---
_id: '3193'
abstract:
- lang: eng
text: 'Optimization techniques based on graph cuts have become a standard tool for
many vision applications. These techniques allow to minimize efficiently certain
energy functions corresponding to pairwise Markov Random Fields (MRFs). Currently,
there is an accepted view within the computer vision community that graph cuts
can only be used for optimizing a limited class of MRF energies (e.g., submodular
functions). In this survey, we review some results that show that graph cuts can
be applied to a much larger class of energy functions (in particular, nonsubmodular
functions). While these results are well-known in the optimization community,
to our knowledge they were not used in the context of computer vision and MRF
optimization. We demonstrate the relevance of these results to vision on the problem
of binary texture restoration. '
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: Kolmogorov V, Rother C. Minimizing nonsubmodular functions with graph cuts
- A review. IEEE Transactions on Pattern Analysis and Machine Intelligence.
2007;29(7):1274-1279. doi:10.1109/TPAMI.2007.1031
apa: Kolmogorov, V., & Rother, C. (2007). Minimizing nonsubmodular functions
with graph cuts - A review. IEEE Transactions on Pattern Analysis and Machine
Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2007.1031
chicago: Kolmogorov, Vladimir, and Carsten Rother. “Minimizing Nonsubmodular Functions
with Graph Cuts - A Review.” IEEE Transactions on Pattern Analysis and Machine
Intelligence. IEEE, 2007. https://doi.org/10.1109/TPAMI.2007.1031.
ieee: V. Kolmogorov and C. Rother, “Minimizing nonsubmodular functions with graph
cuts - A review,” IEEE Transactions on Pattern Analysis and Machine Intelligence,
vol. 29, no. 7. IEEE, pp. 1274–1279, 2007.
ista: Kolmogorov V, Rother C. 2007. Minimizing nonsubmodular functions with graph
cuts - A review. IEEE Transactions on Pattern Analysis and Machine Intelligence.
29(7), 1274–1279.
mla: Kolmogorov, Vladimir, and Carsten Rother. “Minimizing Nonsubmodular Functions
with Graph Cuts - A Review.” IEEE Transactions on Pattern Analysis and Machine
Intelligence, vol. 29, no. 7, IEEE, 2007, pp. 1274–79, doi:10.1109/TPAMI.2007.1031.
short: V. Kolmogorov, C. Rother, IEEE Transactions on Pattern Analysis and Machine
Intelligence 29 (2007) 1274–1279.
date_created: 2018-12-11T12:01:56Z
date_published: 2007-07-01T00:00:00Z
date_updated: 2021-01-12T07:41:42Z
day: '01'
doi: 10.1109/TPAMI.2007.1031
extern: 1
intvolume: ' 29'
issue: '7'
month: '07'
page: 1274 - 1279
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3491'
quality_controlled: 0
status: public
title: Minimizing nonsubmodular functions with graph cuts - A review
type: journal_article
volume: 29
year: '2007'
...
---
_id: '3218'
abstract:
- lang: eng
text: 'A (k, ℓ)-robust combiner for collision-resistant hash-functions is a construction
which from ℓ hash-functions constructs a hash-function which is collision-resistant
if at least k of the components are collision-resistant. One trivially gets a
(k, ℓ)-robust combiner by concatenating the output of any ℓ - k + 1 of the components,
unfortunately this is not very practical as the length of the output of the combiner
is quite large. We show that this is unavoidable as no black-box (k, ℓ)-robust
combiner whose output is significantly shorter than what can be achieved by concatenation
exists. This answers a question of Boneh and Boyen (Crypto''06). '
acknowledgement: Supported by DIAMANT, the Dutch national mathematics cluster for
discrete interactive and algorithmic algebra and number theory.
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. Non-trivial black-box combiners for collision-resistant hash-functions
don’t exist. In: Vol 4515. Springer; 2007:23-33. doi:10.1007/978-3-540-72540-4_2'
apa: 'Pietrzak, K. Z. (2007). Non-trivial black-box combiners for collision-resistant
hash-functions don’t exist (Vol. 4515, pp. 23–33). Presented at the EUROCRYPT:
Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/978-3-540-72540-4_2'
chicago: Pietrzak, Krzysztof Z. “Non-Trivial Black-Box Combiners for Collision-Resistant
Hash-Functions Don’t Exist,” 4515:23–33. Springer, 2007. https://doi.org/10.1007/978-3-540-72540-4_2.
ieee: 'K. Z. Pietrzak, “Non-trivial black-box combiners for collision-resistant
hash-functions don’t exist,” presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, 2007, vol. 4515, pp. 23–33.'
ista: 'Pietrzak KZ. 2007. Non-trivial black-box combiners for collision-resistant
hash-functions don’t exist. EUROCRYPT: Theory and Applications of Cryptographic
Techniques, LNCS, vol. 4515, 23–33.'
mla: Pietrzak, Krzysztof Z. Non-Trivial Black-Box Combiners for Collision-Resistant
Hash-Functions Don’t Exist. Vol. 4515, Springer, 2007, pp. 23–33, doi:10.1007/978-3-540-72540-4_2.
short: K.Z. Pietrzak, in:, Springer, 2007, pp. 23–33.
conference:
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
date_created: 2018-12-11T12:02:05Z
date_published: 2007-06-12T00:00:00Z
date_updated: 2021-01-12T07:41:52Z
day: '12'
doi: 10.1007/978-3-540-72540-4_2
extern: 1
intvolume: ' 4515'
month: '06'
page: 23 - 33
publication_status: published
publisher: Springer
publist_id: '3461'
quality_controlled: 0
status: public
title: Non-trivial black-box combiners for collision-resistant hash-functions don't
exist
type: conference
volume: 4515
year: '2007'
...
---
_id: '3219'
abstract:
- lang: eng
text: 'Many aspects of cryptographic security proofs can be seen as the proof that
a certain system (e.g. a block cipher) is indistinguishable from an ideal system
(e.g. a random permutation), for different types of distinguishers. This paper
presents a new generic approach to proving upper bounds on the information-theoretic
distinguishing advantage (from an ideal system) for a combined system, assuming
upper bounds of certain types for the component systems. For a general type of
combination operation of systems, including the XOR of functions or the cascade
of permutations, we prove two amplification theorems. The first is a product theorem,
in the spirit of XOR-lemmas: The distinguishing advantage of the combination of
two systems is at most twice the product of the individual distinguishing advantages.
This bound is optimal. The second theorem states that the combination of systems
is secure against some strong class of distinguishers, assuming only that the
components are secure against some weaker class of distinguishers. A key technical
tool of the paper is the proof of a tight two-way correspondence, previously only
known to hold in one direction, between the distinguishing advantage of two systems
and the probability of winning an appropriately defined game. © International
Association for Cryptologic Research 2007.'
alternative_title:
- LNCS
author:
- first_name: Ueli
full_name: Maurer, Ueli M
last_name: Maurer
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Renato
full_name: Renner, Renato
last_name: Renner
citation:
ama: 'Maurer U, Pietrzak KZ, Renner R. Indistinguishability amplification. In: Vol
4622. Springer; 2007:130-149. doi:10.1007/978-3-540-74143-5_8'
apa: 'Maurer, U., Pietrzak, K. Z., & Renner, R. (2007). Indistinguishability
amplification (Vol. 4622, pp. 130–149). Presented at the CRYPTO: International
Cryptology Conference, Springer. https://doi.org/10.1007/978-3-540-74143-5_8'
chicago: Maurer, Ueli, Krzysztof Z Pietrzak, and Renato Renner. “Indistinguishability
Amplification,” 4622:130–49. Springer, 2007. https://doi.org/10.1007/978-3-540-74143-5_8.
ieee: 'U. Maurer, K. Z. Pietrzak, and R. Renner, “Indistinguishability amplification,”
presented at the CRYPTO: International Cryptology Conference, 2007, vol. 4622,
pp. 130–149.'
ista: 'Maurer U, Pietrzak KZ, Renner R. 2007. Indistinguishability amplification.
CRYPTO: International Cryptology Conference, LNCS, vol. 4622, 130–149.'
mla: Maurer, Ueli, et al. Indistinguishability Amplification. Vol. 4622,
Springer, 2007, pp. 130–49, doi:10.1007/978-3-540-74143-5_8.
short: U. Maurer, K.Z. Pietrzak, R. Renner, in:, Springer, 2007, pp. 130–149.
conference:
name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:05Z
date_published: 2007-10-03T00:00:00Z
date_updated: 2021-01-12T07:41:53Z
day: '03'
doi: 10.1007/978-3-540-74143-5_8
extern: 1
intvolume: ' 4622'
month: '10'
page: 130 - 149
publication_status: published
publisher: Springer
publist_id: '3462'
quality_controlled: 0
status: public
title: Indistinguishability amplification
type: conference
volume: 4622
year: '2007'
...
---
_id: '3220'
abstract:
- lang: eng
text: We introduce a new primitive called intrusion-resilient secret sharing (IRSS),
whose security proof exploits the fact that there exist functions which can be
efficiently computed interactively using low communication complexity in k, but
not in k-1 rounds. IRSS is a means of sharing a secret message amongst a set of
players which comes with a very strong security guarantee. The shares in an IRSS
are made artificially large so that it is hard to retrieve them completely, and
the reconstruction procedure is interactive requiring the players to exchange
k short messages. The adversaries considered can attack the scheme in rounds,
where in each round the adversary chooses some player to corrupt and some function,
and retrieves the output of that function applied to the share of the corrupted
player. This model captures for example computers connected to a network which
can occasionally he infected by malicious software like viruses, which can compute
any function on the infected machine, but cannot sent out a huge amount of data.
Using methods from the bounded-retrieval model, we construct an IRSS scheme which
is secure against any computationally unbounded adversary as long as the total
amount of information retrieved by the adversary is somewhat less than the length
of the shares, and the adversary makes at most k-1 corruption rounds (as described
above, where k rounds are necessary for reconstruction). We extend our basic scheme
in several ways in order to allow the shares sent by the dealer to be short (the
players then blow them up locally) and to handle even stronger adversaries who
can learn some of the shares completely. As mentioned, there is an obvious connection
between IRSS schemes and the fact that there exist functions with an exponential
gap in their communication complexity for k and k-1 rounds. Our scheme implies
such a separation which is in several aspects stronger than the previously known
ones.
author:
- first_name: Stefan
full_name: Dziembowski, Stefan
last_name: Dziembowski
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Dziembowski S, Pietrzak KZ. Intrusion resilient secret sharing. In: IEEE;
2007:227-237. doi:10.1109/FOCS.2007.63'
apa: 'Dziembowski, S., & Pietrzak, K. Z. (2007). Intrusion resilient secret
sharing (pp. 227–237). Presented at the FOCS: Foundations of Computer Science,
IEEE. https://doi.org/10.1109/FOCS.2007.63'
chicago: Dziembowski, Stefan, and Krzysztof Z Pietrzak. “Intrusion Resilient Secret
Sharing,” 227–37. IEEE, 2007. https://doi.org/10.1109/FOCS.2007.63.
ieee: 'S. Dziembowski and K. Z. Pietrzak, “Intrusion resilient secret sharing,”
presented at the FOCS: Foundations of Computer Science, 2007, pp. 227–237.'
ista: 'Dziembowski S, Pietrzak KZ. 2007. Intrusion resilient secret sharing. FOCS:
Foundations of Computer Science, 227–237.'
mla: Dziembowski, Stefan, and Krzysztof Z. Pietrzak. Intrusion Resilient Secret
Sharing. IEEE, 2007, pp. 227–37, doi:10.1109/FOCS.2007.63.
short: S. Dziembowski, K.Z. Pietrzak, in:, IEEE, 2007, pp. 227–237.
conference:
name: 'FOCS: Foundations of Computer Science'
date_created: 2018-12-11T12:02:05Z
date_published: 2007-10-23T00:00:00Z
date_updated: 2021-01-12T07:41:54Z
day: '23'
doi: 10.1109/FOCS.2007.63
extern: 1
month: '10'
page: 227 - 237
publication_status: published
publisher: IEEE
publist_id: '3459'
quality_controlled: 0
status: public
title: Intrusion resilient secret sharing
type: conference
year: '2007'
...
---
_id: '3221'
abstract:
- lang: eng
text: |-
We investigate a general class of (black-box) constructions for range extension of weak pseudorandom functions: a construction based on m independent functions F 1,...,F m is given by a set of strings over {1,...,m}*, where for example {〈2〉, 〈1,2〉} corresponds to the function X ↦[F 2(X),F 2(F 1(X))]. All efficient constructions for range expansion of weak pseudorandom functions that we are aware of are of this form.
We completely classify such constructions as good, bad or ugly, where the good constructions are those whose security can be proven via a black-box reduction, the bad constructions are those whose insecurity can be proven via a black-box reduction, and the ugly constructions are those which are neither good nor bad.
Our classification shows that the range expansion from [10] is optimal, in the sense that it achieves the best possible expansion (2 m − 1 when using m keys).
Along the way we show that for weak quasirandom functions (i.e. in the information theoretic setting), all constructions which are not bad – in particular all the ugly ones – are secure.
acknowledgement: This work was partially supported by the Zurich Information Security
Center. It represents the views of the authors.
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
- first_name: Johan
full_name: Sjödin, Johan
last_name: Sjödin
citation:
ama: 'Pietrzak KZ, Sjödin J. Range extension for weak PRFs the good the bad and
the ugly. In: Vol 4515. Springer; 2007:517-533. doi:10.1007/978-3-540-72540-4_30'
apa: 'Pietrzak, K. Z., & Sjödin, J. (2007). Range extension for weak PRFs the
good the bad and the ugly (Vol. 4515, pp. 517–533). Presented at the EUROCRYPT:
Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/978-3-540-72540-4_30'
chicago: Pietrzak, Krzysztof Z, and Johan Sjödin. “Range Extension for Weak PRFs
the Good the Bad and the Ugly,” 4515:517–33. Springer, 2007. https://doi.org/10.1007/978-3-540-72540-4_30.
ieee: 'K. Z. Pietrzak and J. Sjödin, “Range extension for weak PRFs the good the
bad and the ugly,” presented at the EUROCRYPT: Theory and Applications of Cryptographic
Techniques, 2007, vol. 4515, pp. 517–533.'
ista: 'Pietrzak KZ, Sjödin J. 2007. Range extension for weak PRFs the good the bad
and the ugly. EUROCRYPT: Theory and Applications of Cryptographic Techniques,
LNCS, vol. 4515, 517–533.'
mla: Pietrzak, Krzysztof Z., and Johan Sjödin. Range Extension for Weak PRFs
the Good the Bad and the Ugly. Vol. 4515, Springer, 2007, pp. 517–33, doi:10.1007/978-3-540-72540-4_30.
short: K.Z. Pietrzak, J. Sjödin, in:, Springer, 2007, pp. 517–533.
conference:
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
date_created: 2018-12-11T12:02:06Z
date_published: 2007-06-12T00:00:00Z
date_updated: 2021-01-12T07:41:54Z
day: '12'
doi: 10.1007/978-3-540-72540-4_30
extern: 1
intvolume: ' 4515'
month: '06'
page: 517 - 533
publication_status: published
publisher: Springer
publist_id: '3460'
quality_controlled: 0
status: public
title: Range extension for weak PRFs the good the bad and the ugly
type: conference
volume: 4515
year: '2007'
...
---
_id: '3222'
abstract:
- lang: eng
text: |-
Parallel repetition is well known to reduce the error probability at an exponential rate for single- and multi-prover interactive proofs.
Bellare, Impagliazzo and Naor (1997) show that this is also true for protocols where the soundness only holds against computationally bounded provers (e.g. interactive arguments) if the protocol has at most three rounds.
On the other hand, for four rounds they give a protocol where this is no longer the case: the error probability does not decrease below some constant even if the protocol is repeated a polynomial number of times. Unfortunately, this protocol is not very convincing as the communication complexity of each instance of the protocol grows linearly with the number of repetitions, and for such protocols the error does not even decrease for some types of interactive proofs. Noticing this, Bellare et al. construct (a quite artificial) oracle relative to which a four round protocol exists whose communication complexity does not depend on the number of parallel repetitions. This shows that there is no “black-box” error reduction theorem for four round protocols.
In this paper we give the first computationally sound protocol where k-fold parallel repetition does not decrease the error probability below some constant for any polynomial k (and where the communication complexity does not depend on k). The protocol has eight rounds and uses the universal arguments of Barak and Goldreich (2001). We also give another four round protocol relative to an oracle, unlike the artificial oracle of Bellare et al., we just need a generic group. This group can then potentially be instantiated with some real group satisfying some well defined hardness assumptions (we do not know of any candidate for such a group at the moment).
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
- first_name: Douglas
full_name: Wikström, Douglas
last_name: Wikström
citation:
ama: 'Pietrzak KZ, Wikström D. Parallel repetition of computationally sound protocols
revisited. In: Vol 4392. Springer; 2007:86-102. doi:10.1007/978-3-540-70936-7_5'
apa: 'Pietrzak, K. Z., & Wikström, D. (2007). Parallel repetition of computationally
sound protocols revisited (Vol. 4392, pp. 86–102). Presented at the TCC: Theory
of Cryptography Conference, Springer. https://doi.org/10.1007/978-3-540-70936-7_5'
chicago: Pietrzak, Krzysztof Z, and Douglas Wikström. “Parallel Repetition of Computationally
Sound Protocols Revisited,” 4392:86–102. Springer, 2007. https://doi.org/10.1007/978-3-540-70936-7_5.
ieee: 'K. Z. Pietrzak and D. Wikström, “Parallel repetition of computationally sound
protocols revisited,” presented at the TCC: Theory of Cryptography Conference,
2007, vol. 4392, pp. 86–102.'
ista: 'Pietrzak KZ, Wikström D. 2007. Parallel repetition of computationally sound
protocols revisited. TCC: Theory of Cryptography Conference, LNCS, vol. 4392,
86–102.'
mla: Pietrzak, Krzysztof Z., and Douglas Wikström. Parallel Repetition of Computationally
Sound Protocols Revisited. Vol. 4392, Springer, 2007, pp. 86–102, doi:10.1007/978-3-540-70936-7_5.
short: K.Z. Pietrzak, D. Wikström, in:, Springer, 2007, pp. 86–102.
conference:
name: 'TCC: Theory of Cryptography Conference'
date_created: 2018-12-11T12:02:06Z
date_published: 2007-03-22T00:00:00Z
date_updated: 2021-01-12T07:41:54Z
day: '22'
doi: 10.1007/978-3-540-70936-7_5
extern: 1
intvolume: ' 4392'
month: '03'
page: 86 - 102
publication_status: published
publisher: Springer
publist_id: '3457'
quality_controlled: 0
status: public
title: Parallel repetition of computationally sound protocols revisited
type: conference
volume: 4392
year: '2007'
...
---
_id: '3223'
abstract:
- lang: eng
text: |-
“Hash then encrypt” is an approach to message authentication, where first the message is hashed down using an ε-universal hash function, and then the resulting k-bit value is encrypted, say with a block-cipher. The security of this scheme is proportional to εq2, where q is the number of MACs the adversary can request. As ε is at least 2−k, the best one can hope for is O(q2/2k) security. Unfortunately, such small ε is not achieved by simple hash functions used in practice, such as the polynomial evaluation or the Merkle-Damg ̊ard construction, where ε grows with the message length L.
The main insight of this work comes from the fact that, by using ran- domized message preprocessing via a short random salt p (which must then be sent as part of the authentication tag), we can use the “hash then encrypt” paradigm with suboptimal “practical” ε-universal hash func- tions, and still improve its exact security to optimal O(q2/2k). Specif- ically, by using at most an O(logL)-bit salt p, one can always regain the optimal exact security O(q2/2k), even in situations where ε grows polynomially with L. We also give very simple preprocessing maps for popular “suboptimal” hash functions, namely polynomial evaluation and the Merkle-Damg ̊ard construction.
Our results come from a general extension of the classical Carter- Wegman paradigm, which we believe is of independent interest. On a high level, it shows that public randomization allows one to use the potentially much smaller “average-case” collision probability in place of the “worst-case” collision probability ε.
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
citation:
ama: 'Dodis Y, Pietrzak KZ. Improving the security of MACs via randomized message
preprocessing. In: Vol 4593. Springer; 2007:414-433. doi:10.1007/978-3-540-74619-5_26'
apa: 'Dodis, Y., & Pietrzak, K. Z. (2007). Improving the security of MACs via
randomized message preprocessing (Vol. 4593, pp. 414–433). Presented at the FSE:
Fast Software Encryption, Springer. https://doi.org/10.1007/978-3-540-74619-5_26'
chicago: Dodis, Yevgeniy, and Krzysztof Z Pietrzak. “Improving the Security of MACs
via Randomized Message Preprocessing,” 4593:414–33. Springer, 2007. https://doi.org/10.1007/978-3-540-74619-5_26.
ieee: 'Y. Dodis and K. Z. Pietrzak, “Improving the security of MACs via randomized
message preprocessing,” presented at the FSE: Fast Software Encryption, 2007,
vol. 4593, pp. 414–433.'
ista: 'Dodis Y, Pietrzak KZ. 2007. Improving the security of MACs via randomized
message preprocessing. FSE: Fast Software Encryption, LNCS, vol. 4593, 414–433.'
mla: Dodis, Yevgeniy, and Krzysztof Z. Pietrzak. Improving the Security of MACs
via Randomized Message Preprocessing. Vol. 4593, Springer, 2007, pp. 414–33,
doi:10.1007/978-3-540-74619-5_26.
short: Y. Dodis, K.Z. Pietrzak, in:, Springer, 2007, pp. 414–433.
conference:
name: 'FSE: Fast Software Encryption'
date_created: 2018-12-11T12:02:06Z
date_published: 2007-10-11T00:00:00Z
date_updated: 2021-01-12T07:41:55Z
day: '11'
doi: 10.1007/978-3-540-74619-5_26
extern: 1
intvolume: ' 4593'
month: '10'
page: 414 - 433
publication_status: published
publisher: Springer
publist_id: '3458'
quality_controlled: 0
status: public
title: Improving the security of MACs via randomized message preprocessing
type: conference
volume: 4593
year: '2007'
...
---
_id: '3305'
abstract:
- lang: eng
text: The accumulation of deleterious mutations plays a major role in evolution,
and key to this are the interactions between their fitness effects, known as epistasis.
Whether mutations tend to interact synergistically (with multiple mutations being
more deleterious than would be expected from their individual fitness effects)
or antagonistically is important for a variety of evolutionary questions, particularly
the evolution of sex. Unfortunately, the experimental evidence on the prevalence
and strength of epistasis is mixed and inconclusive. Here we study theoretically
whether synergistic or antagonistic epistasis is likely to be favored by evolution
and by how much. We find that in the presence of recombination, evolution favors
less synergistic or more antagonistic epistasis whenever mutations that change
the epistasis in this direction are possible. This is because evolution favors
increased buffering against the effects of deleterious mutations. This suggests
that we should not expect synergistic epistasis to be widespread in nature and
hence that the mutational deterministic hypothesis for the advantage of sex may
not apply widely.
author:
- first_name: Michael
full_name: Desai, Michael M
last_name: Desai
- first_name: Daniel
full_name: Daniel Weissman
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Marcus
full_name: Feldman, Marcus W
last_name: Feldman
citation:
ama: Desai M, Weissman D, Feldman M. Evolution can favor antagonistic epistasis.
Genetics. 2007;177(2):1001-1010. doi:10.1534/genetics.107.075812
apa: Desai, M., Weissman, D., & Feldman, M. (2007). Evolution can favor antagonistic
epistasis. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.107.075812
chicago: Desai, Michael, Daniel Weissman, and Marcus Feldman. “Evolution Can Favor
Antagonistic Epistasis.” Genetics. Genetics Society of America, 2007. https://doi.org/10.1534/genetics.107.075812.
ieee: M. Desai, D. Weissman, and M. Feldman, “Evolution can favor antagonistic epistasis,”
Genetics, vol. 177, no. 2. Genetics Society of America, pp. 1001–10, 2007.
ista: Desai M, Weissman D, Feldman M. 2007. Evolution can favor antagonistic epistasis.
Genetics. 177(2), 1001–10.
mla: Desai, Michael, et al. “Evolution Can Favor Antagonistic Epistasis.” Genetics,
vol. 177, no. 2, Genetics Society of America, 2007, pp. 1001–10, doi:10.1534/genetics.107.075812.
short: M. Desai, D. Weissman, M. Feldman, Genetics 177 (2007) 1001–10.
date_created: 2018-12-11T12:02:34Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:32Z
day: '01'
doi: 10.1534/genetics.107.075812
extern: 1
intvolume: ' 177'
issue: '2'
month: '01'
page: 1001 - 10
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3335'
quality_controlled: 0
status: public
title: Evolution can favor antagonistic epistasis
type: journal_article
volume: 177
year: '2007'
...
---
_id: '3411'
abstract:
- lang: eng
text: Mechanical single-molecule techniques offer exciting possibilities to investigate
protein folding and stability in native environments at submolecular resolution.
By applying a free-energy reconstruction procedure developed by Hummer and Szabo,
which is based on a statistical theorem introduced by Jarzynski, we determined
the unfolding free energy of the membrane proteins bacteriorhodopsin (BR), halorhodopsin,
and the sodium-proton antiporter NhaA. The calculated energies ranged from 290.5kcal/mol
for BR to 485.5kcal/mol for NhaA. For the remarkably stable BR, the equilibrium
unfolding free energy was independent of pulling rate and temperature ranging
between 18 and 42°C. Our experiments also revealed heterogeneous energetic properties
in individual transmembrane helices. In halorhodopsin, the stabilization of a
short helical segment yielded a characteristic signature in the energy profile.
In NhaA, a pronounced peak was observed at a functionally important site in the
protein. Since a large variety of single- and multispan membrane proteins can
be tackled in mechanical unfolding experiments, our approach provides a basis
for systematically elucidating energetic properties of membrane proteins with
the resolution of individual secondary-structure elements.
author:
- first_name: Johannes
full_name: Preiner, Johannes
last_name: Preiner
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Christian
full_name: Rankl, Christian
last_name: Rankl
- first_name: Helene
full_name: Knaus, Helene
last_name: Knaus
- first_name: David
full_name: Cisneros, David A
last_name: Cisneros
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: Ferry
full_name: Kienberger, Ferry
last_name: Kienberger
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
- first_name: Peter
full_name: Hinterdorfer, Peter
last_name: Hinterdorfer
citation:
ama: Preiner J, Janovjak HL, Rankl C, et al. Free energy of membrane protein unfolding
derived from single-molecule force measurements. Biophysical Journal. 2007;93(3):930-937.
doi:10.1529/biophysj.106.096982
apa: Preiner, J., Janovjak, H. L., Rankl, C., Knaus, H., Cisneros, D., Kedrov, A.,
… Hinterdorfer, P. (2007). Free energy of membrane protein unfolding derived from
single-molecule force measurements. Biophysical Journal. Biophysical Society.
https://doi.org/10.1529/biophysj.106.096982
chicago: Preiner, Johannes, Harald L Janovjak, Christian Rankl, Helene Knaus, David
Cisneros, Alexej Kedrov, Ferry Kienberger, Daniel Mueller, and Peter Hinterdorfer.
“Free Energy of Membrane Protein Unfolding Derived from Single-Molecule Force
Measurements.” Biophysical Journal. Biophysical Society, 2007. https://doi.org/10.1529/biophysj.106.096982.
ieee: J. Preiner et al., “Free energy of membrane protein unfolding derived
from single-molecule force measurements,” Biophysical Journal, vol. 93,
no. 3. Biophysical Society, pp. 930–937, 2007.
ista: Preiner J, Janovjak HL, Rankl C, Knaus H, Cisneros D, Kedrov A, Kienberger
F, Mueller D, Hinterdorfer P. 2007. Free energy of membrane protein unfolding
derived from single-molecule force measurements. Biophysical Journal. 93(3), 930–937.
mla: Preiner, Johannes, et al. “Free Energy of Membrane Protein Unfolding Derived
from Single-Molecule Force Measurements.” Biophysical Journal, vol. 93,
no. 3, Biophysical Society, 2007, pp. 930–37, doi:10.1529/biophysj.106.096982.
short: J. Preiner, H.L. Janovjak, C. Rankl, H. Knaus, D. Cisneros, A. Kedrov, F.
Kienberger, D. Mueller, P. Hinterdorfer, Biophysical Journal 93 (2007) 930–937.
date_created: 2018-12-11T12:03:11Z
date_published: 2007-08-01T00:00:00Z
date_updated: 2021-01-12T07:43:18Z
day: '01'
doi: 10.1529/biophysj.106.096982
extern: 1
intvolume: ' 93'
issue: '3'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1913163/
month: '08'
oa: 1
page: 930 - 937
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '2990'
quality_controlled: 0
status: public
title: Free energy of membrane protein unfolding derived from single-molecule force
measurements
type: journal_article
volume: 93
year: '2007'
...
---
_id: '3412'
abstract:
- lang: eng
text: |-
Molecular interactions are the basic language of biological processes.
They establish the forces interacting between the building blocks of
proteins and other macromolecules, thus determining their functional
roles. Because molecular interactions trigger virtually every
biological process, approaches to decipher their language are needed.
Single-molecule force spectroscopy (SMFS) has been used to detect
and characterize different types of molecular interactions that occur
between and within native membrane proteins. The first experiments
detected and localized molecular interactions that stabilized
membrane proteins, including how these interactions were established
during folding of α-helical secondary structure elements into
the native protein and how they changed with oligomerization, temperature,
and mutations. SMFS also enables investigators to detect
and locate molecular interactions established during ligand and inhibitor
binding. These exciting applications provide opportunities
for studying the molecular forces of life. Further developments will
elucidate the origins of molecular interactions encoded in their lifetimes,
interaction ranges, interplay, and dynamics characteristic of biological systems.
author:
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Tanuj
full_name: Sapra, Tanuj K
last_name: Sapra
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Kedrov A, Janovjak HL, Sapra T, Mueller D. Deciphering molecular interactions
of native membrane proteins by single-molecule force spectroscopy. Annual Review
of Biophysics. 2007;36:233-260. doi:10.1146/annurev.biophys.36.040306.132640
apa: Kedrov, A., Janovjak, H. L., Sapra, T., & Mueller, D. (2007). Deciphering
molecular interactions of native membrane proteins by single-molecule force spectroscopy.
Annual Review of Biophysics. Annual Reviews. https://doi.org/10.1146/annurev.biophys.36.040306.132640
chicago: Kedrov, Alexej, Harald L Janovjak, Tanuj Sapra, and Daniel Mueller. “Deciphering
Molecular Interactions of Native Membrane Proteins by Single-Molecule Force Spectroscopy.”
Annual Review of Biophysics. Annual Reviews, 2007. https://doi.org/10.1146/annurev.biophys.36.040306.132640.
ieee: A. Kedrov, H. L. Janovjak, T. Sapra, and D. Mueller, “Deciphering molecular
interactions of native membrane proteins by single-molecule force spectroscopy,”
Annual Review of Biophysics, vol. 36. Annual Reviews, pp. 233–260, 2007.
ista: Kedrov A, Janovjak HL, Sapra T, Mueller D. 2007. Deciphering molecular interactions
of native membrane proteins by single-molecule force spectroscopy. Annual Review
of Biophysics. 36, 233–260.
mla: Kedrov, Alexej, et al. “Deciphering Molecular Interactions of Native Membrane
Proteins by Single-Molecule Force Spectroscopy.” Annual Review of Biophysics,
vol. 36, Annual Reviews, 2007, pp. 233–60, doi:10.1146/annurev.biophys.36.040306.132640.
short: A. Kedrov, H.L. Janovjak, T. Sapra, D. Mueller, Annual Review of Biophysics
36 (2007) 233–260.
date_created: 2018-12-11T12:03:11Z
date_published: 2007-06-01T00:00:00Z
date_updated: 2019-04-26T07:22:27Z
day: '01'
doi: 10.1146/annurev.biophys.36.040306.132640
extern: 1
intvolume: ' 36'
month: '06'
page: 233 - 260
publication: Annual Review of Biophysics
publication_status: published
publisher: Annual Reviews
publist_id: '2989'
quality_controlled: 0
status: public
title: Deciphering molecular interactions of native membrane proteins by single-molecule
force spectroscopy
type: review
volume: 36
year: '2007'
...
---
_id: '3427'
abstract:
- lang: eng
text: "We present a general theoretical framework to discuss mechanisms of morphogen
transport and gradient formation in a cell layer. Trafficking events on the cellular
scale lead to transport on larger scales. We discuss in particular the case of
transcytosis where morphogens undergo repeated rounds of internalization into
cells and recycling. Based on a description on the cellular scale, we derive effective
nonlinear transport equations in one and two dimensions which are valid on larger
scales. We derive analytic expressions for the concentration dependence of the
effective diffusion coefficient and the effective degradation rate. We discuss
the effects of a directional bias on morphogen transport and those of the coupling
of the morphogen and receptor kinetics. Furthermore, we discuss general properties
of cellular transport processes such as the robustness of gradients and relate
our results to recent experiments on the morphogen Decapentaplegic (Dpp) that
acts in the wing disk of the fruit fly Drosophila.\r\n© 2007 The American Physical
Society"
article_processing_charge: No
arxiv: 1
author:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Karsten
full_name: Kruse, Karsten
last_name: Kruse
- first_name: Periklis
full_name: Pantazis, Periklis
last_name: Pantazis
- first_name: Marcos
full_name: Gonzalez Gaitan, Marcos
last_name: Gonzalez Gaitan
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
citation:
ama: Bollenbach MT, Kruse K, Pantazis P, Gonzalez Gaitan M, Julicher F. Morphogen
transport in epithelia. Physical Review E Statistical Nonlinear and Soft Matter
Physics. 2007;75(1). doi:10.1103/PhysRevE.75.011901
apa: Bollenbach, M. T., Kruse, K., Pantazis, P., Gonzalez Gaitan, M., & Julicher,
F. (2007). Morphogen transport in epithelia. Physical Review E Statistical
Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.75.011901
chicago: Bollenbach, Mark Tobias, Karsten Kruse, Periklis Pantazis, Marcos Gonzalez
Gaitan, and Frank Julicher. “Morphogen Transport in Epithelia.” Physical Review
E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics,
2007. https://doi.org/10.1103/PhysRevE.75.011901.
ieee: M. T. Bollenbach, K. Kruse, P. Pantazis, M. Gonzalez Gaitan, and F. Julicher,
“Morphogen transport in epithelia,” Physical Review E Statistical Nonlinear
and Soft Matter Physics, vol. 75, no. 1. American Institute of Physics, 2007.
ista: Bollenbach MT, Kruse K, Pantazis P, Gonzalez Gaitan M, Julicher F. 2007. Morphogen
transport in epithelia. Physical Review E Statistical Nonlinear and Soft Matter
Physics. 75(1).
mla: Bollenbach, Mark Tobias, et al. “Morphogen Transport in Epithelia.” Physical
Review E Statistical Nonlinear and Soft Matter Physics, vol. 75, no. 1, American
Institute of Physics, 2007, doi:10.1103/PhysRevE.75.011901.
short: M.T. Bollenbach, K. Kruse, P. Pantazis, M. Gonzalez Gaitan, F. Julicher,
Physical Review E Statistical Nonlinear and Soft Matter Physics 75 (2007).
date_created: 2018-12-11T12:03:16Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:24Z
day: '01'
doi: 10.1103/PhysRevE.75.011901
extern: '1'
external_id:
arxiv:
- q-bio/0609011v1
intvolume: ' 75'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/q-bio/0609011v1
month: '01'
oa: 1
oa_version: Preprint
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '2974'
status: public
title: Morphogen transport in epithelia
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 75
year: '2007'
...
---
_id: '3432'
abstract:
- lang: eng
text: Evolution has left its signature on the molecules and morphology of living
organisms. Ancestral reconstruction offers an excellent tool for understanding
the process of evolution using comparative information. Methods for ancestral
reconstruction have generally focused on reconstructing the ancestral states at
the internal nodes of a phylogeny. Often, we are not interested in particular
nodes of the phylogeny but the whole history of a character. This chapter focuses
on a Bayesian method for estimating these histories, or mutational paths, on phylogenies.
Mutational path methods differ most notably from other approaches in their ability
to estimate not only the ancestral states at the internal nodes of a phylogeny,
but also the order and timing of mutational changes across the phylogeny. The
chapter provides a concise introduction to the statistical tools needed for sampling
mutational paths on a phylogeny.
author:
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Paul
full_name: Gardner, Paul P
last_name: Gardner
- first_name: Rasmus
full_name: Nielsen, Rasmus
last_name: Nielsen
citation:
ama: 'Bollback JP, Gardner P, Nielsen R. Estimating the history of mutations on
a phylogeny. In: Liberles D, ed. Ancestral Sequence Reconstruction. Oxford
University Press; 2007:69-79. doi:10.1093/acprof:oso/9780199299188.003.0006'
apa: Bollback, J. P., Gardner, P., & Nielsen, R. (2007). Estimating the history
of mutations on a phylogeny. In D. Liberles (Ed.), Ancestral Sequence Reconstruction
(pp. 69–79). Oxford University Press. https://doi.org/10.1093/acprof:oso/9780199299188.003.0006
chicago: Bollback, Jonathan P, Paul Gardner, and Rasmus Nielsen. “Estimating the
History of Mutations on a Phylogeny.” In Ancestral Sequence Reconstruction,
edited by David Liberles, 69–79. Oxford University Press, 2007. https://doi.org/10.1093/acprof:oso/9780199299188.003.0006.
ieee: J. P. Bollback, P. Gardner, and R. Nielsen, “Estimating the history of mutations
on a phylogeny,” in Ancestral Sequence Reconstruction, D. Liberles, Ed.
Oxford University Press, 2007, pp. 69–79.
ista: 'Bollback JP, Gardner P, Nielsen R. 2007.Estimating the history of mutations
on a phylogeny. In: Ancestral Sequence Reconstruction. , 69–79.'
mla: Bollback, Jonathan P., et al. “Estimating the History of Mutations on a Phylogeny.”
Ancestral Sequence Reconstruction, edited by David Liberles, Oxford University
Press, 2007, pp. 69–79, doi:10.1093/acprof:oso/9780199299188.003.0006.
short: J.P. Bollback, P. Gardner, R. Nielsen, in:, D. Liberles (Ed.), Ancestral
Sequence Reconstruction, Oxford University Press, 2007, pp. 69–79.
date_created: 2018-12-11T12:03:18Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:26Z
day: '01'
doi: 10.1093/acprof:oso/9780199299188.003.0006
editor:
- first_name: David
full_name: Liberles, David A
last_name: Liberles
extern: 1
month: '01'
page: 69 - 79
publication: Ancestral Sequence Reconstruction
publication_status: published
publisher: Oxford University Press
publist_id: '2968'
quality_controlled: 0
status: public
title: Estimating the history of mutations on a phylogeny
type: book_chapter
year: '2007'
...
---
_id: '3436'
abstract:
- lang: eng
text: 'he potential for di? erences between genetic paternity and paternity inferred
from behavioral observation has long been recognized. These di? erences are associated
with the challenge for females of seeking both genetic and material bene? ts;
this challenge is less severe in species with polygynous, non-resource-based mating
systems (such as leks) than in those with resource-based systems. We pres- ent
the ? rst study of paternity patt erns in a non-resource-based species that does
not form true leks. We compared paternity inferred from observed mating behavior
to genetically assigned paternity in the Satin Bowerbird (Ptilonorhynchus violaceus)
using eight microsatellite markers. Mating behavior was observed and recorded
via automated video-cameras positioned at all bowers (29?34 bowers each year)
in the study site throughout each mating season. We obtained blood samples and
identi- ? ed mothers for 11 chicks in 9 nests. For all chicks, the most likely
genetic father had been observed to mate with the mother in the year the chick
was sampled. All most likely genetic fathers were assigned with high con? dence
and all were bower- holding males. These results demonstrate that genetic paternity
can be inferred from observed mating behavior with reasonable con? dence in Satin
Bowerbirds. Observed male mating-success is therefore a reliable predictor of
reproductive success, and this suggests that high skew in observed male mating-success
translates directly to high skew in reproductive success. '
author:
- first_name: Sheila
full_name: Reynolds, Sheila M
last_name: Reynolds
- first_name: Katie
full_name: Dryer, Katie
last_name: Dryer
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: J Albert
full_name: Uy, J Albert
last_name: Uy
- first_name: Gail
full_name: Patricelli, Gail L
last_name: Patricelli
- first_name: Timothy
full_name: Robson, Timothy
last_name: Robson
- first_name: Gerald
full_name: Borgia, Gerald
last_name: Borgia
- first_name: Michael
full_name: Braun, Michael J
last_name: Braun
citation:
ama: Reynolds S, Dryer K, Bollback JP, et al. Behavioral paternity predicts genetic
paternity in satin bowerbirds, a species with a non-resource-based mating system.
The Auk. 2007;124(3):857-867. doi:10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2
apa: Reynolds, S., Dryer, K., Bollback, J. P., Uy, J. A., Patricelli, G., Robson,
T., … Braun, M. (2007). Behavioral paternity predicts genetic paternity in satin
bowerbirds, a species with a non-resource-based mating system. The Auk.
University of California Press. https://doi.org/10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2
chicago: Reynolds, Sheila, Katie Dryer, Jonathan P Bollback, J Albert Uy, Gail Patricelli,
Timothy Robson, Gerald Borgia, and Michael Braun. “Behavioral Paternity Predicts
Genetic Paternity in Satin Bowerbirds, a Species with a Non-Resource-Based Mating
System.” The Auk. University of California Press, 2007. https://doi.org/10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2.
ieee: S. Reynolds et al., “Behavioral paternity predicts genetic paternity
in satin bowerbirds, a species with a non-resource-based mating system,” The
Auk, vol. 124, no. 3. University of California Press, pp. 857–867, 2007.
ista: Reynolds S, Dryer K, Bollback JP, Uy JA, Patricelli G, Robson T, Borgia G,
Braun M. 2007. Behavioral paternity predicts genetic paternity in satin bowerbirds,
a species with a non-resource-based mating system. The Auk. 124(3), 857–867.
mla: Reynolds, Sheila, et al. “Behavioral Paternity Predicts Genetic Paternity in
Satin Bowerbirds, a Species with a Non-Resource-Based Mating System.” The Auk,
vol. 124, no. 3, University of California Press, 2007, pp. 857–67, doi:10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2.
short: S. Reynolds, K. Dryer, J.P. Bollback, J.A. Uy, G. Patricelli, T. Robson,
G. Borgia, M. Braun, The Auk 124 (2007) 857–867.
date_created: 2018-12-11T12:03:19Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:27Z
day: '01'
doi: 10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2
extern: 1
intvolume: ' 124'
issue: '3'
month: '01'
page: 857 - 867
publication: The Auk
publication_status: published
publisher: University of California Press
publist_id: '2964'
quality_controlled: 0
status: public
title: Behavioral paternity predicts genetic paternity in satin bowerbirds, a species
with a non-resource-based mating system
type: journal_article
volume: 124
year: '2007'
...
---
_id: '3450'
author:
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: György
full_name: Buzsáki, György
last_name: Buzsáki
citation:
ama: Jonas PM, Buzsáki G. Neural inhibition. Scholarpedia. 2007;2. doi:10.4249/scholarpedia.3286
apa: Jonas, P. M., & Buzsáki, G. (2007). Neural inhibition. Scholarpedia.
Scholarpedia. https://doi.org/10.4249/scholarpedia.3286
chicago: Jonas, Peter M, and György Buzsáki. “Neural Inhibition.” Scholarpedia.
Scholarpedia, 2007. https://doi.org/10.4249/scholarpedia.3286.
ieee: P. M. Jonas and G. Buzsáki, “Neural inhibition,” Scholarpedia, vol.
2. Scholarpedia, 2007.
ista: Jonas PM, Buzsáki G. 2007. Neural inhibition. Scholarpedia. 2.
mla: Jonas, Peter M., and György Buzsáki. “Neural Inhibition.” Scholarpedia,
vol. 2, Scholarpedia, 2007, doi:10.4249/scholarpedia.3286.
short: P.M. Jonas, G. Buzsáki, Scholarpedia 2 (2007).
date_created: 2018-12-11T12:03:23Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:32Z
day: '01'
doi: 10.4249/scholarpedia.3286
extern: 1
intvolume: ' 2'
month: '01'
publication: Scholarpedia
publication_status: published
publisher: Scholarpedia
publist_id: '2937'
quality_controlled: 0
status: public
title: Neural inhibition
type: journal_article
volume: 2
year: '2007'
...
---
_id: '3523'
abstract:
- lang: eng
text: On the linear track, the recent firing sequences of CA1 place cells recur
during sharp wave/ripple patterns (SWRs) in a reverse temporal order [Foster &
Wilson (2006) Nature, 440, 680-683]. We have found similar reverse-order reactivation
during SWRs in open-field exploration where the firing sequence of cells varied
before each SWR. Both the onset times and the firing patterns of cells showed
a tendency for reversed sequences during SWRs. These effects were observed for
SWRs that occurred during exploration, but not for those during longer immobility
periods. Additionally, reverse reactivation was stronger when it was preceded
by higher speed (> 5 cm/s) run periods. The trend for reverse-order SWR reactivation
was not significantly different in familiar and novel environments, even though
SWR-associated firing rates of both pyramidal cells and interneurons were reduced
in novel environments as compared with familiar. During exploration-associated
SWRs (eSWR) place cells retain place-selective firing [O'Neill et al. (2006) Neuron,
49, 143-155]. Here, we have shown that each cell's firing onset was more delayed
and firing probability more reduced during eSWRs the further the rat was from
the middle of the cell's place field; that is, cells receiving less momentary
place-related excitatory drive fired later during SWR events. However, even controlling
for place field distance, the recent firing of cells was still significantly correlated
with SWR reactivation sequences. We therefore propose that both place-related
drive and the firing history of cells contribute to reverse reactivation during
eSWRs.
author:
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Joseph
full_name: Joseph O'Neill
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Kevin
full_name: Allen, Kevin
last_name: Allen
- first_name: Timothy
full_name: Senior,Timothy
last_name: Senior
citation:
ama: Csicsvari JL, O’Neill J, Allen K, Senior T. Place-selective firing contributes
to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in
open-field exploration. European Journal of Neuroscience. 2007;26(3):704-716.
doi:10.1111/j.1460-9568.2007.05684.x
apa: Csicsvari, J. L., O’Neill, J., Allen, K., & Senior, T. (2007). Place-selective
firing contributes to the reverse-order reactivation of CA1 pyramidal cells during
sharp waves in open-field exploration. European Journal of Neuroscience.
Wiley-Blackwell. https://doi.org/10.1111/j.1460-9568.2007.05684.x
chicago: Csicsvari, Jozsef L, Joseph O’Neill, Kevin Allen, and Timothy Senior. “Place-Selective
Firing Contributes to the Reverse-Order Reactivation of CA1 Pyramidal Cells during
Sharp Waves in Open-Field Exploration.” European Journal of Neuroscience.
Wiley-Blackwell, 2007. https://doi.org/10.1111/j.1460-9568.2007.05684.x.
ieee: J. L. Csicsvari, J. O’Neill, K. Allen, and T. Senior, “Place-selective firing
contributes to the reverse-order reactivation of CA1 pyramidal cells during sharp
waves in open-field exploration,” European Journal of Neuroscience, vol.
26, no. 3. Wiley-Blackwell, pp. 704–716, 2007.
ista: Csicsvari JL, O’Neill J, Allen K, Senior T. 2007. Place-selective firing contributes
to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in
open-field exploration. European Journal of Neuroscience. 26(3), 704–716.
mla: Csicsvari, Jozsef L., et al. “Place-Selective Firing Contributes to the Reverse-Order
Reactivation of CA1 Pyramidal Cells during Sharp Waves in Open-Field Exploration.”
European Journal of Neuroscience, vol. 26, no. 3, Wiley-Blackwell, 2007,
pp. 704–16, doi:10.1111/j.1460-9568.2007.05684.x.
short: J.L. Csicsvari, J. O’Neill, K. Allen, T. Senior, European Journal of Neuroscience
26 (2007) 704–716.
date_created: 2018-12-11T12:03:46Z
date_published: 2007-08-01T00:00:00Z
date_updated: 2021-01-12T07:44:03Z
day: '01'
doi: 10.1111/j.1460-9568.2007.05684.x
extern: 1
intvolume: ' 26'
issue: '3'
month: '08'
page: 704 - 716
publication: European Journal of Neuroscience
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2862'
quality_controlled: 0
status: public
title: Place-selective firing contributes to the reverse-order reactivation of CA1
pyramidal cells during sharp waves in open-field exploration
type: journal_article
volume: 26
year: '2007'
...
---
_id: '3561'
abstract:
- lang: eng
text: The main result of this paper is an extension of de Silva's Weak Delaunay
Theorem to smoothly embedded curves and surfaces in Euclidean space. Assuming
a sufficiently fine sampling, we prove that i + 1 points in the sample span an
i-simplex in the restricted Delaunay triangulation iff every subset of the i +
1 points has a weak witness.
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Yuriy
full_name: Mileyko, Yuriy
last_name: Mileyko
citation:
ama: 'Attali D, Edelsbrunner H, Mileyko Y. Weak witnesses for Delaunay triangulations
of submanifolds. In: ACM; 2007:143-150. doi:10.1145/1236246.1236267'
apa: 'Attali, D., Edelsbrunner, H., & Mileyko, Y. (2007). Weak witnesses for
Delaunay triangulations of submanifolds (pp. 143–150). Presented at the SPM: Symposium
on Solid and Physical Modeling, ACM. https://doi.org/10.1145/1236246.1236267'
chicago: Attali, Dominique, Herbert Edelsbrunner, and Yuriy Mileyko. “Weak Witnesses
for Delaunay Triangulations of Submanifolds,” 143–50. ACM, 2007. https://doi.org/10.1145/1236246.1236267.
ieee: 'D. Attali, H. Edelsbrunner, and Y. Mileyko, “Weak witnesses for Delaunay
triangulations of submanifolds,” presented at the SPM: Symposium on Solid and
Physical Modeling, 2007, pp. 143–150.'
ista: 'Attali D, Edelsbrunner H, Mileyko Y. 2007. Weak witnesses for Delaunay triangulations
of submanifolds. SPM: Symposium on Solid and Physical Modeling, 143–150.'
mla: Attali, Dominique, et al. Weak Witnesses for Delaunay Triangulations of
Submanifolds. ACM, 2007, pp. 143–50, doi:10.1145/1236246.1236267.
short: D. Attali, H. Edelsbrunner, Y. Mileyko, in:, ACM, 2007, pp. 143–150.
conference:
name: 'SPM: Symposium on Solid and Physical Modeling'
date_created: 2018-12-11T12:03:58Z
date_published: 2007-06-01T00:00:00Z
date_updated: 2021-01-12T07:44:19Z
day: '01'
doi: 10.1145/1236246.1236267
extern: 1
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-00201055
month: '06'
oa: 1
page: 143 - 150
publication_status: published
publisher: ACM
publist_id: '2824'
quality_controlled: 0
status: public
title: Weak witnesses for Delaunay triangulations of submanifolds
type: conference
year: '2007'
...
---
_id: '3601'
abstract:
- lang: eng
text: In this paper, the multiobjective optimal design of space-based reconfigurable
sensor networks with novel adaptive MEMS antennas is investigated by using multiobjective
evolutionary algorithms. The non-dominated sorting genetic algorithm II (NSGA-II)
is employed to obtain multi-criteria Pareto-optimal solutions, which allows system
designers to easily make a reasonable trade-off choice from the set of non-dominated
solutions according to their preferences and system requirements. As a case study,
a cluster-based satellite sensing network is simulated under multiple objectives.
Most importantly, this paper also presents the application of our newly designed
adaptive MEMS antennas together with the NSGA-II to the multiobjective optimal
design of space-based reconfigurable sensor networks.
author:
- first_name: Erfu
full_name: Yang, Erfu
last_name: Yang
- first_name: Nakul
full_name: Haridas, Nakul
last_name: Haridas
- first_name: Ahmed
full_name: El-Rayis, Ahmed O
last_name: El Rayis
- first_name: Ahmet
full_name: Erdogan, Ahmet T
last_name: Erdogan
- first_name: Tughrul
full_name: Arslan, Tughrul
last_name: Arslan
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Yang E, Haridas N, El Rayis A, Erdogan A, Arslan T, Barton NH. Multiobjective
optimal design of MEMS-based reconfigurable and evolvable sensor networks for
space applications. In: IEEE; 2007:27-34. doi:10.1109/AHS.2007.76'
apa: 'Yang, E., Haridas, N., El Rayis, A., Erdogan, A., Arslan, T., & Barton,
N. H. (2007). Multiobjective optimal design of MEMS-based reconfigurable and evolvable
sensor networks for space applications (pp. 27–34). Presented at the AHS: NASA/ESA
Conference on Adaptive Hardware and Systems, IEEE. https://doi.org/10.1109/AHS.2007.76'
chicago: Yang, Erfu, Nakul Haridas, Ahmed El Rayis, Ahmet Erdogan, Tughrul Arslan,
and Nicholas H Barton. “Multiobjective Optimal Design of MEMS-Based Reconfigurable
and Evolvable Sensor Networks for Space Applications,” 27–34. IEEE, 2007. https://doi.org/10.1109/AHS.2007.76.
ieee: 'E. Yang, N. Haridas, A. El Rayis, A. Erdogan, T. Arslan, and N. H. Barton,
“Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor
networks for space applications,” presented at the AHS: NASA/ESA Conference on
Adaptive Hardware and Systems, 2007, pp. 27–34.'
ista: 'Yang E, Haridas N, El Rayis A, Erdogan A, Arslan T, Barton NH. 2007. Multiobjective
optimal design of MEMS-based reconfigurable and evolvable sensor networks for
space applications. AHS: NASA/ESA Conference on Adaptive Hardware and Systems,
27–34.'
mla: Yang, Erfu, et al. Multiobjective Optimal Design of MEMS-Based Reconfigurable
and Evolvable Sensor Networks for Space Applications. IEEE, 2007, pp. 27–34,
doi:10.1109/AHS.2007.76.
short: E. Yang, N. Haridas, A. El Rayis, A. Erdogan, T. Arslan, N.H. Barton, in:,
IEEE, 2007, pp. 27–34.
conference:
name: 'AHS: NASA/ESA Conference on Adaptive Hardware and Systems'
date_created: 2018-12-11T12:04:11Z
date_published: 2007-08-20T00:00:00Z
date_updated: 2021-01-12T07:44:35Z
day: '20'
doi: 10.1109/AHS.2007.76
extern: 1
month: '08'
page: 27 - 34
publication_status: published
publisher: IEEE
publist_id: '2782'
quality_controlled: 0
status: public
title: Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor
networks for space applications
type: conference
year: '2007'
...
---
_id: '3674'
abstract:
- lang: eng
text: "Evolution permeates all of biology. But researchers in molecular and cellular
biology, genetics, developmental biology, microbiology, and neuroscience have
only recently begun to think seriously in terms of evolution. The chief reasons
for this shift are the growing list of organisms with sequenced genomes; the increasingly
sophisticated ways of interpreting those sequences; and the ever more powerful
experimental techniques (and wider range of model organisms) with which to ask
questions about evolution as well as mechanism.\r\n\r\nEvolution serves as a primary
text for undergraduate and graduate courses in evolution. It is also a text working
scientists can use to educate themselves on how evolution affects their fields.
It differs from currently available alternatives in containing more molecular
biology than is traditionally the case. But this is not at the expense of traditional
evolutionary theory. Indeed, a glance at the Table of Contents and the authors'
interests reveals the range of material covered in this book. The authors are
world-renowned in population genetics, bacterial genomics, paleontology, human
genetics, and developmental biology. The integration of molecular biology and
evolutionary biology reflects the current direction of much research among evolutionary
scientists."
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Derek
full_name: Briggs, Derek
last_name: Briggs
- first_name: Jonathan
full_name: Eisen, Jonathan
last_name: Eisen
- first_name: David
full_name: Goldstein, David
last_name: Goldstein
- first_name: Nipam
full_name: Patel, Nipam
last_name: Patel
citation:
ama: Barton NH, Briggs D, Eisen J, Goldstein D, Patel N. Evolution. Cold
Spring Harbor Laboratory Press; 2007.
apa: Barton, N. H., Briggs, D., Eisen, J., Goldstein, D., & Patel, N. (2007).
Evolution. Cold Spring Harbor Laboratory Press.
chicago: Barton, Nicholas H, Derek Briggs, Jonathan Eisen, David Goldstein, and
Nipam Patel. Evolution. Cold Spring Harbor Laboratory Press, 2007.
ieee: N. H. Barton, D. Briggs, J. Eisen, D. Goldstein, and N. Patel, Evolution.
Cold Spring Harbor Laboratory Press, 2007.
ista: Barton NH, Briggs D, Eisen J, Goldstein D, Patel N. 2007. Evolution, Cold
Spring Harbor Laboratory Press, XIV, 833p.
mla: Barton, Nicholas H., et al. Evolution. Cold Spring Harbor Laboratory
Press, 2007.
short: N.H. Barton, D. Briggs, J. Eisen, D. Goldstein, N. Patel, Evolution, Cold
Spring Harbor Laboratory Press, 2007.
date_created: 2018-12-11T12:04:33Z
date_published: 2007-06-30T00:00:00Z
date_updated: 2021-12-21T15:55:28Z
day: '30'
extern: '1'
language:
- iso: eng
month: '06'
oa_version: None
page: XIV, 833
publication_identifier:
isbn:
- 978-087969684-9
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '2709'
quality_controlled: '1'
related_material:
link:
- description: available via catalog IST BookList
relation: other
url: https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=3251&query_desc=au%2Cwrdl%3A%20nicholas%20barton
- relation: supplementary_material
url: http://www.evolution-textbook.org/
status: public
title: Evolution
type: book
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2007'
...
---
_id: '3681'
abstract:
- lang: eng
text: |-
The extraction of a parametric global motion from a motion field is a task with several applications in video processing. We present two probabilistic formulations of the problem and carry out optimization using the RAST algorithm, a geometric matching method novel to motion estimation in video. RAST uses an exhaustive and adaptive search of transformation space and thus gives – in contrast to local sampling optimization techniques used in the past – a globally optimal solution. Among other applications, our framework can thus be used as a source of ground truth for benchmarking motion estimation algorithms.
Our main contributions are: first, the novel combination of a state-of-the-art MAP criterion for dominant motion estimation with a search procedure that guarantees global optimality. Second, experimental results that illustrate the superior performance of our approach on synthetic flow fields as well as real-world video streams. Third, a significant speedup of the search achieved by extending the model with an additional smoothness prior.
alternative_title:
- LCNS
author:
- first_name: Adrian
full_name: Ulges, Adrian
last_name: Ulges
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Daniel
full_name: Keysers,Daniel
last_name: Keysers
- first_name: Thomas
full_name: Breuel,Thomas M
last_name: Breuel
citation:
ama: 'Ulges A, Lampert C, Keysers D, Breuel T. Optimal dominant motion estimation
using adaptive search of transformation space. In: Vol 4713. Springer; 2007:204-213.
doi:10.1007/978-3-540-74936-3_21'
apa: 'Ulges, A., Lampert, C., Keysers, D., & Breuel, T. (2007). Optimal dominant
motion estimation using adaptive search of transformation space (Vol. 4713, pp.
204–213). Presented at the DAGM: German Association For Pattern Recognition, Springer.
https://doi.org/10.1007/978-3-540-74936-3_21'
chicago: Ulges, Adrian, Christoph Lampert, Daniel Keysers, and Thomas Breuel. “Optimal
Dominant Motion Estimation Using Adaptive Search of Transformation Space,” 4713:204–13.
Springer, 2007. https://doi.org/10.1007/978-3-540-74936-3_21.
ieee: 'A. Ulges, C. Lampert, D. Keysers, and T. Breuel, “Optimal dominant motion
estimation using adaptive search of transformation space,” presented at the DAGM:
German Association For Pattern Recognition, 2007, vol. 4713, pp. 204–213.'
ista: 'Ulges A, Lampert C, Keysers D, Breuel T. 2007. Optimal dominant motion estimation
using adaptive search of transformation space. DAGM: German Association For Pattern
Recognition, LCNS, vol. 4713, 204–213.'
mla: Ulges, Adrian, et al. Optimal Dominant Motion Estimation Using Adaptive
Search of Transformation Space. Vol. 4713, Springer, 2007, pp. 204–13, doi:10.1007/978-3-540-74936-3_21.
short: A. Ulges, C. Lampert, D. Keysers, T. Breuel, in:, Springer, 2007, pp. 204–213.
conference:
name: 'DAGM: German Association For Pattern Recognition'
date_created: 2018-12-11T12:04:35Z
date_published: 2007-11-09T00:00:00Z
date_updated: 2021-01-12T07:45:06Z
day: '09'
doi: 10.1007/978-3-540-74936-3_21
extern: 1
intvolume: ' 4713'
month: '11'
page: 204 - 213
publication_status: published
publisher: Springer
publist_id: '2695'
quality_controlled: 0
status: public
title: Optimal dominant motion estimation using adaptive search of transformation
space
type: conference
volume: 4713
year: '2007'
...
---
_id: '3687'
abstract:
- lang: eng
text: |-
Recent years have seen huge advances in object recognition from images. Recognition rates beyond 95% are the rule rather than the exception on many datasets. However, most state-of-the-art methods can only decide if an object is present or not. They are not able to provide information on the object location or extent within in the image.
We report on a simple yet powerful scheme that extends many existing recognition methods to also perform localization of object bounding boxes. This is achieved by maximizing the classification score over all possible subrectangles in the image. Despite the impression that this would be computationally intractable, we show that in many situations efficient algorithms exist which solve a generalized maximum subrectangle problem.
We show how our method is applicable to a variety object detection frameworks and demonstrate its performance by applying it to the popular bag of visual words model, achieving competitive results on the PASCAL VOC 2006 dataset.
author:
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
- first_name: Thomas
full_name: Hofmann,Thomas
last_name: Hofmann
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Blaschko M, Hofmann T, Lampert C. Efficient Subwindow Search for Object
Localization. Max-Planck-Institute for Biological Cybernetics; 2007.
apa: Blaschko, M., Hofmann, T., & Lampert, C. (2007). Efficient subwindow
search for object localization. Unknown. Max-Planck-Institute for Biological
Cybernetics.
chicago: Blaschko, Matthew, Thomas Hofmann, and Christoph Lampert. Efficient
Subwindow Search for Object Localization. Unknown. Max-Planck-Institute
for Biological Cybernetics, 2007.
ieee: M. Blaschko, T. Hofmann, and C. Lampert, Efficient subwindow search for
object localization, no. 164. Max-Planck-Institute for Biological Cybernetics,
2007.
ista: Blaschko M, Hofmann T, Lampert C. 2007. Efficient subwindow search for object
localization, Max-Planck-Institute for Biological Cybernetics,p.
mla: Blaschko, Matthew, et al. “Efficient Subwindow Search for Object Localization.”
Unknown, no. 164, Max-Planck-Institute for Biological Cybernetics, 2007.
short: M. Blaschko, T. Hofmann, C. Lampert, Efficient Subwindow Search for Object
Localization, Max-Planck-Institute for Biological Cybernetics, 2007.
date_created: 2018-12-11T12:04:37Z
date_published: 2007-08-01T00:00:00Z
date_updated: 2019-04-26T07:22:33Z
day: '01'
extern: 1
issue: '164'
main_file_link:
- open_access: '0'
url: http://www.kyb.tuebingen.mpg.de/fileadmin/user_upload/files/publications/TR-164_[0].pdf
month: '08'
publication: Unknown
publication_status: published
publisher: Max-Planck-Institute for Biological Cybernetics
publist_id: '2681'
quality_controlled: 0
status: public
title: Efficient subwindow search for object localization
type: report
year: '2007'
...