---
_id: '3880'
abstract:
- lang: eng
text: We consider imperfect-information parity games in which strategies rely on
observations that provide imperfect information about the history of a play. To
solve such games, i.e., to determine the winning regions of players and corresponding
winning strategies, one can use the subset construction to build an equivalent
perfect-information game. Recently, an algorithm that avoids the inefficient subset
construction has been proposed. The algorithm performs a fixed-point computation
in a lattice of antichains, thus maintaining a succinct representation of state
sets. However, this representation does not allow to recover winning strategies.
In this paper, we build on the antichain approach to develop an algorithm for
constructing the winning strategies in parity games of imperfect information.
We have implemented this algorithm as a prototype. To our knowledge, this is the
first implementation of a procedure for solving imperfect-information parity games
on graphs.
alternative_title:
- LNCS
author:
- first_name: Dietmar
full_name: Berwanger, Dietmar
last_name: Berwanger
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Sangram
full_name: Raje, Sangram
last_name: Raje
citation:
ama: 'Berwanger D, Chatterjee K, Doyen L, Henzinger TA, Raje S. Strategy construction
for parity games with imperfect information. In: Vol 5201. Schloss Dagstuhl -
Leibniz-Zentrum für Informatik; 2008:325-339. doi:10.1007/978-3-540-85361-9'
apa: 'Berwanger, D., Chatterjee, K., Doyen, L., Henzinger, T. A., & Raje, S.
(2008). Strategy construction for parity games with imperfect information (Vol.
5201, pp. 325–339). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-540-85361-9'
chicago: Berwanger, Dietmar, Krishnendu Chatterjee, Laurent Doyen, Thomas A Henzinger,
and Sangram Raje. “Strategy Construction for Parity Games with Imperfect Information,”
5201:325–39. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008. https://doi.org/10.1007/978-3-540-85361-9.
ieee: 'D. Berwanger, K. Chatterjee, L. Doyen, T. A. Henzinger, and S. Raje, “Strategy
construction for parity games with imperfect information,” presented at the CONCUR:
Concurrency Theory, 2008, vol. 5201, pp. 325–339.'
ista: 'Berwanger D, Chatterjee K, Doyen L, Henzinger TA, Raje S. 2008. Strategy
construction for parity games with imperfect information. CONCUR: Concurrency
Theory, LNCS, vol. 5201, 325–339.'
mla: Berwanger, Dietmar, et al. Strategy Construction for Parity Games with Imperfect
Information. Vol. 5201, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2008, pp. 325–39, doi:10.1007/978-3-540-85361-9.
short: D. Berwanger, K. Chatterjee, L. Doyen, T.A. Henzinger, S. Raje, in:, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 325–339.
conference:
name: 'CONCUR: Concurrency Theory'
date_created: 2018-12-11T12:05:40Z
date_published: 2008-07-30T00:00:00Z
date_updated: 2023-02-23T11:46:01Z
day: '30'
doi: 10.1007/978-3-540-85361-9
extern: 1
intvolume: ' 5201'
month: '07'
page: 325 - 339
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '2291'
quality_controlled: 0
related_material:
record:
- id: '3863'
relation: later_version
status: public
status: public
title: Strategy construction for parity games with imperfect information
type: conference
volume: 5201
year: '2008'
...
---
_id: '3903'
abstract:
- lang: eng
text: "Background\r\n\r\nThe invasive garden ant, Lasius neglectus, is the most
recently detected pest ant and the first known invasive ant able to become established
and thrive in the temperate regions of Eurasia. In this study, we aim to reconstruct
the invasion history of this ant in Europe analysing 14 populations with three
complementary approaches: genetic microsatellite analysis, chemical analysis of
cuticular hydrocarbon profiles and behavioural observations of aggression behaviour.
We evaluate the relative informative power of the three methodological approaches
and estimate both the number of independent introduction events from a yet unknown
native range somewhere in the Black Sea area, and the invasive potential of the
existing introduced populations.\r\n\r\nResults\r\n\r\nThree clusters of genetically
similar populations were detected, and all but one population had a similar chemical
profile. Aggression between populations could be predicted from their genetic
and chemical distance, and two major clusters of non-aggressive groups of populations
were found. However, populations of L. neglectus did not separate into clear supercolonial
associations, as is typical for other invasive ants.\r\n\r\nConclusion\r\n\r\nThe
three methodological approaches gave consistent and complementary results. All
joint evidence supports the inference that the 14 introduced populations of L.
neglectus in Europe likely arose from only very few independent introductions
from the native range, and that new infestations were typically started through
introductions from other invasive populations. This indicates that existing introduced
populations have a very high invasive potential when the ants are inadvertently
spread by human transport. "
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: Falko
full_name: Drijfhout, Falko
last_name: Drijfhout
- first_name: Daniel
full_name: Kronauer, Daniel
last_name: Kronauer
- first_name: Jacobus
full_name: Boomsma, Jacobus
last_name: Boomsma
- first_name: Jes
full_name: Pedersen, Jes
last_name: Pedersen
- 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, Drijfhout F, Kronauer D, Boomsma J, Pedersen J, Cremer S. The
introduction history of invasive garden ants in Europe: integrating genetic, chemical
and behavioural approaches. BMC Biology. 2008;6(11). doi:10.1186/1741-7007-6-11'
apa: 'Ugelvig, L. V., Drijfhout, F., Kronauer, D., Boomsma, J., Pedersen, J., &
Cremer, S. (2008). The introduction history of invasive garden ants in Europe:
integrating genetic, chemical and behavioural approaches. BMC Biology.
BioMed Central. https://doi.org/10.1186/1741-7007-6-11'
chicago: 'Ugelvig, Line V, Falko Drijfhout, Daniel Kronauer, Jacobus Boomsma, Jes
Pedersen, and Sylvia Cremer. “The Introduction History of Invasive Garden Ants
in Europe: Integrating Genetic, Chemical and Behavioural Approaches.” BMC Biology.
BioMed Central, 2008. https://doi.org/10.1186/1741-7007-6-11.'
ieee: 'L. V. Ugelvig, F. Drijfhout, D. Kronauer, J. Boomsma, J. Pedersen, and S.
Cremer, “The introduction history of invasive garden ants in Europe: integrating
genetic, chemical and behavioural approaches,” BMC Biology, vol. 6, no.
11. BioMed Central, 2008.'
ista: 'Ugelvig LV, Drijfhout F, Kronauer D, Boomsma J, Pedersen J, Cremer S. 2008.
The introduction history of invasive garden ants in Europe: integrating genetic,
chemical and behavioural approaches. BMC Biology. 6(11).'
mla: 'Ugelvig, Line V., et al. “The Introduction History of Invasive Garden Ants
in Europe: Integrating Genetic, Chemical and Behavioural Approaches.” BMC Biology,
vol. 6, no. 11, BioMed Central, 2008, doi:10.1186/1741-7007-6-11.'
short: L.V. Ugelvig, F. Drijfhout, D. Kronauer, J. Boomsma, J. Pedersen, S. Cremer,
BMC Biology 6 (2008).
date_created: 2018-12-11T12:05:48Z
date_published: 2008-02-26T00:00:00Z
date_updated: 2021-01-12T07:53:05Z
day: '26'
doi: 10.1186/1741-7007-6-11
extern: '1'
intvolume: ' 6'
issue: '11'
language:
- iso: eng
month: '02'
oa_version: None
publication: BMC Biology
publication_status: published
publisher: BioMed Central
publist_id: '2249'
status: public
title: 'The introduction history of invasive garden ants in Europe: integrating genetic,
chemical and behavioural approaches'
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
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2008'
...
---
_id: '3905'
abstract:
- lang: eng
text: Winged and wingless males coexist in the ant Cardiocondyla obscurior. Wingless
(“ergatoid”) males never leave their maternal colony and fight remorselessly among
each other for the access to emerging females. The peaceful winged males disperse
after about 10 days, but beforehand also mate in the nest. In the first 5 days
of their life, winged males perform a chemical female mimicry that protects them
against attack and even makes them sexually attractive to ergatoid males. When
older, the chemical profile of winged males no longer matches that of virgin females;
nevertheless, they are still tolerated, which so far has been puzzling. Contrasting
this general pattern, we have identified a single aberrant colony in which all
winged males were attacked and killed by the ergatoid males. A comparative analysis
of the morphology and chemical profile of these untypical attacked winged males
and the tolerated males from several normal colonies revealed that normal old
males are still performing some chemical mimicry to the virgin queens, though
less perfect than in their young ages. The anomalous attacked winged males, on
the other hand, had a very different odour to the females. Our study thus exemplifies
that the analysis of rare malfunctioning can add valuable insight on functioning
under normal conditions and allows the conclusion that older winged males from
normal colonies of the ant C. obscurior are guarded through an imperfect chemical
female mimicry, still close enough to protect against attacks by the wingless
fighters yet dissimilar enough not to elicit their sexual interest.
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Patrizia
full_name: D'Ettorre, Patrizia
last_name: D'Ettorre
- first_name: Falko
full_name: Drijfhout, Falko
last_name: Drijfhout
- first_name: Matthew
full_name: Sledge, Matthew
last_name: Sledge
- first_name: Stefano
full_name: Turillazzi, Stefano
last_name: Turillazzi
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
citation:
ama: Cremer S, D’Ettorre P, Drijfhout F, Sledge M, Turillazzi S, Heinze J. Imperfect
chemical female mimicry in males of the ant Cardiocondyla obscurior. Naturwissenschaften.
2008;95(11):1101-1105. doi:10.1007/s00114-008-0430-8
apa: Cremer, S., D’Ettorre, P., Drijfhout, F., Sledge, M., Turillazzi, S., &
Heinze, J. (2008). Imperfect chemical female mimicry in males of the ant Cardiocondyla
obscurior. Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-008-0430-8
chicago: Cremer, Sylvia, Patrizia D’Ettorre, Falko Drijfhout, Matthew Sledge, Stefano
Turillazzi, and Jürgen Heinze. “Imperfect Chemical Female Mimicry in Males of
the Ant Cardiocondyla Obscurior.” Naturwissenschaften. Springer, 2008.
https://doi.org/10.1007/s00114-008-0430-8.
ieee: S. Cremer, P. D’Ettorre, F. Drijfhout, M. Sledge, S. Turillazzi, and J. Heinze,
“Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior,”
Naturwissenschaften, vol. 95, no. 11. Springer, pp. 1101–1105, 2008.
ista: Cremer S, D’Ettorre P, Drijfhout F, Sledge M, Turillazzi S, Heinze J. 2008.
Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior.
Naturwissenschaften. 95(11), 1101–1105.
mla: Cremer, Sylvia, et al. “Imperfect Chemical Female Mimicry in Males of the Ant
Cardiocondyla Obscurior.” Naturwissenschaften, vol. 95, no. 11, Springer,
2008, pp. 1101–05, doi:10.1007/s00114-008-0430-8.
short: S. Cremer, P. D’Ettorre, F. Drijfhout, M. Sledge, S. Turillazzi, J. Heinze,
Naturwissenschaften 95 (2008) 1101–1105.
date_created: 2018-12-11T12:05:48Z
date_published: 2008-08-05T00:00:00Z
date_updated: 2021-01-12T07:53:06Z
day: '05'
doi: 10.1007/s00114-008-0430-8
extern: '1'
intvolume: ' 95'
issue: '11'
language:
- iso: eng
month: '08'
oa_version: None
page: 1101 - 1105
publication: Naturwissenschaften
publication_status: published
publisher: Springer
publist_id: '2246'
status: public
title: Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 95
year: '2008'
...
---
_id: '3907'
abstract:
- lang: eng
text: 'Wingless males of the ant genus Cardiocondyla engage in fatal fighting for
access to female sexual nestmates. Older, heavily sclerotized males are usually
capable of eliminating all younger rivals, whose cuticle is still soft. In Cardiocondyla
sp. A, this type of local mate competition (LMC) has turned the standard pattern
of brood production of social insects upside down, in that mother queens in multi-queen
colonies produce extremely long-lived sons very early in the life cycle of the
colony. Here, we investigated the emergence pattern of sexuals in two species
with LMC, in which males are much less long-lived. Queens of Cardiocondyla obscurior
and Cardiocondyla minutior reared their first sons significantly earlier in multi-queen
than in single-queen societies. In addition, first female sexuals also emerged
earlier in multi-queen colonies, so that early males had mating opportunities.
Hence, the timing of sexual production appears to be well predicted by evolutionary
theory, in particular by local mate and queen–queen competition. '
author:
- first_name: Masaki
full_name: Suefuji, Masaki
last_name: Suefuji
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Jan
full_name: Oettler, Jan
last_name: Oettler
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
citation:
ama: Suefuji M, Cremer S, Oettler J, Heinze J. Queen number influences the timing
of the sexual production in colonies of Cardiocondyla ants. Biology Letters.
2008;4(6):670-673. doi:10.1098/rsbl.2008.0355
apa: Suefuji, M., Cremer, S., Oettler, J., & Heinze, J. (2008). Queen number
influences the timing of the sexual production in colonies of Cardiocondyla ants.
Biology Letters. Royal Society, The. https://doi.org/10.1098/rsbl.2008.0355
chicago: Suefuji, Masaki, Sylvia Cremer, Jan Oettler, and Jürgen Heinze. “Queen
Number Influences the Timing of the Sexual Production in Colonies of Cardiocondyla
Ants.” Biology Letters. Royal Society, The, 2008. https://doi.org/10.1098/rsbl.2008.0355.
ieee: M. Suefuji, S. Cremer, J. Oettler, and J. Heinze, “Queen number influences
the timing of the sexual production in colonies of Cardiocondyla ants,” Biology
Letters, vol. 4, no. 6. Royal Society, The, pp. 670–673, 2008.
ista: Suefuji M, Cremer S, Oettler J, Heinze J. 2008. Queen number influences the
timing of the sexual production in colonies of Cardiocondyla ants. Biology Letters.
4(6), 670–673.
mla: Suefuji, Masaki, et al. “Queen Number Influences the Timing of the Sexual Production
in Colonies of Cardiocondyla Ants.” Biology Letters, vol. 4, no. 6, Royal
Society, The, 2008, pp. 670–73, doi:10.1098/rsbl.2008.0355.
short: M. Suefuji, S. Cremer, J. Oettler, J. Heinze, Biology Letters 4 (2008) 670–673.
date_created: 2018-12-11T12:05:49Z
date_published: 2008-12-23T00:00:00Z
date_updated: 2021-01-12T07:53:07Z
day: '23'
doi: 10.1098/rsbl.2008.0355
extern: '1'
intvolume: ' 4'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 670 - 673
publication: Biology Letters
publication_status: published
publisher: Royal Society, The
publist_id: '2248'
status: public
title: Queen number influences the timing of the sexual production in colonies of
Cardiocondyla ants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2008'
...
---
_id: '3906'
acknowledgement: 'Funding was obtained from the European Community: FP5 EU research-training
network ‘INSECTS’ (JJB SC PD FPD DPH) and FP6 Individual Marie Curie EIF grant (SC),
the Alexander-von-Humboldt Foundation (Feodor-Lynen postdoctoral stipend to SC),
the Danish Natural Science Research Council (JSP), the Danish National Research
Foundation (JJB DRN JSP), and the Austrian Science Fund (BCS FMS CS HK).'
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- 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: Falko
full_name: Drijfhout, Falko
last_name: Drijfhout
- first_name: Birgit
full_name: Schlick Steiner, Birgit
last_name: Schlick Steiner
- first_name: Florian
full_name: Steiner, Florian
last_name: Steiner
- first_name: Bernhard
full_name: Seifert, Bernhard
last_name: Seifert
- first_name: David
full_name: Hughes, David
last_name: Hughes
- first_name: Andreas
full_name: Schulz, Andreas
last_name: Schulz
- first_name: Klaus
full_name: Petersen, Klaus
last_name: Petersen
- first_name: Heino
full_name: Konrad, Heino
last_name: Konrad
- first_name: Christian
full_name: Stauffer, Christian
last_name: Stauffer
- first_name: Kadri
full_name: Kiran, Kadri
last_name: Kiran
- first_name: Xavier
full_name: Espadaler, Xavier
last_name: Espadaler
- first_name: Patrizia
full_name: D'Ettorre, Patrizia
last_name: D'Ettorre
- first_name: Nihat
full_name: Aktaç, Nihat
last_name: Aktaç
- first_name: Jørgen
full_name: Eilenberg, Jørgen
last_name: Eilenberg
- first_name: Graeme
full_name: Jones, Graeme
last_name: Jones
- first_name: David
full_name: Nash, David
last_name: Nash
- first_name: Jes
full_name: Pedersen, Jes
last_name: Pedersen
- first_name: Jacobus
full_name: Boomsma, Jacobus
last_name: Boomsma
citation:
ama: Cremer S, Ugelvig LV, Drijfhout F, et al. The evolution of invasiveness in
garden ants. PLoS One. 2008;3(12). doi:10.1371/journal.pone.0003838
apa: Cremer, S., Ugelvig, L. V., Drijfhout, F., Schlick Steiner, B., Steiner, F.,
Seifert, B., … Boomsma, J. (2008). The evolution of invasiveness in garden ants.
PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0003838
chicago: Cremer, Sylvia, Line V Ugelvig, Falko Drijfhout, Birgit Schlick Steiner,
Florian Steiner, Bernhard Seifert, David Hughes, et al. “The Evolution of Invasiveness
in Garden Ants.” PLoS One. Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0003838.
ieee: S. Cremer et al., “The evolution of invasiveness in garden ants,” PLoS
One, vol. 3, no. 12. Public Library of Science, 2008.
ista: Cremer S, Ugelvig LV, Drijfhout F, Schlick Steiner B, Steiner F, Seifert B,
Hughes D, Schulz A, Petersen K, Konrad H, Stauffer C, Kiran K, Espadaler X, D’Ettorre
P, Aktaç N, Eilenberg J, Jones G, Nash D, Pedersen J, Boomsma J. 2008. The evolution
of invasiveness in garden ants. PLoS One. 3(12).
mla: Cremer, Sylvia, et al. “The Evolution of Invasiveness in Garden Ants.” PLoS
One, vol. 3, no. 12, Public Library of Science, 2008, doi:10.1371/journal.pone.0003838.
short: S. Cremer, L.V. Ugelvig, F. Drijfhout, B. Schlick Steiner, F. Steiner, B.
Seifert, D. Hughes, A. Schulz, K. Petersen, H. Konrad, C. Stauffer, K. Kiran,
X. Espadaler, P. D’Ettorre, N. Aktaç, J. Eilenberg, G. Jones, D. Nash, J. Pedersen,
J. Boomsma, PLoS One 3 (2008).
date_created: 2018-12-11T12:05:49Z
date_published: 2008-12-03T00:00:00Z
date_updated: 2021-01-12T07:53:06Z
day: '03'
doi: 10.1371/journal.pone.0003838
extern: '1'
intvolume: ' 3'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '2247'
status: public
title: The evolution of invasiveness in garden ants
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
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2008'
...
---
_id: '3939'
abstract:
- lang: eng
text: The priming of a T cell results from its physical interaction with a dendritic
cell (DC) that presents the cognate antigenic peptide. The success rate of such
interactions is extremely low, because the precursor frequency of a naive T cell
recognizing a specific antigen is in the range of 1:10(5)-10(6). To make this
principle practicable, encounter frequencies between DCs and T cells are maximized
within lymph nodes (LNs) that are compact immunological projections of the peripheral
tissue they drain. But LNs are more than passive meeting places for DCs that immigrated
from the tissue and lymphocytes that recirculated via the blood. The microanatomy
of the LN stroma actively organizes the cellular encounters by providing preformed
migration tracks that create dynamic but highly ordered movement patterns. LN
architecture further acts as a sophisticated filtration system that sieves the
incoming interstitial fluid at different levels and guarantees that immunologically
relevant antigens are loaded on DCs or B cells while inert substances are channeled
back into the blood circulation. This review focuses on the non-hematopoietic
infrastructure of the lymph node. We describe the association between fibroblastic
reticular cell, conduit, DC, and T cell as the essential functional unit of the
T-cell cortex.
author:
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Lämmermann T, Sixt MK. The microanatomy of T-cell responses. Immunological
Reviews. 2008;221(1):26-43. doi:10.1111/j.1600-065X.2008.00592.x
apa: Lämmermann, T., & Sixt, M. K. (2008). The microanatomy of T-cell responses.
Immunological Reviews. Wiley-Blackwell. https://doi.org/10.1111/j.1600-065X.2008.00592.x
chicago: Lämmermann, Tim, and Michael K Sixt. “The Microanatomy of T-Cell Responses.”
Immunological Reviews. Wiley-Blackwell, 2008. https://doi.org/10.1111/j.1600-065X.2008.00592.x.
ieee: T. Lämmermann and M. K. Sixt, “The microanatomy of T-cell responses,” Immunological
Reviews, vol. 221, no. 1. Wiley-Blackwell, pp. 26–43, 2008.
ista: Lämmermann T, Sixt MK. 2008. The microanatomy of T-cell responses. Immunological
Reviews. 221(1), 26–43.
mla: Lämmermann, Tim, and Michael K. Sixt. “The Microanatomy of T-Cell Responses.”
Immunological Reviews, vol. 221, no. 1, Wiley-Blackwell, 2008, pp. 26–43,
doi:10.1111/j.1600-065X.2008.00592.x.
short: T. Lämmermann, M.K. Sixt, Immunological Reviews 221 (2008) 26–43.
date_created: 2018-12-11T12:06:00Z
date_published: 2008-02-07T00:00:00Z
date_updated: 2021-01-12T07:53:20Z
day: '07'
doi: 10.1111/j.1600-065X.2008.00592.x
extern: '1'
intvolume: ' 221'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 26 - 43
publication: Immunological Reviews
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2187'
status: public
title: The microanatomy of T-cell responses
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 221
year: '2008'
...
---
_id: '3940'
abstract:
- lang: eng
text: Until recently little information was available on the molecular details of
the extracellular matrix (ECM) of secondary lymphoid tissues. There is now growing
evidence that these ECMs are unique structures, combining characteristics of basement
membranes and interstitial or fibrillar matrices, resulting in scaffolds that
are strong and highly flexible and, in certain secondary lymphoid compartments,
also forming conduit networks for rapid fluid transport. This review will address
the structural characteristics of the ECM of the murine spleen and its potential
role as an organizer of immune cell compartments, with reference to the lymph
node where relevant.
author:
- first_name: Zerina
full_name: Lokmic, Zerina
last_name: Lokmic
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Susanna
full_name: Cardell, Susanna
last_name: Cardell
- first_name: Rupert
full_name: Hallmann, Rupert
last_name: Hallmann
- first_name: Lydia
full_name: Sorokin, Lydia
last_name: Sorokin
citation:
ama: Lokmic Z, Lämmermann T, Sixt MK, Cardell S, Hallmann R, Sorokin L. The extracellular
matrix of the spleen as a potential organizer of immune cell compartments. Seminars
in Immunology. 2008;20(1):4-13. doi:10.1016/j.smim.2007.12.009
apa: Lokmic, Z., Lämmermann, T., Sixt, M. K., Cardell, S., Hallmann, R., & Sorokin,
L. (2008). The extracellular matrix of the spleen as a potential organizer of
immune cell compartments. Seminars in Immunology. Academic Press. https://doi.org/10.1016/j.smim.2007.12.009
chicago: Lokmic, Zerina, Tim Lämmermann, Michael K Sixt, Susanna Cardell, Rupert
Hallmann, and Lydia Sorokin. “The Extracellular Matrix of the Spleen as a Potential
Organizer of Immune Cell Compartments.” Seminars in Immunology. Academic
Press, 2008. https://doi.org/10.1016/j.smim.2007.12.009.
ieee: Z. Lokmic, T. Lämmermann, M. K. Sixt, S. Cardell, R. Hallmann, and L. Sorokin,
“The extracellular matrix of the spleen as a potential organizer of immune cell
compartments,” Seminars in Immunology, vol. 20, no. 1. Academic Press,
pp. 4–13, 2008.
ista: Lokmic Z, Lämmermann T, Sixt MK, Cardell S, Hallmann R, Sorokin L. 2008. The
extracellular matrix of the spleen as a potential organizer of immune cell compartments.
Seminars in Immunology. 20(1), 4–13.
mla: Lokmic, Zerina, et al. “The Extracellular Matrix of the Spleen as a Potential
Organizer of Immune Cell Compartments.” Seminars in Immunology, vol. 20,
no. 1, Academic Press, 2008, pp. 4–13, doi:10.1016/j.smim.2007.12.009.
short: Z. Lokmic, T. Lämmermann, M.K. Sixt, S. Cardell, R. Hallmann, L. Sorokin,
Seminars in Immunology 20 (2008) 4–13.
date_created: 2018-12-11T12:06:00Z
date_published: 2008-02-01T00:00:00Z
date_updated: 2021-01-12T07:53:20Z
day: '01'
doi: 10.1016/j.smim.2007.12.009
extern: 1
intvolume: ' 20'
issue: '1'
month: '02'
page: 4 - 13
publication: Seminars in Immunology
publication_status: published
publisher: Academic Press
publist_id: '2188'
quality_controlled: 0
status: public
title: The extracellular matrix of the spleen as a potential organizer of immune cell
compartments
type: journal_article
volume: 20
year: '2008'
...
---
_id: '3970'
abstract:
- lang: eng
text: 'While genome-wide gene expression data are generated at an increasing rate,
the repertoire of approaches for pattern discovery in these data is still limited.
Identifying subtle patterns of interest in large amounts of data (tens of thousands
of profiles) associated with a certain level of noise remains a challenge. A microarray
time series was recently generated to study the transcriptional program of the
mouse segmentation clock, a biological oscillator associated with the periodic
formation of the segments of the body axis. A method related to Fourier analysis,
the Lomb-Scargle periodogram, was used to detect periodic profiles in the dataset,
leading to the identification of a novel set of cyclic genes associated with the
segmentation clock. Here, we applied to the same microarray time series dataset
four distinct mathematical methods to identify significant patterns in gene expression
profiles. These methods are called: Phase consistency, Address reduction, Cyclohedron
test and Stable persistence, and are based on different conceptual frameworks
that are either hypothesis- or data-driven. Some of the methods, unlike Fourier
transforms, are not dependent on the assumption of periodicity of the pattern
of interest. Remarkably, these methods identified blindly the expression profiles
of known cyclic genes as the most significant patterns in the dataset. Many candidate
genes predicted by more than one approach appeared to be true positive cyclic
genes and will be of particular interest for future research. In addition, these
methods predicted novel candidate cyclic genes that were consistent with previous
biological knowledge and experimental validation in mouse embryos. Our results
demonstrate the utility of these novel pattern detection strategies, notably for
detection of periodic profiles, and suggest that combining several distinct mathematical
approaches to analyze microarray datasets is a valuable strategy for identifying
genes that exhibit novel, interesting transcriptional patterns.'
acknowledgement: This research was partially supported by DARPA grant HR 0011-05-1-0057.
HE and YM mathematical work was supported by DARPA grant HR0011-05-1-0007. AS research
was supported by a Lucent Technologies Bell Labs Graduate Research. Fellowship;
AK and MR research was supported by NIH grant GM U54 GM74942; and SA research was
supported by Association pour la Recherche sur le Cancer (ARC), France. OP, AM,
MLD, EG and GH research was supported by the Stowers Institute for Medical Research.
OP is a Howard Hughes Medical Institute Investigator.
author:
- first_name: Mary
full_name: Dequéant, Mary-Lee
last_name: Dequéant
- first_name: Sebastian
full_name: Ahnert, Sebastian
last_name: Ahnert
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Thomas
full_name: Fink, Thomas M
last_name: Fink
- first_name: Earl
full_name: Glynn, Earl F
last_name: Glynn
- first_name: Gaye
full_name: Hattem, Gaye
last_name: Hattem
- first_name: Andrzej
full_name: Kudlicki, Andrzej
last_name: Kudlicki
- first_name: Yuriy
full_name: Mileyko, Yuriy
last_name: Mileyko
- first_name: Jason
full_name: Morton, Jason
last_name: Morton
- first_name: Arcady
full_name: Mushegian, Arcady R
last_name: Mushegian
- first_name: Lior
full_name: Pachter, Lior
last_name: Pachter
- first_name: Maga
full_name: Rowicka, Maga
last_name: Rowicka
- first_name: Anne
full_name: Shiu, Anne
last_name: Shiu
- first_name: Bernd
full_name: Sturmfels, Bernd
last_name: Sturmfels
- first_name: Olivier
full_name: Pourquie, Olivier
last_name: Pourquie
citation:
ama: Dequéant M, Ahnert S, Edelsbrunner H, et al. Comparison of pattern detection
methods in microarray time series of the segmentation clock. PLoS One.
2008;3(8). doi:10.1371/journal.pone.0002856
apa: Dequéant, M., Ahnert, S., Edelsbrunner, H., Fink, T., Glynn, E., Hattem, G.,
… Pourquie, O. (2008). Comparison of pattern detection methods in microarray time
series of the segmentation clock. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0002856
chicago: Dequéant, Mary, Sebastian Ahnert, Herbert Edelsbrunner, Thomas Fink, Earl
Glynn, Gaye Hattem, Andrzej Kudlicki, et al. “Comparison of Pattern Detection
Methods in Microarray Time Series of the Segmentation Clock.” PLoS One.
Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0002856.
ieee: M. Dequéant et al., “Comparison of pattern detection methods in microarray
time series of the segmentation clock,” PLoS One, vol. 3, no. 8. Public
Library of Science, 2008.
ista: Dequéant M, Ahnert S, Edelsbrunner H, Fink T, Glynn E, Hattem G, Kudlicki
A, Mileyko Y, Morton J, Mushegian A, Pachter L, Rowicka M, Shiu A, Sturmfels B,
Pourquie O. 2008. Comparison of pattern detection methods in microarray time series
of the segmentation clock. PLoS One. 3(8).
mla: Dequéant, Mary, et al. “Comparison of Pattern Detection Methods in Microarray
Time Series of the Segmentation Clock.” PLoS One, vol. 3, no. 8, Public
Library of Science, 2008, doi:10.1371/journal.pone.0002856.
short: M. Dequéant, S. Ahnert, H. Edelsbrunner, T. Fink, E. Glynn, G. Hattem, A.
Kudlicki, Y. Mileyko, J. Morton, A. Mushegian, L. Pachter, M. Rowicka, A. Shiu,
B. Sturmfels, O. Pourquie, PLoS One 3 (2008).
date_created: 2018-12-11T12:06:11Z
date_published: 2008-08-06T00:00:00Z
date_updated: 2021-01-12T07:53:33Z
day: '06'
doi: 10.1371/journal.pone.0002856
extern: 1
intvolume: ' 3'
issue: '8'
month: '08'
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '2157'
quality_controlled: 0
status: public
title: Comparison of pattern detection methods in microarray time series of the segmentation
clock
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: 3
year: '2008'
...
---
_id: '3971'
abstract:
- lang: eng
text: The Reeb graph is a useful tool in visualizing real-valued data obtained from
computational simulations of physical processes. We characterize the evolution
of the Reeb graph of a time-varying continuous function defined in three-dimensional
space. We show how to maintain the Reeb graph over time and compress the entire
sequence of Reeb graphs into a single, partially persistent data structure, and
augment this data structure with Betti numbers to describe the topology of level
sets and with path seeds to assist in the fast extraction of level sets for visualization.
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Ajith
full_name: Mascarenhas, Ajith
last_name: Mascarenhas
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
- first_name: Jack
full_name: Snoeyink, Jack
last_name: Snoeyink
citation:
ama: 'Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. Time-varying
Reeb graphs for continuous space-time data. Computational Geometry: Theory
and Applications. 2008;41(3):149-166. doi:10.1016/j.comgeo.2007.11.001'
apa: 'Edelsbrunner, H., Harer, J., Mascarenhas, A., Pascucci, V., & Snoeyink,
J. (2008). Time-varying Reeb graphs for continuous space-time data. Computational
Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2007.11.001'
chicago: 'Edelsbrunner, Herbert, John Harer, Ajith Mascarenhas, Valerio Pascucci,
and Jack Snoeyink. “Time-Varying Reeb Graphs for Continuous Space-Time Data.”
Computational Geometry: Theory and Applications. Elsevier, 2008. https://doi.org/10.1016/j.comgeo.2007.11.001.'
ieee: 'H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, and J. Snoeyink,
“Time-varying Reeb graphs for continuous space-time data,” Computational Geometry:
Theory and Applications, vol. 41, no. 3. Elsevier, pp. 149–166, 2008.'
ista: 'Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. 2008. Time-varying
Reeb graphs for continuous space-time data. Computational Geometry: Theory and
Applications. 41(3), 149–166.'
mla: 'Edelsbrunner, Herbert, et al. “Time-Varying Reeb Graphs for Continuous Space-Time
Data.” Computational Geometry: Theory and Applications, vol. 41, no. 3,
Elsevier, 2008, pp. 149–66, doi:10.1016/j.comgeo.2007.11.001.'
short: 'H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, J. Snoeyink, Computational
Geometry: Theory and Applications 41 (2008) 149–166.'
date_created: 2018-12-11T12:06:12Z
date_published: 2008-11-01T00:00:00Z
date_updated: 2021-01-12T07:53:34Z
day: '01'
doi: 10.1016/j.comgeo.2007.11.001
extern: 1
intvolume: ' 41'
issue: '3'
month: '11'
page: 149 - 166
publication: 'Computational Geometry: Theory and Applications'
publication_status: published
publisher: Elsevier
publist_id: '2158'
quality_controlled: 0
status: public
title: Time-varying Reeb graphs for continuous space-time data
type: journal_article
volume: 41
year: '2008'
...
---
_id: '3969'
abstract:
- lang: eng
text: Persistent homology is an algebraic tool for measuring topological features
of shapes and functions. It casts the multi-scale organization we frequently observe
in nature into a mathematical formalism. Here we give a record of the short history
of persistent homology and present its basic concepts. Besides the mathematics
we focus on algorithms and mention the various connections to applications, including
to biomolecules, biological networks, data analysis, and geometric modeling.
acknowledgement: Supported in part by DARPA under grants HR0011-05-1-0007 and HR0011-05-0057
and by the NSF under grant DBI-06-06873.
alternative_title:
- Contemporary Mathematics
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
citation:
ama: 'Edelsbrunner H, Harer J. Persistent homology - a survey. In: Surveys on
Discrete and Computational Geometry: Twenty Years Later. American Mathematical
Society; 2008:257-282.'
apa: 'Edelsbrunner, H., & Harer, J. (2008). Persistent homology - a survey.
In Surveys on Discrete and Computational Geometry: Twenty Years Later (pp.
257–282). American Mathematical Society.'
chicago: 'Edelsbrunner, Herbert, and John Harer. “Persistent Homology - a Survey.”
In Surveys on Discrete and Computational Geometry: Twenty Years Later,
257–82. American Mathematical Society, 2008.'
ieee: 'H. Edelsbrunner and J. Harer, “Persistent homology - a survey,” in Surveys
on Discrete and Computational Geometry: Twenty Years Later, American Mathematical
Society, 2008, pp. 257–282.'
ista: 'Edelsbrunner H, Harer J. 2008.Persistent homology - a survey. In: Surveys
on Discrete and Computational Geometry: Twenty Years Later. Contemporary Mathematics,
, 257–282.'
mla: 'Edelsbrunner, Herbert, and John Harer. “Persistent Homology - a Survey.” Surveys
on Discrete and Computational Geometry: Twenty Years Later, American Mathematical
Society, 2008, pp. 257–82.'
short: 'H. Edelsbrunner, J. Harer, in:, Surveys on Discrete and Computational Geometry:
Twenty Years Later, American Mathematical Society, 2008, pp. 257–282.'
date_created: 2018-12-11T12:06:11Z
date_published: 2008-03-28T00:00:00Z
date_updated: 2021-01-12T07:53:33Z
day: '28'
extern: 1
month: '03'
page: 257 - 282
publication: 'Surveys on Discrete and Computational Geometry: Twenty Years Later'
publication_status: published
publisher: American Mathematical Society
publist_id: '2156'
quality_controlled: 0
status: public
title: Persistent homology - a survey
type: book_chapter
year: '2008'
...
---
_id: '4141'
abstract:
- lang: eng
text: The zyxin-related LPP protein is localized at focal adhesions and cell-cell
contacts and is involved in the regulation of smooth muscle cell migration. A
known interaction partner of LPP in human is the tumor suppressor protein SCRIB.
Knocking down scrib expression c uring zebrafish embryonic development results
in defects of convergence and extension (C&E) movements, which occur during
gastrulation and mediate elongation of the anterior-posterior body axis. Mediolateral
cell polarization underlying C&E is regulated by a noncanonical Writ signaling
pathway constituting the vertebrate planar cell polarity (PCP) pathway. Here,
we investigated the role of Lpp during early zebrafish development. We show that
morpholino knockdown of Ipp results in defects of C&E, phenocopying noncanonical
Wnt signaling mutants. Time-lapse analysis associates the defective dorsal convergence
movements with a reduced ability to migrate along straight paths. In addition,
expression of Lpp is significantly reduced in Wnt11 morphants and in embryos overexpressing
Wnt11 or a dominant-negative form of Rho kinase 2, which is a downstream effector
of Wnt11, Suggesting that Lpp expression is dependent on noncanonical Wnt signaling.
Finally, we demonstrate that Lpp interacts with the PCP protein Scrib in zebrafish,
and that Lpp and Scrib cooperate for the mediation of C&E. (C) 2008 Elsevier
Inc. All rights reserved.
article_processing_charge: No
author:
- first_name: Hilke
full_name: Vervenne, Hilke
last_name: Vervenne
- first_name: Koen
full_name: Crombez, Koen
last_name: Crombez
- first_name: Kathleen
full_name: Lambaerts, Kathleen
last_name: Lambaerts
- first_name: Lara
full_name: Carvalho, Lara
last_name: Carvalho
- first_name: Mathias
full_name: Köppen, Mathias
last_name: Köppen
- 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
- first_name: Wim
full_name: Van De Ven, Wim
last_name: Van De Ven
- first_name: Marleen
full_name: Petit, Marleen
last_name: Petit
citation:
ama: Vervenne H, Crombez K, Lambaerts K, et al. Lpp is involved in Wnt/PCP signaling
and acts together with Scrib to mediate convergence and extension movements during
zebrafish gastrulation. Developmental Biology. 2008;320(1):267-277. doi:10.1016/j.ydbio.2008.05.529
apa: Vervenne, H., Crombez, K., Lambaerts, K., Carvalho, L., Köppen, M., Heisenberg,
C.-P. J., … Petit, M. (2008). Lpp is involved in Wnt/PCP signaling and acts together
with Scrib to mediate convergence and extension movements during zebrafish gastrulation.
Developmental Biology. Elsevier. https://doi.org/10.1016/j.ydbio.2008.05.529
chicago: Vervenne, Hilke, Koen Crombez, Kathleen Lambaerts, Lara Carvalho, Mathias
Köppen, Carl-Philipp J Heisenberg, Wim Van De Ven, and Marleen Petit. “Lpp Is
Involved in Wnt/PCP Signaling and Acts Together with Scrib to Mediate Convergence
and Extension Movements during Zebrafish Gastrulation.” Developmental Biology.
Elsevier, 2008. https://doi.org/10.1016/j.ydbio.2008.05.529.
ieee: H. Vervenne et al., “Lpp is involved in Wnt/PCP signaling and acts
together with Scrib to mediate convergence and extension movements during zebrafish
gastrulation,” Developmental Biology, vol. 320, no. 1. Elsevier, pp. 267–277,
2008.
ista: Vervenne H, Crombez K, Lambaerts K, Carvalho L, Köppen M, Heisenberg C-PJ,
Van De Ven W, Petit M. 2008. Lpp is involved in Wnt/PCP signaling and acts together
with Scrib to mediate convergence and extension movements during zebrafish gastrulation.
Developmental Biology. 320(1), 267–277.
mla: Vervenne, Hilke, et al. “Lpp Is Involved in Wnt/PCP Signaling and Acts Together
with Scrib to Mediate Convergence and Extension Movements during Zebrafish Gastrulation.”
Developmental Biology, vol. 320, no. 1, Elsevier, 2008, pp. 267–77, doi:10.1016/j.ydbio.2008.05.529.
short: H. Vervenne, K. Crombez, K. Lambaerts, L. Carvalho, M. Köppen, C.-P.J. Heisenberg,
W. Van De Ven, M. Petit, Developmental Biology 320 (2008) 267–277.
date_created: 2018-12-11T12:07:11Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2021-01-12T07:54:48Z
day: '01'
doi: 10.1016/j.ydbio.2008.05.529
extern: '1'
intvolume: ' 320'
issue: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 267 - 277
publication: Developmental Biology
publication_status: published
publisher: Elsevier
publist_id: '1978'
status: public
title: Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate
convergence and extension movements during zebrafish gastrulation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 320
year: '2008'
...
---
_id: '4161'
abstract:
- lang: eng
text: Handedness of the vertebrate body plan critically depends on transient embryonic
structures/ organs that generate cilia-dependent leftward fluid flow within constrained
extracellular environments. Although the function of ciliated organs in laterality
determination has been extensively studied, how they are formed during embryogenesis
is still poorly understood. Here we show that Kupffer's vesicle (KV), the zebrafish
organ of laterality, arises from a surface epithelium previously thought to adopt
exclusively extra-embryonic fates. Live multi-photon confocal imaging reveals
that surface epithelial cells undergo Nodal/TGF beta signalling-dependent ingression
at the dorsal germ ring margin prior to gastrulation, to give rise to dorsal forerunner
cells (DFCs), the precursors of KV. DFCs then migrate attached to the overlying
surface epithelium and rearrange into rosette-like epithelial structures at the
end of gastrulation. During early somitogenesis, these epithelial rosettes coalesce
into a single rosette that differentiates into the KV with a ciliated lumen at
its apical centre. Our results provide novel insights into the morphogenetic transformations
that shape the laterality organ in zebrafish and suggest a conserved progenitor
role of the surface epithelium during laterality organ formation in vertebrates.
article_processing_charge: No
author:
- first_name: Pablo
full_name: Oteíza, Pablo
last_name: Oteíza
- first_name: Mathias
full_name: Köppen, Mathias
last_name: Köppen
- first_name: Miguel
full_name: Concha, Miguel
last_name: Concha
- 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: Oteíza P, Köppen M, Concha M, Heisenberg C-PJ. Origin and shaping of the laterality
organ in zebrafish. Development. 2008;135(16):2807-2813. doi:10.1242/dev.022228
apa: Oteíza, P., Köppen, M., Concha, M., & Heisenberg, C.-P. J. (2008). Origin
and shaping of the laterality organ in zebrafish. Development. Company
of Biologists. https://doi.org/10.1242/dev.022228
chicago: Oteíza, Pablo, Mathias Köppen, Miguel Concha, and Carl-Philipp J Heisenberg.
“Origin and Shaping of the Laterality Organ in Zebrafish.” Development.
Company of Biologists, 2008. https://doi.org/10.1242/dev.022228.
ieee: P. Oteíza, M. Köppen, M. Concha, and C.-P. J. Heisenberg, “Origin and shaping
of the laterality organ in zebrafish,” Development, vol. 135, no. 16. Company
of Biologists, pp. 2807–2813, 2008.
ista: Oteíza P, Köppen M, Concha M, Heisenberg C-PJ. 2008. Origin and shaping of
the laterality organ in zebrafish. Development. 135(16), 2807–2813.
mla: Oteíza, Pablo, et al. “Origin and Shaping of the Laterality Organ in Zebrafish.”
Development, vol. 135, no. 16, Company of Biologists, 2008, pp. 2807–13,
doi:10.1242/dev.022228.
short: P. Oteíza, M. Köppen, M. Concha, C.-P.J. Heisenberg, Development 135 (2008)
2807–2813.
date_created: 2018-12-11T12:07:19Z
date_published: 2008-08-15T00:00:00Z
date_updated: 2021-01-12T07:54:57Z
day: '15'
doi: 10.1242/dev.022228
extern: '1'
intvolume: ' 135'
issue: '16'
language:
- iso: eng
month: '08'
oa_version: None
page: 2807 - 2813
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '1956'
status: public
title: Origin and shaping of the laterality organ in zebrafish
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2008'
...
---
_id: '4190'
abstract:
- lang: eng
text: During vertebrate gastrulation, cells forming the prechordal plate undergo
directed migration as a cohesive cluster. Recent studies revealed that E-cadherin-mediated
coherence between these cells plays an important role in effective anterior migration,
and that platelet-derived growth factor (Pdgf) appears to act as a guidance cue
in this process. However, the mechanisms underlying this process at the individual
cell level remain poorly understood. We have identified miles apart (mil) as a
suppressor of defective anterior migration of the prospective prechordal plate
in silberblick (slb)/wnt11 mutant embryos, in which E-cadherin-mediated coherence
of cell movement is reduced. mil encodes Edg5, a sphingosine-1-phosphate (S1P)
receptor belonging to a family of five G-protein-coupled receptors (S1PRs). S1P
is a lipid signalling molecule that has been implicated in regulating cytoskeletal
rearrangements, cell motility and cell adhesion in a variety of cell types. We
examined the roles of Mil in anterior migration of prechordal plate progenitor
cells and found that, in slb embryos injected with mil-MO, cells migrate with
increased motility but decreased directionality, without restoring the coherence
of cell migration. This indicates that prechordal plate progenitor cells can migrate
effectively as individuals, as well as in a coherent cluster of cells. Moreover,
we demonstrate that Mil regulates cell motility and polarisation through Pdgf
and its intracellular effecter PI3K, but modulates cell coherence independently
of the Pdgf/PI3K pathway, thus co-ordinating cell motility and coherence. These
results suggest that the net migration of prechordal plate progenitors is determined
by different parameters, including motility, persistence and coherence.
article_processing_charge: No
author:
- first_name: Masatake
full_name: Kai, Masatake
last_name: Kai
- 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
- first_name: Masazumi
full_name: Tada, Masazumi
last_name: Tada
citation:
ama: Kai M, Heisenberg C-PJ, Tada M. Sphingosine-1-phosphate receptors regulate
individual cell behaviours underlying the directed migration of prechordal plate
progenitor cells during zebrafish gastrulation. Development. 2008;135(18):3043-3051.
doi:10.1242/dev.020396
apa: Kai, M., Heisenberg, C.-P. J., & Tada, M. (2008). Sphingosine-1-phosphate
receptors regulate individual cell behaviours underlying the directed migration
of prechordal plate progenitor cells during zebrafish gastrulation. Development.
Company of Biologists. https://doi.org/10.1242/dev.020396
chicago: Kai, Masatake, Carl-Philipp J Heisenberg, and Masazumi Tada. “Sphingosine-1-Phosphate
Receptors Regulate Individual Cell Behaviours Underlying the Directed Migration
of Prechordal Plate Progenitor Cells during Zebrafish Gastrulation.” Development.
Company of Biologists, 2008. https://doi.org/10.1242/dev.020396.
ieee: M. Kai, C.-P. J. Heisenberg, and M. Tada, “Sphingosine-1-phosphate receptors
regulate individual cell behaviours underlying the directed migration of prechordal
plate progenitor cells during zebrafish gastrulation,” Development, vol.
135, no. 18. Company of Biologists, pp. 3043–3051, 2008.
ista: Kai M, Heisenberg C-PJ, Tada M. 2008. Sphingosine-1-phosphate receptors regulate
individual cell behaviours underlying the directed migration of prechordal plate
progenitor cells during zebrafish gastrulation. Development. 135(18), 3043–3051.
mla: Kai, Masatake, et al. “Sphingosine-1-Phosphate Receptors Regulate Individual
Cell Behaviours Underlying the Directed Migration of Prechordal Plate Progenitor
Cells during Zebrafish Gastrulation.” Development, vol. 135, no. 18, Company
of Biologists, 2008, pp. 3043–51, doi:10.1242/dev.020396.
short: M. Kai, C.-P.J. Heisenberg, M. Tada, Development 135 (2008) 3043–3051.
date_created: 2018-12-11T12:07:29Z
date_published: 2008-09-15T00:00:00Z
date_updated: 2021-01-12T07:55:11Z
day: '15'
doi: 10.1242/dev.020396
extern: '1'
intvolume: ' 135'
issue: '18'
language:
- iso: eng
month: '09'
oa_version: None
page: 3043 - 3051
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '1928'
status: public
title: Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying
the directed migration of prechordal plate progenitor cells during zebrafish gastrulation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2008'
...
---
_id: '4384'
abstract:
- lang: eng
text: |-
Model checking software transactional memories (STMs) is difficult because of the unbounded number, length, and delay of concurrent transactions and the unbounded size of the memory. We show that, under certain conditions, the verification problem can be reduced to a finite-state problem, and we illustrate the use of the method by proving the correctness of several STMs, including two-phase locking, DSTM, TL2, and optimistic concurrency control. The safety properties we consider include strict serializability and opacity; the liveness properties include obstruction freedom, livelock freedom, and wait freedom.
Our main contribution lies in the structure of the proofs, which are largely automated and not restricted to the STMs mentioned above. In a first step we show that every STM that enjoys certain structural properties either violates a safety or liveness requirement on some program with two threads and two shared variables, or satisfies the requirement on all programs. In the second step we use a model checker to prove the requirement for the STM applied to a most general program with two threads and two variables. In the safety case, the model checker constructs a simulation relation between two carefully constructed finite-state transition systems, one representing the given STM applied to a most general program, and the other representing a most liberal safe STM applied to the same program. In the liveness case, the model checker analyzes fairness conditions on the given STM transition system.
author:
- first_name: Rachid
full_name: Guerraoui, Rachid
last_name: Guerraoui
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
- first_name: Vasu
full_name: Vasu Singh
id: 4DAE2708-F248-11E8-B48F-1D18A9856A87
last_name: Singh
citation:
ama: 'Guerraoui R, Henzinger TA, Jobstmann B, Singh V. Model checking transactional
memories. In: ACM; 2008:372-382. doi:10.1145/1375581.1375626'
apa: 'Guerraoui, R., Henzinger, T. A., Jobstmann, B., & Singh, V. (2008). Model
checking transactional memories (pp. 372–382). Presented at the PLDI: Programming
Languages Design and Implementation, ACM. https://doi.org/10.1145/1375581.1375626'
chicago: Guerraoui, Rachid, Thomas A Henzinger, Barbara Jobstmann, and Vasu Singh.
“Model Checking Transactional Memories,” 372–82. ACM, 2008. https://doi.org/10.1145/1375581.1375626.
ieee: 'R. Guerraoui, T. A. Henzinger, B. Jobstmann, and V. Singh, “Model checking
transactional memories,” presented at the PLDI: Programming Languages Design and
Implementation, 2008, pp. 372–382.'
ista: 'Guerraoui R, Henzinger TA, Jobstmann B, Singh V. 2008. Model checking transactional
memories. PLDI: Programming Languages Design and Implementation, 372–382.'
mla: Guerraoui, Rachid, et al. Model Checking Transactional Memories. ACM,
2008, pp. 372–82, doi:10.1145/1375581.1375626.
short: R. Guerraoui, T.A. Henzinger, B. Jobstmann, V. Singh, in:, ACM, 2008, pp.
372–382.
conference:
name: 'PLDI: Programming Languages Design and Implementation'
date_created: 2018-12-11T12:08:34Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:34Z
day: '01'
doi: 10.1145/1375581.1375626
extern: 1
file:
- access_level: open_access
checksum: 1238258a27f212fc1a2050a9a246da20
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:05Z
date_updated: 2020-07-14T12:46:28Z
file_id: '5054'
file_name: IST-2012-74-v1+1_Model_checking_transactional_memories.pdf
file_size: 201583
relation: main_file
file_date_updated: 2020-07-14T12:46:28Z
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/model_checking_transactional_memories.pdf
month: '01'
oa: 1
page: 372 - 382
publication_status: published
publisher: ACM
publist_id: '1073'
quality_controlled: 0
status: public
title: Model checking transactional memories
type: conference
year: '2008'
...
---
_id: '4386'
abstract:
- lang: eng
text: We introduce the notion of permissiveness in transactional memories (TM).
Intuitively, a TM is permissive if it never aborts a transaction when it need
not. More specifically, a TM is permissive with respect to a safety property p
if the TM accepts every history that satisfies p. Permissiveness, like safety
and liveness, can be used as a metric to compare TMs. We illustrate that it is
impractical to achieve permissiveness deterministically, and then show how randomization
can be used to achieve permissiveness efficiently. We introduce Adaptive Validation
STM (AVSTM), which is probabilistically permissive with respect to opacity; that
is, every opaque history is accepted by AVSTM with positive probability. Moreover,
AVSTM guarantees lock freedom. Owing to its permissiveness, AVSTM outperforms
other STMs by up to 40% in read dominated workloads in high contention scenarios.
But, in low contention scenarios, the book-keeping done by AVSTM to achieve permissiveness
makes AVSTM, on average, 20-30% worse than existing STMs.
acknowledgement: This research was supported by the Swiss National Science Foundation.
alternative_title:
- LNCS
author:
- first_name: Rachid
full_name: Guerraoui, Rachid
last_name: Guerraoui
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Vasu
full_name: Vasu Singh
id: 4DAE2708-F248-11E8-B48F-1D18A9856A87
last_name: Singh
citation:
ama: 'Guerraoui R, Henzinger TA, Singh V. Permissiveness in transactional memories.
In: Vol 5218. Springer; 2008:305-319. doi:10.1007/978-3-540-87779-0_21'
apa: 'Guerraoui, R., Henzinger, T. A., & Singh, V. (2008). Permissiveness in
transactional memories (Vol. 5218, pp. 305–319). Presented at the DISC: Distributed
Computing, Springer. https://doi.org/10.1007/978-3-540-87779-0_21'
chicago: Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Permissiveness
in Transactional Memories,” 5218:305–19. Springer, 2008. https://doi.org/10.1007/978-3-540-87779-0_21.
ieee: 'R. Guerraoui, T. A. Henzinger, and V. Singh, “Permissiveness in transactional
memories,” presented at the DISC: Distributed Computing, 2008, vol. 5218, pp.
305–319.'
ista: 'Guerraoui R, Henzinger TA, Singh V. 2008. Permissiveness in transactional
memories. DISC: Distributed Computing, LNCS, vol. 5218, 305–319.'
mla: Guerraoui, Rachid, et al. Permissiveness in Transactional Memories.
Vol. 5218, Springer, 2008, pp. 305–19, doi:10.1007/978-3-540-87779-0_21.
short: R. Guerraoui, T.A. Henzinger, V. Singh, in:, Springer, 2008, pp. 305–319.
conference:
name: 'DISC: Distributed Computing'
date_created: 2018-12-11T12:08:35Z
date_published: 2008-09-10T00:00:00Z
date_updated: 2021-01-12T07:56:35Z
day: '10'
doi: 10.1007/978-3-540-87779-0_21
extern: 1
intvolume: ' 5218'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/permissiveness_in_transactional_memories.pdf
month: '09'
page: 305 - 319
publication_status: published
publisher: Springer
publist_id: '1072'
quality_controlled: 0
status: public
title: Permissiveness in transactional memories
type: conference
volume: 5218
year: '2008'
...
---
_id: '4387'
abstract:
- lang: eng
text: Software transactional memory (STM) offers a disciplined concurrent programming
model for exploiting the parallelism of modern processor architectures. This paper
presents the first deterministic specification automata for strict serializability
and opacity in STMs. Using an antichain-based tool, we show our deterministic
specifications to be equivalent to more intuitive, nondeterministic specification
automata (which are too large to be determinized automatically). Using deterministic
specification automata, we obtain a complete verification tool for STMs. We also
show how to model and verify contention management within STMs. We automatically
check the opacity of popular STM algorithms, such as TL2 and DSTM, with a universal
contention manager. The universal contention manager is nondeterministic and establishes
correctness for all possible contention management schemes.
acknowledgement: This research was supported by the Swiss National Science Foundation.
alternative_title:
- LNCS
author:
- first_name: Rachid
full_name: Guerraoui, Rachid
last_name: Guerraoui
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Vasu
full_name: Vasu Singh
id: 4DAE2708-F248-11E8-B48F-1D18A9856A87
last_name: Singh
citation:
ama: 'Guerraoui R, Henzinger TA, Singh V. Completeness and nondeterminism in model
checking transactional memories. In: Vol 5201. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2008:21-35. doi:10.1007/978-3-540-85361-9_6'
apa: 'Guerraoui, R., Henzinger, T. A., & Singh, V. (2008). Completeness and
nondeterminism in model checking transactional memories (Vol. 5201, pp. 21–35).
Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.1007/978-3-540-85361-9_6'
chicago: Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Completeness and
Nondeterminism in Model Checking Transactional Memories,” 5201:21–35. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2008. https://doi.org/10.1007/978-3-540-85361-9_6.
ieee: 'R. Guerraoui, T. A. Henzinger, and V. Singh, “Completeness and nondeterminism
in model checking transactional memories,” presented at the CONCUR: Concurrency
Theory, 2008, vol. 5201, pp. 21–35.'
ista: 'Guerraoui R, Henzinger TA, Singh V. 2008. Completeness and nondeterminism
in model checking transactional memories. CONCUR: Concurrency Theory, LNCS, vol.
5201, 21–35.'
mla: Guerraoui, Rachid, et al. Completeness and Nondeterminism in Model Checking
Transactional Memories. Vol. 5201, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2008, pp. 21–35, doi:10.1007/978-3-540-85361-9_6.
short: R. Guerraoui, T.A. Henzinger, V. Singh, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2008, pp. 21–35.
conference:
name: 'CONCUR: Concurrency Theory'
date_created: 2018-12-11T12:08:35Z
date_published: 2008-07-30T00:00:00Z
date_updated: 2021-01-12T07:56:35Z
day: '30'
doi: 10.1007/978-3-540-85361-9_6
extern: 1
intvolume: ' 5201'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/completeness_and_nondeterminism_in_model_checking_transactional_memories.pdf
month: '07'
page: 21 - 35
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '1071'
quality_controlled: 0
status: public
title: Completeness and nondeterminism in model checking transactional memories
type: conference
volume: 5201
year: '2008'
...
---
_id: '4397'
alternative_title:
- LNCS 5123
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- first_name: Damien
full_name: Damien Zufferey
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
citation:
ama: 'Beyer D, Zufferey D, Majumdar R. CSIsat: Interpolation for LA+EUF. In: Springer;
2008:304-308.'
apa: 'Beyer, D., Zufferey, D., & Majumdar, R. (2008). CSIsat: Interpolation
for LA+EUF (pp. 304–308). Presented at the CAV: Computer Aided Verification, Springer.'
chicago: 'Beyer, Dirk, Damien Zufferey, and Ritankar Majumdar. “CSIsat: Interpolation
for LA+EUF,” 304–8. Springer, 2008.'
ieee: 'D. Beyer, D. Zufferey, and R. Majumdar, “CSIsat: Interpolation for LA+EUF,”
presented at the CAV: Computer Aided Verification, 2008, pp. 304–308.'
ista: 'Beyer D, Zufferey D, Majumdar R. 2008. CSIsat: Interpolation for LA+EUF.
CAV: Computer Aided Verification, LNCS 5123, , 304–308.'
mla: 'Beyer, Dirk, et al. CSIsat: Interpolation for LA+EUF. Springer, 2008,
pp. 304–08.'
short: D. Beyer, D. Zufferey, R. Majumdar, in:, Springer, 2008, pp. 304–308.
conference:
name: 'CAV: Computer Aided Verification'
date_created: 2018-12-11T12:08:38Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:40Z
day: '01'
extern: 1
month: '01'
page: 304 - 308
publication_status: published
publisher: Springer
publist_id: '1060'
quality_controlled: 0
status: public
title: 'CSIsat: Interpolation for LA+EUF'
type: conference
year: '2008'
...
---
_id: '4400'
author:
- first_name: Adam
full_name: Aviv,Adam J.
last_name: Aviv
- first_name: Pavol
full_name: Pavol Cerny
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Sandy
full_name: Clark,Sandy
last_name: Clark
- first_name: Eric
full_name: Cronin,Eric
last_name: Cronin
- first_name: Gaurav
full_name: Shah,Gaurav
last_name: Shah
- first_name: Micah
full_name: Sherr,Micah
last_name: Sherr
- first_name: Matt
full_name: Blaze,Matt
last_name: Blaze
citation:
ama: 'Aviv A, Cerny P, Clark S, et al. Security Evaluation of ES&S Voting
Machines and Election Management System. In: USENIX; 2008. doi:1545'
apa: Aviv, A., Cerny, P., Clark, S., Cronin, E., Shah, G., Sherr, M., & Blaze,
M. (2008). Security Evaluation of ES&S Voting Machines and Election Management
System. Presented at the Usenix/ Accurate Electronic Voting Technology Workshop
(EVT) 08, USENIX. https://doi.org/1545
chicago: Aviv, Adam, Pavol Cerny, Sandy Clark, Eric Cronin, Gaurav Shah, Micah Sherr,
and Matt Blaze. “Security Evaluation of ES&S Voting Machines and Election
Management System.” USENIX, 2008. https://doi.org/1545.
ieee: A. Aviv et al., “Security Evaluation of ES&S Voting Machines
and Election Management System,” presented at the Usenix/ Accurate Electronic
Voting Technology Workshop (EVT) 08, 2008.
ista: Aviv A, Cerny P, Clark S, Cronin E, Shah G, Sherr M, Blaze M. 2008. Security
Evaluation of ES&S Voting Machines and Election Management System. Usenix/
Accurate Electronic Voting Technology Workshop (EVT) 08.
mla: Aviv, Adam, et al. Security Evaluation of ES&S Voting Machines and
Election Management System. USENIX, 2008, doi:1545.
short: A. Aviv, P. Cerny, S. Clark, E. Cronin, G. Shah, M. Sherr, M. Blaze, in:,
USENIX, 2008.
conference:
name: Usenix/ Accurate Electronic Voting Technology Workshop (EVT) 08
date_created: 2018-12-11T12:08:39Z
date_published: 2008-07-29T00:00:00Z
date_updated: 2021-01-12T07:56:42Z
day: '29'
doi: '1545'
extern: 1
main_file_link:
- open_access: '0'
url: http://www.usenix.org/event/evt08/tech/full_papers/aviv/aviv.pdf
month: '07'
publication_status: published
publisher: USENIX
publist_id: '1057'
quality_controlled: 0
status: public
title: Security Evaluation of ES&S Voting Machines and Election Management System
type: conference
year: '2008'
...
---
_id: '4409'
abstract:
- lang: eng
text: "Models of timed systems must incorporate not only the sequence of system
events, but the timings of these events as well to capture the real-time aspects
of physical systems. Timed automata are models of real-time systems in which states
consist of discrete locations and values for real-time clocks. The presence of
real-time clocks leads to an uncountable state space. This thesis studies verification
problems on timed automata in a game theoretic framework.\r\n\r\nFor untimed systems,
two systems are close if every sequence of events of one system is also observable
in the second system. For timed systems, the difference in timings of the two
corresponding sequences is also of importance. We propose the notion of bisimulation
distance which quantifies timing differences; if the bisimulation distance between
two systems is epsilon, then (a) every sequence of events of one system has a
corresponding matching sequence in the other, and (b) the timings of matching
events in between the two corresponding traces do not differ by more than epsilon.
We show that we can compute the bisimulation distance between two timed automata
to within any desired degree of accuracy. We also show that the timed verification
logic TCTL is robust with respect to our notion of quantitative bisimilarity,
in particular, if a system satisfies a formula, then every close system satisfies
a close formula.\r\n\r\nTimed games are used for distinguishing between the actions
of several agents, typically a controller and an environment. The controller must
achieve its objective against all possible choices of the environment. The modeling
of the passage of time leads to the presence of zeno executions, and corresponding
unrealizable strategies of the controller which may achieve objectives by blocking
time. We disallow such unreasonable strategies by restricting all agents to use
only receptive strategies --strategies which while not being required to ensure
time divergence by any agent, are such that no agent is responsible for blocking
time. Time divergence is guaranteed when all players use receptive strategies.
We show that timed automaton games with receptive strategies can be solved by
a reduction to finite state turn based game graphs. We define the logic timed
alternating-time temporal logic for verification of timed automaton games and
show that the logic can be model checked in EXPTIME. We also show that the minimum
time required by an agent to reach a desired location, and the maximum time an
agent can stay safe within a set of locations, against all possible actions of
its adversaries are both computable.\r\n\r\nWe next study the memory requirements
of winning strategies for timed automaton games. We prove that finite memory strategies
suffice for safety objectives, and that winning strategies for reachability objectives
may require infinite memory in general. We introduce randomized strategies in
which an agent can propose a probabilistic distribution of moves and show that
finite memory randomized strategies suffice for all omega-regular objectives.
We also show that while randomization helps in simplifying winning strategies,
and thus allows the construction of simpler controllers, it does not help a player
in winning at more states, and thus does not allow the construction of more powerful
controllers.\r\n\r\nFinally we study robust winning strategies in timed games.
In a physical system, a controller may propose an action together with a time
delay, but the action cannot be assumed to be executed at the exact proposed time
delay. We present robust strategies which incorporate such jitters and show that
the set of states from which an agent can win robustly is computable."
article_processing_charge: No
author:
- first_name: Vinayak
full_name: Prabhu, Vinayak
last_name: Prabhu
citation:
ama: Prabhu V. Games for the verification of timed systems. 2008:1-137.
apa: Prabhu, V. (2008). Games for the verification of timed systems. University
of California, Berkeley.
chicago: Prabhu, Vinayak. “Games for the Verification of Timed Systems.” University
of California, Berkeley, 2008.
ieee: V. Prabhu, “Games for the verification of timed systems,” University of California,
Berkeley, 2008.
ista: Prabhu V. 2008. Games for the verification of timed systems. University of
California, Berkeley.
mla: Prabhu, Vinayak. Games for the Verification of Timed Systems. University
of California, Berkeley, 2008, pp. 1–137.
short: V. Prabhu, Games for the Verification of Timed Systems, University of California,
Berkeley, 2008.
date_created: 2018-12-11T12:08:42Z
date_published: 2008-09-01T00:00:00Z
date_updated: 2022-02-14T14:35:11Z
day: '01'
degree_awarded: PhD
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www2.eecs.berkeley.edu/Pubs/TechRpts/2008/EECS-2008-97.html
month: '09'
oa: 1
oa_version: None
page: 1 - 137
publication_status: published
publisher: University of California, Berkeley
publist_id: '319'
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: John
full_name: Steel, John
last_name: Steel
- first_name: Pravin
full_name: Varaiya, Pravin
last_name: Varaiya
title: Games for the verification of timed systems
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2008'
...
---
_id: '4415'
abstract:
- lang: eng
text: 'Many computing applications, especially those in safety critical embedded
systems, require highly predictable timing properties. However, time is often
not present in the prevailing computing and networking abstractions. In fact,
most advances in computer architecture, software, and networking favor average-case
performance over timing predictability. This thesis studies several methods for
the design of concurrent and/or distributed embedded systems with precise timing
guarantees. The focus is on flexible and compositional methods for programming
and verification of the timing properties. The presented methods together with
related formalisms cover two levels of design: (1) Programming language/model
level. We propose the distributed variant of Giotto, a coordination programming
language with an explicit temporal semantics—the logical execution time (LET)
semantics. The LET of a task is an interval of time that specifies the time instants
at which task inputs and outputs become available (task release and termination
instants). The LET of a task is always non-zero. This allows us to communicate
values across the network without changing the timing information of the task,
and without introducing nondeterminism. We show how this methodology supports
distributed code generation for distributed real-time systems. The method gives
up some performance in favor of composability and predictability. We characterize
the tradeoff by comparing the LET semantics with the semantics used in Simulink.
(2) Abstract task graph level. We study interface-based design and verification
of applications represented with task graphs. We consider task sequence graphs
with general event models, and cyclic graphs with periodic event models with jitter
and phase. Here an interface of a component exposes time and resource constraints
of the component. Together with interfaces we formally define interface composition
operations and the refinement relation. For efficient and flexible composability
checking two properties are important: incremental design and independent refinement.
According to the incremental design property the composition of interfaces can
be performed in any order, even if interfaces for some components are not known.
The refinement relation is defined such that in a design we can always substitute
a refined interface for an abstract one. We show that the framework supports independent
refinement, i.e., the refinement relation is preserved under composition operations.'
acknowledgement: 978-0-549-83480-9
article_processing_charge: No
author:
- first_name: Slobodan
full_name: Matic, Slobodan
last_name: Matic
citation:
ama: Matic S. Compositionality in deterministic real-time embedded systems. 2008:1-148.
apa: Matic, S. (2008). Compositionality in deterministic real-time embedded systems.
University of California, Berkeley.
chicago: Matic, Slobodan. “Compositionality in Deterministic Real-Time Embedded
Systems.” University of California, Berkeley, 2008.
ieee: S. Matic, “Compositionality in deterministic real-time embedded systems,”
University of California, Berkeley, 2008.
ista: Matic S. 2008. Compositionality in deterministic real-time embedded systems.
University of California, Berkeley.
mla: Matic, Slobodan. Compositionality in Deterministic Real-Time Embedded Systems.
University of California, Berkeley, 2008, pp. 1–148.
short: S. Matic, Compositionality in Deterministic Real-Time Embedded Systems, University
of California, Berkeley, 2008.
date_created: 2018-12-11T12:08:44Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2022-02-14T14:08:50Z
day: '01'
degree_awarded: PhD
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 1 - 148
publication_status: published
publisher: University of California, Berkeley
publist_id: '316'
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Edward
full_name: Lee, Edward
last_name: Lee
- first_name: Raja
full_name: Sengupta, Raja
last_name: Sengupta
title: Compositionality in deterministic real-time embedded systems
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2008'
...
---
_id: '4452'
abstract:
- lang: eng
text: We describe Valigator, a software tool for imperative program verification
that efficiently combines symbolic computation and automated reasoning in a uniform
framework. The system offers support for automatically generating and proving
verification conditions and, most importantly, for automatically inferring loop
invariants and bound assertions by means of symbolic summation, Gröbner basis
computation, and quantifier elimination. We present general principles of the
implementation and illustrate them on examples.
acknowledgement: This research was supported by the Swiss NSF.
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Thibaud
full_name: Hottelier, Thibaud
last_name: Hottelier
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
citation:
ama: 'Henzinger TA, Hottelier T, Kovács L. Valigator: A verification tool with bound
and invariant generation. In: Vol 5330. Springer; 2008:333-342. doi:10.1007/978-3-540-89439-1_24'
apa: 'Henzinger, T. A., Hottelier, T., & Kovács, L. (2008). Valigator: A verification
tool with bound and invariant generation (Vol. 5330, pp. 333–342). Presented at
the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Springer.
https://doi.org/10.1007/978-3-540-89439-1_24'
chicago: 'Henzinger, Thomas A, Thibaud Hottelier, and Laura Kovács. “Valigator:
A Verification Tool with Bound and Invariant Generation,” 5330:333–42. Springer,
2008. https://doi.org/10.1007/978-3-540-89439-1_24.'
ieee: 'T. A. Henzinger, T. Hottelier, and L. Kovács, “Valigator: A verification
tool with bound and invariant generation,” presented at the LPAR: Logic for Programming,
Artificial Intelligence, and Reasoning, 2008, vol. 5330, pp. 333–342.'
ista: 'Henzinger TA, Hottelier T, Kovács L. 2008. Valigator: A verification tool
with bound and invariant generation. LPAR: Logic for Programming, Artificial Intelligence,
and Reasoning, LNCS, vol. 5330, 333–342.'
mla: 'Henzinger, Thomas A., et al. Valigator: A Verification Tool with Bound
and Invariant Generation. Vol. 5330, Springer, 2008, pp. 333–42, doi:10.1007/978-3-540-89439-1_24.'
short: T.A. Henzinger, T. Hottelier, L. Kovács, in:, Springer, 2008, pp. 333–342.
conference:
name: 'LPAR: Logic for Programming, Artificial Intelligence, and Reasoning'
date_created: 2018-12-11T12:08:55Z
date_published: 2008-11-13T00:00:00Z
date_updated: 2021-01-12T07:57:04Z
day: '13'
doi: 10.1007/978-3-540-89439-1_24
extern: 1
intvolume: ' 5330'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/valigator.pdf
month: '11'
page: 333 - 342
publication_status: published
publisher: Springer
publist_id: '277'
quality_controlled: 0
status: public
title: 'Valigator: A verification tool with bound and invariant generation'
type: conference
volume: 5330
year: '2008'
...
---
_id: '4509'
abstract:
- lang: eng
text: 'I discuss two main challenges in embedded systems design: the challenge to
build predictable systems, and that to build robust systems. I suggest how predictability
can be formalized as a form of determinism, and robustness as a form of continuity.'
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Henzinger TA. Two challenges in embedded systems design: Predictability and
robustness. Philosophical Transactions of the Royal Society A Mathematical
Physical and Engineering Sciences. 2008;366(1881):3727-3736. doi:10.1098/rsta.2008.0141'
apa: 'Henzinger, T. A. (2008). Two challenges in embedded systems design: Predictability
and robustness. Philosophical Transactions of the Royal Society A Mathematical
Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rsta.2008.0141'
chicago: 'Henzinger, Thomas A. “Two Challenges in Embedded Systems Design: Predictability
and Robustness.” Philosophical Transactions of the Royal Society A Mathematical
Physical and Engineering Sciences. Royal Society of London, 2008. https://doi.org/10.1098/rsta.2008.0141.'
ieee: 'T. A. Henzinger, “Two challenges in embedded systems design: Predictability
and robustness,” Philosophical Transactions of the Royal Society A Mathematical
Physical and Engineering Sciences, vol. 366, no. 1881. Royal Society of London,
pp. 3727–3736, 2008.'
ista: 'Henzinger TA. 2008. Two challenges in embedded systems design: Predictability
and robustness. Philosophical Transactions of the Royal Society A Mathematical
Physical and Engineering Sciences. 366(1881), 3727–3736.'
mla: 'Henzinger, Thomas A. “Two Challenges in Embedded Systems Design: Predictability
and Robustness.” Philosophical Transactions of the Royal Society A Mathematical
Physical and Engineering Sciences, vol. 366, no. 1881, Royal Society of London,
2008, pp. 3727–36, doi:10.1098/rsta.2008.0141.'
short: T.A. Henzinger, Philosophical Transactions of the Royal Society A Mathematical
Physical and Engineering Sciences 366 (2008) 3727–3736.
date_created: 2018-12-11T12:09:13Z
date_published: 2008-07-31T00:00:00Z
date_updated: 2021-01-12T07:59:19Z
day: '31'
doi: 10.1098/rsta.2008.0141
extern: 1
intvolume: ' 366'
issue: '1881'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/two_challenges_in_embedded_systems_design.pdf
month: '07'
page: 3727 - 3736
publication: Philosophical Transactions of the Royal Society A Mathematical Physical
and Engineering Sciences
publication_status: published
publisher: Royal Society of London
publist_id: '219'
quality_controlled: 0
status: public
title: 'Two challenges in embedded systems design: Predictability and robustness'
type: journal_article
volume: 366
year: '2008'
...
---
_id: '4524'
abstract:
- lang: eng
text: "Complex requirements, time-to-market pressure and regulatory constraints
have made the designing of embedded systems extremely challenging. This is evident
by the increase in effort and expenditure for design of safety-driven real-time
control-dominated applications like automotive and avionic controllers. Design
processes are often challenged by lack of proper programming tools for specifying
and verifying critical requirements (e.g. timing and reliability) of such applications.
Platform based design, an approach for designing embedded systems, addresses the
above concerns by separating requirement from architecture. The requirement specifies
the intended behavior of an application while the architecture specifies the guarantees
(e.g. execution speed, failure rate etc). An implementation, a mapping of the
requirement on the architecture, is then analyzed for correctness. The orthogonalization
of concerns makes the specification and analyses simpler. An effective use of
such design methodology has been proposed in Logical Execution Time (LET) model
of real-time tasks. The model separates the timing requirements (specified by
release and termination instances of a task) from the architecture guarantees
(specified by worst-case execution time of the task).\r\n\r\nThis dissertation
proposes a coordination language, Hierarchical Timing Language (HTL), that captures
the timing and reliability requirements of real-time applications. An implementation
of the program on an architecture is then analyzed to check whether desired timing
and reliability requirements are met or not. The core framework extends the LET
model by accounting for reliability and refinement. The reliability model separates
the reliability requirements of tasks from the reliability guarantees of the architecture.
The requirement expresses the desired long-term reliability while the architecture
provides a short-term reliability guarantee (e.g. failure rate for each iteration).
The analysis checks if the short-term guarantee ensures the desired long-term
reliability. The refinement model allows replacing a task by another task during
program execution. Refinement preserves schedulability and reliability, i.e.,
if a refined task is schedulable and reliable for an implementation, then the
refining task is also schedulable and reliable for the implementation. Refinement
helps in concise specification without overloading analysis.\r\n\r\nThe work presents
the formal model, the analyses (both with and without refinement), and a compiler
for HTL programs. The compiler checks composition and refinement constraints,
performs schedulability and reliability analyses, and generates code for implementation
of an HTL program on a virtual machine. Three real-time controllers, one each
from automatic control, automotive control and avionic control, are used to illustrate
the steps in modeling and analyzing HTL programs."
acknowledgement: 978-0-549-83679-7
article_processing_charge: No
author:
- first_name: Arkadeb
full_name: Ghosal, Arkadeb
last_name: Ghosal
citation:
ama: Ghosal A. A hierarchical coordination language for reliable real-time tasks.
2008:1-210.
apa: Ghosal, A. (2008). A hierarchical coordination language for reliable real-time
tasks. University of California, Berkeley.
chicago: Ghosal, Arkadeb. “A Hierarchical Coordination Language for Reliable Real-Time
Tasks.” University of California, Berkeley, 2008.
ieee: A. Ghosal, “A hierarchical coordination language for reliable real-time tasks,”
University of California, Berkeley, 2008.
ista: Ghosal A. 2008. A hierarchical coordination language for reliable real-time
tasks. University of California, Berkeley.
mla: Ghosal, Arkadeb. A Hierarchical Coordination Language for Reliable Real-Time
Tasks. University of California, Berkeley, 2008, pp. 1–210.
short: A. Ghosal, A Hierarchical Coordination Language for Reliable Real-Time Tasks,
University of California, Berkeley, 2008.
date_created: 2018-12-11T12:09:18Z
date_published: 2008-01-31T00:00:00Z
date_updated: 2021-01-12T07:59:26Z
day: '31'
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 1 - 210
publication_status: published
publisher: University of California, Berkeley
publist_id: '199'
status: public
supervisor:
- first_name: Alberto
full_name: Sangiovanni-Vincentelli, Alberto
last_name: Sangiovanni-Vincentelli
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Edward
full_name: Lee, Edward
last_name: Lee
- first_name: Karl
full_name: Hedrick, Karl
last_name: Hedrick
title: A hierarchical coordination language for reliable real-time tasks
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2008'
...
---
_id: '4521'
abstract:
- lang: eng
text: The search for proof and the search for counterexamples (bugs) are complementary
activities that need to be pursued concurrently in order to maximize the practical
success rate of verification tools.While this is well-understood in safety verification,
the current focus of liveness verification has been almost exclusively on the
search for termination proofs. A counterexample to termination is an infinite
programexecution. In this paper, we propose a method to search for such counterexamples.
The search proceeds in two phases. We first dynamically enumerate lasso-shaped
candidate paths for counterexamples, and then statically prove their feasibility.
We illustrate the utility of our nontermination prover, called TNT, on several
nontrivial examples, some of which require bit-level reasoning about integer representations.
author:
- first_name: Ashutosh
full_name: Ashutosh Gupta
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
- first_name: Ru
full_name: Xu, Ru-Gang
last_name: Xu
citation:
ama: 'Gupta A, Henzinger TA, Majumdar R, Rybalchenko A, Xu R. Proving non-termination.
In: ACM; 2008:147-158. doi:10.1145/1328438.1328459'
apa: 'Gupta, A., Henzinger, T. A., Majumdar, R., Rybalchenko, A., & Xu, R. (2008).
Proving non-termination (pp. 147–158). Presented at the POPL: Principles of Programming
Languages, ACM. https://doi.org/10.1145/1328438.1328459'
chicago: Gupta, Ashutosh, Thomas A Henzinger, Ritankar Majumdar, Andrey Rybalchenko,
and Ru Xu. “Proving Non-Termination,” 147–58. ACM, 2008. https://doi.org/10.1145/1328438.1328459.
ieee: 'A. Gupta, T. A. Henzinger, R. Majumdar, A. Rybalchenko, and R. Xu, “Proving
non-termination,” presented at the POPL: Principles of Programming Languages,
2008, pp. 147–158.'
ista: 'Gupta A, Henzinger TA, Majumdar R, Rybalchenko A, Xu R. 2008. Proving non-termination.
POPL: Principles of Programming Languages, 147–158.'
mla: Gupta, Ashutosh, et al. Proving Non-Termination. ACM, 2008, pp. 147–58,
doi:10.1145/1328438.1328459.
short: A. Gupta, T.A. Henzinger, R. Majumdar, A. Rybalchenko, R. Xu, in:, ACM, 2008,
pp. 147–158.
conference:
name: 'POPL: Principles of Programming Languages'
date_created: 2018-12-11T12:09:17Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:59:25Z
day: '01'
doi: 10.1145/1328438.1328459
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/proving_non-termination.pdf
month: '01'
page: 147 - 158
publication_status: published
publisher: ACM
publist_id: '208'
quality_controlled: 0
status: public
title: Proving non-termination
type: conference
year: '2008'
...
---
_id: '4527'
abstract:
- lang: eng
text: |-
We introduce bounded asynchrony, a notion of concurrency tailored to the modeling of biological cell-cell interactions. Bounded asynchrony is the result of a scheduler that bounds the number of steps that one process gets ahead of other processes; this allows the components of a system to move independently while keeping them coupled. Bounded asynchrony accurately reproduces the experimental observations made about certain cell-cell interactions: its constrained nondeterminism captures the variability observed in cells that, although equally potent, assume distinct fates. Real-life cells are not “scheduled”, but we show that distributed real-time behavior can lead to component interactions that are observationally equivalent to bounded asynchrony; this provides a possible mechanistic explanation for the phenomena observed during cell fate specification.
We use model checking to determine cell fates. The nondeterminism of bounded asynchrony causes state explosion during model checking, but partial-order methods are not directly applicable. We present a new algorithm that reduces the number of states that need to be explored: our optimization takes advantage of the bounded-asynchronous progress and the spatially local interactions of components that model cells. We compare our own communication-based reduction with partial-order reduction (on a restricted form of bounded asynchrony) and experiments illustrate that our algorithm leads to significant savings.
acknowledgement: Supported in part by the Swiss National Science Foundation (grant
205321-111840).
alternative_title:
- LNCS
author:
- first_name: Jasmin
full_name: Fisher, Jasmin
last_name: Fisher
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Maria
full_name: Maria Mateescu
id: 3B43276C-F248-11E8-B48F-1D18A9856A87
last_name: Mateescu
- first_name: Nir
full_name: Piterman, Nir
last_name: Piterman
citation:
ama: 'Fisher J, Henzinger TA, Mateescu M, Piterman N. Bounded asynchrony: Concurrency
for modeling cell-cell interactions. In: Vol 5054. Springer; 2008:17-32. doi:10.1007/978-3-540-68413-8_2'
apa: 'Fisher, J., Henzinger, T. A., Mateescu, M., & Piterman, N. (2008). Bounded
asynchrony: Concurrency for modeling cell-cell interactions (Vol. 5054, pp. 17–32).
Presented at the FMSB: Formal Methods in Systems Biology, Springer. https://doi.org/10.1007/978-3-540-68413-8_2'
chicago: 'Fisher, Jasmin, Thomas A Henzinger, Maria Mateescu, and Nir Piterman.
“Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions,” 5054:17–32.
Springer, 2008. https://doi.org/10.1007/978-3-540-68413-8_2.'
ieee: 'J. Fisher, T. A. Henzinger, M. Mateescu, and N. Piterman, “Bounded asynchrony:
Concurrency for modeling cell-cell interactions,” presented at the FMSB: Formal
Methods in Systems Biology, 2008, vol. 5054, pp. 17–32.'
ista: 'Fisher J, Henzinger TA, Mateescu M, Piterman N. 2008. Bounded asynchrony:
Concurrency for modeling cell-cell interactions. FMSB: Formal Methods in Systems
Biology, LNCS, vol. 5054, 17–32.'
mla: 'Fisher, Jasmin, et al. Bounded Asynchrony: Concurrency for Modeling Cell-Cell
Interactions. Vol. 5054, Springer, 2008, pp. 17–32, doi:10.1007/978-3-540-68413-8_2.'
short: J. Fisher, T.A. Henzinger, M. Mateescu, N. Piterman, in:, Springer, 2008,
pp. 17–32.
conference:
name: 'FMSB: Formal Methods in Systems Biology'
date_created: 2018-12-11T12:09:19Z
date_published: 2008-05-26T00:00:00Z
date_updated: 2021-01-12T07:59:27Z
day: '26'
doi: 10.1007/978-3-540-68413-8_2
extern: 1
intvolume: ' 5054'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/bounded_asynchrony.pdf
month: '05'
page: 17 - 32
publication_status: published
publisher: Springer
publist_id: '196'
quality_controlled: 0
status: public
title: 'Bounded asynchrony: Concurrency for modeling cell-cell interactions'
type: conference
volume: 5054
year: '2008'
...
---
_id: '4532'
abstract:
- lang: eng
text: We consider the equivalence problem for labeled Markov chains (LMCs), where
each state is labeled with an observation. Two LMCs are equivalent if every finite
sequence of observations has the same probability of occurrence in the two LMCs.
We show that equivalence can be decided in polynomial time, using a reduction
to the equivalence problem for probabilistic automata, which is known to be solvable
in polynomial time. We provide an alternative algorithm to solve the equivalence
problem, which is based on a new definition of bisimulation for probabilistic
automata. We also extend the technique to decide the equivalence of weighted probabilistic
automata.
author:
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jean
full_name: Raskin, Jean-François
last_name: Raskin
citation:
ama: Doyen L, Henzinger TA, Raskin J. Equivalence of labeled Markov chains. International
Journal of Foundations of Computer Science. 2008;19(3):549-563. doi:10.1142/S0129054108005814
apa: Doyen, L., Henzinger, T. A., & Raskin, J. (2008). Equivalence of labeled
Markov chains. International Journal of Foundations of Computer Science.
World Scientific Publishing. https://doi.org/10.1142/S0129054108005814
chicago: Doyen, Laurent, Thomas A Henzinger, and Jean Raskin. “Equivalence of Labeled
Markov Chains.” International Journal of Foundations of Computer Science.
World Scientific Publishing, 2008. https://doi.org/10.1142/S0129054108005814 .
ieee: L. Doyen, T. A. Henzinger, and J. Raskin, “Equivalence of labeled Markov chains,”
International Journal of Foundations of Computer Science, vol. 19, no.
3. World Scientific Publishing, pp. 549–563, 2008.
ista: Doyen L, Henzinger TA, Raskin J. 2008. Equivalence of labeled Markov chains.
International Journal of Foundations of Computer Science. 19(3), 549–563.
mla: Doyen, Laurent, et al. “Equivalence of Labeled Markov Chains.” International
Journal of Foundations of Computer Science, vol. 19, no. 3, World Scientific
Publishing, 2008, pp. 549–63, doi:10.1142/S0129054108005814 .
short: L. Doyen, T.A. Henzinger, J. Raskin, International Journal of Foundations
of Computer Science 19 (2008) 549–563.
date_created: 2018-12-11T12:09:20Z
date_published: 2008-06-01T00:00:00Z
date_updated: 2021-01-12T07:59:30Z
day: '01'
doi: '10.1142/S0129054108005814 '
extern: 1
intvolume: ' 19'
issue: '3'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/equivalence_of_labeled_markov_chains.pdf
month: '06'
page: 549 - 563
publication: International Journal of Foundations of Computer Science
publication_status: published
publisher: World Scientific Publishing
publist_id: '192'
quality_controlled: 0
status: public
title: Equivalence of labeled Markov chains
type: journal_article
volume: 19
year: '2008'
...
---
_id: '4533'
abstract:
- lang: eng
text: Interface theories have been proposed to support incremental design and independent
implementability. Incremental design means that the compatibility checking of
interfaces can proceed for partial system descriptions, without knowing the interfaces
of all components. Independent implementability means that compatible interfaces
can be refined separately, maintaining compatibility. We show that these interface
theories provide no formal support for component reuse, meaning that the same
component cannot be used to implement several different interfaces in a design.
We add a new operation to interface theories in order to support such reuse. For
example, different interfaces for the same component may refer to different aspects
such as functionality, timing, and power consumption. We give both stateless and
stateful examples for interface theories with component reuse. To illustrate component
reuse in interface-based design, we show how the stateful theory provides a natural
framework for specifying and refining PCI bus clients.
author:
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
- first_name: Tatjana
full_name: Tatjana Petrov
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: 'Doyen L, Henzinger TA, Jobstmann B, Petrov T. Interface theories with component
reuse. In: ACM; 2008:79-88. doi:10.1145/1450058.1450070'
apa: 'Doyen, L., Henzinger, T. A., Jobstmann, B., & Petrov, T. (2008). Interface
theories with component reuse (pp. 79–88). Presented at the EMSOFT: Embedded Software
, ACM. https://doi.org/10.1145/1450058.1450070'
chicago: Doyen, Laurent, Thomas A Henzinger, Barbara Jobstmann, and Tatjana Petrov.
“Interface Theories with Component Reuse,” 79–88. ACM, 2008. https://doi.org/10.1145/1450058.1450070.
ieee: 'L. Doyen, T. A. Henzinger, B. Jobstmann, and T. Petrov, “Interface theories
with component reuse,” presented at the EMSOFT: Embedded Software , 2008, pp.
79–88.'
ista: 'Doyen L, Henzinger TA, Jobstmann B, Petrov T. 2008. Interface theories with
component reuse. EMSOFT: Embedded Software , 79–88.'
mla: Doyen, Laurent, et al. Interface Theories with Component Reuse. ACM,
2008, pp. 79–88, doi:10.1145/1450058.1450070.
short: L. Doyen, T.A. Henzinger, B. Jobstmann, T. Petrov, in:, ACM, 2008, pp. 79–88.
conference:
name: 'EMSOFT: Embedded Software '
date_created: 2018-12-11T12:09:21Z
date_published: 2008-10-01T00:00:00Z
date_updated: 2021-01-12T07:59:30Z
day: '01'
doi: 10.1145/1450058.1450070
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/interface_theories_with_component_reuse.pdf
month: '10'
page: 79 - 88
publication_status: published
publisher: ACM
publist_id: '193'
quality_controlled: 0
status: public
title: Interface theories with component reuse
type: conference
year: '2008'
...
---
_id: '4534'
abstract:
- lang: eng
text: A stochastic graph game is played by two players on a game graph with probabilistic
transitions. We consider stochastic graph games with ω-regular winning conditions
specified as parity objectives, and mean-payoff (or limit-average) objectives.
These games lie in NP ∩ coNP. We present a polynomial-time Turing reduction of
stochastic parity games to stochastic mean-payoff games.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Chatterjee K, Henzinger TA. Reduction of stochastic parity to stochastic mean-payoff
games. Information Processing Letters. 2008;106(1):1-7. doi:10.1016/j.ipl.2007.08.035
apa: Chatterjee, K., & Henzinger, T. A. (2008). Reduction of stochastic parity
to stochastic mean-payoff games. Information Processing Letters. Elsevier.
https://doi.org/10.1016/j.ipl.2007.08.035
chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Reduction of Stochastic
Parity to Stochastic Mean-Payoff Games.” Information Processing Letters.
Elsevier, 2008. https://doi.org/10.1016/j.ipl.2007.08.035.
ieee: K. Chatterjee and T. A. Henzinger, “Reduction of stochastic parity to stochastic
mean-payoff games,” Information Processing Letters, vol. 106, no. 1. Elsevier,
pp. 1–7, 2008.
ista: Chatterjee K, Henzinger TA. 2008. Reduction of stochastic parity to stochastic
mean-payoff games. Information Processing Letters. 106(1), 1–7.
mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. “Reduction of Stochastic Parity
to Stochastic Mean-Payoff Games.” Information Processing Letters, vol.
106, no. 1, Elsevier, 2008, pp. 1–7, doi:10.1016/j.ipl.2007.08.035.
short: K. Chatterjee, T.A. Henzinger, Information Processing Letters 106 (2008)
1–7.
date_created: 2018-12-11T12:09:21Z
date_published: 2008-03-31T00:00:00Z
date_updated: 2021-01-12T07:59:30Z
day: '31'
doi: 10.1016/j.ipl.2007.08.035
extern: 1
intvolume: ' 106'
issue: '1'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/reduction_of_stochastic_parity_to_stochastic_mean-payoff_games.pdf
month: '03'
page: 1 - 7
publication: Information Processing Letters
publication_status: published
publisher: Elsevier
publist_id: '188'
quality_controlled: 0
status: public
title: Reduction of stochastic parity to stochastic mean-payoff games
type: journal_article
volume: 106
year: '2008'
...
---
_id: '4546'
abstract:
- lang: eng
text: We propose the notion of logical reliability for real-time program tasks that
interact through periodically updated program variables. We describe a reliability
analysis that checks if the given short-term (e.g., single-period) reliability
of a program variable update in an implementation is sufficient to meet the logical
reliability requirement (of the program variable) in the long run. We then present
a notion of design by refinement where a task can be refined by another task that
writes to program variables with less logical reliability. The resulting analysis
can be combined with an incremental schedulability analysis for interacting real-time
tasks proposed earlier for the Hierarchical Timing Language (HTL), a coordination
language for distributed real-time systems. We implemented a logical-reliability-enhanced
prototype of the compiler and runtime infrastructure for HTL.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Arkadeb
full_name: Ghosal, Arkadeb
last_name: Ghosal
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Daniel
full_name: Iercan, Daniel
last_name: Iercan
- first_name: Christoph
full_name: Kirsch, Christoph M
last_name: Kirsch
- first_name: Claudio
full_name: Pinello, Claudio
last_name: Pinello
- first_name: Alberto
full_name: Sangiovanni-Vincentelli, Alberto
last_name: Sangiovanni Vincentelli
citation:
ama: 'Chatterjee K, Ghosal A, Henzinger TA, et al. Logical reliability of interacting
real-time tasks. In: IEEE; 2008:909-914. doi:10.1145/1403375.1403595'
apa: 'Chatterjee, K., Ghosal, A., Henzinger, T. A., Iercan, D., Kirsch, C., Pinello,
C., & Sangiovanni Vincentelli, A. (2008). Logical reliability of interacting
real-time tasks (pp. 909–914). Presented at the DATE: Design, Automation and Test
in Europe, IEEE. https://doi.org/10.1145/1403375.1403595'
chicago: Chatterjee, Krishnendu, Arkadeb Ghosal, Thomas A Henzinger, Daniel Iercan,
Christoph Kirsch, Claudio Pinello, and Alberto Sangiovanni Vincentelli. “Logical
Reliability of Interacting Real-Time Tasks,” 909–14. IEEE, 2008. https://doi.org/10.1145/1403375.1403595.
ieee: 'K. Chatterjee et al., “Logical reliability of interacting real-time
tasks,” presented at the DATE: Design, Automation and Test in Europe, 2008, pp.
909–914.'
ista: 'Chatterjee K, Ghosal A, Henzinger TA, Iercan D, Kirsch C, Pinello C, Sangiovanni
Vincentelli A. 2008. Logical reliability of interacting real-time tasks. DATE:
Design, Automation and Test in Europe, 909–914.'
mla: Chatterjee, Krishnendu, et al. Logical Reliability of Interacting Real-Time
Tasks. IEEE, 2008, pp. 909–14, doi:10.1145/1403375.1403595.
short: K. Chatterjee, A. Ghosal, T.A. Henzinger, D. Iercan, C. Kirsch, C. Pinello,
A. Sangiovanni Vincentelli, in:, IEEE, 2008, pp. 909–914.
conference:
name: 'DATE: Design, Automation and Test in Europe'
date_created: 2018-12-11T12:09:25Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:59:36Z
day: '01'
doi: 10.1145/1403375.1403595
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/logical_reliability_of_interacting_real-time_tasks.pdf
month: '01'
page: 909 - 914
publication_status: published
publisher: IEEE
publist_id: '171'
quality_controlled: 0
status: public
title: Logical reliability of interacting real-time tasks
type: conference
year: '2008'
...
---
_id: '4548'
abstract:
- lang: eng
text: The value of a finite-state two-player zero-sum stochastic game with limit-average
payoff can be approximated to within ε in time exponential in a polynomial in
the size of the game times polynomial in logarithmic in 1/ε, for all ε > 0.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Chatterjee K, Majumdar R, Henzinger TA. Stochastic limit-average games are
in EXPTIME. International Journal of Game Theory. 2008;37(2):219-234. doi:10.1007/s00182-007-0110-5
apa: Chatterjee, K., Majumdar, R., & Henzinger, T. A. (2008). Stochastic limit-average
games are in EXPTIME. International Journal of Game Theory. Springer. https://doi.org/10.1007/s00182-007-0110-5
chicago: Chatterjee, Krishnendu, Ritankar Majumdar, and Thomas A Henzinger. “Stochastic
Limit-Average Games Are in EXPTIME.” International Journal of Game Theory.
Springer, 2008. https://doi.org/10.1007/s00182-007-0110-5.
ieee: K. Chatterjee, R. Majumdar, and T. A. Henzinger, “Stochastic limit-average
games are in EXPTIME,” International Journal of Game Theory, vol. 37, no.
2. Springer, pp. 219–234, 2008.
ista: Chatterjee K, Majumdar R, Henzinger TA. 2008. Stochastic limit-average games
are in EXPTIME. International Journal of Game Theory. 37(2), 219–234.
mla: Chatterjee, Krishnendu, et al. “Stochastic Limit-Average Games Are in EXPTIME.”
International Journal of Game Theory, vol. 37, no. 2, Springer, 2008, pp.
219–34, doi:10.1007/s00182-007-0110-5.
short: K. Chatterjee, R. Majumdar, T.A. Henzinger, International Journal of Game
Theory 37 (2008) 219–234.
date_created: 2018-12-11T12:09:25Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:59:37Z
day: '01'
doi: 10.1007/s00182-007-0110-5
extern: 1
intvolume: ' 37'
issue: '2'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/stochastic_limit-average_games_are_in_exptime.pdf
month: '01'
page: 219 - 234
publication: International Journal of Game Theory
publication_status: published
publisher: Springer
publist_id: '168'
quality_controlled: 0
status: public
title: Stochastic limit-average games are in EXPTIME
type: journal_article
volume: 37
year: '2008'
...
---
_id: '4568'
abstract:
- lang: eng
text: We present and evaluate a framework and tool for combining multiple program
analyses which allows the dynamic (on-line) adjustment of the precision of each
analysis depending on the accumulated results. For example, the explicit tracking
of the values of a variable may be switched off in favor of a predicate abstraction
when and where the number of different variable values that have been encountered
has exceeded a specified threshold. The method is evaluated on verifying the SSH
client/server software and shows significant gains compared with predicate abstraction-based
model checking.
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Grégory
full_name: Théoduloz, Grégory
last_name: Théoduloz
citation:
ama: 'Beyer D, Henzinger TA, Théoduloz G. Program analysis with dynamic change of
precision. In: ACM; 2008:29-38. doi:10.1109/ASE.2008.13'
apa: 'Beyer, D., Henzinger, T. A., & Théoduloz, G. (2008). Program analysis
with dynamic change of precision (pp. 29–38). Presented at the ASE: Automated
Software Engineering, ACM. https://doi.org/10.1109/ASE.2008.13'
chicago: Beyer, Dirk, Thomas A Henzinger, and Grégory Théoduloz. “Program Analysis
with Dynamic Change of Precision,” 29–38. ACM, 2008. https://doi.org/10.1109/ASE.2008.13.
ieee: 'D. Beyer, T. A. Henzinger, and G. Théoduloz, “Program analysis with dynamic
change of precision,” presented at the ASE: Automated Software Engineering, 2008,
pp. 29–38.'
ista: 'Beyer D, Henzinger TA, Théoduloz G. 2008. Program analysis with dynamic change
of precision. ASE: Automated Software Engineering, 29–38.'
mla: Beyer, Dirk, et al. Program Analysis with Dynamic Change of Precision.
ACM, 2008, pp. 29–38, doi:10.1109/ASE.2008.13.
short: D. Beyer, T.A. Henzinger, G. Théoduloz, in:, ACM, 2008, pp. 29–38.
conference:
name: 'ASE: Automated Software Engineering'
date_created: 2018-12-11T12:09:31Z
date_published: 2008-10-07T00:00:00Z
date_updated: 2021-01-12T07:59:46Z
day: '07'
doi: 10.1109/ASE.2008.13
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/program_analysis_with_dynamic_change_of_precision.pdf
month: '10'
page: 29 - 38
publication_status: published
publisher: ACM
publist_id: '140'
quality_controlled: 0
status: public
title: Program analysis with dynamic change of precision
type: conference
year: '2008'
...
---
_id: '581'
abstract:
- lang: eng
text: We have detected a spin-dependent displacement perpendicular to the refractive
index gradient for photons passing through an air-glass interface. The effect
is the photonic version of the spin Hall effect in electronic systems, indicating
the universality of the effect for particles of different nature. Treating the
effect as a weak measurement of the spin projection of the photons, we used a
preselection and postselection technique on the spin state to enhance the original
displacement by nearly four orders of magnitude, attaining sensitivity to displacements
of ∼1 angstrom. The spin Hall effect can be used for manipulating photonic angular
momentum states, and the measurement technique holds promise for precision metrology.
author:
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Paul
full_name: Kwiat, Paul
last_name: Kwiat
citation:
ama: Hosten O, Kwiat P. Observation of the spin hall effect of light via weak measurements.
Science. 2008;319(5864):787-790. doi:10.1126/science.1152697
apa: Hosten, O., & Kwiat, P. (2008). Observation of the spin hall effect of
light via weak measurements. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1152697
chicago: Hosten, Onur, and Paul Kwiat. “Observation of the Spin Hall Effect of Light
via Weak Measurements.” Science. American Association for the Advancement
of Science, 2008. https://doi.org/10.1126/science.1152697.
ieee: O. Hosten and P. Kwiat, “Observation of the spin hall effect of light via
weak measurements,” Science, vol. 319, no. 5864. American Association for
the Advancement of Science, pp. 787–790, 2008.
ista: Hosten O, Kwiat P. 2008. Observation of the spin hall effect of light via
weak measurements. Science. 319(5864), 787–790.
mla: Hosten, Onur, and Paul Kwiat. “Observation of the Spin Hall Effect of Light
via Weak Measurements.” Science, vol. 319, no. 5864, American Association
for the Advancement of Science, 2008, pp. 787–90, doi:10.1126/science.1152697.
short: O. Hosten, P. Kwiat, Science 319 (2008) 787–790.
date_created: 2018-12-11T11:47:19Z
date_published: 2008-02-08T00:00:00Z
date_updated: 2021-01-12T08:03:38Z
day: '08'
doi: 10.1126/science.1152697
extern: 1
intvolume: ' 319'
issue: '5864'
month: '02'
page: 787 - 790
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7226'
quality_controlled: 0
status: public
title: Observation of the spin hall effect of light via weak measurements
type: journal_article
volume: 319
year: '2008'
...
---
_id: '584'
abstract:
- lang: eng
text: Using “quantum weak-measurements” as a coherent enhancement technique for
small signals, we have measured the recently proposed “spin Hall effect” of light
at an air-glass interface, and are working on the smoothly varying refractive-index
case.
alternative_title:
- Optics InfoBase Conference Papers
article_processing_charge: No
author:
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Paul
full_name: Kwiat, Paul
last_name: Kwiat
citation:
ama: 'Hosten O, Kwiat P. Spin hall effect of light via weak measurements: Sharp
and smooth index variations. In: Optica Publishing Group; 2008.'
apa: 'Hosten, O., & Kwiat, P. (2008). Spin hall effect of light via weak measurements:
Sharp and smooth index variations. Presented at the QELS: Quantum Electronics
and Laser Science Conference, San Jose, CA, United States: Optica Publishing Group.'
chicago: 'Hosten, Onur, and Paul Kwiat. “Spin Hall Effect of Light via Weak Measurements:
Sharp and Smooth Index Variations.” Optica Publishing Group, 2008.'
ieee: 'O. Hosten and P. Kwiat, “Spin hall effect of light via weak measurements:
Sharp and smooth index variations,” presented at the QELS: Quantum Electronics
and Laser Science Conference, San Jose, CA, United States, 2008.'
ista: 'Hosten O, Kwiat P. 2008. Spin hall effect of light via weak measurements:
Sharp and smooth index variations. QELS: Quantum Electronics and Laser Science
Conference, Optics InfoBase Conference Papers, .'
mla: 'Hosten, Onur, and Paul Kwiat. Spin Hall Effect of Light via Weak Measurements:
Sharp and Smooth Index Variations. Optica Publishing Group, 2008.'
short: O. Hosten, P. Kwiat, in:, Optica Publishing Group, 2008.
conference:
end_date: 2008-05-09
location: San Jose, CA, United States
name: 'QELS: Quantum Electronics and Laser Science Conference'
start_date: 2008-05-04
date_created: 2018-12-11T11:47:20Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2022-05-24T09:10:41Z
day: '01'
extern: '1'
language:
- iso: eng
main_file_link:
- url: https://opg.optica.org/abstract.cfm?URI=QELS-2008-QFB7
month: '01'
oa_version: None
publication_identifier:
isbn:
- 978-155752859-9
issn:
- '21622701'
publication_status: published
publisher: Optica Publishing Group
publist_id: '7227'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Spin hall effect of light via weak measurements: Sharp and smooth index variations'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2008'
...
---
_id: '6146'
abstract:
- lang: eng
text: Homeostasis of internal carbon dioxide (CO2) and oxygen (O2) levels is fundamental
to all animals. Here we examine the CO2 response of the nematode Caenorhabditis
elegans. This species inhabits rotting material, which typically has a broad CO2
concentration range. We show that well fed C. elegans avoid CO2 levels above 0.5%.
Animals can respond to both absolute CO2 concentrations and changes in CO2 levels
within seconds. Responses to CO2 do not reflect avoidance of acid pH but appear
to define a new sensory response. Sensation of CO2 is promoted by the cGMP-gated
ion channel subunits TAX-2 and TAX-4, but other pathways are also important. Robust
CO2 avoidance in well fed animals requires inhibition of the DAF-16 forkhead transcription
factor by the insulin-like receptor DAF-2. Starvation, which activates DAF-16,
strongly suppresses CO2 avoidance. Exposure to hypoxia (<1% O2) also suppresses
CO2 avoidance via activation of the hypoxia-inducible transcription factor HIF-1.
The npr-1 215V allele of the naturally polymorphic neuropeptide receptor npr-1,
besides inhibiting avoidance of high ambient O2 in feeding C. elegans, also promotes
avoidance of high CO2. C. elegans integrates competing O2 and CO2 sensory inputs
so that one response dominates. Food and allelic variation at NPR-1 regulate which
response prevails. Our results suggest that multiple sensory inputs are coordinated
by C. elegans to generate different coherent foraging strategies.
author:
- first_name: A. J.
full_name: Bretscher, A. J.
last_name: Bretscher
- first_name: K. E.
full_name: Busch, K. E.
last_name: Busch
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Bretscher AJ, Busch KE, de Bono M. A carbon dioxide avoidance behavior is integrated
with responses to ambient oxygen and food in Caenorhabditis elegans. Proceedings
of the National Academy of Sciences. 2008;105(23):8044-8049. doi:10.1073/pnas.0707607105
apa: Bretscher, A. J., Busch, K. E., & de Bono, M. (2008). A carbon dioxide
avoidance behavior is integrated with responses to ambient oxygen and food in
Caenorhabditis elegans. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0707607105
chicago: Bretscher, A. J., K. E. Busch, and Mario de Bono. “A Carbon Dioxide Avoidance
Behavior Is Integrated with Responses to Ambient Oxygen and Food in Caenorhabditis
Elegans.” Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences, 2008. https://doi.org/10.1073/pnas.0707607105.
ieee: A. J. Bretscher, K. E. Busch, and M. de Bono, “A carbon dioxide avoidance
behavior is integrated with responses to ambient oxygen and food in Caenorhabditis
elegans,” Proceedings of the National Academy of Sciences, vol. 105, no.
23. Proceedings of the National Academy of Sciences, pp. 8044–8049, 2008.
ista: Bretscher AJ, Busch KE, de Bono M. 2008. A carbon dioxide avoidance behavior
is integrated with responses to ambient oxygen and food in Caenorhabditis elegans.
Proceedings of the National Academy of Sciences. 105(23), 8044–8049.
mla: Bretscher, A. J., et al. “A Carbon Dioxide Avoidance Behavior Is Integrated
with Responses to Ambient Oxygen and Food in Caenorhabditis Elegans.” Proceedings
of the National Academy of Sciences, vol. 105, no. 23, Proceedings of the
National Academy of Sciences, 2008, pp. 8044–49, doi:10.1073/pnas.0707607105.
short: A.J. Bretscher, K.E. Busch, M. de Bono, Proceedings of the National Academy
of Sciences 105 (2008) 8044–8049.
date_created: 2019-03-21T08:10:15Z
date_published: 2008-06-10T00:00:00Z
date_updated: 2021-01-12T08:06:21Z
day: '10'
ddc:
- '570'
doi: 10.1073/pnas.0707607105
extern: '1'
external_id:
pmid:
- '18524954'
file:
- access_level: open_access
checksum: eac0413064b022c1489f7b6719e7228c
content_type: application/pdf
creator: kschuh
date_created: 2019-03-21T08:14:54Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6147'
file_name: 2008_PNAS_Bretscher.pdf
file_size: 501506
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 105'
issue: '23'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 8044-8049
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: A carbon dioxide avoidance behavior is integrated with responses to ambient
oxygen and food in Caenorhabditis elegans
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 105
year: '2008'
...
---
_id: '6148'
author:
- first_name: Jan E.
full_name: Kammenga, Jan E.
last_name: Kammenga
- first_name: Patrick C.
full_name: Phillips, Patrick C.
last_name: Phillips
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: Agnieszka
full_name: Doroszuk, Agnieszka
last_name: Doroszuk
citation:
ama: 'Kammenga JE, Phillips PC, de Bono M, Doroszuk A. Beyond induced mutants: using
worms to study natural variation in genetic pathways. Trends in Genetics.
2008;24(4):178-185. doi:10.1016/j.tig.2008.01.001'
apa: 'Kammenga, J. E., Phillips, P. C., de Bono, M., & Doroszuk, A. (2008).
Beyond induced mutants: using worms to study natural variation in genetic pathways.
Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2008.01.001'
chicago: 'Kammenga, Jan E., Patrick C. Phillips, Mario de Bono, and Agnieszka Doroszuk.
“Beyond Induced Mutants: Using Worms to Study Natural Variation in Genetic Pathways.”
Trends in Genetics. Elsevier, 2008. https://doi.org/10.1016/j.tig.2008.01.001.'
ieee: 'J. E. Kammenga, P. C. Phillips, M. de Bono, and A. Doroszuk, “Beyond induced
mutants: using worms to study natural variation in genetic pathways,” Trends
in Genetics, vol. 24, no. 4. Elsevier, pp. 178–185, 2008.'
ista: 'Kammenga JE, Phillips PC, de Bono M, Doroszuk A. 2008. Beyond induced mutants:
using worms to study natural variation in genetic pathways. Trends in Genetics.
24(4), 178–185.'
mla: 'Kammenga, Jan E., et al. “Beyond Induced Mutants: Using Worms to Study Natural
Variation in Genetic Pathways.” Trends in Genetics, vol. 24, no. 4, Elsevier,
2008, pp. 178–85, doi:10.1016/j.tig.2008.01.001.'
short: J.E. Kammenga, P.C. Phillips, M. de Bono, A. Doroszuk, Trends in Genetics
24 (2008) 178–185.
date_created: 2019-03-21T08:19:45Z
date_published: 2008-04-01T00:00:00Z
date_updated: 2021-01-12T08:06:21Z
day: '01'
doi: 10.1016/j.tig.2008.01.001
extern: '1'
external_id:
pmid:
- '18325626'
intvolume: ' 24'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 178-185
pmid: 1
publication: Trends in Genetics
publication_identifier:
issn:
- 0168-9525
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Beyond induced mutants: using worms to study natural variation in genetic
pathways'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2008'
...
---
_id: '6149'
article_processing_charge: No
author:
- first_name: Birgitta
full_name: Olofsson, Birgitta
last_name: Olofsson
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: 'Olofsson B, de Bono M. Sleep: dozy worms and sleepy flies. Current Biology.
2008;18(5):R204-R206. doi:10.1016/j.cub.2008.01.002'
apa: 'Olofsson, B., & de Bono, M. (2008). Sleep: dozy worms and sleepy flies.
Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2008.01.002'
chicago: 'Olofsson, Birgitta, and Mario de Bono. “Sleep: Dozy Worms and Sleepy Flies.”
Current Biology. Elsevier, 2008. https://doi.org/10.1016/j.cub.2008.01.002.'
ieee: 'B. Olofsson and M. de Bono, “Sleep: dozy worms and sleepy flies,” Current
Biology, vol. 18, no. 5. Elsevier, pp. R204–R206, 2008.'
ista: 'Olofsson B, de Bono M. 2008. Sleep: dozy worms and sleepy flies. Current
Biology. 18(5), R204–R206.'
mla: 'Olofsson, Birgitta, and Mario de Bono. “Sleep: Dozy Worms and Sleepy Flies.”
Current Biology, vol. 18, no. 5, Elsevier, 2008, pp. R204–06, doi:10.1016/j.cub.2008.01.002.'
short: B. Olofsson, M. de Bono, Current Biology 18 (2008) R204–R206.
date_created: 2019-03-21T08:23:24Z
date_published: 2008-03-11T00:00:00Z
date_updated: 2022-08-25T15:03:41Z
day: '11'
doi: 10.1016/j.cub.2008.01.002
extern: '1'
external_id:
pmid:
- '18334193'
intvolume: ' 18'
issue: '5'
language:
- iso: eng
month: '03'
oa_version: None
page: R204-R206
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Sleep: dozy worms and sleepy flies'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2008'
...
---
_id: '7321'
abstract:
- lang: eng
text: Cell interaction phenomena in polymer electrolyte fuel cell stacks that arise
from imbalance between adjacent cells are investigated in detail experimentally
and theoretically. A specialized two-cell stack with advanced localized diagnostics
was developed and used to analyze the mechanism and effect of cell-to-cell coupling
as a result of operationally relevant variations in reactant feed flow. Contributions
to overall and local voltage changes with respect to uniformly operated cells
are scrutinized. Unequal operation of the cells causes in-plane current in the
bipolar plate to redistribute current and result in inhomogeneous polarization.
Both increasing and decreasing polarization along the air-flow path reduces cell
power as compared to isopotential operation. A two-dimensional model based on
a commercial computational fluid dynamics code is used to back and extend the
experimental results to more general cases. Furthermore, the experimental setup
presented allowed for the first time to perform simultaneous localized electrochemical
impedance spectroscopy beyond the single-cell level. The mechanism of mutual cell
interaction on local and integral spectra is revealed. Results show that virtually
identical operation of the cells is essential to obtain meaningful integral spectra.
article_number: B704
article_processing_charge: No
article_type: original
author:
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Ingo A.
full_name: Schneider, Ingo A.
last_name: Schneider
- first_name: Pang-Chieh
full_name: Sui, Pang-Chieh
last_name: Sui
- first_name: Alexander
full_name: Wokaun, Alexander
last_name: Wokaun
- first_name: Nedjib
full_name: Djilali, Nedjib
last_name: Djilali
- first_name: Felix N.
full_name: Büchi, Felix N.
last_name: Büchi
citation:
ama: Freunberger SA, Schneider IA, Sui P-C, Wokaun A, Djilali N, Büchi FN. Cell
interaction phenomena in polymer electrolyte fuel cell stacks. Journal of The
Electrochemical Society. 2008;155(7). doi:10.1149/1.2913095
apa: Freunberger, S. A., Schneider, I. A., Sui, P.-C., Wokaun, A., Djilali, N.,
& Büchi, F. N. (2008). Cell interaction phenomena in polymer electrolyte
fuel cell stacks. Journal of The Electrochemical Society. The Electrochemical
Society. https://doi.org/10.1149/1.2913095
chicago: Freunberger, Stefan Alexander, Ingo A. Schneider, Pang-Chieh Sui, Alexander
Wokaun, Nedjib Djilali, and Felix N. Büchi. “Cell Interaction Phenomena in Polymer
Electrolyte Fuel Cell Stacks.” Journal of The Electrochemical Society.
The Electrochemical Society, 2008. https://doi.org/10.1149/1.2913095.
ieee: S. A. Freunberger, I. A. Schneider, P.-C. Sui, A. Wokaun, N. Djilali, and
F. N. Büchi, “Cell interaction phenomena in polymer electrolyte fuel cell stacks,”
Journal of The Electrochemical Society, vol. 155, no. 7. The Electrochemical
Society, 2008.
ista: Freunberger SA, Schneider IA, Sui P-C, Wokaun A, Djilali N, Büchi FN. 2008.
Cell interaction phenomena in polymer electrolyte fuel cell stacks. Journal of
The Electrochemical Society. 155(7), B704.
mla: Freunberger, Stefan Alexander, et al. “Cell Interaction Phenomena in Polymer
Electrolyte Fuel Cell Stacks.” Journal of The Electrochemical Society,
vol. 155, no. 7, B704, The Electrochemical Society, 2008, doi:10.1149/1.2913095.
short: S.A. Freunberger, I.A. Schneider, P.-C. Sui, A. Wokaun, N. Djilali, F.N.
Büchi, Journal of The Electrochemical Society 155 (2008).
date_created: 2020-01-15T12:21:47Z
date_published: 2008-05-08T00:00:00Z
date_updated: 2021-01-12T08:13:03Z
day: '08'
doi: 10.1149/1.2913095
extern: '1'
intvolume: ' 155'
issue: '7'
language:
- iso: eng
month: '05'
oa_version: None
publication: Journal of The Electrochemical Society
publication_identifier:
issn:
- 0013-4651
publication_status: published
publisher: The Electrochemical Society
quality_controlled: '1'
status: public
title: Cell interaction phenomena in polymer electrolyte fuel cell stacks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 155
year: '2008'
...
---
_id: '7320'
abstract:
- lang: eng
text: A comparative, experimental diffusivity study of gas diffusion layer (GDL)
materials for polymer electrolyte fuel cells (PEFC) is presented for the first
time. The GDL plays an important role for electrochemical losses due to gas transport
limitations at high current densities. Characterization and optimization of these
layers is therefore essential to improve power density. A recently developed method
which allows for fast diffusimetry is applied and data compared to the literature
values. Measurements are made as a function of direction and compression and the
effect of different binder structures and hydrophobic treatments on effective
diffusivities are discussed. A better understanding of the results is gained by
including novel GDL cross-section images and a meaningful unit cell model for
the interpretation of the data. The diffusivity data is valuable for GDL manufacturers
and future PEFC models. The study reveals that a binder–fiber ratio larger than
50% has a negative impact on the effective diffusion properties. The hydrophobic
treatment which is necessary to improve the water management can impede diffusion
and thus reduce the power density. Furthermore binder has an isotropic effect
while compression pronounces the in-plane orientation of the fibers.
article_processing_charge: No
article_type: original
author:
- first_name: Reto
full_name: Flückiger, Reto
last_name: Flückiger
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Denis
full_name: Kramer, Denis
last_name: Kramer
- first_name: Alexander
full_name: Wokaun, Alexander
last_name: Wokaun
- first_name: Günther G.
full_name: Scherer, Günther G.
last_name: Scherer
- first_name: Felix N.
full_name: Büchi, Felix N.
last_name: Büchi
citation:
ama: Flückiger R, Freunberger SA, Kramer D, Wokaun A, Scherer GG, Büchi FN. Anisotropic,
effective diffusivity of porous gas diffusion layer materials for PEFC. Electrochimica
Acta. 2008;54(2):551-559. doi:10.1016/j.electacta.2008.07.034
apa: Flückiger, R., Freunberger, S. A., Kramer, D., Wokaun, A., Scherer, G. G.,
& Büchi, F. N. (2008). Anisotropic, effective diffusivity of porous gas diffusion
layer materials for PEFC. Electrochimica Acta. Elsevier. https://doi.org/10.1016/j.electacta.2008.07.034
chicago: Flückiger, Reto, Stefan Alexander Freunberger, Denis Kramer, Alexander
Wokaun, Günther G. Scherer, and Felix N. Büchi. “Anisotropic, Effective Diffusivity
of Porous Gas Diffusion Layer Materials for PEFC.” Electrochimica Acta.
Elsevier, 2008. https://doi.org/10.1016/j.electacta.2008.07.034.
ieee: R. Flückiger, S. A. Freunberger, D. Kramer, A. Wokaun, G. G. Scherer, and
F. N. Büchi, “Anisotropic, effective diffusivity of porous gas diffusion layer
materials for PEFC,” Electrochimica Acta, vol. 54, no. 2. Elsevier, pp.
551–559, 2008.
ista: Flückiger R, Freunberger SA, Kramer D, Wokaun A, Scherer GG, Büchi FN. 2008.
Anisotropic, effective diffusivity of porous gas diffusion layer materials for
PEFC. Electrochimica Acta. 54(2), 551–559.
mla: Flückiger, Reto, et al. “Anisotropic, Effective Diffusivity of Porous Gas Diffusion
Layer Materials for PEFC.” Electrochimica Acta, vol. 54, no. 2, Elsevier,
2008, pp. 551–59, doi:10.1016/j.electacta.2008.07.034.
short: R. Flückiger, S.A. Freunberger, D. Kramer, A. Wokaun, G.G. Scherer, F.N.
Büchi, Electrochimica Acta 54 (2008) 551–559.
date_created: 2020-01-15T12:21:36Z
date_published: 2008-12-30T00:00:00Z
date_updated: 2021-01-12T08:13:02Z
day: '30'
doi: 10.1016/j.electacta.2008.07.034
extern: '1'
intvolume: ' 54'
issue: '2'
language:
- iso: eng
month: '12'
oa_version: None
page: 551-559
publication: Electrochimica Acta
publication_identifier:
issn:
- 0013-4686
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Anisotropic, effective diffusivity of porous gas diffusion layer materials
for PEFC
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2008'
...
---
_id: '7322'
abstract:
- lang: eng
text: The gas diffusion layers (GDLs) of a membrane electrode assembly (MEA) serve
as link between flow field and porous electrode within a polymer electrolyte fuel
cell. Beside ensuring sufficient electrical and thermal contact between the whole
electrode area and the flow field, these typically 200–400 μm thick porous structures
enable the access of educts to the electrode area which would be occluded by the
flow field lands if the flow field is directly attached to the electrode. Hence,
the characterisation of properties pertaining to mass transport of educts and
products through these structures is indispensable whilst examining the contribution
of the GDLs to the overall electrochemical characteristics of a MEA. A fast and
cost effective method to measure the effective diffusivity of a GDL is presented.
Electrochemical impedance spectroscopy is applied to measure the effective ionic
conductivity of an electrolyte-soaked GDL. Taking advantage of the analogy between
Ficks and Ohms law, this provides a measure for the effective diffusivity. The
method is described in detail, including experimental as well as theoretical aspects,
and selected results, highlighting the anisotropy and dependence on the degree
of compression, are shown. Moreover, a two-dimensional model consisting of regularly
spaced ellipses is developed to represent the porous structure of the GDL, and
by using conformal maps, the agreement between this model and experiment with
respect to the sensitivity of the effective diffusivity towards compression is
shown.
article_processing_charge: No
article_type: original
author:
- first_name: Denis
full_name: Kramer, Denis
last_name: Kramer
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Reto
full_name: Flückiger, Reto
last_name: Flückiger
- first_name: Ingo A.
full_name: Schneider, Ingo A.
last_name: Schneider
- first_name: Alexander
full_name: Wokaun, Alexander
last_name: Wokaun
- first_name: Felix N.
full_name: Büchi, Felix N.
last_name: Büchi
- first_name: Günther G.
full_name: Scherer, Günther G.
last_name: Scherer
citation:
ama: Kramer D, Freunberger SA, Flückiger R, et al. Electrochemical diffusimetry
of fuel cell gas diffusion layers. Journal of Electroanalytical Chemistry.
2008;612(1):63-77. doi:10.1016/j.jelechem.2007.09.014
apa: Kramer, D., Freunberger, S. A., Flückiger, R., Schneider, I. A., Wokaun, A.,
Büchi, F. N., & Scherer, G. G. (2008). Electrochemical diffusimetry of fuel
cell gas diffusion layers. Journal of Electroanalytical Chemistry. Elsevier.
https://doi.org/10.1016/j.jelechem.2007.09.014
chicago: Kramer, Denis, Stefan Alexander Freunberger, Reto Flückiger, Ingo A. Schneider,
Alexander Wokaun, Felix N. Büchi, and Günther G. Scherer. “Electrochemical Diffusimetry
of Fuel Cell Gas Diffusion Layers.” Journal of Electroanalytical Chemistry.
Elsevier, 2008. https://doi.org/10.1016/j.jelechem.2007.09.014.
ieee: D. Kramer et al., “Electrochemical diffusimetry of fuel cell gas diffusion
layers,” Journal of Electroanalytical Chemistry, vol. 612, no. 1. Elsevier,
pp. 63–77, 2008.
ista: Kramer D, Freunberger SA, Flückiger R, Schneider IA, Wokaun A, Büchi FN, Scherer
GG. 2008. Electrochemical diffusimetry of fuel cell gas diffusion layers. Journal
of Electroanalytical Chemistry. 612(1), 63–77.
mla: Kramer, Denis, et al. “Electrochemical Diffusimetry of Fuel Cell Gas Diffusion
Layers.” Journal of Electroanalytical Chemistry, vol. 612, no. 1, Elsevier,
2008, pp. 63–77, doi:10.1016/j.jelechem.2007.09.014.
short: D. Kramer, S.A. Freunberger, R. Flückiger, I.A. Schneider, A. Wokaun, F.N.
Büchi, G.G. Scherer, Journal of Electroanalytical Chemistry 612 (2008) 63–77.
date_created: 2020-01-15T12:21:57Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T08:13:03Z
day: '01'
doi: 10.1016/j.jelechem.2007.09.014
extern: '1'
intvolume: ' 612'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 63-77
publication: Journal of Electroanalytical Chemistry
publication_identifier:
issn:
- 1572-6657
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Electrochemical diffusimetry of fuel cell gas diffusion layers
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 612
year: '2008'
...
---
_id: '7425'
abstract:
- lang: eng
text: The propagation of single cell performance losses to adjacent cells in a polymer
electrolyte fuel cell stack is studied by means of local current density measurements
in a two cell stack. In this stack, the working conditions of adjacent cells can
be controlled independently in order to deliberately change the performance of
one cell (inducing cell) and study the coupling effects to the adjacent cell (response
cell), while keeping the working conditions of the later one unchanged. The experiments
have shown that changes in the current density distribution caused by lowering
of the air stoichiometry in the inducing cell cause changes in the current density
distribution of the response cell in the order of 60% of the change of the inducing
cell, even when the air stoichiometry of the response cell is kept constant. The
losses in cell voltage of the inducing cell cause losses in cell voltage of the
response cell in a magnitude between 30 and 50%.
article_processing_charge: No
author:
- first_name: Marco
full_name: Santis, Marco
last_name: Santis
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Matthias
full_name: Papra, Matthias
last_name: Papra
- first_name: Felix N.
full_name: Büchi, Felix N.
last_name: Büchi
citation:
ama: 'Santis M, Freunberger SA, Papra M, Büchi FN. Experimental investigation of
the propagation of local current density variations to adjacent cells in PEFC
stacks. In: 3rd International Conference on Fuel Cell Science, Engineering
and Technology. ASMEDC; 2008:763-765. doi:10.1115/fuelcell2005-74116'
apa: 'Santis, M., Freunberger, S. A., Papra, M., & Büchi, F. N. (2008). Experimental
investigation of the propagation of local current density variations to adjacent
cells in PEFC stacks. In 3rd International Conference on Fuel Cell Science,
Engineering and Technology (pp. 763–765). Ypsilanti, MI, United States: ASMEDC.
https://doi.org/10.1115/fuelcell2005-74116'
chicago: Santis, Marco, Stefan Alexander Freunberger, Matthias Papra, and Felix
N. Büchi. “Experimental Investigation of the Propagation of Local Current Density
Variations to Adjacent Cells in PEFC Stacks.” In 3rd International Conference
on Fuel Cell Science, Engineering and Technology, 763–65. ASMEDC, 2008. https://doi.org/10.1115/fuelcell2005-74116.
ieee: M. Santis, S. A. Freunberger, M. Papra, and F. N. Büchi, “Experimental investigation
of the propagation of local current density variations to adjacent cells in PEFC
stacks,” in 3rd International Conference on Fuel Cell Science, Engineering
and Technology, Ypsilanti, MI, United States, 2008, pp. 763–765.
ista: Santis M, Freunberger SA, Papra M, Büchi FN. 2008. Experimental investigation
of the propagation of local current density variations to adjacent cells in PEFC
stacks. 3rd International Conference on Fuel Cell Science, Engineering and Technology.
International conference on fuel cell science, engineering and technology, 763–765.
mla: Santis, Marco, et al. “Experimental Investigation of the Propagation of Local
Current Density Variations to Adjacent Cells in PEFC Stacks.” 3rd International
Conference on Fuel Cell Science, Engineering and Technology, ASMEDC, 2008,
pp. 763–65, doi:10.1115/fuelcell2005-74116.
short: M. Santis, S.A. Freunberger, M. Papra, F.N. Büchi, in:, 3rd International
Conference on Fuel Cell Science, Engineering and Technology, ASMEDC, 2008, pp.
763–765.
conference:
end_date: 2005-05-25
location: Ypsilanti, MI, United States
name: International conference on fuel cell science, engineering and technology
start_date: 2005-05-23
date_created: 2020-01-31T10:14:45Z
date_published: 2008-10-13T00:00:00Z
date_updated: 2021-01-12T08:13:33Z
day: '13'
doi: 10.1115/fuelcell2005-74116
extern: '1'
language:
- iso: eng
month: '10'
oa_version: None
page: 763-765
publication: 3rd International Conference on Fuel Cell Science, Engineering and Technology
publication_identifier:
isbn:
- '0791837645'
- '0791837572'
publication_status: published
publisher: ASMEDC
quality_controlled: '1'
status: public
title: Experimental investigation of the propagation of local current density variations
to adjacent cells in PEFC stacks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2008'
...
---
_id: '753'
abstract:
- lang: eng
text: 'This paper addresses the following question: what is the minimum-sized synchronous
window needed to solve consensus in an otherwise asynchronous system? In answer
to this question, we present the first optimally-resilient algorithm ASAP that
solves consensus as soon as possible in an eventually synchronous system, i.e.,
a system that from some time GST onwards, delivers messages in a timely fashion.
ASAP guarantees that, in an execution with at most f failures, every process decides
no later than round GST + f + 2, which is optimal.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Seth
full_name: Gilbert, Seth
last_name: Gilbert
- first_name: Rachid
full_name: Guerraoui, Rachid
last_name: Guerraoui
- first_name: Corentin
full_name: Travers, Corentin
last_name: Travers
citation:
ama: 'Alistarh D-A, Gilbert S, Guerraoui R, Travers C. How to solve consensus in
the smallest window of synchrony. In: Vol 5218 LNCS. Springer; 2008:32-46. doi:10.1007/978-3-540-87779-0_3'
apa: 'Alistarh, D.-A., Gilbert, S., Guerraoui, R., & Travers, C. (2008). How
to solve consensus in the smallest window of synchrony (Vol. 5218 LNCS, pp. 32–46).
Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-540-87779-0_3'
chicago: Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers.
“How to Solve Consensus in the Smallest Window of Synchrony,” 5218 LNCS:32–46.
Springer, 2008. https://doi.org/10.1007/978-3-540-87779-0_3.
ieee: 'D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “How to solve consensus
in the smallest window of synchrony,” presented at the DISC: Distributed Computing,
2008, vol. 5218 LNCS, pp. 32–46.'
ista: 'Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2008. How to solve consensus
in the smallest window of synchrony. DISC: Distributed Computing, LNCS, vol. 5218
LNCS, 32–46.'
mla: Alistarh, Dan-Adrian, et al. How to Solve Consensus in the Smallest Window
of Synchrony. Vol. 5218 LNCS, Springer, 2008, pp. 32–46, doi:10.1007/978-3-540-87779-0_3.
short: D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, in:, Springer, 2008,
pp. 32–46.
conference:
name: 'DISC: Distributed Computing'
date_created: 2018-12-11T11:48:19Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2023-02-23T13:10:13Z
day: '01'
doi: 10.1007/978-3-540-87779-0_3
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 32 - 46
publication_status: published
publisher: Springer
publist_id: '6904'
status: public
title: How to solve consensus in the smallest window of synchrony
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5218 LNCS
year: '2008'
...
---
_id: '7752'
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Jill G.
full_name: Pilkington, Jill G.
last_name: Pilkington
- first_name: Tim H.
full_name: Clutton-Brock, Tim H.
last_name: Clutton-Brock
- first_name: Josephine M.
full_name: Pemberton, Josephine M.
last_name: Pemberton
- first_name: Loeske. E.B.
full_name: Kruuk, Loeske. E.B.
last_name: Kruuk
citation:
ama: Robinson MR, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. Environmental
heterogeneity generates fluctuating selection on a secondary sexual trait. Current
Biology. 2008;18(10):751-757. doi:10.1016/j.cub.2008.04.059
apa: Robinson, M. R., Pilkington, J. G., Clutton-Brock, T. H., Pemberton, J. M.,
& Kruuk, L. E. B. (2008). Environmental heterogeneity generates fluctuating
selection on a secondary sexual trait. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2008.04.059
chicago: Robinson, Matthew Richard, Jill G. Pilkington, Tim H. Clutton-Brock, Josephine
M. Pemberton, and Loeske. E.B. Kruuk. “Environmental Heterogeneity Generates Fluctuating
Selection on a Secondary Sexual Trait.” Current Biology. Elsevier, 2008.
https://doi.org/10.1016/j.cub.2008.04.059.
ieee: M. R. Robinson, J. G. Pilkington, T. H. Clutton-Brock, J. M. Pemberton, and
L. E. B. Kruuk, “Environmental heterogeneity generates fluctuating selection on
a secondary sexual trait,” Current Biology, vol. 18, no. 10. Elsevier,
pp. 751–757, 2008.
ista: Robinson MR, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. 2008.
Environmental heterogeneity generates fluctuating selection on a secondary sexual
trait. Current Biology. 18(10), 751–757.
mla: Robinson, Matthew Richard, et al. “Environmental Heterogeneity Generates Fluctuating
Selection on a Secondary Sexual Trait.” Current Biology, vol. 18, no. 10,
Elsevier, 2008, pp. 751–57, doi:10.1016/j.cub.2008.04.059.
short: M.R. Robinson, J.G. Pilkington, T.H. Clutton-Brock, J.M. Pemberton, L.E.B.
Kruuk, Current Biology 18 (2008) 751–757.
date_created: 2020-04-30T11:02:13Z
date_published: 2008-05-20T00:00:00Z
date_updated: 2021-01-12T08:15:17Z
day: '20'
doi: 10.1016/j.cub.2008.04.059
extern: '1'
intvolume: ' 18'
issue: '10'
language:
- iso: eng
month: '05'
oa_version: None
page: 751-757
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Environmental heterogeneity generates fluctuating selection on a secondary
sexual trait
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2008'
...
---
_id: '844'
abstract:
- lang: eng
text: Mutation rate varies greatly between nucleotide sites of the human genome
and depends both on the global genomic location and the local sequence context
of a site. In particular, CpG context elevates the mutation rate by an order of
magnitude. Mutations also vary widely in their effect on the molecular function,
phenotype, and fitness. Independence of the probability of occurrence of a new
mutation's effect has been a fundamental premise in genetics. However, highly
mutable contexts may be preserved by negative selection at important sites but
destroyed by mutation at sites under no selection. Thus, there may be a positive
correlation between the rate of mutations at a nucleotide site and the magnitude
of their effect on fitness. We studied the impact of CpG context on the rate of
human-chimpanzee divergence and on intrahuman nucleotide diversity at non-synonymous
coding sites. We compared nucleotides that occupy identical positions within codons
of identical amino acids and only differ by being within versus outside CpG context.
Nucleotides within CpG context are under a stronger negative selection, as revealed
by their lower, proportionally to the mutation rate, rate of evolution and nucleotide
diversity. In particular, the probability of fixation of a non-synonymous transition
at a CpG site is two times lower than at a CpG site. Thus, sites with different
mutation rates are not necessarily selectively equivalent. This suggests that
the mutation rate may complement sequence conservation as a characteristic predictive
of functional importance of nucleotide sites.
acknowledgement: This work was supported in part by NIH grants R01 GM078598 and U54
LM008748.
author:
- first_name: Steffen
full_name: Schmidt, Steffen
last_name: Schmidt
- first_name: Anna
full_name: Gerasimova, Anna
last_name: Gerasimova
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Ivan
full_name: Adzuhbei, Ivan A
last_name: Adzuhbei
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Shamil
full_name: Sunyaev, Shamil R
last_name: Sunyaev
citation:
ama: Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S.
Hypermutable non-synonymous sites are under stronger negative selection. PLoS
Genetics. 2008;4(11). doi:10.1371/journal.pgen.1000281
apa: Schmidt, S., Gerasimova, A., Kondrashov, F., Adzuhbei, I., Kondrashov, A.,
& Sunyaev, S. (2008). Hypermutable non-synonymous sites are under stronger
negative selection. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000281
chicago: Schmidt, Steffen, Anna Gerasimova, Fyodor Kondrashov, Ivan Adzuhbei, Alexey
Kondrashov, and Shamil Sunyaev. “Hypermutable Non-Synonymous Sites Are under Stronger
Negative Selection.” PLoS Genetics. Public Library of Science, 2008. https://doi.org/10.1371/journal.pgen.1000281.
ieee: S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, and
S. Sunyaev, “Hypermutable non-synonymous sites are under stronger negative selection,”
PLoS Genetics, vol. 4, no. 11. Public Library of Science, 2008.
ista: Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S.
2008. Hypermutable non-synonymous sites are under stronger negative selection.
PLoS Genetics. 4(11).
mla: Schmidt, Steffen, et al. “Hypermutable Non-Synonymous Sites Are under Stronger
Negative Selection.” PLoS Genetics, vol. 4, no. 11, Public Library of Science,
2008, doi:10.1371/journal.pgen.1000281.
short: S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, S.
Sunyaev, PLoS Genetics 4 (2008).
date_created: 2018-12-11T11:48:48Z
date_published: 2008-11-01T00:00:00Z
date_updated: 2021-01-12T08:19:16Z
day: '01'
doi: 10.1371/journal.pgen.1000281
extern: 1
intvolume: ' 4'
issue: '11'
month: '11'
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '6800'
quality_controlled: 0
status: public
title: Hypermutable non-synonymous sites are under stronger negative selection
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: 4
year: '2008'
...
---
_id: '8481'
abstract:
- lang: eng
text: 'The copK gene is localized on the pMOL30 plasmid of Cupriavidus metallidurans
CH34 within the complex cop cluster of genes, for which 21 genes have been identified.
The expression of the corresponding periplasmic CopK protein is strongly upregulated
in the presence of copper, leading to a high periplasmic accumulation. The structure
and metal-binding properties of CopK were investigated by NMR and mass spectrometry.
The protein is dimeric in the apo state with a dissociation constant in the range
of 10- 5 M estimated from analytical ultracentrifugation. Mass spectrometry revealed
that CopK has two high-affinity Cu(I)-binding sites per monomer with different
Cu(I) affinities. Binding of Cu(II) was observed but appeared to be non-specific.
The solution structure of apo-CopK revealed an all-β fold formed of two β-sheets
in perpendicular orientation with an unstructured C-terminal tail. The dimer interface
is formed by the surface of the C-terminal β-sheet. Binding of the first Cu(I)-ion
induces a major structural modification involving dissociation of the dimeric
apo-protein. Backbone chemical shifts determined for the 1Cu(I)-bound form confirm
the conservation of the N-terminal β-sheet, while the last strand of the C-terminal
sheet appears in slow conformational exchange. We hypothesize that the partial
disruption of the C-terminal β-sheet is related to dimer dissociation. NH-exchange
data acquired on the apo-protein are consistent with a lower thermodynamic stability
of the C-terminal sheet. CopK contains seven methionine residues, five of which
appear highly conserved. Chemical shift data suggest implication of two or three
methionines (Met54, Met38, Met28) in the first Cu(I) site. Addition of a second
Cu(I) ion further increases protein plasticity. Comparison of the structural and
metal-binding properties of CopK with other periplasmic copper-binding proteins
reveals two conserved features within these functionally related proteins: the
all-β fold and the methionine-rich Cu(I)-binding site.'
article_processing_charge: No
article_type: original
author:
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- first_name: Adrien
full_name: Favier, Adrien
last_name: Favier
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Sébastien
full_name: van Aelst, Sébastien
last_name: van Aelst
- first_name: Tatiana
full_name: Vallaeys, Tatiana
last_name: Vallaeys
- first_name: Jacques
full_name: Covès, Jacques
last_name: Covès
- first_name: Max
full_name: Mergeay, Max
last_name: Mergeay
- first_name: Ruddy
full_name: Wattiez, Ruddy
last_name: Wattiez
citation:
ama: Bersch B, Favier A, Schanda P, et al. Molecular structure and metal-binding
properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans
CH34 during copper challenge. Journal of Molecular Biology. 2008;380(2):386-403.
doi:10.1016/j.jmb.2008.05.017
apa: Bersch, B., Favier, A., Schanda, P., van Aelst, S., Vallaeys, T., Covès, J.,
… Wattiez, R. (2008). Molecular structure and metal-binding properties of the
periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper
challenge. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2008.05.017
chicago: Bersch, Beate, Adrien Favier, Paul Schanda, Sébastien van Aelst, Tatiana
Vallaeys, Jacques Covès, Max Mergeay, and Ruddy Wattiez. “Molecular Structure
and Metal-Binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus
Metallidurans CH34 during Copper Challenge.” Journal of Molecular Biology.
Elsevier, 2008. https://doi.org/10.1016/j.jmb.2008.05.017.
ieee: B. Bersch et al., “Molecular structure and metal-binding properties
of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during
copper challenge,” Journal of Molecular Biology, vol. 380, no. 2. Elsevier,
pp. 386–403, 2008.
ista: Bersch B, Favier A, Schanda P, van Aelst S, Vallaeys T, Covès J, Mergeay M,
Wattiez R. 2008. Molecular structure and metal-binding properties of the periplasmic
CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge.
Journal of Molecular Biology. 380(2), 386–403.
mla: Bersch, Beate, et al. “Molecular Structure and Metal-Binding Properties of
the Periplasmic CopK Protein Expressed in Cupriavidus Metallidurans CH34 during
Copper Challenge.” Journal of Molecular Biology, vol. 380, no. 2, Elsevier,
2008, pp. 386–403, doi:10.1016/j.jmb.2008.05.017.
short: B. Bersch, A. Favier, P. Schanda, S. van Aelst, T. Vallaeys, J. Covès, M.
Mergeay, R. Wattiez, Journal of Molecular Biology 380 (2008) 386–403.
date_created: 2020-09-18T10:12:37Z
date_published: 2008-07-04T00:00:00Z
date_updated: 2021-01-12T08:19:34Z
day: '04'
doi: 10.1016/j.jmb.2008.05.017
extern: '1'
intvolume: ' 380'
issue: '2'
keyword:
- Molecular Biology
language:
- iso: eng
month: '07'
oa_version: None
page: 386-403
publication: Journal of Molecular Biology
publication_identifier:
issn:
- 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Molecular structure and metal-binding properties of the periplasmic CopK protein
expressed in Cupriavidus metallidurans CH34 during copper challenge
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 380
year: '2008'
...
---
_id: '8480'
abstract:
- lang: eng
text: The KIX domain of the transcription co-activator CBP is a three-helix bundle
protein that folds via rapid accumulation of an intermediate state, followed by
a slower folding phase. Recent NMR relaxation dispersion studies revealed the
presence of a low-populated (excited) state of KIX that exists in equilibrium
with the natively folded form under non-denaturing conditions, and likely represents
the equilibrium analog of the folding intermediate. Here, we combine amide hydrogen/deuterium
exchange measurements using rapid NMR data acquisition techniques with backbone
15N and 13C relaxation dispersion experiments to further investigate the equilibrium
folding of the KIX domain. Residual structure within the folding intermediate
is detected by both methods, and their combination enables reliable quantification
of the amount of persistent residual structure. Three well-defined folding subunits
are found, which display variable stability and correspond closely to the individual
helices in the native state. While two of the three helices (α2 and α3) are partially
formed in the folding intermediate (to ∼ 50% and ∼ 80%, respectively, at 20 °C),
the third helix is disordered. The observed helical content within the excited
state exceeds the helical propensities predicted for the corresponding peptide
regions, suggesting that the two helices are weakly mutually stabilized, while
methyl 13C relaxation dispersion data indicate that a defined packing arrangement
is unlikely. Temperature-dependent experiments reveal that the largest enthalpy
and entropy changes along the folding reaction occur during the final transition
from the intermediate to the native state. Our experimental data are consistent
with a folding mechanism where helices α2 and α3 form rapidly, although to different
extents, while helix α1 consolidates only as folding proceeds to complete the
native state-structure.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
- first_name: Robert
full_name: Konrat, Robert
last_name: Konrat
- first_name: Martin
full_name: Tollinger, Martin
last_name: Tollinger
citation:
ama: 'Schanda P, Brutscher B, Konrat R, Tollinger M. Folding of the KIX domain:
Characterization of the equilibrium analog of a folding intermediate using 15N/13C
relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal
of Molecular Biology. 2008;380(4):726-741. doi:10.1016/j.jmb.2008.05.040'
apa: 'Schanda, P., Brutscher, B., Konrat, R., & Tollinger, M. (2008). Folding
of the KIX domain: Characterization of the equilibrium analog of a folding intermediate
using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy.
Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2008.05.040'
chicago: 'Schanda, Paul, Bernhard Brutscher, Robert Konrat, and Martin Tollinger.
“Folding of the KIX Domain: Characterization of the Equilibrium Analog of a Folding
Intermediate Using 15N/13C Relaxation Dispersion and Fast 1H/2H Amide Exchange
NMR Spectroscopy.” Journal of Molecular Biology. Elsevier, 2008. https://doi.org/10.1016/j.jmb.2008.05.040.'
ieee: 'P. Schanda, B. Brutscher, R. Konrat, and M. Tollinger, “Folding of the KIX
domain: Characterization of the equilibrium analog of a folding intermediate using
15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy,”
Journal of Molecular Biology, vol. 380, no. 4. Elsevier, pp. 726–741, 2008.'
ista: 'Schanda P, Brutscher B, Konrat R, Tollinger M. 2008. Folding of the KIX domain:
Characterization of the equilibrium analog of a folding intermediate using 15N/13C
relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal
of Molecular Biology. 380(4), 726–741.'
mla: 'Schanda, Paul, et al. “Folding of the KIX Domain: Characterization of the
Equilibrium Analog of a Folding Intermediate Using 15N/13C Relaxation Dispersion
and Fast 1H/2H Amide Exchange NMR Spectroscopy.” Journal of Molecular Biology,
vol. 380, no. 4, Elsevier, 2008, pp. 726–41, doi:10.1016/j.jmb.2008.05.040.'
short: P. Schanda, B. Brutscher, R. Konrat, M. Tollinger, Journal of Molecular Biology
380 (2008) 726–741.
date_created: 2020-09-18T10:12:29Z
date_published: 2008-07-18T00:00:00Z
date_updated: 2021-01-12T08:19:34Z
day: '18'
doi: 10.1016/j.jmb.2008.05.040
extern: '1'
intvolume: ' 380'
issue: '4'
keyword:
- Molecular Biology
language:
- iso: eng
month: '07'
oa_version: None
page: 726-741
publication: Journal of Molecular Biology
publication_identifier:
issn:
- 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Folding of the KIX domain: Characterization of the equilibrium analog of a
folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange
NMR spectroscopy'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 380
year: '2008'
...
---
_id: '8482'
abstract:
- lang: eng
text: The SOFAST-HMQC experiment [P. Schanda, B. Brutscher, Very fast two-dimensional
NMR spectroscopy for real-time investigation of dynamic events in proteins on
the time scale of seconds, J. Am. Chem. Soc. 127 (2005) 8014–8015] allows recording
two-dimensional correlation spectra of macromolecules such as proteins in only
a few seconds acquisition time. To achieve the highest possible sensitivity, SOFAST-HMQC
experiments are preferably performed on high-field NMR spectrometers equipped
with cryogenically cooled probes. The duty cycle of over 80% in fast-pulsing SOFAST-HMQC
experiments, however, may cause problems when using a cryogenic probe. Here we
introduce SE-IPAP-SOFAST-HMQC, a new pulse sequence that provides comparable sensitivity
to standard SOFAST-HMQC, while avoiding heteronuclear decoupling during 1H detection,
and thus significantly reducing the radiofrequency load of the probe during the
experiment. The experiment is also attractive for fast and sensitive measurement
of heteronuclear one-bond spin coupling constants.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Thomas
full_name: Kern, Thomas
last_name: Kern
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Kern T, Schanda P, Brutscher B. Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing
2D NMR with reduced radiofrequency load. Journal of Magnetic Resonance.
2008;190(2):333-338. doi:10.1016/j.jmr.2007.11.015
apa: Kern, T., Schanda, P., & Brutscher, B. (2008). Sensitivity-enhanced IPAP-SOFAST-HMQC
for fast-pulsing 2D NMR with reduced radiofrequency load. Journal of Magnetic
Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2007.11.015
chicago: Kern, Thomas, Paul Schanda, and Bernhard Brutscher. “Sensitivity-Enhanced
IPAP-SOFAST-HMQC for Fast-Pulsing 2D NMR with Reduced Radiofrequency Load.” Journal
of Magnetic Resonance. Elsevier, 2008. https://doi.org/10.1016/j.jmr.2007.11.015.
ieee: T. Kern, P. Schanda, and B. Brutscher, “Sensitivity-enhanced IPAP-SOFAST-HMQC
for fast-pulsing 2D NMR with reduced radiofrequency load,” Journal of Magnetic
Resonance, vol. 190, no. 2. Elsevier, pp. 333–338, 2008.
ista: Kern T, Schanda P, Brutscher B. 2008. Sensitivity-enhanced IPAP-SOFAST-HMQC
for fast-pulsing 2D NMR with reduced radiofrequency load. Journal of Magnetic
Resonance. 190(2), 333–338.
mla: Kern, Thomas, et al. “Sensitivity-Enhanced IPAP-SOFAST-HMQC for Fast-Pulsing
2D NMR with Reduced Radiofrequency Load.” Journal of Magnetic Resonance,
vol. 190, no. 2, Elsevier, 2008, pp. 333–38, doi:10.1016/j.jmr.2007.11.015.
short: T. Kern, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 190 (2008)
333–338.
date_created: 2020-09-18T10:12:46Z
date_published: 2008-02-01T00:00:00Z
date_updated: 2021-01-12T08:19:35Z
day: '01'
doi: 10.1016/j.jmr.2007.11.015
extern: '1'
intvolume: ' 190'
issue: '2'
keyword:
- Nuclear and High Energy Physics
- Biophysics
- Biochemistry
- Condensed Matter Physics
language:
- iso: eng
month: '02'
oa_version: None
page: 333-338
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced
radiofrequency load
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 190
year: '2008'
...
---
_id: '9537'
abstract:
- lang: eng
text: DNA methylation is an ancient process found in all domains of life. Although
the enzymes that mediate methylation have remained highly conserved, DNA methylation
has been adapted for a variety of uses throughout evolution, including defense
against transposable elements and control of gene expression. Defects in DNA methylation
are linked to human diseases, including cancer. Methylation has been lost several
times in the course of animal and fungal evolution, thus limiting the opportunity
for study in common model organisms. In the past decade, plants have emerged as
a premier model system for genetic dissection of DNA methylation. A recent combination
of plant genetics with powerful genomic approaches has led to a number of exciting
discoveries and promises many more.
article_processing_charge: No
article_type: review
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zilberman D. The evolving functions of DNA methylation. Current Opinion
in Plant Biology. 2008;11(5):554-559. doi:10.1016/j.pbi.2008.07.004
apa: Zilberman, D. (2008). The evolving functions of DNA methylation. Current
Opinion in Plant Biology. Elsevier . https://doi.org/10.1016/j.pbi.2008.07.004
chicago: Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” Current
Opinion in Plant Biology. Elsevier , 2008. https://doi.org/10.1016/j.pbi.2008.07.004.
ieee: D. Zilberman, “The evolving functions of DNA methylation,” Current Opinion
in Plant Biology, vol. 11, no. 5. Elsevier , pp. 554–559, 2008.
ista: Zilberman D. 2008. The evolving functions of DNA methylation. Current Opinion
in Plant Biology. 11(5), 554–559.
mla: Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” Current
Opinion in Plant Biology, vol. 11, no. 5, Elsevier , 2008, pp. 554–59, doi:10.1016/j.pbi.2008.07.004.
short: D. Zilberman, Current Opinion in Plant Biology 11 (2008) 554–559.
date_created: 2021-06-08T13:13:37Z
date_published: 2008-10-01T00:00:00Z
date_updated: 2021-12-14T08:54:07Z
department:
- _id: DaZi
doi: 10.1016/j.pbi.2008.07.004
extern: '1'
external_id:
pmid:
- '18774331'
intvolume: ' 11'
issue: '5'
language:
- iso: eng
month: '10'
oa_version: None
page: 554-559
pmid: 1
publication: Current Opinion in Plant Biology
publication_identifier:
issn:
- 1369-5266
publication_status: published
publisher: 'Elsevier '
quality_controlled: '1'
scopus_import: '1'
status: public
title: The evolving functions of DNA methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 11
year: '2008'
...
---
_id: '965'
abstract:
- lang: eng
text: We give many examples of applying Bogoliubov's forest formula to iterative
solutions of various nonlinear equations. The same formula describes an extremely
wide class of objects, from an ordinary quadratic equation to renormalization
in quantum field theory.
acknowledgement: |-
This work is supported in part by the Dynasty Foundation (M. N. S.), the
Russian Foundation for Basic Research (Grant No
s. 07-02-00878 and 07-02-00645), a joint grant (Grant
No. 06-01-92059-CE), the NWO (Project No. 047.011.2004.026), INTAS (Grant No. 05-1000008-7865), the
Program for Supporting Leading Scientific School
s (Grant No. NSh-8004.2006.2), and also by a project
(Project No. ANR-05-BLAN-0029-01, A. Yu. M.).
author:
- first_name: Alexei
full_name: Morozov, Alexei Y
last_name: Morozov
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Morozov A, Serbyn M. Nonlinear algebra and Bogoliubov’s recursion. Theoretical
and Mathematical Physics. 2008;154(2):270-293. doi:10.1007/s11232-008-0026-7
apa: Morozov, A., & Serbyn, M. (2008). Nonlinear algebra and Bogoliubov’s recursion.
Theoretical and Mathematical Physics. Elsevier. https://doi.org/10.1007/s11232-008-0026-7
chicago: Morozov, Alexei, and Maksym Serbyn. “Nonlinear Algebra and Bogoliubov’s
Recursion.” Theoretical and Mathematical Physics. Elsevier, 2008. https://doi.org/10.1007/s11232-008-0026-7.
ieee: A. Morozov and M. Serbyn, “Nonlinear algebra and Bogoliubov’s recursion,”
Theoretical and Mathematical Physics, vol. 154, no. 2. Elsevier, pp. 270–293,
2008.
ista: Morozov A, Serbyn M. 2008. Nonlinear algebra and Bogoliubov’s recursion. Theoretical
and Mathematical Physics. 154(2), 270–293.
mla: Morozov, Alexei, and Maksym Serbyn. “Nonlinear Algebra and Bogoliubov’s Recursion.”
Theoretical and Mathematical Physics, vol. 154, no. 2, Elsevier, 2008,
pp. 270–93, doi:10.1007/s11232-008-0026-7.
short: A. Morozov, M. Serbyn, Theoretical and Mathematical Physics 154 (2008) 270–293.
date_created: 2018-12-11T11:49:26Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T08:22:17Z
day: '01'
doi: 10.1007/s11232-008-0026-7
extern: 1
intvolume: ' 154'
issue: '2'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/hep-th/0703258
month: '01'
oa: 1
page: 270 - 293
publication: Theoretical and Mathematical Physics
publication_status: published
publisher: Elsevier
publist_id: '6437'
quality_controlled: 0
status: public
title: Nonlinear algebra and Bogoliubov's recursion
type: journal_article
volume: 154
year: '2008'
...
---
_id: '8510'
abstract:
- lang: eng
text: In this paper, using the ideas of Bessi and Mather, we present a simple mechanical
system exhibiting Arnold diffusion. This system of a particle in a small periodic
potential can be also interpreted as ray propagation in a periodic optical medium
with a near-constant index of refraction. Arnold diffusion in this context manifests
itself as an arbitrary finite change of direction for nearly constant index of
refraction.
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Mark
full_name: Levi, Mark
last_name: Levi
citation:
ama: Kaloshin V, Levi M. An example of Arnold diffusion for near-integrable Hamiltonians.
Bulletin of the American Mathematical Society. 2008;45(3):409-427. doi:10.1090/s0273-0979-08-01211-1
apa: Kaloshin, V., & Levi, M. (2008). An example of Arnold diffusion for near-integrable
Hamiltonians. Bulletin of the American Mathematical Society. American Mathematical
Society. https://doi.org/10.1090/s0273-0979-08-01211-1
chicago: Kaloshin, Vadim, and Mark Levi. “An Example of Arnold Diffusion for Near-Integrable
Hamiltonians.” Bulletin of the American Mathematical Society. American
Mathematical Society, 2008. https://doi.org/10.1090/s0273-0979-08-01211-1.
ieee: V. Kaloshin and M. Levi, “An example of Arnold diffusion for near-integrable
Hamiltonians,” Bulletin of the American Mathematical Society, vol. 45,
no. 3. American Mathematical Society, pp. 409–427, 2008.
ista: Kaloshin V, Levi M. 2008. An example of Arnold diffusion for near-integrable
Hamiltonians. Bulletin of the American Mathematical Society. 45(3), 409–427.
mla: Kaloshin, Vadim, and Mark Levi. “An Example of Arnold Diffusion for Near-Integrable
Hamiltonians.” Bulletin of the American Mathematical Society, vol. 45,
no. 3, American Mathematical Society, 2008, pp. 409–27, doi:10.1090/s0273-0979-08-01211-1.
short: V. Kaloshin, M. Levi, Bulletin of the American Mathematical Society 45 (2008)
409–427.
date_created: 2020-09-18T10:48:20Z
date_published: 2008-07-01T00:00:00Z
date_updated: 2021-01-12T08:19:47Z
day: '01'
doi: 10.1090/s0273-0979-08-01211-1
extern: '1'
intvolume: ' 45'
issue: '3'
keyword:
- Applied Mathematics
- General Mathematics
language:
- iso: eng
month: '07'
oa_version: None
page: 409-427
publication: Bulletin of the American Mathematical Society
publication_identifier:
issn:
- 0273-0979
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
status: public
title: An example of Arnold diffusion for near-integrable Hamiltonians
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2008'
...
---
_id: '8509'
abstract:
- lang: eng
text: The goal of this paper is to present to nonspecialists what is perhaps the
simplest possible geometrical picture explaining the mechanism of Arnold diffusion.
We choose to speak of a specific model—that of geometric rays in a periodic optical
medium. This model is equivalent to that of a particle in a periodic potential
in ${\mathbb R}^{n}$ with energy prescribed and to the geodesic flow in a Riemannian
metric on ${\mathbb R}^{n} $.
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Mark
full_name: Levi, Mark
last_name: Levi
citation:
ama: Kaloshin V, Levi M. Geometry of Arnold diffusion. SIAM Review. 2008;50(4):702-720.
doi:10.1137/070703235
apa: Kaloshin, V., & Levi, M. (2008). Geometry of Arnold diffusion. SIAM
Review. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/070703235
chicago: Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” SIAM
Review. Society for Industrial & Applied Mathematics, 2008. https://doi.org/10.1137/070703235.
ieee: V. Kaloshin and M. Levi, “Geometry of Arnold diffusion,” SIAM Review,
vol. 50, no. 4. Society for Industrial & Applied Mathematics, pp. 702–720,
2008.
ista: Kaloshin V, Levi M. 2008. Geometry of Arnold diffusion. SIAM Review. 50(4),
702–720.
mla: Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” SIAM Review,
vol. 50, no. 4, Society for Industrial & Applied Mathematics, 2008, pp. 702–20,
doi:10.1137/070703235.
short: V. Kaloshin, M. Levi, SIAM Review 50 (2008) 702–720.
date_created: 2020-09-18T10:48:12Z
date_published: 2008-11-05T00:00:00Z
date_updated: 2021-01-12T08:19:46Z
day: '05'
doi: 10.1137/070703235
extern: '1'
intvolume: ' 50'
issue: '4'
keyword:
- Theoretical Computer Science
- Applied Mathematics
- Computational Mathematics
language:
- iso: eng
month: '11'
oa_version: None
page: 702-720
publication: SIAM Review
publication_identifier:
issn:
- 0036-1445
- 1095-7200
publication_status: published
publisher: Society for Industrial & Applied Mathematics
quality_controlled: '1'
status: public
title: Geometry of Arnold diffusion
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2008'
...
---
_id: '895'
abstract:
- lang: eng
text: Background. The arginine vasopressin V1a receptor (V1aR) modulates social
cognition and behavior in a wide variety of species. Variation in a repetitive
microsatellite element in the 5′ flanking region of the V1aR gene (AVPR1A) in
rodents has been associated with variation in brain V1aR expression and in social
behavior. In humans, the 5′ flanking region of AVPR1A contains a tandem duplication
of two ∼350 bp, microsatellite-containing elements located approximately 3.5 kb
upstream of the transcription start site. The first block, referred to as DupA,
contains a polymorphic (GT) 25microsatellite; the second block, DupB, has a complex
(CT) 4-(TT)-(CT)8-(GT)24polymorphic motif, known as RS3. Polymorphisms in RS3
have been associated with variation in sociobehavioral traits in humans, including
autism spectrum disorders. Thus, evolution of these regions may have contributed
to variation in social behavior in primates. We examined the structure of these
regions in six ape, six monkey, and one prosimian species. Results. Both tandem
repeat blocks are present upstream of the AVPR1A coding region in five of the
ape species we investigated, while monkeys have only one copy of this region.
As in humans, the microsatellites within DupA and DupB are polymorphic in many
primate species. Furthermore, both single (lacking DupB) and duplicated alleles
(containing both DupA and DupB) are present in chimpanzee (Pan troglodytes) populations
with allele frequencies of 0.795 and 0.205 for the single and duplicated alleles,
respectively, based on the analysis of 47 wild-caught individuals. Finally, a
phylogenetic reconstruction suggests two alternate evolutionary histories for
this locus. Conclusion. There is no obvious relationship between the presence
of the RS3 duplication and social organization in primates. However, polymorphisms
identified in some species may be useful in future genetic association studies.
In particular, the presence of both single and duplicated alleles in chimpanzees
provides a unique opportunity to assess the functional role of this duplication
in contributing to variation in social behavior in primates. While our initial
studies show no signs of directional selection on this locus in chimps, pharmacological
and genetic association studies support a potential role for this region in influencing
V1aR expression and social behavior.
acknowledgement: |
We thank the caretakers at Zoo Atlanta and Yerkes National Primate Center for help with procuring specimens. Additional DNA samples were supplied by Bill Hopkins, Emory University (chimpanzee), Allyson Bennet, Wake Forest University (chimpanzee, rhesus macaque, bonnet macaque), Mar Sanchez, Emory University (rhesus macaque), and Anne Yoder, Duke University (galago). Susan Lambeth, M.D. Anderson Cancer Center, and Katie Chace, Yerkes National Primate Center, helped provide records regarding the origins of wild born chimps at these centers. We would like to thank Dr Lisa McGraw and two anonymous reviewers for their com- ments on this manuscript. This work was supported by NSF IBN-9876754, NIH RR00165, NIMH56897 (LJY), MH64692 (LJY) and a Howard Hughes Predoctoral Fellowship (ZRD).
author:
- first_name: Zoe
full_name: Donaldson, Zoe R
last_name: Donaldson
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Andrea
full_name: Putnam, Andrea S
last_name: Putnam
- first_name: Yaohui
full_name: Bai, Yaohui
last_name: Bai
- first_name: Tara
full_name: Stoinski, Tara S
last_name: Stoinski
- first_name: Elizabeth
full_name: Hammock, Elizabeth A
last_name: Hammock
- first_name: Larry
full_name: Young, Larry
last_name: Young
citation:
ama: Donaldson Z, Kondrashov F, Putnam A, et al. Evolution of a behavior-linked
microsatellite-containing element in the 5′ flanking region of the primate AVPR1A
gene. BMC Evolutionary Biology. 2008;8(1). doi:10.1186/1471-2148-8-180
apa: Donaldson, Z., Kondrashov, F., Putnam, A., Bai, Y., Stoinski, T., Hammock,
E., & Young, L. (2008). Evolution of a behavior-linked microsatellite-containing
element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary
Biology. BioMed Central. https://doi.org/10.1186/1471-2148-8-180
chicago: Donaldson, Zoe, Fyodor Kondrashov, Andrea Putnam, Yaohui Bai, Tara Stoinski,
Elizabeth Hammock, and Larry Young. “Evolution of a Behavior-Linked Microsatellite-Containing
Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary
Biology. BioMed Central, 2008. https://doi.org/10.1186/1471-2148-8-180.
ieee: Z. Donaldson et al., “Evolution of a behavior-linked microsatellite-containing
element in the 5′ flanking region of the primate AVPR1A gene,” BMC Evolutionary
Biology, vol. 8, no. 1. BioMed Central, 2008.
ista: Donaldson Z, Kondrashov F, Putnam A, Bai Y, Stoinski T, Hammock E, Young L.
2008. Evolution of a behavior-linked microsatellite-containing element in the
5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. 8(1).
mla: Donaldson, Zoe, et al. “Evolution of a Behavior-Linked Microsatellite-Containing
Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary
Biology, vol. 8, no. 1, BioMed Central, 2008, doi:10.1186/1471-2148-8-180.
short: Z. Donaldson, F. Kondrashov, A. Putnam, Y. Bai, T. Stoinski, E. Hammock,
L. Young, BMC Evolutionary Biology 8 (2008).
date_created: 2018-12-11T11:49:04Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:29Z
day: '01'
doi: 10.1186/1471-2148-8-180
extern: 1
intvolume: ' 8'
issue: '1'
month: '01'
publication: BMC Evolutionary Biology
publication_status: published
publisher: BioMed Central
publist_id: '6753'
quality_controlled: 0
status: public
title: Evolution of a behavior-linked microsatellite-containing element in the 5′
flanking region of the primate AVPR1A gene
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: 8
year: '2008'
...
---
_id: '907'
abstract:
- lang: eng
text: The most common form of protein-coding gene overlap in eukaryotes is a simple
nested structure, whereby one gene is embedded in an intron of another. Analysis
of nested protein-coding genes in vertebrates, fruit flies and nematodes revealed
substantially higher rates of evolutionary gains than losses. The accumulation
of nested gene structures could not be attributed to any obvious functional relationships
between the genes involved and represents an increase of the organizational complexity
of animal genomes via a neutral process.
author:
- first_name: Raquel
full_name: Assis, Raquel
last_name: Assis
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Eugene
full_name: Koonin, Eugene V
last_name: Koonin
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Assis R, Kondrashov A, Koonin E, Kondrashov F. Nested genes and increasing
organizational complexity of metazoan genomes. Trends in Genetics. 2008;24(10):475-478.
doi:10.1016/j.tig.2008.08.003
apa: Assis, R., Kondrashov, A., Koonin, E., & Kondrashov, F. (2008). Nested
genes and increasing organizational complexity of metazoan genomes. Trends
in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2008.08.003
chicago: Assis, Raquel, Alexey Kondrashov, Eugene Koonin, and Fyodor Kondrashov.
“Nested Genes and Increasing Organizational Complexity of Metazoan Genomes.” Trends
in Genetics. Elsevier, 2008. https://doi.org/10.1016/j.tig.2008.08.003.
ieee: R. Assis, A. Kondrashov, E. Koonin, and F. Kondrashov, “Nested genes and increasing
organizational complexity of metazoan genomes,” Trends in Genetics, vol.
24, no. 10. Elsevier, pp. 475–478, 2008.
ista: Assis R, Kondrashov A, Koonin E, Kondrashov F. 2008. Nested genes and increasing
organizational complexity of metazoan genomes. Trends in Genetics. 24(10), 475–478.
mla: Assis, Raquel, et al. “Nested Genes and Increasing Organizational Complexity
of Metazoan Genomes.” Trends in Genetics, vol. 24, no. 10, Elsevier, 2008,
pp. 475–78, doi:10.1016/j.tig.2008.08.003.
short: R. Assis, A. Kondrashov, E. Koonin, F. Kondrashov, Trends in Genetics 24
(2008) 475–478.
date_created: 2018-12-11T11:49:08Z
date_published: 2008-10-01T00:00:00Z
date_updated: 2021-01-12T08:21:49Z
day: '01'
doi: 10.1016/j.tig.2008.08.003
extern: 1
intvolume: ' 24'
issue: '10'
month: '10'
page: 475 - 478
publication: Trends in Genetics
publication_status: published
publisher: Elsevier
publist_id: '6743'
quality_controlled: 0
status: public
title: Nested genes and increasing organizational complexity of metazoan genomes
type: journal_article
volume: 24
year: '2008'
...
---
_id: '9457'
abstract:
- lang: eng
text: Eukaryotic chromatin is separated into functional domains differentiated by
posttranslational histone modifications, histone variants, and DNA methylation1–6.
Methylation is associated with repression of transcriptional initiation in plants
and animals, and is frequently found in transposable elements. Proper methylation
patterns are critical for eukaryotic development4,5, and aberrant methylation-induced
silencing of tumor suppressor genes is a common feature of human cancer7. In contrast
to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1
ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20.
How DNA methylation and H2A.Z influence transcription remains largely unknown.
Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation
are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of
DNA methylation in the bodies of actively transcribed genes and in methylated
transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses
and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition,
while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads
to genome-wide hypermethylation. Our findings indicate that DNA methylation can
influence chromatin structure and effect gene silencing by excluding H2A.Z, and
that H2A.Z protects genes from DNA methylation.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Devin
full_name: Coleman-Derr, Devin
last_name: Coleman-Derr
- first_name: Tracy
full_name: Ballinger, Tracy
last_name: Ballinger
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA
methylation are mutually antagonistic chromatin marks. Nature. 2008;456(7218):125-129.
doi:10.1038/nature07324
apa: Zilberman, D., Coleman-Derr, D., Ballinger, T., & Henikoff, S. (2008).
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature.
Springer Nature. https://doi.org/10.1038/nature07324
chicago: Zilberman, Daniel, Devin Coleman-Derr, Tracy Ballinger, and Steven Henikoff.
“Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.”
Nature. Springer Nature, 2008. https://doi.org/10.1038/nature07324.
ieee: D. Zilberman, D. Coleman-Derr, T. Ballinger, and S. Henikoff, “Histone H2A.Z
and DNA methylation are mutually antagonistic chromatin marks,” Nature,
vol. 456, no. 7218. Springer Nature, pp. 125–129, 2008.
ista: Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. 2008. Histone H2A.Z
and DNA methylation are mutually antagonistic chromatin marks. Nature. 456(7218),
125–129.
mla: Zilberman, Daniel, et al. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic
Chromatin Marks.” Nature, vol. 456, no. 7218, Springer Nature, 2008, pp.
125–29, doi:10.1038/nature07324.
short: D. Zilberman, D. Coleman-Derr, T. Ballinger, S. Henikoff, Nature 456 (2008)
125–129.
date_created: 2021-06-04T11:49:32Z
date_published: 2008-11-06T00:00:00Z
date_updated: 2021-12-14T08:54:36Z
day: '06'
department:
- _id: DaZi
doi: 10.1038/nature07324
extern: '1'
external_id:
pmid:
- '18815594'
intvolume: ' 456'
issue: '7218'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877514/
month: '11'
oa: 1
oa_version: Submitted Version
page: 125-129
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 456
year: '2008'
...
---
_id: '13423'
abstract:
- lang: eng
text: Supraspheres (SS) composed of hundreds to thousands of metal nanoparticles
(NPs) and crosslinked by dithiol linkers are assembled into larger structures,
which are subsequently converted into nanoporous metals (NMs). Conversion is achieved
by heating which removes organic molecules stabilizing the NPs and allows for
NP fusion. Heating of SS solutions leads to NMs of overall macroscopic dimensions;
localized radiation using collimated electron beam is used to prepare metallized
surface micropatterns. Depending on the composition of supraspherical precursors,
nanoporous materials composed of up to three metals can be obtained. Strategies
for controlling pore size and nanoscale surface roughness of these materials are
discussed.
article_processing_charge: No
article_type: original
author:
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Timothy P.
full_name: Gray, Timothy P.
last_name: Gray
- first_name: Paul J.
full_name: Wesson, Paul J.
last_name: Wesson
- first_name: Benjamin D.
full_name: Myers, Benjamin D.
last_name: Myers
- first_name: Vinayak P.
full_name: Dravid, Vinayak P.
last_name: Dravid
- first_name: Stoyan K.
full_name: Smoukov, Stoyan K.
last_name: Smoukov
- first_name: Bartosz A.
full_name: Grzybowski, Bartosz A.
last_name: Grzybowski
citation:
ama: Klajn R, Gray TP, Wesson PJ, et al. Bulk synthesis and surface patterning of
nanoporous metals and alloys from supraspherical nanoparticle aggregates. Advanced
Functional Materials. 2008;18(18):2763-2769. doi:10.1002/adfm.200800293
apa: Klajn, R., Gray, T. P., Wesson, P. J., Myers, B. D., Dravid, V. P., Smoukov,
S. K., & Grzybowski, B. A. (2008). Bulk synthesis and surface patterning of
nanoporous metals and alloys from supraspherical nanoparticle aggregates. Advanced
Functional Materials. Wiley. https://doi.org/10.1002/adfm.200800293
chicago: Klajn, Rafal, Timothy P. Gray, Paul J. Wesson, Benjamin D. Myers, Vinayak
P. Dravid, Stoyan K. Smoukov, and Bartosz A. Grzybowski. “Bulk Synthesis and Surface
Patterning of Nanoporous Metals and Alloys from Supraspherical Nanoparticle Aggregates.”
Advanced Functional Materials. Wiley, 2008. https://doi.org/10.1002/adfm.200800293.
ieee: R. Klajn et al., “Bulk synthesis and surface patterning of nanoporous
metals and alloys from supraspherical nanoparticle aggregates,” Advanced Functional
Materials, vol. 18, no. 18. Wiley, pp. 2763–2769, 2008.
ista: Klajn R, Gray TP, Wesson PJ, Myers BD, Dravid VP, Smoukov SK, Grzybowski BA.
2008. Bulk synthesis and surface patterning of nanoporous metals and alloys from
supraspherical nanoparticle aggregates. Advanced Functional Materials. 18(18),
2763–2769.
mla: Klajn, Rafal, et al. “Bulk Synthesis and Surface Patterning of Nanoporous Metals
and Alloys from Supraspherical Nanoparticle Aggregates.” Advanced Functional
Materials, vol. 18, no. 18, Wiley, 2008, pp. 2763–69, doi:10.1002/adfm.200800293.
short: R. Klajn, T.P. Gray, P.J. Wesson, B.D. Myers, V.P. Dravid, S.K. Smoukov,
B.A. Grzybowski, Advanced Functional Materials 18 (2008) 2763–2769.
date_created: 2023-08-01T10:30:57Z
date_published: 2008-09-23T00:00:00Z
date_updated: 2023-08-08T11:16:28Z
day: '23'
doi: 10.1002/adfm.200800293
extern: '1'
intvolume: ' 18'
issue: '18'
keyword:
- Electrochemistry
- Condensed Matter Physics
- Biomaterials
- Electronic
- Optical and Magnetic Materials
language:
- iso: eng
month: '09'
oa_version: None
page: 2763-2769
publication: Advanced Functional Materials
publication_identifier:
eissn:
- 1616-3028
issn:
- 1616-301X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bulk synthesis and surface patterning of nanoporous metals and alloys from
supraspherical nanoparticle aggregates
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2008'
...
---
_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'
...