---
_id: '3215'
abstract:
- lang: eng
text: 'Most cryptographic primitives such as encryption, authentication or secret
sharing require randomness. Usually one assumes that perfect randomness is available,
but those primitives might also be realized under weaker assumptions. In this
work we continue the study of building secure cryptographic primitives from imperfect
random sources initiated by Dodis and Spencer (FOCS’02). Their main result shows
that there exists a (high-entropy) source of randomness allowing for perfect encryption
of a bit, and yet from which one cannot extract even a single weakly random bit,
separating encryption from extraction. Our main result separates encryption from
2-out-2 secret sharing (both in the information-theoretic and in the computational
settings): any source which can be used to achieve one-bit encryption also can
be used for 2-out-2 secret sharing of one bit, but the converse is false, even
for high-entropy sources. Therefore, possibility of extraction strictly implies
encryption, which in turn strictly implies 2-out-2 secret sharing.'
acknowledgement: Supported in part by NSF career award CCR-0133806 and NSF grant CCR-0311095.
Supported by the Swiss National Science Foundation, project No. 200020-103847/1.
alternative_title:
- LNCS
author:
- first_name: Yevgeniy
full_name: Dodis, Yevgeniy
last_name: Dodis
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Bartosz
full_name: Przydatek, Bartosz
last_name: Przydatek
citation:
ama: 'Dodis Y, Pietrzak KZ, Przydatek B. Separating sources for encryption and secret
sharing. In: Vol 3876. Springer; 2006:601-616. doi:10.1007/11681878_31'
apa: 'Dodis, Y., Pietrzak, K. Z., & Przydatek, B. (2006). Separating sources
for encryption and secret sharing (Vol. 3876, pp. 601–616). Presented at the TCC:
Theory of Cryptography Conference, Springer. https://doi.org/10.1007/11681878_31'
chicago: Dodis, Yevgeniy, Krzysztof Z Pietrzak, and Bartosz Przydatek. “Separating
Sources for Encryption and Secret Sharing,” 3876:601–16. Springer, 2006. https://doi.org/10.1007/11681878_31.
ieee: 'Y. Dodis, K. Z. Pietrzak, and B. Przydatek, “Separating sources for encryption
and secret sharing,” presented at the TCC: Theory of Cryptography Conference,
2006, vol. 3876, pp. 601–616.'
ista: 'Dodis Y, Pietrzak KZ, Przydatek B. 2006. Separating sources for encryption
and secret sharing. TCC: Theory of Cryptography Conference, LNCS, vol. 3876, 601–616.'
mla: Dodis, Yevgeniy, et al. Separating Sources for Encryption and Secret Sharing.
Vol. 3876, Springer, 2006, pp. 601–16, doi:10.1007/11681878_31.
short: Y. Dodis, K.Z. Pietrzak, B. Przydatek, in:, Springer, 2006, pp. 601–616.
conference:
name: 'TCC: Theory of Cryptography Conference'
date_created: 2018-12-11T12:02:04Z
date_published: 2006-04-11T00:00:00Z
date_updated: 2021-01-12T07:41:51Z
day: '11'
doi: 10.1007/11681878_31
extern: 1
intvolume: ' 3876'
month: '04'
page: 601 - 616
publication_status: published
publisher: Springer
publist_id: '3466'
quality_controlled: 0
status: public
title: Separating sources for encryption and secret sharing
type: conference
volume: 3876
year: '2006'
...
---
_id: '3217'
abstract:
- lang: eng
text: |-
To prove that a secure key-agreement protocol exists one must at least show P ≠NP. Moreover any proof that the sequential composition of two non-adaptively secure pseudorandom functions is secure against at least two adaptive queries must falsify the decisional Diffie-Hellman assumption, a standard assumption from public-key cryptography. Hence proving any of this two seemingly unrelated statements would require a significant breakthrough. We show that at least one of the two statements is true.
To our knowledge this gives the first positive cryptographic result (namely that composition implies some weak adaptive security) which holds in Minicrypt, but not in Cryptomania, i.e. under the assumption that one-way functions exist, but public-key cryptography does not.
acknowledgement: Author was supported during the writing of this work by the Swiss
National Science Foundation, project No. 200020-103847/1. Part of this work is supported
by the Commission of the European Communities through the IST program under contract
IST-2002-507932
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Pietrzak KZ. Composition implies adaptive security in minicrypt. In: Vol 4004.
Springer; 2006:328-338. doi:10.1007/11761679_20'
apa: 'Pietrzak, K. Z. (2006). Composition implies adaptive security in minicrypt
(Vol. 4004, pp. 328–338). Presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, Springer. https://doi.org/10.1007/11761679_20'
chicago: Pietrzak, Krzysztof Z. “Composition Implies Adaptive Security in Minicrypt,”
4004:328–38. Springer, 2006. https://doi.org/10.1007/11761679_20.
ieee: 'K. Z. Pietrzak, “Composition implies adaptive security in minicrypt,” presented
at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2006, vol.
4004, pp. 328–338.'
ista: 'Pietrzak KZ. 2006. Composition implies adaptive security in minicrypt. EUROCRYPT:
Theory and Applications of Cryptographic Techniques, LNCS, vol. 4004, 328–338.'
mla: Pietrzak, Krzysztof Z. Composition Implies Adaptive Security in Minicrypt.
Vol. 4004, Springer, 2006, pp. 328–38, doi:10.1007/11761679_20.
short: K.Z. Pietrzak, in:, Springer, 2006, pp. 328–338.
conference:
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
date_created: 2018-12-11T12:02:04Z
date_published: 2006-07-11T00:00:00Z
date_updated: 2021-01-12T07:41:52Z
day: '11'
doi: 10.1007/11761679_20
extern: 1
intvolume: ' 4004'
month: '07'
page: 328 - 338
publication_status: published
publisher: Springer
publist_id: '3464'
quality_controlled: 0
status: public
title: Composition implies adaptive security in minicrypt
type: conference
volume: 4004
year: '2006'
...
---
_id: '3216'
abstract:
- lang: eng
text: |-
We prove a new upper bound on the advantage of any adversary for distinguishing the encrypted CBC-MAC (EMAC) based on random permutations from a random function. Our proof uses techniques recently introduced in [BPR05], which again were inspired by [DGH + 04].
The bound we prove is tight — in the sense that it matches the advantage of known attacks up to a constant factor — for a wide range of the parameters: let n denote the block-size, q the number of queries the adversary is allowed to make and ℓ an upper bound on the length (i.e. number of blocks) of the messages, then for ℓ ≤ 2 n/8 and q≥ł2 the advantage is in the order of q 2/2 n (and in particular independent of ℓ). This improves on the previous bound of q 2ℓΘ(1/ln ln ℓ)/2 n from [BPR05] and matches the trivial attack (which thus is basically optimal) where one simply asks random queries until a collision is found.
acknowledgement: Part of this work is supported by the Commission of the European
Communities through the IST program under contract IST-2002-507932 ECRYPT.
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Pietrzak KZ. A tight bound for EMAC. In: Vol 4052. Springer; 2006:168-179.
doi:10.1007/11787006_15'
apa: 'Pietrzak, K. Z. (2006). A tight bound for EMAC (Vol. 4052, pp. 168–179). Presented
at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/11787006_15'
chicago: Pietrzak, Krzysztof Z. “A Tight Bound for EMAC,” 4052:168–79. Springer,
2006. https://doi.org/10.1007/11787006_15.
ieee: 'K. Z. Pietrzak, “A tight bound for EMAC,” presented at the ICALP: Automata,
Languages and Programming, 2006, vol. 4052, pp. 168–179.'
ista: 'Pietrzak KZ. 2006. A tight bound for EMAC. ICALP: Automata, Languages and
Programming, LNCS, vol. 4052, 168–179.'
mla: Pietrzak, Krzysztof Z. A Tight Bound for EMAC. Vol. 4052, Springer,
2006, pp. 168–79, doi:10.1007/11787006_15.
short: K.Z. Pietrzak, in:, Springer, 2006, pp. 168–179.
conference:
name: 'ICALP: Automata, Languages and Programming'
date_created: 2018-12-11T12:02:04Z
date_published: 2006-07-28T00:00:00Z
date_updated: 2021-01-12T07:41:52Z
day: '28'
doi: 10.1007/11787006_15
extern: 1
intvolume: ' 4052'
month: '07'
page: 168 - 179
publication_status: published
publisher: Springer
publist_id: '3463'
quality_controlled: 0
status: public
title: A tight bound for EMAC
type: conference
volume: 4052
year: '2006'
...
---
_id: '3522'
abstract:
- lang: eng
text: We observed sharp wave/ripples (SWR) during exploration within brief (<
2.4 s) interruptions of or during theta oscillations. CA1 network responses of
SWRs occurring during exploration (eSWR) and SWRs detected in waking immobility
or sleep were similar. However, neuronal activity during eSWR was location dependent,
and eSWR-related firing was stronger inside the place field than outside. The
eSPW-related firing increase was stronger than the baseline increase inside compared
to outside, suggesting a “supralinear” summation of eSWR and place-selective inputs.
Pairs of cells with similar place fields and/or correlated firing during exploration
showed stronger coactivation during eSWRs and subsequent sleep-SWRs. Sequential
activation of place cells was not required for the reactivation of waking co-firing
patterns; cell pairs with symmetrical cross-correlations still showed reactivated
waking co-firing patterns during sleep-SWRs. We suggest that place-selective firing
during eSWRs facilitates initial associations between cells with similar place
fields that enable place-related ensemble patterns to recur during subsequent
sleep-SWRs.
author:
- first_name: Joseph
full_name: Joseph O'Neill
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Timothy
full_name: Senior,Timothy
last_name: Senior
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: O’Neill J, Senior T, Csicsvari JL. Place-selective firing of CA1 pyramidal
cells during sharp wave/ripple network patterns in exploratory behavior. Neuron.
2006;49(1):143-155. doi:10.1016/j.neuron.2005.10.037
apa: O’Neill, J., Senior, T., & Csicsvari, J. L. (2006). Place-selective firing
of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory
behavior. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2005.10.037
chicago: O’Neill, Joseph, Timothy Senior, and Jozsef L Csicsvari. “Place-Selective
Firing of CA1 Pyramidal Cells during Sharp Wave/Ripple Network Patterns in Exploratory
Behavior.” Neuron. Elsevier, 2006. https://doi.org/10.1016/j.neuron.2005.10.037.
ieee: J. O’Neill, T. Senior, and J. L. Csicsvari, “Place-selective firing of CA1
pyramidal cells during sharp wave/ripple network patterns in exploratory behavior,”
Neuron, vol. 49, no. 1. Elsevier, pp. 143–155, 2006.
ista: O’Neill J, Senior T, Csicsvari JL. 2006. Place-selective firing of CA1 pyramidal
cells during sharp wave/ripple network patterns in exploratory behavior. Neuron.
49(1), 143–155.
mla: O’Neill, Joseph, et al. “Place-Selective Firing of CA1 Pyramidal Cells during
Sharp Wave/Ripple Network Patterns in Exploratory Behavior.” Neuron, vol.
49, no. 1, Elsevier, 2006, pp. 143–55, doi:10.1016/j.neuron.2005.10.037.
short: J. O’Neill, T. Senior, J.L. Csicsvari, Neuron 49 (2006) 143–155.
date_created: 2018-12-11T12:03:46Z
date_published: 2006-01-05T00:00:00Z
date_updated: 2021-01-12T07:44:03Z
day: '05'
doi: 10.1016/j.neuron.2005.10.037
extern: 1
intvolume: ' 49'
issue: '1'
month: '01'
page: 143 - 155
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2863'
quality_controlled: 0
status: public
title: Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network
patterns in exploratory behavior
type: journal_article
volume: 49
year: '2006'
...
---
_id: '3607'
abstract:
- lang: eng
text: We apply new analytical methods to understand the consequences of population
bottlenecks for expected additive genetic variance. We analyze essentially all
models for multilocus epistasis that have been numerically simulated to demonstrate
increased additive variance. We conclude that for biologically plausible models,
large increases in expected additive variance–attributable to epistasis rather
than dominance–are unlikely. Naciri-Graven and Goudet (2003) found that as the
number of epistatically interacting loci increases, additive variance tends to
be inflated more after a bottleneck. We argue that this result reflects biologically
unrealistic aspects of their models. Specifically, as the number of loci increases,
higher-order epistatic interactions become increasingly important in these models,
with an increasing fraction of the genetic variance becoming nonadditive, contrary
to empirical observations. As shown by Barton and Turelli (2004), without dominance,
conversion of nonadditive to additive variance depends only on the variance components
and not on the number of loci per se. Numerical results indicating that more inbreeding
is needed to produce maximal release of additive variance with more loci follow
directly from our analytical results, which show that high levels of inbreeding
(F > 0.5) are needed for significant conversion of higher-order components.
We discuss alternative approaches to modeling multilocus epistasis and understanding
its consequences.
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Turelli M, Barton NH. Will population bottlenecks and multilocus epistasis
increase additive genetic variance? Evolution; International Journal of Organic
Evolution. 2006;60(9):1763-1776. doi:10.1111/j.0014-3820.2006.tb00521.x
apa: Turelli, M., & Barton, N. H. (2006). Will population bottlenecks and multilocus
epistasis increase additive genetic variance? Evolution; International Journal
of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2006.tb00521.x
chicago: Turelli, Michael, and Nicholas H Barton. “Will Population Bottlenecks and
Multilocus Epistasis Increase Additive Genetic Variance?” Evolution; International
Journal of Organic Evolution. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.0014-3820.2006.tb00521.x.
ieee: M. Turelli and N. H. Barton, “Will population bottlenecks and multilocus epistasis
increase additive genetic variance?,” Evolution; International Journal of Organic
Evolution, vol. 60, no. 9. Wiley-Blackwell, pp. 1763–1776, 2006.
ista: Turelli M, Barton NH. 2006. Will population bottlenecks and multilocus epistasis
increase additive genetic variance? Evolution; International Journal of Organic
Evolution. 60(9), 1763–1776.
mla: Turelli, Michael, and Nicholas H. Barton. “Will Population Bottlenecks and
Multilocus Epistasis Increase Additive Genetic Variance?” Evolution; International
Journal of Organic Evolution, vol. 60, no. 9, Wiley-Blackwell, 2006, pp. 1763–76,
doi:10.1111/j.0014-3820.2006.tb00521.x.
short: M. Turelli, N.H. Barton, Evolution; International Journal of Organic Evolution
60 (2006) 1763–1776.
date_created: 2018-12-11T12:04:13Z
date_published: 2006-09-01T00:00:00Z
date_updated: 2021-01-12T07:44:37Z
day: '01'
doi: 10.1111/j.0014-3820.2006.tb00521.x
extern: 1
intvolume: ' 60'
issue: '9'
month: '09'
page: 1763 - 1776
publication: Evolution; International Journal of Organic Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2776'
quality_controlled: 0
status: public
title: Will population bottlenecks and multilocus epistasis increase additive genetic
variance?
type: journal_article
volume: 60
year: '2006'
...
---
_id: '3683'
abstract:
- lang: eng
text: Many algorithms to remove distortion from document images have be proposed
in recent years, but so far there is no reliable method for comparing their performance.
In this paper we propose a collection of methods to measure the quality of such
restoration algorithms for document image which show a non-linear distortion due
to perspective or page curl. For the result from these measurement to be meaningful,
a common data set of ground truth is required. We therefore started with the buildup
of a document image database that is meant to serve as a common data basis for
all kinds of restoration from images of 3D-shaped document. The long term goal
would be to establish this database and following extensions in the area of document
image dewarping as an as fruitful and indispensable tool as e.g. the NIST database
is for OCR, or the Caltech database is for object and face recognition.
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Thomas
full_name: Breuel,Thomas M
last_name: Breuel
citation:
ama: 'Lampert C, Breuel T. Objective quality measurement for geometric document
image restoration. In: Springer; 2006.'
apa: 'Lampert, C., & Breuel, T. (2006). Objective quality measurement for geometric
document image restoration. Presented at the DAS: Document Analysis Systems, Springer.'
chicago: Lampert, Christoph, and Thomas Breuel. “Objective Quality Measurement for
Geometric Document Image Restoration.” Springer, 2006.
ieee: 'C. Lampert and T. Breuel, “Objective quality measurement for geometric document
image restoration,” presented at the DAS: Document Analysis Systems, 2006.'
ista: 'Lampert C, Breuel T. 2006. Objective quality measurement for geometric document
image restoration. DAS: Document Analysis Systems.'
mla: Lampert, Christoph, and Thomas Breuel. Objective Quality Measurement for
Geometric Document Image Restoration. Springer, 2006.
short: C. Lampert, T. Breuel, in:, Springer, 2006.
conference:
name: 'DAS: Document Analysis Systems'
date_created: 2018-12-11T12:04:36Z
date_published: 2006-03-16T00:00:00Z
date_updated: 2021-01-12T07:45:07Z
day: '16'
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/~chl/papers/lampert-das2006.pdf
month: '03'
publication_status: published
publisher: Springer
publist_id: '2692'
quality_controlled: 0
status: public
title: Objective quality measurement for geometric document image restoration
type: conference
year: '2006'
...
---
_id: '3685'
abstract:
- lang: eng
text: 'Video compression currently is dominated by engineering and fine-tuned heuristic
methods. In this paper, we propose to instead apply the well-developed machinery
of machine learning in order to support the optimization of existing video encoders
and the creation of new ones. Exemplarily, we show how by machine learning we
can improve one encoding step that is crucial for the performance of all current
video standards: macroblock mode decision. By formulating the problem in a Bayesian
setup, we show that macroblock mode decision can be reduced to a classification
problem with a cost function for misclassification that is sample dependent. We
demonstrate how to apply different machine learning techniques to obtain suitable
classifiers and we show in detailed experiments that all of these perform better
than the state-of-the-art heuristic method'
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Lampert C. Machine learning for video compression: Macroblock mode decision.
In: IEEE; 2006:936-940. doi:10.1109/ICPR.2006.778'
apa: 'Lampert, C. (2006). Machine learning for video compression: Macroblock mode
decision (pp. 936–940). Presented at the ICPR: International Conference on Pattern
Recognition, IEEE. https://doi.org/10.1109/ICPR.2006.778'
chicago: 'Lampert, Christoph. “Machine Learning for Video Compression: Macroblock
Mode Decision,” 936–40. IEEE, 2006. https://doi.org/10.1109/ICPR.2006.778.'
ieee: 'C. Lampert, “Machine learning for video compression: Macroblock mode decision,”
presented at the ICPR: International Conference on Pattern Recognition, 2006,
pp. 936–940.'
ista: 'Lampert C. 2006. Machine learning for video compression: Macroblock mode
decision. ICPR: International Conference on Pattern Recognition, 936–940.'
mla: 'Lampert, Christoph. Machine Learning for Video Compression: Macroblock
Mode Decision. IEEE, 2006, pp. 936–40, doi:10.1109/ICPR.2006.778.'
short: C. Lampert, in:, IEEE, 2006, pp. 936–940.
conference:
name: 'ICPR: International Conference on Pattern Recognition'
date_created: 2018-12-11T12:04:37Z
date_published: 2006-09-18T00:00:00Z
date_updated: 2021-01-12T07:45:08Z
day: '18'
doi: 10.1109/ICPR.2006.778
extern: 1
month: '09'
page: 936 - 940
publication_status: published
publisher: IEEE
publist_id: '2689'
quality_controlled: 0
status: public
title: 'Machine learning for video compression: Macroblock mode decision'
type: conference
year: '2006'
...
---
_id: '3750'
abstract:
- lang: eng
text: We applied a single-cell assay to characterize how transcription dynamics
affects protein expression levels of a tetracycline-inducible gene expression
system. Transcriptional activity of the tetracycline promoter in response to a
steady level of inducer is steady in ΔacrAB efflux mutant but pulsating in wildtype
Escherichia coli cells. We found that the expression level of the green fluorescent
protein is several folds higher in ΔacrAB efflux mutant than in wildtype cells.
author:
- first_name: Thuc
full_name: Le,Thuc T.
last_name: Le
- first_name: Calin C
full_name: Calin Guet
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Philippe
full_name: Cluzel,Philippe
last_name: Cluzel
citation:
ama: Le T, Guet CC, Cluzel P. Protein expression enhancement in efflux-deleted mutant
bacteria. Protein Expression and Purification. 2006;48(1):28-31.
apa: Le, T., Guet, C. C., & Cluzel, P. (2006). Protein expression enhancement
in efflux-deleted mutant bacteria. Protein Expression and Purification.
Elsevier.
chicago: Le, Thuc, Calin C Guet, and Philippe Cluzel. “Protein Expression Enhancement
in Efflux-Deleted Mutant Bacteria.” Protein Expression and Purification.
Elsevier, 2006.
ieee: T. Le, C. C. Guet, and P. Cluzel, “Protein expression enhancement in efflux-deleted
mutant bacteria,” Protein Expression and Purification, vol. 48, no. 1.
Elsevier, pp. 28–31, 2006.
ista: Le T, Guet CC, Cluzel P. 2006. Protein expression enhancement in efflux-deleted
mutant bacteria. Protein Expression and Purification. 48(1), 28–31.
mla: Le, Thuc, et al. “Protein Expression Enhancement in Efflux-Deleted Mutant Bacteria.”
Protein Expression and Purification, vol. 48, no. 1, Elsevier, 2006, pp.
28–31.
short: T. Le, C.C. Guet, P. Cluzel, Protein Expression and Purification 48 (2006)
28–31.
date_created: 2018-12-11T12:04:58Z
date_published: 2006-07-01T00:00:00Z
date_updated: 2021-01-12T07:51:56Z
day: '01'
extern: 1
intvolume: ' 48'
issue: '1'
month: '07'
page: 28 - 31
publication: Protein Expression and Purification
publication_status: published
publisher: Elsevier
publist_id: '2478'
quality_controlled: 0
status: public
title: Protein expression enhancement in efflux-deleted mutant bacteria
type: journal_article
volume: 48
year: '2006'
...
---
_id: '3767'
abstract:
- lang: eng
text: Models of RNA secondary structure folding are widely used to study evolution
in theory and simulation. However, systematic studies of the parameters involved
are rare. In this paper, we study by simulation how RNA evolution is influenced
by three different factors, namely the mutation rate, scaling of the fitness function,
and distance measure. We found that for low mutation rates the qualitative evolutionary
behavior is robust with respect to the scaling of the fitness function. For efficient
mutation rates, which are close to the error threshold, scaling and distance measure
have a strong influence on the evolutionary behavior. A global distance measure
that takes sequence information additively into account lowers the error threshold.
When using a local sequence-structure alignment for the distance, we observed
a smoother evolution of the fitness over time. Finally, in addition to the well
known error threshold, we identify another threshold of the mutation rate, called
divergence threshold, where the qualitative transient behavior changes from a
localized to an exploratory search.
author:
- first_name: Anne
full_name: Anne Kupczok
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Peter
full_name: Dittrich,Peter
last_name: Dittrich
citation:
ama: Kupczok A, Dittrich P. Determinants of simulated RNA evolution. Journal
of Theoretical Biology. 2006;238(3):726-735. doi:10.1016/j.jtbi.2005.06.019
apa: Kupczok, A., & Dittrich, P. (2006). Determinants of simulated RNA evolution.
Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2005.06.019
chicago: Kupczok, Anne, and Peter Dittrich. “Determinants of Simulated RNA Evolution.”
Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/10.1016/j.jtbi.2005.06.019.
ieee: A. Kupczok and P. Dittrich, “Determinants of simulated RNA evolution.,” Journal
of Theoretical Biology, vol. 238, no. 3. Elsevier, pp. 726–35, 2006.
ista: Kupczok A, Dittrich P. 2006. Determinants of simulated RNA evolution. Journal
of Theoretical Biology. 238(3), 726–35.
mla: Kupczok, Anne, and Peter Dittrich. “Determinants of Simulated RNA Evolution.”
Journal of Theoretical Biology, vol. 238, no. 3, Elsevier, 2006, pp. 726–35,
doi:10.1016/j.jtbi.2005.06.019.
short: A. Kupczok, P. Dittrich, Journal of Theoretical Biology 238 (2006) 726–35.
date_created: 2018-12-11T12:05:03Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:03Z
day: '01'
doi: 10.1016/j.jtbi.2005.06.019
extern: 1
intvolume: ' 238'
issue: '3'
month: '01'
page: 726 - 35
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '2461'
quality_controlled: 0
status: public
title: Determinants of simulated RNA evolution.
type: journal_article
volume: 238
year: '2006'
...
---
_id: '3813'
abstract:
- lang: eng
text: Hyperpolarization-activated channels (Ih or HCN channels) are widely expressed
in principal neurons in the central nervous system. However, Ih in inhibitory
GABAergic interneurons is less well characterized. We examined the functional
properties of Ih in fast-spiking basket cells (BCs) of the dentate gyrus, using
hippocampal slices from 17- to 21-day-old rats. Bath application of the Ih channel
blocker ZD 7288 at a concentration of 30 microm induced a hyperpolarization of
5.7 +/- 1.5 mV, an increase in input resistance and a correlated increase in apparent
membrane time constant. ZD 7288 blocked a hyperpolarization-activated current
in a concentration-dependent manner (IC50, 1.4 microm). The effects of ZD 7288
were mimicked by external Cs+. The reversal potential of Ih was -27.4 mV, corresponding
to a Na+ to K+ permeability ratio (PNa/PK) of 0.36. The midpoint potential of
the activation curve of Ih was -83.9 mV, and the activation time constant at -120
mV was 190 ms. Single-cell expression analysis using reverse transcription followed
by quantitative polymerase chain reaction revealed that BCs coexpress HCN1 and
HCN2 subunit mRNA, suggesting the formation of heteromeric HCN1/2 channels. ZD
7288 increased the current threshold for evoking antidromic action potentials
by extracellular stimulation, consistent with the expression of Ih in BC axons.
Finally, ZD 7288 decreased the frequency of miniature inhibitory postsynaptic
currents (mIPSCs) in hippocampal granule cells, the main target cells of BCs,
to 70 +/- 4% of the control value. In contrast, the amplitude of mIPSCs was unchanged,
consistent with the presence of Ih in inhibitory terminals. In conclusion, our
results suggest that Ih channels are expressed in the somatodendritic region,
axon and presynaptic elements of fast-spiking BCs in the hippocampus.
author:
- first_name: Yexica
full_name: Aponte, Yexica
last_name: Aponte
- first_name: Cheng
full_name: Lien, Cheng-Chang
last_name: Lien
- first_name: Ellen
full_name: Reisinger, Ellen
last_name: Reisinger
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Aponte Y, Lien C, Reisinger E, Jonas PM. Hyperpolarization-activated cation
channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology.
2006;574(Pt 1):229-243. doi:10.1113/jphysiol.2005.104042
apa: Aponte, Y., Lien, C., Reisinger, E., & Jonas, P. M. (2006). Hyperpolarization-activated
cation channels in fast-spiking interneurons of rat hippocampus. Journal of
Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2005.104042
chicago: Aponte, Yexica, Cheng Lien, Ellen Reisinger, and Peter M Jonas. “Hyperpolarization-Activated
Cation Channels in Fast-Spiking Interneurons of Rat Hippocampus.” Journal of
Physiology. Wiley-Blackwell, 2006. https://doi.org/10.1113/jphysiol.2005.104042.
ieee: Y. Aponte, C. Lien, E. Reisinger, and P. M. Jonas, “Hyperpolarization-activated
cation channels in fast-spiking interneurons of rat hippocampus,” Journal of
Physiology, vol. 574, no. Pt 1. Wiley-Blackwell, pp. 229–43, 2006.
ista: Aponte Y, Lien C, Reisinger E, Jonas PM. 2006. Hyperpolarization-activated
cation channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology.
574(Pt 1), 229–43.
mla: Aponte, Yexica, et al. “Hyperpolarization-Activated Cation Channels in Fast-Spiking
Interneurons of Rat Hippocampus.” Journal of Physiology, vol. 574, no.
Pt 1, Wiley-Blackwell, 2006, pp. 229–43, doi:10.1113/jphysiol.2005.104042.
short: Y. Aponte, C. Lien, E. Reisinger, P.M. Jonas, Journal of Physiology 574 (2006)
229–43.
date_created: 2018-12-11T12:05:19Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:23Z
day: '01'
doi: 10.1113/jphysiol.2005.104042
extern: 1
intvolume: ' 574'
issue: Pt 1
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1817792/
month: '01'
oa: 1
page: 229 - 43
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2397'
quality_controlled: 0
status: public
title: Hyperpolarization-activated cation channels in fast-spiking interneurons of
rat hippocampus
type: journal_article
volume: 574
year: '2006'
...
---
_id: '3814'
abstract:
- lang: eng
text: The axon terminals (mossy fibers) of hippocampal dentate granule cells form
characteristic synaptic connections with large spines or excrescences of both
hilar mossy cells and CA3 pyramidal neurons. Interneurons of the hilar region
and area CA3 are also prominent targets of mossy fibers. The tracing of biocytin-filled
mossy fibers and immunolabeling of target cells with interneuron markers has revealed
that the majority of mossy fiber synapses project to gamma aminobutyric acid (GABA)-ergic
inhibitory interneurons rather than to excitatory principal cells, although the
functional implications of these quantitative differences are unclear. Following
a brief description of the "classical" mossy fiber synapse on excrescences
of CA3 pyramidal cells, the present review focuses on the contacts formed between
granule cells and GABAergic interneurons, both normally and after synaptic reorganization.
In response to deafferentation of mossy cell target cells, which include both
granule cells and interneurons, mossy fibers "sprout" new axon collaterals
that form a band of supragranular mossy fibers in the inner molecular layer of
the dentate gyrus. Although most newly formed recurrent mossy fibers establish
synapses with granule cells, there is an apparently convergent input of new mossy
fibers onto GABA-immunoreactive interneuron dendrites that traverse the inner
molecular layer. These mossy fiber-interneuron synapses in the dentate gyrus are
observed in chronically epileptic rats and may be the structural correlate of
the granule cell hyperinhibition observed in these animals in vivo. Together,
the findings reviewed here establish mossy fiber synapses as an important component
of inhibitory circuits in the hippocampus.
author:
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Robert
full_name: Sloviter, Robert S
last_name: Sloviter
citation:
ama: Frotscher M, Jonas PM, Sloviter R. Synapses formed by normal and abnormal hippocampal
mossy fibers (Review). Cell and Tissue Research. 2006;326(2):361-367. doi:10.1007/s00441-006-0269-2
apa: Frotscher, M., Jonas, P. M., & Sloviter, R. (2006). Synapses formed by
normal and abnormal hippocampal mossy fibers (Review). Cell and Tissue Research.
Springer. https://doi.org/10.1007/s00441-006-0269-2
chicago: Frotscher, Michael, Peter M Jonas, and Robert Sloviter. “Synapses Formed
by Normal and Abnormal Hippocampal Mossy Fibers (Review).” Cell and Tissue
Research. Springer, 2006. https://doi.org/10.1007/s00441-006-0269-2.
ieee: M. Frotscher, P. M. Jonas, and R. Sloviter, “Synapses formed by normal and
abnormal hippocampal mossy fibers (Review),” Cell and Tissue Research,
vol. 326, no. 2. Springer, pp. 361–7, 2006.
ista: Frotscher M, Jonas PM, Sloviter R. 2006. Synapses formed by normal and abnormal
hippocampal mossy fibers (Review). Cell and Tissue Research. 326(2), 361–7.
mla: Frotscher, Michael, et al. “Synapses Formed by Normal and Abnormal Hippocampal
Mossy Fibers (Review).” Cell and Tissue Research, vol. 326, no. 2, Springer,
2006, pp. 361–67, doi:10.1007/s00441-006-0269-2.
short: M. Frotscher, P.M. Jonas, R. Sloviter, Cell and Tissue Research 326 (2006)
361–7.
date_created: 2018-12-11T12:05:19Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2019-04-26T07:22:35Z
day: '01'
doi: 10.1007/s00441-006-0269-2
extern: 1
intvolume: ' 326'
issue: '2'
month: '01'
page: 361 - 7
publication: Cell and Tissue Research
publication_status: published
publisher: Springer
publist_id: '2395'
quality_controlled: 0
status: public
title: Synapses formed by normal and abnormal hippocampal mossy fibers (Review)
type: review
volume: 326
year: '2006'
...
---
_id: '3815'
abstract:
- lang: eng
text: It is widely accepted that the hippocampus plays a major role in learning
and memory. The mossy fiber synapse between granule cells in the dentate gyrus
and pyramidal neurons in the CA3 region is a key component of the hippocampal
trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp
recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms
of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+)
channel density in mossy fiber boutons leads to a large amplitude of the presynaptic
action potential. Together with the fast gating of presynaptic Ca(2+) channels,
this generates a large and brief presynaptic Ca(2+) influx, which can trigger
transmitter release with high efficiency and temporal precision. The large number
of release sites, the large size of the releasable pool of vesicles, and the huge
extent of presynaptic plasticity confer unique strength to this synapse, suggesting
a large impact onto the CA3 pyramidal cell network under specific behavioral conditions.
The characteristic properties of the hippocampal mossy fiber synapse may be important
for pattern separation and information storage in the dentate gyrus-CA3 cell network.
author:
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
- first_name: Dominique
full_name: Engel, Dominique
last_name: Engel
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. Timing and efficacy of transmitter
release at mossy fiber synapses in the hippocampal network. Pflugers Archiv :
European Journal of Physiology. 2006;453(3):361-372. doi:10.1007/s00424-006-0093-2'
apa: 'Bischofberger, J., Engel, D., Frotscher, M., & Jonas, P. M. (2006). Timing
and efficacy of transmitter release at mossy fiber synapses in the hippocampal
network. Pflugers Archiv : European Journal of Physiology. Springer. https://doi.org/10.1007/s00424-006-0093-2'
chicago: 'Bischofberger, Josef, Dominique Engel, Michael Frotscher, and Peter M
Jonas. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in
the Hippocampal Network.” Pflugers Archiv : European Journal of Physiology.
Springer, 2006. https://doi.org/10.1007/s00424-006-0093-2.'
ieee: 'J. Bischofberger, D. Engel, M. Frotscher, and P. M. Jonas, “Timing and efficacy
of transmitter release at mossy fiber synapses in the hippocampal network,” Pflugers
Archiv : European Journal of Physiology, vol. 453, no. 3. Springer, pp. 361–72,
2006.'
ista: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. 2006. Timing and efficacy
of transmitter release at mossy fiber synapses in the hippocampal network. Pflugers
Archiv : European Journal of Physiology. 453(3), 361–72.'
mla: 'Bischofberger, Josef, et al. “Timing and Efficacy of Transmitter Release at
Mossy Fiber Synapses in the Hippocampal Network.” Pflugers Archiv : European
Journal of Physiology, vol. 453, no. 3, Springer, 2006, pp. 361–72, doi:10.1007/s00424-006-0093-2.'
short: 'J. Bischofberger, D. Engel, M. Frotscher, P.M. Jonas, Pflugers Archiv :
European Journal of Physiology 453 (2006) 361–72.'
date_created: 2018-12-11T12:05:19Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:24Z
day: '01'
doi: 10.1007/s00424-006-0093-2
extern: 1
intvolume: ' 453'
issue: '3'
month: '01'
page: 361 - 72
publication: 'Pflugers Archiv : European Journal of Physiology'
publication_status: published
publisher: Springer
publist_id: '2396'
quality_controlled: 0
status: public
title: Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal
network
type: journal_article
volume: 453
year: '2006'
...
---
_id: '3811'
abstract:
- lang: eng
text: Networks of GABAergic neurons are key elements in the generation of gamma
oscillations in the brain. Computational studies suggested that the emergence
of coherent oscillations requires hyperpolarizing inhibition. Here, we show that
GABA(A) receptor-mediated inhibition in mature interneurons of the hippocampal
dentate gyrus is shunting rather than hyperpolarizing. Unexpectedly, when shunting
inhibition is incorporated into a structured interneuron network model with fast
and strong synapses, coherent oscillations emerge. In comparison to hyperpolarizing
inhibition, networks with shunting inhibition show several advantages. First,
oscillations are generated with smaller tonic excitatory drive. Second, network
frequencies are tuned to the gamma band. Finally, robustness against heterogeneity
in the excitatory drive is markedly improved. In single interneurons, shunting
inhibition shortens the interspike interval for low levels of drive but prolongs
it for high levels, leading to homogenization of neuronal firing rates. Thus,
shunting inhibition may confer increased robustness to gamma oscillations in the
brain.
author:
- first_name: Imre
full_name: Vida, Imre
last_name: Vida
- first_name: Marlene
full_name: Bartos, Marlene
last_name: Bartos
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Vida I, Bartos M, Jonas PM. Shunting inhibition improves robustness of gamma
oscillations in hippocampal interneuron networks by homogenizing firing rates.
Neuron. 2006;49(1):107-117. doi:10.1016/j.neuron.2005.11.036
apa: Vida, I., Bartos, M., & Jonas, P. M. (2006). Shunting inhibition improves
robustness of gamma oscillations in hippocampal interneuron networks by homogenizing
firing rates. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2005.11.036
chicago: Vida, Imre, Marlene Bartos, and Peter M Jonas. “Shunting Inhibition Improves
Robustness of Gamma Oscillations in Hippocampal Interneuron Networks by Homogenizing
Firing Rates.” Neuron. Elsevier, 2006. https://doi.org/10.1016/j.neuron.2005.11.036.
ieee: I. Vida, M. Bartos, and P. M. Jonas, “Shunting inhibition improves robustness
of gamma oscillations in hippocampal interneuron networks by homogenizing firing
rates,” Neuron, vol. 49, no. 1. Elsevier, pp. 107–17, 2006.
ista: Vida I, Bartos M, Jonas PM. 2006. Shunting inhibition improves robustness
of gamma oscillations in hippocampal interneuron networks by homogenizing firing
rates. Neuron. 49(1), 107–17.
mla: Vida, Imre, et al. “Shunting Inhibition Improves Robustness of Gamma Oscillations
in Hippocampal Interneuron Networks by Homogenizing Firing Rates.” Neuron,
vol. 49, no. 1, Elsevier, 2006, pp. 107–17, doi:10.1016/j.neuron.2005.11.036.
short: I. Vida, M. Bartos, P.M. Jonas, Neuron 49 (2006) 107–17.
date_created: 2018-12-11T12:05:18Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:22Z
day: '01'
doi: 10.1016/j.neuron.2005.11.036
extern: 1
intvolume: ' 49'
issue: '1'
month: '01'
page: 107 - 17
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2398'
quality_controlled: 0
status: public
title: Shunting inhibition improves robustness of gamma oscillations in hippocampal
interneuron networks by homogenizing firing rates
type: journal_article
volume: 49
year: '2006'
...
---
_id: '3817'
author:
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Eckart
full_name: Gundelfinger, Eckart
last_name: Gundelfinger
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Erwin
full_name: Neher, Erwin
last_name: Neher
- first_name: Peter
full_name: Seeburg, Peter
last_name: Seeburg
citation:
ama: Frotscher M, Gundelfinger E, Jonas PM, Neher E, Seeburg P. The most important
recent advances in synapse research from my point of view--and what remains to
be done. Cell and Tissue Research. 2006;326(2):203-204. doi:10.1007/s00441-006-0325-y
apa: Frotscher, M., Gundelfinger, E., Jonas, P. M., Neher, E., & Seeburg, P.
(2006). The most important recent advances in synapse research from my point of
view--and what remains to be done. Cell and Tissue Research. Springer.
https://doi.org/10.1007/s00441-006-0325-y
chicago: Frotscher, Michael, Eckart Gundelfinger, Peter M Jonas, Erwin Neher, and
Peter Seeburg. “The Most Important Recent Advances in Synapse Research from My
Point of View--and What Remains to Be Done.” Cell and Tissue Research.
Springer, 2006. https://doi.org/10.1007/s00441-006-0325-y.
ieee: M. Frotscher, E. Gundelfinger, P. M. Jonas, E. Neher, and P. Seeburg, “The
most important recent advances in synapse research from my point of view--and
what remains to be done,” Cell and Tissue Research, vol. 326, no. 2. Springer,
pp. 203–4, 2006.
ista: Frotscher M, Gundelfinger E, Jonas PM, Neher E, Seeburg P. 2006. The most
important recent advances in synapse research from my point of view--and what
remains to be done. Cell and Tissue Research. 326(2), 203–4.
mla: Frotscher, Michael, et al. “The Most Important Recent Advances in Synapse Research
from My Point of View--and What Remains to Be Done.” Cell and Tissue Research,
vol. 326, no. 2, Springer, 2006, pp. 203–04, doi:10.1007/s00441-006-0325-y.
short: M. Frotscher, E. Gundelfinger, P.M. Jonas, E. Neher, P. Seeburg, Cell and
Tissue Research 326 (2006) 203–4.
date_created: 2018-12-11T12:05:20Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:24Z
day: '01'
doi: 10.1007/s00441-006-0325-y
extern: 1
intvolume: ' 326'
issue: '2'
month: '01'
page: 203 - 4
publication: Cell and Tissue Research
publication_status: published
publisher: Springer
publist_id: '2394'
quality_controlled: 0
status: public
title: The most important recent advances in synapse research from my point of view--and
what remains to be done
type: journal_article
volume: 326
year: '2006'
...
---
_id: '3912'
abstract:
- lang: eng
text: Invasive species often dramatically change native species communities by directly
and indirectly out-competing native species. We studied the direct interference
abilities of the invasive garden ant, Lasius neglectus VAN LOON, BOOMSMA &
ANDRÁSFALVY, 1990, by performing one-to-one aggression tests of L. neglectus workers
towards three native Lasius ant species that occur at the edge of a L. neglectus
supercolony in Seva, Spain. Our results show that L. neglectus is highly aggressive
against all three native Lasius species tested (L. grandis FOREL, 1909, L. emarginatus
(OLIVIER, 1792), and L. cinereus SEIFERT, 1992), expressed as a higher attack
rate of L. neglectus and behavioural dominance throughout the aggressive encounters.
Attacks of L. neglectus were performed fastest and most frequent against L. grandis,
and also the highest antennation frequencies were observed in encounters between
these two species. This could be due to the largest difference in body size, or
due to a greater overlap in ecological niche between L. neglectus and L. grandis
compared to the other two native species. There was only weak support for L. neglectus
workers from the periphery of the supercolony to be more aggressive relative to
workers from the centre, even though the former encounter native ant species on
a daily basis at the edge of the supercolony.
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Suzanne
full_name: Lommen, Suzanne
last_name: Lommen
- first_name: Klaus
full_name: Petersen, Klaus
last_name: Petersen
- first_name: Jes
full_name: Pedersen, Jes
last_name: Pedersen
citation:
ama: 'Cremer S, Ugelvig LV, Lommen S, Petersen K, Pedersen J. Attack of the invasive
garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae)
against native Lasius species in Spain. Myrmecological News. 2006;9:13-19.'
apa: 'Cremer, S., Ugelvig, L. V., Lommen, S., Petersen, K., & Pedersen, J. (2006).
Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera:
Formicidae) against native Lasius species in Spain. Myrmecological News.
Österreichische Gesellschaft für Entomofaunistik.'
chicago: 'Cremer, Sylvia, Line V Ugelvig, Suzanne Lommen, Klaus Petersen, and Jes
Pedersen. “Attack of the Invasive Garden Ant: Aggression Behaviour of Lasius Neglectus
(Hymenoptera: Formicidae) against Native Lasius Species in Spain.” Myrmecological
News. Österreichische Gesellschaft für Entomofaunistik, 2006.'
ieee: 'S. Cremer, L. V. Ugelvig, S. Lommen, K. Petersen, and J. Pedersen, “Attack
of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera:
Formicidae) against native Lasius species in Spain,” Myrmecological News,
vol. 9. Österreichische Gesellschaft für Entomofaunistik, pp. 13–19, 2006.'
ista: 'Cremer S, Ugelvig LV, Lommen S, Petersen K, Pedersen J. 2006. Attack of the
invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae)
against native Lasius species in Spain. Myrmecological News. 9, 13–19.'
mla: 'Cremer, Sylvia, et al. “Attack of the Invasive Garden Ant: Aggression Behaviour
of Lasius Neglectus (Hymenoptera: Formicidae) against Native Lasius Species in
Spain.” Myrmecological News, vol. 9, Österreichische Gesellschaft für Entomofaunistik,
2006, pp. 13–19.'
short: S. Cremer, L.V. Ugelvig, S. Lommen, K. Petersen, J. Pedersen, Myrmecological
News 9 (2006) 13–19.
date_created: 2018-12-11T12:05:51Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2021-01-12T07:53:09Z
day: '01'
extern: '1'
intvolume: ' 9'
language:
- iso: eng
month: '12'
oa_version: None
page: 13 - 19
publication: Myrmecological News
publication_status: published
publisher: Österreichische Gesellschaft für Entomofaunistik
publist_id: '2239'
status: public
title: 'Attack of the invasive garden ant: aggression behaviour of Lasius neglectus
(Hymenoptera: Formicidae) against native Lasius species in Spain'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2006'
...
---
_id: '3914'
abstract:
- lang: eng
text: We compare the performances of established means of character selection for
discriminant analysis in species distinction with a combination procedure for
finding the optimal character combination (minimum classification error, minimum
number of required characters), using morphometric data sets from the ant genera
Cardiocondyla, Lasius and Tetramorium. The established methods are empirical character
selection as well as forward selection, backward elimination and stepwise selection
of discriminant analysis. The combination procedure is clearly superior to the
established methods of character selection, and is widely applicable.
author:
- first_name: Karl
full_name: Moder, Karl
last_name: Moder
- first_name: Birgit
full_name: Schlick Steiner, Birgit
last_name: Schlick Steiner
- first_name: Florian
full_name: Steiner, Florian
last_name: Steiner
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Erhard
full_name: Christian, Erhard
last_name: Christian
- first_name: Bernhard
full_name: Seifert, Bernhard
last_name: Seifert
citation:
ama: 'Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B. Optimal
species distinction by discriminant analysis: comparing established methods of
character selection with a combination procedure using ant morphometrics as a
case study. Journal of Zoological Systematics and Evolutionary Research.
2006;45(1):82-87. doi:10.1111/j.1439-0469.2006.00372.x'
apa: 'Moder, K., Schlick Steiner, B., Steiner, F., Cremer, S., Christian, E., &
Seifert, B. (2006). Optimal species distinction by discriminant analysis: comparing
established methods of character selection with a combination procedure using
ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary
Research. Wiley-Blackwell. https://doi.org/10.1111/j.1439-0469.2006.00372.x'
chicago: 'Moder, Karl, Birgit Schlick Steiner, Florian Steiner, Sylvia Cremer, Erhard
Christian, and Bernhard Seifert. “Optimal Species Distinction by Discriminant
Analysis: Comparing Established Methods of Character Selection with a Combination
Procedure Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics
and Evolutionary Research. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.1439-0469.2006.00372.x.'
ieee: 'K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, and B.
Seifert, “Optimal species distinction by discriminant analysis: comparing established
methods of character selection with a combination procedure using ant morphometrics
as a case study,” Journal of Zoological Systematics and Evolutionary Research,
vol. 45, no. 1. Wiley-Blackwell, pp. 82–87, 2006.'
ista: 'Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B.
2006. Optimal species distinction by discriminant analysis: comparing established
methods of character selection with a combination procedure using ant morphometrics
as a case study. Journal of Zoological Systematics and Evolutionary Research.
45(1), 82–87.'
mla: 'Moder, Karl, et al. “Optimal Species Distinction by Discriminant Analysis:
Comparing Established Methods of Character Selection with a Combination Procedure
Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics
and Evolutionary Research, vol. 45, no. 1, Wiley-Blackwell, 2006, pp. 82–87,
doi:10.1111/j.1439-0469.2006.00372.x.'
short: K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, B. Seifert,
Journal of Zoological Systematics and Evolutionary Research 45 (2006) 82–87.
date_created: 2018-12-11T12:05:52Z
date_published: 2006-08-29T00:00:00Z
date_updated: 2021-01-12T07:53:10Z
day: '29'
doi: 10.1111/j.1439-0469.2006.00372.x
extern: '1'
intvolume: ' 45'
issue: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 82 - 87
publication: Journal of Zoological Systematics and Evolutionary Research
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2241'
status: public
title: 'Optimal species distinction by discriminant analysis: comparing established
methods of character selection with a combination procedure using ant morphometrics
as a case study'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2006'
...
---
_id: '3913'
abstract:
- lang: eng
text: Many invasive ant species, such as the Argentine ant or the red imported fire
ant, have huge colonies with thousands of mass-foraging workers, which quickly
monopolise resources and therefore represent a considerable threat to the native
ant fauna. Cardiocondyla obscurior and several other species of this myrmicine
genus have similarly been transferred throughout the tropics by human activities.
However, because their colonies are tiny and workers forage solitarily, Cardiocondyla
are often not recognized as successful invaders. Here, we document that the life
history of Cardiocondyla closely resembles that of the more conspicuous tramp
species, with polygyny, intranidal mating, budding, worker sterility, low genetic
variability, and possibly also unicoloniality. Given that introduced Cardiocondyla
may locally reach a very high population density, the effects of these stealthy
invaders on the native arthropod fauna should receive more attention.
author:
- 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
- first_name: Norbert
full_name: Eckl, Norbert
last_name: Eckl
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
citation:
ama: 'Heinze J, Cremer S, Eckl N, Schrempf A. Stealthy invaders: the biology of
Cardiocondyla tramp ants. Insectes Sociaux. 2006;53(1):1-7. doi:10.1007/s00040-005-0847-4'
apa: 'Heinze, J., Cremer, S., Eckl, N., & Schrempf, A. (2006). Stealthy invaders:
the biology of Cardiocondyla tramp ants. Insectes Sociaux. Springer. https://doi.org/10.1007/s00040-005-0847-4'
chicago: 'Heinze, Jürgen, Sylvia Cremer, Norbert Eckl, and Alexandra Schrempf. “Stealthy
Invaders: The Biology of Cardiocondyla Tramp Ants.” Insectes Sociaux. Springer,
2006. https://doi.org/10.1007/s00040-005-0847-4.'
ieee: 'J. Heinze, S. Cremer, N. Eckl, and A. Schrempf, “Stealthy invaders: the biology
of Cardiocondyla tramp ants,” Insectes Sociaux, vol. 53, no. 1. Springer,
pp. 1–7, 2006.'
ista: 'Heinze J, Cremer S, Eckl N, Schrempf A. 2006. Stealthy invaders: the biology
of Cardiocondyla tramp ants. Insectes Sociaux. 53(1), 1–7.'
mla: 'Heinze, Jürgen, et al. “Stealthy Invaders: The Biology of Cardiocondyla Tramp
Ants.” Insectes Sociaux, vol. 53, no. 1, Springer, 2006, pp. 1–7, doi:10.1007/s00040-005-0847-4.'
short: J. Heinze, S. Cremer, N. Eckl, A. Schrempf, Insectes Sociaux 53 (2006) 1–7.
date_created: 2018-12-11T12:05:51Z
date_published: 2006-02-01T00:00:00Z
date_updated: 2021-01-12T07:53:09Z
day: '01'
doi: 10.1007/s00040-005-0847-4
extern: '1'
intvolume: ' 53'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 1 - 7
publication: Insectes Sociaux
publication_status: published
publisher: Springer
publist_id: '2240'
status: public
title: 'Stealthy invaders: the biology of Cardiocondyla tramp ants'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2006'
...
---
_id: '3932'
abstract:
- lang: eng
text: 'OBJECTIVES: The EGFR is expressed in malignant ovarian tumor tissue, and
tissue content of EGFR has been directly associated with poor prognosis in patients
with ovarian cancer. The uPA system plays a role in pericellular proteolysis,
cell migration, invasion, and is over-expressed in ovarian cancer. This study
explored the effects of EGF on uPAR expression in the ovarian cancer cell line
OVCAR-3. METHODS: We used OVCAR-3 cells and the following methods: cell migration
assay, time-lapse video microscopy, real-time PCR, assays for cellular binding
of 125I-uPA and cellular degradation of 125I-uPA:PAI-1 complex, biosynthetic labeling
using 35S-methionin, Western blot, Northern blot, and ELISAs for uPA, PAI-1, and
uPAR. RESULTS: EGF up-regulates both protein and mRNA not only for uPAR, but also
for the ligand uPA and its inhibitor PAI-1. Cell surface uPAR, in control as well
as EGF-stimulated cells, is present only in the intact, not the cleaved, form.
Ligand binding experiments showed an increase of endogenously occupied uPAR, whereas
non-occupied receptor sites were not increased. In addition, EGF treatment resulted
in decreased degradation of radiolabeled uPA:PAI-1 complex. This suggests decreased
internalization of uPAR, since the complex is internalized together with uPAR.
Like EGF, colchicine, which inhibits endocytosis, increased cell surface expression
of uPAR. In addition, we found an immediate increase of uPAR after exposing the
cells to EGF and this was accompanied by a transient increase of cell migration.
The increase of cell surface uPAR in response to EGF is accompanied by increased
release of the soluble form of uPAR (suPAR) to the medium as well as by increased
cell migration. Both uPAR and suPAR increased in cells treated with the endocytosis
inhibitor colchicine even though cell migration was inhibited, suggesting that
the mechanism of uPAR shedding is not related to cell migration. CONCLUSION: Increased
cell surface uPAR in response to EGF stimulation results from mobilization of
uPAR from detergent-resistant domains, increased expression of uPAR mRNA, and
decreased internalization and degradation of uPAR. Both the anti-uPAR antibody
R3, which inhibits binding of uPA, and the EGFR phosphorylation inhibitor Iressa
inhibited cell migration in response to uPA as well as to EGF, suggesting that
EGFR and uPAR are engaged in the same multiprotein assembly on the cell surface.'
author:
- first_name: Emir
full_name: Henic, Emir
last_name: Henic
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Stefan
full_name: Hansson, Stefan
last_name: Hansson
- first_name: Gunilla
full_name: Høyer-Hansen, Gunilla
last_name: Høyer Hansen
- first_name: Bertil
full_name: Casslén, Bertil
last_name: Casslén
citation:
ama: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. EGF-stimulated migration
in ovarian cancer cells is associated with decreased internalization, increased
surface expression, and increased shedding of the urokinase plasminogen activator
receptor. Gynecologic Oncology. 2006;101(1):28-39. doi:10.1016/j.ygyno.2005.09.038
apa: Henic, E., Sixt, M. K., Hansson, S., Høyer Hansen, G., & Casslén, B. (2006).
EGF-stimulated migration in ovarian cancer cells is associated with decreased
internalization, increased surface expression, and increased shedding of the urokinase
plasminogen activator receptor. Gynecologic Oncology. Elsevier. https://doi.org/10.1016/j.ygyno.2005.09.038
chicago: Henic, Emir, Michael K Sixt, Stefan Hansson, Gunilla Høyer Hansen, and
Bertil Casslén. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated
with Decreased Internalization, Increased Surface Expression, and Increased Shedding
of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology.
Elsevier, 2006. https://doi.org/10.1016/j.ygyno.2005.09.038.
ieee: E. Henic, M. K. Sixt, S. Hansson, G. Høyer Hansen, and B. Casslén, “EGF-stimulated
migration in ovarian cancer cells is associated with decreased internalization,
increased surface expression, and increased shedding of the urokinase plasminogen
activator receptor,” Gynecologic Oncology, vol. 101, no. 1. Elsevier, pp.
28–39, 2006.
ista: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. 2006. EGF-stimulated
migration in ovarian cancer cells is associated with decreased internalization,
increased surface expression, and increased shedding of the urokinase plasminogen
activator receptor. Gynecologic Oncology. 101(1), 28–39.
mla: Henic, Emir, et al. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated
with Decreased Internalization, Increased Surface Expression, and Increased Shedding
of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology,
vol. 101, no. 1, Elsevier, 2006, pp. 28–39, doi:10.1016/j.ygyno.2005.09.038.
short: E. Henic, M.K. Sixt, S. Hansson, G. Høyer Hansen, B. Casslén, Gynecologic
Oncology 101 (2006) 28–39.
date_created: 2018-12-11T12:05:57Z
date_published: 2006-04-01T00:00:00Z
date_updated: 2021-01-12T07:53:17Z
day: '01'
doi: 10.1016/j.ygyno.2005.09.038
extern: 1
intvolume: ' 101'
issue: '1'
month: '04'
page: 28 - 39
publication: Gynecologic Oncology
publication_status: published
publisher: Elsevier
publist_id: '2194'
quality_controlled: 0
status: public
title: EGF-stimulated migration in ovarian cancer cells is associated with decreased
internalization, increased surface expression, and increased shedding of the urokinase
plasminogen activator receptor
type: journal_article
volume: 101
year: '2006'
...
---
_id: '3978'
abstract:
- lang: eng
text: Evaluating the quality of experimentally determined protein structural models
is an essential step toward identifying potential errors and guiding further structural
refinement. Herein, we report the use of proton local density as a sensitive measure
to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256
high-resolution crystal structures with protons added and optimized, we show that
the local density of different proton types display distinct distributions. These
distributions can be characterized by statistical moments and are used to establish
local density Z-scores for evaluating both global and local packing for individual
protons. Analysis of 546 crystal structures at various resolutions shows that
the local density Z-scores increase as the structural resolution decreases and
correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733)
generated by all atom contact analysis. Local density Z-scores for NMR structures
exhibit a significantly wider range of values than for X-ray structures and demonstrate
a combination of potentially problematic inflation and compression. Water-refined
NMR structures show improved packing quality. Our analysis of a high-quality structural
ensemble of ubiquitin refined against order parameters shows proton density distributions
that correlate nearly perfectly with our standards derived from crystal structures,
further validating our approach. We present an automated analysis and visualization
tool for proton packing to evaluate the quality of NMR structures.
author:
- first_name: Yih
full_name: Ban, Yih-En Andrew
last_name: Ban
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
- first_name: Pei
full_name: Zhou, Pei
last_name: Zhou
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. Evaluating the quality of NMR structures
by local density of protons. Proteins: Structure, Function and Bioinformatics.
2006;62(4):852-864. doi:10.1002/prot.20811'
apa: 'Ban, Y., Rudolph, J., Zhou, P., & Edelsbrunner, H. (2006). Evaluating
the quality of NMR structures by local density of protons. Proteins: Structure,
Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.20811'
chicago: 'Ban, Yih, Johannes Rudolph, Pei Zhou, and Herbert Edelsbrunner. “Evaluating
the Quality of NMR Structures by Local Density of Protons.” Proteins: Structure,
Function and Bioinformatics. Wiley-Blackwell, 2006. https://doi.org/10.1002/prot.20811.'
ieee: 'Y. Ban, J. Rudolph, P. Zhou, and H. Edelsbrunner, “Evaluating the quality
of NMR structures by local density of protons,” Proteins: Structure, Function
and Bioinformatics, vol. 62, no. 4. Wiley-Blackwell, pp. 852–864, 2006.'
ista: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. 2006. Evaluating the quality of
NMR structures by local density of protons. Proteins: Structure, Function and
Bioinformatics. 62(4), 852–864.'
mla: 'Ban, Yih, et al. “Evaluating the Quality of NMR Structures by Local Density
of Protons.” Proteins: Structure, Function and Bioinformatics, vol. 62,
no. 4, Wiley-Blackwell, 2006, pp. 852–64, doi:10.1002/prot.20811.'
short: 'Y. Ban, J. Rudolph, P. Zhou, H. Edelsbrunner, Proteins: Structure, Function
and Bioinformatics 62 (2006) 852–864.'
date_created: 2018-12-11T12:06:14Z
date_published: 2006-03-01T00:00:00Z
date_updated: 2021-01-12T07:53:36Z
day: '01'
doi: 10.1002/prot.20811
extern: 1
intvolume: ' 62'
issue: '4'
month: '03'
page: 852 - 864
publication: 'Proteins: Structure, Function and Bioinformatics'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2146'
quality_controlled: 0
status: public
title: Evaluating the quality of NMR structures by local density of protons
type: journal_article
volume: 62
year: '2006'
...
---
_id: '3979'
abstract:
- lang: eng
text: Protein-protein interactions, which form the basis for most cellular processes,
result in the formation of protein interfaces. Believing that the local shape
of proteins is crucial, we take a geometric approach and present a definition
of an interface surface formed by two or more proteins as a subset of their Voronoi
diagram. The definition deals with the difficult and important problem of specifying
interface boundaries by invoking methods used in the alpha shape representation
of molecules, the discrete flow on Delaunay simplices to define pockets and reconstruct
surfaces, and the assessment of the importance of topological features. We present
an algorithm to construct the surface and define a hierarchy that distinguishes
core and peripheral regions. This hierarchy is shown to have correlation with
hot-spots in protein-protein interactions. Finally, we study the geometric and
topological properties of interface surfaces and show their high degree of contortion.
author:
- first_name: Yih
full_name: Ban, Yih-En Andrew
last_name: Ban
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
citation:
ama: Ban Y, Edelsbrunner H, Rudolph J. Interface surfaces for protein-protein complexes.
Journal of the ACM. 2006;53(3):361-378. doi:10.1145/1147954.1147957
apa: Ban, Y., Edelsbrunner, H., & Rudolph, J. (2006). Interface surfaces for
protein-protein complexes. Journal of the ACM. ACM. https://doi.org/10.1145/1147954.1147957
chicago: Ban, Yih, Herbert Edelsbrunner, and Johannes Rudolph. “Interface Surfaces
for Protein-Protein Complexes.” Journal of the ACM. ACM, 2006. https://doi.org/10.1145/1147954.1147957.
ieee: Y. Ban, H. Edelsbrunner, and J. Rudolph, “Interface surfaces for protein-protein
complexes,” Journal of the ACM, vol. 53, no. 3. ACM, pp. 361–378, 2006.
ista: Ban Y, Edelsbrunner H, Rudolph J. 2006. Interface surfaces for protein-protein
complexes. Journal of the ACM. 53(3), 361–378.
mla: Ban, Yih, et al. “Interface Surfaces for Protein-Protein Complexes.” Journal
of the ACM, vol. 53, no. 3, ACM, 2006, pp. 361–78, doi:10.1145/1147954.1147957.
short: Y. Ban, H. Edelsbrunner, J. Rudolph, Journal of the ACM 53 (2006) 361–378.
date_created: 2018-12-11T12:06:14Z
date_published: 2006-05-01T00:00:00Z
date_updated: 2021-01-12T07:53:37Z
day: '01'
doi: 10.1145/1147954.1147957
extern: 1
intvolume: ' 53'
issue: '3'
month: '05'
page: 361 - 378
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '2147'
quality_controlled: 0
status: public
title: Interface surfaces for protein-protein complexes
type: journal_article
volume: 53
year: '2006'
...