---
_id: '9495'
abstract:
- lang: eng
text: RNA interference is a conserved process in which double-stranded RNA is processed
into 21–25 nucleotide siRNAs that trigger posttranscriptional gene silencing.
In addition, plants display a phenomenon termed RNA-directed DNA methylation (RdDM)
in which DNA with sequence identity to silenced RNA is de novo methylated at its
cytosine residues. This methylation is not only at canonical CpG sites but also
at cytosines in CpNpG and asymmetric sequence contexts. In this report, we study
the role of the DRM and CMT3 DNA methyltransferase genes in the initiation and
maintenance of RdDM. Neither drm nor cmt3 mutants affected the maintenance of
preestablished RNA-directed CpG methylation. However, drm mutants showed a nearly
complete loss of asymmetric methylation and a partial loss of CpNpG methylation.
The remaining asymmetric and CpNpG methylation was dependent on the activity of
CMT3, showing that DRM and CMT3 act redundantly to maintain non-CpG methylation.
These DNA methyltransferases appear to act downstream of siRNAs, since drm1 drm2
cmt3 triple mutants show a lack of non-CpG methylation but elevated levels of
siRNAs. Finally, we demonstrate that DRM activity is required for the initial
establishment of RdDM in all sequence contexts including CpG, CpNpG, and asymmetric
sites.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaofeng
full_name: Cao, Xiaofeng
last_name: Cao
- first_name: Werner
full_name: Aufsatz, Werner
last_name: Aufsatz
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: M.Florian
full_name: Mette, M.Florian
last_name: Mette
- first_name: Michael S.
full_name: Huang, Michael S.
last_name: Huang
- first_name: Marjori
full_name: Matzke, Marjori
last_name: Matzke
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Cao X, Aufsatz W, Zilberman D, et al. Role of the DRM and CMT3 methyltransferases
in RNA-directed DNA methylation. Current Biology. 2003;13(24):2212-2217.
doi:10.1016/j.cub.2003.11.052
apa: Cao, X., Aufsatz, W., Zilberman, D., Mette, M. F., Huang, M. S., Matzke, M.,
& Jacobsen, S. E. (2003). Role of the DRM and CMT3 methyltransferases in RNA-directed
DNA methylation. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2003.11.052
chicago: Cao, Xiaofeng, Werner Aufsatz, Daniel Zilberman, M.Florian Mette, Michael
S. Huang, Marjori Matzke, and Steven E. Jacobsen. “Role of the DRM and CMT3 Methyltransferases
in RNA-Directed DNA Methylation.” Current Biology. Elsevier, 2003. https://doi.org/10.1016/j.cub.2003.11.052.
ieee: X. Cao et al., “Role of the DRM and CMT3 methyltransferases in RNA-directed
DNA methylation,” Current Biology, vol. 13, no. 24. Elsevier, pp. 2212–2217,
2003.
ista: Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE.
2003. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation.
Current Biology. 13(24), 2212–2217.
mla: Cao, Xiaofeng, et al. “Role of the DRM and CMT3 Methyltransferases in RNA-Directed
DNA Methylation.” Current Biology, vol. 13, no. 24, Elsevier, 2003, pp.
2212–17, doi:10.1016/j.cub.2003.11.052.
short: X. Cao, W. Aufsatz, D. Zilberman, M.F. Mette, M.S. Huang, M. Matzke, S.E.
Jacobsen, Current Biology 13 (2003) 2212–2217.
date_created: 2021-06-07T10:43:02Z
date_published: 2003-12-16T00:00:00Z
date_updated: 2021-12-14T08:41:38Z
day: '16'
department:
- _id: DaZi
doi: 10.1016/j.cub.2003.11.052
extern: '1'
external_id:
pmid:
- '14680640'
intvolume: ' 13'
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2003.11.052
month: '12'
oa: 1
oa_version: Published Version
page: 2212-2217
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 the DRM and CMT3 methyltransferases in RNA-directed DNA methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 13
year: '2003'
...
---
_id: '11860'
abstract:
- lang: eng
text: Many daily activities present information in the form of a stream of text,
and often people can benefit from additional information on the topic discussed.
TV broadcast news can be treated as one such stream of text; in this paper we
discuss finding news articles on the web that are relevant to news currently being
broadcast.We evaluated a variety of algorithms for this problem, looking at the
impact of inverse document frequency, stemming, compounds, history, and query
length on the relevance and coverage of news articles returned in real time during
a broadcast. We also evaluated several postprocessing techniques for improving
the precision, including reranking using additional terms, reranking by document
similarity, and filtering on document similarity. For the best algorithm, 84%-91%
of the articles found were relevant, with at least 64% of the articles being on
the exact topic of the broadcast. In addition, a relevant article was found for
at least 70% of the topics.
article_number: 1-10
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
- first_name: Bay-Wei
full_name: Chang, Bay-Wei
last_name: Chang
- first_name: Brian
full_name: Milch, Brian
last_name: Milch
- first_name: Sergey
full_name: Brin, Sergey
last_name: Brin
citation:
ama: 'Henzinger MH, Chang B-W, Milch B, Brin S. Query-free news search. In: Proceedings
of the 12th International Conference on World Wide Web. Association for Computing
Machinery; 2003. doi:10.1145/775152.775154'
apa: 'Henzinger, M. H., Chang, B.-W., Milch, B., & Brin, S. (2003). Query-free
news search. In Proceedings of the 12th international conference on World Wide
Web. Budapest, Hungary: Association for Computing Machinery. https://doi.org/10.1145/775152.775154'
chicago: Henzinger, Monika H, Bay-Wei Chang, Brian Milch, and Sergey Brin. “Query-Free
News Search.” In Proceedings of the 12th International Conference on World
Wide Web. Association for Computing Machinery, 2003. https://doi.org/10.1145/775152.775154.
ieee: M. H. Henzinger, B.-W. Chang, B. Milch, and S. Brin, “Query-free news search,”
in Proceedings of the 12th international conference on World Wide Web,
Budapest, Hungary, 2003.
ista: 'Henzinger MH, Chang B-W, Milch B, Brin S. 2003. Query-free news search. Proceedings
of the 12th international conference on World Wide Web. WWW: International Conference
on World Wide Web, 1–10.'
mla: Henzinger, Monika H., et al. “Query-Free News Search.” Proceedings of the
12th International Conference on World Wide Web, 1–10, Association for Computing
Machinery, 2003, doi:10.1145/775152.775154.
short: M.H. Henzinger, B.-W. Chang, B. Milch, S. Brin, in:, Proceedings of the 12th
International Conference on World Wide Web, Association for Computing Machinery,
2003.
conference:
end_date: 2003-05-24
location: Budapest, Hungary
name: 'WWW: International Conference on World Wide Web'
start_date: 2003-05-20
date_created: 2022-08-16T08:55:05Z
date_published: 2003-05-01T00:00:00Z
date_updated: 2023-02-21T16:32:40Z
day: '01'
doi: 10.1145/775152.775154
extern: '1'
language:
- iso: eng
month: '05'
oa_version: None
publication: Proceedings of the 12th international conference on World Wide Web
publication_identifier:
isbn:
- 978-158113680-7
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '11904'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Query-free news search
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2003'
...
---
_id: '11897'
abstract:
- lang: eng
text: "This paper addresses the problem of topic distillation on the World Wide
Web, namely, given a typical user query to find quality documents related to the
query topic. Connectivity analysis has been shown to be useful in identifying
high quality pages within a topic specific graph of hyperlinked documents. The
essence of our approach is to augment a previous connectivity analysis based algorithm
with content analysis. We identify three problems with the existing approach and
devise algorithms to tackle them. The results of a user evaluation are reported
that show an improvement of precision at 10\r\ndocuments by at least 45% over
pure connectivity analysis. "
article_processing_charge: No
author:
- first_name: Krishna
full_name: Bharat, Krishna
last_name: Bharat
- 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: 'Bharat K, Henzinger MH. Improved algorithms for topic distillation in a hyperlinked
environment. In: 21st Annual International ACM SIGIR Conference on Research
and Development in Information Retrieval. Association for Computing Machinery;
2003:104–111. doi:10.1145/290941.290972'
apa: 'Bharat, K., & Henzinger, M. H. (2003). Improved algorithms for topic distillation
in a hyperlinked environment. In 21st annual international ACM SIGIR conference
on Research and development in information retrieval (pp. 104–111). Melbourne,
Australia: Association for Computing Machinery. https://doi.org/10.1145/290941.290972'
chicago: Bharat, Krishna, and Monika H Henzinger. “Improved Algorithms for Topic
Distillation in a Hyperlinked Environment.” In 21st Annual International ACM
SIGIR Conference on Research and Development in Information Retrieval, 104–111.
Association for Computing Machinery, 2003. https://doi.org/10.1145/290941.290972.
ieee: K. Bharat and M. H. Henzinger, “Improved algorithms for topic distillation
in a hyperlinked environment,” in 21st annual international ACM SIGIR conference
on Research and development in information retrieval, Melbourne, Australia,
2003, pp. 104–111.
ista: 'Bharat K, Henzinger MH. 2003. Improved algorithms for topic distillation
in a hyperlinked environment. 21st annual international ACM SIGIR conference on
Research and development in information retrieval. SIGIR: International Conference
on Research and Development in Information Retrieval, 104–111.'
mla: Bharat, Krishna, and Monika H. Henzinger. “Improved Algorithms for Topic Distillation
in a Hyperlinked Environment.” 21st Annual International ACM SIGIR Conference
on Research and Development in Information Retrieval, Association for Computing
Machinery, 2003, pp. 104–111, doi:10.1145/290941.290972.
short: K. Bharat, M.H. Henzinger, in:, 21st Annual International ACM SIGIR Conference
on Research and Development in Information Retrieval, Association for Computing
Machinery, 2003, pp. 104–111.
conference:
end_date: 1998-08-28
location: Melbourne, Australia
name: 'SIGIR: International Conference on Research and Development in Information
Retrieval'
start_date: 1998-08-24
date_created: 2022-08-17T08:56:18Z
date_published: 2003-08-01T00:00:00Z
date_updated: 2023-02-17T14:47:44Z
day: '01'
doi: 10.1145/290941.290972
extern: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 104–111
publication: 21st annual international ACM SIGIR conference on Research and development
in information retrieval
publication_identifier:
isbn:
- 978-1-58113-015-7
issn:
- '01635840'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Improved algorithms for topic distillation in a hyperlinked environment
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2003'
...
---
_id: '11909'
abstract:
- lang: eng
text: This article presents a high-level discussion of some problems that are unique
to web search engines. The goal is to raise awareness and stimulate research in
these areas.
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
- first_name: Rajeev
full_name: Motwani, Rajeev
last_name: Motwani
- first_name: Craig
full_name: Silverstein, Craig
last_name: Silverstein
citation:
ama: 'Henzinger MH, Motwani R, Silverstein C. Challenges in web search engines.
In: 18th International Joint Conference on Artificial Intelligence. Association
for Computing Machinery; 2003:1573-1579.'
apa: 'Henzinger, M. H., Motwani, R., & Silverstein, C. (2003). Challenges in
web search engines. In 18th International Joint Conference on Artificial Intelligence
(pp. 1573–1579). Acapulco, Mexico: Association for Computing Machinery.'
chicago: Henzinger, Monika H, Rajeev Motwani, and Craig Silverstein. “Challenges
in Web Search Engines.” In 18th International Joint Conference on Artificial
Intelligence, 1573–79. Association for Computing Machinery, 2003.
ieee: M. H. Henzinger, R. Motwani, and C. Silverstein, “Challenges in web search
engines,” in 18th International Joint Conference on Artificial Intelligence,
Acapulco, Mexico, 2003, pp. 1573–1579.
ista: 'Henzinger MH, Motwani R, Silverstein C. 2003. Challenges in web search engines.
18th International Joint Conference on Artificial Intelligence. IJCAI: International
Joint Conference on Artificial Intelligence, 1573–1579.'
mla: Henzinger, Monika H., et al. “Challenges in Web Search Engines.” 18th International
Joint Conference on Artificial Intelligence, Association for Computing Machinery,
2003, pp. 1573–79.
short: M.H. Henzinger, R. Motwani, C. Silverstein, in:, 18th International Joint
Conference on Artificial Intelligence, Association for Computing Machinery, 2003,
pp. 1573–1579.
conference:
end_date: 2003-08-15
location: Acapulco, Mexico
name: 'IJCAI: International Joint Conference on Artificial Intelligence'
start_date: 2003-08-09
date_created: 2022-08-18T06:40:02Z
date_published: 2003-08-01T00:00:00Z
date_updated: 2023-02-09T12:05:25Z
day: '01'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ijcai.org/Proceedings/03/Papers/278.pdf
month: '08'
oa: 1
oa_version: Published Version
page: 1573-1579
publication: 18th International Joint Conference on Artificial Intelligence
publication_identifier:
issn:
- 1045-0823
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Challenges in web search engines
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2003'
...
---
_id: '3425'
alternative_title:
- Nato Science Series II
article_processing_charge: No
author:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: T.
full_name: Strother, T.
last_name: Strother
- first_name: Wolfgang
full_name: Bauer, Wolfgang
last_name: Bauer
citation:
ama: 'Bollenbach MT, Strother T, Bauer W. 3D supernova collapse calculations. In:
Vol 166. Springer; 2003:277-288. doi:10.1007/978-1-4020-2705-5_21'
apa: Bollenbach, M. T., Strother, T., & Bauer, W. (2003). 3D supernova collapse
calculations (Vol. 166, pp. 277–288). Presented at the NATO ASI on Structure and
Dynamics of Elementary Matter, Springer. https://doi.org/10.1007/978-1-4020-2705-5_21
chicago: Bollenbach, Mark Tobias, T. Strother, and Wolfgang Bauer. “3D Supernova
Collapse Calculations,” 166:277–88. Springer, 2003. https://doi.org/10.1007/978-1-4020-2705-5_21.
ieee: M. T. Bollenbach, T. Strother, and W. Bauer, “3D supernova collapse calculations,”
presented at the NATO ASI on Structure and Dynamics of Elementary Matter, 2003,
vol. 166, pp. 277–288.
ista: Bollenbach MT, Strother T, Bauer W. 2003. 3D supernova collapse calculations.
NATO ASI on Structure and Dynamics of Elementary Matter, Nato Science Series II,
vol. 166, 277–288.
mla: Bollenbach, Mark Tobias, et al. 3D Supernova Collapse Calculations.
Vol. 166, Springer, 2003, pp. 277–88, doi:10.1007/978-1-4020-2705-5_21.
short: M.T. Bollenbach, T. Strother, W. Bauer, in:, Springer, 2003, pp. 277–288.
conference:
name: NATO ASI on Structure and Dynamics of Elementary Matter
date_created: 2018-12-11T12:03:16Z
date_published: 2003-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:23Z
day: '01'
doi: 10.1007/978-1-4020-2705-5_21
extern: '1'
intvolume: ' 166'
language:
- iso: eng
month: '01'
oa_version: None
page: 277 - 288
publication_status: published
publisher: Springer
publist_id: '2976'
status: public
title: 3D supernova collapse calculations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 166
year: '2003'
...
---
_id: '3458'
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: Klaus
full_name: Unsicker, Klaus
last_name: Unsicker
citation:
ama: 'Jonas PM, Unsicker K. Molekulare und zelluläre Grundlagen des Nervensystems.
In: Schmidt R, ed. Lehrbuch Vorklinik. Vol B. Deutscher Ärzte Verlag; 2003:3-26.'
apa: Jonas, P. M., & Unsicker, K. (2003). Molekulare und zelluläre Grundlagen
des Nervensystems. In R. Schmidt (Ed.), Lehrbuch Vorklinik (Vol. B, pp.
3–26). Deutscher Ärzte Verlag.
chicago: Jonas, Peter M, and Klaus Unsicker. “Molekulare Und Zelluläre Grundlagen
Des Nervensystems.” In Lehrbuch Vorklinik, edited by R. Schmidt, B:3–26.
Deutscher Ärzte Verlag, 2003.
ieee: P. M. Jonas and K. Unsicker, “Molekulare und zelluläre Grundlagen des Nervensystems.,”
in Lehrbuch Vorklinik, vol. B, R. Schmidt, Ed. Deutscher Ärzte Verlag,
2003, pp. 3–26.
ista: 'Jonas PM, Unsicker K. 2003.Molekulare und zelluläre Grundlagen des Nervensystems.
In: Lehrbuch Vorklinik. vol. B, 3–26.'
mla: Jonas, Peter M., and Klaus Unsicker. “Molekulare Und Zelluläre Grundlagen Des
Nervensystems.” Lehrbuch Vorklinik, edited by R. Schmidt, vol. B, Deutscher
Ärzte Verlag, 2003, pp. 3–26.
short: P.M. Jonas, K. Unsicker, in:, R. Schmidt (Ed.), Lehrbuch Vorklinik, Deutscher
Ärzte Verlag, 2003, pp. 3–26.
date_created: 2018-12-11T12:03:26Z
date_published: 2003-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:35Z
day: '01'
editor:
- first_name: R.
full_name: Schmidt, R. F.
last_name: Schmidt
extern: 1
month: '01'
page: 3 - 26
publication: Lehrbuch Vorklinik
publication_status: published
publisher: Deutscher Ärzte Verlag
publist_id: '2929'
quality_controlled: 0
status: public
title: Molekulare und zelluläre Grundlagen des Nervensystems.
type: book_chapter
volume: B
year: '2003'
...
---
_id: '3526'
abstract:
- lang: eng
text: Neurons can produce action potentials with high temporal precision(1). A fundamental
issue is whether, and how, this capability is used in information processing.
According to the `cell assembly' hypothesis, transient synchrony of anatomically
distributed groups of neurons underlies processing of both external sensory input
and internal cognitive mechanisms(2-4). Accordingly, neuron populations should
be arranged into groups whose synchrony exceeds that predicted by common modulation
by sensory input. Here we find that the spike times of hippocampal pyramidal cells
can be predicted more accurately by using the spike times of simultaneously recorded
neurons in addition to the animals location in space. This improvement remained
when the spatial prediction was refined with a spatially dependent theta phase
modulation(5-8). The time window in which spike times are best predicted from
simultaneous peer activity is 10-30 ms, suggesting that cell assemblies are synchronized
at this timescale. Because this temporal window matches the membrane time constant
of pyramidal neurons(9), the period of the hippocampal gamma oscillation(10) and
the time window for synaptic plasticity(11), we propose that cooperative activity
at this timescale is optimal for information transmission and storage in cortical
circuits.
author:
- first_name: Kenneth
full_name: Harris, Kenneth D
last_name: Harris
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Hajima
full_name: Hirase, Hajima
last_name: Hirase
- first_name: George
full_name: Dragoi, George
last_name: Dragoi
- first_name: György
full_name: Buzsáki, György
last_name: Buzsáki
citation:
ama: Harris K, Csicsvari JL, Hirase H, Dragoi G, Buzsáki G. Organization of cell
assemblies in the hippocampus. Nature. 2003;424(6948):552-556. doi:0.1038/nature01834
apa: Harris, K., Csicsvari, J. L., Hirase, H., Dragoi, G., & Buzsáki, G. (2003).
Organization of cell assemblies in the hippocampus. Nature. Nature Publishing
Group. https://doi.org/0.1038/nature01834
chicago: Harris, Kenneth, Jozsef L Csicsvari, Hajima Hirase, George Dragoi, and
György Buzsáki. “Organization of Cell Assemblies in the Hippocampus.” Nature.
Nature Publishing Group, 2003. https://doi.org/0.1038/nature01834.
ieee: K. Harris, J. L. Csicsvari, H. Hirase, G. Dragoi, and G. Buzsáki, “Organization
of cell assemblies in the hippocampus,” Nature, vol. 424, no. 6948. Nature
Publishing Group, pp. 552–556, 2003.
ista: Harris K, Csicsvari JL, Hirase H, Dragoi G, Buzsáki G. 2003. Organization
of cell assemblies in the hippocampus. Nature. 424(6948), 552–556.
mla: Harris, Kenneth, et al. “Organization of Cell Assemblies in the Hippocampus.”
Nature, vol. 424, no. 6948, Nature Publishing Group, 2003, pp. 552–56,
doi:0.1038/nature01834.
short: K. Harris, J.L. Csicsvari, H. Hirase, G. Dragoi, G. Buzsáki, Nature 424 (2003)
552–556.
date_created: 2018-12-11T12:03:47Z
date_published: 2003-07-31T00:00:00Z
date_updated: 2021-01-12T07:44:04Z
day: '31'
doi: 0.1038/nature01834
extern: 1
intvolume: ' 424'
issue: '6948'
month: '07'
page: 552 - 556
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '2859'
quality_controlled: 0
status: public
title: Organization of cell assemblies in the hippocampus
type: journal_article
volume: 424
year: '2003'
...
---
_id: '3528'
abstract:
- lang: eng
text: Gamma frequency oscillations (30-100 Hz) have been suggested to underlie various
cognitive and motor functions. Here, we examine the generation of gamma oscillation
currents in the hippocampus, using two-dimensional, 96-site silicon probes. Two
gamma generators were identified, one in the dentate gyrus and another in the
CA3-CA1 regions. The coupling strength between the two oscillators varied during
both theta and nontheta states. Both pyramidal cells and interneurons were phase-locked
to gamma waves. Anatomical connectivity, rather than physical distance, determined
the coupling strength of the oscillating neurons. CA3 pyramidal neurons discharged
CA3 and CA1 interneurons at latencies indicative of monosynaptic connections.
Intrahippocampal gamma oscillation emerges in the CA3 recurrent system, which
entrains the CA1 region via its interneurons.
author:
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Brian
full_name: Jamieson, Brian G
last_name: Jamieson
- first_name: Kensall
full_name: Wise, Kensall D
last_name: Wise
- first_name: György
full_name: Buzsáki, György
last_name: Buzsáki
citation:
ama: Csicsvari JL, Jamieson B, Wise K, Buzsáki G. Mechanisms of gamma oscillations
in the hippocampus of the behaving rat. Neuron. 2003;37(2):311-322. doi:10.1016/S0896-6273(02)01169-8
apa: Csicsvari, J. L., Jamieson, B., Wise, K., & Buzsáki, G. (2003). Mechanisms
of gamma oscillations in the hippocampus of the behaving rat. Neuron. Elsevier.
https://doi.org/10.1016/S0896-6273(02)01169-8
chicago: Csicsvari, Jozsef L, Brian Jamieson, Kensall Wise, and György Buzsáki.
“Mechanisms of Gamma Oscillations in the Hippocampus of the Behaving Rat.” Neuron.
Elsevier, 2003. https://doi.org/10.1016/S0896-6273(02)01169-8.
ieee: J. L. Csicsvari, B. Jamieson, K. Wise, and G. Buzsáki, “Mechanisms of gamma
oscillations in the hippocampus of the behaving rat,” Neuron, vol. 37,
no. 2. Elsevier, pp. 311–322, 2003.
ista: Csicsvari JL, Jamieson B, Wise K, Buzsáki G. 2003. Mechanisms of gamma oscillations
in the hippocampus of the behaving rat. Neuron. 37(2), 311–322.
mla: Csicsvari, Jozsef L., et al. “Mechanisms of Gamma Oscillations in the Hippocampus
of the Behaving Rat.” Neuron, vol. 37, no. 2, Elsevier, 2003, pp. 311–22,
doi:10.1016/S0896-6273(02)01169-8.
short: J.L. Csicsvari, B. Jamieson, K. Wise, G. Buzsáki, Neuron 37 (2003) 311–322.
date_created: 2018-12-11T12:03:48Z
date_published: 2003-01-01T00:00:00Z
date_updated: 2021-01-12T07:44:05Z
day: '01'
doi: 10.1016/S0896-6273(02)01169-8
extern: 1
intvolume: ' 37'
issue: '2'
month: '01'
page: 311 - 322
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2857'
quality_controlled: 0
status: public
title: Mechanisms of gamma oscillations in the hippocampus of the behaving rat
type: journal_article
volume: 37
year: '2003'
...
---
_id: '3529'
abstract:
- lang: eng
text: Parallel recording of neuronal activity in the behaving animal is a prerequisite
for our understanding of neuronal representation and storage of information. Here
we describe the development of micro-machined silicon microelectrode arrays for
unit and local field recordings. The two-dimensional probes with 96 or 64 recording
sites provided high-density recording of unit and field activity with minimal
tissue displacement or damage. The on-chip active circuit eliminated movement
and other artifacts and greatly reduced the weight of the headgear. The precise
geometry of the recording tips allowed for the estimation of the spatial location
of the recorded neurons and for high-resolution estimation of extracellular current
source density. Action potentials could be simultaneously recorded from the soma
and dendrites of the same neurons. Silicon technology is a promising approach
for high-density, high-resolution sampling of neuronal activity in both basic
research and prosthetic devices.
author:
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Darrell
full_name: Henze, Darrell A
last_name: Henze
- first_name: Brian
full_name: Jamieson, Brian G
last_name: Jamieson
- first_name: Kenneth
full_name: Harris, Kenneth D
last_name: Harris
- first_name: Anton
full_name: Sirota, Anton M
last_name: Sirota
- first_name: Peter
full_name: Bartho, Peter
last_name: Bartho
- first_name: Kensall
full_name: Wise, Kensall D
last_name: Wise
- first_name: György
full_name: Buzsáki, György
last_name: Buzsáki
citation:
ama: Csicsvari JL, Henze D, Jamieson B, et al. Massively parallel recording of unit
and local field potentials with silicon-based electrodes. Journal of Neurophysiology.
2003;90(2):1314-1323. doi:10.1152/jn.00116.2003
apa: Csicsvari, J. L., Henze, D., Jamieson, B., Harris, K., Sirota, A., Bartho,
P., … Buzsáki, G. (2003). Massively parallel recording of unit and local field
potentials with silicon-based electrodes. Journal of Neurophysiology. American
Physiological Society. https://doi.org/10.1152/jn.00116.2003
chicago: Csicsvari, Jozsef L, Darrell Henze, Brian Jamieson, Kenneth Harris, Anton
Sirota, Peter Bartho, Kensall Wise, and György Buzsáki. “Massively Parallel Recording
of Unit and Local Field Potentials with Silicon-Based Electrodes.” Journal
of Neurophysiology. American Physiological Society, 2003. https://doi.org/10.1152/jn.00116.2003.
ieee: J. L. Csicsvari et al., “Massively parallel recording of unit and local
field potentials with silicon-based electrodes,” Journal of Neurophysiology,
vol. 90, no. 2. American Physiological Society, pp. 1314–1323, 2003.
ista: Csicsvari JL, Henze D, Jamieson B, Harris K, Sirota A, Bartho P, Wise K, Buzsáki
G. 2003. Massively parallel recording of unit and local field potentials with
silicon-based electrodes. Journal of Neurophysiology. 90(2), 1314–1323.
mla: Csicsvari, Jozsef L., et al. “Massively Parallel Recording of Unit and Local
Field Potentials with Silicon-Based Electrodes.” Journal of Neurophysiology,
vol. 90, no. 2, American Physiological Society, 2003, pp. 1314–23, doi:10.1152/jn.00116.2003.
short: J.L. Csicsvari, D. Henze, B. Jamieson, K. Harris, A. Sirota, P. Bartho, K.
Wise, G. Buzsáki, Journal of Neurophysiology 90 (2003) 1314–1323.
date_created: 2018-12-11T12:03:48Z
date_published: 2003-08-01T00:00:00Z
date_updated: 2021-01-12T07:44:05Z
day: '01'
doi: 10.1152/jn.00116.2003
extern: 1
intvolume: ' 90'
issue: '2'
month: '08'
page: 1314 - 1323
publication: Journal of Neurophysiology
publication_status: published
publisher: American Physiological Society
publist_id: '2856'
quality_controlled: 0
status: public
title: Massively parallel recording of unit and local field potentials with silicon-based
electrodes
type: journal_article
volume: 90
year: '2003'
...
---
_id: '3536'
abstract:
- lang: eng
text: 'Genetic engineering of the mouse brain allows investigators to address novel
hypotheses in vivo. Because of the paucity of information on the network patterns
of the mouse hippocampus, we investigated the electrical patterns in the behaving
animal using multisite silicon probes and wire tetrodes. Theta (6-9 Hz) and gamma
(40-100 Hz) oscillations were present during exploration and rapid eye movement
sleep. Gamma power and theta power were comodulated and gamma power varied as
a function of the theta cycle. Pyramidal cells and putative interneurons were
phase-locked to theta oscillations. During immobility, consummatory behaviors
and slow-wave sleep, sharp waves were present in cornu ammonis region CA1 of the
hippocampus stratum radiatum associated with 140-200-Hz “ripples” in the pyramidal
cell layer and population burst of CA1 neurons. In the hilus, large-amplitude
“dentate spikes” occurred in association with increased discharge of hilar neurons.
The amplitude of field patterns was larger in the mouse than in the rat, likely
reflecting the higher neuron density in a smaller brain. We suggest that the main
hippocampal network patterns are mediated by similar pathways and mechanisms in
mouse and rat. '
author:
- first_name: György
full_name: Buzsáki, György
last_name: Buzsáki
- first_name: Derek
full_name: Buhl, Derek L
last_name: Buhl
- first_name: Kenneth
full_name: Harris, Kenneth D
last_name: Harris
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Boldizsár
full_name: Czéh, Boldizsár
last_name: Czéh
- first_name: Alexei
full_name: Morozov, Alexei
last_name: Morozov
citation:
ama: Buzsáki G, Buhl D, Harris K, Csicsvari JL, Czéh B, Morozov A. Hippocampal network
patterns of activity in the mouse. Neuroscience. 2003;116(1):201-211. doi:10.1016/S0306-4522(02)00669-3
apa: Buzsáki, G., Buhl, D., Harris, K., Csicsvari, J. L., Czéh, B., & Morozov,
A. (2003). Hippocampal network patterns of activity in the mouse. Neuroscience.
Elsevier. https://doi.org/10.1016/S0306-4522(02)00669-3
chicago: Buzsáki, György, Derek Buhl, Kenneth Harris, Jozsef L Csicsvari, Boldizsár
Czéh, and Alexei Morozov. “Hippocampal Network Patterns of Activity in the Mouse.”
Neuroscience. Elsevier, 2003. https://doi.org/10.1016/S0306-4522(02)00669-3.
ieee: G. Buzsáki, D. Buhl, K. Harris, J. L. Csicsvari, B. Czéh, and A. Morozov,
“Hippocampal network patterns of activity in the mouse,” Neuroscience,
vol. 116, no. 1. Elsevier, pp. 201–211, 2003.
ista: Buzsáki G, Buhl D, Harris K, Csicsvari JL, Czéh B, Morozov A. 2003. Hippocampal
network patterns of activity in the mouse. Neuroscience. 116(1), 201–211.
mla: Buzsáki, György, et al. “Hippocampal Network Patterns of Activity in the Mouse.”
Neuroscience, vol. 116, no. 1, Elsevier, 2003, pp. 201–11, doi:10.1016/S0306-4522(02)00669-3.
short: G. Buzsáki, D. Buhl, K. Harris, J.L. Csicsvari, B. Czéh, A. Morozov, Neuroscience
116 (2003) 201–211.
date_created: 2018-12-11T12:03:50Z
date_published: 2003-01-15T00:00:00Z
date_updated: 2021-01-12T07:44:09Z
day: '15'
doi: 10.1016/S0306-4522(02)00669-3
extern: 1
intvolume: ' 116'
issue: '1'
month: '01'
page: 201 - 211
publication: Neuroscience
publication_status: published
publisher: Elsevier
publist_id: '2849'
quality_controlled: 0
status: public
title: Hippocampal network patterns of activity in the mouse
type: journal_article
volume: 116
year: '2003'
...
---
_id: '3543'
abstract:
- lang: eng
text: Both neocortical and hippocampal networks organize the firing patterns of
their neurons by prominent oscillations during sleep, but the functional role
of these rhythms is not well understood. Here, we show a robust correlation of
neuronal discharges between the somatosensory cortex and hippocampus on both slow
and fine time scales in the mouse and rat. Neuronal bursts in deep cortical layers,
associated with sleep spindles and delta waves/slow rhythm, effectively triggered
hippocampal discharges related to fast (ripple) oscillations. We hypothesize that
oscillation-mediated temporal links coordinate specific information transfer between
neocortical and hippocampal cell assemblies. Such a neocortical-hippocampal interplay
may be important for memory consolidation.
author:
- first_name: Anton
full_name: Sirota, Anton M
last_name: Sirota
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Derek
full_name: Buhl, Derek L
last_name: Buhl
- first_name: György
full_name: Buzsáki, György
last_name: Buzsáki
citation:
ama: Sirota A, Csicsvari JL, Buhl D, Buzsáki G. Communication between neocortex
and hippocampus during sleep in rodents. PNAS. 2003;100(4):2065-2069. doi:10.1073/pnas.0437938100
apa: Sirota, A., Csicsvari, J. L., Buhl, D., & Buzsáki, G. (2003). Communication
between neocortex and hippocampus during sleep in rodents. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.0437938100
chicago: Sirota, Anton, Jozsef L Csicsvari, Derek Buhl, and György Buzsáki. “Communication
between Neocortex and Hippocampus during Sleep in Rodents.” PNAS. National
Academy of Sciences, 2003. https://doi.org/10.1073/pnas.0437938100.
ieee: A. Sirota, J. L. Csicsvari, D. Buhl, and G. Buzsáki, “Communication between
neocortex and hippocampus during sleep in rodents,” PNAS, vol. 100, no.
4. National Academy of Sciences, pp. 2065–2069, 2003.
ista: Sirota A, Csicsvari JL, Buhl D, Buzsáki G. 2003. Communication between neocortex
and hippocampus during sleep in rodents. PNAS. 100(4), 2065–2069.
mla: Sirota, Anton, et al. “Communication between Neocortex and Hippocampus during
Sleep in Rodents.” PNAS, vol. 100, no. 4, National Academy of Sciences,
2003, pp. 2065–69, doi:10.1073/pnas.0437938100.
short: A. Sirota, J.L. Csicsvari, D. Buhl, G. Buzsáki, PNAS 100 (2003) 2065–2069.
date_created: 2018-12-11T12:03:53Z
date_published: 2003-02-18T00:00:00Z
date_updated: 2021-01-12T07:44:12Z
day: '18'
doi: 10.1073/pnas.0437938100
extern: 1
intvolume: ' 100'
issue: '4'
month: '02'
page: 2065 - 2069
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2841'
quality_controlled: 0
status: public
title: Communication between neocortex and hippocampus during sleep in rodents
type: journal_article
volume: 100
year: '2003'
...
---
_id: '3556'
abstract:
- lang: eng
text: We define the Morse-Smale complex of a Morse function over a 3-manifold as
the overlay of the descending and as- cending manifolds of all critical points.
In the generic case, its 3-dimensional cells are shaped like crystals and are
sepa- rated by quadrangular faces. In this paper, we give a combi- natorial algorithm
for constructing such complexes for piece- wise linear data.
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. Morse-Smale complexes for
piecewise linear 3-manifolds. In: ACM; 2003:361-370. doi:10.1145/777792.777846'
apa: 'Edelsbrunner, H., Harer, J., Natarajan, V., & Pascucci, V. (2003). Morse-Smale
complexes for piecewise linear 3-manifolds (pp. 361–370). Presented at the SCG:
Symposium on Computational Geometry, ACM. https://doi.org/10.1145/777792.777846'
chicago: Edelsbrunner, Herbert, John Harer, Vijay Natarajan, and Valerio Pascucci.
“Morse-Smale Complexes for Piecewise Linear 3-Manifolds,” 361–70. ACM, 2003. https://doi.org/10.1145/777792.777846.
ieee: 'H. Edelsbrunner, J. Harer, V. Natarajan, and V. Pascucci, “Morse-Smale complexes
for piecewise linear 3-manifolds,” presented at the SCG: Symposium on Computational
Geometry, 2003, pp. 361–370.'
ista: 'Edelsbrunner H, Harer J, Natarajan V, Pascucci V. 2003. Morse-Smale complexes
for piecewise linear 3-manifolds. SCG: Symposium on Computational Geometry, 361–370.'
mla: Edelsbrunner, Herbert, et al. Morse-Smale Complexes for Piecewise Linear
3-Manifolds. ACM, 2003, pp. 361–70, doi:10.1145/777792.777846.
short: H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci, in:, ACM, 2003, pp.
361–370.
conference:
name: 'SCG: Symposium on Computational Geometry'
date_created: 2018-12-11T12:03:57Z
date_published: 2003-06-01T00:00:00Z
date_updated: 2021-01-12T07:44:17Z
day: '01'
doi: 10.1145/777792.777846
extern: 1
main_file_link:
- open_access: '0'
url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.14.9592
month: '06'
page: 361 - 370
publication_status: published
publisher: ACM
publist_id: '2829'
quality_controlled: 0
status: public
title: Morse-Smale complexes for piecewise linear 3-manifolds
type: conference
year: '2003'
...
---
_id: '3573'
abstract:
- lang: eng
text: Given a finite point set in R, the surface reconstruction problem asks for
a surface that passes through many but not necessarily all points. We describe
an unambigu- ous definition of such a surface in geometric and topological terms,
and sketch a fast algorithm for constructing it. Our solution overcomes past limitations
to special point distributions and heuristic design decisions.
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. Surface reconstruction by wrapping finite sets in space. In:
Discrete & Computational Geometry. Springer; 2003:379-404. doi:10.1007/978-3-642-55566-4_17'
apa: Edelsbrunner, H. (2003). Surface reconstruction by wrapping finite sets in
space. In Discrete & Computational Geometry (pp. 379–404). Springer.
https://doi.org/10.1007/978-3-642-55566-4_17
chicago: Edelsbrunner, Herbert. “Surface Reconstruction by Wrapping Finite Sets
in Space.” In Discrete & Computational Geometry, 379–404. Springer,
2003. https://doi.org/10.1007/978-3-642-55566-4_17.
ieee: H. Edelsbrunner, “Surface reconstruction by wrapping finite sets in space,”
in Discrete & Computational Geometry, Springer, 2003, pp. 379–404.
ista: 'Edelsbrunner H. 2003.Surface reconstruction by wrapping finite sets in space.
In: Discrete & Computational Geometry. , 379–404.'
mla: Edelsbrunner, Herbert. “Surface Reconstruction by Wrapping Finite Sets in Space.”
Discrete & Computational Geometry, Springer, 2003, pp. 379–404, doi:10.1007/978-3-642-55566-4_17.
short: H. Edelsbrunner, in:, Discrete & Computational Geometry, Springer, 2003,
pp. 379–404.
date_created: 2018-12-11T12:04:02Z
date_published: 2003-06-23T00:00:00Z
date_updated: 2021-01-12T07:44:24Z
day: '23'
doi: 10.1007/978-3-642-55566-4_17
extern: 1
main_file_link:
- open_access: '0'
url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.129.3633
month: '06'
page: 379 - 404
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2812'
quality_controlled: 0
status: public
title: Surface reconstruction by wrapping finite sets in space
type: book_chapter
year: '2003'
...
---
_id: '3584'
abstract:
- lang: eng
text: We develop fast algorithms for computing the linking number of a simplicial
complex within a filtration.We give experimental results in applying our work
toward the detection of non-trivial tangling in biomolecules, modeled as alpha
complexes.
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Afra
full_name: Zomorodian, Afra
last_name: Zomorodian
citation:
ama: Edelsbrunner H, Zomorodian A. Computing linking numbers of a filtration. Homology,
Homotopy and Applications. 2003;5(2):19-37.
apa: Edelsbrunner, H., & Zomorodian, A. (2003). Computing linking numbers of
a filtration. Homology, Homotopy and Applications. International Press.
chicago: Edelsbrunner, Herbert, and Afra Zomorodian. “Computing Linking Numbers
of a Filtration.” Homology, Homotopy and Applications. International Press,
2003.
ieee: H. Edelsbrunner and A. Zomorodian, “Computing linking numbers of a filtration,”
Homology, Homotopy and Applications, vol. 5, no. 2. International Press,
pp. 19–37, 2003.
ista: Edelsbrunner H, Zomorodian A. 2003. Computing linking numbers of a filtration.
Homology, Homotopy and Applications. 5(2), 19–37.
mla: Edelsbrunner, Herbert, and Afra Zomorodian. “Computing Linking Numbers of a
Filtration.” Homology, Homotopy and Applications, vol. 5, no. 2, International
Press, 2003, pp. 19–37.
short: H. Edelsbrunner, A. Zomorodian, Homology, Homotopy and Applications 5 (2003)
19–37.
date_created: 2018-12-11T12:04:05Z
date_published: 2003-04-22T00:00:00Z
date_updated: 2021-01-12T07:44:28Z
day: '22'
extern: '1'
intvolume: ' 5'
issue: '2'
language:
- iso: eng
main_file_link:
- url: http://projecteuclid.org/euclid.hha/1088453320
month: '04'
oa_version: None
page: 19 - 37
publication: Homology, Homotopy and Applications
publication_status: published
publisher: International Press
publist_id: '2801'
quality_controlled: '1'
status: public
title: Computing linking numbers of a filtration
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2003'
...
---
_id: '3593'
abstract:
- lang: eng
text: Temporal logics such as Computation Tree Logic (CTL) and Linear Temporal Logic
(LTL) have become popular for specifying temporal properties over a wide variety
of planning and verification problems. In this paper we work towards building
a generalized framework for automated reasoning based on temporal logics. We present
a powerful extension of CTL with first-order quantification over the set of reachable
states for reasoning about extremal properties of weighted labeled transition
systems in general. The proposed logic, which we call Weighted Quantified Computation
Tree Logic (WQCTL), captures the essential elements common to the domain of planning
and verification problems and can thereby be used as an effective specification
language in both domains. We show that in spite of the rich, expressive power
of the logic, we are able to evaluate WQCTL formulas in time polynomial in the
size of the state space times the length of the formula. Wepresent experimental
results on the WQCTL verifier.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Pallab
full_name: Dasgupta, Pallab
last_name: Dasgupta
- first_name: Partha
full_name: Chakrabarti, Partha P
last_name: Chakrabarti
citation:
ama: Chatterjee K, Dasgupta P, Chakrabarti P. A branching time temporal framework
for quantitative reasoning. Journal of Automated Reasoning. 2003;30(2):205-232.
doi:10.1023/A:1023217515688
apa: Chatterjee, K., Dasgupta, P., & Chakrabarti, P. (2003). A branching time
temporal framework for quantitative reasoning. Journal of Automated Reasoning.
Springer. https://doi.org/10.1023/A:1023217515688
chicago: Chatterjee, Krishnendu, Pallab Dasgupta, and Partha Chakrabarti. “A Branching
Time Temporal Framework for Quantitative Reasoning.” Journal of Automated Reasoning.
Springer, 2003. https://doi.org/10.1023/A:1023217515688.
ieee: K. Chatterjee, P. Dasgupta, and P. Chakrabarti, “A branching time temporal
framework for quantitative reasoning,” Journal of Automated Reasoning,
vol. 30, no. 2. Springer, pp. 205–232, 2003.
ista: Chatterjee K, Dasgupta P, Chakrabarti P. 2003. A branching time temporal framework
for quantitative reasoning. Journal of Automated Reasoning. 30(2), 205–232.
mla: Chatterjee, Krishnendu, et al. “A Branching Time Temporal Framework for Quantitative
Reasoning.” Journal of Automated Reasoning, vol. 30, no. 2, Springer, 2003,
pp. 205–32, doi:10.1023/A:1023217515688.
short: K. Chatterjee, P. Dasgupta, P. Chakrabarti, Journal of Automated Reasoning
30 (2003) 205–232.
date_created: 2018-12-11T12:04:08Z
date_published: 2003-02-01T00:00:00Z
date_updated: 2021-01-12T07:44:31Z
day: '01'
doi: 10.1023/A:1023217515688
extern: 1
intvolume: ' 30'
issue: '2'
month: '02'
page: 205 - 232
publication: Journal of Automated Reasoning
publication_status: published
publisher: Springer
publist_id: '2790'
quality_controlled: 0
status: public
title: A branching time temporal framework for quantitative reasoning
type: journal_article
volume: 30
year: '2003'
...
---
_id: '3618'
abstract:
- lang: eng
text: There are several analyses in evolutionary ecology which assume that a family
of offspring has come from only two parents. Here, we present a simple test for
detecting when a batch involves two or more subfamilies. It is based on the fact
that the mixing of families generates associations amongst unlinked marker loci.
We also present simulations illustrating the power of our method for varying numbers
of loci, alleles per locus and genotyped individuals.
author:
- first_name: Timothy
full_name: Vines, Timothy H
last_name: Vines
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Vines T, Barton NH. A new approach to detecting mixed families. Molecular
Ecology. 2003;12(7):1999-2002. doi:10.1046/j.1365-294X.2003.01867.x
apa: Vines, T., & Barton, N. H. (2003). A new approach to detecting mixed families.
Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1046/j.1365-294X.2003.01867.x
chicago: Vines, Timothy, and Nicholas H Barton. “A New Approach to Detecting Mixed
Families.” Molecular Ecology. Wiley-Blackwell, 2003. https://doi.org/10.1046/j.1365-294X.2003.01867.x.
ieee: T. Vines and N. H. Barton, “A new approach to detecting mixed families,” Molecular
Ecology, vol. 12, no. 7. Wiley-Blackwell, pp. 1999–2002, 2003.
ista: Vines T, Barton NH. 2003. A new approach to detecting mixed families. Molecular
Ecology. 12(7), 1999–2002.
mla: Vines, Timothy, and Nicholas H. Barton. “A New Approach to Detecting Mixed
Families.” Molecular Ecology, vol. 12, no. 7, Wiley-Blackwell, 2003, pp.
1999–2002, doi:10.1046/j.1365-294X.2003.01867.x.
short: T. Vines, N.H. Barton, Molecular Ecology 12 (2003) 1999–2002.
date_created: 2018-12-11T12:04:16Z
date_published: 2003-07-01T00:00:00Z
date_updated: 2021-01-12T07:44:42Z
day: '01'
doi: 10.1046/j.1365-294X.2003.01867.x
extern: 1
intvolume: ' 12'
issue: '7'
month: '07'
page: 1999 - 2002
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2765'
quality_controlled: 0
status: public
title: A new approach to detecting mixed families
type: journal_article
volume: 12
year: '2003'
...
---
_id: '3619'
abstract:
- lang: eng
text: What is the chance that some part of a stretch of genome will survive? In
a population of constant size, and with no selection, the probability of survival
of some part of a stretch of map length y<1 approaches View the MathML source
for View the MathML source. Thus, the whole genome is certain to be lost, but
the rate of loss is extremely slow. This solution extends to give the whole distribution
of surviving block sizes as a function of time. We show that the expected number
of blocks at time t is 1+yt and give expressions for the moments of the number
of blocks and the total amount of genome that survives for a given time. The solution
is based on a branching process and assumes complete interference between crossovers,
so that each descendant carries only a single block of ancestral material. We
consider cases where most individuals carry multiple blocks, either because there
are multiple crossovers in a long genetic map, or because enough time has passed
that most individuals in the population are related to each other. For species
such as ours, which have a long genetic map, the genome of any individual which
leaves descendants (∼80% of the population for a Poisson offspring number with
mean two) is likely to persist for an extremely long time, in the form of a few
short blocks of genome.
author:
- first_name: Stuart
full_name: Baird, Stuart J
last_name: Baird
- 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: Baird S, Barton NH, Etheridge A. The distribution of surviving blocks of an
ancestral genome. Theoretical Population Biology. 2003;64(4):451-471. doi:10.1016/S0040-5809(03)00098-4
apa: Baird, S., Barton, N. H., & Etheridge, A. (2003). The distribution of surviving
blocks of an ancestral genome. Theoretical Population Biology. Academic
Press. https://doi.org/10.1016/S0040-5809(03)00098-4
chicago: Baird, Stuart, Nicholas H Barton, and Alison Etheridge. “The Distribution
of Surviving Blocks of an Ancestral Genome.” Theoretical Population Biology.
Academic Press, 2003. https://doi.org/10.1016/S0040-5809(03)00098-4.
ieee: S. Baird, N. H. Barton, and A. Etheridge, “The distribution of surviving blocks
of an ancestral genome,” Theoretical Population Biology, vol. 64, no. 4.
Academic Press, pp. 451–471, 2003.
ista: Baird S, Barton NH, Etheridge A. 2003. The distribution of surviving blocks
of an ancestral genome. Theoretical Population Biology. 64(4), 451–471.
mla: Baird, Stuart, et al. “The Distribution of Surviving Blocks of an Ancestral
Genome.” Theoretical Population Biology, vol. 64, no. 4, Academic Press,
2003, pp. 451–71, doi:10.1016/S0040-5809(03)00098-4.
short: S. Baird, N.H. Barton, A. Etheridge, Theoretical Population Biology 64 (2003)
451–471.
date_created: 2018-12-11T12:04:17Z
date_published: 2003-12-01T00:00:00Z
date_updated: 2021-01-12T07:44:42Z
day: '01'
doi: 10.1016/S0040-5809(03)00098-4
extern: 1
intvolume: ' 64'
issue: '4'
month: '12'
page: 451 - 471
publication: Theoretical Population Biology
publication_status: published
publisher: Academic Press
publist_id: '2764'
quality_controlled: 0
status: public
title: The distribution of surviving blocks of an ancestral genome
type: journal_article
volume: 64
year: '2003'
...
---
_id: '3620'
abstract:
- lang: eng
text: 'Stable hybrid zones in which ecologically divergent taxa give rise to a range
of recombinants are natural laboratories in which the genetic basis of adaptation
and reproductive isolation can be unraveled. One such hybrid zone is formed by
the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae).
Adaptations to permanent and ephemeral breeding habitats, respectively, have shaped
numerous phenotypic differences between the taxa. All of these are, in principle,
candidates for a genetic dissection via QTL mapping. We present here a linkage
map of 28 codominant and 10 dominant markers in the Bombina genome. In an F2 cross,
markers that were mainly microsatellites, SSCPs or allozymes were mapped to 20
linkage groups. Among the 40 isolated CA microsatellites, we noted a preponderance
of compound and frequently interleaved CA-TA repeats as well as a striking polarity
at the 5′ end of the repeats.'
author:
- first_name: Beate
full_name: Nürnberger, Beate
last_name: Nürnberger
- first_name: Sebastian
full_name: Hofman, Sebastian
last_name: Hofman
- first_name: Bqruni
full_name: Förg-Brey, Bqruni
last_name: Förg Brey
- first_name: Gabriele
full_name: Praetzel, Gabriele
last_name: Praetzel
- first_name: Alan
full_name: Maclean, Alan W
last_name: Maclean
- first_name: Jacek
full_name: Szymura, Jacek M
last_name: Szymura
- first_name: Catherine
full_name: Abbott, Catherine M
last_name: Abbott
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Nürnberger B, Hofman S, Förg Brey B, et al. A linkage map for the hybridising
toads Bombina bombina and B. variegata (Anura: Discoglossidae). Heredity.
2003;91(2):136-142. doi:10.1038/sj.hdy.6800291'
apa: 'Nürnberger, B., Hofman, S., Förg Brey, B., Praetzel, G., Maclean, A., Szymura,
J., … Barton, N. H. (2003). A linkage map for the hybridising toads Bombina bombina
and B. variegata (Anura: Discoglossidae). Heredity. Nature Publishing Group.
https://doi.org/10.1038/sj.hdy.6800291'
chicago: 'Nürnberger, Beate, Sebastian Hofman, Bqruni Förg Brey, Gabriele Praetzel,
Alan Maclean, Jacek Szymura, Catherine Abbott, and Nicholas H Barton. “A Linkage
Map for the Hybridising Toads Bombina Bombina and B. Variegata (Anura: Discoglossidae).”
Heredity. Nature Publishing Group, 2003. https://doi.org/10.1038/sj.hdy.6800291.'
ieee: 'B. Nürnberger et al., “A linkage map for the hybridising toads Bombina
bombina and B. variegata (Anura: Discoglossidae),” Heredity, vol. 91, no.
2. Nature Publishing Group, pp. 136–142, 2003.'
ista: 'Nürnberger B, Hofman S, Förg Brey B, Praetzel G, Maclean A, Szymura J, Abbott
C, Barton NH. 2003. A linkage map for the hybridising toads Bombina bombina and
B. variegata (Anura: Discoglossidae). Heredity. 91(2), 136–142.'
mla: 'Nürnberger, Beate, et al. “A Linkage Map for the Hybridising Toads Bombina
Bombina and B. Variegata (Anura: Discoglossidae).” Heredity, vol. 91, no.
2, Nature Publishing Group, 2003, pp. 136–42, doi:10.1038/sj.hdy.6800291.'
short: B. Nürnberger, S. Hofman, B. Förg Brey, G. Praetzel, A. Maclean, J. Szymura,
C. Abbott, N.H. Barton, Heredity 91 (2003) 136–142.
date_created: 2018-12-11T12:04:17Z
date_published: 2003-08-01T00:00:00Z
date_updated: 2021-01-12T07:44:43Z
day: '01'
doi: 10.1038/sj.hdy.6800291
extern: 1
intvolume: ' 91'
issue: '2'
month: '08'
page: 136 - 142
publication: Heredity
publication_status: published
publisher: Nature Publishing Group
publist_id: '2763'
quality_controlled: 0
status: public
title: 'A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura:
Discoglossidae)'
type: journal_article
volume: 91
year: '2003'
...
---
_id: '3678'
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Lampert C. The Neumann operator in strictly pseudoconvex domains with weighted
Bergman metric . Bonner Mathematische Schriften. 2003;356:1-165.
apa: Lampert, C. (2003). The Neumann operator in strictly pseudoconvex domains
with weighted Bergman metric . Bonner Mathematische Schriften. Universität
Bonn, Fachbibliothek Mathematik.
chicago: Lampert, Christoph. “The Neumann Operator in Strictly Pseudoconvex Domains
with Weighted Bergman Metric .” Bonner Mathematische Schriften. Universität
Bonn, Fachbibliothek Mathematik, 2003.
ieee: C. Lampert, “The Neumann operator in strictly pseudoconvex domains with weighted
Bergman metric ,” Universität Bonn, Fachbibliothek Mathematik, 2003.
ista: Lampert C. 2003. The Neumann operator in strictly pseudoconvex domains with
weighted Bergman metric . Universität Bonn, Fachbibliothek Mathematik.
mla: Lampert, Christoph. “The Neumann Operator in Strictly Pseudoconvex Domains
with Weighted Bergman Metric .” Bonner Mathematische Schriften, vol. 356,
Universität Bonn, Fachbibliothek Mathematik, 2003, pp. 1–165.
short: C. Lampert, The Neumann Operator in Strictly Pseudoconvex Domains with Weighted
Bergman Metric , Universität Bonn, Fachbibliothek Mathematik, 2003.
date_created: 2018-12-11T12:04:34Z
date_published: 2003-03-31T00:00:00Z
date_updated: 2021-01-12T07:45:05Z
day: '31'
extern: 1
intvolume: ' 356'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/~chl/papers/lampert-phd2003.pdf
month: '03'
page: 1 - 165
publication: Bonner Mathematische Schriften
publication_status: published
publisher: Universität Bonn, Fachbibliothek Mathematik
publist_id: '2704'
quality_controlled: 0
status: public
title: 'The Neumann operator in strictly pseudoconvex domains with weighted Bergman
metric '
type: dissertation
volume: 356
year: '2003'
...
---
_id: '3725'
abstract:
- lang: eng
text: The combination of high-resolution atomic force microscopy (AFM) imaging and
single-molecule force-spectroscopy was employed to unfold single bacteriorhodopsins
(BR) from native purple membrane patches at various physiologically relevant temperatures.
The unfolding spectra reveal detailed insight into the stability of individual
structural elements of BR against mechanical unfolding. Intermittent states in
the unfolding process are associated with the stepwise unfolding of alpha-helices,
whereas other states are associated with the unfolding of polypeptide loops connecting
the alpha-helices. It was found that the unfolding forces of the secondary structures
considerably decreased upon increasing the temperature from 8 to 52°C. Associated
with this effect, the probability of individual unfolding pathways of BR was significantly
influenced by the temperature. At lower temperatures, transmembrane alpha-helices
and extracellular polypeptide loops exhibited sufficient stability to individually
establish potential barriers against unfolding, whereas they predominantly unfolded
collectively at elevated temperatures. This suggests that increasing the temperature
decreases the mechanical stability of secondary structural elements and changes
molecular interactions between secondary structures, thereby forcing them to act
as grouped structures.
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: Max
full_name: Kessler, Max
last_name: Kessler
- first_name: Dieter
full_name: Oesterhelt, Dieter
last_name: Oesterhelt
- first_name: Hermann
full_name: Gaub, Hermann
last_name: Gaub
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Janovjak HL, Kessler M, Oesterhelt D, Gaub H, Mueller D. Unfolding pathways
of native bacteriorhodopsin depend on temperature. EMBO Journal. 2003;22(19):5220-5229.
doi:10.1093/emboj/cdg509
apa: Janovjak, H. L., Kessler, M., Oesterhelt, D., Gaub, H., & Mueller, D. (2003).
Unfolding pathways of native bacteriorhodopsin depend on temperature. EMBO
Journal. Wiley-Blackwell. https://doi.org/10.1093/emboj/cdg509
chicago: Janovjak, Harald L, Max Kessler, Dieter Oesterhelt, Hermann Gaub, and Daniel
Mueller. “Unfolding Pathways of Native Bacteriorhodopsin Depend on Temperature.”
EMBO Journal. Wiley-Blackwell, 2003. https://doi.org/10.1093/emboj/cdg509.
ieee: H. L. Janovjak, M. Kessler, D. Oesterhelt, H. Gaub, and D. Mueller, “Unfolding
pathways of native bacteriorhodopsin depend on temperature,” EMBO Journal,
vol. 22, no. 19. Wiley-Blackwell, pp. 5220–5229, 2003.
ista: Janovjak HL, Kessler M, Oesterhelt D, Gaub H, Mueller D. 2003. Unfolding pathways
of native bacteriorhodopsin depend on temperature. EMBO Journal. 22(19), 5220–5229.
mla: Janovjak, Harald L., et al. “Unfolding Pathways of Native Bacteriorhodopsin
Depend on Temperature.” EMBO Journal, vol. 22, no. 19, Wiley-Blackwell,
2003, pp. 5220–29, doi:10.1093/emboj/cdg509.
short: H.L. Janovjak, M. Kessler, D. Oesterhelt, H. Gaub, D. Mueller, EMBO Journal
22 (2003) 5220–5229.
date_created: 2018-12-11T12:04:50Z
date_published: 2003-01-01T00:00:00Z
date_updated: 2021-01-12T07:51:45Z
day: '01'
doi: 10.1093/emboj/cdg509
extern: 1
intvolume: ' 22'
issue: '19'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC204492/
month: '01'
oa: 1
page: 5220 - 5229
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2506'
quality_controlled: 0
status: public
title: Unfolding pathways of native bacteriorhodopsin depend on temperature
type: journal_article
volume: 22
year: '2003'
...