circuitry
controlling motor behavior. Dysregulation of GP activity has been implicated in
a number of psychomotor disorders, including Parkinson''s disease (PD), in which
a cardinal feature of the pathophysiology is an alteration in the pattern and
synchrony of discharge in GP neurons. Yet the determinants of this activity in
GP neurons are poorly understood. To help fill this gap, electrophysiological,
molecular, and computational approaches were used to identify and characterize
GABAergic GP neurons in tissue slices from rodents. In vitro, GABAergic GP neurons
generate a regular, autonomous, single-spike pacemaker activity. Hyperpolarization-activated,
cyclic nucleotide-gated cation (HCN) channels make an important contribution to
this process: their blockade with ZD7288 significantly slowed discharge rate and
decreased its regularity. HCN currents evoked by somatic voltage clamp had fast
and slow components. Single-cell RT-PCR and immunohistochemical approaches revealed
robust expression of HCN2 subunits as well as significant levels of HCN1 subunits
in GABAergic GP neurons. Transient activation of striatal GABAergic input to GP
neurons led to a resetting of rhythmic discharge that was dependent on HCN currents.
Simulations suggested that the ability of transient striatal GABAergic input to
reset pacemaking was dependent on dendritic HCN2/HCN1 channels. Together, these
studies show that HCN channels in GABAergic GP neurons are key determinants of
the regularity and rate of pacemaking as well as striatal resetting of this activity,
implicating HCN channels in the emergence of synchrony in PD.'
author:
- first_name: Savio
full_name: Chan, Savio
last_name: Chan
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Jeff
full_name: Mercer, Jeff N
last_name: Mercer
- first_name: James
full_name: Surmeier, James D
last_name: Surmeier
citation:
ama: Chan S, Shigemoto R, Mercer J, Surmeier J. HCN2 and HCN1 channels govern the
regularity of autonomous pacemaking and synaptic resetting in globus pallidus
neurons. Journal of Neuroscience. 2004;24(44):9921-9932. doi:10.1523/JNEUROSCI.2162-04.2004
apa: Chan, S., Shigemoto, R., Mercer, J., & Surmeier, J. (2004). HCN2 and HCN1
channels govern the regularity of autonomous pacemaking and synaptic resetting
in globus pallidus neurons. Journal of Neuroscience. Society for Neuroscience.
https://doi.org/10.1523/JNEUROSCI.2162-04.2004
chicago: Chan, Savio, Ryuichi Shigemoto, Jeff Mercer, and James Surmeier. “HCN2
and HCN1 Channels Govern the Regularity of Autonomous Pacemaking and Synaptic
Resetting in Globus Pallidus Neurons.” Journal of Neuroscience. Society
for Neuroscience, 2004. https://doi.org/10.1523/JNEUROSCI.2162-04.2004.
ieee: S. Chan, R. Shigemoto, J. Mercer, and J. Surmeier, “HCN2 and HCN1 channels
govern the regularity of autonomous pacemaking and synaptic resetting in globus
pallidus neurons,” Journal of Neuroscience, vol. 24, no. 44. Society for
Neuroscience, pp. 9921–9932, 2004.
ista: Chan S, Shigemoto R, Mercer J, Surmeier J. 2004. HCN2 and HCN1 channels govern
the regularity of autonomous pacemaking and synaptic resetting in globus pallidus
neurons. Journal of Neuroscience. 24(44), 9921–9932.
mla: Chan, Savio, et al. “HCN2 and HCN1 Channels Govern the Regularity of Autonomous
Pacemaking and Synaptic Resetting in Globus Pallidus Neurons.” Journal of Neuroscience,
vol. 24, no. 44, Society for Neuroscience, 2004, pp. 9921–32, doi:10.1523/JNEUROSCI.2162-04.2004.
short: S. Chan, R. Shigemoto, J. Mercer, J. Surmeier, Journal of Neuroscience 24
(2004) 9921–9932.
date_created: 2018-12-11T11:58:51Z
date_published: 2004-11-03T00:00:00Z
date_updated: 2021-01-12T06:58:47Z
day: '03'
doi: 10.1523/JNEUROSCI.2162-04.2004
extern: 1
intvolume: ' 24'
issue: '44'
month: '11'
page: 9921 - 9932
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '4252'
quality_controlled: 0
status: public
title: HCN2 and HCN1 channels govern the regularity of autonomous pacemaking and synaptic
resetting in globus pallidus neurons
type: journal_article
volume: 24
year: '2004'
...
---
_id: '2644'
abstract:
- lang: eng
text: The release of GABA in synapses is modulated by presynaptic metabotropic glutamate
receptors (mGluRs). We tested whether GABA release to identified hippocampal neurons
is influenced by group III mGluR activation using the agonist L-(+)-2-amino-4-phosphonobutyric
acid (L-AP4) on inhibitory postsynaptic currents (IPSCs) evoked in CA1 interneurons
and pyramidal cells. In interneurons, characterized with biocytin and immunolabelling
for somatostatin, evoked IPSCs were depressed by 50 μM L-AP4 (activating mGluR4
and 8) to 68±6% of control, but they were rarely depressed in pyramidal cells
(96±4% of control). At 300-500 μM concentration (activating mGluR4, 7 and 8),
L-AP4 depressed IPSCs in both interneurons (to 70±6%) and pyramidal cells (to
67±4%). The change in trial-to-trial variability and in paired-pulse depression
indicated a presynaptic action. In interneurons, the degree of IPSC depression
was variable (to 9-87%), and a third of IPSCs were not affected by L-AP4. The
L-AP4-evoked IPSC depression was blocked by LY341495. The depression of IPSCs
was similar in O-LM cells and other interneurons. The lack of cell-type selectivity
and the similar efficacy of different concentrations of L-AP4 suggest that several
group III mGluRs are involved in the depression of IPSCs. Electron microscopic
immunocytochemistry confirmed that mGluR4, mGluR7a and mGluR8a occur in the presynaptic
active zone of GABAergic terminals on interneurons, but not on those innervating
pyramidal cells. The high variability of L-AP4-evoked IPSC suppression is in line
with the selective expression of presynaptic mGluRs by several distinct types
of GABAergic neuron innervating each interneuron type.
author:
- first_name: Naoki
full_name: Kogo, Naoki
last_name: Kogo
- first_name: Yannis
full_name: Dalezios, Yannis
last_name: Dalezios
- first_name: Marco
full_name: Capogna,Marco
last_name: Capogna
- first_name: Francesco
full_name: Ferraguti, Francesco
last_name: Ferraguti
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Péter
full_name: Somogyi, Péter
last_name: Somogyi
citation:
ama: Kogo N, Dalezios Y, Capogna M, Ferraguti F, Shigemoto R, Somogyi P. Depression
of GABAergic input to identified hippocampal neurons by group III metabotropic
glutamate receptors in the rat. European Journal of Neuroscience. 2004;19(10):2727-2740.
doi:10.1111/j.0953-816X.2004.03394.x
apa: Kogo, N., Dalezios, Y., Capogna, M., Ferraguti, F., Shigemoto, R., & Somogyi,
P. (2004). Depression of GABAergic input to identified hippocampal neurons by
group III metabotropic glutamate receptors in the rat. European Journal of
Neuroscience. Wiley-Blackwell. https://doi.org/10.1111/j.0953-816X.2004.03394.x
chicago: Kogo, Naoki, Yannis Dalezios, Marco Capogna, Francesco Ferraguti, Ryuichi
Shigemoto, and Péter Somogyi. “Depression of GABAergic Input to Identified Hippocampal
Neurons by Group III Metabotropic Glutamate Receptors in the Rat.” European
Journal of Neuroscience. Wiley-Blackwell, 2004. https://doi.org/10.1111/j.0953-816X.2004.03394.x.
ieee: N. Kogo, Y. Dalezios, M. Capogna, F. Ferraguti, R. Shigemoto, and P. Somogyi,
“Depression of GABAergic input to identified hippocampal neurons by group III
metabotropic glutamate receptors in the rat,” European Journal of Neuroscience,
vol. 19, no. 10. Wiley-Blackwell, pp. 2727–2740, 2004.
ista: Kogo N, Dalezios Y, Capogna M, Ferraguti F, Shigemoto R, Somogyi P. 2004.
Depression of GABAergic input to identified hippocampal neurons by group III metabotropic
glutamate receptors in the rat. European Journal of Neuroscience. 19(10), 2727–2740.
mla: Kogo, Naoki, et al. “Depression of GABAergic Input to Identified Hippocampal
Neurons by Group III Metabotropic Glutamate Receptors in the Rat.” European
Journal of Neuroscience, vol. 19, no. 10, Wiley-Blackwell, 2004, pp. 2727–40,
doi:10.1111/j.0953-816X.2004.03394.x.
short: N. Kogo, Y. Dalezios, M. Capogna, F. Ferraguti, R. Shigemoto, P. Somogyi,
European Journal of Neuroscience 19 (2004) 2727–2740.
date_created: 2018-12-11T11:58:50Z
date_published: 2004-05-01T00:00:00Z
date_updated: 2021-01-12T06:58:46Z
day: '01'
doi: 10.1111/j.0953-816X.2004.03394.x
extern: 1
intvolume: ' 19'
issue: '10'
month: '05'
page: 2727 - 2740
publication: European Journal of Neuroscience
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4255'
quality_controlled: 0
status: public
title: Depression of GABAergic input to identified hippocampal neurons by group III
metabotropic glutamate receptors in the rat
type: journal_article
volume: 19
year: '2004'
...
---
_id: '2646'
abstract:
- lang: eng
text: Metabotropic γ-aminobutyric acid receptors (GABAB) play modulatory roles in
central synaptic transmission and are involved in controlling neuronal migration
during development. We used immunohistochemical methods to elucidate the expression
pattern as well as the cellular and the precise subcellular localization of the
GABAB1a/b and GABAB2 subunits in the rat hippocampus during prenatal and postnatal
development. At the light microscopic level, both GABABB1a/b and GABAB2 were expressed
in the hippocampal primordium from embryonic day E14. During postnatal development,
immunoreactivity for GABAB1a/b and GABAB2 was distributed mainly in pyramidal
cells, with discrete GABABB1a/b-immunopositive cell bodies of interneurons present
throughout the hippocampus. Using double immunofluorescence, we demonstrated that
during the second week of postnatal development, GABAB1a/b but not GABAB2 was
expressed in glial cells throughout the hippocampal formation. At the electron
microscopic level, GABAB1a/b and GABAB2 showed a similar distribution pattern
during postnatal development. Thus, at all ages the two receptor subunits were
located postsynaptically in dendritic spines and shafts at extrasynaptic and perisynaptic
sites in both pyramidal and nonpyramidal cells. We further demonstrated that the
two subunits were localized presynaptically along the extrasynaptic plasma membrane
of axon terminals and along the presynaptic active zone in both asymmetrical and,
to a lesser extent, symmetrical synapses. These results suggest that GABAB receptors
are widely expressed in the hippocampus throughout development and that GABABB1a/b
and GABAB2 form both pre- and postsynaptic receptors.
author:
- first_name: Guillermina
full_name: López-Bendito, Guillermina
last_name: López Bendito
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Ákos
full_name: Kulik, Ákos
last_name: Kulik
- first_name: Imre
full_name: Vida, Imre
last_name: Vida
- first_name: Alfonso
full_name: Fairén, Alfonso
last_name: Fairén
- first_name: Rafael
full_name: Luján, Rafael
last_name: Luján
citation:
ama: López Bendito G, Shigemoto R, Kulik Á, Vida I, Fairén A, Luján R. Distribution
of metabotropic GABA receptor subunits GABAB1a/b and GABAB2 in the rat hippocampus
during prenatal and postnatal development. Hippocampus. 2004;14(7):836-848.
doi:10.1002/hipo.10221
apa: López Bendito, G., Shigemoto, R., Kulik, Á., Vida, I., Fairén, A., & Luján,
R. (2004). Distribution of metabotropic GABA receptor subunits GABAB1a/b and
GABAB2 in the rat hippocampus during prenatal and postnatal development. Hippocampus.
Wiley-Blackwell. https://doi.org/10.1002/hipo.10221
chicago: López Bendito, Guillermina, Ryuichi Shigemoto, Ákos Kulik, Imre Vida, Alfonso
Fairén, and Rafael Luján. “ Distribution of Metabotropic GABA Receptor Subunits
GABAB1a/b and GABAB2 in the Rat Hippocampus during Prenatal and Postnatal Development.”
Hippocampus. Wiley-Blackwell, 2004. https://doi.org/10.1002/hipo.10221.
ieee: G. López Bendito, R. Shigemoto, Á. Kulik, I. Vida, A. Fairén, and R. Luján,
“ Distribution of metabotropic GABA receptor subunits GABAB1a/b and GABAB2 in
the rat hippocampus during prenatal and postnatal development,” Hippocampus,
vol. 14, no. 7. Wiley-Blackwell, pp. 836–848, 2004.
ista: López Bendito G, Shigemoto R, Kulik Á, Vida I, Fairén A, Luján R. 2004. Distribution
of metabotropic GABA receptor subunits GABAB1a/b and GABAB2 in the rat hippocampus
during prenatal and postnatal development. Hippocampus. 14(7), 836–848.
mla: López Bendito, Guillermina, et al. “ Distribution of Metabotropic GABA Receptor
Subunits GABAB1a/b and GABAB2 in the Rat Hippocampus during Prenatal and Postnatal
Development.” Hippocampus, vol. 14, no. 7, Wiley-Blackwell, 2004, pp. 836–48,
doi:10.1002/hipo.10221.
short: G. López Bendito, R. Shigemoto, Á. Kulik, I. Vida, A. Fairén, R. Luján, Hippocampus
14 (2004) 836–848.
date_created: 2018-12-11T11:58:51Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T06:58:47Z
day: '01'
doi: 10.1002/hipo.10221
extern: 1
intvolume: ' 14'
issue: '7'
month: '01'
page: 836 - 848
publication: Hippocampus
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4251'
quality_controlled: 0
status: public
title: ' Distribution of metabotropic GABA receptor subunits GABAB1a/b and GABAB2
in the rat hippocampus during prenatal and postnatal development'
type: journal_article
volume: 14
year: '2004'
...
---
_id: '2706'
abstract:
- lang: eng
text: The Pauli operator describes the energy of a nonrelativistic quantum particle
with spin in a magnetic field and an external potential. Bounds on the sum of
the negative eigenvalues are called magnetic Lieb-Thirring (MLT) inequalities.
The purpose of this paper is twofold. First, we prove a new MLT inequality in
a simple way. Second, we give a short summary of our recent proof of a more refined
MLT inequality(8) and we explain the differences between the two results and methods.
The main feature of both estimates, compared to earlier results, is that in the
large field regime they grow with the optimal (first) power of the strength of
the magnetic field. As a byproduct of the method, we also obtain optimal upper
bounds on the pointwise density of zero energy eigenfunctions of the Dirac operator.
author:
- first_name: László
full_name: László Erdös
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Jan
full_name: Solovej, Jan P
last_name: Solovej
citation:
ama: Erdös L, Solovej J. Magnetic Lieb-Thirring inequalities with optimal dependence
on the field strength. Journal of Statistical Physics. 2004;116(1-4):475-506.
doi:10.1023/B:JOSS.0000037216.45270.1d
apa: Erdös, L., & Solovej, J. (2004). Magnetic Lieb-Thirring inequalities with
optimal dependence on the field strength. Journal of Statistical Physics.
Springer. https://doi.org/10.1023/B:JOSS.0000037216.45270.1d
chicago: Erdös, László, and Jan Solovej. “Magnetic Lieb-Thirring Inequalities with
Optimal Dependence on the Field Strength.” Journal of Statistical Physics.
Springer, 2004. https://doi.org/10.1023/B:JOSS.0000037216.45270.1d.
ieee: L. Erdös and J. Solovej, “Magnetic Lieb-Thirring inequalities with optimal
dependence on the field strength,” Journal of Statistical Physics, vol.
116, no. 1–4. Springer, pp. 475–506, 2004.
ista: Erdös L, Solovej J. 2004. Magnetic Lieb-Thirring inequalities with optimal
dependence on the field strength. Journal of Statistical Physics. 116(1–4), 475–506.
mla: Erdös, László, and Jan Solovej. “Magnetic Lieb-Thirring Inequalities with Optimal
Dependence on the Field Strength.” Journal of Statistical Physics, vol.
116, no. 1–4, Springer, 2004, pp. 475–506, doi:10.1023/B:JOSS.0000037216.45270.1d.
short: L. Erdös, J. Solovej, Journal of Statistical Physics 116 (2004) 475–506.
date_created: 2018-12-11T11:59:10Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2021-01-12T06:59:10Z
day: '01'
doi: 10.1023/B:JOSS.0000037216.45270.1d
extern: 1
intvolume: ' 116'
issue: 1-4
month: '08'
page: 475 - 506
publication: Journal of Statistical Physics
publication_status: published
publisher: Springer
publist_id: '4190'
quality_controlled: 0
status: public
title: Magnetic Lieb-Thirring inequalities with optimal dependence on the field strength
type: journal_article
volume: 116
year: '2004'
...
---
_id: '2707'
abstract:
- lang: eng
text: We give a nonrigorous derivation of the nonlinear Boltzmann equation from
the Schrödinger evolution of interacting fermions. The argument is based mainly
on the assumption that a quasifree initial state satisfies a property called restricted
quasifreeness in the weak coupling limit at any later time. By definition, a state
is called restricted quasifree if the four-point and the eight-point functions
of the state factorize in the same manner as in a quasifree state.
author:
- first_name: László
full_name: László Erdös
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Manfred
full_name: Salmhofer, Manfred
last_name: Salmhofer
- first_name: Horng
full_name: Yau, Horng-Tzer
last_name: Yau
citation:
ama: Erdös L, Salmhofer M, Yau H. On the quantum Boltzmann equation. Journal
of Statistical Physics. 2004;116(1-4):367-380. doi:10.1023/B:JOSS.0000037224.56191.ed
apa: Erdös, L., Salmhofer, M., & Yau, H. (2004). On the quantum Boltzmann equation.
Journal of Statistical Physics. Springer. https://doi.org/10.1023/B:JOSS.0000037224.56191.ed
chicago: Erdös, László, Manfred Salmhofer, and Horng Yau. “On the Quantum Boltzmann
Equation.” Journal of Statistical Physics. Springer, 2004. https://doi.org/10.1023/B:JOSS.0000037224.56191.ed.
ieee: L. Erdös, M. Salmhofer, and H. Yau, “On the quantum Boltzmann equation,” Journal
of Statistical Physics, vol. 116, no. 1–4. Springer, pp. 367–380, 2004.
ista: Erdös L, Salmhofer M, Yau H. 2004. On the quantum Boltzmann equation. Journal
of Statistical Physics. 116(1–4), 367–380.
mla: Erdös, László, et al. “On the Quantum Boltzmann Equation.” Journal of Statistical
Physics, vol. 116, no. 1–4, Springer, 2004, pp. 367–80, doi:10.1023/B:JOSS.0000037224.56191.ed.
short: L. Erdös, M. Salmhofer, H. Yau, Journal of Statistical Physics 116 (2004)
367–380.
date_created: 2018-12-11T11:59:11Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2021-01-12T06:59:11Z
day: '01'
doi: 10.1023/B:JOSS.0000037224.56191.ed
extern: 1
intvolume: ' 116'
issue: 1-4
month: '08'
page: 367 - 380
publication: Journal of Statistical Physics
publication_status: published
publisher: Springer
publist_id: '4189'
quality_controlled: 0
status: public
title: On the quantum Boltzmann equation
type: journal_article
volume: 116
year: '2004'
...
---
_id: '2741'
abstract:
- lang: eng
text: 'The Pauli operator describes the energy of a nonrelativistic quantum particle
with spin 1/2 in a magnetic field and an external potential. A new Lieb-Thirring
type inequality on the sum of the negative eigenvalues is presented. The main
feature compared to earlier results is that in the large field regime the present
estimate grows with the optimal (first) power of the strength of the magnetic
field. As a byproduct of the method, we also obtain an optimal upper bound on
the pointwise density of zero energy eigenfunctions of the Dirac operator. The
main technical tools are: (i) a new localization scheme for the square of the
resolvent of a general class of second order elliptic operators; (ii) a geometric
construction of a Dirac operator with a constant magnetic field that approximates
the original Dirac operator in a tubular neighborhood of a fixed field line. The
errors may depend on the regularity of the magnetic field but they are uniform
in the field strength.'
author:
- first_name: László
full_name: László Erdös
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Jan
full_name: Solovej, Jan P
last_name: Solovej
citation:
ama: Erdös L, Solovej J. Uniform Lieb-Thirring inequality for the three-dimensional
Pauli operator with a strong non-homogeneous magnetic field. Annales Henri
Poincare. 2004;5(4):671-741. doi:10.1007/s00023-004-0180-x
apa: Erdös, L., & Solovej, J. (2004). Uniform Lieb-Thirring inequality for the
three-dimensional Pauli operator with a strong non-homogeneous magnetic field.
Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-004-0180-x
chicago: Erdös, László, and Jan Solovej. “Uniform Lieb-Thirring Inequality for the
Three-Dimensional Pauli Operator with a Strong Non-Homogeneous Magnetic Field.”
Annales Henri Poincare. Birkhäuser, 2004. https://doi.org/10.1007/s00023-004-0180-x.
ieee: L. Erdös and J. Solovej, “Uniform Lieb-Thirring inequality for the three-dimensional
Pauli operator with a strong non-homogeneous magnetic field,” Annales Henri
Poincare, vol. 5, no. 4. Birkhäuser, pp. 671–741, 2004.
ista: Erdös L, Solovej J. 2004. Uniform Lieb-Thirring inequality for the three-dimensional
Pauli operator with a strong non-homogeneous magnetic field. Annales Henri Poincare.
5(4), 671–741.
mla: Erdös, László, and Jan Solovej. “Uniform Lieb-Thirring Inequality for the Three-Dimensional
Pauli Operator with a Strong Non-Homogeneous Magnetic Field.” Annales Henri
Poincare, vol. 5, no. 4, Birkhäuser, 2004, pp. 671–741, doi:10.1007/s00023-004-0180-x.
short: L. Erdös, J. Solovej, Annales Henri Poincare 5 (2004) 671–741.
date_created: 2018-12-11T11:59:21Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2021-01-12T06:59:24Z
day: '01'
doi: 10.1007/s00023-004-0180-x
extern: 1
intvolume: ' 5'
issue: '4'
month: '08'
page: 671 - 741
publication: Annales Henri Poincare
publication_status: published
publisher: Birkhäuser
publist_id: '4151'
quality_controlled: 0
status: public
title: Uniform Lieb-Thirring inequality for the three-dimensional Pauli operator with
a strong non-homogeneous magnetic field
type: journal_article
volume: 5
year: '2004'
...
---
_id: '2742'
abstract:
- lang: eng
text: We consider a system of N weakly interacting fermions with a real analytic
pair interaction. We prove that for a general class of initial data there exists
a fixed time T such that the difference between the one particle density matrix
of this system and the solution of the nonlinear Hartree equation is of order
N−1 for any time t⩽T.
author:
- first_name: Alexander
full_name: Elgart, Alexander
last_name: Elgart
- first_name: László
full_name: László Erdös
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
- first_name: Horng
full_name: Yau, Horng-Tzer
last_name: Yau
citation:
ama: Elgart A, Erdös L, Schlein B, Yau H. Nonlinear Hartree equation as the mean
field limit of weakly coupled fermions. Journal de Mathématiques Pures et Appliquées.
2004;83(10):1241-1273. doi:10.1016/j.matpur.2004.03.006
apa: Elgart, A., Erdös, L., Schlein, B., & Yau, H. (2004). Nonlinear Hartree
equation as the mean field limit of weakly coupled fermions. Journal de Mathématiques
Pures et Appliquées. Elsevier. https://doi.org/10.1016/j.matpur.2004.03.006
chicago: Elgart, Alexander, László Erdös, Benjamin Schlein, and Horng Yau. “Nonlinear
Hartree Equation as the Mean Field Limit of Weakly Coupled Fermions.” Journal
de Mathématiques Pures et Appliquées. Elsevier, 2004. https://doi.org/10.1016/j.matpur.2004.03.006.
ieee: A. Elgart, L. Erdös, B. Schlein, and H. Yau, “Nonlinear Hartree equation as
the mean field limit of weakly coupled fermions,” Journal de Mathématiques
Pures et Appliquées, vol. 83, no. 10. Elsevier, pp. 1241–1273, 2004.
ista: Elgart A, Erdös L, Schlein B, Yau H. 2004. Nonlinear Hartree equation as the
mean field limit of weakly coupled fermions. Journal de Mathématiques Pures et
Appliquées. 83(10), 1241–1273.
mla: Elgart, Alexander, et al. “Nonlinear Hartree Equation as the Mean Field Limit
of Weakly Coupled Fermions.” Journal de Mathématiques Pures et Appliquées,
vol. 83, no. 10, Elsevier, 2004, pp. 1241–73, doi:10.1016/j.matpur.2004.03.006.
short: A. Elgart, L. Erdös, B. Schlein, H. Yau, Journal de Mathématiques Pures et
Appliquées 83 (2004) 1241–1273.
date_created: 2018-12-11T11:59:22Z
date_published: 2004-10-01T00:00:00Z
date_updated: 2021-01-12T06:59:24Z
day: '01'
doi: 10.1016/j.matpur.2004.03.006
extern: 1
intvolume: ' 83'
issue: '10'
month: '10'
page: 1241 - 1273
publication: Journal de Mathématiques Pures et Appliquées
publication_status: published
publisher: Elsevier
publist_id: '4150'
quality_controlled: 0
status: public
title: Nonlinear Hartree equation as the mean field limit of weakly coupled fermions
type: journal_article
volume: 83
year: '2004'
...
---
_id: '2787'
abstract:
- lang: eng
text: The results of experimental and numerical investigations of the onset of oscillatory
convection in a sidewall heated rectangular cavity of molten gallium are reported.
Detailed comparisons are made between experimental observations and calculations
from numerical simulations of a three-dimensional Boussinesq model. The onset
of time-dependence takes place through supercritical Hopf bifurcations and the
loci of critical points in the (Gr, Pr)-plane are qualitatively similar with excellent
agreement between the frequencies of the oscillatory motion. This provides a severe
test of the control of the experiment since the mode of oscillation is extremely
sensitive to imperfections. Detailed numerical investigations reveal that there
are a pair of Hopf bifurcations which exist on two asymmetric states which themselves
arise at a subcritical pitchfork from the symmetric state. There is no evidence
for this in the experiment and this qualitative difference is attributed to non-Boussinesq
perturbations which increase with Gr. However, the antisymmetric spatial structure
of the oscillatory state is robust and is present in both the experiment and the
numerical model. Moreover, the detailed analysis of the numerical results reveals
the origins of the oscillatory instability.
author:
- first_name: Björn
full_name: Björn Hof
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Anne
full_name: Juel, Anne
last_name: Juel
- first_name: Li
full_name: Zhao, Li
last_name: Zhao
- first_name: Daniel
full_name: 'Henry, Daniel '
last_name: Henry
- first_name: Hamda
full_name: Ben Hadid, Hamda
last_name: Ben Hadid
- first_name: Tom
full_name: Mullin, Tom P
last_name: Mullin
citation:
ama: Hof B, Juel A, Zhao L, Henry D, Ben Hadid H, Mullin T. On the onset of oscillatory
convection in molten gallium. Journal of Fluid Mechanics. 2004;515:391-413.
doi:10.1017/S0022112004000527
apa: Hof, B., Juel, A., Zhao, L., Henry, D., Ben Hadid, H., & Mullin, T. (2004).
On the onset of oscillatory convection in molten gallium. Journal of Fluid
Mechanics. Cambridge University Press. https://doi.org/10.1017/S0022112004000527
chicago: Hof, Björn, Anne Juel, Li Zhao, Daniel Henry, Hamda Ben Hadid, and Tom
Mullin. “On the Onset of Oscillatory Convection in Molten Gallium.” Journal
of Fluid Mechanics. Cambridge University Press, 2004. https://doi.org/10.1017/S0022112004000527.
ieee: B. Hof, A. Juel, L. Zhao, D. Henry, H. Ben Hadid, and T. Mullin, “On the onset
of oscillatory convection in molten gallium,” Journal of Fluid Mechanics,
vol. 515. Cambridge University Press, pp. 391–413, 2004.
ista: Hof B, Juel A, Zhao L, Henry D, Ben Hadid H, Mullin T. 2004. On the onset
of oscillatory convection in molten gallium. Journal of Fluid Mechanics. 515,
391–413.
mla: Hof, Björn, et al. “On the Onset of Oscillatory Convection in Molten Gallium.”
Journal of Fluid Mechanics, vol. 515, Cambridge University Press, 2004,
pp. 391–413, doi:10.1017/S0022112004000527.
short: B. Hof, A. Juel, L. Zhao, D. Henry, H. Ben Hadid, T. Mullin, Journal of Fluid
Mechanics 515 (2004) 391–413.
date_created: 2018-12-11T11:59:36Z
date_published: 2004-09-25T00:00:00Z
date_updated: 2021-01-12T06:59:43Z
day: '25'
doi: 10.1017/S0022112004000527
extern: 1
intvolume: ' 515'
month: '09'
page: 391 - 413
publication: Journal of Fluid Mechanics
publication_status: published
publisher: Cambridge University Press
publist_id: '4102'
quality_controlled: 0
status: public
title: On the onset of oscillatory convection in molten gallium
type: journal_article
volume: 515
year: '2004'
...
---
_id: '2786'
abstract:
- lang: eng
text: Transition to turbulence in pipe flow is one of the most fundamental and longest-
standing problems in fluid dynamics. Stability theory suggests that the flow remains
laminar for all flow rates, but in practice pipe flow becomes turbulent even at
moderate speeds. This transition drastically affects the transport efficiency
of mass, momentum, and heat. On the basis of the recent discovery of unstable
traveling waves in computational studies of the Navier-Stokes equations and ideas
from dynamical systems theory, a model for the transition process has been suggested.
We report experimental observation of these traveling waves in pipe flow, confirming
the proposed transition scenario and suggesting that the dynamics associated with
these unstable states may indeed capture the nature of fluid turbulence.
author:
- first_name: Björn
full_name: Björn Hof
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Casimir
full_name: van Doorne, Casimir W
last_name: Van Doorne
- first_name: Jerry
full_name: Westerweel, Jerry
last_name: Westerweel
- first_name: Frans
full_name: Nieuwstadt, Frans T
last_name: Nieuwstadt
- first_name: Holger
full_name: Faisst, Holger
last_name: Faisst
- first_name: Bruno
full_name: Eckhardt, Bruno
last_name: Eckhardt
- first_name: Håkan
full_name: Wedin, Håkan
last_name: Wedin
- first_name: Richard
full_name: Kersweli, Richard R
last_name: Kersweli
- first_name: Fabian
full_name: Waleffe, Fabian
last_name: Waleffe
citation:
ama: Hof B, Van Doorne C, Westerweel J, et al. Experimental observation of nonlinear
traveling waves in turbulent pipe flow. Science. 2004;305(5690):1594-1598.
doi:10.1126/science.1100393
apa: Hof, B., Van Doorne, C., Westerweel, J., Nieuwstadt, F., Faisst, H., Eckhardt,
B., … Waleffe, F. (2004). Experimental observation of nonlinear traveling waves
in turbulent pipe flow. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1100393
chicago: Hof, Björn, Casimir Van Doorne, Jerry Westerweel, Frans Nieuwstadt, Holger
Faisst, Bruno Eckhardt, Håkan Wedin, Richard Kersweli, and Fabian Waleffe. “Experimental
Observation of Nonlinear Traveling Waves in Turbulent Pipe Flow.” Science.
American Association for the Advancement of Science, 2004. https://doi.org/10.1126/science.1100393.
ieee: B. Hof et al., “Experimental observation of nonlinear traveling waves
in turbulent pipe flow,” Science, vol. 305, no. 5690. American Association
for the Advancement of Science, pp. 1594–1598, 2004.
ista: Hof B, Van Doorne C, Westerweel J, Nieuwstadt F, Faisst H, Eckhardt B, Wedin
H, Kersweli R, Waleffe F. 2004. Experimental observation of nonlinear traveling
waves in turbulent pipe flow. Science. 305(5690), 1594–1598.
mla: Hof, Björn, et al. “Experimental Observation of Nonlinear Traveling Waves in
Turbulent Pipe Flow.” Science, vol. 305, no. 5690, American Association
for the Advancement of Science, 2004, pp. 1594–98, doi:10.1126/science.1100393.
short: B. Hof, C. Van Doorne, J. Westerweel, F. Nieuwstadt, H. Faisst, B. Eckhardt,
H. Wedin, R. Kersweli, F. Waleffe, Science 305 (2004) 1594–1598.
date_created: 2018-12-11T11:59:35Z
date_published: 2004-09-10T00:00:00Z
date_updated: 2021-01-12T06:59:42Z
day: '10'
doi: 10.1126/science.1100393
extern: 1
intvolume: ' 305'
issue: '5690'
month: '09'
page: 1594 - 1598
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '4103'
quality_controlled: 0
status: public
title: Experimental observation of nonlinear traveling waves in turbulent pipe flow
type: journal_article
volume: 305
year: '2004'
...
---
_id: '2998'
abstract:
- lang: eng
text: The packaging of the genomic DNA into chromatin in the cell nucleus requires
machineries that facilitate DNA-dependent processes such as transcription in the
presence of repressive chromatin structures. Using co-immunoprecipitation we have
identified in Arabidopsis thaliana cells the FAcilitates Chromatin Transcription
(FACT) complex, consisting of the 120-kDa Spt16 and the 71-kDa SSRP1 proteins.
Indirect immunofluorecence analyses revealed that both FACT subunits co-localize
to nuclei of the majority of cell types in embryos, shoots and roots, whereas
FACT is not present in terminally differentiated cells such as mature trichoblasts
or cells of the root cap. In the nucleus, Spt16 and SSRP1 are found in the cytologically
defined euchromatin of interphase cells independent of the status of DNA replication,
but the proteins are not associated with heterochromatic chromocentres and condensed
mitotic chromosomes. FACT can be detected by chromatin immunoprecipitation over
the entire transcribed region (5′-UTR, coding sequence, 3′-UTR) of actively transcribed
genes, whereas it does not occur at transcriptionally inactive heterochromatic
regions and intergenic regions. FACT localizes to inducible genes only after induction
of transcription, and the association of the complex with the genes correlates
with the level of transcription. Collectively, these results indicate that FACT
assists transcription elongation through plant chromatin.
author:
- first_name: Meg
full_name: Duroux, Meg
last_name: Duroux
- first_name: Andreas
full_name: Houben, Andreas
last_name: Houben
- first_name: Kamil
full_name: Růžička, Kamil
last_name: Růžička
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Klaus
full_name: Grasser, Klaus D
last_name: Grasser
citation:
ama: Duroux M, Houben A, Růžička K, Friml J, Grasser K. The chromatin remodelling
complex FACT associates with actively transcribed regions of the Arabidopsis genome.
Plant Journal. 2004;40(5):660-671. doi:10.1111/j.1365-313X.2004.02242.x
apa: Duroux, M., Houben, A., Růžička, K., Friml, J., & Grasser, K. (2004). The
chromatin remodelling complex FACT associates with actively transcribed regions
of the Arabidopsis genome. Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/j.1365-313X.2004.02242.x
chicago: Duroux, Meg, Andreas Houben, Kamil Růžička, Jiří Friml, and Klaus Grasser.
“The Chromatin Remodelling Complex FACT Associates with Actively Transcribed Regions
of the Arabidopsis Genome.” Plant Journal. Wiley-Blackwell, 2004. https://doi.org/10.1111/j.1365-313X.2004.02242.x.
ieee: M. Duroux, A. Houben, K. Růžička, J. Friml, and K. Grasser, “The chromatin
remodelling complex FACT associates with actively transcribed regions of the Arabidopsis
genome,” Plant Journal, vol. 40, no. 5. Wiley-Blackwell, pp. 660–671, 2004.
ista: Duroux M, Houben A, Růžička K, Friml J, Grasser K. 2004. The chromatin remodelling
complex FACT associates with actively transcribed regions of the Arabidopsis genome.
Plant Journal. 40(5), 660–671.
mla: Duroux, Meg, et al. “The Chromatin Remodelling Complex FACT Associates with
Actively Transcribed Regions of the Arabidopsis Genome.” Plant Journal,
vol. 40, no. 5, Wiley-Blackwell, 2004, pp. 660–71, doi:10.1111/j.1365-313X.2004.02242.x.
short: M. Duroux, A. Houben, K. Růžička, J. Friml, K. Grasser, Plant Journal 40
(2004) 660–671.
date_created: 2018-12-11T12:00:47Z
date_published: 2004-12-01T00:00:00Z
date_updated: 2021-01-12T07:40:20Z
day: '01'
doi: 10.1111/j.1365-313X.2004.02242.x
extern: 1
intvolume: ' 40'
issue: '5'
month: '12'
page: 660 - 671
publication: Plant Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3703'
quality_controlled: 0
status: public
title: The chromatin remodelling complex FACT associates with actively transcribed
regions of the Arabidopsis genome
type: journal_article
volume: 40
year: '2004'
...
---
_id: '2997'
abstract:
- lang: eng
text: Polar transport-dependent local accumulation of auxin provides positional
cues for multiple plant patterning processes. This directional auxin flow depends
on the polar subcellular localization of the PIN auxin efflux regulators. Overexpression
of the PINOID protein kinase induces a basal-to-apical shift in PIN localization,
resulting in the loss of auxin gradients and strong defects in embryo and seedling
roots. Conversely, pid loss of function induces an apical-to-basal shift in PIN1
polar targeting at the inflorescence apex, accompanied by defective organogenesis.
Our results show that a PINOID-dependent binary switch controls PIN polarity and
mediates changes in auxin flow to create local gradients for patterning processes.
author:
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Xiong
full_name: Yang, Xiong
last_name: Yang
- first_name: Marta
full_name: Michniewicz, Marta
last_name: Michniewicz
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Ab
full_name: Quint, Ab
last_name: Quint
- first_name: Olaf
full_name: Tietz, Olaf
last_name: Tietz
- first_name: René
full_name: Benjamins, René
last_name: Benjamins
- first_name: Pieter
full_name: Ouwerkerk, Pieter B
last_name: Ouwerkerk
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Göran
full_name: Sandberg, Göran
last_name: Sandberg
- first_name: Paul
full_name: Hooykaas, Paul J
last_name: Hooykaas
- first_name: Klaus
full_name: Palme, Klaus
last_name: Palme
- first_name: Remko
full_name: Offringa, Remko
last_name: Offringa
citation:
ama: Friml J, Yang X, Michniewicz M, et al. A PINOID-dependent binary switch in
apical-basal PIN polar targeting directs auxin efflux. Science. 2004;306(5697):862-865.
doi:10.1126/science.1100618
apa: Friml, J., Yang, X., Michniewicz, M., Weijers, D., Quint, A., Tietz, O., …
Offringa, R. (2004). A PINOID-dependent binary switch in apical-basal PIN polar
targeting directs auxin efflux. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1100618
chicago: Friml, Jiří, Xiong Yang, Marta Michniewicz, Dolf Weijers, Ab Quint, Olaf
Tietz, René Benjamins, et al. “A PINOID-Dependent Binary Switch in Apical-Basal
PIN Polar Targeting Directs Auxin Efflux.” Science. American Association
for the Advancement of Science, 2004. https://doi.org/10.1126/science.1100618.
ieee: J. Friml et al., “A PINOID-dependent binary switch in apical-basal
PIN polar targeting directs auxin efflux,” Science, vol. 306, no. 5697.
American Association for the Advancement of Science, pp. 862–865, 2004.
ista: Friml J, Yang X, Michniewicz M, Weijers D, Quint A, Tietz O, Benjamins R,
Ouwerkerk P, Ljung K, Sandberg G, Hooykaas P, Palme K, Offringa R. 2004. A PINOID-dependent
binary switch in apical-basal PIN polar targeting directs auxin efflux. Science.
306(5697), 862–865.
mla: Friml, Jiří, et al. “A PINOID-Dependent Binary Switch in Apical-Basal PIN Polar
Targeting Directs Auxin Efflux.” Science, vol. 306, no. 5697, American
Association for the Advancement of Science, 2004, pp. 862–65, doi:10.1126/science.1100618.
short: J. Friml, X. Yang, M. Michniewicz, D. Weijers, A. Quint, O. Tietz, R. Benjamins,
P. Ouwerkerk, K. Ljung, G. Sandberg, P. Hooykaas, K. Palme, R. Offringa, Science
306 (2004) 862–865.
date_created: 2018-12-11T12:00:46Z
date_published: 2004-10-29T00:00:00Z
date_updated: 2021-01-12T07:40:20Z
day: '29'
doi: 10.1126/science.1100618
extern: 1
intvolume: ' 306'
issue: '5697'
month: '10'
page: 862 - 865
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '3705'
quality_controlled: 0
status: public
title: A PINOID-dependent binary switch in apical-basal PIN polar targeting directs
auxin efflux
type: journal_article
volume: 306
year: '2004'
...
---
_id: '2999'
abstract:
- lang: eng
text: Embryogenesis of flowering plants establishes a basic body plan with apical-basal,
radial and bilateral patterns from the single-celled zygote. Arabidopsis embryogenesis
exhibits a nearly invariant cell division pattern and therefore is an ideal system
for studies of early plant development. However, plant embryos are difficult to
access for experimental manipulation, as they develop deeply inside maternal tissues.
Here we present a method for the culture of zygotic Arabidopsis embryos in vitro.
The technique omits excision of the embryo by culturing the entire ovule, thus
greatly facilitating the time and effort involved. It enables external manipulation
of embryo development and culture from the earliest developmental stages up to
maturity. Administration of various chemical treatments as well as the use of
different molecular markers is demonstrated together with standard techniques
for visualizing gene expression and protein localization in in vitro cultivated
embryos. The presented set of techniques allows for so far unavailable molecular
physiology approaches in the study of early plant development.
author:
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Sauer M, Friml J. In vitro culture of Arabidopsis embryos within their ovules.
Plant Journal. 2004;40(5):835-843. doi:10.1111/j.1365-313X.2004.02248.x
apa: Sauer, M., & Friml, J. (2004). In vitro culture of Arabidopsis embryos
within their ovules. Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/j.1365-313X.2004.02248.x
chicago: Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos
within Their Ovules.” Plant Journal. Wiley-Blackwell, 2004. https://doi.org/10.1111/j.1365-313X.2004.02248.x.
ieee: M. Sauer and J. Friml, “In vitro culture of Arabidopsis embryos within their
ovules,” Plant Journal, vol. 40, no. 5. Wiley-Blackwell, pp. 835–843, 2004.
ista: Sauer M, Friml J. 2004. In vitro culture of Arabidopsis embryos within their
ovules. Plant Journal. 40(5), 835–843.
mla: Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos within
Their Ovules.” Plant Journal, vol. 40, no. 5, Wiley-Blackwell, 2004, pp.
835–43, doi:10.1111/j.1365-313X.2004.02248.x.
short: M. Sauer, J. Friml, Plant Journal 40 (2004) 835–843.
date_created: 2018-12-11T12:00:47Z
date_published: 2004-12-01T00:00:00Z
date_updated: 2021-01-12T07:40:20Z
day: '01'
doi: 10.1111/j.1365-313X.2004.02248.x
extern: 1
intvolume: ' 40'
issue: '5'
month: '12'
page: 835 - 843
publication: Plant Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3704'
quality_controlled: 0
status: public
title: In vitro culture of Arabidopsis embryos within their ovules
type: journal_article
volume: 40
year: '2004'
...
---
_id: '3208'
abstract:
- lang: eng
text: |-
A new technique for proving the adaptive indistinguishability of two systems, each composed of some component systems, is presented, using only the fact that corresponding component systems are non-adaptively indistinguishable. The main tool is the definition of a special monotone condition for a random system F, relative to another random system G, whose probability of occurring for a given distinguisher D is closely related to the distinguishing advantage ε of D for F and G, namely it is lower and upper bounded by ε and (1+ln1), respectively.
A concrete instantiation of this result shows that the cascade of two random permutations (with the second one inverted) is indistinguishable from a uniform random permutation by adaptive distinguishers which may query the system from both sides, assuming the components’ security only against non-adaptive one-sided distinguishers.
As applications we provide some results in various fields as almost k-wise independent probability spaces, decorrelation theory and computational indistinguishability (i.e., pseudo-randomness).
alternative_title:
- LNCS
author:
- first_name: Ueli
full_name: Maurer, Ueli M
last_name: Maurer
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Maurer U, Pietrzak KZ. Composition of random systems: When two weak make one
strong. In: Vol 2951. Springer; 2004:410-427. doi:10.1007/978-3-540-24638-1_23'
apa: 'Maurer, U., & Pietrzak, K. Z. (2004). Composition of random systems: When
two weak make one strong (Vol. 2951, pp. 410–427). Presented at the TCC: Theory
of Cryptography Conference, Springer. https://doi.org/10.1007/978-3-540-24638-1_23'
chicago: 'Maurer, Ueli, and Krzysztof Z Pietrzak. “Composition of Random Systems:
When Two Weak Make One Strong,” 2951:410–27. Springer, 2004. https://doi.org/10.1007/978-3-540-24638-1_23.'
ieee: 'U. Maurer and K. Z. Pietrzak, “Composition of random systems: When two weak
make one strong,” presented at the TCC: Theory of Cryptography Conference, 2004,
vol. 2951, pp. 410–427.'
ista: 'Maurer U, Pietrzak KZ. 2004. Composition of random systems: When two weak
make one strong. TCC: Theory of Cryptography Conference, LNCS, vol. 2951, 410–427.'
mla: 'Maurer, Ueli, and Krzysztof Z. Pietrzak. Composition of Random Systems:
When Two Weak Make One Strong. Vol. 2951, Springer, 2004, pp. 410–27, doi:10.1007/978-3-540-24638-1_23.'
short: U. Maurer, K.Z. Pietrzak, in:, Springer, 2004, pp. 410–427.
conference:
name: 'TCC: Theory of Cryptography Conference'
date_created: 2018-12-11T12:02:01Z
date_published: 2004-03-19T00:00:00Z
date_updated: 2021-01-12T07:41:48Z
day: '19'
doi: 10.1007/978-3-540-24638-1_23
extern: 1
intvolume: ' 2951'
month: '03'
page: 410 - 427
publication_status: published
publisher: Springer
publist_id: '3471'
quality_controlled: 0
status: public
title: 'Composition of random systems: When two weak make one strong'
type: conference
volume: 2951
year: '2004'
...
---
_id: '3587'
alternative_title:
- Molecular Aspects of Fish and Marine Biology
article_processing_charge: No
author:
- first_name: Florian
full_name: Ulrich, Florian
last_name: Ulrich
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: 'Ulrich F, Heisenberg C-PJ. Gastrulation in zebrafish. In: Korzh V, Gong Z,
eds. Fish Development and Genetics : The Zebrafish and Medaka Models. Vol
2. World Scientific Publishing; 2004:39-86.'
apa: 'Ulrich, F., & Heisenberg, C.-P. J. (2004). Gastrulation in zebrafish.
In V. Korzh & Z. Gong (Eds.), Fish development and genetics : the zebrafish
and medaka models (Vol. 2, pp. 39–86). World Scientific Publishing.'
chicago: 'Ulrich, Florian, and Carl-Philipp J Heisenberg. “Gastrulation in Zebrafish.”
In Fish Development and Genetics : The Zebrafish and Medaka Models, edited
by Vladimir Korzh and Zhiyuan Gong, 2:39–86. World Scientific Publishing, 2004.'
ieee: 'F. Ulrich and C.-P. J. Heisenberg, “Gastrulation in zebrafish,” in Fish
development and genetics : the zebrafish and medaka models, vol. 2, V. Korzh
and Z. Gong, Eds. World Scientific Publishing, 2004, pp. 39–86.'
ista: 'Ulrich F, Heisenberg C-PJ. 2004.Gastrulation in zebrafish. In: Fish development
and genetics : the zebrafish and medaka models. Molecular Aspects of Fish and
Marine Biology, vol. 2, 39–86.'
mla: 'Ulrich, Florian, and Carl-Philipp J. Heisenberg. “Gastrulation in Zebrafish.”
Fish Development and Genetics : The Zebrafish and Medaka Models, edited
by Vladimir Korzh and Zhiyuan Gong, vol. 2, World Scientific Publishing, 2004,
pp. 39–86.'
short: 'F. Ulrich, C.-P.J. Heisenberg, in:, V. Korzh, Z. Gong (Eds.), Fish Development
and Genetics : The Zebrafish and Medaka Models, World Scientific Publishing, 2004,
pp. 39–86.'
date_created: 2018-12-11T12:04:06Z
date_published: 2004-11-01T00:00:00Z
date_updated: 2021-01-12T07:44:29Z
day: '01'
editor:
- first_name: Vladimir
full_name: Korzh, Vladimir
last_name: Korzh
- first_name: Zhiyuan
full_name: Gong, Zhiyuan
last_name: Gong
extern: '1'
intvolume: ' 2'
language:
- iso: eng
month: '11'
oa_version: None
page: 39 - 86
publication: 'Fish development and genetics : the zebrafish and medaka models'
publication_status: published
publisher: World Scientific Publishing
publist_id: '2796'
status: public
title: Gastrulation in zebrafish
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2004'
...
---
_id: '3617'
abstract:
- lang: eng
text: 'The coalescent process can describe the effects of selection at linked loci
only if selection is so strong that genotype frequencies evolve deterministically.
Here, we develop methods proposed by Kaplan, Darden, and Hudson to find the effects
of weak selection. We show that the overall effect is given by an extension to
Price''s equation: the change in properties such as moments of coalescence times
is equal to the covariance between those properties and the fitness of the sample
of genes. The distribution of coalescence times differs substantially between
allelic classes, even in the absence of selection. However, the average coalescence
time between randomly chosen genes is insensitive to the current allele frequency
and is affected significantly by purifying selection only if deleterious mutations
are common and selection is strong (i.e., the product of population size and selection
coefficient, Ns > 3). Balancing selection increases mean coalescence times,
but the effect becomes large only when mutation rates between allelic classes
are low and when selection is extremely strong. Our analysis supports previous
simulations that show that selection has surprisingly little effect on genealogies.
Moreover, small fluctuations in allele frequency due to random drift can greatly
reduce any such effects. This will make it difficult to detect the action of selection
from neutral variation alone.'
author:
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison M
last_name: Etheridge
citation:
ama: Barton NH, Etheridge A. The effect of selection on genealogies. Genetics.
2004;166(2):1115-1131. doi:10.1534/genetics.166.2.1115
apa: Barton, N. H., & Etheridge, A. (2004). The effect of selection on genealogies.
Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.166.2.1115
chicago: Barton, Nicholas H, and Alison Etheridge. “The Effect of Selection on Genealogies.”
Genetics. Genetics Society of America, 2004. https://doi.org/10.1534/genetics.166.2.1115.
ieee: N. H. Barton and A. Etheridge, “The effect of selection on genealogies,” Genetics,
vol. 166, no. 2. Genetics Society of America, pp. 1115–1131, 2004.
ista: Barton NH, Etheridge A. 2004. The effect of selection on genealogies. Genetics.
166(2), 1115–1131.
mla: Barton, Nicholas H., and Alison Etheridge. “The Effect of Selection on Genealogies.”
Genetics, vol. 166, no. 2, Genetics Society of America, 2004, pp. 1115–31,
doi:10.1534/genetics.166.2.1115.
short: N.H. Barton, A. Etheridge, Genetics 166 (2004) 1115–1131.
date_created: 2018-12-11T12:04:16Z
date_published: 2004-02-01T00:00:00Z
date_updated: 2021-01-12T07:44:41Z
day: '01'
doi: 10.1534/genetics.166.2.1115
extern: 1
intvolume: ' 166'
issue: '2'
month: '02'
page: 1115 - 1131
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '2766'
quality_controlled: 0
status: public
title: The effect of selection on genealogies
type: journal_article
volume: 166
year: '2004'
...
---
_id: '3616'
author:
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Speciation: Why, how, where and when? Current Biology. 2004;14(15):R603-R604.
doi:10.1016/j.cub.2004.07.037'
apa: 'Barton, N. H. (2004). Speciation: Why, how, where and when? Current Biology.
Cell Press. https://doi.org/10.1016/j.cub.2004.07.037'
chicago: 'Barton, Nicholas H. “Speciation: Why, How, Where and When?” Current
Biology. Cell Press, 2004. https://doi.org/10.1016/j.cub.2004.07.037.'
ieee: 'N. H. Barton, “Speciation: Why, how, where and when?,” Current Biology,
vol. 14, no. 15. Cell Press, pp. R603–R604, 2004.'
ista: 'Barton NH. 2004. Speciation: Why, how, where and when? Current Biology. 14(15),
R603–R604.'
mla: 'Barton, Nicholas H. “Speciation: Why, How, Where and When?” Current Biology,
vol. 14, no. 15, Cell Press, 2004, pp. R603–04, doi:10.1016/j.cub.2004.07.037.'
short: N.H. Barton, Current Biology 14 (2004) R603–R604.
date_created: 2018-12-11T12:04:16Z
date_published: 2004-08-10T00:00:00Z
date_updated: 2019-04-26T07:22:31Z
day: '10'
doi: 10.1016/j.cub.2004.07.037
extern: 1
intvolume: ' 14'
issue: '15'
month: '08'
page: R603 - R604
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '2767'
quality_controlled: 0
status: public
title: 'Speciation: Why, how, where and when?'
type: review
volume: 14
year: '2004'
...
---
_id: '3688'
abstract:
- lang: eng
text: Capturing images of documents using handheld digital cameras has a variety
of applications in academia, research, knowledge management, retail, and office
settings. The ultimate goal of such systems is to achieve image quality comparable
to that currently achieved with flatbed scanners even for curved, warped, or curled
pages. This can be achieved by high-accuracy 3D modeling of the page surface,
followed by a "flattening" of the surface. A number of previous systems
have either assumed only perspective distortions, or used techniques like structured
lighting, shading, or side-imaging for obtaining 3D shape. This paper describes
a system for handheld camera-based document capture using general purpose stereo
vision methods followed by a new document dewarping technique. Examples of shape
modeling and dewarping of book images is shown.
author:
- first_name: Adrian
full_name: Ulges, Adrian
last_name: Ulges
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Thomas
full_name: Breuel,Thomas M
last_name: Breuel
citation:
ama: 'Ulges A, Lampert C, Breuel T. Document capture using stereo vision. In: ACM;
2004:198-200. doi:10.1145/1030397.1030434'
apa: 'Ulges, A., Lampert, C., & Breuel, T. (2004). Document capture using stereo
vision (pp. 198–200). Presented at the DocEng: ACM Symposium on Document Engineering,
ACM. https://doi.org/10.1145/1030397.1030434'
chicago: Ulges, Adrian, Christoph Lampert, and Thomas Breuel. “Document Capture
Using Stereo Vision,” 198–200. ACM, 2004. https://doi.org/10.1145/1030397.1030434.
ieee: 'A. Ulges, C. Lampert, and T. Breuel, “Document capture using stereo vision,”
presented at the DocEng: ACM Symposium on Document Engineering, 2004, pp. 198–200.'
ista: 'Ulges A, Lampert C, Breuel T. 2004. Document capture using stereo vision.
DocEng: ACM Symposium on Document Engineering, 198–200.'
mla: Ulges, Adrian, et al. Document Capture Using Stereo Vision. ACM, 2004,
pp. 198–200, doi:10.1145/1030397.1030434.
short: A. Ulges, C. Lampert, T. Breuel, in:, ACM, 2004, pp. 198–200.
conference:
name: 'DocEng: ACM Symposium on Document Engineering'
date_created: 2018-12-11T12:04:38Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:48:58Z
day: '01'
doi: 10.1145/1030397.1030434
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/~chl/papers/ulges-doceng2004.pdf
month: '01'
page: 198 - 200
publication_status: published
publisher: ACM
publist_id: '2679'
quality_controlled: 0
status: public
title: Document capture using stereo vision
type: conference
year: '2004'
...
---
_id: '3810'
abstract:
- lang: eng
text: Voltage-gated potassium (Kv) channels control action potential repolarization,
interspike membrane potential, and action potential frequency in excitable cells.
It is thought that the combinatorial association between distinct alpha and beta
subunits determines whether Kv channels function as non-inactivating delayed rectifiers
or as rapidly inactivating A-type channels. We show that membrane lipids can convert
A-type channels into delayed rectifiers and vice versa. Phosphoinositides remove
N-type inactivation from A-type channels by immobilizing the inactivation domains.
Conversely, arachidonic acid and its amide anandamide endow delayed rectifiers
with rapid voltage-dependent inactivation. The bidirectional control of Kv channel
gating by lipids may provide a mechanism for the dynamic regulation of electrical
signaling in the nervous system.
author:
- first_name: Dominik
full_name: Oliver, Dominik
last_name: Oliver
- first_name: Cheng
full_name: Lien, Cheng-Chang
last_name: Lien
- first_name: Malle
full_name: Soom, Malle
last_name: Soom
- first_name: Thomas
full_name: Baukrowitz, Thomas
last_name: Baukrowitz
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Bernd
full_name: Fakler, Bernd
last_name: Fakler
citation:
ama: Oliver D, Lien C, Soom M, Baukrowitz T, Jonas PM, Fakler B. Functional conversion
between A-type and delayed rectifier K+ channels by membrane lipids. Science.
2004;304(5668):265-270. doi:10.1126/science.1094113
apa: Oliver, D., Lien, C., Soom, M., Baukrowitz, T., Jonas, P. M., & Fakler,
B. (2004). Functional conversion between A-type and delayed rectifier K+ channels
by membrane lipids. Science. American Association for the Advancement of
Science. https://doi.org/10.1126/science.1094113
chicago: Oliver, Dominik, Cheng Lien, Malle Soom, Thomas Baukrowitz, Peter M Jonas,
and Bernd Fakler. “Functional Conversion between A-Type and Delayed Rectifier
K+ Channels by Membrane Lipids.” Science. American Association for the
Advancement of Science, 2004. https://doi.org/10.1126/science.1094113.
ieee: D. Oliver, C. Lien, M. Soom, T. Baukrowitz, P. M. Jonas, and B. Fakler, “Functional
conversion between A-type and delayed rectifier K+ channels by membrane lipids,”
Science, vol. 304, no. 5668. American Association for the Advancement of
Science, pp. 265–70, 2004.
ista: Oliver D, Lien C, Soom M, Baukrowitz T, Jonas PM, Fakler B. 2004. Functional
conversion between A-type and delayed rectifier K+ channels by membrane lipids.
Science. 304(5668), 265–70.
mla: Oliver, Dominik, et al. “Functional Conversion between A-Type and Delayed Rectifier
K+ Channels by Membrane Lipids.” Science, vol. 304, no. 5668, American
Association for the Advancement of Science, 2004, pp. 265–70, doi:10.1126/science.1094113.
short: D. Oliver, C. Lien, M. Soom, T. Baukrowitz, P.M. Jonas, B. Fakler, Science
304 (2004) 265–70.
date_created: 2018-12-11T12:05:18Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:22Z
day: '01'
doi: 10.1126/science.1094113
extern: 1
intvolume: ' 304'
issue: '5668'
month: '01'
page: 265 - 70
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '2402'
quality_controlled: 0
status: public
title: Functional conversion between A-type and delayed rectifier K+ channels by membrane
lipids
type: journal_article
volume: 304
year: '2004'
...
---
_id: '3894'
abstract:
- lang: eng
text: We study infinite stochastic games played by n-players on a finite graph with
goals given by sets of infinite traces. The games are stochastic (each player
simultaneously and independently chooses an action at each round, and the next
state is determined by a probability distribution depending on the current state
and the chosen actions), infinite (the game continues for an infinite number of
rounds), nonzero sum (the players' goals are not necessarily conflicting), and
undiscounted. We show that if each player has a reachability objective, that is,
if the goal for each player i is to visit some subset R-i of the states, then
there exists an epsilon-Nash equilibrium in memoryless strategies, for every epsilon
> 0. However, exact Nash equilibria need not exist. We study the complexity
of finding such Nash equilibria, and show that the payoff of some epsilon-Nash
equilibrium in memoryless strategies can be epsilon-approximated in NP. We study
the important subclass of n-player turn-based probabilistic games, where at each
state at most one player has a nontrivial choice of moves. For turn-based probabilistic
games, we show the existence of epsilon-Nash equilibria in pure strategies for
games where the objective of player i is a Borel set B-i of infinite traces. However,
exact Nash equilibria may not exist. For the special case of omega-regular objectives,
we show exact Nash equilibria exist, and can be computed in NP when the omega-regular
objectives are expressed as parity objectives.
acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327,
ONR grant N00014-02-1-0671, NSF grants CCR-9988172 and CCR-0225610
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: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Marcin
full_name: Jurdziński, Marcin
last_name: Jurdziński
citation:
ama: 'Chatterjee K, Majumdar R, Jurdziński M. On Nash equilibria in stochastic games.
In: Vol 3210. Springer; 2004:26-40. doi:10.1007/978-3-540-30124-0_6'
apa: 'Chatterjee, K., Majumdar, R., & Jurdziński, M. (2004). On Nash equilibria
in stochastic games (Vol. 3210, pp. 26–40). Presented at the CSL: Computer Science
Logic, Springer. https://doi.org/10.1007/978-3-540-30124-0_6'
chicago: Chatterjee, Krishnendu, Ritankar Majumdar, and Marcin Jurdziński. “On Nash
Equilibria in Stochastic Games,” 3210:26–40. Springer, 2004. https://doi.org/10.1007/978-3-540-30124-0_6.
ieee: 'K. Chatterjee, R. Majumdar, and M. Jurdziński, “On Nash equilibria in stochastic
games,” presented at the CSL: Computer Science Logic, 2004, vol. 3210, pp. 26–40.'
ista: 'Chatterjee K, Majumdar R, Jurdziński M. 2004. On Nash equilibria in stochastic
games. CSL: Computer Science Logic, LNCS , vol. 3210, 26–40.'
mla: Chatterjee, Krishnendu, et al. On Nash Equilibria in Stochastic Games.
Vol. 3210, Springer, 2004, pp. 26–40, doi:10.1007/978-3-540-30124-0_6.
short: K. Chatterjee, R. Majumdar, M. Jurdziński, in:, Springer, 2004, pp. 26–40.
conference:
name: 'CSL: Computer Science Logic'
date_created: 2018-12-11T12:05:45Z
date_published: 2004-09-09T00:00:00Z
date_updated: 2021-01-12T07:53:01Z
day: '09'
doi: 10.1007/978-3-540-30124-0_6
extern: 1
intvolume: ' 3210'
month: '09'
page: 26 - 40
publication_status: published
publisher: Springer
publist_id: '2264'
quality_controlled: 0
status: public
title: On Nash equilibria in stochastic games
type: conference
volume: 3210
year: '2004'
...
---
_id: '3895'
abstract:
- lang: eng
text: 'In 2-player non-zero-sum games, Nash equilibria capture the options for rational
behavior if each player attempts to maximize her payoff. In contrast to classical
game theory, we consider lexicographic objectives: first, each player tries to
maximize her own payoff, and then, the player tries to minimize the opponent''s
payoff. Such objectives arise naturally in the verification of systems with multiple
components. There, instead of proving that each component satisfies its specification
no matter how the other components behave, it often suffices to prove that each
component satisfies its specification provided that the other components satisfy
their specifications. We say that a Nash equilibrium is secure if it is an equilibrium
with respect to the lexicographic objectives of both players. We prove that in
graph games with Borel objectives, which include the games that arise in verification,
there may be several Nash equilibria, but there is always a unique maximal payoff
profile of secure equilibria. We show how this equilibrium can be computed in
the case of omega-regular objectives, and we characterize the memory requirements
of strategies that achieve the equilibrium.'
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
- first_name: Marcin
full_name: Jurdziński, Marcin
last_name: Jurdziński
citation:
ama: 'Chatterjee K, Henzinger TA, Jurdziński M. Games with secure equilibria. In:
IEEE; 2004:160-169. doi:10.1109/LICS.2004.1319610'
apa: 'Chatterjee, K., Henzinger, T. A., & Jurdziński, M. (2004). Games with
secure equilibria (pp. 160–169). Presented at the LICS: Logic in Computer Science,
IEEE. https://doi.org/10.1109/LICS.2004.1319610'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Marcin Jurdziński. “Games
with Secure Equilibria,” 160–69. IEEE, 2004. https://doi.org/10.1109/LICS.2004.1319610.
ieee: 'K. Chatterjee, T. A. Henzinger, and M. Jurdziński, “Games with secure equilibria,”
presented at the LICS: Logic in Computer Science, 2004, pp. 160–169.'
ista: 'Chatterjee K, Henzinger TA, Jurdziński M. 2004. Games with secure equilibria.
LICS: Logic in Computer Science, 160–169.'
mla: Chatterjee, Krishnendu, et al. Games with Secure Equilibria. IEEE, 2004,
pp. 160–69, doi:10.1109/LICS.2004.1319610.
short: K. Chatterjee, T.A. Henzinger, M. Jurdziński, in:, IEEE, 2004, pp. 160–169.
conference:
name: 'LICS: Logic in Computer Science'
date_created: 2018-12-11T12:05:45Z
date_published: 2004-08-09T00:00:00Z
date_updated: 2021-01-12T07:53:01Z
day: '09'
doi: 10.1109/LICS.2004.1319610
extern: 1
month: '08'
page: 160 - 169
publication_status: published
publisher: IEEE
publist_id: '2262'
quality_controlled: 0
status: public
title: Games with secure equilibria
type: conference
year: '2004'
...
---
_id: '3931'
abstract:
- lang: eng
text: Hyaluronan is an unsulfated glycosaminoglycan (GAG) that is ubiquitously expressed
in the extracellular matrix (ECM) of all vertebrates, where hyaluronan rich matrices
constitute a particular permissive environment for the development of complex
biological structures and also for tumor progression. Because of its conserved
structure and ubiquitous expression, antibodies for its histochemical detection
cannot be produced. We have engineered a fusion protein, neurocan-GFP, and expressed
it as a secreted molecule in mammalian cells. Neurocan-GFP fusion protein specifically
binds to hyaluronan and directly visualizes hyaluronan on tissue sections, revealing
a very detailed picture of hyaluronan distribution. The fluorescent fusion protein
can be used in combination with antibodies and nuclear markers for double or triple
staining. In addition, it is suitable to visualize hyaluronan on living cells
by time-lapse video microscopy. The successful production and application of the
neurocan-GFP fusion protein opens up new perspectives for using GFP fusion proteins
as detection tools in histological and cytological studies complementing conventional
antibody and biotin/avidin techniques.
author:
- first_name: Hui
full_name: Zhang, Hui
last_name: Zhang
- first_name: Stephan
full_name: Baader, Stephan L
last_name: Baader
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Joachim
full_name: Kappler, Joachim
last_name: Kappler
- first_name: Uwe
full_name: Rauch, Uwe
last_name: Rauch
citation:
ama: 'Zhang H, Baader S, Sixt MK, Kappler J, Rauch U. Neurocan-GFP fusion protein:
a new approach to detect hyaluronan on tissue sections and living cells. Journal
of Histochemistry and Cytochemistry. 2004;52(7):915-922. doi:10.1369/jhc.3A6221.2004'
apa: 'Zhang, H., Baader, S., Sixt, M. K., Kappler, J., & Rauch, U. (2004). Neurocan-GFP
fusion protein: a new approach to detect hyaluronan on tissue sections and living
cells. Journal of Histochemistry and Cytochemistry. Histochemical Society.
https://doi.org/10.1369/jhc.3A6221.2004'
chicago: 'Zhang, Hui, Stephan Baader, Michael K Sixt, Joachim Kappler, and Uwe Rauch.
“Neurocan-GFP Fusion Protein: A New Approach to Detect Hyaluronan on Tissue Sections
and Living Cells.” Journal of Histochemistry and Cytochemistry. Histochemical
Society, 2004. https://doi.org/10.1369/jhc.3A6221.2004.'
ieee: 'H. Zhang, S. Baader, M. K. Sixt, J. Kappler, and U. Rauch, “Neurocan-GFP
fusion protein: a new approach to detect hyaluronan on tissue sections and living
cells,” Journal of Histochemistry and Cytochemistry, vol. 52, no. 7. Histochemical
Society, pp. 915–922, 2004.'
ista: 'Zhang H, Baader S, Sixt MK, Kappler J, Rauch U. 2004. Neurocan-GFP fusion
protein: a new approach to detect hyaluronan on tissue sections and living cells.
Journal of Histochemistry and Cytochemistry. 52(7), 915–922.'
mla: 'Zhang, Hui, et al. “Neurocan-GFP Fusion Protein: A New Approach to Detect
Hyaluronan on Tissue Sections and Living Cells.” Journal of Histochemistry
and Cytochemistry, vol. 52, no. 7, Histochemical Society, 2004, pp. 915–22,
doi:10.1369/jhc.3A6221.2004.'
short: H. Zhang, S. Baader, M.K. Sixt, J. Kappler, U. Rauch, Journal of Histochemistry
and Cytochemistry 52 (2004) 915–922.
date_created: 2018-12-11T12:05:57Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:17Z
day: '01'
doi: 10.1369/jhc.3A6221.2004
extern: 1
intvolume: ' 52'
issue: '7'
month: '01'
page: 915 - 922
publication: Journal of Histochemistry and Cytochemistry
publication_status: published
publisher: Histochemical Society
publist_id: '2196'
quality_controlled: 0
status: public
title: 'Neurocan-GFP fusion protein: a new approach to detect hyaluronan on tissue
sections and living cells'
type: journal_article
volume: 52
year: '2004'
...
---
_id: '3929'
abstract:
- lang: eng
text: The Nef protein of human and simian immunodeficiency virus (HIV/SIV) is believed
to interfere with T cell activation signals by forming a signaling complex at
the plasma membrane. Composition and function of the complex are not fully understood.
Here we report that Nef recruits the Polycomb Group (PcG) protein Eed, so far
known as a nuclear factor and repressor of transcription, to the membrane of cells.
The Nef-induced translocation of Eed led to a potent stimulation of Tat-dependent
HIV transcription, implying that Eed removal from the nucleus is required for
optimal Tat function. Similar to Nef action, activation of integrin receptors
recruited Eed to the plasma membrane, also leading to enhanced Tat/Nef-mediated
transcription. Our results suggest a link between membrane-associated activation
processes and transcriptional derepression and demonstrate how HIV exploits this
mechanism.
author:
- first_name: Vanessa
full_name: Witte, Vanessa
last_name: Witte
- first_name: Bernd
full_name: Laffert, Bernd
last_name: Laffert
- first_name: Olaf
full_name: Rosorius, Olaf
last_name: Rosorius
- first_name: Peter
full_name: Lischka, Peter
last_name: Lischka
- first_name: Katja
full_name: Blume, Katja
last_name: Blume
- first_name: Gunther
full_name: Galler, Gunther
last_name: Galler
- first_name: Andrea
full_name: Stilper, Andrea
last_name: Stilper
- first_name: Dieter
full_name: Willbold, Dieter
last_name: Willbold
- first_name: Paola
full_name: D'Aloja, Paola
last_name: D'Aloja
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Johanna
full_name: Kolanus, Johanna
last_name: Kolanus
- first_name: Melanie
full_name: Ott, Melanie
last_name: Ott
- first_name: Waldemar
full_name: Kolanus, Waldemar
last_name: Kolanus
- first_name: Gerold
full_name: Schuler, Gerold
last_name: Schuler
- first_name: Andreas
full_name: Baur, Andreas S
last_name: Baur
citation:
ama: Witte V, Laffert B, Rosorius O, et al. HIV-1 Nef mimics an integrin receptor
signal that recruits the polycomb group protein Eed to the plasma membrane. Molecular
Cell. 2004;13(2):179-190. doi:10.1016/S1097-2765(04)00004-8
apa: Witte, V., Laffert, B., Rosorius, O., Lischka, P., Blume, K., Galler, G., …
Baur, A. (2004). HIV-1 Nef mimics an integrin receptor signal that recruits the
polycomb group protein Eed to the plasma membrane. Molecular Cell. Cell
Press. https://doi.org/10.1016/S1097-2765(04)00004-8
chicago: Witte, Vanessa, Bernd Laffert, Olaf Rosorius, Peter Lischka, Katja Blume,
Gunther Galler, Andrea Stilper, et al. “HIV-1 Nef Mimics an Integrin Receptor
Signal That Recruits the Polycomb Group Protein Eed to the Plasma Membrane.” Molecular
Cell. Cell Press, 2004. https://doi.org/10.1016/S1097-2765(04)00004-8.
ieee: V. Witte et al., “HIV-1 Nef mimics an integrin receptor signal that
recruits the polycomb group protein Eed to the plasma membrane,” Molecular
Cell, vol. 13, no. 2. Cell Press, pp. 179–190, 2004.
ista: Witte V, Laffert B, Rosorius O, Lischka P, Blume K, Galler G, Stilper A, Willbold
D, D’Aloja P, Sixt MK, Kolanus J, Ott M, Kolanus W, Schuler G, Baur A. 2004. HIV-1
Nef mimics an integrin receptor signal that recruits the polycomb group protein
Eed to the plasma membrane. Molecular Cell. 13(2), 179–190.
mla: Witte, Vanessa, et al. “HIV-1 Nef Mimics an Integrin Receptor Signal That Recruits
the Polycomb Group Protein Eed to the Plasma Membrane.” Molecular Cell,
vol. 13, no. 2, Cell Press, 2004, pp. 179–90, doi:10.1016/S1097-2765(04)00004-8.
short: V. Witte, B. Laffert, O. Rosorius, P. Lischka, K. Blume, G. Galler, A. Stilper,
D. Willbold, P. D’Aloja, M.K. Sixt, J. Kolanus, M. Ott, W. Kolanus, G. Schuler,
A. Baur, Molecular Cell 13 (2004) 179–190.
date_created: 2018-12-11T12:05:56Z
date_published: 2004-01-30T00:00:00Z
date_updated: 2021-01-12T07:53:16Z
day: '30'
doi: 10.1016/S1097-2765(04)00004-8
extern: 1
intvolume: ' 13'
issue: '2'
month: '01'
page: 179 - 190
publication: Molecular Cell
publication_status: published
publisher: Cell Press
publist_id: '2197'
quality_controlled: 0
status: public
title: HIV-1 Nef mimics an integrin receptor signal that recruits the polycomb group
protein Eed to the plasma membrane
type: journal_article
volume: 13
year: '2004'
...
---
_id: '3990'
abstract:
- lang: eng
text: The writhing number measures the global geometry of a closed space curve or
knot. We show that this measure is related to the average winding number of its
Gauss map. Using this relationship, we give an algorithm for computing the writhing
number for a polygonal knot with n edges in time roughly proportional to n(1.6).
We also implement a different, simple algorithm and provide experimental evidence
for its practical efficiency.
acknowledgement: Partially supported by NSF under grants CCR-00-86013, EIA-9972879
and NSF under grant CCR-97-12088.
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: Yusu
full_name: Wang, Yusu
last_name: Wang
citation:
ama: Agarwal P, Edelsbrunner H, Wang Y. Computing the writhing number of a polygonal
knot. Discrete & Computational Geometry. 2004;32(1):37-53. doi:10.1007/s00454-004-2864-x
apa: Agarwal, P., Edelsbrunner, H., & Wang, Y. (2004). Computing the writhing
number of a polygonal knot. Discrete & Computational Geometry. Springer.
https://doi.org/10.1007/s00454-004-2864-x
chicago: Agarwal, Pankaj, Herbert Edelsbrunner, and Yusu Wang. “Computing the Writhing
Number of a Polygonal Knot.” Discrete & Computational Geometry. Springer,
2004. https://doi.org/10.1007/s00454-004-2864-x.
ieee: P. Agarwal, H. Edelsbrunner, and Y. Wang, “Computing the writhing number of
a polygonal knot,” Discrete & Computational Geometry, vol. 32, no.
1. Springer, pp. 37–53, 2004.
ista: Agarwal P, Edelsbrunner H, Wang Y. 2004. Computing the writhing number of
a polygonal knot. Discrete & Computational Geometry. 32(1), 37–53.
mla: Agarwal, Pankaj, et al. “Computing the Writhing Number of a Polygonal Knot.”
Discrete & Computational Geometry, vol. 32, no. 1, Springer, 2004,
pp. 37–53, doi:10.1007/s00454-004-2864-x.
short: P. Agarwal, H. Edelsbrunner, Y. Wang, Discrete & Computational Geometry
32 (2004) 37–53.
date_created: 2018-12-11T12:06:18Z
date_published: 2004-05-01T00:00:00Z
date_updated: 2021-01-12T07:53:42Z
day: '01'
doi: 10.1007/s00454-004-2864-x
extern: 1
intvolume: ' 32'
issue: '1'
month: '05'
page: 37 - 53
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2138'
quality_controlled: 0
status: public
title: Computing the writhing number of a polygonal knot
type: journal_article
volume: 32
year: '2004'
...
---
_id: '4224'
abstract:
- lang: eng
text: Developing cells acquire positional information by reading the graded distribution
of morphogens. In Drosophila, the Dpp morphogen forms a long-range concentration
gradient by spreading from a restricted source in the developing wing. It has
been assumed that Dpp spreads by extracellular diffusion. Under this assumption,
the main role of endocytosis in gradient formation is to downregulate receptors
at the cell surface. These surface receptors bind to the ligand and thereby interfere
with its long-range movement. Recent experiments indicate that Dpp spreading is
mediated by Dynamin-dependent endocytosis in the target tissue, suggesting that
extracellular diffusion alone cannot account for Dpp dispersal. Here, we perform
a theoretical study of a model for morphogen spreading based on extracellular
diffusion, which takes into account receptor binding and trafficking. We compare
profiles of ligand and surface receptors obtained in this model with experimental
data. To this end, we monitored directly the pool of surface receptors and extracellular
Dpp with specific antibodies. We conclude that current models considering pure
extracellular diffusion cannot explain the observed role of endocytosis during
Dpp long-range movement.
article_processing_charge: No
author:
- first_name: Karsten
full_name: Kruse, Karsten
last_name: Kruse
- first_name: Periklis
full_name: Pantazis, Periklis
last_name: Pantazis
- 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: Frank
full_name: Julicher, Frank
last_name: Julicher
- first_name: Marcos
full_name: Gonzalez Gaitan, Marcos
last_name: Gonzalez Gaitan
citation:
ama: 'Kruse K, Pantazis P, Bollenbach MT, Julicher F, Gonzalez Gaitan M. Dpp gradient
formation by dynamin-dependent endocytosis: receptor trafficking and the diffusion
model. Development. 2004;131(19):4843-4856. doi:10.1242/dev.01335'
apa: 'Kruse, K., Pantazis, P., Bollenbach, M. T., Julicher, F., & Gonzalez Gaitan,
M. (2004). Dpp gradient formation by dynamin-dependent endocytosis: receptor trafficking
and the diffusion model. Development. Company of Biologists. https://doi.org/10.1242/dev.01335'
chicago: 'Kruse, Karsten, Periklis Pantazis, Mark Tobias Bollenbach, Frank Julicher,
and Marcos Gonzalez Gaitan. “Dpp Gradient Formation by Dynamin-Dependent Endocytosis:
Receptor Trafficking and the Diffusion Model.” Development. Company of
Biologists, 2004. https://doi.org/10.1242/dev.01335.'
ieee: 'K. Kruse, P. Pantazis, M. T. Bollenbach, F. Julicher, and M. Gonzalez Gaitan,
“Dpp gradient formation by dynamin-dependent endocytosis: receptor trafficking
and the diffusion model,” Development, vol. 131, no. 19. Company of Biologists,
pp. 4843–4856, 2004.'
ista: 'Kruse K, Pantazis P, Bollenbach MT, Julicher F, Gonzalez Gaitan M. 2004.
Dpp gradient formation by dynamin-dependent endocytosis: receptor trafficking
and the diffusion model. Development. 131(19), 4843–4856.'
mla: 'Kruse, Karsten, et al. “Dpp Gradient Formation by Dynamin-Dependent Endocytosis:
Receptor Trafficking and the Diffusion Model.” Development, vol. 131, no.
19, Company of Biologists, 2004, pp. 4843–56, doi:10.1242/dev.01335.'
short: K. Kruse, P. Pantazis, M.T. Bollenbach, F. Julicher, M. Gonzalez Gaitan,
Development 131 (2004) 4843–4856.
date_created: 2018-12-11T12:07:41Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:26Z
day: '01'
doi: 10.1242/dev.01335
extern: '1'
intvolume: ' 131'
issue: '19'
language:
- iso: eng
month: '01'
oa_version: None
page: 4843 - 4856
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '1893'
status: public
title: 'Dpp gradient formation by dynamin-dependent endocytosis: receptor trafficking
and the diffusion model'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2004'
...
---
_id: '4239'
alternative_title:
- Cellular Origin, Life in Extreme Habitats and Astrobiology
author:
- first_name: Harold
full_name: Harold Vladar
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
- first_name: Roberto
full_name: 'Cipriani, Roberto '
last_name: Cipriani
- first_name: Benjamin
full_name: Scharifker, Benjamin
last_name: Scharifker
- first_name: Jose
full_name: Bubis, Jose
last_name: Bubis
citation:
ama: 'de Vladar H, Cipriani R, Scharifker B, Bubis J. A Mechanism for the Prebiotic
Emergence of Proteins. In: Seckbach J, Chela Flores J, Owen T, Raulin F, eds.
Life in the Universe From the Miller Experiment to the Search for Life on Other
Worlds. Vol 7. Springer; 2004:83-87. doi:3807'
apa: de Vladar, H., Cipriani, R., Scharifker, B., & Bubis, J. (2004). A Mechanism
for the Prebiotic Emergence of Proteins. In J. Seckbach, J. Chela Flores, T. Owen,
& F. Raulin (Eds.), Life in the Universe From the Miller Experiment to
the Search for Life on Other Worlds (Vol. 7, pp. 83–87). Springer. https://doi.org/3807
chicago: Vladar, Harold de, Roberto Cipriani, Benjamin Scharifker, and Jose Bubis.
“A Mechanism for the Prebiotic Emergence of Proteins.” In Life in the Universe
From the Miller Experiment to the Search for Life on Other Worlds, edited
by J. Seckbach, J. Chela Flores, T. Owen, and F. Raulin, 7:83–87. Springer, 2004.
https://doi.org/3807.
ieee: H. de Vladar, R. Cipriani, B. Scharifker, and J. Bubis, “A Mechanism for the
Prebiotic Emergence of Proteins,” in Life in the Universe From the Miller Experiment
to the Search for Life on Other Worlds, vol. 7, J. Seckbach, J. Chela Flores,
T. Owen, and F. Raulin, Eds. Springer, 2004, pp. 83–87.
ista: 'de Vladar H, Cipriani R, Scharifker B, Bubis J. 2004.A Mechanism for the
Prebiotic Emergence of Proteins. In: Life in the Universe From the Miller Experiment
to the Search for Life on Other Worlds. Cellular Origin, Life in Extreme Habitats
and Astrobiology, vol. 7, 83–87.'
mla: de Vladar, Harold, et al. “A Mechanism for the Prebiotic Emergence of Proteins.”
Life in the Universe From the Miller Experiment to the Search for Life on Other
Worlds, edited by J. Seckbach et al., vol. 7, Springer, 2004, pp. 83–87, doi:3807.
short: H. de Vladar, R. Cipriani, B. Scharifker, J. Bubis, in:, J. Seckbach, J.
Chela Flores, T. Owen, F. Raulin (Eds.), Life in the Universe From the Miller
Experiment to the Search for Life on Other Worlds, Springer, 2004, pp. 83–87.
date_created: 2018-12-11T12:07:47Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:32Z
day: '01'
doi: '3807'
editor:
- first_name: J.
full_name: Seckbach,J.
last_name: Seckbach
- first_name: J.
full_name: Chela-Flores,J.
last_name: Chela Flores
- first_name: T.
full_name: Owen,T.
last_name: Owen
- first_name: F.
full_name: Raulin,F.
last_name: Raulin
extern: 1
intvolume: ' 7'
month: '01'
page: 83 - 87
publication: Life in the Universe From the Miller Experiment to the Search for Life
on Other Worlds
publication_status: published
publisher: Springer
publist_id: '1875'
quality_controlled: 0
status: public
title: A Mechanism for the Prebiotic Emergence of Proteins
type: book_chapter
volume: 7
year: '2004'
...
---
_id: '4253'
abstract:
- lang: eng
text: We consider a single genetic locus which carries two alleles, labelled P and
Q. This locus experiences selection and mutation. It is linked to a second neutral
locus with recombination rate r. If r = 0, this reduces to the study of a single
selected locus. Assuming a Moran model for the population dynamics, we pass to
a diffusion approximation and, assuming that the allele frequencies at the selected
locus have reached stationarity, establish the joint generating function for the
genealogy of a sample from the population and the frequency of the P allele. In
essence this is the joint generating function for a coalescent and the random
background in which it evolves. We use this to characterize, for the diffusion
approximation, the probability of identity in state at the neutral locus of a
sample of two individuals (whose type at the selected locus is known) as solutions
to a system of ordinary differential equations. The only subtlety is to find the
boundary conditions for this system. Finally, numerical examples are presented
that illustrate the accuracy and predictions of the diffusion approximation. In
particular, a comparison is made between this approach and one in which the frequencies
at the selected locus are estimated by their value in the absence of fluctuations
and a classical structured coalescent model is used.
author:
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison M
last_name: Etheridge
- first_name: Anja
full_name: Sturm, Anja K
last_name: Sturm
citation:
ama: Barton NH, Etheridge A, Sturm A. Coalescence in a Random Background. Annals
of Applied Probability. 2004;14(2):754-785.
apa: Barton, N. H., Etheridge, A., & Sturm, A. (2004). Coalescence in a Random
Background. Annals of Applied Probability. Institute of Mathematical Statistics.
chicago: Barton, Nicholas H, Alison Etheridge, and Anja Sturm. “Coalescence in a
Random Background.” Annals of Applied Probability. Institute of Mathematical
Statistics, 2004.
ieee: N. H. Barton, A. Etheridge, and A. Sturm, “Coalescence in a Random Background,”
Annals of Applied Probability, vol. 14, no. 2. Institute of Mathematical
Statistics, pp. 754–785, 2004.
ista: Barton NH, Etheridge A, Sturm A. 2004. Coalescence in a Random Background.
Annals of Applied Probability. 14(2), 754–785.
mla: Barton, Nicholas H., et al. “Coalescence in a Random Background.” Annals
of Applied Probability, vol. 14, no. 2, Institute of Mathematical Statistics,
2004, pp. 754–85.
short: N.H. Barton, A. Etheridge, A. Sturm, Annals of Applied Probability 14 (2004)
754–785.
date_created: 2018-12-11T12:07:52Z
date_published: 2004-05-01T00:00:00Z
date_updated: 2021-01-12T07:55:38Z
day: '01'
extern: 1
intvolume: ' 14'
issue: '2'
main_file_link:
- open_access: '0'
url: http://www.jstor.org/stable/4140427
month: '05'
page: 754 - 785
publication: Annals of Applied Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '1842'
quality_controlled: 0
status: public
title: Coalescence in a Random Background
type: journal_article
volume: 14
year: '2004'
...
---
_id: '3142'
abstract:
- lang: eng
text: Assembly of neuronal circuits is controlled by the sequential acquisition
of neuronal subpopulation-specific identities at progressive developmental steps.
Whereas neuronal features involved in initial phases of differentiation are already
established at cell-cycle exit, recent findings, based mainly on work in the peripheral
nervous system, suggest that the timely integration of signals encountered en
route to targets and from the target region itself is essential to control late
steps in connectivity. As neurons project towards their targets they require target-derived
signals to establish mature axonal projections and acquire neuronal traits such
as the expression of distinct combinations of neurotransmitters. Recent evidence
presented in this review shows that this principle, of a signaling interplay between
target-derived signals and neuronal cell bodies, is often mediated through transcriptional
events and is evolutionarily conserved.
author:
- first_name: Simon
full_name: Simon Hippenmeyer
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Ina
full_name: Kramer, Ina
last_name: Kramer
- first_name: Silvia
full_name: Arber, Silvia
last_name: Arber
citation:
ama: 'Hippenmeyer S, Kramer I, Arber S. Control of neuronal phenotype: What targets
tell the cell bodies. Trends in Neurosciences. 2004;27(8):482-488. doi:10.1016/j.tins.2004.05.012'
apa: 'Hippenmeyer, S., Kramer, I., & Arber, S. (2004). Control of neuronal phenotype:
What targets tell the cell bodies. Trends in Neurosciences. Elsevier. https://doi.org/10.1016/j.tins.2004.05.012'
chicago: 'Hippenmeyer, Simon, Ina Kramer, and Silvia Arber. “Control of Neuronal
Phenotype: What Targets Tell the Cell Bodies.” Trends in Neurosciences.
Elsevier, 2004. https://doi.org/10.1016/j.tins.2004.05.012.'
ieee: 'S. Hippenmeyer, I. Kramer, and S. Arber, “Control of neuronal phenotype:
What targets tell the cell bodies,” Trends in Neurosciences, vol. 27, no.
8. Elsevier, pp. 482–488, 2004.'
ista: 'Hippenmeyer S, Kramer I, Arber S. 2004. Control of neuronal phenotype: What
targets tell the cell bodies. Trends in Neurosciences. 27(8), 482–488.'
mla: 'Hippenmeyer, Simon, et al. “Control of Neuronal Phenotype: What Targets Tell
the Cell Bodies.” Trends in Neurosciences, vol. 27, no. 8, Elsevier, 2004,
pp. 482–88, doi:10.1016/j.tins.2004.05.012.'
short: S. Hippenmeyer, I. Kramer, S. Arber, Trends in Neurosciences 27 (2004) 482–488.
date_created: 2018-12-11T12:01:38Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2019-04-26T07:22:25Z
day: '01'
doi: 10.1016/j.tins.2004.05.012
extern: 1
intvolume: ' 27'
issue: '8'
month: '08'
page: 482 - 488
publication: Trends in Neurosciences
publication_status: published
publisher: Elsevier
publist_id: '3555'
quality_controlled: 0
status: public
title: 'Control of neuronal phenotype: What targets tell the cell bodies'
type: review
volume: 27
year: '2004'
...
---
_id: '3178'
abstract:
- lang: eng
text: Minimum cut/maximum flow algorithms on graphs have emerged as an increasingly
useful tool for exactor approximate energy minimization in low-level vision. The
combinatorial optimization literature provides many min-cut/max-flow algorithms
with different polynomial time complexity. Their practical efficiency, however,
has to date been studied mainly outside the scope of computer vision. The goal
of this paper is to provide an experimental comparison of the efficiency of min-cut/max
flow algorithms for applications in vision. We compare the running times of several
standard algorithms, as well as a new algorithm that we have recently developed.
The algorithms we study include both Goldberg-Tarjan style "push -relabel"
methods and algorithms based on Ford-Fulkerson style "augmenting paths."
We benchmark these algorithms on a number of typical graphs in the contexts of
image restoration, stereo, and segmentation. In many cases, our new algorithm
works several times faster than any of the other methods, making near real-time
performance possible. An implementation of our max-flow/min-cut algorithm is available
upon request for research purposes.
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
citation:
ama: Boykov Y, Kolmogorov V. An experimental comparison of min-cut/max-flow algorithms
for energy minimization in vision. IEEE Transactions on Pattern Analysis and
Machine Intelligence. 2004;26(9):1124-1137. doi:10.1109/TPAMI.2004.60
apa: Boykov, Y., & Kolmogorov, V. (2004). An experimental comparison of min-cut/max-flow
algorithms for energy minimization in vision. IEEE Transactions on Pattern
Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2004.60
chicago: Boykov, Yuri, and Vladimir Kolmogorov. “An Experimental Comparison of Min-Cut/Max-Flow
Algorithms for Energy Minimization in Vision.” IEEE Transactions on Pattern
Analysis and Machine Intelligence. IEEE, 2004. https://doi.org/10.1109/TPAMI.2004.60.
ieee: Y. Boykov and V. Kolmogorov, “An experimental comparison of min-cut/max-flow
algorithms for energy minimization in vision,” IEEE Transactions on Pattern
Analysis and Machine Intelligence, vol. 26, no. 9. IEEE, pp. 1124–1137, 2004.
ista: Boykov Y, Kolmogorov V. 2004. An experimental comparison of min-cut/max-flow
algorithms for energy minimization in vision. IEEE Transactions on Pattern Analysis
and Machine Intelligence. 26(9), 1124–1137.
mla: Boykov, Yuri, and Vladimir Kolmogorov. “An Experimental Comparison of Min-Cut/Max-Flow
Algorithms for Energy Minimization in Vision.” IEEE Transactions on Pattern
Analysis and Machine Intelligence, vol. 26, no. 9, IEEE, 2004, pp. 1124–37,
doi:10.1109/TPAMI.2004.60.
short: Y. Boykov, V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine
Intelligence 26 (2004) 1124–1137.
date_created: 2018-12-11T12:01:51Z
date_published: 2004-09-01T00:00:00Z
date_updated: 2021-01-12T07:41:36Z
day: '01'
doi: 10.1109/TPAMI.2004.60
extern: 1
intvolume: ' 26'
issue: '9'
month: '09'
page: 1124 - 1137
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3507'
quality_controlled: 0
status: public
title: An experimental comparison of min-cut/max-flow algorithms for energy minimization
in vision
type: journal_article
volume: 26
year: '2004'
...
---
_id: '3173'
abstract:
- lang: eng
text: In the last few years, several new algorithms based on graph cuts have been
developed to solve energy minimization problems in computer vision. Each of these
techniques constructs a graph such that the minimum cut on the graph also minimizes
the energy. Yet, because these graph constructions are complex and highly specific
to a particular energy function, graph cuts have seen limited application to date.
In this paper, we give a characterization of the energy functions that can be
minimized by graph cuts. Our results are restricted to functions of binary variables.
However, our work generalizes many previous constructions and is easily applicable
to vision problems that involve large numbers of labels, such as stereo, motion,
image restoration, and scene reconstruction. We give a precise characterization
of what energy functions can be minimized using graph cuts, among the energy functions
that can be written as a sum of terms containing three or fewer binary variables.
We also provide a general-purpose construction to minimize such an energy function.
Finally, we give a necessary condition for any energy function of binary variables
to be minimized by graph cuts. Researchers who are considering the use of graph
cuts to optimize a particular energy function can use our results to determine
if this is possible and then follow our construction to create the appropriate
graph. A software implementation is freely available.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Ramin
full_name: Zabih, Ramin
last_name: Zabih
citation:
ama: Kolmogorov V, Zabih R. What energy functions can be minimized via graph cuts?
. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2004;26(2):147-159.
doi:10.1109/TPAMI.2004.1262177
apa: Kolmogorov, V., & Zabih, R. (2004). What energy functions can be minimized
via graph cuts? . IEEE Transactions on Pattern Analysis and Machine Intelligence.
IEEE. https://doi.org/10.1109/TPAMI.2004.1262177
chicago: Kolmogorov, Vladimir, and Ramin Zabih. “What Energy Functions Can Be Minimized
via Graph Cuts? .” IEEE Transactions on Pattern Analysis and Machine Intelligence.
IEEE, 2004. https://doi.org/10.1109/TPAMI.2004.1262177.
ieee: V. Kolmogorov and R. Zabih, “What energy functions can be minimized via graph
cuts? ,” IEEE Transactions on Pattern Analysis and Machine Intelligence,
vol. 26, no. 2. IEEE, pp. 147–159, 2004.
ista: Kolmogorov V, Zabih R. 2004. What energy functions can be minimized via graph
cuts? . IEEE Transactions on Pattern Analysis and Machine Intelligence. 26(2),
147–159.
mla: Kolmogorov, Vladimir, and Ramin Zabih. “What Energy Functions Can Be Minimized
via Graph Cuts? .” IEEE Transactions on Pattern Analysis and Machine Intelligence,
vol. 26, no. 2, IEEE, 2004, pp. 147–59, doi:10.1109/TPAMI.2004.1262177.
short: V. Kolmogorov, R. Zabih, IEEE Transactions on Pattern Analysis and Machine
Intelligence 26 (2004) 147–159.
date_created: 2018-12-11T12:01:49Z
date_published: 2004-02-01T00:00:00Z
date_updated: 2021-01-12T07:41:34Z
day: '01'
doi: 10.1109/TPAMI.2004.1262177
extern: 1
intvolume: ' 26'
issue: '2'
month: '02'
page: 147 - 159
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3509'
quality_controlled: 0
status: public
title: 'What energy functions can be minimized via graph cuts? '
type: journal_article
volume: 26
year: '2004'
...
---
_id: '3172'
abstract:
- lang: eng
text: The simultaneous multiple volume (SMV) approach in navigator-gated MRI allows
the use of the whole motion range or the entire scan time for the reconstruction
of final images by simultaneously acquiring different image volumes at different
motion states. The motion tolerance range for each volume is kept small, thus
SMV substantially increases the scan efficiency of navigator methods while maintaining
the effectiveness of motion suppression. This article reports a general implementation
of the SMV approach using a multiprocessor scheduling algorithm. Each motion state
is regarded as a processor and each volume is regarded as a job. An efficient
scheduling that completes all jobs in minimal time is maintained even when the
motion pattern changes. Initial experiments demonstrated that SMV significantly
increased the scan efficiency of navigatorgated MRI.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Thành
full_name: Nguyen, Thành D
last_name: Nguyen
- first_name: Anthony
full_name: Nuval, Anthony
last_name: Nuval
- first_name: Pascal
full_name: Spincemaille, Pascal
last_name: Spincemaille
- first_name: Martin
full_name: Prince, Martin R
last_name: Prince
- first_name: Ramin
full_name: Zabih, Ramin
last_name: Zabih
- first_name: Yusu
full_name: Wang, Yusu
last_name: Wang
citation:
ama: Kolmogorov V, Nguyen T, Nuval A, et al. Multiprocessor scheduling implementation
of the simultaneous multiple volume SMV navigator method. Magnetic Resonance
in Medicine. 2004;52(2):362-367. doi:10.1002/mrm.20162
apa: Kolmogorov, V., Nguyen, T., Nuval, A., Spincemaille, P., Prince, M., Zabih,
R., & Wang, Y. (2004). Multiprocessor scheduling implementation of the simultaneous
multiple volume SMV navigator method. Magnetic Resonance in Medicine. Wiley-Blackwell.
https://doi.org/10.1002/mrm.20162
chicago: Kolmogorov, Vladimir, Thành Nguyen, Anthony Nuval, Pascal Spincemaille,
Martin Prince, Ramin Zabih, and Yusu Wang. “Multiprocessor Scheduling Implementation
of the Simultaneous Multiple Volume SMV Navigator Method.” Magnetic Resonance
in Medicine. Wiley-Blackwell, 2004. https://doi.org/10.1002/mrm.20162.
ieee: V. Kolmogorov et al., “Multiprocessor scheduling implementation of
the simultaneous multiple volume SMV navigator method,” Magnetic Resonance
in Medicine, vol. 52, no. 2. Wiley-Blackwell, pp. 362–367, 2004.
ista: Kolmogorov V, Nguyen T, Nuval A, Spincemaille P, Prince M, Zabih R, Wang Y.
2004. Multiprocessor scheduling implementation of the simultaneous multiple volume
SMV navigator method. Magnetic Resonance in Medicine. 52(2), 362–367.
mla: Kolmogorov, Vladimir, et al. “Multiprocessor Scheduling Implementation of the
Simultaneous Multiple Volume SMV Navigator Method.” Magnetic Resonance in Medicine,
vol. 52, no. 2, Wiley-Blackwell, 2004, pp. 362–67, doi:10.1002/mrm.20162.
short: V. Kolmogorov, T. Nguyen, A. Nuval, P. Spincemaille, M. Prince, R. Zabih,
Y. Wang, Magnetic Resonance in Medicine 52 (2004) 362–367.
date_created: 2018-12-11T12:01:48Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2021-01-12T07:41:34Z
day: '01'
doi: 10.1002/mrm.20162
extern: 1
intvolume: ' 52'
issue: '2'
month: '08'
page: 362 - 367
publication: Magnetic Resonance in Medicine
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3508'
quality_controlled: 0
status: public
title: Multiprocessor scheduling implementation of the simultaneous multiple volume
SMV navigator method
type: journal_article
volume: 52
year: '2004'
...
---
_id: '3177'
abstract:
- lang: eng
text: Feature space clustering is a popular approach to image segmentation, in which
a feature vector of local properties (such as intensity, texture or motion) is
computed at each pixel. The feature space is then clustered, and each pixel is
labeled with the cluster that contains its feature vector. A major limitation
of this approach is that feature space clusters generally lack spatial coherence
(i.e., they do not correspond to a compact grouping of pixels). In this paper,
we propose a segmentation algorithm that operates simultaneously in feature space
and in image space. We define an energy function over both a set of clusters and
a labeling of pixels with clusters. In our framework, a pixel is labeled with
a single cluster (rather than, for example, a distribution over clusters). Our
energy function penalizes clusters that are a poor fit to the data in feature
space, and also penalizes clusters whose pixels lack spatial coherence. The energy
function can be efficiently minimized using graph cuts. Our algorithm can incorporate
both parametric and non-parametric clustering methods. It can be applied to many
optimization-based clustering methods, including k-means and k-medians, and can
handle models which are very close in feature space. Preliminary results are presented
on segmenting real and synthetic images, using both parametric and non-parametric
clustering.
author:
- first_name: Ramin
full_name: Zabih, Ramin
last_name: Zabih
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Zabih R, Kolmogorov V. Spatially coherent clustering using graph cuts. In:
Vol 2. IEEE; 2004:437-444. doi:10.1109/CVPR.2004.1315196'
apa: 'Zabih, R., & Kolmogorov, V. (2004). Spatially coherent clustering using
graph cuts (Vol. 2, pp. 437–444). Presented at the CVPR: Computer Vision and Pattern
Recognition, IEEE. https://doi.org/10.1109/CVPR.2004.1315196'
chicago: Zabih, Ramin, and Vladimir Kolmogorov. “Spatially Coherent Clustering Using
Graph Cuts,” 2:437–44. IEEE, 2004. https://doi.org/10.1109/CVPR.2004.1315196.
ieee: 'R. Zabih and V. Kolmogorov, “Spatially coherent clustering using graph cuts,”
presented at the CVPR: Computer Vision and Pattern Recognition, 2004, vol. 2,
pp. 437–444.'
ista: 'Zabih R, Kolmogorov V. 2004. Spatially coherent clustering using graph cuts.
CVPR: Computer Vision and Pattern Recognition vol. 2, 437–444.'
mla: Zabih, Ramin, and Vladimir Kolmogorov. Spatially Coherent Clustering Using
Graph Cuts. Vol. 2, IEEE, 2004, pp. 437–44, doi:10.1109/CVPR.2004.1315196.
short: R. Zabih, V. Kolmogorov, in:, IEEE, 2004, pp. 437–444.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:50Z
date_published: 2004-06-01T00:00:00Z
date_updated: 2021-01-12T07:41:36Z
day: '01'
doi: 10.1109/CVPR.2004.1315196
extern: 1
intvolume: ' 2'
month: '06'
page: 437 - 444
publication_status: published
publisher: IEEE
publist_id: '3506'
quality_controlled: 0
status: public
title: Spatially coherent clustering using graph cuts
type: conference
volume: 2
year: '2004'
...
---
_id: '3179'
abstract:
- lang: eng
text: The problem of efficient, interactive foreground/background segmentation in
still images is of great practical importance in image editing. Classical image
segmentation tools use either texture (colour) information, e.g. Magic Wand, or
edge (contrast) information, e.g. Intelligent Scissors. Recently, an approach
based on optimization by graph-cut has been developed which successfully combines
both types of information. In this paper we extend the graph-cut approach in three
respects. First, we have developed a more powerful, iterative version of the optimisation.
Secondly, the power of the iterative algorithm is used to simplify substantially
the user interaction needed for a given quality of result. Thirdly, a robust algorithm
for "border matting" has been developed to estimate simultaneously the
alpha-matte around an object boundary and the colours of foreground pixels. We
show that for moderately difficult examples the proposed method outperforms competitive
tools.
author:
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
citation:
ama: 'Rother C, Kolmogorov V, Blake A. "GrabCut" - Interactive
foreground extraction using iterated graph cuts . In: Vol 23. ACM; 2004:309-314.
doi:10.1145/1015706.1015720'
apa: 'Rother, C., Kolmogorov, V., & Blake, A. (2004). "GrabCut"
- Interactive foreground extraction using iterated graph cuts (Vol. 23, pp. 309–314).
Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques, ACM. https://doi.org/10.1145/1015706.1015720'
chicago: Rother, Carsten, Vladimir Kolmogorov, and Andrew Blake. “"GrabCut"
- Interactive Foreground Extraction Using Iterated Graph Cuts ,” 23:309–14. ACM,
2004. https://doi.org/10.1145/1015706.1015720.
ieee: 'C. Rother, V. Kolmogorov, and A. Blake, “"GrabCut" - Interactive
foreground extraction using iterated graph cuts ,” presented at the SIGGRAPH:
Special Interest Group on Computer Graphics and Interactive Techniques, 2004,
vol. 23, no. 3, pp. 309–314.'
ista: 'Rother C, Kolmogorov V, Blake A. 2004. "GrabCut" - Interactive
foreground extraction using iterated graph cuts . SIGGRAPH: Special Interest Group
on Computer Graphics and Interactive Techniques vol. 23, 309–314.'
mla: Rother, Carsten, et al. "GrabCut" - Interactive Foreground
Extraction Using Iterated Graph Cuts . Vol. 23, no. 3, ACM, 2004, pp. 309–14,
doi:10.1145/1015706.1015720.
short: C. Rother, V. Kolmogorov, A. Blake, in:, ACM, 2004, pp. 309–314.
conference:
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
date_created: 2018-12-11T12:01:51Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2021-01-12T07:41:36Z
day: '01'
doi: 10.1145/1015706.1015720
extern: 1
intvolume: ' 23'
issue: '3'
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67890/siggraph04-grabcut.pdf
month: '08'
page: 309 - 314
publication_status: published
publisher: ACM
publist_id: '3505'
quality_controlled: 0
status: public
title: '"GrabCut" - Interactive foreground extraction using iterated graph
cuts '
type: conference
volume: 23
year: '2004'
...
---
_id: '3420'
abstract:
- lang: eng
text: Single-molecule force-spectroscopy was employed to unfold and refold single
sodium-proton antiporters (NhaA) of Escherichia coli from membrane patches. Although
transmembrane α-helices and extracellular polypeptide loops exhibited sufficient
stability to individually establish potential barriers against unfolding, two
helices predominantly unfolded pairwise, thereby acting as one structural unit.
Many of the potential barriers were detected unfolding NhaA either from the C-terminal
or the N-terminal end. It was found that some molecular interactions stabilizing
secondary structural elements were directional, while others were not. Additionally,
some interactions appeared to occur between the secondary structural elements.
After unfolding ten of the 12 helices, the extracted polypeptide was allowed to
refold back into the membrane. After five seconds, the refolded polypeptide established
all secondary structure elements of the native protein. One helical pair showed
a characteristic spring like “snap in” into its folded conformation, while the
refolding process of other helices was not detected in particular. Additionally,
individual helices required characteristic periods of time to fold. Correlating
these results with the primary structure of NhaA allowed us to obtain the first
insights into how potential barriers establish and determine the folding kinetics
of the secondary structure elements.
author:
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: Christine
full_name: Ziegler, Christine
last_name: Ziegler
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- 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, Ziegler C, Janovjak HL, Kühlbrandt W, Mueller D. Controlled unfolding
and refolding of a single sodium/proton antiporter using atomic force microscopy.
Journal of Molecular Biology. 2004;340(5):1143-1152. doi:10.1016/j.jmb.2004.05.026
apa: Kedrov, A., Ziegler, C., Janovjak, H. L., Kühlbrandt, W., & Mueller, D.
(2004). Controlled unfolding and refolding of a single sodium/proton antiporter
using atomic force microscopy. Journal of Molecular Biology. Elsevier.
https://doi.org/10.1016/j.jmb.2004.05.026
chicago: Kedrov, Alexej, Christine Ziegler, Harald L Janovjak, Werner Kühlbrandt,
and Daniel Mueller. “Controlled Unfolding and Refolding of a Single Sodium/Proton
Antiporter Using Atomic Force Microscopy.” Journal of Molecular Biology.
Elsevier, 2004. https://doi.org/10.1016/j.jmb.2004.05.026.
ieee: A. Kedrov, C. Ziegler, H. L. Janovjak, W. Kühlbrandt, and D. Mueller, “Controlled
unfolding and refolding of a single sodium/proton antiporter using atomic force
microscopy,” Journal of Molecular Biology, vol. 340, no. 5. Elsevier, pp.
1143–1152, 2004.
ista: Kedrov A, Ziegler C, Janovjak HL, Kühlbrandt W, Mueller D. 2004. Controlled
unfolding and refolding of a single sodium/proton antiporter using atomic force
microscopy. Journal of Molecular Biology. 340(5), 1143–1152.
mla: Kedrov, Alexej, et al. “Controlled Unfolding and Refolding of a Single Sodium/Proton
Antiporter Using Atomic Force Microscopy.” Journal of Molecular Biology,
vol. 340, no. 5, Elsevier, 2004, pp. 1143–52, doi:10.1016/j.jmb.2004.05.026.
short: A. Kedrov, C. Ziegler, H.L. Janovjak, W. Kühlbrandt, D. Mueller, Journal
of Molecular Biology 340 (2004) 1143–1152.
date_created: 2018-12-11T12:03:14Z
date_published: 2004-07-23T00:00:00Z
date_updated: 2021-01-12T07:43:21Z
day: '23'
doi: 10.1016/j.jmb.2004.05.026
extern: 1
intvolume: ' 340'
issue: '5'
month: '07'
page: 1143 - 1152
publication: Journal of Molecular Biology
publication_status: published
publisher: Elsevier
publist_id: '2981'
quality_controlled: 0
status: public
title: Controlled unfolding and refolding of a single sodium/proton antiporter using
atomic force microscopy
type: journal_article
volume: 340
year: '2004'
...
---
_id: '3419'
abstract:
- lang: eng
text: The folding and stability of transmembrane proteins is a fundamental and unsolved
biological problem. Here, single bacteriorhodopsin molecules were mechanically
unfolded from native purple membranes using atomic force microscopy and force
spectroscopy. The energy landscape of individual transmembrane α helices and polypeptide
loops was mapped by monitoring the pulling speed dependence of the unfolding forces
and applying Monte Carlo simulations. Single helices formed independently stable
units stabilized by a single potential barrier. Mechanical unfolding of the helices
was triggered by 3.9–7.7 Å extension, while natural unfolding rates were of the
order of 10−3 s−1. Besides acting as individually stable units, helices associated
pairwise, establishing a collective potential barrier. The unfolding pathways
of individual proteins reflect distinct pulling speed-dependent unfolding routes
in their energy landscapes. These observations support the two-stage model of
membrane protein folding in which α helices insert into the membrane as stable
units and then assemble into the functional protein.
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: Jens
full_name: Struckmeier, Jens
last_name: Struckmeier
- first_name: Maurice
full_name: Hubain, Maurice
last_name: Hubain
- first_name: Max
full_name: Kessler, Max
last_name: Kessler
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Janovjak HL, Struckmeier J, Hubain M, Kessler M, Kedrov A, Mueller D. Probing
the energy landscape of the membrane protein bacteriorhodopsin. Structure.
2004;12(5):871-879. doi:10.1016/j.str.2004.03.016
apa: Janovjak, H. L., Struckmeier, J., Hubain, M., Kessler, M., Kedrov, A., &
Mueller, D. (2004). Probing the energy landscape of the membrane protein bacteriorhodopsin.
Structure. Cell Press. https://doi.org/10.1016/j.str.2004.03.016
chicago: Janovjak, Harald L, Jens Struckmeier, Maurice Hubain, Max Kessler, Alexej
Kedrov, and Daniel Mueller. “Probing the Energy Landscape of the Membrane Protein
Bacteriorhodopsin.” Structure. Cell Press, 2004. https://doi.org/10.1016/j.str.2004.03.016.
ieee: H. L. Janovjak, J. Struckmeier, M. Hubain, M. Kessler, A. Kedrov, and D. Mueller,
“Probing the energy landscape of the membrane protein bacteriorhodopsin,” Structure,
vol. 12, no. 5. Cell Press, pp. 871–879, 2004.
ista: Janovjak HL, Struckmeier J, Hubain M, Kessler M, Kedrov A, Mueller D. 2004.
Probing the energy landscape of the membrane protein bacteriorhodopsin. Structure.
12(5), 871–879.
mla: Janovjak, Harald L., et al. “Probing the Energy Landscape of the Membrane Protein
Bacteriorhodopsin.” Structure, vol. 12, no. 5, Cell Press, 2004, pp. 871–79,
doi:10.1016/j.str.2004.03.016.
short: H.L. Janovjak, J. Struckmeier, M. Hubain, M. Kessler, A. Kedrov, D. Mueller,
Structure 12 (2004) 871–879.
date_created: 2018-12-11T12:03:14Z
date_published: 2004-05-01T00:00:00Z
date_updated: 2021-01-12T07:43:20Z
day: '01'
doi: 10.1016/j.str.2004.03.016
extern: 1
intvolume: ' 12'
issue: '5'
month: '05'
page: 871 - 879
publication: Structure
publication_status: published
publisher: Cell Press
publist_id: '2982'
quality_controlled: 0
status: public
title: Probing the energy landscape of the membrane protein bacteriorhodopsin
type: journal_article
volume: 12
year: '2004'
...
---
_id: '3575'
abstract:
- lang: eng
text: The Jacobi set of two Morse functions defined on a common - manifold is the
set of critical points of the restrictions of one func- tion to the level sets
of the other function. Equivalently, it is the set of points where the gradients
of the functions are parallel. For a generic pair of Morse functions, the Jacobi
set is a smoothly embed- ded 1-manifold. We give a polynomial-time algorithm that
com- putes the piecewise linear analog of the Jacobi set for functions specified
at the vertices of a triangulation, and we generalize all results to more than
two but at most Morse functions.
alternative_title:
- London Mathematical Society Lecture Note
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
citation:
ama: 'Edelsbrunner H, Harer J. Jacobi sets of multiple Morse functions. In: Foundations
of Computational Mathematics. Vol 312. Springer; 2004:37-57. doi:10.1017/CBO9781139106962.003'
apa: Edelsbrunner, H., & Harer, J. (2004). Jacobi sets of multiple Morse functions.
In Foundations of Computational Mathematics (Vol. 312, pp. 37–57). Springer.
https://doi.org/10.1017/CBO9781139106962.003
chicago: Edelsbrunner, Herbert, and John Harer. “Jacobi Sets of Multiple Morse Functions.”
In Foundations of Computational Mathematics, 312:37–57. Springer, 2004.
https://doi.org/10.1017/CBO9781139106962.003.
ieee: H. Edelsbrunner and J. Harer, “Jacobi sets of multiple Morse functions,” in
Foundations of Computational Mathematics, vol. 312, Springer, 2004, pp.
37–57.
ista: 'Edelsbrunner H, Harer J. 2004.Jacobi sets of multiple Morse functions. In:
Foundations of Computational Mathematics. London Mathematical Society Lecture
Note, vol. 312, 37–57.'
mla: Edelsbrunner, Herbert, and John Harer. “Jacobi Sets of Multiple Morse Functions.”
Foundations of Computational Mathematics, vol. 312, Springer, 2004, pp.
37–57, doi:10.1017/CBO9781139106962.003.
short: H. Edelsbrunner, J. Harer, in:, Foundations of Computational Mathematics,
Springer, 2004, pp. 37–57.
date_created: 2018-12-11T12:04:02Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:44:24Z
day: '01'
doi: 10.1017/CBO9781139106962.003
extern: 1
intvolume: ' 312'
month: '01'
page: 37 - 57
publication: Foundations of Computational Mathematics
publication_status: published
publisher: Springer
publist_id: '2810'
quality_controlled: 0
status: public
title: Jacobi sets of multiple Morse functions
type: book_chapter
volume: 312
year: '2004'
...
---
_id: '3574'
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Edelsbrunner H. Biological applications of computational topology. In: Handbook
of Discrete and Computational Geometry. CRC Press; 2004:1395-1412.'
apa: Edelsbrunner, H. (2004). Biological applications of computational topology.
In Handbook of Discrete and Computational Geometry (pp. 1395–1412). CRC
Press.
chicago: Edelsbrunner, Herbert. “Biological Applications of Computational Topology.”
In Handbook of Discrete and Computational Geometry, 1395–1412. CRC Press,
2004.
ieee: H. Edelsbrunner, “Biological applications of computational topology,” in Handbook
of Discrete and Computational Geometry, CRC Press, 2004, pp. 1395–1412.
ista: 'Edelsbrunner H. 2004.Biological applications of computational topology. In:
Handbook of Discrete and Computational Geometry. , 1395–1412.'
mla: Edelsbrunner, Herbert. “Biological Applications of Computational Topology.”
Handbook of Discrete and Computational Geometry, CRC Press, 2004, pp. 1395–412.
short: H. Edelsbrunner, in:, Handbook of Discrete and Computational Geometry, CRC
Press, 2004, pp. 1395–1412.
date_created: 2018-12-11T12:04:02Z
date_published: 2004-04-15T00:00:00Z
date_updated: 2021-01-12T07:44:24Z
day: '15'
extern: 1
main_file_link:
- open_access: '0'
url: http://www.cs.duke.edu/~edels/Papers/2004-B-01-BiologicalApplicationsTopology.pdf
month: '04'
page: 1395 - 1412
publication: Handbook of Discrete and Computational Geometry
publication_status: published
publisher: CRC Press
publist_id: '2811'
quality_controlled: 0
status: public
title: Biological applications of computational topology
type: book_chapter
year: '2004'
...
---
_id: '3595'
abstract:
- lang: eng
text: Genome sizes vary enormously. This variation in DNA content correlates with
effective population size, suggesting that deleterious additions to the genome
can accumulate in small populations. On this view, the increased complexity of
biological functions associated with large genomes partly reflects evolutionary
degeneration.
author:
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Charlesworth B, Barton NH. Genome size: Does bigger mean worse? Current
Biology. 2004;14(6):R233-R235. doi:10.1016/j.cub.2004.02.054'
apa: 'Charlesworth, B., & Barton, N. H. (2004). Genome size: Does bigger mean
worse? Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2004.02.054'
chicago: 'Charlesworth, Brian, and Nicholas H Barton. “Genome Size: Does Bigger
Mean Worse?” Current Biology. Cell Press, 2004. https://doi.org/10.1016/j.cub.2004.02.054.'
ieee: 'B. Charlesworth and N. H. Barton, “Genome size: Does bigger mean worse?,”
Current Biology, vol. 14, no. 6. Cell Press, pp. R233–R235, 2004.'
ista: 'Charlesworth B, Barton NH. 2004. Genome size: Does bigger mean worse? Current
Biology. 14(6), R233–R235.'
mla: 'Charlesworth, Brian, and Nicholas H. Barton. “Genome Size: Does Bigger Mean
Worse?” Current Biology, vol. 14, no. 6, Cell Press, 2004, pp. R233–35,
doi:10.1016/j.cub.2004.02.054.'
short: B. Charlesworth, N.H. Barton, Current Biology 14 (2004) R233–R235.
date_created: 2018-12-11T12:04:09Z
date_published: 2004-03-01T00:00:00Z
date_updated: 2019-04-26T07:22:31Z
day: '01'
doi: 10.1016/j.cub.2004.02.054
extern: 1
intvolume: ' 14'
issue: '6'
month: '03'
page: R233 - R235
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '2788'
quality_controlled: 0
status: public
title: 'Genome size: Does bigger mean worse?'
type: review
volume: 14
year: '2004'
...
---
_id: '3614'
abstract:
- lang: eng
text: 'We analyze the changes in the mean and variance components of a quantitative
trait caused by changes in allele frequencies, concentrating on the effects of
genetic drift. We use a general representation of epistasis and dominance that
allows an arbitrary relation between genotype and phenotype for any number of
diallelic loci. We assume initial and final Hardy-Weinberg and linkage equilibrium
in our analyses of drift-induced changes. Random drift generates transient linkage
disequilibria that cause correlations between allele frequency fluctuations at
different loci. However, we show that these have negligible effects, at least
for interactions among small numbers of loci. Our analyses are based on diffusion
approximations that summarize the effects of drift in terms of F, the inbreeding
coefficient, interpreted as the expected proportional decrease in heterozygosity
at each locus. For haploids, the variance of the trait mean after a population
bottleneck is var(Δz̄) =inline imagewhere n is the number of loci contributing
to the trait variance, VA(1)=VA is the additive genetic variance, and VA(k) is
the kth-order additive epistatic variance. The expected additive genetic variance
after the bottleneck, denoted (V*A), is closely related to var(Δz̄);
(V*A) (1 –F)inline imageThus, epistasis inflates the expected additive variance
above VA(1 –F), the expectation under additivity. For haploids (and diploids without
dominance), the expected value of every variance component is inflated by the
existence of higher order interactions (e.g., third-order epistasis inflates (V*AA)).
This is not true in general with diploidy, because dominance alone can reduce
(V*A) below VA(1 –F) (e.g., when dominant alleles are rare). Without dominance,
diploidy produces simple expressions: var(Δz̄)=inline image=1 (2F)
kVA(k) and (V*A) = (1 –F)inline imagek(2F)k-1VA(k) With dominance (and even without
epistasis), var(Δz̄)and (V*A) no longer depend solely on the variance
components in the base population. For small F, the expected additive variance
simplifies to (V*A)(1 –F) VA+ 4FVAA+2FVD+2FCAD, where CAD is a sum of two terms
describing covariances between additive effects and dominance and additive × dominance
interactions. Whether population bottlenecks lead to expected increases in additive
variance depends primarily on the ratio of nonadditive to additive genetic variance
in the base population, but dominance precludes simple predictions based solely
on variance components. We illustrate these results using a model in which genotypic
values are drawn at random, allowing extreme and erratic epistatic interactions.
Although our analyses clarify the conditions under which drift is expected to
increase VA, we question the evolutionary importance of such increases.'
author:
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: Barton NH, Turelli M. Effects of allele frequency changes on variance components
under a general model of epistasis. Evolution; International Journal of Organic
Evolution. 2004;58(10):2111-2132. doi:10.1111/j.0014-3820.2004.tb01591.x
apa: Barton, N. H., & Turelli, M. (2004). Effects of allele frequency changes
on variance components under a general model of epistasis. Evolution; International
Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2004.tb01591.x
chicago: Barton, Nicholas H, and Michael Turelli. “Effects of Allele Frequency Changes
on Variance Components under a General Model of Epistasis.” Evolution; International
Journal of Organic Evolution. Wiley-Blackwell, 2004. https://doi.org/10.1111/j.0014-3820.2004.tb01591.x.
ieee: N. H. Barton and M. Turelli, “Effects of allele frequency changes on variance
components under a general model of epistasis,” Evolution; International Journal
of Organic Evolution, vol. 58, no. 10. Wiley-Blackwell, pp. 2111–2132, 2004.
ista: Barton NH, Turelli M. 2004. Effects of allele frequency changes on variance
components under a general model of epistasis. Evolution; International Journal
of Organic Evolution. 58(10), 2111–2132.
mla: Barton, Nicholas H., and Michael Turelli. “Effects of Allele Frequency Changes
on Variance Components under a General Model of Epistasis.” Evolution; International
Journal of Organic Evolution, vol. 58, no. 10, Wiley-Blackwell, 2004, pp.
2111–32, doi:10.1111/j.0014-3820.2004.tb01591.x.
short: N.H. Barton, M. Turelli, Evolution; International Journal of Organic Evolution
58 (2004) 2111–2132.
date_created: 2018-12-11T12:04:15Z
date_published: 2004-10-01T00:00:00Z
date_updated: 2021-01-12T07:44:40Z
day: '01'
doi: 10.1111/j.0014-3820.2004.tb01591.x
extern: 1
intvolume: ' 58'
issue: '10'
month: '10'
page: 2111 - 2132
publication: Evolution; International Journal of Organic Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2769'
quality_controlled: 0
status: public
title: Effects of allele frequency changes on variance components under a general
model of epistasis
type: journal_article
volume: 58
year: '2004'
...
---
_id: '3615'
abstract:
- lang: eng
text: 'We investigate three alternative selection-based scenarios proposed to maintain
polygenic variation: pleiotropic balancing selection, G x E interactions (with
spatial or temporal variation in allelic effects), and sex-dependent allelic effects.
Each analysis assumes an additive polygenic trait with n diallelic loci under
stabilizing selection. We allow loci to have different effects and consider equilibria
at which the population mean departs from the stabilizing-selection optimum. Under
weak selection, each model produces essentially identical, approximate allele-frequency
dynamics. Variation is maintained under pleiotropic balancing selection only at
loci for which the strength of balancing selection exceeds the effective strength
of stabilizing selection. In addition, for all models, polymorphism requires that
the population mean be close enough to the optimum that directional selection
does not overwhelm balancing selection. This balance allows many simultaneously
stable equilibria, and we explore their properties numerically. Both spatial and
temporal G x E can maintain variation at loci for which the coefficient of variation
(across environments) of the effect of a substitution exceeds a critical value
greater than one. The critical value depends on the correlation between substitution
effects at different loci. For large positive correlations (e.g., ρ2ij > 3/4),
even extreme fluctuations in allelic effects cannot maintain variation. Surprisingly,
this constraint on correlations implies that sex-dependent allelic effects cannot
maintain polygenic variation. We present numerical results that support our analytical
approximations and discuss our results in connection to relevant data and alternative
variance-maintaining mechanisms.'
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Turelli M, Barton NH. Polygenic variation maintained by balancing selection:
pleiotropy, sex-dependent allelic effects and GxE interactions. Genetics.
2004;166(2):1053-1079. doi:10.1534/genetics.166.2.1053'
apa: 'Turelli, M., & Barton, N. H. (2004). Polygenic variation maintained by
balancing selection: pleiotropy, sex-dependent allelic effects and GxE interactions.
Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.166.2.1053'
chicago: 'Turelli, Michael, and Nicholas H Barton. “Polygenic Variation Maintained
by Balancing Selection: Pleiotropy, Sex-Dependent Allelic Effects and GxE Interactions.”
Genetics. Genetics Society of America, 2004. https://doi.org/10.1534/genetics.166.2.1053.'
ieee: 'M. Turelli and N. H. Barton, “Polygenic variation maintained by balancing
selection: pleiotropy, sex-dependent allelic effects and GxE interactions,” Genetics,
vol. 166, no. 2. Genetics Society of America, pp. 1053–1079, 2004.'
ista: 'Turelli M, Barton NH. 2004. Polygenic variation maintained by balancing selection:
pleiotropy, sex-dependent allelic effects and GxE interactions. Genetics. 166(2),
1053–1079.'
mla: 'Turelli, Michael, and Nicholas H. Barton. “Polygenic Variation Maintained
by Balancing Selection: Pleiotropy, Sex-Dependent Allelic Effects and GxE Interactions.”
Genetics, vol. 166, no. 2, Genetics Society of America, 2004, pp. 1053–79,
doi:10.1534/genetics.166.2.1053.'
short: M. Turelli, N.H. Barton, Genetics 166 (2004) 1053–1079.
date_created: 2018-12-11T12:04:15Z
date_published: 2004-02-01T00:00:00Z
date_updated: 2021-01-12T07:44:41Z
day: '01'
doi: 10.1534/genetics.166.2.1053
extern: 1
intvolume: ' 166'
issue: '2'
month: '02'
page: 1053 - 1079
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '2768'
quality_controlled: 0
status: public
title: 'Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent
allelic effects and GxE interactions'
type: journal_article
volume: 166
year: '2004'
...
---
_id: '3807'
abstract:
- lang: eng
text: The time course of Mg(2+) block and unblock of NMDA receptors (NMDARs) determines
the extent they are activated by depolarization. Here, we directly measure the
rate of NMDAR channel opening in response to depolarizations at different times
after brief (1 ms) and sustained (4.6 s) applications of glutamate to nucleated
patches from neocortical pyramidal neurons. The kinetics of Mg(2+) unblock were
found to be non-instantaneous and complex, consisting of a prominent fast component
(time constant approximately 100 micros) and slower components (time constants
4 and approximately 300 ms), the relative amplitudes of which depended on the
timing of the depolarizing pulse. Fitting a kinetic model to these data indicated
that Mg(2+) not only blocks the NMDAR channel, but reduces both the open probability
and affinity for glutamate, while enhancing desensitization. These effects slow
the rate of NMDAR channel opening in response to depolarization in a time-dependent
manner such that the slower components of Mg(2+) unblock are enhanced during depolarizations
at later times after glutamate application. One physiological consequence of this
is that brief depolarizations occurring earlier in time after glutamate application
are better able to open NMDAR channels. This finding has important implications
for spike-timing-dependent synaptic plasticity (STDP), where the precise (millisecond)
timing of action potentials relative to synaptic inputs determines the magnitude
and sign of changes in synaptic strength. Indeed, we find that STDP timing curves
of NMDAR channel activation elicited by realistic dendritic action potential waveforms
are narrower than expected assuming instantaneous Mg(2+) unblock, indicating that
slow Mg(2+) unblock of NMDAR channels makes the STDP timing window more precise.
author:
- first_name: Bjorn
full_name: Kampa, Bjorn M
last_name: Kampa
- first_name: John
full_name: Clements, John
last_name: Clements
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Greg
full_name: Stuart, Greg J
last_name: Stuart
citation:
ama: 'Kampa B, Clements J, Jonas PM, Stuart G. Kinetics of Mg(2+) unblock of NMDA
receptors: implications for spike-timing dependent synaptic plasticity. Journal
of Physiology. 2004;556(Pt 2):337-345. doi:10.1113/jphysiol.2003.058842 '
apa: 'Kampa, B., Clements, J., Jonas, P. M., & Stuart, G. (2004). Kinetics of
Mg(2+) unblock of NMDA receptors: implications for spike-timing dependent synaptic
plasticity. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2003.058842 '
chicago: 'Kampa, Bjorn, John Clements, Peter M Jonas, and Greg Stuart. “Kinetics
of Mg(2+) Unblock of NMDA Receptors: Implications for Spike-Timing Dependent Synaptic
Plasticity.” Journal of Physiology. Wiley-Blackwell, 2004. https://doi.org/10.1113/jphysiol.2003.058842 .'
ieee: 'B. Kampa, J. Clements, P. M. Jonas, and G. Stuart, “Kinetics of Mg(2+) unblock
of NMDA receptors: implications for spike-timing dependent synaptic plasticity,”
Journal of Physiology, vol. 556, no. Pt 2. Wiley-Blackwell, pp. 337–45,
2004.'
ista: 'Kampa B, Clements J, Jonas PM, Stuart G. 2004. Kinetics of Mg(2+) unblock
of NMDA receptors: implications for spike-timing dependent synaptic plasticity.
Journal of Physiology. 556(Pt 2), 337–45.'
mla: 'Kampa, Bjorn, et al. “Kinetics of Mg(2+) Unblock of NMDA Receptors: Implications
for Spike-Timing Dependent Synaptic Plasticity.” Journal of Physiology,
vol. 556, no. Pt 2, Wiley-Blackwell, 2004, pp. 337–45, doi:10.1113/jphysiol.2003.058842 .'
short: B. Kampa, J. Clements, P.M. Jonas, G. Stuart, Journal of Physiology 556 (2004)
337–45.
date_created: 2018-12-11T12:05:17Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:20Z
day: '01'
doi: '10.1113/jphysiol.2003.058842 '
extern: 1
intvolume: ' 556'
issue: Pt 2
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664940/
month: '01'
oa: 1
page: 337 - 45
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2403'
quality_controlled: 0
status: public
title: 'Kinetics of Mg(2+) unblock of NMDA receptors: implications for spike-timing
dependent synaptic plasticity'
type: journal_article
volume: 556
year: '2004'
...
---
_id: '3809'
abstract:
- lang: eng
text: Neural stem cells in various regions of the vertebrate brain continuously
generate neurons throughout life. In the mammalian hippocampus, a region important
for spatial and episodic memory, thousands of new granule cells are produced per
day, with the exact number depending on environmental conditions and physical
exercise. The survival of these neurons is improved by learning and conversely
learning may be promoted by neurogenesis. Although it has been suggested that
newly generated neurons may have specific properties to facilitate learning, the
cellular and synaptic mechanisms of plasticity in these neurons are largely unknown.
Here we show that young granule cells in the adult hippocampus differ substantially
from mature granule cells in both active and passive membrane properties. In young
neurons, T-type Ca2+ channels can generate isolated Ca2+ spikes and boost fast
Na+ action potentials, contributing to the induction of synaptic plasticity. Associative
long-term potentiation can be induced more easily in young neurons than in mature
neurons under identical conditions. Thus, newly generated neurons express unique
mechanisms to facilitate synaptic plasticity, which may be important for the formation
of new memories.
author:
- first_name: Christoph
full_name: Schmidt-Hieber, Christoph
last_name: Schmidt Hieber
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
citation:
ama: Schmidt Hieber C, Jonas PM, Bischofberger J. Enhanced synaptic plasticity in
newly generated granule cells of the adult hippocampus. Nature. 2004;429(6988):184-187.
doi:10.1038/nature02553
apa: Schmidt Hieber, C., Jonas, P. M., & Bischofberger, J. (2004). Enhanced
synaptic plasticity in newly generated granule cells of the adult hippocampus.
Nature. Nature Publishing Group. https://doi.org/10.1038/nature02553
chicago: Schmidt Hieber, Christoph, Peter M Jonas, and Josef Bischofberger. “Enhanced
Synaptic Plasticity in Newly Generated Granule Cells of the Adult Hippocampus.”
Nature. Nature Publishing Group, 2004. https://doi.org/10.1038/nature02553.
ieee: C. Schmidt Hieber, P. M. Jonas, and J. Bischofberger, “Enhanced synaptic plasticity
in newly generated granule cells of the adult hippocampus,” Nature, vol.
429, no. 6988. Nature Publishing Group, pp. 184–7, 2004.
ista: Schmidt Hieber C, Jonas PM, Bischofberger J. 2004. Enhanced synaptic plasticity
in newly generated granule cells of the adult hippocampus. Nature. 429(6988),
184–7.
mla: Schmidt Hieber, Christoph, et al. “Enhanced Synaptic Plasticity in Newly Generated
Granule Cells of the Adult Hippocampus.” Nature, vol. 429, no. 6988, Nature
Publishing Group, 2004, pp. 184–87, doi:10.1038/nature02553.
short: C. Schmidt Hieber, P.M. Jonas, J. Bischofberger, Nature 429 (2004) 184–7.
date_created: 2018-12-11T12:05:17Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:21Z
day: '01'
doi: 10.1038/nature02553
extern: 1
intvolume: ' 429'
issue: '6988'
month: '01'
page: 184 - 7
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '2401'
quality_controlled: 0
status: public
title: Enhanced synaptic plasticity in newly generated granule cells of the adult
hippocampus
type: journal_article
volume: 429
year: '2004'
...
---
_id: '3805'
abstract:
- lang: eng
text: The operation of neuronal networks crucially depends on a fast time course
of signaling in inhibitory interneurons. Synapses that excite interneurons generate
fast currents, owing to the expression of glutamate receptors of specific subunit
composition. Interneurons generate brief action potentials in response to transient
synaptic activation and discharge repetitively at very high frequencies during
sustained stimulation. The ability to generate short-duration action potentials
at high frequencies depends on the expression of specific voltage-gated K+ channels.
Factors facilitating fast action potential initiation following synaptic excitation
include depolarized interneuron resting potential, subthreshold conductances and
active dendrites. Finally, GABA release at interneuron output synapses is rapid
and highly synchronized, leading to a faster inhibition in postsynaptic interneurons
than in principal cells. Thus, the expression of distinct transmitter receptors
and voltage-gated ion channels ensures that interneurons operate with high speed
and temporal precision.
author:
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
- first_name: Desdemona
full_name: Fricker, Desdemona
last_name: Fricker
- first_name: Richard
full_name: Miles, Richard
last_name: Miles
citation:
ama: 'Jonas PM, Bischofberger J, Fricker D, Miles R. Interneuron Diversity series:
Fast in, fast out--temporal and spatial signal processing in hippocampal interneurons.
Trends in Neurosciences. 2004;27(1):30-40. doi:doi:10.1016/j.tins.2003.10.010'
apa: 'Jonas, P. M., Bischofberger, J., Fricker, D., & Miles, R. (2004). Interneuron
Diversity series: Fast in, fast out--temporal and spatial signal processing in
hippocampal interneurons. Trends in Neurosciences. Elsevier. https://doi.org/doi:10.1016/j.tins.2003.10.010'
chicago: 'Jonas, Peter M, Josef Bischofberger, Desdemona Fricker, and Richard Miles.
“Interneuron Diversity Series: Fast in, Fast out--Temporal and Spatial Signal
Processing in Hippocampal Interneurons.” Trends in Neurosciences. Elsevier,
2004. https://doi.org/doi:10.1016/j.tins.2003.10.010.'
ieee: 'P. M. Jonas, J. Bischofberger, D. Fricker, and R. Miles, “Interneuron Diversity
series: Fast in, fast out--temporal and spatial signal processing in hippocampal
interneurons,” Trends in Neurosciences, vol. 27, no. 1. Elsevier, pp. 30–40,
2004.'
ista: 'Jonas PM, Bischofberger J, Fricker D, Miles R. 2004. Interneuron Diversity
series: Fast in, fast out--temporal and spatial signal processing in hippocampal
interneurons. Trends in Neurosciences. 27(1), 30–40.'
mla: 'Jonas, Peter M., et al. “Interneuron Diversity Series: Fast in, Fast out--Temporal
and Spatial Signal Processing in Hippocampal Interneurons.” Trends in Neurosciences,
vol. 27, no. 1, Elsevier, 2004, pp. 30–40, doi:doi:10.1016/j.tins.2003.10.010.'
short: P.M. Jonas, J. Bischofberger, D. Fricker, R. Miles, Trends in Neurosciences
27 (2004) 30–40.
date_created: 2018-12-11T12:05:16Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:19Z
day: '01'
doi: doi:10.1016/j.tins.2003.10.010
extern: 1
intvolume: ' 27'
issue: '1'
month: '01'
page: 30 - 40
publication: Trends in Neurosciences
publication_status: published
publisher: Elsevier
publist_id: '2404'
quality_controlled: 0
status: public
title: 'Interneuron Diversity series: Fast in, fast out--temporal and spatial signal
processing in hippocampal interneurons'
type: journal_article
volume: 27
year: '2004'
...
---
_id: '3918'
abstract:
- lang: eng
text: Wingless (ergatoid) males of the tramp ant Cardiocondyla minutior attack and
kill their young ergatoid rivals and thus attempt to monopolize mating with female
sexuals reared in the colony. Because of the different strength of local mate
competition in colonies with one or several reproductive queens, we expected the
production of new ergatoid males to vary with queen number. Sex ratios were mostly
female-biased, but in contrast to the sympatric species C. obscurior (Cremer and
Heinze, 2002) neither the percentage of ergatoid males nor of female sexuals among
the first 20 sexuals produced varied considerably with queen number. As in C.
obscurior, experimental colony fragmentation led to the production of winged males,
whereas in unfragmented control colonies only ergatoid males eclosed.
author:
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: A.
full_name: Böttcher, A.
last_name: Böttcher
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Heinze J, Böttcher A, Cremer S. Production of winged and wingless males in
the ant, Cardiocondyla minutior. Insectes Sociaux. 2004;51(3):275-278.
doi:10.1007/s00040-004-0740-6
apa: Heinze, J., Böttcher, A., & Cremer, S. (2004). Production of winged and
wingless males in the ant, Cardiocondyla minutior. Insectes Sociaux. Springer.
https://doi.org/10.1007/s00040-004-0740-6
chicago: Heinze, Jürgen, A. Böttcher, and Sylvia Cremer. “Production of Winged and
Wingless Males in the Ant, Cardiocondyla Minutior.” Insectes Sociaux. Springer,
2004. https://doi.org/10.1007/s00040-004-0740-6.
ieee: J. Heinze, A. Böttcher, and S. Cremer, “Production of winged and wingless
males in the ant, Cardiocondyla minutior,” Insectes Sociaux, vol. 51, no.
3. Springer, pp. 275–278, 2004.
ista: Heinze J, Böttcher A, Cremer S. 2004. Production of winged and wingless males
in the ant, Cardiocondyla minutior. Insectes Sociaux. 51(3), 275–278.
mla: Heinze, Jürgen, et al. “Production of Winged and Wingless Males in the Ant,
Cardiocondyla Minutior.” Insectes Sociaux, vol. 51, no. 3, Springer, 2004,
pp. 275–78, doi:10.1007/s00040-004-0740-6.
short: J. Heinze, A. Böttcher, S. Cremer, Insectes Sociaux 51 (2004) 275–278.
date_created: 2018-12-11T12:05:53Z
date_published: 2004-08-19T00:00:00Z
date_updated: 2021-01-12T07:53:11Z
day: '19'
doi: 10.1007/s00040-004-0740-6
extern: '1'
intvolume: ' 51'
issue: '3'
language:
- iso: eng
month: '08'
oa_version: None
page: 275 - 278
publication: Insectes Sociaux
publication_status: published
publisher: Springer
publist_id: '2236'
status: public
title: Production of winged and wingless males in the ant, Cardiocondyla minutior
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2004'
...
---
_id: '3988'
abstract:
- lang: eng
text: We give an algorithm that locally improves the fit between two proteins modeled
as space-filling diagrams. The algorithm defines the fit in purely geometric terms
and improves by applying a rigid motion to one of the two proteins. Our implementation
of the algorithm takes between three and ten seconds and converges with high likelihood
to the correct docked configuration, provided it starts at a position away from
the correct one by at most 18 degrees of rotation and at most 3.0Angstrom of translation.
The speed and convergence radius make this an attractive algorithm to use in combination
with a coarse sampling of the six-dimensional space of rigid motions.
acknowledgement: Supported by NSF under grant CCR-00-86013, BGT Postdoc Program from
Duke University and NIH under grant R01 GM61822-01.
alternative_title:
- LNCS
author:
- first_name: Vicky
full_name: Choi, Vicky
last_name: Choi
- first_name: Pankaj
full_name: Agarwal, Pankaj K
last_name: Agarwal
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
citation:
ama: 'Choi V, Agarwal P, Edelsbrunner H, Rudolph J. Local search heuristic for rigid
protein docking. In: Vol 3240. Springer; 2004:218-229. doi:10.1007/978-3-540-30219-3_19'
apa: 'Choi, V., Agarwal, P., Edelsbrunner, H., & Rudolph, J. (2004). Local search
heuristic for rigid protein docking (Vol. 3240, pp. 218–229). Presented at the
WABI: 4th International Workshop on Algorithms in Bioinformatics, Springer. https://doi.org/10.1007/978-3-540-30219-3_19'
chicago: Choi, Vicky, Pankaj Agarwal, Herbert Edelsbrunner, and Johannes Rudolph.
“Local Search Heuristic for Rigid Protein Docking,” 3240:218–29. Springer, 2004.
https://doi.org/10.1007/978-3-540-30219-3_19.
ieee: 'V. Choi, P. Agarwal, H. Edelsbrunner, and J. Rudolph, “Local search heuristic
for rigid protein docking,” presented at the WABI: 4th International Workshop
on Algorithms in Bioinformatics, 2004, vol. 3240, pp. 218–229.'
ista: 'Choi V, Agarwal P, Edelsbrunner H, Rudolph J. 2004. Local search heuristic
for rigid protein docking. WABI: 4th International Workshop on Algorithms in Bioinformatics,
LNCS, vol. 3240, 218–229.'
mla: Choi, Vicky, et al. Local Search Heuristic for Rigid Protein Docking.
Vol. 3240, Springer, 2004, pp. 218–29, doi:10.1007/978-3-540-30219-3_19.
short: V. Choi, P. Agarwal, H. Edelsbrunner, J. Rudolph, in:, Springer, 2004, pp.
218–229.
conference:
name: 'WABI: 4th International Workshop on Algorithms in Bioinformatics'
date_created: 2018-12-11T12:06:17Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:41Z
day: '01'
doi: 10.1007/978-3-540-30219-3_19
extern: 1
intvolume: ' 3240'
month: '01'
page: 218 - 229
publication_status: published
publisher: Springer
publist_id: '2136'
quality_controlled: 0
status: public
title: Local search heuristic for rigid protein docking
type: conference
volume: 3240
year: '2004'
...
---
_id: '3986'
abstract:
- lang: eng
text: The motion of a biomolecule greatly depends on the engulfing solution, which
is mostly water. Instead of representing individual water molecules, it is desirable
to develop implicit solvent models that nevertheless accurately represent the
contribution of the solvent interaction to the motion. In such models, hydrophobicity
is expressed as a weighted sum of atomic surface areas. The derivatives of these
weighted areas contribute to the force that drives the motion. In this paper we
give formulas for the weighted and unweighted area derivatives of a molecule modeled
as a space-filling diagram made up of balls in motion. Other than the radii and
the centers of the balls, the formulas are given in terms of the sizes of circular
arcs of the boundary and edges of the power diagram. We also give inclusion-exclusion
formulas for these sizes.
acknowledgement: Partially supported by NSF under grant CCR-00-86013 and NSF under
grant CCR-97-12088.
author:
- first_name: Robert
full_name: Bryant, Robert
last_name: Bryant
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Patrice
full_name: Koehl, Patrice
last_name: Koehl
- first_name: Michael
full_name: Levitt, Michael
last_name: Levitt
citation:
ama: Bryant R, Edelsbrunner H, Koehl P, Levitt M. The area derivative of a space-filling
diagram. Discrete & Computational Geometry. 2004;32(3):293-308. doi:10.1007/s00454-004-1099-1
apa: Bryant, R., Edelsbrunner, H., Koehl, P., & Levitt, M. (2004). The area
derivative of a space-filling diagram. Discrete & Computational Geometry.
Springer. https://doi.org/10.1007/s00454-004-1099-1
chicago: Bryant, Robert, Herbert Edelsbrunner, Patrice Koehl, and Michael Levitt.
“The Area Derivative of a Space-Filling Diagram.” Discrete & Computational
Geometry. Springer, 2004. https://doi.org/10.1007/s00454-004-1099-1.
ieee: R. Bryant, H. Edelsbrunner, P. Koehl, and M. Levitt, “The area derivative
of a space-filling diagram,” Discrete & Computational Geometry, vol.
32, no. 3. Springer, pp. 293–308, 2004.
ista: Bryant R, Edelsbrunner H, Koehl P, Levitt M. 2004. The area derivative of
a space-filling diagram. Discrete & Computational Geometry. 32(3), 293–308.
mla: Bryant, Robert, et al. “The Area Derivative of a Space-Filling Diagram.” Discrete
& Computational Geometry, vol. 32, no. 3, Springer, 2004, pp. 293–308,
doi:10.1007/s00454-004-1099-1.
short: R. Bryant, H. Edelsbrunner, P. Koehl, M. Levitt, Discrete & Computational
Geometry 32 (2004) 293–308.
date_created: 2018-12-11T12:06:17Z
date_published: 2004-09-01T00:00:00Z
date_updated: 2021-01-12T07:53:40Z
day: '01'
doi: 10.1007/s00454-004-1099-1
extern: 1
intvolume: ' 32'
issue: '3'
month: '09'
page: 293 - 308
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2141'
quality_controlled: 0
status: public
title: The area derivative of a space-filling diagram
type: journal_article
volume: 32
year: '2004'
...
---
_id: '3984'
abstract:
- lang: eng
text: We combine topological and geometric methods to construct a multiresolution
representation for a function over a two-dimensional domain. In a preprocessing
stage, we create the Morse-Smale complex of the function and progressively simplify
its topology by cancelling pairs of critical points. Based on a simple notion
of dependency among these cancellations, we construct a hierarchical data structure
supporting traversal and reconstruction operations similarly to traditional geometry-based
representations. We use this data structure to extract topologically valid approximations
that satisfy error bounds provided at runtime.
author:
- first_name: Peer
full_name: Bremer, Peer-Timo
last_name: Bremer
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Bernd
full_name: Hamann, Bernd
last_name: Hamann
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
citation:
ama: Bremer P, Edelsbrunner H, Hamann B, Pascucci V. A topological hierarchy for
functions on triangulated surfaces. IEEE Transactions on Visualization and
Computer Graphics. 2004;10(4):385-396. doi:10.1109/TVCG.2004.3
apa: Bremer, P., Edelsbrunner, H., Hamann, B., & Pascucci, V. (2004). A topological
hierarchy for functions on triangulated surfaces. IEEE Transactions on Visualization
and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2004.3
chicago: Bremer, Peer, Herbert Edelsbrunner, Bernd Hamann, and Valerio Pascucci.
“A Topological Hierarchy for Functions on Triangulated Surfaces.” IEEE Transactions
on Visualization and Computer Graphics. IEEE, 2004. https://doi.org/10.1109/TVCG.2004.3.
ieee: P. Bremer, H. Edelsbrunner, B. Hamann, and V. Pascucci, “A topological hierarchy
for functions on triangulated surfaces,” IEEE Transactions on Visualization
and Computer Graphics, vol. 10, no. 4. IEEE, pp. 385–396, 2004.
ista: Bremer P, Edelsbrunner H, Hamann B, Pascucci V. 2004. A topological hierarchy
for functions on triangulated surfaces. IEEE Transactions on Visualization and
Computer Graphics. 10(4), 385–396.
mla: Bremer, Peer, et al. “A Topological Hierarchy for Functions on Triangulated
Surfaces.” IEEE Transactions on Visualization and Computer Graphics, vol.
10, no. 4, IEEE, 2004, pp. 385–96, doi:10.1109/TVCG.2004.3.
short: P. Bremer, H. Edelsbrunner, B. Hamann, V. Pascucci, IEEE Transactions on
Visualization and Computer Graphics 10 (2004) 385–396.
date_created: 2018-12-11T12:06:16Z
date_published: 2004-07-01T00:00:00Z
date_updated: 2021-01-12T07:53:39Z
day: '01'
doi: 10.1109/TVCG.2004.3
extern: 1
intvolume: ' 10'
issue: '4'
month: '07'
page: 385 - 396
publication: IEEE Transactions on Visualization and Computer Graphics
publication_status: published
publisher: IEEE
publist_id: '2139'
quality_controlled: 0
status: public
title: A topological hierarchy for functions on triangulated surfaces
type: journal_article
volume: 10
year: '2004'
...
---
_id: '3987'
abstract:
- lang: eng
text: 'We consider scientific data sets that describe density functions over three-dimensional
geometric domains. Such data sets are often large and coarsened representations
are needed for visualization and analysis. Assuming a tetrahedral mesh representation,
we construct such representations with a simplification algorithm that combines
three goals: the approximation of the function, the preservation of the mesh topology,
and the improvement of the mesh quality. The third goal is achieved with a novel
extension of the well-known quadric error metric. We perform a number of computational
experiments to understand the effect of mesh quality improvement on the density
map approximation. In addition, we study the effect of geometric simplification
on the topological features of the function by monitoring its critical points.'
author:
- first_name: Vijay
full_name: Natarajan, Vijay
last_name: Natarajan
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Natarajan V, Edelsbrunner H. Simplification of three-dimensional density maps.
IEEE Transactions on Visualization and Computer Graphics. 2004;10(5):587-597.
doi:10.1109/TVCG.2004.32
apa: Natarajan, V., & Edelsbrunner, H. (2004). Simplification of three-dimensional
density maps. IEEE Transactions on Visualization and Computer Graphics.
IEEE. https://doi.org/10.1109/TVCG.2004.32
chicago: Natarajan, Vijay, and Herbert Edelsbrunner. “Simplification of Three-Dimensional
Density Maps.” IEEE Transactions on Visualization and Computer Graphics.
IEEE, 2004. https://doi.org/10.1109/TVCG.2004.32.
ieee: V. Natarajan and H. Edelsbrunner, “Simplification of three-dimensional density
maps,” IEEE Transactions on Visualization and Computer Graphics, vol. 10,
no. 5. IEEE, pp. 587–597, 2004.
ista: Natarajan V, Edelsbrunner H. 2004. Simplification of three-dimensional density
maps. IEEE Transactions on Visualization and Computer Graphics. 10(5), 587–597.
mla: Natarajan, Vijay, and Herbert Edelsbrunner. “Simplification of Three-Dimensional
Density Maps.” IEEE Transactions on Visualization and Computer Graphics,
vol. 10, no. 5, IEEE, 2004, pp. 587–97, doi:10.1109/TVCG.2004.32.
short: V. Natarajan, H. Edelsbrunner, IEEE Transactions on Visualization and Computer
Graphics 10 (2004) 587–597.
date_created: 2018-12-11T12:06:17Z
date_published: 2004-07-12T00:00:00Z
date_updated: 2021-01-12T07:53:40Z
day: '12'
doi: 10.1109/TVCG.2004.32
extern: 1
intvolume: ' 10'
issue: '5'
month: '07'
page: 587 - 597
publication: IEEE Transactions on Visualization and Computer Graphics
publication_status: published
publisher: IEEE
publist_id: '2142'
quality_controlled: 0
status: public
title: Simplification of three-dimensional density maps
type: journal_article
volume: 10
year: '2004'
...
---
_id: '3985'
abstract:
- lang: eng
text: Given a Morse function f over a 2-manifold with or without boundary, the Reeb
graph is obtained by contracting the connected components of the level sets to
points. We prove tight upper and lower bounds on the number of loops in the Reeb
graph that depend on the genus, the number of boundary components, and whether
or not the 2-manifold is orientable. We also give an algorithm that constructs
the Reeb graph in time O(n log n), where n is the number of edges in the triangulation
used to represent the 2-manifold and the Morse function.
acknowledgement: Partially supported by NSF under Grants EIA-99-72879 and CCR-00-86013.
author:
- first_name: Kree
full_name: Cole-McLaughlin, Kree
last_name: Cole Mclaughlin
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Vijay
full_name: Natarajan, Vijay
last_name: Natarajan
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
citation:
ama: Cole Mclaughlin K, Edelsbrunner H, Harer J, Natarajan V, Pascucci V. Loops
in Reeb graphs of 2-manifolds. Discrete & Computational Geometry. 2004;32(2):231-244.
doi:10.1007/s00454-004-1122-6
apa: Cole Mclaughlin, K., Edelsbrunner, H., Harer, J., Natarajan, V., & Pascucci,
V. (2004). Loops in Reeb graphs of 2-manifolds. Discrete & Computational
Geometry. Springer. https://doi.org/10.1007/s00454-004-1122-6
chicago: Cole Mclaughlin, Kree, Herbert Edelsbrunner, John Harer, Vijay Natarajan,
and Valerio Pascucci. “Loops in Reeb Graphs of 2-Manifolds.” Discrete &
Computational Geometry. Springer, 2004. https://doi.org/10.1007/s00454-004-1122-6.
ieee: K. Cole Mclaughlin, H. Edelsbrunner, J. Harer, V. Natarajan, and V. Pascucci,
“Loops in Reeb graphs of 2-manifolds,” Discrete & Computational Geometry,
vol. 32, no. 2. Springer, pp. 231–244, 2004.
ista: Cole Mclaughlin K, Edelsbrunner H, Harer J, Natarajan V, Pascucci V. 2004.
Loops in Reeb graphs of 2-manifolds. Discrete & Computational Geometry. 32(2),
231–244.
mla: Cole Mclaughlin, Kree, et al. “Loops in Reeb Graphs of 2-Manifolds.” Discrete
& Computational Geometry, vol. 32, no. 2, Springer, 2004, pp. 231–44,
doi:10.1007/s00454-004-1122-6.
short: K. Cole Mclaughlin, H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci,
Discrete & Computational Geometry 32 (2004) 231–244.
date_created: 2018-12-11T12:06:16Z
date_published: 2004-07-01T00:00:00Z
date_updated: 2021-01-12T07:53:39Z
day: '01'
doi: 10.1007/s00454-004-1122-6
extern: 1
intvolume: ' 32'
issue: '2'
month: '07'
page: 231 - 244
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2140'
quality_controlled: 0
status: public
title: Loops in Reeb graphs of 2-manifolds
type: journal_article
volume: 32
year: '2004'
...
---
_id: '3989'
abstract:
- lang: eng
text: We introduce local and global comparison measures for a collection of k less
than or equal to d real-valued smooth functions on a common d-dimensional Riemannian
manifold. For k = d = 2 we relate the measures to the set of critical points of
one function restricted to the level sets of the other. The definition of the
measures extends to piecewise linear functions for which they ace easy to compute.
The computation of the measures forms the centerpiece of a software tool which
we use to study scientific datasets.
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Vijay
full_name: Natarajan, Vijay
last_name: Natarajan
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
citation:
ama: 'Edelsbrunner H, Harer J, Natarajan V, Pascucci V. Local and global comparison
of continuous functions. In: IEEE; 2004:275-280. doi:10.1109/VISUAL.2004.68'
apa: 'Edelsbrunner, H., Harer, J., Natarajan, V., & Pascucci, V. (2004). Local
and global comparison of continuous functions (pp. 275–280). Presented at the
VIS: IEEE Visualization, IEEE. https://doi.org/10.1109/VISUAL.2004.68'
chicago: Edelsbrunner, Herbert, John Harer, Vijay Natarajan, and Valerio Pascucci.
“Local and Global Comparison of Continuous Functions,” 275–80. IEEE, 2004. https://doi.org/10.1109/VISUAL.2004.68.
ieee: 'H. Edelsbrunner, J. Harer, V. Natarajan, and V. Pascucci, “Local and global
comparison of continuous functions,” presented at the VIS: IEEE Visualization,
2004, pp. 275–280.'
ista: 'Edelsbrunner H, Harer J, Natarajan V, Pascucci V. 2004. Local and global
comparison of continuous functions. VIS: IEEE Visualization, 275–280.'
mla: Edelsbrunner, Herbert, et al. Local and Global Comparison of Continuous
Functions. IEEE, 2004, pp. 275–80, doi:10.1109/VISUAL.2004.68.
short: H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci, in:, IEEE, 2004, pp.
275–280.
conference:
name: 'VIS: IEEE Visualization'
date_created: 2018-12-11T12:06:18Z
date_published: 2004-10-01T00:00:00Z
date_updated: 2021-01-12T07:53:41Z
day: '01'
doi: 10.1109/VISUAL.2004.68
extern: 1
month: '10'
page: 275 - 280
publication_status: published
publisher: IEEE
publist_id: '2137'
quality_controlled: 0
status: public
title: Local and global comparison of continuous functions
type: conference
year: '2004'
...
---
_id: '4172'
abstract:
- lang: eng
text: 'During vertebrate gastrulation, a relatively limited number of blastodermal
cells undergoes a stereotypical set of cellular movements that leads to formation
of the three germ layers: ectoderm, mesoderm and endoderm. Gastrulation, therefore,
provides a unique developmental system in which to study cell movements in vivo
in a fairly simple cellular context. Recent advances have been made in elucidating
the cellular and molecular mechanisms that underlie cell movements during zebrafish
gastrulation. These findings can be compared with observations made in other model
systems to identify potential general mechanisms of cell migration during development.'
article_processing_charge: No
author:
- first_name: Juan
full_name: Montero, Juan
last_name: Montero
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: 'Montero J, Heisenberg C-PJ. Gastrulation dynamics: cells move into focus.
Trends in Cell Biology. 2004;14(11):620-627. doi:10.1016/j.tcb.2004.09.008'
apa: 'Montero, J., & Heisenberg, C.-P. J. (2004). Gastrulation dynamics: cells
move into focus. Trends in Cell Biology. Cell Press. https://doi.org/10.1016/j.tcb.2004.09.008'
chicago: 'Montero, Juan, and Carl-Philipp J Heisenberg. “Gastrulation Dynamics:
Cells Move into Focus.” Trends in Cell Biology. Cell Press, 2004. https://doi.org/10.1016/j.tcb.2004.09.008.'
ieee: 'J. Montero and C.-P. J. Heisenberg, “Gastrulation dynamics: cells move into
focus,” Trends in Cell Biology, vol. 14, no. 11. Cell Press, pp. 620–627,
2004.'
ista: 'Montero J, Heisenberg C-PJ. 2004. Gastrulation dynamics: cells move into
focus. Trends in Cell Biology. 14(11), 620–627.'
mla: 'Montero, Juan, and Carl-Philipp J. Heisenberg. “Gastrulation Dynamics: Cells
Move into Focus.” Trends in Cell Biology, vol. 14, no. 11, Cell Press,
2004, pp. 620–27, doi:10.1016/j.tcb.2004.09.008.'
short: J. Montero, C.-P.J. Heisenberg, Trends in Cell Biology 14 (2004) 620–627.
date_created: 2018-12-11T12:07:23Z
date_published: 2004-11-01T00:00:00Z
date_updated: 2021-01-12T07:55:02Z
day: '01'
doi: 10.1016/j.tcb.2004.09.008
extern: '1'
intvolume: ' 14'
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 620 - 627
publication: Trends in Cell Biology
publication_status: published
publisher: Cell Press
publist_id: '1948'
status: public
title: 'Gastrulation dynamics: cells move into focus'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2004'
...
---
_id: '4238'
abstract:
- lang: eng
text: The dynamical basis of tumoral growth has been controversial. Many models
have been proposed to explain cancer development. The descriptions employ exponential,
potential, logistic or Gompertzian growth laws. Some of these models are concerned
with the interaction between cancer and the immunological, system. Among other
properties, these models are concerned with the microscopic behavior of tumors
and the emergence of cancer. We propose a modification of a previous model by
Stepanova, which describes the specific immunological response against cancer.
The modification consists of the substitution of a Gompertian law for the exponential
rate used for tumoral growth. This modification is motivated by the numerous works
confirming that Gompertz's equation correctly describes solid tumor growth. The
modified model predicts that near zero, tumors always tend to grow. Immunological
contraposition never suffices to induce a complete regression of the tumor. Instead,
a stable microscopic equilibrium between cancer and immunological activity can
be attained. In other words, our model predicts that the theory of immune surveillance
is plausible. A macroscopic equilibrium in which the system develops cancer is
also possible. In this case, immunological activity is depleted. This is consistent
with the phenomena of cancer tolerance. Both equilibrium points can coexist or
can exist without the other. In all cases the fixed point at zero tumor size is
unstable. Since immunity cannot induce a complete tumor regression, a therapy
is required. We include constant-dose therapies and show that they are insufficient.
Final levels of immunocompetent cells and tumoral cells are finite, thus post-treatment
regrowth of the tumor is certain. We also evaluate late-intensification therapies
which are successful. They induce an asymptotic regression to zero tumor size.
Immune response is also suppressed by the therapy, and thus plays a negligible
role in the remission. We conclude that treatment evaluation should be successful
without taking into account immunological effects. (C) 2003 Elsevier Ltd. All
rights reserved.
article_processing_charge: No
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: J.
full_name: González, J.
last_name: González
citation:
ama: de Vladar H, González J. Dynamic response of cancer under the influence of
immunological activity and therapy. Journal of Theoretical Biology. 2004;227(3):335-348.
doi:3801
apa: de Vladar, H., & González, J. (2004). Dynamic response of cancer under
the influence of immunological activity and therapy. Journal of Theoretical
Biology. Elsevier. https://doi.org/3801
chicago: Vladar, Harold de, and J. González. “Dynamic Response of Cancer under the
Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology.
Elsevier, 2004. https://doi.org/3801.
ieee: H. de Vladar and J. González, “Dynamic response of cancer under the influence
of immunological activity and therapy,” Journal of Theoretical Biology,
vol. 227, no. 3. Elsevier, pp. 335–348, 2004.
ista: de Vladar H, González J. 2004. Dynamic response of cancer under the influence
of immunological activity and therapy. Journal of Theoretical Biology. 227(3),
335–348.
mla: de Vladar, Harold, and J. González. “Dynamic Response of Cancer under the Influence
of Immunological Activity and Therapy.” Journal of Theoretical Biology,
vol. 227, no. 3, Elsevier, 2004, pp. 335–48, doi:3801.
short: H. de Vladar, J. González, Journal of Theoretical Biology 227 (2004) 335–348.
date_created: 2018-12-11T12:07:46Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:31Z
day: '01'
doi: '3801'
extern: '1'
intvolume: ' 227'
issue: '3'
language:
- iso: eng
month: '01'
oa_version: None
page: 335 - 348
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '1876'
status: public
title: Dynamic response of cancer under the influence of immunological activity and
therapy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 227
year: '2004'
...
---
_id: '4230'
alternative_title:
- Cellular Origin and Life in Extreme Habitats and Astrobiology
author:
- first_name: Harold
full_name: Harold Vladar
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
- first_name: Roberto
full_name: Cipriani, Roberto
last_name: Cipriani
- first_name: Benjamin
full_name: Scharifker, Benjamin
last_name: Scharifker
- first_name: Jose
full_name: Bubis, Jose
last_name: Bubis
citation:
ama: 'de Vladar H, Cipriani R, Scharifker B, Bubis J. A mechanism for the prebiotic
emergence of proteins. In: Hanslmeier A, Kempe S, Seckbach J, eds. Life in
the Universe From the Miller Experiment to the Search for Life on Other Worlds.
Springer; 2004:83-87.'
apa: de Vladar, H., Cipriani, R., Scharifker, B., & Bubis, J. (2004). A mechanism
for the prebiotic emergence of proteins. In A. Hanslmeier, S. Kempe, & J.
Seckbach (Eds.), Life in the Universe From the Miller Experiment to the Search
for Life on Other Worlds (pp. 83–87). Springer.
chicago: Vladar, Harold de, Roberto Cipriani, Benjamin Scharifker, and Jose Bubis.
“A Mechanism for the Prebiotic Emergence of Proteins.” In Life in the Universe
From the Miller Experiment to the Search for Life on Other Worlds, edited
by A. Hanslmeier, S. Kempe, and J. Seckbach, 83–87. Springer, 2004.
ieee: H. de Vladar, R. Cipriani, B. Scharifker, and J. Bubis, “A mechanism for the
prebiotic emergence of proteins,” in Life in the Universe From the Miller Experiment
to the Search for Life on Other Worlds, A. Hanslmeier, S. Kempe, and J. Seckbach,
Eds. Springer, 2004, pp. 83–87.
ista: 'de Vladar H, Cipriani R, Scharifker B, Bubis J. 2004.A mechanism for the
prebiotic emergence of proteins. In: Life in the Universe From the Miller Experiment
to the Search for Life on Other Worlds. Cellular Origin and Life in Extreme Habitats
and Astrobiology, , 83–87.'
mla: de Vladar, Harold, et al. “A Mechanism for the Prebiotic Emergence of Proteins.”
Life in the Universe From the Miller Experiment to the Search for Life on Other
Worlds, edited by A. Hanslmeier et al., Springer, 2004, pp. 83–87.
short: H. de Vladar, R. Cipriani, B. Scharifker, J. Bubis, in:, A. Hanslmeier, S.
Kempe, J. Seckbach (Eds.), Life in the Universe From the Miller Experiment to
the Search for Life on Other Worlds, Springer, 2004, pp. 83–87.
date_created: 2018-12-11T12:07:44Z
date_published: 2004-12-31T00:00:00Z
date_updated: 2021-01-12T07:55:28Z
day: '31'
editor:
- first_name: A.
full_name: Hanslmeier,A.
last_name: Hanslmeier
- first_name: S.
full_name: Kempe,S.
last_name: Kempe
- first_name: J.
full_name: Seckbach,J.
last_name: Seckbach
extern: 1
month: '12'
page: 83 - 87
publication: Life in the Universe From the Miller Experiment to the Search for Life
on Other Worlds
publication_status: published
publisher: Springer
publist_id: '1884'
quality_controlled: 0
status: public
title: A mechanism for the prebiotic emergence of proteins
type: book_chapter
year: '2004'
...
---
_id: '4236'
article_processing_charge: No
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
citation:
ama: de Vladar H. Métodos no lineales y sus aplicaciones en dinámicas aleatorias
de poblaciones celulares. 2004. doi:3810
apa: de Vladar, H. (2004). Métodos no lineales y sus aplicaciones en dinámicas
aleatorias de poblaciones celulares. Centro de estudios avazados, IVIC. https://doi.org/3810
chicago: Vladar, Harold de. “Métodos No Lineales y Sus Aplicaciones En Dinámicas
Aleatorias de Poblaciones Celulares.” Centro de estudios avazados, IVIC, 2004.
https://doi.org/3810.
ieee: H. de Vladar, “Métodos no lineales y sus aplicaciones en dinámicas aleatorias
de poblaciones celulares,” Centro de estudios avazados, IVIC, 2004.
ista: de Vladar H. 2004. Métodos no lineales y sus aplicaciones en dinámicas aleatorias
de poblaciones celulares. Centro de estudios avazados, IVIC.
mla: de Vladar, Harold. Métodos No Lineales y Sus Aplicaciones En Dinámicas Aleatorias
de Poblaciones Celulares. Centro de estudios avazados, IVIC, 2004, doi:3810.
short: H. de Vladar, Métodos No Lineales y Sus Aplicaciones En Dinámicas Aleatorias
de Poblaciones Celulares, Centro de estudios avazados, IVIC, 2004.
date_created: 2018-12-11T12:07:46Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:30Z
day: '01'
doi: '3810'
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication_status: published
publisher: Centro de estudios avazados, IVIC
publist_id: '1877'
status: public
title: Métodos no lineales y sus aplicaciones en dinámicas aleatorias de poblaciones
celulares
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2004'
...
---
_id: '4372'
alternative_title:
- LNCS
author:
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Dejan Nickovic
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
citation:
ama: 'Maler O, Nickovic D. Monitoring Temporal Properties of Continuous Signals.
In: Springer; 2004:152-166. doi:1572'
apa: 'Maler, O., & Nickovic, D. (2004). Monitoring Temporal Properties of Continuous
Signals (pp. 152–166). Presented at the FORMATS: Formal Modeling and Analysis
of Timed Systems, Springer. https://doi.org/1572'
chicago: Maler, Oded, and Dejan Nickovic. “Monitoring Temporal Properties of Continuous
Signals,” 152–66. Springer, 2004. https://doi.org/1572.
ieee: 'O. Maler and D. Nickovic, “Monitoring Temporal Properties of Continuous Signals,”
presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2004,
pp. 152–166.'
ista: 'Maler O, Nickovic D. 2004. Monitoring Temporal Properties of Continuous Signals.
FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, , 152–166.'
mla: Maler, Oded, and Dejan Nickovic. Monitoring Temporal Properties of Continuous
Signals. Springer, 2004, pp. 152–66, doi:1572.
short: O. Maler, D. Nickovic, in:, Springer, 2004, pp. 152–166.
conference:
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
date_created: 2018-12-11T12:08:31Z
date_published: 2004-12-14T00:00:00Z
date_updated: 2021-01-12T07:56:29Z
day: '14'
doi: '1572'
extern: 1
month: '12'
page: 152 - 166
publication_status: published
publisher: Springer
publist_id: '1088'
quality_controlled: 0
status: public
title: Monitoring Temporal Properties of Continuous Signals
type: conference
year: '2004'
...
---
_id: '4424'
abstract:
- lang: eng
text: "The enormous cost and ubiquity of software errors necessitates the need for
techniques and tools that can precisely analyze large systems and prove that they
meet given specifications, or if they don't, return counterexample behaviors showing
how the system fails. Recent advances in model checking, decision procedures,
program analysis and type systems, and a shift of focus to partial specifications
common to several systems (e.g., memory safety and race freedom) have resulted
in several practical verification methods. However, these methods are either precise
or they are scalable, depending on whether they track the values of variables
or only a fixed small set of dataflow facts (e.g., types), and are usually insufficient
for precisely verifying large programs.\r\n\r\nWe describe a new technique called
Lazy Abstraction (LA) which achieves both precision and scalability by localizing
the use of precise information. LA automatically builds, explores and refines
a single abstract model of the program in a way that different parts of the model
exhibit different degrees of precision, namely just enough to verify the desired
property. The algorithm automatically mines the information required by partitioning
mechanical proofs of unsatisfiability of spurious counterexamples into Craig Interpolants.
For multithreaded systems, we give a new technique based on analyzing the behavior
of a single thread executing in a context which is an abstraction of the other
(arbitrarily many) threads. We define novel context models and show how to automatically
infer them and analyze the full system (thread + context) using LA.\r\n\r\nLA
is implemented in BLAST. We have run BLAST on Windows and Linux Device Drivers
to verify API conformance properties, and have used it to find (or guarantee the
absence of) data races in multithreaded Networked Embedded Systems (NESC) applications.
BLAST is able to prove the absence of races in several cases where earlier methods,
which depend on lock-based synchronization, fail."
article_processing_charge: No
author:
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
citation:
ama: Jhala R. Program verification by lazy abstraction. 2004:1-165.
apa: Jhala, R. (2004). Program verification by lazy abstraction. University
of California, Berkeley.
chicago: Jhala, Ranjit. “Program Verification by Lazy Abstraction.” University of
California, Berkeley, 2004.
ieee: R. Jhala, “Program verification by lazy abstraction,” University of California,
Berkeley, 2004.
ista: Jhala R. 2004. Program verification by lazy abstraction. University of California,
Berkeley.
mla: Jhala, Ranjit. Program Verification by Lazy Abstraction. University
of California, Berkeley, 2004, pp. 1–165.
short: R. Jhala, Program Verification by Lazy Abstraction, University of California,
Berkeley, 2004.
date_created: 2018-12-11T12:08:47Z
date_published: 2004-12-01T00:00:00Z
date_updated: 2021-01-12T07:56:52Z
day: '01'
extern: '1'
language:
- iso: eng
month: '12'
oa_version: None
page: 1 - 165
publication_status: published
publisher: University of California, Berkeley
publist_id: '307'
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
title: Program verification by lazy abstraction
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2004'
...
---
_id: '4445'
abstract:
- lang: eng
text: We present a type system for E code, which is an assembly language that manages
the release, interaction, and termination of real-time tasks. E code specifies
a deadline for each task, and the type system ensures that the deadlines are path-insensitive.
We show that typed E programs allow, for given worst-case execution times of tasks,
a simple schedulability analysis. Moreover, the real-time programming language
Giotto can be compiled into typed E~code. This shows that typed E~code identifies
an easily schedulable yet expressive class of real-time programs. We have extended
the Giotto compiler to generate typed E code, and enabled the run-time system
for E code to perform a type and schedulability check before executing the code.
acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327
and by the NSF grants CCR- 0208875 and CCR-0225610.
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Christoph
full_name: Kirsch, Christoph M
last_name: Kirsch
citation:
ama: 'Henzinger TA, Kirsch C. A typed assembly language for real-time programs.
In: ACM; 2004:104-113. doi:10.1145/1017753.1017774'
apa: 'Henzinger, T. A., & Kirsch, C. (2004). A typed assembly language for real-time
programs (pp. 104–113). Presented at the EMSOFT: Embedded Software , ACM. https://doi.org/10.1145/1017753.1017774'
chicago: Henzinger, Thomas A, and Christoph Kirsch. “A Typed Assembly Language for
Real-Time Programs,” 104–13. ACM, 2004. https://doi.org/10.1145/1017753.1017774.
ieee: 'T. A. Henzinger and C. Kirsch, “A typed assembly language for real-time programs,”
presented at the EMSOFT: Embedded Software , 2004, pp. 104–113.'
ista: 'Henzinger TA, Kirsch C. 2004. A typed assembly language for real-time programs.
EMSOFT: Embedded Software , 104–113.'
mla: Henzinger, Thomas A., and Christoph Kirsch. A Typed Assembly Language for
Real-Time Programs. ACM, 2004, pp. 104–13, doi:10.1145/1017753.1017774.
short: T.A. Henzinger, C. Kirsch, in:, ACM, 2004, pp. 104–113.
conference:
name: 'EMSOFT: Embedded Software '
date_created: 2018-12-11T12:08:53Z
date_published: 2004-09-01T00:00:00Z
date_updated: 2021-01-12T07:57:01Z
day: '01'
doi: 10.1145/1017753.1017774
extern: 1
month: '09'
page: 104 - 113
publication_status: published
publisher: ACM
publist_id: '285'
quality_controlled: 0
status: public
title: A typed assembly language for real-time programs
type: conference
year: '2004'
...
---
_id: '4458'
abstract:
- lang: eng
text: 'The success of model checking for large programs depends crucially on the
ability to efficiently construct parsimonious abstractions. A predicate abstraction
is parsimonious if at each control location, it specifies only relationships between
current values of variables, and only those which are required for proving correctness.
Previous methods for automatically refining predicate abstractions until sufficient
precision is obtained do not systematically construct parsimonious abstractions:
predicates usually contain symbolic variables, and are added heuristically and
often uniformly to many or all control locations at once. We use Craig interpolation
to efficiently construct, from a given abstract error trace which cannot be concretized,
a parsominous abstraction that removes the trace. At each location of the trace,
we infer the relevant predicates as an interpolant between the two formulas that
define the past and the future segment of the trace. Each interpolant is a relationship
between current values of program variables, and is relevant only at that particular
program location. It can be found by a linear scan of the proof of infeasibility
of the trace.We develop our method for programs with arithmetic and pointer expressions,
and call-by-value function calls. For function calls, Craig interpolation offers
a systematic way of generating relevant predicates that contain only the local
variables of the function and the values of the formal parameters when the function
was called. We have extended our model checker Blast with predicate discovery
by Craig interpolation, and applied it successfully to C programs with more than
130,000 lines of code, which was not possible with approaches that build less
parsimonious abstractions.'
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Kenneth
full_name: McMillan, Kenneth L
last_name: Mcmillan
citation:
ama: 'Henzinger TA, Jhala R, Majumdar R, Mcmillan K. Abstractions from proofs. In:
ACM; 2004:232-244. doi:10.1145/964001.964021'
apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Mcmillan, K. (2004). Abstractions
from proofs (pp. 232–244). Presented at the POPL: Principles of Programming Languages,
ACM. https://doi.org/10.1145/964001.964021'
chicago: Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Kenneth Mcmillan.
“Abstractions from Proofs,” 232–44. ACM, 2004. https://doi.org/10.1145/964001.964021.
ieee: 'T. A. Henzinger, R. Jhala, R. Majumdar, and K. Mcmillan, “Abstractions from
proofs,” presented at the POPL: Principles of Programming Languages, 2004, pp.
232–244.'
ista: 'Henzinger TA, Jhala R, Majumdar R, Mcmillan K. 2004. Abstractions from proofs.
POPL: Principles of Programming Languages, 232–244.'
mla: Henzinger, Thomas A., et al. Abstractions from Proofs. ACM, 2004, pp.
232–44, doi:10.1145/964001.964021.
short: T.A. Henzinger, R. Jhala, R. Majumdar, K. Mcmillan, in:, ACM, 2004, pp. 232–244.
conference:
name: 'POPL: Principles of Programming Languages'
date_created: 2018-12-11T12:08:57Z
date_published: 2004-04-01T00:00:00Z
date_updated: 2021-01-12T07:57:06Z
day: '01'
doi: 10.1145/964001.964021
extern: 1
month: '04'
page: 232 - 244
publication_status: published
publisher: ACM
publist_id: '270'
quality_controlled: 0
status: public
title: Abstractions from proofs
type: conference
year: '2004'
...
---
_id: '4461'
abstract:
- lang: eng
text: One of the central axioms of extreme programming is the disciplined use of
regression testing during stepwise software development. Due to recent progress
in software model checking, it has become possible to supplement this process
with automatic checks for behavioral safety properties of programs, such as conformance
with locking idioms and other programming protocols and patterns. For efficiency
reasons, all checks must be incremental, i.e., they must reuse partial results
from previous checks in order to avoid all unnecessary repetition of expensive
verification tasks. We show that the lazy-abstraction algorithm, and its implementation
in Blast, can be extended to support the fully automatic and incremental checking
of temporal safety properties during software development.
acknowledgement: 'This work was supported in part by the NSF grants CCR-9988172, CCR-0085949,
and CCR-0234690, the ONR grant N00014-02-1-0671, the DARPA grant F33615-00-C-1693,
and the MARCO grant 98-DT-660. '
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Marco
full_name: Sanvido, Marco A
last_name: Sanvido
citation:
ama: 'Henzinger TA, Jhala R, Majumdar R, Sanvido M. Extreme model checking. In:
Verification: Theory and Practice. Vol 2772. Springer; 2004:332-358. doi:10.1007/978-3-540-39910-0_16'
apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Sanvido, M. (2004). Extreme
model checking. In Verification: Theory and Practice (Vol. 2772, pp. 332–358).
Springer. https://doi.org/10.1007/978-3-540-39910-0_16'
chicago: 'Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Marco Sanvido.
“Extreme Model Checking.” In Verification: Theory and Practice, 2772:332–58.
Springer, 2004. https://doi.org/10.1007/978-3-540-39910-0_16.'
ieee: 'T. A. Henzinger, R. Jhala, R. Majumdar, and M. Sanvido, “Extreme model checking,”
in Verification: Theory and Practice, vol. 2772, Springer, 2004, pp. 332–358.'
ista: 'Henzinger TA, Jhala R, Majumdar R, Sanvido M. 2004.Extreme model checking.
In: Verification: Theory and Practice. LNCS, vol. 2772, 332–358.'
mla: 'Henzinger, Thomas A., et al. “Extreme Model Checking.” Verification: Theory
and Practice, vol. 2772, Springer, 2004, pp. 332–58, doi:10.1007/978-3-540-39910-0_16.'
short: 'T.A. Henzinger, R. Jhala, R. Majumdar, M. Sanvido, in:, Verification: Theory
and Practice, Springer, 2004, pp. 332–358.'
date_created: 2018-12-11T12:08:58Z
date_published: 2004-02-24T00:00:00Z
date_updated: 2021-01-12T07:57:08Z
day: '24'
doi: 10.1007/978-3-540-39910-0_16
extern: 1
intvolume: ' 2772'
month: '02'
page: 332 - 358
publication: 'Verification: Theory and Practice'
publication_status: published
publisher: Springer
publist_id: '269'
quality_controlled: 0
status: public
title: Extreme model checking
type: book_chapter
volume: 2772
year: '2004'
...
---
_id: '4459'
abstract:
- lang: eng
text: Software model checking has been successful for sequential programs, where
predicate abstraction offers suitable models, and counterexample-guided abstraction
refinement permits the automatic inference of models. When checking concurrent
programs, we need to abstract threads as well as the contexts in which they execute.
Stateless context models, such as predicates on global variables, prove insufficient
for showing the absence of race conditions in many examples. We therefore use
richer context models, which combine (1) predicates for abstracting data state,
(2) control flow quotients for abstracting control state, and (3) counters for
abstracting an unbounded number of threads. We infer suitable context models automatically
by a combination of counterexample-guided abstraction refinement, bisimulation
minimization, circular assume-guarantee reasoning, and parametric reasoning about
an unbounded number of threads. This algorithm, called CIRC, has been implemented
in BLAST and succeeds in checking many examples of NESC code for data races. In
particular, BLAST proves the absence of races in several cases where previous
race checkers give false positives.
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
citation:
ama: 'Henzinger TA, Jhala R, Majumdar R. Race checking by context inference. In:
ACM; 2004:1-13. doi:10.1145/996841.996844'
apa: 'Henzinger, T. A., Jhala, R., & Majumdar, R. (2004). Race checking by context
inference (pp. 1–13). Presented at the PLDI: Programming Languages Design and
Implementation, ACM. https://doi.org/10.1145/996841.996844'
chicago: Henzinger, Thomas A, Ranjit Jhala, and Ritankar Majumdar. “Race Checking
by Context Inference,” 1–13. ACM, 2004. https://doi.org/10.1145/996841.996844.
ieee: 'T. A. Henzinger, R. Jhala, and R. Majumdar, “Race checking by context inference,”
presented at the PLDI: Programming Languages Design and Implementation, 2004,
pp. 1–13.'
ista: 'Henzinger TA, Jhala R, Majumdar R. 2004. Race checking by context inference.
PLDI: Programming Languages Design and Implementation, 1–13.'
mla: Henzinger, Thomas A., et al. Race Checking by Context Inference. ACM,
2004, pp. 1–13, doi:10.1145/996841.996844.
short: T.A. Henzinger, R. Jhala, R. Majumdar, in:, ACM, 2004, pp. 1–13.
conference:
name: 'PLDI: Programming Languages Design and Implementation'
date_created: 2018-12-11T12:08:57Z
date_published: 2004-06-01T00:00:00Z
date_updated: 2021-01-12T07:57:07Z
day: '01'
doi: 10.1145/996841.996844
extern: 1
month: '06'
page: 1 - 13
publication_status: published
publisher: ACM
publist_id: '271'
quality_controlled: 0
status: public
title: Race checking by context inference
type: conference
year: '2004'
...
---
_id: '4525'
abstract:
- lang: eng
text: 'We present a new high-level programming language, called xGiotto, for programming
applications with hard real-time constraints. Like its predecessor, xGiotto is
based on the LET (logical execution time) assumption: the programmer specifies
when the outputs of a task become available, and the compiler checks if the specification
can be implemented on a given platform. However, while the predecessor language
xGiotto was purely time-triggered, xGiotto accommodates also asynchronous events.
Indeed, through a mechanism called event scoping, events are the main structuring
principle of the new language. The xGiotto compiler and run-time system implement
event scoping through a tree-based event filter. The compiler also checks programs
for determinism (absence of race conditions).'
acknowledgement: This research is supported by the AFOSR MURI grant F49620-00-1-0327,
the DARPA SEC grant F33615-C-98-3614, the MARCO GSRC grant 98-DT-660, and the NSF
grants CCR-0208875 and CCR-0225610.
alternative_title:
- LNCS
author:
- first_name: Arkadeb
full_name: Ghosal, Arkadeb
last_name: Ghosal
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Christoph
full_name: Kirsch, Christoph M
last_name: Kirsch
- first_name: Marco
full_name: Sanvido, Marco A
last_name: Sanvido
citation:
ama: 'Ghosal A, Henzinger TA, Kirsch C, Sanvido M. Event-driven programming with
logical execution times. In: Vol 2993. Springer; 2004:167-170. doi:10.1007/978-3-540-24743-2_24'
apa: 'Ghosal, A., Henzinger, T. A., Kirsch, C., & Sanvido, M. (2004). Event-driven
programming with logical execution times (Vol. 2993, pp. 167–170). Presented at
the HSCC: Hybrid Systems - Computation and Control, Springer. https://doi.org/10.1007/978-3-540-24743-2_24'
chicago: Ghosal, Arkadeb, Thomas A Henzinger, Christoph Kirsch, and Marco Sanvido.
“Event-Driven Programming with Logical Execution Times,” 2993:167–70. Springer,
2004. https://doi.org/10.1007/978-3-540-24743-2_24.
ieee: 'A. Ghosal, T. A. Henzinger, C. Kirsch, and M. Sanvido, “Event-driven programming
with logical execution times,” presented at the HSCC: Hybrid Systems - Computation
and Control, 2004, vol. 2993, pp. 167–170.'
ista: 'Ghosal A, Henzinger TA, Kirsch C, Sanvido M. 2004. Event-driven programming
with logical execution times. HSCC: Hybrid Systems - Computation and Control,
LNCS, vol. 2993, 167–170.'
mla: Ghosal, Arkadeb, et al. Event-Driven Programming with Logical Execution
Times. Vol. 2993, Springer, 2004, pp. 167–70, doi:10.1007/978-3-540-24743-2_24.
short: A. Ghosal, T.A. Henzinger, C. Kirsch, M. Sanvido, in:, Springer, 2004, pp.
167–170.
conference:
name: 'HSCC: Hybrid Systems - Computation and Control'
date_created: 2018-12-11T12:09:18Z
date_published: 2004-03-12T00:00:00Z
date_updated: 2021-01-12T07:59:26Z
day: '12'
doi: 10.1007/978-3-540-24743-2_24
extern: 1
intvolume: ' 2993'
month: '03'
page: 167 - 170
publication_status: published
publisher: Springer
publist_id: '200'
quality_controlled: 0
status: public
title: Event-driven programming with logical execution times
type: conference
volume: 2993
year: '2004'
...
---
_id: '4555'
abstract:
- lang: eng
text: Strategies in repeated games can be classified as to whether or not they use
memory and/or randomization. We consider Markov decision processes and 2-player
graph games, both of the deterministic and probabilistic varieties. We characterize
when memory and/or randomization are required for winning with respect to various
classes of w-regular objectives, noting particularly when the use of memory can
be traded for the use of randomization. In particular, we show that Markov decision
processes allow randomized memoryless optimal strategies for all M?ller objectives.
Furthermore, we show that 2-player probabilistic graph games allow randomized
memoryless strategies for winning with probability 1 those M?ller objectives which
are upward-closed. Upward-closure means that if a set α of infinitely repeating
vertices is winning, then all supersets of α are also winning.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Luca
full_name: de Alfaro, Luca
last_name: De Alfaro
- 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, De Alfaro L, Henzinger TA. Trading memory for randomness. In:
IEEE; 2004:206-217. doi:10.1109/QEST.2004.10051'
apa: 'Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2004). Trading memory
for randomness (pp. 206–217). Presented at the QEST: Quantitative Evaluation of
Systems, IEEE. https://doi.org/10.1109/QEST.2004.10051'
chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Trading
Memory for Randomness,” 206–17. IEEE, 2004. https://doi.org/10.1109/QEST.2004.10051.
ieee: 'K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Trading memory for randomness,”
presented at the QEST: Quantitative Evaluation of Systems, 2004, pp. 206–217.'
ista: 'Chatterjee K, De Alfaro L, Henzinger TA. 2004. Trading memory for randomness.
QEST: Quantitative Evaluation of Systems, 206–217.'
mla: Chatterjee, Krishnendu, et al. Trading Memory for Randomness. IEEE,
2004, pp. 206–17, doi:10.1109/QEST.2004.10051.
short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, IEEE, 2004, pp. 206–217.
conference:
name: 'QEST: Quantitative Evaluation of Systems'
date_created: 2018-12-11T12:09:27Z
date_published: 2004-09-30T00:00:00Z
date_updated: 2021-01-12T07:59:40Z
day: '30'
doi: 10.1109/QEST.2004.10051
extern: 1
month: '09'
page: 206 - 217
publication_status: published
publisher: IEEE
publist_id: '155'
quality_controlled: 0
status: public
title: Trading memory for randomness
type: conference
year: '2004'
...
---
_id: '4558'
abstract:
- lang: eng
text: We study perfect-information stochastic parity games. These are two-player
nonterminating games which are played on a graph with turn-based probabilistic
transitions. A play results in an infinite path and the conflicting goals of the
two players are ω-regular path properties, formalized as parity winning conditions.
The qualitative solution of such a game amounts to computing the set of vertices
from which a player has a strategy to win with probability 1 (or with positive
probability). The quantitative solution amounts to computing the value of the
game in every vertex, i.e., the highest probability with which a player can guarantee
satisfaction of his own objective in a play that starts from the vertex.For the
important special case of one-player stochastic parity games (parity Markov decision
processes) we give polynomial-time algorithms both for the qualitative and the
quantitative solution. The running time of the qualitative solution is O(d · m3/2)
for graphs with m edges and d priorities. The quantitative solution is based on
a linear-programming formulation.For the two-player case, we establish the existence
of optimal pure memoryless strategies. This has several important ramifications.
First, it implies that the values of the games are rational. This is in contrast
to the concurrent stochastic parity games of de Alfaro et al.; there, values are
in general algebraic numbers, optimal strategies do not exist, and ε-optimal strategies
have to be mixed and with infinite memory. Second, the existence of optimal pure
memoryless strategies together with the polynomial-time solution forone-player
case implies that the quantitative two-player stochastic parity game problem is
in NP ∩ co-NP. This generalizes a result of Condon for stochastic games with reachability
objectives. It also constitutes an exponential improvement over the best previous
algorithm, which is based on a doubly exponential procedure of de Alfaro and Majumdar
for concurrent stochastic parity games and provides only ε-approximations of the
values.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Marcin
full_name: Jurdziński, Marcin
last_name: Jurdziński
- 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, Jurdziński M, Henzinger TA. Quantitative stochastic parity games.
In: SIAM; 2004:121-130.'
apa: 'Chatterjee, K., Jurdziński, M., & Henzinger, T. A. (2004). Quantitative
stochastic parity games (pp. 121–130). Presented at the SODA: Symposium on Discrete
Algorithms, SIAM.'
chicago: Chatterjee, Krishnendu, Marcin Jurdziński, and Thomas A Henzinger. “Quantitative
Stochastic Parity Games,” 121–30. SIAM, 2004.
ieee: 'K. Chatterjee, M. Jurdziński, and T. A. Henzinger, “Quantitative stochastic
parity games,” presented at the SODA: Symposium on Discrete Algorithms, 2004,
pp. 121–130.'
ista: 'Chatterjee K, Jurdziński M, Henzinger TA. 2004. Quantitative stochastic parity
games. SODA: Symposium on Discrete Algorithms, 121–130.'
mla: Chatterjee, Krishnendu, et al. Quantitative Stochastic Parity Games.
SIAM, 2004, pp. 121–30.
short: K. Chatterjee, M. Jurdziński, T.A. Henzinger, in:, SIAM, 2004, pp. 121–130.
conference:
name: 'SODA: Symposium on Discrete Algorithms'
date_created: 2018-12-11T12:09:28Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:59:41Z
day: '01'
extern: 1
month: '01'
page: 121 - 130
publication_status: published
publisher: SIAM
publist_id: '153'
quality_controlled: 0
status: public
title: Quantitative stochastic parity games
type: conference
year: '2004'
...
---
_id: '4556'
abstract:
- lang: eng
text: We study the problem of determining stack boundedness and the exact maximum
stack size for three classes of interrupt-driven programs. Interrupt-driven programs
are used in many real-time applications that require responsive interrupt handling.
In order to ensure responsiveness, programmers often enable interrupt processing
in the body of lower-priority interrupt handlers. In such programs a programming
error can allow interrupt handlers to be interrupted in a cyclic fashion to lead
to an unbounded stack, causing the system to crash. For a restricted class of
interrupt-driven programs, we show that there is a polynomial-time procedure to
check stack boundedness, while determining the exact maximum stack size is PSPACE-complete.
For a larger class of programs, the two problems are both PSPACE-complete, and
for the largest class of programs we consider, the two problems are PSPACE-hard
and can be solved in exponential time. While the complexities are high, our algorithms
are exponential only in the number of handlers, and polynomial in the size of
the program.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Di
full_name: Ma, Di
last_name: Ma
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Tian
full_name: Zhao, Tian
last_name: Zhao
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jens
full_name: Palsberg, Jens
last_name: Palsberg
citation:
ama: Chatterjee K, Ma D, Majumdar R, Zhao T, Henzinger TA, Palsberg J. Stack size
analysis for interrupt-driven programs. Information and Computation. 2004;194(2):144-174.
doi:10.1016/j.ic.2004.06.001
apa: Chatterjee, K., Ma, D., Majumdar, R., Zhao, T., Henzinger, T. A., & Palsberg,
J. (2004). Stack size analysis for interrupt-driven programs. Information and
Computation. Elsevier. https://doi.org/10.1016/j.ic.2004.06.001
chicago: Chatterjee, Krishnendu, Di Ma, Ritankar Majumdar, Tian Zhao, Thomas A Henzinger,
and Jens Palsberg. “Stack Size Analysis for Interrupt-Driven Programs.” Information
and Computation. Elsevier, 2004. https://doi.org/10.1016/j.ic.2004.06.001.
ieee: K. Chatterjee, D. Ma, R. Majumdar, T. Zhao, T. A. Henzinger, and J. Palsberg,
“Stack size analysis for interrupt-driven programs,” Information and Computation,
vol. 194, no. 2. Elsevier, pp. 144–174, 2004.
ista: Chatterjee K, Ma D, Majumdar R, Zhao T, Henzinger TA, Palsberg J. 2004. Stack
size analysis for interrupt-driven programs. Information and Computation. 194(2),
144–174.
mla: Chatterjee, Krishnendu, et al. “Stack Size Analysis for Interrupt-Driven Programs.”
Information and Computation, vol. 194, no. 2, Elsevier, 2004, pp. 144–74,
doi:10.1016/j.ic.2004.06.001.
short: K. Chatterjee, D. Ma, R. Majumdar, T. Zhao, T.A. Henzinger, J. Palsberg,
Information and Computation 194 (2004) 144–174.
date_created: 2018-12-11T12:09:28Z
date_published: 2004-08-11T00:00:00Z
date_updated: 2021-01-12T07:59:40Z
day: '11'
doi: 10.1016/j.ic.2004.06.001
extern: 1
intvolume: ' 194'
issue: '2'
month: '08'
page: 144 - 174
publication: Information and Computation
publication_status: published
publisher: Elsevier
publist_id: '156'
quality_controlled: 0
status: public
title: Stack size analysis for interrupt-driven programs
type: journal_article
volume: 194
year: '2004'
...
---
_id: '4578'
abstract:
- lang: eng
text: 'BLAST is an automatic verification tool for checking temporal safety properties
of C programs. Blast is based on lazy predicate abstraction driven by interpolation-based
predicate discovery. In this paper, we present the Blast specification language.
The language specifies program properties at two levels of precision. At the lower
level, monitor automata are used to specify temporal safety properties of program
executions (traces). At the higher level, relational reachability queries over
program locations are used to combine lower-level trace properties. The two-level
specification language can be used to break down a verification task into several
independent calls of the model-checking engine. In this way, each call to the
model checker may have to analyze only part of the program, or part of the specification,
and may thus succeed in a reduction of the number of predicates needed for the
analysis. In addition, the two-level specification language provides a means for
structuring and maintaining specifications. '
acknowledgement: This research was supported in part by the NSF grants CCR-0085949,
CCR-0234690, and ITR-0326577.
alternative_title:
- LNCS
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- first_name: Adam
full_name: Chlipala, Adam J
last_name: Chlipala
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
citation:
ama: 'Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. The BLAST query language
for software verification. In: Vol 3148. Springer; 2004:2-18. doi:10.1007/978-3-540-27864-1_2'
apa: 'Beyer, D., Chlipala, A., Henzinger, T. A., Jhala, R., & Majumdar, R. (2004).
The BLAST query language for software verification (Vol. 3148, pp. 2–18). Presented
at the SAS: Static Analysis Symposium, Springer. https://doi.org/10.1007/978-3-540-27864-1_2'
chicago: Beyer, Dirk, Adam Chlipala, Thomas A Henzinger, Ranjit Jhala, and Ritankar
Majumdar. “The BLAST Query Language for Software Verification,” 3148:2–18. Springer,
2004. https://doi.org/10.1007/978-3-540-27864-1_2.
ieee: 'D. Beyer, A. Chlipala, T. A. Henzinger, R. Jhala, and R. Majumdar, “The BLAST
query language for software verification,” presented at the SAS: Static Analysis
Symposium, 2004, vol. 3148, pp. 2–18.'
ista: 'Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. 2004. The BLAST query
language for software verification. SAS: Static Analysis Symposium, LNCS, vol.
3148, 2–18.'
mla: Beyer, Dirk, et al. The BLAST Query Language for Software Verification.
Vol. 3148, Springer, 2004, pp. 2–18, doi:10.1007/978-3-540-27864-1_2.
short: D. Beyer, A. Chlipala, T.A. Henzinger, R. Jhala, R. Majumdar, in:, Springer,
2004, pp. 2–18.
conference:
name: 'SAS: Static Analysis Symposium'
date_created: 2018-12-11T12:09:34Z
date_published: 2004-08-17T00:00:00Z
date_updated: 2021-01-12T07:59:50Z
day: '17'
doi: 10.1007/978-3-540-27864-1_2
extern: 1
intvolume: ' 3148'
month: '08'
page: 2 - 18
publication_status: published
publisher: Springer
publist_id: '130'
quality_controlled: 0
status: public
title: The BLAST query language for software verification
type: conference
volume: 3148
year: '2004'
...
---
_id: '4577'
abstract:
- lang: eng
text: While model checking has been successful in uncovering subtle bugs in code,
its adoption in software engineering practice has been hampered by the absence
of a simple interface to the programmer in an integrated development environment.
We describe an integration of the software model checker BLAST into the Eclipse
development environment. We provide a verification interface for practical solutions
for some typical program analysis problems - assertion checking, reachability
analysis, dead code analysis, and test generation - directly on the source code.
The analysis is completely automatic, and assumes no knowledge of model checking
or formal notation. Moreover, the interface supports incremental program verification
to support incremental design and evolution of code.
acknowledgement: This research was supported in part by the NSF grants CCR-0085949,
CCR-0234690, and ITR-0326577.
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
citation:
ama: 'Beyer D, Henzinger TA, Jhala R, Majumdar R. An eclipse plug-in for model checking.
In: IEEE; 2004:251-255. doi:10.1109/WPC.2004.1311069 '
apa: 'Beyer, D., Henzinger, T. A., Jhala, R., & Majumdar, R. (2004). An eclipse
plug-in for model checking (pp. 251–255). Presented at the IWPC: Program Comprehension,
IEEE. https://doi.org/10.1109/WPC.2004.1311069
'
chicago: Beyer, Dirk, Thomas A Henzinger, Ranjit Jhala, and Ritankar Majumdar. “An
Eclipse Plug-in for Model Checking,” 251–55. IEEE, 2004. https://doi.org/10.1109/WPC.2004.1311069 .
ieee: 'D. Beyer, T. A. Henzinger, R. Jhala, and R. Majumdar, “An eclipse plug-in
for model checking,” presented at the IWPC: Program Comprehension, 2004, pp. 251–255.'
ista: 'Beyer D, Henzinger TA, Jhala R, Majumdar R. 2004. An eclipse plug-in for
model checking. IWPC: Program Comprehension, 251–255.'
mla: Beyer, Dirk, et al. An Eclipse Plug-in for Model Checking. IEEE, 2004,
pp. 251–55, doi:10.1109/WPC.2004.1311069
.
short: D. Beyer, T.A. Henzinger, R. Jhala, R. Majumdar, in:, IEEE, 2004, pp. 251–255.
conference:
name: 'IWPC: Program Comprehension'
date_created: 2018-12-11T12:09:34Z
date_published: 2004-07-12T00:00:00Z
date_updated: 2021-01-12T07:59:50Z
day: '12'
doi: '10.1109/WPC.2004.1311069 '
extern: 1
month: '07'
page: 251 - 255
publication_status: published
publisher: IEEE
publist_id: '129'
quality_controlled: 0
status: public
title: An eclipse plug-in for model checking
type: conference
year: '2004'
...
---
_id: '4581'
abstract:
- lang: eng
text: We have extended the software model checker BLAST to automatically generate
test suites that guarantee full coverage with respect to a given predicate. More
precisely, given a C program and a target predicate p, BLAST determines the set
L of program locations which program execution can reach with p true, and automatically
generates a set of test vectors that exhibit the truth of p at all locations in
L. We have used BLAST to generate test suites and to detect dead code in C programs
with up to 30 K lines of code. The analysis and test vector generation is fully
automatic (no user intervention) and exact (no false positives).
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- first_name: Adam
full_name: Chlipala, Adam J
last_name: Chlipala
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
citation:
ama: 'Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. Generating tests from
counterexamples. In: IEEE; 2004:326-335. doi:10.1109/ICSE.2004.1317455'
apa: 'Beyer, D., Chlipala, A., Henzinger, T. A., Jhala, R., & Majumdar, R. (2004).
Generating tests from counterexamples (pp. 326–335). Presented at the ICSE: Software
Engineering, IEEE. https://doi.org/10.1109/ICSE.2004.1317455'
chicago: Beyer, Dirk, Adam Chlipala, Thomas A Henzinger, Ranjit Jhala, and Ritankar
Majumdar. “Generating Tests from Counterexamples,” 326–35. IEEE, 2004. https://doi.org/10.1109/ICSE.2004.1317455.
ieee: 'D. Beyer, A. Chlipala, T. A. Henzinger, R. Jhala, and R. Majumdar, “Generating
tests from counterexamples,” presented at the ICSE: Software Engineering, 2004,
pp. 326–335.'
ista: 'Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. 2004. Generating
tests from counterexamples. ICSE: Software Engineering, 326–335.'
mla: Beyer, Dirk, et al. Generating Tests from Counterexamples. IEEE, 2004,
pp. 326–35, doi:10.1109/ICSE.2004.1317455.
short: D. Beyer, A. Chlipala, T.A. Henzinger, R. Jhala, R. Majumdar, in:, IEEE,
2004, pp. 326–335.
conference:
name: 'ICSE: Software Engineering'
date_created: 2018-12-11T12:09:35Z
date_published: 2004-07-26T00:00:00Z
date_updated: 2021-01-12T07:59:52Z
day: '26'
doi: 10.1109/ICSE.2004.1317455
extern: 1
month: '07'
page: 326 - 335
publication_status: published
publisher: IEEE
publist_id: '128'
quality_controlled: 0
status: public
title: Generating tests from counterexamples
type: conference
year: '2004'
...
---
_id: '4629'
abstract:
- lang: eng
text: 'Temporal logic is two-valued: a property is either true or false. When applied
to the analysis of stochastic systems, or systems with imprecise formal models,
temporal logic is therefore fragile: even small changes in the model can lead
to opposite truth values for a specification. We present a generalization of the
branching-time logic Ctl which achieves robustness with respect to model perturbations
by giving a quantitative interpretation to predicates and logical operators, and
by discounting the importance of events according to how late they occur. In every
state, the value of a formula is a real number in the interval [0,1], where 1
corresponds to truth and 0 to falsehood. The boolean operators and and or are
replaced by min and max, the path quantifiers ∃ and ∀ determine sup and inf over
all paths from a given state, and the temporal operators and □ specify sup and
inf over a given path; a new operator averages all values along a path. Furthermore,
all path operators are discounted by a parameter that can be chosen to give more
weight to states that are closer to the beginning of the path. We interpret the
resulting logic Dctl over transition systems, Markov chains, and Markov decision
processes. We present two semantics for Dctl: a path semantics, inspired by the
standard interpretation of state and path formulas in CTL, and a fixpoint semantics,
inspired by the μ-calculus evaluation of CTL formulas. We show that, while these
semantics coincide for CTL, they differ for Dctl, and we provide model-checking
algorithms for both semantics.'
acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327,
the ONR grant N00014-02-1-0671, and the NSF grants CCR-0132780, CCR-9988172, CCR-0225610,
and CCR-0234690.
alternative_title:
- LNCS
author:
- first_name: Luca
full_name: de Alfaro, Luca
last_name: De Alfaro
- first_name: Marco
full_name: Faella, Marco
last_name: Faella
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Mariëlle
full_name: Stoelinga, Mariëlle
last_name: Stoelinga
citation:
ama: 'De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. Model checking
discounted temporal properties. In: Vol 2988. Springer; 2004:77-92. doi:10.1007/978-3-540-24730-2_6'
apa: 'De Alfaro, L., Faella, M., Henzinger, T. A., Majumdar, R., & Stoelinga,
M. (2004). Model checking discounted temporal properties (Vol. 2988, pp. 77–92).
Presented at the TACAS: Tools and Algorithms for the Construction and Analysis
of Systems, Springer. https://doi.org/10.1007/978-3-540-24730-2_6'
chicago: De Alfaro, Luca, Marco Faella, Thomas A Henzinger, Ritankar Majumdar, and
Mariëlle Stoelinga. “Model Checking Discounted Temporal Properties,” 2988:77–92.
Springer, 2004. https://doi.org/10.1007/978-3-540-24730-2_6.
ieee: 'L. De Alfaro, M. Faella, T. A. Henzinger, R. Majumdar, and M. Stoelinga,
“Model checking discounted temporal properties,” presented at the TACAS: Tools
and Algorithms for the Construction and Analysis of Systems, 2004, vol. 2988,
pp. 77–92.'
ista: 'De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. 2004. Model
checking discounted temporal properties. TACAS: Tools and Algorithms for the Construction
and Analysis of Systems, LNCS, vol. 2988, 77–92.'
mla: De Alfaro, Luca, et al. Model Checking Discounted Temporal Properties.
Vol. 2988, Springer, 2004, pp. 77–92, doi:10.1007/978-3-540-24730-2_6.
short: L. De Alfaro, M. Faella, T.A. Henzinger, R. Majumdar, M. Stoelinga, in:,
Springer, 2004, pp. 77–92.
conference:
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
date_created: 2018-12-11T12:09:50Z
date_published: 2004-03-18T00:00:00Z
date_updated: 2021-01-12T08:00:38Z
day: '18'
doi: 10.1007/978-3-540-24730-2_6
extern: 1
intvolume: ' 2988'
month: '03'
page: 77 - 92
publication_status: published
publisher: Springer
publist_id: '79'
quality_controlled: 0
status: public
title: Model checking discounted temporal properties
type: conference
volume: 2988
year: '2004'
...
---
_id: '6155'
abstract:
- lang: eng
text: 'The genome of the nematode Caenorhabditis elegans encodes seven soluble guanylate
cyclases (sGCs) [1]. In mammals, sGCs function as α/β heterodimers activated by
gaseous ligands binding to a haem prosthetic group 2, 3. The principal activator
is nitric oxide, which acts through sGCs to regulate diverse cellular events.
In C. elegans the function of sGCs is mysterious: the worm genome does not appear
to encode nitric oxide synthase, and all C. elegans sGC subunits are more closely
related to mammalian β than α subunits [1]. Here, we show that two of the seven
C. elegans sGCs, GCY-35 and GCY-36, promote aggregation behavior. gcy-35 and gcy-36
are expressed in a small number of neurons. These include the body cavity neurons
AQR, PQR, and URX, which are directly exposed to the blood equivalent of C. elegans
and regulate aggregation behavior [4]. We show that GCY-35 and GCY-36 act as α-like
and β-like sGC subunits and that their function in the URX sensory neurons is
sufficient for strong nematode aggregation. Neither GCY-35 nor GCY-36 is absolutely
required for C. elegans to aggregate. Instead, these molecules may transduce one
of several pathways that induce C. elegans to aggregate or may modulate aggregation
by responding to cues in C. elegans body fluid.'
author:
- first_name: Benny H.H
full_name: Cheung, Benny H.H
last_name: Cheung
- first_name: Fausto
full_name: Arellano-Carbajal, Fausto
last_name: Arellano-Carbajal
- first_name: Irene
full_name: Rybicki, Irene
last_name: Rybicki
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Cheung BH., Arellano-Carbajal F, Rybicki I, de Bono M. Soluble guanylate cyclases
act in neurons exposed to the body fluid to promote C. elegans aggregation behavior.
Current Biology. 2004;14(12):1105-1111. doi:10.1016/j.cub.2004.06.027
apa: Cheung, B. H. ., Arellano-Carbajal, F., Rybicki, I., & de Bono, M. (2004).
Soluble guanylate cyclases act in neurons exposed to the body fluid to promote
C. elegans aggregation behavior. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2004.06.027
chicago: Cheung, Benny H.H, Fausto Arellano-Carbajal, Irene Rybicki, and Mario de
Bono. “Soluble Guanylate Cyclases Act in Neurons Exposed to the Body Fluid to
Promote C. Elegans Aggregation Behavior.” Current Biology. Elsevier, 2004.
https://doi.org/10.1016/j.cub.2004.06.027.
ieee: B. H. . Cheung, F. Arellano-Carbajal, I. Rybicki, and M. de Bono, “Soluble
guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans
aggregation behavior,” Current Biology, vol. 14, no. 12. Elsevier, pp.
1105–1111, 2004.
ista: Cheung BH., Arellano-Carbajal F, Rybicki I, de Bono M. 2004. Soluble guanylate
cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation
behavior. Current Biology. 14(12), 1105–1111.
mla: Cheung, Benny H. .., et al. “Soluble Guanylate Cyclases Act in Neurons Exposed
to the Body Fluid to Promote C. Elegans Aggregation Behavior.” Current Biology,
vol. 14, no. 12, Elsevier, 2004, pp. 1105–11, doi:10.1016/j.cub.2004.06.027.
short: B.H.. Cheung, F. Arellano-Carbajal, I. Rybicki, M. de Bono, Current Biology
14 (2004) 1105–1111.
date_created: 2019-03-21T09:42:01Z
date_published: 2004-06-22T00:00:00Z
date_updated: 2021-01-12T08:06:25Z
day: '22'
doi: 10.1016/j.cub.2004.06.027
extern: '1'
external_id:
pmid:
- '15203005'
intvolume: ' 14'
issue: '12'
language:
- iso: eng
month: '06'
oa_version: None
page: 1105-1111
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Soluble guanylate cyclases act in neurons exposed to the body fluid to promote
C. elegans aggregation behavior
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2004'
...
---
_id: '7334'
abstract:
- lang: eng
text: 'Fundamental and phenomenological models for cells, stacks, and complete systems
of PEFC and SOFC are reviewed and their predictive power is assessed by comparing
model simulations against experiments. Computationally efficient models suited
for engineering design include the (1+1) dimensionality approach, which decouples
the membrane in-plane and through-plane processes, and the volume-averaged-method
(VAM) that considers only the lumped effect of pre-selected system components.
The former model was shown to capture the measured lateral current density inhomogeneities
in a PEFC and the latter was used for the optimization of commercial SOFC systems.
State Space Modeling (SSM) was used to identify the main reaction pathways in
SOFC and, in conjunction with the implementation of geometrically well-defined
electrodes, has opened a new direction for the understanding of electrochemical
reactions. Furthermore, SSM has advanced the understanding of the COpoisoning-induced
anode impedance in PEFC. Detailed numerical models such as the Lattice Boltzmann
(LB) method for transport in porous media and the full 3-D Computational Fluid
Dynamics (CFD) Navier-Stokes simulations are addressed. These models contain all
components of the relevant physics and they can improve the understanding of the
related phenomena, a necessary condition for the development of both appropriate
simplified models as well as reliable technologies. Within the LB framework, a
technique for the characterization and computer-reconstruction of the porous electrode
structure was developed using advanced pattern recognition algorithms. In CFD
modeling, 3-D simulations were used to investigate SOFC with internal methane
steam reforming and have exemplified the significance of porous and novel fractal
channel distributors for the fuel and oxidant delivery, as well as for the cooling
of PEFC. As importantly, the novel concept has been put forth of functionally
designed, fractal-shaped fuel cells, showing promise of significant performance
improvements over the conventional rectangular shaped units. Thermo-economic modeling
for the optimization of PEFC is finally addressed. '
article_processing_charge: No
article_type: original
author:
- first_name: John
full_name: Mantzaras, John
last_name: Mantzaras
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Felix N.
full_name: Büchi, Felix N.
last_name: Büchi
- first_name: Markus
full_name: Roos, Markus
last_name: Roos
- first_name: Wilhelm
full_name: Brandstätter, Wilhelm
last_name: Brandstätter
- first_name: Michel
full_name: Prestat, Michel
last_name: Prestat
- first_name: Ludwig J.
full_name: Gauckler, Ludwig J.
last_name: Gauckler
- first_name: Bernhard
full_name: Andreaus, Bernhard
last_name: Andreaus
- first_name: Faegheh
full_name: Hajbolouri, Faegheh
last_name: Hajbolouri
- first_name: Stephan M.
full_name: Senn, Stephan M.
last_name: Senn
- first_name: Dimos
full_name: Poulikakos, Dimos
last_name: Poulikakos
- first_name: Andreas K.
full_name: Chaniotis, Andreas K.
last_name: Chaniotis
- first_name: Diego
full_name: Larrain, Diego
last_name: Larrain
- first_name: Nordahl
full_name: Autissier, Nordahl
last_name: Autissier
- first_name: François
full_name: Maréchal, François
last_name: Maréchal
citation:
ama: Mantzaras J, Freunberger SA, Büchi FN, et al. Fuel cell modeling and simulations.
CHIMIA International Journal for Chemistry. 2004;58(12):857-868. doi:10.2533/000942904777677029
apa: Mantzaras, J., Freunberger, S. A., Büchi, F. N., Roos, M., Brandstätter, W.,
Prestat, M., … Maréchal, F. (2004). Fuel cell modeling and simulations. CHIMIA
International Journal for Chemistry. Swiss Chemical Society. https://doi.org/10.2533/000942904777677029
chicago: Mantzaras, John, Stefan Alexander Freunberger, Felix N. Büchi, Markus Roos,
Wilhelm Brandstätter, Michel Prestat, Ludwig J. Gauckler, et al. “Fuel Cell Modeling
and Simulations.” CHIMIA International Journal for Chemistry. Swiss Chemical
Society, 2004. https://doi.org/10.2533/000942904777677029.
ieee: J. Mantzaras et al., “Fuel cell modeling and simulations,” CHIMIA
International Journal for Chemistry, vol. 58, no. 12. Swiss Chemical Society,
pp. 857–868, 2004.
ista: Mantzaras J, Freunberger SA, Büchi FN, Roos M, Brandstätter W, Prestat M,
Gauckler LJ, Andreaus B, Hajbolouri F, Senn SM, Poulikakos D, Chaniotis AK, Larrain
D, Autissier N, Maréchal F. 2004. Fuel cell modeling and simulations. CHIMIA International
Journal for Chemistry. 58(12), 857–868.
mla: Mantzaras, John, et al. “Fuel Cell Modeling and Simulations.” CHIMIA International
Journal for Chemistry, vol. 58, no. 12, Swiss Chemical Society, 2004, pp.
857–68, doi:10.2533/000942904777677029.
short: J. Mantzaras, S.A. Freunberger, F.N. Büchi, M. Roos, W. Brandstätter, M.
Prestat, L.J. Gauckler, B. Andreaus, F. Hajbolouri, S.M. Senn, D. Poulikakos,
A.K. Chaniotis, D. Larrain, N. Autissier, F. Maréchal, CHIMIA International Journal
for Chemistry 58 (2004) 857–868.
date_created: 2020-01-15T12:24:23Z
date_published: 2004-12-01T00:00:00Z
date_updated: 2021-01-12T08:13:09Z
day: '01'
doi: 10.2533/000942904777677029
extern: '1'
intvolume: ' 58'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 857-868
publication: CHIMIA International Journal for Chemistry
publication_identifier:
issn:
- 0009-4293
publication_status: published
publisher: Swiss Chemical Society
quality_controlled: '1'
status: public
title: Fuel cell modeling and simulations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2004'
...
---
_id: '7333'
abstract:
- lang: eng
text: The analysis of the complete H2/air polymer electrolyte fuel cell system shows
that process air humidification is one of the biggest obstacles for a high performance
portable system in the kW range. Therefore, a new concept, with passive process
air humidification integrated into the stack, has been developed. Humidification
in each cell makes the process independent from the number of cells and the operation
mode, thus making the concept fully scalable. Without external humidification
the system is simpler, smaller, and cheaper. The humidification of the process
air is achieved by transfer of product water from the exhaust air, through part
of the membrane, to the dry intake air. Tests have shown that cells using the
concept of internal humidification and operated with dry air at 70 ° have almost
the same performance as when operated with external humidification. A 42‐cell
stack with this internal humidification concept was built and integrated into
a portable 1 kW power generator system.
article_processing_charge: No
article_type: original
author:
- first_name: M.
full_name: Santis, M.
last_name: Santis
- first_name: D.
full_name: Schmid, D.
last_name: Schmid
- first_name: M.
full_name: Ruge, M.
last_name: Ruge
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: F.N.
full_name: Büchi, F.N.
last_name: Büchi
citation:
ama: Santis M, Schmid D, Ruge M, Freunberger SA, Büchi FN. Modular stack-internal
air humidification concept-verification in a 1 kW stack. Fuel Cells. 2004;4(3):214-218.
doi:10.1002/fuce.200400028
apa: Santis, M., Schmid, D., Ruge, M., Freunberger, S. A., & Büchi, F. N. (2004).
Modular stack-internal air humidification concept-verification in a 1 kW stack.
Fuel Cells. Wiley. https://doi.org/10.1002/fuce.200400028
chicago: Santis, M., D. Schmid, M. Ruge, Stefan Alexander Freunberger, and F.N.
Büchi. “Modular Stack-Internal Air Humidification Concept-Verification in a 1 KW
Stack.” Fuel Cells. Wiley, 2004. https://doi.org/10.1002/fuce.200400028.
ieee: M. Santis, D. Schmid, M. Ruge, S. A. Freunberger, and F. N. Büchi, “Modular
stack-internal air humidification concept-verification in a 1 kW stack,” Fuel
Cells, vol. 4, no. 3. Wiley, pp. 214–218, 2004.
ista: Santis M, Schmid D, Ruge M, Freunberger SA, Büchi FN. 2004. Modular stack-internal
air humidification concept-verification in a 1 kW stack. Fuel Cells. 4(3), 214–218.
mla: Santis, M., et al. “Modular Stack-Internal Air Humidification Concept-Verification
in a 1 KW Stack.” Fuel Cells, vol. 4, no. 3, Wiley, 2004, pp. 214–18, doi:10.1002/fuce.200400028.
short: M. Santis, D. Schmid, M. Ruge, S.A. Freunberger, F.N. Büchi, Fuel Cells 4
(2004) 214–218.
date_created: 2020-01-15T12:24:14Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2021-01-12T08:13:08Z
day: '01'
doi: 10.1002/fuce.200400028
extern: '1'
intvolume: ' 4'
issue: '3'
language:
- iso: eng
month: '08'
oa_version: None
page: 214-218
publication: Fuel Cells
publication_identifier:
issn:
- 1615-6846
- 1615-6854
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Modular stack-internal air humidification concept-verification in a 1 kW stack
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2004'
...
---
_id: '864'
abstract:
- lang: eng
text: 'We present a method for prediction of functional sites in a set of aligned
protein sequences. The method selects sites which are both well conserved and
clustered together in space, as inferred from the 3D structures of proteins included
in the alignment. We tested the method using 86 alignments from the NCBI CDD database,
where the sites of experimentally determined ligand and/or macromolecular interactions
are annotated. In agreement with earlier investigations, we found that functional
site predictions are most successful when overall background sequence conservation
is low, such that sites under evolutionary constraint become apparent. In addition,
we found that averaging of conservation values across spatially clustered sites
improves predictions under certain conditions: that is, when overall conservation
is relatively high and when the site in question involves a large macromolecular
binding interface. Under these conditions it is better to look for clusters of
conserved sites than to look for particular conserved sites.'
acknowledgement: We thank John Spouge, Ben Shoemaker, and Michael Galperin forhelpful
suggestions, and the NIH Intramural Research Program forsupport.
author:
- first_name: Anna
full_name: Panchenko, Anna R
last_name: Panchenko
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Stephen
full_name: Bryant, Stephen H
last_name: Bryant
citation:
ama: Panchenko A, Kondrashov F, Bryant S. Prediction of functional sites by analysis
of sequence and structure conservation. Protein Science. 2004;13(4):884-892.
doi:10.1110/ps.03465504
apa: Panchenko, A., Kondrashov, F., & Bryant, S. (2004). Prediction of functional
sites by analysis of sequence and structure conservation. Protein Science.
Wiley-Blackwell. https://doi.org/10.1110/ps.03465504
chicago: Panchenko, Anna, Fyodor Kondrashov, and Stephen Bryant. “Prediction of
Functional Sites by Analysis of Sequence and Structure Conservation.” Protein
Science. Wiley-Blackwell, 2004. https://doi.org/10.1110/ps.03465504.
ieee: A. Panchenko, F. Kondrashov, and S. Bryant, “Prediction of functional sites
by analysis of sequence and structure conservation,” Protein Science, vol.
13, no. 4. Wiley-Blackwell, pp. 884–892, 2004.
ista: Panchenko A, Kondrashov F, Bryant S. 2004. Prediction of functional sites
by analysis of sequence and structure conservation. Protein Science. 13(4), 884–892.
mla: Panchenko, Anna, et al. “Prediction of Functional Sites by Analysis of Sequence
and Structure Conservation.” Protein Science, vol. 13, no. 4, Wiley-Blackwell,
2004, pp. 884–92, doi:10.1110/ps.03465504.
short: A. Panchenko, F. Kondrashov, S. Bryant, Protein Science 13 (2004) 884–892.
date_created: 2018-12-11T11:48:55Z
date_published: 2004-04-01T00:00:00Z
date_updated: 2021-01-12T08:20:22Z
day: '01'
doi: 10.1110/ps.03465504
extern: 1
intvolume: ' 13'
issue: '4'
month: '04'
page: 884 - 892
publication: Protein Science
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6786'
quality_controlled: 0
status: public
title: Prediction of functional sites by analysis of sequence and structure conservation
type: journal_article
volume: 13
year: '2004'
...
---
_id: '870'
abstract:
- lang: eng
text: Only a fraction of eukaryotic genes affect the phenotype drastically. We compared
18 parameters in 1273 human morbid genes, known to cause diseases, and in the
remaining 16 580 unambiguous human genes. Morbid genes evolve more slowly, have
wider phylogenetic distributions, are more similar to essential genes of Drosophila
melanogaster, code for longer proteins containing more alanine and glycine and
less histidine, lysine and methionine, possess larger numbers of longer introns
with more accurate splicing signals and have higher and broader expressions. These
differences make it possible to classify as non-morbid 34% of human genes with
unknown morbidity, when only 5% of known morbid genes are incorrectly classified
as non-morbid. This classification can help to identify disease-causing genes
among multiple candidates.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Aleksey
full_name: Ogurtsov, Aleksey Yu
last_name: Ogurtsov
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
citation:
ama: Kondrashov F, Ogurtsov A, Kondrashov A. Bioinformatical assay of human gene
morbidity. Nucleic Acids Research. 2004;32(5):1731-1737. doi:10.1093/nar/gkh330
apa: Kondrashov, F., Ogurtsov, A., & Kondrashov, A. (2004). Bioinformatical
assay of human gene morbidity. Nucleic Acids Research. Oxford University
Press. https://doi.org/10.1093/nar/gkh330
chicago: Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Bioinformatical
Assay of Human Gene Morbidity.” Nucleic Acids Research. Oxford University
Press, 2004. https://doi.org/10.1093/nar/gkh330.
ieee: F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Bioinformatical assay of human
gene morbidity,” Nucleic Acids Research, vol. 32, no. 5. Oxford University
Press, pp. 1731–1737, 2004.
ista: Kondrashov F, Ogurtsov A, Kondrashov A. 2004. Bioinformatical assay of human
gene morbidity. Nucleic Acids Research. 32(5), 1731–1737.
mla: Kondrashov, Fyodor, et al. “Bioinformatical Assay of Human Gene Morbidity.”
Nucleic Acids Research, vol. 32, no. 5, Oxford University Press, 2004,
pp. 1731–37, doi:10.1093/nar/gkh330.
short: F. Kondrashov, A. Ogurtsov, A. Kondrashov, Nucleic Acids Research 32 (2004)
1731–1737.
date_created: 2018-12-11T11:48:56Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:37Z
day: '01'
doi: 10.1093/nar/gkh330
extern: 1
intvolume: ' 32'
issue: '5'
month: '01'
page: 1731 - 1737
publication: Nucleic Acids Research
publication_status: published
publisher: Oxford University Press
publist_id: '6780'
quality_controlled: 0
status: public
title: Bioinformatical assay of human gene morbidity
type: journal_article
volume: 32
year: '2004'
...
---
_id: '875'
abstract:
- lang: eng
text: The dominance of wild-type alleles and the concomitant recessivity of deleterious
mutant alleles might have evolved by natural selection or could be a by-product
of the molecular and physiological mechanisms of gene action. We compared the
properties of human haplosufficient genes, whose wild-type alleles are dominant
over loss-of-function alleles, with haploinsufficient (recessive wild-type) genes,
which produce an abnormal phenotype when heterozygous for a loss-of-function allele.
The fraction of haplosufficient genes is the highest among the genes that encode
enzymes, which is best compatible with the physiological theory. Haploinsufficient
genes, on average, have more paralogs than haplosufficient genes, supporting the
idea that gene dosage could be important for the initial fixation of duplications.
Thus, haplo(in)sufficiency of a gene and its propensity for duplication might
have a common evolutionary basis.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Eugene
full_name: Koonin, Eugene V
last_name: Koonin
citation:
ama: Kondrashov F, Koonin E. A common framework for understanding the origin of
genetic dominance and evolutionary fates of gene duplications. Trends in Genetics.
2004;20(7):287-291. doi:10.1016/j.tig.2004.05.001
apa: Kondrashov, F., & Koonin, E. (2004). A common framework for understanding
the origin of genetic dominance and evolutionary fates of gene duplications. Trends
in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2004.05.001
chicago: Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding
the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.”
Trends in Genetics. Elsevier, 2004. https://doi.org/10.1016/j.tig.2004.05.001.
ieee: F. Kondrashov and E. Koonin, “A common framework for understanding the origin
of genetic dominance and evolutionary fates of gene duplications,” Trends in
Genetics, vol. 20, no. 7. Elsevier, pp. 287–291, 2004.
ista: Kondrashov F, Koonin E. 2004. A common framework for understanding the origin
of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics.
20(7), 287–291.
mla: Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding
the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.”
Trends in Genetics, vol. 20, no. 7, Elsevier, 2004, pp. 287–91, doi:10.1016/j.tig.2004.05.001.
short: F. Kondrashov, E. Koonin, Trends in Genetics 20 (2004) 287–291.
date_created: 2018-12-11T11:48:58Z
date_published: 2004-07-01T00:00:00Z
date_updated: 2021-01-12T08:20:54Z
day: '01'
doi: 10.1016/j.tig.2004.05.001
extern: 1
intvolume: ' 20'
issue: '7'
month: '07'
page: 287 - 291
publication: Trends in Genetics
publication_status: published
publisher: Elsevier
publist_id: '6775'
quality_controlled: 0
status: public
title: A common framework for understanding the origin of genetic dominance and evolutionary
fates of gene duplications
type: journal_article
volume: 20
year: '2004'
...
---
_id: '889'
abstract:
- lang: eng
text: 'The function of protein and RNA molecules depends on complex epistatic interactions
between sites. Therefore, the deleterious effect of a mutation can be suppressed
by a compensatory second-site substitution. In relating a list of 86 pathogenic
mutations in human IRNAs encoded by mitochondrial genes to the sequences of their
mammalian orthologs, we noted that 52 pathogenic mutations were present in normal
tRNAs of one or several nonhuman mammals. We found at least five mechanisms of
compensation for 32 pathogenic mutations that destroyed a Watson-Crick pair in
one of the four tRNA stems: restoration of the affected Watson-Crick interaction
(25 cases), strengthening of another pair (4 cases), creation of a new pair (8
cases), changes of multiple interactions in the affected stem (11 cases) and changes
involving the interaction between the loop and stem structures (3 cases). A pathogenic
mutation and its compensating substitution are fixed in a lineage in rapid succession,
and often a compensatory interaction evolves convergently in different clades.
At least 10%, and perhaps as many as 50%, of all nucleotide substitutions in evolving
mammalian (RNAs participate in such interactions, indicating that the evolution
of tRNAs proceeds along highly epistatic fitness ridges.'
acknowledgement: We thank J. Gillespie, M. Hahn, L. Horth, A. Kondrashov, A. Kopp,
S. Nuzhdin, M. Turelli and D. Weinreich for their contributions. The authors were
supported by a grant from the US National Institutes of Health to S. Nuzhdin, and
A.D.K. is a Howard Hughes
author:
- first_name: Andrew
full_name: Kern, Andrew D
last_name: Kern
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kern A, Kondrashov F. Mechanisms and convergence of compensatory evolution
in mammalian mitochondrial tRNAs. Nature Genetics. 2004;36(11):1207-1212.
doi:10.1038/ng1451
apa: Kern, A., & Kondrashov, F. (2004). Mechanisms and convergence of compensatory
evolution in mammalian mitochondrial tRNAs. Nature Genetics. Nature Publishing
Group. https://doi.org/10.1038/ng1451
chicago: Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory
Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics. Nature Publishing
Group, 2004. https://doi.org/10.1038/ng1451.
ieee: A. Kern and F. Kondrashov, “Mechanisms and convergence of compensatory evolution
in mammalian mitochondrial tRNAs,” Nature Genetics, vol. 36, no. 11. Nature
Publishing Group, pp. 1207–1212, 2004.
ista: Kern A, Kondrashov F. 2004. Mechanisms and convergence of compensatory evolution
in mammalian mitochondrial tRNAs. Nature Genetics. 36(11), 1207–1212.
mla: Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory
Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics, vol. 36,
no. 11, Nature Publishing Group, 2004, pp. 1207–12, doi:10.1038/ng1451.
short: A. Kern, F. Kondrashov, Nature Genetics 36 (2004) 1207–1212.
date_created: 2018-12-11T11:49:02Z
date_published: 2004-11-01T00:00:00Z
date_updated: 2021-01-12T08:21:17Z
day: '01'
doi: 10.1038/ng1451
extern: 1
intvolume: ' 36'
issue: '11'
month: '11'
page: 1207 - 1212
publication: Nature Genetics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6759'
quality_controlled: 0
status: public
title: Mechanisms and convergence of compensatory evolution in mammalian mitochondrial
tRNAs
type: journal_article
volume: 36
year: '2004'
...
---
_id: '9493'
abstract:
- lang: eng
text: In a number of organisms, transgenes containing transcribed inverted repeats
(IRs) that produce hairpin RNA can trigger RNA-mediated silencing, which is associated
with 21-24 nucleotide small interfering RNAs (siRNAs). In plants, IR-driven RNA
silencing also causes extensive cytosine methylation of homologous DNA in both
the transgene "trigger" and any other homologous DNA sequences--"targets". Endogenous
genomic sequences, including transposable elements and repeated elements, are
also subject to RNA-mediated silencing. The RNA silencing gene ARGONAUTE4 (AGO4)
is required for maintenance of DNA methylation at several endogenous loci and
for the establishment of methylation at the FWA gene. Here, we show that mutation
of AGO4 substantially reduces the maintenance of DNA methylation triggered by
IR transgenes, but AGO4 loss-of-function does not block the initiation of DNA
methylation by IRs. AGO4 primarily affects non-CG methylation of the target sequences,
while the IR trigger sequences lose methylation in all sequence contexts. Finally,
we find that AGO4 and the DRM methyltransferase genes are required for maintenance
of siRNAs at a subset of endogenous sequences, but AGO4 is not required for the
accumulation of IR-induced siRNAs or a number of endogenous siRNAs, suggesting
that AGO4 may function downstream of siRNA production.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Xiaofeng
full_name: Cao, Xiaofeng
last_name: Cao
- first_name: Lisa K.
full_name: Johansen, Lisa K.
last_name: Johansen
- first_name: Zhixin
full_name: Xie, Zhixin
last_name: Xie
- first_name: James C.
full_name: Carrington, James C.
last_name: Carrington
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of
Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats.
Current Biology. 2004;14(13):1214-1220. doi:10.1016/j.cub.2004.06.055
apa: Zilberman, D., Cao, X., Johansen, L. K., Xie, Z., Carrington, J. C., &
Jacobsen, S. E. (2004). Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation
triggered by inverted repeats. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2004.06.055
chicago: Zilberman, Daniel, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C.
Carrington, and Steven E. Jacobsen. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed
DNA Methylation Triggered by Inverted Repeats.” Current Biology. Elsevier,
2004. https://doi.org/10.1016/j.cub.2004.06.055.
ieee: D. Zilberman, X. Cao, L. K. Johansen, Z. Xie, J. C. Carrington, and S. E.
Jacobsen, “Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered
by inverted repeats,” Current Biology, vol. 14, no. 13. Elsevier, pp. 1214–1220,
2004.
ista: Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. 2004.
Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted
repeats. Current Biology. 14(13), 1214–1220.
mla: Zilberman, Daniel, et al. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA
Methylation Triggered by Inverted Repeats.” Current Biology, vol. 14, no.
13, Elsevier, 2004, pp. 1214–20, doi:10.1016/j.cub.2004.06.055.
short: D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, S.E. Jacobsen,
Current Biology 14 (2004) 1214–1220.
date_created: 2021-06-07T10:33:00Z
date_published: 2004-07-13T00:00:00Z
date_updated: 2021-12-14T08:52:00Z
day: '13'
department:
- _id: DaZi
doi: 10.1016/j.cub.2004.06.055
extern: '1'
external_id:
pmid:
- '15242620 '
intvolume: ' 14'
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2004.06.055
month: '07'
oa: 1
oa_version: Published Version
page: 1214-1220
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by
inverted repeats
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 14
year: '2004'
...