---
_id: '3207'
abstract:
- lang: eng
text: 'Cosegmentation is typically defined as the task of jointly segmenting something
similar in a given set of images. Existing methods are too generic and so far
have not demonstrated competitive results for any specific task. In this paper
we overcome this limitation by adding two new aspects to cosegmentation: (1) the
"something" has to be an object, and (2) the "similarity"
measure is learned. In this way, we are able to achieve excellent results on the
recently introduced iCoseg dataset, which contains small sets of images of either
the same object instance or similar objects of the same class. The challenge of
this dataset lies in the extreme changes in viewpoint, lighting, and object deformations
within each set. We are able to considerably outperform several competitors. To
achieve this performance, we borrow recent ideas from object recognition: the
use of powerful features extracted from a pool of candidate object-like segmentations.
We believe that our work will be beneficial to several application areas, such
as image retrieval.'
author:
- first_name: Sara
full_name: Vicente, Sara
last_name: Vicente
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Vicente S, Rother C, Kolmogorov V. Object cosegmentation. In: IEEE; 2011:2217-2224.
doi:10.1109/CVPR.2011.5995530'
apa: 'Vicente, S., Rother, C., & Kolmogorov, V. (2011). Object cosegmentation
(pp. 2217–2224). Presented at the CVPR: Computer Vision and Pattern Recognition,
IEEE. https://doi.org/10.1109/CVPR.2011.5995530'
chicago: Vicente, Sara, Carsten Rother, and Vladimir Kolmogorov. “Object Cosegmentation,”
2217–24. IEEE, 2011. https://doi.org/10.1109/CVPR.2011.5995530.
ieee: 'S. Vicente, C. Rother, and V. Kolmogorov, “Object cosegmentation,” presented
at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 2217–2224.'
ista: 'Vicente S, Rother C, Kolmogorov V. 2011. Object cosegmentation. CVPR: Computer
Vision and Pattern Recognition, 2217–2224.'
mla: Vicente, Sara, et al. Object Cosegmentation. IEEE, 2011, pp. 2217–24,
doi:10.1109/CVPR.2011.5995530.
short: S. Vicente, C. Rother, V. Kolmogorov, in:, IEEE, 2011, pp. 2217–2224.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:02:01Z
date_published: 2011-08-22T00:00:00Z
date_updated: 2021-01-12T07:41:48Z
day: '22'
doi: 10.1109/CVPR.2011.5995530
extern: 1
month: '08'
page: 2217 - 2224
publication_status: published
publisher: IEEE
publist_id: '3477'
quality_controlled: 0
status: public
title: Object cosegmentation
type: conference
year: '2011'
...
---
_id: '3236'
abstract:
- lang: eng
text: 'If a cryptographic primitive remains secure even if ℓ bits about the secret
key are leaked to the adversary, one would expect that at least one of n independent
instantiations of the scheme remains secure given n·ℓ bits of leakage. This intuition
has been proven true for schemes satisfying some special information-theoretic
properties by Alwen et al. [Eurocrypt''10]. On the negative side, Lewko and Waters
[FOCS''10] construct a CPA secure public-key encryption scheme for which this
intuition fails. The counterexample of Lewko and Waters leaves open the interesting
possibility that for any scheme there exists a constant c>0, such that n fold
repetition remains secure against c·n·ℓ bits of leakage. Furthermore, their counterexample
requires the n copies of the encryption scheme to share a common reference parameter,
leaving open the possibility that the intuition is true for all schemes without
common setup. In this work we give a stronger counterexample ruling out these
possibilities. We construct a signature scheme such that: 1. a single instantiation
remains secure given ℓ = log(k) bits of leakage where k is a security parameter.
2. any polynomial number of independent instantiations can be broken (in the strongest
sense of key-recovery) given ℓ′ = poly(k) bits of leakage. Note that ℓ does not
depend on the number of instances. The computational assumption underlying our
counterexample is that non-interactive computationally sound proofs exist. Moreover,
under a stronger (non-standard) assumption about such proofs, our counterexample
does not require a common reference parameter. The underlying idea of our counterexample
is rather generic and can be applied to other primitives like encryption schemes.
© 2011 International Association for Cryptologic Research.'
alternative_title:
- LNCS
author:
- first_name: Abhishek
full_name: Jain, Abhishek
last_name: Jain
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Jain A, Pietrzak KZ. Parallel repetition for leakage resilience amplification
revisited. In: Vol 6597. Springer; 2011:58-69. doi:10.1007/978-3-642-19571-6_5'
apa: 'Jain, A., & Pietrzak, K. Z. (2011). Parallel repetition for leakage resilience
amplification revisited (Vol. 6597, pp. 58–69). Presented at the TCC: Theory of
Cryptography Conference, Springer. https://doi.org/10.1007/978-3-642-19571-6_5'
chicago: Jain, Abhishek, and Krzysztof Z Pietrzak. “Parallel Repetition for Leakage
Resilience Amplification Revisited,” 6597:58–69. Springer, 2011. https://doi.org/10.1007/978-3-642-19571-6_5.
ieee: 'A. Jain and K. Z. Pietrzak, “Parallel repetition for leakage resilience amplification
revisited,” presented at the TCC: Theory of Cryptography Conference, 2011, vol.
6597, pp. 58–69.'
ista: 'Jain A, Pietrzak KZ. 2011. Parallel repetition for leakage resilience amplification
revisited. TCC: Theory of Cryptography Conference, LNCS, vol. 6597, 58–69.'
mla: Jain, Abhishek, and Krzysztof Z. Pietrzak. Parallel Repetition for Leakage
Resilience Amplification Revisited. Vol. 6597, Springer, 2011, pp. 58–69,
doi:10.1007/978-3-642-19571-6_5.
short: A. Jain, K.Z. Pietrzak, in:, Springer, 2011, pp. 58–69.
conference:
name: 'TCC: Theory of Cryptography Conference'
date_created: 2018-12-11T12:02:11Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:00Z
day: '01'
doi: 10.1007/978-3-642-19571-6_5
extern: 1
month: '01'
page: 58 - 69
publication_status: published
publisher: Springer
publist_id: '3443'
quality_controlled: 0
status: public
title: Parallel repetition for leakage resilience amplification revisited
type: conference
volume: '6597 '
year: '2011'
...
---
_id: '3238'
abstract:
- lang: eng
text: We construct efficient authentication protocols and message-authentication
codes (MACs) whose security can be reduced to the learning parity with noise (LPN)
problem. Despite a large body of work - starting with the HB protocol of Hopper
and Blum in 2001 - until now it was not even known how to construct an efficient
authentication protocol from LPN which is secure against man-in-the-middle (MIM)
attacks. A MAC implies such a (two-round) protocol. © 2011 International Association
for Cryptologic Research
acknowledgement: The European Regional Development Fund (ERDF),Guardtime,Qualcomm,Swedbank
alternative_title:
- LNCS
author:
- first_name: Eike
full_name: Kiltz, Eike
last_name: Kiltz
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: David
full_name: Cash, David
last_name: Cash
- first_name: Abhishek
full_name: Jain, Abhishek
last_name: Jain
- first_name: Daniele
full_name: Venturi, Daniele
last_name: Venturi
citation:
ama: 'Kiltz E, Pietrzak KZ, Cash D, Jain A, Venturi D. Efficient authentication
from hard learning problems. In: Vol 6632. Springer; 2011:7-26. doi:10.1007/978-3-642-20465-4_3'
apa: 'Kiltz, E., Pietrzak, K. Z., Cash, D., Jain, A., & Venturi, D. (2011).
Efficient authentication from hard learning problems (Vol. 6632, pp. 7–26). Presented
at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Tallinn,
Estonia: Springer. https://doi.org/10.1007/978-3-642-20465-4_3'
chicago: Kiltz, Eike, Krzysztof Z Pietrzak, David Cash, Abhishek Jain, and Daniele
Venturi. “Efficient Authentication from Hard Learning Problems,” 6632:7–26. Springer,
2011. https://doi.org/10.1007/978-3-642-20465-4_3.
ieee: 'E. Kiltz, K. Z. Pietrzak, D. Cash, A. Jain, and D. Venturi, “Efficient authentication
from hard learning problems,” presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, Tallinn, Estonia, 2011, vol. 6632, pp. 7–26.'
ista: 'Kiltz E, Pietrzak KZ, Cash D, Jain A, Venturi D. 2011. Efficient authentication
from hard learning problems. EUROCRYPT: Theory and Applications of Cryptographic
Techniques, LNCS, vol. 6632, 7–26.'
mla: Kiltz, Eike, et al. Efficient Authentication from Hard Learning Problems.
Vol. 6632, Springer, 2011, pp. 7–26, doi:10.1007/978-3-642-20465-4_3.
short: E. Kiltz, K.Z. Pietrzak, D. Cash, A. Jain, D. Venturi, in:, Springer, 2011,
pp. 7–26.
conference:
end_date: 2011-05-19
location: Tallinn, Estonia
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
start_date: 2011-05-15
date_created: 2018-12-11T12:02:11Z
date_published: 2011-05-01T00:00:00Z
date_updated: 2023-09-20T11:20:57Z
day: '01'
doi: 10.1007/978-3-642-20465-4_3
extern: '1'
intvolume: ' 6632'
language:
- iso: eng
month: '05'
oa_version: None
page: 7 - 26
publication_status: published
publisher: Springer
publist_id: '3442'
quality_controlled: '1'
related_material:
record:
- id: '1187'
relation: later_version
status: public
status: public
title: Efficient authentication from hard learning problems
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6632
year: '2011'
...
---
_id: '3239'
abstract:
- lang: eng
text: Tampering attacks are cryptanalytic attacks on the implementation of cryptographic
algorithms (e.g., smart cards), where an adversary introduces faults with the
hope that the tampered device will reveal secret information. Inspired by the
work of Ishai et al. [Eurocrypt'06], we propose a compiler that transforms any
circuit into a new circuit with the same functionality, but which is resilient
against a well-defined and powerful tampering adversary. More concretely, our
transformed circuits remain secure even if the adversary can adaptively tamper
with every wire in the circuit as long as the tampering fails with some probability
δ>0. This additional requirement is motivated by practical tampering attacks,
where it is often difficult to guarantee the success of a specific attack. Formally,
we show that a q-query tampering attack against the transformed circuit can be
"simulated" with only black-box access to the original circuit and log(q)
bits of additional auxiliary information. Thus, if the implemented cryptographic
scheme is secure against log(q) bits of leakage, then our implementation is tamper-proof
in the above sense. Surprisingly, allowing for this small amount of information
leakage allows for much more efficient compilers, which moreover do not require
randomness during evaluation. Similar to earlier works our compiler requires small,
stateless and computation-independent tamper-proof gadgets. Thus, our result can
be interpreted as reducing the problem of shielding arbitrary complex computation
to protecting simple components. © 2011 Springer-Verlag.
alternative_title:
- LNCS
author:
- first_name: Sebastian
full_name: Faust, Sebastian
last_name: Faust
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Daniele
full_name: Venturi, Daniele
last_name: Venturi
citation:
ama: 'Faust S, Pietrzak KZ, Venturi D. Tamper proof circuits How to trade leakage
for tamper resilience. In: Vol 6755. Springer; 2011:391-402. doi:10.1007/978-3-642-22006-7_33'
apa: 'Faust, S., Pietrzak, K. Z., & Venturi, D. (2011). Tamper proof circuits
How to trade leakage for tamper resilience (Vol. 6755, pp. 391–402). Presented
at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/978-3-642-22006-7_33'
chicago: Faust, Sebastian, Krzysztof Z Pietrzak, and Daniele Venturi. “Tamper Proof
Circuits How to Trade Leakage for Tamper Resilience,” 6755:391–402. Springer,
2011. https://doi.org/10.1007/978-3-642-22006-7_33.
ieee: 'S. Faust, K. Z. Pietrzak, and D. Venturi, “Tamper proof circuits How to trade
leakage for tamper resilience,” presented at the ICALP: Automata, Languages and
Programming, 2011, vol. 6755, no. Part 1, pp. 391–402.'
ista: 'Faust S, Pietrzak KZ, Venturi D. 2011. Tamper proof circuits How to trade
leakage for tamper resilience. ICALP: Automata, Languages and Programming, LNCS,
vol. 6755, 391–402.'
mla: Faust, Sebastian, et al. Tamper Proof Circuits How to Trade Leakage for
Tamper Resilience. Vol. 6755, no. Part 1, Springer, 2011, pp. 391–402, doi:10.1007/978-3-642-22006-7_33.
short: S. Faust, K.Z. Pietrzak, D. Venturi, in:, Springer, 2011, pp. 391–402.
conference:
name: 'ICALP: Automata, Languages and Programming'
date_created: 2018-12-11T12:02:12Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:02Z
day: '01'
doi: 10.1007/978-3-642-22006-7_33
extern: 1
issue: Part 1
month: '01'
page: 391 - 402
publication_status: published
publisher: Springer
publist_id: '3441'
quality_controlled: 0
status: public
title: Tamper proof circuits How to trade leakage for tamper resilience
type: conference
volume: '6755 '
year: '2011'
...
---
_id: '3240'
abstract:
- lang: eng
text: 'The famous Leftover Hash Lemma (LHL) states that (almost) universal hash
functions are good randomness extractors. Despite its numerous applications, LHL-based
extractors suffer from the following two limitations: - Large Entropy Loss: to
extract v bits from distribution X of min-entropy m which are ε-close to uniform,
one must set v ≤ m - 2log(1/ε), meaning that the entropy loss L = def m - v ≥
2 log(1/ε). For many applications, such entropy loss is too large. - Large Seed
Length: the seed length n of (almost) universal hash function required by the
LHL must be at least n ≥ min (u - v, v + 2log(1/ε)) - O(1), where u is the length
of the source, and must grow with the number of extracted bits. Quite surprisingly,
we show that both limitations of the LHL - large entropy loss and large seed -
can be overcome (or, at least, mitigated) in various important scenarios. First,
we show that entropy loss could be reduced to L = log(1/ε) for the setting of
deriving secret keys for a wide range of cryptographic applications. Specifically,
the security of these schemes with an LHL-derived key gracefully degrades from
ε to at most ε + √ε2-L. (Notice that, unlike standard LHL, this bound is meaningful
even when one extracts more bits than the min-entropy we have!) Based on these
results we build a general computational extractor that enjoys low entropy loss
and can be used to instantiate a generic key derivation function for any cryptographic
application. Second, we study the soundness of the natural expand-then-extract
approach, where one uses a pseudorandom generator (PRG) to expand a short "input
seed" S into a longer "output seed" S′, and then use the resulting
S′ as the seed required by the LHL (or, more generally, by any randomness extractor).
We show that, in general, the expand-then-extract approach is not sound if the
Decisional Diffie-Hellman assumption is true. Despite that, we show that it is
sound either: (1) when extracting a "small" (logarithmic in the security
of the PRG) number of bits; or (2) in minicrypt. Implication (2) suggests that
the expand-then-extract approach is likely secure when used with "practical"
PRGs, despite lacking a reductionist proof of security! © 2011 International Association
for Cryptologic Research.'
alternative_title:
- LNCS
author:
- first_name: Boaz
full_name: Barak, Boaz
last_name: Barak
- first_name: Yevgeniy
full_name: Dodis, Yevgeniy
last_name: Dodis
- first_name: Hugo
full_name: Krawczyk, Hugo
last_name: Krawczyk
- first_name: Olivier
full_name: Pereira, Olivier
last_name: Pereira
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: François
full_name: Standaert, François-Xavier
last_name: Standaert
- first_name: Yu
full_name: Yu, Yu
last_name: Yu
citation:
ama: 'Barak B, Dodis Y, Krawczyk H, et al. Leftover hash lemma revisited. In: Vol
6841. Springer; 2011:1-20. doi:
10.1007/978-3-642-22792-9_1'
apa: 'Barak, B., Dodis, Y., Krawczyk, H., Pereira, O., Pietrzak, K. Z., Standaert,
F., & Yu, Y. (2011). Leftover hash lemma revisited (Vol. 6841, pp. 1–20).
Presented at the CRYPTO: International Cryptology Conference, Springer. https://doi.org/ 10.1007/978-3-642-22792-9_1'
chicago: Barak, Boaz, Yevgeniy Dodis, Hugo Krawczyk, Olivier Pereira, Krzysztof
Z Pietrzak, François Standaert, and Yu Yu. “Leftover Hash Lemma Revisited,” 6841:1–20.
Springer, 2011. https://doi.org/
10.1007/978-3-642-22792-9_1.
ieee: 'B. Barak et al., “Leftover hash lemma revisited,” presented at the
CRYPTO: International Cryptology Conference, 2011, vol. 6841, pp. 1–20.'
ista: 'Barak B, Dodis Y, Krawczyk H, Pereira O, Pietrzak KZ, Standaert F, Yu Y.
2011. Leftover hash lemma revisited. CRYPTO: International Cryptology Conference,
LNCS, vol. 6841, 1–20.'
mla: Barak, Boaz, et al. Leftover Hash Lemma Revisited. Vol. 6841, Springer,
2011, pp. 1–20, doi: 10.1007/978-3-642-22792-9_1.
short: B. Barak, Y. Dodis, H. Krawczyk, O. Pereira, K.Z. Pietrzak, F. Standaert,
Y. Yu, in:, Springer, 2011, pp. 1–20.
conference:
name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:12Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:03Z
day: '01'
doi: ' 10.1007/978-3-642-22792-9_1'
extern: 1
intvolume: ' 6841'
month: '01'
page: 1 - 20
publication_status: published
publisher: Springer
publist_id: '3440'
quality_controlled: 0
status: public
title: Leftover hash lemma revisited
type: conference
volume: 6841
year: '2011'
...
---
_id: '3264'
abstract:
- lang: eng
text: Verification of programs with procedures, multi-threaded programs, and higher-order
functional programs can be effectively au- tomated using abstraction and refinement
schemes that rely on spurious counterexamples for abstraction discovery. The analysis
of counterexam- ples can be automated by a series of interpolation queries, or,
alterna- tively, as a constraint solving query expressed by a set of recursion
free Horn clauses. (A set of interpolation queries can be formulated as a single
constraint over Horn clauses with linear dependency structure between the unknown
relations.) In this paper we present an algorithm for solving recursion free Horn
clauses over a combined theory of linear real/rational arithmetic and uninterpreted
functions. Our algorithm performs resolu- tion to deal with the clausal structure
and relies on partial solutions to deal with (non-local) instances of functionality
axioms.
alternative_title:
- LNCS
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Corneliu
full_name: Popeea, Corneliu
last_name: Popeea
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
citation:
ama: 'Gupta A, Popeea C, Rybalchenko A. Solving recursion-free Horn clauses over
LI+UIF. In: Yang H, ed. Vol 7078. Springer; 2011:188-203. doi:10.1007/978-3-642-25318-8_16'
apa: 'Gupta, A., Popeea, C., & Rybalchenko, A. (2011). Solving recursion-free
Horn clauses over LI+UIF. In H. Yang (Ed.) (Vol. 7078, pp. 188–203). Presented
at the APLAS: Asian Symposium on Programming Languages and Systems, Kenting, Taiwan:
Springer. https://doi.org/10.1007/978-3-642-25318-8_16'
chicago: Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Solving Recursion-Free
Horn Clauses over LI+UIF.” edited by Hongseok Yang, 7078:188–203. Springer, 2011.
https://doi.org/10.1007/978-3-642-25318-8_16.
ieee: 'A. Gupta, C. Popeea, and A. Rybalchenko, “Solving recursion-free Horn clauses
over LI+UIF,” presented at the APLAS: Asian Symposium on Programming Languages
and Systems, Kenting, Taiwan, 2011, vol. 7078, pp. 188–203.'
ista: 'Gupta A, Popeea C, Rybalchenko A. 2011. Solving recursion-free Horn clauses
over LI+UIF. APLAS: Asian Symposium on Programming Languages and Systems, LNCS,
vol. 7078, 188–203.'
mla: Gupta, Ashutosh, et al. Solving Recursion-Free Horn Clauses over LI+UIF.
Edited by Hongseok Yang, vol. 7078, Springer, 2011, pp. 188–203, doi:10.1007/978-3-642-25318-8_16.
short: A. Gupta, C. Popeea, A. Rybalchenko, in:, H. Yang (Ed.), Springer, 2011,
pp. 188–203.
conference:
end_date: 2011-12-07
location: Kenting, Taiwan
name: 'APLAS: Asian Symposium on Programming Languages and Systems'
start_date: 2011-12-05
date_created: 2018-12-11T12:02:20Z
date_published: 2011-12-05T00:00:00Z
date_updated: 2021-01-12T07:42:15Z
day: '05'
department:
- _id: ToHe
doi: 10.1007/978-3-642-25318-8_16
ec_funded: 1
editor:
- first_name: Hongseok
full_name: Yang, Hongseok
last_name: Yang
intvolume: ' 7078'
language:
- iso: eng
month: '12'
oa_version: None
page: 188 - 203
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Springer
publist_id: '3383'
quality_controlled: '1'
status: public
title: Solving recursion-free Horn clauses over LI+UIF
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 7078
year: '2011'
...
---
_id: '3266'
abstract:
- lang: eng
text: We present a joint image segmentation and labeling model (JSL) which, given
a bag of figure-ground segment hypotheses extracted at multiple image locations
and scales, constructs a joint probability distribution over both the compatible
image interpretations (tilings or image segmentations) composed from those segments,
and over their labeling into categories. The process of drawing samples from the
joint distribution can be interpreted as first sampling tilings, modeled as maximal
cliques, from a graph connecting spatially non-overlapping segments in the bag
[1], followed by sampling labels for those segments, conditioned on the choice
of a particular tiling. We learn the segmentation and labeling parameters jointly,
based on Maximum Likelihood with a novel Incremental Saddle Point estimation procedure.
The partition function over tilings and labelings is increasingly more accurately
approximated by including incorrect configurations that a not-yet-competent model
rates probable during learning. We show that the proposed methodologymatches the
current state of the art in the Stanford dataset [2], as well as in VOC2010, where
41.7% accuracy on the test set is achieved.
author:
- first_name: Adrian
full_name: Ion, Adrian
id: 29F89302-F248-11E8-B48F-1D18A9856A87
last_name: Ion
- first_name: Joao
full_name: Carreira, Joao
last_name: Carreira
- first_name: Cristian
full_name: Sminchisescu, Cristian
last_name: Sminchisescu
citation:
ama: 'Ion A, Carreira J, Sminchisescu C. Probabilistic joint image segmentation
and labeling. In: NIPS Proceedings. Vol 24. Neural Information Processing
Systems Foundation; 2011:1827-1835.'
apa: 'Ion, A., Carreira, J., & Sminchisescu, C. (2011). Probabilistic joint
image segmentation and labeling. In NIPS Proceedings (Vol. 24, pp. 1827–1835).
Granada, Spain: Neural Information Processing Systems Foundation.'
chicago: Ion, Adrian, Joao Carreira, and Cristian Sminchisescu. “Probabilistic Joint
Image Segmentation and Labeling.” In NIPS Proceedings, 24:1827–35. Neural
Information Processing Systems Foundation, 2011.
ieee: A. Ion, J. Carreira, and C. Sminchisescu, “Probabilistic joint image segmentation
and labeling,” in NIPS Proceedings, Granada, Spain, 2011, vol. 24, pp.
1827–1835.
ista: 'Ion A, Carreira J, Sminchisescu C. 2011. Probabilistic joint image segmentation
and labeling. NIPS Proceedings. NIPS: Neural Information Processing Systems vol.
24, 1827–1835.'
mla: Ion, Adrian, et al. “Probabilistic Joint Image Segmentation and Labeling.”
NIPS Proceedings, vol. 24, Neural Information Processing Systems Foundation,
2011, pp. 1827–35.
short: A. Ion, J. Carreira, C. Sminchisescu, in:, NIPS Proceedings, Neural Information
Processing Systems Foundation, 2011, pp. 1827–1835.
conference:
end_date: 2011-12-14
location: Granada, Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2011-12-12
date_created: 2018-12-11T12:02:21Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2021-01-12T07:42:15Z
day: '01'
department:
- _id: HeEd
intvolume: ' 24'
language:
- iso: eng
month: '12'
oa_version: None
page: 1827 - 1835
publication: NIPS Proceedings
publication_status: published
publisher: Neural Information Processing Systems Foundation
publist_id: '3381'
quality_controlled: '1'
scopus_import: 1
status: public
title: Probabilistic joint image segmentation and labeling
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2011'
...
---
_id: '3267'
abstract:
- lang: eng
text: 'We address the problem of localizing homology classes, namely, finding the
cycle representing a given class with the most concise geometric measure. We study
the problem with different measures: volume, diameter and radius. For volume,
that is, the 1-norm of a cycle, two main results are presented. First, we prove
that the problem is NP-hard to approximate within any constant factor. Second,
we prove that for homology of dimension two or higher, the problem is NP-hard
to approximate even when the Betti number is O(1). The latter result leads to
the inapproximability of the problem of computing the nonbounding cycle with the
smallest volume and computing cycles representing a homology basis with the minimal
total volume. As for the other two measures defined by pairwise geodesic distance,
diameter and radius, we show that the localization problem is NP-hard for diameter
but is polynomial for radius. Our work is restricted to homology over the ℤ2 field.'
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Daniel
full_name: Freedman, Daniel
last_name: Freedman
citation:
ama: Chen C, Freedman D. Hardness results for homology localization. Discrete
& Computational Geometry. 2011;45(3):425-448. doi:10.1007/s00454-010-9322-8
apa: Chen, C., & Freedman, D. (2011). Hardness results for homology localization.
Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-010-9322-8
chicago: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.”
Discrete & Computational Geometry. Springer, 2011. https://doi.org/10.1007/s00454-010-9322-8.
ieee: C. Chen and D. Freedman, “Hardness results for homology localization,” Discrete
& Computational Geometry, vol. 45, no. 3. Springer, pp. 425–448, 2011.
ista: Chen C, Freedman D. 2011. Hardness results for homology localization. Discrete
& Computational Geometry. 45(3), 425–448.
mla: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.”
Discrete & Computational Geometry, vol. 45, no. 3, Springer, 2011,
pp. 425–48, doi:10.1007/s00454-010-9322-8.
short: C. Chen, D. Freedman, Discrete & Computational Geometry 45 (2011) 425–448.
date_created: 2018-12-11T12:02:21Z
date_published: 2011-01-14T00:00:00Z
date_updated: 2023-02-21T16:07:10Z
day: '14'
department:
- _id: HeEd
doi: 10.1007/s00454-010-9322-8
intvolume: ' 45'
issue: '3'
language:
- iso: eng
month: '01'
oa_version: None
page: 425 - 448
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '3379'
quality_controlled: '1'
related_material:
record:
- id: '10909'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Hardness results for homology localization
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2011'
...
---
_id: '3268'
abstract:
- lang: eng
text: 'Algebraic topology is generally considered one of the purest subfield of
mathematics. However, over the last decade two interesting new lines of research
have emerged, one focusing on algorithms for algebraic topology, and the other
on applications of algebraic topology in engineering and science. Amongst the
new areas in which the techniques have been applied are computer vision and image
processing. In this paper, we survey the results of these endeavours. Because
algebraic topology is an area of mathematics with which most computer vision practitioners
have no experience, we review the machinery behind the theories of homology and
persistent homology; our review emphasizes intuitive explanations. In terms of
applications to computer vision, we focus on four illustrative problems: shape
signatures, natural image statistics, image denoising, and segmentation. Our hope
is that this review will stimulate interest on the part of computer vision researchers
to both use and extend the tools of this new field. '
alternative_title:
- Computer Science, Technology and Applications
author:
- first_name: Daniel
full_name: Freedman, Daniel
last_name: Freedman
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
citation:
ama: 'Freedman D, Chen C. Algebraic topology for computer vision. In: Computer
Vision. Nova Science Publishers; 2011:239-268.'
apa: Freedman, D., & Chen, C. (2011). Algebraic topology for computer vision.
In Computer Vision (pp. 239–268). Nova Science Publishers.
chicago: Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.”
In Computer Vision, 239–68. Nova Science Publishers, 2011.
ieee: D. Freedman and C. Chen, “Algebraic topology for computer vision,” in Computer
Vision, Nova Science Publishers, 2011, pp. 239–268.
ista: 'Freedman D, Chen C. 2011.Algebraic topology for computer vision. In: Computer
Vision. Computer Science, Technology and Applications, , 239–268.'
mla: Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.”
Computer Vision, Nova Science Publishers, 2011, pp. 239–68.
short: D. Freedman, C. Chen, in:, Computer Vision, Nova Science Publishers, 2011,
pp. 239–268.
date_created: 2018-12-11T12:02:22Z
date_published: 2011-11-30T00:00:00Z
date_updated: 2021-01-12T07:42:16Z
day: '30'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://www.hpl.hp.com/techreports/2009/HPL-2009-375.pdf
month: '11'
oa_version: None
page: 239 - 268
publication: Computer Vision
publication_status: published
publisher: Nova Science Publishers
publist_id: '3378'
quality_controlled: '1'
status: public
title: Algebraic topology for computer vision
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3269'
abstract:
- lang: eng
text: The unintentional scattering of light between neighboring surfaces in complex
projection environments increases the brightness and decreases the contrast, disrupting
the appearance of the desired imagery. To achieve satisfactory projection results,
the inverse problem of global illumination must be solved to cancel this secondary
scattering. In this paper, we propose a global illumination cancellation method
that minimizes the perceptual difference between the desired imagery and the actual
total illumination in the resulting physical environment. Using Gauss-Newton and
active set methods, we design a fast solver for the bound constrained nonlinear
least squares problem raised by the perceptual error metrics. Our solver is further
accelerated with a CUDA implementation and multi-resolution method to achieve
1–2 fps for problems with approximately 3000 variables. We demonstrate the global
illumination cancellation algorithm with our multi-projector system. Results show
that our method preserves the color fidelity of the desired imagery significantly
better than previous methods.
article_processing_charge: No
article_type: original
author:
- first_name: Yu
full_name: Sheng, Yu
last_name: Sheng
- first_name: Barbara
full_name: Cutler, Barbara
last_name: Cutler
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Joshua
full_name: Nasman, Joshua
last_name: Nasman
citation:
ama: Sheng Y, Cutler B, Chen C, Nasman J. Perceptual global illumination cancellation
in complex projection environments. Computer Graphics Forum. 2011;30(4):1261-1268.
doi:10.1111/j.1467-8659.2011.01985.x
apa: Sheng, Y., Cutler, B., Chen, C., & Nasman, J. (2011). Perceptual global
illumination cancellation in complex projection environments. Computer Graphics
Forum. Wiley-Blackwell. https://doi.org/10.1111/j.1467-8659.2011.01985.x
chicago: Sheng, Yu, Barbara Cutler, Chao Chen, and Joshua Nasman. “Perceptual Global
Illumination Cancellation in Complex Projection Environments.” Computer Graphics
Forum. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1467-8659.2011.01985.x.
ieee: Y. Sheng, B. Cutler, C. Chen, and J. Nasman, “Perceptual global illumination
cancellation in complex projection environments,” Computer Graphics Forum,
vol. 30, no. 4. Wiley-Blackwell, pp. 1261–1268, 2011.
ista: Sheng Y, Cutler B, Chen C, Nasman J. 2011. Perceptual global illumination
cancellation in complex projection environments. Computer Graphics Forum. 30(4),
1261–1268.
mla: Sheng, Yu, et al. “Perceptual Global Illumination Cancellation in Complex Projection
Environments.” Computer Graphics Forum, vol. 30, no. 4, Wiley-Blackwell,
2011, pp. 1261–68, doi:10.1111/j.1467-8659.2011.01985.x.
short: Y. Sheng, B. Cutler, C. Chen, J. Nasman, Computer Graphics Forum 30 (2011)
1261–1268.
date_created: 2018-12-11T12:02:22Z
date_published: 2011-07-19T00:00:00Z
date_updated: 2021-01-12T07:42:16Z
day: '19'
department:
- _id: HeEd
doi: 10.1111/j.1467-8659.2011.01985.x
intvolume: ' 30'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.cs.cmu.edu/%7Eshengyu/download/egsr2011_paper.pdf
month: '07'
oa: 1
oa_version: Published Version
page: 1261 - 1268
publication: Computer Graphics Forum
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3377'
quality_controlled: '1'
scopus_import: 1
status: public
title: Perceptual global illumination cancellation in complex projection environments
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2011'
...
---
_id: '3270'
abstract:
- lang: eng
text: 'The persistence diagram of a filtered simplicial com- plex is usually computed
by reducing the boundary matrix of the complex. We introduce a simple op- timization
technique: by processing the simplices of the complex in decreasing dimension,
we can “kill” columns (i.e., set them to zero) without reducing them. This technique
completely avoids reduction on roughly half of the columns. We demonstrate that
this idea significantly improves the running time of the reduction algorithm in
practice. We also give an output-sensitive complexity analysis for the new al-
gorithm which yields to sub-cubic asymptotic bounds under certain assumptions.'
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
citation:
ama: 'Chen C, Kerber M. Persistent homology computation with a twist. In: TU Dortmund;
2011:197-200.'
apa: 'Chen, C., & Kerber, M. (2011). Persistent homology computation with a
twist (pp. 197–200). Presented at the EuroCG: European Workshop on Computational
Geometry, Morschach, Switzerland: TU Dortmund.'
chicago: Chen, Chao, and Michael Kerber. “Persistent Homology Computation with a
Twist,” 197–200. TU Dortmund, 2011.
ieee: 'C. Chen and M. Kerber, “Persistent homology computation with a twist,” presented
at the EuroCG: European Workshop on Computational Geometry, Morschach, Switzerland,
2011, pp. 197–200.'
ista: 'Chen C, Kerber M. 2011. Persistent homology computation with a twist. EuroCG:
European Workshop on Computational Geometry, 197–200.'
mla: Chen, Chao, and Michael Kerber. Persistent Homology Computation with a Twist.
TU Dortmund, 2011, pp. 197–200.
short: C. Chen, M. Kerber, in:, TU Dortmund, 2011, pp. 197–200.
conference:
end_date: 2011-03-30
location: Morschach, Switzerland
name: 'EuroCG: European Workshop on Computational Geometry'
start_date: 2011-03-28
date_created: 2018-12-11T12:02:22Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:17Z
day: '01'
department:
- _id: HeEd
language:
- iso: eng
month: '01'
oa_version: None
page: 197 - 200
publication_status: published
publisher: TU Dortmund
publist_id: '3376'
quality_controlled: '1'
status: public
title: Persistent homology computation with a twist
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3271'
abstract:
- lang: eng
text: In this paper we present an efficient framework for computation of persis-
tent homology of cubical data in arbitrary dimensions. An existing algorithm using
simplicial complexes is adapted to the setting of cubical complexes. The proposed
approach enables efficient application of persistent homology in domains where
the data is naturally given in a cubical form. By avoiding triangulation of the
data, we significantly reduce the size of the complex. We also present a data-structure
de- signed to compactly store and quickly manipulate cubical complexes. By means
of numerical experiments, we show high speed and memory efficiency of our ap-
proach. We compare our framework to other available implementations, showing its
superiority. Finally, we report performance on selected 3D and 4D data-sets.
alternative_title:
- Theory, Algorithms, and Applications
author:
- first_name: Hubert
full_name: Wagner, Hubert
last_name: Wagner
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Erald
full_name: Vuçini, Erald
last_name: Vuçini
citation:
ama: 'Wagner H, Chen C, Vuçini E. Efficient computation of persistent homology for
cubical data. In: Peikert R, Hauser H, Carr H, Fuchs R, eds. Topological Methods
in Data Analysis and Visualization II. Springer; 2011:91-106. doi:10.1007/978-3-642-23175-9_7'
apa: Wagner, H., Chen, C., & Vuçini, E. (2011). Efficient computation of persistent
homology for cubical data. In R. Peikert, H. Hauser, H. Carr, & R. Fuchs (Eds.),
Topological Methods in Data Analysis and Visualization II (pp. 91–106).
Springer. https://doi.org/10.1007/978-3-642-23175-9_7
chicago: Wagner, Hubert, Chao Chen, and Erald Vuçini. “Efficient Computation of
Persistent Homology for Cubical Data.” In Topological Methods in Data Analysis
and Visualization II, edited by Ronald Peikert, Helwig Hauser, Hamish Carr,
and Raphael Fuchs, 91–106. Springer, 2011. https://doi.org/10.1007/978-3-642-23175-9_7.
ieee: H. Wagner, C. Chen, and E. Vuçini, “Efficient computation of persistent homology
for cubical data,” in Topological Methods in Data Analysis and Visualization
II, R. Peikert, H. Hauser, H. Carr, and R. Fuchs, Eds. Springer, 2011, pp.
91–106.
ista: 'Wagner H, Chen C, Vuçini E. 2011.Efficient computation of persistent homology
for cubical data. In: Topological Methods in Data Analysis and Visualization II.
Theory, Algorithms, and Applications, , 91–106.'
mla: Wagner, Hubert, et al. “Efficient Computation of Persistent Homology for Cubical
Data.” Topological Methods in Data Analysis and Visualization II, edited
by Ronald Peikert et al., Springer, 2011, pp. 91–106, doi:10.1007/978-3-642-23175-9_7.
short: H. Wagner, C. Chen, E. Vuçini, in:, R. Peikert, H. Hauser, H. Carr, R. Fuchs
(Eds.), Topological Methods in Data Analysis and Visualization II, Springer, 2011,
pp. 91–106.
date_created: 2018-12-11T12:02:23Z
date_published: 2011-11-14T00:00:00Z
date_updated: 2021-01-12T07:42:18Z
day: '14'
department:
- _id: HeEd
doi: 10.1007/978-3-642-23175-9_7
editor:
- first_name: Ronald
full_name: Peikert, Ronald
last_name: Peikert
- first_name: Helwig
full_name: Hauser, Helwig
last_name: Hauser
- first_name: Hamish
full_name: Carr, Hamish
last_name: Carr
- first_name: Raphael
full_name: Fuchs, Raphael
last_name: Fuchs
language:
- iso: eng
month: '11'
oa_version: None
page: 91 - 106
publication: Topological Methods in Data Analysis and Visualization II
publication_status: published
publisher: Springer
publist_id: '3375'
quality_controlled: '1'
scopus_import: 1
status: public
title: Efficient computation of persistent homology for cubical data
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3273'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
citation:
ama: Maître J-L. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors.
2011.
apa: Maître, J.-L. (2011). Mechanics of adhesion and de‐adhesion in zebrafish
germ layer progenitors. Institute of Science and Technology Austria.
chicago: Maître, Jean-Léon. “Mechanics of Adhesion and De‐adhesion in Zebrafish
Germ Layer Progenitors.” Institute of Science and Technology Austria, 2011.
ieee: J.-L. Maître, “Mechanics of adhesion and de‐adhesion in zebrafish germ layer
progenitors,” Institute of Science and Technology Austria, 2011.
ista: Maître J-L. 2011. Mechanics of adhesion and de‐adhesion in zebrafish germ
layer progenitors. Institute of Science and Technology Austria.
mla: Maître, Jean-Léon. Mechanics of Adhesion and De‐adhesion in Zebrafish Germ
Layer Progenitors. Institute of Science and Technology Austria, 2011.
short: J.-L. Maître, Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer
Progenitors, Institute of Science and Technology Austria, 2011.
date_created: 2018-12-11T12:02:23Z
date_published: 2011-12-12T00:00:00Z
date_updated: 2023-09-07T11:30:16Z
day: '12'
degree_awarded: PhD
department:
- _id: CaHe
language:
- iso: eng
month: '12'
oa_version: None
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '3373'
status: public
supervisor:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
title: Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2011'
...
---
_id: '3275'
abstract:
- lang: eng
text: 'Chemokines organize immune cell trafficking by inducing either directed (tactic)
or random (kinetic) migration and by activating integrins in order to support
surface adhesion (haptic). Beyond that the same chemokines can establish clearly
defined functional areas in secondary lymphoid organs. Until now it is unclear
how chemokines can fulfill such diverse functions. One decisive prerequisite to
explain these capacities is to know how chemokines are presented in tissue. In
theory chemokines could occur either soluble or immobilized, and could be distributed
either homogenously or as a concentration gradient. To dissect if and how the
presenting mode of chemokines influences immune cells, I tested the response of
dendritic cells (DCs) to differentially displayed chemokines. DCs are antigen
presenting cells that reside in the periphery and migrate into draining lymph
nodes (LNs) once exposed to inflammatory stimuli to activate naïve T cells. DCs
are guided to and within the LN by the chemokine receptor CCR7, which has two
ligands, the chemokines CCL19 and CCL21. Both CCR7 ligands are expressed by fibroblastic
reticular cells in the LN, but differ in their ability to bind to heparan sulfate
residues. CCL21 has a highly charged C-terminal extension, which mediates binding
to anionic surfaces, whereas CCL19 is lacking such residues and likely distributes
as a soluble molecule. This study shows that surface-bound CCL21 causes random,
haptokinetic DC motility, which is confined to the chemokine coated area by insideout
activation of β2 integrins that mediate cell binding to the surface. CCL19 on
the other hand forms concentration gradients which trigger directional, chemotactic
movement, but no surface adhesion. In addition DCs can actively manipulate this
system by recruiting and activating serine proteases on their surfaces, which
create - by proteolytically removing the adhesive C-terminus - a solubilized variant
of CCL21 that functionally resembles CCL19. By generating a CCL21 concentration
gradient DCs establish a positive feedback loop to recruit further DCs from the
periphery to the CCL21 coated region. In addition DCs can sense chemotactic gradients
as well as immobilized haptokinetic fields at the same time and integrate these
signals. The result is chemotactically biased haptokinesis - directional migration
confined to a chemokine coated track or area - which could explain the dynamic
but spatially tightly controlled swarming leukocyte locomotion patterns that have
been observed in lymphatic organs by intravital microscopists. The finding that
DCs can approach soluble cues in a non-adhesive manner while they attach to surfaces
coated with immobilized cues raises the question how these cells transmit intracellular
forces to the environment, especially in the non-adherent migration mode. In order
to migrate, cells have to generate and transmit force to the extracellular substrate.
Force transmission is the prerequisite to procure an expansion of the leading
edge and a forward motion of the whole cell body. In the current conceptions actin
polymerization at the leading edge is coupled to extracellular ligands via the
integrin family of transmembrane receptors, which allows the transmission of intracellular
force. Against the paradigm of force transmission during migration, leukocytes,
like DCs, are able to migrate in threedimensional environments without using integrin
transmembrane receptors (Lämmermann et al., 2008). This reflects the biological
function of leukocytes, as they can invade almost all tissues, whereby their migration
has to be independent from the extracellular environment. How the cells can achieve
this is unclear. For this study I examined DC migration in a defined threedimensional
environment and highlighted actin-dynamics with the probe Lifeact-GFP. The result
was that chemotactic DCs can switch between integrin-dependent and integrin- independent
locomotion and can thereby adapt to the adhesive properties of their environment.
If the cells are able to couple their actin cytoskeleton to the substrate, actin
polymerization is entirely converted into protrusion. Without coupling the actin
cortex undergoes slippage and retrograde actin flow can be observed. But retrograde
actin flow can be completely compensated by higher actin polymerization rate keeping
the migration velocity and the shape of the cells unaltered. Mesenchymal cells
like fibroblast cannot balance the loss of adhesive interaction, cannot protrude
into open space and, therefore, strictly depend on integrinmediated force coupling.
This leukocyte specific phenomenon of “adaptive force transmission” endows these
cells with the unique ability to transit and invade almost every type of tissue. '
acknowledgement: "I would like to express my sincere gratitude to the following people
who made with their continuous support and encouragement this thesis possible: First,
I want to thank Prof. Dr. Michael Sixt for his excellent supervision and mentoring,
especially for the nice, relaxed working atmosphere, a lot of brilliant ideas and
the freedom to work in my own way.\r\n\r\nProf. Dr. Reinhard Fässler for his constant
support of the Sixt lab and for providing excellent working conditions. \r\n\r\nProf.
Dr. Sanjiv Luther and Prof. Dr. Tobias Bollenbach for agreeing to be member of my
thesis committee and to evaluate my work.\r\n\r\nDr. Walther Göhring, Carmen Schmitz,
the Recombinant Protein Production core facility and the animal care takers for
providing the “infrastructure” for this thesis. \r\n\r\nProf. Dr. Daniel Legler,
Markus Bruckner and Dr. Julien Polleux for very fruitful collaborations and discussions.\r\n\r\nMy
labmates for their help, a lot of discussions and to make the Sixt lab to a convenient
place to work : Karin Hirsch, Tim Lämmeramnn, Holger Pflicke, Jörg Renkawitz, Michele
Weber and Alexander Eichner All members of the Department of Molecular Medicine
for their help. Especially I want to thank Sarah Schmidt, Karin Hirsch and Raphael
Ruppert for their friendship, nice chats and their uncensored point of view. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Kathrin
full_name: Schumann, Kathrin
id: F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F
last_name: Schumann
citation:
ama: Schumann K. The role of chemotactic gradients in dendritic cell migration.
2011.
apa: Schumann, K. (2011). The role of chemotactic gradients in dendritic cell
migration. Institute of Science and Technology Austria.
chicago: Schumann, Kathrin. “The Role of Chemotactic Gradients in Dendritic Cell
Migration.” Institute of Science and Technology Austria, 2011.
ieee: K. Schumann, “The role of chemotactic gradients in dendritic cell migration,”
Institute of Science and Technology Austria, 2011.
ista: Schumann K. 2011. The role of chemotactic gradients in dendritic cell migration.
Institute of Science and Technology Austria.
mla: Schumann, Kathrin. The Role of Chemotactic Gradients in Dendritic Cell Migration.
Institute of Science and Technology Austria, 2011.
short: K. Schumann, The Role of Chemotactic Gradients in Dendritic Cell Migration,
Institute of Science and Technology Austria, 2011.
date_created: 2018-12-11T12:02:24Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2023-09-07T11:31:48Z
day: '01'
ddc:
- '570'
- '579'
degree_awarded: PhD
department:
- _id: MiSi
file:
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creator: dernst
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success: 1
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has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '141'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '3371'
pubrep_id: '11'
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
title: The role of chemotactic gradients in dendritic cell migration
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2011'
...
---
_id: '3276'
abstract:
- lang: eng
text: 'We present an algorithm to identify individual neural spikes observed on
high-density multi-electrode arrays (MEAs). Our method can distinguish large numbers
of distinct neural units, even when spikes overlap, and accounts for intrinsic
variability of spikes from each unit. As MEAs grow larger, it is important to
find spike-identification methods that are scalable, that is, the computational
cost of spike fitting should scale well with the number of units observed. Our
algorithm accomplishes this goal, and is fast, because it exploits the spatial
locality of each unit and the basic biophysics of extracellular signal propagation.
Human interaction plays a key role in our method; but effort is minimized and
streamlined via a graphical interface. We illustrate our method on data from guinea
pig retinal ganglion cells and document its performance on simulated data consisting
of spikes added to experimentally measured background noise. We present several
tests demonstrating that the algorithm is highly accurate: it exhibits low error
rates on fits to synthetic data, low refractory violation rates, good receptive
field coverage, and consistency across users.'
acknowledgement: |+
This work was supported by National Science Foundation (NSF) grants IBN-0344678, EF-0928048, National Institutes of Health (NIH) grant RO1 EY08124, NIH training grant T32-07035, and NIH training grant 5T90DA022763-04.
Michael Berry and Olivier Marre have developed an algorithm similar to, but different from, ours (manuscript in preparation). We thank them for discussions of their work, and specifically thank Olivier Marre for suggesting to us that the most complete subtraction of a spike can be obtained by refitting the spike without a prior.
author:
- first_name: Jason
full_name: Prentice, Jason S
last_name: Prentice
- first_name: Jan
full_name: Homann, Jan
last_name: Homann
- first_name: Kristina
full_name: Simmons, Kristina D
last_name: Simmons
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Vijay
full_name: Balasubramanian, Vijay
last_name: Balasubramanian
- first_name: Philip
full_name: Nelson, Philip C
last_name: Nelson
citation:
ama: Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. Fast,
scalable, Bayesian spike identification for multi-electrode arrays. PLoS One.
2011;6(7). doi:10.1371/journal.pone.0019884
apa: Prentice, J., Homann, J., Simmons, K., Tkačik, G., Balasubramanian, V., &
Nelson, P. (2011). Fast, scalable, Bayesian spike identification for multi-electrode
arrays. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0019884
chicago: Prentice, Jason, Jan Homann, Kristina Simmons, Gašper Tkačik, Vijay Balasubramanian,
and Philip Nelson. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode
Arrays.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0019884.
ieee: J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, and P.
Nelson, “Fast, scalable, Bayesian spike identification for multi-electrode arrays,”
PLoS One, vol. 6, no. 7. Public Library of Science, 2011.
ista: Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. 2011.
Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS
One. 6(7).
mla: Prentice, Jason, et al. “Fast, Scalable, Bayesian Spike Identification for
Multi-Electrode Arrays.” PLoS One, vol. 6, no. 7, Public Library of Science,
2011, doi:10.1371/journal.pone.0019884.
short: J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, P. Nelson,
PLoS One 6 (2011).
date_created: 2018-12-11T12:02:24Z
date_published: 2011-07-20T00:00:00Z
date_updated: 2021-01-12T07:42:19Z
day: '20'
doi: 10.1371/journal.pone.0019884
extern: 1
file:
- access_level: open_access
checksum: 654464e99683b55a699734213d5356f1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:38Z
date_updated: 2020-07-14T12:46:06Z
file_id: '4894'
file_name: IST-2015-381-v1+1_journal.pone.0019884.pdf
file_size: 885464
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
intvolume: ' 6'
issue: '7'
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3370'
pubrep_id: '381'
quality_controlled: 0
status: public
title: Fast, scalable, Bayesian spike identification for multi-electrode arrays
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 6
year: '2011'
...
...
---
_id: '3278'
abstract:
- lang: eng
text: |-
Despite much research on the socially parasitic large blue butterflies (genus Maculinea) in the past 40 years, their relationship to their closest relatives, Phengaris, is controversial and the relationships among the remaining genera in the Glaucopsyche section are largely unresolved. The evolutionary history of this butterfly section is particularly important to understand the evolution of life history diversity con- nected to food-plant and host-ant associations in the larval stage. In the present study, we use a combi- nation of four nuclear and two mitochondrial genes to reconstruct the phylogeny of the Glaucopsyche section, and in particular, to study the relationships among and within the Phengaris–Maculinea species.
We find a clear pattern between the clades recovered in the Glaucopsyche section phylogeny and their food-plant associations, with only the Phengaris–Maculinea clade utilising more than one plant family. Maculinea is, for the first time, recovered with strong support as a monophyletic group nested within Phengaris, with the closest relative being the rare genus Caerulea. The genus Glaucopsyche is polyphyletic, including the genera Sinia and Iolana. Interestingly, we find evidence for additional potential cryptic spe- cies within the highly endangered Maculinea, which has long been suspected from morphological, ecolog- ical and molecular studies.
author:
- first_name: Roger
full_name: Vila, Roger
last_name: Vila
- first_name: Naomi
full_name: Pierce, Naomi E
last_name: Pierce
- first_name: David
full_name: Nash, David R
last_name: Nash
- first_name: Line V
full_name: Line Ugelvig
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
citation:
ama: 'Vila R, Pierce N, Nash D, Ugelvig LV. A phylogenetic revision of the Glaucopsyche
section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea
clade. Molecular Phylogenetics and Evolution. 2011;61(1):237-243. doi:10.1016/j.ympev.2011.05.016'
apa: 'Vila, R., Pierce, N., Nash, D., & Ugelvig, L. V. (2011). A phylogenetic
revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus
on the Phengaris-Maculinea clade. Molecular Phylogenetics and Evolution.
Elsevier. https://doi.org/10.1016/j.ympev.2011.05.016'
chicago: 'Vila, Roger, Naomi Pierce, David Nash, and Line V Ugelvig. “A Phylogenetic
Revision of the Glaucopsyche Section (Lepidoptera: Lycaenidae), with Special Focus
on the Phengaris-Maculinea Clade.” Molecular Phylogenetics and Evolution.
Elsevier, 2011. https://doi.org/10.1016/j.ympev.2011.05.016.'
ieee: 'R. Vila, N. Pierce, D. Nash, and L. V. Ugelvig, “A phylogenetic revision
of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the
Phengaris-Maculinea clade,” Molecular Phylogenetics and Evolution, vol.
61, no. 1. Elsevier, pp. 237–243, 2011.'
ista: 'Vila R, Pierce N, Nash D, Ugelvig LV. 2011. A phylogenetic revision of the
Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea
clade. Molecular Phylogenetics and Evolution. 61(1), 237–243.'
mla: 'Vila, Roger, et al. “A Phylogenetic Revision of the Glaucopsyche Section (Lepidoptera:
Lycaenidae), with Special Focus on the Phengaris-Maculinea Clade.” Molecular
Phylogenetics and Evolution, vol. 61, no. 1, Elsevier, 2011, pp. 237–43, doi:10.1016/j.ympev.2011.05.016.'
short: R. Vila, N. Pierce, D. Nash, L.V. Ugelvig, Molecular Phylogenetics and Evolution
61 (2011) 237–243.
date_created: 2018-12-11T12:02:25Z
date_published: 2011-10-01T00:00:00Z
date_updated: 2021-01-12T07:42:20Z
day: '01'
doi: 10.1016/j.ympev.2011.05.016
extern: 1
intvolume: ' 61'
issue: '1'
month: '10'
page: 237 - 243
publication: Molecular Phylogenetics and Evolution
publication_status: published
publisher: Elsevier
publist_id: '3368'
quality_controlled: 0
status: public
title: 'A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae),
with special focus on the Phengaris-Maculinea clade'
type: journal_article
volume: 61
year: '2011'
...
---
_id: '3285'
abstract:
- lang: eng
text: Resolving the dynamical interplay of proteins and lipids in the live-cell
plasma membrane represents a central goal in current cell biology. Superresolution
concepts have introduced a means of capturing spatial heterogeneity at a nanoscopic
length scale. Similar concepts for detecting dynamical transitions (superresolution
chronoscopy) are still lacking. Here, we show that recently introduced spot-variation
fluorescence correlation spectroscopy allows for sensing transient confinement
times of membrane constituents at dramatically improved resolution. Using standard
diffraction-limited optics, spot-variation fluorescence correlation spectroscopy
captures signatures of single retardation events far below the transit time of
the tracer through the focal spot. We provide an analytical description of special
cases of transient binding of a tracer to pointlike traps, or association of a
tracer with nanodomains. The influence of trap mobility and the underlying binding
kinetics are quantified. Experimental approaches are suggested that allow for
gaining quantitative mechanistic insights into the interaction processes of membrane
constituents.
acknowledgement: Y 250-B03/Austrian Science Fund FWF/Austria
author:
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Didier
full_name: Marguet, Didier
last_name: Marguet
- first_name: Gerhard
full_name: Schuetz, Gerhard
last_name: Schuetz
citation:
ama: Ruprecht V, Wieser S, Marguet D, Schuetz G. Spot variation fluorescence correlation
spectroscopy allows for superresolution chronoscopy of confinement times in membranes.
Biophysical Journal. 2011;100(11):2839-2845. doi:10.1016/j.bpj.2011.04.035
apa: Ruprecht, V., Wieser, S., Marguet, D., & Schuetz, G. (2011). Spot variation
fluorescence correlation spectroscopy allows for superresolution chronoscopy of
confinement times in membranes. Biophysical Journal. Biophysical Society.
https://doi.org/10.1016/j.bpj.2011.04.035
chicago: Ruprecht, Verena, Stefan Wieser, Didier Marguet, and Gerhard Schuetz. “Spot
Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy
of Confinement Times in Membranes.” Biophysical Journal. Biophysical Society,
2011. https://doi.org/10.1016/j.bpj.2011.04.035.
ieee: V. Ruprecht, S. Wieser, D. Marguet, and G. Schuetz, “Spot variation fluorescence
correlation spectroscopy allows for superresolution chronoscopy of confinement
times in membranes,” Biophysical Journal, vol. 100, no. 11. Biophysical
Society, pp. 2839–2845, 2011.
ista: Ruprecht V, Wieser S, Marguet D, Schuetz G. 2011. Spot variation fluorescence
correlation spectroscopy allows for superresolution chronoscopy of confinement
times in membranes. Biophysical Journal. 100(11), 2839–2845.
mla: Ruprecht, Verena, et al. “Spot Variation Fluorescence Correlation Spectroscopy
Allows for Superresolution Chronoscopy of Confinement Times in Membranes.” Biophysical
Journal, vol. 100, no. 11, Biophysical Society, 2011, pp. 2839–45, doi:10.1016/j.bpj.2011.04.035.
short: V. Ruprecht, S. Wieser, D. Marguet, G. Schuetz, Biophysical Journal 100 (2011)
2839–2845.
date_created: 2018-12-11T12:02:27Z
date_published: 2011-06-08T00:00:00Z
date_updated: 2021-01-12T07:42:23Z
day: '08'
doi: 10.1016/j.bpj.2011.04.035
extern: '1'
intvolume: ' 100'
issue: '11'
language:
- iso: eng
month: '06'
oa_version: None
page: 2839 - 2845
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '3360'
status: public
title: Spot variation fluorescence correlation spectroscopy allows for superresolution
chronoscopy of confinement times in membranes
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2011'
...
---
_id: '3286'
abstract:
- lang: eng
text: Cationic antimicrobial peptides (CAMPs) selectively target bacterial membranes
by electrostatic interactions with negatively charged lipids. It turned out that
for inhibition of microbial growth a high CAMP membrane concentration is required,
which can be realized by the incorporation of hydrophobic groups within the peptide.
Increasing hydrophobicity, however, reduces the CAMP selectivity for bacterial
over eukaryotic host membranes, thereby causing the risk of detrimental side-effects.
In this study we addressed how cationic amphipathic peptides—in particular a CAMP
with Lysine–Leucine–Lysine repeats (termed KLK)—affect the localization and dynamics
of molecules in eukaryotic membranes. We found KLK to selectively inhibit the
endocytosis of a subgroup of membrane proteins and lipids by electrostatically
interacting with negatively charged sialic acid moieties. Ultrastructural characterization
revealed the formation of membrane invaginations representing fission or fusion
intermediates, in which the sialylated proteins and lipids were immobilized. Experiments
on structurally different cationic amphipathic peptides (KLK, 6-MO-LF11-322 and
NK14-2) indicated a cooperation of electrostatic and hydrophobic forces that selectively
arrest sialylated membrane constituents.
acknowledgement: "This work was funded by the GEN-AU project of the Austrian Research
Promotion Agency, the Austrian Science Fund (FWF; project Y250-B03) and Intercell
AG.\nWe thank the following colleagues for providing plasmids and cells: Daniel
Legler (University of Konstanz, Switzerland), Jennifer Lippincott-Schwartz (NIH,
Bethesda, USA), Hannes Stockinger (Medical University Vienna, Austria), Katharina
Strub (University of Geneva, Switzerland), Lawrence Rajendran (ETH Zurich, Switzerland),
Eileen M. Lafer (UTHSC San Antonio, Texas, USA), Mark McNiven (Mayo Clinic, Minnesota,
USA), John Silvius (McGill University, Montreal, Canada), Christoph Romanin (JKU
Linz, Austria), Herbert Stangl (Medical University Vienna, Austria) and Anton van
der Merwe (Oxford University, Oxford, UK). We thank Harald Kotisch (MFPL, Vienna)
for excellent technical assistance in the processing of samples for electron microscopy
and Sergio Grinstein (Hospital for Sick Children Research Institute, Toronto) for
fruitful discussions. "
author:
- first_name: Julian
full_name: Weghuber, Julian
last_name: Weghuber
- first_name: Michael
full_name: Aichinger, Michael C.
last_name: Aichinger
- first_name: Mario
full_name: Brameshuber, Mario
last_name: Brameshuber
- first_name: Stefan
full_name: Stefan Wieser
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Verena
full_name: Verena Ruprecht
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Birgit
full_name: Plochberger, Birgit
last_name: Plochberger
- first_name: Josef
full_name: Madl, Josef
last_name: Madl
- first_name: Andreas
full_name: Horner, Andreas
last_name: Horner
- first_name: Siegfried
full_name: Reipert, Siegfried
last_name: Reipert
- first_name: Karl
full_name: Lohner, Karl
last_name: Lohner
- first_name: Tamas
full_name: Henics, Tamas
last_name: Henics
- first_name: Gerhard
full_name: Schuetz, Gerhard J
last_name: Schuetz
citation:
ama: Weghuber J, Aichinger M, Brameshuber M, et al. Cationic amphipathic peptides
accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic
host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2011;1808(10):2581-2590.
doi:10.1016/j.bbamem.2011.06.007
apa: Weghuber, J., Aichinger, M., Brameshuber, M., Wieser, S., Ruprecht, V., Plochberger,
B., … Schuetz, G. (2011). Cationic amphipathic peptides accumulate sialylated
proteins and lipids in the plasma membrane of eukaryotic host cells. Biochimica
et Biophysica Acta (BBA) - Biomembranes. Elsevier. https://doi.org/10.1016/j.bbamem.2011.06.007
chicago: Weghuber, Julian, Michael Aichinger, Mario Brameshuber, Stefan Wieser,
Verena Ruprecht, Birgit Plochberger, Josef Madl, et al. “Cationic Amphipathic
Peptides Accumulate Sialylated Proteins and Lipids in the Plasma Membrane of Eukaryotic
Host Cells.” Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier,
2011. https://doi.org/10.1016/j.bbamem.2011.06.007.
ieee: J. Weghuber et al., “Cationic amphipathic peptides accumulate sialylated
proteins and lipids in the plasma membrane of eukaryotic host cells,” Biochimica
et Biophysica Acta (BBA) - Biomembranes, vol. 1808, no. 10. Elsevier, pp.
2581–2590, 2011.
ista: Weghuber J, Aichinger M, Brameshuber M, Wieser S, Ruprecht V, Plochberger
B, Madl J, Horner A, Reipert S, Lohner K, Henics T, Schuetz G. 2011. Cationic
amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane
of eukaryotic host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes.
1808(10), 2581–2590.
mla: Weghuber, Julian, et al. “Cationic Amphipathic Peptides Accumulate Sialylated
Proteins and Lipids in the Plasma Membrane of Eukaryotic Host Cells.” Biochimica
et Biophysica Acta (BBA) - Biomembranes, vol. 1808, no. 10, Elsevier, 2011,
pp. 2581–90, doi:10.1016/j.bbamem.2011.06.007.
short: J. Weghuber, M. Aichinger, M. Brameshuber, S. Wieser, V. Ruprecht, B. Plochberger,
J. Madl, A. Horner, S. Reipert, K. Lohner, T. Henics, G. Schuetz, Biochimica et
Biophysica Acta (BBA) - Biomembranes 1808 (2011) 2581–2590.
date_created: 2018-12-11T12:02:28Z
date_published: 2011-10-01T00:00:00Z
date_updated: 2021-01-12T07:42:24Z
day: '01'
doi: 10.1016/j.bbamem.2011.06.007
extern: 1
intvolume: ' 1808'
issue: '10'
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
page: 2581 - 2590
publication: Biochimica et Biophysica Acta (BBA) - Biomembranes
publication_status: published
publisher: Elsevier
publist_id: '3359'
quality_controlled: 0
status: public
title: Cationic amphipathic peptides accumulate sialylated proteins and lipids in
the plasma membrane of eukaryotic host cells
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
volume: 1808
year: '2011'
...
---
_id: '3287'
abstract:
- lang: eng
text: 'Diffusing membrane constituents are constantly exposed to a variety of forces
that influence their stochastic path. Single molecule experiments allow for resolving
trajectories at extremely high spatial and temporal accuracy, thereby offering
insights into en route interactions of the tracer. In this review we discuss approaches
to derive information about the underlying processes, based on single molecule
tracking experiments. In particular, we focus on a new versatile way to analyze
single molecule diffusion in the absence of a full analytical treatment. The method
is based on comprehensive comparison of an experimental data set against the hypothetical
outcome of multiple experiments performed on the computer. Since Monte Carlo simulations
can be easily and rapidly performed even on state-of-the-art PCs, our method provides
a simple way for testing various - even complicated - diffusion models. We describe
the new method in detail, and show the applicability on two specific examples:
firstly, kinetic rate constants can be derived for the transient interaction of
mobile membrane proteins; secondly, residence time and corral size can be extracted
for confined diffusion.'
author:
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Markus
full_name: Axmann, Markus
last_name: Axmann
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Gerhard
full_name: Schuetz, Gerhard
last_name: Schuetz
citation:
ama: Ruprecht V, Axmann M, Wieser S, Schuetz G. What can we learn from single molecule
trajectories? Current Protein & Peptide Science. 2011;12(8):714-724.
doi:10.2174/138920311798841753
apa: Ruprecht, V., Axmann, M., Wieser, S., & Schuetz, G. (2011). What can we
learn from single molecule trajectories? Current Protein & Peptide Science.
Bentham Science Publishers. https://doi.org/10.2174/138920311798841753
chicago: Ruprecht, Verena, Markus Axmann, Stefan Wieser, and Gerhard Schuetz. “What
Can We Learn from Single Molecule Trajectories?” Current Protein & Peptide
Science. Bentham Science Publishers, 2011. https://doi.org/10.2174/138920311798841753.
ieee: V. Ruprecht, M. Axmann, S. Wieser, and G. Schuetz, “What can we learn from
single molecule trajectories?,” Current Protein & Peptide Science,
vol. 12, no. 8. Bentham Science Publishers, pp. 714–724, 2011.
ista: Ruprecht V, Axmann M, Wieser S, Schuetz G. 2011. What can we learn from single
molecule trajectories? Current Protein & Peptide Science. 12(8), 714–724.
mla: Ruprecht, Verena, et al. “What Can We Learn from Single Molecule Trajectories?”
Current Protein & Peptide Science, vol. 12, no. 8, Bentham Science
Publishers, 2011, pp. 714–24, doi:10.2174/138920311798841753.
short: V. Ruprecht, M. Axmann, S. Wieser, G. Schuetz, Current Protein & Peptide
Science 12 (2011) 714–724.
date_created: 2018-12-11T12:02:28Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2021-01-12T07:42:24Z
day: '01'
department:
- _id: CaHe
- _id: MiSi
doi: 10.2174/138920311798841753
intvolume: ' 12'
issue: '8'
language:
- iso: eng
month: '12'
oa_version: None
page: 714 - 724
publication: Current Protein & Peptide Science
publication_status: published
publisher: Bentham Science Publishers
publist_id: '3358'
quality_controlled: '1'
scopus_import: 1
status: public
title: What can we learn from single molecule trajectories?
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2011'
...
---
_id: '3288'
abstract:
- lang: eng
text: 'The zonula adherens (ZA) of epithelial cells is a site of cell-cell adhesion
where cellular forces are exerted and resisted. Increasing evidence indicates
that E-cadherin adhesion molecules at the ZA serve to sense force applied on the
junctions and coordinate cytoskeletal responses to those forces. Efforts to understand
the role that cadherins play in mechanotransduction have been limited by the lack
of assays to measure the impact of forces on the ZA. In this study we used 4D
imaging of GFP-tagged E-cadherin to analyse the movement of the ZA. Junctions
in confluent epithelial monolayers displayed prominent movements oriented orthogonal
(perpendicular) to the ZA itself. Two components were identified in these movements:
a relatively slow unidirectional (translational) component that could be readily
fitted by least-squares regression analysis, upon which were superimposed more
rapid oscillatory movements. Myosin IIB was a dominant factor responsible for
driving the unilateral translational movements. In contrast, frequency spectrum
analysis revealed that depletion of Myosin IIA increased the power of the oscillatory
movements. This implies that Myosin IIA may serve to dampen oscillatory movements
of the ZA. This extends our recent analysis of Myosin II at the ZA to demonstrate
that Myosin IIA and Myosin IIB make distinct contributions to junctional movement
at the ZA.'
acknowledgement: his work was funded by the National Health and Medical Research Council
(NHMRC) of Australia. M.S. was an Erwin Schroedinger postdoctoral fellow of the
Austrian Science Fund (FWF), S.K.W. is supported by a UQ International Research
Tuition Award and Research Scholarship, S.M .by an ANZ Trustees PhD Scholarship.
A.S.Y. is a Research Fellow of the NHMRC. Confocal imaging was performed at the
Australian Cancer Research Foundation (ACRF) Cancer Biology Imaging Centre at the
Institute for Molecular Bioscience, established with the generous support of the
ACRF.
author:
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Selwin
full_name: Wu, Selwin
last_name: Wu
- first_name: Guillermo
full_name: Gomez, Guillermo
last_name: Gomez
- first_name: Sabine
full_name: Mangold, Sabine
last_name: Mangold
- first_name: Alpha
full_name: Yap, Alpha
last_name: Yap
- first_name: Nicholas
full_name: Hamilton, Nicholas
last_name: Hamilton
citation:
ama: Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. Multicomponent analysis
of junctional movements regulated by Myosin II isoforms at the epithelial zonula
adherens. PLoS One. 2011;6(7). doi:10.1371/journal.pone.0022458
apa: Smutny, M., Wu, S., Gomez, G., Mangold, S., Yap, A., & Hamilton, N. (2011).
Multicomponent analysis of junctional movements regulated by Myosin II isoforms
at the epithelial zonula adherens. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0022458
chicago: Smutny, Michael, Selwin Wu, Guillermo Gomez, Sabine Mangold, Alpha Yap,
and Nicholas Hamilton. “Multicomponent Analysis of Junctional Movements Regulated
by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One. Public
Library of Science, 2011. https://doi.org/10.1371/journal.pone.0022458.
ieee: M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, and N. Hamilton, “Multicomponent
analysis of junctional movements regulated by Myosin II isoforms at the epithelial
zonula adherens,” PLoS One, vol. 6, no. 7. Public Library of Science, 2011.
ista: Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. 2011. Multicomponent
analysis of junctional movements regulated by Myosin II isoforms at the epithelial
zonula adherens. PLoS One. 6(7).
mla: Smutny, Michael, et al. “Multicomponent Analysis of Junctional Movements Regulated
by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One, vol.
6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0022458.
short: M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, N. Hamilton, PLoS One 6 (2011).
date_created: 2018-12-11T12:02:28Z
date_published: 2011-07-22T00:00:00Z
date_updated: 2021-01-12T07:42:25Z
day: '22'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1371/journal.pone.0022458
file:
- access_level: open_access
checksum: 57a5eb11dd05241c48c44f492b3ec3ac
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T10:51:43Z
date_updated: 2020-07-14T12:46:06Z
file_id: '6399'
file_name: 2011_PLOS_Smutny.PDF
file_size: 1984567
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3357'
quality_controlled: '1'
status: public
title: Multicomponent analysis of junctional movements regulated by Myosin II isoforms
at the epithelial zonula adherens
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2011'
...