---
_id: '3198'
abstract:
- lang: eng
text: 'In this paper we present a new approach for establishing correspondences
between sparse image features related by an unknown non-rigid mapping and corrupted
by clutter and occlusion, such as points extracted from a pair of images containing
a human figure in distinct poses. We formulate this matching task as an energy
minimization problem by defining a complex objective function of the appearance
and the spatial arrangement of the features. Optimization of this energy is an
instance of graph matching, which is in general a NP-hard problem. We describe
a novel graph matching optimization technique, which we refer to as dual decomposition
(DD), and demonstrate on a variety of examples that this method outperforms existing
graph matching algorithms. In the majority of our examples DD is able to find
the global minimum within a minute. The ability to globally optimize the objective
allows us to accurately learn the parameters of our matching model from training
examples. We show on several matching tasks that our learned model yields results
superior to those of state-of-the-art methods. '
alternative_title:
- LNCS
author:
- first_name: Lorenzo
full_name: Torresani, Lorenzo
last_name: Torresani
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: 'Torresani L, Kolmogorov V, Rother C. Feature correspondence via graph matching:
Models and global optimization. In: Vol 5303. Springer; 2008:596-609. doi:10.1007/978-3-540-88688-4_44'
apa: 'Torresani, L., Kolmogorov, V., & Rother, C. (2008). Feature correspondence
via graph matching: Models and global optimization (Vol. 5303, pp. 596–609). Presented
at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/978-3-540-88688-4_44'
chicago: 'Torresani, Lorenzo, Vladimir Kolmogorov, and Carsten Rother. “Feature
Correspondence via Graph Matching: Models and Global Optimization,” 5303:596–609.
Springer, 2008. https://doi.org/10.1007/978-3-540-88688-4_44.'
ieee: 'L. Torresani, V. Kolmogorov, and C. Rother, “Feature correspondence via graph
matching: Models and global optimization,” presented at the ECCV: European Conference
on Computer Vision, 2008, vol. 5303, pp. 596–609.'
ista: 'Torresani L, Kolmogorov V, Rother C. 2008. Feature correspondence via graph
matching: Models and global optimization. ECCV: European Conference on Computer
Vision, LNCS, vol. 5303, 596–609.'
mla: 'Torresani, Lorenzo, et al. Feature Correspondence via Graph Matching: Models
and Global Optimization. Vol. 5303, Springer, 2008, pp. 596–609, doi:10.1007/978-3-540-88688-4_44.'
short: L. Torresani, V. Kolmogorov, C. Rother, in:, Springer, 2008, pp. 596–609.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:01:58Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:44Z
day: '01'
doi: 10.1007/978-3-540-88688-4_44
extern: 1
intvolume: ' 5303'
main_file_link:
- open_access: '0'
url: http://research-srv.microsoft.com/pubs/70610/eccv08-MatchingMRF.pdf
month: '01'
page: 596 - 609
publication_status: published
publisher: Springer
publist_id: '3485'
quality_controlled: 0
status: public
title: 'Feature correspondence via graph matching: Models and global optimization'
type: conference
volume: 5303
year: '2008'
...
---
_id: '3195'
abstract:
- lang: eng
text: 'Graph cut is a popular technique for interactive image segmentation. However,
it has certain shortcomings. In particular, graph cut has problems with segmenting
thin elongated objects due to the ldquoshrinking biasrdquo. To overcome this problem,
we propose to impose an additional connectivity prior, which is a very natural
assumption about objects. We formulate several versions of the connectivity constraint
and show that the corresponding optimization problems are all NP-hard. For some
of these versions we propose two optimization algorithms: (i) a practical heuristic
technique which we call DijkstraGC, and (ii) a slow method based on problem decomposition
which provides a lower bound on the problem. We use the second technique to verify
that for some practical examples DijkstraGC is able to find the global minimum.'
author:
- first_name: Sara
full_name: Vicente, Sara
last_name: Vicente
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: 'Vicente S, Kolmogorov V, Rother C. Graph cut based image segmentation with
connectivity priors. In: IEEE; 2008. doi:10.1109/CVPR.2008.4587440'
apa: 'Vicente, S., Kolmogorov, V., & Rother, C. (2008). Graph cut based image
segmentation with connectivity priors. Presented at the CVPR: Computer Vision
and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2008.4587440'
chicago: Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Graph Cut Based
Image Segmentation with Connectivity Priors.” IEEE, 2008. https://doi.org/10.1109/CVPR.2008.4587440.
ieee: 'S. Vicente, V. Kolmogorov, and C. Rother, “Graph cut based image segmentation
with connectivity priors,” presented at the CVPR: Computer Vision and Pattern
Recognition, 2008.'
ista: 'Vicente S, Kolmogorov V, Rother C. 2008. Graph cut based image segmentation
with connectivity priors. CVPR: Computer Vision and Pattern Recognition.'
mla: Vicente, Sara, et al. Graph Cut Based Image Segmentation with Connectivity
Priors. IEEE, 2008, doi:10.1109/CVPR.2008.4587440.
short: S. Vicente, V. Kolmogorov, C. Rother, in:, IEEE, 2008.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:57Z
date_published: 2008-08-05T00:00:00Z
date_updated: 2021-01-12T07:41:43Z
day: '05'
doi: 10.1109/CVPR.2008.4587440
extern: 1
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/80485/CVPR08-ConnectedGC.pdf
month: '08'
publication_status: published
publisher: IEEE
publist_id: '3487'
quality_controlled: 0
status: public
title: Graph cut based image segmentation with connectivity priors
type: conference
year: '2008'
...
---
_id: '3224'
abstract:
- lang: eng
text: 'We propose a new mode of operation, enciphered CBC, for domain extension
of length-preserving functions (like block ciphers), which is a variation on the
popular CBC mode of operation. Our new mode is twice slower than CBC, but has
many (property-preserving) properties not enjoyed by CBC and other known modes.
Most notably, it yields the first constant-rate Variable Input Length (VIL) MAC
from any length preserving Fixed Input Length (FIL) MAC. This answers the question
of Dodis and Puniya from Eurocrypt 2007. Further, our mode is a secure domain
extender for PRFs (with basically the same security as encrypted CBC). This provides
a hedge against the security of the block cipher: if the block cipher is pseudorandom,
one gets a VIL-PRF, while if it is "only" unpredictable, one "at
least" gets a VIL-MAC. Additionally, our mode yields a VIL random oracle
(and, hence, a collision-resistant hash function) when instantiated with length-preserving
random functions, or even random permutations (which can be queried from both
sides). This means that one does not have to re-key the block cipher during the
computation, which was critically used in most previous constructions (analyzed
in the ideal cipher model). '
alternative_title:
- LNCS
author:
- first_name: Yevgeniy
full_name: Dodis, Yevgeniy
last_name: Dodis
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Prashant
full_name: Puniya, Prashant
last_name: Puniya
citation:
ama: 'Dodis Y, Pietrzak KZ, Puniya P. A new mode of operation for block ciphers
and length preserving MACs. In: Vol 4965. Springer; 2008:198-219. doi:10.1007/978-3-540-78967-3_12'
apa: 'Dodis, Y., Pietrzak, K. Z., & Puniya, P. (2008). A new mode of operation
for block ciphers and length preserving MACs (Vol. 4965, pp. 198–219). Presented
at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer.
https://doi.org/10.1007/978-3-540-78967-3_12'
chicago: Dodis, Yevgeniy, Krzysztof Z Pietrzak, and Prashant Puniya. “A New Mode
of Operation for Block Ciphers and Length Preserving MACs,” 4965:198–219. Springer,
2008. https://doi.org/10.1007/978-3-540-78967-3_12.
ieee: 'Y. Dodis, K. Z. Pietrzak, and P. Puniya, “A new mode of operation for block
ciphers and length preserving MACs,” presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, 2008, vol. 4965, pp. 198–219.'
ista: 'Dodis Y, Pietrzak KZ, Puniya P. 2008. A new mode of operation for block ciphers
and length preserving MACs. EUROCRYPT: Theory and Applications of Cryptographic
Techniques, LNCS, vol. 4965, 198–219.'
mla: Dodis, Yevgeniy, et al. A New Mode of Operation for Block Ciphers and Length
Preserving MACs. Vol. 4965, Springer, 2008, pp. 198–219, doi:10.1007/978-3-540-78967-3_12.
short: Y. Dodis, K.Z. Pietrzak, P. Puniya, in:, Springer, 2008, pp. 198–219.
conference:
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
date_created: 2018-12-11T12:02:07Z
date_published: 2008-04-28T00:00:00Z
date_updated: 2021-01-12T07:41:55Z
day: '28'
doi: 10.1007/978-3-540-78967-3_12
extern: 1
intvolume: ' 4965'
month: '04'
page: 198 - 219
publication_status: published
publisher: Springer
publist_id: '3456'
quality_controlled: 0
status: public
title: A new mode of operation for block ciphers and length preserving MACs
type: conference
volume: 4965
year: '2008'
...
---
_id: '3225'
abstract:
- lang: eng
text: 'A robust multi-property combiner for a set of security properties merges
two hash functions such that the resulting function satisfies each of the properties
which at least one of the two starting functions has. Fischlin and Lehmann (TCC
2008) recently constructed a combiner which simultaneously preserves collision-resistance,
target collision-resistance, message authentication, pseudorandomness and indifferentiability
from a random oracle (IRO). Their combiner produces outputs of 5n bits, where
n denotes the output length of the underlying hash functions. In this paper we
propose improved combiners with shorter outputs. By sacrificing the indifferentiability
from random oracles we obtain a combiner which preserves all of the other aforementioned
properties but with output length 2n only. This matches a lower bound for black-box
combiners for collision-resistance as the only property, showing that the other
properties can be achieved without penalizing the length of the hash values. We
then propose a combiner which also preserves the IRO property, slightly increasing
the output length to 2n + ω(logn). Finally, we show that a twist on our combiners
also makes them robust for one-wayness (but at the price of a fixed input length). '
alternative_title:
- LNCS
author:
- first_name: Marc
full_name: Fischlin, Marc
last_name: Fischlin
- first_name: Anja
full_name: Lehmann, Anja
last_name: Lehmann
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Fischlin M, Lehmann A, Pietrzak KZ. Robust multi property combiners for hash
functions revisited. In: Vol 5126. Springer; 2008:655-666. doi:10.1007/978-3-540-70583-3_53'
apa: 'Fischlin, M., Lehmann, A., & Pietrzak, K. Z. (2008). Robust multi property
combiners for hash functions revisited (Vol. 5126, pp. 655–666). Presented at
the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/978-3-540-70583-3_53'
chicago: Fischlin, Marc, Anja Lehmann, and Krzysztof Z Pietrzak. “Robust Multi Property
Combiners for Hash Functions Revisited,” 5126:655–66. Springer, 2008. https://doi.org/10.1007/978-3-540-70583-3_53.
ieee: 'M. Fischlin, A. Lehmann, and K. Z. Pietrzak, “Robust multi property combiners
for hash functions revisited,” presented at the ICALP: Automata, Languages and
Programming, 2008, vol. 5126, no. PART 2, pp. 655–666.'
ista: 'Fischlin M, Lehmann A, Pietrzak KZ. 2008. Robust multi property combiners
for hash functions revisited. ICALP: Automata, Languages and Programming, LNCS,
vol. 5126, 655–666.'
mla: Fischlin, Marc, et al. Robust Multi Property Combiners for Hash Functions
Revisited. Vol. 5126, no. PART 2, Springer, 2008, pp. 655–66, doi:10.1007/978-3-540-70583-3_53.
short: M. Fischlin, A. Lehmann, K.Z. Pietrzak, in:, Springer, 2008, pp. 655–666.
conference:
name: 'ICALP: Automata, Languages and Programming'
date_created: 2018-12-11T12:02:07Z
date_published: 2008-08-06T00:00:00Z
date_updated: 2023-02-23T11:01:10Z
day: '06'
doi: 10.1007/978-3-540-70583-3_53
extern: 1
intvolume: ' 5126'
issue: PART 2
month: '08'
page: 655 - 666
publication_status: published
publisher: Springer
publist_id: '3454'
quality_controlled: 0
related_material:
record:
- id: '2852'
relation: later_version
status: public
status: public
title: Robust multi property combiners for hash functions revisited
type: conference
volume: 5126
year: '2008'
...
---
_id: '3291'
abstract:
- lang: eng
text: 'The filamentous fungus Aspergillus fumigatus is responsible for a lethal
disease called Invasive Aspergillosis that affects immunocompromised patients.
This disease, like other human fungal diseases, is generally treated by compounds
targeting the primary fungal cell membrane sterol. Recently, glucan synthesis
inhibitors were added to the limited antifungal arsenal and encouraged the search
for novel targets in cell wall biosynthesis. Although galactomannan is a major
component of the A. fumigatus cell wall and extracellular matrix, the biosynthesis
and role of galactomannan are currently unknown. By a targeted gene deletion approach,
we demonstrate that UDP-galactopyranose mutase, a key enzyme of galactofuranose
metabolism, controls the biosynthesis of galactomannan and galactofuranose containing
glycoconjugates. The glfA deletion mutant generated in this study is devoid of
galactofuranose and displays attenuated virulence in a low-dose mouse model of
invasive aspergillosis that likely reflects the impaired growth of the mutant
at mammalian body temperature. Furthermore, the absence of galactofuranose results
in a thinner cell wall that correlates with an increased susceptibility to several
antifungal agents. The UDP-galactopyranose mutase thus appears to be an appealing
adjunct therapeutic target in combination with other drugs against A. fumigatus.
Its absence from mammalian cells indeed offers a considerable advantage to achieve
therapeutic selectivity. '
author:
- first_name: Philipp S
full_name: Philipp Schmalhorst
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Sven
full_name: Krappmann, Sven
last_name: Krappmann
- first_name: Wouter
full_name: Vervecken, Wouter
last_name: Vervecken
- first_name: Manfred
full_name: Rohde, Manfred
last_name: Rohde
- first_name: Meike
full_name: Müller, Meike
last_name: Müller
- first_name: Gerhard
full_name: Braus, Gerhard H.
last_name: Braus
- first_name: Roland
full_name: Contreras, Roland
last_name: Contreras
- first_name: Armin
full_name: Braun, Armin
last_name: Braun
- first_name: Hans
full_name: Bakker, Hans
last_name: Bakker
- first_name: Françoise
full_name: Routier, Françoise H
last_name: Routier
citation:
ama: Schmalhorst PS, Krappmann S, Vervecken W, et al. Contribution of galactofuranose
to the virulence of the opportunistic pathogen Aspergillus fumigatus. Eukaryotic
Cell. 2008;7(8):1268-1277. doi:10.1128/EC.00065-08
apa: Schmalhorst, P. S., Krappmann, S., Vervecken, W., Rohde, M., Müller, M., Braus,
G., … Routier, F. (2008). Contribution of galactofuranose to the virulence of
the opportunistic pathogen Aspergillus fumigatus. Eukaryotic Cell. American
Society for Microbiology. https://doi.org/10.1128/EC.00065-08
chicago: Schmalhorst, Philipp S, Sven Krappmann, Wouter Vervecken, Manfred Rohde,
Meike Müller, Gerhard Braus, Roland Contreras, Armin Braun, Hans Bakker, and Françoise
Routier. “Contribution of Galactofuranose to the Virulence of the Opportunistic
Pathogen Aspergillus Fumigatus.” Eukaryotic Cell. American Society for
Microbiology, 2008. https://doi.org/10.1128/EC.00065-08.
ieee: P. S. Schmalhorst et al., “Contribution of galactofuranose to the virulence
of the opportunistic pathogen Aspergillus fumigatus,” Eukaryotic Cell,
vol. 7, no. 8. American Society for Microbiology, pp. 1268–1277, 2008.
ista: Schmalhorst PS, Krappmann S, Vervecken W, Rohde M, Müller M, Braus G, Contreras
R, Braun A, Bakker H, Routier F. 2008. Contribution of galactofuranose to the
virulence of the opportunistic pathogen Aspergillus fumigatus. Eukaryotic Cell.
7(8), 1268–1277.
mla: Schmalhorst, Philipp S., et al. “Contribution of Galactofuranose to the Virulence
of the Opportunistic Pathogen Aspergillus Fumigatus.” Eukaryotic Cell,
vol. 7, no. 8, American Society for Microbiology, 2008, pp. 1268–77, doi:10.1128/EC.00065-08.
short: P.S. Schmalhorst, S. Krappmann, W. Vervecken, M. Rohde, M. Müller, G. Braus,
R. Contreras, A. Braun, H. Bakker, F. Routier, Eukaryotic Cell 7 (2008) 1268–1277.
date_created: 2018-12-11T12:02:29Z
date_published: 2008-06-13T00:00:00Z
date_updated: 2021-01-12T07:42:26Z
day: '13'
doi: 10.1128/EC.00065-08
extern: 1
intvolume: ' 7'
issue: '8'
month: '06'
page: 1268 - 1277
publication: Eukaryotic Cell
publication_status: published
publisher: American Society for Microbiology
publist_id: '3354'
quality_controlled: 0
status: public
title: Contribution of galactofuranose to the virulence of the opportunistic pathogen
Aspergillus fumigatus
type: journal_article
volume: 7
year: '2008'
...
---
_id: '3307'
abstract:
- lang: eng
text: A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000
year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8
Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally
establishes that the Neandertal mtDNA falls outside the variation of extant human
mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages
of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2
of cytochrome c oxidase of the mitochondrial electron transport chain has experienced
the largest number of amino acid substitutions in human ancestors since the separation
from Neandertals. There is evidence that purifying selection in the Neandertal
mtDNA was reduced compared with other primate lineages, suggesting that the effective
population size of Neandertals was small.
author:
- first_name: Richard
full_name: Green, Richard E
last_name: Green
- first_name: Anna
full_name: 'Malaspinas, Anna-Sapfo '
last_name: Malaspinas
- first_name: Johannes
full_name: Krause, Johannes
last_name: Krause
- first_name: Adrian
full_name: Briggs, Adrian W
last_name: Briggs
- first_name: Philip
full_name: Johnson, Philip L
last_name: Johnson
- first_name: Caroline
full_name: Caroline Uhler
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Matthias
full_name: Meyer, Matthias
last_name: Meyer
- first_name: Jeffrey
full_name: Good, Jeffrey M
last_name: Good
- first_name: Tomislav
full_name: Maricic, Tomislav
last_name: Maricic
- first_name: Udo
full_name: Stenzel, Udo
last_name: Stenzel
- first_name: Kay
full_name: Prüfer, Kay
last_name: Prüfer
- first_name: Michael
full_name: Siebauer, Michael F
last_name: Siebauer
- first_name: Hernän
full_name: Burbano, Hernän A
last_name: Burbano
- first_name: Michael
full_name: Ronan, Michael T
last_name: Ronan
- first_name: Jonathan
full_name: Rothberg, Jonathan M
last_name: Rothberg
- first_name: Michael
full_name: Egholm, Michael
last_name: Egholm
- first_name: Pavao
full_name: Rudan, Pavao
last_name: Rudan
- first_name: Dejana
full_name: Brajković, Dejana
last_name: Brajković
- first_name: Željko
full_name: Kućan, Željko
last_name: Kućan
- first_name: Ivan
full_name: Gušić, Ivan
last_name: Gušić
- first_name: Mårten
full_name: Wikström, Mårten K
last_name: Wikström
- first_name: Liisa
full_name: Laakkonen, Liisa J
last_name: Laakkonen
- first_name: Janet
full_name: Kelso, Janet F
last_name: Kelso
- first_name: Montgomery
full_name: Slatkin, Montgomery
last_name: Slatkin
- first_name: Svante
full_name: Pääbo, Svante H
last_name: Pääbo
citation:
ama: Green R, Malaspinas A, Krause J, et al. A complete neandertal mitochondrial
genome sequence determined by highhhroughput sequencing. Cell. 2008;134:416-426.
doi:10.1016/j.cell.2008.06.021
apa: Green, R., Malaspinas, A., Krause, J., Briggs, A., Johnson, P., Uhler, C.,
… Pääbo, S. (2008). A complete neandertal mitochondrial genome sequence determined
by highhhroughput sequencing. Cell. Cell Press. https://doi.org/10.1016/j.cell.2008.06.021
chicago: Green, Richard, Anna Malaspinas, Johannes Krause, Adrian Briggs, Philip
Johnson, Caroline Uhler, Matthias Meyer, et al. “A Complete Neandertal Mitochondrial
Genome Sequence Determined by Highhhroughput Sequencing.” Cell. Cell Press,
2008. https://doi.org/10.1016/j.cell.2008.06.021.
ieee: R. Green et al., “A complete neandertal mitochondrial genome sequence
determined by highhhroughput sequencing,” Cell, vol. 134. Cell Press, pp.
416–426, 2008.
ista: Green R, Malaspinas A, Krause J, Briggs A, Johnson P, Uhler C, Meyer M, Good
J, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano H, Ronan M, Rothberg J,
Egholm M, Rudan P, Brajković D, Kućan Ž, Gušić I, Wikström M, Laakkonen L, Kelso
J, Slatkin M, Pääbo S. 2008. A complete neandertal mitochondrial genome sequence
determined by highhhroughput sequencing. Cell. 134, 416–426.
mla: Green, Richard, et al. “A Complete Neandertal Mitochondrial Genome Sequence
Determined by Highhhroughput Sequencing.” Cell, vol. 134, Cell Press, 2008,
pp. 416–26, doi:10.1016/j.cell.2008.06.021.
short: R. Green, A. Malaspinas, J. Krause, A. Briggs, P. Johnson, C. Uhler, M. Meyer,
J. Good, T. Maricic, U. Stenzel, K. Prüfer, M. Siebauer, H. Burbano, M. Ronan,
J. Rothberg, M. Egholm, P. Rudan, D. Brajković, Ž. Kućan, I. Gušić, M. Wikström,
L. Laakkonen, J. Kelso, M. Slatkin, S. Pääbo, Cell 134 (2008) 416–426.
date_created: 2018-12-11T12:02:35Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2021-01-12T07:42:32Z
day: '01'
doi: 10.1016/j.cell.2008.06.021
extern: 1
intvolume: ' 134'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2602844/
month: '08'
oa: 1
page: 416 - 426
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3333'
quality_controlled: 0
status: public
title: A complete neandertal mitochondrial genome sequence determined by highhhroughput
sequencing
type: journal_article
volume: 134
year: '2008'
...
---
_id: '3435'
abstract:
- lang: eng
text: We develop a new method for estimating effective population sizes, Ne, and
selection coefficients, s, from time-series data of allele frequencies sampled
from a single diallelic locus. The method is based on calculating transition probabilities,
using a numerical solution of the diffusion process, and assuming independent
binomial sampling from this diffusion process at each time point. We apply the
method in two example applications. First, we estimate selection coefficients
acting on the CCR5-Δ32 mutation on the basis of published samples of contemporary
and ancient human DNA. We show that the data are compatible with the assumption
of s = 0, although moderate amounts of selection acting on this mutation cannot
be excluded. In our second example, we estimate the selection coefficient acting
on a mutation segregating in an experimental phage population. We show that the
selection coefficient acting on this mutation is ~0.43.
author:
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Thomas
full_name: York, Thomas L
last_name: York
- first_name: Rasmus
full_name: Nielsen, Rasmus
last_name: Nielsen
citation:
ama: Bollback JP, York T, Nielsen R. Estimation of 2Nes From Temporal Allele Frequency
Data. Genetics. 2008;179(1):497-502. doi:10.1534/genetics.107.085019
apa: Bollback, J. P., York, T., & Nielsen, R. (2008). Estimation of 2Nes From
Temporal Allele Frequency Data. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.107.085019
chicago: Bollback, Jonathan P, Thomas York, and Rasmus Nielsen. “Estimation of 2Nes
From Temporal Allele Frequency Data.” Genetics. Genetics Society of America,
2008. https://doi.org/10.1534/genetics.107.085019.
ieee: J. P. Bollback, T. York, and R. Nielsen, “Estimation of 2Nes From Temporal
Allele Frequency Data,” Genetics, vol. 179, no. 1. Genetics Society of
America, pp. 497–502, 2008.
ista: Bollback JP, York T, Nielsen R. 2008. Estimation of 2Nes From Temporal Allele
Frequency Data. Genetics. 179(1), 497–502.
mla: Bollback, Jonathan P., et al. “Estimation of 2Nes From Temporal Allele Frequency
Data.” Genetics, vol. 179, no. 1, Genetics Society of America, 2008, pp.
497–502, doi:10.1534/genetics.107.085019.
short: J.P. Bollback, T. York, R. Nielsen, Genetics 179 (2008) 497–502.
date_created: 2018-12-11T12:03:19Z
date_published: 2008-05-01T00:00:00Z
date_updated: 2021-01-12T07:43:27Z
day: '01'
doi: 10.1534/genetics.107.085019
extern: 1
intvolume: ' 179'
issue: '1'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390626
month: '05'
oa: 1
page: 497 - 502
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '2965'
quality_controlled: 0
status: public
title: Estimation of 2Nes From Temporal Allele Frequency Data
type: journal_article
volume: 179
year: '2008'
...
---
_id: '3516'
abstract:
- lang: eng
text: Temporal coding is a means of representing information by the time, as opposed
to the rate, at which neurons fire. Evidence of temporal coding in the hippocampus
comes from place cells, whose spike times relative to theta oscillations reflect
a rat's position while running along stereotyped trajectories. This arises from
the backwards shift in cell firing relative to local theta oscillations (phase
precession). Here we demonstrate phase precession during place-field crossings
in an open-field foraging task. This produced spike sequences in each theta cycle
that disambiguate the rat's trajectory through two-dimensional space and can be
used to predict movement direction. Furthermore, position and movement direction
were maximally predicted from firing in the early and late portions of the theta
cycle, respectively. This represents the first direct evidence of a combined representation
of position, trajectory and heading in the hippocampus, organized on a fine temporal
scale by theta oscillations.
author:
- first_name: John
full_name: Huxter,John R
last_name: Huxter
- first_name: Timothy
full_name: Senior,Timothy J
last_name: Senior
- first_name: Kevin
full_name: Allen, Kevin
last_name: Allen
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Huxter J, Senior T, Allen K, Csicsvari JL. Theta phase-specific codes for two-dimensional
position, trajectory and heading in the hippocampus. Nature Neuroscience.
2008;11(5):587-594. doi:10.1038/nn.2106
apa: Huxter, J., Senior, T., Allen, K., & Csicsvari, J. L. (2008). Theta phase-specific
codes for two-dimensional position, trajectory and heading in the hippocampus.
Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.2106
chicago: Huxter, John, Timothy Senior, Kevin Allen, and Jozsef L Csicsvari. “Theta
Phase-Specific Codes for Two-Dimensional Position, Trajectory and Heading in the
Hippocampus.” Nature Neuroscience. Nature Publishing Group, 2008. https://doi.org/10.1038/nn.2106.
ieee: J. Huxter, T. Senior, K. Allen, and J. L. Csicsvari, “Theta phase-specific
codes for two-dimensional position, trajectory and heading in the hippocampus,”
Nature Neuroscience, vol. 11, no. 5. Nature Publishing Group, pp. 587–594,
2008.
ista: Huxter J, Senior T, Allen K, Csicsvari JL. 2008. Theta phase-specific codes
for two-dimensional position, trajectory and heading in the hippocampus. Nature
Neuroscience. 11(5), 587–594.
mla: Huxter, John, et al. “Theta Phase-Specific Codes for Two-Dimensional Position,
Trajectory and Heading in the Hippocampus.” Nature Neuroscience, vol. 11,
no. 5, Nature Publishing Group, 2008, pp. 587–94, doi:10.1038/nn.2106.
short: J. Huxter, T. Senior, K. Allen, J.L. Csicsvari, Nature Neuroscience 11 (2008)
587–594.
date_created: 2018-12-11T12:03:44Z
date_published: 2008-05-29T00:00:00Z
date_updated: 2021-01-12T07:44:00Z
day: '29'
doi: 10.1038/nn.2106
extern: 1
intvolume: ' 11'
issue: '5'
month: '05'
page: 587 - 594
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '2869'
quality_controlled: 0
status: public
title: Theta phase-specific codes for two-dimensional position, trajectory and heading
in the hippocampus
type: journal_article
volume: 11
year: '2008'
...
---
_id: '3530'
abstract:
- lang: eng
text: In the cerebral cortex, GABAergic interneurons are often regarded as fast-spiking
cells. We have identified a type of slow-spiking interneuron that offers distinct
contributions to network activity. “Ivy” cells, named after their dense and fine
axons innervating mostly basal and oblique pyramidal cell dendrites, are more
numerous than the parvalbumin-expressing basket, bistratified, or axo-axonic cells.
Ivy cells express nitric oxide synthase, neuropeptide Y, and high levels of GABA(A)
receptor alpha 1 subunit; they discharge at a low frequency with wide spikes in
vivo, yet are distinctively phase-locked to behaviorally relevant network rhythms
including theta, gamma, and ripple oscillations. Paired recordings in vitro showed
that Ivy cells receive depressing EPSPs from pyramidal cells, which in turn receive
slowly rising and decaying inhibitory input from Ivy cells. In contrast to fast-spiking
interneurons operating with millisecond precision, the highly abundant Ivy cells
express presynaptically acting neuromodulators and regulate the excitability of
pyramidal cell dendrites through slowly rising and decaying GABAergic inputs.
author:
- first_name: Pablo
full_name: Fuentealba,Pablo
last_name: Fuentealba
- first_name: Rahima
full_name: Begum,Rahima
last_name: Begum
- first_name: Marco
full_name: Capogna,Marco
last_name: Capogna
- first_name: Shozo
full_name: Jinno,Shozo
last_name: Jinno
- first_name: Laszlo
full_name: Marton,Laszlo F
last_name: Marton
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Alex
full_name: Thomson,Alex
last_name: Thomson
- first_name: Péter
full_name: Somogyi, Péter
last_name: Somogyi
- first_name: Thomas
full_name: Klausberger,Thomas
last_name: Klausberger
citation:
ama: 'Fuentealba P, Begum R, Capogna M, et al. Ivy cells: A population of nitric-oxide-producing,
slow-spiking GABAergic neurons and their involvement in hippocampal network activity.
Neuron. 2008;57(6):917-929. doi:10.1016/j.neuron.2008.01.034'
apa: 'Fuentealba, P., Begum, R., Capogna, M., Jinno, S., Marton, L., Csicsvari,
J. L., … Klausberger, T. (2008). Ivy cells: A population of nitric-oxide-producing,
slow-spiking GABAergic neurons and their involvement in hippocampal network activity.
Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2008.01.034'
chicago: 'Fuentealba, Pablo, Rahima Begum, Marco Capogna, Shozo Jinno, Laszlo Marton,
Jozsef L Csicsvari, Alex Thomson, Péter Somogyi, and Thomas Klausberger. “Ivy
Cells: A Population of Nitric-Oxide-Producing, Slow-Spiking GABAergic Neurons
and Their Involvement in Hippocampal Network Activity.” Neuron. Elsevier,
2008. https://doi.org/10.1016/j.neuron.2008.01.034.'
ieee: 'P. Fuentealba et al., “Ivy cells: A population of nitric-oxide-producing,
slow-spiking GABAergic neurons and their involvement in hippocampal network activity,”
Neuron, vol. 57, no. 6. Elsevier, pp. 917–929, 2008.'
ista: 'Fuentealba P, Begum R, Capogna M, Jinno S, Marton L, Csicsvari JL, Thomson
A, Somogyi P, Klausberger T. 2008. Ivy cells: A population of nitric-oxide-producing,
slow-spiking GABAergic neurons and their involvement in hippocampal network activity.
Neuron. 57(6), 917–929.'
mla: 'Fuentealba, Pablo, et al. “Ivy Cells: A Population of Nitric-Oxide-Producing,
Slow-Spiking GABAergic Neurons and Their Involvement in Hippocampal Network Activity.”
Neuron, vol. 57, no. 6, Elsevier, 2008, pp. 917–29, doi:10.1016/j.neuron.2008.01.034.'
short: P. Fuentealba, R. Begum, M. Capogna, S. Jinno, L. Marton, J.L. Csicsvari,
A. Thomson, P. Somogyi, T. Klausberger, Neuron 57 (2008) 917–929.
date_created: 2018-12-11T12:03:49Z
date_published: 2008-03-27T00:00:00Z
date_updated: 2021-01-12T07:44:06Z
day: '27'
doi: 10.1016/j.neuron.2008.01.034
extern: 1
intvolume: ' 57'
issue: '6'
month: '03'
page: 917 - 929
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2855'
quality_controlled: 0
status: public
title: 'Ivy cells: A population of nitric-oxide-producing, slow-spiking GABAergic
neurons and their involvement in hippocampal network activity'
type: journal_article
volume: 57
year: '2008'
...
---
_id: '3544'
abstract:
- lang: eng
text: In the subthalamic nucleus (STN) of Parkinson's disease (PD) patients, a pronounced
synchronization of oscillatory activity at beta frequencies (15-30 Hz) accompanies
movement difficulties. Abnormal beta oscillations and motor symptoms are concomitantly
and acutely suppressed by dopaminergic therapies, suggesting that these inappropriate
rhythms might also emerge acutely from disrupted dopamine transmission. The neural
basis of these abnormal beta oscillations is unclear, and how they might compromise
information processing, or how they arise, is unknown. Using a 6-hydroxydopamine-lesioned
rodent model of PD, we demonstrate that beta oscillations are inappropriately
exaggerated, compared with controls, in a brain-state-dependent manner after chronic
dopamine loss. Exaggerated beta oscillations are expressed at the levels of single
neurons and small neuronal ensembles, and are focally present and spatially distributed
within STN. They are also expressed in synchronous population activities, as evinced
by oscillatory local field potentials, in STN and cortex. Excessively synchronized
beta oscillations reduce the information coding capacity of STN neuronal ensembles,
which may contribute to parkinsonian motor impairment. Acute disruption of dopamine
transmission in control animals with antagonists of D-1/D-2 receptors did not
exaggerate STN or cortical beta oscillations. Moreover, beta oscillations were
not exaggerated until several days after 6-hydroxydopamine injections. Thus, contrary
to predictions, abnormally amplified beta oscillations in cortico-STN circuits
do not result simply from an acute absence of dopamine receptor stimulation, but
are instead delayed sequelae of chronic dopamine depletion. Targeting the plastic
processes underlying the delayed emergence of pathological beta oscillations after
continuing dopaminergic dysfunction may offer considerable therapeutic promise.
author:
- first_name: Nicolas
full_name: Mallet,Nicolas
last_name: Mallet
- first_name: Alek
full_name: Pogosyan,Alek
last_name: Pogosyan
- first_name: Andrew
full_name: Sharott,Andrew
last_name: Sharott
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: John
full_name: Bolam, John Paul
last_name: Bolam
- first_name: Peter
full_name: Brown,Peter
last_name: Brown
- first_name: Peter
full_name: Magill,Peter J
last_name: Magill
citation:
ama: Mallet N, Pogosyan A, Sharott A, et al. Disrupted dopamine transmission and
the emergence of exaggerated beta oscillations in subthalamic nucleus and cerebral
cortex. Journal of Neuroscience. 2008;28(18):4795-4806. doi:10.1523/JNEUROSCI.0123-08.2008
apa: Mallet, N., Pogosyan, A., Sharott, A., Csicsvari, J. L., Bolam, J., Brown,
P., & Magill, P. (2008). Disrupted dopamine transmission and the emergence
of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex. Journal
of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0123-08.2008
chicago: Mallet, Nicolas, Alek Pogosyan, Andrew Sharott, Jozsef L Csicsvari, John
Bolam, Peter Brown, and Peter Magill. “Disrupted Dopamine Transmission and the
Emergence of Exaggerated Beta Oscillations in Subthalamic Nucleus and Cerebral
Cortex.” Journal of Neuroscience. Society for Neuroscience, 2008. https://doi.org/10.1523/JNEUROSCI.0123-08.2008.
ieee: N. Mallet et al., “Disrupted dopamine transmission and the emergence
of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex,”
Journal of Neuroscience, vol. 28, no. 18. Society for Neuroscience, pp.
4795–4806, 2008.
ista: Mallet N, Pogosyan A, Sharott A, Csicsvari JL, Bolam J, Brown P, Magill P.
2008. Disrupted dopamine transmission and the emergence of exaggerated beta oscillations
in subthalamic nucleus and cerebral cortex. Journal of Neuroscience. 28(18), 4795–4806.
mla: Mallet, Nicolas, et al. “Disrupted Dopamine Transmission and the Emergence
of Exaggerated Beta Oscillations in Subthalamic Nucleus and Cerebral Cortex.”
Journal of Neuroscience, vol. 28, no. 18, Society for Neuroscience, 2008,
pp. 4795–806, doi:10.1523/JNEUROSCI.0123-08.2008.
short: N. Mallet, A. Pogosyan, A. Sharott, J.L. Csicsvari, J. Bolam, P. Brown, P.
Magill, Journal of Neuroscience 28 (2008) 4795–4806.
date_created: 2018-12-11T12:03:53Z
date_published: 2008-04-30T00:00:00Z
date_updated: 2021-01-12T07:44:12Z
day: '30'
doi: 10.1523/JNEUROSCI.0123-08.2008
extern: 1
intvolume: ' 28'
issue: '18'
month: '04'
page: 4795 - 4806
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '2842'
quality_controlled: 0
status: public
title: Disrupted dopamine transmission and the emergence of exaggerated beta oscillations
in subthalamic nucleus and cerebral cortex
type: journal_article
volume: 28
year: '2008'
...
---
_id: '3577'
alternative_title:
- Mathematics and Visualization
author:
- first_name: Silvia
full_name: Biasotti, Silvia
last_name: Biasotti
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: Jean
full_name: Boissonnat, Jean-Daniel
last_name: Boissonnat
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Gershon
full_name: Elber, Gershon
last_name: Elber
- first_name: Michela
full_name: Mortara, Michela
last_name: Mortara
- first_name: Gabriella
full_name: Sanniti di Baja, Gabriella
last_name: Sanniti Di Baja
- first_name: Michela
full_name: Spagnuolo, Michela
last_name: Spagnuolo
- first_name: Mirela
full_name: Tanase, Mirela
last_name: Tanase
- first_name: Remco
full_name: Veltkam, Remco
last_name: Veltkam
citation:
ama: 'Biasotti S, Attali D, Boissonnat J, et al. Skeletal structures. In: Shape
Analysis and Structuring. Springer; 2008:145-183. doi:10.1007/978-3-540-33265-7_5'
apa: Biasotti, S., Attali, D., Boissonnat, J., Edelsbrunner, H., Elber, G., Mortara,
M., … Veltkam, R. (2008). Skeletal structures. In Shape Analysis and Structuring
(pp. 145–183). Springer. https://doi.org/10.1007/978-3-540-33265-7_5
chicago: Biasotti, Silvia, Dominique Attali, Jean Boissonnat, Herbert Edelsbrunner,
Gershon Elber, Michela Mortara, Gabriella Sanniti Di Baja, Michela Spagnuolo,
Mirela Tanase, and Remco Veltkam. “Skeletal Structures.” In Shape Analysis
and Structuring, 145–83. Springer, 2008. https://doi.org/10.1007/978-3-540-33265-7_5.
ieee: S. Biasotti et al., “Skeletal structures,” in Shape Analysis and
Structuring, Springer, 2008, pp. 145–183.
ista: 'Biasotti S, Attali D, Boissonnat J, Edelsbrunner H, Elber G, Mortara M, Sanniti
Di Baja G, Spagnuolo M, Tanase M, Veltkam R. 2008.Skeletal structures. In: Shape
Analysis and Structuring. Mathematics and Visualization, , 145–183.'
mla: Biasotti, Silvia, et al. “Skeletal Structures.” Shape Analysis and Structuring,
Springer, 2008, pp. 145–83, doi:10.1007/978-3-540-33265-7_5.
short: S. Biasotti, D. Attali, J. Boissonnat, H. Edelsbrunner, G. Elber, M. Mortara,
G. Sanniti Di Baja, M. Spagnuolo, M. Tanase, R. Veltkam, in:, Shape Analysis and
Structuring, Springer, 2008, pp. 145–183.
date_created: 2018-12-11T12:04:03Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:44:25Z
day: '01'
doi: 10.1007/978-3-540-33265-7_5
extern: 1
month: '01'
page: 145 - 183
publication: Shape Analysis and Structuring
publication_status: published
publisher: Springer
publist_id: '2808'
quality_controlled: 0
status: public
title: Skeletal structures
type: book_chapter
year: '2008'
...
---
_id: '3591'
abstract:
- lang: eng
text: The controlled internalization of membrane receptors and lipids is crucial
for cells to control signaling pathways and interact with their environment. During
clathrin-mediated endocytosis, membrane constituents are transported via endocytic
vesicles into early endosomes, from which they are further distributed within
the cell. The small guanosine triphosphatase (GTPase) Rab5 is both required and
sufficient for the formation of these early endosomes and can be used to experimentally
address endocytic processes. Recent evidence shows that endocytic turnover of
E-cadherin regulates the migration of mesendodermal cells during zebrafish gastrulation
by modulating their adhesive interactions with neighboring cells. This in turn
leads to effective and synchronized movement within the embryo. In this review,
we discuss techniques to manipulate E-cadherin endocytosis by morpholino-mediated
knockdown of rab5 during zebrafish gastrulation. We describe the use of antibodies
specifically directed against zebrafish E-cadherin to detect its intracellular
localization and of in situ hybridization and primary cell culture to reveal patterns
of cell migration and adhesion, respectively
article_processing_charge: No
author:
- first_name: Florian
full_name: Ulrich, Florian
last_name: Ulrich
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Ulrich F, Heisenberg C-PJ. Probing E-cadherin endocytosis by morpholino-mediated
Rab5 knock-down in zebrafish. Methods in Molecular Biology. 2008;440:371-387.
doi:10.1007/978-1-59745-178-9_27
apa: Ulrich, F., & Heisenberg, C.-P. J. (2008). Probing E-cadherin endocytosis
by morpholino-mediated Rab5 knock-down in zebrafish. Methods in Molecular Biology.
Springer. https://doi.org/10.1007/978-1-59745-178-9_27
chicago: Ulrich, Florian, and Carl-Philipp J Heisenberg. “Probing E-Cadherin Endocytosis
by Morpholino-Mediated Rab5 Knock-down in Zebrafish.” Methods in Molecular
Biology. Springer, 2008. https://doi.org/10.1007/978-1-59745-178-9_27.
ieee: F. Ulrich and C.-P. J. Heisenberg, “Probing E-cadherin endocytosis by morpholino-mediated
Rab5 knock-down in zebrafish.,” Methods in Molecular Biology, vol. 440.
Springer, pp. 371–387, 2008.
ista: Ulrich F, Heisenberg C-PJ. 2008. Probing E-cadherin endocytosis by morpholino-mediated
Rab5 knock-down in zebrafish. Methods in Molecular Biology. 440, 371–387.
mla: Ulrich, Florian, and Carl-Philipp J. Heisenberg. “Probing E-Cadherin Endocytosis
by Morpholino-Mediated Rab5 Knock-down in Zebrafish.” Methods in Molecular
Biology, vol. 440, Springer, 2008, pp. 371–87, doi:10.1007/978-1-59745-178-9_27.
short: F. Ulrich, C.-P.J. Heisenberg, Methods in Molecular Biology 440 (2008) 371–387.
date_created: 2018-12-11T12:04:08Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:44:31Z
day: '01'
doi: 10.1007/978-1-59745-178-9_27
extern: '1'
intvolume: ' 440'
language:
- iso: eng
month: '01'
oa_version: None
page: 371 - 387
publication: Methods in Molecular Biology
publication_status: published
publisher: Springer
publist_id: '2792'
status: public
title: Probing E-cadherin endocytosis by morpholino-mediated Rab5 knock-down in zebrafish.
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 440
year: '2008'
...
---
_id: '3599'
abstract:
- lang: eng
text: In this paper, adaptive formation control and bio-inspired optimization are
jointly addressed for a cluster-based satellite wireless sensor network in which
there are multiple satellites flying in formation (MSFF) in the presence of unknown
disturbances. The full nonlinear dynamics model describing the relative positioning
of the MSFF system is used to develop an adaptive formation controller. First,
the original nonlinear system is transformed into a linear controllable system
with aperturbation term by invoking the input-output feedback linearization technique.
Second, by using the integral feedback design scheme, the adaptive formation controller
is presented for improving the steady-state performance of the MSFF system in
the presence of unknown disturbances. Third, as a currently popular bio-inspired
algorithm, PSO (particle swarm optimizer) is employed to minimize the total energy
consumption under the required quality of service by jointly optimizing the transmission
power and rate for each satellite. Simulation results are provided to demonstrate
the effectiveness of the adaptive formation controller and the PSO-based optimization
for saving the total communication energy.
author:
- first_name: Erfu
full_name: Yang, Erfu
last_name: Yang
- first_name: Ahmet
full_name: Erdogan, Ahmet T
last_name: Erdogan
- first_name: Tughrul
full_name: Arslan, Tughrul
last_name: Arslan
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Yang E, Erdogan A, Arslan T, Barton NH. Adaptive formation control and bio-inspired
optimization of a cluster-based satellite wireless sensor network . In: IEEE;
2008:432-439. doi:10.1109/AHS.2008.60'
apa: 'Yang, E., Erdogan, A., Arslan, T., & Barton, N. H. (2008). Adaptive formation
control and bio-inspired optimization of a cluster-based satellite wireless sensor
network (pp. 432–439). Presented at the AHS: NASA/ESA Conference on Adaptive
Hardware and Systems, IEEE. https://doi.org/10.1109/AHS.2008.60'
chicago: Yang, Erfu, Ahmet Erdogan, Tughrul Arslan, and Nicholas H Barton. “Adaptive
Formation Control and Bio-Inspired Optimization of a Cluster-Based Satellite Wireless
Sensor Network ,” 432–39. IEEE, 2008. https://doi.org/10.1109/AHS.2008.60.
ieee: 'E. Yang, A. Erdogan, T. Arslan, and N. H. Barton, “Adaptive formation control
and bio-inspired optimization of a cluster-based satellite wireless sensor network
,” presented at the AHS: NASA/ESA Conference on Adaptive Hardware and Systems,
2008, pp. 432–439.'
ista: 'Yang E, Erdogan A, Arslan T, Barton NH. 2008. Adaptive formation control
and bio-inspired optimization of a cluster-based satellite wireless sensor network
. AHS: NASA/ESA Conference on Adaptive Hardware and Systems, 432–439.'
mla: Yang, Erfu, et al. Adaptive Formation Control and Bio-Inspired Optimization
of a Cluster-Based Satellite Wireless Sensor Network . IEEE, 2008, pp. 432–39,
doi:10.1109/AHS.2008.60.
short: E. Yang, A. Erdogan, T. Arslan, N.H. Barton, in:, IEEE, 2008, pp. 432–439.
conference:
name: 'AHS: NASA/ESA Conference on Adaptive Hardware and Systems'
date_created: 2018-12-11T12:04:10Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2021-01-12T07:44:34Z
day: '01'
doi: 10.1109/AHS.2008.60
extern: 1
month: '08'
page: 432 - 439
publication_status: published
publisher: IEEE
publist_id: '2784'
quality_controlled: 0
status: public
title: 'Adaptive formation control and bio-inspired optimization of a cluster-based
satellite wireless sensor network '
type: conference
year: '2008'
...
---
_id: '3698'
abstract:
- lang: eng
text: Kernel canonical correlation analysis (KCCA) is a dimensionality reduction
technique for paired data. By finding directions that maximize correlation, KCCA
learns representations that are more closely tied to the underlying semantics
of the data rather than noise. However, meaningful directions are not only those
that have high correlation to another modality, but also those that capture the
manifold structure of the data. We propose a method that is simultaneously able
to find highly correlated directions that are also located on high variance directions
along the data manifold. This is achieved by the use of semi-supervised Laplacian
regularization of KCCA. We show experimentally that Laplacian regularized training
improves class separation over KCCA with only Tikhonov regularization, while causing
no degradation in the correlation between modalities. We propose a model selection
criterion based on the Hilbert-Schmidt norm of the semi-supervised Laplacian regularized
cross-covariance operator, which we compute in closed form.
alternative_title:
- LNCS
author:
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Arthur
full_name: Gretton,Arthur
last_name: Gretton
citation:
ama: 'Blaschko M, Lampert C, Gretton A. Semi-supervised Laplacian regularization
of kernel canonical correlation analysis. In: Vol 5211. Springer; 2008:133-145.
doi:10.1007/978-3-540-87479-9_27'
apa: 'Blaschko, M., Lampert, C., & Gretton, A. (2008). Semi-supervised Laplacian
regularization of kernel canonical correlation analysis (Vol. 5211, pp. 133–145).
Presented at the ECML: European Conference on Machine Learning, Springer. https://doi.org/10.1007/978-3-540-87479-9_27'
chicago: Blaschko, Matthew, Christoph Lampert, and Arthur Gretton. “Semi-Supervised
Laplacian Regularization of Kernel Canonical Correlation Analysis,” 5211:133–45.
Springer, 2008. https://doi.org/10.1007/978-3-540-87479-9_27.
ieee: 'M. Blaschko, C. Lampert, and A. Gretton, “Semi-supervised Laplacian regularization
of kernel canonical correlation analysis,” presented at the ECML: European Conference
on Machine Learning, 2008, vol. 5211, no. Part 1, pp. 133–145.'
ista: 'Blaschko M, Lampert C, Gretton A. 2008. Semi-supervised Laplacian regularization
of kernel canonical correlation analysis. ECML: European Conference on Machine
Learning, LNCS, vol. 5211, 133–145.'
mla: Blaschko, Matthew, et al. Semi-Supervised Laplacian Regularization of Kernel
Canonical Correlation Analysis. Vol. 5211, no. Part 1, Springer, 2008, pp.
133–45, doi:10.1007/978-3-540-87479-9_27.
short: M. Blaschko, C. Lampert, A. Gretton, in:, Springer, 2008, pp. 133–145.
conference:
name: 'ECML: European Conference on Machine Learning'
date_created: 2018-12-11T12:04:41Z
date_published: 2008-10-21T00:00:00Z
date_updated: 2021-01-12T07:49:02Z
day: '21'
doi: 10.1007/978-3-540-87479-9_27
extern: 1
intvolume: ' 5211'
issue: Part 1
month: '10'
page: 133 - 145
publication_status: published
publisher: Springer
publist_id: '2662'
quality_controlled: 0
status: public
title: Semi-supervised Laplacian regularization of kernel canonical correlation analysis
type: conference
volume: 5211
year: '2008'
...
---
_id: '3694'
abstract:
- lang: eng
text: Distributed Denial of Service (DDoS) attacks are today the most destabilizing
factor in the global internet and there is a strong need for sophisticated solutions.
We introduce a formal statistical framework and derive a Bayes optimal packet
classifier from it. Our proposed practical algorithm "Adaptive History-Based
IP Filtering" (AHIF) mitigates DDoS attacks near the victim and outperforms
existing methods by at least 32% in terms of collateral damage. Furthermore, it
adjusts to the strength of an ongoing attack and ensures availability of the attacked
server. In contrast to other adaptive solutions, firewall rulesets used to resist
an attack can be precalculated before an attack takes place. This ensures an immediate
response in a DDoS emergency. For evaluation, simulated DDoS attacks and two real-world
user traffic datasets are used.
author:
- first_name: Markus
full_name: Goldstein,Markus
last_name: Goldstein
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Matthias
full_name: Reif,Matthias
last_name: Reif
- first_name: Armin
full_name: Stahl,Armin
last_name: Stahl
- first_name: Thomas
full_name: Breuel,Thomas M
last_name: Breuel
citation:
ama: 'Goldstein M, Lampert C, Reif M, Stahl A, Breuel T. Bayes optimal DDoS mitigation
by adaptive history-based IP filtering. In: IEEE; 2008:174-179. doi:10.1109/ICN.2008.64'
apa: 'Goldstein, M., Lampert, C., Reif, M., Stahl, A., & Breuel, T. (2008).
Bayes optimal DDoS mitigation by adaptive history-based IP filtering (pp. 174–179).
Presented at the ICN: International Conference on Networking, IEEE. https://doi.org/10.1109/ICN.2008.64'
chicago: Goldstein, Markus, Christoph Lampert, Matthias Reif, Armin Stahl, and Thomas
Breuel. “Bayes Optimal DDoS Mitigation by Adaptive History-Based IP Filtering,”
174–79. IEEE, 2008. https://doi.org/10.1109/ICN.2008.64.
ieee: 'M. Goldstein, C. Lampert, M. Reif, A. Stahl, and T. Breuel, “Bayes optimal
DDoS mitigation by adaptive history-based IP filtering,” presented at the ICN:
International Conference on Networking, 2008, pp. 174–179.'
ista: 'Goldstein M, Lampert C, Reif M, Stahl A, Breuel T. 2008. Bayes optimal DDoS
mitigation by adaptive history-based IP filtering. ICN: International Conference
on Networking, 174–179.'
mla: Goldstein, Markus, et al. Bayes Optimal DDoS Mitigation by Adaptive History-Based
IP Filtering. IEEE, 2008, pp. 174–79, doi:10.1109/ICN.2008.64.
short: M. Goldstein, C. Lampert, M. Reif, A. Stahl, T. Breuel, in:, IEEE, 2008,
pp. 174–179.
conference:
name: 'ICN: International Conference on Networking'
date_created: 2018-12-11T12:04:39Z
date_published: 2008-04-13T00:00:00Z
date_updated: 2021-01-12T07:49:01Z
day: '13'
doi: 10.1109/ICN.2008.64
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/~chl/papers/goldstein-icn2008.pdf
month: '04'
page: 174 - 179
publication_status: published
publisher: IEEE
publist_id: '2671'
quality_controlled: 0
status: public
title: Bayes optimal DDoS mitigation by adaptive history-based IP filtering
type: conference
year: '2008'
...
---
_id: '3706'
abstract:
- lang: eng
text: We present a new technique for structured prediction that works in a hybrid
generative/discriminative way, using a one-class support vector machine to model
the joint probability of (input, output)-pairs in a joint reproducing kernel Hilbert
space. Compared to discriminative techniques, like conditional random fields or
structured output SVMs?, the proposed method has the advantage that its training
time depends only on the number of training examples, not on the size of the label
space. Due to its generative aspect, it is also very tolerant against ambiguous,
incomplete or incorrect labels. Experiments on realistic data show that our method
works efficiently and robustly in situations that discriminative techniques have
problems with or that are computationally infeasible for them.
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
citation:
ama: 'Lampert C, Blaschko M. Joint kernel support estimation for structured prediction.
In: Curran Associates, Inc.; 2008:1-4.'
apa: 'Lampert, C., & Blaschko, M. (2008). Joint kernel support estimation for
structured prediction (pp. 1–4). Presented at the NIPS SISO: NIPS Workshop on
“Structured Input - Structured Output,” Curran Associates, Inc.'
chicago: Lampert, Christoph, and Matthew Blaschko. “Joint Kernel Support Estimation
for Structured Prediction,” 1–4. Curran Associates, Inc., 2008.
ieee: 'C. Lampert and M. Blaschko, “Joint kernel support estimation for structured
prediction,” presented at the NIPS SISO: NIPS Workshop on “Structured Input -
Structured Output,” 2008, pp. 1–4.'
ista: 'Lampert C, Blaschko M. 2008. Joint kernel support estimation for structured
prediction. NIPS SISO: NIPS Workshop on ‘Structured Input - Structured Output’,
1–4.'
mla: Lampert, Christoph, and Matthew Blaschko. Joint Kernel Support Estimation
for Structured Prediction. Curran Associates, Inc., 2008, pp. 1–4.
short: C. Lampert, M. Blaschko, in:, Curran Associates, Inc., 2008, pp. 1–4.
conference:
name: 'NIPS SISO: NIPS Workshop on "Structured Input - Structured Output"'
date_created: 2018-12-11T12:04:43Z
date_published: 2008-12-12T00:00:00Z
date_updated: 2021-01-12T07:51:37Z
day: '12'
extern: 1
main_file_link:
- open_access: '0'
url: http://agbs.kyb.tuebingen.mpg.de/wikis/bg/siso2008/Blaschkoetal.pdf
month: '12'
page: 1 - 4
publication_status: published
publisher: Curran Associates, Inc.
publist_id: '2650'
quality_controlled: 0
status: public
title: Joint kernel support estimation for structured prediction
type: conference
year: '2008'
...
---
_id: '3712'
abstract:
- lang: eng
text: We present a new method for spectral clustering with paired data based on
kernel canonical correlation analysis, called correlational spectral clustering.
Paired data are common in real world data sources, such as images with text captions.
Traditional spectral clustering algorithms either assume that data can be represented
by a single similarity measure, or by co-occurrence matrices that are then used
in biclustering. In contrast, the proposed method uses separate similarity measures
for each data representation, and allows for projection of previously unseen data
that are only observed in one representation (e.g. images but not text). We show
that this algorithm generalizes traditional spectral clustering algorithms and
show consistent empirical improvement over spectral clustering on a variety of
datasets of images with associated text.
author:
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Blaschko M, Lampert C. Correlational spectral clustering. In: IEEE; 2008:1-8.
doi:10.1109/CVPR.2008.4587353'
apa: 'Blaschko, M., & Lampert, C. (2008). Correlational spectral clustering
(pp. 1–8). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE.
https://doi.org/10.1109/CVPR.2008.4587353'
chicago: Blaschko, Matthew, and Christoph Lampert. “Correlational Spectral Clustering,”
1–8. IEEE, 2008. https://doi.org/10.1109/CVPR.2008.4587353.
ieee: 'M. Blaschko and C. Lampert, “Correlational spectral clustering,” presented
at the CVPR: Computer Vision and Pattern Recognition, 2008, pp. 1–8.'
ista: 'Blaschko M, Lampert C. 2008. Correlational spectral clustering. CVPR: Computer
Vision and Pattern Recognition, 1–8.'
mla: Blaschko, Matthew, and Christoph Lampert. Correlational Spectral Clustering.
IEEE, 2008, pp. 1–8, doi:10.1109/CVPR.2008.4587353.
short: M. Blaschko, C. Lampert, in:, IEEE, 2008, pp. 1–8.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:04:45Z
date_published: 2008-09-18T00:00:00Z
date_updated: 2021-01-12T07:51:40Z
day: '18'
doi: 10.1109/CVPR.2008.4587353
extern: 1
month: '09'
page: 1 - 8
publication_status: published
publisher: IEEE
publist_id: '2646'
quality_controlled: 0
status: public
title: Correlational spectral clustering
type: conference
year: '2008'
...
---
_id: '3726'
abstract:
- lang: eng
text: Single-molecule atomic force microscopy (AFM) provides novel ways to characterize
the structure-function relationship of native membrane proteins. High-resolution
AFM topographs allow observing the structure of single proteins at sub-nanometer
resolution as well as their conformational changes, oligomeric state, molecular
dynamics and assembly. We will review these feasibilities illustrating examples
of membrane proteins in native and reconstituted membranes. Classification of
individual topographs of single proteins allows understanding the principles of
motions of their extrinsic domains, to learn about their local structural flexibilities
and to find the entropy minima of certain conformations. Combined with the visualization
of functionally related conformational changes these insights allow understanding
why certain flexibilities are required for the protein to function and how structurally
flexible regions allow certain conformational changes. Complementary to AFM imaging,
single-molecule force spectroscopy (SMFS) experiments detect molecular interactions
established within and between membrane proteins. The sensitivity of this method
makes it possible to measure interactions that stabilize secondary structures
such as transmembrane α-helices, polypeptide loops and segments within. Changes
in temperature or protein-protein assembly do not change the locations of stable
structural segments, but influence their stability established by collective molecular
interactions. Such changes alter the probability of proteins to choose a certain
unfolding pathway. Recent examples have elucidated unfolding and refolding pathways
of membrane proteins as well as their energy landscapes.
author:
- first_name: Andreas
full_name: Engel, Andreas
last_name: Engel
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Dimtrios
full_name: Fotiadis, Dimtrios
last_name: Fotiadis
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: David
full_name: Cisneros, David
last_name: Cisneros
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: 'Engel A, Janovjak HL, Fotiadis D, Kedrov A, Cisneros D, Mueller D. Single-molecule
microscopy and force spectroscopy of membrane proteins. In: Single Molecules
and Nanotechnology. Vol 12. Springer; 2008:279-311. doi:10.1007/978-3-540-73924-1_11'
apa: Engel, A., Janovjak, H. L., Fotiadis, D., Kedrov, A., Cisneros, D., & Mueller,
D. (2008). Single-molecule microscopy and force spectroscopy of membrane proteins.
In Single Molecules and Nanotechnology (Vol. 12, pp. 279–311). Springer.
https://doi.org/10.1007/978-3-540-73924-1_11
chicago: Engel, Andreas, Harald L Janovjak, Dimtrios Fotiadis, Alexej Kedrov, David
Cisneros, and Daniel Mueller. “Single-Molecule Microscopy and Force Spectroscopy
of Membrane Proteins.” In Single Molecules and Nanotechnology, 12:279–311.
Springer, 2008. https://doi.org/10.1007/978-3-540-73924-1_11.
ieee: A. Engel, H. L. Janovjak, D. Fotiadis, A. Kedrov, D. Cisneros, and D. Mueller,
“Single-molecule microscopy and force spectroscopy of membrane proteins,” in Single
Molecules and Nanotechnology, vol. 12, Springer, 2008, pp. 279–311.
ista: 'Engel A, Janovjak HL, Fotiadis D, Kedrov A, Cisneros D, Mueller D. 2008.Single-molecule
microscopy and force spectroscopy of membrane proteins. In: Single Molecules and
Nanotechnology. vol. 12, 279–311.'
mla: Engel, Andreas, et al. “Single-Molecule Microscopy and Force Spectroscopy of
Membrane Proteins.” Single Molecules and Nanotechnology, vol. 12, Springer,
2008, pp. 279–311, doi:10.1007/978-3-540-73924-1_11.
short: A. Engel, H.L. Janovjak, D. Fotiadis, A. Kedrov, D. Cisneros, D. Mueller,
in:, Single Molecules and Nanotechnology, Springer, 2008, pp. 279–311.
date_created: 2018-12-11T12:04:50Z
date_published: 2008-01-08T00:00:00Z
date_updated: 2021-01-12T07:51:45Z
day: '08'
doi: 10.1007/978-3-540-73924-1_11
extern: 1
intvolume: ' 12'
month: '01'
page: 279 - 311
publication: Single Molecules and Nanotechnology
publication_status: published
publisher: Springer
publist_id: '2503'
quality_controlled: 0
status: public
title: Single-molecule microscopy and force spectroscopy of membrane proteins
type: book_chapter
volume: 12
year: '2008'
...
---
_id: '3739'
abstract:
- lang: eng
text: 'Changes in a cell''s external or internal conditions are usually reflected
in the concentrations of the relevant transcription factors. These proteins in
turn modulate the expression levels of the genes under their control and sometimes
need to perform nontrivial computations that integrate several inputs and affect
multiple genes. At the same time, the activities of the regulated genes would
fluctuate even if the inputs were held fixed, as a consequence of the intrinsic
noise in the system, and such noise must fundamentally limit the reliability of
any genetic computation. Here we use information theory to formalize the notion
of information transmission in simple genetic regulatory elements in the presence
of physically realistic noise sources. The dependence of this "channel capacity"
on noise parameters, cooperativity and cost of making signaling molecules is explored
systematically. We find that, in the range of parameters probed by recent in vivo
measurements, capacities higher than one bit should be achievable. It is of course
generally accepted that gene regulatory elements must, in order to function properly,
have a capacity of at least one bit. The central point of our analysis is the
demonstration that simple physical models of noisy gene transcription, with realistic
parameters, can indeed achieve this capacity: it was not self-evident that this
should be so. We also demonstrate that capacities significantly greater than one
bit are possible, so that transcriptional regulation need not be limited to simple
"on-off" components. The question whether real systems actually exploit
this richer possibility is beyond the scope of this investigation.'
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Curtis
full_name: Callan,Curtis G
last_name: Callan
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Tkačik G, Callan C, Bialek W. Information capacity of genetic regulatory elements.
Physical Review E Statistical Nonlinear and Soft Matter Physics. 2008;78(1).
doi:10.1103/PhysRevE.78.011910
apa: Tkačik, G., Callan, C., & Bialek, W. (2008). Information capacity of genetic
regulatory elements. Physical Review E Statistical Nonlinear and Soft Matter
Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.78.011910
chicago: Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Capacity
of Genetic Regulatory Elements.” Physical Review E Statistical Nonlinear and
Soft Matter Physics. American Institute of Physics, 2008. https://doi.org/10.1103/PhysRevE.78.011910.
ieee: G. Tkačik, C. Callan, and W. Bialek, “Information capacity of genetic regulatory
elements,” Physical Review E Statistical Nonlinear and Soft Matter Physics,
vol. 78, no. 1. American Institute of Physics, 2008.
ista: Tkačik G, Callan C, Bialek W. 2008. Information capacity of genetic regulatory
elements. Physical Review E Statistical Nonlinear and Soft Matter Physics. 78(1).
mla: Tkačik, Gašper, et al. “Information Capacity of Genetic Regulatory Elements.”
Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 78,
no. 1, American Institute of Physics, 2008, doi:10.1103/PhysRevE.78.011910.
short: G. Tkačik, C. Callan, W. Bialek, Physical Review E Statistical Nonlinear
and Soft Matter Physics 78 (2008).
date_created: 2018-12-11T12:04:54Z
date_published: 2008-07-21T00:00:00Z
date_updated: 2021-01-12T07:51:51Z
day: '21'
doi: 10.1103/PhysRevE.78.011910
extern: 1
intvolume: ' 78'
issue: '1'
month: '07'
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '2488'
quality_controlled: 0
status: public
title: Information capacity of genetic regulatory elements
type: journal_article
volume: 78
year: '2008'
...
---
_id: '3740'
abstract:
- lang: eng
text: In the simplest view of transcriptional regulation, the expression of a gene
is turned on or off by changes in the concentration of a transcription factor
(TF). We use recent data on noise levels in gene expression to show that it should
be possible to transmit much more than just one regulatory bit. Realizing this
optimal information capacity would require that the dynamic range of TF concentrations
used by the cell, the input/output relation of the regulatory module, and the
noise in gene expression satisfy certain matching relations, which we derive.
These results provide parameter-free, quantitative predictions connecting independently
measurable quantities. Although we have considered only the simplified problem
of a single gene responding to a single TF, we find that these predictions are
in surprisingly good agreement with recent experiments on the Bicoid/Hunchback
system in the early Drosophila embryo and that this system achieves approximately
90% of its theoretical maximum information transmission.
acknowledgement: P50 GM071508/GM/NIGMS NIH HHS/United States; R01 GM077599/GM/NIGMS
NIH HHS/United States
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Curtis
full_name: Callan,Curtis G
last_name: Callan
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Tkačik G, Callan C, Bialek W. Information flow and optimization in transcriptional
regulation. PNAS. 2008;105(34):12265-12270. doi:10.1073/pnas.0806077105
apa: Tkačik, G., Callan, C., & Bialek, W. (2008). Information flow and optimization
in transcriptional regulation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0806077105
chicago: Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Flow and
Optimization in Transcriptional Regulation.” PNAS. National Academy of
Sciences, 2008. https://doi.org/10.1073/pnas.0806077105.
ieee: G. Tkačik, C. Callan, and W. Bialek, “Information flow and optimization in
transcriptional regulation,” PNAS, vol. 105, no. 34. National Academy of
Sciences, pp. 12265–12270, 2008.
ista: Tkačik G, Callan C, Bialek W. 2008. Information flow and optimization in transcriptional
regulation. PNAS. 105(34), 12265–12270.
mla: Tkačik, Gašper, et al. “Information Flow and Optimization in Transcriptional
Regulation.” PNAS, vol. 105, no. 34, National Academy of Sciences, 2008,
pp. 12265–70, doi:10.1073/pnas.0806077105.
short: G. Tkačik, C. Callan, W. Bialek, PNAS 105 (2008) 12265–12270.
date_created: 2018-12-11T12:04:54Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:51:52Z
day: '01'
doi: 10.1073/pnas.0806077105
extern: 1
intvolume: ' 105'
issue: '34'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527900
month: '01'
oa: 1
page: 12265 - 12270
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2489'
quality_controlled: 0
status: public
title: Information flow and optimization in transcriptional regulation
type: journal_article
volume: 105
year: '2008'
...
---
_id: '3744'
abstract:
- lang: eng
text: It is widely acknowledged that detailed timing of action potentials is used
to encode information, for example, in auditory pathways; however, the computational
tools required to analyze encoding through timing are still in their infancy.
We present a simple example of encoding, based on a recent model of time-frequency
analysis, in which units fire action potentials when a certain condition is met,
but the timing of the action potential depends also on other features of the stimulus.
We show that, as a result, spike-triggered averages are smoothed so much that
they do not represent the true features of the encoding. Inspired by this example,
we present a simple method, differential reverse correlations, that can separate
an analysis of what causes a neuron to spike, and what controls its timing. We
analyze with this method the leaky integrate-and-fire neuron and show the method
accurately reconstructs the model's kernel.
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Marcelo
full_name: Magnasco, Marcelo O
last_name: Magnasco
citation:
ama: 'Tkačik G, Magnasco M. Decoding spike timing: The differential reverse-correlation
method. Biosystems. 2008;93(1-2):90-100. doi:10.1016/j.biosystems.2008.04.011'
apa: 'Tkačik, G., & Magnasco, M. (2008). Decoding spike timing: The differential
reverse-correlation method. Biosystems. Elsevier. https://doi.org/10.1016/j.biosystems.2008.04.011'
chicago: 'Tkačik, Gašper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential
Reverse-Correlation Method.” Biosystems. Elsevier, 2008. https://doi.org/10.1016/j.biosystems.2008.04.011.'
ieee: 'G. Tkačik and M. Magnasco, “Decoding spike timing: The differential reverse-correlation
method,” Biosystems, vol. 93, no. 1–2. Elsevier, pp. 90–100, 2008.'
ista: 'Tkačik G, Magnasco M. 2008. Decoding spike timing: The differential reverse-correlation
method. Biosystems. 93(1–2), 90–100.'
mla: 'Tkačik, Gašper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential
Reverse-Correlation Method.” Biosystems, vol. 93, no. 1–2, Elsevier, 2008,
pp. 90–100, doi:10.1016/j.biosystems.2008.04.011.'
short: G. Tkačik, M. Magnasco, Biosystems 93 (2008) 90–100.
date_created: 2018-12-11T12:04:56Z
date_published: 2008-07-01T00:00:00Z
date_updated: 2021-01-12T07:51:53Z
day: '01'
doi: 10.1016/j.biosystems.2008.04.011
extern: 1
intvolume: ' 93'
issue: 1-2
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2792887
month: '07'
oa: 1
page: 90 - 100
publication: Biosystems
publication_status: published
publisher: Elsevier
publist_id: '2482'
quality_controlled: 0
status: public
title: 'Decoding spike timing: The differential reverse-correlation method'
type: journal_article
volume: 93
year: '2008'
...
---
_id: '3760'
abstract:
- lang: eng
text: We introduce a method for efficiently animating a wide range of deformable
materials. We combine a high resolution surface mesh with a tetrahedral finite
element simulator that makes use of frequent re-meshing. This combination allows
for fast and detailed simulations of complex elastic and plastic behavior. We
significantly expand the range of physical parameters that can be simulated with
a single technique, and the results are free from common artifacts such as volume-loss,
smoothing, popping, and the absence of thin features like strands and sheets.
Our decision to couple a high resolution surface with low-resolution physics leads
to efficient simulation and detailed surface features, and our approach to creating
the tetrahedral mesh leads to an order-of-magnitude speedup over previous techniques
in the time spent re-meshing. We compute masses, collisions, and surface tension
forces on the scale of the fine mesh, which helps avoid visual artifacts due to
the differing mesh resolutions. The result is a method that can simulate a large
array of different material behaviors with high resolution features in a short
amount of time.
article_processing_charge: No
author:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
citation:
ama: Wojtan C, Turk G. Fast viscoelastic behavior with thin features. ACM Transactions
on Graphics. 2008;27(3). doi:10.1145/1360612.1360646
apa: Wojtan, C., & Turk, G. (2008). Fast viscoelastic behavior with thin features.
ACM Transactions on Graphics. ACM. https://doi.org/10.1145/1360612.1360646
chicago: Wojtan, Chris, and Greg Turk. “Fast Viscoelastic Behavior with Thin Features.”
ACM Transactions on Graphics. ACM, 2008. https://doi.org/10.1145/1360612.1360646.
ieee: C. Wojtan and G. Turk, “Fast viscoelastic behavior with thin features,” ACM
Transactions on Graphics, vol. 27, no. 3. ACM, 2008.
ista: Wojtan C, Turk G. 2008. Fast viscoelastic behavior with thin features. ACM
Transactions on Graphics. 27(3).
mla: Wojtan, Chris, and Greg Turk. “Fast Viscoelastic Behavior with Thin Features.”
ACM Transactions on Graphics, vol. 27, no. 3, ACM, 2008, doi:10.1145/1360612.1360646.
short: C. Wojtan, G. Turk, ACM Transactions on Graphics 27 (2008).
date_created: 2018-12-11T12:05:01Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2023-02-23T11:41:29Z
day: '01'
doi: 10.1145/1360612.1360646
extern: '1'
intvolume: ' 27'
issue: '3'
language:
- iso: eng
main_file_link:
- url: http://www.cc.gatech.edu/~turk/my_papers/fast_goop_2008.pdf
month: '08'
oa_version: None
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '2467'
status: public
title: Fast viscoelastic behavior with thin features
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2008'
...
---
_id: '3825'
abstract:
- lang: eng
text: Fast-spiking parvalbumin-expressing basket cells (BCs) represent a major type
of inhibitory interneuron in the hippocampus. These cells inhibit principal cells
in a temporally precise manner and are involved in the generation of network oscillations.
Although BCs show a unique expression profile of Ca(2+)-permeable receptors, Ca(2+)-binding
proteins and Ca(2+)-dependent signalling molecules, physiological Ca(2+) signalling
in these interneurons has not been investigated. To study action potential (AP)-induced
dendritic Ca(2+) influx and buffering, we combined whole-cell patch-clamp recordings
with ratiometric Ca(2+) imaging from the proximal apical dendrites of rigorously
identified BCs in acute slices, using the high-affinity Ca(2+) indicator fura-2
or the low-affinity dye fura-FF. Single APs evoked dendritic Ca(2+) transients
with small amplitude. Bursts of APs evoked Ca(2+) transients with amplitudes that
increased linearly with AP number. Analysis of Ca(2+) transients under steady-state
conditions with different fura-2 concentrations and during loading with 200 microm
fura-2 indicated that the endogenous Ca(2+)-binding ratio was approximately 200
(kappa(S) = 202 +/- 26 for the loading experiments). The peak amplitude of the
Ca(2+) transients measured directly with 100 microm fura-FF was 39 nm AP(-1).
At approximately 23 degrees C, the decay time constant of the Ca(2+) transients
was 390 ms, corresponding to an extrusion rate of approximately 600 s(-1). At
34 degrees C, the decay time constant was 203 ms and the corresponding extrusion
rate was approximately 1100 s(-1). At both temperatures, continuous theta-burst
activity with three to five APs per theta cycle, as occurs in vivo during exploration,
led to a moderate increase in the global Ca(2+) concentration that was proportional
to AP number, whereas more intense stimulation was required to reach micromolar
Ca(2+) concentrations and to shift Ca(2+) signalling into a non-linear regime.
In conclusion, dentate gyrus BCs show a high endogenous Ca(2+)-binding ratio,
a small AP-induced dendritic Ca(2+) influx, and a relatively slow Ca(2+) extrusion.
These specific buffering properties of BCs will sharpen the time course of local
Ca(2+) signals, while prolonging the decay of global Ca(2+) signals.
author:
- first_name: Yexica
full_name: Aponte, Yexica
last_name: Aponte
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Aponte Y, Bischofberger J, Jonas PM. Efficient Ca(2+) buffering in fast-spiking
basket cells of rat hippocampus. Journal of Physiology. 2008;586(8):2061-2075.
doi:10.1113/jphysiol.2007.147298
apa: Aponte, Y., Bischofberger, J., & Jonas, P. M. (2008). Efficient Ca(2+)
buffering in fast-spiking basket cells of rat hippocampus. Journal of Physiology.
Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2007.147298
chicago: Aponte, Yexica, Josef Bischofberger, and Peter M Jonas. “Efficient Ca(2+)
Buffering in Fast-Spiking Basket Cells of Rat Hippocampus.” Journal of Physiology.
Wiley-Blackwell, 2008. https://doi.org/10.1113/jphysiol.2007.147298.
ieee: Y. Aponte, J. Bischofberger, and P. M. Jonas, “Efficient Ca(2+) buffering
in fast-spiking basket cells of rat hippocampus,” Journal of Physiology,
vol. 586, no. 8. Wiley-Blackwell, pp. 2061–75, 2008.
ista: Aponte Y, Bischofberger J, Jonas PM. 2008. Efficient Ca(2+) buffering in fast-spiking
basket cells of rat hippocampus. Journal of Physiology. 586(8), 2061–75.
mla: Aponte, Yexica, et al. “Efficient Ca(2+) Buffering in Fast-Spiking Basket Cells
of Rat Hippocampus.” Journal of Physiology, vol. 586, no. 8, Wiley-Blackwell,
2008, pp. 2061–75, doi:10.1113/jphysiol.2007.147298.
short: Y. Aponte, J. Bischofberger, P.M. Jonas, Journal of Physiology 586 (2008)
2061–75.
date_created: 2018-12-11T12:05:22Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:28Z
day: '01'
doi: 10.1113/jphysiol.2007.147298
extern: 1
intvolume: ' 586'
issue: '8'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2465201/
month: '01'
oa: 1
page: 2061 - 75
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2386'
quality_controlled: 0
status: public
title: Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus
type: journal_article
volume: 586
year: '2008'
...
---
_id: '3822'
abstract:
- lang: eng
text: Dentate gyrus granule cells transmit action potentials (APs) along their unmyelinated
mossy fibre axons to the CA3 region. Although the initiation and propagation of
APs are fundamental steps during neural computation, little is known about the
site of AP initiation and the speed of propagation in mossy fibre axons. To address
these questions, we performed simultaneous somatic and axonal whole-cell recordings
from granule cells in acute hippocampal slices of adult mice at approximately
23 degrees C. Injection of short current pulses or synaptic stimulation evoked
axonal and somatic APs with similar amplitudes. By contrast, the time course was
significantly different, as axonal APs had a higher maximal rate of rise (464
+/- 30 V s(-1) in the axon versus 297 +/- 12 V s(-1) in the soma, mean +/- s.e.m.).
Furthermore, analysis of latencies between the axonal and somatic signals showed
that APs were initiated in the proximal axon at approximately 20-30 mum distance
from the soma, and propagated orthodromically with a velocity of 0.24 m s(-1).
Qualitatively similar results were obtained at a recording temperature of approximately
34 degrees C. Modelling of AP propagation in detailed cable models of granule
cells suggested that a approximately 4 times higher Na(+) channel density ( approximately
1000 pS mum(-2)) in the axon might account for both the higher rate of rise of
axonal APs and the robust AP initiation in the proximal mossy fibre axon. This
may be of critical importance to separate dendritic integration of thousands of
synaptic inputs from the generation and transmission of a common AP output.
author:
- first_name: Christoph
full_name: Schmidt-Hieber, Christoph
last_name: Schmidt Hieber
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
citation:
ama: Schmidt Hieber C, Jonas PM, Bischofberger J. Action potential initiation and
propagation in hippocampal mossy fibre axons. Journal of Physiology. 2008;586(7):1849-1857.
doi:10.1113/jphysiol.2007.150151
apa: Schmidt Hieber, C., Jonas, P. M., & Bischofberger, J. (2008). Action potential
initiation and propagation in hippocampal mossy fibre axons. Journal of Physiology.
Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2007.150151
chicago: Schmidt Hieber, Christoph, Peter M Jonas, and Josef Bischofberger. “Action
Potential Initiation and Propagation in Hippocampal Mossy Fibre Axons.” Journal
of Physiology. Wiley-Blackwell, 2008. https://doi.org/10.1113/jphysiol.2007.150151 .
ieee: C. Schmidt Hieber, P. M. Jonas, and J. Bischofberger, “Action potential initiation
and propagation in hippocampal mossy fibre axons,” Journal of Physiology,
vol. 586, no. 7. Wiley-Blackwell, pp. 1849–57, 2008.
ista: Schmidt Hieber C, Jonas PM, Bischofberger J. 2008. Action potential initiation
and propagation in hippocampal mossy fibre axons. Journal of Physiology. 586(7),
1849–57.
mla: Schmidt Hieber, Christoph, et al. “Action Potential Initiation and Propagation
in Hippocampal Mossy Fibre Axons.” Journal of Physiology, vol. 586, no.
7, Wiley-Blackwell, 2008, pp. 1849–57, doi:10.1113/jphysiol.2007.150151 .
short: C. Schmidt Hieber, P.M. Jonas, J. Bischofberger, Journal of Physiology 586
(2008) 1849–57.
date_created: 2018-12-11T12:05:21Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:27Z
day: '01'
doi: '10.1113/jphysiol.2007.150151 '
extern: 1
intvolume: ' 586'
issue: '7'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375716/
month: '01'
oa: 1
page: 1849 - 57
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2387'
quality_controlled: 0
status: public
title: Action potential initiation and propagation in hippocampal mossy fibre axons
type: journal_article
volume: 586
year: '2008'
...
---
_id: '3824'
abstract:
- lang: eng
text: It is generally thought that transmitter release at mammalian central synapses
is triggered by Ca2+ microdomains, implying loose coupling between presynaptic
Ca2+ channels and Ca2+ sensors of exocytosis. Here we show that Ca2+ channel subunit
immunoreactivity is highly concentrated in the active zone of GABAergic presynaptic
terminals of putative parvalbumin-containing basket cells in the hippocampus.
Paired recording combined with presynaptic patch pipette perfusion revealed that
GABA release at basket cell-granule cell synapses is sensitive to millimolar concentrations
of the fast Ca2+ chelator BAPTA but insensitive to the slow Ca2+ chelator EGTA.
These results show that Ca2+ source and Ca2+ sensor are tightly coupled at this
synapse, with distances in the range of 10-20 nm. Models of Ca2+ inflow-exocytosis
coupling further reveal that the tightness of coupling increases efficacy, speed,
and temporal precision of transmitter release. Thus, tight coupling contributes
to fast feedforward and feedback inhibition in the hippocampal network.
author:
- first_name: Iancu
full_name: Bucurenciu, Iancu
last_name: Bucurenciu
- first_name: Ákos
full_name: Kulik, Ákos
last_name: Kulik
- first_name: Beat
full_name: Schwaller, Beat
last_name: Schwaller
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Bucurenciu I, Kulik Á, Schwaller B, Frotscher M, Jonas PM. Nanodomain coupling
between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter
release at a cortical GABAergic synapse. Neuron. 2008;57(4):536-545. doi:10.1016/j.neuron.2007.12.026
apa: Bucurenciu, I., Kulik, Á., Schwaller, B., Frotscher, M., & Jonas, P. M.
(2008). Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes
fast and efficient transmitter release at a cortical GABAergic synapse. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2007.12.026
chicago: Bucurenciu, Iancu, Ákos Kulik, Beat Schwaller, Michael Frotscher, and Peter
M Jonas. “Nanodomain Coupling between Ca(2+) Channels and Ca2+ Sensors Promotes
Fast and Efficient Transmitter Release at a Cortical GABAergic Synapse.” Neuron.
Elsevier, 2008. https://doi.org/10.1016/j.neuron.2007.12.026.
ieee: I. Bucurenciu, Á. Kulik, B. Schwaller, M. Frotscher, and P. M. Jonas, “Nanodomain
coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient
transmitter release at a cortical GABAergic synapse,” Neuron, vol. 57,
no. 4. Elsevier, pp. 536–45, 2008.
ista: Bucurenciu I, Kulik Á, Schwaller B, Frotscher M, Jonas PM. 2008. Nanodomain
coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient
transmitter release at a cortical GABAergic synapse. Neuron. 57(4), 536–45.
mla: Bucurenciu, Iancu, et al. “Nanodomain Coupling between Ca(2+) Channels and
Ca2+ Sensors Promotes Fast and Efficient Transmitter Release at a Cortical GABAergic
Synapse.” Neuron, vol. 57, no. 4, Elsevier, 2008, pp. 536–45, doi:10.1016/j.neuron.2007.12.026.
short: I. Bucurenciu, Á. Kulik, B. Schwaller, M. Frotscher, P.M. Jonas, Neuron 57
(2008) 536–45.
date_created: 2018-12-11T12:05:22Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:27Z
day: '01'
doi: 10.1016/j.neuron.2007.12.026
extern: 1
intvolume: ' 57'
issue: '4'
month: '01'
page: 536 - 45
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2385'
quality_controlled: 0
status: public
title: Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast
and efficient transmitter release at a cortical GABAergic synapse
type: journal_article
volume: 57
year: '2008'
...
---
_id: '3823'
abstract:
- lang: eng
text: Two studies in this issue of Neuron (Kwon and Castillo and Rebola et al.)
show that the mossy fiber-CA3 pyramidal neuron synapse, a hippocampal synapse
well known for its presynaptic plasticity, exhibits a novel form of long-term
potentiation of NMDAR-mediated currents, which is induced and expressed postsynaptically.
author:
- first_name: Angharad
full_name: Kerr, Angharad M
last_name: Kerr
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Kerr A, Jonas PM. The two sides of hippocampal mossy fiber plasticity (Review).
Neuron. 2008;57(1):5-7. doi:10.1016/j.neuron.2007.12.015
apa: Kerr, A., & Jonas, P. M. (2008). The two sides of hippocampal mossy fiber
plasticity (Review). Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2007.12.015
chicago: Kerr, Angharad, and Peter M Jonas. “The Two Sides of Hippocampal Mossy
Fiber Plasticity (Review).” Neuron. Elsevier, 2008. https://doi.org/10.1016/j.neuron.2007.12.015.
ieee: A. Kerr and P. M. Jonas, “The two sides of hippocampal mossy fiber plasticity
(Review),” Neuron, vol. 57, no. 1. Elsevier, pp. 5–7, 2008.
ista: Kerr A, Jonas PM. 2008. The two sides of hippocampal mossy fiber plasticity
(Review). Neuron. 57(1), 5–7.
mla: Kerr, Angharad, and Peter M. Jonas. “The Two Sides of Hippocampal Mossy Fiber
Plasticity (Review).” Neuron, vol. 57, no. 1, Elsevier, 2008, pp. 5–7,
doi:10.1016/j.neuron.2007.12.015.
short: A. Kerr, P.M. Jonas, Neuron 57 (2008) 5–7.
date_created: 2018-12-11T12:05:22Z
date_published: 2008-01-10T00:00:00Z
date_updated: 2021-01-12T07:52:27Z
day: '10'
doi: 10.1016/j.neuron.2007.12.015
extern: 1
intvolume: ' 57'
issue: '1'
month: '01'
page: 5 - 7
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2388'
quality_controlled: 0
status: public
title: The two sides of hippocampal mossy fiber plasticity (Review)
type: journal_article
volume: 57
year: '2008'
...
---
_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
license: https://creativecommons.org/licenses/by/4.0/
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'
...