---
_id: '3388'
abstract:
- lang: eng
text: 'Background: Fragmentation of terrestrial ecosystems has had detrimental effects
on metapopulations of habitat specialists. Maculinea butterflies have been particularly
affected because of their specialized lifecycles, requiring both specific food-plants
and host-ants. However, the interaction between dispersal, effective population
size, and long-term genetic erosion of these endangered butterflies remains unknown.
Using non-destructive sampling, we investigated the genetic diversity of the last
extant population of M. arion in Denmark, which experienced critically low numbers
in the 1980s. Results: Using nine microsatellite markers, we show that the population
is genetically impoverished compared to nearby populations in Sweden, but less
so than monitoring programs suggested. Ten additional short repeat microsatellites
were used to reconstruct changes in genetic diversity and population structure
over the last 77 years from museum specimens. We also tested amplification efficiency
in such historical samples as a function of repeat length and sample age. Low
population numbers in the 1980s did not affect genetic diversity, but considerable
turnover of alleles has characterized this population throughout the time-span
of our analysis. Conclusions: Our results suggest that M. arion is less sensitive
to genetic erosion via population bottlenecks than previously thought, and that
managing clusters of high quality habitat may be key for long-term conservation.'
article_number: '201'
article_processing_charge: No
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: Per
full_name: Nielsen, Per
last_name: Nielsen
- first_name: Jacobus
full_name: Boomsma, Jacobus
last_name: Boomsma
- first_name: David
full_name: Nash, David
last_name: Nash
citation:
ama: Ugelvig LV, Nielsen P, Boomsma J, Nash D. Reconstructing eight decades of genetic
variation in an isolated Danish population of the large blue butterfly Maculinea
arion. BMC Evolutionary Biology. 2011;11(201). doi:10.1186/1471-2148-11-201
apa: Ugelvig, L. V., Nielsen, P., Boomsma, J., & Nash, D. (2011). Reconstructing
eight decades of genetic variation in an isolated Danish population of the large
blue butterfly Maculinea arion. BMC Evolutionary Biology. BioMed Central.
https://doi.org/10.1186/1471-2148-11-201
chicago: Ugelvig, Line V, Per Nielsen, Jacobus Boomsma, and David Nash. “Reconstructing
Eight Decades of Genetic Variation in an Isolated Danish Population of the Large
Blue Butterfly Maculinea Arion.” BMC Evolutionary Biology. BioMed Central,
2011. https://doi.org/10.1186/1471-2148-11-201.
ieee: L. V. Ugelvig, P. Nielsen, J. Boomsma, and D. Nash, “Reconstructing eight
decades of genetic variation in an isolated Danish population of the large blue
butterfly Maculinea arion,” BMC Evolutionary Biology, vol. 11, no. 201.
BioMed Central, 2011.
ista: Ugelvig LV, Nielsen P, Boomsma J, Nash D. 2011. Reconstructing eight decades
of genetic variation in an isolated Danish population of the large blue butterfly
Maculinea arion. BMC Evolutionary Biology. 11(201), 201.
mla: Ugelvig, Line V., et al. “Reconstructing Eight Decades of Genetic Variation
in an Isolated Danish Population of the Large Blue Butterfly Maculinea Arion.”
BMC Evolutionary Biology, vol. 11, no. 201, 201, BioMed Central, 2011,
doi:10.1186/1471-2148-11-201.
short: L.V. Ugelvig, P. Nielsen, J. Boomsma, D. Nash, BMC Evolutionary Biology 11
(2011).
corr_author: '1'
date_created: 2018-12-11T12:03:03Z
date_published: 2011-07-11T00:00:00Z
date_updated: 2025-09-30T08:46:17Z
day: '11'
ddc:
- '576'
department:
- _id: SyCr
doi: 10.1186/1471-2148-11-201
external_id:
isi:
- '000293275300002'
file:
- access_level: open_access
checksum: 9ebfed0740f1fa071d02ec32c2b8c17f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:18Z
date_updated: 2020-07-14T12:46:11Z
file_id: '5069'
file_name: IST-2015-371-v1+1_1471-2148-11-201.pdf
file_size: 2166556
relation: main_file
file_date_updated: 2020-07-14T12:46:11Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '201'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: BMC Evolutionary Biology
publication_status: published
publisher: BioMed Central
publist_id: '3220'
pubrep_id: '371'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reconstructing eight decades of genetic variation in an isolated Danish population
of the large blue butterfly Maculinea arion
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 11
year: '2011'
...
---
_id: '3389'
abstract:
- lang: eng
text: Kernel canonical correlation analysis (KCCA) is a general technique for subspace
learning that incorporates principal components analysis (PCA) and Fisher linear
discriminant analysis (LDA) as special cases. By finding directions that maximize
correlation, KCCA learns representations that are more closely tied to the underlying
process that generates the data and can ignore high-variance noise directions.
However, for data where acquisition in one or more modalities is expensive or
otherwise limited, KCCA may suffer from small sample effects. We propose to use
semi-supervised Laplacian regularization to utilize data that are present in only
one modality. This approach is able to find highly correlated directions that
also lie along the data manifold, resulting in a more robust estimate of correlated
subspaces. Functional magnetic resonance imaging (fMRI) acquired data are naturally
amenable to subspace techniques as data are well aligned. fMRI data of the human
brain are a particularly interesting candidate. In this study we implemented various
supervised and semi-supervised versions of KCCA on human fMRI data, with regression
to single and multi-variate labels (corresponding to video content subjects viewed
during the image acquisition). In each variate condition, the semi-supervised
variants of KCCA performed better than the supervised variants, including a supervised
variant with Laplacian regularization. We additionally analyze the weights learned
by the regression in order to infer brain regions that are important to different
types of visual processing.
acknowledgement: The research leading to these results has received funding from the
European Research Council under the European Community’s Seventh Framework Programme
(FP7/2007-2013)/ERC Grant Agreement No. 228180. This work was funded in part by
the EC project CLASS, IST 027978, and the PASCAL2 network of excellence, IST 2002-506778.
article_processing_charge: No
author:
- first_name: Matthew
full_name: Blaschko, Matthew
last_name: Blaschko
- first_name: Jacquelyn
full_name: Shelton, Jacquelyn
last_name: Shelton
- first_name: Andreas
full_name: Bartels, Andreas
last_name: Bartels
- first_name: Christoph
full_name: Lampert, Christoph
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, Shelton J, Bartels A, Lampert C, Gretton A. Semi supervised kernel
canonical correlation analysis with application to human fMRI. Pattern Recognition
Letters. 2011;32(11):1572-1583. doi:10.1016/j.patrec.2011.02.011
apa: Blaschko, M., Shelton, J., Bartels, A., Lampert, C., & Gretton, A. (2011).
Semi supervised kernel canonical correlation analysis with application to human
fMRI. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2011.02.011
chicago: Blaschko, Matthew, Jacquelyn Shelton, Andreas Bartels, Christoph Lampert,
and Arthur Gretton. “Semi Supervised Kernel Canonical Correlation Analysis with
Application to Human FMRI.” Pattern Recognition Letters. Elsevier, 2011.
https://doi.org/10.1016/j.patrec.2011.02.011.
ieee: M. Blaschko, J. Shelton, A. Bartels, C. Lampert, and A. Gretton, “Semi supervised
kernel canonical correlation analysis with application to human fMRI,” Pattern
Recognition Letters, vol. 32, no. 11. Elsevier, pp. 1572–1583, 2011.
ista: Blaschko M, Shelton J, Bartels A, Lampert C, Gretton A. 2011. Semi supervised
kernel canonical correlation analysis with application to human fMRI. Pattern
Recognition Letters. 32(11), 1572–1583.
mla: Blaschko, Matthew, et al. “Semi Supervised Kernel Canonical Correlation Analysis
with Application to Human FMRI.” Pattern Recognition Letters, vol. 32,
no. 11, Elsevier, 2011, pp. 1572–83, doi:10.1016/j.patrec.2011.02.011.
short: M. Blaschko, J. Shelton, A. Bartels, C. Lampert, A. Gretton, Pattern Recognition
Letters 32 (2011) 1572–1583.
date_created: 2018-12-11T12:03:03Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2025-09-30T08:45:21Z
day: '01'
department:
- _id: ChLa
doi: 10.1016/j.patrec.2011.02.011
external_id:
isi:
- '000293050700010'
intvolume: ' 32'
isi: 1
issue: '11'
language:
- iso: eng
month: '08'
oa_version: None
page: 1572 - 1583
publication: Pattern Recognition Letters
publication_status: published
publisher: Elsevier
publist_id: '3218'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Semi supervised kernel canonical correlation analysis with application to human
fMRI
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 32
year: '2011'
...
---
_id: '3390'
abstract:
- lang: eng
text: 'What determines the genetic contribution that an individual makes to future
generations? With biparental reproduction, each individual leaves a ''pedigree''
of descendants, determined by the biparental relationships in the population.
The pedigree of an individual constrains the lines of descent of each of its genes.
An individual''s reproductive value is the expected number of copies of each of
its genes that is passed on to distant generations conditional on its pedigree.
For the simplest model of biparental reproduction analogous to the Wright-Fisher
model, an individual''s reproductive value is determined within ~10 generations,
independent of population size. Partial selfing and subdivision do not greatly
slow this convergence. Our central result is that the probability that a gene
will survive is proportional to the reproductive value of the individual that
carries it, and that conditional on survival, after a few tens of generations,
the distribution of the number of surviving copies is the same for all individuals,
whatever their reproductive value. These results can be generalized to the joint
distribution of surviving blocks of ancestral genome. Selection on unlinked loci
in the genetic background may greatly increase the variance in reproductive value,
but the above results nevertheless still hold. The almost linear relationship
between survival probability and reproductive value also holds for weakly favored
alleles. Thus, the influence of the complex pedigree of descendants on an individual''s
genetic contribution to the population can be summarized through a single number:
its reproductive value.'
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
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: Barton NH, Etheridge A. The relation between reproductive value and genetic
contribution. Genetics. 2011;188(4):953-973. doi:10.1534/genetics.111.127555
apa: Barton, N. H., & Etheridge, A. (2011). The relation between reproductive
value and genetic contribution. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.111.127555
chicago: Barton, Nicholas H, and Alison Etheridge. “The Relation between Reproductive
Value and Genetic Contribution.” Genetics. Genetics Society of America,
2011. https://doi.org/10.1534/genetics.111.127555.
ieee: N. H. Barton and A. Etheridge, “The relation between reproductive value and
genetic contribution,” Genetics, vol. 188, no. 4. Genetics Society of America,
pp. 953–973, 2011.
ista: Barton NH, Etheridge A. 2011. The relation between reproductive value and
genetic contribution. Genetics. 188(4), 953–973.
mla: Barton, Nicholas H., and Alison Etheridge. “The Relation between Reproductive
Value and Genetic Contribution.” Genetics, vol. 188, no. 4, Genetics Society
of America, 2011, pp. 953–73, doi:10.1534/genetics.111.127555.
short: N.H. Barton, A. Etheridge, Genetics 188 (2011) 953–973.
corr_author: '1'
date_created: 2018-12-11T12:03:04Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2025-09-30T08:44:55Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.111.127555
ec_funded: 1
external_id:
isi:
- '000293700000018'
intvolume: ' 188'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176105/
month: '08'
oa: 1
oa_version: Submitted Version
page: 953 - 973
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3217'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The relation between reproductive value and genetic contribution
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 188
year: '2011'
...
---
_id: '3391'
abstract:
- lang: eng
text: 'Evolutionary biology shares many concepts with statistical physics: both
deal with populations, whether of molecules or organisms, and both seek to simplify
evolution in very many dimensions. Often, methodologies have undergone parallel
and independent development, as with stochastic methods in population genetics.
Here, we discuss aspects of population genetics that have embraced methods from
physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo
methods, among others, have been used to study polygenic evolution, rates of adaptation
and range expansions. These applications indicate that evolutionary biology can
further benefit from interactions with other areas of statistical physics; for
example, by following the distribution of paths taken by a population through
time'
article_processing_charge: No
arxiv: 1
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- 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: de Vladar H, Barton NH. The contribution of statistical physics to evolutionary
biology. Trends in Ecology and Evolution. 2011;26(8):424-432. doi:10.1016/j.tree.2011.04.002
apa: de Vladar, H., & Barton, N. H. (2011). The contribution of statistical
physics to evolutionary biology. Trends in Ecology and Evolution. Cell
Press. https://doi.org/10.1016/j.tree.2011.04.002
chicago: Vladar, Harold de, and Nicholas H Barton. “The Contribution of Statistical
Physics to Evolutionary Biology.” Trends in Ecology and Evolution. Cell
Press, 2011. https://doi.org/10.1016/j.tree.2011.04.002.
ieee: H. de Vladar and N. H. Barton, “The contribution of statistical physics to
evolutionary biology,” Trends in Ecology and Evolution, vol. 26, no. 8.
Cell Press, pp. 424–432, 2011.
ista: de Vladar H, Barton NH. 2011. The contribution of statistical physics to evolutionary
biology. Trends in Ecology and Evolution. 26(8), 424–432.
mla: de Vladar, Harold, and Nicholas H. Barton. “The Contribution of Statistical
Physics to Evolutionary Biology.” Trends in Ecology and Evolution, vol.
26, no. 8, Cell Press, 2011, pp. 424–32, doi:10.1016/j.tree.2011.04.002.
short: H. de Vladar, N.H. Barton, Trends in Ecology and Evolution 26 (2011) 424–432.
corr_author: '1'
date_created: 2018-12-11T12:03:04Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2025-09-30T08:44:25Z
day: '01'
department:
- _id: NiBa
doi: 10.1016/j.tree.2011.04.002
ec_funded: 1
external_id:
arxiv:
- '1104.2854'
isi:
- '000293940800010'
intvolume: ' 26'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1104.2854
month: '08'
oa: 1
oa_version: Submitted Version
page: 424 - 432
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Trends in Ecology and Evolution
publication_status: published
publisher: Cell Press
publist_id: '3216'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The contribution of statistical physics to evolutionary biology
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 26
year: '2011'
...
---
_id: '3392'
abstract:
- lang: eng
text: Migrating lymphocytes acquire a polarized phenotype with a leading and a trailing
edge, or uropod. Although in vitro experiments in cell lines or activated primary
cell cultures have established that Rho-p160 coiled-coil kinase (ROCK)-myosin
II-mediated uropod contractility is required for integrin de-adhesion on two-dimensional
surfaces and nuclear propulsion through narrow pores in three-dimensional matrices,
less is known about the role of these two events during the recirculation of primary,
nonactivated lymphocytes. Using pharmacological antagonists of ROCK and myosin
II, we report that inhibition of uropod contractility blocked integrin-independent
mouse T cell migration through narrow, but not large, pores in vitro. T cell crawling
on chemokine-coated endothelial cells under shear was severely impaired by ROCK
inhibition, whereas transendothelial migration was only reduced through endothelial
cells with high, but not low, barrier properties. Using three-dimensional thick-tissue
imaging and dynamic two-photon microscopy of T cell motility in lymphoid tissue,
we demonstrated a significant role for uropod contractility in intraluminal crawling
and transendothelial migration through lymph node, but not bone marrow, endothelial
cells. Finally, we demonstrated that ICAM-1, but not anatomical constraints or
integrin-independent interactions, reduced parenchymal motility of inhibitor-treated
T cells within the dense lymphoid microenvironment, thus assigning context-dependent
roles for uropod contraction during lymphocyte recirculation.
article_processing_charge: No
article_type: original
author:
- first_name: Silvia
full_name: Soriano, Silvia
last_name: Soriano
- first_name: Miroslav
full_name: Hons, Miroslav
last_name: Hons
orcid: 0000-0002-6625-3348
- first_name: Kathrin
full_name: Schumann, Kathrin
last_name: Schumann
- first_name: Varsha
full_name: Kumar, Varsha
last_name: Kumar
- first_name: Timo
full_name: Dennier, Timo
last_name: Dennier
- first_name: Ruth
full_name: Lyck, Ruth
last_name: Lyck
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Jens
full_name: Stein, Jens
last_name: Stein
citation:
ama: Soriano S, Hons M, Schumann K, et al. In vivo analysis of uropod function during
physiological T cell trafficking. Journal of Immunology. 2011;187(5):2356-2364.
doi:10.4049/jimmunol.1100935
apa: Soriano, S., Hons, M., Schumann, K., Kumar, V., Dennier, T., Lyck, R., … Stein,
J. (2011). In vivo analysis of uropod function during physiological T cell trafficking.
Journal of Immunology. American Association of Immunologists. https://doi.org/10.4049/jimmunol.1100935
chicago: Soriano, Silvia, Miroslav Hons, Kathrin Schumann, Varsha Kumar, Timo Dennier,
Ruth Lyck, Michael K Sixt, and Jens Stein. “In Vivo Analysis of Uropod Function
during Physiological T Cell Trafficking.” Journal of Immunology. American
Association of Immunologists, 2011. https://doi.org/10.4049/jimmunol.1100935.
ieee: S. Soriano et al., “In vivo analysis of uropod function during physiological
T cell trafficking,” Journal of Immunology, vol. 187, no. 5. American Association
of Immunologists, pp. 2356–2364, 2011.
ista: Soriano S, Hons M, Schumann K, Kumar V, Dennier T, Lyck R, Sixt MK, Stein
J. 2011. In vivo analysis of uropod function during physiological T cell trafficking.
Journal of Immunology. 187(5), 2356–2364.
mla: Soriano, Silvia, et al. “In Vivo Analysis of Uropod Function during Physiological
T Cell Trafficking.” Journal of Immunology, vol. 187, no. 5, American Association
of Immunologists, 2011, pp. 2356–64, doi:10.4049/jimmunol.1100935.
short: S. Soriano, M. Hons, K. Schumann, V. Kumar, T. Dennier, R. Lyck, M.K. Sixt,
J. Stein, Journal of Immunology 187 (2011) 2356–2364.
date_created: 2018-12-11T12:03:04Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2025-09-30T08:43:55Z
day: '01'
department:
- _id: MiSi
doi: 10.4049/jimmunol.1100935
external_id:
isi:
- '000294059500040'
intvolume: ' 187'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa_version: None
page: 2356 - 2364
publication: Journal of Immunology
publication_identifier:
eissn:
- 1550-6606
issn:
- 0022-1767
publication_status: published
publisher: American Association of Immunologists
publist_id: '3215'
quality_controlled: '1'
scopus_import: '1'
status: public
title: In vivo analysis of uropod function during physiological T cell trafficking
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 187
year: '2011'
...
---
_id: '3393'
abstract:
- lang: eng
text: 'Unlike unconditionally advantageous “Fisherian” variants that tend to spread
throughout a species range once introduced anywhere, “bistable” variants, such
as chromosome translocations, have two alternative stable frequencies, absence
and (near) fixation. Analogous to populations with Allee effects, bistable variants
tend to increase locally only once they become sufficiently common, and their
spread depends on their rate of increase averaged over all frequencies. Several
proposed manipulations of insect populations, such as using Wolbachia or “engineered
underdominance” to suppress vector-borne diseases, produce bistable rather than
Fisherian dynamics. We synthesize and extend theoretical analyses concerning three
features of their spatial behavior: rate of spread, conditions to initiate spread
from a localized introduction, and wave stopping caused by variation in population
densities or dispersal rates. Unlike Fisherian variants, bistable variants tend
to spread spatially only for particular parameter combinations and initial conditions.
Wave initiation requires introduction over an extended region, while subsequent
spatial spread is slower than for Fisherian waves and can easily be halted by
local spatial inhomogeneities. We present several new results, including robust
sufficient conditions to initiate (and stop) spread, using a one-parameter cubic
approximation applicable to several models. The results have both basic and applied
implications.'
article_processing_charge: No
article_type: original
author:
- 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: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: 'Barton NH, Turelli M. Spatial waves of advance with bistable dynamics: Cytoplasmic
and genetic analogues of Allee effects. American Naturalist. 2011;178(3):E48-E75.
doi:10.1086/661246'
apa: 'Barton, N. H., & Turelli, M. (2011). Spatial waves of advance with bistable
dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist.
The University of Chicago Press. https://doi.org/10.1086/661246'
chicago: 'Barton, Nicholas H, and Michael Turelli. “Spatial Waves of Advance with
Bistable Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” American
Naturalist. The University of Chicago Press, 2011. https://doi.org/10.1086/661246.'
ieee: 'N. H. Barton and M. Turelli, “Spatial waves of advance with bistable dynamics:
Cytoplasmic and genetic analogues of Allee effects,” American Naturalist,
vol. 178, no. 3. The University of Chicago Press, pp. E48–E75, 2011.'
ista: 'Barton NH, Turelli M. 2011. Spatial waves of advance with bistable dynamics:
Cytoplasmic and genetic analogues of Allee effects. American Naturalist. 178(3),
E48–E75.'
mla: 'Barton, Nicholas H., and Michael Turelli. “Spatial Waves of Advance with Bistable
Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” American Naturalist,
vol. 178, no. 3, The University of Chicago Press, 2011, pp. E48–75, doi:10.1086/661246.'
short: N.H. Barton, M. Turelli, American Naturalist 178 (2011) E48–E75.
date_created: 2018-12-11T12:03:05Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2025-09-30T08:43:28Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1086/661246
external_id:
isi:
- '000294256800001'
file:
- access_level: open_access
checksum: 7fd22a2ef3321a6fca6a439b3be5d8f4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:31Z
date_updated: 2020-07-14T12:46:11Z
file_id: '4692'
file_name: IST-2016-554-v1+1_BartonTurelli2011_copy.pdf
file_size: 629130
relation: main_file
file_date_updated: 2020-07-14T12:46:11Z
has_accepted_license: '1'
intvolume: ' 178'
isi: 1
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: E48 - E75
publication: American Naturalist
publication_identifier:
eissn:
- 1537-5323
issn:
- 0003-0147
publication_status: published
publisher: The University of Chicago Press
publist_id: '3214'
pubrep_id: '554'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues
of Allee effects'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 178
year: '2011'
...
---
_id: '3394'
abstract:
- lang: eng
text: 'Random genetic drift shifts clines in space, alters their width, and distorts
their shape. Such random fluctuations complicate inferences from cline width and
position. Notably, the effect of genetic drift on the expected shape of the cline
is opposite to the naive (but quite common) misinterpretation of classic results
on the expected cline. While random drift on average broadens the overall cline
in expected allele frequency, it narrows the width of any particular cline. The
opposing effects arise because locally, drift drives alleles to fixation—but fluctuations
in position widen the expected cline. The effect of genetic drift can be predicted
from standardized variance in allele frequencies, averaged across the habitat:
〈F〉. A cline maintained by spatially varying selection (step change) is expected
to be narrower by a factor of relative to the cline in the absence of drift.
The expected cline is broader by the inverse of this factor. In a tension zone
maintained by underdominance, the expected cline width is narrower by about 1
– 〈F〉relative to the width in the absence of drift. Individual clines can differ
substantially from the expectation, and we give quantitative predictions for the
variance in cline position and width. The predictions apply to clines in almost
one-dimensional circumstances such as hybrid zones in rivers, deep valleys, or
along a coast line and give a guide to what patterns to expect in two dimensions.'
article_processing_charge: No
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- 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: Polechova J, Barton NH. Genetic drift widens the expected cline but narrows
the expected cline width. Genetics. 2011;189(1):227-235. doi:10.1534/genetics.111.129817
apa: Polechova, J., & Barton, N. H. (2011). Genetic drift widens the expected
cline but narrows the expected cline width. Genetics. Genetics Society
of America. https://doi.org/10.1534/genetics.111.129817
chicago: Polechova, Jitka, and Nicholas H Barton. “Genetic Drift Widens the Expected
Cline but Narrows the Expected Cline Width.” Genetics. Genetics Society
of America, 2011. https://doi.org/10.1534/genetics.111.129817.
ieee: J. Polechova and N. H. Barton, “Genetic drift widens the expected cline but
narrows the expected cline width,” Genetics, vol. 189, no. 1. Genetics
Society of America, pp. 227–235, 2011.
ista: Polechova J, Barton NH. 2011. Genetic drift widens the expected cline but
narrows the expected cline width. Genetics. 189(1), 227–235.
mla: Polechova, Jitka, and Nicholas H. Barton. “Genetic Drift Widens the Expected
Cline but Narrows the Expected Cline Width.” Genetics, vol. 189, no. 1,
Genetics Society of America, 2011, pp. 227–35, doi:10.1534/genetics.111.129817.
short: J. Polechova, N.H. Barton, Genetics 189 (2011) 227–235.
corr_author: '1'
date_created: 2018-12-11T12:03:05Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2025-09-30T08:42:59Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.111.129817
ec_funded: 1
external_id:
isi:
- '000294721600018'
intvolume: ' 189'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176109/
month: '09'
oa: 1
oa_version: Submitted Version
page: 227 - 235
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3213'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic drift widens the expected cline but narrows the expected cline width
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 189
year: '2011'
...
---
_id: '3395'
abstract:
- lang: eng
text: Defining population structure and genetic diversity levels is of the utmost
importance for developing efficient conservation strategies. Overfishing has caused
mean annual catches of the European spiny lobster (Palinurus elephas) to decrease
alarmingly along its distribution area. In this context, there is a need for comprehensive
studies aiming to evaluate the genetic health of the exploited populations. The
present study is based on a set of ten nuclear markers amplified in 331 individuals
from ten different localities covering most of P. elephas distribution area. Samples
from Atlantic and Mediterranean basins showed small but significant differences,
indicating that P. elephas populations do not behave as a single panmictic unit
but form two partially-overlapping groups. Despite intense overfishing, our dataset
did not recover a recent bottleneck signal, and instead showed a large and stable
historical effective size. This result could be accounted for by specific life-history
traits (reproduction and longevity) and the limitations of molecular markers in
covering recent timescales for nontemporal samples. The findings of the present
study emphasize the need to integrate information on effective population sizes
and life-history parameters when evaluating population connectivity levels from
genetic data.
acknowledgement: This work was supported by a pre-doctoral fellowship awarded by the
Autonomous Government of Catalonia to F.P. (2006FIC-00082). Research was funded
by projects FBBVA-BIOCON 08-187/09, CGL2006-13423, and CTM2007-66635. The authors
are part of the research group 2009SGR-636, 2009SGR-655, and 2009SGR-1364 of the
Generalitat de Catalunya. F.P. acknowledges EU-Synthesys grant (GB-TAF-4474).
article_processing_charge: No
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
- first_name: Enrique
full_name: Macpherson, Enrique
last_name: Macpherson
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
citation:
ama: Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Effect of oceanographic
barriers and overfishing on the population genetic structure of the European spiny
lobster Palinurus elephas. Biological Journal of the Linnean Society. 2011;104(2):407-418.
doi:10.1111/j.1095-8312.2011.01728.x
apa: Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011).
Effect of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster Palinurus elephas. Biological Journal of the
Linnean Society. Wiley-Blackwell. https://doi.org/10.1111/j.1095-8312.2011.01728.x
chicago: Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta
Pascual. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic
Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal
of the Linnean Society. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1095-8312.2011.01728.x.
ieee: F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Effect
of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster Palinurus elephas,” Biological Journal of the
Linnean Society, vol. 104, no. 2. Wiley-Blackwell, pp. 407–418, 2011.
ista: Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Effect of oceanographic
barriers and overfishing on the population genetic structure of the European spiny
lobster Palinurus elephas. Biological Journal of the Linnean Society. 104(2),
407–418.
mla: Palero, Ferran, et al. “Effect of Oceanographic Barriers and Overfishing on
the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.”
Biological Journal of the Linnean Society, vol. 104, no. 2, Wiley-Blackwell,
2011, pp. 407–18, doi:10.1111/j.1095-8312.2011.01728.x.
short: F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, Biological
Journal of the Linnean Society 104 (2011) 407–418.
corr_author: '1'
date_created: 2018-12-11T12:03:06Z
date_published: 2011-09-14T00:00:00Z
date_updated: 2025-09-30T08:42:31Z
day: '14'
department:
- _id: NiBa
doi: 10.1111/j.1095-8312.2011.01728.x
external_id:
isi:
- '000294902700013'
intvolume: ' 104'
isi: 1
issue: '2'
language:
- iso: eng
month: '09'
oa_version: None
page: 407 - 418
publication: Biological Journal of the Linnean Society
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3212'
quality_controlled: '1'
related_material:
record:
- id: '9762'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Effect of oceanographic barriers and overfishing on the population genetic
structure of the European spiny lobster Palinurus elephas
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 104
year: '2011'
...
---
_id: '3396'
abstract:
- lang: eng
text: Facial branchiomotor neurons (FBMNs) in zebrafish and mouse embryonic hindbrain
undergo a characteristic tangential migration from rhombomere (r) 4, where they
are born, to r6/7. Cohesion among neuroepithelial cells (NCs) has been suggested
to function in FBMN migration by inhibiting FBMNs positioned in the basal neuroepithelium
such that they move apically between NCs towards the midline of the neuroepithelium
instead of tangentially along the basal side of the neuroepithelium towards r6/7.
However, direct experimental evaluation of this hypothesis is still lacking. Here,
we have used a combination of biophysical cell adhesion measurements and high-resolution
time-lapse microscopy to determine the role of NC cohesion in FBMN migration.
We show that reducing NC cohesion by interfering with Cadherin 2 (Cdh2) activity
results in FBMNs positioned at the basal side of the neuroepithelium moving apically
towards the neural tube midline instead of tangentially towards r6/7. In embryos
with strongly reduced NC cohesion, ectopic apical FBMN movement frequently results
in fusion of the bilateral FBMN clusters over the apical midline of the neural
tube. By contrast, reducing cohesion among FBMNs by interfering with Contactin
2 (Cntn2) expression in these cells has little effect on apical FBMN movement,
but reduces the fusion of the bilateral FBMN clusters in embryos with strongly
diminished NC cohesion. These data provide direct experimental evidence that NC
cohesion functions in tangential FBMN migration by restricting their apical movement.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
article_processing_charge: No
article_type: original
author:
- first_name: Petra
full_name: Stockinger, Petra
id: 261CB030-E90D-11E9-B182-F697D44B663C
last_name: Stockinger
- 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: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
citation:
ama: Stockinger P, Heisenberg C-PJ, Maître J-L. Defective neuroepithelial cell cohesion
affects tangential branchiomotor neuron migration in the zebrafish neural tube.
Development. 2011;138(21):4673-4683. doi:10.1242/dev.071233
apa: Stockinger, P., Heisenberg, C.-P. J., & Maître, J.-L. (2011). Defective
neuroepithelial cell cohesion affects tangential branchiomotor neuron migration
in the zebrafish neural tube. Development. Company of Biologists. https://doi.org/10.1242/dev.071233
chicago: Stockinger, Petra, Carl-Philipp J Heisenberg, and Jean-Léon Maître. “Defective
Neuroepithelial Cell Cohesion Affects Tangential Branchiomotor Neuron Migration
in the Zebrafish Neural Tube.” Development. Company of Biologists, 2011.
https://doi.org/10.1242/dev.071233.
ieee: P. Stockinger, C.-P. J. Heisenberg, and J.-L. Maître, “Defective neuroepithelial
cell cohesion affects tangential branchiomotor neuron migration in the zebrafish
neural tube,” Development, vol. 138, no. 21. Company of Biologists, pp.
4673–4683, 2011.
ista: Stockinger P, Heisenberg C-PJ, Maître J-L. 2011. Defective neuroepithelial
cell cohesion affects tangential branchiomotor neuron migration in the zebrafish
neural tube. Development. 138(21), 4673–4683.
mla: Stockinger, Petra, et al. “Defective Neuroepithelial Cell Cohesion Affects
Tangential Branchiomotor Neuron Migration in the Zebrafish Neural Tube.” Development,
vol. 138, no. 21, Company of Biologists, 2011, pp. 4673–83, doi:10.1242/dev.071233.
short: P. Stockinger, C.-P.J. Heisenberg, J.-L. Maître, Development 138 (2011) 4673–4683.
corr_author: '1'
date_created: 2018-12-11T12:03:06Z
date_published: 2011-09-28T00:00:00Z
date_updated: 2025-09-30T08:41:19Z
day: '28'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1242/dev.071233
external_id:
isi:
- '000296060100011'
file:
- access_level: open_access
checksum: ca12b79e01ef36c1ef1aea31cf7e7139
content_type: application/pdf
creator: dernst
date_created: 2019-10-07T14:19:42Z
date_updated: 2020-07-14T12:46:12Z
file_id: '6930'
file_name: 2011_Development_Stockinger.pdf
file_size: 4672439
relation: main_file
file_date_updated: 2020-07-14T12:46:12Z
has_accepted_license: '1'
intvolume: ' 138'
isi: 1
issue: '21'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 4673 - 4683
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '3210'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron
migration in the zebrafish neural tube
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 138
year: '2011'
...
---
_id: '3397'
abstract:
- lang: eng
text: Recent advances in microscopy techniques and biophysical measurements have
provided novel insight into the molecular, cellular and biophysical basis of cell
adhesion. However, comparably little is known about a core element of cell–cell
adhesion—the energy of adhesion at the cell–cell contact. In this review, we discuss
approaches to understand the nature and regulation of adhesion energy, and propose
strategies to determine adhesion energy between cells in vitro and in vivo.
article_processing_charge: No
author:
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
- 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: Maître J-L, Heisenberg C-PJ. The role of adhesion energy in controlling cell-cell
contacts. Current Opinion in Cell Biology. 2011;23(5):508-514. doi:10.1016/j.ceb.2011.07.004
apa: Maître, J.-L., & Heisenberg, C.-P. J. (2011). The role of adhesion energy
in controlling cell-cell contacts. Current Opinion in Cell Biology. Elsevier.
https://doi.org/10.1016/j.ceb.2011.07.004
chicago: Maître, Jean-Léon, and Carl-Philipp J Heisenberg. “The Role of Adhesion
Energy in Controlling Cell-Cell Contacts.” Current Opinion in Cell Biology.
Elsevier, 2011. https://doi.org/10.1016/j.ceb.2011.07.004.
ieee: J.-L. Maître and C.-P. J. Heisenberg, “The role of adhesion energy in controlling
cell-cell contacts,” Current Opinion in Cell Biology, vol. 23, no. 5. Elsevier,
pp. 508–514, 2011.
ista: Maître J-L, Heisenberg C-PJ. 2011. The role of adhesion energy in controlling
cell-cell contacts. Current Opinion in Cell Biology. 23(5), 508–514.
mla: Maître, Jean-Léon, and Carl-Philipp J. Heisenberg. “The Role of Adhesion Energy
in Controlling Cell-Cell Contacts.” Current Opinion in Cell Biology, vol.
23, no. 5, Elsevier, 2011, pp. 508–14, doi:10.1016/j.ceb.2011.07.004.
short: J.-L. Maître, C.-P.J. Heisenberg, Current Opinion in Cell Biology 23 (2011)
508–514.
corr_author: '1'
date_created: 2018-12-11T12:03:06Z
date_published: 2011-10-01T00:00:00Z
date_updated: 2025-09-30T08:42:02Z
day: '01'
department:
- _id: CaHe
doi: 10.1016/j.ceb.2011.07.004
external_id:
isi:
- '000296040800002'
intvolume: ' 23'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188705/
month: '10'
oa: 1
oa_version: Submitted Version
page: 508 - 514
publication: Current Opinion in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '3211'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The role of adhesion energy in controlling cell-cell contacts
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 23
year: '2011'
...
---
_id: '3399'
abstract:
- lang: eng
text: Context-dependent adjustment of mating tactics can drastically increase the
mating success of behaviourally flexible animals. We used the ant Cardiocondyla
obscurior as a model system to study adaptive adjustment of male mating tactics.
This species shows a male diphenism of wingless fighter males and peaceful winged
males. Whereas the wingless males stay and exclusively mate in the maternal colony,
the mating behaviour of winged males is plastic. They copulate with female sexuals
in their natal nests early in life but later disperse in search for sexuals outside.
In this study, we observed the nest-leaving behaviour of winged males under different
conditions and found that they adaptively adjust the timing of their dispersal
to the availability of mating partners, as well as the presence, and even the
type of competitors in their natal nests. In colonies with virgin female queens
winged males stayed longest when they were the only male in the nest. They left
earlier when mating partners were not available or when other males were present.
In the presence of wingless, locally mating fighter males, winged males dispersed
earlier than in the presence of docile, winged competitors. This suggests that
C. obscurior males are capable of estimating their local breeding chances and
adaptively adjust their dispersal behaviour in both an opportunistic and a risk-sensitive
way, thus showing hitherto unknown behavioural plasticity in social insect males.
acknowledgement: This work was supported by the German Science Foundation (www.dfg.de,
He 1623/23).
article_number: e17323
article_processing_charge: No
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
citation:
ama: Cremer S, Schrempf A, Heinze J. Competition and opportunity shape the reproductive
tactics of males in the ant Cardiocondyla obscurior. PLoS One. 2011;6(3).
doi:10.1371/journal.pone.0017323
apa: Cremer, S., Schrempf, A., & Heinze, J. (2011). Competition and opportunity
shape the reproductive tactics of males in the ant Cardiocondyla obscurior. PLoS
One. Public Library of Science. https://doi.org/10.1371/journal.pone.0017323
chicago: Cremer, Sylvia, Alexandra Schrempf, and Jürgen Heinze. “Competition and
Opportunity Shape the Reproductive Tactics of Males in the Ant Cardiocondyla Obscurior.”
PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0017323.
ieee: S. Cremer, A. Schrempf, and J. Heinze, “Competition and opportunity shape
the reproductive tactics of males in the ant Cardiocondyla obscurior,” PLoS
One, vol. 6, no. 3. Public Library of Science, 2011.
ista: Cremer S, Schrempf A, Heinze J. 2011. Competition and opportunity shape the
reproductive tactics of males in the ant Cardiocondyla obscurior. PLoS One. 6(3),
e17323.
mla: Cremer, Sylvia, et al. “Competition and Opportunity Shape the Reproductive
Tactics of Males in the Ant Cardiocondyla Obscurior.” PLoS One, vol. 6,
no. 3, e17323, Public Library of Science, 2011, doi:10.1371/journal.pone.0017323.
short: S. Cremer, A. Schrempf, J. Heinze, PLoS One 6 (2011).
corr_author: '1'
date_created: 2018-12-11T12:03:07Z
date_published: 2011-03-29T00:00:00Z
date_updated: 2025-09-30T08:40:50Z
day: '29'
ddc:
- '576'
department:
- _id: SyCr
doi: 10.1371/journal.pone.0017323
external_id:
isi:
- '000289054600009'
file:
- access_level: open_access
checksum: 46f8cbde61f06fcacf8fa297cacfa0e5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:40Z
date_updated: 2020-07-14T12:46:12Z
file_id: '5162'
file_name: IST-2015-377-v1+1_journal.pone.0017323.pdf
file_size: 147367
relation: main_file
file_date_updated: 2020-07-14T12:46:12Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3059'
pubrep_id: '377'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Competition and opportunity shape the reproductive tactics of males in the
ant Cardiocondyla obscurior
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2011'
...
---
_id: '3401'
abstract:
- lang: eng
text: The Bicoid morphogen gradient directs the patterning of cell fates along the
anterior-posterior axis of the syncytial Drosophila embryo and serves as a paradigm
of morphogen-mediated patterning. The simplest models of gradient formation rely
on constant protein synthesis and diffusion from anteriorly localized source mRNA,
coupled with uniform protein degradation. However, currently such models cannot
account for all known gradient characteristics. Recent work has proposed that
bicoid mRNA spatial distribution is sufficient to produce the observed protein
gradient, minimizing the role of protein transport. Here, we adapt a novel method
of fluorescent in situ hybridization to quantify the global spatio-temporal dynamics
of bicoid mRNA particles. We determine that >90% of all bicoid mRNA is continuously
present within the anterior 20% of the embryo. bicoid mRNA distribution along
the body axis remains nearly unchanged despite dynamic mRNA translocation from
the embryo core to the cortex. To evaluate the impact of mRNA distribution on
protein gradient dynamics, we provide detailed quantitative measurements of nuclear
Bicoid levels during the formation of the protein gradient. We find that gradient
establishment begins 45 minutes after fertilization and that the gradient requires
about 50 minutes to reach peak levels. In numerical simulations of gradient formation,
we find that incorporating the actual bicoid mRNA distribution yields a closer
prediction of the observed protein dynamics compared to modeling protein production
from a point source at the anterior pole. We conclude that the spatial distribution
of bicoid mRNA contributes to, but cannot account for, protein gradient formation,
and therefore that protein movement, either active or passive, is required for
gradient formation.
article_number: e1000596
article_type: original
author:
- first_name: Shawn
full_name: Little, Shawn
last_name: Little
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Thomas
full_name: Kneeland, Thomas
last_name: Kneeland
- first_name: Eric
full_name: Wieschaus, Eric
last_name: Wieschaus
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
citation:
ama: Little S, Tkačik G, Kneeland T, Wieschaus E, Gregor T. The formation of the
Bicoid morphogen gradient requires protein movement from anteriorly localized
source. PLoS Biology. 2011;9(3). doi:10.1371/journal.pbio.1000596
apa: Little, S., Tkačik, G., Kneeland, T., Wieschaus, E., & Gregor, T. (2011).
The formation of the Bicoid morphogen gradient requires protein movement from
anteriorly localized source. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000596
chicago: Little, Shawn, Gašper Tkačik, Thomas Kneeland, Eric Wieschaus, and Thomas
Gregor. “The Formation of the Bicoid Morphogen Gradient Requires Protein Movement
from Anteriorly Localized Source.” PLoS Biology. Public Library of Science,
2011. https://doi.org/10.1371/journal.pbio.1000596.
ieee: S. Little, G. Tkačik, T. Kneeland, E. Wieschaus, and T. Gregor, “The formation
of the Bicoid morphogen gradient requires protein movement from anteriorly localized
source,” PLoS Biology, vol. 9, no. 3. Public Library of Science, 2011.
ista: Little S, Tkačik G, Kneeland T, Wieschaus E, Gregor T. 2011. The formation
of the Bicoid morphogen gradient requires protein movement from anteriorly localized
source. PLoS Biology. 9(3), e1000596.
mla: Little, Shawn, et al. “The Formation of the Bicoid Morphogen Gradient Requires
Protein Movement from Anteriorly Localized Source.” PLoS Biology, vol.
9, no. 3, e1000596, Public Library of Science, 2011, doi:10.1371/journal.pbio.1000596.
short: S. Little, G. Tkačik, T. Kneeland, E. Wieschaus, T. Gregor, PLoS Biology
9 (2011).
date_created: 2018-12-11T12:03:08Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2021-01-12T07:43:14Z
day: '01'
doi: 10.1371/journal.pbio.1000596
extern: '1'
intvolume: ' 9'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '3057'
quality_controlled: '1'
status: public
title: The formation of the Bicoid morphogen gradient requires protein movement from
anteriorly localized source
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2011'
...
---
_id: '3405'
abstract:
- lang: eng
text: Glutamate is the major excitatory neurotransmitter in the mammalian central
nervous system and gates non-selective cation channels. The origins of glutamate
receptors are not well understood as they differ structurally and functionally
from simple bacterial ligand-gated ion channels. Here we report the discovery
of an ionotropic glutamate receptor that combines the typical eukaryotic domain
architecture with the 'TXVGYG' signature sequence of the selectivity filter found
in K+ channels. This receptor exhibits functional properties intermediate between
bacterial and eukaryotic glutamate-gated ion channels, suggesting a link in the
evolution of ionotropic glutamate receptors.
article_processing_charge: No
author:
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Guillaume
full_name: Sandoz, Guillaume
last_name: Sandoz
- first_name: Ehud
full_name: Isacoff, Ehud
last_name: Isacoff
citation:
ama: Janovjak HL, Sandoz G, Isacoff E. Modern ionotropic glutamate receptor with
a K+ selectivity signature sequence. Nature Communications. 2011;2(232):1-6.
doi:10.1038/ncomms1231
apa: Janovjak, H. L., Sandoz, G., & Isacoff, E. (2011). Modern ionotropic glutamate
receptor with a K+ selectivity signature sequence. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms1231
chicago: Janovjak, Harald L, Guillaume Sandoz, and Ehud Isacoff. “Modern Ionotropic
Glutamate Receptor with a K+ Selectivity Signature Sequence.” Nature Communications.
Nature Publishing Group, 2011. https://doi.org/10.1038/ncomms1231.
ieee: H. L. Janovjak, G. Sandoz, and E. Isacoff, “Modern ionotropic glutamate receptor
with a K+ selectivity signature sequence,” Nature Communications, vol.
2, no. 232. Nature Publishing Group, pp. 1–6, 2011.
ista: Janovjak HL, Sandoz G, Isacoff E. 2011. Modern ionotropic glutamate receptor
with a K+ selectivity signature sequence. Nature Communications. 2(232), 1–6.
mla: Janovjak, Harald L., et al. “Modern Ionotropic Glutamate Receptor with a K+
Selectivity Signature Sequence.” Nature Communications, vol. 2, no. 232,
Nature Publishing Group, 2011, pp. 1–6, doi:10.1038/ncomms1231.
short: H.L. Janovjak, G. Sandoz, E. Isacoff, Nature Communications 2 (2011) 1–6.
corr_author: '1'
date_created: 2018-12-11T12:03:09Z
date_published: 2011-03-08T00:00:00Z
date_updated: 2025-09-30T08:40:22Z
day: '08'
ddc:
- '570'
- '571'
department:
- _id: HaJa
doi: 10.1038/ncomms1231
external_id:
isi:
- '000289982600022'
file:
- access_level: open_access
checksum: 6b68d65aadd97c18d663eb117a0a9d35
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:36Z
date_updated: 2020-07-14T12:46:12Z
file_id: '4891'
file_name: IST-2017-832-v1+1_janovjak.pdf
file_size: 387654
relation: main_file
file_date_updated: 2020-07-14T12:46:12Z
has_accepted_license: '1'
intvolume: ' 2'
isi: 1
issue: '232'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 1 - 6
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '2997'
pubrep_id: '832'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modern ionotropic glutamate receptor with a K+ selectivity signature sequence
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 2
year: '2011'
...
---
_id: '341'
abstract:
- lang: eng
text: An oriented attachment and growth mechanism allows an accurate control of
the size and morphology of Cu2-xS nanocrystals, from spheres and disks to tetradecahedrons
and dodecahedrons. The synthesis conditions and the growth mechanism are detailed
here.
acknowledgement: "This work was supported by the Spanish MICINN projects\r\nMAT2008-05779,
MAT2008-03400-E/MAT, ENE2008-03277-E/\r\nCON, MAT2010-15138, MAT-2010-21510, CDS2009-00050
and\r\nCSD2009-00013 and by Generalitat de Catalunya 2009-SGR-770\r\nand XaRMAE."
article_processing_charge: No
article_type: original
author:
- first_name: Wenhua
full_name: Li, Wenhua
last_name: Li
- first_name: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Roger
full_name: Guzman, Roger
last_name: Guzman
- first_name: Javier
full_name: Rubio Garcia, Javier
last_name: Rubio Garcia
- first_name: Cristina
full_name: Flox, Cristina
last_name: Flox
- first_name: Jiandong
full_name: Fan, Jiandong
last_name: Fan
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Joan
full_name: Morante, Joan
last_name: Morante
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: 'Li W, Shavel A, Guzman R, et al. Morphology evolution of Cu2−xS nanoparticles:
from spheres to dodecahedrons. Chemical Communications. 2011;47(37):10332-10334.
doi:10.1039/c1cc13803k'
apa: 'Li, W., Shavel, A., Guzman, R., Rubio Garcia, J., Flox, C., Fan, J., … Cabot,
A. (2011). Morphology evolution of Cu2−xS nanoparticles: from spheres to dodecahedrons.
Chemical Communications. Royal Society of Chemistry (RSC) . https://doi.org/10.1039/c1cc13803k'
chicago: 'Li, Wenhua, Alexey Shavel, Roger Guzman, Javier Rubio Garcia, Cristina
Flox, Jiandong Fan, Doris Cadavid, et al. “Morphology Evolution of Cu2−xS Nanoparticles:
From Spheres to Dodecahedrons.” Chemical Communications. Royal Society
of Chemistry (RSC) , 2011. https://doi.org/10.1039/c1cc13803k.'
ieee: 'W. Li et al., “Morphology evolution of Cu2−xS nanoparticles: from
spheres to dodecahedrons,” Chemical Communications, vol. 47, no. 37. Royal
Society of Chemistry (RSC) , pp. 10332–10334, 2011.'
ista: 'Li W, Shavel A, Guzman R, Rubio Garcia J, Flox C, Fan J, Cadavid D, Ibáñez
M, Arbiol J, Morante J, Cabot A. 2011. Morphology evolution of Cu2−xS nanoparticles:
from spheres to dodecahedrons. Chemical Communications. 47(37), 10332–10334.'
mla: 'Li, Wenhua, et al. “Morphology Evolution of Cu2−xS Nanoparticles: From Spheres
to Dodecahedrons.” Chemical Communications, vol. 47, no. 37, Royal Society
of Chemistry (RSC) , 2011, pp. 10332–34, doi:10.1039/c1cc13803k.'
short: W. Li, A. Shavel, R. Guzman, J. Rubio Garcia, C. Flox, J. Fan, D. Cadavid,
M. Ibáñez, J. Arbiol, J. Morante, A. Cabot, Chemical Communications 47 (2011)
10332–10334.
date_created: 2018-12-11T11:45:55Z
date_published: 2011-10-07T00:00:00Z
date_updated: 2021-01-12T07:43:17Z
day: '07'
doi: 10.1039/c1cc13803k
extern: '1'
intvolume: ' 47'
issue: '37'
language:
- iso: eng
month: '10'
oa_version: None
page: 10332 - 10334
publication: Chemical Communications
publication_status: published
publisher: 'Royal Society of Chemistry (RSC) '
publist_id: '7491'
quality_controlled: '1'
status: public
title: 'Morphology evolution of Cu2−xS nanoparticles: from spheres to dodecahedrons'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2011'
...
---
_id: '14305'
abstract:
- lang: eng
text: Understanding the mechanism of protein folding requires a detailed knowledge
of the structural properties of the barriers separating unfolded from native conformations.
The S-peptide from ribonuclease S forms its α-helical structure only upon binding
to the folded S-protein. We characterized the transition state for this binding-induced
folding reaction at high resolution by determining the effect of site-specific
backbone thioxylation and side-chain modifications on the kinetics and thermodynamics
of the reaction, which allows us to monitor formation of backbone hydrogen bonds
and side-chain interactions in the transition state. The experiments reveal that
α-helical structure in the S-peptide is absent in the transition state of binding.
Recognition between the unfolded S-peptide and the S-protein is mediated by loosely
packed hydrophobic side-chain interactions in two well defined regions on the
S-peptide. Close packing and helix formation occurs rapidly after binding. Introducing
hydrophobic residues at positions outside the recognition region can drastically
slow down association.
article_processing_charge: No
article_type: original
author:
- first_name: Annett
full_name: Bachmann, Annett
last_name: Bachmann
- first_name: Dirk
full_name: Wildemann, Dirk
last_name: Wildemann
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Gunter
full_name: Fischer, Gunter
last_name: Fischer
- first_name: Thomas
full_name: Kiefhaber, Thomas
last_name: Kiefhaber
citation:
ama: Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. Mapping backbone
and side-chain interactions in the transition state of a coupled protein folding
and binding reaction. PNAS. 2011;108(10):3952-3957. doi:10.1073/pnas.1012668108
apa: Bachmann, A., Wildemann, D., Praetorius, F. M., Fischer, G., & Kiefhaber,
T. (2011). Mapping backbone and side-chain interactions in the transition state
of a coupled protein folding and binding reaction. PNAS. Proceedings of
the National Academy of Sciences. https://doi.org/10.1073/pnas.1012668108
chicago: Bachmann, Annett, Dirk Wildemann, Florian M Praetorius, Gunter Fischer,
and Thomas Kiefhaber. “Mapping Backbone and Side-Chain Interactions in the Transition
State of a Coupled Protein Folding and Binding Reaction.” PNAS. Proceedings
of the National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1012668108.
ieee: A. Bachmann, D. Wildemann, F. M. Praetorius, G. Fischer, and T. Kiefhaber,
“Mapping backbone and side-chain interactions in the transition state of a coupled
protein folding and binding reaction,” PNAS, vol. 108, no. 10. Proceedings
of the National Academy of Sciences, pp. 3952–3957, 2011.
ista: Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. 2011. Mapping
backbone and side-chain interactions in the transition state of a coupled protein
folding and binding reaction. PNAS. 108(10), 3952–3957.
mla: Bachmann, Annett, et al. “Mapping Backbone and Side-Chain Interactions in the
Transition State of a Coupled Protein Folding and Binding Reaction.” PNAS,
vol. 108, no. 10, Proceedings of the National Academy of Sciences, 2011, pp. 3952–57,
doi:10.1073/pnas.1012668108.
short: A. Bachmann, D. Wildemann, F.M. Praetorius, G. Fischer, T. Kiefhaber, PNAS
108 (2011) 3952–3957.
date_created: 2023-09-06T12:54:36Z
date_published: 2011-01-12T00:00:00Z
date_updated: 2023-11-07T11:50:29Z
day: '12'
doi: 10.1073/pnas.1012668108
extern: '1'
external_id:
pmid:
- '21325613'
intvolume: ' 108'
issue: '10'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1012668108
month: '01'
oa: 1
oa_version: Published Version
page: 3952-3957
pmid: 1
publication: PNAS
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mapping backbone and side-chain interactions in the transition state of a coupled
protein folding and binding reaction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2011'
...
---
_id: '1467'
abstract:
- lang: eng
text: We propose a general conjecture for the mixed Hodge polynomial of the generic
character varieties of representations of the fundamental group of a Riemann surface
of genus g to GLn(C) with fixed generic semisimple conjugacy classes at k punctures.
This conjecture generalizes the Cauchy identity for Macdonald polynomials and
is a common generalization of two formulas that we prove in this paper. The first
is a formula for the E-polynomial of these character varieties which we obtain
using the character table of GLn(Fq). We use this formula to compute the Euler
characteristic of character varieties. The second formula gives the Poincaré polynomial
of certain associated quiver varieties which we obtain using the character table
of gln(Fq). In the last main result we prove that the Poincaré polynomials of
the quiver varieties equal certain multiplicities in the tensor product of irreducible
characters of GLn(Fq). As a consequence we find a curious connection between Kac-Moody
algebras associated with comet-shaped, and typically wild, quivers and the representation
theory of GLn(Fq).
acknowledgement: |-
Hausel’s work was supported by National Science Foundation grants DMS-0305505 and DMS-0604775, by an Alfred Sloan Fellowship, and by a Royal Society University Research Fellowship. Letellier’s work supported by Agence Nationale de la Recherche grant ANR-09-JCJC-0102-01.
Rodriguez-Villegas’s work supported by National Science Foundation grant DMS-0200605, by an FRA from the University of Texas at Austin, by EPSRC grant EP/G027110/1, by visiting fellowships at All Souls and Wadham Colleges in Oxford, and by a Research Scholarship from the Clay Mathematical Institute.
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Emmanuel
full_name: Letellier, Emmanuel
last_name: Letellier
- first_name: Fernando
full_name: Rodríguez Villegas, Fernando
last_name: Rodríguez Villegas
citation:
ama: Hausel T, Letellier E, Rodríguez Villegas F. Arithmetic harmonic analysis on
character and quiver varieties. Duke Mathematical Journal. 2011;160(2):323-400.
doi:10.1215/00127094-1444258
apa: Hausel, T., Letellier, E., & Rodríguez Villegas, F. (2011). Arithmetic
harmonic analysis on character and quiver varieties. Duke Mathematical Journal.
Duke University Press. https://doi.org/10.1215/00127094-1444258
chicago: Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Arithmetic
Harmonic Analysis on Character and Quiver Varieties.” Duke Mathematical Journal.
Duke University Press, 2011. https://doi.org/10.1215/00127094-1444258.
ieee: T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Arithmetic harmonic analysis
on character and quiver varieties,” Duke Mathematical Journal, vol. 160,
no. 2. Duke University Press, pp. 323–400, 2011.
ista: Hausel T, Letellier E, Rodríguez Villegas F. 2011. Arithmetic harmonic analysis
on character and quiver varieties. Duke Mathematical Journal. 160(2), 323–400.
mla: Hausel, Tamás, et al. “Arithmetic Harmonic Analysis on Character and Quiver
Varieties.” Duke Mathematical Journal, vol. 160, no. 2, Duke University
Press, 2011, pp. 323–400, doi:10.1215/00127094-1444258.
short: T. Hausel, E. Letellier, F. Rodríguez Villegas, Duke Mathematical Journal
160 (2011) 323–400.
date_created: 2018-12-11T11:52:11Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:56Z
day: '01'
doi: 10.1215/00127094-1444258
extern: 1
intvolume: ' 160'
issue: '2'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0810.2076
month: '01'
oa: 1
page: 323 - 400
publication: Duke Mathematical Journal
publication_status: published
publisher: Duke University Press
publist_id: '5728'
quality_controlled: 0
status: public
title: Arithmetic harmonic analysis on character and quiver varieties
type: journal_article
volume: 160
year: '2011'
...
---
_id: '1781'
abstract:
- lang: eng
text: Microwave cavities with high quality factors enable coherent coupling of distant
quantum systems. Virtual photons lead to a transverse interaction between qubits
when they are nonresonant with the cavity but resonant with each other. We experimentally
investigate the inverse scaling of the interqubit coupling with the detuning from
a cavity mode and its proportionality to the qubit-cavity interaction strength.
We demonstrate that the enhanced coupling at higher frequencies is mediated by
multiple higher-harmonic cavity modes. Moreover, we observe dark states of the
coupled qubit-qubit system and analyze their relation to the symmetry of the applied
driving field at different frequencies.
acknowledgement: This work was supported by the Swiss National Science Foundation
(SNF), the Austrian Science Foundation (FWF), and ETH Zurich
author:
- first_name: Stefan
full_name: Filipp, Stefan
last_name: Filipp
- 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: L.
full_name: Steffen, L. Kraig
last_name: Steffen
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Filipp S, Göppl M, Fink JM, et al. Multimode mediated qubit-qubit coupling
and dark-state symmetries in circuit quantum electrodynamics. Physical Review
A - Atomic, Molecular, and Optical Physics. 2011;83(6). doi:10.1103/PhysRevA.83.063827
apa: Filipp, S., Göppl, M., Fink, J. M., Baur, M., Bianchetti, R., Steffen, L.,
& Wallraff, A. (2011). Multimode mediated qubit-qubit coupling and dark-state
symmetries in circuit quantum electrodynamics. Physical Review A - Atomic,
Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.83.063827
chicago: Filipp, Stefan, M Göppl, Johannes M Fink, Matthias Baur, R Bianchetti,
L. Steffen, and Andreas Wallraff. “Multimode Mediated Qubit-Qubit Coupling and
Dark-State Symmetries in Circuit Quantum Electrodynamics.” Physical Review
A - Atomic, Molecular, and Optical Physics. American Physical Society, 2011.
https://doi.org/10.1103/PhysRevA.83.063827.
ieee: S. Filipp et al., “Multimode mediated qubit-qubit coupling and dark-state
symmetries in circuit quantum electrodynamics,” Physical Review A - Atomic,
Molecular, and Optical Physics, vol. 83, no. 6. American Physical Society,
2011.
ista: Filipp S, Göppl M, Fink JM, Baur M, Bianchetti R, Steffen L, Wallraff A. 2011.
Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum
electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. 83(6).
mla: Filipp, Stefan, et al. “Multimode Mediated Qubit-Qubit Coupling and Dark-State
Symmetries in Circuit Quantum Electrodynamics.” Physical Review A - Atomic,
Molecular, and Optical Physics, vol. 83, no. 6, American Physical Society,
2011, doi:10.1103/PhysRevA.83.063827.
short: S. Filipp, M. Göppl, J.M. Fink, M. Baur, R. Bianchetti, L. Steffen, A. Wallraff,
Physical Review A - Atomic, Molecular, and Optical Physics 83 (2011).
date_created: 2018-12-11T11:53:58Z
date_published: 2011-06-22T00:00:00Z
date_updated: 2021-01-12T06:53:09Z
day: '22'
doi: 10.1103/PhysRevA.83.063827
extern: 1
intvolume: ' 83'
issue: '6'
month: '06'
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '5335'
quality_controlled: 0
status: public
title: Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit
quantum electrodynamics
type: journal_article
volume: 83
year: '2011'
...
---
OA_type: closed access
_id: '18012'
abstract:
- lang: eng
text: We report the first concurrent determination of conductance (G) and thermopower
(S) of single-molecule junctions via direct measurement of electrical and thermoelectric
currents using a scanning tunneling microscope-based break-junction technique.
We explore several amine-Au and pyridine-Au linked molecules that are predicted
to conduct through either the highest occupied molecular orbital (HOMO) or the
lowest unoccupied molecular orbital (LUMO), respectively. We find that the Seebeck
coefficient is negative for pyridine-Au linked LUMO-conducting junctions and positive
for amine-Au linked HOMO-conducting junctions. Within the accessible temperature
gradients (<30 K), we do not observe a strong dependence of the junction Seebeck
coefficient on temperature. From histograms of thousands of junctions, we use
the most probable Seebeck coefficient to determine a power factor, GS2, for each
junction studied, and find that GS2 increases with G. Finally, we find that conductance
and Seebeck coefficient values are in good quantitative agreement with our self-energy
corrected density functional theory calculations.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Jonathan R.
full_name: Widawsky, Jonathan R.
last_name: Widawsky
- first_name: Pierre
full_name: Darancet, Pierre
last_name: Darancet
- first_name: Jeffrey B.
full_name: Neaton, Jeffrey B.
last_name: Neaton
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
citation:
ama: Widawsky JR, Darancet P, Neaton JB, Venkataraman L. Simultaneous determination
of conductance and thermopower of single molecule junctions. Nano Letters.
2011;12(1):354-358. doi:10.1021/nl203634m
apa: Widawsky, J. R., Darancet, P., Neaton, J. B., & Venkataraman, L. (2011).
Simultaneous determination of conductance and thermopower of single molecule junctions.
Nano Letters. American Chemical Society. https://doi.org/10.1021/nl203634m
chicago: Widawsky, Jonathan R., Pierre Darancet, Jeffrey B. Neaton, and Latha Venkataraman.
“Simultaneous Determination of Conductance and Thermopower of Single Molecule
Junctions.” Nano Letters. American Chemical Society, 2011. https://doi.org/10.1021/nl203634m.
ieee: J. R. Widawsky, P. Darancet, J. B. Neaton, and L. Venkataraman, “Simultaneous
determination of conductance and thermopower of single molecule junctions,” Nano
Letters, vol. 12, no. 1. American Chemical Society, pp. 354–358, 2011.
ista: Widawsky JR, Darancet P, Neaton JB, Venkataraman L. 2011. Simultaneous determination
of conductance and thermopower of single molecule junctions. Nano Letters. 12(1),
354–358.
mla: Widawsky, Jonathan R., et al. “Simultaneous Determination of Conductance and
Thermopower of Single Molecule Junctions.” Nano Letters, vol. 12, no. 1,
American Chemical Society, 2011, pp. 354–58, doi:10.1021/nl203634m.
short: J.R. Widawsky, P. Darancet, J.B. Neaton, L. Venkataraman, Nano Letters 12
(2011) 354–358.
date_created: 2024-09-09T12:32:14Z
date_published: 2011-11-30T00:00:00Z
date_updated: 2025-01-03T09:26:26Z
day: '30'
doi: 10.1021/nl203634m
extern: '1'
external_id:
pmid:
- '22128800'
intvolume: ' 12'
issue: '1'
language:
- iso: eng
month: '11'
oa_version: None
page: 354-358
pmid: 1
publication: Nano Letters
publication_identifier:
eissn:
- 1530-6992
issn:
- 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Simultaneous determination of conductance and thermopower of single molecule
junctions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2011'
...
---
OA_place: repository
OA_type: green
_id: '18014'
abstract:
- lang: eng
text: We measure electronic conductance through single conjugated molecules bonded
to Au metal electrodes with direct Au–C covalent bonds using the scanning tunneling
microscope based break-junction technique. We start with molecules terminated
with trimethyltin end groups that cleave off in situ, resulting in formation of
a direct covalent σ bond between the carbon backbone and the gold metal electrodes.
The molecular carbon backbone used in this study consist of a conjugated π system
that has one terminal methylene group on each end, which bonds to the electrodes,
achieving large electronic coupling of the electrodes to the π system. The junctions
formed with the prototypical example of 1,4-dimethylenebenzene show a conductance
approaching one conductance quantum (G0 = 2e2/h). Junctions formed with methylene-terminated
oligophenyls with two to four phenyl units show a 100-fold increase in conductance
compared with junctions formed with amine-linked oligophenyls. The conduction
mechanism for these longer oligophenyls is tunneling, as they exhibit an exponential
dependence of conductance on oligomer length. In addition, density functional
theory based calculations for the Au–xylylene–Au junction show near-resonant transmission,
with a crossover to tunneling for the longer oligomers.
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Wenbo
full_name: Chen, Wenbo
last_name: Chen
- first_name: Jonathan R.
full_name: Widawsky, Jonathan R.
last_name: Widawsky
- first_name: Héctor
full_name: Vázquez, Héctor
last_name: Vázquez
- first_name: Severin T.
full_name: Schneebeli, Severin T.
last_name: Schneebeli
- first_name: Mark S.
full_name: Hybertsen, Mark S.
last_name: Hybertsen
- first_name: Ronald
full_name: Breslow, Ronald
last_name: Breslow
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
citation:
ama: Chen W, Widawsky JR, Vázquez H, et al. Highly conducting π-conjugated molecular
junctions covalently bonded to gold electrodes. Journal of the American Chemical
Society. 2011;133(43):17160-17163. doi:10.1021/ja208020j
apa: Chen, W., Widawsky, J. R., Vázquez, H., Schneebeli, S. T., Hybertsen, M. S.,
Breslow, R., & Venkataraman, L. (2011). Highly conducting π-conjugated molecular
junctions covalently bonded to gold electrodes. Journal of the American Chemical
Society. American Chemical Society. https://doi.org/10.1021/ja208020j
chicago: Chen, Wenbo, Jonathan R. Widawsky, Héctor Vázquez, Severin T. Schneebeli,
Mark S. Hybertsen, Ronald Breslow, and Latha Venkataraman. “Highly Conducting
π-Conjugated Molecular Junctions Covalently Bonded to Gold Electrodes.” Journal
of the American Chemical Society. American Chemical Society, 2011. https://doi.org/10.1021/ja208020j.
ieee: W. Chen et al., “Highly conducting π-conjugated molecular junctions
covalently bonded to gold electrodes,” Journal of the American Chemical Society,
vol. 133, no. 43. American Chemical Society, pp. 17160–17163, 2011.
ista: Chen W, Widawsky JR, Vázquez H, Schneebeli ST, Hybertsen MS, Breslow R, Venkataraman
L. 2011. Highly conducting π-conjugated molecular junctions covalently bonded
to gold electrodes. Journal of the American Chemical Society. 133(43), 17160–17163.
mla: Chen, Wenbo, et al. “Highly Conducting π-Conjugated Molecular Junctions Covalently
Bonded to Gold Electrodes.” Journal of the American Chemical Society, vol.
133, no. 43, American Chemical Society, 2011, pp. 17160–63, doi:10.1021/ja208020j.
short: W. Chen, J.R. Widawsky, H. Vázquez, S.T. Schneebeli, M.S. Hybertsen, R. Breslow,
L. Venkataraman, Journal of the American Chemical Society 133 (2011) 17160–17163.
date_created: 2024-09-09T12:33:46Z
date_published: 2011-09-22T00:00:00Z
date_updated: 2025-01-03T09:34:24Z
day: '22'
doi: 10.1021/ja208020j
extern: '1'
external_id:
arxiv:
- '1110.0344'
pmid:
- '21939263'
intvolume: ' 133'
issue: '43'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1110.0344
month: '09'
oa: 1
oa_version: Preprint
page: 17160-17163
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Highly conducting π-conjugated molecular junctions covalently bonded to gold
electrodes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 133
year: '2011'
...
---
OA_type: closed access
_id: '18015'
abstract:
- lang: eng
text: We investigate the binding and energy level alignment of 2,3,5,6-tetramethyl-1,4-benzenediamine
(TMBDA) on Au(111) through a combination of helium atom scattering (HAS), X-ray
photoemission (XPS), and scanning tunneling microscopy (STM). We show that TMBDA
binds to step edges and to flat Au (111) terraces in a nearly flat-lying configuration.
Through combination of HAS and STM data, we determine that the molecules are bound
on step edges with an adsorption energy of about 1.2 eV, which is about 0.2 eV
stronger than the adsorption energy we measure on flat surface. Preferential bonding
to the under-coordinated Au atoms on step edges suggests that the molecules bind
to Au through the nitrogen lone pair. Finally, STM measurements on TMBDA in these
two different adsorption configurations show that the highest-occupied molecular
orbital is deeper relative to Fermi for the more strongly bound molecules on step
edges, confirming that the nitrogen bonds through charge donation to the Au.
article_processing_charge: No
article_type: original
author:
- first_name: M.
full_name: Kamenetska, M.
last_name: Kamenetska
- first_name: M.
full_name: Dell’Angela, M.
last_name: Dell’Angela
- first_name: J.R.
full_name: Widawsky, J.R.
last_name: Widawsky
- first_name: G.
full_name: Kladnik, G.
last_name: Kladnik
- first_name: A.
full_name: Verdini, A.
last_name: Verdini
- first_name: A.
full_name: Cossaro, A.
last_name: Cossaro
- first_name: D.
full_name: Cvetko, D.
last_name: Cvetko
- first_name: A.
full_name: Morgante, A.
last_name: Morgante
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
citation:
ama: Kamenetska M, Dell’Angela M, Widawsky JR, et al. Structure and energy level
alignment of tetramethyl benzenediamine on Au(111). The Journal of Physical
Chemistry C. 2011;115(25):12625-12630. doi:10.1021/jp202555d
apa: Kamenetska, M., Dell’Angela, M., Widawsky, J. R., Kladnik, G., Verdini, A.,
Cossaro, A., … Venkataraman, L. (2011). Structure and energy level alignment of
tetramethyl benzenediamine on Au(111). The Journal of Physical Chemistry C.
American Chemical Society. https://doi.org/10.1021/jp202555d
chicago: Kamenetska, M., M. Dell’Angela, J.R. Widawsky, G. Kladnik, A. Verdini,
A. Cossaro, D. Cvetko, A. Morgante, and Latha Venkataraman. “Structure and Energy
Level Alignment of Tetramethyl Benzenediamine on Au(111).” The Journal of Physical
Chemistry C. American Chemical Society, 2011. https://doi.org/10.1021/jp202555d.
ieee: M. Kamenetska et al., “Structure and energy level alignment of tetramethyl
benzenediamine on Au(111),” The Journal of Physical Chemistry C, vol. 115,
no. 25. American Chemical Society, pp. 12625–12630, 2011.
ista: Kamenetska M, Dell’Angela M, Widawsky JR, Kladnik G, Verdini A, Cossaro A,
Cvetko D, Morgante A, Venkataraman L. 2011. Structure and energy level alignment
of tetramethyl benzenediamine on Au(111). The Journal of Physical Chemistry C.
115(25), 12625–12630.
mla: Kamenetska, M., et al. “Structure and Energy Level Alignment of Tetramethyl
Benzenediamine on Au(111).” The Journal of Physical Chemistry C, vol. 115,
no. 25, American Chemical Society, 2011, pp. 12625–30, doi:10.1021/jp202555d.
short: M. Kamenetska, M. Dell’Angela, J.R. Widawsky, G. Kladnik, A. Verdini, A.
Cossaro, D. Cvetko, A. Morgante, L. Venkataraman, The Journal of Physical Chemistry
C 115 (2011) 12625–12630.
date_created: 2024-09-09T12:34:26Z
date_published: 2011-05-17T00:00:00Z
date_updated: 2025-01-03T09:36:40Z
day: '17'
doi: 10.1021/jp202555d
extern: '1'
intvolume: ' 115'
issue: '25'
language:
- iso: eng
month: '05'
oa_version: None
page: 12625-12630
publication: The Journal of Physical Chemistry C
publication_identifier:
eissn:
- 1932-7455
issn:
- 1932-7447
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure and energy level alignment of tetramethyl benzenediamine on Au(111)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2011'
...