---
_id: '3200'
abstract:
- lang: eng
  text: Motivated by various applications to computer vision, we consider the convex
    cost tension problem, which is the dual of the convex cost flow problem. In this
    paper, we first propose a primal algorithm for computing an optimal solution of
    the problem. Our primal algorithm iteratively updates primal variables by solving
    associated minimum cut problems. We show that the time complexity of the primal
    algorithm is O (K {dot operator} T (n, m)), where K is the range of primal variables
    and T (n, m) is the time needed to compute a minimum cut in a graph with n nodes
    and m edges. We then develop an improved version of the primal algorithm, called
    the primal-dual algorithm, by making good use of dual variables in addition to
    primal variables. Although its time complexity is the same as that of the primal
    algorithm, we can expect a better performance in practice. We finally consider
    an application to a computer vision problem called the panoramic image stitching.
author:
- first_name: Vladimir
  full_name: Vladimir Kolmogorov
  id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kolmogorov
- first_name: Akiyoshi
  full_name: Shioura, Akiyoshi
  last_name: Shioura
citation:
  ama: Kolmogorov V, Shioura A. New algorithms for convex cost tension problem with
    application to computer vision. <i>Discrete Optimization</i>. 2009;6(4):378-393.
    doi:<a href="https://doi.org/10.1016/j.disopt.2009.04.006">10.1016/j.disopt.2009.04.006</a>
  apa: Kolmogorov, V., &#38; Shioura, A. (2009). New algorithms for convex cost tension
    problem with application to computer vision. <i>Discrete Optimization</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.disopt.2009.04.006">https://doi.org/10.1016/j.disopt.2009.04.006</a>
  chicago: Kolmogorov, Vladimir, and Akiyoshi Shioura. “New Algorithms for Convex
    Cost Tension Problem with Application to Computer Vision.” <i>Discrete Optimization</i>.
    Elsevier, 2009. <a href="https://doi.org/10.1016/j.disopt.2009.04.006">https://doi.org/10.1016/j.disopt.2009.04.006</a>.
  ieee: V. Kolmogorov and A. Shioura, “New algorithms for convex cost tension problem
    with application to computer vision,” <i>Discrete Optimization</i>, vol. 6, no.
    4. Elsevier, pp. 378–393, 2009.
  ista: Kolmogorov V, Shioura A. 2009. New algorithms for convex cost tension problem
    with application to computer vision. Discrete Optimization. 6(4), 378–393.
  mla: Kolmogorov, Vladimir, and Akiyoshi Shioura. “New Algorithms for Convex Cost
    Tension Problem with Application to Computer Vision.” <i>Discrete Optimization</i>,
    vol. 6, no. 4, Elsevier, 2009, pp. 378–93, doi:<a href="https://doi.org/10.1016/j.disopt.2009.04.006">10.1016/j.disopt.2009.04.006</a>.
  short: V. Kolmogorov, A. Shioura, Discrete Optimization 6 (2009) 378–393.
date_created: 2018-12-11T12:01:58Z
date_published: 2009-11-01T00:00:00Z
date_updated: 2021-01-12T07:41:45Z
day: '01'
doi: 10.1016/j.disopt.2009.04.006
extern: 1
intvolume: '         6'
issue: '4'
month: '11'
page: 378 - 393
publication: Discrete Optimization
publication_status: published
publisher: Elsevier
publist_id: '3483'
quality_controlled: 0
status: public
title: New algorithms for convex cost tension problem with application to computer
  vision
type: journal_article
volume: 6
year: '2009'
...
---
_id: '3203'
abstract:
- lang: eng
  text: In recent years the Markov Random Field (MRF) has become the de facto probabilistic
    model for low-level vision applications. However, in a maximum a posteriori (MAP)
    framework, MRFs inherently encourage delta function marginal statistics. By contrast,
    many low-level vision problems have heavy tailed marginal statistics, making the
    MRF model unsuitable. In this paper we introduce a more general Marginal Probability
    Field (MPF), of which the MRF is a special, linear case, and show that convex
    energy MPFs can be used to encourage arbitrary marginal statistics. We introduce
    a flexible, extensible framework for effectively optimizing the resulting NP-hard
    MAP problem, based around dual-decomposition and a modified mincost flow algorithm,
    and which achieves global optimality in some instances. We use a range of applications,
    including image denoising and texture synthesis, to demonstrate the benefits of
    this class of MPF over MRFs.
author:
- first_name: Oliver
  full_name: Woodford, Oliver J
  last_name: Woodford
- 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: 'Woodford O, Rother C, Kolmogorov V. A global perspective on MAP inference
    for low level vision. In: IEEE; 2009:2319-2326. doi:<a href="https://doi.org/10.1109/ICCV.2009.5459434">10.1109/ICCV.2009.5459434</a>'
  apa: 'Woodford, O., Rother, C., &#38; Kolmogorov, V. (2009). A global perspective
    on MAP inference for low level vision (pp. 2319–2326). Presented at the ICCV:
    International Conference on Computer Vision, IEEE. <a href="https://doi.org/10.1109/ICCV.2009.5459434">https://doi.org/10.1109/ICCV.2009.5459434</a>'
  chicago: Woodford, Oliver, Carsten Rother, and Vladimir Kolmogorov. “A Global Perspective
    on MAP Inference for Low Level Vision,” 2319–26. IEEE, 2009. <a href="https://doi.org/10.1109/ICCV.2009.5459434">https://doi.org/10.1109/ICCV.2009.5459434</a>.
  ieee: 'O. Woodford, C. Rother, and V. Kolmogorov, “A global perspective on MAP inference
    for low level vision,” presented at the ICCV: International Conference on Computer
    Vision, 2009, pp. 2319–2326.'
  ista: 'Woodford O, Rother C, Kolmogorov V. 2009. A global perspective on MAP inference
    for low level vision. ICCV: International Conference on Computer Vision, 2319–2326.'
  mla: Woodford, Oliver, et al. <i>A Global Perspective on MAP Inference for Low Level
    Vision</i>. IEEE, 2009, pp. 2319–26, doi:<a href="https://doi.org/10.1109/ICCV.2009.5459434">10.1109/ICCV.2009.5459434</a>.
  short: O. Woodford, C. Rother, V. Kolmogorov, in:, IEEE, 2009, pp. 2319–2326.
conference:
  name: 'ICCV: International Conference on Computer Vision'
date_created: 2018-12-11T12:01:59Z
date_published: 2009-05-01T00:00:00Z
date_updated: 2021-01-12T07:41:46Z
day: '01'
doi: 10.1109/ICCV.2009.5459434
extern: 1
month: '05'
page: 2319 - 2326
publication_status: published
publisher: IEEE
publist_id: '3481'
quality_controlled: 0
status: public
title: A global perspective on MAP inference for low level vision
type: conference
year: '2009'
...
---
_id: '3230'
abstract:
- lang: eng
  text: 'We present a new approach to the design of IND-CCA2 secure hybrid encryption
    schemes in the standard model. Our approach provides an efficient generic transformation
    from 1-universal to 2-universal hash proof systems. The transformation involves
    a randomness extractor based on a 4-wise independent hash function as the key
    derivation function. Our methodology can be instantiated with efficient schemes
    based on standard intractability assumptions such as Decisional Diffie-Hellman,
    Quadratic Residuosity, and Paillier''s Decisional Composite Residuosity. Interestingly,
    our framework also allows to prove IND-CCA2 security of a hybrid version of 1991''s
    Damgård''s ElGamal public-key encryption scheme under the DDH assumption. '
alternative_title:
- LNCS
author:
- first_name: Eike
  full_name: Kiltz, Eike
  last_name: Kiltz
- first_name: Krzysztof Z
  full_name: Krzysztof Pietrzak
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
- first_name: Martijn
  full_name: Stam, Martijn
  last_name: Stam
- first_name: Moti
  full_name: Yung, Moti
  last_name: Yung
citation:
  ama: 'Kiltz E, Pietrzak KZ, Stam M, Yung M. A new randomness extraction paradigm
    for hybrid encryption. In: Vol 5479. Springer; 2009:590-609. doi:<a href="https://doi.org/10.1007/978-3-642-01001-9_34">10.1007/978-3-642-01001-9_34</a>'
  apa: 'Kiltz, E., Pietrzak, K. Z., Stam, M., &#38; Yung, M. (2009). A new randomness
    extraction paradigm for hybrid encryption (Vol. 5479, pp. 590–609). Presented
    at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer.
    <a href="https://doi.org/10.1007/978-3-642-01001-9_34">https://doi.org/10.1007/978-3-642-01001-9_34</a>'
  chicago: Kiltz, Eike, Krzysztof Z Pietrzak, Martijn Stam, and Moti Yung. “A New
    Randomness Extraction Paradigm for Hybrid Encryption,” 5479:590–609. Springer,
    2009. <a href="https://doi.org/10.1007/978-3-642-01001-9_34">https://doi.org/10.1007/978-3-642-01001-9_34</a>.
  ieee: 'E. Kiltz, K. Z. Pietrzak, M. Stam, and M. Yung, “A new randomness extraction
    paradigm for hybrid encryption,” presented at the EUROCRYPT: Theory and Applications
    of Cryptographic Techniques, 2009, vol. 5479, pp. 590–609.'
  ista: 'Kiltz E, Pietrzak KZ, Stam M, Yung M. 2009. A new randomness extraction paradigm
    for hybrid encryption. EUROCRYPT: Theory and Applications of Cryptographic Techniques,
    LNCS, vol. 5479, 590–609.'
  mla: Kiltz, Eike, et al. <i>A New Randomness Extraction Paradigm for Hybrid Encryption</i>.
    Vol. 5479, Springer, 2009, pp. 590–609, doi:<a href="https://doi.org/10.1007/978-3-642-01001-9_34">10.1007/978-3-642-01001-9_34</a>.
  short: E. Kiltz, K.Z. Pietrzak, M. Stam, M. Yung, in:, Springer, 2009, pp. 590–609.
conference:
  name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
date_created: 2018-12-11T12:02:09Z
date_published: 2009-05-28T00:00:00Z
date_updated: 2021-01-12T07:41:58Z
day: '28'
doi: 10.1007/978-3-642-01001-9_34
extern: 1
intvolume: '      5479'
month: '05'
page: 590 - 609
publication_status: published
publisher: Springer
publist_id: '3449'
quality_controlled: 0
status: public
title: A new randomness extraction paradigm for hybrid encryption
type: conference
volume: 5479
year: '2009'
...
---
_id: '3231'
abstract:
- lang: eng
  text: 'We investigate the security of &quot;padding-based&quot; encryption schemes
    in the standard model. This class contains all public-key encryption schemes where
    the encryption algorithm first applies some invertible public transformation to
    the message (the &quot;padding&quot;), followed by a trapdoor permutation. In
    particular, this class contains OAEP and its variants. Our main result is a black-box
    impossibility result showing that one cannot prove any such padding-based scheme
    chosen-ciphertext secure even assuming the existence of ideal trapdoor permutations.
    The latter is a strong ideal abstraction of trapdoor permutations which inherits
    all security properties of uniform random permutations. '
alternative_title:
- LNCS
author:
- first_name: Eike
  full_name: Kiltz, Eike
  last_name: Kiltz
- first_name: Krzysztof Z
  full_name: Krzysztof Pietrzak
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
citation:
  ama: 'Kiltz E, Pietrzak KZ. On the security of padding based encryption schemes
    Why We cannot prove OAEP secure in the standard model. In: Vol 5479. Springer;
    2009:389-406. doi:<a href="https://doi.org/10.1007/978-3-642-01001-9_23">10.1007/978-3-642-01001-9_23</a>'
  apa: 'Kiltz, E., &#38; Pietrzak, K. Z. (2009). On the security of padding based
    encryption schemes Why We cannot prove OAEP secure in the standard model (Vol.
    5479, pp. 389–406). Presented at the EUROCRYPT: Theory and Applications of Cryptographic
    Techniques, Springer. <a href="https://doi.org/10.1007/978-3-642-01001-9_23">https://doi.org/10.1007/978-3-642-01001-9_23</a>'
  chicago: Kiltz, Eike, and Krzysztof Z Pietrzak. “On the Security of Padding Based
    Encryption Schemes Why We Cannot Prove OAEP Secure in the Standard Model,” 5479:389–406.
    Springer, 2009. <a href="https://doi.org/10.1007/978-3-642-01001-9_23">https://doi.org/10.1007/978-3-642-01001-9_23</a>.
  ieee: 'E. Kiltz and K. Z. Pietrzak, “On the security of padding based encryption
    schemes Why We cannot prove OAEP secure in the standard model,” presented at the
    EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2009, vol. 5479,
    pp. 389–406.'
  ista: 'Kiltz E, Pietrzak KZ. 2009. On the security of padding based encryption schemes
    Why We cannot prove OAEP secure in the standard model. EUROCRYPT: Theory and Applications
    of Cryptographic Techniques, LNCS, vol. 5479, 389–406.'
  mla: Kiltz, Eike, and Krzysztof Z. Pietrzak. <i>On the Security of Padding Based
    Encryption Schemes Why We Cannot Prove OAEP Secure in the Standard Model</i>.
    Vol. 5479, Springer, 2009, pp. 389–406, doi:<a href="https://doi.org/10.1007/978-3-642-01001-9_23">10.1007/978-3-642-01001-9_23</a>.
  short: E. Kiltz, K.Z. Pietrzak, in:, Springer, 2009, pp. 389–406.
conference:
  name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
date_created: 2018-12-11T12:02:09Z
date_published: 2009-05-28T00:00:00Z
date_updated: 2021-01-12T07:41:58Z
day: '28'
doi: 10.1007/978-3-642-01001-9_23
extern: 1
intvolume: '      5479'
month: '05'
page: 389 - 406
publication_status: published
publisher: Springer
publist_id: '3450'
quality_controlled: 0
status: public
title: On the security of padding based encryption schemes Why We cannot prove OAEP
  secure in the standard model
type: conference
volume: 5479
year: '2009'
...
---
_id: '3232'
abstract:
- lang: eng
  text: 'A weak pseudorandom function (wPRF) is a cryptographic primitive similar
    to - but weaker than - a pseudorandom function: for wPRFs one only requires that
    the output is pseudorandom when queried on random inputs.We show that unlike &quot;normal&quot;
    PRFs, wPRFs are seedincompressible, in the sense that the output of a wPRF is
    pseudorandom even if a bounded amount of information about the key is leaked.
    As an application of this result we construct a simple mode of operation which
    - when instantiated with any wPRF - gives a leakage-resilient stream-cipher. The
    implementation of such a cipher is secure against every side-channel attack, as
    long as the amount of information leaked per round is bounded, but overall can
    be arbitrary large. The construction is simpler than the previous one (Dziembowski-Pietrzak
    FOCS''08) as it only uses a single primitive (a wPRF) in a straight forward manner. '
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
  full_name: Krzysztof Pietrzak
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
citation:
  ama: 'Pietrzak KZ. A leakage resilient mode of operation. In: Vol 5479. Springer;
    2009:462-482. doi:<a href="https://doi.org/10.1007/978-3-642-01001-9_27">10.1007/978-3-642-01001-9_27</a>'
  apa: 'Pietrzak, K. Z. (2009). A leakage resilient mode of operation (Vol. 5479,
    pp. 462–482). Presented at the CRYPTO: International Cryptology Conference, Springer.
    <a href="https://doi.org/10.1007/978-3-642-01001-9_27">https://doi.org/10.1007/978-3-642-01001-9_27</a>'
  chicago: Pietrzak, Krzysztof Z. “A Leakage Resilient Mode of Operation,” 5479:462–82.
    Springer, 2009. <a href="https://doi.org/10.1007/978-3-642-01001-9_27">https://doi.org/10.1007/978-3-642-01001-9_27</a>.
  ieee: 'K. Z. Pietrzak, “A leakage resilient mode of operation,” presented at the
    CRYPTO: International Cryptology Conference, 2009, vol. 5479, pp. 462–482.'
  ista: 'Pietrzak KZ. 2009. A leakage resilient mode of operation. CRYPTO: International
    Cryptology Conference, LNCS, vol. 5479, 462–482.'
  mla: Pietrzak, Krzysztof Z. <i>A Leakage Resilient Mode of Operation</i>. Vol. 5479,
    Springer, 2009, pp. 462–82, doi:<a href="https://doi.org/10.1007/978-3-642-01001-9_27">10.1007/978-3-642-01001-9_27</a>.
  short: K.Z. Pietrzak, in:, Springer, 2009, pp. 462–482.
conference:
  name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:09Z
date_published: 2009-05-28T00:00:00Z
date_updated: 2021-01-12T07:41:59Z
day: '28'
doi: 10.1007/978-3-642-01001-9_27
extern: 1
intvolume: '      5479'
month: '05'
page: 462 - 482
publication_status: published
publisher: Springer
publist_id: '3448'
quality_controlled: 0
status: public
title: A leakage resilient mode of operation
type: conference
volume: 5479
year: '2009'
...
---
_id: '3292'
abstract:
- lang: eng
  text: Galactofuranose (Galf) containing molecules have been described at the cell
    surface of several eukaryotes and shown to contribute to the virulence of the
    parasite Leishmania major and the fungus Aspergillus fumigatus. It is anticipated
    that a number of the surface glycoconjugates such as N-glycans or glycolipids
    are galactofuranosylated in the Golgi apparatus. This raises the question of how
    the substrate for galactofuranosylation reactions, UDP-Galf, which is synthesized
    in the cytosol, translocates into the organelles of the secretory pathway. Here
    we report the first identification of a Golgi-localized nucleotide sugar transporter,
    named GlfB, with specificity for a UDP-Galf. In vitro transport assays established
    binding of UDP-Galf to GlfB and excluded transport of several other nucleotide
    sugars. Furthermore, the implication of glfB in the galactofuranosylation of A.
    fumigatus glycoconjugates and galactomannan was demonstrated by a targeted gene
    deletion approach. Our data reveal a direct connection between galactomannan and
    the organelles of the secretory pathway that strongly suggests that the cell wall-bound
    polysaccharide originates from its glycosylphosphatidylinositol-anchored form.
author:
- first_name: Jakob
  full_name: Engel, Jakob
  last_name: Engel
- first_name: Philipp S
  full_name: Schmalhorst, Philipp S
  id: 309D50DA-F248-11E8-B48F-1D18A9856A87
  last_name: Schmalhorst
  orcid: 0000-0002-5795-0133
- first_name: Thilo
  full_name: Dörk Bousset, Thilo
  last_name: Dörk Bousset
- first_name: Vincent
  full_name: Ferrières, Vincent
  last_name: Ferrières
- first_name: Françoise
  full_name: Routier, Françoise
  last_name: Routier
citation:
  ama: Engel J, Schmalhorst PS, Dörk Bousset T, Ferrières V, Routier F. A single UDP
    galactofuranose transporter is required for galactofuranosylation in Aspergillus
    fumigatus. <i>Journal of Biological Chemistry</i>. 2009;284(49):33859-33868. doi:<a
    href="https://doi.org/10.1074/jbc.M109.070219 ">10.1074/jbc.M109.070219 </a>
  apa: Engel, J., Schmalhorst, P. S., Dörk Bousset, T., Ferrières, V., &#38; Routier,
    F. (2009). A single UDP galactofuranose transporter is required for galactofuranosylation
    in Aspergillus fumigatus. <i>Journal of Biological Chemistry</i>. American Society
    for Biochemistry and Molecular Biology. <a href="https://doi.org/10.1074/jbc.M109.070219
    ">https://doi.org/10.1074/jbc.M109.070219 </a>
  chicago: Engel, Jakob, Philipp S Schmalhorst, Thilo Dörk Bousset, Vincent Ferrières,
    and Françoise Routier. “A Single UDP Galactofuranose Transporter Is Required for
    Galactofuranosylation in Aspergillus Fumigatus.” <i>Journal of Biological Chemistry</i>.
    American Society for Biochemistry and Molecular Biology, 2009. <a href="https://doi.org/10.1074/jbc.M109.070219
    ">https://doi.org/10.1074/jbc.M109.070219 </a>.
  ieee: J. Engel, P. S. Schmalhorst, T. Dörk Bousset, V. Ferrières, and F. Routier,
    “A single UDP galactofuranose transporter is required for galactofuranosylation
    in Aspergillus fumigatus,” <i>Journal of Biological Chemistry</i>, vol. 284, no.
    49. American Society for Biochemistry and Molecular Biology, pp. 33859–33868,
    2009.
  ista: Engel J, Schmalhorst PS, Dörk Bousset T, Ferrières V, Routier F. 2009. A single
    UDP galactofuranose transporter is required for galactofuranosylation in Aspergillus
    fumigatus. Journal of Biological Chemistry. 284(49), 33859–33868.
  mla: Engel, Jakob, et al. “A Single UDP Galactofuranose Transporter Is Required
    for Galactofuranosylation in Aspergillus Fumigatus.” <i>Journal of Biological
    Chemistry</i>, vol. 284, no. 49, American Society for Biochemistry and Molecular
    Biology, 2009, pp. 33859–68, doi:<a href="https://doi.org/10.1074/jbc.M109.070219
    ">10.1074/jbc.M109.070219 </a>.
  short: J. Engel, P.S. Schmalhorst, T. Dörk Bousset, V. Ferrières, F. Routier, Journal
    of Biological Chemistry 284 (2009) 33859–33868.
date_created: 2018-12-11T12:02:30Z
date_published: 2009-12-04T00:00:00Z
date_updated: 2021-01-12T07:42:26Z
day: '04'
doi: '10.1074/jbc.M109.070219 '
extern: '1'
intvolume: '       284'
issue: '49'
language:
- iso: eng
month: '12'
oa_version: None
page: 33859 - 33868
publication: Journal of Biological Chemistry
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '3353'
quality_controlled: '1'
status: public
title: A single UDP galactofuranose transporter is required for galactofuranosylation
  in Aspergillus fumigatus
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 284
year: '2009'
...
---
_id: '3293'
abstract:
- lang: eng
  text: Chemotactic responses of Drosophila to certain esters and alcohols are experience
    dependent. When the flies are exposed after eclosion to these chemicals, the odorants
    become strongly attractive. We show that behavioral conditioning is accompanied
    by an increase in the electrophysiological responses of single neurons in sensilla
    basiconica. Sensitization involves odorants that act on a common olfactory receptor.
    The possible mechanism of imaginal conditioning and its ecological and evolutionary
    significance are discussed.
author:
- first_name: Subhra
  full_name: Chakraborty Tuhin, Subhra
  last_name: Chakraborty Tuhin
- first_name: Sarit
  full_name: Sarit Goswami
  id: 3A578F32-F248-11E8-B48F-1D18A9856A87
  last_name: Goswami
- first_name: Obaid
  full_name: Siddiqi, Obaid
  last_name: Siddiqi
citation:
  ama: Chakraborty Tuhin S, Goswami S, Siddiqi O. Sensory correlates of imaginal conditioning
    in Drosophila melanogaster. <i>Journal of Neurogenetics</i>. 2009;23(1-2):210-219.
    doi:<a href="https://doi.org/10.1080/01677060802491559 ">10.1080/01677060802491559
    </a>
  apa: Chakraborty Tuhin, S., Goswami, S., &#38; Siddiqi, O. (2009). Sensory correlates
    of imaginal conditioning in Drosophila melanogaster. <i>Journal of Neurogenetics</i>.
    Informa Healthcare. <a href="https://doi.org/10.1080/01677060802491559 ">https://doi.org/10.1080/01677060802491559
    </a>
  chicago: Chakraborty Tuhin, Subhra, Sarit Goswami, and Obaid Siddiqi. “Sensory Correlates
    of Imaginal Conditioning in Drosophila Melanogaster.” <i>Journal of Neurogenetics</i>.
    Informa Healthcare, 2009. <a href="https://doi.org/10.1080/01677060802491559 ">https://doi.org/10.1080/01677060802491559
    </a>.
  ieee: S. Chakraborty Tuhin, S. Goswami, and O. Siddiqi, “Sensory correlates of imaginal
    conditioning in Drosophila melanogaster,” <i>Journal of Neurogenetics</i>, vol.
    23, no. 1–2. Informa Healthcare, pp. 210–9, 2009.
  ista: Chakraborty Tuhin S, Goswami S, Siddiqi O. 2009. Sensory correlates of imaginal
    conditioning in Drosophila melanogaster. Journal of Neurogenetics. 23(1–2), 210–9.
  mla: Chakraborty Tuhin, Subhra, et al. “Sensory Correlates of Imaginal Conditioning
    in Drosophila Melanogaster.” <i>Journal of Neurogenetics</i>, vol. 23, no. 1–2,
    Informa Healthcare, 2009, pp. 210–19, doi:<a href="https://doi.org/10.1080/01677060802491559
    ">10.1080/01677060802491559 </a>.
  short: S. Chakraborty Tuhin, S. Goswami, O. Siddiqi, Journal of Neurogenetics 23
    (2009) 210–9.
date_created: 2018-12-11T12:02:30Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:27Z
day: '01'
doi: '10.1080/01677060802491559 '
extern: 1
intvolume: '        23'
issue: 1-2
month: '01'
page: 210 - 9
publication: Journal of Neurogenetics
publication_status: published
publisher: Informa Healthcare
publist_id: '3348'
quality_controlled: 0
status: public
title: Sensory correlates of imaginal conditioning in Drosophila melanogaster
type: journal_article
volume: 23
year: '2009'
...
---
_id: '3304'
abstract:
- lang: eng
  text: Complex traits often involve interactions between different genetic loci.
    This can lead to sign epistasis, whereby mutations that are individually deleterious
    or neutral combine to confer a fitness benefit. In order to acquire the beneficial
    genotype, an asexual population must cross a fitness valley or plateau by first
    acquiring the deleterious or neutral intermediates. Here, we present a complete,
    intuitive theoretical description of the valley-crossing process across the full
    spectrum of possible parameter regimes. We calculate the rate at which a population
    crosses a fitness valley or plateau of arbitrary width, as a function of the mutation
    rates, the population size, and the fitnesses of the intermediates. We find that
    when intermediates are close to neutral, a large population can cross even wide
    fitness valleys remarkably quickly, so that valley-crossing dynamics may be common
    even when mutations that directly increase fitness are also possible. Thus the
    evolutionary dynamics of large populations can be sensitive to the structure of
    an extended region of the fitness landscape — the population may not take directly
    uphill paths in favor of paths across valleys and plateaus that lead eventually
    to fitter genotypes. In smaller populations, we find that below a threshold size,
    which depends on the width of the fitness valley and the strength of selection
    against intermediate genotypes, valley-crossing is much less likely and hence
    the evolutionary dynamics are less influenced by distant regions of the fitness
    landscape.
author:
- first_name: Daniel
  full_name: Daniel Weissman
  id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
  last_name: Weissman
- first_name: Michael
  full_name: Desai, Michael M
  last_name: Desai
- first_name: Daniel
  full_name: Fisher, Daniel S
  last_name: Fisher
- first_name: Marcus
  full_name: Feldman, Marcus W
  last_name: Feldman
citation:
  ama: Weissman D, Desai M, Fisher D, Feldman M. The rate at which asexual populations
    cross fitness valleys. <i>Theoretical Population Biology</i>. 2009;75(4):286-300.
    doi:<a href="https://doi.org/10.1016/j.tpb.2009.02.006">10.1016/j.tpb.2009.02.006</a>
  apa: Weissman, D., Desai, M., Fisher, D., &#38; Feldman, M. (2009). The rate at
    which asexual populations cross fitness valleys. <i>Theoretical Population Biology</i>.
    Academic Press. <a href="https://doi.org/10.1016/j.tpb.2009.02.006">https://doi.org/10.1016/j.tpb.2009.02.006</a>
  chicago: Weissman, Daniel, Michael Desai, Daniel Fisher, and Marcus Feldman. “The
    Rate at Which Asexual Populations Cross Fitness Valleys.” <i>Theoretical Population
    Biology</i>. Academic Press, 2009. <a href="https://doi.org/10.1016/j.tpb.2009.02.006">https://doi.org/10.1016/j.tpb.2009.02.006</a>.
  ieee: D. Weissman, M. Desai, D. Fisher, and M. Feldman, “The rate at which asexual
    populations cross fitness valleys,” <i>Theoretical Population Biology</i>, vol.
    75, no. 4. Academic Press, pp. 286–300, 2009.
  ista: Weissman D, Desai M, Fisher D, Feldman M. 2009. The rate at which asexual
    populations cross fitness valleys. Theoretical Population Biology. 75(4), 286–300.
  mla: Weissman, Daniel, et al. “The Rate at Which Asexual Populations Cross Fitness
    Valleys.” <i>Theoretical Population Biology</i>, vol. 75, no. 4, Academic Press,
    2009, pp. 286–300, doi:<a href="https://doi.org/10.1016/j.tpb.2009.02.006">10.1016/j.tpb.2009.02.006</a>.
  short: D. Weissman, M. Desai, D. Fisher, M. Feldman, Theoretical Population Biology
    75 (2009) 286–300.
date_created: 2018-12-11T12:02:34Z
date_published: 2009-06-01T00:00:00Z
date_updated: 2021-01-12T07:42:31Z
day: '01'
doi: 10.1016/j.tpb.2009.02.006
extern: 1
intvolume: '        75'
issue: '4'
month: '06'
page: 286 - 300
publication: Theoretical Population Biology
publication_status: published
publisher: Academic Press
publist_id: '3336'
quality_controlled: 0
status: public
title: The rate at which asexual populations cross fitness valleys
type: journal_article
volume: 75
year: '2009'
...
---
_id: '3309'
abstract:
- lang: eng
  text: |2-


    Mastitis, a worldwide endemic disease of dairy cows, is an important cause of decreased efficiency in milk production. Early medical treatment can reduce the nonreversible losses in milk production caused by this infection. Various diagnostic tests for mastitis are available, including a test measuring the electrical conductivity of milk (MEC test), the industry standard of somatic cell counting (SCC test), a bacteriological test, and a recently developed test measuring mammary associated amyloid A (MAA test). None of these tests is considered a gold standard, however. The aim of the present study was to determine which of these tests provides the best results, and at what cost, to improve the efficiency of milk production. For this study, 25 cows were tested at all four quarters of the udder with each of the aforementioned mastitis diagnostic tests. Based on the data, the disease prevalence as well as the sensitivity and the specificity of the four tests were estimated with a Bayesian approach by extending the Hui and Walter model with two independent tests and two populations to a model with four partially dependent tests and one population. This model was further combined with a receiver operating characteristics analysis to estimate the overall test accuracy.
author:
- first_name: Caroline
  full_name: Caroline Uhler
  id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
  last_name: Uhler
  orcid: 0000-0002-7008-0216
citation:
  ama: 'Uhler C. Mastitis in dairy production: Estimation of sensitivity, specificity
    and disease prevalence in the absence of a gold standard. <i>Journal of Agricultural
    Biological and Environmental Statistics</i>. 2009;14(1):79-98. doi:<a href="https://doi.org/10.1198/jabes.2009.0005">10.1198/jabes.2009.0005</a>'
  apa: 'Uhler, C. (2009). Mastitis in dairy production: Estimation of sensitivity,
    specificity and disease prevalence in the absence of a gold standard. <i>Journal
    of Agricultural Biological and Environmental Statistics</i>. Springer. <a href="https://doi.org/10.1198/jabes.2009.0005">https://doi.org/10.1198/jabes.2009.0005</a>'
  chicago: 'Uhler, Caroline. “Mastitis in Dairy Production: Estimation of Sensitivity,
    Specificity and Disease Prevalence in the Absence of a Gold Standard.” <i>Journal
    of Agricultural Biological and Environmental Statistics</i>. Springer, 2009. <a
    href="https://doi.org/10.1198/jabes.2009.0005">https://doi.org/10.1198/jabes.2009.0005</a>.'
  ieee: 'C. Uhler, “Mastitis in dairy production: Estimation of sensitivity, specificity
    and disease prevalence in the absence of a gold standard,” <i>Journal of Agricultural
    Biological and Environmental Statistics</i>, vol. 14, no. 1. Springer, pp. 79–98,
    2009.'
  ista: 'Uhler C. 2009. Mastitis in dairy production: Estimation of sensitivity, specificity
    and disease prevalence in the absence of a gold standard. Journal of Agricultural
    Biological and Environmental Statistics. 14(1), 79–98.'
  mla: 'Uhler, Caroline. “Mastitis in Dairy Production: Estimation of Sensitivity,
    Specificity and Disease Prevalence in the Absence of a Gold Standard.” <i>Journal
    of Agricultural Biological and Environmental Statistics</i>, vol. 14, no. 1, Springer,
    2009, pp. 79–98, doi:<a href="https://doi.org/10.1198/jabes.2009.0005">10.1198/jabes.2009.0005</a>.'
  short: C. Uhler, Journal of Agricultural Biological and Environmental Statistics
    14 (2009) 79–98.
date_created: 2018-12-11T12:02:35Z
date_published: 2009-03-01T00:00:00Z
date_updated: 2021-01-12T07:42:33Z
day: '01'
doi: 10.1198/jabes.2009.0005
extern: 1
intvolume: '        14'
issue: '1'
month: '03'
page: 79 - 98
publication: Journal of Agricultural Biological and Environmental Statistics
publication_status: published
publisher: Springer
publist_id: '3331'
quality_controlled: 0
status: public
title: 'Mastitis in dairy production: Estimation of sensitivity, specificity and disease
  prevalence in the absence of a gold standard'
type: journal_article
volume: 14
year: '2009'
...
---
_id: '337'
abstract:
- lang: eng
  text: 'The formation of hollow vs solid particles by means of the oxidation reaction
    of solid metal particles depends on the differential self-diffusivities of the
    reactants through the composite shell, the reaction probabilities at each interface,
    and the concentration and diffusivity of the element in solution. By means of
    a kinetic model of the oxidation process, we determine the phase diagrams for
    the geometry of the oxidized particles and propose four shell growth regimes.
    We experimentally illustrate the different growth scenarios by changing the conditions
    of oxidation of cadmium spherical crystals using different chalcogen precursors. '
article_processing_charge: No
article_type: original
author:
- first_name: Andreu
  full_name: Cabot, Andreu
  last_name: Cabot
- first_name: Maria
  full_name: Ibáñez, Maria
  id: 43C61214-F248-11E8-B48F-1D18A9856A87
  last_name: Ibáñez
  orcid: 0000-0001-5013-2843
- first_name: Pablo
  full_name: Guardia, Pablo
  last_name: Guardia
- first_name: Paul
  full_name: Alivisatos, Paul
  last_name: Alivisatos
citation:
  ama: Cabot A, Ibáñez M, Guardia P, Alivisatos P. Reaction regimes on the synthesis
    of hollow particles by the Kirkendall effect. <i>Journal of the American Chemical
    Society</i>. 2009;131(32):11326-11328. doi:<a href="https://doi.org/10.1021/ja903751p">10.1021/ja903751p</a>
  apa: Cabot, A., Ibáñez, M., Guardia, P., &#38; Alivisatos, P. (2009). Reaction regimes
    on the synthesis of hollow particles by the Kirkendall effect. <i>Journal of the
    American Chemical Society</i>. ACS. <a href="https://doi.org/10.1021/ja903751p">https://doi.org/10.1021/ja903751p</a>
  chicago: Cabot, Andreu, Maria Ibáñez, Pablo Guardia, and Paul Alivisatos. “Reaction
    Regimes on the Synthesis of Hollow Particles by the Kirkendall Effect.” <i>Journal
    of the American Chemical Society</i>. ACS, 2009. <a href="https://doi.org/10.1021/ja903751p">https://doi.org/10.1021/ja903751p</a>.
  ieee: A. Cabot, M. Ibáñez, P. Guardia, and P. Alivisatos, “Reaction regimes on the
    synthesis of hollow particles by the Kirkendall effect,” <i>Journal of the American
    Chemical Society</i>, vol. 131, no. 32. ACS, pp. 11326–11328, 2009.
  ista: Cabot A, Ibáñez M, Guardia P, Alivisatos P. 2009. Reaction regimes on the
    synthesis of hollow particles by the Kirkendall effect. Journal of the American
    Chemical Society. 131(32), 11326–11328.
  mla: Cabot, Andreu, et al. “Reaction Regimes on the Synthesis of Hollow Particles
    by the Kirkendall Effect.” <i>Journal of the American Chemical Society</i>, vol.
    131, no. 32, ACS, 2009, pp. 11326–28, doi:<a href="https://doi.org/10.1021/ja903751p">10.1021/ja903751p</a>.
  short: A. Cabot, M. Ibáñez, P. Guardia, P. Alivisatos, Journal of the American Chemical
    Society 131 (2009) 11326–11328.
date_created: 2018-12-11T11:45:53Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:00Z
day: '01'
doi: 10.1021/ja903751p
extern: '1'
intvolume: '       131'
issue: '32'
language:
- iso: eng
month: '01'
oa_version: None
page: 11326 - 11328
publication: Journal of the American Chemical Society
publication_status: published
publisher: ACS
publist_id: '7494'
quality_controlled: '1'
status: public
title: Reaction regimes on the synthesis of hollow particles by the Kirkendall effect
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2009'
...
---
_id: '3398'
abstract:
- lang: eng
  text: Why is a particular architecture for a pathway chosen over seemingly equivalent
    alternatives? Çağatay et al. (2009) use a synthetic biology approach to show that
    fluctuations—or noise—in protein levels may play a key role in determining which
    network design is selected during evolution.
article_processing_charge: No
author:
- first_name: Tobias
  full_name: Bollenbach, Tobias
  id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
  last_name: Bollenbach
  orcid: 0000-0003-4398-476X
- first_name: Roy
  full_name: Kishony, Roy
  last_name: Kishony
citation:
  ama: Bollenbach MT, Kishony R. Quiet gene circuit more fragile than its noisy peer.
    <i>Cell</i>. 2009;139(3):460-461. doi:<a href="https://doi.org/10.1016/j.cell.2009.10.005">10.1016/j.cell.2009.10.005</a>
  apa: Bollenbach, M. T., &#38; Kishony, R. (2009). Quiet gene circuit more fragile
    than its noisy peer. <i>Cell</i>. Cell Press. <a href="https://doi.org/10.1016/j.cell.2009.10.005">https://doi.org/10.1016/j.cell.2009.10.005</a>
  chicago: Bollenbach, Mark Tobias, and Roy Kishony. “Quiet Gene Circuit More Fragile
    than Its Noisy Peer.” <i>Cell</i>. Cell Press, 2009. <a href="https://doi.org/10.1016/j.cell.2009.10.005">https://doi.org/10.1016/j.cell.2009.10.005</a>.
  ieee: M. T. Bollenbach and R. Kishony, “Quiet gene circuit more fragile than its
    noisy peer,” <i>Cell</i>, vol. 139, no. 3. Cell Press, pp. 460–461, 2009.
  ista: Bollenbach MT, Kishony R. 2009. Quiet gene circuit more fragile than its noisy
    peer. Cell. 139(3), 460–461.
  mla: Bollenbach, Mark Tobias, and Roy Kishony. “Quiet Gene Circuit More Fragile
    than Its Noisy Peer.” <i>Cell</i>, vol. 139, no. 3, Cell Press, 2009, pp. 460–61,
    doi:<a href="https://doi.org/10.1016/j.cell.2009.10.005">10.1016/j.cell.2009.10.005</a>.
  short: M.T. Bollenbach, R. Kishony, Cell 139 (2009) 460–461.
date_created: 2018-12-11T12:03:07Z
date_published: 2009-10-30T00:00:00Z
date_updated: 2021-01-12T07:43:12Z
day: '30'
doi: 10.1016/j.cell.2009.10.005
extern: '1'
intvolume: '       139'
issue: '3'
language:
- iso: eng
month: '10'
oa_version: None
page: 460 - 461
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3061'
status: public
title: Quiet gene circuit more fragile than its noisy peer
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 139
year: '2009'
...
---
_id: '3400'
abstract:
- lang: eng
  text: |-
    Invasive fungal infections pose a serious threat to immunocompromised people. Most of these infections are caused by either Candida or Aspergillus species, with A. fumigatus being the predominant causative agent of Invasive Aspergillosis. Affected people comprise mainly haematopoietic stem cell or solid organ transplant patients who receive either high-dose corticosteroids or immunosuppressants. These risk factors predispose to the development of Invasive
    Aspergillosis which is lethal in 20 to 80 % of the cases, largely due to insufficient efficacy of current antifungal therapy. Thus one major aim in current mycological research is the identification of new drug targets.
    The polysaccharide-based fungal cell wall is both essential to fungi and absent from human cells which makes it appear an attractive new target. Notably, many components of the A. fumigatus cell wall, including the polysaccharide galactomannan, glycoproteins, and glycolipids, contain the unusual sugar galactofuranose (Galf). In contrast to the other cell wall monosaccharides, Galf does not occur on human cells but is known as component of cell surface molecules of many pathogenic bacteria and protozoa, such as Mycobacterium tuberculosis or Leishmania major. These molecules are often essential for virulence or viability of these organisms which suggested a possible role of Galf in the pathogenicity of A. fumigatus.
    To address the importance of Galf in A. fumigatus, the key biosynthesis gene glfA, encoding UDPgalactopyranose mutase (UGM), was deleted. In different experimental approaches it was demonstrated that the absence of the glfA gene led to a complete loss of Galf-containing glycans.
    Analysis of the DeltaglfA phenotype revealed growth and sporulation defects, reduced thermotolerance and an increased susceptibility to antifungal drugs. Electron Microscopy indicated a cell wall defect as a likely cause for the observed impairments. Furthermore, the virulence of the DeltaglfA mutant was found to be severely attenuated in a murine model of Invasive Aspergillosis.
    The second focus of this study was laid on further elucidation of the galactofuranosylation pathway in A. fumigatus. In eukaryotes, a UDP-Galf transporter is likely required to transport UDP-Galf from the
    cytosol into the organelles of the secretory pathway, but no such activity had been described. Sixteen candidate genes were identified in the A. fumigatus genome of which one, glfB, was found in close proximity to the glfA gene. In vitro transport assays revealed specificity of GlfB for UDP-Galf suggesting that glfB encoded indeed a UDP-Galf transporter. The influence of glfB on
    galactofuranosylation was determined by a DeltaglfB deletion mutant, which closely recapitulated the DeltaglfA phenotype and was likewise found to be completely devoid of Galf. It could be concluded that all galactofuranosylation processes in A. fumigatus occur in the secretory pathway, including the biosynthesis of the cell wall polysaccharide galactomannan whose subcellular origin was previously disputed.

    Thus in the course of this study the first UDP-Galf specific nucleotide sugar transporter was identified and its requirement for galactofuranosylation in A. fumigatus demonstrated. Moreover, it was shown that blocking the galactofuranosylation pathway impaired virulence of A. fumigatus which suggests the UDP-Galf biosynthesis enzyme UGM as a target for new antifungal drugs.
author:
- first_name: Philipp S
  full_name: Philipp Schmalhorst
  id: 309D50DA-F248-11E8-B48F-1D18A9856A87
  last_name: Schmalhorst
  orcid: 0000-0002-5795-0133
citation:
  ama: Schmalhorst PS. Biosynthesis of Galactofuranose Containing Glycans and Their
    Relevance for the Pathogenic Fungus Aspergillus fumigatus. 2009:1-72.
  apa: Schmalhorst, P. S. (2009). <i>Biosynthesis of Galactofuranose Containing Glycans
    and Their Relevance for the Pathogenic Fungus Aspergillus fumigatus</i>. Gottfried
    Wilhelm Leibniz Universität Hannover.
  chicago: Schmalhorst, Philipp S. “Biosynthesis of Galactofuranose Containing Glycans
    and Their Relevance for the Pathogenic Fungus Aspergillus Fumigatus.” Gottfried
    Wilhelm Leibniz Universität Hannover, 2009.
  ieee: P. S. Schmalhorst, “Biosynthesis of Galactofuranose Containing Glycans and
    Their Relevance for the Pathogenic Fungus Aspergillus fumigatus,” Gottfried Wilhelm
    Leibniz Universität Hannover, 2009.
  ista: Schmalhorst PS. 2009. Biosynthesis of Galactofuranose Containing Glycans and
    Their Relevance for the Pathogenic Fungus Aspergillus fumigatus. Gottfried Wilhelm
    Leibniz Universität Hannover.
  mla: Schmalhorst, Philipp S. <i>Biosynthesis of Galactofuranose Containing Glycans
    and Their Relevance for the Pathogenic Fungus Aspergillus Fumigatus</i>. Gottfried
    Wilhelm Leibniz Universität Hannover, 2009, pp. 1–72.
  short: P.S. Schmalhorst, Biosynthesis of Galactofuranose Containing Glycans and
    Their Relevance for the Pathogenic Fungus Aspergillus Fumigatus, Gottfried Wilhelm
    Leibniz Universität Hannover, 2009.
date_created: 2018-12-11T12:03:07Z
date_published: 2009-08-13T00:00:00Z
date_updated: 2021-01-12T07:43:13Z
day: '13'
extern: 1
main_file_link:
- open_access: '0'
  url: http://edok01.tib.uni-hannover.de/edoks/e01dh09/609861891.pdf
month: '08'
page: 1 - 72
publication_status: published
publisher: Gottfried Wilhelm Leibniz Universität Hannover
publist_id: '3058'
quality_controlled: 0
status: public
title: Biosynthesis of Galactofuranose Containing Glycans and Their Relevance for
  the Pathogenic Fungus Aspergillus fumigatus
type: dissertation
year: '2009'
...
---
_id: '3408'
abstract:
- lang: eng
  text: Mechanical forces govern physiological processes in all living organisms.
    Many cellular forces, for example, those generated in cyclic conformational changes
    of biological machines, have repetitive components. In apparent contrast, little
    is known about how dynamic protein structures respond to periodic mechanical information.
    Ubiquitin is a small protein found in all eukaryotes. We developed molecular dynamics
    simulations to unfold single and multimeric ubiquitins with periodic forces. By
    using a coarse-grained representation, we were able to model forces with periods
    about 2 orders of magnitude longer than the protein's relaxation time. We found
    that even a moderate periodic force weakened the protein and shifted its unfolding
    pathways in a frequency- and amplitude-dependent manner. A complex dynamic response
    with secondary structure refolding and an increasing importance of local interactions
    was revealed. Importantly, repetitive forces with broadly distributed frequencies
    elicited very similar molecular responses compared to fixed-frequency forces.
    When testing the influence of pulling geometry on ubiquitin's mechanical stability,
    it was found that the linkage involved in the mechanical degradation of cellular
    proteins renders the protein remarkably insensitive to periodic forces. We also
    devised a complementary kinetic energy landscape model that traces these observations
    and explains periodic-force, single-molecule measurements. In turn, this analytical
    model is capable of predicting dynamic protein responses. These results provide
    new insights into ubiquitin mechanics and a potential mechanical role during protein
    degradation, as well as first frameworks for dynamic protein stability and the
    modeling of repetitive mechanical processes.
author:
- first_name: Piotr
  full_name: Szymczak, Piotr
  last_name: Szymczak
- first_name: Harald L
  full_name: Harald Janovjak
  id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
  last_name: Janovjak
  orcid: 0000-0002-8023-9315
citation:
  ama: Szymczak P, Janovjak HL. Periodic forces trigger a complex mechanical response
    in ubiquitin. <i>Journal of Molecular Biology</i>. 2009;390(3):443-456. doi:<a
    href="https://doi.org/10.1016/j.jmb.2009.04.071">10.1016/j.jmb.2009.04.071</a>
  apa: Szymczak, P., &#38; Janovjak, H. L. (2009). Periodic forces trigger a complex
    mechanical response in ubiquitin. <i>Journal of Molecular Biology</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.jmb.2009.04.071">https://doi.org/10.1016/j.jmb.2009.04.071</a>
  chicago: Szymczak, Piotr, and Harald L Janovjak. “Periodic Forces Trigger a Complex
    Mechanical Response in Ubiquitin.” <i>Journal of Molecular Biology</i>. Elsevier,
    2009. <a href="https://doi.org/10.1016/j.jmb.2009.04.071">https://doi.org/10.1016/j.jmb.2009.04.071</a>.
  ieee: P. Szymczak and H. L. Janovjak, “Periodic forces trigger a complex mechanical
    response in ubiquitin,” <i>Journal of Molecular Biology</i>, vol. 390, no. 3.
    Elsevier, pp. 443–456, 2009.
  ista: Szymczak P, Janovjak HL. 2009. Periodic forces trigger a complex mechanical
    response in ubiquitin. Journal of Molecular Biology. 390(3), 443–456.
  mla: Szymczak, Piotr, and Harald L. Janovjak. “Periodic Forces Trigger a Complex
    Mechanical Response in Ubiquitin.” <i>Journal of Molecular Biology</i>, vol. 390,
    no. 3, Elsevier, 2009, pp. 443–56, doi:<a href="https://doi.org/10.1016/j.jmb.2009.04.071">10.1016/j.jmb.2009.04.071</a>.
  short: P. Szymczak, H.L. Janovjak, Journal of Molecular Biology 390 (2009) 443–456.
date_created: 2018-12-11T12:03:10Z
date_published: 2009-07-17T00:00:00Z
date_updated: 2021-01-12T07:43:16Z
day: '17'
doi: 10.1016/j.jmb.2009.04.071
extern: 1
intvolume: '       390'
issue: '3'
month: '07'
page: 443 - 456
publication: Journal of Molecular Biology
publication_status: published
publisher: Elsevier
publist_id: '2994'
quality_controlled: 0
status: public
title: Periodic forces trigger a complex mechanical response in ubiquitin
type: journal_article
volume: 390
year: '2009'
...
---
_id: '3428'
abstract:
- lang: eng
  text: In this issue of Molecular Cell, Davies et al. (2009) work out a sequence
    of active cellular events that lead to the death of Escherichia coli in the presence
    of the drug hydroxyurea.
article_processing_charge: No
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: Roy
  full_name: Kishony, Roy
  last_name: Kishony
citation:
  ama: Bollenbach MT, Kishony R. Hydroxyurea triggers cellular responses that actively
    cause bacterial cell death. <i>Molecular Cell</i>. 2009;36(5):728-729. doi:<a
    href="https://doi.org/10.1016/j.molcel.2009.11.027">10.1016/j.molcel.2009.11.027</a>
  apa: Bollenbach, M. T., &#38; Kishony, R. (2009). Hydroxyurea triggers cellular
    responses that actively cause bacterial cell death. <i>Molecular Cell</i>. Cell
    Press. <a href="https://doi.org/10.1016/j.molcel.2009.11.027">https://doi.org/10.1016/j.molcel.2009.11.027</a>
  chicago: Bollenbach, Mark Tobias, and Roy Kishony. “Hydroxyurea Triggers Cellular
    Responses That Actively Cause Bacterial Cell Death.” <i>Molecular Cell</i>. Cell
    Press, 2009. <a href="https://doi.org/10.1016/j.molcel.2009.11.027">https://doi.org/10.1016/j.molcel.2009.11.027</a>.
  ieee: M. T. Bollenbach and R. Kishony, “Hydroxyurea triggers cellular responses
    that actively cause bacterial cell death,” <i>Molecular Cell</i>, vol. 36, no.
    5. Cell Press, pp. 728–729, 2009.
  ista: Bollenbach MT, Kishony R. 2009. Hydroxyurea triggers cellular responses that
    actively cause bacterial cell death. Molecular Cell. 36(5), 728–729.
  mla: Bollenbach, Mark Tobias, and Roy Kishony. “Hydroxyurea Triggers Cellular Responses
    That Actively Cause Bacterial Cell Death.” <i>Molecular Cell</i>, vol. 36, no.
    5, Cell Press, 2009, pp. 728–29, doi:<a href="https://doi.org/10.1016/j.molcel.2009.11.027">10.1016/j.molcel.2009.11.027</a>.
  short: M.T. Bollenbach, R. Kishony, Molecular Cell 36 (2009) 728–729.
date_created: 2018-12-11T12:03:17Z
date_published: 2009-12-11T00:00:00Z
date_updated: 2021-01-12T07:43:24Z
day: '11'
doi: 10.1016/j.molcel.2009.11.027
extern: '1'
intvolume: '        36'
issue: '5'
language:
- iso: eng
month: '12'
oa_version: None
page: 728 - 729
publication: Molecular Cell
publication_status: published
publisher: Cell Press
publist_id: '2972'
status: public
title: Hydroxyurea triggers cellular responses that actively cause bacterial cell
  death
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2009'
...
---
_id: '3503'
abstract:
- lang: eng
  text: 'We give polynomial-time algorithms for computing the values of Markov decision
    processes (MDPs) with limsup and liminf objectives. A real-valued reward is assigned
    to each state, and the value of an infinite path in the MDP is the limsup (resp.
    liminf) of all rewards along the path. The value of an MDP is the maximal expected
    value of an infinite path that can be achieved by resolving the decisions of the
    MDP. Using our result on MDPs, we show that turn-based stochastic games with limsup
    and liminf objectives can be solved in NP ∩ coNP. '
alternative_title:
- LNCS
author:
- first_name: Krishnendu
  full_name: Krishnendu Chatterjee
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Thomas A
  full_name: Thomas Henzinger
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
citation:
  ama: 'Chatterjee K, Henzinger TA. Probabilistic systems with limsup and liminf objectives.
    In: Vol 5489. Springer; 2009:32-45. doi:<a href="https://doi.org/10.1007/978-3-642-03092-5_4">10.1007/978-3-642-03092-5_4</a>'
  apa: 'Chatterjee, K., &#38; Henzinger, T. A. (2009). Probabilistic systems with
    limsup and liminf objectives (Vol. 5489, pp. 32–45). Presented at the ILC: Infinity
    in Logic and Computation, Springer. <a href="https://doi.org/10.1007/978-3-642-03092-5_4">https://doi.org/10.1007/978-3-642-03092-5_4</a>'
  chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Probabilistic Systems
    with Limsup and Liminf Objectives,” 5489:32–45. Springer, 2009. <a href="https://doi.org/10.1007/978-3-642-03092-5_4">https://doi.org/10.1007/978-3-642-03092-5_4</a>.
  ieee: 'K. Chatterjee and T. A. Henzinger, “Probabilistic systems with limsup and
    liminf objectives,” presented at the ILC: Infinity in Logic and Computation, 2009,
    vol. 5489, pp. 32–45.'
  ista: 'Chatterjee K, Henzinger TA. 2009. Probabilistic systems with limsup and liminf
    objectives. ILC: Infinity in Logic and Computation, LNCS, vol. 5489, 32–45.'
  mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. <i>Probabilistic Systems with
    Limsup and Liminf Objectives</i>. Vol. 5489, Springer, 2009, pp. 32–45, doi:<a
    href="https://doi.org/10.1007/978-3-642-03092-5_4">10.1007/978-3-642-03092-5_4</a>.
  short: K. Chatterjee, T.A. Henzinger, in:, Springer, 2009, pp. 32–45.
conference:
  name: 'ILC: Infinity in Logic and Computation'
date_created: 2018-12-11T12:03:40Z
date_published: 2009-12-15T00:00:00Z
date_updated: 2021-01-12T07:43:54Z
day: '15'
doi: 10.1007/978-3-642-03092-5_4
extern: 1
intvolume: '      5489'
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/0809.1465
month: '12'
oa: 1
page: 32 - 45
publication_status: published
publisher: Springer
publist_id: '2884'
quality_controlled: 0
status: public
title: Probabilistic systems with limsup and liminf objectives
type: conference
volume: 5489
year: '2009'
...
---
_id: '3547'
abstract:
- lang: eng
  text: Neurons possess elaborate dendritic arbors which receive and integrate excitatory
    synaptic signals. Individual dendritic subbranches exhibit local membrane potential
    supralinearities, termed dendritic spikes, which control transfer of local synaptic
    input to the soma. Here, we show that dendritic spikes in CA1 pyramidal cells
    are strongly regulated by specific types of prior input. While input in the linear
    range is without effect, supralinear input inhibits subsequent spikes, causing
    them to attenuate and ultimately fail due to dendritic Na+ channel inactivation.
    This mechanism acts locally within the boundaries of the input branch. If an input
    is sufficiently strong to trigger axonal action potentials, their back-propagation
    into the dendritic tree causes a widespread global reduction in dendritic excitability
    which is prominent after firing patterns occurring in vivo. Together, these mechanisms
    control the capability of individual dendritic branches to trigger somatic action
    potential output. They are invoked at frequencies encountered during learning,
    and impose limits on the storage and retrieval rates of information encoded as
    branch excitability.
author:
- first_name: Stefan
  full_name: Remy,Stefan
  last_name: Remy
- first_name: Jozsef L
  full_name: Jozsef Csicsvari
  id: 3FA14672-F248-11E8-B48F-1D18A9856A87
  last_name: Csicsvari
  orcid: 0000-0002-5193-4036
- first_name: Heinz
  full_name: Beck,Heinz
  last_name: Beck
citation:
  ama: Remy S, Csicsvari JL, Beck H. Activity-dependent control of neuronal output
    by local and global dendritic spike attenuation. <i>Neuron</i>. 2009;61(6):906-916.
    doi:<a href="https://doi.org/10.1016/j.neuron.2009.01.032">10.1016/j.neuron.2009.01.032</a>
  apa: Remy, S., Csicsvari, J. L., &#38; Beck, H. (2009). Activity-dependent control
    of neuronal output by local and global dendritic spike attenuation. <i>Neuron</i>.
    Elsevier. <a href="https://doi.org/10.1016/j.neuron.2009.01.032">https://doi.org/10.1016/j.neuron.2009.01.032</a>
  chicago: Remy, Stefan, Jozsef L Csicsvari, and Heinz Beck. “Activity-Dependent Control
    of Neuronal Output by Local and Global Dendritic Spike Attenuation.” <i>Neuron</i>.
    Elsevier, 2009. <a href="https://doi.org/10.1016/j.neuron.2009.01.032">https://doi.org/10.1016/j.neuron.2009.01.032</a>.
  ieee: S. Remy, J. L. Csicsvari, and H. Beck, “Activity-dependent control of neuronal
    output by local and global dendritic spike attenuation,” <i>Neuron</i>, vol. 61,
    no. 6. Elsevier, pp. 906–916, 2009.
  ista: Remy S, Csicsvari JL, Beck H. 2009. Activity-dependent control of neuronal
    output by local and global dendritic spike attenuation. Neuron. 61(6), 906–916.
  mla: Remy, Stefan, et al. “Activity-Dependent Control of Neuronal Output by Local
    and Global Dendritic Spike Attenuation.” <i>Neuron</i>, vol. 61, no. 6, Elsevier,
    2009, pp. 906–16, doi:<a href="https://doi.org/10.1016/j.neuron.2009.01.032">10.1016/j.neuron.2009.01.032</a>.
  short: S. Remy, J.L. Csicsvari, H. Beck, Neuron 61 (2009) 906–916.
date_created: 2018-12-11T12:03:54Z
date_published: 2009-03-26T00:00:00Z
date_updated: 2021-01-12T07:44:13Z
day: '26'
doi: 10.1016/j.neuron.2009.01.032
extern: 1
intvolume: '        61'
issue: '6'
month: '03'
page: 906 - 916
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2838'
quality_controlled: 0
status: public
title: Activity-dependent control of neuronal output by local and global dendritic
  spike attenuation
type: journal_article
volume: 61
year: '2009'
...
---
_id: '3578'
abstract:
- lang: eng
  text: The medial axis of a geometric shape captures its connectivity. In spite of
    its inherent instability, it has found applications in a number of areas that
    deal with shapes. In this survey paper, we focus on results that shed light on
    this instability and use the new insights to generate simplified and stable modifications
    of the medial axis.
alternative_title:
- Mathematics and Visualization
author:
- first_name: Dominique
  full_name: Attali, Dominique
  last_name: Attali
- first_name: Jean
  full_name: Boissonnat, Jean-Daniel
  last_name: Boissonnat
- first_name: Herbert
  full_name: Herbert Edelsbrunner
  id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
  last_name: Edelsbrunner
  orcid: 0000-0002-9823-6833
citation:
  ama: 'Attali D, Boissonnat J, Edelsbrunner H. Stability and computation of medial
    axes: a state-of-the-art report. In: <i>Mathematical Foundations of Scientific
    Visualization, Computer Graphics, and Massive Data Exploration</i>. Springer;
    2009:109-125. doi:<a href="https://doi.org/10.1007/b106657_6">10.1007/b106657_6</a>'
  apa: 'Attali, D., Boissonnat, J., &#38; Edelsbrunner, H. (2009). Stability and computation
    of medial axes: a state-of-the-art report. In <i>Mathematical Foundations of Scientific
    Visualization, Computer Graphics, and Massive Data Exploration</i> (pp. 109–125).
    Springer. <a href="https://doi.org/10.1007/b106657_6">https://doi.org/10.1007/b106657_6</a>'
  chicago: 'Attali, Dominique, Jean Boissonnat, and Herbert Edelsbrunner. “Stability
    and Computation of Medial Axes: A State-of-the-Art Report.” In <i>Mathematical
    Foundations of Scientific Visualization, Computer Graphics, and Massive Data Exploration</i>,
    109–25. Springer, 2009. <a href="https://doi.org/10.1007/b106657_6">https://doi.org/10.1007/b106657_6</a>.'
  ieee: 'D. Attali, J. Boissonnat, and H. Edelsbrunner, “Stability and computation
    of medial axes: a state-of-the-art report,” in <i>Mathematical Foundations of
    Scientific Visualization, Computer Graphics, and Massive Data Exploration</i>,
    Springer, 2009, pp. 109–125.'
  ista: 'Attali D, Boissonnat J, Edelsbrunner H. 2009.Stability and computation of
    medial axes: a state-of-the-art report. In: Mathematical Foundations of Scientific
    Visualization, Computer Graphics, and Massive Data Exploration. Mathematics and
    Visualization, , 109–125.'
  mla: 'Attali, Dominique, et al. “Stability and Computation of Medial Axes: A State-of-the-Art
    Report.” <i>Mathematical Foundations of Scientific Visualization, Computer Graphics,
    and Massive Data Exploration</i>, Springer, 2009, pp. 109–25, doi:<a href="https://doi.org/10.1007/b106657_6">10.1007/b106657_6</a>.'
  short: D. Attali, J. Boissonnat, H. Edelsbrunner, in:, Mathematical Foundations
    of Scientific Visualization, Computer Graphics, and Massive Data Exploration,
    Springer, 2009, pp. 109–125.
date_created: 2018-12-11T12:04:03Z
date_published: 2009-06-22T00:00:00Z
date_updated: 2021-01-12T07:44:25Z
day: '22'
doi: 10.1007/b106657_6
extern: 1
main_file_link:
- open_access: '0'
  url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.103.9122
month: '06'
page: 109 - 125
publication: Mathematical Foundations of Scientific Visualization, Computer Graphics,
  and Massive Data Exploration
publication_status: published
publisher: Springer
publist_id: '2807'
quality_controlled: 0
status: public
title: 'Stability and computation of medial axes: a state-of-the-art report'
type: book_chapter
year: '2009'
...
---
_id: '3675'
abstract:
- lang: eng
  text: "Sex and recombination have long been seen as adaptations that facilitate
    natural selection by generating favorable variations. If recombination is to aid
    selection, there must be negative linkage disequilibria—favorable alleles must
    be found together less often than expected by chance. These negative linkage disequilibria
    can be generated directly by selection, but this must involve negative epistasis
    of just the right strength, which is not expected, from either experiment or theory.
    Random drift provides a more general source of negative associations: Favorable
    mutations almost always arise on different genomes, and negative associations
    tend to persist, precisely because they shield variation from selection.\r\n\r\nWe
    can understand how recombination aids adaptation by determining the maximum possible
    rate of adaptation. With unlinked loci, this rate increases only logarithmically
    with the influx of favorable mutations. With a linear genome, a scaling argument
    shows that in a large population, the rate of adaptive substitution depends only
    on the expected rate in the absence of interference, divided by the total rate
    of recombination. A two-locus approximation predicts an upper bound on the rate
    of substitution, proportional to recombination rate.\r\n\r\nIf associations between
    linked loci do impede adaptation, there can be substantial selection for modifiers
    that increase recombination. Whether this can account for the maintenance of high
    rates of sex and recombination depends on the extent of selection. It is clear
    that the rate of species-wide substitutions is typically far too low to generate
    appreciable selection for recombination. However, local sweeps within a subdivided
    population may be effective."
acknowledgement: Royal Society and the Engineering and Physical Sciences for support
  (GR/ T11753/01)
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
citation:
  ama: 'Barton NH. Why sex and recombination? In: <i>Cold Spring Harbor Symposia on
    Quantitative Biology</i>. Vol 74. Cold Spring Harbor Laboratory Press; 2009:187-195.
    doi:<a href="https://doi.org/10.1101/sqb.2009.74.030">10.1101/sqb.2009.74.030</a>'
  apa: Barton, N. H. (2009). Why sex and recombination? In <i>Cold Spring Harbor Symposia
    on Quantitative Biology</i> (Vol. 74, pp. 187–195). Cold Spring Harbor Laboratory
    Press. <a href="https://doi.org/10.1101/sqb.2009.74.030">https://doi.org/10.1101/sqb.2009.74.030</a>
  chicago: Barton, Nicholas H. “Why Sex and Recombination?” In <i>Cold Spring Harbor
    Symposia on Quantitative Biology</i>, 74:187–95. Cold Spring Harbor Laboratory
    Press, 2009. <a href="https://doi.org/10.1101/sqb.2009.74.030">https://doi.org/10.1101/sqb.2009.74.030</a>.
  ieee: N. H. Barton, “Why sex and recombination?,” in <i>Cold Spring Harbor Symposia
    on Quantitative Biology</i>, vol. 74, Cold Spring Harbor Laboratory Press, 2009,
    pp. 187–195.
  ista: 'Barton NH. 2009.Why sex and recombination? In: Cold Spring Harbor Symposia
    on Quantitative Biology. vol. 74, 187–195.'
  mla: Barton, Nicholas H. “Why Sex and Recombination?” <i>Cold Spring Harbor Symposia
    on Quantitative Biology</i>, vol. 74, Cold Spring Harbor Laboratory Press, 2009,
    pp. 187–95, doi:<a href="https://doi.org/10.1101/sqb.2009.74.030">10.1101/sqb.2009.74.030</a>.
  short: N.H. Barton, in:, Cold Spring Harbor Symposia on Quantitative Biology, Cold
    Spring Harbor Laboratory Press, 2009, pp. 187–195.
corr_author: '1'
date_created: 2018-12-11T12:04:33Z
date_published: 2009-11-10T00:00:00Z
date_updated: 2025-09-30T09:56:29Z
day: '10'
department:
- _id: NiBa
doi: 10.1101/sqb.2009.74.030
external_id:
  isi:
  - '000578380600022'
intvolume: '        74'
isi: 1
language:
- iso: eng
month: '11'
oa_version: None
page: 187 - 195
publication: Cold Spring Harbor Symposia on Quantitative Biology
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '2708'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Why sex and recombination?
type: book_chapter
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 74
year: '2009'
...
---
_id: '3696'
abstract:
- lang: eng
  text: Discriminative techniques, such as conditional random fields (CRFs) or structure
    aware maximum-margin techniques (maximum margin Markov networks (M3N), structured
    output support vector machines (S-SVM)), are state-of-the-art in the prediction
    of structured data. However, to achieve good results these techniques require
    complete and reliable ground truth, which is not always available in realistic
    problems. Furthermore, training either CRFs or margin-based techniques is computationally
    costly, because the runtime of current training methods depends not only on the
    size of the training set but also on properties of the output space to which the
    training samples are assigned. We propose an alternative model for structured
    output prediction, Joint Kernel Support Estimation (JKSE), which is rather generative
    in nature as it relies on estimating the joint probability density of samples
    and labels in the training set. This makes it tolerant against incomplete or incorrect
    labels and also opens the possibility of learning in situations where more than
    one output label can be considered correct. At the same time, we avoid typical
    problems of generative models as we do not attempt to learn the full joint probability
    distribution, but we model only its support in a joint reproducing kernel Hilbert
    space. As a consequence, JKSE training is possible by an adaption of the classical
    one-class SVM procedure. The resulting optimization problem is convex and efficiently
    solvable even with tens of thousands of training examples. A particular advantage
    of JKSE is that the training speed depends only on the size of the training set,
    and not on the total size of the label space. No inference step during training
    is required (as M3N and S-SVM would) nor do we have calculate a partition function
    (as CRFs do). Experiments on realistic data show that, for suitable kernel functions,
    our method works efficiently and robustly in situations that discriminative techniques
    have problems with or that are computationally infeasible for them.
author:
- first_name: Christoph
  full_name: Christoph Lampert
  id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
  last_name: Lampert
  orcid: 0000-0001-8622-7887
- first_name: Matthew
  full_name: Blaschko,Matthew B
  last_name: Blaschko
citation:
  ama: Lampert C, Blaschko M. Structured prediction by joint kernel support estimation.
    <i>Machine Learning</i>. 2009;77(2-3):249-269. doi:<a href="https://doi.org/10.1007/s10994-009-5111-0">10.1007/s10994-009-5111-0</a>
  apa: Lampert, C., &#38; Blaschko, M. (2009). Structured prediction by joint kernel
    support estimation. <i>Machine Learning</i>. Springer. <a href="https://doi.org/10.1007/s10994-009-5111-0">https://doi.org/10.1007/s10994-009-5111-0</a>
  chicago: Lampert, Christoph, and Matthew Blaschko. “Structured Prediction by Joint
    Kernel Support Estimation.” <i>Machine Learning</i>. Springer, 2009. <a href="https://doi.org/10.1007/s10994-009-5111-0">https://doi.org/10.1007/s10994-009-5111-0</a>.
  ieee: C. Lampert and M. Blaschko, “Structured prediction by joint kernel support
    estimation,” <i>Machine Learning</i>, vol. 77, no. 2–3. Springer, pp. 249–269,
    2009.
  ista: Lampert C, Blaschko M. 2009. Structured prediction by joint kernel support
    estimation. Machine Learning. 77(2–3), 249–269.
  mla: Lampert, Christoph, and Matthew Blaschko. “Structured Prediction by Joint Kernel
    Support Estimation.” <i>Machine Learning</i>, vol. 77, no. 2–3, Springer, 2009,
    pp. 249–69, doi:<a href="https://doi.org/10.1007/s10994-009-5111-0">10.1007/s10994-009-5111-0</a>.
  short: C. Lampert, M. Blaschko, Machine Learning 77 (2009) 249–269.
date_created: 2018-12-11T12:04:40Z
date_published: 2009-04-07T00:00:00Z
date_updated: 2021-01-12T07:49:01Z
day: '07'
doi: 10.1007/s10994-009-5111-0
extern: 1
intvolume: '        77'
issue: 2-3
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '04'
page: 249 - 269
publication: Machine Learning
publication_status: published
publisher: Springer
publist_id: '2663'
quality_controlled: 0
status: public
title: Structured prediction by joint kernel support estimation
tmp:
  image: /images/cc_by_nc.png
  legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
  short: CC BY-NC (4.0)
type: journal_article
volume: 77
year: '2009'
...
---
_id: '3699'
abstract:
- lang: eng
  text: Kernel Canonical Correlation Analysis (KCCA) is a general technique for subspace
    learning that incorporates principal components analysis (PCA) and Fisher linear
    discriminant analysis (LDA) as special cases. By finding directions that maximize
    correlation, CCA learns representations tied more closely to underlying process
    generating the the data and can ignore high-variance noise directions. However,
    for data where acquisition in a given modality is expensive or otherwise limited,
    CCA may suffer from small sample effects. We propose to use semisupervised Laplacian
    regularization to utilize data that are present in only one modality. This approach
    is able to find highly correlated directions that also lie along the data manifold,
    resulting in a more robust estimate of correlated subspaces. Functional magnetic
    resonance imaging (fMRI) acquired data are naturally amenable to subspace techniques
    as data are well aligned. fMRI data of the human brain are a particularly interesting
    candidate. In this study we implemented various supervised and semi-supervised
    versions of CCA on human fMRI data, with regression to single and multivariate
    labels (corresponding to video content subjects viewed during the image acquisition).
    In each variate condition, the semi-supervised variants of CCA performed better
    than the supervised variants, including a supervised variant with Laplacian regularization.
    We additionally analyze the weights learned by the regression in order to infer
    brain regions that are important to different types of visual processing.
author:
- first_name: Matthew
  full_name: Blaschko,Matthew B
  last_name: Blaschko
- first_name: Christoph
  full_name: Christoph Lampert
  id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
  last_name: Lampert
  orcid: 0000-0001-8622-7887
- first_name: Andreas
  full_name: Bartels, Andreas
  last_name: Bartels
citation:
  ama: Blaschko M, Lampert C, Bartels A. <i>Semi-Supervised Analysis of Human FMRI
    Data</i>. Berlin Institute of Technology; 2009.
  apa: 'Blaschko, M., Lampert, C., &#38; Bartels, A. (2009). <i>Semi-supervised analysis
    of human fMRI data</i>. <i>BBCI: Berlin Brain-Computer Interface Workshop - Advances
    in Neurotechnology</i>. Berlin Institute of Technology.'
  chicago: 'Blaschko, Matthew, Christoph Lampert, and Andreas Bartels. <i>Semi-Supervised
    Analysis of Human FMRI Data</i>. <i>BBCI: Berlin Brain-Computer Interface Workshop
    - Advances in Neurotechnology</i>. Berlin Institute of Technology, 2009.'
  ieee: M. Blaschko, C. Lampert, and A. Bartels, <i>Semi-supervised analysis of human
    fMRI data</i>. Berlin Institute of Technology, 2009.
  ista: Blaschko M, Lampert C, Bartels A. 2009. Semi-supervised analysis of human
    fMRI data, Berlin Institute of Technology,p.
  mla: 'Blaschko, Matthew, et al. “Semi-Supervised Analysis of Human FMRI Data.” <i>BBCI:
    Berlin Brain-Computer Interface Workshop - Advances in Neurotechnology</i>, Berlin
    Institute of Technology, 2009.'
  short: M. Blaschko, C. Lampert, A. Bartels, Semi-Supervised Analysis of Human FMRI
    Data, Berlin Institute of Technology, 2009.
date_created: 2018-12-11T12:04:41Z
date_published: 2009-07-10T00:00:00Z
date_updated: 2019-04-26T07:22:33Z
day: '10'
extern: 1
main_file_link:
- open_access: '0'
  url: http://pubman.mpdl.mpg.de/pubman/faces/viewItemOverviewPage.jsp?itemId=escidoc:1789281
month: '07'
publication: 'BBCI: Berlin Brain-Computer Interface Workshop - Advances in Neurotechnology'
publication_status: published
publisher: Berlin Institute of Technology
publist_id: '2661'
quality_controlled: 0
status: public
title: Semi-supervised analysis of human fMRI data
type: conference_poster
year: '2009'
...