---
_id: '7773'
abstract:
- lang: eng
text: 'For more than a century, physicists have described real solids in terms of
perturbations about perfect crystalline order1. Such an approach takes us only
so far: a glass, another ubiquitous form of rigid matter, cannot be described
in any meaningful sense as a defected crystal2. Is there an opposite extreme to
a crystal—a solid with complete disorder—that forms an alternative starting point
for understanding real materials? Here, we argue that the solid comprising particles
with finite-ranged interactions at the jamming transition3,4,5 constitutes such
a limit. It has been shown that the physics associated with this transition can
be extended to interactions that are long ranged6. We demonstrate that jamming
physics is not restricted to amorphous systems, but dominates the behaviour of
solids with surprisingly high order. Just as the free-electron and tight-binding
models represent two idealized cases from which to understand electronic structure1,
we identify two extreme limits of mechanical behaviour. Thus, the physics of jamming
can be set side by side with the physics of crystals to provide an organizing
structure for understanding the mechanical properties of solids over the entire
spectrum of disorder.'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Goodrich CP, Liu AJ, Nagel SR. Solids between the mechanical extremes of order
and disorder. Nature Physics. 2014;10(8):578-581. doi:10.1038/nphys3006
apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Solids between the
mechanical extremes of order and disorder. Nature Physics. Springer Nature.
https://doi.org/10.1038/nphys3006
chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Solids between
the Mechanical Extremes of Order and Disorder.” Nature Physics. Springer
Nature, 2014. https://doi.org/10.1038/nphys3006.
ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Solids between the mechanical
extremes of order and disorder,” Nature Physics, vol. 10, no. 8. Springer
Nature, pp. 578–581, 2014.
ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Solids between the mechanical extremes
of order and disorder. Nature Physics. 10(8), 578–581.
mla: Goodrich, Carl Peter, et al. “Solids between the Mechanical Extremes of Order
and Disorder.” Nature Physics, vol. 10, no. 8, Springer Nature, 2014, pp.
578–81, doi:10.1038/nphys3006.
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Nature Physics 10 (2014) 578–581.
date_created: 2020-04-30T11:43:29Z
date_published: 2014-07-06T00:00:00Z
date_updated: 2021-01-12T08:15:26Z
day: '06'
doi: 10.1038/nphys3006
extern: '1'
intvolume: ' 10'
issue: '8'
language:
- iso: eng
month: '07'
oa_version: None
page: 578-581
publication: Nature Physics
publication_identifier:
issn:
- 1745-2473
- 1745-2481
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Solids between the mechanical extremes of order and disorder
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2014'
...
---
_id: '7769'
abstract:
- lang: eng
text: 'Athermal packings of soft repulsive spheres exhibit a sharp jamming transition
in the thermodynamic limit. Upon further compression, various structural and mechanical
properties display clean power-law behavior over many decades in pressure. As
with any phase transition, the rounding of such behavior in finite systems close
to the transition plays an important role in understanding the nature of the transition
itself. The situation for jamming is surprisingly rich: the assumption that jammed
packings are isotropic is only strictly true in the large-size limit, and finite-size
has a profound effect on the very meaning of jamming. Here, we provide a comprehensive
numerical study of finite-size effects in sphere packings above the jamming transition,
focusing on stability as well as the scaling of the contact number and the elastic
response.'
article_number: '022138'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Simon
full_name: Dagois-Bohy, Simon
last_name: Dagois-Bohy
- first_name: Brian P.
full_name: Tighe, Brian P.
last_name: Tighe
- first_name: Martin
full_name: van Hecke, Martin
last_name: van Hecke
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: 'Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. Jamming
in finite systems: Stability, anisotropy, fluctuations, and scaling. Physical
Review E. 2014;90(2). doi:10.1103/physreve.90.022138'
apa: 'Goodrich, C. P., Dagois-Bohy, S., Tighe, B. P., van Hecke, M., Liu, A. J.,
& Nagel, S. R. (2014). Jamming in finite systems: Stability, anisotropy, fluctuations,
and scaling. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.90.022138'
chicago: 'Goodrich, Carl Peter, Simon Dagois-Bohy, Brian P. Tighe, Martin van Hecke,
Andrea J. Liu, and Sidney R. Nagel. “Jamming in Finite Systems: Stability, Anisotropy,
Fluctuations, and Scaling.” Physical Review E. American Physical Society,
2014. https://doi.org/10.1103/physreve.90.022138.'
ieee: 'C. P. Goodrich, S. Dagois-Bohy, B. P. Tighe, M. van Hecke, A. J. Liu, and
S. R. Nagel, “Jamming in finite systems: Stability, anisotropy, fluctuations,
and scaling,” Physical Review E, vol. 90, no. 2. American Physical Society,
2014.'
ista: 'Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. 2014.
Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. Physical
Review E. 90(2), 022138.'
mla: 'Goodrich, Carl Peter, et al. “Jamming in Finite Systems: Stability, Anisotropy,
Fluctuations, and Scaling.” Physical Review E, vol. 90, no. 2, 022138,
American Physical Society, 2014, doi:10.1103/physreve.90.022138.'
short: C.P. Goodrich, S. Dagois-Bohy, B.P. Tighe, M. van Hecke, A.J. Liu, S.R. Nagel,
Physical Review E 90 (2014).
date_created: 2020-04-30T11:42:09Z
date_published: 2014-08-27T00:00:00Z
date_updated: 2021-01-12T08:15:24Z
day: '27'
doi: 10.1103/physreve.90.022138
extern: '1'
intvolume: ' 90'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 90
year: '2014'
...
---
_id: '7770'
abstract:
- lang: eng
text: Packings of frictionless athermal particles that interact only when they overlap
experience a jamming transition as a function of packing density. Such packings
provide the foundation for the theory of jamming. This theory rests on the observation
that, despite the multitude of disordered configurations, the mechanical response
to linear order depends only on the distance to the transition. We investigate
the validity and utility of such measurements that invoke the harmonic approximation
and show that, despite particles coming in and out of contact, there is a well-defined
linear regime in the thermodynamic limit.
article_number: '022201'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Goodrich CP, Liu AJ, Nagel SR. Contact nonlinearities and linear response in
jammed particulate packings. Physical Review E. 2014;90(2). doi:10.1103/physreve.90.022201
apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Contact nonlinearities
and linear response in jammed particulate packings. Physical Review E.
American Physical Society. https://doi.org/10.1103/physreve.90.022201
chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Contact Nonlinearities
and Linear Response in Jammed Particulate Packings.” Physical Review E.
American Physical Society, 2014. https://doi.org/10.1103/physreve.90.022201.
ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Contact nonlinearities and linear
response in jammed particulate packings,” Physical Review E, vol. 90, no.
2. American Physical Society, 2014.
ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Contact nonlinearities and linear response
in jammed particulate packings. Physical Review E. 90(2), 022201.
mla: Goodrich, Carl Peter, et al. “Contact Nonlinearities and Linear Response in
Jammed Particulate Packings.” Physical Review E, vol. 90, no. 2, 022201,
American Physical Society, 2014, doi:10.1103/physreve.90.022201.
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review E 90 (2014).
date_created: 2020-04-30T11:42:24Z
date_published: 2014-08-04T00:00:00Z
date_updated: 2021-01-12T08:15:25Z
day: '04'
doi: 10.1103/physreve.90.022201
extern: '1'
intvolume: ' 90'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Contact nonlinearities and linear response in jammed particulate packings
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 90
year: '2014'
...
---
_id: '8021'
abstract:
- lang: eng
text: 'Most excitatory inputs in the mammalian brain are made on dendritic spines,
rather than on dendritic shafts. Spines compartmentalize calcium, and this biochemical
isolation can underlie input-specific synaptic plasticity, providing a raison
d''etre for spines. However, recent results indicate that the spine can experience
a membrane potential different from that in the parent dendrite, as though the
spine neck electrically isolated the spine. Here we use two-photon calcium imaging
of mouse neocortical pyramidal neurons to analyze the correlation between the
morphologies of spines activated under minimal synaptic stimulation and the excitatory
postsynaptic potentials they generate. We find that excitatory postsynaptic potential
amplitudes are inversely correlated with spine neck lengths. Furthermore, a spike
timing-dependent plasticity protocol, in which two-photon glutamate uncaging over
a spine is paired with postsynaptic spikes, produces rapid shrinkage of the spine
neck and concomitant increases in the amplitude of the evoked spine potentials.
Using numerical simulations, we explore the parameter regimes for the spine neck
resistance and synaptic conductance changes necessary to explain our observations.
Our data, directly correlating synaptic and morphological plasticity, imply that
long-necked spines have small or negligible somatic voltage contributions, but
that, upon synaptic stimulation paired with postsynaptic activity, they can shorten
their necks and increase synaptic efficacy, thus changing the input/output gain
of pyramidal neurons. '
article_processing_charge: No
article_type: original
author:
- first_name: R.
full_name: Araya, R.
last_name: Araya
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: R.
full_name: Yuste, R.
last_name: Yuste
citation:
ama: Araya R, Vogels TP, Yuste R. Activity-dependent dendritic spine neck changes
are correlated with synaptic strength. Proceedings of the National Academy
of Sciences. 2014;111(28):E2895-E2904. doi:10.1073/pnas.1321869111
apa: Araya, R., Vogels, T. P., & Yuste, R. (2014). Activity-dependent dendritic
spine neck changes are correlated with synaptic strength. Proceedings of the
National Academy of Sciences. Proceedings of the National Academy of Sciences.
https://doi.org/10.1073/pnas.1321869111
chicago: Araya, R., Tim P Vogels, and R. Yuste. “Activity-Dependent Dendritic Spine
Neck Changes Are Correlated with Synaptic Strength.” Proceedings of the National
Academy of Sciences. Proceedings of the National Academy of Sciences, 2014.
https://doi.org/10.1073/pnas.1321869111.
ieee: R. Araya, T. P. Vogels, and R. Yuste, “Activity-dependent dendritic spine
neck changes are correlated with synaptic strength,” Proceedings of the National
Academy of Sciences, vol. 111, no. 28. Proceedings of the National Academy
of Sciences, pp. E2895–E2904, 2014.
ista: Araya R, Vogels TP, Yuste R. 2014. Activity-dependent dendritic spine neck
changes are correlated with synaptic strength. Proceedings of the National Academy
of Sciences. 111(28), E2895–E2904.
mla: Araya, R., et al. “Activity-Dependent Dendritic Spine Neck Changes Are Correlated
with Synaptic Strength.” Proceedings of the National Academy of Sciences,
vol. 111, no. 28, Proceedings of the National Academy of Sciences, 2014, pp. E2895–904,
doi:10.1073/pnas.1321869111.
short: R. Araya, T.P. Vogels, R. Yuste, Proceedings of the National Academy of Sciences
111 (2014) E2895–E2904.
date_created: 2020-06-25T13:06:24Z
date_published: 2014-07-15T00:00:00Z
date_updated: 2021-01-12T08:16:34Z
day: '15'
doi: 10.1073/pnas.1321869111
extern: '1'
external_id:
pmid:
- '24982196'
intvolume: ' 111'
issue: '28'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104910/
month: '07'
oa: 1
oa_version: Published Version
page: E2895-E2904
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Activity-dependent dendritic spine neck changes are correlated with synaptic
strength
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 111
year: '2014'
...
---
_id: '8023'
abstract:
- lang: eng
text: Uniform random sparse network architectures are ubiquitous in computational
neuroscience, but the implicit hypothesis that they are a good representation
of real neuronal networks has been met with skepticism. Here we used two experimental
data sets, a study of triplet connectivity statistics and a data set measuring
neuronal responses to channelrhodopsin stimuli, to evaluate the fidelity of thousands
of model networks. Network architectures comprised three neuron types (excitatory,
fast spiking, and nonfast spiking inhibitory) and were created from a set of rules
that govern the statistics of the resulting connection types. In a high-dimensional
parameter scan, we varied the degree distributions (i.e., how many cells each
neuron connects with) and the synaptic weight correlations of synapses from or
onto the same neuron. These variations converted initially uniform random and
homogeneously connected networks, in which every neuron sent and received equal
numbers of synapses with equal synaptic strength distributions, to highly heterogeneous
networks in which the number of synapses per neuron, as well as average synaptic
strength of synapses from or to a neuron were variable. By evaluating the impact
of each variable on the network structure and dynamics, and their similarity to
the experimental data, we could falsify the uniform random sparse connectivity
hypothesis for 7 of 36 connectivity parameters, but we also confirmed the hypothesis
in 8 cases. Twenty-one parameters had no substantial impact on the results of
the test protocols we used.
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Tomm, Christian
last_name: Tomm
- first_name: Michael
full_name: Avermann, Michael
last_name: Avermann
- first_name: Carl
full_name: Petersen, Carl
last_name: Petersen
- first_name: Wulfram
full_name: Gerstner, Wulfram
last_name: Gerstner
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. Connection-type-specific
biases make uniform random network models consistent with cortical recordings.
Journal of Neurophysiology. 2014;112(8):1801-1814. doi:10.1152/jn.00629.2013
apa: Tomm, C., Avermann, M., Petersen, C., Gerstner, W., & Vogels, T. P. (2014).
Connection-type-specific biases make uniform random network models consistent
with cortical recordings. Journal of Neurophysiology. American Physiological
Society. https://doi.org/10.1152/jn.00629.2013
chicago: Tomm, Christian, Michael Avermann, Carl Petersen, Wulfram Gerstner, and
Tim P Vogels. “Connection-Type-Specific Biases Make Uniform Random Network Models
Consistent with Cortical Recordings.” Journal of Neurophysiology. American
Physiological Society, 2014. https://doi.org/10.1152/jn.00629.2013.
ieee: C. Tomm, M. Avermann, C. Petersen, W. Gerstner, and T. P. Vogels, “Connection-type-specific
biases make uniform random network models consistent with cortical recordings,”
Journal of Neurophysiology, vol. 112, no. 8. American Physiological Society,
pp. 1801–1814, 2014.
ista: Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. 2014. Connection-type-specific
biases make uniform random network models consistent with cortical recordings.
Journal of Neurophysiology. 112(8), 1801–1814.
mla: Tomm, Christian, et al. “Connection-Type-Specific Biases Make Uniform Random
Network Models Consistent with Cortical Recordings.” Journal of Neurophysiology,
vol. 112, no. 8, American Physiological Society, 2014, pp. 1801–14, doi:10.1152/jn.00629.2013.
short: C. Tomm, M. Avermann, C. Petersen, W. Gerstner, T.P. Vogels, Journal of Neurophysiology
112 (2014) 1801–1814.
date_created: 2020-06-25T13:08:30Z
date_published: 2014-10-15T00:00:00Z
date_updated: 2021-01-12T08:16:35Z
day: '15'
ddc:
- '570'
doi: 10.1152/jn.00629.2013
extern: '1'
external_id:
pmid:
- '24944218'
file:
- access_level: open_access
checksum: 7c06a086da6f924342650de6dc555c3f
content_type: application/pdf
creator: cziletti
date_created: 2020-07-16T10:12:13Z
date_updated: 2020-07-16T10:12:13Z
file_id: '8122'
file_name: 2014_JNeurophysiol_Tomm.pdf
file_size: 1632295
relation: main_file
success: 1
file_date_updated: 2020-07-16T10:12:13Z
has_accepted_license: '1'
intvolume: ' 112'
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '10'
oa: 1
oa_version: Published Version
page: 1801-1814
pmid: 1
publication: Journal of Neurophysiology
publication_identifier:
eissn:
- 1522-1598
issn:
- 0022-3077
publication_status: published
publisher: American Physiological Society
quality_controlled: '1'
status: public
title: Connection-type-specific biases make uniform random network models consistent
with cortical recordings
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 112
year: '2014'
...
---
_id: '8022'
abstract:
- lang: eng
text: Populations of neurons in motor cortex engage in complex transient dynamics
of large amplitude during the execution of limb movements. Traditional network
models with stochastically assigned synapses cannot reproduce this behavior. Here
we introduce a class of cortical architectures with strong and random excitatory
recurrence that is stabilized by intricate, fine-tuned inhibition, optimized from
a control theory perspective. Such networks transiently amplify specific activity
states and can be used to reliably execute multidimensional movement patterns.
Similar to the experimental observations, these transients must be preceded by
a steady-state initialization phase from which the network relaxes back into the
background state by way of complex internal dynamics. In our networks, excitation
and inhibition are as tightly balanced as recently reported in experiments across
several brain areas, suggesting inhibitory control of complex excitatory recurrence
as a generic organizational principle in cortex.
article_processing_charge: No
article_type: original
author:
- first_name: Guillaume
full_name: Hennequin, Guillaume
last_name: Hennequin
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Wulfram
full_name: Gerstner, Wulfram
last_name: Gerstner
citation:
ama: Hennequin G, Vogels TP, Gerstner W. Optimal control of transient dynamics in
balanced networks supports generation of complex movements. Neuron. 2014;82(6):1394-1406.
doi:10.1016/j.neuron.2014.04.045
apa: Hennequin, G., Vogels, T. P., & Gerstner, W. (2014). Optimal control of
transient dynamics in balanced networks supports generation of complex movements.
Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.04.045
chicago: Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Optimal Control
of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.”
Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.045.
ieee: G. Hennequin, T. P. Vogels, and W. Gerstner, “Optimal control of transient
dynamics in balanced networks supports generation of complex movements,” Neuron,
vol. 82, no. 6. Elsevier, pp. 1394–1406, 2014.
ista: Hennequin G, Vogels TP, Gerstner W. 2014. Optimal control of transient dynamics
in balanced networks supports generation of complex movements. Neuron. 82(6),
1394–1406.
mla: Hennequin, Guillaume, et al. “Optimal Control of Transient Dynamics in Balanced
Networks Supports Generation of Complex Movements.” Neuron, vol. 82, no.
6, Elsevier, 2014, pp. 1394–406, doi:10.1016/j.neuron.2014.04.045.
short: G. Hennequin, T.P. Vogels, W. Gerstner, Neuron 82 (2014) 1394–1406.
date_created: 2020-06-25T13:07:37Z
date_published: 2014-06-18T00:00:00Z
date_updated: 2021-01-12T08:16:35Z
day: '18'
doi: 10.1016/j.neuron.2014.04.045
extern: '1'
external_id:
pmid:
- '24945778'
intvolume: ' 82'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364799/
month: '06'
oa: 1
oa_version: Submitted Version
page: 1394-1406
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Optimal control of transient dynamics in balanced networks supports generation
of complex movements
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 82
year: '2014'
...
---
_id: '809'
abstract:
- lang: eng
text: The assembly of HIV-1 is mediated by oligomerization of the major structural
polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the
infected cell. This leads to budding and release of progeny immature virus particles.
Subsequent proteolytic cleavage of Gag triggers rearrangement of the particles
to form mature infectious virions. Obtaining a structural model of the assembled
lattice of Gag within immature virus particles is necessary to understand the
interactions that mediate assembly of HIV-1 particles in the infected cell, and
to describe the substrate that is subsequently cleaved by the viral protease.
An 8-Å resolution structure of an immature virus-like tubular array assembled
from a Gag-derived protein of the related retrovirus Mason-Pfizer monkey virus
(M-PMV) has previously been reported, and a model for the arrangement of the HIV-1
capsid (CA) domains has been generated based on homology to this structure. Here
we have assembled tubular arrays of a HIV-1 Gag-derived protein with an immature-like
arrangement of the C-terminal CA domains and have solved their structure by using
hybrid cryo-EM and tomography analysis. The structure reveals the arrangement
of the C-terminal domain of CA within an immature-like HIV-1 Gag lattice, and
provides, to our knowledge, the first high-resolution view of the region immediately
downstream of CA, which is essential for assembly, and is significantly different
from the respective region in M-PMV. Our results reveal a hollow column of density
for this region in HIV-1 that is compatible with the presence of a six-helix bundle
at this position.
acknowledgement: 'The authors thank Leonardo Trabuco for help with running MDFF, Maria
Anders for preparing amprenavir-inhibited virus, Marie-Christine Vaney for help
with X-ray data processing and structure refinement, Ahmed Haouz and Patrick Weber
(robotized crystallization facility Proteopole, Institut Pasteur) for help in crystal
screening, and the European Molecular Biology Laboratory (EMBL) Information Technology
Services Unit and Frank Thommen for technical support. This study was supported
by Deutsche Forschungsgemeinschaft Grants BR 3635/2-1 (to J.A.G.B.) and KR 906/7-1
(to H.-G.K.) and a Federation of European Biochemical Societies long-term fellowship
(to T.A.M.B.). The laboratory of J.A.G.B. acknowledges financial support from EMBL
and the Chica und Heinz Schaller Stiftung. '
author:
- first_name: Tanmay
full_name: Bharata, Tanmay A
last_name: Bharata
- first_name: Luis
full_name: Menendez, Luis R
last_name: Menendez
- first_name: Wim
full_name: Hagena, Wim J
last_name: Hagena
- first_name: Vanda
full_name: Luxd, Vanda
last_name: Luxd
- first_name: Sebastien
full_name: Igonete, Sebastien
last_name: Igonete
- first_name: Martin
full_name: Schorba, Martin
last_name: Schorba
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Hans
full_name: Kraüsslich, Hans Georg
last_name: Kraüsslich
- first_name: John
full_name: Briggsa, John A
last_name: Briggsa
citation:
ama: Bharata T, Menendez L, Hagena W, et al. Cryo electron microscopy of tubular
arrays of HIV-1 Gag resolves structures essential for immature virus assembly.
PNAS. 2014;111(22):8233-8238. doi:10.1073/pnas.1401455111
apa: Bharata, T., Menendez, L., Hagena, W., Luxd, V., Igonete, S., Schorba, M.,
… Briggsa, J. (2014). Cryo electron microscopy of tubular arrays of HIV-1 Gag
resolves structures essential for immature virus assembly. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1401455111
chicago: Bharata, Tanmay, Luis Menendez, Wim Hagena, Vanda Luxd, Sebastien Igonete,
Martin Schorba, Florian KM Schur, Hans Kraüsslich, and John Briggsa. “Cryo Electron
Microscopy of Tubular Arrays of HIV-1 Gag Resolves Structures Essential for Immature
Virus Assembly.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1401455111.
ieee: T. Bharata et al., “Cryo electron microscopy of tubular arrays of HIV-1
Gag resolves structures essential for immature virus assembly,” PNAS, vol.
111, no. 22. National Academy of Sciences, pp. 8233–8238, 2014.
ista: Bharata T, Menendez L, Hagena W, Luxd V, Igonete S, Schorba M, Schur FK, Kraüsslich
H, Briggsa J. 2014. Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves
structures essential for immature virus assembly. PNAS. 111(22), 8233–8238.
mla: Bharata, Tanmay, et al. “Cryo Electron Microscopy of Tubular Arrays of HIV-1
Gag Resolves Structures Essential for Immature Virus Assembly.” PNAS, vol.
111, no. 22, National Academy of Sciences, 2014, pp. 8233–38, doi:10.1073/pnas.1401455111.
short: T. Bharata, L. Menendez, W. Hagena, V. Luxd, S. Igonete, M. Schorba, F.K.
Schur, H. Kraüsslich, J. Briggsa, PNAS 111 (2014) 8233–8238.
date_created: 2018-12-11T11:48:37Z
date_published: 2014-06-03T00:00:00Z
date_updated: 2021-01-12T08:16:50Z
day: '03'
doi: 10.1073/pnas.1401455111
extern: 1
intvolume: ' 111'
issue: '22'
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '06'
page: 8233 - 8238
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6838'
quality_controlled: 0
status: public
title: Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures
essential for immature virus assembly
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
volume: 111
year: '2014'
...
---
_id: '8244'
abstract:
- lang: eng
text: Passive immunotherapy with monoclonal antibodies represents a cornerstone
of human anticancer therapies, but has not been established in veterinary medicine
yet. As the tumor-associated antigen EGFR (ErbB-1) is highly conserved between
humans and dogs, and considering the effectiveness of the anti-EGFR antibody cetuximab
in human clinical oncology, we present here a “caninized” version of this antibody,
can225IgG, for comparative oncology studies. Variable region genes of 225, the
murine precursor of cetuximab, were fused with canine constant heavy gamma and
kappa chain genes, respectively, and transfected into Chinese hamster ovary (CHO)
DUKX-B11 cells. Of note, 480 clones were screened and the best clones were selected
according to productivity and highest specificity in EGFR-coated ELISA. Upon purification
with Protein G, the recombinant cetuximab-like canine IgG was tested for integrity,
correct assembly, and functionality. Specific binding to the surface of EGFR-overexpressing
cells was assessed by flow cytometry and immunofluorescence; moreover, binding
to canine mammary tissue was demonstrated by immunohistochemistry. In cell viability
and proliferation assays, incubation with can225IgG led to significant tumor cell
growth inhibition. Moreover, this antibody mediated significant tumor cell killing
via phagocytosis in vitro. We thus present here, for the first time, the generation
of a canine IgG antibody and its hypothetical structure. On the basis of its cetuximab-like
binding site, on the one hand, and the expression of a 91% homologous EGFR molecule
in canine cancer, on the other hand, this antibody may be a promising research
compound to establish passive immunotherapy in dog patients with cancer.
article_processing_charge: No
article_type: original
author:
- first_name: J.
full_name: Singer, J.
last_name: Singer
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: W.
full_name: Wang, W.
last_name: Wang
- first_name: M.
full_name: Weichselbaumer, M.
last_name: Weichselbaumer
- first_name: M.
full_name: Matz, M.
last_name: Matz
- first_name: A.
full_name: Mader, A.
last_name: Mader
- first_name: W.
full_name: Steinfellner, W.
last_name: Steinfellner
- first_name: S.
full_name: Meitz, S.
last_name: Meitz
- first_name: D.
full_name: Mechtcheriakova, D.
last_name: Mechtcheriakova
- first_name: Y.
full_name: Sobanov, Y.
last_name: Sobanov
- first_name: M.
full_name: Willmann, M.
last_name: Willmann
- first_name: T.
full_name: Stockner, T.
last_name: Stockner
- first_name: E.
full_name: Spillner, E.
last_name: Spillner
- first_name: R.
full_name: Kunert, R.
last_name: Kunert
- first_name: E.
full_name: Jensen-Jarolim, E.
last_name: Jensen-Jarolim
citation:
ama: Singer J, Singer J, Wang W, et al. Generation of a canine anti-EGFR (ErbB-1)
antibody for passive immunotherapy in dog cancer patients. Molecular Cancer
Therapeutics. 2014;13(7):1777-1790. doi:10.1158/1535-7163.mct-13-0288
apa: Singer, J., Singer, J., Wang, W., Weichselbaumer, M., Matz, M., Mader, A.,
… Jensen-Jarolim, E. (2014). Generation of a canine anti-EGFR (ErbB-1) antibody
for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics.
American Association for Cancer Research. https://doi.org/10.1158/1535-7163.mct-13-0288
chicago: Singer, J., Judit Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader,
W. Steinfellner, et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for
Passive Immunotherapy in Dog Cancer Patients.” Molecular Cancer Therapeutics.
American Association for Cancer Research, 2014. https://doi.org/10.1158/1535-7163.mct-13-0288.
ieee: J. Singer et al., “Generation of a canine anti-EGFR (ErbB-1) antibody
for passive immunotherapy in dog cancer patients,” Molecular Cancer Therapeutics,
vol. 13, no. 7. American Association for Cancer Research, pp. 1777–1790, 2014.
ista: Singer J, Singer J, Wang W, Weichselbaumer M, Matz M, Mader A, Steinfellner
W, Meitz S, Mechtcheriakova D, Sobanov Y, Willmann M, Stockner T, Spillner E,
Kunert R, Jensen-Jarolim E. 2014. Generation of a canine anti-EGFR (ErbB-1) antibody
for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics.
13(7), 1777–1790.
mla: Singer, J., et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for
Passive Immunotherapy in Dog Cancer Patients.” Molecular Cancer Therapeutics,
vol. 13, no. 7, American Association for Cancer Research, 2014, pp. 1777–90, doi:10.1158/1535-7163.mct-13-0288.
short: J. Singer, J. Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader, W. Steinfellner,
S. Meitz, D. Mechtcheriakova, Y. Sobanov, M. Willmann, T. Stockner, E. Spillner,
R. Kunert, E. Jensen-Jarolim, Molecular Cancer Therapeutics 13 (2014) 1777–1790.
date_created: 2020-08-10T11:54:29Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2021-01-12T08:17:42Z
day: '01'
doi: 10.1158/1535-7163.mct-13-0288
extern: '1'
intvolume: ' 13'
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
page: 1777-1790
publication: Molecular Cancer Therapeutics
publication_identifier:
issn:
- 1535-7163
- 1538-8514
publication_status: published
publisher: American Association for Cancer Research
quality_controlled: '1'
status: public
title: Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy
in dog cancer patients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2014'
...
---
_id: '8459'
abstract:
- lang: eng
text: Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion
of biomolecules at the atomic level. One technique, the analysis of relaxation
dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics
of biological processes. Built on top of the relax computational environment for
NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate
and easy-to-use. The software supports more models, both numeric and analytic,
than current solutions. An automated protocol, available for scripting and driving
the graphical user interface (GUI), is designed to simplify the analysis of dispersion
data for NMR spectroscopists. Decreases in optimization time are granted by parallelization
for running on computer clusters and by skipping an initial grid search by using
parameters from one solution as the starting point for another —using analytic
model results for the numeric models, taking advantage of model nesting, and using
averaged non-clustered results for the clustered analysis.
article_processing_charge: No
article_type: original
author:
- first_name: Sébastien
full_name: Morin, Sébastien
last_name: Morin
- first_name: Troels E
full_name: Linnet, Troels E
last_name: Linnet
- first_name: Mathilde
full_name: Lescanne, Mathilde
last_name: Lescanne
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Gary S
full_name: Thompson, Gary S
last_name: Thompson
- first_name: Martin
full_name: Tollinger, Martin
last_name: Tollinger
- first_name: Kaare
full_name: Teilum, Kaare
last_name: Teilum
- first_name: Stéphane
full_name: Gagné, Stéphane
last_name: Gagné
- first_name: Dominique
full_name: Marion, Dominique
last_name: Marion
- first_name: Christian
full_name: Griesinger, Christian
last_name: Griesinger
- first_name: Martin
full_name: Blackledge, Martin
last_name: Blackledge
- first_name: Edward J
full_name: d’Auvergne, Edward J
last_name: d’Auvergne
citation:
ama: 'Morin S, Linnet TE, Lescanne M, et al. Relax: The analysis of biomolecular
kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics.
2014;30(15):2219-2220. doi:10.1093/bioinformatics/btu166'
apa: 'Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger,
M., … d’Auvergne, E. J. (2014). Relax: The analysis of biomolecular kinetics and
thermodynamics using NMR relaxation dispersion data. Bioinformatics. Oxford
University Press. https://doi.org/10.1093/bioinformatics/btu166'
chicago: 'Morin, Sébastien, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary
S Thompson, Martin Tollinger, Kaare Teilum, et al. “Relax: The Analysis of Biomolecular
Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics.
Oxford University Press, 2014. https://doi.org/10.1093/bioinformatics/btu166.'
ieee: 'S. Morin et al., “Relax: The analysis of biomolecular kinetics and
thermodynamics using NMR relaxation dispersion data,” Bioinformatics, vol.
30, no. 15. Oxford University Press, pp. 2219–2220, 2014.'
ista: 'Morin S, Linnet TE, Lescanne M, Schanda P, Thompson GS, Tollinger M, Teilum
K, Gagné S, Marion D, Griesinger C, Blackledge M, d’Auvergne EJ. 2014. Relax:
The analysis of biomolecular kinetics and thermodynamics using NMR relaxation
dispersion data. Bioinformatics. 30(15), 2219–2220.'
mla: 'Morin, Sébastien, et al. “Relax: The Analysis of Biomolecular Kinetics and
Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics, vol.
30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:10.1093/bioinformatics/btu166.'
short: S. Morin, T.E. Linnet, M. Lescanne, P. Schanda, G.S. Thompson, M. Tollinger,
K. Teilum, S. Gagné, D. Marion, C. Griesinger, M. Blackledge, E.J. d’Auvergne,
Bioinformatics 30 (2014) 2219–2220.
date_created: 2020-09-18T10:08:07Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '01'
doi: 10.1093/bioinformatics/btu166
extern: '1'
intvolume: ' 30'
issue: '15'
keyword:
- Statistics and Probability
- Computational Theory and Mathematics
- Biochemistry
- Molecular Biology
- Computational Mathematics
- Computer Science Applications
language:
- iso: eng
month: '08'
oa_version: None
page: 2219-2220
publication: Bioinformatics
publication_identifier:
issn:
- 1367-4803
- 1460-2059
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1093/bioinformatics/btz397
status: public
title: 'Relax: The analysis of biomolecular kinetics and thermodynamics using NMR
relaxation dispersion data'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2014'
...
---
_id: '8458'
abstract:
- lang: eng
text: The maintenance of bacterial cell shape and integrity is largely attributed
to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform
this cross-linking are important targets for antibiotics. Despite this biomedical
importance, to date no structure of a protein in complex with an intact bacterial
peptidoglycan has been resolved, primarily due to the large size and flexibility
of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for
the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis
bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly,
the model obtained from protein chemical shift perturbation data shows that both
domains—the catalytic domain as well as the proposed peptidoglycan recognition
domain—are important for the interaction and reveals a novel binding motif that
involves residues outside of the classical enzymatic pocket. Experiments on mutants
and truncated protein constructs independently confirm the binding site and the
implication of both domains. Through measurements of dipolar-coupling derived
order parameters of bond motion we show that protein binding reduces the flexibility
of peptidoglycan. This first report of an atomic model of a protein–peptidoglycan
complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases.
The strategy developed here can be extended to the study of a large variety of
enzymes involved in peptidoglycan morphogenesis.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Sébastien
full_name: Triboulet, Sébastien
last_name: Triboulet
- first_name: Cédric
full_name: Laguri, Cédric
last_name: Laguri
- first_name: Catherine M.
full_name: Bougault, Catherine M.
last_name: Bougault
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Morgane
full_name: Callon, Morgane
last_name: Callon
- first_name: Michel
full_name: Arthur, Michel
last_name: Arthur
- first_name: Jean-Pierre
full_name: Simorre, Jean-Pierre
last_name: Simorre
citation:
ama: Schanda P, Triboulet S, Laguri C, et al. Atomic model of a cell-wall cross-linking
enzyme in complex with an intact bacterial peptidoglycan. Journal of the American
Chemical Society. 2014;136(51):17852-17860. doi:10.1021/ja5105987
apa: Schanda, P., Triboulet, S., Laguri, C., Bougault, C. M., Ayala, I., Callon,
M., … Simorre, J.-P. (2014). Atomic model of a cell-wall cross-linking enzyme
in complex with an intact bacterial peptidoglycan. Journal of the American
Chemical Society. American Chemical Society. https://doi.org/10.1021/ja5105987
chicago: Schanda, Paul, Sébastien Triboulet, Cédric Laguri, Catherine M. Bougault,
Isabel Ayala, Morgane Callon, Michel Arthur, and Jean-Pierre Simorre. “Atomic
Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial
Peptidoglycan.” Journal of the American Chemical Society. American Chemical
Society, 2014. https://doi.org/10.1021/ja5105987.
ieee: P. Schanda et al., “Atomic model of a cell-wall cross-linking enzyme
in complex with an intact bacterial peptidoglycan,” Journal of the American
Chemical Society, vol. 136, no. 51. American Chemical Society, pp. 17852–17860,
2014.
ista: Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M,
Simorre J-P. 2014. Atomic model of a cell-wall cross-linking enzyme in complex
with an intact bacterial peptidoglycan. Journal of the American Chemical Society.
136(51), 17852–17860.
mla: Schanda, Paul, et al. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in
Complex with an Intact Bacterial Peptidoglycan.” Journal of the American Chemical
Society, vol. 136, no. 51, American Chemical Society, 2014, pp. 17852–60,
doi:10.1021/ja5105987.
short: P. Schanda, S. Triboulet, C. Laguri, C.M. Bougault, I. Ayala, M. Callon,
M. Arthur, J.-P. Simorre, Journal of the American Chemical Society 136 (2014)
17852–17860.
date_created: 2020-09-18T10:07:52Z
date_published: 2014-11-27T00:00:00Z
date_updated: 2021-01-12T08:19:24Z
day: '27'
doi: 10.1021/ja5105987
extern: '1'
intvolume: ' 136'
issue: '51'
language:
- iso: eng
month: '11'
oa_version: None
page: 17852-17860
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Atomic model of a cell-wall cross-linking enzyme in complex with an intact
bacterial peptidoglycan
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2014'
...
---
_id: '8460'
abstract:
- lang: eng
text: The function of proteins depends on their ability to sample a variety of states
differing in structure and free energy. Deciphering how the various thermally
accessible conformations are connected, and understanding their structures and
relative energies is crucial in rationalizing protein function. Many biomolecular
reactions take place within microseconds to milliseconds, and this timescale is
therefore of central functional importance. Here we show that R1ρ relaxation dispersion
experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible
to investigate the thermodynamics and kinetics of such exchange process, and gain
insight into structural features of short‐lived states.
article_processing_charge: No
article_type: original
author:
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Jens D.
full_name: Haller, Jens D.
last_name: Haller
- first_name: Jérémy
full_name: Zajakala, Jérémy
last_name: Zajakala
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Astrid C.
full_name: Sivertsen, Astrid C.
last_name: Sivertsen
- first_name: Dieter
full_name: Willbold, Dieter
last_name: Willbold
- first_name: Jérôme
full_name: Boisbouvier, Jérôme
last_name: Boisbouvier
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Ma P, Haller JD, Zajakala J, et al. Probing transient conformational states
of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte
Chemie International Edition. 2014;53(17):4312-4317. doi:10.1002/anie.201311275
apa: Ma, P., Haller, J. D., Zajakala, J., Macek, P., Sivertsen, A. C., Willbold,
D., … Schanda, P. (2014). Probing transient conformational states of proteins
by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie
International Edition. Wiley. https://doi.org/10.1002/anie.201311275
chicago: Ma, Peixiang, Jens D. Haller, Jérémy Zajakala, Pavel Macek, Astrid C. Sivertsen,
Dieter Willbold, Jérôme Boisbouvier, and Paul Schanda. “Probing Transient Conformational
States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.”
Angewandte Chemie International Edition. Wiley, 2014. https://doi.org/10.1002/anie.201311275.
ieee: P. Ma et al., “Probing transient conformational states of proteins
by solid-state R1ρ relaxation-dispersion NMR spectroscopy,” Angewandte Chemie
International Edition, vol. 53, no. 17. Wiley, pp. 4312–4317, 2014.
ista: Ma P, Haller JD, Zajakala J, Macek P, Sivertsen AC, Willbold D, Boisbouvier
J, Schanda P. 2014. Probing transient conformational states of proteins by solid-state
R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition.
53(17), 4312–4317.
mla: Ma, Peixiang, et al. “Probing Transient Conformational States of Proteins by
Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” Angewandte Chemie
International Edition, vol. 53, no. 17, Wiley, 2014, pp. 4312–17, doi:10.1002/anie.201311275.
short: P. Ma, J.D. Haller, J. Zajakala, P. Macek, A.C. Sivertsen, D. Willbold, J.
Boisbouvier, P. Schanda, Angewandte Chemie International Edition 53 (2014) 4312–4317.
date_created: 2020-09-18T10:08:53Z
date_published: 2014-03-18T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '18'
doi: 10.1002/anie.201311275
extern: '1'
intvolume: ' 53'
issue: '17'
language:
- iso: eng
month: '03'
oa_version: None
page: 4312-4317
publication: Angewandte Chemie International Edition
publication_identifier:
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion
NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2014'
...
---
_id: '8501'
abstract:
- lang: eng
text: In this paper, we study small perturbations of a class of non-convex integrable
Hamiltonians with two degrees of freedom, and we prove a result of diffusion for
an open and dense set of perturbations, with an optimal time of diffusion which
grows linearly with respect to the inverse of the size of the perturbation.
article_processing_charge: No
article_type: original
author:
- first_name: Abed
full_name: Bounemoura, Abed
last_name: Bounemoura
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Bounemoura A, Kaloshin V. Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom. Moscow Mathematical Journal.
2014;14(2):181-203. doi:10.17323/1609-4514-2014-14-2-181-203
apa: Bounemoura, A., & Kaloshin, V. (2014). Generic fast diffusion for a class
of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical
Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2014-14-2-181-203
chicago: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class
of Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical
Journal. Independent University of Moscow, 2014. https://doi.org/10.17323/1609-4514-2014-14-2-181-203.
ieee: A. Bounemoura and V. Kaloshin, “Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom,” Moscow Mathematical Journal,
vol. 14, no. 2. Independent University of Moscow, pp. 181–203, 2014.
ista: Bounemoura A, Kaloshin V. 2014. Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 14(2),
181–203.
mla: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of
Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical Journal,
vol. 14, no. 2, Independent University of Moscow, 2014, pp. 181–203, doi:10.17323/1609-4514-2014-14-2-181-203.
short: A. Bounemoura, V. Kaloshin, Moscow Mathematical Journal 14 (2014) 181–203.
date_created: 2020-09-18T10:47:09Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T08:19:43Z
day: '01'
doi: 10.17323/1609-4514-2014-14-2-181-203
extern: '1'
external_id:
arxiv:
- '1304.3050'
intvolume: ' 14'
issue: '2'
keyword:
- General Mathematics
language:
- iso: eng
month: '04'
oa_version: Preprint
page: 181-203
publication: Moscow Mathematical Journal
publication_identifier:
issn:
- 1609-3321
- 1609-4514
publication_status: published
publisher: Independent University of Moscow
quality_controlled: '1'
status: public
title: Generic fast diffusion for a class of non-convex Hamiltonians with two degrees
of freedom
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2014'
...
---
_id: '8500'
abstract:
- lang: eng
text: The main model studied in this paper is a lattice of pendula with a nearest‐neighbor
coupling. If the coupling is weak, then the system is near‐integrable and KAM
tori fill most of the phase space. For all KAM trajectories the energy of each
pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily
weak coupling of a certain localized type, the neighboring pendula can exchange
energy. In fact, the energy can be transferred between the pendula in any prescribed
way.
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Mark
full_name: Levi, Mark
last_name: Levi
- first_name: Maria
full_name: Saprykina, Maria
last_name: Saprykina
citation:
ama: Kaloshin V, Levi M, Saprykina M. Arnol′d diffusion in a pendulum lattice. Communications
on Pure and Applied Mathematics. 2014;67(5):748-775. doi:10.1002/cpa.21509
apa: Kaloshin, V., Levi, M., & Saprykina, M. (2014). Arnol′d diffusion in a
pendulum lattice. Communications on Pure and Applied Mathematics. Wiley.
https://doi.org/10.1002/cpa.21509
chicago: Kaloshin, Vadim, Mark Levi, and Maria Saprykina. “Arnol′d Diffusion in
a Pendulum Lattice.” Communications on Pure and Applied Mathematics. Wiley,
2014. https://doi.org/10.1002/cpa.21509.
ieee: V. Kaloshin, M. Levi, and M. Saprykina, “Arnol′d diffusion in a pendulum lattice,”
Communications on Pure and Applied Mathematics, vol. 67, no. 5. Wiley,
pp. 748–775, 2014.
ista: Kaloshin V, Levi M, Saprykina M. 2014. Arnol′d diffusion in a pendulum lattice.
Communications on Pure and Applied Mathematics. 67(5), 748–775.
mla: Kaloshin, Vadim, et al. “Arnol′d Diffusion in a Pendulum Lattice.” Communications
on Pure and Applied Mathematics, vol. 67, no. 5, Wiley, 2014, pp. 748–75,
doi:10.1002/cpa.21509.
short: V. Kaloshin, M. Levi, M. Saprykina, Communications on Pure and Applied Mathematics
67 (2014) 748–775.
date_created: 2020-09-18T10:47:01Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2022-08-25T13:58:13Z
day: '01'
doi: 10.1002/cpa.21509
extern: '1'
intvolume: ' 67'
issue: '5'
keyword:
- Applied Mathematics
- General Mathematics
language:
- iso: eng
month: '05'
oa_version: None
page: 748-775
publication: Communications on Pure and Applied Mathematics
publication_identifier:
issn:
- 0010-3640
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Arnol′d diffusion in a pendulum lattice
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 67
year: '2014'
...
---
_id: '852'
abstract:
- lang: eng
text: 'Rapid divergence of gene copies after duplication is thought to determine
the fate of the copies and evolution of novel protein functions. However, data
on howlong the gene copies continue to experience an elevated rate of evolution
remain scarce. Standard theory of gene duplications based on some level of genetic
redundancy of gene copies predicts that the period of accelerated evolutionmust
end relatively quickly. Using a maximum-likelihood approach we estimate preduplication,
initial postduplication, and recent postduplication rates of evolution that occurred
in themammalian lineage.Wefind that both gene copies experience a similar in magnitude
acceleration in their rate of evolution. The copy located in the original genomic
position typically returns to the preduplication rates of evolution in a short
period of time. The burst of faster evolution of the copy that is located in a
new genomic position typically lasts longer. Furthermore, the fast-evolving copies
on average continue to evolve faster than the preduplication rates far longer
than predicted by standard theory of gene duplications.We hypothesize that the
prolonged elevated rates of evolution are determined by functional properties
that were acquired during, or soon after, the gene duplication event. '
author:
- first_name: Oriol
full_name: Rosello, Oriol P
last_name: Rosello
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Rosello O, Kondrashov F. Long-Term asymmetrical acceleration of protein evolution
after gene duplication. Genome Biology and Evolution. 2014;6(8):1949-1955.
doi:10.1093/gbe/evu159
apa: Rosello, O., & Kondrashov, F. (2014). Long-Term asymmetrical acceleration
of protein evolution after gene duplication. Genome Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/gbe/evu159
chicago: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration
of Protein Evolution after Gene Duplication.” Genome Biology and Evolution.
Oxford University Press, 2014. https://doi.org/10.1093/gbe/evu159.
ieee: O. Rosello and F. Kondrashov, “Long-Term asymmetrical acceleration of protein
evolution after gene duplication,” Genome Biology and Evolution, vol. 6,
no. 8. Oxford University Press, pp. 1949–1955, 2014.
ista: Rosello O, Kondrashov F. 2014. Long-Term asymmetrical acceleration of protein
evolution after gene duplication. Genome Biology and Evolution. 6(8), 1949–1955.
mla: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration
of Protein Evolution after Gene Duplication.” Genome Biology and Evolution,
vol. 6, no. 8, Oxford University Press, 2014, pp. 1949–55, doi:10.1093/gbe/evu159.
short: O. Rosello, F. Kondrashov, Genome Biology and Evolution 6 (2014) 1949–1955.
date_created: 2018-12-11T11:48:51Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:51Z
day: '01'
doi: 10.1093/gbe/evu159
extern: 1
intvolume: ' 6'
issue: '8'
license: https://creativecommons.org/licenses/by/4.0/
month: '08'
page: 1949 - 1955
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6797'
quality_controlled: 0
status: public
title: Long-Term asymmetrical acceleration of protein evolution after gene duplication
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 6
year: '2014'
...
---
_id: '856'
abstract:
- lang: eng
text: The emergence of new genes throughout evolution requires rewiring and extension
of regulatory networks. However, the molecular details of how the transcriptional
regulation of new gene copies evolves remain largely unexplored. Here we show
how duplication of a transcription factor gene allowed the emergence of two independent
regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous
and could bind different motifs in its target promoters. After duplication, one
paralogue evolved increased binding specificity so that it only binds one type
of motif, whereas the other copy evolved a decreased activity so that it only
activates promoters that contain multiple binding sites. Interestingly, only a
few mutations in both the DNA-binding domains and in the promoter binding sites
were required to gradually disentangle the two networks. These results reveal
how duplication of a promiscuous transcription factor followed by concerted cis
and trans mutations allows expansion of a regulatory network.
acknowledgement: 'K.P. acknowledges financial support from TRIPLE I and a Belspo mobility
grant from the Belgian Federal Science Policy Office co-funded by the Marie Curie
Actions from the European Commission. Research in the lab of K.J.V. is supported
by ERC Starting Grant 241426, HFSP programme grant RGP0050/2013, VIB, EMBO YIP programme,
KU Leuven Programme Financing, FWO, and IWT. A.V. acknowledges RIKEN for the FPR
grant. The work of F.A.K. was supported by a grant of the HHMI International Early
Career Scientist Programme (grant #55007424), the Spanish Ministry of Economy and
Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP programme, two grants
from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia
Severo Ochoa 2013–2017 (grant #Sev-2012-0208)’ and (grant #BES-2013-064004) funded
by the European Regional Development Fund (ERDF), the European Union and the European
Research Council (grant #335980_EinME). K.V. is supported by an FWO postdoctoral
fellowship. Funders had no role in study design, data collection and analysis, decision
to publish or preparation of the manuscript.'
author:
- first_name: Ksenia
full_name: Pougach, Ksenia S
last_name: Pougach
- first_name: Arnout
full_name: Voet, Arnout R
last_name: Voet
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Karin
full_name: Voordeckers, Karin
last_name: Voordeckers
- first_name: Joaquin
full_name: Christiaens, Joaquin F
last_name: Christiaens
- first_name: Bianka
full_name: Baying, Bianka
last_name: Baying
- first_name: Vladimı́R
full_name: Bénès, Vladimı́r
last_name: Bénès
- first_name: Ryo
full_name: Sakai, Ryo
last_name: Sakai
- first_name: Jan
full_name: Aerts, Jan A
last_name: Aerts
- first_name: Bo
full_name: Zhu, Bo
last_name: Zhu
- first_name: Patrick
full_name: Van Dijck, Patrick
last_name: Van Dijck
- first_name: Kevin
full_name: Verstrepen, Kevin J
last_name: Verstrepen
citation:
ama: Pougach K, Voet A, Kondrashov F, et al. Duplication of a promiscuous transcription
factor drives the emergence of a new regulatory network. Nature Communications.
2014;5. doi:10.1038/ncomms5868
apa: Pougach, K., Voet, A., Kondrashov, F., Voordeckers, K., Christiaens, J., Baying,
B., … Verstrepen, K. (2014). Duplication of a promiscuous transcription factor
drives the emergence of a new regulatory network. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms5868
chicago: Pougach, Ksenia, Arnout Voet, Fyodor Kondrashov, Karin Voordeckers, Joaquin
Christiaens, Bianka Baying, Vladimı́R Bénès, et al. “Duplication of a Promiscuous
Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature
Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms5868.
ieee: K. Pougach et al., “Duplication of a promiscuous transcription factor
drives the emergence of a new regulatory network,” Nature Communications,
vol. 5. Nature Publishing Group, 2014.
ista: Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens J, Baying B, Bénès
V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen K. 2014. Duplication of a
promiscuous transcription factor drives the emergence of a new regulatory network.
Nature Communications. 5.
mla: Pougach, Ksenia, et al. “Duplication of a Promiscuous Transcription Factor
Drives the Emergence of a New Regulatory Network.” Nature Communications,
vol. 5, Nature Publishing Group, 2014, doi:10.1038/ncomms5868.
short: K. Pougach, A. Voet, F. Kondrashov, K. Voordeckers, J. Christiaens, B. Baying,
V. Bénès, R. Sakai, J. Aerts, B. Zhu, P. Van Dijck, K. Verstrepen, Nature Communications
5 (2014).
date_created: 2018-12-11T11:48:52Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:01Z
day: '01'
doi: 10.1038/ncomms5868
extern: 1
intvolume: ' 5'
month: '01'
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '6790'
quality_controlled: 0
status: public
title: Duplication of a promiscuous transcription factor drives the emergence of a
new regulatory network
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 5
year: '2014'
...
---
_id: '863'
abstract:
- lang: eng
text: The origins of neural systems remain unresolved. In contrast to other basal
metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived
muscular systems. These holoplanktonic predators also have sophisticated ciliated
locomotion, behaviour and distinct development. Here we present the draft genome
of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore
transcriptomes, and show that they are remarkably distinct from other animal genomes
in their content of neurogenic, immune and developmental genes. Our integrative
analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis
is supported by comparative analysis of multiple gene families, including the
apparent absence of HOX genes, canonical microRNA machinery, and reduced immune
complement in ctenophores. Although two distinct nervous systems are well recognized
in ctenophores, many bilaterian neuron-specific genes and genes of 'classical'
neurotransmitter pathways either are absent or, if present, are not expressed
in neurons. Our metabolomic and physiological data are consistent with the hypothesis
that ctenophore neural systems, and possibly muscle specification, evolved independently
from those in other animals.
acknowledgement: We thank Friday Harbor Laboratories for facilities during animal
collection and Marine Genomics apprenticeships (L.L.M., B.J.S.); E. Dabe, G. Winters,
J. Netherton, N. Churches and C. Bostwick for help with animal, tissue, in situ,
RNA and DNA assays; and X.-X. Tan, F. Lu and T. Tyazelova for sequencing. We thank
F. Nivens for videos and P. L. Williams for database support. This work was supported
by NSF (NSF-0744649 and NSF CNS-0821622 to L.L.M.; NSF CHE-1111705 to J.V.S.), NIH
(1R01GM097502, R01MH097062, R21RR025699 and 5R21DA030118 to L.L.M.; P30 DA018310
to J.V.S.; R01 AG029360 and 1S10RR027052 to E.I.R.), NASA NNX13AJ31G (to K.M.H.,
L.L.M. and K.M.K.), NSERC 458115 and 211598 (J.P.R.), University of Florida Opportunity
Funds/McKnight Brain Research and Florida Biodiversity Institute (L.L.M.), Rostock
Inc./A.V. Chikunov (E.I.R.), grant from Russian Federation Government 14.B25.31.0033
(Resolution No.220) (E.I.R.). F.A.K., I.S.P. and R.D. were supported by HHMI (55007424),
EMBO and MINECO (BFU2012-31329 and Sev-2012-0208). Contributions of AU Marine Biology
Program 117 and Molette laboratory 22.
author:
- first_name: Leonid
full_name: Moroz, Leonid L
last_name: Moroz
- first_name: Kevin
full_name: Kocot, Kevin M
last_name: Kocot
- first_name: Mathew
full_name: Citarella, Mathew R
last_name: Citarella
- first_name: Sohn
full_name: Dosung, Sohn
last_name: Dosung
- first_name: Tigran
full_name: Norekian, Tigran P
last_name: Norekian
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Anastasia
full_name: Grigorenko, Anastasia P
last_name: Grigorenko
- first_name: Christopher
full_name: Dailey, Christopher A
last_name: Dailey
- first_name: Eugene
full_name: Berezikov, Eugene
last_name: Berezikov
- first_name: Katherine
full_name: Buckley, Katherine M
last_name: Buckley
- first_name: Andrey
full_name: Ptitsyn, Andrey A
last_name: Ptitsyn
- first_name: Denis
full_name: Reshetov, Denis A
last_name: Reshetov
- first_name: Krishanu
full_name: Mukherjee, Krishanu
last_name: Mukherjee
- first_name: Tatiana
full_name: Moroz, Tatiana P
last_name: Moroz
- first_name: Yelena
full_name: Bobkova, Yelena V
last_name: Bobkova
- first_name: Fahong
full_name: Yu, Fahong
last_name: Yu
- first_name: Vladimir
full_name: Kapitonov, Vladimir V
last_name: Kapitonov
- first_name: Jerzy
full_name: Jurka, Jerzy W
last_name: Jurka
- first_name: Yuriy
full_name: Bobkov, Yuriy V
last_name: Bobkov
- first_name: Joshua
full_name: Swore, Joshua J
last_name: Swore
- first_name: David
full_name: Girardo, David O
last_name: Girardo
- first_name: Alexander
full_name: Fodor, Alexander
last_name: Fodor
- first_name: Fedor
full_name: Gusev, Fedor E
last_name: Gusev
- first_name: Rachel
full_name: Sanford, Rachel S
last_name: Sanford
- first_name: Rebecca
full_name: Bruders, Rebecca
last_name: Bruders
- first_name: Ellen
full_name: Kittler, Ellen L
last_name: Kittler
- first_name: Claudia
full_name: Mills, Claudia E
last_name: Mills
- first_name: Jonathan
full_name: Rast, Jonathan P
last_name: Rast
- first_name: Romain
full_name: Derelle, Romain
last_name: Derelle
- first_name: Victor
full_name: Solovyev, Victor
last_name: Solovyev
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Billie
full_name: Swalla, Billie J
last_name: Swalla
- first_name: Jonathan
full_name: Sweedler, Jonathan V
last_name: Sweedler
- first_name: Evgeny
full_name: Rogaev, Evgeny I
last_name: Rogaev
- first_name: Kenneth
full_name: Halanych, Kenneth M
last_name: Halanych
- first_name: Andrea
full_name: Kohn, Andrea B
last_name: Kohn
citation:
ama: Moroz L, Kocot K, Citarella M, et al. The ctenophore genome and the evolutionary
origins of neural systems. Nature. 2014;510(7503):109-114. doi:10.1038/nature13400
apa: Moroz, L., Kocot, K., Citarella, M., Dosung, S., Norekian, T., Povolotskaya,
I., … Kohn, A. (2014). The ctenophore genome and the evolutionary origins of neural
systems. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13400
chicago: Moroz, Leonid, Kevin Kocot, Mathew Citarella, Sohn Dosung, Tigran Norekian,
Inna Povolotskaya, Anastasia Grigorenko, et al. “The Ctenophore Genome and the
Evolutionary Origins of Neural Systems.” Nature. Nature Publishing Group,
2014. https://doi.org/10.1038/nature13400.
ieee: L. Moroz et al., “The ctenophore genome and the evolutionary origins
of neural systems,” Nature, vol. 510, no. 7503. Nature Publishing Group,
pp. 109–114, 2014.
ista: Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko
A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz
T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor
A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev
V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The
ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503),
109–114.
mla: Moroz, Leonid, et al. “The Ctenophore Genome and the Evolutionary Origins of
Neural Systems.” Nature, vol. 510, no. 7503, Nature Publishing Group, 2014,
pp. 109–14, doi:10.1038/nature13400.
short: L. Moroz, K. Kocot, M. Citarella, S. Dosung, T. Norekian, I. Povolotskaya,
A. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, A. Ptitsyn, D. Reshetov, K.
Mukherjee, T. Moroz, Y. Bobkova, F. Yu, V. Kapitonov, J. Jurka, Y. Bobkov, J.
Swore, D. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C.
Mills, J. Rast, R. Derelle, V. Solovyev, F. Kondrashov, B. Swalla, J. Sweedler,
E. Rogaev, K. Halanych, A. Kohn, Nature 510 (2014) 109–114.
date_created: 2018-12-11T11:48:54Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:21Z
day: '01'
doi: 10.1038/nature13400
extern: 1
intvolume: ' 510'
issue: '7503'
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '01'
page: 109 - 114
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6785'
quality_controlled: 0
status: public
title: The ctenophore genome and the evolutionary origins of neural systems
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
volume: 510
year: '2014'
...
---
_id: '865'
abstract:
- lang: eng
text: Research on existing drugs often discovers novel mechanisms of their action
and leads to the expansion of their therapeutic scope and subsequent remarketing.
The Wnt signaling pathway is of the immediate therapeutic relevance, as it plays
critical roles in cancer development and progression. However, drugs which disrupt
this pathway are unavailable despite the high demand. Here we report an attempt
to identify antagonists of the Wnt-FZD interaction among the library of the FDA-approved
drugs. We performed an in silico screening which brought up several potential
antagonists of the ligand-receptor interaction. 14 of these substances were tested
using the TopFlash luciferase reporter assay and four of them identified as active
and specific inhibitors of the Wnt3a-induced signaling. However, further analysis
through GTP-binding and β-catenin stabilization assays showed that the compounds
do not target the Wnt-FZD pair, but inhibit the signaling at downstream levels.
We further describe the previously unknown inhibitory activity of an anti-leprosy
drug clofazimine in the Wnt pathway and provide data demonstrating its efficiency
in suppressing growth of Wnt-dependent triple-negative breast cancer cells. These
data provide a basis for further investigations of the efficiency of clofazimine
in treatment of Wnt-dependent cancers.
author:
- first_name: Alexey
full_name: Koval, Alexey V
last_name: Koval
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Polina
full_name: Shichkova, Polina
last_name: Shichkova
- first_name: S
full_name: Khunderyakova, S
last_name: Khunderyakova
- first_name: Yury
full_name: Markov, Yury
last_name: Markov
- first_name: J
full_name: Panchenko, J
last_name: Panchenko
- first_name: A
full_name: Volodina, A
last_name: Volodina
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Vladimir
full_name: Katanaev, Vladimir L
last_name: Katanaev
citation:
ama: Koval A, Vlasov P, Shichkova P, et al. Anti leprosy drug clofazimine inhibits
growth of triple-negative breast cancer cells via inhibition of canonical Wnt
signaling. Biochemical Pharmacology. 2014;87(4):571-578. doi:10.1016/j.bcp.2013.12.007
apa: Koval, A., Vlasov, P., Shichkova, P., Khunderyakova, S., Markov, Y., Panchenko,
J., … Katanaev, V. (2014). Anti leprosy drug clofazimine inhibits growth of triple-negative
breast cancer cells via inhibition of canonical Wnt signaling. Biochemical
Pharmacology. Elsevier. https://doi.org/10.1016/j.bcp.2013.12.007
chicago: Koval, Alexey, Peter Vlasov, Polina Shichkova, S Khunderyakova, Yury Markov,
J Panchenko, A Volodina, Fyodor Kondrashov, and Vladimir Katanaev. “Anti Leprosy
Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition
of Canonical Wnt Signaling.” Biochemical Pharmacology. Elsevier, 2014.
https://doi.org/10.1016/j.bcp.2013.12.007.
ieee: A. Koval et al., “Anti leprosy drug clofazimine inhibits growth of
triple-negative breast cancer cells via inhibition of canonical Wnt signaling,”
Biochemical Pharmacology, vol. 87, no. 4. Elsevier, pp. 571–578, 2014.
ista: Koval A, Vlasov P, Shichkova P, Khunderyakova S, Markov Y, Panchenko J, Volodina
A, Kondrashov F, Katanaev V. 2014. Anti leprosy drug clofazimine inhibits growth
of triple-negative breast cancer cells via inhibition of canonical Wnt signaling.
Biochemical Pharmacology. 87(4), 571–578.
mla: Koval, Alexey, et al. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative
Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical
Pharmacology, vol. 87, no. 4, Elsevier, 2014, pp. 571–78, doi:10.1016/j.bcp.2013.12.007.
short: A. Koval, P. Vlasov, P. Shichkova, S. Khunderyakova, Y. Markov, J. Panchenko,
A. Volodina, F. Kondrashov, V. Katanaev, Biochemical Pharmacology 87 (2014) 571–578.
date_created: 2018-12-11T11:48:55Z
date_published: 2014-02-15T00:00:00Z
date_updated: 2021-01-12T08:20:24Z
day: '15'
doi: 10.1016/j.bcp.2013.12.007
extern: 1
intvolume: ' 87'
issue: '4'
month: '02'
page: 571 - 578
publication: Biochemical Pharmacology
publication_status: published
publisher: Elsevier
publist_id: '6782'
quality_controlled: 0
status: public
title: Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer
cells via inhibition of canonical Wnt signaling
type: journal_article
volume: 87
year: '2014'
...
---
_id: '925'
abstract:
- lang: eng
text: The morphological stability of biological tubes is crucial for the efficient
circulation of fluids and gases. Failure of this stability causes irregularly
shaped tubes found in multiple pathological conditions. Here, we report that Drosophila
mutants of the ESCRT III component Shrub/Vps32 exhibit a strikingly elongated
sinusoidal tube phenotype. This is caused by excessive apical membrane synthesis
accompanied by the ectopic accumulation and overactivation of Crumbs in swollen
endosomes. Furthermore, we demonstrate that the apical extracellular matrix (aECM)
of the tracheal tube is a viscoelastic material coupled with the apical membrane.
We present a simple mechanical model in which aECM elasticity, apical membrane
growth, and their interaction are three vital parameters determining the stability
of biological tubes. Our findings demonstrate a mechanical role for the extracellular
matrix and suggest that the interaction of the apical membrane and an elastic
aECM determines the final morphology of biological tubes independent of cell shape.
acknowledgement: We thank F. Gao, R.E. Ward, S. Luschnig, T. Okajima, M. Affolter,
D. Bilder, E. Knust, T. Tanaka, A. Nakamura, C. Samakovlis, K. Saigo, M. Furuse,
the Bloomington Stock Center, Drosophila Genetic Resource Center in Kyoto, Japan,
and the Developmental Studies Hybridoma Bank for generously providing antibodies
and fly stocks; H. Wada for UAS-3×TagRFP fly and dye injection; Y.H. Zhang for plasmid
and protocol for CBP preparation; and J. Prost and J.F. Joanny for their support
for the project and discussion. We also thank T. Shibata, Y. Morishita, T. Kondo,
and G. Sheng for critically reading the manuscript. This work was supported by a
Grant-in-Aid for Scientific Research on Innovative Areas from MEXT Japan to S.H.
and the RIKEN Foreign Postdoctoral Researcher Program to B.D.
article_processing_charge: No
author:
- first_name: Bo
full_name: Dong, Bo
last_name: Dong
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Shigeo
full_name: Hayashi, Shigeo
last_name: Hayashi
citation:
ama: Dong B, Hannezo EB, Hayashi S. Balance between apical membrane growth and luminal
matrix resistance determines epithelial tubule shape. Cell Reports. 2014;7(4):941-950.
doi:10.1016/j.celrep.2014.03.066
apa: Dong, B., Hannezo, E. B., & Hayashi, S. (2014). Balance between apical
membrane growth and luminal matrix resistance determines epithelial tubule shape.
Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2014.03.066
chicago: Dong, Bo, Edouard B Hannezo, and Shigeo Hayashi. “Balance between Apical
Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.”
Cell Reports. Cell Press, 2014. https://doi.org/10.1016/j.celrep.2014.03.066.
ieee: B. Dong, E. B. Hannezo, and S. Hayashi, “Balance between apical membrane growth
and luminal matrix resistance determines epithelial tubule shape,” Cell Reports,
vol. 7, no. 4. Cell Press, pp. 941–950, 2014.
ista: Dong B, Hannezo EB, Hayashi S. 2014. Balance between apical membrane growth
and luminal matrix resistance determines epithelial tubule shape. Cell Reports.
7(4), 941–950.
mla: Dong, Bo, et al. “Balance between Apical Membrane Growth and Luminal Matrix
Resistance Determines Epithelial Tubule Shape.” Cell Reports, vol. 7, no.
4, Cell Press, 2014, pp. 941–50, doi:10.1016/j.celrep.2014.03.066.
short: B. Dong, E.B. Hannezo, S. Hayashi, Cell Reports 7 (2014) 941–950.
date_created: 2018-12-11T11:49:14Z
date_published: 2014-05-22T00:00:00Z
date_updated: 2021-01-12T08:21:57Z
day: '22'
doi: 10.1016/j.celrep.2014.03.066
extern: '1'
intvolume: ' 7'
issue: '4'
language:
- iso: eng
month: '05'
oa_version: None
page: 941 - 950
publication: Cell Reports
publication_status: published
publisher: Cell Press
publist_id: '6515'
status: public
title: Balance between apical membrane growth and luminal matrix resistance determines
epithelial tubule shape
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2014'
...
---
_id: '927'
abstract:
- lang: eng
text: Morphogenesis during embryo development requires the coordination of mechanical
forces to generate the macroscopic shapes of organs. We propose a minimal theoretical
model, based on cell adhesion and actomyosin contractility, which describes the
various shapes of epithelial cells and the bending and buckling of epithelial
sheets, as well as the relative stability of cellular tubes and spheres. We show
that, to understand these processes, a full 3D description of the cells is needed,
but that simple scaling laws can still be derived. The morphologies observed in
vivo can be understood as stable points of mechanical equations and the transitions
between them are either continuous or discontinuous. We then focus on epithelial
sheet bending, a ubiquitous morphogenetic process. We calculate the curvature
of an epithelium as a function of actin belt tension as well as of cell-cell and
and cell-substrate tension. The model allows for a comparison of the relative
stabilities of spherical or cylindrical cellular structures (acini or tubes).
Finally, we propose a unique type of buckling instability of epithelia, driven
by a flattening of individual cell shapes, and discuss experimental tests to verify
our predictions.
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jacques
full_name: Prost, Jacques
last_name: Prost
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
citation:
ama: Hannezo EB, Prost J, Joanny J. Theory of epithelial sheet morphology in three
dimensions. PNAS. 2014;111(1):27-32. doi:10.1073/pnas.1312076111
apa: Hannezo, E. B., Prost, J., & Joanny, J. (2014). Theory of epithelial sheet
morphology in three dimensions. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1312076111
chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Theory of Epithelial
Sheet Morphology in Three Dimensions.” PNAS. National Academy of Sciences,
2014. https://doi.org/10.1073/pnas.1312076111.
ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Theory of epithelial sheet morphology
in three dimensions,” PNAS, vol. 111, no. 1. National Academy of Sciences,
pp. 27–32, 2014.
ista: Hannezo EB, Prost J, Joanny J. 2014. Theory of epithelial sheet morphology
in three dimensions. PNAS. 111(1), 27–32.
mla: Hannezo, Edouard B., et al. “Theory of Epithelial Sheet Morphology in Three
Dimensions.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014,
pp. 27–32, doi:10.1073/pnas.1312076111.
short: E.B. Hannezo, J. Prost, J. Joanny, PNAS 111 (2014) 27–32.
date_created: 2018-12-11T11:49:14Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:58Z
day: '01'
doi: 10.1073/pnas.1312076111
extern: '1'
intvolume: ' 111'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 27 - 32
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6517'
status: public
title: Theory of epithelial sheet morphology in three dimensions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2014'
...
---
_id: '9519'
abstract:
- lang: eng
text: Transposons are selfish genetic sequences that can increase their copy number
and inflict substantial damage on their hosts. To combat these genomic parasites,
plants have evolved multiple pathways to identify and silence transposons by methylating
their DNA. Plants have also evolved mechanisms to limit the collateral damage
from the antitransposon machinery. In this review, we examine recent developments
that have elucidated many of the molecular workings of these pathways. We also
highlight the evidence that the methylation and demethylation pathways interact,
indicating that plants have a highly sophisticated, integrated system of transposon
defense that has an important role in the regulation of gene expression.
article_processing_charge: No
article_type: review
author:
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity.
Trends in Plant Science. 2014;19(5):320-326. doi:10.1016/j.tplants.2014.01.014
apa: Kim, M. Y., & Zilberman, D. (2014). DNA methylation as a system of plant
genomic immunity. Trends in Plant Science. Elsevier. https://doi.org/10.1016/j.tplants.2014.01.014
chicago: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant
Genomic Immunity.” Trends in Plant Science. Elsevier, 2014. https://doi.org/10.1016/j.tplants.2014.01.014.
ieee: M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic
immunity,” Trends in Plant Science, vol. 19, no. 5. Elsevier, pp. 320–326,
2014.
ista: Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity.
Trends in Plant Science. 19(5), 320–326.
mla: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant
Genomic Immunity.” Trends in Plant Science, vol. 19, no. 5, Elsevier, 2014,
pp. 320–26, doi:10.1016/j.tplants.2014.01.014.
short: M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.
date_created: 2021-06-07T14:38:09Z
date_published: 2014-05-04T00:00:00Z
date_updated: 2021-12-14T08:24:48Z
day: '04'
department:
- _id: DaZi
doi: 10.1016/j.tplants.2014.01.014
extern: '1'
external_id:
pmid:
- '24618094 '
intvolume: ' 19'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 320-326
pmid: 1
publication: Trends in Plant Science
publication_identifier:
eissn:
- 1878-4372
issn:
- 1360-1385
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation as a system of plant genomic immunity
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 19
year: '2014'
...
---
_id: '96'
abstract:
- lang: eng
text: Multielectron spin qubits are demonstrated, and performance examined by comparing
coherent exchange oscillations in coupled single-electron and multielectron quantum
dots, measured in the same device. Fast (>1 GHz) exchange oscillations with
a quality factor Q∼15 are found for the multielectron case, compared to Q∼2 for
the single-electron case, the latter consistent with experiments in the literature.
A model of dephasing that includes voltage and hyperfine noise is developed that
is in good agreement with both single- and multielectron data, though in both
cases additional exchange-independent dephasing is needed to obtain quantitative
agreement across a broad parameter range.
acknowledgement: The research is supported by the Intelligence Advanced Research Projects
Activity (IARPA), through the Army Research Office Grant No. W911NF-12-1-0354, the
DARPA QuEST Program, the Department of Energy, Office of Science, and the Danish
National Research Foundation.
article_number: '026801'
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
- first_name: Micah
full_name: Hanson, Micah
last_name: Hanson
- first_name: Arthur
full_name: Gossard, Arthur
last_name: Gossard
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
citation:
ama: Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. Coherent operations
and screening in multielectron spin qubits. APS Physics, Physical Review Letters.
2014;112(2). doi:10.1103/PhysRevLett.112.026801
apa: Higginbotham, A. P., Kuemmeth, F., Hanson, M., Gossard, A., & Marcus, C.
(2014). Coherent operations and screening in multielectron spin qubits. APS
Physics, Physical Review Letters. American Physiological Society. https://doi.org/10.1103/PhysRevLett.112.026801
chicago: Higginbotham, Andrew P, Ferdinand Kuemmeth, Micah Hanson, Arthur Gossard,
and Charles Marcus. “Coherent Operations and Screening in Multielectron Spin Qubits.”
APS Physics, Physical Review Letters. American Physiological Society, 2014.
https://doi.org/10.1103/PhysRevLett.112.026801.
ieee: A. P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, and C. Marcus, “Coherent
operations and screening in multielectron spin qubits,” APS Physics, Physical
Review Letters, vol. 112, no. 2. American Physiological Society, 2014.
ista: Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. 2014. Coherent
operations and screening in multielectron spin qubits. APS Physics, Physical Review
Letters. 112(2), 026801.
mla: Higginbotham, Andrew P., et al. “Coherent Operations and Screening in Multielectron
Spin Qubits.” APS Physics, Physical Review Letters, vol. 112, no. 2, 026801,
American Physiological Society, 2014, doi:10.1103/PhysRevLett.112.026801.
short: A.P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, C. Marcus, APS Physics,
Physical Review Letters 112 (2014).
date_created: 2018-12-11T11:44:36Z
date_published: 2014-01-14T00:00:00Z
date_updated: 2021-01-12T08:22:14Z
day: '14'
doi: 10.1103/PhysRevLett.112.026801
extern: '1'
external_id:
arxiv:
- '1306.2720'
intvolume: ' 112'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1306.2720
month: '01'
oa: 1
oa_version: Preprint
publication: APS Physics, Physical Review Letters
publication_status: published
publisher: American Physiological Society
publist_id: '7958'
quality_controlled: '1'
status: public
title: Coherent operations and screening in multielectron spin qubits
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2014'
...
---
_id: '9594'
abstract:
- lang: eng
text: Let d≥3 be a fixed integer. We give an asympotic formula for the expected
number of spanning trees in a uniformly random d-regular graph with n vertices.
(The asymptotics are as n→∞, restricted to even n if d is odd.) We also obtain
the asymptotic distribution of the number of spanning trees in a uniformly random
cubic graph, and conjecture that the corresponding result holds for arbitrary
(fixed) d. Numerical evidence is presented which supports our conjecture.
article_number: P1.45
article_processing_charge: No
article_type: original
author:
- first_name: Catherine
full_name: Greenhill, Catherine
last_name: Greenhill
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: David
full_name: Wind, David
last_name: Wind
citation:
ama: Greenhill C, Kwan MA, Wind D. On the number of spanning trees in random regular
graphs. The Electronic Journal of Combinatorics. 2014;21(1). doi:10.37236/3752
apa: Greenhill, C., Kwan, M. A., & Wind, D. (2014). On the number of spanning
trees in random regular graphs. The Electronic Journal of Combinatorics.
The Electronic Journal of Combinatorics. https://doi.org/10.37236/3752
chicago: Greenhill, Catherine, Matthew Alan Kwan, and David Wind. “On the Number
of Spanning Trees in Random Regular Graphs.” The Electronic Journal of Combinatorics.
The Electronic Journal of Combinatorics, 2014. https://doi.org/10.37236/3752.
ieee: C. Greenhill, M. A. Kwan, and D. Wind, “On the number of spanning trees in
random regular graphs,” The Electronic Journal of Combinatorics, vol. 21,
no. 1. The Electronic Journal of Combinatorics, 2014.
ista: Greenhill C, Kwan MA, Wind D. 2014. On the number of spanning trees in random
regular graphs. The Electronic Journal of Combinatorics. 21(1), P1.45.
mla: Greenhill, Catherine, et al. “On the Number of Spanning Trees in Random Regular
Graphs.” The Electronic Journal of Combinatorics, vol. 21, no. 1, P1.45,
The Electronic Journal of Combinatorics, 2014, doi:10.37236/3752.
short: C. Greenhill, M.A. Kwan, D. Wind, The Electronic Journal of Combinatorics
21 (2014).
date_created: 2021-06-23T06:29:35Z
date_published: 2014-02-28T00:00:00Z
date_updated: 2023-02-23T14:02:12Z
day: '28'
doi: 10.37236/3752
extern: '1'
external_id:
arxiv:
- '1309.6710'
intvolume: ' 21'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.37236/3752
month: '02'
oa: 1
oa_version: Published Version
publication: The Electronic Journal of Combinatorics
publication_identifier:
eissn:
- 1077-8926
publication_status: published
publisher: The Electronic Journal of Combinatorics
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the number of spanning trees in random regular graphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 21
year: '2014'
...
---
_id: '9655'
abstract:
- lang: eng
text: Correlative microscopy incorporates the specificity of fluorescent protein
labeling into high-resolution electron micrographs. Several approaches exist for
correlative microscopy, most of which have used the green fluorescent protein
(GFP) as the label for light microscopy. Here we use chemical tagging and synthetic
fluorophores instead, in order to achieve protein-specific labeling, and to perform
multicolor imaging. We show that synthetic fluorophores preserve their post-embedding
fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is
of such quality that the specimen can be prepared with identical protocols for
scanning electron microscopy (SEM) and transmission electron microscopy (TEM);
this is particularly valuable when singular or otherwise difficult samples are
examined. We show that synthetic fluorophores give bright, well-resolved signals
in super-resolution light microscopy, enabling us to superimpose light microscopic
images with a precision of up to 25 nm in the x–y plane on electron micrographs.
To exemplify the preservation quality of our new method we visualize the molecular
arrangement of cadherins in adherens junctions of mouse epithelial cells.
article_processing_charge: No
article_type: original
author:
- first_name: Mario
full_name: Perkovic, Mario
last_name: Perkovic
- first_name: Michael
full_name: Kunz, Michael
last_name: Kunz
- first_name: Ulrike
full_name: Endesfelder, Ulrike
last_name: Endesfelder
- first_name: Stefanie
full_name: Bunse, Stefanie
last_name: Bunse
- first_name: Christoph
full_name: Wigge, Christoph
last_name: Wigge
- first_name: Zhou
full_name: Yu, Zhou
last_name: Yu
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Margot P.
full_name: Scheffer, Margot P.
last_name: Scheffer
- first_name: Anja
full_name: Seybert, Anja
last_name: Seybert
- first_name: Sebastian
full_name: Malkusch, Sebastian
last_name: Malkusch
- first_name: Erin M.
full_name: Schuman, Erin M.
last_name: Schuman
- first_name: Mike
full_name: Heilemann, Mike
last_name: Heilemann
- first_name: Achilleas S.
full_name: Frangakis, Achilleas S.
last_name: Frangakis
citation:
ama: Perkovic M, Kunz M, Endesfelder U, et al. Correlative light- and electron microscopy
with chemical tags. Journal of Structural Biology. 2014;186(2):205-213.
doi:10.1016/j.jsb.2014.03.018
apa: Perkovic, M., Kunz, M., Endesfelder, U., Bunse, S., Wigge, C., Yu, Z., … Frangakis,
A. S. (2014). Correlative light- and electron microscopy with chemical tags. Journal
of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2014.03.018
chicago: Perkovic, Mario, Michael Kunz, Ulrike Endesfelder, Stefanie Bunse, Christoph
Wigge, Zhou Yu, Victor-Valentin Hodirnau, et al. “Correlative Light- and Electron
Microscopy with Chemical Tags.” Journal of Structural Biology. Elsevier,
2014. https://doi.org/10.1016/j.jsb.2014.03.018.
ieee: M. Perkovic et al., “Correlative light- and electron microscopy with
chemical tags,” Journal of Structural Biology, vol. 186, no. 2. Elsevier,
pp. 205–213, 2014.
ista: Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau V-V, Scheffer
MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS. 2014. Correlative
light- and electron microscopy with chemical tags. Journal of Structural Biology.
186(2), 205–213.
mla: Perkovic, Mario, et al. “Correlative Light- and Electron Microscopy with Chemical
Tags.” Journal of Structural Biology, vol. 186, no. 2, Elsevier, 2014,
pp. 205–13, doi:10.1016/j.jsb.2014.03.018.
short: M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V.-V. Hodirnau,
M.P. Scheffer, A. Seybert, S. Malkusch, E.M. Schuman, M. Heilemann, A.S. Frangakis,
Journal of Structural Biology 186 (2014) 205–213.
date_created: 2021-07-14T09:05:42Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2021-07-22T08:26:32Z
day: '01'
ddc:
- '570'
doi: 10.1016/j.jsb.2014.03.018
extern: '1'
external_id:
pmid:
- '24698954'
file:
- access_level: open_access
checksum: a322991b43cdc5935c99db88d285aa3a
content_type: application/pdf
creator: asandaue
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date_updated: 2021-07-22T08:06:34Z
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month: '05'
oa: 1
oa_version: Published Version
page: 205-213
pmid: 1
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Correlative light- and electron microscopy with chemical tags
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND
3.0)
short: CC BY-NC-ND (3.0)
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 186
year: '2014'
...
---
_id: '9686'
abstract:
- lang: eng
text: It is well known that ultrasonic vibration can soften metals, and this phenomenon
has been widely exploited in industrial applications concerning metal forming
and bonding. Recent experiments show that the simultaneous application of oscillatory
stresses from audible to ultrasonic frequency ranges can lead to not only softening
but also significant dislocation annihilation and subgrain formation in metal
samples from the nano- to macro-size range. These findings indicate that the existing
understanding of ultrasound softening – that the vibrations either impose additional
stress waves to augment the quasi-static applied load, or cause heating of the
metal, whereas the metal’s intrinsic deformation resistance or mechanism remains
unaltered – is far from complete. To understand the softening and the associated
enhanced subgrain formation and dislocation annihilation, a new simulator based
on the dynamics of dislocation-density functions is employed. This new simulator
considers the flux, production and annihilation, as well as the Taylor and elastic
interactions between dislocation densities. Softening during vibrations as well
as enhanced cell formation is predicted. The simulations reveal the main mechanism
for subcell formation under oscillatory loadings to be the enhanced elimination
of statistically stored dislocations (SSDs) by the oscillatory stress, leaving
behind geometrically necessary dislocations with low Schmid factors which then
form the subgrain walls. The oscillatory stress helps the depletion of the SSDs,
because the chance for them to meet up and annihilate is increased with reversals
of dislocation motions. This is the first simulation effort to successfully predict
the cell formation phenomenon under vibratory loadings.
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: H.S.
full_name: Leung, H.S.
last_name: Leung
- first_name: A.H.W.
full_name: Ngan, A.H.W.
last_name: Ngan
citation:
ama: Cheng B, Leung HS, Ngan AHW. Strength of metals under vibrations – dislocation-density-function
dynamics simulations. Philosophical Magazine. 2014;95(16-18):1845-1865.
doi:10.1080/14786435.2014.897008
apa: Cheng, B., Leung, H. S., & Ngan, A. H. W. (2014). Strength of metals under
vibrations – dislocation-density-function dynamics simulations. Philosophical
Magazine. Taylor & Francis. https://doi.org/10.1080/14786435.2014.897008
chicago: Cheng, Bingqing, H.S. Leung, and A.H.W. Ngan. “Strength of Metals under
Vibrations – Dislocation-Density-Function Dynamics Simulations.” Philosophical
Magazine. Taylor & Francis, 2014. https://doi.org/10.1080/14786435.2014.897008.
ieee: B. Cheng, H. S. Leung, and A. H. W. Ngan, “Strength of metals under vibrations
– dislocation-density-function dynamics simulations,” Philosophical Magazine,
vol. 95, no. 16–18. Taylor & Francis, pp. 1845–1865, 2014.
ista: Cheng B, Leung HS, Ngan AHW. 2014. Strength of metals under vibrations – dislocation-density-function
dynamics simulations. Philosophical Magazine. 95(16–18), 1845–1865.
mla: Cheng, Bingqing, et al. “Strength of Metals under Vibrations – Dislocation-Density-Function
Dynamics Simulations.” Philosophical Magazine, vol. 95, no. 16–18, Taylor
& Francis, 2014, pp. 1845–65, doi:10.1080/14786435.2014.897008.
short: B. Cheng, H.S. Leung, A.H.W. Ngan, Philosophical Magazine 95 (2014) 1845–1865.
date_created: 2021-07-19T09:27:15Z
date_published: 2014-06-23T00:00:00Z
date_updated: 2023-02-23T14:04:59Z
day: '23'
doi: 10.1080/14786435.2014.897008
extern: '1'
intvolume: ' 95'
issue: 16-18
language:
- iso: eng
month: '06'
oa_version: None
page: 1845-1865
publication: Philosophical Magazine
publication_identifier:
eissn:
- 1478-6443
issn:
- 1478-6435
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strength of metals under vibrations – dislocation-density-function dynamics
simulations
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 95
year: '2014'
...
---
_id: '2083'
abstract:
- lang: eng
text: Understanding the effects of sex and migration on adaptation to novel environments
remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas
reinhardtii, we investigated how sex and migration affected rates of evolutionary
rescue in a sink environment, and subsequent changes in fitness following evolutionary
rescue. We show that sex and migration affect both the rate of evolutionary rescue
and subsequent adaptation. However, their combined effects change as the populations
adapt to a sink habitat. Both sex and migration independently increased rates
of evolutionary rescue, but the effect of sex on subsequent fitness improvements,
following initial rescue, changed with migration, as sex was beneficial in the
absence of migration but constraining adaptation when combined with migration.
These results suggest that sex and migration are beneficial during the initial
stages of adaptation, but can become detrimental as the population adapts to its
environment.
acknowledgement: The authors are grateful to the Leverhulme Trust (F/00 215/AW) for
funding this work.
article_processing_charge: No
article_type: original
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Andrew
full_name: Morgan, Andrew
last_name: Morgan
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
citation:
ama: Lagator M, Morgan A, Neve P, Colegrave N. Role of sex and migration in adaptation
to sink environments. Evolution. 2014;68(8):2296-2305. doi:10.1111/evo.12440
apa: Lagator, M., Morgan, A., Neve, P., & Colegrave, N. (2014). Role of sex
and migration in adaptation to sink environments. Evolution. Wiley. https://doi.org/10.1111/evo.12440
chicago: Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Role of Sex
and Migration in Adaptation to Sink Environments.” Evolution. Wiley, 2014.
https://doi.org/10.1111/evo.12440.
ieee: M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Role of sex and migration
in adaptation to sink environments,” Evolution, vol. 68, no. 8. Wiley,
pp. 2296–2305, 2014.
ista: Lagator M, Morgan A, Neve P, Colegrave N. 2014. Role of sex and migration
in adaptation to sink environments. Evolution. 68(8), 2296–2305.
mla: Lagator, Mato, et al. “Role of Sex and Migration in Adaptation to Sink Environments.”
Evolution, vol. 68, no. 8, Wiley, 2014, pp. 2296–305, doi:10.1111/evo.12440.
short: M. Lagator, A. Morgan, P. Neve, N. Colegrave, Evolution 68 (2014) 2296–2305.
date_created: 2018-12-11T11:55:36Z
date_published: 2014-04-25T00:00:00Z
date_updated: 2023-02-23T14:06:51Z
day: '25'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1111/evo.12440
file:
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checksum: 8d459b07e4a11bb5fde92d969184fe48
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has_accepted_license: '1'
intvolume: ' 68'
issue: '8'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 2296 - 2305
publication: Evolution
publication_status: published
publisher: Wiley
publist_id: '4954'
quality_controlled: '1'
related_material:
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- id: '9747'
relation: research_data
status: public
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status: public
title: Role of sex and migration in adaptation to sink environments
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68
year: '2014'
...
---
_id: '9747'
abstract:
- lang: eng
text: Understanding the effects of sex and migration on adaptation to novel environments
remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas
reinhardtii, we investigated how sex and migration affected rates of evolutionary
rescue in a sink environment, and subsequent changes in fitness following evolutionary
rescue. We show that sex and migration affect both the rate of evolutionary rescue
and subsequent adaptation. However, their combined effects change as the populations
adapt to a sink habitat. Both sex and migration independently increased rates
of evolutionary rescue, but the effect of sex on subsequent fitness improvements,
following initial rescue, changed with migration, as sex was beneficial in the
absence of migration but constraining adaptation when combined with migration.
These results suggest that sex and migration are beneficial during the initial
stages of adaptation, but can become detrimental as the population adapts to its
environment.
article_processing_charge: No
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Andrew
full_name: Morgan, Andrew
last_name: Morgan
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
citation:
ama: 'Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration
in adaptation to sink environments. 2014. doi:10.5061/dryad.s42n1'
apa: 'Lagator, M., Morgan, A., Neve, P., & Colegrave, N. (2014). Data from:
Role of sex and migration in adaptation to sink environments. Dryad. https://doi.org/10.5061/dryad.s42n1'
chicago: 'Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from:
Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. https://doi.org/10.5061/dryad.s42n1.'
ieee: 'M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex
and migration in adaptation to sink environments.” Dryad, 2014.'
ista: 'Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and
migration in adaptation to sink environments, Dryad, 10.5061/dryad.s42n1.'
mla: 'Lagator, Mato, et al. Data from: Role of Sex and Migration in Adaptation
to Sink Environments. Dryad, 2014, doi:10.5061/dryad.s42n1.'
short: M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014).
date_created: 2021-07-28T15:32:55Z
date_published: 2014-04-17T00:00:00Z
date_updated: 2023-02-23T10:27:31Z
day: '17'
department:
- _id: CaGu
doi: 10.5061/dryad.s42n1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.s42n1
month: '04'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2083'
relation: used_in_publication
status: public
status: public
title: 'Data from: Role of sex and migration in adaptation to sink environments'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '977'
abstract:
- lang: eng
text: We propose a method for detecting many-body localization (MBL) in disordered
spin systems. The method involves pulsed coherent spin manipulations that probe
the dephasing of a given spin due to its entanglement with a set of distant spins.
It allows one to distinguish the MBL phase from a noninteracting localized phase
and a delocalized phase. In particular, we show that for a properly chosen pulse
sequence the MBL phase exhibits a characteristic power-law decay reflecting its
slow growth of entanglement. We find that this power-law decay is robust with
respect to thermal and disorder averaging, provide numerical simulations supporting
our results, and discuss possible experimental realizations in solid-state and
cold-atom systems.
acknowledgement: |-
We thank E. Altman, Y. Bahri, I. Bloch, T. Giamarchi, D. Huse, V. Oganesyan, A. Pal, D. Pekker, and G. Refael for insightful discussions. The authors acknowledge support from the Harvard Quantum Optics Center, Harvard-MIT CUA, the DARPA OLE program, AFOSR Quantum Simulation MURI, ARO-MURI on Atomtronics, the ARO-MURI Quism program, the Austrian Science Fund (FWF) Project No. J 3361-N20, NSERC grant, and Sloan Research Fellowship. Simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University and the Research Computing Center at Harvard University. Research at Perimeter Institute was supported by the Government of Canada and by the Province of Ontario.
M. S., M. K., and S. G. contributed equally to this work.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Michael
full_name: Knap, Michael J
last_name: Knap
- first_name: Sarang
full_name: Gopalakrishnan, Sarang
last_name: Gopalakrishnan
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Norman
full_name: Yao, Norman Y
last_name: Yao
- first_name: Chris
full_name: Laumann, Chris R
last_name: Laumann
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
- first_name: Mikhail
full_name: Lukin, Mikhail D
last_name: Lukin
- first_name: Eugene
full_name: Demler, Eugene A
last_name: Demler
citation:
ama: Serbyn M, Knap M, Gopalakrishnan S, et al. Interferometric probes of many-body
localization. Physical Review Letters. 2014;113(14). doi:10.1103/PhysRevLett.113.147204
apa: Serbyn, M., Knap, M., Gopalakrishnan, S., Papić, Z., Yao, N., Laumann, C.,
… Demler, E. (2014). Interferometric probes of many-body localization. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.113.147204
chicago: Serbyn, Maksym, Michael Knap, Sarang Gopalakrishnan, Zlatko Papić, Norman
Yao, Chris Laumann, Dmitry Abanin, Mikhail Lukin, and Eugene Demler. “Interferometric
Probes of Many-Body Localization.” Physical Review Letters. American Physical
Society, 2014. https://doi.org/10.1103/PhysRevLett.113.147204.
ieee: M. Serbyn et al., “Interferometric probes of many-body localization,”
Physical Review Letters, vol. 113, no. 14. American Physical Society, 2014.
ista: Serbyn M, Knap M, Gopalakrishnan S, Papić Z, Yao N, Laumann C, Abanin D, Lukin
M, Demler E. 2014. Interferometric probes of many-body localization. Physical
Review Letters. 113(14).
mla: Serbyn, Maksym, et al. “Interferometric Probes of Many-Body Localization.”
Physical Review Letters, vol. 113, no. 14, American Physical Society, 2014,
doi:10.1103/PhysRevLett.113.147204.
short: M. Serbyn, M. Knap, S. Gopalakrishnan, Z. Papić, N. Yao, C. Laumann, D. Abanin,
M. Lukin, E. Demler, Physical Review Letters 113 (2014).
date_created: 2018-12-11T11:49:30Z
date_published: 2014-10-03T00:00:00Z
date_updated: 2021-01-12T08:22:22Z
day: '03'
doi: 10.1103/PhysRevLett.113.147204
extern: 1
intvolume: ' 113'
issue: '14'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.0693
month: '10'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6421'
quality_controlled: 0
status: public
title: Interferometric probes of many-body localization
type: journal_article
volume: 113
year: '2014'
...
---
_id: '980'
abstract:
- lang: eng
text: Many-body localized (MBL) systems are characterized by the absence of transport
and thermalization and, therefore, cannot be described by conventional statistical
mechanics. In this paper, using analytic arguments and numerical simulations,
we study the behavior of local observables in an isolated MBL system following
a quantum quench. For the case of a global quench, we find that the local observables
reach stationary, highly nonthermal values at long times as a result of slow dephasing
characteristic of the MBL phase. These stationary values retain the local memory
of the initial state due to the existence of local integrals of motion in the
MBL phase. The temporal fluctuations around stationary values exhibit universal
power-law decay in time, with an exponent set by the localization length and the
diagonal entropy of the initial state. Such a power-law decay holds for any local
observable and is related to the logarithmic in time growth of entanglement in
the MBL phase. This behavior distinguishes the MBL phase from both the Anderson
insulator (where no stationary state is reached) and from the ergodic phase (where
relaxation is expected to be exponential). For the case of a local quench, we
also find a power-law approach of local observables to their stationary values
when the system is prepared in a mixed state. Quench protocols considered in this
paper can be naturally implemented in systems of ultracold atoms in disordered
optical lattices, and the behavior of local observables provides a direct experimental
signature of many-body localization.
acknowledgement: Research at Perimeter Institute is supported by the Government of
Canada through Industry Canada and by the Province of Ontario through the Ministry
of Economic Development & Innovation. We acknowledge support by NSERC Discovery
Grant (D.A.).
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
citation:
ama: Serbyn M, Papić Z, Abanin D. Quantum quenches in the many-body localized phase.
Physical Review B - Condensed Matter and Materials Physics. 2014;90(17).
doi:10.1103/PhysRevB.90.174302
apa: Serbyn, M., Papić, Z., & Abanin, D. (2014). Quantum quenches in the many-body
localized phase. Physical Review B - Condensed Matter and Materials Physics.
American Physical Society. https://doi.org/10.1103/PhysRevB.90.174302
chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Quantum Quenches in the
Many-Body Localized Phase.” Physical Review B - Condensed Matter and Materials
Physics. American Physical Society, 2014. https://doi.org/10.1103/PhysRevB.90.174302.
ieee: M. Serbyn, Z. Papić, and D. Abanin, “Quantum quenches in the many-body localized
phase,” Physical Review B - Condensed Matter and Materials Physics, vol.
90, no. 17. American Physical Society, 2014.
ista: Serbyn M, Papić Z, Abanin D. 2014. Quantum quenches in the many-body localized
phase. Physical Review B - Condensed Matter and Materials Physics. 90(17).
mla: Serbyn, Maksym, et al. “Quantum Quenches in the Many-Body Localized Phase.”
Physical Review B - Condensed Matter and Materials Physics, vol. 90, no.
17, American Physical Society, 2014, doi:10.1103/PhysRevB.90.174302.
short: M. Serbyn, Z. Papić, D. Abanin, Physical Review B - Condensed Matter and
Materials Physics 90 (2014).
date_created: 2018-12-11T11:49:31Z
date_published: 2014-11-06T00:00:00Z
date_updated: 2021-01-12T08:22:24Z
day: '06'
doi: 10.1103/PhysRevB.90.174302
extern: 1
intvolume: ' 90'
issue: '17'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1408.4105
month: '11'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6420'
quality_controlled: 0
status: public
title: Quantum quenches in the many-body localized phase
type: journal_article
volume: 90
year: '2014'
...
---
_id: '98'
abstract:
- lang: eng
text: Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si
nanowire double quantum dot using a fast pulsed-gate method and dispersive readout.
An inhomogeneous dephasing time T2* ∼ 0.18 μs exceeds corresponding measurements
in III-V semiconductors by more than an order of magnitude, as expected for predominately
nuclear-spin-free materials. Dephasing is observed to be exponential in time,
indicating the presence of a broadband noise source, rather than Gaussian, previously
seen in systems with nuclear-spin-dominated dephasing.
acknowledgement: Funding from the Department of Energy, Office of Science & SCGF,
the EC FP7-ICT project SiSPIN no. 323841, and the Danish National Research Foundation
is acknowledged.
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Thorvald
full_name: Larsen, Thorvald
last_name: Larsen
- first_name: Jun
full_name: Yao, Jun
last_name: Yao
- first_name: Hao
full_name: Yan, Hao
last_name: Yan
- first_name: Charles
full_name: Lieber, Charles
last_name: Lieber
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
- first_name: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
citation:
ama: Higginbotham AP, Larsen T, Yao J, et al. Hole spin coherence in a Ge/Si heterostructure
nanowire. Nano Letters. 2014;14(6):3582-3586. doi:10.1021/nl501242b
apa: Higginbotham, A. P., Larsen, T., Yao, J., Yan, H., Lieber, C., Marcus, C.,
& Kuemmeth, F. (2014). Hole spin coherence in a Ge/Si heterostructure nanowire.
Nano Letters. American Chemical Society. https://doi.org/10.1021/nl501242b
chicago: Higginbotham, Andrew P, Thorvald Larsen, Jun Yao, Hao Yan, Charles Lieber,
Charles Marcus, and Ferdinand Kuemmeth. “Hole Spin Coherence in a Ge/Si Heterostructure
Nanowire.” Nano Letters. American Chemical Society, 2014. https://doi.org/10.1021/nl501242b.
ieee: A. P. Higginbotham et al., “Hole spin coherence in a Ge/Si heterostructure
nanowire,” Nano Letters, vol. 14, no. 6. American Chemical Society, pp.
3582–3586, 2014.
ista: Higginbotham AP, Larsen T, Yao J, Yan H, Lieber C, Marcus C, Kuemmeth F. 2014.
Hole spin coherence in a Ge/Si heterostructure nanowire. Nano Letters. 14(6),
3582–3586.
mla: Higginbotham, Andrew P., et al. “Hole Spin Coherence in a Ge/Si Heterostructure
Nanowire.” Nano Letters, vol. 14, no. 6, American Chemical Society, 2014,
pp. 3582–86, doi:10.1021/nl501242b.
short: A.P. Higginbotham, T. Larsen, J. Yao, H. Yan, C. Lieber, C. Marcus, F. Kuemmeth,
Nano Letters 14 (2014) 3582–3586.
date_created: 2018-12-11T11:44:37Z
date_published: 2014-05-05T00:00:00Z
date_updated: 2021-01-12T08:22:24Z
day: '05'
doi: 10.1021/nl501242b
extern: '1'
external_id:
arxiv:
- '1403.2093'
intvolume: ' 14'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.2093
month: '05'
oa: 1
oa_version: Preprint
page: 3582 - 3586
publication: Nano Letters
publication_status: published
publisher: American Chemical Society
publist_id: '7956'
quality_controlled: '1'
status: public
title: Hole spin coherence in a Ge/Si heterostructure nanowire
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2014'
...
---
_id: '2086'
abstract:
- lang: eng
text: Pathogens may gain a fitness advantage through manipulation of the behaviour
of their hosts. Likewise, host behavioural changes can be a defence mechanism,
counteracting the impact of pathogens on host fitness. We apply harmonic radar
technology to characterize the impact of an emerging pathogen - Nosema ceranae
(Microsporidia) - on honeybee (Apis mellifera) flight and orientation performance
in the field. Honeybees are the most important commercial pollinators. Emerging
diseases have been proposed to play a prominent role in colony decline, partly
through sub-lethal behavioural manipulation of their hosts. We found that homing
success was significantly reduced in diseased (65.8%) versus healthy foragers
(92.5%). Although lost bees had significantly reduced continuous flight times
and prolonged resting times, other flight characteristics and navigational abilities
showed no significant difference between infected and non-infected bees. Our results
suggest that infected bees express normal flight characteristics but are constrained
in their homing ability, potentially compromising the colony by reducing its resource
inputs, but also counteracting the intra-colony spread of infection. We provide
the first high-resolution analysis of sub-lethal effects of an emerging disease
on insect flight behaviour. The potential causes and the implications for both
host and parasite are discussed.
acknowledgement: This study was funded jointly by a grant from BBSRC, Defra, NERC,
the Scottish Government and the Wellcome Trust, under the Insect Pollinators Initiative
(grant numbers BB/I00097/1 and BB/I000100/1). Rothamsted Research is a national
institute of bioscience strategically funded by the UK Biotechnology and Biological
Sciences Research Council (BBSRC).
article_number: e103989
author:
- first_name: Stephan
full_name: Wolf, Stephan
last_name: Wolf
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Ka
full_name: Lim, Ka
last_name: Lim
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Suzanne
full_name: Clark, Suzanne
last_name: Clark
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
- first_name: Juliet
full_name: Osborne, Juliet
last_name: Osborne
citation:
ama: 'Wolf S, Mcmahon D, Lim K, et al. So near and yet so far: Harmonic radar reveals
reduced homing ability of Nosema infected honeybees. PLoS One. 2014;9(8).
doi:10.1371/journal.pone.0103989'
apa: 'Wolf, S., Mcmahon, D., Lim, K., Pull, C., Clark, S., Paxton, R., & Osborne,
J. (2014). So near and yet so far: Harmonic radar reveals reduced homing ability
of Nosema infected honeybees. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0103989'
chicago: 'Wolf, Stephan, Dino Mcmahon, Ka Lim, Christopher Pull, Suzanne Clark,
Robert Paxton, and Juliet Osborne. “So near and yet so Far: Harmonic Radar Reveals
Reduced Homing Ability of Nosema Infected Honeybees.” PLoS One. Public
Library of Science, 2014. https://doi.org/10.1371/journal.pone.0103989.'
ieee: 'S. Wolf et al., “So near and yet so far: Harmonic radar reveals reduced
homing ability of Nosema infected honeybees,” PLoS One, vol. 9, no. 8.
Public Library of Science, 2014.'
ista: 'Wolf S, Mcmahon D, Lim K, Pull C, Clark S, Paxton R, Osborne J. 2014. So
near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected
honeybees. PLoS One. 9(8), e103989.'
mla: 'Wolf, Stephan, et al. “So near and yet so Far: Harmonic Radar Reveals Reduced
Homing Ability of Nosema Infected Honeybees.” PLoS One, vol. 9, no. 8,
e103989, Public Library of Science, 2014, doi:10.1371/journal.pone.0103989.'
short: S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, PLoS
One 9 (2014).
date_created: 2018-12-11T11:55:37Z
date_published: 2014-08-06T00:00:00Z
date_updated: 2023-02-23T14:11:56Z
day: '06'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1371/journal.pone.0103989
file:
- access_level: open_access
checksum: 2fc62c6739eada4bddf026afbae669db
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:55Z
date_updated: 2020-07-14T12:45:28Z
file_id: '5042'
file_name: IST-2016-437-v1+1_journal.pone.0103989.pdf
file_size: 1013386
relation: main_file
file_date_updated: 2020-07-14T12:45:28Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '4949'
pubrep_id: '437'
quality_controlled: '1'
related_material:
record:
- id: '9888'
relation: research_data
status: public
scopus_import: 1
status: public
title: 'So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema
infected honeybees'
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2014'
...
---
_id: '9888'
abstract:
- lang: eng
text: Detailed description of the experimental prodedures, data analyses and additional
statistical analyses of the results.
article_processing_charge: No
author:
- first_name: Stephan
full_name: Wolf, Stephan
last_name: Wolf
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Ka
full_name: Lim, Ka
last_name: Lim
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Suzanne
full_name: Clark, Suzanne
last_name: Clark
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
- first_name: Juliet
full_name: Osborne, Juliet
last_name: Osborne
citation:
ama: Wolf S, Mcmahon D, Lim K, et al. Supporting information. 2014. doi:10.1371/journal.pone.0103989.s003
apa: Wolf, S., Mcmahon, D., Lim, K., Pull, C., Clark, S., Paxton, R., & Osborne,
J. (2014). Supporting information. Public Library of Science. https://doi.org/10.1371/journal.pone.0103989.s003
chicago: Wolf, Stephan, Dino Mcmahon, Ka Lim, Christopher Pull, Suzanne Clark, Robert
Paxton, and Juliet Osborne. “Supporting Information.” Public Library of Science,
2014. https://doi.org/10.1371/journal.pone.0103989.s003.
ieee: S. Wolf et al., “Supporting information.” Public Library of Science,
2014.
ista: Wolf S, Mcmahon D, Lim K, Pull C, Clark S, Paxton R, Osborne J. 2014. Supporting
information, Public Library of Science, 10.1371/journal.pone.0103989.s003.
mla: Wolf, Stephan, et al. Supporting Information. Public Library of Science,
2014, doi:10.1371/journal.pone.0103989.s003.
short: S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, (2014).
date_created: 2021-08-11T14:17:53Z
date_updated: 2023-02-23T10:27:38Z
day: '06'
department:
- _id: SyCr
doi: 10.1371/journal.pone.0103989.s003
month: '08'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '2086'
relation: used_in_publication
status: public
status: public
title: Supporting information
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '845'
abstract:
- lang: eng
text: Recombination between double-stranded DNA molecules is a key genetic process
which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs
during meiosis between genotypes with 98.0-99.9% sequence identity, because within-population
nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable
and it is unclear how CO can occur between genotypes with less than 90% sequence
identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan
basidiomycete mushroom, a frequently encountered decayer of woody substrates.
We crossed two haploid individuals, from the United States and from Russia, and
obtained genome sequences for their 17 offspring. The average genetic distance
between the parents was 14%, making it possible to study CO at very high resolution.
We found reduced levels of linkage disequilibrium between loci flanking the CO
sites indicating that they are mostly confined to hotspots of recombination. Furthermore,
CO events preferentially occurred in regions under stronger negative selection,
in particular within exons that showed reduced levels of nucleotide diversity.
Apparently, in hypervariable species CO must avoid regions of higher divergence
between the recombining genomes due to limitations imposed by the mismatch repair
system, with regions under strong negative selection providing the opportunity
for recombination. These patterns are opposite to those observed in a number of
less variable species indicating that population genomics of hypervariable species
may reveal novel biological phenomena.
acknowledgement: The authors are grateful to Georgii Bazykin for valuable discussion
and to the DNA sequencing facility at Engelhardt Institute of Molecular Biology
for Sanger sequencing. This study was supported by the Russian government grant
No 11.G34.31.0008 and by Plan Nacional (BFU2012-31329), Howard Hughes Medical Institute
International Early Career Scientist Award and EMBO Young Investigator Program,
and core funds provided by the University of Michigan.
author:
- first_name: Vladimir
full_name: Seplyarskiy, Vladimir B
last_name: Seplyarskiy
- first_name: Maria
full_name: Logacheva, Maria D
last_name: Logacheva
- first_name: Aleksey
full_name: Penin, Aleksey A
last_name: Penin
- first_name: Maria
full_name: Baranová, Maria A
last_name: Baranová
- first_name: Evgeny
full_name: Leushkin, Evgeny V
last_name: Leushkin
- first_name: Natalia
full_name: Demidenko, Natalia V
last_name: Demidenko
- first_name: Anna
full_name: Klepikova, Anna V
last_name: Klepikova
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Timothy
full_name: James, Timothy Y
last_name: James
citation:
ama: Seplyarskiy V, Logacheva M, Penin A, et al. Crossing-over in a hypervariable
species preferentially occurs in regions of high local similarity. Molecular
Biology and Evolution. 2014;31(11):3016-3025. doi:10.1093/molbev/msu242
apa: Seplyarskiy, V., Logacheva, M., Penin, A., Baranová, M., Leushkin, E., Demidenko,
N., … James, T. (2014). Crossing-over in a hypervariable species preferentially
occurs in regions of high local similarity. Molecular Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/molbev/msu242
chicago: Seplyarskiy, Vladimir, Maria Logacheva, Aleksey Penin, Maria Baranová,
Evgeny Leushkin, Natalia Demidenko, Anna Klepikova, Fyodor Kondrashov, Alexey
Kondrashov, and Timothy James. “Crossing-over in a Hypervariable Species Preferentially
Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution.
Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu242.
ieee: V. Seplyarskiy et al., “Crossing-over in a hypervariable species preferentially
occurs in regions of high local similarity,” Molecular Biology and Evolution,
vol. 31, no. 11. Oxford University Press, pp. 3016–3025, 2014.
ista: Seplyarskiy V, Logacheva M, Penin A, Baranová M, Leushkin E, Demidenko N,
Klepikova A, Kondrashov F, Kondrashov A, James T. 2014. Crossing-over in a hypervariable
species preferentially occurs in regions of high local similarity. Molecular Biology
and Evolution. 31(11), 3016–3025.
mla: Seplyarskiy, Vladimir, et al. “Crossing-over in a Hypervariable Species Preferentially
Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution,
vol. 31, no. 11, Oxford University Press, 2014, pp. 3016–25, doi:10.1093/molbev/msu242.
short: V. Seplyarskiy, M. Logacheva, A. Penin, M. Baranová, E. Leushkin, N. Demidenko,
A. Klepikova, F. Kondrashov, A. Kondrashov, T. James, Molecular Biology and Evolution
31 (2014) 3016–3025.
date_created: 2018-12-11T11:48:48Z
date_published: 2014-11-01T00:00:00Z
date_updated: 2021-01-12T08:19:21Z
day: '01'
doi: 10.1093/molbev/msu242
extern: 1
intvolume: ' 31'
issue: '11'
month: '11'
page: 3016 - 3025
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6801'
quality_controlled: 0
status: public
title: Crossing-over in a hypervariable species preferentially occurs in regions of
high local similarity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 31
year: '2014'
...
---
_id: '892'
abstract:
- lang: eng
text: The study of molecular evolution is important because it reveals how protein
functions emerge and evolve. Recently, several types of studies indicated that
substitutions in molecular evolution occur in a compensatory manner, whereby the
occurrence of a substitution depends on the amino acid residues at other sites.
However, a molecular or structural basis behind the compensation often remains
obscure. Here, we review studies on the interface of structural biology and molecular
evolution that revealed novel aspects of compensatory evolution. In many cases
structural studies benefit from evolutionary data while structural data often
add a functional dimension to the study of molecular evolution.
acknowledgement: |
The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)’ and (BFU2012-31329), the European Union and the European Research Council grant (335980_EinME), RFBR (13-04-00253a), MCB RAS (01201358029) and MES RK Grants.
author:
- first_name: Dmitry
full_name: Ivankov, Dmitry N
last_name: Ivankov
- first_name: Alexei
full_name: Finkelstein, Alexei V
last_name: Finkelstein
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Ivankov D, Finkelstein A, Kondrashov F. A structural perspective of compensatory
evolution. Current Opinion in Structural Biology. 2014;26(1):104-112. doi:10.1016/j.sbi.2014.05.004
apa: Ivankov, D., Finkelstein, A., & Kondrashov, F. (2014). A structural perspective
of compensatory evolution. Current Opinion in Structural Biology. Elsevier.
https://doi.org/10.1016/j.sbi.2014.05.004
chicago: Ivankov, Dmitry, Alexei Finkelstein, and Fyodor Kondrashov. “A Structural
Perspective of Compensatory Evolution.” Current Opinion in Structural Biology.
Elsevier, 2014. https://doi.org/10.1016/j.sbi.2014.05.004.
ieee: D. Ivankov, A. Finkelstein, and F. Kondrashov, “A structural perspective of
compensatory evolution,” Current Opinion in Structural Biology, vol. 26,
no. 1. Elsevier, pp. 104–112, 2014.
ista: Ivankov D, Finkelstein A, Kondrashov F. 2014. A structural perspective of
compensatory evolution. Current Opinion in Structural Biology. 26(1), 104–112.
mla: Ivankov, Dmitry, et al. “A Structural Perspective of Compensatory Evolution.”
Current Opinion in Structural Biology, vol. 26, no. 1, Elsevier, 2014,
pp. 104–12, doi:10.1016/j.sbi.2014.05.004.
short: D. Ivankov, A. Finkelstein, F. Kondrashov, Current Opinion in Structural
Biology 26 (2014) 104–112.
date_created: 2018-12-11T11:49:03Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2021-01-12T08:21:21Z
day: '01'
doi: 10.1016/j.sbi.2014.05.004
extern: 1
intvolume: ' 26'
issue: '1'
month: '06'
page: 104 - 112
publication: Current Opinion in Structural Biology
publication_status: published
publisher: Elsevier
publist_id: '6756'
quality_controlled: 0
status: public
title: A structural perspective of compensatory evolution
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
volume: 26
year: '2014'
...
---
_id: '9050'
abstract:
- lang: eng
text: Self-propelled particles can exhibit surprising non-equilibrium behaviors,
and how they interact with obstacles or boundaries remains an important open problem.
Here we show that chemically propelled micro-rods can be captured, with little
change in their speed, into close orbits around solid spheres resting on or near
a horizontal plane. We show that this interaction between sphere and particle
is short-range, occurring even for spheres smaller than the particle length, and
for a variety of sphere materials. We consider a simple model, based on lubrication
theory, of a force- and torque-free swimmer driven by a surface slip (the phoretic
propulsion mechanism) and moving near a solid surface. The model demonstrates
capture, or movement towards the surface, and yields speeds independent of distance.
This study reveals the crucial aspects of activity–driven interactions of self-propelled
particles with passive objects, and brings into question the use of colloidal
tracers as probes of active matter.
article_number: '1784'
article_processing_charge: No
article_type: original
author:
- first_name: Daisuke
full_name: Takagi, Daisuke
last_name: Takagi
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Adam B.
full_name: Braunschweig, Adam B.
last_name: Braunschweig
- first_name: Michael J.
full_name: Shelley, Michael J.
last_name: Shelley
- first_name: Jun
full_name: Zhang, Jun
last_name: Zhang
citation:
ama: Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. Hydrodynamic capture
of microswimmers into sphere-bound orbits. Soft Matter. 2014;10(11). doi:10.1039/c3sm52815d
apa: Takagi, D., Palacci, J. A., Braunschweig, A. B., Shelley, M. J., & Zhang,
J. (2014). Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft
Matter. Royal Society of Chemistry . https://doi.org/10.1039/c3sm52815d
chicago: Takagi, Daisuke, Jérémie A Palacci, Adam B. Braunschweig, Michael J. Shelley,
and Jun Zhang. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.”
Soft Matter. Royal Society of Chemistry , 2014. https://doi.org/10.1039/c3sm52815d.
ieee: D. Takagi, J. A. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang,
“Hydrodynamic capture of microswimmers into sphere-bound orbits,” Soft Matter,
vol. 10, no. 11. Royal Society of Chemistry , 2014.
ista: Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. 2014. Hydrodynamic
capture of microswimmers into sphere-bound orbits. Soft Matter. 10(11), 1784.
mla: Takagi, Daisuke, et al. “Hydrodynamic Capture of Microswimmers into Sphere-Bound
Orbits.” Soft Matter, vol. 10, no. 11, 1784, Royal Society of Chemistry
, 2014, doi:10.1039/c3sm52815d.
short: D. Takagi, J.A. Palacci, A.B. Braunschweig, M.J. Shelley, J. Zhang, Soft
Matter 10 (2014).
date_created: 2021-02-01T13:43:31Z
date_published: 2014-03-21T00:00:00Z
date_updated: 2023-02-23T13:47:35Z
day: '21'
doi: 10.1039/c3sm52815d
extern: '1'
external_id:
arxiv:
- '1309.5662'
pmid:
- '24800268'
intvolume: ' 10'
issue: '11'
keyword:
- General Chemistry
- Condensed Matter Physics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1309.5662
month: '03'
oa: 1
oa_version: Preprint
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: 'Royal Society of Chemistry '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hydrodynamic capture of microswimmers into sphere-bound orbits
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 10
year: '2014'
...
---
_id: '9166'
abstract:
- lang: eng
text: Light-activated self-propelled colloids are synthesized and their active motion
is studied using optical microscopy. We propose a versatile route using different
photoactive materials, and demonstrate a multiwavelength activation and propulsion.
Thanks to the photoelectrochemical properties of two semiconductor materials (α-Fe2O3
and TiO2), a light with an energy higher than the bandgap triggers the reaction
of decomposition of hydrogen peroxide and produces a chemical cloud around the
particle. It induces a phoretic attraction with neighbouring colloids as well
as an osmotic self-propulsion of the particle on the substrate. We use these mechanisms
to form colloidal cargos as well as self-propelled particles where the light-activated
component is embedded into a dielectric sphere. The particles are self-propelled
along a direction otherwise randomized by thermal fluctuations, and exhibit a
persistent random walk. For sufficient surface density, the particles spontaneously
form ‘living crystals’ which are mobile, break apart and reform. Steering the
particle with an external magnetic field, we show that the formation of the dense
phase results from the collisions heads-on of the particles. This effect is intrinsically
non-equilibrium and a novel principle of organization for systems without detailed
balance. Engineering families of particles self-propelled by different wavelength
demonstrate a good understanding of both the physics and the chemistry behind
the system and points to a general route for designing new families of self-propelled
particles.
article_number: '20130372'
article_processing_charge: No
article_type: original
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: S.
full_name: Sacanna, S.
last_name: Sacanna
- first_name: S.-H.
full_name: Kim, S.-H.
last_name: Kim
- first_name: G.-R.
full_name: Yi, G.-R.
last_name: Yi
- first_name: D. J.
full_name: Pine, D. J.
last_name: Pine
- first_name: P. M.
full_name: Chaikin, P. M.
last_name: Chaikin
citation:
ama: 'Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. Light-activated
self-propelled colloids. Philosophical Transactions of the Royal Society A:
Mathematical, Physical and Engineering Sciences. 2014;372(2029). doi:10.1098/rsta.2013.0372'
apa: 'Palacci, J. A., Sacanna, S., Kim, S.-H., Yi, G.-R., Pine, D. J., & Chaikin,
P. M. (2014). Light-activated self-propelled colloids. Philosophical Transactions
of the Royal Society A: Mathematical, Physical and Engineering Sciences. The
Royal Society. https://doi.org/10.1098/rsta.2013.0372'
chicago: 'Palacci, Jérémie A, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P.
M. Chaikin. “Light-Activated Self-Propelled Colloids.” Philosophical Transactions
of the Royal Society A: Mathematical, Physical and Engineering Sciences. The
Royal Society, 2014. https://doi.org/10.1098/rsta.2013.0372.'
ieee: 'J. A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin,
“Light-activated self-propelled colloids,” Philosophical Transactions of the
Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 372,
no. 2029. The Royal Society, 2014.'
ista: 'Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. 2014. Light-activated
self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical,
Physical and Engineering Sciences. 372(2029), 20130372.'
mla: 'Palacci, Jérémie A., et al. “Light-Activated Self-Propelled Colloids.” Philosophical
Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences,
vol. 372, no. 2029, 20130372, The Royal Society, 2014, doi:10.1098/rsta.2013.0372.'
short: 'J.A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D.J. Pine, P.M. Chaikin,
Philosophical Transactions of the Royal Society A: Mathematical, Physical and
Engineering Sciences 372 (2014).'
date_created: 2021-02-18T14:31:11Z
date_published: 2014-11-28T00:00:00Z
date_updated: 2021-02-22T10:44:16Z
day: '28'
doi: 10.1098/rsta.2013.0372
extern: '1'
external_id:
arxiv:
- '1410.7278'
pmid:
- '25332383'
intvolume: ' 372'
issue: '2029'
keyword:
- General Engineering
- General Physics and Astronomy
- General Mathematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rsta.2013.0372
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Philosophical Transactions of the Royal Society A: Mathematical, Physical
and Engineering Sciences'
publication_identifier:
eissn:
- 1471-2962
issn:
- 1364-503X
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Light-activated self-propelled colloids
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 372
year: '2014'
...
---
_id: '926'
abstract:
- lang: eng
text: 'The regulation of cell growth in animal tissues is a question of critical
importance: most tissues contain different types of cells in interconversion and
the fraction of each type has to be controlled in a precise way, by mechanisms
that remain unclear. Here, we provide a theoretical framework for the homeostasis
of stem-cell-containing epithelial tissues using mechanical equations, which describe
the size of the tissue and kinetic equations, which describe the interconversions
of the cell populations. We show that several features, such as the evolution
of stem cell fractions during intestinal development, the shape of a developing
intestinal wall, as well as the increase in the proliferative compartment in cancer
initiation, can be studied and understood from generic modelling which does not
rely on a particular regulatory mechanism. Finally, inspired by recent experiments,
we propose a model where cell division rates are regulated by the mechanical stresses
in the epithelial sheet. We show that pressure-controlled growth can, in addition
to the previous features, also explain with few parameters the formation of stem
cell compartments as well as the morphologies observed when a colonic crypt becomes
cancerous. We also discuss optimal strategies of wound healing, in connection
with experiments on the cornea.'
acknowledgement: We thank Jens Elgeti and Silvia Fre for fruitful discussions.
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jacques
full_name: Prost, Jacques
last_name: Prost
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
citation:
ama: Hannezo EB, Prost J, Joanny J. Growth homeostatic regulation and stem cell
dynamics in tissues. Journal of the Royal Society Interface. 2014;11(93).
doi:10.1098/rsif.2013.0895
apa: Hannezo, E. B., Prost, J., & Joanny, J. (2014). Growth homeostatic regulation
and stem cell dynamics in tissues. Journal of the Royal Society Interface.
Royal Society of London. https://doi.org/10.1098/rsif.2013.0895
chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Growth Homeostatic
Regulation and Stem Cell Dynamics in Tissues.” Journal of the Royal Society
Interface. Royal Society of London, 2014. https://doi.org/10.1098/rsif.2013.0895.
ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Growth homeostatic regulation and
stem cell dynamics in tissues,” Journal of the Royal Society Interface,
vol. 11, no. 93. Royal Society of London, 2014.
ista: Hannezo EB, Prost J, Joanny J. 2014. Growth homeostatic regulation and stem
cell dynamics in tissues. Journal of the Royal Society Interface. 11(93).
mla: Hannezo, Edouard B., et al. “Growth Homeostatic Regulation and Stem Cell Dynamics
in Tissues.” Journal of the Royal Society Interface, vol. 11, no. 93, Royal
Society of London, 2014, doi:10.1098/rsif.2013.0895.
short: E.B. Hannezo, J. Prost, J. Joanny, Journal of the Royal Society Interface
11 (2014).
date_created: 2018-12-11T11:49:14Z
date_published: 2014-04-06T00:00:00Z
date_updated: 2021-01-12T08:21:57Z
day: '06'
doi: 10.1098/rsif.2013.0895
extern: '1'
intvolume: ' 11'
issue: '93'
language:
- iso: eng
month: '04'
oa_version: None
publication: Journal of the Royal Society Interface
publication_status: published
publisher: Royal Society of London
publist_id: '6516'
status: public
title: Growth homeostatic regulation and stem cell dynamics in tissues
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2014'
...
---
_id: '9458'
abstract:
- lang: eng
text: Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes.
Their genomes are typically depleted of CG dinucleotides because of imperfect
repair of deaminated methylcytosines. Here, we extensively survey diverse species
lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless
frequently present and catalyzed by a different DNA methyltransferase family,
Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years
ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered
methylation occurs at unprecedented densities and directly disfavors nucleosomes,
contributing to nucleosome positioning between clusters. Dense methylation is
enabled by a regime of genomic sequence evolution that enriches CG dinucleotides
and drives the highest CG frequencies known. Species with linker methylation have
small, transcriptionally active nuclei that approach the physical limits of chromatin
compaction. These features constitute a previously unappreciated genome architecture,
in which dense methylation influences nucleosome positions, likely facilitating
nuclear processes under extreme spatial constraints.
article_processing_charge: No
article_type: original
author:
- first_name: Jason T.
full_name: Huff, Jason T.
last_name: Huff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome
positioning in diverse eukaryotes. Cell. 2014;156(6):1286-1297. doi:10.1016/j.cell.2014.01.029
apa: Huff, J. T., & Zilberman, D. (2014). Dnmt1-independent CG methylation contributes
to nucleosome positioning in diverse eukaryotes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.01.029
chicago: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation
Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell. Elsevier,
2014. https://doi.org/10.1016/j.cell.2014.01.029.
ieee: J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes
to nucleosome positioning in diverse eukaryotes,” Cell, vol. 156, no. 6.
Elsevier, pp. 1286–1297, 2014.
ista: Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to
nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.
mla: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes
to Nucleosome Positioning in Diverse Eukaryotes.” Cell, vol. 156, no. 6,
Elsevier, 2014, pp. 1286–97, doi:10.1016/j.cell.2014.01.029.
short: J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.
date_created: 2021-06-04T12:00:16Z
date_published: 2014-03-13T00:00:00Z
date_updated: 2021-12-14T08:22:36Z
day: '13'
department:
- _id: DaZi
doi: 10.1016/j.cell.2014.01.029
extern: '1'
external_id:
pmid:
- '24630728'
intvolume: ' 156'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2014.01.029
month: '03'
oa: 1
oa_version: Published Version
page: 1286-1297
pmid: 1
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse
eukaryotes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 156
year: '2014'
...
---
_id: '9479'
abstract:
- lang: eng
text: Centromeres mediate chromosome segregation and are defined by the centromere-specific
histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from
centromeres is a general property of terminally differentiated cells, and the
persistence of CenH3 increases the risk of diseases such as cancer. However, active
mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen
vegetative cells, which transport engulfed sperm by extended tip growth, undergo
loss of CenH3; centromeric heterochromatin decondensation; and bulk activation
of silent rRNA genes, accompanied by their translocation into the nucleolus. Here,
we show that these processes are blocked by mutations in the evolutionarily conserved
AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97
proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier
(SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates
with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as
well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations.
In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are
uniquely clustered together within the nucleolus and all major rRNA gene variants,
including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant
vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed
centromeric heterochromatin at the external periphery of the nucleolus. Our results
indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres
and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus
for ribosome production, which fuels single nucleus-driven pollen tube growth
and is essential for plant reproduction.
article_processing_charge: No
article_type: original
author:
- first_name: Zsuzsanna
full_name: Mérai, Zsuzsanna
last_name: Mérai
- first_name: Nina
full_name: Chumak, Nina
last_name: Chumak
- first_name: Marcelina
full_name: García-Aguilar, Marcelina
last_name: García-Aguilar
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Vera K.
full_name: Schoft, Vera K.
last_name: Schoft
- first_name: János
full_name: Bindics, János
last_name: Bindics
- first_name: Lucyna
full_name: Ślusarz, Lucyna
last_name: Ślusarz
- first_name: Stéphanie
full_name: Arnoux, Stéphanie
last_name: Arnoux
- first_name: Susanne
full_name: Opravil, Susanne
last_name: Opravil
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Hisashi
full_name: Tamaru, Hisashi
last_name: Tamaru
citation:
ama: Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone
Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and
activates ribosomal RNA genes. Proceedings of the National Academy of Sciences.
2014;111(45):16166-16171. doi:10.1073/pnas.1418564111
apa: Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft,
V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles
sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA
genes. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1418564111
chicago: Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh,
Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular
Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin,
and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of
Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1418564111.
ieee: Z. Mérai et al., “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles
sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA
genes,” Proceedings of the National Academy of Sciences, vol. 111, no.
45. National Academy of Sciences, pp. 16166–16171, 2014.
ista: Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics
J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru
H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated
centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings
of the National Academy of Sciences. 111(45), 16166–16171.
mla: Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles
Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA
Genes.” Proceedings of the National Academy of Sciences, vol. 111, no.
45, National Academy of Sciences, 2014, pp. 16166–71, doi:10.1073/pnas.1418564111.
short: Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft,
J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L.
Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014)
16166–16171.
date_created: 2021-06-07T07:23:43Z
date_published: 2014-11-11T00:00:00Z
date_updated: 2021-12-14T08:23:26Z
day: '11'
department:
- _id: DaZi
doi: 10.1073/pnas.1418564111
extern: '1'
external_id:
pmid:
- '25344531'
intvolume: ' 111'
issue: '45'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1418564111
month: '11'
oa: 1
oa_version: Published Version
page: 16166-16171
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres,
decondenses heterochromatin, and activates ribosomal RNA genes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2014'
...
---
_id: '9662'
abstract:
- lang: eng
text: Fractionation of isotopes among distinct molecules or phases is a quantum
effect which is often exploited to obtain insights on reaction mechanisms, biochemical,
geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios
in atomistic simulations is challenging, because one needs to perform a thermodynamic
integration with respect to the isotope mass, along with time-consuming path integral
calculations. By re-formulating the problem as a particle exchange in the ring
polymer partition function, we derive new estimators giving direct access to the
differential partitioning of isotopes, which can simplify the calculations by
avoiding thermodynamic integration. We demonstrate the efficiency of these estimators
by applying them to investigate the isotope fractionation ratios in the gas-phase
Zundel cation, and in a few simple hydrocarbons.
article_number: '244112'
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Ceriotti M. Direct path integral estimators for isotope fractionation
ratios. The Journal of Chemical Physics. 2014;141(24). doi:10.1063/1.4904293
apa: Cheng, B., & Ceriotti, M. (2014). Direct path integral estimators for isotope
fractionation ratios. The Journal of Chemical Physics. AIP Publishing.
https://doi.org/10.1063/1.4904293
chicago: Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators
for Isotope Fractionation Ratios.” The Journal of Chemical Physics. AIP
Publishing, 2014. https://doi.org/10.1063/1.4904293.
ieee: B. Cheng and M. Ceriotti, “Direct path integral estimators for isotope fractionation
ratios,” The Journal of Chemical Physics, vol. 141, no. 24. AIP Publishing,
2014.
ista: Cheng B, Ceriotti M. 2014. Direct path integral estimators for isotope fractionation
ratios. The Journal of Chemical Physics. 141(24), 244112.
mla: Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for
Isotope Fractionation Ratios.” The Journal of Chemical Physics, vol. 141,
no. 24, 244112, AIP Publishing, 2014, doi:10.1063/1.4904293.
short: B. Cheng, M. Ceriotti, The Journal of Chemical Physics 141 (2014).
date_created: 2021-07-15T09:22:49Z
date_published: 2014-12-28T00:00:00Z
date_updated: 2021-08-09T12:32:24Z
day: '28'
doi: 10.1063/1.4904293
extern: '1'
external_id:
arxiv:
- '1412.1308'
pmid:
- '25554138'
intvolume: ' 141'
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1412.1308
month: '12'
oa: 1
oa_version: Preprint
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Direct path integral estimators for isotope fractionation ratios
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 141
year: '2014'
...
---
_id: '97'
abstract:
- lang: eng
text: The distribution of Coulomb blockade peak heights as a function of magnetic
field is investigated experimentally in a Ge-Si nanowire quantum dot. Strong spin-orbit
coupling in this hole-gas system leads to antilocalization of Coulomb blockade
peaks, consistent with theory. In particular, the peak height distribution has
its maximum away from zero at zero magnetic field, with an average that decreases
with increasing field. Magnetoconductance in the open-wire regime places a bound
on the spin-orbit length (lso < 20 nm), consistent with values extracted in the
Coulomb blockade regime (lso < 25 nm).
acknowledgement: Research supported by the Danish National Research Foundation, the
Office of Science at the U.S. Department of Energy, the National Science Foundation
(PHY-1104528), and the Defense Advanced Research Projects Agency through the QuEST
Program.
article_number: '216806'
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
- first_name: Thorvald
full_name: Larsen, Thorvald
last_name: Larsen
- first_name: Mattias
full_name: Fitzpatrick, Mattias
last_name: Fitzpatrick
- first_name: Jun
full_name: Yao, Jun
last_name: Yao
- first_name: Hao
full_name: Yan, Hao
last_name: Yan
- first_name: Charles
full_name: Lieber, Charles
last_name: Lieber
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
citation:
ama: Higginbotham AP, Kuemmeth F, Larsen T, et al. Antilocalization of coulomb blockade
in a Ge/Si nanowire. APS Physics, Physical Review Letters. 2014;112(21).
doi:10.1103/PhysRevLett.112.216806
apa: Higginbotham, A. P., Kuemmeth, F., Larsen, T., Fitzpatrick, M., Yao, J., Yan,
H., … Marcus, C. (2014). Antilocalization of coulomb blockade in a Ge/Si nanowire.
APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.112.216806
chicago: Higginbotham, Andrew P, Ferdinand Kuemmeth, Thorvald Larsen, Mattias Fitzpatrick,
Jun Yao, Hao Yan, Charles Lieber, and Charles Marcus. “Antilocalization of Coulomb
Blockade in a Ge/Si Nanowire.” APS Physics, Physical Review Letters. American
Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.112.216806.
ieee: A. P. Higginbotham et al., “Antilocalization of coulomb blockade in
a Ge/Si nanowire,” APS Physics, Physical Review Letters, vol. 112, no.
21. American Physical Society, 2014.
ista: Higginbotham AP, Kuemmeth F, Larsen T, Fitzpatrick M, Yao J, Yan H, Lieber
C, Marcus C. 2014. Antilocalization of coulomb blockade in a Ge/Si nanowire. APS
Physics, Physical Review Letters. 112(21), 216806.
mla: Higginbotham, Andrew P., et al. “Antilocalization of Coulomb Blockade in a
Ge/Si Nanowire.” APS Physics, Physical Review Letters, vol. 112, no. 21,
216806, American Physical Society, 2014, doi:10.1103/PhysRevLett.112.216806.
short: A.P. Higginbotham, F. Kuemmeth, T. Larsen, M. Fitzpatrick, J. Yao, H. Yan,
C. Lieber, C. Marcus, APS Physics, Physical Review Letters 112 (2014).
date_created: 2018-12-11T11:44:36Z
date_published: 2014-05-29T00:00:00Z
date_updated: 2021-01-12T08:22:19Z
day: '29'
doi: 10.1103/PhysRevLett.112.216806
extern: '1'
external_id:
arxiv:
- '1401.2948'
intvolume: ' 112'
issue: '21'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1401.2948
month: '05'
oa: 1
oa_version: None
publication: APS Physics, Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7957'
quality_controlled: '1'
status: public
title: Antilocalization of coulomb blockade in a Ge/Si nanowire
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2014'
...
---
_id: '2004'
abstract:
- lang: eng
text: We have assembled a network of cell-fate determining transcription factors
that play a key role in the specification of the ventral neuronal subtypes of
the spinal cord on the basis of published transcriptional interactions. Asynchronous
Boolean modelling of the network was used to compare simulation results with reported
experimental observations. Such comparison highlighted the need to include additional
regulatory connections in order to obtain the fixed point attractors of the model
associated with the five known progenitor cell types located in the ventral spinal
cord. The revised gene regulatory network reproduced previously observed cell
state switches between progenitor cells observed in knock-out animal models or
in experiments where the transcription factors were overexpressed. Furthermore
the network predicted the inhibition of Irx3 by Nkx2.2 and this prediction was
tested experimentally. Our results provide evidence for the existence of an as
yet undescribed inhibitory connection which could potentially have significance
beyond the ventral spinal cord. The work presented in this paper demonstrates
the strength of Boolean modelling for identifying gene regulatory networks.
article_number: e111430
author:
- first_name: Anna
full_name: Lovrics, Anna
last_name: Lovrics
- first_name: Yu
full_name: Gao, Yu
last_name: Gao
- first_name: Bianka
full_name: Juhász, Bianka
last_name: Juhász
- first_name: István
full_name: Bock, István
last_name: Bock
- first_name: Helen
full_name: Byrne, Helen
last_name: Byrne
- first_name: András
full_name: Dinnyés, András
last_name: Dinnyés
- first_name: Krisztián
full_name: Kovács, Krisztián
id: 2AB5821E-F248-11E8-B48F-1D18A9856A87
last_name: Kovács
citation:
ama: Lovrics A, Gao Y, Juhász B, et al. Boolean modelling reveals new regulatory
connections between transcription factors orchestrating the development of the
ventral spinal cord. PLoS One. 2014;9(11). doi:10.1371/journal.pone.0111430
apa: Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H., Dinnyés, A., & Kovács,
K. (2014). Boolean modelling reveals new regulatory connections between transcription
factors orchestrating the development of the ventral spinal cord. PLoS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0111430
chicago: Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen Byrne, András
Dinnyés, and Krisztián Kovács. “Boolean Modelling Reveals New Regulatory Connections
between Transcription Factors Orchestrating the Development of the Ventral Spinal
Cord.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0111430.
ieee: A. Lovrics et al., “Boolean modelling reveals new regulatory connections
between transcription factors orchestrating the development of the ventral spinal
cord,” PLoS One, vol. 9, no. 11. Public Library of Science, 2014.
ista: Lovrics A, Gao Y, Juhász B, Bock I, Byrne H, Dinnyés A, Kovács K. 2014. Boolean
modelling reveals new regulatory connections between transcription factors orchestrating
the development of the ventral spinal cord. PLoS One. 9(11), e111430.
mla: Lovrics, Anna, et al. “Boolean Modelling Reveals New Regulatory Connections
between Transcription Factors Orchestrating the Development of the Ventral Spinal
Cord.” PLoS One, vol. 9, no. 11, e111430, Public Library of Science, 2014,
doi:10.1371/journal.pone.0111430.
short: A. Lovrics, Y. Gao, B. Juhász, I. Bock, H. Byrne, A. Dinnyés, K. Kovács,
PLoS One 9 (2014).
date_created: 2018-12-11T11:55:09Z
date_published: 2014-11-14T00:00:00Z
date_updated: 2023-02-23T14:06:14Z
day: '14'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1371/journal.pone.0111430
ec_funded: 1
file:
- access_level: open_access
checksum: a2289b843f7463eb1233f9ce45e6a943
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:58Z
date_updated: 2020-07-14T12:45:24Z
file_id: '4850'
file_name: IST-2016-435-v1+1_journal.pone.0111430.pdf
file_size: 829363
relation: main_file
file_date_updated: 2020-07-14T12:45:24Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5072'
pubrep_id: '435'
quality_controlled: '1'
related_material:
record:
- id: '9722'
relation: research_data
status: public
scopus_import: 1
status: public
title: Boolean modelling reveals new regulatory connections between transcription
factors orchestrating the development of the ventral spinal cord
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2014'
...
---
_id: '9722'
article_processing_charge: No
author:
- first_name: Anna
full_name: Lovrics, Anna
last_name: Lovrics
- first_name: Yu
full_name: Gao, Yu
last_name: Gao
- first_name: Bianka
full_name: Juhász, Bianka
last_name: Juhász
- first_name: István
full_name: Bock, István
last_name: Bock
- first_name: Helen M.
full_name: Byrne, Helen M.
last_name: Byrne
- first_name: András
full_name: Dinnyés, András
last_name: Dinnyés
- first_name: Krisztián
full_name: Kovács, Krisztián
id: 2AB5821E-F248-11E8-B48F-1D18A9856A87
last_name: Kovács
citation:
ama: Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression
states when Dbx2 inhibits Nkx2.2. 2014. doi:10.1371/journal.pone.0111430.s006
apa: Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., &
Kovács, K. (2014). Transition probability between TF expression states when Dbx2
inhibits Nkx2.2. Public Library of Science. https://doi.org/10.1371/journal.pone.0111430.s006
chicago: Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András
Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States
When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0111430.s006.
ieee: A. Lovrics et al., “Transition probability between TF expression states
when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014.
ista: Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition
probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library
of Science, 10.1371/journal.pone.0111430.s006.
mla: Lovrics, Anna, et al. Transition Probability between TF Expression States
When Dbx2 Inhibits Nkx2.2. Public Library of Science, 2014, doi:10.1371/journal.pone.0111430.s006.
short: A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács,
(2014).
date_created: 2021-07-26T14:35:00Z
date_published: 2014-11-14T00:00:00Z
date_updated: 2023-02-23T10:24:07Z
day: '14'
department:
- _id: JoCs
doi: 10.1371/journal.pone.0111430.s006
month: '11'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '2004'
relation: used_in_publication
status: public
status: public
title: Transition probability between TF expression states when Dbx2 inhibits Nkx2.2
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '2039'
abstract:
- lang: eng
text: 'A fundamental question in biology is the following: what is the time scale
that is needed for evolutionary innovations? There are many results that characterize
single steps in terms of the fixation time of new mutants arising in populations
of certain size and structure. But here we ask a different question, which is
concerned with the much longer time scale of evolutionary trajectories: how long
does it take for a population exploring a fitness landscape to find target sequences
that encode new biological functions? Our key variable is the length, (Formula
presented.) of the genetic sequence that undergoes adaptation. In computer science
there is a crucial distinction between problems that require algorithms which
take polynomial or exponential time. The latter are considered to be intractable.
Here we develop a theoretical approach that allows us to estimate the time of
evolution as function of (Formula presented.) We show that adaptation on many
fitness landscapes takes time that is exponential in (Formula presented.) even
if there are broad selection gradients and many targets uniformly distributed
in sequence space. These negative results lead us to search for specific mechanisms
that allow evolution to work on polynomial time scales. We study a regeneration
process and show that it enables evolution to work in polynomial time.'
article_number: 7p
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Ben
full_name: Adlam, Ben
last_name: Adlam
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. The time scale of evolutionary
innovation. PLoS Computational Biology. 2014;10(9). doi:10.1371/journal.pcbi.1003818
apa: Chatterjee, K., Pavlogiannis, A., Adlam, B., & Nowak, M. (2014). The time
scale of evolutionary innovation. PLoS Computational Biology. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1003818
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Nowak.
“The Time Scale of Evolutionary Innovation.” PLoS Computational Biology.
Public Library of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003818.
ieee: K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Nowak, “The time scale of
evolutionary innovation,” PLoS Computational Biology, vol. 10, no. 9. Public
Library of Science, 2014.
ista: Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. 2014. The time scale of evolutionary
innovation. PLoS Computational Biology. 10(9), 7p.
mla: Chatterjee, Krishnendu, et al. “The Time Scale of Evolutionary Innovation.”
PLoS Computational Biology, vol. 10, no. 9, 7p, Public Library of Science,
2014, doi:10.1371/journal.pcbi.1003818.
short: K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Nowak, PLoS Computational Biology
10 (2014).
date_created: 2018-12-11T11:55:22Z
date_published: 2014-09-11T00:00:00Z
date_updated: 2023-02-23T14:06:36Z
day: '11'
ddc:
- '510'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1003818
ec_funded: 1
file:
- access_level: open_access
checksum: 712d4c5787ddf97809cfc962507f0738
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:35Z
date_updated: 2020-07-14T12:45:26Z
file_id: '4890'
file_name: IST-2016-440-v1+1_journal.pcbi.1003818.pdf
file_size: 1399093
relation: main_file
file_date_updated: 2020-07-14T12:45:26Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5012'
pubrep_id: '440'
quality_controlled: '1'
related_material:
record:
- id: '9739'
relation: research_data
status: public
scopus_import: 1
status: public
title: The time scale of evolutionary innovation
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2014'
...
---
_id: '2161'
abstract:
- lang: eng
text: 'Repeated pathogen exposure is a common threat in colonies of social insects,
posing selection pressures on colony members to respond with improved disease-defense
performance. We here tested whether experience gained by repeated tending of low-level
fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary
brood care in the clonal ant, Platythyrea punctata. We trained ants individually
over nine consecutive trials to either sham-treated or fungus-exposed larvae.
We then compared the larval grooming behavior of naive and trained ants and measured
how effectively they removed infectious fungal conidiospores from the fungus-exposed
larvae. We found that the ants changed the duration of larval grooming in response
to both, larval treatment and their level of experience: (1) sham-treated larvae
received longer grooming than the fungus-exposed larvae and (2) trained ants performed
less self-grooming but longer larval grooming than naive ants, which was true
for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants
that groomed the fungus-exposed larvae for longer periods removed a higher number
of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced
ants performed longer larval grooming, they were more effective in fungal removal,
thus making them better caretakers under pathogen attack of the colony. By studying
this clonal ant, we can thus conclude that even in the absence of genetic variation
between colony members, differences in experience levels of brood care may affect
performance of sanitary brood care in social insects.'
acknowledgement: "We thank Katrin Kellner for colony establishment and characterization,
Mike Bidochka for the fungal strain, Meghan Vyleta for fungal strain characterization,
Martina Klatt and Simon Tragust for help in the laboratory, Dimitri Missoh for developing
the software BioLogic, and Mark Brown and Raphaël Jeanson for discussion and help
with data analysis. The study was funded by the European Research Council (ERC Starting
Grant to SC; Marie Curie IEF to LVU) and the German Research Foundation DFG (to
SC and to JH), and CW received funding by the doctoral school Diversité du Vivant
(Cotutelle project to CD and SC).\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Claudia
full_name: Westhus, Claudia
id: ca9c6ca9-e8aa-11ec-a586-b9471ede0494
last_name: Westhus
- 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: Edouard
full_name: Tourdot, Edouard
last_name: Tourdot
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Claudie
full_name: Doums, Claudie
last_name: Doums
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. Increased grooming
after repeated brood care provides sanitary benefits in a clonal ant. Behavioral
Ecology and Sociobiology. 2014;68(10):1701-1710. doi:10.1007/s00265-014-1778-8
apa: Westhus, C., Ugelvig, L. V., Tourdot, E., Heinze, J., Doums, C., & Cremer,
S. (2014). Increased grooming after repeated brood care provides sanitary benefits
in a clonal ant. Behavioral Ecology and Sociobiology. Springer. https://doi.org/10.1007/s00265-014-1778-8
chicago: Westhus, Claudia, Line V Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie
Doums, and Sylvia Cremer. “Increased Grooming after Repeated Brood Care Provides
Sanitary Benefits in a Clonal Ant.” Behavioral Ecology and Sociobiology.
Springer, 2014. https://doi.org/10.1007/s00265-014-1778-8.
ieee: C. Westhus, L. V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, and S. Cremer,
“Increased grooming after repeated brood care provides sanitary benefits in a
clonal ant,” Behavioral Ecology and Sociobiology, vol. 68, no. 10. Springer,
pp. 1701–1710, 2014.
ista: Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. 2014. Increased
grooming after repeated brood care provides sanitary benefits in a clonal ant.
Behavioral Ecology and Sociobiology. 68(10), 1701–1710.
mla: Westhus, Claudia, et al. “Increased Grooming after Repeated Brood Care Provides
Sanitary Benefits in a Clonal Ant.” Behavioral Ecology and Sociobiology,
vol. 68, no. 10, Springer, 2014, pp. 1701–10, doi:10.1007/s00265-014-1778-8.
short: C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, Behavioral
Ecology and Sociobiology 68 (2014) 1701–1710.
date_created: 2018-12-11T11:56:03Z
date_published: 2014-07-23T00:00:00Z
date_updated: 2023-02-23T14:06:46Z
day: '23'
department:
- _id: SyCr
doi: 10.1007/s00265-014-1778-8
ec_funded: 1
intvolume: ' 68'
issue: '10'
language:
- iso: eng
month: '07'
oa_version: None
page: 1701 - 1710
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
publication: Behavioral Ecology and Sociobiology
publication_identifier:
issn:
- 0340-5443
publication_status: published
publisher: Springer
publist_id: '4823'
quality_controlled: '1'
related_material:
record:
- id: '9742'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Increased grooming after repeated brood care provides sanitary benefits in
a clonal ant
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68
year: '2014'
...
---
_id: '2036'
abstract:
- lang: eng
text: ' In rapidly changing environments, selection history may impact the dynamics
of adaptation. Mutations selected in one environment may result in pleiotropic
fitness trade-offs in subsequent novel environments, slowing the rates of adaptation.
Epistatic interactions between mutations selected in sequential stressful environments
may slow or accelerate subsequent rates of adaptation, depending on the nature
of that interaction. We explored the dynamics of adaptation during sequential
exposure to herbicides with different modes of action in Chlamydomonas reinhardtii.
Evolution of resistance to two of the herbicides was largely independent of selection
history. For carbetamide, previous adaptation to other herbicide modes of action
positively impacted the likelihood of adaptation to this herbicide. Furthermore,
while adaptation to all individual herbicides was associated with pleiotropic
fitness costs in stress-free environments, we observed that accumulation of resistance
mechanisms was accompanied by a reduction in overall fitness costs. We suggest
that antagonistic epistasis may be a driving mechanism that enables populations
to more readily adapt in novel environments. These findings highlight the potential
for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug
and -pesticide resistance, as well as the potential for epistatic interactions
between adaptive mutations to facilitate evolutionary rescue in rapidly changing
environments. '
acknowledgement: The project was supported by Leverhulme Trust.
article_number: '20141679'
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
citation:
ama: Lagator M, Colegrave N, Neve P. Selection history and epistatic interactions
impact dynamics of adaptation to novel environmental stresses. Proceedings
of the Royal Society of London Series B Biological Sciences. 2014;281(1794).
doi:10.1098/rspb.2014.1679
apa: Lagator, M., Colegrave, N., & Neve, P. (2014). Selection history and epistatic
interactions impact dynamics of adaptation to novel environmental stresses. Proceedings
of the Royal Society of London Series B Biological Sciences. Royal Society,
The. https://doi.org/10.1098/rspb.2014.1679
chicago: Lagator, Mato, Nick Colegrave, and Paul Neve. “Selection History and Epistatic
Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Proceedings
of the Royal Society of London Series B Biological Sciences. Royal Society,
The, 2014. https://doi.org/10.1098/rspb.2014.1679.
ieee: M. Lagator, N. Colegrave, and P. Neve, “Selection history and epistatic interactions
impact dynamics of adaptation to novel environmental stresses,” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 281, no.
1794. Royal Society, The, 2014.
ista: Lagator M, Colegrave N, Neve P. 2014. Selection history and epistatic interactions
impact dynamics of adaptation to novel environmental stresses. Proceedings of
the Royal Society of London Series B Biological Sciences. 281(1794), 20141679.
mla: Lagator, Mato, et al. “Selection History and Epistatic Interactions Impact
Dynamics of Adaptation to Novel Environmental Stresses.” Proceedings of the
Royal Society of London Series B Biological Sciences, vol. 281, no. 1794,
20141679, Royal Society, The, 2014, doi:10.1098/rspb.2014.1679.
short: M. Lagator, N. Colegrave, P. Neve, Proceedings of the Royal Society of London
Series B Biological Sciences 281 (2014).
date_created: 2018-12-11T11:55:21Z
date_published: 2014-09-17T00:00:00Z
date_updated: 2023-02-23T14:06:44Z
day: '17'
department:
- _id: CaGu
doi: 10.1098/rspb.2014.1679
intvolume: ' 281'
issue: '1794'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211454/
month: '09'
oa: 1
oa_version: Submitted Version
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '5019'
quality_controlled: '1'
related_material:
record:
- id: '9741'
relation: research_data
status: public
scopus_import: 1
status: public
title: Selection history and epistatic interactions impact dynamics of adaptation
to novel environmental stresses
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 281
year: '2014'
...
---
_id: '9740'
abstract:
- lang: eng
text: The fitness effects of symbionts on their hosts can be context-dependent,
with usually benign symbionts causing detrimental effects when their hosts are
stressed, or typically parasitic symbionts providing protection towards their
hosts (e.g. against pathogen infection). Here, we studied the novel association
between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia
formicarum for potential costs and benefits. We tested ants with different Laboulbenia
levels for their survival and immunity under resource limitation and exposure
to the obligate killing entomopathogen Metarhizium brunneum. While survival of
L. neglectus workers under starvation was significantly decreased with increasing
Laboulbenia levels, host survival under Metarhizium exposure increased with higher
levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection,
which seems to be driven mechanistically by both improved sanitary behaviours
and an upregulated immune system. Ants with high Laboulbenia levels showed significantly
longer self-grooming and elevated expression of immune genes relevant for wound
repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase),
compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont
Laboulbenia formicarum weakens its ant host by either direct resource exploitation
or the costs of an upregulated behavioural and immunological response, which,
however, provides a prophylactic protection upon later exposure to pathogens.
article_processing_charge: No
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Konrad M, Grasse AV, Tragust S, Cremer S. Data from: Anti-pathogen protection
versus survival costs mediated by an ectosymbiont in an ant host. 2014. doi:10.5061/dryad.vm0vc'
apa: 'Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2014). Data from:
Anti-pathogen protection versus survival costs mediated by an ectosymbiont in
an ant host. Dryad. https://doi.org/10.5061/dryad.vm0vc'
chicago: 'Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Data
from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont
in an Ant Host.” Dryad, 2014. https://doi.org/10.5061/dryad.vm0vc.'
ieee: 'M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Data from: Anti-pathogen
protection versus survival costs mediated by an ectosymbiont in an ant host.”
Dryad, 2014.'
ista: 'Konrad M, Grasse AV, Tragust S, Cremer S. 2014. Data from: Anti-pathogen
protection versus survival costs mediated by an ectosymbiont in an ant host, Dryad,
10.5061/dryad.vm0vc.'
mla: 'Konrad, Matthias, et al. Data from: Anti-Pathogen Protection versus Survival
Costs Mediated by an Ectosymbiont in an Ant Host. Dryad, 2014, doi:10.5061/dryad.vm0vc.'
short: M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, (2014).
date_created: 2021-07-28T08:38:40Z
date_published: 2014-11-13T00:00:00Z
date_updated: 2023-02-23T10:23:32Z
day: '13'
department:
- _id: SyCr
doi: 10.5061/dryad.vm0vc
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.vm0vc
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1993'
relation: used_in_publication
status: public
status: public
title: 'Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont
in an ant host'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9741'
abstract:
- lang: eng
text: In rapidly changing environments, selection history may impact the dynamics
of adaptation. Mutations selected in one environment may result in pleiotropic
fitness trade-offs in subsequent novel environments, slowing the rates of adaptation.
Epistatic interactions between mutations selected in sequential stressful environments
may slow or accelerate subsequent rates of adaptation, depending on the nature
of that interaction. We explored the dynamics of adaptation during sequential
exposure to herbicides with different modes of action in Chlamydomonas reinhardtii.
Evolution of resistance to two of the herbicides was largely independent of selection
history. For carbetamide, previous adaptation to other herbicide modes of action
positively impacted the likelihood of adaptation to this herbicide. Furthermore,
while adaptation to all individual herbicides was associated with pleiotropic
fitness costs in stress-free environments, we observed that accumulation of resistance
mechanisms was accompanied by a reduction in overall fitness costs. We suggest
that antagonistic epistasis may be a driving mechanism that enables populations
to more readily adapt in novel environments. These findings highlight the potential
for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug
and -pesticide resistance, as well as the potential for epistatic interactions
between adaptive mutations to facilitate evolutionary rescue in rapidly changing
environments.
article_processing_charge: No
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
citation:
ama: 'Lagator M, Colegrave N, Neve P. Data from: Selection history and epistatic
interactions impact dynamics of adaptation to novel environmental stresses. 2014.
doi:10.5061/dryad.85dn7'
apa: 'Lagator, M., Colegrave, N., & Neve, P. (2014). Data from: Selection history
and epistatic interactions impact dynamics of adaptation to novel environmental
stresses. Dryad. https://doi.org/10.5061/dryad.85dn7'
chicago: 'Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History
and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental
Stresses.” Dryad, 2014. https://doi.org/10.5061/dryad.85dn7.'
ieee: 'M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and
epistatic interactions impact dynamics of adaptation to novel environmental stresses.”
Dryad, 2014.'
ista: 'Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic
interactions impact dynamics of adaptation to novel environmental stresses, Dryad,
10.5061/dryad.85dn7.'
mla: 'Lagator, Mato, et al. Data from: Selection History and Epistatic Interactions
Impact Dynamics of Adaptation to Novel Environmental Stresses. Dryad, 2014,
doi:10.5061/dryad.85dn7.'
short: M. Lagator, N. Colegrave, P. Neve, (2014).
date_created: 2021-07-28T08:48:06Z
date_published: 2014-08-21T00:00:00Z
date_updated: 2023-02-23T10:25:31Z
day: '21'
department:
- _id: CaGu
doi: 10.5061/dryad.85dn7
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.85dn7
month: '08'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2036'
relation: used_in_publication
status: public
status: public
title: 'Data from: Selection history and epistatic interactions impact dynamics of
adaptation to novel environmental stresses'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9739'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Ben
full_name: Adlam, Ben
last_name: Adlam
- first_name: Martin
full_name: Novak, Martin
last_name: Novak
citation:
ama: Chatterjee K, Pavlogiannis A, Adlam B, Novak M. Detailed proofs for “The time
scale of evolutionary innovation.” 2014. doi:10.1371/journal.pcbi.1003818.s001
apa: Chatterjee, K., Pavlogiannis, A., Adlam, B., & Novak, M. (2014). Detailed
proofs for “The time scale of evolutionary innovation.” Public Library of Science.
https://doi.org/10.1371/journal.pcbi.1003818.s001
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Novak.
“Detailed Proofs for ‘The Time Scale of Evolutionary Innovation.’” Public Library
of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003818.s001.
ieee: K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for
‘The time scale of evolutionary innovation.’” Public Library of Science, 2014.
ista: Chatterjee K, Pavlogiannis A, Adlam B, Novak M. 2014. Detailed proofs for
“The time scale of evolutionary innovation”, Public Library of Science, 10.1371/journal.pcbi.1003818.s001.
mla: Chatterjee, Krishnendu, et al. Detailed Proofs for “The Time Scale of Evolutionary
Innovation.” Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003818.s001.
short: K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014).
date_created: 2021-07-28T08:13:57Z
date_published: 2014-09-11T00:00:00Z
date_updated: 2023-02-23T10:25:37Z
day: '11'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1003818.s001
month: '09'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '2039'
relation: used_in_publication
status: public
status: public
title: Detailed proofs for “The time scale of evolutionary innovation”
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '2170'
abstract:
- lang: eng
text: ' Short-read sequencing technologies have in principle made it feasible to
draw detailed inferences about the recent history of any organism. In practice,
however, this remains challenging due to the difficulty of genome assembly in
most organisms and the lack of statistical methods powerful enough to discriminate
between recent, nonequilibrium histories. We address both the assembly and inference
challenges. We develop a bioinformatic pipeline for generating outgroup-rooted
alignments of orthologous sequence blocks from de novo low-coverage short-read
data for a small number of genomes, and show how such sequence blocks can be used
to fit explicit models of population divergence and admixture in a likelihood
framework. To illustrate our approach, we reconstruct the Pleistocene history
of an oak-feeding insect (the oak gallwasp Biorhiza pallida), which, in common
with many other taxa, was restricted during Pleistocene ice ages to a longitudinal
series of southern refugia spanning the Western Palaearctic. Our analysis of sequence
blocks sampled from a single genome from each of three major glacial refugia reveals
support for an unexpected history dominated by recent admixture. Despite the fact
that 80% of the genome is affected by admixture during the last glacial cycle,
we are able to infer the deeper divergence history of these populations. These
inferences are robust to variation in block length, mutation model and the sampling
location of individual genomes within refugia. This combination of de novo assembly
and numerical likelihood calculation provides a powerful framework for estimating
recent population history that can be applied to any organism without the need
for prior genetic resources.'
acknowledgement: This work was funded by NERC grants to G Stone, J Nicholls, K Lohse
and N Barton (NE/J010499, NBAF375, NE/E014453/1 and NER/B/S2003/00856).
author:
- first_name: Jack
full_name: Hearn, Jack
last_name: Hearn
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
- first_name: Lynsey
full_name: Bunnefeld, Lynsey
last_name: Bunnefeld
- first_name: James
full_name: Nicholls, James
last_name: Nicholls
- 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: Konrad
full_name: Lohse, Konrad
last_name: Lohse
citation:
ama: Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. Likelihood-based
inference of population history from low-coverage de novo genome assemblies. Molecular
Ecology. 2014;23(1):198-211. doi:10.1111/mec.12578
apa: Hearn, J., Stone, G., Bunnefeld, L., Nicholls, J., Barton, N. H., & Lohse,
K. (2014). Likelihood-based inference of population history from low-coverage
de novo genome assemblies. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12578
chicago: Hearn, Jack, Graham Stone, Lynsey Bunnefeld, James Nicholls, Nicholas H
Barton, and Konrad Lohse. “Likelihood-Based Inference of Population History from
Low-Coverage de Novo Genome Assemblies.” Molecular Ecology. Wiley-Blackwell,
2014. https://doi.org/10.1111/mec.12578.
ieee: J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N. H. Barton, and K. Lohse,
“Likelihood-based inference of population history from low-coverage de novo genome
assemblies,” Molecular Ecology, vol. 23, no. 1. Wiley-Blackwell, pp. 198–211,
2014.
ista: Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. 2014. Likelihood-based
inference of population history from low-coverage de novo genome assemblies. Molecular
Ecology. 23(1), 198–211.
mla: Hearn, Jack, et al. “Likelihood-Based Inference of Population History from
Low-Coverage de Novo Genome Assemblies.” Molecular Ecology, vol. 23, no.
1, Wiley-Blackwell, 2014, pp. 198–211, doi:10.1111/mec.12578.
short: J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N.H. Barton, K. Lohse, Molecular
Ecology 23 (2014) 198–211.
date_created: 2018-12-11T11:56:07Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T14:07:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.12578
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creator: system
date_created: 2018-12-12T10:07:52Z
date_updated: 2020-07-14T12:45:31Z
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file_size: 807444
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checksum: 01a8073e071c088500425f910b0f1f71
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creator: system
date_created: 2018-12-12T10:07:53Z
date_updated: 2020-07-14T12:45:31Z
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has_accepted_license: '1'
intvolume: ' 23'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 198 - 211
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4814'
pubrep_id: '559'
quality_controlled: '1'
related_material:
record:
- id: '9754'
relation: research_data
status: public
scopus_import: 1
status: public
title: Likelihood-based inference of population history from low-coverage de novo
genome assemblies
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2014'
...
---
_id: '9753'
abstract:
- lang: eng
text: 'Background: The brood of ants and other social insects is highly susceptible
to pathogens, particularly those that penetrate the soft larval and pupal cuticle.
We here test whether the presence of a pupal cocoon, which occurs in some ant
species but not in others, affects the sanitary brood care and fungal infection
patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We
use a) a comparative approach analysing four species with either naked or cocooned
pupae and b) a within-species analysis of a single ant species, in which both
pupal types co-exist in the same colony. Results: We found that the presence of
a cocoon did not compromise fungal pathogen detection by the ants and that species
with cocooned pupae increased brood grooming after pathogen exposure. All tested
ant species further removed brood from their nests, which was predominantly expressed
towards larvae and naked pupae treated with the live fungal pathogen. In contrast,
cocooned pupae exposed to live fungus were not removed at higher rates than cocooned
pupae exposed to dead fungus or a sham control. Consistent with this, exposure
to the live fungus caused high numbers of infections and fungal outgrowth in larvae
and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed
the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion:
Our study suggests that the pupal cocoon has a protective effect against fungal
infection, causing an adaptive change in sanitary behaviours by the ants. It further
demonstrates that brood removal - originally described for honeybees as “hygienic
behaviour” – is a widespread sanitary behaviour in ants, which likely has important
implications on disease dynamics in social insect colonies.'
article_processing_charge: No
author:
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- 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: Michel
full_name: Chapuisat, Michel
last_name: Chapuisat
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Data from: Pupal cocoons
affect sanitary brood care and limit fungal infections in ant colonies. 2014.
doi:10.5061/dryad.nc0gc'
apa: 'Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., & Cremer, S. (2014).
Data from: Pupal cocoons affect sanitary brood care and limit fungal infections
in ant colonies. Dryad. https://doi.org/10.5061/dryad.nc0gc'
chicago: 'Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia
Cremer. “Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal
Infections in Ant Colonies.” Dryad, 2014. https://doi.org/10.5061/dryad.nc0gc.'
ieee: 'S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Data
from: Pupal cocoons affect sanitary brood care and limit fungal infections in
ant colonies.” Dryad, 2014.'
ista: 'Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2014. Data from:
Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies,
Dryad, 10.5061/dryad.nc0gc.'
mla: 'Tragust, Simon, et al. Data from: Pupal Cocoons Affect Sanitary Brood Care
and Limit Fungal Infections in Ant Colonies. Dryad, 2014, doi:10.5061/dryad.nc0gc.'
short: S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, (2014).
date_created: 2021-07-30T08:24:11Z
date_published: 2014-10-08T00:00:00Z
date_updated: 2023-02-23T10:36:17Z
day: '08'
department:
- _id: SyCr
doi: 10.5061/dryad.nc0gc
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.nc0gc
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2284'
relation: used_in_publication
status: public
status: public
title: 'Data from: Pupal cocoons affect sanitary brood care and limit fungal infections
in ant colonies'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9752'
abstract:
- lang: eng
text: Redundancies and correlations in the responses of sensory neurons may seem
to waste neural resources, but they can also carry cues about structured stimuli
and may help the brain to correct for response errors. To investigate the effect
of stimulus structure on redundancy in retina, we measured simultaneous responses
from populations of retinal ganglion cells presented with natural and artificial
stimuli that varied greatly in correlation structure; these stimuli and recordings
are publicly available online. Responding to spatio-temporally structured stimuli
such as natural movies, pairs of ganglion cells were modestly more correlated
than in response to white noise checkerboards, but they were much less correlated
than predicted by a non-adapting functional model of retinal response. Meanwhile,
responding to stimuli with purely spatial correlations, pairs of ganglion cells
showed increased correlations consistent with a static, non-adapting receptive
field and nonlinearity. We found that in response to spatio-temporally correlated
stimuli, ganglion cells had faster temporal kernels and tended to have stronger
surrounds. These properties of individual cells, along with gain changes that
opposed changes in effective contrast at the ganglion cell input, largely explained
the pattern of pairwise correlations across stimuli where receptive field measurements
were possible.
article_processing_charge: No
author:
- first_name: Kristina
full_name: Simmons, Kristina
last_name: Simmons
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Jan
full_name: Homann, Jan
last_name: Homann
- first_name: Heather
full_name: Yee, Heather
last_name: Yee
- first_name: Stephanie
full_name: Palmer, Stephanie
last_name: Palmer
- first_name: Philip
full_name: Nelson, Philip
last_name: Nelson
- first_name: Vijay
full_name: Balasubramanian, Vijay
last_name: Balasubramanian
citation:
ama: 'Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus
correlations by the retina. 2014. doi:10.5061/dryad.246qg'
apa: 'Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., …
Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations
by the retina. Dryad. https://doi.org/10.5061/dryad.246qg'
chicago: 'Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather
Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation
of Stimulus Correlations by the Retina.” Dryad, 2014. https://doi.org/10.5061/dryad.246qg.'
ieee: 'K. Simmons et al., “Data from: Transformation of stimulus correlations
by the retina.” Dryad, 2014.'
ista: 'Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian
V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad,
10.5061/dryad.246qg.'
mla: 'Simmons, Kristina, et al. Data from: Transformation of Stimulus Correlations
by the Retina. Dryad, 2014, doi:10.5061/dryad.246qg.'
short: K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson,
V. Balasubramanian, (2014).
date_created: 2021-07-30T08:13:52Z
date_published: 2014-11-07T00:00:00Z
date_updated: 2023-02-23T10:35:57Z
day: '07'
department:
- _id: GaTk
doi: 10.5061/dryad.246qg
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.246qg
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2277'
relation: used_in_publication
status: public
status: public
title: 'Data from: Transformation of stimulus correlations by the retina'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '978'
abstract:
- lang: eng
text: The newly discovered topological crystalline insulators feature a complex
band structure involving multiple Dirac cones, and are potentially highly tunable
by external electric field, temperature or strain. Theoretically, it has been
predicted that the various Dirac cones, which are offset in energy and momentum,
might harbour vastly different orbital character. However, their orbital texture,
which is of immense importance in determining a variety of a materialâ €™ s properties
remains elusive. Here, we unveil the orbital texture of Pb 1â ̂'x Sn x Se, a prototypical
topological crystalline insulator. By using Fourier-transform scanning tunnelling
spectroscopy we measure the interference patterns produced by the scattering of
surface-state electrons. We discover that the intensity and energy dependences
of the Fourier transforms show distinct characteristics, which can be directly
attributed to orbital effects. Our experiments reveal a complex band topology
involving two Lifshitz transitions and establish the orbital nature of the Dirac
bands, which could provide an alternative pathway towards future quantum applications.
acknowledgement: V.M. gratefully acknowledges funding from the US Department of Energy,
Scanned Probe Division under Award Number DE-FG02-12ER46880 for the primary support
of I.Z. and Y.O. (experiments, data analysis and writing the paper) and NSF-ECCS-1232105
for the partial support of W.Z. and D.W. (data acquisition). Work at Massachusetts
Institute of Technology is supported by US Department of Energy, Office of Basic
Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526
(L.F.), and NSF DMR 1104498 (M.S.). H.L. acknowledges the Singapore National Research
Foundation for support under NRF Award No. NRF-NRFF2013-03. The work at Northeastern
University is supported by the US Department of Energy grant number DE-FG02-07ER46352,
and benefited from Northeastern University’s Advanced Scientific Computation Center
(ASCC), theory support at the Advanced Light Source, Berkeley and the allocation
of time at the NERSC supercomputing centre through DOE grant number DE-AC02-05CH11231.
W-F.T. and C-Y.H. were supported by the NSC in Taiwan under Grant No. 102-2112-M-110-009.
W-F.T. also thanks C. Fang for useful discussions. Work at Princeton University
is supported by the US National Science Foundation Grant, NSF-DMR-1006492. F.C.
acknowledges the support provided by MOST-Taiwan under project number NSC-102-2119-M-002-004.
author:
- first_name: Ilija
full_name: Zeljkovic, Ilija
last_name: Zeljkovic
- first_name: Yoshinori
full_name: Okada, Yoshinori
last_name: Okada
- first_name: Chengyi
full_name: Huang, Chengyi
last_name: Huang
- first_name: Raman
full_name: Sankar, Raman
last_name: Sankar
- first_name: Daniel
full_name: Walkup, Daniel
last_name: Walkup
- first_name: Wenwen
full_name: Zhou, Wenwen
last_name: Zhou
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Fangcheng
full_name: Chou, Fangcheng
last_name: Chou
- first_name: Wei
full_name: Tsai, Wei-Feng
last_name: Tsai
- first_name: Hsin
full_name: Lin, Hsin
last_name: Lin
- first_name: Arun
full_name: Bansil, Arun
last_name: Bansil
- first_name: Liang
full_name: Fu, Liang
last_name: Fu
- first_name: Md
full_name: Hasan, Md Z
last_name: Hasan
- first_name: Vidya
full_name: Madhavan, Vidya
last_name: Madhavan
citation:
ama: Zeljkovic I, Okada Y, Huang C, et al. Mapping the unconventional orbital texture
in topological crystalline insulators. Nature Physics. 2014;10(8):572-577.
doi:10.1038/nphys3012
apa: Zeljkovic, I., Okada, Y., Huang, C., Sankar, R., Walkup, D., Zhou, W., … Madhavan,
V. (2014). Mapping the unconventional orbital texture in topological crystalline
insulators. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3012
chicago: Zeljkovic, Ilija, Yoshinori Okada, Chengyi Huang, Raman Sankar, Daniel
Walkup, Wenwen Zhou, Maksym Serbyn, et al. “Mapping the Unconventional Orbital
Texture in Topological Crystalline Insulators.” Nature Physics. Nature
Publishing Group, 2014. https://doi.org/10.1038/nphys3012.
ieee: I. Zeljkovic et al., “Mapping the unconventional orbital texture in
topological crystalline insulators,” Nature Physics, vol. 10, no. 8. Nature
Publishing Group, pp. 572–577, 2014.
ista: Zeljkovic I, Okada Y, Huang C, Sankar R, Walkup D, Zhou W, Serbyn M, Chou
F, Tsai W, Lin H, Bansil A, Fu L, Hasan M, Madhavan V. 2014. Mapping the unconventional
orbital texture in topological crystalline insulators. Nature Physics. 10(8),
572–577.
mla: Zeljkovic, Ilija, et al. “Mapping the Unconventional Orbital Texture in Topological
Crystalline Insulators.” Nature Physics, vol. 10, no. 8, Nature Publishing
Group, 2014, pp. 572–77, doi:10.1038/nphys3012.
short: I. Zeljkovic, Y. Okada, C. Huang, R. Sankar, D. Walkup, W. Zhou, M. Serbyn,
F. Chou, W. Tsai, H. Lin, A. Bansil, L. Fu, M. Hasan, V. Madhavan, Nature Physics
10 (2014) 572–577.
date_created: 2018-12-11T11:49:30Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:22:23Z
day: '01'
doi: 10.1038/nphys3012
extern: 1
intvolume: ' 10'
issue: '8'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1312.0164
month: '08'
oa: 1
page: 572 - 577
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6423'
quality_controlled: 0
status: public
title: Mapping the unconventional orbital texture in topological crystalline insulators
type: journal_article
volume: 10
year: '2014'
...
---
_id: '979'
abstract:
- lang: eng
text: In the recently discovered topological crystalline insulators SnTe and Pb1-xSnx(Te,
Se), crystal symmetry and electronic topology intertwine to create topological
surface states with many interesting features including Lifshitz transition, Van-Hove
singularity, and fermion mass generation. These surface states are protected by
mirror symmetry with respect to the (110) plane. In this work we present a comprehensive
study of the effects of different mirror-symmetry-breaking perturbations on the
(001) surface band structure. Pristine (001) surface states have four branches
of Dirac fermions at low energy. We show that ferroelectric-type structural distortion
generates a mass and gaps out some or all of these Dirac points, while strain
shifts Dirac points in the Brillouin zone. An in-plane magnetic field leaves the
surface state gapless, but introduces asymmetry between Dirac points. Finally,
an out-of-plane magnetic field leads to discrete Landau levels. We show that the
Landau level spectrum has an unusual pattern of degeneracy and interesting features
due to the unique underlying band structure. This suggests that Landau level spectroscopy
can detect and distinguish between different mechanisms of symmetry breaking in
topological crystalline insulators.
acknowledgement: We thank V. Madhavan and Y. Okada for related collaborations, and
P. A. Lee for discussions. M.S. was supported by P. A. Lee via Grant No. NSF DMR
1104498. L.F. is supported by the DOE Office of Basic Energy Sciences, Division
of Materials Sciences and Engineering under award DE-SC0010526.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Liang
full_name: Fu, Liang
last_name: Fu
citation:
ama: Serbyn M, Fu L. Symmetry breaking and Landau quantization in topological crystalline
insulators. Physical Review B - Condensed Matter and Materials Physics.
2014;90(3). doi:10.1103/PhysRevB.90.035402
apa: Serbyn, M., & Fu, L. (2014). Symmetry breaking and Landau quantization
in topological crystalline insulators. Physical Review B - Condensed Matter
and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.90.035402
chicago: Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization
in Topological Crystalline Insulators.” Physical Review B - Condensed Matter
and Materials Physics. American Physical Society, 2014. https://doi.org/10.1103/PhysRevB.90.035402.
ieee: M. Serbyn and L. Fu, “Symmetry breaking and Landau quantization in topological
crystalline insulators,” Physical Review B - Condensed Matter and Materials
Physics, vol. 90, no. 3. American Physical Society, 2014.
ista: Serbyn M, Fu L. 2014. Symmetry breaking and Landau quantization in topological
crystalline insulators. Physical Review B - Condensed Matter and Materials Physics.
90(3).
mla: Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization in
Topological Crystalline Insulators.” Physical Review B - Condensed Matter and
Materials Physics, vol. 90, no. 3, American Physical Society, 2014, doi:10.1103/PhysRevB.90.035402.
short: M. Serbyn, L. Fu, Physical Review B - Condensed Matter and Materials Physics
90 (2014).
date_created: 2018-12-11T11:49:31Z
date_published: 2014-07-03T00:00:00Z
date_updated: 2021-01-12T08:22:23Z
day: '03'
doi: 10.1103/PhysRevB.90.035402
extern: 1
intvolume: ' 90'
issue: '3'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.8153
month: '07'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6422'
quality_controlled: 0
status: public
title: Symmetry breaking and Landau quantization in topological crystalline insulators
type: journal_article
volume: 90
year: '2014'
...
---
_id: '9931'
abstract:
- lang: eng
text: Gene duplication is important in evolution, because it provides new raw material
for evolutionary adaptations. Several existing hypotheses about the causes of
duplicate retention and diversification differ in their emphasis on gene dosage,
subfunctionalization, and neofunctionalization. Little experimental data exist
on the relative importance of gene expression changes and changes in coding regions
for the evolution of duplicate genes. Furthermore, we do not know how strongly
the environment could affect this importance. To address these questions, we performed
evolution experiments with the TEM-1 beta lactamase gene in Escherichia coli to
study the initial stages of duplicate gene evolution in the laboratory. We mimicked
tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid.
We then subjected these copies to repeated cycles of mutagenesis and selection
in various environments that contained antibiotics in different combinations and
concentrations. Our experiments showed that gene dosage is the most important
factor in the initial stages of duplicate gene evolution, and overshadows the
importance of point mutations in the coding region.
acknowledgement: We thank the Functional Genomics Center Zurich for its service in
generating sequencing data, M. Ackermann and E. Hayden for helpful discussions,
A. de Visser for comments on earlier versions of this manuscript, and M. Moser for
help with quantitative PCR. This work was supported by Swiss National Science Foundation
(grant 315230–129708), as well as through the YeastX project of SystemsX.ch, and
the University Priority Research Program in Systems Biology at the University of
Zurich. RD acknowledges support from the Forschungskredit program of the University
of Zurich. The authors declare no conflict of interest.
article_processing_charge: No
article_type: original
author:
- first_name: Riddhiman
full_name: Dhar, Riddhiman
last_name: Dhar
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Andreas
full_name: Wagner, Andreas
last_name: Wagner
citation:
ama: Dhar R, Bergmiller T, Wagner A. Increased gene dosage plays a predominant role
in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution.
2014;68(6):1775-1791. doi:10.1111/evo.12373
apa: Dhar, R., Bergmiller, T., & Wagner, A. (2014). Increased gene dosage plays
a predominant role in the initial stages of evolution of duplicate TEM-1 beta
lactamase genes. Evolution. Wiley. https://doi.org/10.1111/evo.12373
chicago: Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Increased Gene
Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate
TEM-1 Beta Lactamase Genes.” Evolution. Wiley, 2014. https://doi.org/10.1111/evo.12373.
ieee: R. Dhar, T. Bergmiller, and A. Wagner, “Increased gene dosage plays a predominant
role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes,”
Evolution, vol. 68, no. 6. Wiley, pp. 1775–1791, 2014.
ista: Dhar R, Bergmiller T, Wagner A. 2014. Increased gene dosage plays a predominant
role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes.
Evolution. 68(6), 1775–1791.
mla: Dhar, Riddhiman, et al. “Increased Gene Dosage Plays a Predominant Role in
the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” Evolution,
vol. 68, no. 6, Wiley, 2014, pp. 1775–91, doi:10.1111/evo.12373.
short: R. Dhar, T. Bergmiller, A. Wagner, Evolution 68 (2014) 1775–1791.
date_created: 2021-08-17T09:03:09Z
date_published: 2014-06-03T00:00:00Z
date_updated: 2023-02-23T14:13:27Z
day: '03'
department:
- _id: CaGu
doi: 10.1111/evo.12373
external_id:
pmid:
- '24495000'
intvolume: ' 68'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 1775-1791
pmid: 1
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '9932'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Increased gene dosage plays a predominant role in the initial stages of evolution
of duplicate TEM-1 beta lactamase genes
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 68
year: '2014'
...
---
_id: '9932'
abstract:
- lang: eng
text: Gene duplication is important in evolution, because it provides new raw material
for evolutionary adaptations. Several existing hypotheses about the causes of
duplicate retention and diversification differ in their emphasis on gene dosage,
sub-functionalization, and neo-functionalization. Little experimental data exists
on the relative importance of gene expression changes and changes in coding regions
for the evolution of duplicate genes. Furthermore, we do not know how strongly
the environment could affect this importance. To address these questions, we performed
evolution experiments with the TEM-1 beta lactamase gene in E. coli to study the
initial stages of duplicate gene evolution in the laboratory. We mimicked tandem
duplication by inserting two copies of the TEM-1 gene on the same plasmid. We
then subjected these copies to repeated cycles of mutagenesis and selection in
various environments that contained antibiotics in different combinations and
concentrations. Our experiments showed that gene dosage is the most important
factor in the initial stages of duplicate gene evolution, and overshadows the
importance of point mutations in the coding region.
article_processing_charge: No
author:
- first_name: Riddhiman
full_name: Dhar, Riddhiman
last_name: Dhar
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Andreas
full_name: Wagner, Andreas
last_name: Wagner
citation:
ama: 'Dhar R, Bergmiller T, Wagner A. Data from: Increased gene dosage plays a predominant
role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes.
2014. doi:10.5061/dryad.jc402'
apa: 'Dhar, R., Bergmiller, T., & Wagner, A. (2014). Data from: Increased gene
dosage plays a predominant role in the initial stages of evolution of duplicate
TEM-1 beta lactamase genes. Dryad. https://doi.org/10.5061/dryad.jc402'
chicago: 'Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Data from: Increased
Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate
TEM-1 Beta Lactamase Genes.” Dryad, 2014. https://doi.org/10.5061/dryad.jc402.'
ieee: 'R. Dhar, T. Bergmiller, and A. Wagner, “Data from: Increased gene dosage
plays a predominant role in the initial stages of evolution of duplicate TEM-1
beta lactamase genes.” Dryad, 2014.'
ista: 'Dhar R, Bergmiller T, Wagner A. 2014. Data from: Increased gene dosage plays
a predominant role in the initial stages of evolution of duplicate TEM-1 beta
lactamase genes, Dryad, 10.5061/dryad.jc402.'
mla: 'Dhar, Riddhiman, et al. Data from: Increased Gene Dosage Plays a Predominant
Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.
Dryad, 2014, doi:10.5061/dryad.jc402.'
short: R. Dhar, T. Bergmiller, A. Wagner, (2014).
date_created: 2021-08-17T09:11:40Z
date_published: 2014-01-27T00:00:00Z
date_updated: 2023-02-23T14:13:24Z
day: '27'
department:
- _id: CaGu
doi: 10.5061/dryad.jc402
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.jc402
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9931'
relation: used_in_publication
status: public
status: public
title: 'Data from: Increased gene dosage plays a predominant role in the initial stages
of evolution of duplicate TEM-1 beta lactamase genes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '12637'
abstract:
- lang: eng
text: The performance of glaciohydrological models which simulate catchment response
to climate variability depends to a large degree on the data used to force the
models. The forcing data become increasingly important in high-elevation, glacierized
catchments where the interplay between extreme topography, climate, and the cryosphere
is complex. It is challenging to generate a reliable forcing data set that captures
this spatial heterogeneity. In this paper, we analyze the results of a 1 year
field campaign focusing on air temperature and precipitation observations in the
Langtang valley in the Nepalese Himalayas. We use the observed time series to
characterize both temperature lapse rates (LRs) and precipitation gradients (PGs).
We study their spatial and temporal variability, and we attempt to identify possible
controlling factors. We show that very clear LRs exist in the valley and that
there are strong seasonal differences related to the water vapor content in the
atmosphere. Results also show that the LRs are generally shallower than the commonly
used environmental lapse rates. The analysis of the precipitation observations
reveals that there is great variability in precipitation over short horizontal
distances. A uniform valley wide PG cannot be established, and several scale-dependent
mechanisms may explain our observations. We complete our analysis by showing the
impact of the observed LRs and PGs on the outputs of the TOPKAPI-ETH glaciohydrological
model. We conclude that LRs and PGs have a very large impact on the water balance
composition and that short-term monitoring campaigns have the potential to improve
model quality considerably.
article_processing_charge: No
article_type: original
author:
- first_name: W. W.
full_name: Immerzeel, W. W.
last_name: Immerzeel
- first_name: L.
full_name: Petersen, L.
last_name: Petersen
- first_name: S.
full_name: Ragettli, S.
last_name: Ragettli
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: Immerzeel WW, Petersen L, Ragettli S, Pellicciotti F. The importance of observed
gradients of air temperature and precipitation for modeling runoff from a glacierized
watershed in the Nepalese Himalayas. Water Resources Research. 2014;50(3):2212-2226.
doi:10.1002/2013wr014506
apa: Immerzeel, W. W., Petersen, L., Ragettli, S., & Pellicciotti, F. (2014).
The importance of observed gradients of air temperature and precipitation for
modeling runoff from a glacierized watershed in the Nepalese Himalayas. Water
Resources Research. American Geophysical Union. https://doi.org/10.1002/2013wr014506
chicago: Immerzeel, W. W., L. Petersen, S. Ragettli, and Francesca Pellicciotti.
“The Importance of Observed Gradients of Air Temperature and Precipitation for
Modeling Runoff from a Glacierized Watershed in the Nepalese Himalayas.” Water
Resources Research. American Geophysical Union, 2014. https://doi.org/10.1002/2013wr014506.
ieee: W. W. Immerzeel, L. Petersen, S. Ragettli, and F. Pellicciotti, “The importance
of observed gradients of air temperature and precipitation for modeling runoff
from a glacierized watershed in the Nepalese Himalayas,” Water Resources Research,
vol. 50, no. 3. American Geophysical Union, pp. 2212–2226, 2014.
ista: Immerzeel WW, Petersen L, Ragettli S, Pellicciotti F. 2014. The importance
of observed gradients of air temperature and precipitation for modeling runoff
from a glacierized watershed in the Nepalese Himalayas. Water Resources Research.
50(3), 2212–2226.
mla: Immerzeel, W. W., et al. “The Importance of Observed Gradients of Air Temperature
and Precipitation for Modeling Runoff from a Glacierized Watershed in the Nepalese
Himalayas.” Water Resources Research, vol. 50, no. 3, American Geophysical
Union, 2014, pp. 2212–26, doi:10.1002/2013wr014506.
short: W.W. Immerzeel, L. Petersen, S. Ragettli, F. Pellicciotti, Water Resources
Research 50 (2014) 2212–2226.
date_created: 2023-02-20T08:17:01Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2023-02-24T08:28:23Z
day: '01'
doi: 10.1002/2013wr014506
extern: '1'
intvolume: ' 50'
issue: '3'
keyword:
- Water Science and Technology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/2013WR014506
month: '03'
oa: 1
oa_version: Published Version
page: 2212-2226
publication: Water Resources Research
publication_identifier:
eissn:
- 1944-7973
issn:
- 0043-1397
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: The importance of observed gradients of air temperature and precipitation for
modeling runoff from a glacierized watershed in the Nepalese Himalayas
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2014'
...
---
_id: '12636'
abstract:
- lang: eng
text: Himalayan glacier tongues are commonly debris covered and they are an important
source of melt water. However, they remain relatively unstudied because of the
inaccessibility of the terrain and the difficulties in field work caused by the
thick debris mantles. Observations of debris-covered glaciers are therefore scarce
and airborne remote sensing may bridge the gap between scarce field observations
and coarse resolution space-borne remote sensing. In this study we deploy an Unmanned
Aerial Vehicle (UAV) before and after the melt and monsoon season (May and October
2013) over the debris-covered tongue of the Lirung Glacier in Nepal. Based on
stereo-imaging and the structure for motion algorithm we derive highly detailed
ortho-mosaics and digital elevation models (DEMs), which we geometrically correct
using differential GPS observations collected in the field. Based on DEM differencing
and manual feature tracking we derive the mass loss and the surface velocity of
the glacier at a high spatial accuracy. On average, mass loss is limited and the
surface velocity is very small. However, the spatial variability of melt rates
is very high, and ice cliffs and supra-glacial ponds show mass losses that can
be an order of magnitude higher than the average. We suggest that future research
should focus on the interaction between supra-glacial ponds, ice cliffs and englacial
hydrology to further understand the dynamics of debris-covered glaciers. Finally,
we conclude that UAV deployment has large potential in glaciology and it may revolutionize
methods currently applied in studying glacier surface features.
article_processing_charge: No
article_type: original
author:
- first_name: W.W.
full_name: Immerzeel, W.W.
last_name: Immerzeel
- first_name: P.D.A.
full_name: Kraaijenbrink, P.D.A.
last_name: Kraaijenbrink
- first_name: J.M.
full_name: Shea, J.M.
last_name: Shea
- first_name: A.B.
full_name: Shrestha, A.B.
last_name: Shrestha
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: M.F.P.
full_name: Bierkens, M.F.P.
last_name: Bierkens
- first_name: S.M.
full_name: de Jong, S.M.
last_name: de Jong
citation:
ama: Immerzeel WW, Kraaijenbrink PDA, Shea JM, et al. High-resolution monitoring
of Himalayan glacier dynamics using unmanned aerial vehicles. Remote Sensing
of Environment. 2014;150(7):93-103. doi:10.1016/j.rse.2014.04.025
apa: Immerzeel, W. W., Kraaijenbrink, P. D. A., Shea, J. M., Shrestha, A. B., Pellicciotti,
F., Bierkens, M. F. P., & de Jong, S. M. (2014). High-resolution monitoring
of Himalayan glacier dynamics using unmanned aerial vehicles. Remote Sensing
of Environment. Elsevier. https://doi.org/10.1016/j.rse.2014.04.025
chicago: Immerzeel, W.W., P.D.A. Kraaijenbrink, J.M. Shea, A.B. Shrestha, Francesca
Pellicciotti, M.F.P. Bierkens, and S.M. de Jong. “High-Resolution Monitoring of
Himalayan Glacier Dynamics Using Unmanned Aerial Vehicles.” Remote Sensing
of Environment. Elsevier, 2014. https://doi.org/10.1016/j.rse.2014.04.025.
ieee: W. W. Immerzeel et al., “High-resolution monitoring of Himalayan glacier
dynamics using unmanned aerial vehicles,” Remote Sensing of Environment,
vol. 150, no. 7. Elsevier, pp. 93–103, 2014.
ista: Immerzeel WW, Kraaijenbrink PDA, Shea JM, Shrestha AB, Pellicciotti F, Bierkens
MFP, de Jong SM. 2014. High-resolution monitoring of Himalayan glacier dynamics
using unmanned aerial vehicles. Remote Sensing of Environment. 150(7), 93–103.
mla: Immerzeel, W. W., et al. “High-Resolution Monitoring of Himalayan Glacier Dynamics
Using Unmanned Aerial Vehicles.” Remote Sensing of Environment, vol. 150,
no. 7, Elsevier, 2014, pp. 93–103, doi:10.1016/j.rse.2014.04.025.
short: W.W. Immerzeel, P.D.A. Kraaijenbrink, J.M. Shea, A.B. Shrestha, F. Pellicciotti,
M.F.P. Bierkens, S.M. de Jong, Remote Sensing of Environment 150 (2014) 93–103.
date_created: 2023-02-20T08:16:56Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2023-02-24T08:32:39Z
day: '01'
doi: 10.1016/j.rse.2014.04.025
extern: '1'
intvolume: ' 150'
issue: '7'
keyword:
- Computers in Earth Sciences
- Geology
- Soil Science
language:
- iso: eng
month: '07'
oa_version: None
page: 93-103
publication: Remote Sensing of Environment
publication_identifier:
issn:
- 0034-4257
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: High-resolution monitoring of Himalayan glacier dynamics using unmanned aerial
vehicles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 150
year: '2014'
...
---
_id: '12635'
abstract:
- lang: eng
text: 'Switzerland is one of the countries with some of the longest and best glaciological
data sets. Its glaciers and their changes in response to climate have been extensively
investigated, and the number and quality of related studies are notable. However,
a comprehensive review of glacier changes and their impact on the hydrology of
glacierised catchments for Switzerland is missing and we use the opportunity provided
by the EU-FP7 ACQWA project to review the current state of knowledge about past
changes and future projections. We examine the type of models that have been applied
to infer glacier evolution and identify knowledge gaps that should be addressed
in future research in addition to those indicated in previous publications. Common
characteristics in long-term series of projected future glacier runoff are an
initial peak followed by a decline, associated with shifts in seasonality, earlier
melt onset and reduced summer runoff. However, the quantitative predictions are
difficult to compare, as studies differ in terms of model structure, calibration
strategies, input data, temporal and spatial resolution as well as future scenarios
used for impact studies. We identify two sources of uncertainties among those
emerging from recent research, and use simulations over four glaciers to: i) quantify
the importance of the correct extrapolation of air temperature, and ii) point
at the key role played by debris cover in modulating glacier response.'
article_processing_charge: No
article_type: review
author:
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: M.
full_name: Carenzo, M.
last_name: Carenzo
- first_name: R.
full_name: Bordoy, R.
last_name: Bordoy
- first_name: M.
full_name: Stoffel, M.
last_name: Stoffel
citation:
ama: 'Pellicciotti F, Carenzo M, Bordoy R, Stoffel M. Changes in glaciers in the
Swiss Alps and impact on basin hydrology: Current state of the art and future
research. Science of The Total Environment. 2014;493:1152-1170. doi:10.1016/j.scitotenv.2014.04.022'
apa: 'Pellicciotti, F., Carenzo, M., Bordoy, R., & Stoffel, M. (2014). Changes
in glaciers in the Swiss Alps and impact on basin hydrology: Current state of
the art and future research. Science of The Total Environment. Elsevier.
https://doi.org/10.1016/j.scitotenv.2014.04.022'
chicago: 'Pellicciotti, Francesca, M. Carenzo, R. Bordoy, and M. Stoffel. “Changes
in Glaciers in the Swiss Alps and Impact on Basin Hydrology: Current State of
the Art and Future Research.” Science of The Total Environment. Elsevier,
2014. https://doi.org/10.1016/j.scitotenv.2014.04.022.'
ieee: 'F. Pellicciotti, M. Carenzo, R. Bordoy, and M. Stoffel, “Changes in glaciers
in the Swiss Alps and impact on basin hydrology: Current state of the art and
future research,” Science of The Total Environment, vol. 493. Elsevier,
pp. 1152–1170, 2014.'
ista: 'Pellicciotti F, Carenzo M, Bordoy R, Stoffel M. 2014. Changes in glaciers
in the Swiss Alps and impact on basin hydrology: Current state of the art and
future research. Science of The Total Environment. 493, 1152–1170.'
mla: 'Pellicciotti, Francesca, et al. “Changes in Glaciers in the Swiss Alps and
Impact on Basin Hydrology: Current State of the Art and Future Research.” Science
of The Total Environment, vol. 493, Elsevier, 2014, pp. 1152–70, doi:10.1016/j.scitotenv.2014.04.022.'
short: F. Pellicciotti, M. Carenzo, R. Bordoy, M. Stoffel, Science of The Total
Environment 493 (2014) 1152–1170.
date_created: 2023-02-20T08:16:51Z
date_published: 2014-09-15T00:00:00Z
date_updated: 2023-02-24T08:36:04Z
day: '15'
doi: 10.1016/j.scitotenv.2014.04.022
extern: '1'
intvolume: ' 493'
keyword:
- Pollution
- Waste Management and Disposal
- Environmental Chemistry
- Environmental Engineering
language:
- iso: eng
month: '09'
oa_version: None
page: 1152-1170
publication: Science of The Total Environment
publication_identifier:
issn:
- 0048-9697
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Changes in glaciers in the Swiss Alps and impact on basin hydrology: Current
state of the art and future research'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 493
year: '2014'
...
---
_id: '12632'
abstract:
- lang: eng
text: We investigate the performance of five glacier melt models over a multi-decadal
period in order to assess their ability to model future glacier response. The
models range from a simple degree-day model, based solely on air temperature,
to more-sophisticated models, including the full shortwave radiation balance.
In addition to the empirical models, the performance of a physically based energy-balance
(EB) model is examined. The melt models are coupled to an accumulation and a surface
evolution model and applied in a distributed manner to Rhonegletscher, Switzerland,
over the period 1929–2012 at hourly resolution. For calibration, seasonal mass-balance
measurements (2006–12) are used. Decadal ice volume changes for six periods in
the years 1929–2012 serve for model validation. Over the period 2006–12, there
are almost no differences in performance between the models, except for EB, which
is less consistent with observations, likely due to lack of meteorological in
situ data. However, simulations over the long term (1929–2012) reveal that models
which include a separate term for shortwave radiation agree best with the observed
ice volume changes, indicating that their melt relationships are robust in time
and thus suitable for long-term modelling, in contrast to more empirical approaches
that are oversensitive to temperature fluctuations.
article_processing_charge: No
article_type: original
author:
- first_name: Jeannette
full_name: Gabbi, Jeannette
last_name: Gabbi
- first_name: Marco
full_name: Carenzo, Marco
last_name: Carenzo
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Andreas
full_name: Bauder, Andreas
last_name: Bauder
- first_name: Martin
full_name: Funk, Martin
last_name: Funk
citation:
ama: Gabbi J, Carenzo M, Pellicciotti F, Bauder A, Funk M. A comparison of empirical
and physically based glacier surface melt models for long-term simulations of
glacier response. Journal of Glaciology. 2014;60(224):1140-1154. doi:10.3189/2014jog14j011
apa: Gabbi, J., Carenzo, M., Pellicciotti, F., Bauder, A., & Funk, M. (2014).
A comparison of empirical and physically based glacier surface melt models for
long-term simulations of glacier response. Journal of Glaciology. International
Glaciological Society. https://doi.org/10.3189/2014jog14j011
chicago: Gabbi, Jeannette, Marco Carenzo, Francesca Pellicciotti, Andreas Bauder,
and Martin Funk. “A Comparison of Empirical and Physically Based Glacier Surface
Melt Models for Long-Term Simulations of Glacier Response.” Journal of Glaciology.
International Glaciological Society, 2014. https://doi.org/10.3189/2014jog14j011.
ieee: J. Gabbi, M. Carenzo, F. Pellicciotti, A. Bauder, and M. Funk, “A comparison
of empirical and physically based glacier surface melt models for long-term simulations
of glacier response,” Journal of Glaciology, vol. 60, no. 224. International
Glaciological Society, pp. 1140–1154, 2014.
ista: Gabbi J, Carenzo M, Pellicciotti F, Bauder A, Funk M. 2014. A comparison of
empirical and physically based glacier surface melt models for long-term simulations
of glacier response. Journal of Glaciology. 60(224), 1140–1154.
mla: Gabbi, Jeannette, et al. “A Comparison of Empirical and Physically Based Glacier
Surface Melt Models for Long-Term Simulations of Glacier Response.” Journal
of Glaciology, vol. 60, no. 224, International Glaciological Society, 2014,
pp. 1140–54, doi:10.3189/2014jog14j011.
short: J. Gabbi, M. Carenzo, F. Pellicciotti, A. Bauder, M. Funk, Journal of Glaciology
60 (2014) 1140–1154.
date_created: 2023-02-20T08:16:34Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2023-02-24T08:56:35Z
day: '01'
doi: 10.3189/2014jog14j011
extern: '1'
intvolume: ' 60'
issue: '224'
keyword:
- Earth-Surface Processes
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3189/2014JoG14J011
month: '08'
oa: 1
oa_version: Published Version
page: 1140-1154
publication: Journal of Glaciology
publication_identifier:
eissn:
- 1727-5652
issn:
- 0022-1430
publication_status: published
publisher: International Glaciological Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: A comparison of empirical and physically based glacier surface melt models
for long-term simulations of glacier response
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2014'
...
---
_id: '12634'
abstract:
- lang: eng
text: 'Glaciers in the Andes of Chile seem to be shrinking and possibly loosing
mass, but the number and types of studies conducted, constrained mainly by data
availability, are not sufficient to provide a synopsis of glacier changes for
the past or future or explain in an explicit way causes of the observed changes.
In this paper, we provide a systematic review of changes in glaciers for the entire
country, followed by a discussion of the studies that have provided evidence of
such changes. We identify a missing type of work in distributed, physically-oriented
modelling studies that are needed to bridge the gap between the numerous remote
sensing studies and the specific, point scale works focused on process understanding.
We use an advanced mass balance model applied to one of the best monitored glaciers
in the region to investigate four main research issues that should be addressed
in modelling studies for a sound assessment of glacier changes: 1) the use of
physically-based models of glacier ablation (energy balance models) versus more
empirical models (enhanced temperature index approaches); 2) the importance of
the correct extrapolation of air temperature forcing on glaciers and in high elevation
areas and the large uncertainty in model outputs associated with it; 3) the role
played by snow gravitational redistribution; and 4) the uncertainty associated
with future climate scenarios. We quantify differences in model outputs associated
with each of these choices, and conclude with suggestions for future work directions.'
article_processing_charge: No
article_type: review
author:
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: S.
full_name: Ragettli, S.
last_name: Ragettli
- first_name: M.
full_name: Carenzo, M.
last_name: Carenzo
- first_name: J.
full_name: McPhee, J.
last_name: McPhee
citation:
ama: Pellicciotti F, Ragettli S, Carenzo M, McPhee J. Changes of glaciers in the
Andes of Chile and priorities for future work. Science of The Total Environment.
2014;493:1197-1210. doi:10.1016/j.scitotenv.2013.10.055
apa: Pellicciotti, F., Ragettli, S., Carenzo, M., & McPhee, J. (2014). Changes
of glaciers in the Andes of Chile and priorities for future work. Science of
The Total Environment. Elsevier. https://doi.org/10.1016/j.scitotenv.2013.10.055
chicago: Pellicciotti, Francesca, S. Ragettli, M. Carenzo, and J. McPhee. “Changes
of Glaciers in the Andes of Chile and Priorities for Future Work.” Science
of The Total Environment. Elsevier, 2014. https://doi.org/10.1016/j.scitotenv.2013.10.055.
ieee: F. Pellicciotti, S. Ragettli, M. Carenzo, and J. McPhee, “Changes of glaciers
in the Andes of Chile and priorities for future work,” Science of The Total
Environment, vol. 493. Elsevier, pp. 1197–1210, 2014.
ista: Pellicciotti F, Ragettli S, Carenzo M, McPhee J. 2014. Changes of glaciers
in the Andes of Chile and priorities for future work. Science of The Total Environment.
493, 1197–1210.
mla: Pellicciotti, Francesca, et al. “Changes of Glaciers in the Andes of Chile
and Priorities for Future Work.” Science of The Total Environment, vol.
493, Elsevier, 2014, pp. 1197–210, doi:10.1016/j.scitotenv.2013.10.055.
short: F. Pellicciotti, S. Ragettli, M. Carenzo, J. McPhee, Science of The Total
Environment 493 (2014) 1197–1210.
date_created: 2023-02-20T08:16:46Z
date_published: 2014-09-15T00:00:00Z
date_updated: 2023-02-24T08:37:57Z
day: '15'
doi: 10.1016/j.scitotenv.2013.10.055
extern: '1'
intvolume: ' 493'
keyword:
- Pollution
- Waste Management and Disposal
- Environmental Chemistry
- Environmental Engineering
language:
- iso: eng
month: '09'
oa_version: None
page: 1197-1210
publication: Science of The Total Environment
publication_identifier:
issn:
- 0048-9697
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Changes of glaciers in the Andes of Chile and priorities for future work
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 493
year: '2014'
...
---
_id: '13399'
abstract:
- lang: eng
text: Nature has long inspired scientists with its seemingly unlimited ability to
harness solar energy and to utilize it to drive various physiological processes.
With the help of man-made molecular photoswitches, we now have the potential to
outperform natural systems in many ways, with the ultimate goal of fabricating
multifunctional materials that operate at different light wavelengths. An important
challenge in developing light-controlled artificial molecular machines lies in
attaining a detailed understanding of the photoisomerization-coupled conformational
changes that occur in macromolecules and molecular assemblies. In this issue of
ACS Nano, Bléger, Rabe, and co-workers use force microscopy to provide interesting
insights into the behavior of individual photoresponsive molecules and to identify
contraction, extension, and crawling events accompanying light-induced isomerization.
article_processing_charge: No
article_type: original
author:
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Kundu PK, Klajn R. Watching single molecules move in response to light. ACS
Nano. 2014;8(12):11913-11916. doi:10.1021/nn506656r
apa: Kundu, P. K., & Klajn, R. (2014). Watching single molecules move in response
to light. ACS Nano. American Chemical Society. https://doi.org/10.1021/nn506656r
chicago: Kundu, Pintu K., and Rafal Klajn. “Watching Single Molecules Move in Response
to Light.” ACS Nano. American Chemical Society, 2014. https://doi.org/10.1021/nn506656r.
ieee: P. K. Kundu and R. Klajn, “Watching single molecules move in response to light,”
ACS Nano, vol. 8, no. 12. American Chemical Society, pp. 11913–11916, 2014.
ista: Kundu PK, Klajn R. 2014. Watching single molecules move in response to light.
ACS Nano. 8(12), 11913–11916.
mla: Kundu, Pintu K., and Rafal Klajn. “Watching Single Molecules Move in Response
to Light.” ACS Nano, vol. 8, no. 12, American Chemical Society, 2014, pp.
11913–16, doi:10.1021/nn506656r.
short: P.K. Kundu, R. Klajn, ACS Nano 8 (2014) 11913–11916.
date_created: 2023-08-01T09:45:42Z
date_published: 2014-12-23T00:00:00Z
date_updated: 2023-08-08T07:18:58Z
day: '23'
doi: 10.1021/nn506656r
extern: '1'
external_id:
pmid:
- '25474733'
intvolume: ' 8'
issue: '12'
keyword:
- General Physics and Astronomy
- General Engineering
- General Materials Science
language:
- iso: eng
month: '12'
oa_version: None
page: 11913-11916
pmid: 1
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086X
issn:
- 1936-0851
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Watching single molecules move in response to light
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2014'
...
---
_id: '13402'
abstract:
- lang: eng
text: Nanoporous frameworks are polymeric materials built from rigid molecules,
which give rise to their nanoporous structures with applications in gas sorption
and storage, catalysis and others. Conceptually new applications could emerge,
should these beneficial properties be manipulated by external stimuli in a reversible
manner. One approach to render nanoporous frameworks responsive to external signals
would be to immobilize molecular switches within their nanopores. Although the
majority of molecular switches require conformational freedom to isomerize, and
switching in the solid state is prohibited, the nanopores may provide enough room
for the switches to efficiently isomerize. Here we describe two families of nanoporous
materials incorporating the spiropyran molecular switch. These materials exhibit
a variety of interesting properties, including reversible photochromism and acidochromism
under solvent-free conditions, light-controlled capture and release of metal ions,
as well reversible chromism induced by solvation/desolvation.
article_number: '3588'
article_processing_charge: No
article_type: original
author:
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Gregory L.
full_name: Olsen, Gregory L.
last_name: Olsen
- first_name: Vladimir
full_name: Kiss, Vladimir
last_name: Kiss
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Kundu PK, Olsen GL, Kiss V, Klajn R. Nanoporous frameworks exhibiting multiple
stimuli responsiveness. Nature Communications. 2014;5. doi:10.1038/ncomms4588
apa: Kundu, P. K., Olsen, G. L., Kiss, V., & Klajn, R. (2014). Nanoporous frameworks
exhibiting multiple stimuli responsiveness. Nature Communications. Springer
Nature. https://doi.org/10.1038/ncomms4588
chicago: Kundu, Pintu K., Gregory L. Olsen, Vladimir Kiss, and Rafal Klajn. “Nanoporous
Frameworks Exhibiting Multiple Stimuli Responsiveness.” Nature Communications.
Springer Nature, 2014. https://doi.org/10.1038/ncomms4588.
ieee: P. K. Kundu, G. L. Olsen, V. Kiss, and R. Klajn, “Nanoporous frameworks exhibiting
multiple stimuli responsiveness,” Nature Communications, vol. 5. Springer
Nature, 2014.
ista: Kundu PK, Olsen GL, Kiss V, Klajn R. 2014. Nanoporous frameworks exhibiting
multiple stimuli responsiveness. Nature Communications. 5, 3588.
mla: Kundu, Pintu K., et al. “Nanoporous Frameworks Exhibiting Multiple Stimuli
Responsiveness.” Nature Communications, vol. 5, 3588, Springer Nature,
2014, doi:10.1038/ncomms4588.
short: P.K. Kundu, G.L. Olsen, V. Kiss, R. Klajn, Nature Communications 5 (2014).
date_created: 2023-08-01T09:46:27Z
date_published: 2014-04-07T00:00:00Z
date_updated: 2023-08-08T07:28:10Z
day: '07'
doi: 10.1038/ncomms4588
extern: '1'
external_id:
pmid:
- '24709950'
intvolume: ' 5'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/ncomms4588
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nanoporous frameworks exhibiting multiple stimuli responsiveness
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2014'
...
---
_id: '13400'
abstract:
- lang: eng
text: Organizing inorganic nanocrystals into complex architectures is challenging
and typically relies on preexisting templates, such as properly folded DNA or
polypeptide chains. We found that under carefully controlled conditions, cubic
nanocrystals of magnetite self-assemble into arrays of helical superstructures
in a template-free manner with >99% yield. Computer simulations revealed that
the formation of helices is determined by the interplay of van der Waals and magnetic
dipole-dipole interactions, Zeeman coupling, and entropic forces and can be attributed
to spontaneous formation of chiral nanocube clusters. Neighboring helices within
their densely packed ensembles tended to adopt the same handedness in order to
maximize packing, thus revealing a novel mechanism of symmetry breaking and chirality
amplification.
article_processing_charge: No
article_type: original
author:
- first_name: Gurvinder
full_name: Singh, Gurvinder
last_name: Singh
- first_name: Henry
full_name: Chan, Henry
last_name: Chan
- first_name: Artem
full_name: Baskin, Artem
last_name: Baskin
- first_name: Elijah
full_name: Gelman, Elijah
last_name: Gelman
- first_name: Nikita
full_name: Repnin, Nikita
last_name: Repnin
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Singh G, Chan H, Baskin A, et al. Self-assembly of magnetite nanocubes into
helical superstructures. Science. 2014;345(6201):1149-1153. doi:10.1126/science.1254132
apa: Singh, G., Chan, H., Baskin, A., Gelman, E., Repnin, N., Král, P., & Klajn,
R. (2014). Self-assembly of magnetite nanocubes into helical superstructures.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1254132
chicago: Singh, Gurvinder, Henry Chan, Artem Baskin, Elijah Gelman, Nikita Repnin,
Petr Král, and Rafal Klajn. “Self-Assembly of Magnetite Nanocubes into Helical
Superstructures.” Science. American Association for the Advancement of
Science, 2014. https://doi.org/10.1126/science.1254132.
ieee: G. Singh et al., “Self-assembly of magnetite nanocubes into helical
superstructures,” Science, vol. 345, no. 6201. American Association for
the Advancement of Science, pp. 1149–1153, 2014.
ista: Singh G, Chan H, Baskin A, Gelman E, Repnin N, Král P, Klajn R. 2014. Self-assembly
of magnetite nanocubes into helical superstructures. Science. 345(6201), 1149–1153.
mla: Singh, Gurvinder, et al. “Self-Assembly of Magnetite Nanocubes into Helical
Superstructures.” Science, vol. 345, no. 6201, American Association for
the Advancement of Science, 2014, pp. 1149–53, doi:10.1126/science.1254132.
short: G. Singh, H. Chan, A. Baskin, E. Gelman, N. Repnin, P. Král, R. Klajn, Science
345 (2014) 1149–1153.
date_created: 2023-08-01T09:45:56Z
date_published: 2014-07-24T00:00:00Z
date_updated: 2023-08-08T07:23:05Z
day: '24'
doi: 10.1126/science.1254132
extern: '1'
external_id:
pmid:
- '25061133'
intvolume: ' 345'
issue: '6201'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '07'
oa_version: None
page: 1149-1153
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-assembly of magnetite nanocubes into helical superstructures
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 345
year: '2014'
...
---
_id: '13404'
abstract:
- lang: eng
text: In the past few years, spiropyran has emerged as the molecule-of-choice for
the construction of novel dynamic materials. This unique molecular switch undergoes
structural isomerisation in response to a variety of orthogonal stimuli, e.g.
light, temperature, metal ions, redox potential, and mechanical stress. Incorporation
of this switch onto macromolecular supports or inorganic scaffolds allows for
the creation of robust dynamic materials. This review discusses the synthesis,
switching conditions, and use of dynamic materials in which spiropyran has been
attached to the surfaces of polymers, biomacromolecules, inorganic nanoparticles,
as well as solid surfaces. The resulting materials show fascinating properties
whereby the state of the switch intimately affects a multitude of useful properties
of the support. The utility of the spiropyran switch will undoubtedly endow these
materials with far-reaching applications in the near future.
article_processing_charge: No
article_type: original
author:
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Klajn R. Spiropyran-based dynamic materials. Chemical Society Reviews.
2014;43(1):148-184. doi:10.1039/c3cs60181a
apa: Klajn, R. (2014). Spiropyran-based dynamic materials. Chemical Society Reviews.
Royal Society of Chemistry. https://doi.org/10.1039/c3cs60181a
chicago: Klajn, Rafal. “Spiropyran-Based Dynamic Materials.” Chemical Society
Reviews. Royal Society of Chemistry, 2014. https://doi.org/10.1039/c3cs60181a.
ieee: R. Klajn, “Spiropyran-based dynamic materials,” Chemical Society Reviews,
vol. 43, no. 1. Royal Society of Chemistry, pp. 148–184, 2014.
ista: Klajn R. 2014. Spiropyran-based dynamic materials. Chemical Society Reviews.
43(1), 148–184.
mla: Klajn, Rafal. “Spiropyran-Based Dynamic Materials.” Chemical Society Reviews,
vol. 43, no. 1, Royal Society of Chemistry, 2014, pp. 148–84, doi:10.1039/c3cs60181a.
short: R. Klajn, Chemical Society Reviews 43 (2014) 148–184.
date_created: 2023-08-01T09:47:03Z
date_published: 2014-01-27T00:00:00Z
date_updated: 2023-08-08T07:41:38Z
day: '27'
doi: 10.1039/c3cs60181a
extern: '1'
external_id:
pmid:
- '23979515'
intvolume: ' 43'
issue: '1'
keyword:
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1039/C3CS60181A
month: '01'
oa: 1
oa_version: Published Version
page: 148-184
pmid: 1
publication: Chemical Society Reviews
publication_identifier:
eissn:
- 1460-4744
issn:
- 0306-0012
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spiropyran-based dynamic materials
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2014'
...
---
_id: '13401'
abstract:
- lang: eng
text: A compound combining the features of a molecular rotor and a photoswitch was
synthesized and was shown to exist as three diastereomers, which interconvert
via a reversible cyclic reaction scheme. Each of the three diastereomers was isolated,
and by following the equilibration kinetics, activation barriers for all reactions
were calculated. The results indicate that the properties of molecular switches
depend heavily on their immediate chemical environment. The conclusions are important
in the context of designing new switchable molecules and materials.
article_processing_charge: No
article_type: original
author:
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Avishai
full_name: Lerner, Avishai
last_name: Lerner
- first_name: Kristina
full_name: Kučanda, Kristina
last_name: Kučanda
- first_name: Gregory
full_name: Leitus, Gregory
last_name: Leitus
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Kundu PK, Lerner A, Kučanda K, Leitus G, Klajn R. Cyclic kinetics during thermal
equilibration of an axially chiral bis-spiropyran. Journal of the American
Chemical Society. 2014;136(32):11276-11279. doi:10.1021/ja505948q
apa: Kundu, P. K., Lerner, A., Kučanda, K., Leitus, G., & Klajn, R. (2014).
Cyclic kinetics during thermal equilibration of an axially chiral bis-spiropyran.
Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja505948q
chicago: Kundu, Pintu K., Avishai Lerner, Kristina Kučanda, Gregory Leitus, and
Rafal Klajn. “Cyclic Kinetics during Thermal Equilibration of an Axially Chiral
Bis-Spiropyran.” Journal of the American Chemical Society. American Chemical
Society, 2014. https://doi.org/10.1021/ja505948q.
ieee: P. K. Kundu, A. Lerner, K. Kučanda, G. Leitus, and R. Klajn, “Cyclic kinetics
during thermal equilibration of an axially chiral bis-spiropyran,” Journal
of the American Chemical Society, vol. 136, no. 32. American Chemical Society,
pp. 11276–11279, 2014.
ista: Kundu PK, Lerner A, Kučanda K, Leitus G, Klajn R. 2014. Cyclic kinetics during
thermal equilibration of an axially chiral bis-spiropyran. Journal of the American
Chemical Society. 136(32), 11276–11279.
mla: Kundu, Pintu K., et al. “Cyclic Kinetics during Thermal Equilibration of an
Axially Chiral Bis-Spiropyran.” Journal of the American Chemical Society,
vol. 136, no. 32, American Chemical Society, 2014, pp. 11276–79, doi:10.1021/ja505948q.
short: P.K. Kundu, A. Lerner, K. Kučanda, G. Leitus, R. Klajn, Journal of the American
Chemical Society 136 (2014) 11276–11279.
date_created: 2023-08-01T09:46:12Z
date_published: 2014-08-13T00:00:00Z
date_updated: 2023-08-08T07:25:37Z
day: '13'
doi: 10.1021/ja505948q
extern: '1'
external_id:
pmid:
- '25072292'
intvolume: ' 136'
issue: '32'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '08'
oa_version: None
page: 11276-11279
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: Cyclic kinetics during thermal equilibration of an axially chiral bis-spiropyran
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2014'
...
---
_id: '13403'
abstract:
- lang: eng
text: We show that bimolecular reactions between species confined to the surfaces
of nanoparticles can be manipulated by the nature of the linker, as well as by
the curvature of the underlying particles.
article_processing_charge: No
article_type: original
author:
- first_name: Tino
full_name: Zdobinsky, Tino
last_name: Zdobinsky
- first_name: Pradipta
full_name: Sankar Maiti, Pradipta
last_name: Sankar Maiti
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Zdobinsky T, Sankar Maiti P, Klajn R. Support curvature and conformational
freedom control chemical reactivity of immobilized species. Journal of the
American Chemical Society. 2014;136(7):2711-2714. doi:10.1021/ja411573a
apa: Zdobinsky, T., Sankar Maiti, P., & Klajn, R. (2014). Support curvature
and conformational freedom control chemical reactivity of immobilized species.
Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja411573a
chicago: Zdobinsky, Tino, Pradipta Sankar Maiti, and Rafal Klajn. “Support Curvature
and Conformational Freedom Control Chemical Reactivity of Immobilized Species.”
Journal of the American Chemical Society. American Chemical Society, 2014.
https://doi.org/10.1021/ja411573a.
ieee: T. Zdobinsky, P. Sankar Maiti, and R. Klajn, “Support curvature and conformational
freedom control chemical reactivity of immobilized species,” Journal of the
American Chemical Society, vol. 136, no. 7. American Chemical Society, pp.
2711–2714, 2014.
ista: Zdobinsky T, Sankar Maiti P, Klajn R. 2014. Support curvature and conformational
freedom control chemical reactivity of immobilized species. Journal of the American
Chemical Society. 136(7), 2711–2714.
mla: Zdobinsky, Tino, et al. “Support Curvature and Conformational Freedom Control
Chemical Reactivity of Immobilized Species.” Journal of the American Chemical
Society, vol. 136, no. 7, American Chemical Society, 2014, pp. 2711–14, doi:10.1021/ja411573a.
short: T. Zdobinsky, P. Sankar Maiti, R. Klajn, Journal of the American Chemical
Society 136 (2014) 2711–2714.
date_created: 2023-08-01T09:46:44Z
date_published: 2014-02-19T00:00:00Z
date_updated: 2023-08-08T07:32:11Z
day: '19'
doi: 10.1021/ja411573a
extern: '1'
external_id:
pmid:
- '24320557'
intvolume: ' 136'
issue: '7'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '02'
oa_version: None
page: 2711-2714
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: Support curvature and conformational freedom control chemical reactivity of
immobilized species
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2014'
...
---
_id: '14018'
abstract:
- lang: eng
text: The sensitivities of high-harmonic generation (HHG) and strong-field ionization
(SFI) to coupled electronic and nuclear dynamics are studied, using the nitric
oxide (NO) molecule as an example. A coherent superposition of electronic and
rotational states of NO is prepared by impulsive stimulated Raman scattering and
probed by simultaneous detection of HHG and SFI yields. We observe a fourfold
higher sensitivity of high-harmonic generation to electronic dynamics and attribute
it to the presence of inelastic quantum paths connecting coherently related electronic
states [Kraus et al., Phys. Rev. Lett.111, 243005 (2013)]. Whereas different harmonic
orders display very different sensitivities to rotational or electronic dynamics,
strong-field ionization is found to be most sensitive to electronic motion. We
introduce a general theoretical formalism for high-harmonic generation from coupled
nuclear-electronic wave packets. We show that the unequal sensitivities of different
harmonic orders to electronic or rotational dynamics result from the angle dependence
of the photorecombination matrix elements which encode several autoionizing and
shape resonances in the photoionization continuum of NO. We further study the
dependence of rotational and electronic coherences on the intensity of the excitation
pulse and support the observations with calculations.
article_processing_charge: No
article_type: original
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Peter M.
full_name: Kraus, Peter M.
last_name: Kraus
- first_name: Song Bin
full_name: Zhang, Song Bin
last_name: Zhang
- first_name: Nina
full_name: Rohringer, Nina
last_name: Rohringer
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Baykusheva DR, Kraus PM, Zhang SB, Rohringer N, Wörner HJ. The sensitivities
of high-harmonic generation and strong-field ionization to coupled electronic
and nuclear dynamics. Faraday Discussions. 2014;171:113-132. doi:10.1039/c4fd00018h
apa: Baykusheva, D. R., Kraus, P. M., Zhang, S. B., Rohringer, N., & Wörner,
H. J. (2014). The sensitivities of high-harmonic generation and strong-field ionization
to coupled electronic and nuclear dynamics. Faraday Discussions. Royal
Society of Chemistry. https://doi.org/10.1039/c4fd00018h
chicago: Baykusheva, Denitsa Rangelova, Peter M. Kraus, Song Bin Zhang, Nina Rohringer,
and Hans Jakob Wörner. “The Sensitivities of High-Harmonic Generation and Strong-Field
Ionization to Coupled Electronic and Nuclear Dynamics.” Faraday Discussions.
Royal Society of Chemistry, 2014. https://doi.org/10.1039/c4fd00018h.
ieee: D. R. Baykusheva, P. M. Kraus, S. B. Zhang, N. Rohringer, and H. J. Wörner,
“The sensitivities of high-harmonic generation and strong-field ionization to
coupled electronic and nuclear dynamics,” Faraday Discussions, vol. 171.
Royal Society of Chemistry, pp. 113–132, 2014.
ista: Baykusheva DR, Kraus PM, Zhang SB, Rohringer N, Wörner HJ. 2014. The sensitivities
of high-harmonic generation and strong-field ionization to coupled electronic
and nuclear dynamics. Faraday Discussions. 171, 113–132.
mla: Baykusheva, Denitsa Rangelova, et al. “The Sensitivities of High-Harmonic Generation
and Strong-Field Ionization to Coupled Electronic and Nuclear Dynamics.” Faraday
Discussions, vol. 171, Royal Society of Chemistry, 2014, pp. 113–32, doi:10.1039/c4fd00018h.
short: D.R. Baykusheva, P.M. Kraus, S.B. Zhang, N. Rohringer, H.J. Wörner, Faraday
Discussions 171 (2014) 113–132.
date_created: 2023-08-10T06:38:19Z
date_published: 2014-04-14T00:00:00Z
date_updated: 2023-08-22T08:58:12Z
day: '14'
doi: 10.1039/c4fd00018h
extern: '1'
external_id:
pmid:
- '25415558'
intvolume: ' 171'
keyword:
- Physical and Theoretical Chemistry
language:
- iso: eng
month: '04'
oa_version: None
page: 113-132
pmid: 1
publication: Faraday Discussions
publication_identifier:
eissn:
- 1364-5498
issn:
- 1359-6640
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: The sensitivities of high-harmonic generation and strong-field ionization to
coupled electronic and nuclear dynamics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 171
year: '2014'
...
---
_id: '14019'
abstract:
- lang: eng
text: The cyclopropene radical cation (c-C3H₄⁺) is an important but poorly characterized
three-membered-ring hydrocarbon. We report on a measurement of the high-resolution
photoelectron and photoionization spectra of cyclopropene and several deuterated
isotopomers, from which we have determined the rovibrational energy level structure
of the X⁺ (2)B2 ground electronic state of c-C3H₄⁺ at low energies for the first
time. The synthesis of the partially deuterated isotopomers always resulted in
mixtures of several isotopomers, differing in their number of D atoms and in the
location of these atoms, so that the photoelectron spectra of deuterated samples
are superpositions of the spectra of several isotopomers. The rotationally resolved
spectra indicate a C(2v)-symmetric R0 structure for the ground electronic state
of c-C3H₄⁺. Two vibrational modes of c-C3H₄⁺ are found to have vibrational wave
numbers below 300 cm(-1), which is surprising for such a small cyclic hydrocarbon.
The analysis of the isotopic shifts of the vibrational levels enabled the assignment
of the lowest-frequency mode (fundamental wave number of ≈110 cm(-1) in c-C3H₄⁺)
to the CH2 torsional mode (ν₈⁺, A2 symmetry) and of the second-lowest-frequency
mode (≈210 cm(-1) in c-C3H₄⁺) to a mode combining a CH out-of-plane with a CH2
rocking motion (ν₁₅⁺, B2 symmetry). The potential energy along the CH2 torsional
coordinate is flat near the equilibrium structure and leads to a pronounced anharmonicity.
article_number: '064317'
article_processing_charge: No
article_type: original
author:
- first_name: K.
full_name: Vasilatou, K.
last_name: Vasilatou
- first_name: J. M.
full_name: Michaud, J. M.
last_name: Michaud
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: G.
full_name: Grassi, G.
last_name: Grassi
- first_name: F.
full_name: Merkt, F.
last_name: Merkt
citation:
ama: 'Vasilatou K, Michaud JM, Baykusheva DR, Grassi G, Merkt F. The cyclopropene
radical cation: Rovibrational level structure at low energies from high-resolution
photoelectron spectra. The Journal of Chemical Physics. 2014;141(6). doi:10.1063/1.4890744'
apa: 'Vasilatou, K., Michaud, J. M., Baykusheva, D. R., Grassi, G., & Merkt,
F. (2014). The cyclopropene radical cation: Rovibrational level structure at low
energies from high-resolution photoelectron spectra. The Journal of Chemical
Physics. AIP Publishing. https://doi.org/10.1063/1.4890744'
chicago: 'Vasilatou, K., J. M. Michaud, Denitsa Rangelova Baykusheva, G. Grassi,
and F. Merkt. “The Cyclopropene Radical Cation: Rovibrational Level Structure
at Low Energies from High-Resolution Photoelectron Spectra.” The Journal of
Chemical Physics. AIP Publishing, 2014. https://doi.org/10.1063/1.4890744.'
ieee: 'K. Vasilatou, J. M. Michaud, D. R. Baykusheva, G. Grassi, and F. Merkt, “The
cyclopropene radical cation: Rovibrational level structure at low energies from
high-resolution photoelectron spectra,” The Journal of Chemical Physics,
vol. 141, no. 6. AIP Publishing, 2014.'
ista: 'Vasilatou K, Michaud JM, Baykusheva DR, Grassi G, Merkt F. 2014. The cyclopropene
radical cation: Rovibrational level structure at low energies from high-resolution
photoelectron spectra. The Journal of Chemical Physics. 141(6), 064317.'
mla: 'Vasilatou, K., et al. “The Cyclopropene Radical Cation: Rovibrational Level
Structure at Low Energies from High-Resolution Photoelectron Spectra.” The
Journal of Chemical Physics, vol. 141, no. 6, 064317, AIP Publishing, 2014,
doi:10.1063/1.4890744.'
short: K. Vasilatou, J.M. Michaud, D.R. Baykusheva, G. Grassi, F. Merkt, The Journal
of Chemical Physics 141 (2014).
date_created: 2023-08-10T06:38:30Z
date_published: 2014-08-14T00:00:00Z
date_updated: 2023-08-22T09:01:31Z
day: '14'
doi: 10.1063/1.4890744
extern: '1'
external_id:
pmid:
- '25134581'
intvolume: ' 141'
issue: '6'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
month: '08'
oa_version: None
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The cyclopropene radical cation: Rovibrational level structure at low energies
from high-resolution photoelectron spectra'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 141
year: '2014'
...
---
_id: '14021'
abstract:
- lang: eng
text: We present the detailed analysis of a new two-pulse orientation scheme that
achieves macroscopic field-free orientation at the high particle densities required
for attosecond and high-harmonic spectroscopies (Kraus et al 2013 arXiv:1311.3923).
Carbon monoxide molecules are oriented by combining one-colour and delayed two-colour
non-resonant femtosecond laser pulses. High-harmonic generation is used to probe
the oriented wave-packet dynamics and reveals that a very high degree of orientation
(Nup/Ntotal = 0.73–0.82) is achieved. We further extend this approach to orienting
carbonyl sulphide molecules. We show that the present two-pulse scheme selectively
enhances orientation created by the hyperpolarizability interaction whereas the
ionization-depletion mechanism plays no role. We further control and optimize
orientation through the delay between the one- and two-colour pump pulses. Finally,
we demonstrate a complementary encoding of electronic-structure features, such
as shape resonances, in the even- and odd-harmonic spectrum. The achieved progress
makes two-pulse field-free orientation an attractive tool for a broad class of
time-resolved measurements.
article_number: '124030'
article_processing_charge: No
article_type: original
author:
- first_name: P M
full_name: Kraus, P M
last_name: Kraus
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: H J
full_name: Wörner, H J
last_name: Wörner
citation:
ama: 'Kraus PM, Baykusheva DR, Wörner HJ. Two-pulse orientation dynamics and high-harmonic
spectroscopy of strongly-oriented molecules. Journal of Physics B: Atomic,
Molecular and Optical Physics. 2014;47(12). doi:10.1088/0953-4075/47/12/124030'
apa: 'Kraus, P. M., Baykusheva, D. R., & Wörner, H. J. (2014). Two-pulse orientation
dynamics and high-harmonic spectroscopy of strongly-oriented molecules. Journal
of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing. https://doi.org/10.1088/0953-4075/47/12/124030'
chicago: 'Kraus, P M, Denitsa Rangelova Baykusheva, and H J Wörner. “Two-Pulse Orientation
Dynamics and High-Harmonic Spectroscopy of Strongly-Oriented Molecules.” Journal
of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing, 2014.
https://doi.org/10.1088/0953-4075/47/12/124030.'
ieee: 'P. M. Kraus, D. R. Baykusheva, and H. J. Wörner, “Two-pulse orientation dynamics
and high-harmonic spectroscopy of strongly-oriented molecules,” Journal of
Physics B: Atomic, Molecular and Optical Physics, vol. 47, no. 12. IOP Publishing,
2014.'
ista: 'Kraus PM, Baykusheva DR, Wörner HJ. 2014. Two-pulse orientation dynamics
and high-harmonic spectroscopy of strongly-oriented molecules. Journal of Physics
B: Atomic, Molecular and Optical Physics. 47(12), 124030.'
mla: 'Kraus, P. M., et al. “Two-Pulse Orientation Dynamics and High-Harmonic Spectroscopy
of Strongly-Oriented Molecules.” Journal of Physics B: Atomic, Molecular and
Optical Physics, vol. 47, no. 12, 124030, IOP Publishing, 2014, doi:10.1088/0953-4075/47/12/124030.'
short: 'P.M. Kraus, D.R. Baykusheva, H.J. Wörner, Journal of Physics B: Atomic,
Molecular and Optical Physics 47 (2014).'
date_created: 2023-08-10T06:38:48Z
date_published: 2014-06-10T00:00:00Z
date_updated: 2023-08-22T09:04:30Z
day: '10'
doi: 10.1088/0953-4075/47/12/124030
extern: '1'
external_id:
arxiv:
- '1311.3923'
intvolume: ' 47'
issue: '12'
keyword:
- Condensed Matter Physics
- Atomic and Molecular Physics
- and Optics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1311.3923
month: '06'
oa: 1
oa_version: Preprint
publication: 'Journal of Physics B: Atomic, Molecular and Optical Physics'
publication_identifier:
eissn:
- 1361-6455
issn:
- 0953-4075
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented
molecules
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2014'
...
---
_id: '14020'
abstract:
- lang: eng
text: We report the observation of macroscopic field-free orientation, i.e., more
than 73% of CO molecules pointing in the same direction. This is achieved through
an all-optical scheme operating at high particle densities (>10(17) cm(-3)) that
combines one-color (ω) and two-color (ω+2ω) nonresonant femtosecond laser pulses.
We show that the achieved orientation solely relies on the hyperpolarizability
interaction as opposed to an ionization-depletion mechanism, thus, opening a wide
range of applications. The achieved strong orientation enables us to reveal the
molecular-frame anisotropies of the photorecombination amplitudes and phases caused
by a shape resonance. The resonance appears as a local maximum in the even-harmonic
emission around 28 eV. In contrast, the odd-harmonic emission is suppressed in
this spectral region through the combined effects of an asymmetric photorecombination
phase and a subcycle Stark effect, generic for polar molecules, that we experimentally
identify.
article_number: '023001'
article_processing_charge: No
article_type: original
author:
- first_name: P. M.
full_name: Kraus, P. M.
last_name: Kraus
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: H. J.
full_name: Wörner, H. J.
last_name: Wörner
citation:
ama: Kraus PM, Baykusheva DR, Wörner HJ. Two-pulse field-free orientation reveals
anisotropy of molecular shape resonance. Physical Review Letters. 2014;113(2).
doi:10.1103/physrevlett.113.023001
apa: Kraus, P. M., Baykusheva, D. R., & Wörner, H. J. (2014). Two-pulse field-free
orientation reveals anisotropy of molecular shape resonance. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/physrevlett.113.023001
chicago: Kraus, P. M., Denitsa Rangelova Baykusheva, and H. J. Wörner. “Two-Pulse
Field-Free Orientation Reveals Anisotropy of Molecular Shape Resonance.” Physical
Review Letters. American Physical Society, 2014. https://doi.org/10.1103/physrevlett.113.023001.
ieee: P. M. Kraus, D. R. Baykusheva, and H. J. Wörner, “Two-pulse field-free orientation
reveals anisotropy of molecular shape resonance,” Physical Review Letters,
vol. 113, no. 2. American Physical Society, 2014.
ista: Kraus PM, Baykusheva DR, Wörner HJ. 2014. Two-pulse field-free orientation
reveals anisotropy of molecular shape resonance. Physical Review Letters. 113(2),
023001.
mla: Kraus, P. M., et al. “Two-Pulse Field-Free Orientation Reveals Anisotropy of
Molecular Shape Resonance.” Physical Review Letters, vol. 113, no. 2, 023001,
American Physical Society, 2014, doi:10.1103/physrevlett.113.023001.
short: P.M. Kraus, D.R. Baykusheva, H.J. Wörner, Physical Review Letters 113 (2014).
date_created: 2023-08-10T06:38:38Z
date_published: 2014-07-11T00:00:00Z
date_updated: 2023-08-22T09:02:56Z
day: '11'
doi: 10.1103/physrevlett.113.023001
extern: '1'
external_id:
arxiv:
- '1311.3923'
pmid:
- '25062172'
intvolume: ' 113'
issue: '2'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1311.3923
month: '07'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Two-pulse field-free orientation reveals anisotropy of molecular shape resonance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2014'
...
---
_id: '535'
abstract:
- lang: eng
text: Energy games belong to a class of turn-based two-player infinite-duration
games played on a weighted directed graph. It is one of the rare and intriguing
combinatorial problems that lie in NP∩co-NP, but are not known to be in P. The
existence of polynomial-time algorithms has been a major open problem for decades
and apart from pseudopolynomial algorithms there is no algorithm that solves any
non-trivial subclass in polynomial time. In this paper, we give several results
based on the weight structures of the graph. First, we identify a notion of penalty
and present a polynomial-time algorithm when the penalty is large. Our algorithm
is the first polynomial-time algorithm on a large class of weighted graphs. It
includes several worst-case instances on which previous algorithms, such as value
iteration and random facet algorithms, require at least sub-exponential time.
Our main technique is developing the first non-trivial approximation algorithm
and showing how to convert it to an exact algorithm. Moreover, we show that in
a practical case in verification where weights are clustered around a constant
number of values, the energy game problem can be solved in polynomial time. We
also show that the problem is still as hard as in general when the clique-width
is bounded or the graph is strongly ergodic, suggesting that restricting the graph
structure does not necessarily help.
article_processing_charge: No
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. Polynomial-time algorithms
for energy games with special weight structures. Algorithmica. 2014;70(3):457-492.
doi:10.1007/s00453-013-9843-7
apa: Chatterjee, K., Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014).
Polynomial-time algorithms for energy games with special weight structures. Algorithmica.
Springer. https://doi.org/10.1007/s00453-013-9843-7
chicago: Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, and Danupon
Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.”
Algorithmica. Springer, 2014. https://doi.org/10.1007/s00453-013-9843-7.
ieee: K. Chatterjee, M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time
algorithms for energy games with special weight structures,” Algorithmica,
vol. 70, no. 3. Springer, pp. 457–492, 2014.
ista: Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. 2014. Polynomial-time
algorithms for energy games with special weight structures. Algorithmica. 70(3),
457–492.
mla: Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games
with Special Weight Structures.” Algorithmica, vol. 70, no. 3, Springer,
2014, pp. 457–92, doi:10.1007/s00453-013-9843-7.
short: K. Chatterjee, M.H. Henzinger, S. Krinninger, D. Nanongkai, Algorithmica
70 (2014) 457–492.
date_created: 2018-12-11T11:47:01Z
date_published: 2014-11-01T00:00:00Z
date_updated: 2023-09-05T14:09:29Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/s00453-013-9843-7
ec_funded: 1
external_id:
arxiv:
- '1604.08234'
intvolume: ' 70'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.08234
month: '11'
oa: 1
oa_version: Preprint
page: 457 - 492
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Algorithmica
publication_status: published
publisher: Springer
publist_id: '7282'
quality_controlled: '1'
related_material:
record:
- id: '10905'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Polynomial-time algorithms for energy games with special weight structures
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 70
year: '2014'
...
---
_id: '10886'
abstract:
- lang: eng
text: We propose a method for visualizing two-dimensional symmetric positive definite
tensor fields using the Heat Kernel Signature (HKS). The HKS is derived from the
heat kernel and was originally introduced as an isometry invariant shape signature.
Each positive definite tensor field defines a Riemannian manifold by considering
the tensor field as a Riemannian metric. On this Riemmanian manifold we can apply
the definition of the HKS. The resulting scalar quantity is used for the visualization
of tensor fields. The HKS is closely related to the Gaussian curvature of the
Riemannian manifold and the time parameter of the heat kernel allows a multiscale
analysis in a natural way. In this way, the HKS represents field related scale
space properties, enabling a level of detail analysis of tensor fields. This makes
the HKS an interesting new scalar quantity for tensor fields, which differs significantly
from usual tensor invariants like the trace or the determinant. A method for visualization
and a numerical realization of the HKS for tensor fields is proposed in this chapter.
To validate the approach we apply it to some illustrating simple examples as isolated
critical points and to a medical diffusion tensor data set.
acknowledgement: This research is partially supported by the TOPOSYS project FP7-ICT-318493-STREP.
alternative_title:
- Mathematics and Visualization
article_processing_charge: No
author:
- first_name: Valentin
full_name: Zobel, Valentin
last_name: Zobel
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Ingrid
full_name: Hotz, Ingrid
last_name: Hotz
citation:
ama: 'Zobel V, Reininghaus J, Hotz I. Visualization of two-dimensional symmetric
positive definite tensor fields using the heat kernel signature. In: Topological
Methods in Data Analysis and Visualization III . Springer; 2014:249-262. doi:10.1007/978-3-319-04099-8_16'
apa: Zobel, V., Reininghaus, J., & Hotz, I. (2014). Visualization of two-dimensional
symmetric positive definite tensor fields using the heat kernel signature. In
Topological Methods in Data Analysis and Visualization III (pp. 249–262).
Springer. https://doi.org/10.1007/978-3-319-04099-8_16
chicago: Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualization of Two-Dimensional
Symmetric Positive Definite Tensor Fields Using the Heat Kernel Signature.” In
Topological Methods in Data Analysis and Visualization III , 249–62. Springer,
2014. https://doi.org/10.1007/978-3-319-04099-8_16.
ieee: V. Zobel, J. Reininghaus, and I. Hotz, “Visualization of two-dimensional symmetric
positive definite tensor fields using the heat kernel signature,” in Topological
Methods in Data Analysis and Visualization III , 2014, pp. 249–262.
ista: Zobel V, Reininghaus J, Hotz I. 2014. Visualization of two-dimensional symmetric
positive definite tensor fields using the heat kernel signature. Topological Methods
in Data Analysis and Visualization III . , Mathematics and Visualization, , 249–262.
mla: Zobel, Valentin, et al. “Visualization of Two-Dimensional Symmetric Positive
Definite Tensor Fields Using the Heat Kernel Signature.” Topological Methods
in Data Analysis and Visualization III , Springer, 2014, pp. 249–62, doi:10.1007/978-3-319-04099-8_16.
short: V. Zobel, J. Reininghaus, I. Hotz, in:, Topological Methods in Data Analysis
and Visualization III , Springer, 2014, pp. 249–262.
date_created: 2022-03-18T13:05:39Z
date_published: 2014-03-19T00:00:00Z
date_updated: 2023-09-05T14:13:16Z
day: '19'
department:
- _id: HeEd
doi: 10.1007/978-3-319-04099-8_16
language:
- iso: eng
month: '03'
oa_version: None
page: 249-262
publication: 'Topological Methods in Data Analysis and Visualization III '
publication_identifier:
eisbn:
- '9783319040998'
eissn:
- 2197-666X
isbn:
- '9783319040981'
issn:
- 1612-3786
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Visualization of two-dimensional symmetric positive definite tensor fields
using the heat kernel signature
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2014'
...
---
_id: '6178'
abstract:
- lang: eng
text: Mechanically coupled cells can generate forces driving cell and tissue morphogenesis
during development. Visualization and measuring of these forces is of major importance
to better understand the complexity of the biomechanic processes that shape cells
and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively
assess mechanical tension in different tissues of the developing zebrafish and
in cultures of primary germ layer progenitor cells ex vivo.
article_processing_charge: No
author:
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Pedro
full_name: Campinho, Pedro
id: 3AFBBC42-F248-11E8-B48F-1D18A9856A87
last_name: Campinho
orcid: 0000-0002-8526-5416
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- 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: 'Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. UV laser ablation
to measure cell and tissue-generated forces in the zebrafish embryo in vivo and
ex vivo. In: Nelson C, ed. Tissue Morphogenesis. Vol 1189. Methods in Molecular
Biology. New York, NY: Springer; 2014:219-235. doi:10.1007/978-1-4939-1164-6_15'
apa: 'Smutny, M., Behrndt, M., Campinho, P., Ruprecht, V., & Heisenberg, C.-P.
J. (2014). UV laser ablation to measure cell and tissue-generated forces in the
zebrafish embryo in vivo and ex vivo. In C. Nelson (Ed.), Tissue Morphogenesis
(Vol. 1189, pp. 219–235). New York, NY: Springer. https://doi.org/10.1007/978-1-4939-1164-6_15'
chicago: 'Smutny, Michael, Martin Behrndt, Pedro Campinho, Verena Ruprecht, and
Carl-Philipp J Heisenberg. “UV Laser Ablation to Measure Cell and Tissue-Generated
Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” In Tissue Morphogenesis,
edited by Celeste Nelson, 1189:219–35. Methods in Molecular Biology. New York,
NY: Springer, 2014. https://doi.org/10.1007/978-1-4939-1164-6_15.'
ieee: 'M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, and C.-P. J. Heisenberg,
“UV laser ablation to measure cell and tissue-generated forces in the zebrafish
embryo in vivo and ex vivo,” in Tissue Morphogenesis, vol. 1189, C. Nelson,
Ed. New York, NY: Springer, 2014, pp. 219–235.'
ista: 'Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. 2014.UV laser
ablation to measure cell and tissue-generated forces in the zebrafish embryo in
vivo and ex vivo. In: Tissue Morphogenesis. vol. 1189, 219–235.'
mla: Smutny, Michael, et al. “UV Laser Ablation to Measure Cell and Tissue-Generated
Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” Tissue Morphogenesis,
edited by Celeste Nelson, vol. 1189, Springer, 2014, pp. 219–35, doi:10.1007/978-1-4939-1164-6_15.
short: M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, C.-P.J. Heisenberg, in:,
C. Nelson (Ed.), Tissue Morphogenesis, Springer, New York, NY, 2014, pp. 219–235.
date_created: 2019-03-26T08:55:59Z
date_published: 2014-08-22T00:00:00Z
date_updated: 2023-09-05T14:12:00Z
day: '22'
department:
- _id: CaHe
doi: 10.1007/978-1-4939-1164-6_15
editor:
- first_name: Celeste
full_name: Nelson, Celeste
last_name: Nelson
external_id:
pmid:
- '25245697'
intvolume: ' 1189'
language:
- iso: eng
month: '08'
oa_version: None
page: 219-235
place: New York, NY
pmid: 1
publication: Tissue Morphogenesis
publication_identifier:
eissn:
- 1940-6029
isbn:
- '9781493911639'
- '9781493911646'
issn:
- 1064-3745
publication_status: published
publisher: Springer
quality_controlled: '1'
series_title: Methods in Molecular Biology
status: public
title: UV laser ablation to measure cell and tissue-generated forces in the zebrafish
embryo in vivo and ex vivo
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 1189
year: '2014'
...
---
_id: '10814'
abstract:
- lang: eng
text: We review recent progress towards a rigorous understanding of the excitation
spectrum of bosonic quantum many-body systems. In particular, we explain how one
can rigorously establish the predictions resulting from the Bogoliubov approximation
in the mean field limit. The latter predicts that the spectrum is made up of elementary
excitations, whose energy behaves linearly in the momentum for small momentum.
This property is crucial for the superfluid behavior of the system. We also discuss
a list of open problems in this field.
article_processing_charge: No
article_type: original
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Seiringer R. The excitation spectrum for Bose fluids with weak interactions.
Jahresbericht der Deutschen Mathematiker-Vereinigung. 2014;116:21-41. doi:10.1365/s13291-014-0083-9
apa: Seiringer, R. (2014). The excitation spectrum for Bose fluids with weak interactions.
Jahresbericht Der Deutschen Mathematiker-Vereinigung. Springer Nature.
https://doi.org/10.1365/s13291-014-0083-9
chicago: Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.”
Jahresbericht Der Deutschen Mathematiker-Vereinigung. Springer Nature,
2014. https://doi.org/10.1365/s13291-014-0083-9.
ieee: R. Seiringer, “The excitation spectrum for Bose fluids with weak interactions,”
Jahresbericht der Deutschen Mathematiker-Vereinigung, vol. 116. Springer
Nature, pp. 21–41, 2014.
ista: Seiringer R. 2014. The excitation spectrum for Bose fluids with weak interactions.
Jahresbericht der Deutschen Mathematiker-Vereinigung. 116, 21–41.
mla: Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.”
Jahresbericht Der Deutschen Mathematiker-Vereinigung, vol. 116, Springer
Nature, 2014, pp. 21–41, doi:10.1365/s13291-014-0083-9.
short: R. Seiringer, Jahresbericht Der Deutschen Mathematiker-Vereinigung 116 (2014)
21–41.
date_created: 2022-03-04T07:54:39Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2023-09-05T14:19:47Z
day: '01'
department:
- _id: RoSe
doi: 10.1365/s13291-014-0083-9
intvolume: ' 116'
keyword:
- General Medicine
language:
- iso: eng
month: '03'
oa_version: None
page: 21-41
publication: Jahresbericht der Deutschen Mathematiker-Vereinigung
publication_identifier:
eissn:
- 1869-7135
issn:
- 0012-0456
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The excitation spectrum for Bose fluids with weak interactions
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 116
year: '2014'
...
---
_id: '10817'
abstract:
- lang: eng
text: The Morse-Smale complex can be either explicitly or implicitly represented.
Depending on the type of representation, the simplification of the Morse-Smale
complex works differently. In the explicit representation, the Morse-Smale complex
is directly simplified by explicitly reconnecting the critical points during the
simplification. In the implicit representation, on the other hand, the Morse-Smale
complex is given by a combinatorial gradient field. In this setting, the simplification
changes the combinatorial flow, which yields an indirect simplification of the
Morse-Smale complex. The topological complexity of the Morse-Smale complex is
reduced in both representations. However, the simplifications generally yield
different results. In this chapter, we emphasize properties of the two representations
that cause these differences. We also provide a complexity analysis of the two
schemes with respect to running time and memory consumption.
acknowledgement: This research is supported and funded by the Digiteo unTopoVis project,
the TOPOSYS project FP7-ICT-318493-STREP, and MPC-VCC.
article_processing_charge: No
author:
- first_name: David
full_name: Günther, David
last_name: Günther
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Hans-Peter
full_name: Seidel, Hans-Peter
last_name: Seidel
- first_name: Tino
full_name: Weinkauf, Tino
last_name: Weinkauf
citation:
ama: 'Günther D, Reininghaus J, Seidel H-P, Weinkauf T. Notes on the simplification
of the Morse-Smale complex. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds.
Topological Methods in Data Analysis and Visualization III. Mathematics
and Visualization. Cham: Springer Nature; 2014:135-150. doi:10.1007/978-3-319-04099-8_9'
apa: 'Günther, D., Reininghaus, J., Seidel, H.-P., & Weinkauf, T. (2014). Notes
on the simplification of the Morse-Smale complex. In P.-T. Bremer, I. Hotz, V.
Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and
Visualization III. (pp. 135–150). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-04099-8_9'
chicago: 'Günther, David, Jan Reininghaus, Hans-Peter Seidel, and Tino Weinkauf.
“Notes on the Simplification of the Morse-Smale Complex.” In Topological Methods
in Data Analysis and Visualization III., edited by Peer-Timo Bremer, Ingrid
Hotz, Valerio Pascucci, and Ronald Peikert, 135–50. Mathematics and Visualization.
Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-319-04099-8_9.'
ieee: 'D. Günther, J. Reininghaus, H.-P. Seidel, and T. Weinkauf, “Notes on the
simplification of the Morse-Smale complex,” in Topological Methods in Data
Analysis and Visualization III., P.-T. Bremer, I. Hotz, V. Pascucci, and R.
Peikert, Eds. Cham: Springer Nature, 2014, pp. 135–150.'
ista: 'Günther D, Reininghaus J, Seidel H-P, Weinkauf T. 2014.Notes on the simplification
of the Morse-Smale complex. In: Topological Methods in Data Analysis and Visualization
III. , 135–150.'
mla: Günther, David, et al. “Notes on the Simplification of the Morse-Smale Complex.”
Topological Methods in Data Analysis and Visualization III., edited by
Peer-Timo Bremer et al., Springer Nature, 2014, pp. 135–50, doi:10.1007/978-3-319-04099-8_9.
short: D. Günther, J. Reininghaus, H.-P. Seidel, T. Weinkauf, in:, P.-T. Bremer,
I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis
and Visualization III., Springer Nature, Cham, 2014, pp. 135–150.
date_created: 2022-03-04T08:33:57Z
date_published: 2014-03-19T00:00:00Z
date_updated: 2023-09-05T15:33:45Z
day: '19'
department:
- _id: HeEd
doi: 10.1007/978-3-319-04099-8_9
ec_funded: 1
editor:
- first_name: Peer-Timo
full_name: Bremer, Peer-Timo
last_name: Bremer
- first_name: Ingrid
full_name: Hotz, Ingrid
last_name: Hotz
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
- first_name: Ronald
full_name: Peikert, Ronald
last_name: Peikert
language:
- iso: eng
month: '03'
oa_version: None
page: 135-150
place: Cham
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Topological Methods in Data Analysis and Visualization III.
publication_identifier:
eisbn:
- '9783319040998'
eissn:
- 2197-666X
isbn:
- '9783319040981'
issn:
- 1612-3786
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: Mathematics and Visualization
status: public
title: Notes on the simplification of the Morse-Smale complex
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2014'
...
---
_id: '1395'
abstract:
- lang: eng
text: In this thesis I studied various individual and social immune defences employed
by the invasive garden ant Lasius neglectus mostly against entomopathogenic fungi. The
first two chapters of this thesis address the phenomenon of 'social immunisation'.
Social immunisation, that is the immunological protection of group members due
to social contact to a pathogen-exposed nestmate, has been described in various
social insect species against different types of pathogens. However, in the case
of entomopathogenic fungi it has, so far, only been demonstrated that social immunisation
exists at all. Its underlying mechanisms r any other properties were, however,
unknown. In the first chapter of this thesis I identified the mechanistic basis
of social immunisation in L. neglectus against the entomopathogenous fungus Metarhizium.
I could show that nestmates of a pathogen-exposed individual contract low-level
infections due to social interactions. These low-level infections are, however,
non-lethal and cause an active stimulation of the immune system, which protects
the nestmates upon subsequent pathogen encounters. In the second chapter of this
thesis I investigated the specificity and colony level effects of social immunisation.
I demonstrated that the protection conferred by social immunisation is highly
specific, protecting ants only against the same pathogen strain. In addition,
depending on the respective context, social immunisation may even cause fitness
costs. I further showed that social immunisation crucially affects sanitary behaviour
and disease dynamics within ant groups. In the third chapter of this thesis I
studied the effects of the ectosymbiotic fungus Laboulbenia formicarum on its
host L. neglectus. Although Laboulbeniales are the largest order of insect-parasitic
fungi, research concerning host fitness consequence is sparse. I showed that highly
Laboulbenia-infected ants sustain fitness costs under resource limitation, however,
gain fitness benefits when exposed to an entomopathogenus fungus. These effects
are probably cause by a prophylactic upregulation of behavioural as well as physiological
immune defences in highly infected ants.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
citation:
ama: 'Konrad M. Immune defences in ants: Effects of social immunisation and a fungal
ectosymbiont in the ant Lasius neglectus. 2014.'
apa: 'Konrad, M. (2014). Immune defences in ants: Effects of social immunisation
and a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science
and Technology Austria.'
chicago: 'Konrad, Matthias. “Immune Defences in Ants: Effects of Social Immunisation
and a Fungal Ectosymbiont in the Ant Lasius Neglectus.” Institute of Science and
Technology Austria, 2014.'
ieee: 'M. Konrad, “Immune defences in ants: Effects of social immunisation and a
fungal ectosymbiont in the ant Lasius neglectus,” Institute of Science and Technology
Austria, 2014.'
ista: 'Konrad M. 2014. Immune defences in ants: Effects of social immunisation and
a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science and Technology
Austria.'
mla: 'Konrad, Matthias. Immune Defences in Ants: Effects of Social Immunisation
and a Fungal Ectosymbiont in the Ant Lasius Neglectus. Institute of Science
and Technology Austria, 2014.'
short: 'M. Konrad, Immune Defences in Ants: Effects of Social Immunisation and a
Fungal Ectosymbiont in the Ant Lasius Neglectus, Institute of Science and Technology
Austria, 2014.'
date_created: 2018-12-11T11:51:46Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2023-09-07T11:38:56Z
day: '01'
degree_awarded: PhD
department:
- _id: SyCr
language:
- iso: eng
month: '02'
oa_version: None
page: '131'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5814'
status: public
supervisor:
- first_name: Sylvia M
full_name: Cremer, Sylvia M
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: 'Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont
in the ant Lasius neglectus'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2014'
...
---
_id: '1402'
abstract:
- lang: eng
text: Phosphatidylinositol (Ptdlns) is a structural phospholipid that can be phosphorylated
into various lipid signaling molecules, designated polyphosphoinositides (PPIs).
The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol
is performed by a set of organelle-specific kinases and phosphatases, and the
characteristic head groups make these molecules ideal for regulating biological
processes in time and space. In yeast and mammals, Ptdlns3P and Ptdlns(3,5)P2
play crucial roles in trafficking toward the lytic compartments, whereas the role
in plants is not yet fully understood. Here we identified the role of a land plant-specific
subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during
vauolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize
to the tonoplast along with Ptdlns3P, the presumable product of their activity.
in SAC gain- and loss-of-function mutants, the levels of Ptdlns monophosphates
and bisphosphates were changed, with opposite effects on the morphology of storage
and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover,
multiple sac knockout mutants had an increased number of smaller storage and lytic
vacuoles, whereas extralarge vacuoles were observed in the overexpression lines,
correlating with various growth and developmental defects. The fragmented vacuolar
phenotype of sac mutants could be mimicked by treating wild-type seedlings with
Ptdlns(3,5)P2, corroborating that this PPI is important for vacuole morphology.
Taken together, these results provide evidence that PPIs, together with their
metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar
morphology and function in plants.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Petra
full_name: Marhavá, Petra
id: 44E59624-F248-11E8-B48F-1D18A9856A87
last_name: Marhavá
citation:
ama: Marhavá P. Molecular mechanisms of patterning and subcellular trafficking in
Arabidopsis thaliana. 2014.
apa: Marhavá, P. (2014). Molecular mechanisms of patterning and subcellular trafficking
in Arabidopsis thaliana. Institute of Science and Technology Austria.
chicago: Marhavá, Petra. “Molecular Mechanisms of Patterning and Subcellular Trafficking
in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2014.
ieee: P. Marhavá, “Molecular mechanisms of patterning and subcellular trafficking
in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2014.
ista: Marhavá P. 2014. Molecular mechanisms of patterning and subcellular trafficking
in Arabidopsis thaliana. Institute of Science and Technology Austria.
mla: Marhavá, Petra. Molecular Mechanisms of Patterning and Subcellular Trafficking
in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2014.
short: P. Marhavá, Molecular Mechanisms of Patterning and Subcellular Trafficking
in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2014.
date_created: 2018-12-11T11:51:49Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2023-09-07T11:39:38Z
day: '01'
degree_awarded: PhD
department:
- _id: JiFr
language:
- iso: eng
month: '12'
oa_version: None
page: '90'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5805'
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis
thaliana
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2014'
...
---
_id: '2255'
abstract:
- lang: eng
text: Motivated by applications in biology, we present an algorithm for estimating
the length of tube-like shapes in 3-dimensional Euclidean space. In a first step,
we combine the tube formula of Weyl with integral geometric methods to obtain
an integral representation of the length, which we approximate using a variant
of the Koksma-Hlawka Theorem. In a second step, we use tools from computational
topology to decrease the dependence on small perturbations of the shape. We present
computational experiments that shed light on the stability and the convergence
rate of our algorithm.
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes. Journal
of Mathematical Imaging and Vision. 2014;50(1):164-177. doi:10.1007/s10851-013-0468-x
apa: Edelsbrunner, H., & Pausinger, F. (2014). Stable length estimates of tube-like
shapes. Journal of Mathematical Imaging and Vision. Springer. https://doi.org/10.1007/s10851-013-0468-x
chicago: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates
of Tube-like Shapes.” Journal of Mathematical Imaging and Vision. Springer,
2014. https://doi.org/10.1007/s10851-013-0468-x.
ieee: H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,”
Journal of Mathematical Imaging and Vision, vol. 50, no. 1. Springer, pp.
164–177, 2014.
ista: Edelsbrunner H, Pausinger F. 2014. Stable length estimates of tube-like shapes.
Journal of Mathematical Imaging and Vision. 50(1), 164–177.
mla: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like
Shapes.” Journal of Mathematical Imaging and Vision, vol. 50, no. 1, Springer,
2014, pp. 164–77, doi:10.1007/s10851-013-0468-x.
short: H. Edelsbrunner, F. Pausinger, Journal of Mathematical Imaging and Vision
50 (2014) 164–177.
date_created: 2018-12-11T11:56:36Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2023-09-07T11:41:25Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/s10851-013-0468-x
ec_funded: 1
file:
- access_level: open_access
checksum: 2f93f3e63a38a85cd4404d7953913b14
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:18Z
date_updated: 2020-07-14T12:45:35Z
file_id: '5204'
file_name: IST-2016-549-v1+1_2014-J-06-LengthEstimate.pdf
file_size: 3941391
relation: main_file
file_date_updated: 2020-07-14T12:45:35Z
has_accepted_license: '1'
intvolume: ' 50'
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 164 - 177
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Journal of Mathematical Imaging and Vision
publication_identifier:
issn:
- '09249907'
publication_status: published
publisher: Springer
publist_id: '4691'
pubrep_id: '549'
quality_controlled: '1'
related_material:
record:
- id: '2843'
relation: earlier_version
status: public
- id: '1399'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Stable length estimates of tube-like shapes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2014'
...
---
_id: '2159'
abstract:
- lang: eng
text: 'Motivated by topological Tverberg-type problems, we consider multiple (double,
triple, and higher multiplicity) selfintersection points of maps from finite simplicial
complexes (compact polyhedra) into ℝd and study conditions under which such multiple
points can be eliminated. The most classical case is that of embeddings (i.e.,
maps without double points) of a κ-dimensional complex K into ℝ2κ. For this problem,
the work of van Kampen, Shapiro, and Wu provides an efficiently testable necessary
condition for embeddability (namely, vanishing of the van Kampen ob-struction).
For κ ≥ 3, the condition is also sufficient, and yields a polynomial-time algorithm
for deciding embeddability: One starts with an arbitrary map f : K→ℝ2κ, which
generically has finitely many double points; if k ≥ 3 and if the obstruction vanishes
then one can successively remove these double points by local modifications of
the map f. One of the main tools is the famous Whitney trick that permits eliminating
pairs of double points of opposite intersection sign. We are interested in generalizing
this approach to intersection points of higher multiplicity. We call a point y
2 ℝd an r-fold Tverberg point of a map f : Kκ →ℝd if y lies in the intersection
f(σ1)∩. ∩f(σr) of the images of r pairwise disjoint simplices of K. The analogue
of (non-)embeddability that we study is the problem Tverbergκ r→d: Given a κ-dimensional
complex K, does it satisfy a Tverberg-type theorem with parameters r and d, i.e.,
does every map f : K κ → ℝd have an r-fold Tverberg point? Here, we show that
for fixed r, κ and d of the form d = rm and k = (r-1)m, m ≥ 3, there is a polynomial-time
algorithm for deciding this (based on the vanishing of a cohomological obstruction,
as in the case of embeddings). Our main tool is an r-fold analogue of the Whitney
trick: Given r pairwise disjoint simplices of K such that the intersection of
their images contains two r-fold Tverberg points y+ and y- of opposite intersection
sign, we can eliminate y+ and y- by a local isotopy of f. In a subsequent paper,
we plan to develop this further and present a generalization of the classical
Haeiger-Weber Theorem (which yields a necessary and sufficient condition for embeddability
of κ-complexes into ℝd for a wider range of dimensions) to intersection points
of higher multiplicity.'
acknowledgement: Swiss National Science Foundation (Project SNSF-PP00P2-138948)
author:
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Mabillard I, Wagner U. Eliminating Tverberg points, I. An analogue of the
Whitney trick. In: Proceedings of the Annual Symposium on Computational Geometry.
ACM; 2014:171-180. doi:10.1145/2582112.2582134'
apa: 'Mabillard, I., & Wagner, U. (2014). Eliminating Tverberg points, I. An
analogue of the Whitney trick. In Proceedings of the Annual Symposium on Computational
Geometry (pp. 171–180). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582134'
chicago: Mabillard, Isaac, and Uli Wagner. “Eliminating Tverberg Points, I. An Analogue
of the Whitney Trick.” In Proceedings of the Annual Symposium on Computational
Geometry, 171–80. ACM, 2014. https://doi.org/10.1145/2582112.2582134.
ieee: I. Mabillard and U. Wagner, “Eliminating Tverberg points, I. An analogue of
the Whitney trick,” in Proceedings of the Annual Symposium on Computational
Geometry, Kyoto, Japan, 2014, pp. 171–180.
ista: 'Mabillard I, Wagner U. 2014. Eliminating Tverberg points, I. An analogue
of the Whitney trick. Proceedings of the Annual Symposium on Computational Geometry.
SoCG: Symposium on Computational Geometry, 171–180.'
mla: Mabillard, Isaac, and Uli Wagner. “Eliminating Tverberg Points, I. An Analogue
of the Whitney Trick.” Proceedings of the Annual Symposium on Computational
Geometry, ACM, 2014, pp. 171–80, doi:10.1145/2582112.2582134.
short: I. Mabillard, U. Wagner, in:, Proceedings of the Annual Symposium on Computational
Geometry, ACM, 2014, pp. 171–180.
conference:
end_date: 2014-06-11
location: Kyoto, Japan
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2014-06-08
date_created: 2018-12-11T11:56:03Z
date_published: 2014-06-08T00:00:00Z
date_updated: 2023-09-07T11:56:27Z
day: '08'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1145/2582112.2582134
file:
- access_level: open_access
checksum: 2aae223fee8ffeaf57bbabd8d92b6a2c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:12Z
date_updated: 2020-07-14T12:45:30Z
file_id: '4735'
file_name: IST-2016-534-v1+1_Eliminating_Tverberg_points_I._An_analogue_of_the_Whitney_trick.pdf
file_size: 914396
relation: main_file
file_date_updated: 2020-07-14T12:45:30Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 171 - 180
publication: Proceedings of the Annual Symposium on Computational Geometry
publication_status: published
publisher: ACM
publist_id: '4847'
pubrep_id: '534'
quality_controlled: '1'
related_material:
record:
- id: '1123'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Eliminating Tverberg points, I. An analogue of the Whitney trick
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2023'
abstract:
- lang: eng
text: 'Understanding the evolution of dispersal is essential for understanding and
predicting the dynamics of natural populations. Two main factors are known to
influence dispersal evolution: spatio-temporal variation in the environment and
relatedness between individuals. However, the relation between these factors is
still poorly understood, and they are usually treated separately. In this article,
I present a theoretical framework that contains and connects effects of both environmental
variation and relatedness, and reproduces and extends their known features. Spatial
habitat variation selects for balanced dispersal strategies, whereby the population
is kept at an ideal free distribution. Within this class of dispersal strategies,
I explain how increased dispersal is promoted by perturbations to the dispersal
type frequencies. An explicit formula shows the magnitude of the selective advantage
of increased dispersal in terms of the spatial variability in the frequencies
of the different dispersal strategies present. These variances are capable of
capturing various sources of stochasticity and hence establish a common scale
for their effects on the evolution of dispersal. The results furthermore indicate
an alternative approach to identifying effects of relatedness on dispersal evolution.'
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
citation:
ama: Novak S. Habitat heterogeneities versus spatial type frequency variances as
driving forces of dispersal evolution. Ecology and Evolution. 2014;4(24):4589-4597.
doi:10.1002/ece3.1289
apa: Novak, S. (2014). Habitat heterogeneities versus spatial type frequency variances
as driving forces of dispersal evolution. Ecology and Evolution. Wiley-Blackwell.
https://doi.org/10.1002/ece3.1289
chicago: Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency
Variances as Driving Forces of Dispersal Evolution.” Ecology and Evolution.
Wiley-Blackwell, 2014. https://doi.org/10.1002/ece3.1289.
ieee: S. Novak, “Habitat heterogeneities versus spatial type frequency variances
as driving forces of dispersal evolution,” Ecology and Evolution, vol.
4, no. 24. Wiley-Blackwell, pp. 4589–4597, 2014.
ista: Novak S. 2014. Habitat heterogeneities versus spatial type frequency variances
as driving forces of dispersal evolution. Ecology and Evolution. 4(24), 4589–4597.
mla: Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances
as Driving Forces of Dispersal Evolution.” Ecology and Evolution, vol.
4, no. 24, Wiley-Blackwell, 2014, pp. 4589–97, doi:10.1002/ece3.1289.
short: S. Novak, Ecology and Evolution 4 (2014) 4589–4597.
date_created: 2018-12-11T11:55:16Z
date_published: 2014-11-27T00:00:00Z
date_updated: 2023-09-07T11:55:53Z
day: '27'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/ece3.1289
ec_funded: 1
file:
- access_level: open_access
checksum: 9ab43db1b0fede7bfe560ed77e177b76
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:28Z
date_updated: 2020-07-14T12:45:25Z
file_id: '4946'
file_name: IST-2016-462-v1+1_Novak-2014-Ecology_and_Evolution.pdf
file_size: 118813
relation: main_file
file_date_updated: 2020-07-14T12:45:25Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '24'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 4589 - 4597
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Ecology and Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5049'
pubrep_id: '462'
quality_controlled: '1'
related_material:
record:
- id: '1125'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Habitat heterogeneities versus spatial type frequency variances as driving
forces of dispersal evolution
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2014'
...
---
_id: '2218'
abstract:
- lang: eng
text: While fixing concurrency bugs, program repair algorithms may introduce new
concurrency bugs. We present an algorithm that avoids such regressions. The solution
space is given by a set of program transformations we consider in the repair process.
These include reordering of instructions within a thread and inserting atomic
sections. The new algorithm learns a constraint on the space of candidate solutions,
from both positive examples (error-free traces) and counterexamples (error traces).
From each counterexample, the algorithm learns a constraint necessary to remove
the errors. From each positive examples, it learns a constraint that is necessary
in order to prevent the repair from turning the trace into an error trace. We
implemented the algorithm and evaluated it on simplified Linux device drivers
with known bugs.
alternative_title:
- LNCS
author:
- first_name: Pavol
full_name: Cerny, Pavol
last_name: Cerny
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Leonid
full_name: Ryzhyk, Leonid
last_name: Ryzhyk
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: 'Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. Regression-free
synthesis for concurrency. In: Vol 8559. Springer; 2014:568-584. doi:10.1007/978-3-319-08867-9_38'
apa: 'Cerny, P., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., & Tarrach,
T. (2014). Regression-free synthesis for concurrency (Vol. 8559, pp. 568–584).
Presented at the CAV: Computer Aided Verification, Vienna, Austria: Springer.
https://doi.org/10.1007/978-3-319-08867-9_38'
chicago: Cerny, Pavol, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, and
Thorsten Tarrach. “Regression-Free Synthesis for Concurrency,” 8559:568–84. Springer,
2014. https://doi.org/10.1007/978-3-319-08867-9_38.
ieee: 'P. Cerny, T. A. Henzinger, A. Radhakrishna, L. Ryzhyk, and T. Tarrach, “Regression-free
synthesis for concurrency,” presented at the CAV: Computer Aided Verification,
Vienna, Austria, 2014, vol. 8559, pp. 568–584.'
ista: 'Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. 2014. Regression-free
synthesis for concurrency. CAV: Computer Aided Verification, LNCS, vol. 8559,
568–584.'
mla: Cerny, Pavol, et al. Regression-Free Synthesis for Concurrency. Vol.
8559, Springer, 2014, pp. 568–84, doi:10.1007/978-3-319-08867-9_38.
short: P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer,
2014, pp. 568–584.
conference:
end_date: 2014-07-22
location: Vienna, Austria
name: 'CAV: Computer Aided Verification'
start_date: 2014-07-18
date_created: 2018-12-11T11:56:23Z
date_published: 2014-07-22T00:00:00Z
date_updated: 2023-09-07T11:57:01Z
day: '22'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-08867-9_38
ec_funded: 1
file:
- access_level: open_access
checksum: a631d3105509f239724644e77a1212e2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:14Z
date_updated: 2020-07-14T12:45:33Z
file_id: '4995'
file_name: IST-2014-297-v1+1_cav14-final.pdf
file_size: 416732
relation: main_file
- access_level: open_access
checksum: f8b0f748cc9fa697ca992cc56c87bc4e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:15Z
date_updated: 2020-07-14T12:45:33Z
file_id: '4996'
file_name: IST-2014-297-v2+1_cav14-final2.pdf
file_size: 616293
relation: main_file
file_date_updated: 2020-07-14T12:45:33Z
has_accepted_license: '1'
intvolume: ' 8559'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://link.springer.com/chapter/10.1007%2F978-3-319-08867-9_38
month: '07'
oa: 1
oa_version: Submitted Version
page: 568 - 584
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication_identifier:
isbn:
- 978-331908866-2
publication_status: published
publisher: Springer
publist_id: '4749'
pubrep_id: '297'
quality_controlled: '1'
related_material:
record:
- id: '1130'
relation: dissertation_contains
status: public
status: public
title: Regression-free synthesis for concurrency
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8559
year: '2014'
...
---
_id: '2167'
abstract:
- lang: eng
text: Model-based testing is a promising technology for black-box software and hardware
testing, in which test cases are generated automatically from high-level specifications.
Nowadays, systems typically consist of multiple interacting components and, due
to their complexity, testing presents a considerable portion of the effort and
cost in the design process. Exploiting the compositional structure of system specifications
can considerably reduce the effort in model-based testing. Moreover, inferring
properties about the system from testing its individual components allows the
designer to reduce the amount of integration testing. In this paper, we study
compositional properties of the ioco-testing theory. We propose a new approach
to composition and hiding operations, inspired by contract-based design and interface
theories. These operations preserve behaviors that are compatible under composition
and hiding, and prune away incompatible ones. The resulting specification characterizes
the input sequences for which the unit testing of components is sufficient to
infer the correctness of component integration without the need for further tests.
We provide a methodology that uses these results to minimize integration testing
effort, but also to detect potential weaknesses in specifications. While we focus
on asynchronous models and the ioco conformance relation, the resulting methodology
can be applied to a broader class of systems.
article_number: '6823899'
article_processing_charge: No
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Willibald
full_name: Krenn, Willibald
last_name: Krenn
- first_name: Dejan
full_name: Nickovic, Dejan
last_name: Nickovic
citation:
ama: 'Daca P, Henzinger TA, Krenn W, Nickovic D. Compositional specifications for
IOCO testing. In: IEEE 7th International Conference on Software Testing, Verification
and Validation. IEEE; 2014. doi:10.1109/ICST.2014.50'
apa: 'Daca, P., Henzinger, T. A., Krenn, W., & Nickovic, D. (2014). Compositional
specifications for IOCO testing. In IEEE 7th International Conference on Software
Testing, Verification and Validation. Cleveland, USA: IEEE. https://doi.org/10.1109/ICST.2014.50'
chicago: Daca, Przemyslaw, Thomas A Henzinger, Willibald Krenn, and Dejan Nickovic.
“Compositional Specifications for IOCO Testing.” In IEEE 7th International
Conference on Software Testing, Verification and Validation. IEEE, 2014. https://doi.org/10.1109/ICST.2014.50.
ieee: P. Daca, T. A. Henzinger, W. Krenn, and D. Nickovic, “Compositional specifications
for IOCO testing,” in IEEE 7th International Conference on Software Testing,
Verification and Validation, Cleveland, USA, 2014.
ista: 'Daca P, Henzinger TA, Krenn W, Nickovic D. 2014. Compositional specifications
for IOCO testing. IEEE 7th International Conference on Software Testing, Verification
and Validation. ICST: International Conference on Software Testing, Verification
and Validation, 6823899.'
mla: Daca, Przemyslaw, et al. “Compositional Specifications for IOCO Testing.” IEEE
7th International Conference on Software Testing, Verification and Validation,
6823899, IEEE, 2014, doi:10.1109/ICST.2014.50.
short: P. Daca, T.A. Henzinger, W. Krenn, D. Nickovic, in:, IEEE 7th International
Conference on Software Testing, Verification and Validation, IEEE, 2014.
conference:
end_date: 2014-04-04
location: Cleveland, USA
name: 'ICST: International Conference on Software Testing, Verification and Validation'
start_date: 2014-03-31
date_created: 2018-12-11T11:56:06Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '01'
department:
- _id: ToHe
doi: 10.1109/ICST.2014.50
ec_funded: 1
external_id:
arxiv:
- '1904.07083'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1904.07083
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication: IEEE 7th International Conference on Software Testing, Verification and
Validation
publication_identifier:
isbn:
- 978-1-4799-2255-0
issn:
- 2159-4848
publication_status: published
publisher: IEEE
publist_id: '4817'
quality_controlled: '1'
related_material:
record:
- id: '5411'
relation: earlier_version
status: public
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Compositional specifications for IOCO testing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2063'
abstract:
- lang: eng
text: We consider Markov decision processes (MDPs) which are a standard model for
probabilistic systems.We focus on qualitative properties forMDPs that can express
that desired behaviors of the system arise almost-surely (with probability 1)
or with positive probability. We introduce a new simulation relation to capture
the refinement relation ofMDPs with respect to qualitative properties, and present
discrete graph theoretic algorithms with quadratic complexity to compute the simulation
relation.We present an automated technique for assume-guarantee style reasoning
for compositional analysis ofMDPs with qualitative properties by giving a counterexample
guided abstraction-refinement approach to compute our new simulation relation.
We have implemented our algorithms and show that the compositional analysis leads
to significant improvements.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
citation:
ama: 'Chatterjee K, Chmelik M, Daca P. CEGAR for qualitative analysis of probabilistic
systems. In: Vol 8559. Springer; 2014:473-490. doi:10.1007/978-3-319-08867-9_31'
apa: 'Chatterjee, K., Chmelik, M., & Daca, P. (2014). CEGAR for qualitative
analysis of probabilistic systems (Vol. 8559, pp. 473–490). Presented at the CAV:
Computer Aided Verification, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-319-08867-9_31'
chicago: Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for
Qualitative Analysis of Probabilistic Systems,” 8559:473–90. Springer, 2014. https://doi.org/10.1007/978-3-319-08867-9_31.
ieee: 'K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for qualitative analysis of
probabilistic systems,” presented at the CAV: Computer Aided Verification, Vienna,
Austria, 2014, vol. 8559, pp. 473–490.'
ista: 'Chatterjee K, Chmelik M, Daca P. 2014. CEGAR for qualitative analysis of
probabilistic systems. CAV: Computer Aided Verification, LNCS, vol. 8559, 473–490.'
mla: Chatterjee, Krishnendu, et al. CEGAR for Qualitative Analysis of Probabilistic
Systems. Vol. 8559, Springer, 2014, pp. 473–90, doi:10.1007/978-3-319-08867-9_31.
short: K. Chatterjee, M. Chmelik, P. Daca, in:, Springer, 2014, pp. 473–490.
conference:
end_date: 2014-07-22
location: Vienna, Austria
name: 'CAV: Computer Aided Verification'
start_date: 2014-07-18
date_created: 2018-12-11T11:55:30Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-08867-9_31
ec_funded: 1
intvolume: ' 8559'
language:
- iso: eng
month: '07'
oa_version: None
page: 473 - 490
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Springer
publist_id: '4978'
quality_controlled: '1'
related_material:
record:
- id: '5412'
relation: earlier_version
status: public
- id: '5413'
relation: earlier_version
status: public
- id: '5414'
relation: earlier_version
status: public
- id: '1155'
relation: dissertation_contains
status: public
status: public
title: CEGAR for qualitative analysis of probabilistic systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8559
year: '2014'
...
---
_id: '2001'
abstract:
- lang: eng
text: Antibiotics affect bacterial cell physiology at many levels. Rather than just
compensating for the direct cellular defects caused by the drug, bacteria respond
to antibiotics by changing their morphology, macromolecular composition, metabolism,
gene expression and possibly even their mutation rate. Inevitably, these processes
affect each other, resulting in a complex response with changes in the expression
of numerous genes. Genome‐wide approaches can thus help in gaining a comprehensive
understanding of bacterial responses to antibiotics. In addition, a combination
of experimental and theoretical approaches is needed for identifying general principles
that underlie these responses. Here, we review recent progress in our understanding
of bacterial responses to antibiotics and their combinations, focusing on effects
at the levels of growth rate and gene expression. We concentrate on studies performed
in controlled laboratory conditions, which combine promising experimental techniques
with quantitative data analysis and mathematical modeling. While these basic research
approaches are not immediately applicable in the clinic, uncovering the principles
and mechanisms underlying bacterial responses to antibiotics may, in the long
term, contribute to the development of new treatment strategies to cope with and
prevent the rise of resistant pathogenic bacteria.
author:
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Mitosch K, Bollenbach MT. Bacterial responses to antibiotics and their combinations.
Environmental Microbiology Reports. 2014;6(6):545-557. doi:10.1111/1758-2229.12190
apa: Mitosch, K., & Bollenbach, M. T. (2014). Bacterial responses to antibiotics
and their combinations. Environmental Microbiology Reports. Wiley. https://doi.org/10.1111/1758-2229.12190
chicago: Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics
and Their Combinations.” Environmental Microbiology Reports. Wiley, 2014.
https://doi.org/10.1111/1758-2229.12190.
ieee: K. Mitosch and M. T. Bollenbach, “Bacterial responses to antibiotics and their
combinations,” Environmental Microbiology Reports, vol. 6, no. 6. Wiley,
pp. 545–557, 2014.
ista: Mitosch K, Bollenbach MT. 2014. Bacterial responses to antibiotics and their
combinations. Environmental Microbiology Reports. 6(6), 545–557.
mla: Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics
and Their Combinations.” Environmental Microbiology Reports, vol. 6, no.
6, Wiley, 2014, pp. 545–57, doi:10.1111/1758-2229.12190.
short: K. Mitosch, M.T. Bollenbach, Environmental Microbiology Reports 6 (2014)
545–557.
date_created: 2018-12-11T11:55:08Z
date_published: 2014-06-22T00:00:00Z
date_updated: 2023-09-07T12:00:25Z
day: '22'
department:
- _id: ToBo
doi: 10.1111/1758-2229.12190
ec_funded: 1
intvolume: ' 6'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 545 - 557
project:
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
publication: Environmental Microbiology Reports
publication_status: published
publisher: Wiley
publist_id: '5076'
quality_controlled: '1'
related_material:
record:
- id: '818'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Bacterial responses to antibiotics and their combinations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2014'
...
---
_id: '2082'
abstract:
- lang: eng
text: 'NMAC is a mode of operation which turns a fixed input-length keyed hash function
f into a variable input-length function. A practical single-key variant of NMAC
called HMAC is a very popular and widely deployed message authentication code
(MAC). Security proofs and attacks for NMAC can typically be lifted to HMAC. NMAC
was introduced by Bellare, Canetti and Krawczyk [Crypto''96], who proved it to
be a secure pseudorandom function (PRF), and thus also a MAC, assuming that (1)
f is a PRF and (2) the function we get when cascading f is weakly collision-resistant.
Unfortunately, HMAC is typically instantiated with cryptographic hash functions
like MD5 or SHA-1 for which (2) has been found to be wrong. To restore the provable
guarantees for NMAC, Bellare [Crypto''06] showed its security based solely on
the assumption that f is a PRF, albeit via a non-uniform reduction. - Our first
contribution is a simpler and uniform proof for this fact: If f is an ε-secure
PRF (against q queries) and a δ-non-adaptively secure PRF (against q queries),
then NMAC f is an (ε+ℓqδ)-secure PRF against q queries of length at most ℓ blocks
each. - We then show that this ε+ℓqδ bound is basically tight. For the most interesting
case where ℓqδ ≥ ε we prove this by constructing an f for which an attack with
advantage ℓqδ exists. This also violates the bound O(ℓε) on the PRF-security of
NMAC recently claimed by Koblitz and Menezes. - Finally, we analyze the PRF-security
of a modification of NMAC called NI [An and Bellare, Crypto''99] that differs
mainly by using a compression function with an additional keying input. This avoids
the constant rekeying on multi-block messages in NMAC and allows for a security
proof starting by the standard switch from a PRF to a random function, followed
by an information-theoretic analysis. We carry out such an analysis, obtaining
a tight ℓq2/2 c bound for this step, improving over the trivial bound of ℓ2q2/2c.
The proof borrows combinatorial techniques originally developed for proving the
security of CBC-MAC [Bellare et al., Crypto''05].'
alternative_title:
- LNCS
author:
- first_name: Peter
full_name: Gazi, Peter
id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
last_name: Gazi
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Michal
full_name: Rybar, Michal
id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87
last_name: Rybar
citation:
ama: 'Gazi P, Pietrzak KZ, Rybar M. The exact PRF-security of NMAC and HMAC. In:
Garay J, Gennaro R, eds. Vol 8616. Springer; 2014:113-130. doi:10.1007/978-3-662-44371-2_7'
apa: 'Gazi, P., Pietrzak, K. Z., & Rybar, M. (2014). The exact PRF-security
of NMAC and HMAC. In J. Garay & R. Gennaro (Eds.) (Vol. 8616, pp. 113–130).
Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, USA:
Springer. https://doi.org/10.1007/978-3-662-44371-2_7'
chicago: Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact PRF-Security
of NMAC and HMAC.” edited by Juan Garay and Rosario Gennaro, 8616:113–30. Springer,
2014. https://doi.org/10.1007/978-3-662-44371-2_7.
ieee: 'P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact PRF-security of NMAC and
HMAC,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara,
USA, 2014, vol. 8616, no. 1, pp. 113–130.'
ista: 'Gazi P, Pietrzak KZ, Rybar M. 2014. The exact PRF-security of NMAC and HMAC.
CRYPTO: International Cryptology Conference, LNCS, vol. 8616, 113–130.'
mla: Gazi, Peter, et al. The Exact PRF-Security of NMAC and HMAC. Edited
by Juan Garay and Rosario Gennaro, vol. 8616, no. 1, Springer, 2014, pp. 113–30,
doi:10.1007/978-3-662-44371-2_7.
short: P. Gazi, K.Z. Pietrzak, M. Rybar, in:, J. Garay, R. Gennaro (Eds.), Springer,
2014, pp. 113–130.
conference:
end_date: 2014-08-21
location: Santa Barbara, USA
name: 'CRYPTO: International Cryptology Conference'
start_date: 2014-08-17
date_created: 2018-12-11T11:55:36Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-09-07T12:02:27Z
day: '01'
ddc:
- '000'
- '004'
department:
- _id: KrPi
doi: 10.1007/978-3-662-44371-2_7
ec_funded: 1
editor:
- first_name: Juan
full_name: Garay, Juan
last_name: Garay
- first_name: Rosario
full_name: Gennaro, Rosario
last_name: Gennaro
file:
- access_level: open_access
checksum: dab6ab36a5f6af94f2b597e6404ed11d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:17Z
date_updated: 2020-07-14T12:45:28Z
file_id: '4999'
file_name: IST-2016-682-v1+1_578.pdf
file_size: 492310
relation: main_file
file_date_updated: 2020-07-14T12:45:28Z
has_accepted_license: '1'
intvolume: ' 8616'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 113 - 130
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '4955'
pubrep_id: '682'
quality_controlled: '1'
related_material:
record:
- id: '838'
relation: dissertation_contains
status: public
status: public
title: The exact PRF-security of NMAC and HMAC
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8616
year: '2014'
...
---
_id: '1912'
abstract:
- lang: eng
text: Kupffer's vesicle (KV) is the zebrafish organ of laterality, patterning the
embryo along its left-right (LR) axis. Regional differences in cell shape within
the lumen-lining KV epithelium are essential for its LR patterning function. However,
the processes by which KV cells acquire their characteristic shapes are largely
unknown. Here, we show that the notochord induces regional differences in cell
shape within KV by triggering extracellular matrix (ECM) accumulation adjacent
to anterior-dorsal (AD) regions of KV. This localized ECM deposition restricts
apical expansion of lumen-lining epithelial cells in AD regions of KV during lumen
growth. Our study provides mechanistic insight into the processes by which KV
translates global embryonic patterning into regional cell shape differences required
for its LR symmetry-breaking function.
acknowledgement: We are grateful to members of the C.-P.H. lab, M. Concha, D. Siekhaus,
and J. Vermot for comments on the manuscript and to M. Furutani-Seiki for sharing
reagents. This work was supported by the Institute of Science and Technology Austria
and an Alexander von Humboldt Foundation fellowship to J.C.
article_processing_charge: No
author:
- first_name: Julien
full_name: Compagnon, Julien
id: 2E3E0988-F248-11E8-B48F-1D18A9856A87
last_name: Compagnon
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Srivarsha
full_name: Rajshekar, Srivarsha
last_name: Rajshekar
- first_name: Rita
full_name: Kottmeier, Rita
last_name: Kottmeier
- first_name: Kornelija
full_name: Pranjic-Ferscha, Kornelija
id: 4362B3C2-F248-11E8-B48F-1D18A9856A87
last_name: Pranjic-Ferscha
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- 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: Compagnon J, Barone V, Rajshekar S, et al. The notochord breaks bilateral symmetry
by controlling cell shapes in the Zebrafish laterality organ. Developmental
Cell. 2014;31(6):774-783. doi:10.1016/j.devcel.2014.11.003
apa: Compagnon, J., Barone, V., Rajshekar, S., Kottmeier, R., Pranjic-Ferscha, K.,
Behrndt, M., & Heisenberg, C.-P. J. (2014). The notochord breaks bilateral
symmetry by controlling cell shapes in the Zebrafish laterality organ. Developmental
Cell. Cell Press. https://doi.org/10.1016/j.devcel.2014.11.003
chicago: Compagnon, Julien, Vanessa Barone, Srivarsha Rajshekar, Rita Kottmeier,
Kornelija Pranjic-Ferscha, Martin Behrndt, and Carl-Philipp J Heisenberg. “The
Notochord Breaks Bilateral Symmetry by Controlling Cell Shapes in the Zebrafish
Laterality Organ.” Developmental Cell. Cell Press, 2014. https://doi.org/10.1016/j.devcel.2014.11.003.
ieee: J. Compagnon et al., “The notochord breaks bilateral symmetry by controlling
cell shapes in the Zebrafish laterality organ,” Developmental Cell, vol.
31, no. 6. Cell Press, pp. 774–783, 2014.
ista: Compagnon J, Barone V, Rajshekar S, Kottmeier R, Pranjic-Ferscha K, Behrndt
M, Heisenberg C-PJ. 2014. The notochord breaks bilateral symmetry by controlling
cell shapes in the Zebrafish laterality organ. Developmental Cell. 31(6), 774–783.
mla: Compagnon, Julien, et al. “The Notochord Breaks Bilateral Symmetry by Controlling
Cell Shapes in the Zebrafish Laterality Organ.” Developmental Cell, vol.
31, no. 6, Cell Press, 2014, pp. 774–83, doi:10.1016/j.devcel.2014.11.003.
short: J. Compagnon, V. Barone, S. Rajshekar, R. Kottmeier, K. Pranjic-Ferscha,
M. Behrndt, C.-P.J. Heisenberg, Developmental Cell 31 (2014) 774–783.
date_created: 2018-12-11T11:54:41Z
date_published: 2014-12-22T00:00:00Z
date_updated: 2023-09-07T12:05:08Z
day: '22'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2014.11.003
external_id:
pmid:
- '25535919'
intvolume: ' 31'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/25535919
month: '12'
oa: 1
oa_version: Published Version
page: 774 - 783
pmid: 1
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '5182'
quality_controlled: '1'
related_material:
record:
- id: '961'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish
laterality organ
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2014'
...
---
_id: '2084'
abstract:
- lang: eng
text: Receptor tyrosine kinases (RTKs) are a large family of cell surface receptors
that sense growth factors and hormones and regulate a variety of cell behaviours
in health and disease. Contactless activation of RTKs with spatial and temporal
precision is currently not feasible. Here, we generated RTKs that are insensitive
to endogenous ligands but can be selectively activated by low-intensity blue light.
We screened light-oxygen-voltage (LOV)-sensing domains for their ability to activate
RTKs by light-activated dimerization. Incorporation of LOV domains found in aureochrome
photoreceptors of stramenopiles resulted in robust activation of the fibroblast
growth factor receptor 1 (FGFR1), epidermal growth factor receptor (EGFR) and
rearranged during transfection (RET). In human cancer and endothelial cells, light
induced cellular signalling with spatial and temporal precision. Furthermore,
light faithfully mimicked complex mitogenic and morphogenic cell behaviour induced
by growth factors. RTKs under optical control (Opto-RTKs) provide a powerful optogenetic
approach to actuate cellular signals and manipulate cell behaviour.
acknowledgement: European Union Seventh Framework Programme; Human Frontier Science
Program; Oesterreichische Nationalbank Anniversary Fund 14211; Austrian Research
Promotion Agency; FemTech
author:
- first_name: Michael
full_name: Grusch, Michael
last_name: Grusch
- first_name: Karin
full_name: Schelch, Karin
last_name: Schelch
- first_name: Robert
full_name: Riedler, Robert
last_name: Riedler
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
- first_name: Christopher
full_name: Differ, Christopher
last_name: Differ
- first_name: Walter
full_name: Berger, Walter
last_name: Berger
- first_name: Álvaro
full_name: Inglés Prieto, Álvaro
id: 2A9DB292-F248-11E8-B48F-1D18A9856A87
last_name: Inglés Prieto
orcid: 0000-0002-5409-8571
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Grusch M, Schelch K, Riedler R, et al. Spatio-temporally precise activation
of engineered receptor tyrosine kinases by light. EMBO Journal. 2014;33(15):1713-1726.
doi:10.15252/embj.201387695
apa: Grusch, M., Schelch, K., Riedler, R., Gschaider-Reichhart, E., Differ, C.,
Berger, W., … Janovjak, H. L. (2014). Spatio-temporally precise activation of
engineered receptor tyrosine kinases by light. EMBO Journal. Wiley-Blackwell.
https://doi.org/10.15252/embj.201387695
chicago: Grusch, Michael, Karin Schelch, Robert Riedler, Eva Gschaider-Reichhart,
Christopher Differ, Walter Berger, Álvaro Inglés Prieto, and Harald L Janovjak.
“Spatio-Temporally Precise Activation of Engineered Receptor Tyrosine Kinases
by Light.” EMBO Journal. Wiley-Blackwell, 2014. https://doi.org/10.15252/embj.201387695.
ieee: M. Grusch et al., “Spatio-temporally precise activation of engineered
receptor tyrosine kinases by light,” EMBO Journal, vol. 33, no. 15. Wiley-Blackwell,
pp. 1713–1726, 2014.
ista: Grusch M, Schelch K, Riedler R, Gschaider-Reichhart E, Differ C, Berger W,
Inglés Prieto Á, Janovjak HL. 2014. Spatio-temporally precise activation of engineered
receptor tyrosine kinases by light. EMBO Journal. 33(15), 1713–1726.
mla: Grusch, Michael, et al. “Spatio-Temporally Precise Activation of Engineered
Receptor Tyrosine Kinases by Light.” EMBO Journal, vol. 33, no. 15, Wiley-Blackwell,
2014, pp. 1713–26, doi:10.15252/embj.201387695.
short: M. Grusch, K. Schelch, R. Riedler, E. Gschaider-Reichhart, C. Differ, W.
Berger, Á. Inglés Prieto, H.L. Janovjak, EMBO Journal 33 (2014) 1713–1726.
date_created: 2018-12-11T11:55:37Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2023-09-07T12:49:09Z
day: '01'
department:
- _id: HaJa
doi: 10.15252/embj.201387695
intvolume: ' 33'
issue: '15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194103/
month: '07'
oa: 1
oa_version: Submitted Version
page: 1713 - 1726
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4953'
quality_controlled: '1'
related_material:
record:
- id: '418'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Spatio-temporally precise activation of engineered receptor tyrosine kinases
by light
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2014'
...
---
_id: '2157'
abstract:
- lang: eng
text: 'We show that the following algorithmic problem is decidable: given a 2-dimensional
simplicial complex, can it be embedded (topologically, or equivalently, piecewise
linearly) in ℝ3? By a known reduction, it suffices to decide the embeddability
of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which
allows us to simplify X and recurse, is in proving that if X can be embedded in
S3, then there is also an embedding in which X has a short meridian, i.e., an
essential curve in the boundary of X bounding a disk in S3 nX with length bounded
by a computable function of the number of tetrahedra of X.'
acknowledgement: ERC Advanced Grant No. 267165; Grant GRADR Eurogiga GIG/11/E023 (SNSF-PP00P2-138948);
Swiss National Science Foundation (SNSF-200020-138230).
author:
- first_name: Jiří
full_name: Matoušek, Jiří
last_name: Matoušek
- first_name: Eric
full_name: Sedgwick, Eric
last_name: Sedgwick
- first_name: Martin
full_name: Tancer, Martin
id: 38AC689C-F248-11E8-B48F-1D18A9856A87
last_name: Tancer
orcid: 0000-0002-1191-6714
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3 sphere
is decidable. In: Proceedings of the Annual Symposium on Computational Geometry.
ACM; 2014:78-84. doi:10.1145/2582112.2582137'
apa: 'Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2014). Embeddability
in the 3 sphere is decidable. In Proceedings of the Annual Symposium on Computational
Geometry (pp. 78–84). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582137'
chicago: Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability
in the 3 Sphere Is Decidable.” In Proceedings of the Annual Symposium on Computational
Geometry, 78–84. ACM, 2014. https://doi.org/10.1145/2582112.2582137.
ieee: J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the
3 sphere is decidable,” in Proceedings of the Annual Symposium on Computational
Geometry, Kyoto, Japan, 2014, pp. 78–84.
ista: 'Matoušek J, Sedgwick E, Tancer M, Wagner U. 2014. Embeddability in the 3
sphere is decidable. Proceedings of the Annual Symposium on Computational Geometry.
SoCG: Symposium on Computational Geometry, 78–84.'
mla: Matoušek, Jiří, et al. “Embeddability in the 3 Sphere Is Decidable.” Proceedings
of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 78–84, doi:10.1145/2582112.2582137.
short: J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, in:, Proceedings of the Annual
Symposium on Computational Geometry, ACM, 2014, pp. 78–84.
conference:
end_date: 2014-06-11
location: Kyoto, Japan
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2014-06-08
date_created: 2018-12-11T11:56:02Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2023-09-11T13:38:49Z
day: '01'
department:
- _id: UlWa
doi: 10.1145/2582112.2582137
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1402.0815
month: '06'
oa: 1
oa_version: Submitted Version
page: 78 - 84
publication: Proceedings of the Annual Symposium on Computational Geometry
publication_status: published
publisher: ACM
publist_id: '4849'
quality_controlled: '1'
related_material:
record:
- id: '425'
relation: later_version
status: public
scopus_import: 1
status: public
title: Embeddability in the 3 sphere is decidable
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '10894'
abstract:
- lang: eng
text: PHAT is a C++ library for the computation of persistent homology by matrix
reduction. We aim for a simple generic design that decouples algorithms from data
structures without sacrificing efficiency or user-friendliness. This makes PHAT
a versatile platform for experimenting with algorithmic ideas and comparing them
to state of the art implementations.
article_processing_charge: No
author:
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
- first_name: Michael
full_name: Kerber, Michael
last_name: Kerber
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Hubert
full_name: Wagner, Hubert
last_name: Wagner
citation:
ama: 'Bauer U, Kerber M, Reininghaus J, Wagner H. PHAT – Persistent Homology Algorithms
Toolbox. In: ICMS 2014: International Congress on Mathematical Software.
Vol 8592. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg; 2014:137-143.
doi:10.1007/978-3-662-44199-2_24'
apa: 'Bauer, U., Kerber, M., Reininghaus, J., & Wagner, H. (2014). PHAT – Persistent
Homology Algorithms Toolbox. In ICMS 2014: International Congress on Mathematical
Software (Vol. 8592, pp. 137–143). Berlin, Heidelberg: Springer Berlin Heidelberg.
https://doi.org/10.1007/978-3-662-44199-2_24'
chicago: 'Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “PHAT
– Persistent Homology Algorithms Toolbox.” In ICMS 2014: International Congress
on Mathematical Software, 8592:137–43. LNCS. Berlin, Heidelberg: Springer
Berlin Heidelberg, 2014. https://doi.org/10.1007/978-3-662-44199-2_24.'
ieee: 'U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “PHAT – Persistent Homology
Algorithms Toolbox,” in ICMS 2014: International Congress on Mathematical Software,
Seoul, South Korea, 2014, vol. 8592, pp. 137–143.'
ista: 'Bauer U, Kerber M, Reininghaus J, Wagner H. 2014. PHAT – Persistent Homology
Algorithms Toolbox. ICMS 2014: International Congress on Mathematical Software.
ICMS: International Congress on Mathematical SoftwareLNCS vol. 8592, 137–143.'
mla: 'Bauer, Ulrich, et al. “PHAT – Persistent Homology Algorithms Toolbox.” ICMS
2014: International Congress on Mathematical Software, vol. 8592, Springer
Berlin Heidelberg, 2014, pp. 137–43, doi:10.1007/978-3-662-44199-2_24.'
short: 'U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, in:, ICMS 2014: International
Congress on Mathematical Software, Springer Berlin Heidelberg, Berlin, Heidelberg,
2014, pp. 137–143.'
conference:
end_date: 2014-08-09
location: Seoul, South Korea
name: 'ICMS: International Congress on Mathematical Software'
start_date: 2014-08-05
date_created: 2022-03-21T07:12:16Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2023-09-20T09:42:40Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-662-44199-2_24
intvolume: ' 8592'
language:
- iso: eng
month: '09'
oa_version: None
page: 137-143
place: Berlin, Heidelberg
publication: 'ICMS 2014: International Congress on Mathematical Software'
publication_identifier:
eisbn:
- '9783662441992'
eissn:
- 1611-3349
isbn:
- '9783662441985'
issn:
- 0302-9743
publication_status: published
publisher: Springer Berlin Heidelberg
quality_controlled: '1'
related_material:
record:
- id: '1433'
relation: later_version
status: public
scopus_import: '1'
series_title: LNCS
status: public
title: PHAT – Persistent Homology Algorithms Toolbox
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8592
year: '2014'
...
---
_id: '5428'
abstract:
- lang: eng
text: "Simulation is an attractive alternative for language inclusion for automata
as it is an under-approximation of language inclusion, but usually has much lower
complexity. For non-deterministic automata, while language inclusion is PSPACE-complete,
simulation can be computed in polynomial time. Simulation has also been extended
in two orthogonal directions, namely, (1) fair simulation, for simulation over
specified set of infinite runs; and (2) quantitative simulation, for simulation
between weighted automata. Again, while fair trace inclusion is PSPACE-complete,
fair simulation can be computed in polynomial time. For weighted automata, the
(quantitative) language inclusion problem is undecidable for mean-payoff automata
and the decidability is open for discounted-sum automata, whereas the (quantitative)
simulation reduce to mean-payoff games and discounted-sum games, which admit pseudo-polynomial
time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted
automata with Büchi acceptance conditions, i.e., we generalize fair simulation
from non-weighted automata to weighted automata. We show that imposing Büchi acceptance
conditions on weighted automata changes many fundamental properties of the simulation
games. For example, whereas for mean-payoff and discounted-sum games, the players
do not need memory to play optimally; we show in contrast that for simulation
games with Büchi acceptance conditions, (i) for mean-payoff objectives, optimal
strategies for both players require infinite memory in general, and (ii) for discounted-sum
objectives, optimal strategies need not exist for both players. While the simulation
games with Büchi acceptance conditions are more complicated (e.g., due to infinite-memory
requirements for mean-payoff objectives) as compared to their counterpart without
Büchi acceptance conditions, we still present pseudo-polynomial time algorithms
to solve simulation games with Büchi acceptance conditions for both weighted mean-payoff
and weighted discounted-sum automata."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative Fair Simulation
Games. IST Austria; 2014. doi:10.15479/AT:IST-2014-315-v1-1
apa: Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2014). Quantitative
fair simulation games. IST Austria. https://doi.org/10.15479/AT:IST-2014-315-v1-1
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner.
Quantitative Fair Simulation Games. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-315-v1-1.
ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, Quantitative fair
simulation games. IST Austria, 2014.
ista: Chatterjee K, Henzinger TA, Otop J, Velner Y. 2014. Quantitative fair simulation
games, IST Austria, 26p.
mla: Chatterjee, Krishnendu, et al. Quantitative Fair Simulation Games. IST
Austria, 2014, doi:10.15479/AT:IST-2014-315-v1-1.
short: K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Quantitative Fair Simulation
Games, IST Austria, 2014.
date_created: 2018-12-12T11:39:16Z
date_published: 2014-12-05T00:00:00Z
date_updated: 2023-09-20T12:07:48Z
day: '05'
ddc:
- '004'
department:
- _id: ToHe
- _id: KrCh
doi: 10.15479/AT:IST-2014-315-v1-1
file:
- access_level: open_access
checksum: b1d573bc04365625ff9974880c0aa807
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:59Z
date_updated: 2020-07-14T12:46:52Z
file_id: '5521'
file_name: IST-2014-315-v1+1_report.pdf
file_size: 531046
relation: main_file
file_date_updated: 2020-07-14T12:46:52Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '26'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '315'
related_material:
record:
- id: '1066'
relation: later_version
status: public
status: public
title: Quantitative fair simulation games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1887'
article_processing_charge: No
article_type: original
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Cremer S. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie.
2014:23-30.
apa: Cremer, S. (2014). Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie.
Deutsche Zoologische Gesellschaft.
chicago: Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.”
Zoologie. Deutsche Zoologische Gesellschaft, 2014.
ieee: S. Cremer, “Gemeinsame Krankheitsabwehr in Ameisengesellschaften,” Zoologie.
Deutsche Zoologische Gesellschaft, pp. 23–30, 2014.
ista: Cremer S. 2014. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie.,
23–30.
mla: Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” Zoologie,
Deutsche Zoologische Gesellschaft, 2014, pp. 23–30.
short: S. Cremer, Zoologie (2014) 23–30.
date_created: 2018-12-11T11:54:33Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-10-17T07:54:57Z
day: '01'
department:
- _id: SyCr
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.dzg-ev.de/wp-content/uploads/2019/05/zoologie2014.pdf
month: '01'
oa: 1
oa_version: Published Version
page: 23 - 30
publication: Zoologie
publication_status: published
publisher: Deutsche Zoologische Gesellschaft
publist_id: '5208'
quality_controlled: '1'
status: public
title: Gemeinsame Krankheitsabwehr in Ameisengesellschaften
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2175'
abstract:
- lang: eng
text: The cerebral cortex, the seat of our cognitive abilities, is composed of an
intricate network of billions of excitatory projection and inhibitory interneurons.
Postmitotic cortical neurons are generated by a diverse set of neural stem cell
progenitors within dedicated zones and defined periods of neurogenesis during
embryonic development. Disruptions in neurogenesis can lead to alterations in
the neuronal cytoarchitecture, which is thought to represent a major underlying
cause for several neurological disorders, including microcephaly, autism and epilepsy.
Although a number of signaling pathways regulating neurogenesis have been described,
the precise cellular and molecular mechanisms regulating the functional neural
stem cell properties in cortical neurogenesis remain unclear. Here, we discuss
the most up-to-date strategies to monitor the fundamental mechanistic parameters
of neuronal progenitor proliferation, and recent advances deciphering the logic
and dynamics of neurogenesis.
article_processing_charge: No
author:
- first_name: Maria P
full_name: Postiglione, Maria P
id: 2C67902A-F248-11E8-B48F-1D18A9856A87
last_name: Postiglione
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: 'Postiglione MP, Hippenmeyer S. Monitoring neurogenesis in the cerebral cortex:
an update. Future Neurology. 2014;9(3):323-340. doi:10.2217/fnl.14.18'
apa: 'Postiglione, M. P., & Hippenmeyer, S. (2014). Monitoring neurogenesis
in the cerebral cortex: an update. Future Neurology. Future Science Group.
https://doi.org/10.2217/fnl.14.18'
chicago: 'Postiglione, Maria P, and Simon Hippenmeyer. “Monitoring Neurogenesis
in the Cerebral Cortex: An Update.” Future Neurology. Future Science Group,
2014. https://doi.org/10.2217/fnl.14.18.'
ieee: 'M. P. Postiglione and S. Hippenmeyer, “Monitoring neurogenesis in the cerebral
cortex: an update,” Future Neurology, vol. 9, no. 3. Future Science Group,
pp. 323–340, 2014.'
ista: 'Postiglione MP, Hippenmeyer S. 2014. Monitoring neurogenesis in the cerebral
cortex: an update. Future Neurology. 9(3), 323–340.'
mla: 'Postiglione, Maria P., and Simon Hippenmeyer. “Monitoring Neurogenesis in
the Cerebral Cortex: An Update.” Future Neurology, vol. 9, no. 3, Future
Science Group, 2014, pp. 323–40, doi:10.2217/fnl.14.18.'
short: M.P. Postiglione, S. Hippenmeyer, Future Neurology 9 (2014) 323–340.
date_created: 2018-12-11T11:56:09Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2023-10-17T08:34:27Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.2217/fnl.14.18
ec_funded: 1
file:
- access_level: open_access
checksum: ba06659ecadabceec9a37dd8c4586dce
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:25Z
date_updated: 2020-07-14T12:45:31Z
file_id: '4812'
file_name: IST-2016-528-v1+1_fnl.14.18.pdf
file_size: 3848424
relation: main_file
file_date_updated: 2020-07-14T12:45:31Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '3'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 323 - 340
project:
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
publication: Future Neurology
publication_identifier:
eissn:
- 1748-6971
issn:
- 1479-6708
publication_status: published
publisher: Future Science Group
publist_id: '4806'
pubrep_id: '528'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Monitoring neurogenesis in the cerebral cortex: an update'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2014'
...
---
_id: '1913'
abstract:
- lang: eng
text: 'Deposits of phosphorylated tau protein and convergence of pathology in the
hippocampus are the hallmarks of neurodegenerative tauopathies. Thus we aimed
to evaluate whether regional and cellular vulnerability patterns in the hippocampus
distinguish tauopathies or are influenced by their concomitant presence. Methods:
We created a heat map of phospho-tau (AT8) immunoreactivity patterns in 24 hippocampal
subregions/layers in individuals with Alzheimer''s disease (AD)-related neurofibrillary
degeneration (n = 40), Pick''s disease (n = 8), progressive supranuclear palsy
(n = 7), corticobasal degeneration (n = 6), argyrophilic grain disease (AGD, n
= 18), globular glial tauopathy (n = 5), and tau-astrogliopathy of the elderly
(n = 10). AT8 immunoreactivity patterns were compared by mathematical analysis.
Results: Our study reveals disease-specific hot spots and regional selective vulnerability
for these disorders. The pattern of hippocampal AD-related tau pathology is strongly
influenced by concomitant AGD. Mathematical analysis reveals that hippocampal
involvement in primary tauopathies is distinguishable from early-stage AD-related
neurofibrillary degeneration. Conclusion: Our data demonstrate disease-specific
AT8 immunoreactivity patterns and hot spots in the hippocampus even in tauopathies,
which primarily do not affect the hippocampus. These hot spots can be shifted
to other regions by the co-occurrence of tauopathies like AGD. Our observations
support the notion that globular glial tauopathies and tau-astrogliopathy of the
elderly are distinct entities.'
acknowledgement: This study was supported by the European Commission’s 7th Framework
Programme under GA No. 278486, ‘DEVELAGE’.
article_processing_charge: No
article_type: original
author:
- first_name: Ivan
full_name: Milenković, Ivan
last_name: Milenković
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
- first_name: Gábor
full_name: Kovács, Gábor
last_name: Kovács
citation:
ama: Milenković I, Petrov T, Kovács G. Patterns of hippocampal tau pathology differentiate
neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders.
2014;38(5-6):375-388. doi:10.1159/000365548
apa: Milenković, I., Petrov, T., & Kovács, G. (2014). Patterns of hippocampal
tau pathology differentiate neurodegenerative dementias. Dementia and Geriatric
Cognitive Disorders. Karger Publishers. https://doi.org/10.1159/000365548
chicago: Milenković, Ivan, Tatjana Petrov, and Gábor Kovács. “Patterns of Hippocampal
Tau Pathology Differentiate Neurodegenerative Dementias.” Dementia and Geriatric
Cognitive Disorders. Karger Publishers, 2014. https://doi.org/10.1159/000365548.
ieee: I. Milenković, T. Petrov, and G. Kovács, “Patterns of hippocampal tau pathology
differentiate neurodegenerative dementias,” Dementia and Geriatric Cognitive
Disorders, vol. 38, no. 5–6. Karger Publishers, pp. 375–388, 2014.
ista: Milenković I, Petrov T, Kovács G. 2014. Patterns of hippocampal tau pathology
differentiate neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders.
38(5–6), 375–388.
mla: Milenković, Ivan, et al. “Patterns of Hippocampal Tau Pathology Differentiate
Neurodegenerative Dementias.” Dementia and Geriatric Cognitive Disorders,
vol. 38, no. 5–6, Karger Publishers, 2014, pp. 375–88, doi:10.1159/000365548.
short: I. Milenković, T. Petrov, G. Kovács, Dementia and Geriatric Cognitive Disorders
38 (2014) 375–388.
date_created: 2018-12-11T11:54:41Z
date_published: 2014-11-07T00:00:00Z
date_updated: 2023-10-17T10:21:17Z
day: '07'
department:
- _id: CaGu
doi: 10.1159/000365548
external_id:
pmid:
- '25195847'
intvolume: ' 38'
issue: 5-6
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://kops.uni-konstanz.de/bitstream/123456789/42127/1/Milenkovic_2-17ivylo2up0798.pdf
month: '11'
oa: 1
oa_version: Published Version
page: 375 - 388
pmid: 1
publication: Dementia and Geriatric Cognitive Disorders
publication_identifier:
issn:
- 1420-8008
publication_status: published
publisher: Karger Publishers
publist_id: '5181'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Patterns of hippocampal tau pathology differentiate neurodegenerative dementias
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2014'
...
---
_id: '1507'
abstract:
- lang: eng
text: The Wigner-Dyson-Gaudin-Mehta conjecture asserts that the local eigenvalue
statistics of large real and complex Hermitian matrices with independent, identically
distributed entries are universal in a sense that they depend only on the symmetry
class of the matrix and otherwise are independent of the details of the distribution.
We present the recent solution to this half-century old conjecture. We explain
how stochastic tools, such as the Dyson Brownian motion, and PDE ideas, such as
De Giorgi-Nash-Moser regularity theory, were combined in the solution. We also
show related results for log-gases that represent a universal model for strongly
correlated systems. Finally, in the spirit of Wigner’s original vision, we discuss
the extensions of these universality results to more realistic physical systems
such as random band matrices.
acknowledgement: The author is partially supported by SFB-TR 12 Grant of the German
Research Council.
article_processing_charge: No
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
citation:
ama: 'Erdös L. Random matrices, log-gases and Hölder regularity. In: Proceedings
of the International Congress of Mathematicians. Vol 3. International Congress
of Mathematicians; 2014:214-236.'
apa: 'Erdös, L. (2014). Random matrices, log-gases and Hölder regularity. In Proceedings
of the International Congress of Mathematicians (Vol. 3, pp. 214–236). Seoul,
Korea: International Congress of Mathematicians.'
chicago: Erdös, László. “Random Matrices, Log-Gases and Hölder Regularity.” In Proceedings
of the International Congress of Mathematicians, 3:214–36. International Congress
of Mathematicians, 2014.
ieee: L. Erdös, “Random matrices, log-gases and Hölder regularity,” in Proceedings
of the International Congress of Mathematicians, Seoul, Korea, 2014, vol.
3, pp. 214–236.
ista: 'Erdös L. 2014. Random matrices, log-gases and Hölder regularity. Proceedings
of the International Congress of Mathematicians. ICM: International Congress of
Mathematicians vol. 3, 214–236.'
mla: Erdös, László. “Random Matrices, Log-Gases and Hölder Regularity.” Proceedings
of the International Congress of Mathematicians, vol. 3, International Congress
of Mathematicians, 2014, pp. 214–36.
short: L. Erdös, in:, Proceedings of the International Congress of Mathematicians,
International Congress of Mathematicians, 2014, pp. 214–236.
conference:
end_date: 2014-08-21
location: Seoul, Korea
name: 'ICM: International Congress of Mathematicians'
start_date: 2014-08-13
date_created: 2018-12-11T11:52:25Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2023-10-17T11:12:55Z
day: '01'
department:
- _id: LaEr
ec_funded: 1
intvolume: ' 3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1407.5752
month: '08'
oa: 1
oa_version: Submitted Version
page: 214 - 236
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Proceedings of the International Congress of Mathematicians
publication_status: published
publisher: International Congress of Mathematicians
publist_id: '5670'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Random matrices, log-gases and Hölder regularity
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2014'
...
---
_id: '8044'
abstract:
- lang: eng
text: Many questions concerning models in quantum mechanics require a detailed analysis
of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable
Hilbert space. Of particular relevance for an understanding of the low-temperature
properties of a system is the structure of the excitation spectrum, which is the
part of the spectrum close to the spectral bottom. We present recent progress
on this question for bosonic many-body quantum systems with weak two-body interactions.
Such system are currently of great interest, due to their experimental realization
in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations,
which predicts that the low-energy spectrum is made up of sums of elementary excitations,
with linear dispersion law at low momentum. The latter property is crucial for
the superfluid behavior the system.
article_processing_charge: No
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Seiringer R. Structure of the excitation spectrum for many-body quantum systems.
In: Proceeding of the International Congress of Mathematicans. Vol 3. International
Congress of Mathematicians; 2014:1175-1194.'
apa: 'Seiringer, R. (2014). Structure of the excitation spectrum for many-body quantum
systems. In Proceeding of the International Congress of Mathematicans (Vol.
3, pp. 1175–1194). Seoul, South Korea: International Congress of Mathematicians.'
chicago: Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body
Quantum Systems.” In Proceeding of the International Congress of Mathematicans,
3:1175–94. International Congress of Mathematicians, 2014.
ieee: R. Seiringer, “Structure of the excitation spectrum for many-body quantum
systems,” in Proceeding of the International Congress of Mathematicans,
Seoul, South Korea, 2014, vol. 3, pp. 1175–1194.
ista: 'Seiringer R. 2014. Structure of the excitation spectrum for many-body quantum
systems. Proceeding of the International Congress of Mathematicans. ICM: International
Congress of Mathematicans vol. 3, 1175–1194.'
mla: Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum
Systems.” Proceeding of the International Congress of Mathematicans, vol.
3, International Congress of Mathematicians, 2014, pp. 1175–94.
short: R. Seiringer, in:, Proceeding of the International Congress of Mathematicans,
International Congress of Mathematicians, 2014, pp. 1175–1194.
conference:
end_date: 2014-08-21
location: Seoul, South Korea
name: 'ICM: International Congress of Mathematicans'
start_date: 2014-08-13
date_created: 2020-06-29T07:59:35Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2023-10-17T11:12:33Z
day: '01'
department:
- _id: RoSe
intvolume: ' 3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.icm2014.org/en/vod/proceedings.html
month: '08'
oa: 1
oa_version: Published Version
page: 1175-1194
publication: Proceeding of the International Congress of Mathematicans
publication_identifier:
isbn:
- '9788961058063'
publication_status: published
publisher: International Congress of Mathematicians
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure of the excitation spectrum for many-body quantum systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2014'
...
---
_id: '2160'
abstract:
- lang: eng
text: Transfer learning has received a lot of attention in the machine learning
community over the last years, and several effective algorithms have been developed.
However, relatively little is known about their theoretical properties, especially
in the setting of lifelong learning, where the goal is to transfer information
to tasks for which no data have been observed so far. In this work we study lifelong
learning from a theoretical perspective. Our main result is a PAC-Bayesian generalization
bound that offers a unified view on existing paradigms for transfer learning,
such as the transfer of parameters or the transfer of low-dimensional representations.
We also use the bound to derive two principled lifelong learning algorithms, and
we show that these yield results comparable with existing methods.
article_processing_charge: No
author:
- first_name: Anastasia
full_name: Pentina, Anastasia
id: 42E87FC6-F248-11E8-B48F-1D18A9856A87
last_name: Pentina
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Pentina A, Lampert C. A PAC-Bayesian bound for Lifelong Learning. In: Vol
32. ML Research Press; 2014:991-999.'
apa: 'Pentina, A., & Lampert, C. (2014). A PAC-Bayesian bound for Lifelong Learning
(Vol. 32, pp. 991–999). Presented at the ICML: International Conference on Machine
Learning, Beijing, China: ML Research Press.'
chicago: Pentina, Anastasia, and Christoph Lampert. “A PAC-Bayesian Bound for Lifelong
Learning,” 32:991–99. ML Research Press, 2014.
ieee: 'A. Pentina and C. Lampert, “A PAC-Bayesian bound for Lifelong Learning,”
presented at the ICML: International Conference on Machine Learning, Beijing,
China, 2014, vol. 32, pp. 991–999.'
ista: 'Pentina A, Lampert C. 2014. A PAC-Bayesian bound for Lifelong Learning. ICML:
International Conference on Machine Learning vol. 32, 991–999.'
mla: Pentina, Anastasia, and Christoph Lampert. A PAC-Bayesian Bound for Lifelong
Learning. Vol. 32, ML Research Press, 2014, pp. 991–99.
short: A. Pentina, C. Lampert, in:, ML Research Press, 2014, pp. 991–999.
conference:
end_date: 2014-06-26
location: Beijing, China
name: 'ICML: International Conference on Machine Learning'
start_date: 2014-06-21
date_created: 2018-12-11T11:56:03Z
date_published: 2014-05-10T00:00:00Z
date_updated: 2023-10-17T11:54:24Z
day: '10'
department:
- _id: ChLa
intvolume: ' 32'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://dl.acm.org/citation.cfm?id=3045003
month: '05'
oa: 1
oa_version: Submitted Version
page: 991 - 999
publication_status: published
publisher: ML Research Press
publist_id: '4844'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A PAC-Bayesian bound for Lifelong Learning
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2014'
...
---
_id: '1403'
abstract:
- lang: eng
text: A variety of developmental and disease related processes depend on epithelial
cell sheet spreading. In order to gain insight into the biophysical mechanism(s)
underlying the tissue morphogenesis we studied the spreading of an epithelium
during the early development of the zebrafish embryo. In zebrafish epiboly the
enveloping cell layer (EVL), a simple squamous epithelium, spreads over the yolk
cell to completely engulf it at the end of gastrulation. Previous studies have
proposed that an actomyosin ring forming within the yolk syncytial layer (YSL)
acts as purse string that through constriction along its circumference pulls on
the margin of the EVL. Direct biophysical evidence for this hypothesis has however
been missing. The aim of the thesis was to understand how the actomyosin ring
may generate pulling forces onto the EVL and what cellular mechanism(s) may facilitate
the spreading of the epithelium. Using laser ablation to measure cortical tension
within the actomyosin ring we found an anisotropic tension distribution, which
was highest along the circumference of the ring. However the low degree of anisotropy
was incompatible with the actomyosin ring functioning as a purse string only.
Additionally, we observed retrograde cortical flow from vegetal parts of the ring
into the EVL margin. Interpreting the experimental data using a theoretical distribution
that models the tissues as active viscous gels led us to proposen that the actomyosin
ring has a twofold contribution to EVL epiboly. It not only acts as a purse string
through constriction along its circumference, but in addition constriction along
the width of the ring generates pulling forces through friction-resisted cortical
flow. Moreover, when rendering the purse string mechanism unproductive EVL epiboly
proceeded normally indicating that the flow-friction mechanism is sufficient to
drive the process. Aiming to understand what cellular mechanism(s) may facilitate
the spreading of the epithelium we found that tension-oriented EVL cell divisions
limit tissue anisotropy by releasing tension along the division axis and promote
epithelial spreading. Notably, EVL cells undergo ectopic cell fusion in conditions
in which oriented-cell division is impaired or the epithelium is mechanically
challenged. Taken together our study of EVL epiboly suggests a novel mechanism
of force generation for actomyosin rings through friction-resisted cortical flow
and highlights the importance of tension-oriented cell divisions in epithelial
morphogenesis.
acknowledged_ssus:
- _id: SSU
alternative_title:
- IST Austria Thesis
author:
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
citation:
ama: Behrndt M. Forces driving epithelial spreading in zebrafish epiboly. 2014.
apa: Behrndt, M. (2014). Forces driving epithelial spreading in zebrafish epiboly.
IST Austria.
chicago: Behrndt, Martin. “Forces Driving Epithelial Spreading in Zebrafish Epiboly.”
IST Austria, 2014.
ieee: M. Behrndt, “Forces driving epithelial spreading in zebrafish epiboly,” IST
Austria, 2014.
ista: Behrndt M. 2014. Forces driving epithelial spreading in zebrafish epiboly.
IST Austria.
mla: Behrndt, Martin. Forces Driving Epithelial Spreading in Zebrafish Epiboly.
IST Austria, 2014.
short: M. Behrndt, Forces Driving Epithelial Spreading in Zebrafish Epiboly, IST
Austria, 2014.
date_created: 2018-12-11T11:51:49Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2023-10-17T12:16:58Z
day: '01'
department:
- _id: CaHe
language:
- iso: eng
month: '08'
oa_version: None
page: '91'
publication_status: published
publisher: IST Austria
publist_id: '5804'
related_material:
record:
- id: '2282'
relation: part_of_dissertation
status: public
- id: '2950'
relation: part_of_dissertation
status: public
- id: '3373'
relation: part_of_dissertation
status: public
status: public
supervisor:
- 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
title: Forces driving epithelial spreading in zebrafish epiboly
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1888'
abstract:
- lang: ger
text: 'Im Rahmen meiner Arbeit mit der kollektiven Krankheitsabwehr in Ameisengesellschaften
interessiert mich vor allem, wie sich die Kolonien als Ganzes gegen Krankheiten
wehren können. Warum ist dieses Thema der Krankheitsdynamik in Gruppen so wichtig?
Ein Vergleich von solitär lebenden Individuen mit Individuen, die in sozialen
Gruppen zusammenleben, zeigt die Kosten und die Vorteile des Gruppenlebens: Einerseits
haben Individuen in sozialen Gruppen aufgrund der hohen Dichte, in der die Tiere
zusammenleben, den hohen Interaktionsraten, die sie miteinander haben, und der
engen Verwandtschaft, die sie verbindet, ein höheres Ansteckungsrisiko. Andererseits
kann die individuelle Krankheitsabwehr durch die kollektive Abwehr in den Gruppen
ergänzt werden.'
alternative_title:
- Rundgespräche der Kommission für Ökologie
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
citation:
ama: 'Cremer S. Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt Bayerische
Akademie der Wissenschaften. In: Soziale Insekten in Einer Sich Wandelnden
Welt. Vol 43. Verlag Dr. Friedrich Pfeil; 2014:65-72.'
apa: 'Cremer, S. (2014). Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt
Bayerische Akademie der Wissenschaften. In Soziale Insekten in einer sich wandelnden
Welt (Vol. 43, pp. 65–72). Verlag Dr. Friedrich Pfeil.'
chicago: 'Cremer, Sylvia. “Soziale Immunität: Wie Sich Der Staat Gegen Pathogene
Wehrt Bayerische Akademie Der Wissenschaften.” In Soziale Insekten in Einer
Sich Wandelnden Welt, 43:65–72. Verlag Dr. Friedrich Pfeil, 2014.'
ieee: 'S. Cremer, “Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt
Bayerische Akademie der Wissenschaften,” in Soziale Insekten in einer sich
wandelnden Welt, vol. 43, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72.'
ista: 'Cremer S. 2014.Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt
Bayerische Akademie der Wissenschaften. In: Soziale Insekten in einer sich wandelnden
Welt. Rundgespräche der Kommission für Ökologie, vol. 43, 65–72.'
mla: 'Cremer, Sylvia. “Soziale Immunität: Wie Sich Der Staat Gegen Pathogene Wehrt
Bayerische Akademie Der Wissenschaften.” Soziale Insekten in Einer Sich Wandelnden
Welt, vol. 43, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72.'
short: S. Cremer, in:, Soziale Insekten in Einer Sich Wandelnden Welt, Verlag Dr.
Friedrich Pfeil, 2014, pp. 65–72.
date_created: 2018-12-11T11:54:33Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-10-17T12:28:45Z
day: '01'
department:
- _id: SyCr
intvolume: ' 43'
language:
- iso: eng
month: '01'
oa_version: None
page: 65 - 72
publication: Soziale Insekten in einer sich wandelnden Welt
publication_identifier:
issn:
- 2366-2875
publication_status: published
publisher: Verlag Dr. Friedrich Pfeil
publist_id: '5207'
quality_controlled: '1'
status: public
title: 'Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt Bayerische Akademie
der Wissenschaften'
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2014'
...
---
_id: '2012'
abstract:
- lang: eng
text: The classical sphere packing problem asks for the best (infinite) arrangement
of non-overlapping unit balls which cover as much space as possible. We define
a generalized version of the problem, where we allow each ball a limited amount
of overlap with other balls. We study two natural choices of overlap measures
and obtain the optimal lattice packings in a parameterized family of lattices
which contains the FCC, BCC, and integer lattice.
acknowledgement: We thank Herbert Edelsbrunner for his valuable discussions and ideas
on the topic of this paper. The second author has been supported by the Max Planck
Center for Visual Computing and Communication
article_number: '1401.0468'
article_processing_charge: No
author:
- first_name: Mabel
full_name: Iglesias Ham, Mabel
id: 41B58C0C-F248-11E8-B48F-1D18A9856A87
last_name: Iglesias Ham
- first_name: Michael
full_name: Kerber, Michael
last_name: Kerber
orcid: 0000-0002-8030-9299
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. arXiv.
doi:10.48550/arXiv.1401.0468
apa: Iglesias Ham, M., Kerber, M., & Uhler, C. (n.d.). Sphere packing with limited
overlap. arXiv. https://doi.org/10.48550/arXiv.1401.0468
chicago: Iglesias Ham, Mabel, Michael Kerber, and Caroline Uhler. “Sphere Packing
with Limited Overlap.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1401.0468.
ieee: M. Iglesias Ham, M. Kerber, and C. Uhler, “Sphere packing with limited overlap,”
arXiv. .
ista: Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. arXiv,
1401.0468.
mla: Iglesias Ham, Mabel, et al. “Sphere Packing with Limited Overlap.” ArXiv,
1401.0468, doi:10.48550/arXiv.1401.0468.
short: M. Iglesias Ham, M. Kerber, C. Uhler, ArXiv (n.d.).
date_created: 2018-12-11T11:55:12Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-10-18T08:06:45Z
day: '01'
department:
- _id: HeEd
- _id: CaUh
doi: 10.48550/arXiv.1401.0468
external_id:
arxiv:
- '1401.0468'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://cccg.ca/proceedings/2014/papers/paper23.pdf
month: '01'
oa: 1
oa_version: Submitted Version
publication: arXiv
publication_status: submitted
publist_id: '5064'
status: public
title: Sphere packing with limited overlap
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '14301'
abstract:
- lang: eng
text: DNA has become a prime material for assembling complex three-dimensional objects
that promise utility in various areas of application. However, achieving user-defined
goals with DNA objects has been hampered by the difficulty to prepare them at
arbitrary concentrations and in user-defined solution conditions. Here, we describe
a method that solves this problem. The method is based on poly(ethylene glycol)-induced
depletion of species with high molecular weight. We demonstrate that our method
is applicable to a wide spectrum of DNA shapes and that it achieves excellent
recovery yields of target objects up to 97 %, while providing efficient separation
from non-integrated DNA strands. DNA objects may be prepared at concentrations
up to the limit of solubility, including the possibility for bringing DNA objects
into a solid phase. Due to the fidelity and simplicity of our method we anticipate
that it will help to catalyze the development of new types of applications that
use self-assembled DNA objects.
article_processing_charge: No
article_type: original
author:
- first_name: Evi
full_name: Stahl, Evi
last_name: Stahl
- first_name: Thomas
full_name: Martin, Thomas
last_name: Martin
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
citation:
ama: Stahl E, Martin T, Praetorius FM, Dietz H. Facile and scalable preparation
of pure and dense DNA origami solutions. Angewandte Chemie International Edition.
2014;126(47):12949-12954. doi:10.1002/ange.201405991
apa: Stahl, E., Martin, T., Praetorius, F. M., & Dietz, H. (2014). Facile and
scalable preparation of pure and dense DNA origami solutions. Angewandte Chemie
International Edition. Wiley. https://doi.org/10.1002/ange.201405991
chicago: Stahl, Evi, Thomas Martin, Florian M Praetorius, and Hendrik Dietz. “Facile
and Scalable Preparation of Pure and Dense DNA Origami Solutions.” Angewandte
Chemie International Edition. Wiley, 2014. https://doi.org/10.1002/ange.201405991.
ieee: E. Stahl, T. Martin, F. M. Praetorius, and H. Dietz, “Facile and scalable
preparation of pure and dense DNA origami solutions,” Angewandte Chemie International
Edition, vol. 126, no. 47. Wiley, pp. 12949–12954, 2014.
ista: Stahl E, Martin T, Praetorius FM, Dietz H. 2014. Facile and scalable preparation
of pure and dense DNA origami solutions. Angewandte Chemie International Edition.
126(47), 12949–12954.
mla: Stahl, Evi, et al. “Facile and Scalable Preparation of Pure and Dense DNA Origami
Solutions.” Angewandte Chemie International Edition, vol. 126, no. 47,
Wiley, 2014, pp. 12949–54, doi:10.1002/ange.201405991.
short: E. Stahl, T. Martin, F.M. Praetorius, H. Dietz, Angewandte Chemie International
Edition 126 (2014) 12949–12954.
date_created: 2023-09-06T12:51:14Z
date_published: 2014-11-17T00:00:00Z
date_updated: 2023-11-07T12:14:30Z
day: '17'
doi: 10.1002/ange.201405991
extern: '1'
external_id:
pmid:
- '25346175'
intvolume: ' 126'
issue: '47'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/ange.201405991
month: '11'
oa: 1
oa_version: Published Version
page: 12949-12954
pmid: 1
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Facile and scalable preparation of pure and dense DNA origami solutions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 126
year: '2014'
...