---
_id: '13422'
abstract:
- lang: eng
text: 'Make like a leaf: The synthesis and characterization of a family of “flowerlike”
Au/Fe3O4 nanoparticles is described, whereby Fe3O4 “leaves” adhere to a gold core
(see image). The size and numbers of iron oxide domains can be adjusted flexibly
by changing the proportion of the starting materials and the reaction time.'
article_processing_charge: No
article_type: original
author:
- first_name: Yanhu
full_name: Wei, Yanhu
last_name: Wei
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Anatoliy O.
full_name: Pinchuk, Anatoliy O.
last_name: Pinchuk
- first_name: Bartosz A.
full_name: Grzybowski, Bartosz A.
last_name: Grzybowski
citation:
ama: Wei Y, Klajn R, Pinchuk AO, Grzybowski BA. Synthesis, shape control, and optical
properties of hybrid Au/Fe3O4 “nanoflowers.” Small. 2008;4(10):1635-1639.
doi:10.1002/smll.200800511
apa: Wei, Y., Klajn, R., Pinchuk, A. O., & Grzybowski, B. A. (2008). Synthesis,
shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers.” Small.
Wiley. https://doi.org/10.1002/smll.200800511
chicago: Wei, Yanhu, Rafal Klajn, Anatoliy O. Pinchuk, and Bartosz A. Grzybowski.
“Synthesis, Shape Control, and Optical Properties of Hybrid Au/Fe3O4 ‘Nanoflowers.’”
Small. Wiley, 2008. https://doi.org/10.1002/smll.200800511.
ieee: Y. Wei, R. Klajn, A. O. Pinchuk, and B. A. Grzybowski, “Synthesis, shape control,
and optical properties of hybrid Au/Fe3O4 ‘nanoflowers,’” Small, vol. 4,
no. 10. Wiley, pp. 1635–1639, 2008.
ista: Wei Y, Klajn R, Pinchuk AO, Grzybowski BA. 2008. Synthesis, shape control,
and optical properties of hybrid Au/Fe3O4 “nanoflowers”. Small. 4(10), 1635–1639.
mla: Wei, Yanhu, et al. “Synthesis, Shape Control, and Optical Properties of Hybrid
Au/Fe3O4 ‘Nanoflowers.’” Small, vol. 4, no. 10, Wiley, 2008, pp. 1635–39,
doi:10.1002/smll.200800511.
short: Y. Wei, R. Klajn, A.O. Pinchuk, B.A. Grzybowski, Small 4 (2008) 1635–1639.
date_created: 2023-08-01T10:30:42Z
date_published: 2008-10-09T00:00:00Z
date_updated: 2023-08-08T11:14:50Z
day: '09'
doi: 10.1002/smll.200800511
extern: '1'
external_id:
pmid:
- '18636405'
intvolume: ' 4'
issue: '10'
keyword:
- Biomaterials
- Biotechnology
- General Materials Science
- General Chemistry
language:
- iso: eng
month: '10'
oa_version: None
page: 1635-1639
pmid: 1
publication: Small
publication_identifier:
eissn:
- 1613-6829
issn:
- 1613-6810
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers”
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2008'
...
---
_id: '517'
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Identity and coalescence in structured populations: A commentary
on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. Genetics
Research. 2008;89(5-6):475-477. doi:10.1017/S0016672308009683'
apa: 'Barton, N. H. (2008). Identity and coalescence in structured populations:
A commentary on “Inbreeding coefficients and coalescence times” by Montgomery
Slatkin. Genetics Research. Cambridge University Press. https://doi.org/10.1017/S0016672308009683'
chicago: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations:
A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery
Slatkin.” Genetics Research. Cambridge University Press, 2008. https://doi.org/10.1017/S0016672308009683.'
ieee: 'N. H. Barton, “Identity and coalescence in structured populations: A commentary
on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin,” Genetics
Research, vol. 89, no. 5–6. Cambridge University Press, pp. 475–477, 2008.'
ista: 'Barton NH. 2008. Identity and coalescence in structured populations: A commentary
on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin. Genetics
Research. 89(5–6), 475–477.'
mla: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A
Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.”
Genetics Research, vol. 89, no. 5–6, Cambridge University Press, 2008,
pp. 475–77, doi:10.1017/S0016672308009683.'
short: N.H. Barton, Genetics Research 89 (2008) 475–477.
date_created: 2018-12-11T11:46:55Z
date_published: 2008-10-29T00:00:00Z
date_updated: 2024-02-14T09:51:09Z
day: '29'
department:
- _id: NiBa
doi: 10.1017/S0016672308009683
intvolume: ' 89'
issue: 5-6
language:
- iso: eng
month: '10'
oa_version: None
page: 475 - 477
publication: Genetics Research
publication_status: published
publisher: Cambridge University Press
publist_id: '7302'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Identity and coalescence in structured populations: A commentary on ''Inbreeding
coefficients and coalescence times'' by Montgomery Slatkin'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2008'
...
---
_id: '1035'
abstract:
- lang: eng
text: We explore the rich internal structure of Cs2 Feshbach molecules. Pure ultracold
molecular samples are prepared in a CO2 -laser trap, and a multitude of weakly
bound states is populated by elaborate magnetic-field ramping techniques. Our
methods use different Feshbach resonances as input ports and various internal
level crossings for controlled state transfer. We populate higher partial-wave
states of up to eight units of rotational angular momentum (l -wave states). We
investigate the molecular structure by measurements of the magnetic moments for
various states. Avoided level crossings between different molecular states are
characterized through the changes in magnetic moment and by a Landau-Zener tunneling
method. Based on microwave spectroscopy, we present a precise measurement of the
magnetic-field-dependent binding energy of the weakly bound s -wave state that
is responsible for the large background scattering length of Cs. This state is
of particular interest because of its quantum-halo character.
acknowledgement: The authors thank E. Tiesinga, P. Julienne, and C. Williams for providing
invaluable theoretical input and J. Hutson and A. Simoni for helpful discussions.
The authors acknowledge support by the Austrian Science Fund (FWF) within SFB 15
(project part 16) and by the European Union within the Cold Molecules TMR Network
under Contract No. HPRN-CT-2002-00290. One of the authors (M.M.) acknowledges support
within the Ph.D. program DOC of the Austrian Academy of Sciences, and two of the
authors (F.F., C.C.) acknowledge support within the Lise Meitner program of the
FWF. One of the authors (S.K.) is supported by the European Community, Marie Curie
Intra-European program.
article_processing_charge: No
author:
- first_name: Michael
full_name: Mark, Michael
last_name: Mark
- first_name: Francesca
full_name: Ferlaino, Francesca
last_name: Ferlaino
- first_name: Steven
full_name: Knoop, Steven
last_name: Knoop
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Tobias
full_name: Kraemer, Tobias
last_name: Kraemer
- first_name: Cheng
full_name: Chin, Cheng
last_name: Chin
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
- first_name: Rudolf
full_name: Grimm, Rudolf
last_name: Grimm
citation:
ama: Mark M, Ferlaino F, Knoop S, et al. Spectroscopy of ultracold trapped cesium
Feshbach molecules. Physical Review A - Atomic, Molecular, and Optical Physics.
2007;76(4). doi:10.1103/PhysRevA.76.042514
apa: Mark, M., Ferlaino, F., Knoop, S., Danzl, J. G., Kraemer, T., Chin, C., … Grimm,
R. (2007). Spectroscopy of ultracold trapped cesium Feshbach molecules. Physical
Review A - Atomic, Molecular, and Optical Physics. American Physical Society.
https://doi.org/10.1103/PhysRevA.76.042514
chicago: Mark, Michael, Francesca Ferlaino, Steven Knoop, Johann G Danzl, Tobias
Kraemer, Cheng Chin, Hanns Nägerl, and Rudolf Grimm. “Spectroscopy of Ultracold
Trapped Cesium Feshbach Molecules.” Physical Review A - Atomic, Molecular,
and Optical Physics. American Physical Society, 2007. https://doi.org/10.1103/PhysRevA.76.042514.
ieee: M. Mark et al., “Spectroscopy of ultracold trapped cesium Feshbach
molecules,” Physical Review A - Atomic, Molecular, and Optical Physics,
vol. 76, no. 4. American Physical Society, 2007.
ista: Mark M, Ferlaino F, Knoop S, Danzl JG, Kraemer T, Chin C, Nägerl H, Grimm
R. 2007. Spectroscopy of ultracold trapped cesium Feshbach molecules. Physical
Review A - Atomic, Molecular, and Optical Physics. 76(4).
mla: Mark, Michael, et al. “Spectroscopy of Ultracold Trapped Cesium Feshbach Molecules.”
Physical Review A - Atomic, Molecular, and Optical Physics, vol. 76, no.
4, American Physical Society, 2007, doi:10.1103/PhysRevA.76.042514.
short: M. Mark, F. Ferlaino, S. Knoop, J.G. Danzl, T. Kraemer, C. Chin, H. Nägerl,
R. Grimm, Physical Review A - Atomic, Molecular, and Optical Physics 76 (2007).
date_created: 2018-12-11T11:49:48Z
date_published: 2007-10-25T00:00:00Z
date_updated: 2021-01-12T06:47:49Z
day: '25'
doi: 10.1103/PhysRevA.76.042514
extern: '1'
intvolume: ' 76'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0706.1041
month: '10'
oa: 1
oa_version: None
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '6354'
status: public
title: Spectroscopy of ultracold trapped cesium Feshbach molecules
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 76
year: '2007'
...
---
_id: '11116'
abstract:
- lang: eng
text: The metazoan nuclear envelope (NE) breaks down and re-forms during each cell
cycle. Nuclear pore complexes (NPCs), which allow nucleocytoplasmic transport
during interphase, assemble into the re-forming NE at the end of mitosis. Using
in vitro NE assembly, we show that the vertebrate homologue of MEL-28 (maternal
effect lethal), a recently discovered NE component in Caenorhabditis elegans,
functions in postmitotic NPC assembly. MEL-28 interacts with the Nup107–160 complex
(Nup for nucleoporin), an important building block of the NPC, and is essential
for the recruitment of the Nup107–160 complex to chromatin. We suggest that MEL-28
acts as a seeding point for NPC assembly.
article_processing_charge: No
article_type: original
author:
- first_name: Cerstin
full_name: Franz, Cerstin
last_name: Franz
- first_name: Rudolf
full_name: Walczak, Rudolf
last_name: Walczak
- first_name: Sevil
full_name: Yavuz, Sevil
last_name: Yavuz
- first_name: Rachel
full_name: Santarella, Rachel
last_name: Santarella
- first_name: Marc
full_name: Gentzel, Marc
last_name: Gentzel
- first_name: Peter
full_name: Askjaer, Peter
last_name: Askjaer
- first_name: Vincent
full_name: Galy, Vincent
last_name: Galy
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Iain W
full_name: Mattaj, Iain W
last_name: Mattaj
- first_name: Wolfram
full_name: Antonin, Wolfram
last_name: Antonin
citation:
ama: Franz C, Walczak R, Yavuz S, et al. MEL‐28/ELYS is required for the recruitment
of nucleoporins to chromatin and postmitotic nuclear pore complex assembly. EMBO
reports. 2007;8(2):165-172. doi:10.1038/sj.embor.7400889
apa: Franz, C., Walczak, R., Yavuz, S., Santarella, R., Gentzel, M., Askjaer, P.,
… Antonin, W. (2007). MEL‐28/ELYS is required for the recruitment of nucleoporins
to chromatin and postmitotic nuclear pore complex assembly. EMBO Reports.
EMBO. https://doi.org/10.1038/sj.embor.7400889
chicago: Franz, Cerstin, Rudolf Walczak, Sevil Yavuz, Rachel Santarella, Marc Gentzel,
Peter Askjaer, Vincent Galy, Martin Hetzer, Iain W Mattaj, and Wolfram Antonin.
“MEL‐28/ELYS Is Required for the Recruitment of Nucleoporins to Chromatin and
Postmitotic Nuclear Pore Complex Assembly.” EMBO Reports. EMBO, 2007. https://doi.org/10.1038/sj.embor.7400889.
ieee: C. Franz et al., “MEL‐28/ELYS is required for the recruitment of nucleoporins
to chromatin and postmitotic nuclear pore complex assembly,” EMBO reports,
vol. 8, no. 2. EMBO, pp. 165–172, 2007.
ista: Franz C, Walczak R, Yavuz S, Santarella R, Gentzel M, Askjaer P, Galy V, Hetzer
M, Mattaj IW, Antonin W. 2007. MEL‐28/ELYS is required for the recruitment of
nucleoporins to chromatin and postmitotic nuclear pore complex assembly. EMBO
reports. 8(2), 165–172.
mla: Franz, Cerstin, et al. “MEL‐28/ELYS Is Required for the Recruitment of Nucleoporins
to Chromatin and Postmitotic Nuclear Pore Complex Assembly.” EMBO Reports,
vol. 8, no. 2, EMBO, 2007, pp. 165–72, doi:10.1038/sj.embor.7400889.
short: C. Franz, R. Walczak, S. Yavuz, R. Santarella, M. Gentzel, P. Askjaer, V.
Galy, M. Hetzer, I.W. Mattaj, W. Antonin, EMBO Reports 8 (2007) 165–172.
date_created: 2022-04-07T07:56:13Z
date_published: 2007-01-19T00:00:00Z
date_updated: 2022-07-18T08:56:40Z
day: '19'
doi: 10.1038/sj.embor.7400889
extern: '1'
external_id:
pmid:
- '17235358'
intvolume: ' 8'
issue: '2'
keyword:
- Genetics
- Molecular Biology
- Biochemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/sj.embor.7400889
month: '01'
oa: 1
oa_version: Published Version
page: 165-172
pmid: 1
publication: EMBO reports
publication_identifier:
eissn:
- 1469-3178
issn:
- 1469-221X
publication_status: published
publisher: EMBO
quality_controlled: '1'
scopus_import: '1'
status: public
title: MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and
postmitotic nuclear pore complex assembly
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 8
year: '2007'
...
---
_id: '11115'
abstract:
- lang: eng
text: The formation of the nuclear envelope (NE) around chromatin is a major membrane-remodelling
event that occurs during cell division of metazoa. It is unclear whether the nuclear
membrane reforms by the fusion of NE fragments or if it re-emerges from an intact
tubular network of the endoplasmic reticulum (ER). Here, we show that NE formation
and expansion requires a tubular ER network and occurs efficiently in the presence
of the membrane fusion inhibitor GTPγS. Chromatin recruitment of membranes, which
is initiated by tubule-end binding, followed by the formation, expansion and sealing
of flat membrane sheets, is mediated by DNA-binding proteins residing in the ER.
Thus, chromatin plays an active role in reshaping of the ER during NE formation.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel J.
full_name: Anderson, Daniel J.
last_name: Anderson
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Anderson DJ, Hetzer M. Nuclear envelope formation by chromatin-mediated reorganization
of the endoplasmic reticulum. Nature Cell Biology. 2007;9(10):1160-1166.
doi:10.1038/ncb1636
apa: Anderson, D. J., & Hetzer, M. (2007). Nuclear envelope formation by chromatin-mediated
reorganization of the endoplasmic reticulum. Nature Cell Biology. Springer
Nature. https://doi.org/10.1038/ncb1636
chicago: Anderson, Daniel J., and Martin Hetzer. “Nuclear Envelope Formation by
Chromatin-Mediated Reorganization of the Endoplasmic Reticulum.” Nature Cell
Biology. Springer Nature, 2007. https://doi.org/10.1038/ncb1636.
ieee: D. J. Anderson and M. Hetzer, “Nuclear envelope formation by chromatin-mediated
reorganization of the endoplasmic reticulum,” Nature Cell Biology, vol.
9, no. 10. Springer Nature, pp. 1160–1166, 2007.
ista: Anderson DJ, Hetzer M. 2007. Nuclear envelope formation by chromatin-mediated
reorganization of the endoplasmic reticulum. Nature Cell Biology. 9(10), 1160–1166.
mla: Anderson, Daniel J., and Martin Hetzer. “Nuclear Envelope Formation by Chromatin-Mediated
Reorganization of the Endoplasmic Reticulum.” Nature Cell Biology, vol.
9, no. 10, Springer Nature, 2007, pp. 1160–66, doi:10.1038/ncb1636.
short: D.J. Anderson, M. Hetzer, Nature Cell Biology 9 (2007) 1160–1166.
date_created: 2022-04-07T07:56:04Z
date_published: 2007-09-09T00:00:00Z
date_updated: 2022-07-18T08:56:38Z
day: '09'
doi: 10.1038/ncb1636
extern: '1'
external_id:
pmid:
- '17828249'
intvolume: ' 9'
issue: '10'
keyword:
- Cell Biology
language:
- iso: eng
month: '09'
oa_version: None
page: 1160-1166
pmid: 1
publication: Nature Cell Biology
publication_identifier:
eissn:
- 1476-4679
issn:
- 1465-7392
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic
reticulum
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 9
year: '2007'
...
---
_id: '11884'
abstract:
- lang: eng
text: About 20% of the world's population uses the Web, and a large majority thereof
uses Web search engines to find information. As a result, many Web researchers
are devoting much effort to improving the speed and capability of search technology.
article_processing_charge: No
article_type: review
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. Search technologies for the internet. Science. 2007;317(5837):468-471.
doi:10.1126/science.1126557
apa: Henzinger, M. H. (2007). Search technologies for the internet. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.1126557
chicago: Henzinger, Monika H. “Search Technologies for the Internet.” Science.
American Association for the Advancement of Science, 2007. https://doi.org/10.1126/science.1126557.
ieee: M. H. Henzinger, “Search technologies for the internet,” Science, vol.
317, no. 5837. American Association for the Advancement of Science, pp. 468–471,
2007.
ista: Henzinger MH. 2007. Search technologies for the internet. Science. 317(5837),
468–471.
mla: Henzinger, Monika H. “Search Technologies for the Internet.” Science,
vol. 317, no. 5837, American Association for the Advancement of Science, 2007,
pp. 468–71, doi:10.1126/science.1126557.
short: M.H. Henzinger, Science 317 (2007) 468–471.
date_created: 2022-08-17T07:30:07Z
date_published: 2007-07-27T00:00:00Z
date_updated: 2023-02-17T14:07:49Z
day: '27'
doi: 10.1126/science.1126557
extern: '1'
external_id:
pmid:
- '17656714'
intvolume: ' 317'
issue: '5837'
language:
- iso: eng
month: '07'
oa_version: None
page: 468-471
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Search technologies for the internet
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 317
year: '2007'
...
---
_id: '11924'
abstract:
- lang: eng
text: 'How much can smart combinatorial algorithms improve web search engines? To
address this question we will describe three algorithms that have had a positive
impact on web search engines: The PageRank algorithm, algorithms for finding near-duplicate
web pages, and algorithms for index server loadbalancing.'
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. Combinatorial algorithms for web search engines: three success
stories. In: 18th Annual ACM-SIAM Symposium on Discrete Algorithms. Society
for Industrial & Applied Mathematics; 2007:1022-1026.'
apa: 'Henzinger, M. H. (2007). Combinatorial algorithms for web search engines:
three success stories. In 18th Annual ACM-SIAM Symposium on Discrete Algorithms
(pp. 1022–1026). New Orleans, LA, United States: Society for Industrial &
Applied Mathematics.'
chicago: 'Henzinger, Monika H. “Combinatorial Algorithms for Web Search Engines:
Three Success Stories.” In 18th Annual ACM-SIAM Symposium on Discrete Algorithms,
1022–26. Society for Industrial & Applied Mathematics, 2007.'
ieee: 'M. H. Henzinger, “Combinatorial algorithms for web search engines: three
success stories,” in 18th Annual ACM-SIAM Symposium on Discrete Algorithms,
New Orleans, LA, United States, 2007, pp. 1022–1026.'
ista: 'Henzinger MH. 2007. Combinatorial algorithms for web search engines: three
success stories. 18th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA:
Symposium on Discrete Algorithms, 1022–1026.'
mla: 'Henzinger, Monika H. “Combinatorial Algorithms for Web Search Engines: Three
Success Stories.” 18th Annual ACM-SIAM Symposium on Discrete Algorithms,
Society for Industrial & Applied Mathematics, 2007, pp. 1022–26.'
short: M.H. Henzinger, in:, 18th Annual ACM-SIAM Symposium on Discrete Algorithms,
Society for Industrial & Applied Mathematics, 2007, pp. 1022–1026.
conference:
end_date: 2007-01-09
location: New Orleans, LA, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2007-01-07
date_created: 2022-08-18T12:37:03Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2023-02-17T12:06:29Z
day: '01'
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 1022-1026
publication: 18th Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
isbn:
- '9780898716245'
publication_status: published
publisher: Society for Industrial & Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Combinatorial algorithms for web search engines: three success stories'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2007'
...
---
_id: '128'
abstract:
- lang: eng
text: 'A 671 nm diode laser with a mode-hop-free tuning range of 40 GHz is described.
This long tuning range is achieved by simultaneously ramping the external cavity
length with the laser injection current. The laser output pointing remains fixed,
independent of its frequency because of the cover slip cavity design. This system
is simple, economical, robust, and easy to use for spectroscopy, as we demonstrate
with lithium vapor and lithium atom beam experiments. '
acknowledgement: "National Science Foundation\r\nThis work was supported with NSF
Grant No. PHY-0653623. We thank Dr. W. Bickel and Dr. J. Jones for diagnostic equipment,
K. Guerin for assistance with mechanical drawings, and M. Parker of Rincon Research
Inc. for optics components."
article_number: '106108'
author:
- first_name: Adra
full_name: Carr, Adra
last_name: Carr
- first_name: Yancey
full_name: Serchest, Yancey
last_name: Serchest
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: John
full_name: Perreault, John
last_name: Perreault
- first_name: Vincent
full_name: Lonij, Vincent
last_name: Lonij
- first_name: Alexander
full_name: Cronin, Alexander
last_name: Cronin
citation:
ama: Carr A, Serchest Y, Waitukaitis SR, Perreault J, Lonij V, Cronin A. Cover slip
external cavity diode laser. Review of Scientific Instruments. 2007;78(10).
doi:10.1063/1.2801006
apa: Carr, A., Serchest, Y., Waitukaitis, S. R., Perreault, J., Lonij, V., &
Cronin, A. (2007). Cover slip external cavity diode laser. Review of Scientific
Instruments. American Institute of Physics. https://doi.org/10.1063/1.2801006
chicago: Carr, Adra, Yancey Serchest, Scott R Waitukaitis, John Perreault, Vincent
Lonij, and Alexander Cronin. “Cover Slip External Cavity Diode Laser.” Review
of Scientific Instruments. American Institute of Physics, 2007. https://doi.org/10.1063/1.2801006.
ieee: A. Carr, Y. Serchest, S. R. Waitukaitis, J. Perreault, V. Lonij, and A. Cronin,
“Cover slip external cavity diode laser,” Review of Scientific Instruments,
vol. 78, no. 10. American Institute of Physics, 2007.
ista: Carr A, Serchest Y, Waitukaitis SR, Perreault J, Lonij V, Cronin A. 2007.
Cover slip external cavity diode laser. Review of Scientific Instruments. 78(10),
106108.
mla: Carr, Adra, et al. “Cover Slip External Cavity Diode Laser.” Review of Scientific
Instruments, vol. 78, no. 10, 106108, American Institute of Physics, 2007,
doi:10.1063/1.2801006.
short: A. Carr, Y. Serchest, S.R. Waitukaitis, J. Perreault, V. Lonij, A. Cronin,
Review of Scientific Instruments 78 (2007).
date_created: 2018-12-11T11:44:46Z
date_published: 2007-10-29T00:00:00Z
date_updated: 2021-01-12T06:49:35Z
day: '29'
doi: 10.1063/1.2801006
extern: '1'
external_id:
arxiv:
- '0708.0014'
intvolume: ' 78'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0708.0014
month: '10'
oa: 1
oa_version: Preprint
publication: Review of Scientific Instruments
publication_status: published
publisher: American Institute of Physics
publist_id: '7925'
quality_controlled: '1'
status: public
title: Cover slip external cavity diode laser
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
year: '2007'
...
---
_id: '1297'
abstract:
- lang: eng
text: In flies, the large tangential cells of the lobula plate represent an important
processing center for visual navigation based on optic flow. Although the visual
response properties of these cells have been well studied in blowflies, information
on their synaptic organization is mostly lacking. Here we study the distribution
of presynaptic release and postsynaptic inhibitory sites in the same set of cells
in Drosophila melanogaster. By making use of transgenic tools and immunohistochemistry,
our results suggest that HS and VS cells of Drosophila express γ-aminobutyric
acid (GABA) receptors in their dendritic region within the lobula plate, thus
being postsynaptic to inhibitory input there. At their axon terminals in the protocerebrum,
both cell types express synaptobrevin, suggesting the presence of presynaptic
specializations there. HS- and VS-cell terminals additionally show evidence for
postsynaptic GABAergic input, superimposed on this synaptic polarity. Our findings
are in line with the general circuit for visual motion detection and receptive
field properties as postulated from electrophysiological and optical recordings
in blowflies, suggesting a similar functional organization of lobula plate tangential
cells in the two species.
author:
- first_name: Shamprasad
full_name: Raghu, Shamprasad V
last_name: Raghu
- first_name: Maximilian A
full_name: Maximilian Jösch
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Alexander
full_name: Borst, Alexander
last_name: Borst
- first_name: Dierk
full_name: Reiff, Dierk F
last_name: Reiff
citation:
ama: 'Raghu S, Jösch MA, Borst A, Reiff D. Synaptic organization of lobula plate
tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release
sites. Journal of Comparative Neurology. 2007;502(4):598-610. doi:10.1002/cne.21319'
apa: 'Raghu, S., Jösch, M. A., Borst, A., & Reiff, D. (2007). Synaptic organization
of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors
and chemical release sites. Journal of Comparative Neurology. Wiley-Blackwell.
https://doi.org/10.1002/cne.21319'
chicago: 'Raghu, Shamprasad, Maximilian A Jösch, Alexander Borst, and Dierk Reiff.
“Synaptic Organization of Lobula Plate Tangential Cells in Drosophila: γ-Aminobutyric
Acid Receptors and Chemical Release Sites.” Journal of Comparative Neurology.
Wiley-Blackwell, 2007. https://doi.org/10.1002/cne.21319.'
ieee: 'S. Raghu, M. A. Jösch, A. Borst, and D. Reiff, “Synaptic organization of
lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and
chemical release sites,” Journal of Comparative Neurology, vol. 502, no.
4. Wiley-Blackwell, pp. 598–610, 2007.'
ista: 'Raghu S, Jösch MA, Borst A, Reiff D. 2007. Synaptic organization of lobula
plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical
release sites. Journal of Comparative Neurology. 502(4), 598–610.'
mla: 'Raghu, Shamprasad, et al. “Synaptic Organization of Lobula Plate Tangential
Cells in Drosophila: γ-Aminobutyric Acid Receptors and Chemical Release Sites.”
Journal of Comparative Neurology, vol. 502, no. 4, Wiley-Blackwell, 2007,
pp. 598–610, doi:10.1002/cne.21319.'
short: S. Raghu, M.A. Jösch, A. Borst, D. Reiff, Journal of Comparative Neurology
502 (2007) 598–610.
date_created: 2018-12-11T11:51:13Z
date_published: 2007-06-01T00:00:00Z
date_updated: 2021-01-12T06:49:42Z
day: '01'
doi: 10.1002/cne.21319
extern: 1
intvolume: ' 502'
issue: '4'
month: '06'
page: 598 - 610
publication: Journal of Comparative Neurology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5974'
quality_controlled: 0
status: public
title: 'Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric
acid receptors and chemical release sites'
type: journal_article
volume: 502
year: '2007'
...
---
_id: '167'
abstract:
- lang: eng
text: This book contains research articles on Diophantine Geometry, written by participants
of a research program held at the Ennio De Giorgi Mathematical Research Center
in Pisa, Italy, during the period April – July 2005. The authors are eminent experts
in the field. Several subfields of the main topic are presented; the volume thus
is particularly useful to get a broad overview of recent research developments.
alternative_title:
- CRM Series
article_processing_charge: No
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Roger
full_name: Heath Brown, Roger
last_name: Heath Brown
citation:
ama: 'Browning TD, Heath Brown R. Simultaneous equal sums of three powers. In: Zannier
U, ed. Diophantine Geometry. Vol 4. Edizioni della Normale; 2007:93-100.'
apa: Browning, T. D., & Heath Brown, R. (2007). Simultaneous equal sums of three
powers. In U. Zannier (Ed.), Diophantine Geometry (Vol. 4, pp. 93–100).
Edizioni della Normale.
chicago: Browning, Timothy D, and Roger Heath Brown. “Simultaneous Equal Sums of
Three Powers.” In Diophantine Geometry, edited by Umberto Zannier, 4:93–100.
Edizioni della Normale, 2007.
ieee: T. D. Browning and R. Heath Brown, “Simultaneous equal sums of three powers,”
in Diophantine Geometry, vol. 4, U. Zannier, Ed. Edizioni della Normale,
2007, pp. 93–100.
ista: 'Browning TD, Heath Brown R. 2007.Simultaneous equal sums of three powers.
In: Diophantine Geometry. CRM Series, vol. 4, 93–100.'
mla: Browning, Timothy D., and Roger Heath Brown. “Simultaneous Equal Sums of Three
Powers.” Diophantine Geometry, edited by Umberto Zannier, vol. 4, Edizioni
della Normale, 2007, pp. 93–100.
short: T.D. Browning, R. Heath Brown, in:, U. Zannier (Ed.), Diophantine Geometry,
Edizioni della Normale, 2007, pp. 93–100.
date_created: 2018-12-11T11:44:59Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:24Z
day: '01'
editor:
- first_name: Umberto
full_name: Zannier, Umberto
last_name: Zannier
extern: '1'
external_id:
arxiv:
- '0509152'
intvolume: ' 4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/math/0509152
month: '01'
oa: 1
oa_version: Preprint
page: 93 - 100
publication: Diophantine Geometry
publication_status: published
publisher: Edizioni della Normale
publist_id: '7754'
quality_controlled: '1'
status: public
title: Simultaneous equal sums of three powers
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2007'
...
---
_id: '1750'
abstract:
- lang: eng
text: The authors investigate the composition profile of SiGe islands after capping
with Si to form quantum dots, using a two step etching procedure and atomic force
microscopy. Initially, the Si capping layers are removed by etching selectively
Si over Ge and then the composition of the disclosed islands is addressed by selectively
etching Ge over Si. For samples grown at 580 °C the authors show that even when
overgrowth leads to a flat Si surface and the islands undergo strong morphological
changes, a Ge-rich core region is still preserved in the dot. At high growth and
overgrowth temperatures (740 °C), the experiments show that the newly formed base
of the buried islands is more Si rich than their top. Furthermore, the authors
find that for the growth conditions used, no lateral motion takes place during
capping.
author:
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
- first_name: Jerry
full_name: Tersoff, Jerry
last_name: Tersoff
citation:
ama: Katsaros G, Stoffel M, Rastelli A, Schmidt O, Kern K, Tersoff J. Three-dimensional
isocompositional profiles of buried SiGeSi (001) islands. Applied Physics Letters.
2007;91(1). doi:10.1063/1.2752730
apa: Katsaros, G., Stoffel, M., Rastelli, A., Schmidt, O., Kern, K., & Tersoff,
J. (2007). Three-dimensional isocompositional profiles of buried SiGeSi (001)
islands. Applied Physics Letters. American Institute of Physics. https://doi.org/10.1063/1.2752730
chicago: Katsaros, Georgios, Mathieu Stoffel, Armando Rastelli, Oliver Schmidt,
Klaus Kern, and Jerry Tersoff. “Three-Dimensional Isocompositional Profiles of
Buried SiGeSi (001) Islands.” Applied Physics Letters. American Institute
of Physics, 2007. https://doi.org/10.1063/1.2752730.
ieee: G. Katsaros, M. Stoffel, A. Rastelli, O. Schmidt, K. Kern, and J. Tersoff,
“Three-dimensional isocompositional profiles of buried SiGeSi (001) islands,”
Applied Physics Letters, vol. 91, no. 1. American Institute of Physics,
2007.
ista: Katsaros G, Stoffel M, Rastelli A, Schmidt O, Kern K, Tersoff J. 2007. Three-dimensional
isocompositional profiles of buried SiGeSi (001) islands. Applied Physics Letters.
91(1).
mla: Katsaros, Georgios, et al. “Three-Dimensional Isocompositional Profiles of
Buried SiGeSi (001) Islands.” Applied Physics Letters, vol. 91, no. 1,
American Institute of Physics, 2007, doi:10.1063/1.2752730.
short: G. Katsaros, M. Stoffel, A. Rastelli, O. Schmidt, K. Kern, J. Tersoff, Applied
Physics Letters 91 (2007).
date_created: 2018-12-11T11:53:48Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:58Z
day: '01'
doi: 10.1063/1.2752730
extern: 1
intvolume: ' 91'
issue: '1'
month: '01'
publication: Applied Physics Letters
publication_status: published
publisher: American Institute of Physics
publist_id: '5375'
quality_controlled: 0
status: public
title: Three-dimensional isocompositional profiles of buried SiGeSi (001) islands
type: journal_article
volume: 91
year: '2007'
...
---
_id: '1762'
abstract:
- lang: eng
text: In quantum information science, the phase of a wave function plays an important
role in encoding information. Although most experiments in this field rely on
dynamic effects to manipulate this information, an alternative approach is to
use geometric phase, which has been argued to have potential fault tolerance.
We demonstrated the controlled accumulation of a geometric phase, Berry's phase,
in a superconducting qubit; we manipulated the qubit geometrically by means of
microwave radiation and observed the accumulated phase in an interference experiment.
We found excellent agreement with Berry's predictions and also observed a geometry-dependent
contribution to dephasing.
acknowledgement: Supported by the EC via an Intra-European Marie Curie Fellowship
(P.J.L.), the Natural Sciences and Engineering Research Council of Canada, Canadian
Institute for Advanced Research, and Fonds Québécois de la Recherche sur la Nature
et les Technologies (A.B.), the National Security Agency under the Army Research
Office, NSF, and Yale University (D.I.S., L.F., and R.J.S.), Consiglio Nazionale
delle Ricerche–Istituto di Cibernetica, Pozzuoli, Italy (L.F.), the Ontario Research
Development Challenge Fund and Mathematics of Information Technology and Complex
Systems (J.M.G.), the Swiss National Science Foundation, and ETH Zürich
author:
- first_name: Peter
full_name: Leek, Peter J
last_name: Leek
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Alexandre
full_name: Blais, Alexandre
last_name: Blais
- first_name: R
full_name: Bianchetti, R
last_name: Bianchetti
- first_name: M
full_name: Göppl, M
last_name: Göppl
- first_name: Jay
full_name: Gambetta, Jay M
last_name: Gambetta
- first_name: David
full_name: Schuster, David I
last_name: Schuster
- first_name: Luigi
full_name: Frunzio, Luigi
last_name: Frunzio
- first_name: Robert
full_name: Schoelkopf, Robert J
last_name: Schoelkopf
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Leek P, Fink JM, Blais A, et al. Observation of Berry’s phase in a solid-state
qubit. Science. 2007;318(5858):1889-1892. doi:10.1126/science.1149858
apa: Leek, P., Fink, J. M., Blais, A., Bianchetti, R., Göppl, M., Gambetta, J.,
… Wallraff, A. (2007). Observation of Berry’s phase in a solid-state qubit. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.1149858
chicago: Leek, Peter, Johannes M Fink, Alexandre Blais, R Bianchetti, M Göppl, Jay
Gambetta, David Schuster, Luigi Frunzio, Robert Schoelkopf, and Andreas Wallraff.
“Observation of Berry’s Phase in a Solid-State Qubit.” Science. American
Association for the Advancement of Science, 2007. https://doi.org/10.1126/science.1149858.
ieee: P. Leek et al., “Observation of Berry’s phase in a solid-state qubit,”
Science, vol. 318, no. 5858. American Association for the Advancement of
Science, pp. 1889–1892, 2007.
ista: Leek P, Fink JM, Blais A, Bianchetti R, Göppl M, Gambetta J, Schuster D, Frunzio
L, Schoelkopf R, Wallraff A. 2007. Observation of Berry’s phase in a solid-state
qubit. Science. 318(5858), 1889–1892.
mla: Leek, Peter, et al. “Observation of Berry’s Phase in a Solid-State Qubit.”
Science, vol. 318, no. 5858, American Association for the Advancement of
Science, 2007, pp. 1889–92, doi:10.1126/science.1149858.
short: P. Leek, J.M. Fink, A. Blais, R. Bianchetti, M. Göppl, J. Gambetta, D. Schuster,
L. Frunzio, R. Schoelkopf, A. Wallraff, Science 318 (2007) 1889–1892.
date_created: 2018-12-11T11:53:52Z
date_published: 2007-12-27T00:00:00Z
date_updated: 2021-01-12T06:53:02Z
day: '27'
doi: 10.1126/science.1149858
extern: 1
intvolume: ' 318'
issue: '5858'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0711.0218
month: '12'
oa: 1
page: 1889 - 1892
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5360'
quality_controlled: 0
status: public
title: Observation of Berry's phase in a solid-state qubit
type: journal_article
volume: 318
year: '2007'
...
---
_id: '1797'
abstract:
- lang: eng
text: Intrinsically photosensitive melanopsin-containing retinal ganglion cells
(ipRGCs) control important physiological processes, including the circadian rhythm,
the pupillary reflex, and the suppression of locomotor behavior (reviewed in [1]).
ipRGCs are also activated by classical photoreceptors, the rods and cones, through
local retinal circuits [2, 3]. ipRGCs can be transsynaptically labeled through
the pupillary-reflex circuit with the derivatives of the Bartha strain of the
alphaherpesvirus pseudorabies virus(PRV) [4, 5] that express GFP [6-12]. Bartha-strain
derivatives spread only in the retrograde direction [13]. There is evidence that
infected cells function normally for a while during GFP expression [7]. Here we
combine transsynaptic PRV labeling, two-photon laser microscopy, and electrophysiological
techniques to trace the local circuit of different ipRGC subtypes in the mouse
retina and record light-evoked activity from the transsynaptically labeled ganglion
cells. First, we show that ipRGCs are connected by monostratified amacrine cells
that provide strong inhibition from classical-photoreceptor-driven circuits. Second,
we show evidence that dopaminergic interplexiform cells are synaptically connected
to ipRGCs. The latter finding provides a circuitry link between light-dark adaptation
and ipRGC function.
acknowledgement: This study was supported by Office of Naval Research Multidisciplinary
University Research Initiative [ONR MURI] and Naval International Cooperative Opportunities
in Science and Technology Program [NICOP] grants, a Marie Curie Excellence Grant,
a Human Frontier Science Program [HFSP] Young Investigator grant, and Friedrich
Miescher Institute funds to B.R.
author:
- first_name: Tim
full_name: Viney, Tim J
last_name: Viney
- first_name: Kamill
full_name: Bálint, Kamill
last_name: Bálint
- first_name: Dániel
full_name: Hillier, Dániel
last_name: Hillier
- first_name: Sandra
full_name: Sandra Siegert
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
- first_name: Zsolt
full_name: Boldogköi, Zsolt S
last_name: Boldogköi
- first_name: Lynn
full_name: Enquist, Lynn W
last_name: Enquist
- first_name: Markus
full_name: Meister, Markus
last_name: Meister
- first_name: Constance
full_name: Cepko, Constance L
last_name: Cepko
- first_name: Botond
full_name: Roska, Botond M
last_name: Roska
citation:
ama: Viney T, Bálint K, Hillier D, et al. Local retinal circuits of melanopsin-containing
ganglion cells identified by transsynaptic viral tracing. Current Biology.
2007;17(11):981-988. doi:10.1016/j.cub.2007.04.058
apa: Viney, T., Bálint, K., Hillier, D., Siegert, S., Boldogköi, Z., Enquist, L.,
… Roska, B. (2007). Local retinal circuits of melanopsin-containing ganglion cells
identified by transsynaptic viral tracing. Current Biology. Cell Press.
https://doi.org/10.1016/j.cub.2007.04.058
chicago: Viney, Tim, Kamill Bálint, Dániel Hillier, Sandra Siegert, Zsolt Boldogköi,
Lynn Enquist, Markus Meister, Constance Cepko, and Botond Roska. “Local Retinal
Circuits of Melanopsin-Containing Ganglion Cells Identified by Transsynaptic Viral
Tracing.” Current Biology. Cell Press, 2007. https://doi.org/10.1016/j.cub.2007.04.058.
ieee: T. Viney et al., “Local retinal circuits of melanopsin-containing ganglion
cells identified by transsynaptic viral tracing,” Current Biology, vol.
17, no. 11. Cell Press, pp. 981–988, 2007.
ista: Viney T, Bálint K, Hillier D, Siegert S, Boldogköi Z, Enquist L, Meister M,
Cepko C, Roska B. 2007. Local retinal circuits of melanopsin-containing ganglion
cells identified by transsynaptic viral tracing. Current Biology. 17(11), 981–988.
mla: Viney, Tim, et al. “Local Retinal Circuits of Melanopsin-Containing Ganglion
Cells Identified by Transsynaptic Viral Tracing.” Current Biology, vol.
17, no. 11, Cell Press, 2007, pp. 981–88, doi:10.1016/j.cub.2007.04.058.
short: T. Viney, K. Bálint, D. Hillier, S. Siegert, Z. Boldogköi, L. Enquist, M.
Meister, C. Cepko, B. Roska, Current Biology 17 (2007) 981–988.
date_created: 2018-12-11T11:54:04Z
date_published: 2007-06-05T00:00:00Z
date_updated: 2021-01-12T06:53:15Z
day: '05'
doi: 10.1016/j.cub.2007.04.058
extern: 1
intvolume: ' 17'
issue: '11'
month: '06'
page: 981 - 988
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '5313'
quality_controlled: 0
status: public
title: Local retinal circuits of melanopsin-containing ganglion cells identified by
transsynaptic viral tracing
type: journal_article
volume: 17
year: '2007'
...
---
_id: '1965'
abstract:
- lang: eng
text: Respiratory complex I (NADH:ubiquinone oxidoreductase) is an L-shaped multisubunit
protein assembly consisting of a hydrophobic membrane arm and a hydrophilic peripheral
arm. It catalyses the transfer of two electrons from NADH to quinone coupled to
the translocation of four protons across the membrane. Although we have solved
recently the crystal structure of the peripheral arm, the structure of the complete
enzyme and the coupling mechanism are not yet known. The membrane domain of Escherichia
coli complex I consists of seven different subunits with total molecular mass
of 258 kDa. It is significantly more stable than the whole enzyme, which allowed
us to obtain well-ordered two-dimensional crystals of the domain, belonging to
the space group p22121. Comparison of the projection map of negatively stained
crystals with previously published low-resolution structures indicated that the
characteristic curved shape of the membrane domain is remarkably well conserved
between bacterial and mitochondrial enzymes, helping us to interpret projection
maps in the context of the intact complex. Two pronounced stain-excluding densities
at the distal end of the membrane domain are likely to represent the two large
antiporter-like subunits NuoL and NuoM. Cryo-electron microscopy on frozen-hydrated
crystals allowed us to calculate a projection map at 8 Å resolution. About 60
transmembrane α-helices, both perpendicular to the membrane plane and tilted,
are present within one membrane domain, which is consistent with secondary structure
predictions. A possible binding site and access channel for quinone are found
at the interface with the peripheral arm. Tentative assignment of individual subunits
to the features of the map has been made. The location of subunits NuoL and NuoM
at substantial distance from the peripheral arm, which contains all the redox
centres of the complex, indicates that conformational changes are likely to play
a role in the mechanism of coupling between electron transfer and proton pumping.
author:
- first_name: Ekaterina
full_name: Baranova, Ekaterina A
last_name: Baranova
- first_name: Peter
full_name: Holt, Peter J
last_name: Holt
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Baranova E, Holt P, Sazanov LA. Projection structure of the membrane domain
of Escherichia coli respiratory Complex I at 8 Å resolution. Journal of Molecular
Biology. 2007;366(1):140-154. doi:10.1016/j.jmb.2006.11.026
apa: Baranova, E., Holt, P., & Sazanov, L. A. (2007). Projection structure of
the membrane domain of Escherichia coli respiratory Complex I at 8 Å resolution.
Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2006.11.026
chicago: Baranova, Ekaterina, Peter Holt, and Leonid A Sazanov. “Projection Structure
of the Membrane Domain of Escherichia Coli Respiratory Complex I at 8 Å Resolution.”
Journal of Molecular Biology. Elsevier, 2007. https://doi.org/10.1016/j.jmb.2006.11.026.
ieee: E. Baranova, P. Holt, and L. A. Sazanov, “Projection structure of the membrane
domain of Escherichia coli respiratory Complex I at 8 Å resolution,” Journal
of Molecular Biology, vol. 366, no. 1. Elsevier, pp. 140–154, 2007.
ista: Baranova E, Holt P, Sazanov LA. 2007. Projection structure of the membrane
domain of Escherichia coli respiratory Complex I at 8 Å resolution. Journal of
Molecular Biology. 366(1), 140–154.
mla: Baranova, Ekaterina, et al. “Projection Structure of the Membrane Domain of
Escherichia Coli Respiratory Complex I at 8 Å Resolution.” Journal of Molecular
Biology, vol. 366, no. 1, Elsevier, 2007, pp. 140–54, doi:10.1016/j.jmb.2006.11.026.
short: E. Baranova, P. Holt, L.A. Sazanov, Journal of Molecular Biology 366 (2007)
140–154.
date_created: 2018-12-11T11:54:57Z
date_published: 2007-02-09T00:00:00Z
date_updated: 2021-01-12T06:54:23Z
day: '09'
doi: 10.1016/j.jmb.2006.11.026
extern: 1
intvolume: ' 366'
issue: '1'
month: '02'
page: 140 - 154
publication: Journal of Molecular Biology
publication_status: published
publisher: Elsevier
publist_id: '5119'
quality_controlled: 0
status: public
title: Projection structure of the membrane domain of Escherichia coli respiratory
Complex I at 8 Å resolution
type: journal_article
volume: 366
year: '2007'
...
---
_id: '1969'
abstract:
- lang: eng
text: Respiratory complex I catalyses the transfer of electrons from NADH to quinone
coupled to the translocation of protons across the membrane. The mechanism of
coupling and the structure of the complete enzyme are not known. The membrane
domain of the complex contains three similar antiporter-like subunits NuoL/M/N,
probably involved in proton pumping. We have previously shown that subunits NuoL/M
can be removed from the rest of the complex, suggesting their location at the
distal end of the membrane domain. Here, using electron microscopy and single
particle analysis, we show that subunits NuoL and M jointly occupy a distal half
of the membrane domain, separated by about 10 nm from the interface with the peripheral
arm. This indicates that coupling mechanism of complex I is likely to involve
long range conformational changes.
author:
- first_name: Ekaterina
full_name: Baranova, Ekaterina A
last_name: Baranova
- first_name: David
full_name: Morgan, David J
last_name: Morgan
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Baranova E, Morgan D, Sazanov LA. Single particle analysis confirms distal
location of subunits NuoL and NuoM in Escherichia coli complex I. Journal of
Structural Biology. 2007;159(2 SPEC. ISS.):238-242. doi:10.1016/j.jsb.2007.01.009
apa: Baranova, E., Morgan, D., & Sazanov, L. A. (2007). Single particle analysis
confirms distal location of subunits NuoL and NuoM in Escherichia coli complex
I. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2007.01.009
chicago: Baranova, Ekaterina, David Morgan, and Leonid A Sazanov. “Single Particle
Analysis Confirms Distal Location of Subunits NuoL and NuoM in Escherichia Coli
Complex I.” Journal of Structural Biology. Academic Press, 2007. https://doi.org/10.1016/j.jsb.2007.01.009.
ieee: E. Baranova, D. Morgan, and L. A. Sazanov, “Single particle analysis confirms
distal location of subunits NuoL and NuoM in Escherichia coli complex I,” Journal
of Structural Biology, vol. 159, no. 2 SPEC. ISS. Academic Press, pp. 238–242,
2007.
ista: Baranova E, Morgan D, Sazanov LA. 2007. Single particle analysis confirms
distal location of subunits NuoL and NuoM in Escherichia coli complex I. Journal
of Structural Biology. 159(2 SPEC. ISS.), 238–242.
mla: Baranova, Ekaterina, et al. “Single Particle Analysis Confirms Distal Location
of Subunits NuoL and NuoM in Escherichia Coli Complex I.” Journal of Structural
Biology, vol. 159, no. 2 SPEC. ISS., Academic Press, 2007, pp. 238–42, doi:10.1016/j.jsb.2007.01.009.
short: E. Baranova, D. Morgan, L.A. Sazanov, Journal of Structural Biology 159 (2007)
238–242.
date_created: 2018-12-11T11:54:58Z
date_published: 2007-08-01T00:00:00Z
date_updated: 2021-01-12T06:54:24Z
day: '01'
doi: 10.1016/j.jsb.2007.01.009
extern: 1
intvolume: ' 159'
issue: 2 SPEC. ISS.
month: '08'
page: 238 - 242
publication: Journal of Structural Biology
publication_status: published
publisher: Academic Press
publist_id: '5117'
quality_controlled: 0
status: public
title: Single particle analysis confirms distal location of subunits NuoL and NuoM
in Escherichia coli complex I
type: journal_article
volume: 159
year: '2007'
...
---
_id: '1964'
abstract:
- lang: eng
text: Complex I of respiratory chains plays a central role in cellular energy production.
Mutations in its subunits lead to many human neurodegenerative diseases. Recently,
a first atomic structure of the hydrophilic domain of complex I from Thermus thermophilus
was determined. This domain represents a catalytic core of the enzyme. It consists
of eight different subunits, contains all the redox centers, and comprises more
than half of the entire complex. In this review, novel mechanistic implications
of the structure are discussed, and the effects of many known mutations of complex
I subunits are interpreted in a structural context.
author:
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: 'Sazanov LA. Respiratory complex I: Mechanistic and structural insights provided
by the crystal structure of the hydrophilic domain. Biochemistry. 2007;46(9):2275-2288.
doi:10.1021/bi602508x'
apa: 'Sazanov, L. A. (2007). Respiratory complex I: Mechanistic and structural insights
provided by the crystal structure of the hydrophilic domain. Biochemistry.
ACS. https://doi.org/10.1021/bi602508x'
chicago: 'Sazanov, Leonid A. “Respiratory Complex I: Mechanistic and Structural
Insights Provided by the Crystal Structure of the Hydrophilic Domain.” Biochemistry.
ACS, 2007. https://doi.org/10.1021/bi602508x.'
ieee: 'L. A. Sazanov, “Respiratory complex I: Mechanistic and structural insights
provided by the crystal structure of the hydrophilic domain,” Biochemistry,
vol. 46, no. 9. ACS, pp. 2275–2288, 2007.'
ista: 'Sazanov LA. 2007. Respiratory complex I: Mechanistic and structural insights
provided by the crystal structure of the hydrophilic domain. Biochemistry. 46(9),
2275–2288.'
mla: 'Sazanov, Leonid A. “Respiratory Complex I: Mechanistic and Structural Insights
Provided by the Crystal Structure of the Hydrophilic Domain.” Biochemistry,
vol. 46, no. 9, ACS, 2007, pp. 2275–88, doi:10.1021/bi602508x.'
short: L.A. Sazanov, Biochemistry 46 (2007) 2275–2288.
date_created: 2018-12-11T11:54:57Z
date_published: 2007-03-06T00:00:00Z
date_updated: 2021-01-12T06:54:23Z
day: '06'
doi: 10.1021/bi602508x
extern: 1
intvolume: ' 46'
issue: '9'
month: '03'
page: 2275 - 2288
publication: Biochemistry
publication_status: published
publisher: ACS
publist_id: '5118'
quality_controlled: 0
status: public
title: 'Respiratory complex I: Mechanistic and structural insights provided by the
crystal structure of the hydrophilic domain'
type: journal_article
volume: 46
year: '2007'
...
---
_id: '2091'
abstract:
- lang: eng
text: 'We present a novel multi-scale representation and acquisition method for
the animation of high-resolution facial geometry and wrinkles. We first acquire
a static scan of the face including reflectance data at the highest possible quality.
We then augment a traditional marker-based facial motion-capture system by two
synchronized video cameras to track expression wrinkles. The resulting model consists
of high-resolution geometry, motion-capture data, and expression wrinkles in 2D
parametric form. This combination represents the facial shape and its salient
features at multiple scales. During motion synthesis the motion-capture data deforms
the high-resolution geometry using a linear shell-based mesh-deformation method.
The wrinkle geometry is added to the facial base mesh using nonlinear energy optimization.
We present the results of our approach for performance replay as well as for wrinkle
editing. '
acknowledgement: This research has been supported by the NCCR Co-Me of the Swiss National
Science Foundation.
author:
- first_name: Bernd
full_name: Bernd Bickel
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Mario
full_name: Botsch, Mario
last_name: Botsch
- first_name: Roland
full_name: Angst, Roland
last_name: Angst
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
- first_name: Miguel
full_name: Otaduy, Miguel A
last_name: Otaduy
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
- first_name: Markus
full_name: Groß, Markus S
last_name: Groß
citation:
ama: 'Bickel B, Botsch M, Angst R, et al. Multi scale capture of facial geometry
and motion. In: ACM; 2007. doi:doi:10.1145/1275808.1276419'
apa: 'Bickel, B., Botsch, M., Angst, R., Matusik, W., Otaduy, M., Pfister, H., &
Groß, M. (2007). Multi scale capture of facial geometry and motion. Presented
at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques,
ACM. https://doi.org/doi:10.1145/1275808.1276419'
chicago: Bickel, Bernd, Mario Botsch, Roland Angst, Wojciech Matusik, Miguel Otaduy,
Hanspeter Pfister, and Markus Groß. “Multi Scale Capture of Facial Geometry and
Motion.” ACM, 2007. https://doi.org/doi:10.1145/1275808.1276419.
ieee: 'B. Bickel et al., “Multi scale capture of facial geometry and motion,”
presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques, 2007.'
ista: 'Bickel B, Botsch M, Angst R, Matusik W, Otaduy M, Pfister H, Groß M. 2007.
Multi scale capture of facial geometry and motion. SIGGRAPH: Special Interest
Group on Computer Graphics and Interactive Techniques.'
mla: Bickel, Bernd, et al. Multi Scale Capture of Facial Geometry and Motion.
ACM, 2007, doi:doi:10.1145/1275808.1276419.
short: B. Bickel, M. Botsch, R. Angst, W. Matusik, M. Otaduy, H. Pfister, M. Groß,
in:, ACM, 2007.
conference:
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
date_created: 2018-12-11T11:55:39Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T06:55:15Z
day: '01'
doi: doi:10.1145/1275808.1276419
extern: 1
main_file_link:
- open_access: '1'
url: http://nrs.harvard.edu/urn-3:HUL.InstRepos:4726184
month: '01'
oa: 1
publication_status: published
publisher: ACM
publist_id: '4942'
quality_controlled: 0
status: public
title: Multi scale capture of facial geometry and motion
type: conference
year: '2007'
...
---
_id: '2093'
abstract:
- lang: eng
text: 'We present a novel multi-scale representation and acquisition method for
the animation of high-resolution facial geometry and wrinkles. We first acquire
a static scan of the face including reflectance data at the highest possible quality.
We then augment a traditional marker-based facial motion-capture system by two
synchronized video cameras to track expression wrinkles. The resulting model consists
of high-resolution geometry, motion-capture data, and expression wrinkles in 2D
parametric form. This combination represents the facial shape and its salient
features at multiple scales. During motion synthesis the motion-capture data deforms
the high-resolution geometry using a linear shell-based mesh-deformation method.
The wrinkle geometry is added to the facial base mesh using nonlinear energy optimization.
We present the results of our approach for performance replay as well as for wrinkle
editing. '
acknowledgement: This research has been supported by the NCCR Co-Me of the Swiss National
Science Foundation
author:
- first_name: Bernd
full_name: Bernd Bickel
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Mario
full_name: Botsch, Mario
last_name: Botsch
- first_name: Roland
full_name: Angst, Roland
last_name: Angst
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
- first_name: Miguel
full_name: Otaduy, Miguel A
last_name: Otaduy
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
- first_name: Markus
full_name: Groß, Markus S
last_name: Groß
citation:
ama: Bickel B, Botsch M, Angst R, et al. Multi scale capture of facial geometry
and motion. ACM Transactions on Graphics. 2007;26(3). doi:10.1145/1276377.1276419
apa: Bickel, B., Botsch, M., Angst, R., Matusik, W., Otaduy, M., Pfister, H., &
Groß, M. (2007). Multi scale capture of facial geometry and motion. ACM Transactions
on Graphics. ACM. https://doi.org/10.1145/1276377.1276419
chicago: Bickel, Bernd, Mario Botsch, Roland Angst, Wojciech Matusik, Miguel Otaduy,
Hanspeter Pfister, and Markus Groß. “Multi Scale Capture of Facial Geometry and
Motion.” ACM Transactions on Graphics. ACM, 2007. https://doi.org/10.1145/1276377.1276419.
ieee: B. Bickel et al., “Multi scale capture of facial geometry and motion,”
ACM Transactions on Graphics, vol. 26, no. 3. ACM, 2007.
ista: Bickel B, Botsch M, Angst R, Matusik W, Otaduy M, Pfister H, Groß M. 2007.
Multi scale capture of facial geometry and motion. ACM Transactions on Graphics.
26(3).
mla: Bickel, Bernd, et al. “Multi Scale Capture of Facial Geometry and Motion.”
ACM Transactions on Graphics, vol. 26, no. 3, ACM, 2007, doi:10.1145/1276377.1276419.
short: B. Bickel, M. Botsch, R. Angst, W. Matusik, M. Otaduy, H. Pfister, M. Groß,
ACM Transactions on Graphics 26 (2007).
date_created: 2018-12-11T11:55:40Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T06:55:15Z
day: '01'
doi: 10.1145/1276377.1276419
extern: 1
intvolume: ' 26'
issue: '3'
main_file_link:
- open_access: '1'
url: http://nrs.harvard.edu/urn-3:HUL.InstRepos:4726184
month: '01'
oa: 1
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '4944'
quality_controlled: 0
status: public
title: Multi scale capture of facial geometry and motion
type: journal_article
volume: 26
year: '2007'
...
---
_id: '2092'
abstract:
- lang: eng
text: We introduce a new appearance-modeling paradigm for synthesizing the internal
structure of a 3D model from photographs of a few cross-sections of a real object.
When the internal surfaces of the 3D model are revealed as it is cut, carved,
or simply clipped, we synthesize their texture from the input photographs. Our
texture synthesis algorithm is best classified as a morphing technique, which
efficiently outputs the texture attributes of each surface point on demand. For
determining source points and their weights in the morphing algorithm, we propose
an interpolation domain based on BSP trees that naturally resembles planar splitting
of real objects. In the context of the interpolation domain, we define efficient
warping and morphing operations that allow for real-time synthesis of textures.
Overall, our modeling paradigm, together with its realization through our texture
morphing algorithm, allow users to author 3D models that reveal highly realistic
internal surfaces in a variety of artistic flavors.
acknowledgement: 'This research was supported in part by the NCCR Co-Me of the Swiss
National Science Foundation. '
author:
- first_name: Nico
full_name: Pietroni, Nico
last_name: Pietroni
- first_name: Miguel
full_name: Otaduy, Miguel A
last_name: Otaduy
- first_name: Bernd
full_name: Bernd Bickel
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Fabio
full_name: Ganovelli, Fabio
last_name: Ganovelli
- first_name: Markus
full_name: Groß, Markus S
last_name: Groß
citation:
ama: Pietroni N, Otaduy M, Bickel B, Ganovelli F, Groß M. Texturing internal surfaces
from a few cross-sections. Computer Graphics Forum. 2007;26(3):637-644.
doi:10.1111/j.1467-8659.2007.01087.x
apa: Pietroni, N., Otaduy, M., Bickel, B., Ganovelli, F., & Groß, M. (2007).
Texturing internal surfaces from a few cross-sections. Computer Graphics Forum.
Wiley-Blackwell. https://doi.org/10.1111/j.1467-8659.2007.01087.x
chicago: Pietroni, Nico, Miguel Otaduy, Bernd Bickel, Fabio Ganovelli, and Markus
Groß. “Texturing Internal Surfaces from a Few Cross-Sections.” Computer Graphics
Forum. Wiley-Blackwell, 2007. https://doi.org/10.1111/j.1467-8659.2007.01087.x.
ieee: N. Pietroni, M. Otaduy, B. Bickel, F. Ganovelli, and M. Groß, “Texturing internal
surfaces from a few cross-sections,” Computer Graphics Forum, vol. 26,
no. 3. Wiley-Blackwell, pp. 637–644, 2007.
ista: Pietroni N, Otaduy M, Bickel B, Ganovelli F, Groß M. 2007. Texturing internal
surfaces from a few cross-sections. Computer Graphics Forum. 26(3), 637–644.
mla: Pietroni, Nico, et al. “Texturing Internal Surfaces from a Few Cross-Sections.”
Computer Graphics Forum, vol. 26, no. 3, Wiley-Blackwell, 2007, pp. 637–44,
doi:10.1111/j.1467-8659.2007.01087.x.
short: N. Pietroni, M. Otaduy, B. Bickel, F. Ganovelli, M. Groß, Computer Graphics
Forum 26 (2007) 637–644.
date_created: 2018-12-11T11:55:39Z
date_published: 2007-09-01T00:00:00Z
date_updated: 2021-01-12T06:55:15Z
day: '01'
doi: 10.1111/j.1467-8659.2007.01087.x
extern: 1
intvolume: ' 26'
issue: '3'
month: '09'
page: 637 - 644
publication: Computer Graphics Forum
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4943'
quality_controlled: 0
status: public
title: Texturing internal surfaces from a few cross-sections
type: journal_article
volume: 26
year: '2007'
...
---
_id: '2118'
abstract:
- lang: eng
text: 'We extend to infinite dimensions an explicit formula of Chill, Fašangová,
Metafune, and Pallara for the optimal angle of analyticity of analytic Ornstein-Uhlenbeck
semigroups. The main ingredient is an abstract representation of the Ornstein-Uhlenbeck
operator in divergence form. '
acknowledgement: The authors are supported by the ‘VIDI subsidie’ 639.032.201 of the
Netherlands Organization for Scientific Research (NWO) and by the Research Training
Network HPRN-CT-2002-00281.
author:
- first_name: Jan
full_name: Jan Maas
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Jan
full_name: van Neerven, Jan M
last_name: Van Neerven
citation:
ama: Maas J, Van Neerven J. On analytic Ornstein-Uhlenbeck semigroups in infinite
dimensions. Archiv der Mathematik. 2007;89(3):226-236. doi:10.1007/s00013-007-2082-x
apa: Maas, J., & Van Neerven, J. (2007). On analytic Ornstein-Uhlenbeck semigroups
in infinite dimensions. Archiv Der Mathematik. Birkhäuser. https://doi.org/10.1007/s00013-007-2082-x
chicago: Maas, Jan, and Jan Van Neerven. “On Analytic Ornstein-Uhlenbeck Semigroups
in Infinite Dimensions.” Archiv Der Mathematik. Birkhäuser, 2007. https://doi.org/10.1007/s00013-007-2082-x.
ieee: J. Maas and J. Van Neerven, “On analytic Ornstein-Uhlenbeck semigroups in
infinite dimensions,” Archiv der Mathematik, vol. 89, no. 3. Birkhäuser,
pp. 226–236, 2007.
ista: Maas J, Van Neerven J. 2007. On analytic Ornstein-Uhlenbeck semigroups in
infinite dimensions. Archiv der Mathematik. 89(3), 226–236.
mla: Maas, Jan, and Jan Van Neerven. “On Analytic Ornstein-Uhlenbeck Semigroups
in Infinite Dimensions.” Archiv Der Mathematik, vol. 89, no. 3, Birkhäuser,
2007, pp. 226–36, doi:10.1007/s00013-007-2082-x.
short: J. Maas, J. Van Neerven, Archiv Der Mathematik 89 (2007) 226–236.
date_created: 2018-12-11T11:55:49Z
date_published: 2007-08-06T00:00:00Z
date_updated: 2021-01-12T06:55:25Z
day: '06'
doi: 10.1007/s00013-007-2082-x
extern: 1
intvolume: ' 89'
issue: '3'
main_file_link:
- open_access: '1'
url: http://repository.tudelft.nl/view/ir/uuid:c2cc3bd8-822b-4e72-ae42-1da0424e8a22/
month: '08'
oa: 1
page: 226 - 236
publication: Archiv der Mathematik
publication_status: published
publisher: Birkhäuser
publist_id: '4916'
quality_controlled: 0
status: public
title: On analytic Ornstein-Uhlenbeck semigroups in infinite dimensions
type: journal_article
volume: 89
year: '2007'
...
---
_id: '2135'
abstract:
- lang: eng
text: We use the x-ray absorption fine structure spectroscopy at Nb K edge to reveal
the local atomic structure of KxNa1−xNbO3 (PSN) solid solutions. The study is
performed over the temperature range 10–1023K for six different x values. We show
that only the combined analysis of extended x-ray absorption fine structure and
preedge fine structure provides complete and reliable information about the local
structure of NbO6 octahedra. Such extensive treatment of the experimental data
shows that the local structure of PSN could be described within the spherical
model proposed earlier as a hypothesis for perovskite-type ferroelectric zirconates.
We reveal that the Nb atoms are localized near their average positions on the
sphere surfaces for all temperatures and x values. With regard to previous results
we point out the features of microscopic structure common for PSN and perovskite-type
zirconates.
acknowledgement: This work was partially supported by Russian Foundation for Basic
Research Grant No. 07-02-00796a. The authors are indebted to the French Government
for financial support of E.S.N. and M.P.L. within the CNOUS program.
author:
- first_name: Mikhail
full_name: Mikhail Lemeshko
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Elena
full_name: Nazarenko, Elena S
last_name: Nazarenko
- first_name: A.A
full_name: Gonchar, A.A
last_name: Gonchar
- first_name: Larisa
full_name: Reznichenko, Larisa A
last_name: Reznichenko
- first_name: Tatiana
full_name: Nedoseykina, Tatiana I
last_name: Nedoseykina
- first_name: Alexander
full_name: Novakovich, Alexander A
last_name: Novakovich
- first_name: Olivier
full_name: Mathon, Olivier
last_name: Mathon
- first_name: Yves
full_name: Joly, Yves
last_name: Joly
- first_name: Rostislav
full_name: Vedrinskiǐ, Rostislav V
last_name: Vedrinskiǐ
citation:
ama: Lemeshko M, Nazarenko E, Gonchar A., et al. EXAFS studies of the local atomic
structure of the lead-free piezoelectric ceramics KxNa1−xNbO3 over the temperature
range 10–1023K. Physical Review B - Condensed Matter and Materials Physics.
2007;76. doi:http://dx.doi.org/10.1103/PhysRevB.76.134106
apa: Lemeshko, M., Nazarenko, E., Gonchar, A. ., Reznichenko, L., Nedoseykina, T.,
Novakovich, A., … Vedrinskiǐ, R. (2007). EXAFS studies of the local atomic structure
of the lead-free piezoelectric ceramics KxNa1−xNbO3 over the temperature range
10–1023K. Physical Review B - Condensed Matter and Materials Physics. American
Physical Society. http://dx.doi.org/10.1103/PhysRevB.76.134106
chicago: Lemeshko, Mikhail, Elena Nazarenko, A.A Gonchar, Larisa Reznichenko, Tatiana
Nedoseykina, Alexander Novakovich, Olivier Mathon, Yves Joly, and Rostislav Vedrinskiǐ.
“EXAFS Studies of the Local Atomic Structure of the Lead-Free Piezoelectric Ceramics
KxNa1−xNbO3 over the Temperature Range 10–1023K.” Physical Review B - Condensed
Matter and Materials Physics. American Physical Society, 2007. http://dx.doi.org/10.1103/PhysRevB.76.134106.
ieee: M. Lemeshko et al., “EXAFS studies of the local atomic structure of
the lead-free piezoelectric ceramics KxNa1−xNbO3 over the temperature range 10–1023K,”
Physical Review B - Condensed Matter and Materials Physics, vol. 76. American
Physical Society, 2007.
ista: Lemeshko M, Nazarenko E, Gonchar A., Reznichenko L, Nedoseykina T, Novakovich
A, Mathon O, Joly Y, Vedrinskiǐ R. 2007. EXAFS studies of the local atomic structure
of the lead-free piezoelectric ceramics KxNa1−xNbO3 over the temperature range
10–1023K. Physical Review B - Condensed Matter and Materials Physics. 76.
mla: Lemeshko, Mikhail, et al. “EXAFS Studies of the Local Atomic Structure of the
Lead-Free Piezoelectric Ceramics KxNa1−xNbO3 over the Temperature Range 10–1023K.”
Physical Review B - Condensed Matter and Materials Physics, vol. 76, American
Physical Society, 2007, doi:http://dx.doi.org/10.1103/PhysRevB.76.134106.
short: M. Lemeshko, E. Nazarenko, A.. Gonchar, L. Reznichenko, T. Nedoseykina, A.
Novakovich, O. Mathon, Y. Joly, R. Vedrinskiǐ, Physical Review B - Condensed Matter
and Materials Physics 76 (2007).
date_created: 2018-12-11T11:55:54Z
date_published: 2007-10-09T00:00:00Z
date_updated: 2021-01-12T06:55:31Z
day: '09'
doi: http://dx.doi.org/10.1103/PhysRevB.76.134106
extern: 1
intvolume: ' 76'
month: '10'
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '4899'
quality_controlled: 0
status: public
title: EXAFS studies of the local atomic structure of the lead-free piezoelectric
ceramics KxNa1−xNbO3 over the temperature range 10–1023K
type: journal_article
volume: 76
year: '2007'
...
---
_id: '2143'
abstract:
- lang: eng
text: 'Local atomic structure of the piezoelectric ceramics KxNa 1-xNbO3 (x≤0.00,
0.05, 0.30, 0.40, 0.50 and 0.65) is studied in all phase regions (10 K-1023 K)
using Nb K-edge extended X-ray absorption fine-structure (EXAFS) spectroscopy.
We have shown the validity of a new spherical model for phase transitions on the
basis of both fitting of EXAFS signal in the R-space and differential EXAFS analysis.
Within this model the Nb atoms are located on the surfaces of small spheres of
constant radii surrounding centers of NbO6 octahedrons in all phases. The distribution
of the Nb atom on this surface changes during phase transitions. Besides, the
analysis of local structure reveals that the geometry of NbO6 octahedra does not
depend on the x value at each temperature, whereas the octahedra rotation angles
do. '
author:
- first_name: Mikhail
full_name: Mikhail Lemeshko
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Elena
full_name: Nazarenko, Elena S
last_name: Nazarenko
- first_name: Anastasia
full_name: Gonchar, Anastasia A
last_name: Gonchar
- first_name: Larisa
full_name: Reznichenko, Larisa A
last_name: Reznichenko
- first_name: Olivier
full_name: Mathon, Olivier
last_name: Mathon
- first_name: Yves
full_name: Joly, Yves
last_name: Joly
- first_name: Rostislav
full_name: Vedrinskiǐ, Rostislav V
last_name: Vedrinskiǐ
citation:
ama: 'Lemeshko M, Nazarenko E, Gonchar A, et al. Phase transitions in lead-free
piezoelectric ceramics: Study of local atomic structure. EPL. 2007;77(2).
doi:10.1209/0295-5075/77/26003
'
apa: 'Lemeshko, M., Nazarenko, E., Gonchar, A., Reznichenko, L., Mathon, O., Joly,
Y., & Vedrinskiǐ, R. (2007). Phase transitions in lead-free piezoelectric
ceramics: Study of local atomic structure. EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/77/26003
'
chicago: 'Lemeshko, Mikhail, Elena Nazarenko, Anastasia Gonchar, Larisa Reznichenko,
Olivier Mathon, Yves Joly, and Rostislav Vedrinskiǐ. “Phase Transitions in Lead-Free
Piezoelectric Ceramics: Study of Local Atomic Structure.” EPL. IOP Publishing
Ltd., 2007. https://doi.org/10.1209/0295-5075/77/26003
.'
ieee: 'M. Lemeshko et al., “Phase transitions in lead-free piezoelectric
ceramics: Study of local atomic structure,” EPL, vol. 77, no. 2. IOP Publishing
Ltd., 2007.'
ista: 'Lemeshko M, Nazarenko E, Gonchar A, Reznichenko L, Mathon O, Joly Y, Vedrinskiǐ
R. 2007. Phase transitions in lead-free piezoelectric ceramics: Study of local
atomic structure. EPL. 77(2).'
mla: 'Lemeshko, Mikhail, et al. “Phase Transitions in Lead-Free Piezoelectric Ceramics:
Study of Local Atomic Structure.” EPL, vol. 77, no. 2, IOP Publishing Ltd.,
2007, doi:10.1209/0295-5075/77/26003
.'
short: M. Lemeshko, E. Nazarenko, A. Gonchar, L. Reznichenko, O. Mathon, Y. Joly,
R. Vedrinskiǐ, EPL 77 (2007).
date_created: 2018-12-11T11:55:57Z
date_published: 2007-01-11T00:00:00Z
date_updated: 2021-01-12T06:55:34Z
day: '11'
doi: '10.1209/0295-5075/77/26003 '
extern: 1
intvolume: ' 77'
issue: '2'
month: '01'
publication: EPL
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '4880'
quality_controlled: 0
status: public
title: 'Phase transitions in lead-free piezoelectric ceramics: Study of local atomic
structure'
type: journal_article
volume: 77
year: '2007'
...
---
_id: '2145'
abstract:
- lang: eng
text: 'We use the x-ray absorption fine structure spectroscopy at Nb K edge to reveal
the local atomic structure of Kx Na1-x Nb O3 (PSN) solid solutions. The study
is performed over the temperature range 10-1023 K for six different x values.
We show that only the combined analysis of extended x-ray absorption fine structure
and preedge fine structure provides complete and reliable information about the
local structure of Nb O6 octahedra. Such extensive treatment of the experimental
data shows that the local structure of PSN could be described within the spherical
model proposed earlier as a hypothesis for perovskite-type ferroelectric zirconates.
We reveal that the Nb atoms are localized near their average positions on the
sphere surfaces for all temperatures and x values. With regard to previous results
we point out the features of microscopic structure common for PSN and perovskite-type
zirconates. '
acknowledgement: This work was partially supported by Russian Foundation for Basic
Research Grant No. 07-02-00796a
author:
- first_name: Mikhail
full_name: Mikhail Lemeshko
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Elena
full_name: Nazarenko, Elena S
last_name: Nazarenko
- first_name: Anastasia
full_name: Gonchar, Anastasia A
last_name: Gonchar
- first_name: Larisa
full_name: Reznichenko, Larisa A
last_name: Reznichenko
- first_name: Tatiana
full_name: Nedoseykina, Tatiana I
last_name: Nedoseykina
- first_name: Alexander
full_name: Novakovich, Alexander A
last_name: Novakovich
- first_name: Olivier
full_name: Mathon, Olivier
last_name: Mathon
- first_name: Yves
full_name: Joly, Yves
last_name: Joly
- first_name: Rostislav
full_name: Vedrinskiǐ, Rostislav V
last_name: Vedrinskiǐ
citation:
ama: Lemeshko M, Nazarenko E, Gonchar A, et al. EXAFS studies of the local atomic
structure of the lead free piezoelectric ceramics Kx Na1-x Nb O3 over the temperature
range 10-1023 K. Physical Review B - Condensed Matter and Materials Physics.
2007;76(13). doi:10.1103/PhysRevB.76.134106
apa: Lemeshko, M., Nazarenko, E., Gonchar, A., Reznichenko, L., Nedoseykina, T.,
Novakovich, A., … Vedrinskiǐ, R. (2007). EXAFS studies of the local atomic structure
of the lead free piezoelectric ceramics Kx Na1-x Nb O3 over the temperature range
10-1023 K. Physical Review B - Condensed Matter and Materials Physics.
American Physical Society. https://doi.org/10.1103/PhysRevB.76.134106
chicago: Lemeshko, Mikhail, Elena Nazarenko, Anastasia Gonchar, Larisa Reznichenko,
Tatiana Nedoseykina, Alexander Novakovich, Olivier Mathon, Yves Joly, and Rostislav
Vedrinskiǐ. “EXAFS Studies of the Local Atomic Structure of the Lead Free Piezoelectric
Ceramics Kx Na1-x Nb O3 over the Temperature Range 10-1023 K.” Physical Review
B - Condensed Matter and Materials Physics. American Physical Society, 2007.
https://doi.org/10.1103/PhysRevB.76.134106.
ieee: M. Lemeshko et al., “EXAFS studies of the local atomic structure of
the lead free piezoelectric ceramics Kx Na1-x Nb O3 over the temperature range
10-1023 K,” Physical Review B - Condensed Matter and Materials Physics,
vol. 76, no. 13. American Physical Society, 2007.
ista: Lemeshko M, Nazarenko E, Gonchar A, Reznichenko L, Nedoseykina T, Novakovich
A, Mathon O, Joly Y, Vedrinskiǐ R. 2007. EXAFS studies of the local atomic structure
of the lead free piezoelectric ceramics Kx Na1-x Nb O3 over the temperature range
10-1023 K. Physical Review B - Condensed Matter and Materials Physics. 76(13).
mla: Lemeshko, Mikhail, et al. “EXAFS Studies of the Local Atomic Structure of the
Lead Free Piezoelectric Ceramics Kx Na1-x Nb O3 over the Temperature Range 10-1023
K.” Physical Review B - Condensed Matter and Materials Physics, vol. 76,
no. 13, American Physical Society, 2007, doi:10.1103/PhysRevB.76.134106.
short: M. Lemeshko, E. Nazarenko, A. Gonchar, L. Reznichenko, T. Nedoseykina, A.
Novakovich, O. Mathon, Y. Joly, R. Vedrinskiǐ, Physical Review B - Condensed Matter
and Materials Physics 76 (2007).
date_created: 2018-12-11T11:55:58Z
date_published: 2007-10-09T00:00:00Z
date_updated: 2021-01-12T06:55:35Z
day: '09'
doi: 10.1103/PhysRevB.76.134106
extern: 1
intvolume: ' 76'
issue: '13'
month: '10'
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '4879'
quality_controlled: 0
status: public
title: EXAFS studies of the local atomic structure of the lead free piezoelectric
ceramics Kx Na1-x Nb O3 over the temperature range 10-1023 K
type: journal_article
volume: 76
year: '2007'
...
---
_id: '219'
abstract:
- lang: eng
text: This paper contains a proof of the Manin conjecture for the singular cubic
surface S ⊂ P3 that is defined by the equation x1 x22 + x2 x02 + x33 = 0. In fact
if U ⊂ S is the Zariski open subset obtained by deleting the unique line from
S, and H is the usual exponential height on P3 (Q), then the height zeta function
∑x ∈ U (Q) H (x)- s is analytically continued to the half-plane R e (s) > 9
/ 10.
acknowledgement: EPSRC grant number GR/R93155/01
author:
- first_name: Régis
full_name: De La Bretèche, Régis
last_name: De La Bretèche
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Ulrich
full_name: Derenthal, Ulrich
last_name: Derenthal
citation:
ama: De La Bretèche R, Browning TD, Derenthal U. On Manin’s conjecture for a certain
singular cubic surface. Annales Scientifiques de l’Ecole Normale Superieure.
2007;40(1):1-50. doi:10.1016/j.ansens.2006.12.002
apa: De La Bretèche, R., Browning, T. D., & Derenthal, U. (2007). On Manin’s
conjecture for a certain singular cubic surface. Annales Scientifiques de l’Ecole
Normale Superieure. Societe Mathematique de France. https://doi.org/10.1016/j.ansens.2006.12.002
chicago: De La Bretèche, Régis, Timothy D Browning, and Ulrich Derenthal. “On Manin’s
Conjecture for a Certain Singular Cubic Surface.” Annales Scientifiques de
l’Ecole Normale Superieure. Societe Mathematique de France, 2007. https://doi.org/10.1016/j.ansens.2006.12.002.
ieee: R. De La Bretèche, T. D. Browning, and U. Derenthal, “On Manin’s conjecture
for a certain singular cubic surface,” Annales Scientifiques de l’Ecole Normale
Superieure, vol. 40, no. 1. Societe Mathematique de France, pp. 1–50, 2007.
ista: De La Bretèche R, Browning TD, Derenthal U. 2007. On Manin’s conjecture for
a certain singular cubic surface. Annales Scientifiques de l’Ecole Normale Superieure.
40(1), 1–50.
mla: De La Bretèche, Régis, et al. “On Manin’s Conjecture for a Certain Singular
Cubic Surface.” Annales Scientifiques de l’Ecole Normale Superieure, vol.
40, no. 1, Societe Mathematique de France, 2007, pp. 1–50, doi:10.1016/j.ansens.2006.12.002.
short: R. De La Bretèche, T.D. Browning, U. Derenthal, Annales Scientifiques de
l’Ecole Normale Superieure 40 (2007) 1–50.
date_created: 2018-12-11T11:45:16Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T06:55:53Z
day: '01'
doi: 10.1016/j.ansens.2006.12.002
extern: '1'
intvolume: ' 40'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 1 - 50
publication: Annales Scientifiques de l'Ecole Normale Superieure
publication_status: published
publisher: Societe Mathematique de France
publist_id: '7693'
status: public
title: On Manin's conjecture for a certain singular cubic surface
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2007'
...
---
_id: '220'
abstract:
- lang: eng
text: Let X ⊂ ℙN be a geometrically integral cubic hypersurface defined over ℚ,
with singular locus of dimension at most dim X - 4. The main result in this paper
is a proof of the fact that X(ℚ) contains OεX,(BdimX+ε) points of height at most
B.
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Browning TD. Counting rational points on cubic hypersurfaces. Mathematika.
2007;54(1-2):93-112. doi:10.1112/S0025579300000243
apa: Browning, T. D. (2007). Counting rational points on cubic hypersurfaces. Mathematika.
University College London. https://doi.org/10.1112/S0025579300000243
chicago: Browning, Timothy D. “Counting Rational Points on Cubic Hypersurfaces.”
Mathematika. University College London, 2007. https://doi.org/10.1112/S0025579300000243.
ieee: T. D. Browning, “Counting rational points on cubic hypersurfaces,” Mathematika,
vol. 54, no. 1–2. University College London, pp. 93–112, 2007.
ista: Browning TD. 2007. Counting rational points on cubic hypersurfaces. Mathematika.
54(1–2), 93–112.
mla: Browning, Timothy D. “Counting Rational Points on Cubic Hypersurfaces.” Mathematika,
vol. 54, no. 1–2, University College London, 2007, pp. 93–112, doi:10.1112/S0025579300000243.
short: T.D. Browning, Mathematika 54 (2007) 93–112.
date_created: 2018-12-11T11:45:16Z
date_published: 2007-12-21T00:00:00Z
date_updated: 2021-01-12T06:55:56Z
day: '21'
doi: 10.1112/S0025579300000243
extern: 1
intvolume: ' 54'
issue: 1-2
month: '12'
page: 93 - 112
publication: Mathematika
publication_status: published
publisher: University College London
publist_id: '7692'
quality_controlled: 0
status: public
title: Counting rational points on cubic hypersurfaces
type: journal_article
volume: 54
year: '2007'
...
---
_id: '221'
author:
- first_name: Régis
full_name: De La Bretèche, Régis
last_name: De La Bretèche
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: De La Bretèche R, Browning TD. On Manin’s conjecture for singular del Pezzo
surfaces of degree four, I. Michigan Mathematical Journal. 2007;55(1):51-80.
doi:10.1307/mmj/1177681985
apa: De La Bretèche, R., & Browning, T. D. (2007). On Manin’s conjecture for
singular del Pezzo surfaces of degree four, I. Michigan Mathematical Journal.
Project Euclid. https://doi.org/10.1307/mmj/1177681985
chicago: De La Bretèche, Régis, and Timothy D Browning. “On Manin’s Conjecture for
Singular Del Pezzo Surfaces of Degree Four, I.” Michigan Mathematical Journal.
Project Euclid, 2007. https://doi.org/10.1307/mmj/1177681985.
ieee: R. De La Bretèche and T. D. Browning, “On Manin’s conjecture for singular
del Pezzo surfaces of degree four, I,” Michigan Mathematical Journal, vol.
55, no. 1. Project Euclid, pp. 51–80, 2007.
ista: De La Bretèche R, Browning TD. 2007. On Manin’s conjecture for singular del
Pezzo surfaces of degree four, I. Michigan Mathematical Journal. 55(1), 51–80.
mla: De La Bretèche, Régis, and Timothy D. Browning. “On Manin’s Conjecture for
Singular Del Pezzo Surfaces of Degree Four, I.” Michigan Mathematical Journal,
vol. 55, no. 1, Project Euclid, 2007, pp. 51–80, doi:10.1307/mmj/1177681985.
short: R. De La Bretèche, T.D. Browning, Michigan Mathematical Journal 55 (2007)
51–80.
date_created: 2018-12-11T11:45:17Z
date_published: 2007-04-27T00:00:00Z
date_updated: 2021-01-12T06:56:00Z
day: '27'
ddc:
- '510'
doi: 10.1307/mmj/1177681985
extern: '1'
external_id:
arxiv:
- math/0412086
file:
- access_level: open_access
checksum: 37663dde30b00d2af8a2606c6630a82f
content_type: application/pdf
creator: dernst
date_created: 2019-04-30T08:27:34Z
date_updated: 2020-07-14T12:45:32Z
file_id: '6361'
file_name: 2007_MichiganMath_Breteche.pdf
file_size: 256111
relation: main_file
file_date_updated: 2020-07-14T12:45:32Z
has_accepted_license: '1'
intvolume: ' 55'
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 51 - 80
publication: Michigan Mathematical Journal
publication_status: published
publisher: Project Euclid
publist_id: '7691'
quality_controlled: '1'
status: public
title: On Manin's conjecture for singular del Pezzo surfaces of degree four, I
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2007'
...
---
_id: '222'
abstract:
- lang: eng
text: Acknowledgements. The authors are grateful to Ulrich Derenthal and Brendan
Hassett for several useful conversations relating to universal torsors for singular
del Pezzo surfaces. Special thanks are due to Roger Heath–Brown whose ideas led
us to the proof of Lemma 6. The paper was finalised while the first author was
at the École Normale Supérieure, and the second author was at Oxford University
supported by EPSRC grant number GR/R93155/01. The hospitality and financial support
of these institutions is gratefully acknowledged. Finally, the authors would like
to thank the anonymous referee for his careful reading of the manuscript and numerous
useful suggestions.
acknowledgement: GR/R93155/01
author:
- first_name: Régis
full_name: de la Bretèche, Régis
last_name: De La Bretèche
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: De La Bretèche R, Browning TD. On Manin’s conjecture for singular del Pezzo
surfaces of degree four, II. Mathematical Proceedings of the Cambridge Philosophical
Society. 2007;143(3):579-605. doi:10.1017/S0305004107000205
apa: De La Bretèche, R., & Browning, T. D. (2007). On Manin’s conjecture for
singular del Pezzo surfaces of degree four, II. Mathematical Proceedings of
the Cambridge Philosophical Society. Unknown. https://doi.org/10.1017/S0305004107000205
chicago: De La Bretèche, Régis, and Timothy D Browning. “On Manin’s Conjecture for
Singular Del Pezzo Surfaces of Degree Four, II.” Mathematical Proceedings of
the Cambridge Philosophical Society. Unknown, 2007. https://doi.org/10.1017/S0305004107000205.
ieee: R. De La Bretèche and T. D. Browning, “On Manin’s conjecture for singular
del Pezzo surfaces of degree four, II,” Mathematical Proceedings of the Cambridge
Philosophical Society, vol. 143, no. 3. Unknown, pp. 579–605, 2007.
ista: De La Bretèche R, Browning TD. 2007. On Manin’s conjecture for singular del
Pezzo surfaces of degree four, II. Mathematical Proceedings of the Cambridge Philosophical
Society. 143(3), 579–605.
mla: De La Bretèche, Régis, and Timothy D. Browning. “On Manin’s Conjecture for
Singular Del Pezzo Surfaces of Degree Four, II.” Mathematical Proceedings of
the Cambridge Philosophical Society, vol. 143, no. 3, Unknown, 2007, pp. 579–605,
doi:10.1017/S0305004107000205.
short: R. De La Bretèche, T.D. Browning, Mathematical Proceedings of the Cambridge
Philosophical Society 143 (2007) 579–605.
date_created: 2018-12-11T11:45:17Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:05Z
day: '01'
doi: 10.1017/S0305004107000205
extern: 1
intvolume: ' 143'
issue: '3'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/math/0502510v4
month: '01'
oa: 1
page: 579 - 605
publication: Mathematical Proceedings of the Cambridge Philosophical Society
publication_status: published
publisher: Unknown
publist_id: '7689'
quality_controlled: 0
status: public
title: On Manin's conjecture for singular del Pezzo surfaces of degree four, II
type: journal_article
volume: 143
year: '2007'
...
---
_id: '223'
abstract:
- lang: eng
text: Let Q be a non-singular diagonal quadratic form in at least four variables.
We provide upper bounds for the number of integer solutions to the equation Q
= 0, which lie in a box with sides of length 2B, as B → ∞. The estimates obtained
are completely uniform in the coefficients of the form, and become sharper as
they grow larger in modulus.
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Browning TD. Density of integer solutions to diagonal quadratic forms. Monatshefte
fur Mathematik. 2007;152(1):13-38. doi:10.1007/s00605-007-0457-5
apa: Browning, T. D. (2007). Density of integer solutions to diagonal quadratic
forms. Monatshefte Fur Mathematik. Springer. https://doi.org/10.1007/s00605-007-0457-5
chicago: Browning, Timothy D. “Density of Integer Solutions to Diagonal Quadratic
Forms.” Monatshefte Fur Mathematik. Springer, 2007. https://doi.org/10.1007/s00605-007-0457-5.
ieee: T. D. Browning, “Density of integer solutions to diagonal quadratic forms,”
Monatshefte fur Mathematik, vol. 152, no. 1. Springer, pp. 13–38, 2007.
ista: Browning TD. 2007. Density of integer solutions to diagonal quadratic forms.
Monatshefte fur Mathematik. 152(1), 13–38.
mla: Browning, Timothy D. “Density of Integer Solutions to Diagonal Quadratic Forms.”
Monatshefte Fur Mathematik, vol. 152, no. 1, Springer, 2007, pp. 13–38,
doi:10.1007/s00605-007-0457-5.
short: T.D. Browning, Monatshefte Fur Mathematik 152 (2007) 13–38.
date_created: 2018-12-11T11:45:17Z
date_published: 2007-09-01T00:00:00Z
date_updated: 2021-01-12T06:56:09Z
day: '01'
doi: 10.1007/s00605-007-0457-5
extern: 1
intvolume: ' 152'
issue: '1'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/math/0603569
month: '09'
oa: 1
page: 13 - 38
publication: Monatshefte fur Mathematik
publication_status: published
publisher: Springer
publist_id: '7690'
quality_controlled: 0
status: public
title: Density of integer solutions to diagonal quadratic forms
type: journal_article
volume: 152
year: '2007'
...
---
_id: '2367'
abstract:
- lang: eng
text: It was recently shown by Hansen that the Wigner-Yanase entropy is, for general
states of quantum systems, not subadditive with respect to decomposition into
two subsystems, although this property is known to hold for pure states. We investigate
the question whether the weaker property of subadditivity for pure states with
respect to decomposition into more than two subsystems holds. This property would
have interesting applications in quantum chemistry. We show, however, that it
does not hold in general, and provide a counterexample.
author:
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Seiringer R. On the failure of subadditivity of the Wigner-Yanase entropy.
Letters in Mathematical Physics. 2007;80(3):285-288. doi:10.1007/s11005-007-0159-x
apa: Seiringer, R. (2007). On the failure of subadditivity of the Wigner-Yanase
entropy. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-007-0159-x
chicago: Seiringer, Robert. “On the Failure of Subadditivity of the Wigner-Yanase
Entropy.” Letters in Mathematical Physics. Springer, 2007. https://doi.org/10.1007/s11005-007-0159-x.
ieee: R. Seiringer, “On the failure of subadditivity of the Wigner-Yanase entropy,”
Letters in Mathematical Physics, vol. 80, no. 3. Springer, pp. 285–288,
2007.
ista: Seiringer R. 2007. On the failure of subadditivity of the Wigner-Yanase entropy.
Letters in Mathematical Physics. 80(3), 285–288.
mla: Seiringer, Robert. “On the Failure of Subadditivity of the Wigner-Yanase Entropy.”
Letters in Mathematical Physics, vol. 80, no. 3, Springer, 2007, pp. 285–88,
doi:10.1007/s11005-007-0159-x.
short: R. Seiringer, Letters in Mathematical Physics 80 (2007) 285–288.
date_created: 2018-12-11T11:57:15Z
date_published: 2007-06-01T00:00:00Z
date_updated: 2021-01-12T06:57:03Z
day: '01'
doi: 10.1007/s11005-007-0159-x
extern: 1
intvolume: ' 80'
issue: '3'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0704.1435
month: '06'
oa: 1
page: 285 - 288
publication: Letters in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4557'
quality_controlled: 0
status: public
title: On the failure of subadditivity of the Wigner-Yanase entropy
type: journal_article
volume: 80
year: '2007'
...
---
_id: '2372'
abstract:
- lang: eng
text: The increasing interest in the Müller density-matrix-functional theory has
led us to a systematic mathematical investigation of its properties. This functional
is similar to the Hartree-Fock (HF) functional, but with a modified exchange term
in which the square of the density matrix γ(x, x′) is replaced by the square of
γ1 2 (x, x′). After an extensive introductory discussion of density-matrix-functional
theory we show, among other things, that this functional is convex (unlike the
HF functional) and that energy minimizing γ 's have unique densities ρ(r), which
is a physically desirable property often absent in HF theory. We show that minimizers
exist if N≤Z, and derive various properties of the minimal energy and the corresponding
minimizers. We also give a precise statement about the equation for the orbitals
of γ, which is more complex than for HF theory. We state some open mathematical
questions about the theory together with conjectured solutions.
author:
- first_name: Rupert
full_name: Frank, Rupert L
last_name: Frank
- first_name: Élliott
full_name: Lieb, Élliott H
last_name: Lieb
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Heinz
full_name: Siedentop, Heinz K
last_name: Siedentop
citation:
ama: Frank R, Lieb É, Seiringer R, Siedentop H. Müller’s exchange-correlation energy
in density-matrix-functional theory. Physical Review A - Atomic, Molecular,
and Optical Physics. 2007;76(5). doi:10.1103/PhysRevA.76.052517
apa: Frank, R., Lieb, É., Seiringer, R., & Siedentop, H. (2007). Müller’s exchange-correlation
energy in density-matrix-functional theory. Physical Review A - Atomic, Molecular,
and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.76.052517
chicago: Frank, Rupert, Élliott Lieb, Robert Seiringer, and Heinz Siedentop. “Müller’s
Exchange-Correlation Energy in Density-Matrix-Functional Theory.” Physical
Review A - Atomic, Molecular, and Optical Physics. American Physical Society,
2007. https://doi.org/10.1103/PhysRevA.76.052517.
ieee: R. Frank, É. Lieb, R. Seiringer, and H. Siedentop, “Müller’s exchange-correlation
energy in density-matrix-functional theory,” Physical Review A - Atomic, Molecular,
and Optical Physics, vol. 76, no. 5. American Physical Society, 2007.
ista: Frank R, Lieb É, Seiringer R, Siedentop H. 2007. Müller’s exchange-correlation
energy in density-matrix-functional theory. Physical Review A - Atomic, Molecular,
and Optical Physics. 76(5).
mla: Frank, Rupert, et al. “Müller’s Exchange-Correlation Energy in Density-Matrix-Functional
Theory.” Physical Review A - Atomic, Molecular, and Optical Physics, vol.
76, no. 5, American Physical Society, 2007, doi:10.1103/PhysRevA.76.052517.
short: R. Frank, É. Lieb, R. Seiringer, H. Siedentop, Physical Review A - Atomic,
Molecular, and Optical Physics 76 (2007).
date_created: 2018-12-11T11:57:17Z
date_published: 2007-11-30T00:00:00Z
date_updated: 2021-01-12T06:57:05Z
day: '30'
doi: 10.1103/PhysRevA.76.052517
extern: 1
intvolume: ' 76'
issue: '5'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0705.1587
month: '11'
oa: 1
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '4554'
quality_controlled: 0
status: public
title: Müller's exchange-correlation energy in density-matrix-functional theory
type: journal_article
volume: 76
year: '2007'
...
---
_id: '2370'
abstract:
- lang: eng
text: After recalling briefly the connection between spontaneous symmetry breaking
and off-diagonal long-range order for models of magnets a general proof of spontaneous
breaking of gauge symmetry as a consequence of Bose-Einstein condensation is presented.
The proof is based on a rigorous validation of Bogoliubov's c-number substitution
for the k = 0 mode operator α0.
author:
- first_name: Élliott
full_name: Lieb, Élliott H
last_name: Lieb
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jakob
full_name: Yngvason, Jakob
last_name: Yngvason
citation:
ama: Lieb É, Seiringer R, Yngvason J. Bose-Einstein condensation and spontaneous
symmetry breaking. Reports on Mathematical Physics. 2007;59(3):389-399.
doi:10.1016/S0034-4877(07)80074-7
apa: Lieb, É., Seiringer, R., & Yngvason, J. (2007). Bose-Einstein condensation
and spontaneous symmetry breaking. Reports on Mathematical Physics. Elsevier.
https://doi.org/10.1016/S0034-4877(07)80074-7
chicago: Lieb, Élliott, Robert Seiringer, and Jakob Yngvason. “Bose-Einstein Condensation
and Spontaneous Symmetry Breaking.” Reports on Mathematical Physics. Elsevier,
2007. https://doi.org/10.1016/S0034-4877(07)80074-7.
ieee: É. Lieb, R. Seiringer, and J. Yngvason, “Bose-Einstein condensation and spontaneous
symmetry breaking,” Reports on Mathematical Physics, vol. 59, no. 3. Elsevier,
pp. 389–399, 2007.
ista: Lieb É, Seiringer R, Yngvason J. 2007. Bose-Einstein condensation and spontaneous
symmetry breaking. Reports on Mathematical Physics. 59(3), 389–399.
mla: Lieb, Élliott, et al. “Bose-Einstein Condensation and Spontaneous Symmetry
Breaking.” Reports on Mathematical Physics, vol. 59, no. 3, Elsevier, 2007,
pp. 389–99, doi:10.1016/S0034-4877(07)80074-7.
short: É. Lieb, R. Seiringer, J. Yngvason, Reports on Mathematical Physics 59 (2007)
389–399.
date_created: 2018-12-11T11:57:16Z
date_published: 2007-06-01T00:00:00Z
date_updated: 2021-01-12T06:57:04Z
day: '01'
doi: 10.1016/S0034-4877(07)80074-7
extern: 1
intvolume: ' 59'
issue: '3'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math-ph/0610034
month: '06'
oa: 1
page: 389 - 399
publication: Reports on Mathematical Physics
publication_status: published
publisher: Elsevier
publist_id: '4556'
quality_controlled: 0
status: public
title: Bose-Einstein condensation and spontaneous symmetry breaking
type: journal_article
volume: 59
year: '2007'
...
---
_id: '2375'
abstract:
- lang: eng
text: We give a Cwikel-Lieb-Rozenblum type bound on the number of bound states of
Schrödinger operators with matrix-valued potentials using the functional integral
method of Lieb. This significantly improves the constant in this inequality obtained
earlier by Hundertmark.
author:
- first_name: Rupert
full_name: Frank, Rupert L
last_name: Frank
- first_name: Élliott
full_name: Lieb, Élliott H
last_name: Lieb
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Frank R, Lieb É, Seiringer R. Number of bound states of Schrödinger operators
with matrix-valued potentials. Letters in Mathematical Physics. 2007;82(2-3):107-116.
doi:10.1007/s11005-007-0211-x
apa: Frank, R., Lieb, É., & Seiringer, R. (2007). Number of bound states of
Schrödinger operators with matrix-valued potentials. Letters in Mathematical
Physics. Springer. https://doi.org/10.1007/s11005-007-0211-x
chicago: Frank, Rupert, Élliott Lieb, and Robert Seiringer. “Number of Bound States
of Schrödinger Operators with Matrix-Valued Potentials.” Letters in Mathematical
Physics. Springer, 2007. https://doi.org/10.1007/s11005-007-0211-x.
ieee: R. Frank, É. Lieb, and R. Seiringer, “Number of bound states of Schrödinger
operators with matrix-valued potentials,” Letters in Mathematical Physics,
vol. 82, no. 2–3. Springer, pp. 107–116, 2007.
ista: Frank R, Lieb É, Seiringer R. 2007. Number of bound states of Schrödinger
operators with matrix-valued potentials. Letters in Mathematical Physics. 82(2–3),
107–116.
mla: Frank, Rupert, et al. “Number of Bound States of Schrödinger Operators with
Matrix-Valued Potentials.” Letters in Mathematical Physics, vol. 82, no.
2–3, Springer, 2007, pp. 107–16, doi:10.1007/s11005-007-0211-x.
short: R. Frank, É. Lieb, R. Seiringer, Letters in Mathematical Physics 82 (2007)
107–116.
date_created: 2018-12-11T11:57:18Z
date_published: 2007-12-01T00:00:00Z
date_updated: 2021-01-12T06:57:06Z
day: '01'
doi: 10.1007/s11005-007-0211-x
extern: 1
intvolume: ' 82'
issue: 2-3
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0710.1877
month: '12'
oa: 1
page: 107 - 116
publication: Letters in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4552'
quality_controlled: 0
status: public
title: Number of bound states of Schrödinger operators with matrix-valued potentials
type: journal_article
volume: 82
year: '2007'
...
---
_id: '2373'
abstract:
- lang: eng
text: For the BCS equation with local two-body interaction λV(x), we give a rigorous
analysis of the asymptotic behavior of the critical temperature as γ"0. We
derive necessary and sufficient conditions onV(x) for the existence of a nontrivial
solution for all values of γ>0.
author:
- first_name: Rupert
full_name: Frank, Rupert L
last_name: Frank
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Serguei
full_name: Naboko, Serguei N
last_name: Naboko
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Frank R, Hainzl C, Naboko S, Seiringer R. The critical temperature for the
BCS equation at weak coupling. Journal of Geometric Analysis. 2007;17(4):559-567.
doi:10.1007/BF02937429
apa: Frank, R., Hainzl, C., Naboko, S., & Seiringer, R. (2007). The critical
temperature for the BCS equation at weak coupling. Journal of Geometric Analysis.
Springer. https://doi.org/10.1007/BF02937429
chicago: Frank, Rupert, Christian Hainzl, Serguei Naboko, and Robert Seiringer.
“The Critical Temperature for the BCS Equation at Weak Coupling.” Journal of
Geometric Analysis. Springer, 2007. https://doi.org/10.1007/BF02937429.
ieee: R. Frank, C. Hainzl, S. Naboko, and R. Seiringer, “The critical temperature
for the BCS equation at weak coupling,” Journal of Geometric Analysis,
vol. 17, no. 4. Springer, pp. 559–567, 2007.
ista: Frank R, Hainzl C, Naboko S, Seiringer R. 2007. The critical temperature for
the BCS equation at weak coupling. Journal of Geometric Analysis. 17(4), 559–567.
mla: Frank, Rupert, et al. “The Critical Temperature for the BCS Equation at Weak
Coupling.” Journal of Geometric Analysis, vol. 17, no. 4, Springer, 2007,
pp. 559–67, doi:10.1007/BF02937429.
short: R. Frank, C. Hainzl, S. Naboko, R. Seiringer, Journal of Geometric Analysis
17 (2007) 559–567.
date_created: 2018-12-11T11:57:17Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T06:57:05Z
day: '01'
doi: 10.1007/BF02937429
extern: 1
intvolume: ' 17'
issue: '4'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0704.3564
month: '01'
oa: 1
page: 559 - 567
publication: Journal of Geometric Analysis
publication_status: published
publisher: Springer
publist_id: '4553'
quality_controlled: 0
status: public
title: The critical temperature for the BCS equation at weak coupling
type: journal_article
volume: 17
year: '2007'
...
---
_id: '2371'
abstract:
- lang: eng
text: We give a proof of stability of relativistic matter with magnetic fields all
the way up to the critical value of the nuclear charge Zα = 2/π.
author:
- first_name: Rupert
full_name: Frank, Rupert L
last_name: Frank
- first_name: Élliott
full_name: Lieb, Élliott H
last_name: Lieb
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Frank R, Lieb É, Seiringer R. Stability of relativistic matter with magnetic
fields for nuclear charges up to the critical value. Communications in Mathematical
Physics. 2007;275(2):479-489. doi:10.1007/s00220-007-0307-2
apa: Frank, R., Lieb, É., & Seiringer, R. (2007). Stability of relativistic
matter with magnetic fields for nuclear charges up to the critical value. Communications
in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-007-0307-2
chicago: Frank, Rupert, Élliott Lieb, and Robert Seiringer. “Stability of Relativistic
Matter with Magnetic Fields for Nuclear Charges up to the Critical Value.” Communications
in Mathematical Physics. Springer, 2007. https://doi.org/10.1007/s00220-007-0307-2.
ieee: R. Frank, É. Lieb, and R. Seiringer, “Stability of relativistic matter with
magnetic fields for nuclear charges up to the critical value,” Communications
in Mathematical Physics, vol. 275, no. 2. Springer, pp. 479–489, 2007.
ista: Frank R, Lieb É, Seiringer R. 2007. Stability of relativistic matter with
magnetic fields for nuclear charges up to the critical value. Communications in
Mathematical Physics. 275(2), 479–489.
mla: Frank, Rupert, et al. “Stability of Relativistic Matter with Magnetic Fields
for Nuclear Charges up to the Critical Value.” Communications in Mathematical
Physics, vol. 275, no. 2, Springer, 2007, pp. 479–89, doi:10.1007/s00220-007-0307-2.
short: R. Frank, É. Lieb, R. Seiringer, Communications in Mathematical Physics 275
(2007) 479–489.
date_created: 2018-12-11T11:57:16Z
date_published: 2007-10-01T00:00:00Z
date_updated: 2021-01-12T06:57:05Z
day: '01'
doi: 10.1007/s00220-007-0307-2
extern: 1
intvolume: ' 275'
issue: '2'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math-ph/0610062
month: '10'
oa: 1
page: 479 - 489
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4555'
quality_controlled: 0
status: public
title: Stability of relativistic matter with magnetic fields for nuclear charges up
to the critical value
type: journal_article
volume: 275
year: '2007'
...
---
_id: '2451'
abstract:
- lang: eng
text: Signal molecules known as phytohormones play a decisive role in processing
signals coming to plants from the surrounding environment. They include auxin
— a simple compound with a large range of effects. Auxin is irregularly deposited
in plant tissues, it accumulates in certain cellules and through activation of
a signal cascade it causes changes in the development programme of these cellules.
This article forms a part of the series prepared in honour of the anniversary
of the important plant physiologist — Bohumil Němec.
author:
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Friml J. Auxin - Universal development signal in plant life. Živa. 2007;1.
apa: Friml, J. (2007). Auxin - Universal development signal in plant life. Živa.
CSAV.
chicago: Friml, Jiří. “Auxin - Universal development signal in plant life.” Živa.
CSAV, 2007.
ieee: J. Friml, “Auxin - Universal development signal in plant life,” Živa,
vol. 1. CSAV, 2007.
ista: Friml J. 2007. Auxin - Universal development signal in plant life. Živa. 1.
mla: Friml, Jiří. “Auxin - Universal development signal in plant life.” Živa,
vol. 1, CSAV, 2007.
short: J. Friml, Živa 1 (2007).
date_created: 2018-12-11T11:57:44Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T06:57:34Z
day: '01'
extern: '1'
intvolume: ' 1'
language:
- iso: cze
month: '01'
oa_version: None
publication: Živa
publication_status: published
publisher: CSAV
publist_id: '4452'
quality_controlled: '1'
status: public
title: Auxin - Universal development signal in plant life
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2007'
...
---
_id: '2462'
author:
- first_name: Marta
full_name: Michniewicz, Marta
last_name: Michniewicz
- first_name: Philip
full_name: Brewer, Philip B
last_name: Brewer
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Michniewicz M, Brewer P, Friml J. Polar auxin transport and asymmetric auxin
distribution. The Arabidopsis Book. 2007;5. doi:10.1199/tab.0108
apa: Michniewicz, M., Brewer, P., & Friml, J. (2007). Polar auxin transport
and asymmetric auxin distribution. The Arabidopsis Book. The American Society
of Plant Biologists. https://doi.org/10.1199/tab.0108
chicago: Michniewicz, Marta, Philip Brewer, and Jiří Friml. “Polar Auxin Transport
and Asymmetric Auxin Distribution.” The Arabidopsis Book. The American
Society of Plant Biologists, 2007. https://doi.org/10.1199/tab.0108.
ieee: M. Michniewicz, P. Brewer, and J. Friml, “Polar auxin transport and asymmetric
auxin distribution,” The Arabidopsis Book, vol. 5. The American Society
of Plant Biologists, 2007.
ista: Michniewicz M, Brewer P, Friml J. 2007. Polar auxin transport and asymmetric
auxin distribution. The Arabidopsis Book. 5.
mla: Michniewicz, Marta, et al. “Polar Auxin Transport and Asymmetric Auxin Distribution.”
The Arabidopsis Book, vol. 5, The American Society of Plant Biologists,
2007, doi:10.1199/tab.0108.
short: M. Michniewicz, P. Brewer, J. Friml, The Arabidopsis Book 5 (2007).
date_created: 2018-12-11T11:57:48Z
date_published: 2007-08-21T00:00:00Z
date_updated: 2021-01-12T06:57:38Z
day: '21'
doi: 10.1199/tab.0108
extern: 1
intvolume: ' 5'
month: '08'
publication: The Arabidopsis Book
publication_status: published
publisher: The American Society of Plant Biologists
publist_id: '4441'
quality_controlled: 0
status: public
title: Polar auxin transport and asymmetric auxin distribution
type: journal_article
volume: 5
year: '2007'
...
---
_id: '2495'
abstract:
- lang: eng
text: 'Metabotropic glutamate receptor 4 (mGluR4) is localized mainly to presynaptic
membranes in the brain. Rat neostriatum has been reported to contain two types
of mGluR4-immunoreactive axon varicosities: small, weakly immunoreactive varicosities
that were distributed randomly (type 1) and large, intensely immunoreactive ones
that were often aligned linearly (type 2). In the present study, most type 1 terminals
formed asymmetric synapses on dendritic spines, whereas type 2 terminals made
symmetric synapses on dendritic shafts, showing immunoreactivity for GABAergic
markers. After depletion of neostriatal neurons, type 2 but not type 1 varicosities
were largely decreased in the damaged region. When medium-sized spiny neurons
(MSNs) were labeled with Sindbis virus expressing membrane-targeted green fluorescent
protein, mGluR4 immunoreactivity was observed on some varicosities of their axon
collaterals in immunofluorescence and immunoelectron microscopies. Furthermore,
type 2 varicosities were often positive for substance P but mostly negative for
striatal interneuron markers and preproenkephalin. Thus, striatonigral/striato-
entopeduncular MSNs are likely to be the largest source of type 2 mGluR4-immunopositive
axon terminals in the neostriatum. Next, in the double-immunofluorescence study,
almost all choline acetyltransferase (ChAT)-immunopositive and 41% of NK1 receptor-positive
dendrites were heavily associated with type 2 mGluR4-immunoreactive varicosities.
Neuronal nitric oxide synthase (nNOS)-positive dendrites, in contrast, seemed
associated with only a few type 2 varicosities. Conversely, almost all type 2
varicosities were closely apposed to NK1 receptor-positive dendrites that were
known to be derived from cholinergic and nNOS-producing interneurons. These findings
indicate that the mGluR4-positive terminals of MSN axon collaterals selectively
form synapses with neostriatal cholinergic interneurons.'
author:
- first_name: Eriko
full_name: Kuramoto, Eriko
last_name: Kuramoto
- first_name: Fumino
full_name: Fujiyama, Fumino
last_name: Fujiyama
- first_name: Tomo
full_name: Unzai, Tomo
last_name: Unzai
- first_name: Kouichi
full_name: Nakamura, Kouichi
last_name: Nakamura
- first_name: Hiroyuki
full_name: Hioki, Hiroyuki
last_name: Hioki
- first_name: Takahiro
full_name: Furuta, Takahiro
last_name: Furuta
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Francesco
full_name: Ferraguti, Francesco
last_name: Ferraguti
- first_name: Takeshi
full_name: Kaneko, Takeshi
last_name: Kaneko
citation:
ama: Kuramoto E, Fujiyama F, Unzai T, et al. Metabotropic glutamate receptor 4-immunopositive
terminals of medium-sized spiny neurons selectively form synapses with cholinergic
interneurons in the rat neostriatum. Journal of Comparative Neurology.
2007;500(5):908-922. doi:10.1002/cne.21216
apa: Kuramoto, E., Fujiyama, F., Unzai, T., Nakamura, K., Hioki, H., Furuta, T.,
… Kaneko, T. (2007). Metabotropic glutamate receptor 4-immunopositive terminals
of medium-sized spiny neurons selectively form synapses with cholinergic interneurons
in the rat neostriatum. Journal of Comparative Neurology. Wiley-Blackwell.
https://doi.org/10.1002/cne.21216
chicago: Kuramoto, Eriko, Fumino Fujiyama, Tomo Unzai, Kouichi Nakamura, Hiroyuki
Hioki, Takahiro Furuta, Ryuichi Shigemoto, Francesco Ferraguti, and Takeshi Kaneko.
“Metabotropic Glutamate Receptor 4-Immunopositive Terminals of Medium-Sized Spiny
Neurons Selectively Form Synapses with Cholinergic Interneurons in the Rat Neostriatum.”
Journal of Comparative Neurology. Wiley-Blackwell, 2007. https://doi.org/10.1002/cne.21216.
ieee: E. Kuramoto et al., “Metabotropic glutamate receptor 4-immunopositive
terminals of medium-sized spiny neurons selectively form synapses with cholinergic
interneurons in the rat neostriatum,” Journal of Comparative Neurology,
vol. 500, no. 5. Wiley-Blackwell, pp. 908–922, 2007.
ista: Kuramoto E, Fujiyama F, Unzai T, Nakamura K, Hioki H, Furuta T, Shigemoto
R, Ferraguti F, Kaneko T. 2007. Metabotropic glutamate receptor 4-immunopositive
terminals of medium-sized spiny neurons selectively form synapses with cholinergic
interneurons in the rat neostriatum. Journal of Comparative Neurology. 500(5),
908–922.
mla: Kuramoto, Eriko, et al. “Metabotropic Glutamate Receptor 4-Immunopositive Terminals
of Medium-Sized Spiny Neurons Selectively Form Synapses with Cholinergic Interneurons
in the Rat Neostriatum.” Journal of Comparative Neurology, vol. 500, no.
5, Wiley-Blackwell, 2007, pp. 908–22, doi:10.1002/cne.21216.
short: E. Kuramoto, F. Fujiyama, T. Unzai, K. Nakamura, H. Hioki, T. Furuta, R.
Shigemoto, F. Ferraguti, T. Kaneko, Journal of Comparative Neurology 500 (2007)
908–922.
date_created: 2018-12-11T11:58:00Z
date_published: 2007-02-10T00:00:00Z
date_updated: 2021-01-12T06:57:49Z
day: '10'
doi: 10.1002/cne.21216
extern: 1
intvolume: ' 500'
issue: '5'
month: '02'
page: 908 - 922
publication: Journal of Comparative Neurology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4406'
quality_controlled: 0
status: public
title: Metabotropic glutamate receptor 4-immunopositive terminals of medium-sized
spiny neurons selectively form synapses with cholinergic interneurons in the rat
neostriatum
type: journal_article
volume: 500
year: '2007'
...
---
_id: '2496'
abstract:
- lang: eng
text: 'Glutamate is one candidate for the neurotransmitters and/or neuromodulators
involved in taste signaling in taste buds. Group II metabotropic glutamate receptors
(mGluRs: mGluR2 and mGluR3) are known to function as presynaptic receptors that
regulate the release of glutamate and/or other neurotransmitters in the central
nervous system. Group II mGluRs are negatively linked to adenylyl cyclase through
Gαi subunits and thereby reduce the turnover of cAMP. In rat taste tissues, a
subset of adenylyl-cyclase-8-expressing taste cells coexpress the Gαi subunits
gustducin and Gαi2. However, the expression patterns of group II mGluRs in rat
taste tissues have not yet been elucidated. We have therefore examined the expression
patterns of mGluR2, mGluR3, and gustducin in rat gustatory tissues. Reverse transcription/polymerase
chain reaction assays have revealed that mGluR2 and mGluR3 mRNAs are expressed
in the circumvallate papillae. In situ hybridization analyses have detected positive
signals for mGluR2 and mGluR3 mRNAs only in the circumvallate taste buds. Among
the fungiform, foliate, and circumvallate papillae, an antibody against mGluR2/3
labels a subset of taste bud cells and nerve fibers immediately beneath the taste
lingual epithelium. Double-labeling experiments have demonstrated that mGluR2/3-positive
cells coexpress gustducin. These results indicate that mGluR2 and mGluR3 are coupled
to Gαi subunits and play roles in glutamate-mediated signaling in taste transductions.'
author:
- first_name: Takashi
full_name: Toyono, Takashi
last_name: Toyono
- first_name: Shinji
full_name: Kataoka, Shinji
last_name: Kataoka
- first_name: Yuji
full_name: Seta, Yuji
last_name: Seta
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Kuniaki
full_name: Toyoshima, Kuniaki
last_name: Toyoshima
citation:
ama: Toyono T, Kataoka S, Seta Y, Shigemoto R, Toyoshima K. Expression of group
II metabotropic glutamate receptors in rat gustatory papillae. Cell and Tissue
Research. 2007;328(1):57-63. doi:10.1007/s00441-006-0351-9
apa: Toyono, T., Kataoka, S., Seta, Y., Shigemoto, R., & Toyoshima, K. (2007).
Expression of group II metabotropic glutamate receptors in rat gustatory papillae.
Cell and Tissue Research. Springer. https://doi.org/10.1007/s00441-006-0351-9
chicago: Toyono, Takashi, Shinji Kataoka, Yuji Seta, Ryuichi Shigemoto, and Kuniaki
Toyoshima. “Expression of Group II Metabotropic Glutamate Receptors in Rat Gustatory
Papillae.” Cell and Tissue Research. Springer, 2007. https://doi.org/10.1007/s00441-006-0351-9.
ieee: T. Toyono, S. Kataoka, Y. Seta, R. Shigemoto, and K. Toyoshima, “Expression
of group II metabotropic glutamate receptors in rat gustatory papillae,” Cell
and Tissue Research, vol. 328, no. 1. Springer, pp. 57–63, 2007.
ista: Toyono T, Kataoka S, Seta Y, Shigemoto R, Toyoshima K. 2007. Expression of
group II metabotropic glutamate receptors in rat gustatory papillae. Cell and
Tissue Research. 328(1), 57–63.
mla: Toyono, Takashi, et al. “Expression of Group II Metabotropic Glutamate Receptors
in Rat Gustatory Papillae.” Cell and Tissue Research, vol. 328, no. 1,
Springer, 2007, pp. 57–63, doi:10.1007/s00441-006-0351-9.
short: T. Toyono, S. Kataoka, Y. Seta, R. Shigemoto, K. Toyoshima, Cell and Tissue
Research 328 (2007) 57–63.
date_created: 2018-12-11T11:58:00Z
date_published: 2007-04-01T00:00:00Z
date_updated: 2021-01-12T06:57:50Z
day: '01'
doi: 10.1007/s00441-006-0351-9
extern: 1
intvolume: ' 328'
issue: '1'
month: '04'
page: 57 - 63
publication: Cell and Tissue Research
publication_status: published
publisher: Springer
publist_id: '4405'
quality_controlled: 0
status: public
title: Expression of group II metabotropic glutamate receptors in rat gustatory papillae
type: journal_article
volume: 328
year: '2007'
...
---
_id: '2665'
abstract:
- lang: eng
text: Substance P (SP) is known to be a peptide that facilitates epileptic activity
of principal cells in the hippocampus. Paradoxically, in other models, it was
found to be protective against seizures by activating substance P receptor (SPR)-expressing
interneurons. Thus, these cells appear to play an important role in the generation
and regulation of epileptic seizures. The number, distribution, morphological
features and input characteristics of SPR-immunoreactive cells were analyzed in
surgically removed hippocampi of 28 temporal lobe epileptic patients and eight
control hippocampi in order to examine their changes in epileptic tissues. SPR
is expressed in a subset of inhibitory cells in the control human hippocampus,
they are multipolar interneurons with smooth dendrites, present in all hippocampal
subfields. This cell population is considerably different from SPR-positive cells
of the rat hippocampus. The CA1 (cornu Ammonis subfield 1) region was chosen for
the detailed morphological analysis of the SPR-immunoreactive cells because of
its extreme vulnerability in epilepsy. The presence of various neurochemical markers
identifies functionally distinct interneuron types, such as those responsible
for perisomatic, dendritic or interneuron-selective inhibition. We found considerable
colocalization of SPR with calbindin but not with parvalbumin, calretinin, cholecystokinin
and somatostatin, therefore we suppose that SPR-positive cells participate mainly
in dendritic inhibition. In the non-sclerotic CA1 region they are mainly preserved,
whereas their number is decreased in the sclerotic cases. In the epileptic samples
their morphology is considerably altered, they possessed more dendritic branches,
which often became beaded. Analyses of synaptic coverage revealed that the ratio
of symmetric synaptic input of SPR-immunoreactive cells has increased in epileptic
samples. Our results suggest that SPR-positive cells are preserved while principal
cells are present in the CA1 region, but show reactive changes in epilepsy including
intense branching and growth of their dendritic arborization.
author:
- first_name: Kinga
full_name: Tóth, Kinga
last_name: Tóth
- first_name: Lucia
full_name: Wittner, Lucia
last_name: Wittner
- first_name: Z
full_name: Urbán, Z
last_name: Urbán
- first_name: Werner
full_name: Doyle, Werner K
last_name: Doyle
- first_name: György
full_name: Buzsáki, György
last_name: Buzsáki
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Tamás
full_name: Freund, Tamás F
last_name: Freund
- first_name: Zsófia
full_name: Maglóczky, Zsófia
last_name: Maglóczky
citation:
ama: Tóth K, Wittner L, Urbán Z, et al. Morphology and synaptic input of substance
P receptor-immunoreactive interneurons in control and epileptic human hippocampus.
Neuroscience. 2007;144(2):495-508. doi:10.1016/j.neuroscience.2006.09.039
apa: Tóth, K., Wittner, L., Urbán, Z., Doyle, W., Buzsáki, G., Shigemoto, R., …
Maglóczky, Z. (2007). Morphology and synaptic input of substance P receptor-immunoreactive
interneurons in control and epileptic human hippocampus. Neuroscience.
Elsevier. https://doi.org/10.1016/j.neuroscience.2006.09.039
chicago: Tóth, Kinga, Lucia Wittner, Z Urbán, Werner Doyle, György Buzsáki, Ryuichi
Shigemoto, Tamás Freund, and Zsófia Maglóczky. “Morphology and Synaptic Input
of Substance P Receptor-Immunoreactive Interneurons in Control and Epileptic Human
Hippocampus.” Neuroscience. Elsevier, 2007. https://doi.org/10.1016/j.neuroscience.2006.09.039.
ieee: K. Tóth et al., “Morphology and synaptic input of substance P receptor-immunoreactive
interneurons in control and epileptic human hippocampus,” Neuroscience,
vol. 144, no. 2. Elsevier, pp. 495–508, 2007.
ista: Tóth K, Wittner L, Urbán Z, Doyle W, Buzsáki G, Shigemoto R, Freund T, Maglóczky
Z. 2007. Morphology and synaptic input of substance P receptor-immunoreactive
interneurons in control and epileptic human hippocampus. Neuroscience. 144(2),
495–508.
mla: Tóth, Kinga, et al. “Morphology and Synaptic Input of Substance P Receptor-Immunoreactive
Interneurons in Control and Epileptic Human Hippocampus.” Neuroscience,
vol. 144, no. 2, Elsevier, 2007, pp. 495–508, doi:10.1016/j.neuroscience.2006.09.039.
short: K. Tóth, L. Wittner, Z. Urbán, W. Doyle, G. Buzsáki, R. Shigemoto, T. Freund,
Z. Maglóczky, Neuroscience 144 (2007) 495–508.
date_created: 2018-12-11T11:58:57Z
date_published: 2007-01-19T00:00:00Z
date_updated: 2021-01-12T06:58:55Z
day: '19'
doi: 10.1016/j.neuroscience.2006.09.039
extern: 1
intvolume: ' 144'
issue: '2'
month: '01'
page: 495 - 508
publication: Neuroscience
publication_status: published
publisher: Elsevier
publist_id: '4232'
quality_controlled: 0
status: public
title: Morphology and synaptic input of substance P receptor-immunoreactive interneurons
in control and epileptic human hippocampus
type: journal_article
volume: 144
year: '2007'
...
---
_id: '2666'
abstract:
- lang: eng
text: GABAB receptors (GABABRs) are involved in early events during neuronal development.
The presence of GABABRs in developing oligodendrocytes has not been established.
Using immunofluorescent co-localization, we have identified GABABR proteins in
O4 marker-positive oligodendrocyte precursor cells (OPCs) in 4-day-old mouse brain
periventricular white matter. In culture, OPCs, differentiated oligodendrocytes
(DOs) and type 2 astrocytes (ASTs) express both the GABAB1abcdf and GABAB2 subunits
of the GABABR. Using semiquantitative PCR analysis with GABABR isoform-selective
primers we found that the expression level of GABAB1abd was substantially higher
in OPCs or ASTs than in DOs. In contrast, the GABAB2 isoform showed a similar
level of expression in OPCs and DOs, and a significantly higher level in ASTs.
This indicates that the expression of GABAB1 and GABAB2 subunits are under independent
control during oligodendroglial development. Activation of GABABRs using the selective
agonist baclofen demonstrated that these receptors are functionally active and
negatively coupled to adenylyl cyclase. Manipulation of GABABR activity had no
effect on OPC migration in a conventional agarose drop assay, whereas baclofen
significantly increased OPC migration in a more sensitive transwell microchamber-based
assay. Exposure of cultured OPCs to baclofen increased their proliferation, providing
evidence for a functional role of GABABRs in oligodendrocyte development. The
presence of GABABRs in developing oligodendrocytes provides a new mechanism for
neuronal-glial interactions during development and may offer a novel target for
promoting remyelination following white matter injury.
author:
- first_name: Karen
full_name: Luyt, Karen
last_name: Luyt
- first_name: Timothy
full_name: Slade, Timothy P
last_name: Slade
- first_name: Jienchi
full_name: Dorward, Jienchi J
last_name: Dorward
- first_name: Claire
full_name: Durant, Claire F
last_name: Durant
- first_name: Yue
full_name: Wu, Yue
last_name: Wu
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Stuart
full_name: Mundell, Stuart J
last_name: Mundell
- first_name: Anikó
full_name: Váradi, Anikó
last_name: Váradi
- first_name: Elek
full_name: Molnár, Elek
last_name: Molnár
citation:
ama: Luyt K, Slade T, Dorward J, et al. Developing oligodendrocytes express functional
GABAB receptors that stimulate cell proliferation and migration. Journal of
Neurochemistry. 2007;100(3):822-840. doi:10.1111/j.1471-4159.2006.04255.x
apa: Luyt, K., Slade, T., Dorward, J., Durant, C., Wu, Y., Shigemoto, R., … Molnár,
E. (2007). Developing oligodendrocytes express functional GABAB receptors that
stimulate cell proliferation and migration. Journal of Neurochemistry.
Wiley-Blackwell. https://doi.org/10.1111/j.1471-4159.2006.04255.x
chicago: Luyt, Karen, Timothy Slade, Jienchi Dorward, Claire Durant, Yue Wu, Ryuichi
Shigemoto, Stuart Mundell, Anikó Váradi, and Elek Molnár. “Developing Oligodendrocytes
Express Functional GABAB Receptors That Stimulate Cell Proliferation and Migration.”
Journal of Neurochemistry. Wiley-Blackwell, 2007. https://doi.org/10.1111/j.1471-4159.2006.04255.x.
ieee: K. Luyt et al., “Developing oligodendrocytes express functional GABAB
receptors that stimulate cell proliferation and migration,” Journal of Neurochemistry,
vol. 100, no. 3. Wiley-Blackwell, pp. 822–840, 2007.
ista: Luyt K, Slade T, Dorward J, Durant C, Wu Y, Shigemoto R, Mundell S, Váradi
A, Molnár E. 2007. Developing oligodendrocytes express functional GABAB receptors
that stimulate cell proliferation and migration. Journal of Neurochemistry. 100(3),
822–840.
mla: Luyt, Karen, et al. “Developing Oligodendrocytes Express Functional GABAB Receptors
That Stimulate Cell Proliferation and Migration.” Journal of Neurochemistry,
vol. 100, no. 3, Wiley-Blackwell, 2007, pp. 822–40, doi:10.1111/j.1471-4159.2006.04255.x.
short: K. Luyt, T. Slade, J. Dorward, C. Durant, Y. Wu, R. Shigemoto, S. Mundell,
A. Váradi, E. Molnár, Journal of Neurochemistry 100 (2007) 822–840.
date_created: 2018-12-11T11:58:57Z
date_published: 2007-02-01T00:00:00Z
date_updated: 2021-01-12T06:58:55Z
day: '01'
doi: 10.1111/j.1471-4159.2006.04255.x
extern: 1
intvolume: ' 100'
issue: '3'
month: '02'
page: 822 - 840
publication: Journal of Neurochemistry
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4231'
quality_controlled: 0
status: public
title: Developing oligodendrocytes express functional GABAB receptors that stimulate
cell proliferation and migration
type: journal_article
volume: 100
year: '2007'
...
---
_id: '2668'
abstract:
- lang: eng
text: Hyperpolarization-activated, cyclic nucleotide-gated cation (HCN) channels
are expressed postsynaptically in the rodent globus pallidus (GP), where they
play several important roles in controlling GP neuronal activity. To further elucidate
the role of HCN channels in the GP, immunocytochemical and electrophysiological
approaches were used to test the hypothesis that HCN channels are also expressed
presynaptically on the local axon collaterals of GP neurons. At the electron microscopic
level, immunoperoxidase labelling for HCN1 and HCN2 was localized in GP somata
and dendritic processes, myelinated and unmyelinated axons, and axon terminals.
One population of labelled terminals formed symmetric synapses with somata and
proximal dendrites and were immunoreactive for parvalbumin, consistent with the
axon collaterals of GABAergic GP projection neurons. In addition, labelling for
HCN2 and, to a lesser degree, HCN1 was observed in axon terminals that formed
asymmetric synapses and were immunoreactive for the vesicular glutamate transporter
2. Immunogold labelling demonstrated that HCN1 and HCN2 were located predominantly
at extrasynaptic sites along the plasma membrane of both types of terminal. To
determine the function of presynaptic HCN channels in the GP, we performed whole-cell
recordings from GP neurons in vitro. Bath application of the HCN channel blocker
ZD7288 resulted in an increase in the frequency of mIPSCs but had no effect on
their amplitude, implying that HCN channels tonically regulate the release of
GABA. Their presence, and predicted role in modulating transmitter release, represents
a hitherto unidentified mechanism whereby HCN channels influence the activity
of GP neurons.
author:
- first_name: Justin
full_name: Boyes, Justin
last_name: Boyes
- first_name: John
full_name: Bolam, John P
last_name: Bolam
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Ian
full_name: Stanford, Ian M
last_name: Stanford
citation:
ama: Boyes J, Bolam J, Shigemoto R, Stanford I. Functional presynaptic HCN channels
in the rat globus pallidus. European Journal of Neuroscience. 2007;25(7):2081-2092.
doi:10.1111/j.1460-9568.2007.05463.x
apa: Boyes, J., Bolam, J., Shigemoto, R., & Stanford, I. (2007). Functional
presynaptic HCN channels in the rat globus pallidus. European Journal of Neuroscience.
Wiley-Blackwell. https://doi.org/10.1111/j.1460-9568.2007.05463.x
chicago: Boyes, Justin, John Bolam, Ryuichi Shigemoto, and Ian Stanford. “Functional
Presynaptic HCN Channels in the Rat Globus Pallidus.” European Journal of Neuroscience.
Wiley-Blackwell, 2007. https://doi.org/10.1111/j.1460-9568.2007.05463.x.
ieee: J. Boyes, J. Bolam, R. Shigemoto, and I. Stanford, “Functional presynaptic
HCN channels in the rat globus pallidus,” European Journal of Neuroscience,
vol. 25, no. 7. Wiley-Blackwell, pp. 2081–2092, 2007.
ista: Boyes J, Bolam J, Shigemoto R, Stanford I. 2007. Functional presynaptic HCN
channels in the rat globus pallidus. European Journal of Neuroscience. 25(7),
2081–2092.
mla: Boyes, Justin, et al. “Functional Presynaptic HCN Channels in the Rat Globus
Pallidus.” European Journal of Neuroscience, vol. 25, no. 7, Wiley-Blackwell,
2007, pp. 2081–92, doi:10.1111/j.1460-9568.2007.05463.x.
short: J. Boyes, J. Bolam, R. Shigemoto, I. Stanford, European Journal of Neuroscience
25 (2007) 2081–2092.
date_created: 2018-12-11T11:58:58Z
date_published: 2007-04-01T00:00:00Z
date_updated: 2021-01-12T06:58:56Z
day: '01'
doi: 10.1111/j.1460-9568.2007.05463.x
extern: 1
intvolume: ' 25'
issue: '7'
month: '04'
page: 2081 - 2092
publication: European Journal of Neuroscience
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4228'
quality_controlled: 0
status: public
title: Functional presynaptic HCN channels in the rat globus pallidus
type: journal_article
volume: 25
year: '2007'
...
---
_id: '2667'
abstract:
- lang: eng
text: The number of AMPA receptor (AMPAR) is the major determinant of synaptic strength
at glutamatergic synapses, but little is known about the absolute number and density
of AMPARs in individual synapses. Using SDS-digested freeze-fracture replica labeling,
which has high detection efficiency comparable with electrophysiological noise
analysis for functional AMPAR, we analyzed three kinds of excitatory synapses
in the molecular layer of the adult rat cerebellum. In parallel fiber (PF)-Purkinje
cell (PC) synapses, we found large variability in the number (38.1 ± 34.4 particles
per synapse, mean ± SD; range, 2-178 particles per synapse) and density (437 ±
277 particles/μm2; range, 48-1210 particles/μm2) of immunogold-labeled AMPARs.
Two-dimensional view and high sensitivity of this method revealed irregular-shaped
small AMPAR clusters within synapses. Climbing fiber (CF)-PC synapses had higher
number of AMPAR labeling (68.6 ± 34.5 particles per synapse) than PF-PC and PF-interneuron
synapses (36.8 ± 14.4 particles per synapse). Furthermore, AMPAR density at CF-PC
and PF-interneuron synapses was approximately five times higher and more uniform
than that at PF-PC synapses. These results suggest input- and target-dependent
regulation of AMPAR-mediated synaptic strength.
author:
- first_name: Miwako
full_name: Masugi-Tokita, Miwako
last_name: Masugi Tokita
- first_name: Etsuko
full_name: Tarusawa, Etsuko
last_name: Tarusawa
- first_name: Masahiko
full_name: Watanabe, Masahiko
last_name: Watanabe
- first_name: Elek
full_name: Molnár, Elek
last_name: Molnár
- first_name: Kazushi
full_name: Fujimoto, Kazushi
last_name: Fujimoto
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Masugi Tokita M, Tarusawa E, Watanabe M, Molnár E, Fujimoto K, Shigemoto R.
Number and density of AMPA receptors in individual synapses in the rat cerebellum
as revealed by SDS-digested freeze-fracture replica labeling. Journal of Neuroscience.
2007;27(8):2135-2144. doi:10.1523/JNEUROSCI.2861-06.2007
apa: Masugi Tokita, M., Tarusawa, E., Watanabe, M., Molnár, E., Fujimoto, K., &
Shigemoto, R. (2007). Number and density of AMPA receptors in individual synapses
in the rat cerebellum as revealed by SDS-digested freeze-fracture replica labeling.
Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2861-06.2007
chicago: Masugi Tokita, Miwako, Etsuko Tarusawa, Masahiko Watanabe, Elek Molnár,
Kazushi Fujimoto, and Ryuichi Shigemoto. “Number and Density of AMPA Receptors
in Individual Synapses in the Rat Cerebellum as Revealed by SDS-Digested Freeze-Fracture
Replica Labeling.” Journal of Neuroscience. Society for Neuroscience, 2007.
https://doi.org/10.1523/JNEUROSCI.2861-06.2007.
ieee: M. Masugi Tokita, E. Tarusawa, M. Watanabe, E. Molnár, K. Fujimoto, and R.
Shigemoto, “Number and density of AMPA receptors in individual synapses in the
rat cerebellum as revealed by SDS-digested freeze-fracture replica labeling,”
Journal of Neuroscience, vol. 27, no. 8. Society for Neuroscience, pp.
2135–2144, 2007.
ista: Masugi Tokita M, Tarusawa E, Watanabe M, Molnár E, Fujimoto K, Shigemoto R.
2007. Number and density of AMPA receptors in individual synapses in the rat cerebellum
as revealed by SDS-digested freeze-fracture replica labeling. Journal of Neuroscience.
27(8), 2135–2144.
mla: Masugi Tokita, Miwako, et al. “Number and Density of AMPA Receptors in Individual
Synapses in the Rat Cerebellum as Revealed by SDS-Digested Freeze-Fracture Replica
Labeling.” Journal of Neuroscience, vol. 27, no. 8, Society for Neuroscience,
2007, pp. 2135–44, doi:10.1523/JNEUROSCI.2861-06.2007.
short: M. Masugi Tokita, E. Tarusawa, M. Watanabe, E. Molnár, K. Fujimoto, R. Shigemoto,
Journal of Neuroscience 27 (2007) 2135–2144.
date_created: 2018-12-11T11:58:58Z
date_published: 2007-02-21T00:00:00Z
date_updated: 2021-01-12T06:58:55Z
day: '21'
doi: 10.1523/JNEUROSCI.2861-06.2007
extern: 1
intvolume: ' 27'
issue: '8'
month: '02'
page: 2135 - 2144
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '4230'
quality_controlled: 0
status: public
title: Number and density of AMPA receptors in individual synapses in the rat cerebellum
as revealed by SDS-digested freeze-fracture replica labeling
type: journal_article
volume: 27
year: '2007'
...
---
_id: '2669'
abstract:
- lang: eng
text: The properties of the hyperpolarization-activated current (Ih) and its roles
in hippocampal network function evolve radically during development. Because Ih
is conducted by the hyperpolarization- activated cyclic nucleotide-gated (HCN)
cation channels, we tested the hypothesis that understanding the quantitative
developmental profiles of HCN1, HCN2, and HCN4 expression, and the isoform- and
age-specific progression of their subcellular distribution, should shed light
on the established modifications of the properties of Ih throughout development.
Combined quantitative in situ hybridization, regional western blots, and high-resolution,
dual-label immunocytochemistry revealed striking and novel information about the
expression and distribution of the HCN channel isoforms in the developing hippocampal
formation. In cornus ammon 1 (CA) pyramidal cell layer, a robust increase of HCN1
mRNA and protein expression occurred with age, with reciprocal reduction of HCN4
and relatively stable HCN2 levels. These distinct expression patterns raised the
contribution of HCN1 to the total HCN channel pool from 33% to 65% consonant with
acceleration and reduced cyclic adenosine mono phosphate (cAMP) sensitivity of
Ih in this region with age. In CA3, strong expression of HCN1 already neonatally
supports the recently established role of this conductance in neonatal, age-specific,
hippocampal oscillations (giant depolarizing potentials). Notably, HCN1 channels
were present and probably transported to dendritic compartments already on postnatal
day (P) 2, whereas HCN2 channel protein was not evident in dendrites for the first
2 weeks of life. HCN2 mRNA and protein expression remained fairly constant subsequent
to the first week of life in all hippocampal subfields examined, whereas HCN4
mRNA and protein expression declined after maximal neonatal expression, so that
the contribution of this isoform to the total HCN channel pool dropped from 43%
(CA1) and 34% (CA3) on P11 to 8% (CA1) and 19% (CA3) on P90. Interneuronal expression
of all HCN channel isoforms in stratum pyramidale was robust in parvalbumin-but
not in cholecystokinin-expressing populations and with a subunit-specific subcellular
distribution. Taken together, these data suggest that early in life, HCN4 may
contribute significantly to the functions of Ih in specific hippocampal regions.
In addition, these evolving, differential quantitative, and subcellular expression
patterns of the HCN channel isoforms support age-specific properties and functions
of Ih within the developing hippocampal formation.
author:
- first_name: Amy
full_name: Brewster, Amy L
last_name: Brewster
- first_name: Yuncai
full_name: Chen, Yuncai
last_name: Chen
- first_name: Roland
full_name: Bender, Roland A
last_name: Bender
- first_name: Amy
full_name: Yeh, Amy
last_name: Yeh
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Tallie
full_name: Baram, Tallie Z
last_name: Baram
citation:
ama: Brewster A, Chen Y, Bender R, Yeh A, Shigemoto R, Baram T. Quantitative analysis
and subcellular distribution of mRNA and protein expression of the hyperpolarization-activated
cyclic nucleotide-gated channels throughout development in rat hippocampus. Cerebral
Cortex. 2007;17(3):702-712. doi:10.1093/cercor/bhk021
apa: Brewster, A., Chen, Y., Bender, R., Yeh, A., Shigemoto, R., & Baram, T.
(2007). Quantitative analysis and subcellular distribution of mRNA and protein
expression of the hyperpolarization-activated cyclic nucleotide-gated channels
throughout development in rat hippocampus. Cerebral Cortex. Oxford University
Press. https://doi.org/10.1093/cercor/bhk021
chicago: Brewster, Amy, Yuncai Chen, Roland Bender, Amy Yeh, Ryuichi Shigemoto,
and Tallie Baram. “Quantitative Analysis and Subcellular Distribution of MRNA
and Protein Expression of the Hyperpolarization-Activated Cyclic Nucleotide-Gated
Channels throughout Development in Rat Hippocampus.” Cerebral Cortex. Oxford
University Press, 2007. https://doi.org/10.1093/cercor/bhk021.
ieee: A. Brewster, Y. Chen, R. Bender, A. Yeh, R. Shigemoto, and T. Baram, “Quantitative
analysis and subcellular distribution of mRNA and protein expression of the hyperpolarization-activated
cyclic nucleotide-gated channels throughout development in rat hippocampus,” Cerebral
Cortex, vol. 17, no. 3. Oxford University Press, pp. 702–712, 2007.
ista: Brewster A, Chen Y, Bender R, Yeh A, Shigemoto R, Baram T. 2007. Quantitative
analysis and subcellular distribution of mRNA and protein expression of the hyperpolarization-activated
cyclic nucleotide-gated channels throughout development in rat hippocampus. Cerebral
Cortex. 17(3), 702–712.
mla: Brewster, Amy, et al. “Quantitative Analysis and Subcellular Distribution of
MRNA and Protein Expression of the Hyperpolarization-Activated Cyclic Nucleotide-Gated
Channels throughout Development in Rat Hippocampus.” Cerebral Cortex, vol.
17, no. 3, Oxford University Press, 2007, pp. 702–12, doi:10.1093/cercor/bhk021.
short: A. Brewster, Y. Chen, R. Bender, A. Yeh, R. Shigemoto, T. Baram, Cerebral
Cortex 17 (2007) 702–712.
date_created: 2018-12-11T11:58:58Z
date_published: 2007-03-01T00:00:00Z
date_updated: 2021-01-12T06:58:56Z
day: '01'
doi: 10.1093/cercor/bhk021
extern: 1
intvolume: ' 17'
issue: '3'
month: '03'
page: 702 - 712
publication: Cerebral Cortex
publication_status: published
publisher: Oxford University Press
publist_id: '4229'
quality_controlled: 0
status: public
title: Quantitative analysis and subcellular distribution of mRNA and protein expression
of the hyperpolarization-activated cyclic nucleotide-gated channels throughout development
in rat hippocampus
type: journal_article
volume: 17
year: '2007'
...
---
_id: '2673'
abstract:
- lang: eng
text: Excitatory synaptic transmission is inhibited by G protein coupled receptors,
including the adenosine A1, GABAB, and metabotropic glutamate receptor 7. These
receptors are present in nerve terminals where they reduce the release of glutamate
through activating signaling pathways negatively coupled to Ca2+ channels and
adenylyl cyclase. However, it is not clear whether these receptors operate in
distinct subpopulations of nerve terminals or if they are co-expressed in the
same nerve terminals, despite the functional consequences that such distributions
may have on synaptic transmission. Applying Ca2+ imaging and immunocytochemistry,
we show that these three G protein coupled receptors coexist in a subpopulation
of cerebrocortical nerve terminals. The three receptors share an intracellular
signaling pathway through which their inhibitory responses are integrated and
coactivation of these receptors produced an integrated response. Indeed, this
response was highly variable, from a synergistic response at subthreshold agonist
concentrations to an occluded response at high agonist concentrations. The presence
of multiple receptors in a nerve terminal could be responsible for the physiological
effects of neurotransmitter spillover from neighboring synapses or alternatively,
the co-release of transmitters by the same nerve terminal.
author:
- first_name: Carolina
full_name: Ladera, Carolina
last_name: Ladera
- first_name: María
full_name: Godino, María D
last_name: Godino
- first_name: Ricardo
full_name: Martín, Ricardo J
last_name: Martín
- first_name: Rafael
full_name: Luján, Rafael
last_name: Luján
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Francisco
full_name: Ciruela, Francisco
last_name: Ciruela
- first_name: Magdalena
full_name: Torres, Magdalena
last_name: Torres
- first_name: José
full_name: Sánchez-Prieto, José
last_name: Sánchez Prieto
citation:
ama: Ladera C, Godino M, Martín R, et al. The coexistence of multiple receptors
in a single nerve terminal provides evidence for pre-synaptic integration. Journal
of Neurochemistry. 2007;103(6):2314-2326. doi:10.1111/j.1471-4159.2007.04964.x
apa: Ladera, C., Godino, M., Martín, R., Luján, R., Shigemoto, R., Ciruela, F.,
… Sánchez Prieto, J. (2007). The coexistence of multiple receptors in a single
nerve terminal provides evidence for pre-synaptic integration. Journal of Neurochemistry.
Wiley-Blackwell. https://doi.org/10.1111/j.1471-4159.2007.04964.x
chicago: Ladera, Carolina, María Godino, Ricardo Martín, Rafael Luján, Ryuichi Shigemoto,
Francisco Ciruela, Magdalena Torres, and José Sánchez Prieto. “ The Coexistence
of Multiple Receptors in a Single Nerve Terminal Provides Evidence for Pre-Synaptic
Integration.” Journal of Neurochemistry. Wiley-Blackwell, 2007. https://doi.org/10.1111/j.1471-4159.2007.04964.x.
ieee: C. Ladera et al., “ The coexistence of multiple receptors in a single
nerve terminal provides evidence for pre-synaptic integration,” Journal of
Neurochemistry, vol. 103, no. 6. Wiley-Blackwell, pp. 2314–2326, 2007.
ista: Ladera C, Godino M, Martín R, Luján R, Shigemoto R, Ciruela F, Torres M, Sánchez
Prieto J. 2007. The coexistence of multiple receptors in a single nerve terminal
provides evidence for pre-synaptic integration. Journal of Neurochemistry. 103(6),
2314–2326.
mla: Ladera, Carolina, et al. “ The Coexistence of Multiple Receptors in a Single
Nerve Terminal Provides Evidence for Pre-Synaptic Integration.” Journal of
Neurochemistry, vol. 103, no. 6, Wiley-Blackwell, 2007, pp. 2314–26, doi:10.1111/j.1471-4159.2007.04964.x.
short: C. Ladera, M. Godino, R. Martín, R. Luján, R. Shigemoto, F. Ciruela, M. Torres,
J. Sánchez Prieto, Journal of Neurochemistry 103 (2007) 2314–2326.
date_created: 2018-12-11T11:58:59Z
date_published: 2007-12-01T00:00:00Z
date_updated: 2021-01-12T06:58:58Z
day: '01'
doi: 10.1111/j.1471-4159.2007.04964.x
extern: 1
intvolume: ' 103'
issue: '6'
month: '12'
page: 2314 - 2326
publication: Journal of Neurochemistry
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4224'
quality_controlled: 0
status: public
title: ' The coexistence of multiple receptors in a single nerve terminal provides
evidence for pre-synaptic integration'
type: journal_article
volume: 103
year: '2007'
...
---
_id: '2671'
abstract:
- lang: eng
text: 'Increasing evidence supports roles for the current mediated by hyperpolarization-activated
cyclic nucleotide-gated (HCN) channels, I h, in hippocampal maturation and specifically
in the evolving changes of intrinsic properties as well as network responses of
hippocampal neurons. Here, we describe a novel developmental plasticity of HCN
channel expression in axonal and presynaptic compartments: HCN1 channels were
localized to axon terminals of the perforant path (the major hippocampal afferent
pathway) of immature rats, where they modulated synaptic efficacy. However, presynaptic
expression and functions of the channels disappeared with maturation. This was
a result of altered channel transport to the axons, because HCN1 mRNA and protein
levels in entorhinal cortex neurons, where the perforant path axons originate,
were stable through adulthood. Blocking action potential firing in vitro increased
presynaptic expression of HCN1 channels in the perforant path, suggesting that
network activity contributed to regulating this expression. These findings support
a novel developmentally regulated axonal transport of functional ion channels
and suggest a role for HCN1 channel-mediated presynaptic I h in hippocampal maturation.'
author:
- first_name: Roland
full_name: Bender, Roland A
last_name: Bender
- first_name: Timo
full_name: Kirschstein, Timo
last_name: Kirschstein
- first_name: Oliver
full_name: Kretz, Oliver
last_name: Kretz
- first_name: Amy
full_name: Brewster, Amy L
last_name: Brewster
- first_name: Cristina
full_name: Richichi, Cristina
last_name: Richichi
- first_name: Christiane
full_name: Rüschenschmidt, Christiane
last_name: Rüschenschmidt
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Heinz
full_name: Beck,Heinz
last_name: Beck
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Tallie
full_name: Baram, Tallie Z
last_name: Baram
citation:
ama: 'Bender R, Kirschstein T, Kretz O, et al. Localization of HCN1 channels to
presynaptic compartments: Novel plasticity that may contribute to hippocampal
maturation. Journal of Neuroscience. 2007;27(17):4697-4706. doi:10.1523/JNEUROSCI.4699-06.2007'
apa: 'Bender, R., Kirschstein, T., Kretz, O., Brewster, A., Richichi, C., Rüschenschmidt,
C., … Baram, T. (2007). Localization of HCN1 channels to presynaptic compartments:
Novel plasticity that may contribute to hippocampal maturation. Journal of
Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.4699-06.2007'
chicago: 'Bender, Roland, Timo Kirschstein, Oliver Kretz, Amy Brewster, Cristina
Richichi, Christiane Rüschenschmidt, Ryuichi Shigemoto, Heinz Beck, Michael Frotscher,
and Tallie Baram. “Localization of HCN1 Channels to Presynaptic Compartments:
Novel Plasticity That May Contribute to Hippocampal Maturation.” Journal of
Neuroscience. Society for Neuroscience, 2007. https://doi.org/10.1523/JNEUROSCI.4699-06.2007.'
ieee: 'R. Bender et al., “Localization of HCN1 channels to presynaptic compartments:
Novel plasticity that may contribute to hippocampal maturation,” Journal of
Neuroscience, vol. 27, no. 17. Society for Neuroscience, pp. 4697–4706, 2007.'
ista: 'Bender R, Kirschstein T, Kretz O, Brewster A, Richichi C, Rüschenschmidt
C, Shigemoto R, Beck H, Frotscher M, Baram T. 2007. Localization of HCN1 channels
to presynaptic compartments: Novel plasticity that may contribute to hippocampal
maturation. Journal of Neuroscience. 27(17), 4697–4706.'
mla: 'Bender, Roland, et al. “Localization of HCN1 Channels to Presynaptic Compartments:
Novel Plasticity That May Contribute to Hippocampal Maturation.” Journal of
Neuroscience, vol. 27, no. 17, Society for Neuroscience, 2007, pp. 4697–706,
doi:10.1523/JNEUROSCI.4699-06.2007.'
short: R. Bender, T. Kirschstein, O. Kretz, A. Brewster, C. Richichi, C. Rüschenschmidt,
R. Shigemoto, H. Beck, M. Frotscher, T. Baram, Journal of Neuroscience 27 (2007)
4697–4706.
date_created: 2018-12-11T11:58:59Z
date_published: 2007-04-25T00:00:00Z
date_updated: 2021-01-12T06:58:57Z
day: '25'
doi: 10.1523/JNEUROSCI.4699-06.2007
extern: 1
intvolume: ' 27'
issue: '17'
month: '04'
page: 4697 - 4706
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '4227'
quality_controlled: 0
status: public
title: 'Localization of HCN1 channels to presynaptic compartments: Novel plasticity
that may contribute to hippocampal maturation'
type: journal_article
volume: 27
year: '2007'
...
---
_id: '2672'
abstract:
- lang: eng
text: Hyperpolarization-activated cyclic nucleotide-modulated (HCN) "pacemaker"
channel subunits are integral membrane proteins that assemble as tetramers to
form channels in cardiac conduction tissue and nerve cells. Previous studies have
suggested that the HCN2 and HCN4 channel isoforms physically interact when overexpressed
in mammalian cells, but whether they are able to co-assemble and form functional
channels remains unclear. The extent to which co-assembly occurs over self-assembly
and whether HCN2-HCN4 heteromeric channels are formed in native tissue are not
known. In this study, we show co-assembly of HCN2 and HCN4 in live Chinese hamster
ovary cells using bioluminescence resonance energy transfer (BRET2), a novel approach
for studying tetramerization of ion channel subunits. Together with results from
electrophysiological and imaging approaches, the BRET2 data show that HCN2 and
HCN4 subunits self-assemble and co-assemble with equal preference. We also demonstrate
colocalization of HCN2 and HCN4 and a positive correlation of their intensities
in the embryonic mouse heart using immunohistochemistry, as well as physical interactions
between these isoforms in the rat thalamus by coimmunoprecipitation. Together,
these data support the formation of HCN2-HCN4 heteromeric channels in native tissue.
author:
- first_name: Gina
full_name: Whitaker, Gina M
last_name: Whitaker
- first_name: Damiano
full_name: Angoli, Damiano
last_name: Angoli
- first_name: Hamed
full_name: Nazzari, Hamed
last_name: Nazzari
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Eric
full_name: Accili, Eric A
last_name: Accili
citation:
ama: Whitaker G, Angoli D, Nazzari H, Shigemoto R, Accili E. HCN2 and HCN4 isoforms
self-assemble and co-assemble with equal preference to form functional pacemaker
channels. Journal of Biological Chemistry. 2007;282(31):22900-22909. doi:10.1074/jbc.M610978200
apa: Whitaker, G., Angoli, D., Nazzari, H., Shigemoto, R., & Accili, E. (2007).
HCN2 and HCN4 isoforms self-assemble and co-assemble with equal preference to
form functional pacemaker channels. Journal of Biological Chemistry. American
Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M610978200
chicago: Whitaker, Gina, Damiano Angoli, Hamed Nazzari, Ryuichi Shigemoto, and Eric
Accili. “HCN2 and HCN4 Isoforms Self-Assemble and Co-Assemble with Equal Preference
to Form Functional Pacemaker Channels.” Journal of Biological Chemistry.
American Society for Biochemistry and Molecular Biology, 2007. https://doi.org/10.1074/jbc.M610978200.
ieee: G. Whitaker, D. Angoli, H. Nazzari, R. Shigemoto, and E. Accili, “HCN2 and
HCN4 isoforms self-assemble and co-assemble with equal preference to form functional
pacemaker channels,” Journal of Biological Chemistry, vol. 282, no. 31.
American Society for Biochemistry and Molecular Biology, pp. 22900–22909, 2007.
ista: Whitaker G, Angoli D, Nazzari H, Shigemoto R, Accili E. 2007. HCN2 and HCN4
isoforms self-assemble and co-assemble with equal preference to form functional
pacemaker channels. Journal of Biological Chemistry. 282(31), 22900–22909.
mla: Whitaker, Gina, et al. “HCN2 and HCN4 Isoforms Self-Assemble and Co-Assemble
with Equal Preference to Form Functional Pacemaker Channels.” Journal of Biological
Chemistry, vol. 282, no. 31, American Society for Biochemistry and Molecular
Biology, 2007, pp. 22900–09, doi:10.1074/jbc.M610978200.
short: G. Whitaker, D. Angoli, H. Nazzari, R. Shigemoto, E. Accili, Journal of Biological
Chemistry 282 (2007) 22900–22909.
date_created: 2018-12-11T11:58:59Z
date_published: 2007-08-03T00:00:00Z
date_updated: 2021-01-12T06:58:58Z
day: '03'
doi: 10.1074/jbc.M610978200
extern: 1
intvolume: ' 282'
issue: '31'
month: '08'
page: 22900 - 22909
publication: Journal of Biological Chemistry
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '4225'
quality_controlled: 0
status: public
title: HCN2 and HCN4 isoforms self-assemble and co-assemble with equal preference
to form functional pacemaker channels
type: journal_article
volume: 282
year: '2007'
...
---
_id: '2670'
abstract:
- lang: eng
text: Glutamate and GABA are the main transmitters in the central nervous system
and their effects are mediated by ionotropic and metabotropic receptors. Immunogold
electron microscopy has revealed the quantitative localization of these receptors
at 20-30 nm resolution. SDS-digested freeze-fracture replica labeling (SDS-FRL),
a newly developed immunogold method, provides an accurate estimate of molecule
numbers. Here, we summarize the recent advances in quantitative receptor localization,
including use of SDS-FRL analyses to determine numbers of AMPA-type glutamate
receptors in the cerebellum. The two-dimensional view and high sensitivity of
SDS-FRL have revealed small, irregularly shaped AMPA receptor clusters within
cerebellar synapses.
author:
- first_name: Miwako
full_name: Masugi-Tokita, Miwako
last_name: Masugi Tokita
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Masugi Tokita M, Shigemoto R. High-resolution quantitative visualization of
glutamate and GABA receptors at central synapses. Current Opinion in Neurobiology.
2007;17(3):387-393. doi:10.1016/j.conb.2007.04.012
apa: Masugi Tokita, M., & Shigemoto, R. (2007). High-resolution quantitative
visualization of glutamate and GABA receptors at central synapses. Current
Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2007.04.012
chicago: Masugi Tokita, Miwako, and Ryuichi Shigemoto. “High-Resolution Quantitative
Visualization of Glutamate and GABA Receptors at Central Synapses.” Current
Opinion in Neurobiology. Elsevier, 2007. https://doi.org/10.1016/j.conb.2007.04.012.
ieee: M. Masugi Tokita and R. Shigemoto, “High-resolution quantitative visualization
of glutamate and GABA receptors at central synapses,” Current Opinion in Neurobiology,
vol. 17, no. 3. Elsevier, pp. 387–393, 2007.
ista: Masugi Tokita M, Shigemoto R. 2007. High-resolution quantitative visualization
of glutamate and GABA receptors at central synapses. Current Opinion in Neurobiology.
17(3), 387–393.
mla: Masugi Tokita, Miwako, and Ryuichi Shigemoto. “High-Resolution Quantitative
Visualization of Glutamate and GABA Receptors at Central Synapses.” Current
Opinion in Neurobiology, vol. 17, no. 3, Elsevier, 2007, pp. 387–93, doi:10.1016/j.conb.2007.04.012.
short: M. Masugi Tokita, R. Shigemoto, Current Opinion in Neurobiology 17 (2007)
387–393.
date_created: 2018-12-11T11:58:58Z
date_published: 2007-06-01T00:00:00Z
date_updated: 2020-07-14T12:45:44Z
day: '01'
doi: 10.1016/j.conb.2007.04.012
extern: 1
intvolume: ' 17'
issue: '3'
month: '06'
page: 387 - 393
publication: Current Opinion in Neurobiology
publication_status: published
publisher: Elsevier
publist_id: '4226'
quality_controlled: 0
status: public
title: High-resolution quantitative visualization of glutamate and GABA receptors
at central synapses
type: review
volume: 17
year: '2007'
...
---
_id: '2705'
alternative_title:
- Proceedings of Symposia in Pure Mathematics
author:
- first_name: László
full_name: László Erdös
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
citation:
ama: 'Erdös L. Recent developments in quantum mechanics with magnetic fields. In:
Gesztesy F, Deift P, Galvez P, Perry P, Schlag W, eds. Spectral Theory and
Mathematical Physics: A Festschrift in Honor of Barry Simon’s 60th Birthday .
Vol 76. American Mathematical Society; 2007:401-428.'
apa: 'Erdös, L. (2007). Recent developments in quantum mechanics with magnetic fields.
In F. Gesztesy, P. Deift, P. Galvez, P. Perry, & W. Schlag (Eds.), Spectral
Theory and Mathematical Physics: a Festschrift in Honor of Barry Simon’s 60th
Birthday (Vol. 76, pp. 401–428). American Mathematical Society.'
chicago: 'Erdös, László. “Recent Developments in Quantum Mechanics with Magnetic
Fields.” In Spectral Theory and Mathematical Physics: A Festschrift in Honor
of Barry Simon’s 60th Birthday , edited by Fritz Gesztesy, Percy Deift, Percy
Galvez, Peter Perry, and Wilhelm Schlag, 76:401–28. American Mathematical Society,
2007.'
ieee: 'L. Erdös, “Recent developments in quantum mechanics with magnetic fields,”
in Spectral Theory and Mathematical Physics: a Festschrift in Honor of Barry
Simon’s 60th Birthday , vol. 76, F. Gesztesy, P. Deift, P. Galvez, P. Perry,
and W. Schlag, Eds. American Mathematical Society, 2007, pp. 401–428.'
ista: 'Erdös L. 2007.Recent developments in quantum mechanics with magnetic fields.
In: Spectral Theory and Mathematical Physics: a Festschrift in Honor of Barry
Simon’s 60th Birthday . Proceedings of Symposia in Pure Mathematics, vol. 76,
401–428.'
mla: 'Erdös, László. “Recent Developments in Quantum Mechanics with Magnetic Fields.”
Spectral Theory and Mathematical Physics: A Festschrift in Honor of Barry Simon’s
60th Birthday , edited by Fritz Gesztesy et al., vol. 76, American Mathematical
Society, 2007, pp. 401–28.'
short: 'L. Erdös, in:, F. Gesztesy, P. Deift, P. Galvez, P. Perry, W. Schlag (Eds.),
Spectral Theory and Mathematical Physics: A Festschrift in Honor of Barry Simon’s
60th Birthday , American Mathematical Society, 2007, pp. 401–428.'
date_created: 2018-12-11T11:59:10Z
date_published: 2007-03-30T00:00:00Z
date_updated: 2021-01-12T06:59:10Z
day: '30'
editor:
- first_name: Fritz
full_name: Gesztesy, Fritz
last_name: Gesztesy
- first_name: Percy
full_name: Deift, Percy
last_name: Deift
- first_name: Percy
full_name: Galvez, Percy
last_name: Galvez
- first_name: Peter
full_name: Perry, Peter
last_name: Perry
- first_name: Wilhelm
full_name: Schlag, Wilhelm
last_name: Schlag
extern: 1
intvolume: ' 76'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math-ph/0510055v2
month: '03'
oa: 1
page: 401 - 428
publication: 'Spectral Theory and Mathematical Physics: a Festschrift in Honor of
Barry Simon''s 60th Birthday '
publication_status: published
publisher: American Mathematical Society
publist_id: '4191'
quality_controlled: 0
status: public
title: Recent developments in quantum mechanics with magnetic fields
type: book_chapter
volume: 76
year: '2007'
...
---
_id: '2750'
abstract:
- lang: eng
text: We consider random Schrödinger equations on ℝd for d ≥ 3 with a homogeneous
Anderson-Poisson type random potential. Denote by λ the coupling constant and
ψt the solution with initial data ψ0. The space and time variables scale as χ
≃λ-2-κ/2, t ≃λ-2-κ with 0 < kappa; < kappa;0(d). We prove that, in the limit
λ → 0, the expectation of the Wigner distribution of ψt converges weakly to the
solution of a heat equation in the space variable x for arbitrary L2 initial data.
The proof is based on a rigorous analysis of Feynman diagrams. In the companion
paper [10] the analysis of the non-repetition diagrams was presented. In this
paper we complete the proof by estimating the recollision diagrams and showing
that the main terms, i.e. the ladder diagrams with renormalized propagator, converge
to the heat equation.
author:
- first_name: László
full_name: László Erdös
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Manfred
full_name: Salmhofer, Manfred
last_name: Salmhofer
- first_name: Horng
full_name: Yau, Horng-Tzer
last_name: Yau
citation:
ama: Erdös L, Salmhofer M, Yau H. Quantum diffusion of the random Schrödinger evolution
in the scaling limit II. The recollision diagrams. Communications in Mathematical
Physics. 2007;271(1):1-53. doi:10.1007/s00220-006-0158-2
apa: Erdös, L., Salmhofer, M., & Yau, H. (2007). Quantum diffusion of the random
Schrödinger evolution in the scaling limit II. The recollision diagrams. Communications
in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-006-0158-2
chicago: Erdös, László, Manfred Salmhofer, and Horng Yau. “Quantum Diffusion of
the Random Schrödinger Evolution in the Scaling Limit II. The Recollision Diagrams.”
Communications in Mathematical Physics. Springer, 2007. https://doi.org/10.1007/s00220-006-0158-2.
ieee: L. Erdös, M. Salmhofer, and H. Yau, “Quantum diffusion of the random Schrödinger
evolution in the scaling limit II. The recollision diagrams,” Communications
in Mathematical Physics, vol. 271, no. 1. Springer, pp. 1–53, 2007.
ista: Erdös L, Salmhofer M, Yau H. 2007. Quantum diffusion of the random Schrödinger
evolution in the scaling limit II. The recollision diagrams. Communications in
Mathematical Physics. 271(1), 1–53.
mla: Erdös, László, et al. “Quantum Diffusion of the Random Schrödinger Evolution
in the Scaling Limit II. The Recollision Diagrams.” Communications in Mathematical
Physics, vol. 271, no. 1, Springer, 2007, pp. 1–53, doi:10.1007/s00220-006-0158-2.
short: L. Erdös, M. Salmhofer, H. Yau, Communications in Mathematical Physics 271
(2007) 1–53.
date_created: 2018-12-11T11:59:24Z
date_published: 2007-04-01T00:00:00Z
date_updated: 2021-01-12T06:59:27Z
day: '01'
doi: 10.1007/s00220-006-0158-2
extern: 1
intvolume: ' 271'
issue: '1'
month: '04'
page: 1 - 53
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4142'
quality_controlled: 0
status: public
title: Quantum diffusion of the random Schrödinger evolution in the scaling limit
II. The recollision diagrams
type: journal_article
volume: 271
year: '2007'
...
---
_id: '2751'
abstract:
- lang: eng
text: We consider random Schrödinger equations on ℤd for d ≥ 3 with identically
distributed random potential. Denote by λ the coupling constant and ψ t the solution
with initial data ψ 0. The space and time variables scale as x ∼ λ -2-κ/2,t ∼
λ-2-κ with 0 < κ < κ0(d). We prove that, in the limit λ → 0, the expectation
of the Wigner distribution of ψ t converges weakly to a solution of a heat equation
in the space variable x for arbitrary L 2 initial data. The diffusion coefficient
is uniquely determined by the kinetic energy associated to the momentum υ. This
work is an extension to the lattice case of our previous result in the continuum
[8,9]. Due to the non-convexity of the level surfaces of the dispersion relation,
the estimates of several Feynman graphs are more involved.
author:
- first_name: László
full_name: László Erdös
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Manfred
full_name: Salmhofer, Manfred
last_name: Salmhofer
- first_name: Horng
full_name: Yau, Horng-Tzer
last_name: Yau
citation:
ama: Erdös L, Salmhofer M, Yau H. Quantum diffusion for the Anderson model in the
scaling limit. Annales Henri Poincare. 2007;8(4):621-685. doi:10.1007/s00023-006-0318-0
apa: Erdös, L., Salmhofer, M., & Yau, H. (2007). Quantum diffusion for the Anderson
model in the scaling limit. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-006-0318-0
chicago: Erdös, László, Manfred Salmhofer, and Horng Yau. “Quantum Diffusion for
the Anderson Model in the Scaling Limit.” Annales Henri Poincare. Birkhäuser,
2007. https://doi.org/10.1007/s00023-006-0318-0.
ieee: L. Erdös, M. Salmhofer, and H. Yau, “Quantum diffusion for the Anderson model
in the scaling limit,” Annales Henri Poincare, vol. 8, no. 4. Birkhäuser,
pp. 621–685, 2007.
ista: Erdös L, Salmhofer M, Yau H. 2007. Quantum diffusion for the Anderson model
in the scaling limit. Annales Henri Poincare. 8(4), 621–685.
mla: Erdös, László, et al. “Quantum Diffusion for the Anderson Model in the Scaling
Limit.” Annales Henri Poincare, vol. 8, no. 4, Birkhäuser, 2007, pp. 621–85,
doi:10.1007/s00023-006-0318-0.
short: L. Erdös, M. Salmhofer, H. Yau, Annales Henri Poincare 8 (2007) 621–685.
date_created: 2018-12-11T11:59:24Z
date_published: 2007-07-01T00:00:00Z
date_updated: 2021-01-12T06:59:27Z
day: '01'
doi: 10.1007/s00023-006-0318-0
extern: 1
intvolume: ' 8'
issue: '4'
month: '07'
page: 621 - 685
publication: Annales Henri Poincare
publication_status: published
publisher: Birkhäuser
publist_id: '4141'
quality_controlled: 0
status: public
title: Quantum diffusion for the Anderson model in the scaling limit
type: journal_article
volume: 8
year: '2007'
...
---
_id: '2752'
abstract:
- lang: eng
text: We prove L p -bounds on the Fourier transform of measures μ supported on two
dimensional surfaces. Our method allows to consider surfaces whose Gauss curvature
vanishes on a one-dimensional submanifold. Under a certain non-degeneracy condition,
we prove that μ ∧ ε L 4+β, β > 0, and we give a logarithmically divergent bound
on the L 4-norm. We use this latter bound to estimate almost singular integrals
involving the dispersion relation, e(p)= ∑13 [1-\cos p_j]} , of the discrete Laplace
operator on the cubic lattice. We briefly explain our motivation for this bound
originating in the theory of random Schrödinger operators.
author:
- first_name: László
full_name: László Erdös
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Manfred
full_name: Salmhofer, Manfred
last_name: Salmhofer
citation:
ama: Erdös L, Salmhofer M. Decay of the Fourier transform of surfaces with vanishing
curvature. Mathematische Zeitschrift. 2007;257(2):261-294. doi:10.1007/s00209-007-0125-4
apa: Erdös, L., & Salmhofer, M. (2007). Decay of the Fourier transform of surfaces
with vanishing curvature. Mathematische Zeitschrift. Springer. https://doi.org/10.1007/s00209-007-0125-4
chicago: Erdös, László, and Manfred Salmhofer. “Decay of the Fourier Transform of
Surfaces with Vanishing Curvature.” Mathematische Zeitschrift. Springer,
2007. https://doi.org/10.1007/s00209-007-0125-4.
ieee: L. Erdös and M. Salmhofer, “Decay of the Fourier transform of surfaces with
vanishing curvature,” Mathematische Zeitschrift, vol. 257, no. 2. Springer,
pp. 261–294, 2007.
ista: Erdös L, Salmhofer M. 2007. Decay of the Fourier transform of surfaces with
vanishing curvature. Mathematische Zeitschrift. 257(2), 261–294.
mla: Erdös, László, and Manfred Salmhofer. “Decay of the Fourier Transform of Surfaces
with Vanishing Curvature.” Mathematische Zeitschrift, vol. 257, no. 2,
Springer, 2007, pp. 261–94, doi:10.1007/s00209-007-0125-4.
short: L. Erdös, M. Salmhofer, Mathematische Zeitschrift 257 (2007) 261–294.
date_created: 2018-12-11T11:59:25Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T06:59:28Z
day: '01'
doi: 10.1007/s00209-007-0125-4
extern: 1
intvolume: ' 257'
issue: '2'
month: '01'
page: 261 - 294
publication: Mathematische Zeitschrift
publication_status: published
publisher: Springer
publist_id: '4140'
quality_controlled: 0
status: public
title: Decay of the Fourier transform of surfaces with vanishing curvature
type: journal_article
volume: 257
year: '2007'
...
---
_id: '2749'
abstract:
- lang: eng
text: 'We prove rigorously that the one-particle density matrix of three dimensional
interacting Bose systems with a short-scale repulsive pair interaction converges
to the solution of the cubic non-linear Schrödinger equation in a suitable scaling
limit. The result is extended to k-particle density matrices for all positive
integer k. '
author:
- first_name: László
full_name: László Erdös
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
- first_name: Horng
full_name: Yau, Horng-Tzer
last_name: Yau
citation:
ama: Erdös L, Schlein B, Yau H. Derivation of the cubic non linear Schrödinger equation
from quantum dynamics of many body systems. Inventiones Mathematicae. 2007;167(3):515-614.
doi:10.1007/s00222-006-0022-1
apa: Erdös, L., Schlein, B., & Yau, H. (2007). Derivation of the cubic non linear
Schrödinger equation from quantum dynamics of many body systems. Inventiones
Mathematicae. Springer. https://doi.org/10.1007/s00222-006-0022-1
chicago: Erdös, László, Benjamin Schlein, and Horng Yau. “Derivation of the Cubic
Non Linear Schrödinger Equation from Quantum Dynamics of Many Body Systems.” Inventiones
Mathematicae. Springer, 2007. https://doi.org/10.1007/s00222-006-0022-1.
ieee: L. Erdös, B. Schlein, and H. Yau, “Derivation of the cubic non linear Schrödinger
equation from quantum dynamics of many body systems,” Inventiones Mathematicae,
vol. 167, no. 3. Springer, pp. 515–614, 2007.
ista: Erdös L, Schlein B, Yau H. 2007. Derivation of the cubic non linear Schrödinger
equation from quantum dynamics of many body systems. Inventiones Mathematicae.
167(3), 515–614.
mla: Erdös, László, et al. “Derivation of the Cubic Non Linear Schrödinger Equation
from Quantum Dynamics of Many Body Systems.” Inventiones Mathematicae,
vol. 167, no. 3, Springer, 2007, pp. 515–614, doi:10.1007/s00222-006-0022-1.
short: L. Erdös, B. Schlein, H. Yau, Inventiones Mathematicae 167 (2007) 515–614.
date_created: 2018-12-11T11:59:24Z
date_published: 2007-03-01T00:00:00Z
date_updated: 2019-04-26T07:22:19Z
day: '01'
doi: 10.1007/s00222-006-0022-1
extern: 1
intvolume: ' 167'
issue: '3'
month: '03'
page: 515 - 614
publication: Inventiones Mathematicae
publication_status: published
publisher: Springer
publist_id: '4143'
quality_controlled: 0
status: public
title: Derivation of the cubic non linear Schrödinger equation from quantum dynamics
of many body systems
type: review
volume: 167
year: '2007'
...
---
_id: '2748'
abstract:
- lang: eng
text: The time-dependent Gross-Pitaevskii equation describes the dynamics of initially
trapped Bose-Einstein condensates. We present a rigorous proof of this fact starting
from a many-body bosonic Schrödinger equation with a short-scale repulsive interaction
in the dilute limit. Our proof shows the persistence of an explicit short-scale
correlation structure in the condensate.
author:
- first_name: László
full_name: László Erdös
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
- first_name: Horng
full_name: Yau, Horng-Tzer
last_name: Yau
citation:
ama: Erdös L, Schlein B, Yau H. Rigorous derivation of the Gross-Pitaevskii equation.
Physical Review Letters. 2007;98(4). doi:10.1103/PhysRevLett.98.040404
apa: Erdös, L., Schlein, B., & Yau, H. (2007). Rigorous derivation of the Gross-Pitaevskii
equation. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.98.040404
chicago: Erdös, László, Benjamin Schlein, and Horng Yau. “Rigorous Derivation of
the Gross-Pitaevskii Equation.” Physical Review Letters. American Physical
Society, 2007. https://doi.org/10.1103/PhysRevLett.98.040404.
ieee: L. Erdös, B. Schlein, and H. Yau, “Rigorous derivation of the Gross-Pitaevskii
equation,” Physical Review Letters, vol. 98, no. 4. American Physical Society,
2007.
ista: Erdös L, Schlein B, Yau H. 2007. Rigorous derivation of the Gross-Pitaevskii
equation. Physical Review Letters. 98(4).
mla: Erdös, László, et al. “Rigorous Derivation of the Gross-Pitaevskii Equation.”
Physical Review Letters, vol. 98, no. 4, American Physical Society, 2007,
doi:10.1103/PhysRevLett.98.040404.
short: L. Erdös, B. Schlein, H. Yau, Physical Review Letters 98 (2007).
date_created: 2018-12-11T11:59:23Z
date_published: 2007-01-26T00:00:00Z
date_updated: 2021-01-12T06:59:26Z
day: '26'
doi: 10.1103/PhysRevLett.98.040404
extern: 1
intvolume: ' 98'
issue: '4'
month: '01'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '4144'
quality_controlled: 0
status: public
title: Rigorous derivation of the Gross-Pitaevskii equation
type: journal_article
volume: 98
year: '2007'
...
---
_id: '2793'
abstract:
- lang: eng
text: Pipe flow is a prominent example among the shear flows that undergo transition
to turbulence without mediation by a linear instability of the laminar profile.
Experiments on pipe flow, as well as plane Couette and plane Poiseuille flow,
show that triggering turbulence depends sensitively on initial conditions, that
between the laminar and the turbulent states there exists no intermediate state
with simple spatial or temporal characteristics, and that turbulence is not persistent,
i.e., it can decay again, if the observation time is long enough. All these features
can consistently be explained on the assumption that the turbulent state corresponds
to a chaotic saddle in state space. The goal of this review is to explain this
concept, summarize the numerical and experimental evidence for pipe flow, and
outline the consequences for related flows.
author:
- first_name: Bruno
full_name: Eckhardt, Bruno
last_name: Eckhardt
- first_name: Tobias
full_name: Schneider, Tobias M
last_name: Schneider
- first_name: Björn
full_name: Björn Hof
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Jerry
full_name: Westerweel, Jerry
last_name: Westerweel
citation:
ama: Eckhardt B, Schneider T, Hof B, Westerweel J. Turbulence transition in pipe
flow. Annual Review of Fluid Mechanics. 2007;39:447-468. doi:10.1146/annurev.fluid.39.050905.110308
apa: Eckhardt, B., Schneider, T., Hof, B., & Westerweel, J. (2007). Turbulence
transition in pipe flow. Annual Review of Fluid Mechanics. Annual Reviews.
https://doi.org/10.1146/annurev.fluid.39.050905.110308
chicago: Eckhardt, Bruno, Tobias Schneider, Björn Hof, and Jerry Westerweel. “Turbulence
Transition in Pipe Flow.” Annual Review of Fluid Mechanics. Annual Reviews,
2007. https://doi.org/10.1146/annurev.fluid.39.050905.110308.
ieee: B. Eckhardt, T. Schneider, B. Hof, and J. Westerweel, “Turbulence transition
in pipe flow,” Annual Review of Fluid Mechanics, vol. 39. Annual Reviews,
pp. 447–468, 2007.
ista: Eckhardt B, Schneider T, Hof B, Westerweel J. 2007. Turbulence transition
in pipe flow. Annual Review of Fluid Mechanics. 39, 447–468.
mla: Eckhardt, Bruno, et al. “Turbulence Transition in Pipe Flow.” Annual Review
of Fluid Mechanics, vol. 39, Annual Reviews, 2007, pp. 447–68, doi:10.1146/annurev.fluid.39.050905.110308.
short: B. Eckhardt, T. Schneider, B. Hof, J. Westerweel, Annual Review of Fluid
Mechanics 39 (2007) 447–468.
date_created: 2018-12-11T11:59:38Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2019-04-26T07:22:20Z
day: '01'
doi: 10.1146/annurev.fluid.39.050905.110308
extern: 1
intvolume: ' 39'
month: '01'
page: 447 - 468
publication: Annual Review of Fluid Mechanics
publication_status: published
publisher: Annual Reviews
publist_id: '4096'
quality_controlled: 0
status: public
title: Turbulence transition in pipe flow
type: review
volume: 39
year: '2007'
...
---
_id: '2794'
alternative_title:
- Springer Proceedings in Physics
author:
- first_name: Björn
full_name: Björn Hof
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Wilco
full_name: Tax, Wilco
last_name: Tax
- first_name: Jerry
full_name: Westerweel, Jerry
last_name: Westerweel
citation:
ama: 'Hof B, Tax W, Westerweel J. Lifetime of turbulence in pipe flow. In: Vol 117.
Springer; 2007:556-558. doi:10.1007/978-3-540-72604-3_177'
apa: 'Hof, B., Tax, W., & Westerweel, J. (2007). Lifetime of turbulence in pipe
flow (Vol. 117, pp. 556–558). Presented at the EETC11: European Turbulence Conference,
Springer. https://doi.org/10.1007/978-3-540-72604-3_177'
chicago: Hof, Björn, Wilco Tax, and Jerry Westerweel. “Lifetime of Turbulence in
Pipe Flow,” 117:556–58. Springer, 2007. https://doi.org/10.1007/978-3-540-72604-3_177.
ieee: 'B. Hof, W. Tax, and J. Westerweel, “Lifetime of turbulence in pipe flow,”
presented at the EETC11: European Turbulence Conference, 2007, vol. 117, pp. 556–558.'
ista: 'Hof B, Tax W, Westerweel J. 2007. Lifetime of turbulence in pipe flow. EETC11:
European Turbulence Conference, Springer Proceedings in Physics, vol. 117, 556–558.'
mla: Hof, Björn, et al. Lifetime of Turbulence in Pipe Flow. Vol. 117, Springer,
2007, pp. 556–58, doi:10.1007/978-3-540-72604-3_177.
short: B. Hof, W. Tax, J. Westerweel, in:, Springer, 2007, pp. 556–558.
conference:
name: 'EETC11: European Turbulence Conference'
date_created: 2018-12-11T11:59:38Z
date_published: 2007-06-01T00:00:00Z
date_updated: 2021-01-12T06:59:45Z
day: '01'
doi: 10.1007/978-3-540-72604-3_177
extern: 1
intvolume: ' 117'
month: '06'
page: 556 - 558
publication_status: published
publisher: Springer
publist_id: '4095'
quality_controlled: 0
status: public
title: Lifetime of turbulence in pipe flow
type: conference
volume: 117
year: '2007'
...
---
_id: '2893'
abstract:
- lang: eng
text: 'Summary: Regulatory CD4+ T cells, enriched in the CD25 pool of healthy individuals,
mediate natural tolerance and prevent autoimmune diseases. Despite their fundamental
and potential clinical significance, regulatory T (TR) cells have not yet been
incorporated in a coherent theory of the immune system. This article reviews experimental
evidence and theoretical arguments supporting a model of TR cell dynamics, uncovering
some of its most relevant biological implications. According to this model, the
persistence and expansion of TR cell populations depend strictly on specific interactions
they make with antigen-presenting cells (APCs) and conventional effector T (TE)
cells. This three-partner crossregulation imposes that TR cells feed on the specific
autoimmune activities they suppress, with implications ranging from their interactions
with other cells to their repertoire selection in the periphery and in the thymus,
and to the relationship between these cells and the innate immune system. These
implications stem from the basic prediction that the peripheral dynamics sort
the CD4+ T-cell repertoire into two subsets: a less diverse set of small clones
of autoreactive effector and regulatory cells that regulate each other’s growth,
and a more diverse set of barely autoreactive TE cell clones, whose expansion
is limited only by APC availability. It is argued that such partitioning of the
repertoire sets the ground for self–non-self discrimination. '
author:
- first_name: Jorge
full_name: Carneiro, Jorge
last_name: Carneiro
- first_name: Kalet
full_name: Leon, Kalet
last_name: Leon
- first_name: Íris
full_name: Caramalho, Íris
last_name: Caramalho
- first_name: Carline
full_name: Van Den Dool, Carline
last_name: Van Den Dool
- first_name: Rui
full_name: Gardner, Rui
last_name: Gardner
- first_name: Vanessa
full_name: Oliveira, Vanessa
last_name: Oliveira
- first_name: Marie
full_name: Bergman, Marie L
last_name: Bergman
- first_name: Nuno
full_name: Sepúlveda, Nuno
last_name: Sepúlveda
- first_name: Tiago
full_name: Tiago Paixao
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Jose
full_name: Faro, Jose
last_name: Faro
- first_name: Jocelyne
full_name: Demengeot, Jocelyne
last_name: Demengeot
citation:
ama: Carneiro J, Leon K, Caramalho Í, et al. When three is not a crowd a Crossregulation
Model of the dynamics and repertoire selection of regulatory CD4 T cells. Immunological
Reviews. 2007;216(1):48-68. doi:10.1111/j.1600-065X.2007.00487.x
apa: Carneiro, J., Leon, K., Caramalho, Í., Van Den Dool, C., Gardner, R., Oliveira,
V., … Demengeot, J. (2007). When three is not a crowd a Crossregulation Model
of the dynamics and repertoire selection of regulatory CD4 T cells. Immunological
Reviews. Wiley-Blackwell. https://doi.org/10.1111/j.1600-065X.2007.00487.x
chicago: Carneiro, Jorge, Kalet Leon, Íris Caramalho, Carline Van Den Dool, Rui
Gardner, Vanessa Oliveira, Marie Bergman, et al. “When Three Is Not a Crowd a
Crossregulation Model of the Dynamics and Repertoire Selection of Regulatory CD4
T Cells.” Immunological Reviews. Wiley-Blackwell, 2007. https://doi.org/10.1111/j.1600-065X.2007.00487.x.
ieee: J. Carneiro et al., “When three is not a crowd a Crossregulation Model
of the dynamics and repertoire selection of regulatory CD4 T cells,” Immunological
Reviews, vol. 216, no. 1. Wiley-Blackwell, pp. 48–68, 2007.
ista: Carneiro J, Leon K, Caramalho Í, Van Den Dool C, Gardner R, Oliveira V, Bergman
M, Sepúlveda N, Paixao T, Faro J, Demengeot J. 2007. When three is not a crowd
a Crossregulation Model of the dynamics and repertoire selection of regulatory
CD4 T cells. Immunological Reviews. 216(1), 48–68.
mla: Carneiro, Jorge, et al. “When Three Is Not a Crowd a Crossregulation Model
of the Dynamics and Repertoire Selection of Regulatory CD4 T Cells.” Immunological
Reviews, vol. 216, no. 1, Wiley-Blackwell, 2007, pp. 48–68, doi:10.1111/j.1600-065X.2007.00487.x.
short: J. Carneiro, K. Leon, Í. Caramalho, C. Van Den Dool, R. Gardner, V. Oliveira,
M. Bergman, N. Sepúlveda, T. Paixao, J. Faro, J. Demengeot, Immunological Reviews
216 (2007) 48–68.
date_created: 2018-12-11T12:00:11Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:31Z
day: '01'
doi: 10.1111/j.1600-065X.2007.00487.x
extern: 1
intvolume: ' 216'
issue: '1'
month: '01'
page: 48 - 68
publication: Immunological Reviews
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3865'
quality_controlled: 0
status: public
title: When three is not a crowd a Crossregulation Model of the dynamics and repertoire
selection of regulatory CD4 T cells
type: journal_article
volume: 216
year: '2007'
...
---
_id: '2896'
abstract:
- lang: eng
text: Gene expression from both parental alleles is beneficial by masking the effects
of deleterious recessive mutations and by reducing the noise in gene expression
in diploid organisms. However, a class of genes are expressed preferentially or
strictly from a single allele. The selective advantage of avoiding biallelic expression
is clear for allelic-excluded antigen receptor and odorant receptor genes, genes
undergoing X-chromosome inactivation in females and parental genomic imprinted
genes. In contrast, there is no clear biological rationale for the predominant
and stochastic monoallelic expression of cytokine genes in the immune system,
and the underlying mechanism is elusive and controversial. A clarification of
the mechanism of predominant monoallelic expression would be instrumental in better
understanding its eventual biological functional. This prompted the development
of a quantitative framework that could describe the dynamics of the pattern of
allele expression of the IL-10 gene, from which general quantitative insights
could be gained. We report that the experimental observations on these patterns
of allelic expression cannot be easily reconciled with a simple model of stochastic
transcriptional activation, in which the two alleles are, at any time, equally
competent for transcription. Instead, these observations call into action a general
model of eukaryotic transcriptional regulation according to which the locus competence
for transcription is dynamic, involving multiple, cooperative and stochastic modification
steps. In this model, the probability that an allele becomes transcriptionally
active is a function of the number of chromatin modifications that it accumulated.
On the basis of the properties of this model, we argue that predominant monoallelic
expression might have had no adaptive role, and may have evolved under indirect
selection for low frequency of expressing cells.
acknowledgement: Calado and Paixão acknowledge the financial support of Fundação para
a Ciência e a Tecnologia (fellowships SFRH/BD/2973/2000 and SFRH/BD/10550/2002,
respectively).
author:
- first_name: Tiago
full_name: Tiago Paixao
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Tiago
full_name: Carvalho, Tiago P
last_name: Carvalho
- first_name: Dinis
full_name: Calado, Dinis P
last_name: Calado
- first_name: Jorge
full_name: Carneiro, Jorge
last_name: Carneiro
citation:
ama: Paixao T, Carvalho T, Calado D, Carneiro J. Quantitative insights into stochastic
monoallelic expression of cytokine genes. Immunology and Cell Biology.
2007;85(4):315-322. doi:10.1038/sj.icb.7100057
apa: Paixao, T., Carvalho, T., Calado, D., & Carneiro, J. (2007). Quantitative
insights into stochastic monoallelic expression of cytokine genes. Immunology
and Cell Biology. Nature Publishing Group. https://doi.org/10.1038/sj.icb.7100057
chicago: Paixao, Tiago, Tiago Carvalho, Dinis Calado, and Jorge Carneiro. “Quantitative
Insights into Stochastic Monoallelic Expression of Cytokine Genes.” Immunology
and Cell Biology. Nature Publishing Group, 2007. https://doi.org/10.1038/sj.icb.7100057.
ieee: T. Paixao, T. Carvalho, D. Calado, and J. Carneiro, “Quantitative insights
into stochastic monoallelic expression of cytokine genes,” Immunology and Cell
Biology, vol. 85, no. 4. Nature Publishing Group, pp. 315–322, 2007.
ista: Paixao T, Carvalho T, Calado D, Carneiro J. 2007. Quantitative insights into
stochastic monoallelic expression of cytokine genes. Immunology and Cell Biology.
85(4), 315–322.
mla: Paixao, Tiago, et al. “Quantitative Insights into Stochastic Monoallelic Expression
of Cytokine Genes.” Immunology and Cell Biology, vol. 85, no. 4, Nature
Publishing Group, 2007, pp. 315–22, doi:10.1038/sj.icb.7100057.
short: T. Paixao, T. Carvalho, D. Calado, J. Carneiro, Immunology and Cell Biology
85 (2007) 315–322.
date_created: 2018-12-11T12:00:12Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:32Z
day: '01'
doi: 10.1038/sj.icb.7100057
extern: 1
intvolume: ' 85'
issue: '4'
month: '01'
page: 315 - 322
publication: Immunology and Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3862'
quality_controlled: 0
status: public
title: Quantitative insights into stochastic monoallelic expression of cytokine genes
type: journal_article
volume: 85
year: '2007'
...
---
_id: '2933'
author:
- first_name: M Pawan
full_name: Kumar, M Pawan
last_name: Kumar
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Philip
full_name: Torr, Philip H
last_name: Torr
citation:
ama: 'Kumar MP, Kolmogorov V, Torr P. An Analysis of Convex Relaxations for MAP
Estimation. In: Neural Information Processing Systems; 2007.'
apa: Kumar, M. P., Kolmogorov, V., & Torr, P. (2007). An Analysis of Convex
Relaxations for MAP Estimation. Presented at the Neural Information Processing
Systems, Neural Information Processing Systems.
chicago: Kumar, M Pawan, Vladimir Kolmogorov, and Philip Torr. “An Analysis of Convex
Relaxations for MAP Estimation.” Neural Information Processing Systems, 2007.
ieee: M. P. Kumar, V. Kolmogorov, and P. Torr, “An Analysis of Convex Relaxations
for MAP Estimation,” presented at the Neural Information Processing Systems, 2007.
ista: Kumar MP, Kolmogorov V, Torr P. 2007. An Analysis of Convex Relaxations for
MAP Estimation. Neural Information Processing Systems.
mla: Kumar, M. Pawan, et al. An Analysis of Convex Relaxations for MAP Estimation.
Neural Information Processing Systems, 2007.
short: M.P. Kumar, V. Kolmogorov, P. Torr, in:, Neural Information Processing Systems,
2007.
conference:
name: Neural Information Processing Systems
date_created: 2018-12-11T12:00:25Z
date_published: 2007-12-01T00:00:00Z
date_updated: 2021-01-12T07:39:52Z
day: '01'
extern: 1
month: '12'
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '3803'
quality_controlled: 0
status: public
title: An Analysis of Convex Relaxations for MAP Estimation
type: conference
year: '2007'
...
---
_id: '3019'
abstract:
- lang: eng
text: |2-
Directional transport of the phytohormone auxin is established primarily at the point of cellular afflux and is required for the establishment and maintenance of plant polarity. Studies in whole plants and heterologous systems indicate that PIN-FORMED (PIN) and P-glycoprotein (PGP) transport proteins mediate the cellular efflux of natural and synthetic auxins. However, aromatic anion transport resulting from PGP and PIN expression in nonplant systems was also found to lack tha high level of substrate specificity seen in planta. Furthermore, previous reports that PGP19 stabilizes PIN1 on the plasma membrane suggested that PIN-PGP interactions might regulate polar auxin efflux. Hare, we show that PGP1 and PGP19 colocalized with PIN1 in the shoot apax in Arabidopsis thaliana and with PIN1 and PIN2 in root tissues. Specific PGP-PIN interactions were seen in yeast two-hybrid and colmmunoprecipitation assays. PIN-PGP interactions appeared to enhance transport activity and, to a greater extent, substrate/inhibitor specificities when coexpressed in heterologous systems. By contrast, no interactions between PGPs and the AUXIN1 influx carrier were observed. Phenotypes of pin and pgp mutants suggest discrete functional roles in auxin transport, but pin pgp mutants exhibited phenotypes that are both additive and synergistic. These results suggest that PINs and PGPs characterize coordinated, Independent auxin transport mechanisms but also function interactively in a tissue-specific manner.
author:
- first_name: Joshua
full_name: Blakeslee, Joshua
last_name: Blakeslee
- first_name: Anindita
full_name: Bandyopadhyay, Anindita
last_name: Bandyopadhyay
- first_name: Ran
full_name: Ok, Ran Lee
last_name: Ok
- first_name: Jozef
full_name: Mravec, Jozef
last_name: Mravec
- first_name: Boosaree
full_name: Titapiwatanakun, Boosaree
last_name: Titapiwatanakun
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Srinivas
full_name: Makam, Srinivas N
last_name: Makam
- first_name: Yan
full_name: Cheng, Yan
last_name: Cheng
- first_name: Rodolphe
full_name: Bouchard, Rodolphe
last_name: Bouchard
- first_name: Jiří
full_name: Adamec, Jiří
last_name: Adamec
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Akitomo
full_name: Nagashima, Akitomo
last_name: Nagashima
- first_name: Tatsuya
full_name: Sakai, Tatsuya
last_name: Sakai
- first_name: Enrico
full_name: Martinoia, Enrico
last_name: Martinoia
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Wendy
full_name: Peer, Wendy A
last_name: Peer
- first_name: Angus
full_name: Murphy, Angus S
last_name: Murphy
citation:
ama: Blakeslee J, Bandyopadhyay A, Ok R, et al. Interactions among PIN FORMED and
P glycoprotein auxin transporters in Arabidopsis. Plant Cell. 2007;19(1):131-147.
doi:10.1105/tpc.106.040782
apa: Blakeslee, J., Bandyopadhyay, A., Ok, R., Mravec, J., Titapiwatanakun, B.,
Sauer, M., … Murphy, A. (2007). Interactions among PIN FORMED and P glycoprotein
auxin transporters in Arabidopsis. Plant Cell. American Society of Plant
Biologists. https://doi.org/10.1105/tpc.106.040782
chicago: Blakeslee, Joshua, Anindita Bandyopadhyay, Ran Ok, Jozef Mravec, Boosaree
Titapiwatanakun, Michael Sauer, Srinivas Makam, et al. “Interactions among PIN
FORMED and P Glycoprotein Auxin Transporters in Arabidopsis.” Plant Cell.
American Society of Plant Biologists, 2007. https://doi.org/10.1105/tpc.106.040782.
ieee: J. Blakeslee et al., “Interactions among PIN FORMED and P glycoprotein
auxin transporters in Arabidopsis,” Plant Cell, vol. 19, no. 1. American
Society of Plant Biologists, pp. 131–147, 2007.
ista: Blakeslee J, Bandyopadhyay A, Ok R, Mravec J, Titapiwatanakun B, Sauer M,
Makam S, Cheng Y, Bouchard R, Adamec J, Geisler M, Nagashima A, Sakai T, Martinoia
E, Friml J, Peer W, Murphy A. 2007. Interactions among PIN FORMED and P glycoprotein
auxin transporters in Arabidopsis. Plant Cell. 19(1), 131–147.
mla: Blakeslee, Joshua, et al. “Interactions among PIN FORMED and P Glycoprotein
Auxin Transporters in Arabidopsis.” Plant Cell, vol. 19, no. 1, American
Society of Plant Biologists, 2007, pp. 131–47, doi:10.1105/tpc.106.040782.
short: J. Blakeslee, A. Bandyopadhyay, R. Ok, J. Mravec, B. Titapiwatanakun, M.
Sauer, S. Makam, Y. Cheng, R. Bouchard, J. Adamec, M. Geisler, A. Nagashima, T.
Sakai, E. Martinoia, J. Friml, W. Peer, A. Murphy, Plant Cell 19 (2007) 131–147.
date_created: 2018-12-11T12:00:54Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:29Z
day: '01'
doi: 10.1105/tpc.106.040782
extern: 1
intvolume: ' 19'
issue: '1'
month: '01'
page: 131 - 147
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3682'
quality_controlled: 0
status: public
title: Interactions among PIN FORMED and P glycoprotein auxin transporters in Arabidopsis
type: journal_article
volume: 19
year: '2007'
...
---
_id: '3023'
abstract:
- lang: eng
text: 'Cytokinesis ensures proper partitioning of the nucleocytoplasmic contents
into two daughter cells. It has generally been thought that cytokinesis is accomplished
differently in animals and plants because of the differences in the preparatory
phases, into the centrosomal or acentrosomal nature of the process, the presence
or absence of rigid cell walls, and on the basis of ‘outside‐in’ or ‘inside‐out’
mechanism. However, this long‐standing paradigm needs further reevaluation based
on new findings. Recent advances reveal that plant cells, similarly to animal
cells, possess astral microtubules that regulate the cell division plane. Furthermore,
endocytosis has been found to be important for cytokinesis in animal and plant
cells: vesicles containing endocytosed cargo provide material for the cell plate
formation in plants and for closure of the midbody channel in animals. Thus, although
the preparatory phases of the cell division process differ between plant and animal
cells, the later phases show similarities. We unify these findings in a model
that suggests a conserved mode of cytokinesis.'
author:
- first_name: Pankaj
full_name: Dhonukshe, Pankaj
last_name: Dhonukshe
- first_name: Jozef
full_name: Šamaj, Jozef
last_name: Šamaj
- first_name: František
full_name: Baluška, František
last_name: Baluška
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Dhonukshe P, Šamaj J, Baluška F, Friml J. A unifying new model of cytokinesis
for the dividing plant and animal cells. Bioessays : News and Reviews in Molecular,
Cellular and Developmental Biology. 2007;29(4):371-381. doi:10.1002/bies.20559'
apa: 'Dhonukshe, P., Šamaj, J., Baluška, F., & Friml, J. (2007). A unifying
new model of cytokinesis for the dividing plant and animal cells. Bioessays :
News and Reviews in Molecular, Cellular and Developmental Biology. Wiley-Blackwell.
https://doi.org/10.1002/bies.20559'
chicago: 'Dhonukshe, Pankaj, Jozef Šamaj, František Baluška, and Jiří Friml. “A
Unifying New Model of Cytokinesis for the Dividing Plant and Animal Cells.” Bioessays :
News and Reviews in Molecular, Cellular and Developmental Biology. Wiley-Blackwell,
2007. https://doi.org/10.1002/bies.20559.'
ieee: 'P. Dhonukshe, J. Šamaj, F. Baluška, and J. Friml, “A unifying new model of
cytokinesis for the dividing plant and animal cells,” Bioessays : News and
Reviews in Molecular, Cellular and Developmental Biology, vol. 29, no. 4.
Wiley-Blackwell, pp. 371–381, 2007.'
ista: 'Dhonukshe P, Šamaj J, Baluška F, Friml J. 2007. A unifying new model of cytokinesis
for the dividing plant and animal cells. Bioessays : News and Reviews in Molecular,
Cellular and Developmental Biology. 29(4), 371–381.'
mla: 'Dhonukshe, Pankaj, et al. “A Unifying New Model of Cytokinesis for the Dividing
Plant and Animal Cells.” Bioessays : News and Reviews in Molecular, Cellular
and Developmental Biology, vol. 29, no. 4, Wiley-Blackwell, 2007, pp. 371–81,
doi:10.1002/bies.20559.'
short: 'P. Dhonukshe, J. Šamaj, F. Baluška, J. Friml, Bioessays : News and Reviews
in Molecular, Cellular and Developmental Biology 29 (2007) 371–381.'
date_created: 2018-12-11T12:00:55Z
date_published: 2007-04-01T00:00:00Z
date_updated: 2021-01-12T07:40:31Z
day: '01'
doi: 10.1002/bies.20559
extern: '1'
external_id:
pmid:
- ' 17373659'
intvolume: ' 29'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 371 - 381
pmid: 1
publication: 'Bioessays : News and Reviews in Molecular, Cellular and Developmental
Biology'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3678'
quality_controlled: '1'
status: public
title: A unifying new model of cytokinesis for the dividing plant and animal cells
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2007'
...
---
_id: '3021'
abstract:
- lang: eng
text: Polarized transport of the plant hormone auxin influences multiple growth
processes in plants and is regulated by plasma-membrane-localized efflux and uptake
carriers. The PGP (P-glycoprotein) ABC transporters (ATP-binding-cassette transporters),
PIN (pin-formed) subfamily of major facilitator proteins and members of AUX/LAX
families have been shown to independently transport auxin both in planta and in
heterologous systems. However, PIN- and PGP-mediated transport in heterologous
systems exhibits decreased substrate specificity and inhibitor-sensitivity compared
with what is seen in plants and plant cells. To determine whether PIN-PGP interactions
enhance transport specificity, we analysed interactions of the representative
auxin-transporting PGPs with PIN1 and AUX1 in planta and in heterologous systems.
Here, we provide evidence that PINs and PGPs interact and function both independently
and co-ordinately to control polar auxin transport and impart transport specificity
and directionality. These interactions take place in protein complexes stabilized
by PGPs in detergent-resistant microdomains.
alternative_title:
- Biochemical Society Transactions
author:
- first_name: Anindita
full_name: Bandyopadhyay, Anindita
last_name: Bandyopadhyay
- first_name: Joshua
full_name: Blakeslee, Joshua
last_name: Blakeslee
- first_name: Ok
full_name: Lee, Ok Ran
last_name: Lee
- first_name: Jozef
full_name: Mravec, Jozef
last_name: Mravec
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Boosaree
full_name: Titapiwatanakun, Boosaree
last_name: Titapiwatanakun
- first_name: Srinivas
full_name: Makam, Srinivas N
last_name: Makam
- first_name: Rodolphe
full_name: Bouchard, Rodolphe
last_name: Bouchard
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Enrico
full_name: Martinoia, Enrico
last_name: Martinoia
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Wendy
full_name: Peer, Wendy A
last_name: Peer
- first_name: Angus
full_name: Murphy, Angus S
last_name: Murphy
citation:
ama: 'Bandyopadhyay A, Blakeslee J, Lee O, et al. Interactions of PIN and PGP auxin
transport mechanisms. In: Vol 35. Portland Press; 2007:137-141. doi:10.1042/BST0350137'
apa: Bandyopadhyay, A., Blakeslee, J., Lee, O., Mravec, J., Sauer, M., Titapiwatanakun,
B., … Murphy, A. (2007). Interactions of PIN and PGP auxin transport mechanisms
(Vol. 35, pp. 137–141). Presented at the Intercellular Signalling in Plants, Portland
Press. https://doi.org/10.1042/BST0350137
chicago: Bandyopadhyay, Anindita, Joshua Blakeslee, Ok Lee, Jozef Mravec, Michael
Sauer, Boosaree Titapiwatanakun, Srinivas Makam, et al. “Interactions of PIN and
PGP Auxin Transport Mechanisms,” 35:137–41. Portland Press, 2007. https://doi.org/10.1042/BST0350137.
ieee: A. Bandyopadhyay et al., “Interactions of PIN and PGP auxin transport
mechanisms,” presented at the Intercellular Signalling in Plants, 2007, vol. 35,
no. 1, pp. 137–141.
ista: Bandyopadhyay A, Blakeslee J, Lee O, Mravec J, Sauer M, Titapiwatanakun B,
Makam S, Bouchard R, Geisler M, Martinoia E, Friml J, Peer W, Murphy A. 2007.
Interactions of PIN and PGP auxin transport mechanisms. Intercellular Signalling
in Plants, Biochemical Society Transactions, vol. 35, 137–141.
mla: Bandyopadhyay, Anindita, et al. Interactions of PIN and PGP Auxin Transport
Mechanisms. Vol. 35, no. 1, Portland Press, 2007, pp. 137–41, doi:10.1042/BST0350137.
short: A. Bandyopadhyay, J. Blakeslee, O. Lee, J. Mravec, M. Sauer, B. Titapiwatanakun,
S. Makam, R. Bouchard, M. Geisler, E. Martinoia, J. Friml, W. Peer, A. Murphy,
in:, Portland Press, 2007, pp. 137–141.
conference:
name: Intercellular Signalling in Plants
date_created: 2018-12-11T12:00:54Z
date_published: 2007-02-01T00:00:00Z
date_updated: 2021-01-12T07:40:30Z
day: '01'
doi: 10.1042/BST0350137
extern: 1
intvolume: ' 35'
issue: '1'
month: '02'
page: 137 - 141
publication_status: published
publisher: Portland Press
publist_id: '3681'
quality_controlled: 0
status: public
title: Interactions of PIN and PGP auxin transport mechanisms
type: conference
volume: 35
year: '2007'
...
---
_id: '3029'
abstract:
- lang: eng
text: In Arabidopsis thaliana, lateral roots are formed from root pericycle cells
adjacent to the xylem poles. Lateral root development is regulated antagonistically
by the plant hormones auxin and cytokinin. While a great deal is known about how
auxin promotes lateral root development, the mechanism of cytokinin repression
is still unclear. Elevating cytokinin levels was observed to disrupt lateral root
initiation and the regular pattern of divisions that characterizes lateral root
development in Arabidopsis. To identify the stage of lateral root development
that is sensitive to cytokinins, we targeted the expression of the Agrobacterium
tumefaciens cytokinin biosynthesis enzyme isopentenyltransferase to either xylem-pole
pericycle cells or young lateral root primordia using GAL4-GFP enhancer trap lines.
Transactivation experiments revealed that xylem-pole pericycle cells are sensitive
to cytokinins, whereas young lateral root primordia are not. This effect is physiologically
significant because transactivation of the Arabidopsis cytokinin degrading enzyme
cytokinin oxidase 1 in lateral root founder cells results in increased lateral
root formation. We observed that cytokinins perturb the expression of PIN genes
in lateral root founder cells and prevent the formation of an auxin gradient that
is required to pattern lateral root primordia.
author:
- first_name: Laurent
full_name: Laplaze, Laurent
last_name: Laplaze
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Ilda
full_name: Casimiro, Ilda
last_name: Casimiro
- first_name: Lies
full_name: Maes, Lies
last_name: Maes
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Ranjan
full_name: Swarup, Ranjan
last_name: Swarup
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Vanessa
full_name: Calvo, Vanessa
last_name: Calvo
- first_name: Boris
full_name: Parizot, Boris
last_name: Parizot
- first_name: Maria
full_name: Herrera-Rodriguez, Maria Begoña
last_name: Herrera Rodriguez
- first_name: Remko
full_name: Offringa, Remko
last_name: Offringa
- first_name: Neil
full_name: Graham, Neil
last_name: Graham
- first_name: Patrick
full_name: Doumas, Patrick
last_name: Doumas
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Didier
full_name: Bogusz, Didier
last_name: Bogusz
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Malcolm
full_name: Bennett, Malcolm
last_name: Bennett
citation:
ama: Laplaze L, Benková E, Casimiro I, et al. Cytokinins act directly on lateral
root founder cells to inhibit root initiation. Plant Cell. 2007;19(12):3889-3900.
doi:10.1105/tpc.107.055863
apa: Laplaze, L., Benková, E., Casimiro, I., Maes, L., Vanneste, S., Swarup, R.,
… Bennett, M. (2007). Cytokinins act directly on lateral root founder cells to
inhibit root initiation. Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.107.055863
chicago: Laplaze, Laurent, Eva Benková, Ilda Casimiro, Lies Maes, Steffen Vanneste,
Ranjan Swarup, Dolf Weijers, et al. “Cytokinins Act Directly on Lateral Root Founder
Cells to Inhibit Root Initiation.” Plant Cell. American Society of Plant
Biologists, 2007. https://doi.org/10.1105/tpc.107.055863.
ieee: L. Laplaze et al., “Cytokinins act directly on lateral root founder
cells to inhibit root initiation,” Plant Cell, vol. 19, no. 12. American
Society of Plant Biologists, pp. 3889–3900, 2007.
ista: Laplaze L, Benková E, Casimiro I, Maes L, Vanneste S, Swarup R, Weijers D,
Calvo V, Parizot B, Herrera Rodriguez M, Offringa R, Graham N, Doumas P, Friml
J, Bogusz D, Beeckman T, Bennett M. 2007. Cytokinins act directly on lateral root
founder cells to inhibit root initiation. Plant Cell. 19(12), 3889–3900.
mla: Laplaze, Laurent, et al. “Cytokinins Act Directly on Lateral Root Founder Cells
to Inhibit Root Initiation.” Plant Cell, vol. 19, no. 12, American Society
of Plant Biologists, 2007, pp. 3889–900, doi:10.1105/tpc.107.055863.
short: L. Laplaze, E. Benková, I. Casimiro, L. Maes, S. Vanneste, R. Swarup, D.
Weijers, V. Calvo, B. Parizot, M. Herrera Rodriguez, R. Offringa, N. Graham, P.
Doumas, J. Friml, D. Bogusz, T. Beeckman, M. Bennett, Plant Cell 19 (2007) 3889–3900.
date_created: 2018-12-11T12:00:57Z
date_published: 2007-12-01T00:00:00Z
date_updated: 2021-01-12T07:40:33Z
day: '01'
doi: 10.1105/tpc.107.055863
extern: 1
intvolume: ' 19'
issue: '12'
month: '12'
page: 3889 - 3900
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3673'
quality_controlled: 0
status: public
title: Cytokinins act directly on lateral root founder cells to inhibit root initiation
type: journal_article
volume: 19
year: '2007'
...
---
_id: '3026'
abstract:
- lang: eng
text: In plants, each developmental process integrates a network of signaling events
that are regulated by different phytohormones, and interactions among hormonal
pathways are essential to modulate their effect. Continuous growth of roots results
from the postembryonic activity of cells within the root meristem that is controlled
by the coordinated action of several phytohormones, including auxin and ethylene.
Although their interaction has been studied intensively, the molecular and cellular
mechanisms underlying this interplay are unknown. We show that the effect of ethylene
on root growth is largely mediated by the regulation of the auxin biosynthesis
and transport-dependent local auxin distribution. Ethylene stimulates auxin biosynthesis
and basipetal auxin transport toward the elongation zone, where it activates a
local auxin response leading to inhibition of cell elongation. Consistently, in
mutants affected in auxin perception or basipetal auxin transport, ethylene cannot
activate the auxin response nor regulate the root growth. In addition, ethylene
modulates the transcription of several components of the auxin transport machinery.
Thus, ethylene achieves a local activation of the auxin signaling pathway and
regulates root growth by both stimulating the auxin biosynthesis and by modulating
the auxin transport machinery.
author:
- first_name: Kamil
full_name: Růžička, Kamil
last_name: Růžička
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Radka
full_name: Podhorská, Radka
last_name: Podhorská
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Růžička K, Ljung K, Vanneste S, et al. Ethylene regulates root growth through
effects on auxin biosynthesis and transport dependent auxin distribution. Plant
Cell. 2007;19(7):2197-2212. doi:10.1105/tpc.107.052126
apa: Růžička, K., Ljung, K., Vanneste, S., Podhorská, R., Beeckman, T., Friml, J.,
& Benková, E. (2007). Ethylene regulates root growth through effects on auxin
biosynthesis and transport dependent auxin distribution. Plant Cell. American
Society of Plant Biologists. https://doi.org/10.1105/tpc.107.052126
chicago: Růžička, Kamil, Karin Ljung, Steffen Vanneste, Radka Podhorská, Tom Beeckman,
Jiří Friml, and Eva Benková. “Ethylene Regulates Root Growth through Effects on
Auxin Biosynthesis and Transport Dependent Auxin Distribution.” Plant Cell.
American Society of Plant Biologists, 2007. https://doi.org/10.1105/tpc.107.052126.
ieee: K. Růžička et al., “Ethylene regulates root growth through effects
on auxin biosynthesis and transport dependent auxin distribution,” Plant Cell,
vol. 19, no. 7. American Society of Plant Biologists, pp. 2197–2212, 2007.
ista: Růžička K, Ljung K, Vanneste S, Podhorská R, Beeckman T, Friml J, Benková
E. 2007. Ethylene regulates root growth through effects on auxin biosynthesis
and transport dependent auxin distribution. Plant Cell. 19(7), 2197–2212.
mla: Růžička, Kamil, et al. “Ethylene Regulates Root Growth through Effects on Auxin
Biosynthesis and Transport Dependent Auxin Distribution.” Plant Cell, vol.
19, no. 7, American Society of Plant Biologists, 2007, pp. 2197–212, doi:10.1105/tpc.107.052126.
short: K. Růžička, K. Ljung, S. Vanneste, R. Podhorská, T. Beeckman, J. Friml, E.
Benková, Plant Cell 19 (2007) 2197–2212.
date_created: 2018-12-11T12:00:56Z
date_published: 2007-07-01T00:00:00Z
date_updated: 2021-01-12T07:40:32Z
day: '01'
doi: 10.1105/tpc.107.052126
extern: 1
intvolume: ' 19'
issue: '7'
month: '07'
page: 2197 - 2212
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3676'
quality_controlled: 0
status: public
title: Ethylene regulates root growth through effects on auxin biosynthesis and transport
dependent auxin distribution
type: journal_article
volume: 19
year: '2007'
...
---
_id: '3028'
abstract:
- lang: eng
text: In plants, cell polarity and tissue patterning are connected by intercellular
flow of the phytohormone auxin, whose directional signaling depends on polar subcellular
localization of PIN auxin transport proteins. The mechanism of polar targeting
of PINs or other cargos in plants is largely unidentified, with the PINOID kinase
being the only known molecular component. Here, we identify PP2A phosphatase as
an important regulator of PIN apical-basal targeting and auxin distribution. Genetic
analysis, localization, and phosphorylation studies demonstrate that PP2A and
PINOID both partially colocalize with PINs and act antagonistically on the phosphorylation
state of their central hydrophilic loop, hence mediating PIN apical-basal polar
targeting. Thus, in plants, polar sorting by the reversible phosphorylation of
cargos allows for their conditional delivery to specific intracellular destinations.
In the case of PIN proteins, this mechanism enables switches in the direction
of intercellular auxin fluxes, which mediate differential growth, tissue patterning,
and organogenesis.
author:
- first_name: Marta
full_name: Michniewicz, Marta
last_name: Michniewicz
- first_name: Marcelo
full_name: Zago, Marcelo K
last_name: Zago
- first_name: Lindy
full_name: Abas, Lindy
last_name: Abas
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Alois
full_name: Schweighofer, Alois
last_name: Schweighofer
- first_name: Irute
full_name: Meskiene, Irute
last_name: Meskiene
- first_name: Marcus
full_name: Heisler, Marcus G
last_name: Heisler
- first_name: Carolyn
full_name: Ohno, Carolyn
last_name: Ohno
- first_name: Jing
full_name: Zhang, Jing
last_name: Zhang
- first_name: Fang
full_name: Huang, Fang
last_name: Huang
- first_name: Rebecca
full_name: Schwab, Rebecca
last_name: Schwab
- first_name: Detlef
full_name: Weigel, Detlef
last_name: Weigel
- first_name: Elliot
full_name: Meyerowitz, Elliot M
last_name: Meyerowitz
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
- first_name: Remko
full_name: Offringa, Remko
last_name: Offringa
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Michniewicz M, Zago M, Abas L, et al. Antagonistic regulation of PIN phosphorylation
by PP2A and PINOID directs auxin flux. Cell. 2007;130(6):1044-1056. doi:10.1016/j.cell.2007.07.033
apa: Michniewicz, M., Zago, M., Abas, L., Weijers, D., Schweighofer, A., Meskiene,
I., … Friml, J. (2007). Antagonistic regulation of PIN phosphorylation by PP2A
and PINOID directs auxin flux. Cell. Cell Press. https://doi.org/10.1016/j.cell.2007.07.033
chicago: Michniewicz, Marta, Marcelo Zago, Lindy Abas, Dolf Weijers, Alois Schweighofer,
Irute Meskiene, Marcus Heisler, et al. “Antagonistic Regulation of PIN Phosphorylation
by PP2A and PINOID Directs Auxin Flux.” Cell. Cell Press, 2007. https://doi.org/10.1016/j.cell.2007.07.033.
ieee: M. Michniewicz et al., “Antagonistic regulation of PIN phosphorylation
by PP2A and PINOID directs auxin flux,” Cell, vol. 130, no. 6. Cell Press,
pp. 1044–1056, 2007.
ista: Michniewicz M, Zago M, Abas L, Weijers D, Schweighofer A, Meskiene I, Heisler
M, Ohno C, Zhang J, Huang F, Schwab R, Weigel D, Meyerowitz E, Luschnig C, Offringa
R, Friml J. 2007. Antagonistic regulation of PIN phosphorylation by PP2A and PINOID
directs auxin flux. Cell. 130(6), 1044–1056.
mla: Michniewicz, Marta, et al. “Antagonistic Regulation of PIN Phosphorylation
by PP2A and PINOID Directs Auxin Flux.” Cell, vol. 130, no. 6, Cell Press,
2007, pp. 1044–56, doi:10.1016/j.cell.2007.07.033.
short: M. Michniewicz, M. Zago, L. Abas, D. Weijers, A. Schweighofer, I. Meskiene,
M. Heisler, C. Ohno, J. Zhang, F. Huang, R. Schwab, D. Weigel, E. Meyerowitz,
C. Luschnig, R. Offringa, J. Friml, Cell 130 (2007) 1044–1056.
date_created: 2018-12-11T12:00:57Z
date_published: 2007-09-21T00:00:00Z
date_updated: 2021-01-12T07:40:33Z
day: '21'
doi: 10.1016/j.cell.2007.07.033
extern: 1
intvolume: ' 130'
issue: '6'
month: '09'
page: 1044 - 1056
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3674'
quality_controlled: 0
status: public
title: Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin
flux
type: journal_article
volume: 130
year: '2007'
...
---
_id: '3024'
abstract:
- lang: eng
text: The plant hormone auxin is frequently observed to be asymmetrically distributed
across adjacent cells during crucial stages of growth and development. These auxin
gradients depend on polar transport and regulate a wide variety of processes,
including embryogenesis, organogenesis, vascular tissue differentiation, root
meristem maintenance and tropic growth. Auxin can mediate such a perplexing array
of developmental processes by acting as a general trigger for the change in developmental
program in cells where it accumulates and by providing vectorial information to
the tissues by its polar intercellular flow. In recent years, a wealth of molecular
data on the mechanism of auxin transport and its regulation has been generated,
providing significant insights into the action of this versatile coordinative
signal.
author:
- first_name: Anne
full_name: Vieten, Anne
last_name: Vieten
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Philip
full_name: Brewer, Philip
last_name: Brewer
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Vieten A, Sauer M, Brewer P, Friml J. Molecular and cellular aspects of auxin-transport-mediated
development. Trends in Plant Science. 2007;12(4):160-168. doi:10.1016/j.tplants.2007.03.006
apa: Vieten, A., Sauer, M., Brewer, P., & Friml, J. (2007). Molecular and cellular
aspects of auxin-transport-mediated development. Trends in Plant Science.
Cell Press. https://doi.org/10.1016/j.tplants.2007.03.006
chicago: Vieten, Anne, Michael Sauer, Philip Brewer, and Jiří Friml. “Molecular
and Cellular Aspects of Auxin-Transport-Mediated Development.” Trends in Plant
Science. Cell Press, 2007. https://doi.org/10.1016/j.tplants.2007.03.006.
ieee: A. Vieten, M. Sauer, P. Brewer, and J. Friml, “Molecular and cellular aspects
of auxin-transport-mediated development,” Trends in Plant Science, vol.
12, no. 4. Cell Press, pp. 160–168, 2007.
ista: Vieten A, Sauer M, Brewer P, Friml J. 2007. Molecular and cellular aspects
of auxin-transport-mediated development. Trends in Plant Science. 12(4), 160–168.
mla: Vieten, Anne, et al. “Molecular and Cellular Aspects of Auxin-Transport-Mediated
Development.” Trends in Plant Science, vol. 12, no. 4, Cell Press, 2007,
pp. 160–68, doi:10.1016/j.tplants.2007.03.006.
short: A. Vieten, M. Sauer, P. Brewer, J. Friml, Trends in Plant Science 12 (2007)
160–168.
date_created: 2018-12-11T12:00:55Z
date_published: 2007-04-01T00:00:00Z
date_updated: 2021-01-12T07:40:31Z
day: '01'
doi: 10.1016/j.tplants.2007.03.006
extern: '1'
external_id:
pmid:
- ' 17369077'
intvolume: ' 12'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 160 - 168
pmid: 1
publication: Trends in Plant Science
publication_status: published
publisher: Cell Press
publist_id: '3679'
quality_controlled: '1'
status: public
title: Molecular and cellular aspects of auxin-transport-mediated development
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2007'
...
---
_id: '3192'
abstract:
- lang: eng
text: Many computer vision applications rely on the efficient optimization of challenging,
so-called non-submodular, binary pairwise MRFs. A promising graph cut based approach
for optimizing such MRFs known as "roof duality" was recently introduced
into computer vision. We study two methods which extend this approach. First,
we discuss an efficient implementation of the "probing" technique introduced
recently by Boros et al. [5]. It simplifies the MRF while preserving the global
optimum. Our code is 400-700 faster on some graphs than the implementation of
[5]. Second, we present a new technique which takes an arbitrary input labeling
and tries to improve its energy. We give theoretical characterizations of local
minima of this procedure. We applied both techniques to many applications, including
image segmentation, new view synthesis, superresolution, diagram recognition,
parameter learning, texture restoration, and image deconvolution. For several
applications we see that we are able to find the global minimum very efficiently,
and considerably outperform the original roof duality approach. In comparison
to existing techniques, such as graph cut, TRW, BP, ICM, and simulated annealing,
we nearly always find a lower energy.
author:
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Victor
full_name: Lempitsky, Victor
last_name: Lempitsky
- first_name: Martin
full_name: Szummer, Martin
last_name: Szummer
citation:
ama: 'Rother C, Kolmogorov V, Lempitsky V, Szummer M. Optimizing binary MRFs via
extended roof duality. In: IEEE; 2007. doi:10.1109/CVPR.2007.383203'
apa: 'Rother, C., Kolmogorov, V., Lempitsky, V., & Szummer, M. (2007). Optimizing
binary MRFs via extended roof duality. Presented at the CVPR: Computer Vision
and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2007.383203'
chicago: Rother, Carsten, Vladimir Kolmogorov, Victor Lempitsky, and Martin Szummer.
“Optimizing Binary MRFs via Extended Roof Duality.” IEEE, 2007. https://doi.org/10.1109/CVPR.2007.383203.
ieee: 'C. Rother, V. Kolmogorov, V. Lempitsky, and M. Szummer, “Optimizing binary
MRFs via extended roof duality,” presented at the CVPR: Computer Vision and Pattern
Recognition, 2007.'
ista: 'Rother C, Kolmogorov V, Lempitsky V, Szummer M. 2007. Optimizing binary MRFs
via extended roof duality. CVPR: Computer Vision and Pattern Recognition.'
mla: Rother, Carsten, et al. Optimizing Binary MRFs via Extended Roof Duality.
IEEE, 2007, doi:10.1109/CVPR.2007.383203.
short: C. Rother, V. Kolmogorov, V. Lempitsky, M. Szummer, in:, IEEE, 2007.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:55Z
date_published: 2007-07-16T00:00:00Z
date_updated: 2021-01-12T07:41:42Z
day: '16'
doi: 10.1109/CVPR.2007.383203
extern: 1
main_file_link:
- open_access: '0'
url: http://www.robots.ox.ac.uk/~vilem/QPBOPI.pdf
month: '07'
publication_status: published
publisher: IEEE
publist_id: '3490'
quality_controlled: 0
status: public
title: Optimizing binary MRFs via extended roof duality
type: conference
year: '2007'
...
---
_id: '3191'
abstract:
- lang: eng
text: 'The maximum flow algorithm for minimizing energy functions of binary variables
has become a standard tool in computer vision. In many cases, unary costs of the
energy depend linearly on parameter lambda. In this paper we study vision applications
for which it is important to solve the maxflow problem for different lambda''s.
An example is a weighting between data and regularization terms in image segmentation
or stereo: it is desirable to vary it both during training (to learn lambda from
ground truth data) and testing (to select best lambda using high-knowledge constraints,
e.g. user input). We review algorithmic aspects of this parametric maximum flow
problem previously unknown in vision, such as the ability to compute all breakpoints
of lambda and corresponding optimal configurations infinite time. These results
allow, in particular, to minimize the ratio of some geometric functional, such
as flux of a vector field over length (or area). Previously, such functional were
tackled with shortest path techniques applicable only in 2D. We give theoretical
improvements for "PDE cuts" [5]. We present experimental results for
image segmentation, 3D reconstruction, and the cosegmentation problem.'
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Yuri
full_name: Boykov, Yuri
last_name: Boykov
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: 'Kolmogorov V, Boykov Y, Rother C. Applications of parametric maxflow in computer
vision. In: IEEE; 2007. doi:10.1109/ICCV.2007.4408910'
apa: 'Kolmogorov, V., Boykov, Y., & Rother, C. (2007). Applications of parametric
maxflow in computer vision. Presented at the ICCV: International Conference on
Computer Vision, IEEE. https://doi.org/10.1109/ICCV.2007.4408910'
chicago: Kolmogorov, Vladimir, Yuri Boykov, and Carsten Rother. “Applications of
Parametric Maxflow in Computer Vision.” IEEE, 2007. https://doi.org/10.1109/ICCV.2007.4408910.
ieee: 'V. Kolmogorov, Y. Boykov, and C. Rother, “Applications of parametric maxflow
in computer vision,” presented at the ICCV: International Conference on Computer
Vision, 2007.'
ista: 'Kolmogorov V, Boykov Y, Rother C. 2007. Applications of parametric maxflow
in computer vision. ICCV: International Conference on Computer Vision.'
mla: Kolmogorov, Vladimir, et al. Applications of Parametric Maxflow in Computer
Vision. IEEE, 2007, doi:10.1109/ICCV.2007.4408910.
short: V. Kolmogorov, Y. Boykov, C. Rother, in:, IEEE, 2007.
conference:
name: 'ICCV: International Conference on Computer Vision'
date_created: 2018-12-11T12:01:55Z
date_published: 2007-12-26T00:00:00Z
date_updated: 2021-01-12T07:41:41Z
day: '26'
doi: 10.1109/ICCV.2007.4408910
extern: 1
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/70474/iccv07-paramaxflow.pdf
month: '12'
publication_status: published
publisher: IEEE
publist_id: '3489'
quality_controlled: 0
status: public
title: Applications of parametric maxflow in computer vision
type: conference
year: '2007'
...
---
_id: '3193'
abstract:
- lang: eng
text: 'Optimization techniques based on graph cuts have become a standard tool for
many vision applications. These techniques allow to minimize efficiently certain
energy functions corresponding to pairwise Markov Random Fields (MRFs). Currently,
there is an accepted view within the computer vision community that graph cuts
can only be used for optimizing a limited class of MRF energies (e.g., submodular
functions). In this survey, we review some results that show that graph cuts can
be applied to a much larger class of energy functions (in particular, nonsubmodular
functions). While these results are well-known in the optimization community,
to our knowledge they were not used in the context of computer vision and MRF
optimization. We demonstrate the relevance of these results to vision on the problem
of binary texture restoration. '
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: Kolmogorov V, Rother C. Minimizing nonsubmodular functions with graph cuts
- A review. IEEE Transactions on Pattern Analysis and Machine Intelligence.
2007;29(7):1274-1279. doi:10.1109/TPAMI.2007.1031
apa: Kolmogorov, V., & Rother, C. (2007). Minimizing nonsubmodular functions
with graph cuts - A review. IEEE Transactions on Pattern Analysis and Machine
Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2007.1031
chicago: Kolmogorov, Vladimir, and Carsten Rother. “Minimizing Nonsubmodular Functions
with Graph Cuts - A Review.” IEEE Transactions on Pattern Analysis and Machine
Intelligence. IEEE, 2007. https://doi.org/10.1109/TPAMI.2007.1031.
ieee: V. Kolmogorov and C. Rother, “Minimizing nonsubmodular functions with graph
cuts - A review,” IEEE Transactions on Pattern Analysis and Machine Intelligence,
vol. 29, no. 7. IEEE, pp. 1274–1279, 2007.
ista: Kolmogorov V, Rother C. 2007. Minimizing nonsubmodular functions with graph
cuts - A review. IEEE Transactions on Pattern Analysis and Machine Intelligence.
29(7), 1274–1279.
mla: Kolmogorov, Vladimir, and Carsten Rother. “Minimizing Nonsubmodular Functions
with Graph Cuts - A Review.” IEEE Transactions on Pattern Analysis and Machine
Intelligence, vol. 29, no. 7, IEEE, 2007, pp. 1274–79, doi:10.1109/TPAMI.2007.1031.
short: V. Kolmogorov, C. Rother, IEEE Transactions on Pattern Analysis and Machine
Intelligence 29 (2007) 1274–1279.
date_created: 2018-12-11T12:01:56Z
date_published: 2007-07-01T00:00:00Z
date_updated: 2021-01-12T07:41:42Z
day: '01'
doi: 10.1109/TPAMI.2007.1031
extern: 1
intvolume: ' 29'
issue: '7'
month: '07'
page: 1274 - 1279
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3491'
quality_controlled: 0
status: public
title: Minimizing nonsubmodular functions with graph cuts - A review
type: journal_article
volume: 29
year: '2007'
...
---
_id: '3187'
abstract:
- lang: eng
text: Stereo vision has numerous applications in robotics, graphics, inspection
and other areas. A prime application, one which has driven work on stereo in our
laboratory, is teleconferencing in which the use of a stereo webcam already makes
possible various transformations of the video stream. These include digital camera
control, insertion of virtual objects, background substitution, and eye-gaze correction
[9, 8].
author:
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Antonio
full_name: Criminisi, Antonio
last_name: Criminisi
- first_name: Geoffrey
full_name: Cross, Geoffrey
last_name: Cross
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: Blake A, Criminisi A, Cross G, Kolmogorov V, Rother C. Fusion of stereo colour
and contrast. Springer Tracts in Advanced Robotics. 2007;28:295-304. doi:10.1007/978-3-540-48113-3_27
apa: Blake, A., Criminisi, A., Cross, G., Kolmogorov, V., & Rother, C. (2007).
Fusion of stereo colour and contrast. Springer Tracts in Advanced Robotics.
Springer. https://doi.org/10.1007/978-3-540-48113-3_27
chicago: Blake, Andrew, Antonio Criminisi, Geoffrey Cross, Vladimir Kolmogorov,
and Carsten Rother. “Fusion of Stereo Colour and Contrast.” Springer Tracts
in Advanced Robotics. Springer, 2007. https://doi.org/10.1007/978-3-540-48113-3_27.
ieee: A. Blake, A. Criminisi, G. Cross, V. Kolmogorov, and C. Rother, “Fusion of
stereo colour and contrast,” Springer Tracts in Advanced Robotics, vol.
28. Springer, pp. 295–304, 2007.
ista: Blake A, Criminisi A, Cross G, Kolmogorov V, Rother C. 2007. Fusion of stereo
colour and contrast. Springer Tracts in Advanced Robotics. 28, 295–304.
mla: Blake, Andrew, et al. “Fusion of Stereo Colour and Contrast.” Springer Tracts
in Advanced Robotics, vol. 28, Springer, 2007, pp. 295–304, doi:10.1007/978-3-540-48113-3_27.
short: A. Blake, A. Criminisi, G. Cross, V. Kolmogorov, C. Rother, Springer Tracts
in Advanced Robotics 28 (2007) 295–304.
date_created: 2018-12-11T12:01:54Z
date_published: 2007-02-05T00:00:00Z
date_updated: 2021-01-12T07:41:40Z
day: '05'
doi: 10.1007/978-3-540-48113-3_27
extern: 1
intvolume: ' 28'
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67417/criminisi_isrr2005.pdf
month: '02'
page: 295 - 304
publication: Springer Tracts in Advanced Robotics
publication_status: published
publisher: Springer
publist_id: '3492'
quality_controlled: 0
status: public
title: Fusion of stereo colour and contrast
type: journal_article
volume: 28
year: '2007'
...
---
_id: '3218'
abstract:
- lang: eng
text: 'A (k, ℓ)-robust combiner for collision-resistant hash-functions is a construction
which from ℓ hash-functions constructs a hash-function which is collision-resistant
if at least k of the components are collision-resistant. One trivially gets a
(k, ℓ)-robust combiner by concatenating the output of any ℓ - k + 1 of the components,
unfortunately this is not very practical as the length of the output of the combiner
is quite large. We show that this is unavoidable as no black-box (k, ℓ)-robust
combiner whose output is significantly shorter than what can be achieved by concatenation
exists. This answers a question of Boneh and Boyen (Crypto''06). '
acknowledgement: Supported by DIAMANT, the Dutch national mathematics cluster for
discrete interactive and algorithmic algebra and number theory.
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Pietrzak KZ. Non-trivial black-box combiners for collision-resistant hash-functions
don’t exist. In: Vol 4515. Springer; 2007:23-33. doi:10.1007/978-3-540-72540-4_2'
apa: 'Pietrzak, K. Z. (2007). Non-trivial black-box combiners for collision-resistant
hash-functions don’t exist (Vol. 4515, pp. 23–33). Presented at the EUROCRYPT:
Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/978-3-540-72540-4_2'
chicago: Pietrzak, Krzysztof Z. “Non-Trivial Black-Box Combiners for Collision-Resistant
Hash-Functions Don’t Exist,” 4515:23–33. Springer, 2007. https://doi.org/10.1007/978-3-540-72540-4_2.
ieee: 'K. Z. Pietrzak, “Non-trivial black-box combiners for collision-resistant
hash-functions don’t exist,” presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, 2007, vol. 4515, pp. 23–33.'
ista: 'Pietrzak KZ. 2007. Non-trivial black-box combiners for collision-resistant
hash-functions don’t exist. EUROCRYPT: Theory and Applications of Cryptographic
Techniques, LNCS, vol. 4515, 23–33.'
mla: Pietrzak, Krzysztof Z. Non-Trivial Black-Box Combiners for Collision-Resistant
Hash-Functions Don’t Exist. Vol. 4515, Springer, 2007, pp. 23–33, doi:10.1007/978-3-540-72540-4_2.
short: K.Z. Pietrzak, in:, Springer, 2007, pp. 23–33.
conference:
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
date_created: 2018-12-11T12:02:05Z
date_published: 2007-06-12T00:00:00Z
date_updated: 2021-01-12T07:41:52Z
day: '12'
doi: 10.1007/978-3-540-72540-4_2
extern: 1
intvolume: ' 4515'
month: '06'
page: 23 - 33
publication_status: published
publisher: Springer
publist_id: '3461'
quality_controlled: 0
status: public
title: Non-trivial black-box combiners for collision-resistant hash-functions don't
exist
type: conference
volume: 4515
year: '2007'
...
---
_id: '3305'
abstract:
- lang: eng
text: The accumulation of deleterious mutations plays a major role in evolution,
and key to this are the interactions between their fitness effects, known as epistasis.
Whether mutations tend to interact synergistically (with multiple mutations being
more deleterious than would be expected from their individual fitness effects)
or antagonistically is important for a variety of evolutionary questions, particularly
the evolution of sex. Unfortunately, the experimental evidence on the prevalence
and strength of epistasis is mixed and inconclusive. Here we study theoretically
whether synergistic or antagonistic epistasis is likely to be favored by evolution
and by how much. We find that in the presence of recombination, evolution favors
less synergistic or more antagonistic epistasis whenever mutations that change
the epistasis in this direction are possible. This is because evolution favors
increased buffering against the effects of deleterious mutations. This suggests
that we should not expect synergistic epistasis to be widespread in nature and
hence that the mutational deterministic hypothesis for the advantage of sex may
not apply widely.
author:
- first_name: Michael
full_name: Desai, Michael M
last_name: Desai
- first_name: Daniel
full_name: Daniel Weissman
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Marcus
full_name: Feldman, Marcus W
last_name: Feldman
citation:
ama: Desai M, Weissman D, Feldman M. Evolution can favor antagonistic epistasis.
Genetics. 2007;177(2):1001-1010. doi:10.1534/genetics.107.075812
apa: Desai, M., Weissman, D., & Feldman, M. (2007). Evolution can favor antagonistic
epistasis. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.107.075812
chicago: Desai, Michael, Daniel Weissman, and Marcus Feldman. “Evolution Can Favor
Antagonistic Epistasis.” Genetics. Genetics Society of America, 2007. https://doi.org/10.1534/genetics.107.075812.
ieee: M. Desai, D. Weissman, and M. Feldman, “Evolution can favor antagonistic epistasis,”
Genetics, vol. 177, no. 2. Genetics Society of America, pp. 1001–10, 2007.
ista: Desai M, Weissman D, Feldman M. 2007. Evolution can favor antagonistic epistasis.
Genetics. 177(2), 1001–10.
mla: Desai, Michael, et al. “Evolution Can Favor Antagonistic Epistasis.” Genetics,
vol. 177, no. 2, Genetics Society of America, 2007, pp. 1001–10, doi:10.1534/genetics.107.075812.
short: M. Desai, D. Weissman, M. Feldman, Genetics 177 (2007) 1001–10.
date_created: 2018-12-11T12:02:34Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:32Z
day: '01'
doi: 10.1534/genetics.107.075812
extern: 1
intvolume: ' 177'
issue: '2'
month: '01'
page: 1001 - 10
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3335'
quality_controlled: 0
status: public
title: Evolution can favor antagonistic epistasis
type: journal_article
volume: 177
year: '2007'
...
---
_id: '3411'
abstract:
- lang: eng
text: Mechanical single-molecule techniques offer exciting possibilities to investigate
protein folding and stability in native environments at submolecular resolution.
By applying a free-energy reconstruction procedure developed by Hummer and Szabo,
which is based on a statistical theorem introduced by Jarzynski, we determined
the unfolding free energy of the membrane proteins bacteriorhodopsin (BR), halorhodopsin,
and the sodium-proton antiporter NhaA. The calculated energies ranged from 290.5kcal/mol
for BR to 485.5kcal/mol for NhaA. For the remarkably stable BR, the equilibrium
unfolding free energy was independent of pulling rate and temperature ranging
between 18 and 42°C. Our experiments also revealed heterogeneous energetic properties
in individual transmembrane helices. In halorhodopsin, the stabilization of a
short helical segment yielded a characteristic signature in the energy profile.
In NhaA, a pronounced peak was observed at a functionally important site in the
protein. Since a large variety of single- and multispan membrane proteins can
be tackled in mechanical unfolding experiments, our approach provides a basis
for systematically elucidating energetic properties of membrane proteins with
the resolution of individual secondary-structure elements.
author:
- first_name: Johannes
full_name: Preiner, Johannes
last_name: Preiner
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Christian
full_name: Rankl, Christian
last_name: Rankl
- first_name: Helene
full_name: Knaus, Helene
last_name: Knaus
- first_name: David
full_name: Cisneros, David A
last_name: Cisneros
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: Ferry
full_name: Kienberger, Ferry
last_name: Kienberger
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
- first_name: Peter
full_name: Hinterdorfer, Peter
last_name: Hinterdorfer
citation:
ama: Preiner J, Janovjak HL, Rankl C, et al. Free energy of membrane protein unfolding
derived from single-molecule force measurements. Biophysical Journal. 2007;93(3):930-937.
doi:10.1529/biophysj.106.096982
apa: Preiner, J., Janovjak, H. L., Rankl, C., Knaus, H., Cisneros, D., Kedrov, A.,
… Hinterdorfer, P. (2007). Free energy of membrane protein unfolding derived from
single-molecule force measurements. Biophysical Journal. Biophysical Society.
https://doi.org/10.1529/biophysj.106.096982
chicago: Preiner, Johannes, Harald L Janovjak, Christian Rankl, Helene Knaus, David
Cisneros, Alexej Kedrov, Ferry Kienberger, Daniel Mueller, and Peter Hinterdorfer.
“Free Energy of Membrane Protein Unfolding Derived from Single-Molecule Force
Measurements.” Biophysical Journal. Biophysical Society, 2007. https://doi.org/10.1529/biophysj.106.096982.
ieee: J. Preiner et al., “Free energy of membrane protein unfolding derived
from single-molecule force measurements,” Biophysical Journal, vol. 93,
no. 3. Biophysical Society, pp. 930–937, 2007.
ista: Preiner J, Janovjak HL, Rankl C, Knaus H, Cisneros D, Kedrov A, Kienberger
F, Mueller D, Hinterdorfer P. 2007. Free energy of membrane protein unfolding
derived from single-molecule force measurements. Biophysical Journal. 93(3), 930–937.
mla: Preiner, Johannes, et al. “Free Energy of Membrane Protein Unfolding Derived
from Single-Molecule Force Measurements.” Biophysical Journal, vol. 93,
no. 3, Biophysical Society, 2007, pp. 930–37, doi:10.1529/biophysj.106.096982.
short: J. Preiner, H.L. Janovjak, C. Rankl, H. Knaus, D. Cisneros, A. Kedrov, F.
Kienberger, D. Mueller, P. Hinterdorfer, Biophysical Journal 93 (2007) 930–937.
date_created: 2018-12-11T12:03:11Z
date_published: 2007-08-01T00:00:00Z
date_updated: 2021-01-12T07:43:18Z
day: '01'
doi: 10.1529/biophysj.106.096982
extern: 1
intvolume: ' 93'
issue: '3'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1913163/
month: '08'
oa: 1
page: 930 - 937
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '2990'
quality_controlled: 0
status: public
title: Free energy of membrane protein unfolding derived from single-molecule force
measurements
type: journal_article
volume: 93
year: '2007'
...
---
_id: '3412'
abstract:
- lang: eng
text: |-
Molecular interactions are the basic language of biological processes.
They establish the forces interacting between the building blocks of
proteins and other macromolecules, thus determining their functional
roles. Because molecular interactions trigger virtually every
biological process, approaches to decipher their language are needed.
Single-molecule force spectroscopy (SMFS) has been used to detect
and characterize different types of molecular interactions that occur
between and within native membrane proteins. The first experiments
detected and localized molecular interactions that stabilized
membrane proteins, including how these interactions were established
during folding of α-helical secondary structure elements into
the native protein and how they changed with oligomerization, temperature,
and mutations. SMFS also enables investigators to detect
and locate molecular interactions established during ligand and inhibitor
binding. These exciting applications provide opportunities
for studying the molecular forces of life. Further developments will
elucidate the origins of molecular interactions encoded in their lifetimes,
interaction ranges, interplay, and dynamics characteristic of biological systems.
author:
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Tanuj
full_name: Sapra, Tanuj K
last_name: Sapra
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Kedrov A, Janovjak HL, Sapra T, Mueller D. Deciphering molecular interactions
of native membrane proteins by single-molecule force spectroscopy. Annual Review
of Biophysics. 2007;36:233-260. doi:10.1146/annurev.biophys.36.040306.132640
apa: Kedrov, A., Janovjak, H. L., Sapra, T., & Mueller, D. (2007). Deciphering
molecular interactions of native membrane proteins by single-molecule force spectroscopy.
Annual Review of Biophysics. Annual Reviews. https://doi.org/10.1146/annurev.biophys.36.040306.132640
chicago: Kedrov, Alexej, Harald L Janovjak, Tanuj Sapra, and Daniel Mueller. “Deciphering
Molecular Interactions of Native Membrane Proteins by Single-Molecule Force Spectroscopy.”
Annual Review of Biophysics. Annual Reviews, 2007. https://doi.org/10.1146/annurev.biophys.36.040306.132640.
ieee: A. Kedrov, H. L. Janovjak, T. Sapra, and D. Mueller, “Deciphering molecular
interactions of native membrane proteins by single-molecule force spectroscopy,”
Annual Review of Biophysics, vol. 36. Annual Reviews, pp. 233–260, 2007.
ista: Kedrov A, Janovjak HL, Sapra T, Mueller D. 2007. Deciphering molecular interactions
of native membrane proteins by single-molecule force spectroscopy. Annual Review
of Biophysics. 36, 233–260.
mla: Kedrov, Alexej, et al. “Deciphering Molecular Interactions of Native Membrane
Proteins by Single-Molecule Force Spectroscopy.” Annual Review of Biophysics,
vol. 36, Annual Reviews, 2007, pp. 233–60, doi:10.1146/annurev.biophys.36.040306.132640.
short: A. Kedrov, H.L. Janovjak, T. Sapra, D. Mueller, Annual Review of Biophysics
36 (2007) 233–260.
date_created: 2018-12-11T12:03:11Z
date_published: 2007-06-01T00:00:00Z
date_updated: 2019-04-26T07:22:27Z
day: '01'
doi: 10.1146/annurev.biophys.36.040306.132640
extern: 1
intvolume: ' 36'
month: '06'
page: 233 - 260
publication: Annual Review of Biophysics
publication_status: published
publisher: Annual Reviews
publist_id: '2989'
quality_controlled: 0
status: public
title: Deciphering molecular interactions of native membrane proteins by single-molecule
force spectroscopy
type: review
volume: 36
year: '2007'
...
---
_id: '3427'
abstract:
- lang: eng
text: "We present a general theoretical framework to discuss mechanisms of morphogen
transport and gradient formation in a cell layer. Trafficking events on the cellular
scale lead to transport on larger scales. We discuss in particular the case of
transcytosis where morphogens undergo repeated rounds of internalization into
cells and recycling. Based on a description on the cellular scale, we derive effective
nonlinear transport equations in one and two dimensions which are valid on larger
scales. We derive analytic expressions for the concentration dependence of the
effective diffusion coefficient and the effective degradation rate. We discuss
the effects of a directional bias on morphogen transport and those of the coupling
of the morphogen and receptor kinetics. Furthermore, we discuss general properties
of cellular transport processes such as the robustness of gradients and relate
our results to recent experiments on the morphogen Decapentaplegic (Dpp) that
acts in the wing disk of the fruit fly Drosophila.\r\n© 2007 The American Physical
Society"
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: Karsten
full_name: Kruse, Karsten
last_name: Kruse
- first_name: Periklis
full_name: Pantazis, Periklis
last_name: Pantazis
- first_name: Marcos
full_name: Gonzalez Gaitan, Marcos
last_name: Gonzalez Gaitan
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
citation:
ama: Bollenbach MT, Kruse K, Pantazis P, Gonzalez Gaitan M, Julicher F. Morphogen
transport in epithelia. Physical Review E Statistical Nonlinear and Soft Matter
Physics. 2007;75(1). doi:10.1103/PhysRevE.75.011901
apa: Bollenbach, M. T., Kruse, K., Pantazis, P., Gonzalez Gaitan, M., & Julicher,
F. (2007). Morphogen transport in epithelia. Physical Review E Statistical
Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.75.011901
chicago: Bollenbach, Mark Tobias, Karsten Kruse, Periklis Pantazis, Marcos Gonzalez
Gaitan, and Frank Julicher. “Morphogen Transport in Epithelia.” Physical Review
E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics,
2007. https://doi.org/10.1103/PhysRevE.75.011901.
ieee: M. T. Bollenbach, K. Kruse, P. Pantazis, M. Gonzalez Gaitan, and F. Julicher,
“Morphogen transport in epithelia,” Physical Review E Statistical Nonlinear
and Soft Matter Physics, vol. 75, no. 1. American Institute of Physics, 2007.
ista: Bollenbach MT, Kruse K, Pantazis P, Gonzalez Gaitan M, Julicher F. 2007. Morphogen
transport in epithelia. Physical Review E Statistical Nonlinear and Soft Matter
Physics. 75(1).
mla: Bollenbach, Mark Tobias, et al. “Morphogen Transport in Epithelia.” Physical
Review E Statistical Nonlinear and Soft Matter Physics, vol. 75, no. 1, American
Institute of Physics, 2007, doi:10.1103/PhysRevE.75.011901.
short: M.T. Bollenbach, K. Kruse, P. Pantazis, M. Gonzalez Gaitan, F. Julicher,
Physical Review E Statistical Nonlinear and Soft Matter Physics 75 (2007).
date_created: 2018-12-11T12:03:16Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:24Z
day: '01'
doi: 10.1103/PhysRevE.75.011901
extern: '1'
external_id:
arxiv:
- q-bio/0609011v1
intvolume: ' 75'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/q-bio/0609011v1
month: '01'
oa: 1
oa_version: Preprint
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '2974'
status: public
title: Morphogen transport in epithelia
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 75
year: '2007'
...
---
_id: '3523'
abstract:
- lang: eng
text: On the linear track, the recent firing sequences of CA1 place cells recur
during sharp wave/ripple patterns (SWRs) in a reverse temporal order [Foster &
Wilson (2006) Nature, 440, 680-683]. We have found similar reverse-order reactivation
during SWRs in open-field exploration where the firing sequence of cells varied
before each SWR. Both the onset times and the firing patterns of cells showed
a tendency for reversed sequences during SWRs. These effects were observed for
SWRs that occurred during exploration, but not for those during longer immobility
periods. Additionally, reverse reactivation was stronger when it was preceded
by higher speed (> 5 cm/s) run periods. The trend for reverse-order SWR reactivation
was not significantly different in familiar and novel environments, even though
SWR-associated firing rates of both pyramidal cells and interneurons were reduced
in novel environments as compared with familiar. During exploration-associated
SWRs (eSWR) place cells retain place-selective firing [O'Neill et al. (2006) Neuron,
49, 143-155]. Here, we have shown that each cell's firing onset was more delayed
and firing probability more reduced during eSWRs the further the rat was from
the middle of the cell's place field; that is, cells receiving less momentary
place-related excitatory drive fired later during SWR events. However, even controlling
for place field distance, the recent firing of cells was still significantly correlated
with SWR reactivation sequences. We therefore propose that both place-related
drive and the firing history of cells contribute to reverse reactivation during
eSWRs.
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: Joseph
full_name: Joseph O'Neill
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Kevin
full_name: Allen, Kevin
last_name: Allen
- first_name: Timothy
full_name: Senior,Timothy
last_name: Senior
citation:
ama: Csicsvari JL, O’Neill J, Allen K, Senior T. Place-selective firing contributes
to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in
open-field exploration. European Journal of Neuroscience. 2007;26(3):704-716.
doi:10.1111/j.1460-9568.2007.05684.x
apa: Csicsvari, J. L., O’Neill, J., Allen, K., & Senior, T. (2007). Place-selective
firing contributes to the reverse-order reactivation of CA1 pyramidal cells during
sharp waves in open-field exploration. European Journal of Neuroscience.
Wiley-Blackwell. https://doi.org/10.1111/j.1460-9568.2007.05684.x
chicago: Csicsvari, Jozsef L, Joseph O’Neill, Kevin Allen, and Timothy Senior. “Place-Selective
Firing Contributes to the Reverse-Order Reactivation of CA1 Pyramidal Cells during
Sharp Waves in Open-Field Exploration.” European Journal of Neuroscience.
Wiley-Blackwell, 2007. https://doi.org/10.1111/j.1460-9568.2007.05684.x.
ieee: J. L. Csicsvari, J. O’Neill, K. Allen, and T. Senior, “Place-selective firing
contributes to the reverse-order reactivation of CA1 pyramidal cells during sharp
waves in open-field exploration,” European Journal of Neuroscience, vol.
26, no. 3. Wiley-Blackwell, pp. 704–716, 2007.
ista: Csicsvari JL, O’Neill J, Allen K, Senior T. 2007. Place-selective firing contributes
to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in
open-field exploration. European Journal of Neuroscience. 26(3), 704–716.
mla: Csicsvari, Jozsef L., et al. “Place-Selective Firing Contributes to the Reverse-Order
Reactivation of CA1 Pyramidal Cells during Sharp Waves in Open-Field Exploration.”
European Journal of Neuroscience, vol. 26, no. 3, Wiley-Blackwell, 2007,
pp. 704–16, doi:10.1111/j.1460-9568.2007.05684.x.
short: J.L. Csicsvari, J. O’Neill, K. Allen, T. Senior, European Journal of Neuroscience
26 (2007) 704–716.
date_created: 2018-12-11T12:03:46Z
date_published: 2007-08-01T00:00:00Z
date_updated: 2021-01-12T07:44:03Z
day: '01'
doi: 10.1111/j.1460-9568.2007.05684.x
extern: 1
intvolume: ' 26'
issue: '3'
month: '08'
page: 704 - 716
publication: European Journal of Neuroscience
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2862'
quality_controlled: 0
status: public
title: Place-selective firing contributes to the reverse-order reactivation of CA1
pyramidal cells during sharp waves in open-field exploration
type: journal_article
volume: 26
year: '2007'
...
---
_id: '3601'
abstract:
- lang: eng
text: In this paper, the multiobjective optimal design of space-based reconfigurable
sensor networks with novel adaptive MEMS antennas is investigated by using multiobjective
evolutionary algorithms. The non-dominated sorting genetic algorithm II (NSGA-II)
is employed to obtain multi-criteria Pareto-optimal solutions, which allows system
designers to easily make a reasonable trade-off choice from the set of non-dominated
solutions according to their preferences and system requirements. As a case study,
a cluster-based satellite sensing network is simulated under multiple objectives.
Most importantly, this paper also presents the application of our newly designed
adaptive MEMS antennas together with the NSGA-II to the multiobjective optimal
design of space-based reconfigurable sensor networks.
author:
- first_name: Erfu
full_name: Yang, Erfu
last_name: Yang
- first_name: Nakul
full_name: Haridas, Nakul
last_name: Haridas
- first_name: Ahmed
full_name: El-Rayis, Ahmed O
last_name: El Rayis
- first_name: Ahmet
full_name: Erdogan, Ahmet T
last_name: Erdogan
- first_name: Tughrul
full_name: Arslan, Tughrul
last_name: Arslan
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Yang E, Haridas N, El Rayis A, Erdogan A, Arslan T, Barton NH. Multiobjective
optimal design of MEMS-based reconfigurable and evolvable sensor networks for
space applications. In: IEEE; 2007:27-34. doi:10.1109/AHS.2007.76'
apa: 'Yang, E., Haridas, N., El Rayis, A., Erdogan, A., Arslan, T., & Barton,
N. H. (2007). Multiobjective optimal design of MEMS-based reconfigurable and evolvable
sensor networks for space applications (pp. 27–34). Presented at the AHS: NASA/ESA
Conference on Adaptive Hardware and Systems, IEEE. https://doi.org/10.1109/AHS.2007.76'
chicago: Yang, Erfu, Nakul Haridas, Ahmed El Rayis, Ahmet Erdogan, Tughrul Arslan,
and Nicholas H Barton. “Multiobjective Optimal Design of MEMS-Based Reconfigurable
and Evolvable Sensor Networks for Space Applications,” 27–34. IEEE, 2007. https://doi.org/10.1109/AHS.2007.76.
ieee: 'E. Yang, N. Haridas, A. El Rayis, A. Erdogan, T. Arslan, and N. H. Barton,
“Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor
networks for space applications,” presented at the AHS: NASA/ESA Conference on
Adaptive Hardware and Systems, 2007, pp. 27–34.'
ista: 'Yang E, Haridas N, El Rayis A, Erdogan A, Arslan T, Barton NH. 2007. Multiobjective
optimal design of MEMS-based reconfigurable and evolvable sensor networks for
space applications. AHS: NASA/ESA Conference on Adaptive Hardware and Systems,
27–34.'
mla: Yang, Erfu, et al. Multiobjective Optimal Design of MEMS-Based Reconfigurable
and Evolvable Sensor Networks for Space Applications. IEEE, 2007, pp. 27–34,
doi:10.1109/AHS.2007.76.
short: E. Yang, N. Haridas, A. El Rayis, A. Erdogan, T. Arslan, N.H. Barton, in:,
IEEE, 2007, pp. 27–34.
conference:
name: 'AHS: NASA/ESA Conference on Adaptive Hardware and Systems'
date_created: 2018-12-11T12:04:11Z
date_published: 2007-08-20T00:00:00Z
date_updated: 2021-01-12T07:44:35Z
day: '20'
doi: 10.1109/AHS.2007.76
extern: 1
month: '08'
page: 27 - 34
publication_status: published
publisher: IEEE
publist_id: '2782'
quality_controlled: 0
status: public
title: Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor
networks for space applications
type: conference
year: '2007'
...
---
_id: '3687'
abstract:
- lang: eng
text: |-
Recent years have seen huge advances in object recognition from images. Recognition rates beyond 95% are the rule rather than the exception on many datasets. However, most state-of-the-art methods can only decide if an object is present or not. They are not able to provide information on the object location or extent within in the image.
We report on a simple yet powerful scheme that extends many existing recognition methods to also perform localization of object bounding boxes. This is achieved by maximizing the classification score over all possible subrectangles in the image. Despite the impression that this would be computationally intractable, we show that in many situations efficient algorithms exist which solve a generalized maximum subrectangle problem.
We show how our method is applicable to a variety object detection frameworks and demonstrate its performance by applying it to the popular bag of visual words model, achieving competitive results on the PASCAL VOC 2006 dataset.
author:
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
- first_name: Thomas
full_name: Hofmann,Thomas
last_name: Hofmann
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Blaschko M, Hofmann T, Lampert C. Efficient Subwindow Search for Object
Localization. Max-Planck-Institute for Biological Cybernetics; 2007.
apa: Blaschko, M., Hofmann, T., & Lampert, C. (2007). Efficient subwindow
search for object localization. Unknown. Max-Planck-Institute for Biological
Cybernetics.
chicago: Blaschko, Matthew, Thomas Hofmann, and Christoph Lampert. Efficient
Subwindow Search for Object Localization. Unknown. Max-Planck-Institute
for Biological Cybernetics, 2007.
ieee: M. Blaschko, T. Hofmann, and C. Lampert, Efficient subwindow search for
object localization, no. 164. Max-Planck-Institute for Biological Cybernetics,
2007.
ista: Blaschko M, Hofmann T, Lampert C. 2007. Efficient subwindow search for object
localization, Max-Planck-Institute for Biological Cybernetics,p.
mla: Blaschko, Matthew, et al. “Efficient Subwindow Search for Object Localization.”
Unknown, no. 164, Max-Planck-Institute for Biological Cybernetics, 2007.
short: M. Blaschko, T. Hofmann, C. Lampert, Efficient Subwindow Search for Object
Localization, Max-Planck-Institute for Biological Cybernetics, 2007.
date_created: 2018-12-11T12:04:37Z
date_published: 2007-08-01T00:00:00Z
date_updated: 2019-04-26T07:22:33Z
day: '01'
extern: 1
issue: '164'
main_file_link:
- open_access: '0'
url: http://www.kyb.tuebingen.mpg.de/fileadmin/user_upload/files/publications/TR-164_[0].pdf
month: '08'
publication: Unknown
publication_status: published
publisher: Max-Planck-Institute for Biological Cybernetics
publist_id: '2681'
quality_controlled: 0
status: public
title: Efficient subwindow search for object localization
type: report
year: '2007'
...
---
_id: '3701'
abstract:
- lang: eng
text: |-
The extraction of a parametric global motion from a motion field is a task with several applications in video processing. We present two probabilistic formulations of the problem and carry out optimization using the RAST algorithm, a geometric matching method novel to motion estimation in video. RAST uses an exhaustive and adaptive search of transformation space and thus gives – in contrast to local sampling optimization techniques used in the past – a globally optimal solution. Among other applications, our framework can thus be used as a source of ground truth for benchmarking motion estimation algorithms.
Our main contributions are: first, the novel combination of a state-of-the-art MAP criterion for dominant motion estimation with a search procedure that guarantees global optimality. Second, experimental results that illustrate the superior performance of our approach on synthetic flow fields as well as real-world video streams. Third, a significant speedup of the search achieved by extending the model with an additional smoothness prior.
alternative_title:
- LNCS
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: Daniel
full_name: Keysers,Daniel
last_name: Keysers
- first_name: Thomas
full_name: Breuel,Thomas M
last_name: Breuel
citation:
ama: 'Ulges A, Lampert C, Keysers D, Breuel T. Optimal dominant motion estimation
using adaptive search of transformation space. In: Vol 4713. Springer; 2007:204-213.
doi:10.1007/978-3-540-74936-3_21'
apa: 'Ulges, A., Lampert, C., Keysers, D., & Breuel, T. (2007). Optimal dominant
motion estimation using adaptive search of transformation space (Vol. 4713, pp.
204–213). Presented at the DAGM: German Association For Pattern Recognition, Springer.
https://doi.org/10.1007/978-3-540-74936-3_21'
chicago: Ulges, Adrian, Christoph Lampert, Daniel Keysers, and Thomas Breuel. “Optimal
Dominant Motion Estimation Using Adaptive Search of Transformation Space,” 4713:204–13.
Springer, 2007. https://doi.org/10.1007/978-3-540-74936-3_21.
ieee: 'A. Ulges, C. Lampert, D. Keysers, and T. Breuel, “Optimal dominant motion
estimation using adaptive search of transformation space,” presented at the DAGM:
German Association For Pattern Recognition, 2007, vol. 4713, pp. 204–213.'
ista: 'Ulges A, Lampert C, Keysers D, Breuel T. 2007. Optimal dominant motion estimation
using adaptive search of transformation space. DAGM: German Association For Pattern
Recognition, LNCS, vol. 4713, 204–213.'
mla: Ulges, Adrian, et al. Optimal Dominant Motion Estimation Using Adaptive
Search of Transformation Space. Vol. 4713, Springer, 2007, pp. 204–13, doi:10.1007/978-3-540-74936-3_21.
short: A. Ulges, C. Lampert, D. Keysers, T. Breuel, in:, Springer, 2007, pp. 204–213.
conference:
name: 'DAGM: German Association For Pattern Recognition'
date_created: 2018-12-11T12:04:42Z
date_published: 2007-11-09T00:00:00Z
date_updated: 2021-01-12T07:51:35Z
day: '09'
doi: 10.1007/978-3-540-74936-3_21
extern: 1
intvolume: ' 4713'
month: '11'
page: 204 - 213
publication_status: published
publisher: Springer
publist_id: '2656'
quality_controlled: 0
status: public
title: Optimal dominant motion estimation using adaptive search of transformation
space
type: conference
volume: 4713
year: '2007'
...
---
_id: '3731'
abstract:
- lang: eng
text: A cell's ability to regulate gene transcription depends in large part on the
energy with which transcription factors (TFs) bind their DNA regulatory sites.
Obtaining accurate models of this binding energy is therefore an important goal
for quantitative biology. In this article, we present a principled likelihood-based
approach for inferring physical models of TF-DNA binding energy from the data
produced by modern high-throughput binding assays. Central to our analysis is
the ability to assess the relative likelihood of different model parameters given
experimental observations. We take a unique approach to this problem and show
how to compute likelihood without any explicit assumptions about the noise that
inevitably corrupts such measurements. Sampling possible choices for model parameters
according to this likelihood function, we can then make probabilistic predictions
for the identities of binding sites and their physical binding energies. Applying
this procedure to previously published data on the Saccharomyces cerevisiae TF
Abf1p, we find models of TF binding whose parameters are determined with remarkable
precision. Evidence for the accuracy of these models is provided by an astonishing
level of phylogenetic conservation in the predicted energies of putative binding
sites. Results from in vivo and in vitro experiments also provide highly consistent
characterizations of Abf1p, a result that contrasts with a previous analysis of
the same data.
author:
- first_name: Justin
full_name: Kinney,Justin B
last_name: Kinney
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Curtis
full_name: Callan,Curtis G
last_name: Callan
citation:
ama: Kinney J, Tkačik G, Callan C. Precise physical models of protein-DNA interaction
from high-throughput data. PNAS. 2007;104(2):501-506. doi:10.1073/pnas.0609908104
apa: Kinney, J., Tkačik, G., & Callan, C. (2007). Precise physical models of
protein-DNA interaction from high-throughput data. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.0609908104
chicago: Kinney, Justin, Gašper Tkačik, and Curtis Callan. “Precise Physical Models
of Protein-DNA Interaction from High-Throughput Data.” PNAS. National Academy
of Sciences, 2007. https://doi.org/10.1073/pnas.0609908104.
ieee: J. Kinney, G. Tkačik, and C. Callan, “Precise physical models of protein-DNA
interaction from high-throughput data,” PNAS, vol. 104, no. 2. National
Academy of Sciences, pp. 501–506, 2007.
ista: Kinney J, Tkačik G, Callan C. 2007. Precise physical models of protein-DNA
interaction from high-throughput data. PNAS. 104(2), 501–506.
mla: Kinney, Justin, et al. “Precise Physical Models of Protein-DNA Interaction
from High-Throughput Data.” PNAS, vol. 104, no. 2, National Academy of
Sciences, 2007, pp. 501–06, doi:10.1073/pnas.0609908104.
short: J. Kinney, G. Tkačik, C. Callan, PNAS 104 (2007) 501–506.
date_created: 2018-12-11T12:04:51Z
date_published: 2007-01-09T00:00:00Z
date_updated: 2021-01-12T07:51:48Z
day: '09'
doi: 10.1073/pnas.0609908104
extern: 1
intvolume: ' 104'
issue: '2'
main_file_link:
- open_access: '0'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1766414
month: '01'
page: 501 - 506
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2495'
quality_controlled: 0
status: public
title: Precise physical models of protein-DNA interaction from high-throughput data
type: journal_article
volume: 104
year: '2007'
...
---
_id: '3765'
abstract:
- lang: eng
text: We present an extension to Lagrangian finite element methods to allow for
large plastic deformations of solid materials. These behaviors are seen in such
everyday materials as shampoo, dough, and clay as well as in fantastic gooey and
blobby creatures in special effects scenes. To account for plastic deformation,
we explicitly update the linear basis functions defined over the finite elements
during each simulation step. When these updates cause the basis functions to become
ill-conditioned, we remesh the simulation domain to produce a new high-quality
finite-element mesh, taking care to preserve the original boundary. We also introduce
an enhanced plasticity model that preserves volume and includes creep and work
hardening/softening. We demonstrate our approach with simulations of synthetic
objects that squish, dent, and flow. To validate our methods, we compare simulation
results to videos of real materials.
article_processing_charge: No
author:
- first_name: Adam
full_name: Bargteil, Adam
last_name: Bargteil
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Jessica
full_name: Hodgins, Jessica
last_name: Hodgins
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
citation:
ama: Bargteil A, Wojtan C, Hodgins J, Turk G. A finite element method for animating
large viscoplastic flow. ACM Transactions on Graphics. 2007;26(3). doi:10.1145/1276377.1276397
apa: Bargteil, A., Wojtan, C., Hodgins, J., & Turk, G. (2007). A finite element
method for animating large viscoplastic flow. ACM Transactions on Graphics.
ACM. https://doi.org/10.1145/1276377.1276397
chicago: Bargteil, Adam, Chris Wojtan, Jessica Hodgins, and Greg Turk. “A Finite
Element Method for Animating Large Viscoplastic Flow.” ACM Transactions on
Graphics. ACM, 2007. https://doi.org/10.1145/1276377.1276397.
ieee: A. Bargteil, C. Wojtan, J. Hodgins, and G. Turk, “A finite element method
for animating large viscoplastic flow,” ACM Transactions on Graphics, vol.
26, no. 3. ACM, 2007.
ista: Bargteil A, Wojtan C, Hodgins J, Turk G. 2007. A finite element method for
animating large viscoplastic flow. ACM Transactions on Graphics. 26(3).
mla: Bargteil, Adam, et al. “A Finite Element Method for Animating Large Viscoplastic
Flow.” ACM Transactions on Graphics, vol. 26, no. 3, ACM, 2007, doi:10.1145/1276377.1276397.
short: A. Bargteil, C. Wojtan, J. Hodgins, G. Turk, ACM Transactions on Graphics
26 (2007).
date_created: 2018-12-11T12:05:03Z
date_published: 2007-07-29T00:00:00Z
date_updated: 2023-02-23T11:41:41Z
day: '29'
doi: 10.1145/1276377.1276397
extern: '1'
intvolume: ' 26'
issue: '3'
language:
- iso: eng
month: '07'
oa_version: None
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '2462'
status: public
title: A finite element method for animating large viscoplastic flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2007'
...
---
_id: '3762'
abstract:
- lang: eng
text: In this paper, we present a simple method for animating natural phenomena
such as erosion, sedimentation, and acidic corrosion. We discretize the appropriate
physical or chemical equations using finite differences, and we use the results
to modify the shape of a solid body. We remove mass from an object by treating
its surface as a level set and advecting it inward, and we deposit the chemical
and physical byproducts into simulated fluid. Similarly, our technique deposits
sediment onto a surface by advecting the level set outward. Our idea can be used
for off-line high quality animations as well as interactive applications such
as games, and we demonstrate both in this paper.
article_processing_charge: No
author:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Mark
full_name: Carlson, Mark
last_name: Carlson
- first_name: Peter
full_name: Mucha, Peter
last_name: Mucha
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
citation:
ama: 'Wojtan C, Carlson M, Mucha P, Turk G. Animating corrosion and erosion. In:
Eurographics Association; 2007:15-22. doi:10.2312/NPH/NPH07/015-022'
apa: 'Wojtan, C., Carlson, M., Mucha, P., & Turk, G. (2007). Animating corrosion
and erosion (pp. 15–22). Presented at the EGWNP: Eurographics Workshop on Natural
Phenomena, Eurographics Association. https://doi.org/10.2312/NPH/NPH07/015-022'
chicago: Wojtan, Chris, Mark Carlson, Peter Mucha, and Greg Turk. “Animating Corrosion
and Erosion,” 15–22. Eurographics Association, 2007. https://doi.org/10.2312/NPH/NPH07/015-022.
ieee: 'C. Wojtan, M. Carlson, P. Mucha, and G. Turk, “Animating corrosion and erosion,”
presented at the EGWNP: Eurographics Workshop on Natural Phenomena, 2007, pp.
15–22.'
ista: 'Wojtan C, Carlson M, Mucha P, Turk G. 2007. Animating corrosion and erosion.
EGWNP: Eurographics Workshop on Natural Phenomena, 15–22.'
mla: Wojtan, Chris, et al. Animating Corrosion and Erosion. Eurographics
Association, 2007, pp. 15–22, doi:10.2312/NPH/NPH07/015-022.
short: C. Wojtan, M. Carlson, P. Mucha, G. Turk, in:, Eurographics Association,
2007, pp. 15–22.
conference:
name: 'EGWNP: Eurographics Workshop on Natural Phenomena'
date_created: 2018-12-11T12:05:02Z
date_published: 2007-09-01T00:00:00Z
date_updated: 2023-02-23T11:41:34Z
day: '01'
doi: 10.2312/NPH/NPH07/015-022
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://www.amath.unc.edu/Faculty/mucha/Reprints/EGNPerosion.pdf
month: '09'
oa_version: None
page: 15 - 22
publication_status: published
publisher: Eurographics Association
publist_id: '2464'
status: public
title: Animating corrosion and erosion
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2007'
...
---
_id: '3816'
abstract:
- lang: eng
text: Gamma frequency oscillations are thought to provide a temporal structure for
information processing in the brain. They contribute to cognitive functions, such
as memory formation and sensory processing, and are disturbed in some psychiatric
disorders. Fast-spiking, parvalbumin-expressing, soma-inhibiting interneurons
have a key role in the generation of these oscillations. Experimental analysis
in the hippocampus and the neocortex reveals that synapses among these interneurons
are highly specialized. Computational analysis further suggests that synaptic
specialization turns interneuron networks into robust gamma frequency oscillators.
author:
- first_name: Marlene
full_name: Bartos, Marlene
last_name: Bartos
- first_name: Imre
full_name: Vida, Imre
last_name: Vida
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Bartos M, Vida I, Jonas PM. Synaptic mechanisms of synchronized gamma oscillations
in inhibitory interneuron networks (Review). Nature Reviews Neuroscience.
2007;8(1):45-56. doi:10.1038/nrn2044
apa: Bartos, M., Vida, I., & Jonas, P. M. (2007). Synaptic mechanisms of synchronized
gamma oscillations in inhibitory interneuron networks (Review). Nature Reviews
Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nrn2044
chicago: Bartos, Marlene, Imre Vida, and Peter M Jonas. “Synaptic Mechanisms of
Synchronized Gamma Oscillations in Inhibitory Interneuron Networks (Review).”
Nature Reviews Neuroscience. Nature Publishing Group, 2007. https://doi.org/10.1038/nrn2044 .
ieee: M. Bartos, I. Vida, and P. M. Jonas, “Synaptic mechanisms of synchronized
gamma oscillations in inhibitory interneuron networks (Review),” Nature Reviews
Neuroscience, vol. 8, no. 1. Nature Publishing Group, pp. 45–56, 2007.
ista: Bartos M, Vida I, Jonas PM. 2007. Synaptic mechanisms of synchronized gamma
oscillations in inhibitory interneuron networks (Review). Nature Reviews Neuroscience.
8(1), 45–56.
mla: Bartos, Marlene, et al. “Synaptic Mechanisms of Synchronized Gamma Oscillations
in Inhibitory Interneuron Networks (Review).” Nature Reviews Neuroscience,
vol. 8, no. 1, Nature Publishing Group, 2007, pp. 45–56, doi:10.1038/nrn2044 .
short: M. Bartos, I. Vida, P.M. Jonas, Nature Reviews Neuroscience 8 (2007) 45–56.
date_created: 2018-12-11T12:05:20Z
date_published: 2007-01-21T00:00:00Z
date_updated: 2021-01-12T07:52:24Z
day: '21'
doi: '10.1038/nrn2044 '
extern: 1
intvolume: ' 8'
issue: '1'
month: '01'
page: 45 - 56
publication: Nature Reviews Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '2393'
quality_controlled: 0
status: public
title: Synaptic mechanisms of synchronized gamma oscillations in inhibitory interneuron
networks (Review)
type: journal_article
volume: 8
year: '2007'
...
---
_id: '3911'
abstract:
- lang: eng
text: Life in a social group increases the risk of disease transmission. To counteract
this threat, social insects have evolved manifold antiparasite defenses, ranging
from social exclusion of infected group members to intensive care. It is generally
assumed that individuals performing hygienic behaviors risk infecting themselves,
suggesting a high direct cost of helping. Our work instead indicates the opposite
for garden ants. Social contact with individual workers, which were experimentally
exposed to a fungal parasite, provided a clear survival benefit to nontreated,
naive group members upon later challenge with the same parasite. This first demonstration
of contact immunity in Social Hymenoptera and complementary results from other
animal groups and plants suggest its general importance in both antiparasite and
antiherbivore defense. In addition to this physiological prophylaxis of adult
ants, infection of the brood was prevented in our experiment by behavioral changes
of treated and naive workers. Parasite-treated ants stayed away from the brood
chamber, whereas their naive nestmates increased brood-care activities. Our findings
reveal a direct benefit for individuals to perform hygienic behaviors toward others,
and this might explain the widely observed maintenance of social cohesion under
parasite attack in insect societies.
author:
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Ugelvig LV, Cremer S. Social prophylaxis: group interaction promotes collective
immunity in ant colonies. Current Biology. 2007;17(22):1967-1971. doi:10.1016/j.cub.2007.10.029'
apa: 'Ugelvig, L. V., & Cremer, S. (2007). Social prophylaxis: group interaction
promotes collective immunity in ant colonies. Current Biology. Cell Press.
https://doi.org/10.1016/j.cub.2007.10.029'
chicago: 'Ugelvig, Line V, and Sylvia Cremer. “Social Prophylaxis: Group Interaction
Promotes Collective Immunity in Ant Colonies.” Current Biology. Cell Press,
2007. https://doi.org/10.1016/j.cub.2007.10.029.'
ieee: 'L. V. Ugelvig and S. Cremer, “Social prophylaxis: group interaction promotes
collective immunity in ant colonies,” Current Biology, vol. 17, no. 22.
Cell Press, pp. 1967–1971, 2007.'
ista: 'Ugelvig LV, Cremer S. 2007. Social prophylaxis: group interaction promotes
collective immunity in ant colonies. Current Biology. 17(22), 1967–1971.'
mla: 'Ugelvig, Line V., and Sylvia Cremer. “Social Prophylaxis: Group Interaction
Promotes Collective Immunity in Ant Colonies.” Current Biology, vol. 17,
no. 22, Cell Press, 2007, pp. 1967–71, doi:10.1016/j.cub.2007.10.029.'
short: L.V. Ugelvig, S. Cremer, Current Biology 17 (2007) 1967–1971.
date_created: 2018-12-11T12:05:51Z
date_published: 2007-11-20T00:00:00Z
date_updated: 2021-01-12T07:53:08Z
day: '20'
doi: 10.1016/j.cub.2007.10.029
extern: '1'
intvolume: ' 17'
issue: '22'
language:
- iso: eng
month: '11'
oa_version: None
page: 1967 - 1971
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '2245'
status: public
title: 'Social prophylaxis: group interaction promotes collective immunity in ant
colonies'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2007'
...
---
_id: '3909'
abstract:
- lang: eng
text: Social insect colonies have evolved collective immune defences against parasites.
These ‘social immune systems’ result from the cooperation of the individual group
members to combat the increased risk of disease transmission that arises from
sociality and group living. In this review we illustrate the pathways that parasites
can take to infect a social insect colony and use these pathways as a framework
to predict colony defence mechanisms and present the existing evidence. We find
that the collective defences can be both prophylactic and activated on demand
and consist of behavioural, physiological and organisational adaptations of the
colony that prevent parasite entrance, establishment and spread. We discuss the
regulation of collective immunity, which requires complex integration of information
about both the parasites and the internal status of the insect colony. Our review
concludes with an examination of the evolution of social immunity, which is based
on the consequences of selection at both the individual and the colony level.
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Sophie
full_name: Armitage, Sophie
last_name: Armitage
- first_name: Paul
full_name: Schmid Hempel, Paul
last_name: Schmid Hempel
citation:
ama: Cremer S, Armitage S, Schmid Hempel P. Social immunity. Current Biology.
2007;17(16):R693-R702. doi:10.1016/j.cub.2007.06.008
apa: Cremer, S., Armitage, S., & Schmid Hempel, P. (2007). Social immunity.
Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2007.06.008
chicago: Cremer, Sylvia, Sophie Armitage, and Paul Schmid Hempel. “Social Immunity.”
Current Biology. Cell Press, 2007. https://doi.org/10.1016/j.cub.2007.06.008.
ieee: S. Cremer, S. Armitage, and P. Schmid Hempel, “Social immunity,” Current
Biology, vol. 17, no. 16. Cell Press, pp. R693–R702, 2007.
ista: Cremer S, Armitage S, Schmid Hempel P. 2007. Social immunity. Current Biology.
17(16), R693–R702.
mla: Cremer, Sylvia, et al. “Social Immunity.” Current Biology, vol. 17,
no. 16, Cell Press, 2007, pp. R693–702, doi:10.1016/j.cub.2007.06.008.
short: S. Cremer, S. Armitage, P. Schmid Hempel, Current Biology 17 (2007) R693–R702.
date_created: 2018-12-11T12:05:50Z
date_published: 2007-08-21T00:00:00Z
date_updated: 2021-01-12T07:53:07Z
day: '21'
doi: 10.1016/j.cub.2007.06.008
extern: '1'
intvolume: ' 17'
issue: '16'
language:
- iso: eng
month: '08'
oa_version: None
page: R693 - R702
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '2243'
status: public
title: Social immunity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2007'
...
---
_id: '3910'
author:
- first_name: David
full_name: Hughes, David
last_name: Hughes
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Hughes D, Cremer S. Plasticity in anti-parasite behaviours and its suggested
role in invasion biology. Animal Behaviour. 2007;74(5):1593-1599. doi:10.1016/j.anbehav.2006.12.025
apa: Hughes, D., & Cremer, S. (2007). Plasticity in anti-parasite behaviours
and its suggested role in invasion biology. Animal Behaviour. Elsevier.
https://doi.org/10.1016/j.anbehav.2006.12.025
chicago: Hughes, David, and Sylvia Cremer. “Plasticity in Anti-Parasite Behaviours
and Its Suggested Role in Invasion Biology.” Animal Behaviour. Elsevier,
2007. https://doi.org/10.1016/j.anbehav.2006.12.025.
ieee: D. Hughes and S. Cremer, “Plasticity in anti-parasite behaviours and its suggested
role in invasion biology,” Animal Behaviour, vol. 74, no. 5. Elsevier,
pp. 1593–1599, 2007.
ista: Hughes D, Cremer S. 2007. Plasticity in anti-parasite behaviours and its suggested
role in invasion biology. Animal Behaviour. 74(5), 1593–1599.
mla: Hughes, David, and Sylvia Cremer. “Plasticity in Anti-Parasite Behaviours and
Its Suggested Role in Invasion Biology.” Animal Behaviour, vol. 74, no.
5, Elsevier, 2007, pp. 1593–99, doi:10.1016/j.anbehav.2006.12.025.
short: D. Hughes, S. Cremer, Animal Behaviour 74 (2007) 1593–1599.
date_created: 2018-12-11T12:05:50Z
date_published: 2007-11-01T00:00:00Z
date_updated: 2021-01-12T07:53:08Z
day: '01'
doi: 10.1016/j.anbehav.2006.12.025
extern: '1'
intvolume: ' 74'
issue: '5'
language:
- iso: eng
month: '11'
oa_version: None
page: 1593 - 1599
publication: Animal Behaviour
publication_status: published
publisher: Elsevier
publist_id: '2244'
status: public
title: Plasticity in anti-parasite behaviours and its suggested role in invasion biology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2007'
...
---
_id: '3976'
abstract:
- lang: eng
text: Herein, we study the interfaces of a set of 146 transient protein-protein
interfaces in order to better understand the principles of their interactions.
We define and generate the protein interface using tools from computational geometry
and topology and then apply statistical analysis to its residue composition. In
addition to counting individual occurrences, we evaluate pairing preferences,
both across and as neighbors on one side of an interface. Likelihood correction
emphasizes novel and unexpected pairs, such as the His-Cys pair found in most
complexes of serine proteases with their diverse inhibitors and the Met-Met neighbor
pair found in unrelated protein interfaces. We also present a visualization of
the protein interface that allows for facile identification of residue-residue
contacts and other biochemical properties.
author:
- first_name: Jeffrey
full_name: Headd, Jeffrey J
last_name: Headd
- first_name: Y E Andrew
full_name: Ban, Y E Andrew
last_name: Ban
- first_name: Paul
full_name: Brown, Paul
last_name: Brown
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Madhuwanti
full_name: Vaidya, Madhuwanti
last_name: Vaidya
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
citation:
ama: 'Headd J, Ban YEA, Brown P, Edelsbrunner H, Vaidya M, Rudolph J. Protein-protein
interfaces: Properties, preferences, and projections. Journal of Proteome Research.
2007;6(7):2576-2586. doi:10.1021/pr070018+'
apa: 'Headd, J., Ban, Y. E. A., Brown, P., Edelsbrunner, H., Vaidya, M., & Rudolph,
J. (2007). Protein-protein interfaces: Properties, preferences, and projections.
Journal of Proteome Research. American Chemical Society. https://doi.org/10.1021/pr070018+'
chicago: 'Headd, Jeffrey, Y E Andrew Ban, Paul Brown, Herbert Edelsbrunner, Madhuwanti
Vaidya, and Johannes Rudolph. “Protein-Protein Interfaces: Properties, Preferences,
and Projections.” Journal of Proteome Research. American Chemical Society,
2007. https://doi.org/10.1021/pr070018+.'
ieee: 'J. Headd, Y. E. A. Ban, P. Brown, H. Edelsbrunner, M. Vaidya, and J. Rudolph,
“Protein-protein interfaces: Properties, preferences, and projections,” Journal
of Proteome Research, vol. 6, no. 7. American Chemical Society, pp. 2576–2586,
2007.'
ista: 'Headd J, Ban YEA, Brown P, Edelsbrunner H, Vaidya M, Rudolph J. 2007. Protein-protein
interfaces: Properties, preferences, and projections. Journal of Proteome Research.
6(7), 2576–2586.'
mla: 'Headd, Jeffrey, et al. “Protein-Protein Interfaces: Properties, Preferences,
and Projections.” Journal of Proteome Research, vol. 6, no. 7, American
Chemical Society, 2007, pp. 2576–86, doi:10.1021/pr070018+.'
short: J. Headd, Y.E.A. Ban, P. Brown, H. Edelsbrunner, M. Vaidya, J. Rudolph, Journal
of Proteome Research 6 (2007) 2576–2586.
date_created: 2018-12-11T12:06:13Z
date_published: 2007-06-02T00:00:00Z
date_updated: 2021-01-12T07:53:36Z
day: '02'
doi: 10.1021/pr070018+
extern: 1
intvolume: ' 6'
issue: '7'
month: '06'
page: 2576 - 2586
publication: Journal of Proteome Research
publication_status: published
publisher: American Chemical Society
publist_id: '2151'
quality_controlled: 0
status: public
title: 'Protein-protein interfaces: Properties, preferences, and projections'
type: journal_article
volume: 6
year: '2007'
...
---
_id: '3981'
abstract:
- lang: eng
text: Building on the work of Martinetz, Schulten and de Silva, Carlsson, we introduce
a 2-parameter family of witness complexes and algorithms for constructing them.
This family can be used to determine the gross topology of point cloud data in
R-d or other metric spaces. The 2-parameter family is sensitive to differences
in sampling density and thus amenable to detecting patterns within the data set.
It also lends itself to theoretical analysis. For example, we can prove that in
the limit, when the witnesses cover the entire domain, witness complexes in the
family that share the first, scale parameter have the same homotopy type.
acknowledgement: Research by the authors is partially supported by DARPA under grant
HR0011-05-1-0007, by CNRS under grant PICS-3416 and by IST Program of the EU under
Contract IST-2002-506766.
alternative_title:
- LNCS
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- 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: Yuriy
full_name: Mileyko, Yuriy
last_name: Mileyko
citation:
ama: 'Attali D, Edelsbrunner H, Harer J, Mileyko Y. Alpha-beta witness complexes.
In: Vol 4619. Springer; 2007:386-397. doi:10.1007/978-3-540-73951-7_34'
apa: 'Attali, D., Edelsbrunner, H., Harer, J., & Mileyko, Y. (2007). Alpha-beta
witness complexes (Vol. 4619, pp. 386–397). Presented at the WADS: International
Workshop on Algrithms and Data Structures, Springer. https://doi.org/10.1007/978-3-540-73951-7_34'
chicago: Attali, Dominique, Herbert Edelsbrunner, John Harer, and Yuriy Mileyko.
“Alpha-Beta Witness Complexes,” 4619:386–97. Springer, 2007. https://doi.org/10.1007/978-3-540-73951-7_34.
ieee: 'D. Attali, H. Edelsbrunner, J. Harer, and Y. Mileyko, “Alpha-beta witness
complexes,” presented at the WADS: International Workshop on Algrithms and Data
Structures, 2007, vol. 4619, pp. 386–397.'
ista: 'Attali D, Edelsbrunner H, Harer J, Mileyko Y. 2007. Alpha-beta witness complexes.
WADS: International Workshop on Algrithms and Data Structures, LNCS, vol. 4619,
386–397.'
mla: Attali, Dominique, et al. Alpha-Beta Witness Complexes. Vol. 4619, Springer,
2007, pp. 386–97, doi:10.1007/978-3-540-73951-7_34.
short: D. Attali, H. Edelsbrunner, J. Harer, Y. Mileyko, in:, Springer, 2007, pp.
386–397.
conference:
name: 'WADS: International Workshop on Algrithms and Data Structures'
date_created: 2018-12-11T12:06:15Z
date_published: 2007-08-21T00:00:00Z
date_updated: 2021-01-12T07:53:38Z
day: '21'
doi: 10.1007/978-3-540-73951-7_34
extern: 1
intvolume: ' 4619'
month: '08'
page: 386 - 397
publication_status: published
publisher: Springer
publist_id: '2149'
quality_controlled: 0
status: public
title: Alpha-beta witness complexes
type: conference
volume: 4619
year: '2007'
...
---
_id: '3975'
abstract:
- lang: eng
text: We study the reconstruction of a stratified space from a possibly noisy point
sample. Specifically, we use the vineyard of the distance function restricted
to a I-parameter family of neighborhoods of a point to assess the local homology
of the stratified space at that point. We prove the correctness of this assessment
under the assumption of a sufficiently dense sample. We also give an algorithm
that constructs the vineyard and makes the local assessment in time at most cubic
in the size of the Delaunay triangulation of the point sample.
author:
- first_name: Paul
full_name: Paul Bendich
id: 43F6EC54-F248-11E8-B48F-1D18A9856A87
last_name: Bendich
- first_name: David
full_name: Cohen-Steiner, David
last_name: Cohen Steiner
- 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: Dmitriy
full_name: Morozov, Dmitriy
last_name: Morozov
citation:
ama: 'Bendich P, Cohen Steiner D, Edelsbrunner H, Harer J, Morozov D. Inferring
local homology from sampled stratified spaces. In: IEEE; 2007:536-546. doi:10.1109/FOCS.2007.33'
apa: 'Bendich, P., Cohen Steiner, D., Edelsbrunner, H., Harer, J., & Morozov,
D. (2007). Inferring local homology from sampled stratified spaces (pp. 536–546).
Presented at the FOCS: Foundations of Computer Science, IEEE. https://doi.org/10.1109/FOCS.2007.33'
chicago: Bendich, Paul, David Cohen Steiner, Herbert Edelsbrunner, John Harer, and
Dmitriy Morozov. “Inferring Local Homology from Sampled Stratified Spaces,” 536–46.
IEEE, 2007. https://doi.org/10.1109/FOCS.2007.33.
ieee: 'P. Bendich, D. Cohen Steiner, H. Edelsbrunner, J. Harer, and D. Morozov,
“Inferring local homology from sampled stratified spaces,” presented at the FOCS:
Foundations of Computer Science, 2007, pp. 536–546.'
ista: 'Bendich P, Cohen Steiner D, Edelsbrunner H, Harer J, Morozov D. 2007. Inferring
local homology from sampled stratified spaces. FOCS: Foundations of Computer Science,
536–546.'
mla: Bendich, Paul, et al. Inferring Local Homology from Sampled Stratified Spaces.
IEEE, 2007, pp. 536–46, doi:10.1109/FOCS.2007.33.
short: P. Bendich, D. Cohen Steiner, H. Edelsbrunner, J. Harer, D. Morozov, in:,
IEEE, 2007, pp. 536–546.
conference:
name: 'FOCS: Foundations of Computer Science'
date_created: 2018-12-11T12:06:13Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:35Z
day: '01'
doi: 10.1109/FOCS.2007.33
extern: 1
month: '01'
page: 536 - 546
publication_status: published
publisher: IEEE
publist_id: '2150'
quality_controlled: 0
status: public
title: Inferring local homology from sampled stratified spaces
type: conference
year: '2007'
...
---
_id: '3977'
abstract:
- lang: eng
text: Using inclusion-exclusion, we can write the indicator function of a union
of finitely many balls as an alternating sum of indicator functions of common
intersections of balls. We exhibit abstract simplicial complexes that correspond
to minimal inclusion-exclusion formulas. They include the dual complex, as defined
in [3], and are characterized by the independence of their simplices and by geometric
realizations with the same underlying space as the dual complex.
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Attali D, Edelsbrunner H. Inclusion-exclusion formulas from independent complexes.
Discrete & Computational Geometry. 2007;37(1):59-77. doi:10.1007/s00454-006-1274-7
apa: Attali, D., & Edelsbrunner, H. (2007). Inclusion-exclusion formulas from
independent complexes. Discrete & Computational Geometry. Springer.
https://doi.org/10.1007/s00454-006-1274-7
chicago: Attali, Dominique, and Herbert Edelsbrunner. “Inclusion-Exclusion Formulas
from Independent Complexes.” Discrete & Computational Geometry. Springer,
2007. https://doi.org/10.1007/s00454-006-1274-7.
ieee: D. Attali and H. Edelsbrunner, “Inclusion-exclusion formulas from independent
complexes,” Discrete & Computational Geometry, vol. 37, no. 1. Springer,
pp. 59–77, 2007.
ista: Attali D, Edelsbrunner H. 2007. Inclusion-exclusion formulas from independent
complexes. Discrete & Computational Geometry. 37(1), 59–77.
mla: Attali, Dominique, and Herbert Edelsbrunner. “Inclusion-Exclusion Formulas
from Independent Complexes.” Discrete & Computational Geometry, vol.
37, no. 1, Springer, 2007, pp. 59–77, doi:10.1007/s00454-006-1274-7.
short: D. Attali, H. Edelsbrunner, Discrete & Computational Geometry 37 (2007)
59–77.
date_created: 2018-12-11T12:06:14Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:36Z
day: '01'
doi: 10.1007/s00454-006-1274-7
extern: 1
intvolume: ' 37'
issue: '1'
month: '01'
page: 59 - 77
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2152'
quality_controlled: 0
status: public
title: Inclusion-exclusion formulas from independent complexes
type: journal_article
volume: 37
year: '2007'
...
---
_id: '4152'
abstract:
- lang: eng
text: 'Gastrulation is a morphogenetic process that results in the formation of
the embryonic germ layers. Here we detail the major cell movements that occur
during zebrafish gastrulation: epiboly, internalization, and convergent extension.
Although gastrulation is known to be regulated by signaling pathways such as the
Wnt/planar cell polarity pathway, many questions remain about the underlying molecular
and cellular mechanisms. Key factors that may play a role in gastrulation cell
movements are cell adhesion and cytoskeletal rearrangement. In addition, some
of the driving force for gastrulation may derive from tissue interactions such
as those described between the enveloping layer and the yolk syncytial layer.
Future exploration of gastrulation mechanisms relies on the development of sensitive
and quantitative techniques to characterize embryonic germ-layer properties.'
author:
- first_name: Laurel
full_name: Rohde, Laurel
last_name: Rohde
- 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: 'Rohde L, Heisenberg C-PJ. Zebrafish gastrulation: Cell movements, signals,
and mechanisms. International Review of Cytology - A Survey of Cell Biology.
2007;261:159-192. doi:10.1016/S0074-7696(07)61004-3'
apa: 'Rohde, L., & Heisenberg, C.-P. J. (2007). Zebrafish gastrulation: Cell
movements, signals, and mechanisms. International Review of Cytology - A Survey
of Cell Biology. Academic Press. https://doi.org/10.1016/S0074-7696(07)61004-3'
chicago: 'Rohde, Laurel, and Carl-Philipp J Heisenberg. “Zebrafish Gastrulation:
Cell Movements, Signals, and Mechanisms.” International Review of Cytology
- A Survey of Cell Biology. Academic Press, 2007. https://doi.org/10.1016/S0074-7696(07)61004-3.'
ieee: 'L. Rohde and C.-P. J. Heisenberg, “Zebrafish gastrulation: Cell movements,
signals, and mechanisms,” International Review of Cytology - A Survey of Cell
Biology, vol. 261. Academic Press, pp. 159–192, 2007.'
ista: 'Rohde L, Heisenberg C-PJ. 2007. Zebrafish gastrulation: Cell movements, signals,
and mechanisms. International Review of Cytology - A Survey of Cell Biology. 261,
159–192.'
mla: 'Rohde, Laurel, and Carl-Philipp J. Heisenberg. “Zebrafish Gastrulation: Cell
Movements, Signals, and Mechanisms.” International Review of Cytology - A Survey
of Cell Biology, vol. 261, Academic Press, 2007, pp. 159–92, doi:10.1016/S0074-7696(07)61004-3.'
short: L. Rohde, C.-P.J. Heisenberg, International Review of Cytology - A Survey
of Cell Biology 261 (2007) 159–192.
date_created: 2018-12-11T12:07:15Z
date_published: 2007-06-06T00:00:00Z
date_updated: 2021-01-12T07:54:53Z
day: '06'
doi: 10.1016/S0074-7696(07)61004-3
extern: '1'
intvolume: ' 261'
language:
- iso: eng
month: '06'
oa_version: None
page: 159 - 192
publication: International Review of Cytology - A Survey of Cell Biology
publication_status: published
publisher: Academic Press
publist_id: '1967'
status: public
title: 'Zebrafish gastrulation: Cell movements, signals, and mechanisms'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2007'
...
---
_id: '4182'
abstract:
- lang: eng
text: We are interested in the cellular and molecular mechanisms underlying tissue
morphogenesis during zebrafish gastrulation. Both differential cell adhesion and
contractility have been proposed to be key mechanisms by which tissues form and
rearrange in development. To obtain insight into the potential roles of differential
cell adhesion and contraction for germ layer morphogenesis during gastrulation,
we are analyzing cell adhesion and contraction of germ layer progenitor cells
using atomic force microscopy, primary tissue culture and transplantation assays.
I will present and discuss data about the differential adhesiveness and contractility
of germ layer progenitor cells in the context of germ layer formation during vertebrate
gastrulation.
acknowledgement: Abstract for the Annual Meeting of the German Societey for Cell Biology.
article_processing_charge: No
author:
- first_name: Michael
full_name: Krieg, Michael
last_name: Krieg
- first_name: Yohanna
full_name: Arboleda, Yohanna
last_name: Arboleda
- first_name: Daniel
full_name: Müller, Daniel
last_name: Müller
- 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: Krieg M, Arboleda Y, Müller D, Heisenberg C-PJ. The role of cell adhesion and
contractility for germ layer morphogenesis during zebrafish gastrulation. European
Journal of Cell Biology. 2007;86(Supplement 1):39-39. doi:10.1016/j.ejcb.2007.02.002
apa: Krieg, M., Arboleda, Y., Müller, D., & Heisenberg, C.-P. J. (2007). The
role of cell adhesion and contractility for germ layer morphogenesis during zebrafish
gastrulation. European Journal of Cell Biology. Elsevier. https://doi.org/10.1016/j.ejcb.2007.02.002
chicago: Krieg, Michael, Yohanna Arboleda, Daniel Müller, and Carl-Philipp J Heisenberg.
“The Role of Cell Adhesion and Contractility for Germ Layer Morphogenesis during
Zebrafish Gastrulation.” European Journal of Cell Biology. Elsevier, 2007.
https://doi.org/10.1016/j.ejcb.2007.02.002.
ieee: M. Krieg, Y. Arboleda, D. Müller, and C.-P. J. Heisenberg, “The role of cell
adhesion and contractility for germ layer morphogenesis during zebrafish gastrulation,”
European Journal of Cell Biology, vol. 86, no. Supplement 1. Elsevier,
pp. 39–39, 2007.
ista: Krieg M, Arboleda Y, Müller D, Heisenberg C-PJ. 2007. The role of cell adhesion
and contractility for germ layer morphogenesis during zebrafish gastrulation.
European Journal of Cell Biology. 86(Supplement 1), 39–39.
mla: Krieg, Michael, et al. “The Role of Cell Adhesion and Contractility for Germ
Layer Morphogenesis during Zebrafish Gastrulation.” European Journal of Cell
Biology, vol. 86, no. Supplement 1, Elsevier, 2007, pp. 39–39, doi:10.1016/j.ejcb.2007.02.002.
short: M. Krieg, Y. Arboleda, D. Müller, C.-P.J. Heisenberg, European Journal of
Cell Biology 86 (2007) 39–39.
date_created: 2018-12-11T12:07:26Z
date_published: 2007-03-22T00:00:00Z
date_updated: 2021-01-12T07:55:07Z
day: '22'
doi: 10.1016/j.ejcb.2007.02.002
extern: '1'
intvolume: ' 86'
issue: Supplement 1
language:
- iso: eng
month: '03'
oa_version: None
page: 39 - 39
publication: European Journal of Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '1937'
status: public
title: The role of cell adhesion and contractility for germ layer morphogenesis during
zebrafish gastrulation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 86
year: '2007'
...
---
_id: '4225'
abstract:
- lang: eng
text: The discovery of the genetic code was one of the most important advances of
modern biology. But there is more to a DNA code than protein sequence; DNA carries
signals for splicing, localization, folding, and regulation that are often embedded
within the protein-coding sequence. In this issue, Itzkovitz and Alon show that
the specific 64-to-20 mapping found in the genetic code may have been optimized
for permitting protein-coding regions to carry this extra information and suggest
that this property may have evolved as a side benefit of selection to minimize
the negative effects of frameshift errors.
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: Kalin
full_name: Vetsigian, Kalin
last_name: Vetsigian
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Bollenbach MT, Vetsigian K, Kishony R. Evolution and multilevel optimization
of the genetic code. Genome Research. 2007;17(4):401-404. doi:10.1101/gr.6144007
apa: Bollenbach, M. T., Vetsigian, K., & Kishony, R. (2007). Evolution and multilevel
optimization of the genetic code. Genome Research. Cold Spring Harbor Laboratory
Press. https://doi.org/10.1101/gr.6144007
chicago: Bollenbach, Mark Tobias, Kalin Vetsigian, and Roy Kishony. “Evolution and
Multilevel Optimization of the Genetic Code.” Genome Research. Cold Spring
Harbor Laboratory Press, 2007. https://doi.org/10.1101/gr.6144007.
ieee: M. T. Bollenbach, K. Vetsigian, and R. Kishony, “Evolution and multilevel
optimization of the genetic code,” Genome Research, vol. 17, no. 4. Cold
Spring Harbor Laboratory Press, pp. 401–404, 2007.
ista: Bollenbach MT, Vetsigian K, Kishony R. 2007. Evolution and multilevel optimization
of the genetic code. Genome Research. 17(4), 401–404.
mla: Bollenbach, Mark Tobias, et al. “Evolution and Multilevel Optimization of the
Genetic Code.” Genome Research, vol. 17, no. 4, Cold Spring Harbor Laboratory
Press, 2007, pp. 401–04, doi:10.1101/gr.6144007.
short: M.T. Bollenbach, K. Vetsigian, R. Kishony, Genome Research 17 (2007) 401–404.
date_created: 2018-12-11T12:07:42Z
date_published: 2007-03-09T00:00:00Z
date_updated: 2021-01-12T07:55:26Z
day: '09'
doi: 10.1101/gr.6144007
extern: '1'
intvolume: ' 17'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 401 - 404
publication: Genome Research
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '1891'
status: public
title: Evolution and multilevel optimization of the genetic code
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2007'
...
---
_id: '4226'
abstract:
- lang: eng
text: 'In the developing fly wing, secreted morphogens such as Decapentaplegic (Dpp)
and Wingless (Wg) form gradients of concentration providing positional information.
Dpp forms a longer-range gradient than Wg. To understand how the range is controlled,
we measured the four key kinetic parameters governing morphogen spreading: the
production rate, the effective diffusion coefficient, the degradation rate, and
the immobile fraction. The four parameters had different values for Dpp versus
Wg. In addition, Dynamin-dependent endocytosis was required for spreading of Dpp,
but not Wg. Thus, the cellular mechanisms of Dpp and Wingless spreading are different:
Dpp spreading requires endocytic, intracellular trafficking.'
author:
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Periklis
full_name: Pantazis, Periklis
last_name: Pantazis
- first_name: Tobias
full_name: Bollenbach, Tobias
last_name: Bollenbach
- first_name: Yannis
full_name: Kalaidzidis, Yannis
last_name: Kalaidzidis
- first_name: Thomas
full_name: Bittig, Thomas
last_name: Bittig
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
- first_name: Marcos
full_name: Gonzalez-Gaitan, Marcos
last_name: Gonzalez Gaitan
citation:
ama: Kicheva A, Pantazis P, Bollenbach T, et al. Kinetics of morphogen gradient
formation. Science. 2007;315(5811):521-525. doi:10.1126/science.1135774
apa: Kicheva, A., Pantazis, P., Bollenbach, T., Kalaidzidis, Y., Bittig, T., Julicher,
F., & Gonzalez Gaitan, M. (2007). Kinetics of morphogen gradient formation.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1135774
chicago: Kicheva, Anna, Periklis Pantazis, Tobias Bollenbach, Yannis Kalaidzidis,
Thomas Bittig, Frank Julicher, and Marcos Gonzalez Gaitan. “Kinetics of Morphogen
Gradient Formation.” Science. American Association for the Advancement
of Science, 2007. https://doi.org/10.1126/science.1135774.
ieee: A. Kicheva et al., “Kinetics of morphogen gradient formation,” Science,
vol. 315, no. 5811. American Association for the Advancement of Science, pp. 521–525,
2007.
ista: Kicheva A, Pantazis P, Bollenbach T, Kalaidzidis Y, Bittig T, Julicher F,
Gonzalez Gaitan M. 2007. Kinetics of morphogen gradient formation. Science. 315(5811),
521–525.
mla: Kicheva, Anna, et al. “Kinetics of Morphogen Gradient Formation.” Science,
vol. 315, no. 5811, American Association for the Advancement of Science, 2007,
pp. 521–25, doi:10.1126/science.1135774.
short: A. Kicheva, P. Pantazis, T. Bollenbach, Y. Kalaidzidis, T. Bittig, F. Julicher,
M. Gonzalez Gaitan, Science 315 (2007) 521–525.
date_created: 2018-12-11T12:07:42Z
date_published: 2007-01-26T00:00:00Z
date_updated: 2021-01-12T07:55:26Z
day: '26'
doi: 10.1126/science.1135774
extern: 1
intvolume: ' 315'
issue: '5811'
month: '01'
page: 521 - 525
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '1892'
quality_controlled: 0
status: public
title: Kinetics of morphogen gradient formation
type: journal_article
volume: 315
year: '2007'
...
---
_id: '4342'
abstract:
- lang: eng
text: "Library 2.0 and user-generated content are two terms, which are closely connected.
In the\r\n\r\npresentation, I will briefly define both terms. Two example projects
where user- generated content and libraries interact will be presented. The cooperation
of Wikipedia and the Personennamendatei, the German cooperative name authority
files is the first. The second will be Wikisource where users provide transcribed
source material. Another important area of user-generated content is social tagging
where users index different resources. And if the users will do so much in the
future, is there still a place for librarians? But in the future user\r\n\r\nand
librarians become partners and the library will provide the platform: the library
2.0."
author:
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
citation:
ama: 'Danowski P. Library 2.0 and User-Generated Content - What can the users do
for us? In: IFLA; 2007. doi:601'
apa: 'Danowski, P. (2007). Library 2.0 and User-Generated Content - What can the
users do for us? Presented at the WLIC: World Library and Information Congress,
Durban, South Africa: IFLA. https://doi.org/601'
chicago: Danowski, Patrick. “Library 2.0 and User-Generated Content - What Can the
Users Do for Us?” IFLA, 2007. https://doi.org/601.
ieee: 'P. Danowski, “Library 2.0 and User-Generated Content - What can the users
do for us?,” presented at the WLIC: World Library and Information Congress, Durban,
South Africa, 2007.'
ista: 'Danowski P. 2007. Library 2.0 and User-Generated Content - What can the users
do for us? WLIC: World Library and Information Congress.'
mla: Danowski, Patrick. Library 2.0 and User-Generated Content - What Can the
Users Do for Us? IFLA, 2007, doi:601.
short: P. Danowski, in:, IFLA, 2007.
conference:
end_date: 2007-08-23
location: Durban, South Africa
name: 'WLIC: World Library and Information Congress'
start_date: 2007-08-19
date_created: 2018-12-11T12:08:22Z
date_published: 2007-05-25T00:00:00Z
date_updated: 2021-01-12T07:56:16Z
day: '25'
doi: '601'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://www.ifla.org/IV/ifla73/papers/113-Danowski-en.pdf
month: '05'
oa_version: None
publication_status: published
publisher: IFLA
publist_id: '1232'
status: public
title: Library 2.0 and User-Generated Content - What can the users do for us?
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2007'
...
---
_id: '4343'
author:
- first_name: Patrick
full_name: Patrick Danowski
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
- first_name: Barbara
full_name: Pfeifer,Barbara
last_name: Pfeifer
citation:
ama: 'Danowski P, Pfeifer B. Wikipedia und Normdateien: Wege der Vernetzung am Beispiel
der Kooperation mit der Personennamendatei. Bibliothek - Forschung Und Praxis.
2007;31(2):149-155. doi:485'
apa: 'Danowski, P., & Pfeifer, B. (2007). Wikipedia und Normdateien: Wege der
Vernetzung am Beispiel der Kooperation mit der Personennamendatei. Bibliothek
- Forschung Und Praxis. De Gruyter. https://doi.org/485'
chicago: 'Danowski, Patrick, and Barbara Pfeifer. “Wikipedia Und Normdateien: Wege
Der Vernetzung Am Beispiel Der Kooperation Mit Der Personennamendatei.” Bibliothek
- Forschung Und Praxis. De Gruyter, 2007. https://doi.org/485.'
ieee: 'P. Danowski and B. Pfeifer, “Wikipedia und Normdateien: Wege der Vernetzung
am Beispiel der Kooperation mit der Personennamendatei,” Bibliothek - Forschung
Und Praxis, vol. 31, no. 2. De Gruyter, pp. 149–155, 2007.'
ista: 'Danowski P, Pfeifer B. 2007. Wikipedia und Normdateien: Wege der Vernetzung
am Beispiel der Kooperation mit der Personennamendatei. Bibliothek - Forschung
Und Praxis. 31(2), 149–155.'
mla: 'Danowski, Patrick, and Barbara Pfeifer. “Wikipedia Und Normdateien: Wege Der
Vernetzung Am Beispiel Der Kooperation Mit Der Personennamendatei.” Bibliothek
- Forschung Und Praxis, vol. 31, no. 2, De Gruyter, 2007, pp. 149–55, doi:485.'
short: P. Danowski, B. Pfeifer, Bibliothek - Forschung Und Praxis 31 (2007) 149–155.
date_created: 2018-12-11T12:08:22Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:17Z
day: '01'
doi: '485'
extern: 1
intvolume: ' 31'
issue: '2'
month: '01'
page: 149 - 155
publication: Bibliothek - Forschung Und Praxis
publication_status: published
publisher: De Gruyter
publist_id: '1231'
quality_controlled: 0
status: public
title: 'Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation
mit der Personennamendatei'
type: journal_article
volume: 31
year: '2007'
...
---
_id: '4344'
author:
- first_name: Patrick
full_name: Patrick Danowski
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
- first_name: Lambert
full_name: Heller,Lambert
last_name: Heller
citation:
ama: Danowski P, Heller L. Bibliothek 2.0 ? Wird alles anders? Bibliothek - Forschung
Und Praxis. 2007;31(2007):130-136. doi:45
apa: Danowski, P., & Heller, L. (2007). Bibliothek 2.0 ? Wird alles anders?
Bibliothek - Forschung Und Praxis. De Gruyter. https://doi.org/45
chicago: Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 ? Wird Alles Anders?”
Bibliothek - Forschung Und Praxis. De Gruyter, 2007. https://doi.org/45.
ieee: P. Danowski and L. Heller, “Bibliothek 2.0 ? Wird alles anders?,” Bibliothek
- Forschung Und Praxis, vol. 31, no. 2007. De Gruyter, pp. 130–136, 2007.
ista: Danowski P, Heller L. 2007. Bibliothek 2.0 ? Wird alles anders? Bibliothek
- Forschung Und Praxis. 31(2007), 130–136.
mla: Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 ? Wird Alles Anders?”
Bibliothek - Forschung Und Praxis, vol. 31, no. 2007, De Gruyter, 2007,
pp. 130–36, doi:45.
short: P. Danowski, L. Heller, Bibliothek - Forschung Und Praxis 31 (2007) 130–136.
date_created: 2018-12-11T12:08:22Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:17Z
day: '01'
doi: '45'
extern: 1
intvolume: ' 31'
issue: '2007'
main_file_link:
- open_access: '0'
url: http://www.bibliothek-saur.de/2007_2/130-136.pdf
month: '01'
page: 130 - 136
publication: Bibliothek - Forschung Und Praxis
publication_status: published
publisher: De Gruyter
publist_id: '1230'
quality_controlled: 0
status: public
title: Bibliothek 2.0 ? Wird alles anders?
type: journal_article
volume: 31
year: '2007'
...
---
_id: '4353'
abstract:
- lang: eng
text: 'BACKGROUND: The invention of the Genome Sequence 20 DNA Sequencing System
(454 parallel sequencing platform) has enabled the rapid and high-volume production
of sequence data. Until now, however, individual emulsion PCR (emPCR) reactions
and subsequent sequencing runs have been unable to combine template DNA from multiple
individuals, as homologous sequences cannot be subsequently assigned to their
original sources. METHODOLOGY: We use conventional PCR with 5''-nucleotide tagged
primers to generate homologous DNA amplification products from multiple specimens,
followed by sequencing through the high-throughput Genome Sequence 20 DNA Sequencing
System (GS20, Roche/454 Life Sciences). Each DNA sequence is subsequently traced
back to its individual source through 5''tag-analysis. CONCLUSIONS: We demonstrate
that this new approach enables the assignment of virtually all the generated DNA
sequences to the correct source once sequencing anomalies are accounted for (miss-assignment
rate<0.4%). Therefore, the method enables accurate sequencing and assignment
of homologous DNA sequences from multiple sources in single high-throughput GS20
run. We observe a bias in the distribution of the differently tagged primers that
is dependent on the 5'' nucleotide of the tag. In particular, primers 5'' labelled
with a cytosine are heavily overrepresented among the final sequences, while those
5'' labelled with a thymine are strongly underrepresented. A weaker bias also
exists with regards to the distribution of the sequences as sorted by the second
nucleotide of the dinucleotide tags. As the results are based on a single GS20
run, the general applicability of the approach requires confirmation. However,
our experiments demonstrate that 5''primer tagging is a useful method in which
the sequencing power of the GS20 can be applied to PCR-based assays of multiple
homologous PCR products. The new approach will be of value to a broad range of
research areas, such as those of comparative genomics, complete mitochondrial
analyses, population genetics, and phylogenetics.'
acknowledgement: JB and EW were supported by the Wellcome Trust, UK, the Carlsberg
Foundation, DK, and the National Science Foundation, DK. MTPG acknowledges the Marie
Curie Actions FP6-MEIF-CT-2005-025002 ‘FORMAPLEX’ grant for funding his research.
JPB and RN were funded by the Danish FSS and the National Science Foundation, DK.
None of the sponsors or funders have had any influence on the data or manuscript
presented here.
author:
- first_name: Jonas
full_name: Binladen, Jonas
last_name: Binladen
- first_name: M Thomas
full_name: Gilbert, M Thomas
last_name: Gilbert
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Frank
full_name: Panitz, Frank
last_name: Panitz
- first_name: Christian
full_name: Bendixen, Christian
last_name: Bendixen
- first_name: Rasmus
full_name: Nielsen, Rasmus
last_name: Nielsen
- first_name: Eske
full_name: Willerslev, Eske
last_name: Willerslev
citation:
ama: Binladen J, Gilbert MT, Bollback JP, et al. The use of coded PCR primers enables
high-throughput sequencing of multiple homolog amplification products by 454 parallel
sequencing. PLoS One. 2007;2(2). doi:10.1371/journal.pone.0000197
apa: Binladen, J., Gilbert, M. T., Bollback, J. P., Panitz, F., Bendixen, C., Nielsen,
R., & Willerslev, E. (2007). The use of coded PCR primers enables high-throughput
sequencing of multiple homolog amplification products by 454 parallel sequencing.
PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0000197
chicago: Binladen, Jonas, M Thomas Gilbert, Jonathan P Bollback, Frank Panitz, Christian
Bendixen, Rasmus Nielsen, and Eske Willerslev. “The Use of Coded PCR Primers Enables
High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel
Sequencing.” PLoS One. Public Library of Science, 2007. https://doi.org/10.1371/journal.pone.0000197.
ieee: J. Binladen et al., “The use of coded PCR primers enables high-throughput
sequencing of multiple homolog amplification products by 454 parallel sequencing,”
PLoS One, vol. 2, no. 2. Public Library of Science, 2007.
ista: Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev
E. 2007. The use of coded PCR primers enables high-throughput sequencing of multiple
homolog amplification products by 454 parallel sequencing. PLoS One. 2(2).
mla: Binladen, Jonas, et al. “The Use of Coded PCR Primers Enables High-Throughput
Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing.”
PLoS One, vol. 2, no. 2, Public Library of Science, 2007, doi:10.1371/journal.pone.0000197.
short: J. Binladen, M.T. Gilbert, J.P. Bollback, F. Panitz, C. Bendixen, R. Nielsen,
E. Willerslev, PLoS One 2 (2007).
date_created: 2018-12-11T12:08:25Z
date_published: 2007-02-14T00:00:00Z
date_updated: 2021-01-12T07:56:21Z
day: '14'
doi: 10.1371/journal.pone.0000197
extern: 1
intvolume: ' 2'
issue: '2'
month: '02'
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '1105'
quality_controlled: 0
status: public
title: The use of coded PCR primers enables high-throughput sequencing of multiple
homolog amplification products by 454 parallel sequencing
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 2
year: '2007'
...
---
_id: '4356'
abstract:
- lang: eng
text: We used a comparative genomics approach to identify genes that are under positive
selection in six strains of Escherichia coli and Shigella flexneri, including
five strains that are human pathogens. We find that positive selection targets
a wide range of different functions in the E. coli genome, including cell surface
proteins such as beta barrel porins, presumably because of the involvement of
these genes in evolutionary arms races with other bacteria, phages, and/or the
host immune system. Structural mapping of positively selected sites on trans-membrane
beta barrel porins reveals that the residues under positive selection occur almost
exclusively in the extracellular region of the proteins that are enriched with
sites known to be targets of phages, colicins, or the host immune system. More
surprisingly, we also find a number of other categories of genes that show very
strong evidence for positive selection, such as the enigmatic rhs elements and
transposases. Based on structural evidence, we hypothesize that the selection
acting on transposases is related to the genomic conflict between transposable
elements and the host genome.
author:
- first_name: Lise
full_name: Petersen, Lise
last_name: Petersen
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Matt
full_name: Dimmic, Matt
last_name: Dimmic
- first_name: Melissa
full_name: Hubisz, Melissa
last_name: Hubisz
- first_name: Rasmus
full_name: Nielsen, Rasmus
last_name: Nielsen
citation:
ama: Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R. Genes under positive
selection in Escherichia coli. Genome Research. 2007;17(9):1336-1343. doi:10.1101/gr.6254707
apa: Petersen, L., Bollback, J. P., Dimmic, M., Hubisz, M., & Nielsen, R. (2007).
Genes under positive selection in Escherichia coli. Genome Research. Cold
Spring Harbor Laboratory Press. https://doi.org/10.1101/gr.6254707
chicago: Petersen, Lise, Jonathan P Bollback, Matt Dimmic, Melissa Hubisz, and Rasmus
Nielsen. “Genes under Positive Selection in Escherichia Coli.” Genome Research.
Cold Spring Harbor Laboratory Press, 2007. https://doi.org/10.1101/gr.6254707.
ieee: L. Petersen, J. P. Bollback, M. Dimmic, M. Hubisz, and R. Nielsen, “Genes
under positive selection in Escherichia coli,” Genome Research, vol. 17,
no. 9. Cold Spring Harbor Laboratory Press, pp. 1336–1343, 2007.
ista: Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R. 2007. Genes under
positive selection in Escherichia coli. Genome Research. 17(9), 1336–1343.
mla: Petersen, Lise, et al. “Genes under Positive Selection in Escherichia Coli.”
Genome Research, vol. 17, no. 9, Cold Spring Harbor Laboratory Press, 2007,
pp. 1336–43, doi:10.1101/gr.6254707.
short: L. Petersen, J.P. Bollback, M. Dimmic, M. Hubisz, R. Nielsen, Genome Research
17 (2007) 1336–1343.
date_created: 2018-12-11T12:08:26Z
date_published: 2007-08-03T00:00:00Z
date_updated: 2021-01-12T07:56:22Z
day: '03'
doi: 10.1101/gr.6254707
extern: 1
intvolume: ' 17'
issue: '9'
month: '08'
page: 1336 - 1343
publication: Genome Research
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '1103'
quality_controlled: 0
status: public
title: Genes under positive selection in Escherichia coli
type: journal_article
volume: 17
year: '2007'
...
---
_id: '4355'
abstract:
- lang: eng
text: When a beneficial mutation is fixed in a population that lacks recombination,
the genetic background linked to that mutation is fixed. As a result, beneficial
mutations on different backgrounds experience competition, or "clonal interference,"
that can cause asexual populations to evolve more slowly than their sexual counterparts.
Factors such as a large population size (N) and high mutation rates (mu) increase
the number of competing beneficial mutations, and hence are expected to increase
the intensity of clonal interference. However, recent theory suggests that, with
very large values of Nmu, the severity of clonal interference may instead decline.
The reason is that, with large Nmu, genomes including both beneficial mutations
are rapidly created by recurrent mutation, obviating the need for recombination.
Here, we analyze data from experimentally evolved asexual populations of a bacteriophage
and find that, in these nonrecombining populations with very large Nmu, recurrent
mutation does appear to ameliorate this cost of asexuality.
acknowledgement: R01 GM069801-08/GM/NIGMS NIH HHS/United States
author:
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: John
full_name: Huelsenbeck, John P
last_name: Huelsenbeck
citation:
ama: Bollback JP, Huelsenbeck J. Clonal interference is alleviated by high mutation
rates in large populations. Molecular Biology and Evolution. 2007;24(6):1397-1406.
doi:10.1093/molbev/msm056
apa: Bollback, J. P., & Huelsenbeck, J. (2007). Clonal interference is alleviated
by high mutation rates in large populations. Molecular Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/molbev/msm056
chicago: Bollback, Jonathan P, and John Huelsenbeck. “Clonal Interference Is Alleviated
by High Mutation Rates in Large Populations.” Molecular Biology and Evolution.
Oxford University Press, 2007. https://doi.org/10.1093/molbev/msm056.
ieee: J. P. Bollback and J. Huelsenbeck, “Clonal interference is alleviated by high
mutation rates in large populations,” Molecular Biology and Evolution,
vol. 24, no. 6. Oxford University Press, pp. 1397–1406, 2007.
ista: Bollback JP, Huelsenbeck J. 2007. Clonal interference is alleviated by high
mutation rates in large populations. Molecular Biology and Evolution. 24(6), 1397–1406.
mla: Bollback, Jonathan P., and John Huelsenbeck. “Clonal Interference Is Alleviated
by High Mutation Rates in Large Populations.” Molecular Biology and Evolution,
vol. 24, no. 6, Oxford University Press, 2007, pp. 1397–406, doi:10.1093/molbev/msm056.
short: J.P. Bollback, J. Huelsenbeck, Molecular Biology and Evolution 24 (2007)
1397–1406.
date_created: 2018-12-11T12:08:26Z
date_published: 2007-03-22T00:00:00Z
date_updated: 2021-01-12T07:56:22Z
day: '22'
doi: 10.1093/molbev/msm056
extern: 1
intvolume: ' 24'
issue: '6'
month: '03'
page: 1397 - 1406
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '1104'
quality_controlled: 0
status: public
title: Clonal interference is alleviated by high mutation rates in large populations
type: journal_article
volume: 24
year: '2007'
...
---
_id: '4354'
abstract:
- lang: eng
text: Homology search is one of the most ubiquitous bioinformatic tasks, yet it
is unknown how effective the currently available tools are for identifying noncoding
RNAs (ncRNAs). In this work, we use reliable ncRNA data sets to assess the effectiveness
of methods such as BLAST, FASTA, HMMer, and Infernal. Surprisingly, the most popular
homology search methods are often the least accurate. As a result, many studies
have used inappropriate tools for their analyses. On the basis of our results,
we suggest homology search strategies using the currently available tools and
some directions for future development.
author:
- first_name: Eva
full_name: Freyhult, Eva K
last_name: Freyhult
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Paul
full_name: Gardner, Paul P
last_name: Gardner
citation:
ama: 'Freyhult E, Bollback JP, Gardner P. Exploring genomic dark matter: a critical
assessment of the performance of homology search methods on noncoding RNA. Genome
Research. 2007;17(1):117-125. doi:10.1101/gr.5890907'
apa: 'Freyhult, E., Bollback, J. P., & Gardner, P. (2007). Exploring genomic
dark matter: a critical assessment of the performance of homology search methods
on noncoding RNA. Genome Research. Cold Spring Harbor Laboratory Press.
https://doi.org/10.1101/gr.5890907'
chicago: 'Freyhult, Eva, Jonathan P Bollback, and Paul Gardner. “Exploring Genomic
Dark Matter: A Critical Assessment of the Performance of Homology Search Methods
on Noncoding RNA.” Genome Research. Cold Spring Harbor Laboratory Press,
2007. https://doi.org/10.1101/gr.5890907.'
ieee: 'E. Freyhult, J. P. Bollback, and P. Gardner, “Exploring genomic dark matter:
a critical assessment of the performance of homology search methods on noncoding
RNA,” Genome Research, vol. 17, no. 1. Cold Spring Harbor Laboratory Press,
pp. 117–25, 2007.'
ista: 'Freyhult E, Bollback JP, Gardner P. 2007. Exploring genomic dark matter:
a critical assessment of the performance of homology search methods on noncoding
RNA. Genome Research. 17(1), 117–25.'
mla: 'Freyhult, Eva, et al. “Exploring Genomic Dark Matter: A Critical Assessment
of the Performance of Homology Search Methods on Noncoding RNA.” Genome Research,
vol. 17, no. 1, Cold Spring Harbor Laboratory Press, 2007, pp. 117–25, doi:10.1101/gr.5890907.'
short: E. Freyhult, J.P. Bollback, P. Gardner, Genome Research 17 (2007) 117–25.
date_created: 2018-12-11T12:08:25Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:21Z
day: '01'
doi: 10.1101/gr.5890907
extern: 1
intvolume: ' 17'
issue: '1'
main_file_link:
- open_access: '0'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716261
month: '01'
page: 117 - 25
publication: Genome Research
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '1106'
quality_controlled: 0
status: public
title: 'Exploring genomic dark matter: a critical assessment of the performance of
homology search methods on noncoding RNA'
type: journal_article
volume: 17
year: '2007'
...