---
OA_type: free access
_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.
article_processing_charge: No
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
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: 2026-05-29T09:15:13Z
day: '01'
doi: 10.1016/j.comgeo.2007.11.001
extern: '1'
intvolume: ' 41'
issue: '3'
language:
- iso: eng
month: '11'
oa_version: None
page: 149 - 166
publication: 'Computational Geometry: Theory and Applications'
publication_identifier:
eissn:
- 1879-081X
issn:
- 0925-7721
publication_status: published
publisher: Elsevier
publist_id: '2158'
status: public
title: Time-varying Reeb graphs for continuous space-time data
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 41
year: '2008'
...
---
_id: '3974'
abstract:
- lang: eng
text: Generalizing the concept of a Reeb graph, the Reeb space of a multivariate
continuous mapping identifies points of the domain that belong to a common component
of the preimage of a point in the range. We study the local and global structure
of this space for generic, piecewise linear mappings on a combinatorial manifold.
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
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: Amit
full_name: Patel, Amit
id: 34A254A0-F248-11E8-B48F-1D18A9856A87
last_name: Patel
citation:
ama: 'Edelsbrunner H, Harer J, Patel A. Reeb spaces of piecewise linear mappings.
In: Proceedings of the Twenty-Fourth Annual Symposium on Computational Geometry.
Association for Computing Machinery; 2008:242-250. doi:10.1145/1377676.1377720'
apa: 'Edelsbrunner, H., Harer, J., & Patel, A. (2008). Reeb spaces of piecewise
linear mappings. In Proceedings of the twenty-fourth annual symposium on Computational
geometry (pp. 242–250). College Park, MD, United States: Association for Computing
Machinery. https://doi.org/10.1145/1377676.1377720'
chicago: Edelsbrunner, Herbert, John Harer, and Amit Patel. “Reeb Spaces of Piecewise
Linear Mappings.” In Proceedings of the Twenty-Fourth Annual Symposium on Computational
Geometry, 242–50. Association for Computing Machinery, 2008. https://doi.org/10.1145/1377676.1377720.
ieee: H. Edelsbrunner, J. Harer, and A. Patel, “Reeb spaces of piecewise linear
mappings,” in Proceedings of the twenty-fourth annual symposium on Computational
geometry, College Park, MD, United States, 2008, pp. 242–250.
ista: 'Edelsbrunner H, Harer J, Patel A. 2008. Reeb spaces of piecewise linear mappings.
Proceedings of the twenty-fourth annual symposium on Computational geometry. SCG:
Symposium on Computational Geometry, 242–250.'
mla: Edelsbrunner, Herbert, et al. “Reeb Spaces of Piecewise Linear Mappings.” Proceedings
of the Twenty-Fourth Annual Symposium on Computational Geometry, Association
for Computing Machinery, 2008, pp. 242–50, doi:10.1145/1377676.1377720.
short: H. Edelsbrunner, J. Harer, A. Patel, in:, Proceedings of the Twenty-Fourth
Annual Symposium on Computational Geometry, Association for Computing Machinery,
2008, pp. 242–250.
conference:
end_date: 2008-06-11
location: College Park, MD, United States
name: 'SCG: Symposium on Computational Geometry'
start_date: 2008-06-09
date_created: 2018-12-11T12:06:13Z
date_published: 2008-06-09T00:00:00Z
date_updated: 2026-05-29T09:01:13Z
day: '09'
doi: 10.1145/1377676.1377720
extern: '1'
language:
- iso: eng
month: '06'
oa_version: None
page: 242 - 250
publication: Proceedings of the twenty-fourth annual symposium on Computational geometry
publication_identifier:
isbn:
- '9781605580715'
publication_status: published
publisher: Association for Computing Machinery
publist_id: '2155'
status: public
title: Reeb spaces of piecewise linear mappings
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2008'
...
---
_id: '4135'
abstract:
- lang: eng
text: There have been several attempts to build a unified framework for macroecological
patterns. However, these have mostly been based either on questionable assumptions
or have had to be parameterized to obtain realistic predictions. Here, we propose
a new model explicitly considering patterns of aggregated species distributions
on multiple spatial scales, the property which lies behind all spatial macroecological
patterns, using the idea we term ‘generalized fractals’. Species’ spatial distributions
were modelled by a random hierarchical process in which the original ‘habitat’
patches were randomly replaced by sets of smaller patches nested within them,
and the statistical properties of modelled species assemblages were compared with
macroecological patterns in observed bird data. Without parameterization based
on observed patterns, this simple model predicts realistic patterns of species
abundance, distribution and diversity, including fractal-like spatial distributions,
the frequency distribution of species occupancies/abundances and the species–area
relationship. Although observed macroecological patterns may differ in some quantitative
properties, our concept of random hierarchical aggregation can be considered as
an appropriate null model of fundamental macroecological patterns which can potentially
be modified to accommodate ecologically important variables.
article_processing_charge: No
author:
- first_name: D.
full_name: Storch, D.
last_name: Storch
- first_name: A.
full_name: Šizling, A.
last_name: Šizling
- first_name: J.
full_name: Reif, J.
last_name: Reif
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: E.
full_name: Šizlingová, E.
last_name: Šizlingová
- first_name: K.
full_name: Gaston, K.
last_name: Gaston
citation:
ama: 'Storch D, Šizling A, Reif J, Polechova J, Šizlingová E, Gaston K. The quest
for a null model for macroecological patterns: Geometry of species distributions
at multiple spatial scales. Ecology Letters. 2008;11(8):771-784. doi:10.1111/j.1461-0248.2008.01206.x'
apa: 'Storch, D., Šizling, A., Reif, J., Polechova, J., Šizlingová, E., & Gaston,
K. (2008). The quest for a null model for macroecological patterns: Geometry of
species distributions at multiple spatial scales. Ecology Letters. Wiley.
https://doi.org/10.1111/j.1461-0248.2008.01206.x'
chicago: 'Storch, D., A. Šizling, J. Reif, Jitka Polechova, E. Šizlingová, and K.
Gaston. “The Quest for a Null Model for Macroecological Patterns: Geometry of
Species Distributions at Multiple Spatial Scales.” Ecology Letters. Wiley,
2008. https://doi.org/10.1111/j.1461-0248.2008.01206.x.'
ieee: 'D. Storch, A. Šizling, J. Reif, J. Polechova, E. Šizlingová, and K. Gaston,
“The quest for a null model for macroecological patterns: Geometry of species
distributions at multiple spatial scales,” Ecology Letters, vol. 11, no.
8. Wiley, pp. 771–784, 2008.'
ista: 'Storch D, Šizling A, Reif J, Polechova J, Šizlingová E, Gaston K. 2008. The
quest for a null model for macroecological patterns: Geometry of species distributions
at multiple spatial scales. Ecology Letters. 11(8), 771–784.'
mla: 'Storch, D., et al. “The Quest for a Null Model for Macroecological Patterns:
Geometry of Species Distributions at Multiple Spatial Scales.” Ecology Letters,
vol. 11, no. 8, Wiley, 2008, pp. 771–84, doi:10.1111/j.1461-0248.2008.01206.x.'
short: D. Storch, A. Šizling, J. Reif, J. Polechova, E. Šizlingová, K. Gaston, Ecology
Letters 11 (2008) 771–784.
date_created: 2018-12-11T12:07:09Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2025-07-02T05:52:43Z
day: '01'
doi: 10.1111/j.1461-0248.2008.01206.x
extern: '1'
intvolume: ' 11'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 771 - 784
publication: Ecology Letters
publication_status: published
publisher: Wiley
publist_id: '1985'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The quest for a null model for macroecological patterns: Geometry of species
distributions at multiple spatial scales'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2008'
...
---
OA_type: free access
_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
article_type: original
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: 2026-05-29T08:31:06Z
day: '01'
doi: 10.1016/j.ydbio.2008.05.529
extern: '1'
external_id:
pmid:
- '18582857'
intvolume: ' 320'
issue: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 267 - 277
pmid: 1
publication: Developmental Biology
publication_identifier:
issn:
- 0012-1606
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 320
year: '2008'
...
---
OA_place: publisher
OA_type: free access
_id: '4150'
abstract:
- lang: eng
text: This study provides direct functional evidence that differential adhesion,
measurable as quantitative differences in tissue surface tension, influences spatial
positioning between zebrafish germ layer tissues. We show that embryonic ectodermal
and mesendodermal tissues generated by mRNA-overexpression behave on long-time
scales like immiscible fluids. When mixed in hanging drop culture, their cells
segregate into discrete phases with ectoderm adopting an internal position relative
to the mesendoderm. The position adopted directly correlates with differences
in tissue surface tension. We also show that germ layer tissues from untreated
embryos, when extirpated and placed in culture, adopt a configuration similar
to those of their mRNA-overexpressing counterparts. Down-regulating E-cadherin
expression in the ectoderm leads to reduced surface tension and results in phase
reversal with E-cadherin-depleted ectoderm cells now adopting an external position
relative to the mesendoderm. These results show that in vitro cell sorting of
zebrafish mesendoderm and ectoderm tissues is specified by tissue interfacial
tensions. We perform a mathematical analysis indicating that tissue interfacial
tension between actively motile cells contributes to the spatial organization
and dynamics of these zebrafish germ layers in vivo.
article_processing_charge: No
article_type: original
author:
- first_name: Eva
full_name: Schötz, Eva
last_name: Schötz
- first_name: Rebecca
full_name: Burdine, Rebecca
last_name: Burdine
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
- first_name: Malcolm
full_name: Steinberg, Malcolm
last_name: Steinberg
- 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: Ramsey
full_name: Foty, Ramsey
last_name: Foty
citation:
ama: Schötz E, Burdine R, Julicher F, Steinberg M, Heisenberg C-PJ, Foty R. Quantitative
differences in tissue surface tension influence zebrafish germ layer positioning.
HFSP Journal. 2008;2(1):42-56. doi:10.2976/1.2834817
apa: Schötz, E., Burdine, R., Julicher, F., Steinberg, M., Heisenberg, C.-P. J.,
& Foty, R. (2008). Quantitative differences in tissue surface tension influence
zebrafish germ layer positioning. HFSP Journal. HFSP Publishing. https://doi.org/10.2976/1.2834817
chicago: Schötz, Eva, Rebecca Burdine, Frank Julicher, Malcolm Steinberg, Carl-Philipp
J Heisenberg, and Ramsey Foty. “Quantitative Differences in Tissue Surface Tension
Influence Zebrafish Germ Layer Positioning.” HFSP Journal. HFSP Publishing,
2008. https://doi.org/10.2976/1.2834817.
ieee: E. Schötz, R. Burdine, F. Julicher, M. Steinberg, C.-P. J. Heisenberg, and
R. Foty, “Quantitative differences in tissue surface tension influence zebrafish
germ layer positioning,” HFSP Journal, vol. 2, no. 1. HFSP Publishing,
pp. 42–56, 2008.
ista: Schötz E, Burdine R, Julicher F, Steinberg M, Heisenberg C-PJ, Foty R. 2008.
Quantitative differences in tissue surface tension influence zebrafish germ layer
positioning. HFSP Journal. 2(1), 42–56.
mla: Schötz, Eva, et al. “Quantitative Differences in Tissue Surface Tension Influence
Zebrafish Germ Layer Positioning.” HFSP Journal, vol. 2, no. 1, HFSP Publishing,
2008, pp. 42–56, doi:10.2976/1.2834817.
short: E. Schötz, R. Burdine, F. Julicher, M. Steinberg, C.-P.J. Heisenberg, R.
Foty, HFSP Journal 2 (2008) 42–56.
date_created: 2018-12-11T12:07:14Z
date_published: 2008-02-01T00:00:00Z
date_updated: 2026-06-02T09:01:41Z
day: '01'
doi: 10.2976/1.2834817
extern: '1'
external_id:
pmid:
- '19404452'
intvolume: ' 2'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.2976/1.2834817
month: '02'
oa: 1
oa_version: Published Version
page: 42 - 56
pmid: 1
publication: HFSP Journal
publication_status: published
publisher: HFSP Publishing
publist_id: '1969'
status: public
title: Quantitative differences in tissue surface tension influence zebrafish germ
layer positioning
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2008'
...
---
OA_type: closed access
_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
article_type: original
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: 2026-05-29T07:25:53Z
day: '15'
doi: 10.1242/dev.022228
extern: '1'
external_id:
pmid:
- '18635607'
intvolume: ' 135'
issue: '16'
language:
- iso: eng
month: '08'
oa_version: None
page: 2807 - 2813
pmid: 1
publication: Development
publication_identifier:
eissn:
- 1477-9129
issn:
- 0950-1991
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 135
year: '2008'
...
---
OA_type: closed access
_id: '4180'
abstract:
- lang: eng
text: '(Figure Presented) The name''s Bond: Separated cells form membranous nanotubes
whose tips are tethered by adhesive bonds (see picture). The lifetime of receptor-ligand
interactions can be measured by using membrane nanotubes of living cells as constant
force actuators. Because the nanotubes are extruded from living cells at conditions
approaching the physiological, cellular processes can be both studied and utilized. '
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Krieg, Michael
last_name: Krieg
- first_name: Jonne
full_name: Helenius, Jonne
last_name: Helenius
- 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: Daniel
full_name: Mueller, Daniel
last_name: Mueller
citation:
ama: 'Krieg M, Helenius J, Heisenberg C-PJ, Mueller D. A Bond for a Lifetime: Employing
Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics. Angewandte
Chemie - International Edition. 2008;47(50):9775-9777. doi:10.1002/anie.200803552'
apa: 'Krieg, M., Helenius, J., Heisenberg, C.-P. J., & Mueller, D. (2008). A
Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine
Receptor-Ligand Kinetics. Angewandte Chemie - International Edition. Wiley-Blackwell.
https://doi.org/10.1002/anie.200803552'
chicago: 'Krieg, Michael, Jonne Helenius, Carl-Philipp J Heisenberg, and Daniel
Mueller. “A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells
to Determine Receptor-Ligand Kinetics.” Angewandte Chemie - International Edition.
Wiley-Blackwell, 2008. https://doi.org/10.1002/anie.200803552.'
ieee: 'M. Krieg, J. Helenius, C.-P. J. Heisenberg, and D. Mueller, “A Bond for a
Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand
Kinetics,” Angewandte Chemie - International Edition, vol. 47, no. 50.
Wiley-Blackwell, pp. 9775–9777, 2008.'
ista: 'Krieg M, Helenius J, Heisenberg C-PJ, Mueller D. 2008. A Bond for a Lifetime:
Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics.
Angewandte Chemie - International Edition. 47(50), 9775–9777.'
mla: 'Krieg, Michael, et al. “A Bond for a Lifetime: Employing Membrane Nanotubes
from Living Cells to Determine Receptor-Ligand Kinetics.” Angewandte Chemie
- International Edition, vol. 47, no. 50, Wiley-Blackwell, 2008, pp. 9775–77,
doi:10.1002/anie.200803552.'
short: M. Krieg, J. Helenius, C.-P.J. Heisenberg, D. Mueller, Angewandte Chemie
- International Edition 47 (2008) 9775–9777.
date_created: 2018-12-11T12:07:26Z
date_published: 2008-11-26T00:00:00Z
date_updated: 2026-05-29T07:20:40Z
day: '26'
doi: 10.1002/anie.200803552
extern: '1'
external_id:
pmid:
- '19035533'
intvolume: ' 47'
issue: '50'
language:
- iso: eng
month: '11'
oa_version: None
page: 9775 - 9777
pmid: 1
publication: Angewandte Chemie - International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1939'
status: public
title: 'A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine
Receptor-Ligand Kinetics'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 47
year: '2008'
...
---
OA_type: closed access
_id: '4181'
abstract:
- lang: eng
text: Understanding the factors that direct tissue organization during development
is one of the most fundamental goals in developmental biology. Various hypotheses
explain cell sorting and tissue organization on the basis of the adhesive and
mechanical properties of the constituent cells(1). However, validating these hypotheses
has been difficult due to the lack of appropriate tools to measure these parameters.
Here we use atomic force microscopy ( AFM) to quantify the adhesive and mechanical
properties of individual ectoderm, mesoderm and endoderm progenitor cells from
gastrulating zebrafish embryos. Combining these data with tissue self-assembly
in vitro and the sorting behaviour of progenitors in vivo, we have shown that
differential actomyosin-dependent cell-cortex tension, regulated by Nodal/ TGF
beta-signalling ( transforming growth factor beta), constitutes a key factor that
directs progenitor-cell sorting. These results demonstrate a previously unrecognized
role for Nodal-controlled cell-cortex tension in germ-layer organization during
gastrulation.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Michael
full_name: Krieg, Michael
last_name: Krieg
- first_name: Yohanna
full_name: Arboleda Estudillo, Yohanna
last_name: Arboleda Estudillo
- first_name: Pierre
full_name: Puech, Pierre
last_name: Puech
- first_name: Jos
full_name: Käfer, Jos
last_name: Käfer
- first_name: François
full_name: Graner, François
last_name: Graner
- first_name: Daniel
full_name: Mueller, Daniel
last_name: Mueller
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Krieg M, Arboleda Estudillo Y, Puech P, et al. Tensile forces govern germ-layer
organization in zebrafish. Nature Cell Biology. 2008;10(4):429-436. doi:10.1038/ncb1705
apa: Krieg, M., Arboleda Estudillo, Y., Puech, P., Käfer, J., Graner, F., Mueller,
D., & Heisenberg, C.-P. J. (2008). Tensile forces govern germ-layer organization
in zebrafish. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb1705
chicago: Krieg, Michael, Yohanna Arboleda Estudillo, Pierre Puech, Jos Käfer, François
Graner, Daniel Mueller, and Carl-Philipp J Heisenberg. “Tensile Forces Govern
Germ-Layer Organization in Zebrafish.” Nature Cell Biology. Nature Publishing
Group, 2008. https://doi.org/10.1038/ncb1705.
ieee: M. Krieg et al., “Tensile forces govern germ-layer organization in
zebrafish,” Nature Cell Biology, vol. 10, no. 4. Nature Publishing Group,
pp. 429–436, 2008.
ista: Krieg M, Arboleda Estudillo Y, Puech P, Käfer J, Graner F, Mueller D, Heisenberg
C-PJ. 2008. Tensile forces govern germ-layer organization in zebrafish. Nature
Cell Biology. 10(4), 429–436.
mla: Krieg, Michael, et al. “Tensile Forces Govern Germ-Layer Organization in Zebrafish.”
Nature Cell Biology, vol. 10, no. 4, Nature Publishing Group, 2008, pp.
429–36, doi:10.1038/ncb1705.
short: M. Krieg, Y. Arboleda Estudillo, P. Puech, J. Käfer, F. Graner, D. Mueller,
C.-P.J. Heisenberg, Nature Cell Biology 10 (2008) 429–436.
date_created: 2018-12-11T12:07:26Z
date_published: 2008-03-23T00:00:00Z
date_updated: 2026-05-29T07:13:59Z
day: '23'
doi: 10.1038/ncb1705
extern: '1'
external_id:
pmid:
- '18364700 '
intvolume: ' 10'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 429 - 436
pmid: 1
publication: Nature Cell Biology
publication_identifier:
eissn:
- 1476-4679
issn:
- 1465-7392
publication_status: published
publisher: Nature Publishing Group
publist_id: '1938'
status: public
title: Tensile forces govern germ-layer organization in zebrafish
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 10
year: '2008'
...
---
OA_place: repository
OA_type: green
_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
article_type: original
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: 2026-05-21T08:53:00Z
day: '15'
doi: 10.1242/dev.020396
extern: '1'
external_id:
pmid:
- '18701549'
intvolume: ' 135'
issue: '18'
language:
- iso: eng
month: '09'
oa_version: None
page: 3043 - 3051
pmid: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 135
year: '2008'
...
---
OA_place: repository
OA_type: green
_id: '4193'
abstract:
- lang: eng
text: The controlled adhesion of cells to each other and to the extracellular matrix
is crucial for tissue development and maintenance. Numerous assays have been developed
to quantify cell adhesion. Among these, the use of atomic force microscopy (AFM)
for single-cell force spectroscopy (SCFS) has recently been established. This
assay permits the adhesion of living cells to be studied in near-physiological
conditions. This implementation of AFM allows unrivaled spatial and temporal control
of cells, as well as highly quantitative force actuation and force measurement
that is sufficiently sensitive to characterize the interaction of single molecules.
Therefore, not only overall cell adhesion but also the properties of single adhesion-receptor-ligand
interactions can be studied. Here we describe current implementations and applications
of SCFS, as well as potential pitfalls, and outline how developments will provide
insight into the forces, energetics and kinetics of cell-adhesion processes.
article_processing_charge: No
article_type: comment
author:
- first_name: Jonne
full_name: Helenius, Jonne
last_name: Helenius
- 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: Hermann
full_name: Gaub, Hermann
last_name: Gaub
- first_name: Daniel
full_name: Mueller, Daniel
last_name: Mueller
citation:
ama: Helenius J, Heisenberg C-PJ, Gaub H, Mueller D. Single-cell force spectroscopy.
Journal of Cell Science. 2008;121(11):1785-1791. doi:10.1242/jcs.030999
apa: Helenius, J., Heisenberg, C.-P. J., Gaub, H., & Mueller, D. (2008). Single-cell
force spectroscopy. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.030999
chicago: Helenius, Jonne, Carl-Philipp J Heisenberg, Hermann Gaub, and Daniel Mueller.
“Single-Cell Force Spectroscopy.” Journal of Cell Science. Company of Biologists,
2008. https://doi.org/10.1242/jcs.030999.
ieee: J. Helenius, C.-P. J. Heisenberg, H. Gaub, and D. Mueller, “Single-cell force
spectroscopy,” Journal of Cell Science, vol. 121, no. 11. Company of Biologists,
pp. 1785–1791, 2008.
ista: Helenius J, Heisenberg C-PJ, Gaub H, Mueller D. 2008. Single-cell force spectroscopy.
Journal of Cell Science. 121(11), 1785–1791.
mla: Helenius, Jonne, et al. “Single-Cell Force Spectroscopy.” Journal of Cell
Science, vol. 121, no. 11, Company of Biologists, 2008, pp. 1785–91, doi:10.1242/jcs.030999.
short: J. Helenius, C.-P.J. Heisenberg, H. Gaub, D. Mueller, Journal of Cell Science
121 (2008) 1785–1791.
date_created: 2018-12-11T12:07:30Z
date_published: 2008-06-01T00:00:00Z
date_updated: 2026-05-28T14:11:54Z
day: '01'
doi: 10.1242/jcs.030999
extern: '1'
external_id:
pmid:
- '18492792'
intvolume: ' 121'
issue: '11'
language:
- iso: eng
month: '06'
oa_version: None
page: 1785 - 1791
pmid: 1
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: Company of Biologists
publist_id: '1924'
status: public
title: Single-cell force spectroscopy
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 121
year: '2008'
...
---
OA_type: closed access
_id: '4198'
abstract:
- lang: eng
text: Animal body plan arises during gastrulation and organogenesis by the coordination
of inductive events and cell movements. Several signaling pathways, such as BMP,
FGF, Hedgehog, Nodal, and Wnt have well-recognized instructive roles in cell fate
specification during vertebrate embryogenesis. Growing evidence indicates that
BMP, Nodal, and FGF signaling also regulate cell movements, and that they do so
through mechanisms distinct from those that specify cell fates. Moreover, pathways
controlling cell movements can also indirectly influence cell fate specification
by regulating dimensions and relative positions of interacting tissues. The current
challenge is to delineate the molecular mechanisms via which the major signaling
pathways regulate cell fate specification and movements, and how these two processes
are coordinated to ensure normal development.
article_processing_charge: No
article_type: review
author:
- 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: Lilianna
full_name: Solnica Krezel, Lilianna
last_name: Solnica Krezel
citation:
ama: Heisenberg C-PJ, Solnica Krezel L. Back and forth between cell fate specification
and movement during vertebrate gastrulation. Current Opinion in Genetics &
Development. 2008;18(4):311-316. doi:10.1016/j.gde.2008.07.011
apa: Heisenberg, C.-P. J., & Solnica Krezel, L. (2008). Back and forth between
cell fate specification and movement during vertebrate gastrulation. Current
Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2008.07.011
chicago: Heisenberg, Carl-Philipp J, and Lilianna Solnica Krezel. “Back and Forth
between Cell Fate Specification and Movement during Vertebrate Gastrulation.”
Current Opinion in Genetics & Development. Elsevier, 2008. https://doi.org/10.1016/j.gde.2008.07.011.
ieee: C.-P. J. Heisenberg and L. Solnica Krezel, “Back and forth between cell fate
specification and movement during vertebrate gastrulation,” Current Opinion
in Genetics & Development, vol. 18, no. 4. Elsevier, pp. 311–316, 2008.
ista: Heisenberg C-PJ, Solnica Krezel L. 2008. Back and forth between cell fate
specification and movement during vertebrate gastrulation. Current Opinion in
Genetics & Development. 18(4), 311–316.
mla: Heisenberg, Carl-Philipp J., and Lilianna Solnica Krezel. “Back and Forth between
Cell Fate Specification and Movement during Vertebrate Gastrulation.” Current
Opinion in Genetics & Development, vol. 18, no. 4, Elsevier, 2008, pp.
311–16, doi:10.1016/j.gde.2008.07.011.
short: C.-P.J. Heisenberg, L. Solnica Krezel, Current Opinion in Genetics &
Development 18 (2008) 311–316.
date_created: 2018-12-11T12:07:32Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2026-05-28T14:03:47Z
day: '01'
doi: 10.1016/j.gde.2008.07.011
extern: '1'
external_id:
pmid:
- '18721878'
intvolume: ' 18'
issue: '4'
language:
- iso: eng
month: '01'
oa_version: None
page: 311 - 316
pmid: 1
publication: Current Opinion in Genetics & Development
publication_identifier:
eissn:
- 1879-0380
issn:
- 0959-437X
publication_status: published
publisher: Elsevier
publist_id: '1918'
status: public
title: Back and forth between cell fate specification and movement during vertebrate
gastrulation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 18
year: '2008'
...
---
OA_type: closed access
_id: '4227'
abstract:
- lang: eng
text: 'Morphogen concentration gradients provide positional information by activating
target genes in a concentration-dependent manner. Recent reports show that the
gradient of the syncytial morphogen Bicoid seems to provide precise positional
information to determine target gene domains. For secreted morphogenetic ligands,
the precision of the gradients, the signal transduction and the reliability of
target gene expression domains have not been studied. Here we investigate these
issues for the TGF-beta-type morphogen Dpp. We first studied theoretically how
cell-to-cell variability in the source, the target tissue, or both, contribute
to the variations of the gradient. Fluctuations in the source and target generate
a local maximum of precision at a finite distance to the source. We then determined
experimentally in the wing epithelium: (1) the precision of the Dpp concentration
gradient; (2) the precision of the Dpp signaling activity profile; and (3) the
precision of activation of the Dpp target gene spalt. As captured by our theoretical
description, the Dpp gradient provides positional information with a maximal precision
a few cells away from the source. This maximal precision corresponds to a positional
uncertainly of about a single cell diameter. The precision of the Dpp gradient
accounts for the precision of the spalt expression range, implying that Dpp can
act as a morphogen to coarsely determine the expression pattern of target genes.'
article_processing_charge: No
article_type: original
author:
- first_name: Tobias
full_name: Bollenbach, Tobias
last_name: Bollenbach
- first_name: Periklis
full_name: Pantazis, Periklis
last_name: Pantazis
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Christian
full_name: Bokel, Christian
last_name: Bokel
- first_name: Marcos
full_name: González Gaitán, Marcos
last_name: González Gaitán
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
citation:
ama: Bollenbach T, Pantazis P, Kicheva A, Bokel C, González Gaitán M, Julicher F.
Precision of the Dpp gradient. Development. 2008;135(6):1137-1146. doi:10.1242/dev.012062
apa: Bollenbach, T., Pantazis, P., Kicheva, A., Bokel, C., González Gaitán, M.,
& Julicher, F. (2008). Precision of the Dpp gradient. Development.
Company of Biologists. https://doi.org/10.1242/dev.012062
chicago: Bollenbach, Tobias, Periklis Pantazis, Anna Kicheva, Christian Bokel, Marcos
González Gaitán, and Frank Julicher. “Precision of the Dpp Gradient.” Development.
Company of Biologists, 2008. https://doi.org/10.1242/dev.012062.
ieee: T. Bollenbach, P. Pantazis, A. Kicheva, C. Bokel, M. González Gaitán, and
F. Julicher, “Precision of the Dpp gradient,” Development, vol. 135, no.
6. Company of Biologists, pp. 1137–1146, 2008.
ista: Bollenbach T, Pantazis P, Kicheva A, Bokel C, González Gaitán M, Julicher
F. 2008. Precision of the Dpp gradient. Development. 135(6), 1137–1146.
mla: Bollenbach, Tobias, et al. “Precision of the Dpp Gradient.” Development,
vol. 135, no. 6, Company of Biologists, 2008, pp. 1137–46, doi:10.1242/dev.012062.
short: T. Bollenbach, P. Pantazis, A. Kicheva, C. Bokel, M. González Gaitán, F.
Julicher, Development 135 (2008) 1137–1146.
date_created: 2018-12-11T12:07:42Z
date_published: 2008-03-15T00:00:00Z
date_updated: 2026-05-28T13:59:30Z
day: '15'
doi: 10.1242/dev.012062
extern: '1'
external_id:
pmid:
- '18296653'
intvolume: ' 135'
issue: '6'
language:
- iso: eng
month: '03'
oa_version: None
page: 1137 - 1146
pmid: 1
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '1889'
status: public
title: Precision of the Dpp gradient
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 135
year: '2008'
...
---
OA_type: closed access
_id: '4244'
abstract:
- lang: eng
text: This paper presents a new approach to optimization of an energy-constrained
modulation scheme for wireless sensor networks by taking advantage of a novel
bio-inspired optimization algorithm. The algorithm is inspired by Wrightpsilas
shifting balance theory (SBT) of evolution in population genetics. The total energy
consumption of an energy-constrained modulation scheme is minimized by using the
new SBT-based optimization algorithm. The results obtained by this new algorithm
are compared with other popular optimization algorithms. Numerical experiments
are performed to demonstrate that the SBT-based algorithm could be used as an
efficient optimizer for solving the optimization problems arising from currently
emerging energy-efficient wireless sensor networks.
article_processing_charge: No
author:
- first_name: Erfu
full_name: Yang, Erfu
last_name: Yang
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Tughrul
full_name: Arslan, Tughrul
last_name: Arslan
- first_name: Ahmet
full_name: Erdogan, Ahmet
last_name: Erdogan
citation:
ama: 'Yang E, Barton NH, Arslan T, Erdogan A. A novel shifting balance theory-based
approach to optimization of an energy-constrained modulation scheme for wireless
sensor networks. In: IEEE; 2008:2749-2756. doi:10.1109/CEC.2008.4631167'
apa: 'Yang, E., Barton, N. H., Arslan, T., & Erdogan, A. (2008). A novel shifting
balance theory-based approach to optimization of an energy-constrained modulation
scheme for wireless sensor networks (pp. 2749–2756). Presented at the WCCI: IEEE
World Congress on Computational Intelligence, Hong Kong: IEEE. https://doi.org/10.1109/CEC.2008.4631167'
chicago: Yang, Erfu, Nicholas H Barton, Tughrul Arslan, and Ahmet Erdogan. “A Novel
Shifting Balance Theory-Based Approach to Optimization of an Energy-Constrained
Modulation Scheme for Wireless Sensor Networks,” 2749–56. IEEE, 2008. https://doi.org/10.1109/CEC.2008.4631167.
ieee: 'E. Yang, N. H. Barton, T. Arslan, and A. Erdogan, “A novel shifting balance
theory-based approach to optimization of an energy-constrained modulation scheme
for wireless sensor networks,” presented at the WCCI: IEEE World Congress on Computational
Intelligence, Hong Kong, 2008, pp. 2749–2756.'
ista: 'Yang E, Barton NH, Arslan T, Erdogan A. 2008. A novel shifting balance theory-based
approach to optimization of an energy-constrained modulation scheme for wireless
sensor networks. WCCI: IEEE World Congress on Computational Intelligence, 2749–2756.'
mla: Yang, Erfu, et al. A Novel Shifting Balance Theory-Based Approach to Optimization
of an Energy-Constrained Modulation Scheme for Wireless Sensor Networks. IEEE,
2008, pp. 2749–56, doi:10.1109/CEC.2008.4631167.
short: E. Yang, N.H. Barton, T. Arslan, A. Erdogan, in:, IEEE, 2008, pp. 2749–2756.
conference:
end_date: 2008-06-06
location: Hong Kong
name: 'WCCI: IEEE World Congress on Computational Intelligence'
start_date: 2008-06-01
date_created: 2018-12-11T12:07:49Z
date_published: 2008-09-23T00:00:00Z
date_updated: 2026-05-28T13:57:07Z
day: '23'
doi: 10.1109/CEC.2008.4631167
extern: '1'
language:
- iso: eng
month: '09'
oa_version: None
page: 2749 - 2756
publication_identifier:
isbn:
- '9781424418237'
publication_status: published
publisher: IEEE
publist_id: '1861'
status: public
title: A novel shifting balance theory-based approach to optimization of an energy-constrained
modulation scheme for wireless sensor networks
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2008'
...
---
OA_type: closed access
_id: '4245'
abstract:
- lang: eng
text: Sex allocation theory has proved extremely successful at predicting when individuals
should adjust the sex of their offspring in response to environmental conditions.
However, we know rather little about the underlying genetics of sex ratio or how
genetic architecture might constrain adaptive sex-ratio behavior. We examined
how mutation influenced genetic variation in the sex ratios produced by the parasitoid
wasp Nasonia vitripennis. In a mutation accumulation experiment, we determined
the mutability of sex ratio, and compared this with the amount of genetic variation
observed in natural populations. We found that the mutability (h2m) ranges from
0.001 to 0.002, similar to estimates for life-history traits in other organisms.
These estimates suggest one mutation every 5–60 generations, which shift the sex
ratio by approximately 0.01 (proportion males). In this and other studies, the
genetic variation in N. vitripennis sex ratio ranged from 0.02 to 0.17 (broad-sense
heritability, H2). If sex ratio is maintained by mutation–selection balance, a
higher genetic variance would be expected given our mutational parameters. Instead,
the observed genetic variance perhaps suggests additional selection against sex-ratio
mutations with deleterious effects on other fitness traits as well as sex ratio
(i.e., pleiotropy), as has been argued to be the case more generally.
article_processing_charge: No
article_type: original
author:
- first_name: Bart
full_name: Pannebakker, Bart
last_name: Pannebakker
- first_name: Daniel
full_name: Halligan, Daniel
last_name: Halligan
- first_name: K Tracy
full_name: Reynolds, K Tracy
last_name: Reynolds
- first_name: Gavin
full_name: Ballantyne, Gavin
last_name: Ballantyne
- first_name: David
full_name: Shuker, David
last_name: Shuker
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Stuart
full_name: West, Stuart
last_name: West
citation:
ama: Pannebakker B, Halligan D, Reynolds KT, et al. Effects of spontaneous mutation
accumulation on sex ratio traits. Evolution; International Journal of Organic
Evolution. 2008;62(8):1921-1935. doi:10.1111/j.1558-5646.2008.00434.x
apa: Pannebakker, B., Halligan, D., Reynolds, K. T., Ballantyne, G., Shuker, D.,
Barton, N. H., & West, S. (2008). Effects of spontaneous mutation accumulation
on sex ratio traits. Evolution; International Journal of Organic Evolution.
Oxford Academic. https://doi.org/10.1111/j.1558-5646.2008.00434.x
chicago: Pannebakker, Bart, Daniel Halligan, K Tracy Reynolds, Gavin Ballantyne,
David Shuker, Nicholas H Barton, and Stuart West. “Effects of Spontaneous Mutation
Accumulation on Sex Ratio Traits.” Evolution; International Journal of Organic
Evolution. Oxford Academic, 2008. https://doi.org/10.1111/j.1558-5646.2008.00434.x.
ieee: B. Pannebakker et al., “Effects of spontaneous mutation accumulation
on sex ratio traits,” Evolution; International Journal of Organic Evolution,
vol. 62, no. 8. Oxford Academic, pp. 1921–1935, 2008.
ista: Pannebakker B, Halligan D, Reynolds KT, Ballantyne G, Shuker D, Barton NH,
West S. 2008. Effects of spontaneous mutation accumulation on sex ratio traits.
Evolution; International Journal of Organic Evolution. 62(8), 1921–1935.
mla: Pannebakker, Bart, et al. “Effects of Spontaneous Mutation Accumulation on
Sex Ratio Traits.” Evolution; International Journal of Organic Evolution,
vol. 62, no. 8, Oxford Academic, 2008, pp. 1921–35, doi:10.1111/j.1558-5646.2008.00434.x.
short: B. Pannebakker, D. Halligan, K.T. Reynolds, G. Ballantyne, D. Shuker, N.H.
Barton, S. West, Evolution; International Journal of Organic Evolution 62 (2008)
1921–1935.
date_created: 2018-12-11T12:07:49Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2026-05-28T13:46:48Z
day: '01'
doi: 10.1111/j.1558-5646.2008.00434.x
extern: '1'
external_id:
pmid:
- '18522711'
intvolume: ' 62'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 1921 - 1935
pmid: 1
publication: Evolution; International Journal of Organic Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Oxford Academic
publist_id: '1860'
status: public
title: Effects of spontaneous mutation accumulation on sex ratio traits
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 62
year: '2008'
...
---
_id: '1749'
abstract:
- lang: eng
text: Scanning probe microscopy; Semiconductor quantum dots; Composition gradients;
Composition profiles; Nanotomography; Single quantum dots; Strained sige/si; Three-dimensional
(3D); Wet-chemical etchings; X-ray scattering measurements; quantum dot; methodology;
nanotechnology; optical tomography; scanning probe microscopy; three dimensional
imaging; Imaging, Three-Dimensional; Materials Testing; Microscopy, Scanning Probe;
Nanotechnology; Quantum Dots; Tomography,
acknowledgement: This work was supported by the BMBF (No. 03N8711) and the EU project
D-DotFET (No. 012150)
author:
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Ângelo
full_name: Malachias, Ângelo S
last_name: Malachias
- first_name: Tsvetelina
full_name: Merdzhanova, Tsvetelina
last_name: Merdzhanova
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
- first_name: Till
full_name: Metzger, Till H
last_name: Metzger
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
citation:
ama: Rastelli A, Stoffel M, Malachias Â, et al. Three-dimensional composition profiles
of single quantum dots determined by scanning-probe-microscopy-based nanotomography.
Nano Letters. 2008;8(5):1404-1409. doi:10.1021/nl080290y
apa: Rastelli, A., Stoffel, M., Malachias, Â., Merdzhanova, T., Katsaros, G., Kern,
K., … Schmidt, O. (2008). Three-dimensional composition profiles of single quantum
dots determined by scanning-probe-microscopy-based nanotomography. Nano Letters.
American Chemical Society. https://doi.org/10.1021/nl080290y
chicago: Rastelli, Armando, Mathieu Stoffel, Ângelo Malachias, Tsvetelina Merdzhanova,
Georgios Katsaros, Klaus Kern, Till Metzger, and Oliver Schmidt. “Three-Dimensional
Composition Profiles of Single Quantum Dots Determined by Scanning-Probe-Microscopy-Based
Nanotomography.” Nano Letters. American Chemical Society, 2008. https://doi.org/10.1021/nl080290y.
ieee: A. Rastelli et al., “Three-dimensional composition profiles of single
quantum dots determined by scanning-probe-microscopy-based nanotomography,” Nano
Letters, vol. 8, no. 5. American Chemical Society, pp. 1404–1409, 2008.
ista: Rastelli A, Stoffel M, Malachias Â, Merdzhanova T, Katsaros G, Kern K, Metzger
T, Schmidt O. 2008. Three-dimensional composition profiles of single quantum dots
determined by scanning-probe-microscopy-based nanotomography. Nano Letters. 8(5),
1404–1409.
mla: Rastelli, Armando, et al. “Three-Dimensional Composition Profiles of Single
Quantum Dots Determined by Scanning-Probe-Microscopy-Based Nanotomography.” Nano
Letters, vol. 8, no. 5, American Chemical Society, 2008, pp. 1404–09, doi:10.1021/nl080290y.
short: A. Rastelli, M. Stoffel, Â. Malachias, T. Merdzhanova, G. Katsaros, K. Kern,
T. Metzger, O. Schmidt, Nano Letters 8 (2008) 1404–1409.
date_created: 2018-12-11T11:53:48Z
date_published: 2008-05-01T00:00:00Z
date_updated: 2021-01-12T06:52:57Z
day: '01'
doi: 10.1021/nl080290y
extern: 1
intvolume: ' 8'
issue: '5'
month: '05'
page: 1404 - 1409
publication: Nano Letters
publication_status: published
publisher: American Chemical Society
publist_id: '5374'
quality_controlled: 0
status: public
title: Three-dimensional composition profiles of single quantum dots determined by
scanning-probe-microscopy-based nanotomography
type: journal_article
volume: 8
year: '2008'
...
---
_id: '1751'
abstract:
- lang: eng
text: When strained Stranski-Krastanow islands are used as "self-assembled
quantum dots," a key goal is to control the island position. Here we show
that nanoscale grooves can control the nucleation of epitaxial Ge islands on Si(001),
and can drive lateral motion of existing islands onto the grooves, even when the
grooves are very narrow and shallow compared to the islands. A position centered
on the groove minimizes energy. We use as prototype grooves the trenches which
form naturally around islands. During coarsening, the shrinking islands move laterally
to sit directly astride that trench. In subsequent growth, we demonstrate that
islands nucleate on the "empty trenches" which remain on the surface
after complete dissolution of the original islands.
author:
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Jerry
full_name: Tersoff, Jerry
last_name: Tersoff
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: P
full_name: Acosta-Diaz, P
last_name: Acosta Diaz
- first_name: Gouranga
full_name: Kar, Gouranga S
last_name: Kar
- first_name: Giovanni
full_name: Costantini, Giovanni
last_name: Costantini
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
citation:
ama: Katsaros G, Tersoff J, Stoffel M, et al. Positioning of strained islands by
interaction with surface nanogrooves. Physical Review Letters. 2008;101(9).
doi:10.1103/PhysRevLett.101.096103
apa: Katsaros, G., Tersoff, J., Stoffel, M., Rastelli, A., Acosta Diaz, P., Kar,
G., … Kern, K. (2008). Positioning of strained islands by interaction with surface
nanogrooves. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.101.096103
chicago: Katsaros, Georgios, Jerry Tersoff, Mathieu Stoffel, Armando Rastelli, P
Acosta Diaz, Gouranga Kar, Giovanni Costantini, Oliver Schmidt, and Klaus Kern.
“Positioning of Strained Islands by Interaction with Surface Nanogrooves.” Physical
Review Letters. American Physical Society, 2008. https://doi.org/10.1103/PhysRevLett.101.096103.
ieee: G. Katsaros et al., “Positioning of strained islands by interaction
with surface nanogrooves,” Physical Review Letters, vol. 101, no. 9. American
Physical Society, 2008.
ista: Katsaros G, Tersoff J, Stoffel M, Rastelli A, Acosta Diaz P, Kar G, Costantini
G, Schmidt O, Kern K. 2008. Positioning of strained islands by interaction with
surface nanogrooves. Physical Review Letters. 101(9).
mla: Katsaros, Georgios, et al. “Positioning of Strained Islands by Interaction
with Surface Nanogrooves.” Physical Review Letters, vol. 101, no. 9, American
Physical Society, 2008, doi:10.1103/PhysRevLett.101.096103.
short: G. Katsaros, J. Tersoff, M. Stoffel, A. Rastelli, P. Acosta Diaz, G. Kar,
G. Costantini, O. Schmidt, K. Kern, Physical Review Letters 101 (2008).
date_created: 2018-12-11T11:53:49Z
date_published: 2008-08-29T00:00:00Z
date_updated: 2021-01-12T06:52:58Z
day: '29'
doi: 10.1103/PhysRevLett.101.096103
extern: 1
intvolume: ' 101'
issue: '9'
month: '08'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5373'
quality_controlled: 0
status: public
title: Positioning of strained islands by interaction with surface nanogrooves
type: journal_article
volume: 101
year: '2008'
...
---
_id: '1763'
abstract:
- lang: eng
text: The field of cavity quantum electrodynamics (QED), traditionally studied in
atomic systems, has gained new momentum by recent reports of quantum optical experiments
with solid-state semiconducting and superconducting systems. In cavity QED, the
observation of the vacuum Rabi mode splitting is used to investigate the nature
of matter-light interaction at a quantum-mechanical level. However, this effect
can, at least in principle, be explained classically as the normal mode splitting
of two coupled linear oscillators. It has been suggested that an observation of
the scaling of the resonant atom-photon coupling strength in the Jaynes-Cummings
energy ladder with the square root of photon number n is sufficient to prove that
the system is quantum mechanical in nature. Here we report a direct spectroscopic
observation of this characteristic quantum nonlinearity. Measuring the photonic
degree of freedom of the coupled system, our measurements provide unambiguous
spectroscopic evidence for the quantum nature of the resonant atom-field interaction
in cavity QED. We explore atom-photon superposition states involving up to two
photons, using a spectroscopic pump and probe technique. The experiments have
been performed in a circuit QED set-up, in which very strong coupling is realized
by the large dipole coupling strength and the long coherence time of a superconducting
qubit embedded in a high-quality on-chip microwave cavity. Circuit QED systems
also provide a natural quantum interface between flying qubits (photons) and stationary
qubits for applications in quantum information processing and communication.
acknowledgement: This work was supported by SNF and ETHZ. P.J.L. was supported by
the EU with an MC-EIF. A.B. was supported by NSERC, CIFAR and FQRNT
author:
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: M
full_name: Göppl, M
last_name: Göppl
- first_name: Matthias
full_name: Baur, Matthias P
last_name: Baur
- first_name: R
full_name: Bianchetti, R
last_name: Bianchetti
- first_name: Peter
full_name: Leek, Peter J
last_name: Leek
- first_name: Alexandre
full_name: Blais, Alexandre
last_name: Blais
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Fink JM, Göppl M, Baur M, et al. Climbing the Jaynes-Cummings ladder and observing
its √n nonlinearity in a cavity QED system. Nature. 2008;454(7202):315-318.
doi:10.1038/nature07112
apa: Fink, J. M., Göppl, M., Baur, M., Bianchetti, R., Leek, P., Blais, A., &
Wallraff, A. (2008). Climbing the Jaynes-Cummings ladder and observing its √n
nonlinearity in a cavity QED system. Nature. Nature Publishing Group. https://doi.org/10.1038/nature07112
chicago: Fink, Johannes M, M Göppl, Matthias Baur, R Bianchetti, Peter Leek, Alexandre
Blais, and Andreas Wallraff. “Climbing the Jaynes-Cummings Ladder and Observing
Its √n Nonlinearity in a Cavity QED System.” Nature. Nature Publishing
Group, 2008. https://doi.org/10.1038/nature07112.
ieee: J. M. Fink et al., “Climbing the Jaynes-Cummings ladder and observing
its √n nonlinearity in a cavity QED system,” Nature, vol. 454, no. 7202.
Nature Publishing Group, pp. 315–318, 2008.
ista: Fink JM, Göppl M, Baur M, Bianchetti R, Leek P, Blais A, Wallraff A. 2008.
Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity
QED system. Nature. 454(7202), 315–318.
mla: Fink, Johannes M., et al. “Climbing the Jaynes-Cummings Ladder and Observing
Its √n Nonlinearity in a Cavity QED System.” Nature, vol. 454, no. 7202,
Nature Publishing Group, 2008, pp. 315–18, doi:10.1038/nature07112.
short: J.M. Fink, M. Göppl, M. Baur, R. Bianchetti, P. Leek, A. Blais, A. Wallraff,
Nature 454 (2008) 315–318.
date_created: 2018-12-11T11:53:53Z
date_published: 2008-07-17T00:00:00Z
date_updated: 2021-01-12T06:53:03Z
day: '17'
doi: 10.1038/nature07112
extern: 1
intvolume: ' 454'
issue: '7202'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0902.1827
month: '07'
oa: 1
page: 315 - 318
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5358'
quality_controlled: 0
status: public
title: Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a
cavity QED system
type: journal_article
volume: 454
year: '2008'
...
---
_id: '1764'
abstract:
- lang: eng
text: Quantum theory predicts that empty space is not truly empty. Even in the absence
of any particles or radiation, in pure vacuum, virtual particles are constantly
created and annihilated. In an electromagnetic field, the presence of virtual
photons manifests itself as a small renormalization of the energy of a quantum
system, known as the Lamb shift. We present an experimental observation of the
Lamb shift in a solid-state system. The strong dispersive coupling of a superconducting
electronic circuit acting as a quantum bit (qubit) to the vacuum field in a transmission-line
resonator leads to measurable Lamb shifts of up to 1.4% of the qubit transition
frequency. The qubit is also observed to couple more strongly to the vacuum field
than to a single photon inside the cavity, an effect that is explained by taking
into account the limited anharmonicity of the higher excited qubit states.
acknowledgement: This work was supported by the Swiss National Science Foundation
and ETHZ. P.J.L. was supported by the European Commission with a Marie Curie Intra-European
Fellowship. A.B. was supported by 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
author:
- first_name: A
full_name: Fragner, A
last_name: Fragner
- first_name: M
full_name: Göppl, M
last_name: Göppl
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Matthias
full_name: Baur, Matthias P
last_name: Baur
- first_name: R
full_name: Bianchetti, R
last_name: Bianchetti
- first_name: Peter
full_name: Leek, Peter J
last_name: Leek
- first_name: Alexandre
full_name: Blais, Alexandre
last_name: Blais
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Fragner A, Göppl M, Fink JM, et al. Resolving vacuum fluctuations in an electrical
circuit by measuring the lamb shift. Science. 2008;322(5906):1357-1360.
doi:10.1126/science.1164482
apa: Fragner, A., Göppl, M., Fink, J. M., Baur, M., Bianchetti, R., Leek, P., …
Wallraff, A. (2008). Resolving vacuum fluctuations in an electrical circuit by
measuring the lamb shift. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1164482
chicago: Fragner, A, M Göppl, Johannes M Fink, Matthias Baur, R Bianchetti, Peter
Leek, Alexandre Blais, and Andreas Wallraff. “Resolving Vacuum Fluctuations in
an Electrical Circuit by Measuring the Lamb Shift.” Science. American Association
for the Advancement of Science, 2008. https://doi.org/10.1126/science.1164482.
ieee: A. Fragner et al., “Resolving vacuum fluctuations in an electrical
circuit by measuring the lamb shift,” Science, vol. 322, no. 5906. American
Association for the Advancement of Science, pp. 1357–1360, 2008.
ista: Fragner A, Göppl M, Fink JM, Baur M, Bianchetti R, Leek P, Blais A, Wallraff
A. 2008. Resolving vacuum fluctuations in an electrical circuit by measuring the
lamb shift. Science. 322(5906), 1357–1360.
mla: Fragner, A., et al. “Resolving Vacuum Fluctuations in an Electrical Circuit
by Measuring the Lamb Shift.” Science, vol. 322, no. 5906, American Association
for the Advancement of Science, 2008, pp. 1357–60, doi:10.1126/science.1164482.
short: A. Fragner, M. Göppl, J.M. Fink, M. Baur, R. Bianchetti, P. Leek, A. Blais,
A. Wallraff, Science 322 (2008) 1357–1360.
date_created: 2018-12-11T11:53:53Z
date_published: 2008-11-28T00:00:00Z
date_updated: 2021-01-12T06:53:03Z
day: '28'
doi: 10.1126/science.1164482
extern: 1
intvolume: ' 322'
issue: '5906'
month: '11'
page: 1357 - 1360
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5357'
quality_controlled: 0
status: public
title: Resolving vacuum fluctuations in an electrical circuit by measuring the lamb
shift
type: journal_article
volume: 322
year: '2008'
...
---
_id: '1765'
abstract:
- lang: eng
text: High quality on-chip microwave resonators have recently found prominent new
applications in quantum optics and quantum information processing experiments
with superconducting electronic circuits, a field now known as circuit quantum
electrodynamics (QED). They are also used as single photon detectors and parametric
amplifiers. Here we analyze the physical properties of coplanar waveguide resonators
and their relation to the materials properties for use in circuit QED. We have
designed and fabricated resonators with fundamental frequencies from 2 to 9 GHz
and quality factors ranging from a few hundreds to a several hundred thousands
controlled by appropriately designed input and output coupling capacitors. The
microwave transmission spectra measured at temperatures of 20 mK are shown to
be in good agreement with theoretical lumped element and distributed element transmission
matrix models. In particular, the experimentally determined resonance frequencies,
quality factors, and insertion losses are fully and consistently explained by
the two models for all measured devices. The high level of control and flexibility
in design renders these resonators ideal for storing and manipulating quantum
electromagnetic fields in integrated superconducting electronic circuits.
acknowledgement: This work was supported by Swiss National Fund (SNF) and ETH Zürich.
P.J.L. was supported by the EC with a MC-EIF
author:
- first_name: M
full_name: Göppl, M
last_name: Göppl
- first_name: A
full_name: Fragner, A
last_name: Fragner
- first_name: Matthias
full_name: Baur, Matthias P
last_name: Baur
- first_name: R
full_name: Bianchetti, R
last_name: Bianchetti
- first_name: Stefan
full_name: Filipp, Stefan
last_name: Filipp
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Peter
full_name: Leek, Peter J
last_name: Leek
- first_name: G
full_name: Puebla, G
last_name: Puebla
- first_name: L.
full_name: Steffen, L. Kraig
last_name: Steffen
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Göppl M, Fragner A, Baur M, et al. Coplanar waveguide resonators for circuit
quantum electrodynamics. Journal of Applied Physics. 2008;104(11). doi:10.1063/1.3010859
apa: Göppl, M., Fragner, A., Baur, M., Bianchetti, R., Filipp, S., Fink, J. M.,
… Wallraff, A. (2008). Coplanar waveguide resonators for circuit quantum electrodynamics.
Journal of Applied Physics. American Institute of Physics. https://doi.org/10.1063/1.3010859
chicago: Göppl, M, A Fragner, Matthias Baur, R Bianchetti, Stefan Filipp, Johannes
M Fink, Peter Leek, G Puebla, L. Steffen, and Andreas Wallraff. “Coplanar Waveguide
Resonators for Circuit Quantum Electrodynamics.” Journal of Applied Physics.
American Institute of Physics, 2008. https://doi.org/10.1063/1.3010859.
ieee: M. Göppl et al., “Coplanar waveguide resonators for circuit quantum
electrodynamics,” Journal of Applied Physics, vol. 104, no. 11. American
Institute of Physics, 2008.
ista: Göppl M, Fragner A, Baur M, Bianchetti R, Filipp S, Fink JM, Leek P, Puebla
G, Steffen L, Wallraff A. 2008. Coplanar waveguide resonators for circuit quantum
electrodynamics. Journal of Applied Physics. 104(11).
mla: Göppl, M., et al. “Coplanar Waveguide Resonators for Circuit Quantum Electrodynamics.”
Journal of Applied Physics, vol. 104, no. 11, American Institute of Physics,
2008, doi:10.1063/1.3010859.
short: M. Göppl, A. Fragner, M. Baur, R. Bianchetti, S. Filipp, J.M. Fink, P. Leek,
G. Puebla, L. Steffen, A. Wallraff, Journal of Applied Physics 104 (2008).
date_created: 2018-12-11T11:53:53Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:03Z
day: '01'
doi: 10.1063/1.3010859
extern: 1
intvolume: ' 104'
issue: '11'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0807.4094
month: '01'
oa: 1
publication: Journal of Applied Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5355'
quality_controlled: 0
status: public
title: Coplanar waveguide resonators for circuit quantum electrodynamics
type: journal_article
volume: 104
year: '2008'
...
---
_id: '17721'
abstract:
- lang: eng
text: High-redshift quasars (z >~ 6) drive ionization fronts into the intergalactic
medium (IGM). If the thickness of the front can be measured, it can provide a
novel constraint on the ionizing spectral energy distribution (SED). Here we follow
the propagation of an I-front into a uniform IGM, and compute its thickness for
a range of possible quasar spectra and ages. We also explore the effects of uniform
and non-uniform ionizing backgrounds. We find that even for hard spectra, the
fronts are initially thin, with a thickness much smaller than the mean free path
of ionizing photons, but the thickness increases as the front approaches equilibrium
in 10^8 - 10^9 years, and can eventually significantly exceed simple estimates
based on the mean free path. With a high intrinsic hydrogen column density obscuring
the source (log(N_H/cm^-2) >~ 19.2) or a hard power-law spectrum combined with
some obscuration (e.g. dlog(F_\nu)/dlog(\nu) >~ -1.2 at log(N_H/cm^-2) >~ 18.0),
the thickness of the front exceeds ~1 physical Mpc and may be measurable from
the morphology of its redshifted 21cm signal. We find that the highly ionized
inner part of the front, which may be probed by Lyman line absorption spectra,
remains sharp for bright quasars unless a large obscuring column (log(N_H/cm^-2)
>~ 19.2) removes most of their ionizing photons up to ~40 eV. For obscured sources
with log(N_H/cm^-2) >~ 19.8, embedded in a significantly neutral IGM, the black
Lyman-alpha trough (where the neutral fraction is ~10^-3) underestimates the size
of the HII region by a factor of >~4.
article_processing_charge: No
article_type: original
author:
- first_name: R. H.
full_name: Kramer, R. H.
last_name: Kramer
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
citation:
ama: Kramer RH, Haiman Z. The thickness of high-redshift quasar ionization fronts
as a constraint on the ionizing spectral energy distribution. Monthly Notices
of the Royal Astronomical Society. 2008;385(3):1561-1575. doi:10.1111/j.1365-2966.2008.12945.x
apa: Kramer, R. H., & Haiman, Z. (2008). The thickness of high-redshift quasar
ionization fronts as a constraint on the ionizing spectral energy distribution.
Monthly Notices of the Royal Astronomical Society. Oxford University Press.
https://doi.org/10.1111/j.1365-2966.2008.12945.x
chicago: Kramer, R. H., and Zoltán Haiman. “The Thickness of High-Redshift Quasar
Ionization Fronts as a Constraint on the Ionizing Spectral Energy Distribution.”
Monthly Notices of the Royal Astronomical Society. Oxford University Press,
2008. https://doi.org/10.1111/j.1365-2966.2008.12945.x.
ieee: R. H. Kramer and Z. Haiman, “The thickness of high-redshift quasar ionization
fronts as a constraint on the ionizing spectral energy distribution,” Monthly
Notices of the Royal Astronomical Society, vol. 385, no. 3. Oxford University
Press, pp. 1561–1575, 2008.
ista: Kramer RH, Haiman Z. 2008. The thickness of high-redshift quasar ionization
fronts as a constraint on the ionizing spectral energy distribution. Monthly Notices
of the Royal Astronomical Society. 385(3), 1561–1575.
mla: Kramer, R. H., and Zoltán Haiman. “The Thickness of High-Redshift Quasar Ionization
Fronts as a Constraint on the Ionizing Spectral Energy Distribution.” Monthly
Notices of the Royal Astronomical Society, vol. 385, no. 3, Oxford University
Press, 2008, pp. 1561–75, doi:10.1111/j.1365-2966.2008.12945.x.
short: R.H. Kramer, Z. Haiman, Monthly Notices of the Royal Astronomical Society
385 (2008) 1561–1575.
date_created: 2024-09-06T09:09:01Z
date_published: 2008-03-13T00:00:00Z
date_updated: 2024-09-25T13:54:14Z
day: '13'
doi: 10.1111/j.1365-2966.2008.12945.x
extern: '1'
intvolume: ' 385'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/j.1365-2966.2008.12945.x
month: '03'
oa: 1
oa_version: Published Version
page: 1561-1575
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
issn:
- 0035-8711
- 1365-2966
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The thickness of high-redshift quasar ionization fronts as a constraint on
the ionizing spectral energy distribution
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 385
year: '2008'
...