---
_id: '9517'
abstract:
- lang: eng
text: Multicellular eukaryotes produce small RNA molecules (approximately 21–24
nucleotides) of two general types, microRNA (miRNA) and short interfering RNA
(siRNA). They collectively function as sequence-specific guides to silence or
regulate genes, transposons, and viruses and to modify chromatin and genome structure.
Formation or activity of small RNAs requires factors belonging to gene families
that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case
of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals,
plants encode multiple DCL and RDR proteins. Using a series of insertion mutants
of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1),
endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One
RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of
endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic
marks and increased transcript accumulation at some loci. Defects in siRNA-generation
activity in response to turnip crinkle virus in dcl2 mutant plants correlated
with increased virus susceptibility. We conclude that proliferation and diversification
of DCL and RDR genes during evolution of plants contributed to specialization
of small RNA-directed pathways for development, chromatin structure, and defense.
article_processing_charge: No
article_type: original
author:
- first_name: Zhixin
full_name: Xie, Zhixin
last_name: Xie
- first_name: Lisa K.
full_name: Johansen, Lisa K.
last_name: Johansen
- first_name: Adam M.
full_name: Gustafson, Adam M.
last_name: Gustafson
- first_name: Kristin D.
full_name: Kasschau, Kristin D.
last_name: Kasschau
- first_name: 'Andrew D. '
full_name: 'Lellis, Andrew D. '
last_name: Lellis
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
- first_name: James C.
full_name: Carrington, James C.
last_name: Carrington
citation:
ama: Xie Z, Johansen LK, Gustafson AM, et al. Genetic and functional diversification
of small RNA pathways in plants. PLoS Biology. 2004;2(5):0642-0652. doi:10.1371/journal.pbio.0020104
apa: Xie, Z., Johansen, L. K., Gustafson, A. M., Kasschau, K. D., Lellis, A. D.,
Zilberman, D., … Carrington, J. C. (2004). Genetic and functional diversification
of small RNA pathways in plants. PLoS Biology. Public Library of Science.
https://doi.org/10.1371/journal.pbio.0020104
chicago: Xie, Zhixin, Lisa K. Johansen, Adam M. Gustafson, Kristin D. Kasschau,
Andrew D. Lellis, Daniel Zilberman, Steven E. Jacobsen, and James C. Carrington.
“Genetic and Functional Diversification of Small RNA Pathways in Plants.” PLoS
Biology. Public Library of Science, 2004. https://doi.org/10.1371/journal.pbio.0020104.
ieee: Z. Xie et al., “Genetic and functional diversification of small RNA
pathways in plants,” PLoS Biology, vol. 2, no. 5. Public Library of Science,
pp. 0642–0652, 2004.
ista: Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen
SE, Carrington JC. 2004. Genetic and functional diversification of small RNA pathways
in plants. PLoS Biology. 2(5), 0642–0652.
mla: Xie, Zhixin, et al. “Genetic and Functional Diversification of Small RNA Pathways
in Plants.” PLoS Biology, vol. 2, no. 5, Public Library of Science, 2004,
pp. 0642–52, doi:10.1371/journal.pbio.0020104.
short: Z. Xie, L.K. Johansen, A.M. Gustafson, K.D. Kasschau, A.D. Lellis, D. Zilberman,
S.E. Jacobsen, J.C. Carrington, PLoS Biology 2 (2004) 0642–0652.
date_created: 2021-06-07T14:12:08Z
date_published: 2004-02-24T00:00:00Z
date_updated: 2021-12-14T08:43:57Z
day: '24'
department:
- _id: DaZi
doi: 10.1371/journal.pbio.0020104
extern: '1'
external_id:
pmid:
- '15024409'
intvolume: ' 2'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pbio.0020104
month: '02'
oa: 1
oa_version: Published Version
page: 0642-0652
pmid: 1
publication: PLoS Biology
publication_identifier:
eissn:
- 1545-7885
issn:
- 1544-9173
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic and functional diversification of small RNA pathways in plants
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2
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: '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: '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: '12203'
abstract:
- lang: eng
text: 'Geranylgeranyl diphosphate synthase (GGPPS, EC: 2.5.1.29) catalyzes the biosynthesis
of geranylgeranyl diphosphate (GGPP), which is a key precursor for ginkgolide
biosynthesis. Here we reported for the first time the cloning of a new full-length
cDNA encoding GGPPS from the living fossil plant Ginkgo biloba. The full-length
cDNA encoding G. biloba GGPPS (designated as GbGGPPS) was 1657bp long and contained
a 1176bp open reading frame encoding a 391 amino acid protein. Comparative analysis
showed that GbGGPPS possessed a 79 amino acid transit peptide at its N-terminal,
which directed GbGGPPS to target to the plastids. Bioinformatic analysis revealed
that GbGGPPS was a member of polyprenyltransferases with two highly conserved
aspartate-rich motifs like other plant GGPPSs. Phylogenetic tree analysis indicated
that plant GGPPSs could be classified into two groups, angiosperm and gymnosperm
GGPPSs, while GbGGPPS had closer relationship with gymnosperm plant GGPPSs.'
acknowledgement: This study was financially supported by China National High-Tech
“863” Program. The authors are very thankful to Dr Li Wang (School of Life Sciences,
Fudan University, Shanghai, China) for her kind help with constructing the phylogenetic
tree.
article_processing_charge: No
article_type: original
author:
- first_name: Zhihua
full_name: Liao, Zhihua
last_name: Liao
- first_name: Min
full_name: Chen, Min
last_name: Chen
- first_name: Yifu
full_name: Gong, Yifu
last_name: Gong
- first_name: Liang
full_name: Guo, Liang
last_name: Guo
- first_name: Qiumin
full_name: Tan, Qiumin
last_name: Tan
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Xiaofen
full_name: Sun, Xiaofen
last_name: Sun
- first_name: Feng
full_name: Tan, Feng
last_name: Tan
- first_name: Kexuan
full_name: Tang, Kexuan
last_name: Tang
citation:
ama: Liao Z, Chen M, Gong Y, et al. A new geranylgeranyl Diphosphate synthase gene
from Ginkgo biloba, which intermediates the biosynthesis of the key precursor
for ginkgolides. DNA Sequence. 2004;15(2):153-158. doi:10.1080/10425170410001667348
apa: Liao, Z., Chen, M., Gong, Y., Guo, L., Tan, Q., Feng, X., … Tang, K. (2004).
A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates
the biosynthesis of the key precursor for ginkgolides. DNA Sequence. Informa
UK Limited. https://doi.org/10.1080/10425170410001667348
chicago: Liao, Zhihua, Min Chen, Yifu Gong, Liang Guo, Qiumin Tan, Xiaoqi Feng,
Xiaofen Sun, Feng Tan, and Kexuan Tang. “A New Geranylgeranyl Diphosphate Synthase
Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor
for Ginkgolides.” DNA Sequence. Informa UK Limited, 2004. https://doi.org/10.1080/10425170410001667348.
ieee: Z. Liao et al., “A new geranylgeranyl Diphosphate synthase gene from
Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides,”
DNA Sequence, vol. 15, no. 2. Informa UK Limited, pp. 153–158, 2004.
ista: Liao Z, Chen M, Gong Y, Guo L, Tan Q, Feng X, Sun X, Tan F, Tang K. 2004.
A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates
the biosynthesis of the key precursor for ginkgolides. DNA Sequence. 15(2), 153–158.
mla: Liao, Zhihua, et al. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo
Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.”
DNA Sequence, vol. 15, no. 2, Informa UK Limited, 2004, pp. 153–58, doi:10.1080/10425170410001667348.
short: Z. Liao, M. Chen, Y. Gong, L. Guo, Q. Tan, X. Feng, X. Sun, F. Tan, K. Tang,
DNA Sequence 15 (2004) 153–158.
date_created: 2023-01-16T09:24:50Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2023-05-08T10:58:29Z
department:
- _id: XiFe
doi: 10.1080/10425170410001667348
extern: '1'
external_id:
pmid:
- '15352294'
intvolume: ' 15'
issue: '2'
keyword:
- Endocrinology
- Genetics
- Molecular Biology
- Biochemistry
language:
- iso: eng
oa_version: None
page: 153-158
pmid: 1
publication: DNA Sequence
publication_identifier:
issn:
- 1042-5179
publication_status: published
publisher: Informa UK Limited
quality_controlled: '1'
scopus_import: '1'
status: public
title: A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates
the biosynthesis of the key precursor for ginkgolides
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
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: '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: '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: '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: '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: '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: '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: '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: '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: '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: '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: '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'
...