---
_id: '2895'
abstract:
- lang: eng
  text: One of the fundamental properties of the immune system is its capacity to
    avoid autoimmune diseases. The mechanism underlying this process, known as self-tolerance,
    is hitherto unresolved but seems to involve the control of clonal expansion of
    autoreactive lymphocytes. This article reviews mathematical modeling of self-tolerance,
    addressing two specific hypotheses. The first hypothesis posits that self-tolerance
    is mediated by tuning of activation thresholds, which makes autoreactive T lymphocytes
    reversibly &quot;anergic&quot; and unable to proliferate. The second hypothesis
    posits that the proliferation of autoreactive T lymphocytes is instead controlled
    by specific regulatory T lymphocytes. Models representing the population dynamics
    of autoreactive T lymphocytes according to these two hypotheses were derived.
    For each model we identified how cell density affects tolerance, and predicted
    the corresponding phase spaces and bifurcations. We show that the simple induction
    of proliferative anergy, as modeled here, has a density dependence that is only
    partially compatible with adoptive transfers of tolerance, and that the models
    of tolerance mediated by specific regulatory T cells are closer to the observations.
acknowledgement: 'The work was financially supported by Fundação para a Ciência e
  Tecnologia: grants  P/BIA/10094/1998,  POCTI/36413/99,  and  POCTI/MGI/46477/2002;
  and fellowships to JF (Praxis/BCC/18972/98), JS (BD/13546/97), KL (SFRH/BPD+/1157/2002),
  DM (SFRH/BD/2960/2000) and TP (SFRH/BD/10550/2002).'
author:
- first_name: Jorge
  full_name: Carneiro, Jorge
  last_name: Carneiro
- first_name: Tiago
  full_name: Tiago Paixao
  id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
  last_name: Paixao
  orcid: 0000-0003-2361-3953
- first_name: Dejan
  full_name: Milutinovic, Dejan
  last_name: Milutinovic
- first_name: João
  full_name: Sousa, João
  last_name: Sousa
- first_name: Kalet
  full_name: Leon, Kalet
  last_name: Leon
- first_name: Rui
  full_name: Gardner, Rui
  last_name: Gardner
- first_name: Jose
  full_name: Faro, Jose
  last_name: Faro
citation:
  ama: 'Carneiro J, Paixao T, Milutinovic D, et al. Immunological self tolerance:
    Lessons from mathematical modeling. <i>Journal of Computational and Applied Mathematics</i>.
    2005;184(1):77-100. doi:<a href="https://doi.org/10.1016/j.cam.2004.10.025">10.1016/j.cam.2004.10.025</a>'
  apa: 'Carneiro, J., Paixao, T., Milutinovic, D., Sousa, J., Leon, K., Gardner, R.,
    &#38; Faro, J. (2005). Immunological self tolerance: Lessons from mathematical
    modeling. <i>Journal of Computational and Applied Mathematics</i>. Elsevier. <a
    href="https://doi.org/10.1016/j.cam.2004.10.025">https://doi.org/10.1016/j.cam.2004.10.025</a>'
  chicago: 'Carneiro, Jorge, Tiago Paixao, Dejan Milutinovic, João Sousa, Kalet Leon,
    Rui Gardner, and Jose Faro. “Immunological Self Tolerance: Lessons from Mathematical
    Modeling.” <i>Journal of Computational and Applied Mathematics</i>. Elsevier,
    2005. <a href="https://doi.org/10.1016/j.cam.2004.10.025">https://doi.org/10.1016/j.cam.2004.10.025</a>.'
  ieee: 'J. Carneiro <i>et al.</i>, “Immunological self tolerance: Lessons from mathematical
    modeling,” <i>Journal of Computational and Applied Mathematics</i>, vol. 184,
    no. 1. Elsevier, pp. 77–100, 2005.'
  ista: 'Carneiro J, Paixao T, Milutinovic D, Sousa J, Leon K, Gardner R, Faro J.
    2005. Immunological self tolerance: Lessons from mathematical modeling. Journal
    of Computational and Applied Mathematics. 184(1), 77–100.'
  mla: 'Carneiro, Jorge, et al. “Immunological Self Tolerance: Lessons from Mathematical
    Modeling.” <i>Journal of Computational and Applied Mathematics</i>, vol. 184,
    no. 1, Elsevier, 2005, pp. 77–100, doi:<a href="https://doi.org/10.1016/j.cam.2004.10.025">10.1016/j.cam.2004.10.025</a>.'
  short: J. Carneiro, T. Paixao, D. Milutinovic, J. Sousa, K. Leon, R. Gardner, J.
    Faro, Journal of Computational and Applied Mathematics 184 (2005) 77–100.
date_created: 2018-12-11T12:00:12Z
date_published: 2005-12-01T00:00:00Z
date_updated: 2021-01-12T07:00:32Z
day: '01'
doi: 10.1016/j.cam.2004.10.025
extern: 1
intvolume: '       184'
issue: '1'
month: '12'
page: 77 - 100
publication: Journal of Computational and Applied Mathematics
publication_status: published
publisher: Elsevier
publist_id: '3863'
quality_controlled: 0
status: public
title: 'Immunological self tolerance: Lessons from mathematical modeling'
type: journal_article
volume: 184
year: '2005'
...
---
_id: '3000'
abstract:
- lang: eng
  text: In plants, cell polarity is an issue more recurring than in other systems,
    because plants, due to their adaptive and flexible development, often change cell
    polarity postembryonically according to intrinsic cues and demands of the environment.
    Recent findings on the directional movement of the plant signalling molecule auxin
    provide a unique connection between individual cell polarity and the establishment
    of polarity at the tissue, organ, and whole-plant levels. Decisions about the
    subcellular polar targeting of PIN auxin transport components determine the direction
    of auxin flow between cells and consequently mediate multiple developmental events.
    In addition, mutations or chemical interference with PIN-based auxin transport
    result in abnormal cell divisions. Thus, the complicated links between cell polarity
    establishment, auxin transport, cytoskeleton, and oriented cell divisions now
    begin to emerge. Here we review the available literature on the issues of cell
    polarity in both plants and animals to extend our understanding on the generation,
    maintenance, and transmission of cell polarity in plants.
author:
- first_name: Pankaj
  full_name: Dhonukshe, Pankaj
  last_name: Dhonukshe
- first_name: Jürgen
  full_name: Kleine Vehn, Jürgen
  last_name: Kleine Vehn
- first_name: Jirí
  full_name: Friml, Jirí
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: 'Dhonukshe P, Kleine Vehn J, Friml J. Cell polarity, auxin transport and cytoskeleton
    mediated division planes: Who comes first? <i>Protoplasma</i>. 2005;226(1-2):67-73.
    doi:<a href="https://doi.org/10.1007/s00709-005-0104-8">10.1007/s00709-005-0104-8</a>'
  apa: 'Dhonukshe, P., Kleine Vehn, J., &#38; Friml, J. (2005). Cell polarity, auxin
    transport and cytoskeleton mediated division planes: Who comes first? <i>Protoplasma</i>.
    Springer. <a href="https://doi.org/10.1007/s00709-005-0104-8">https://doi.org/10.1007/s00709-005-0104-8</a>'
  chicago: 'Dhonukshe, Pankaj, Jürgen Kleine Vehn, and Jiří Friml. “Cell Polarity,
    Auxin Transport and Cytoskeleton Mediated Division Planes: Who Comes First?” <i>Protoplasma</i>.
    Springer, 2005. <a href="https://doi.org/10.1007/s00709-005-0104-8">https://doi.org/10.1007/s00709-005-0104-8</a>.'
  ieee: 'P. Dhonukshe, J. Kleine Vehn, and J. Friml, “Cell polarity, auxin transport
    and cytoskeleton mediated division planes: Who comes first?,” <i>Protoplasma</i>,
    vol. 226, no. 1–2. Springer, pp. 67–73, 2005.'
  ista: 'Dhonukshe P, Kleine Vehn J, Friml J. 2005. Cell polarity, auxin transport
    and cytoskeleton mediated division planes: Who comes first? Protoplasma. 226(1–2),
    67–73.'
  mla: 'Dhonukshe, Pankaj, et al. “Cell Polarity, Auxin Transport and Cytoskeleton
    Mediated Division Planes: Who Comes First?” <i>Protoplasma</i>, vol. 226, no.
    1–2, Springer, 2005, pp. 67–73, doi:<a href="https://doi.org/10.1007/s00709-005-0104-8">10.1007/s00709-005-0104-8</a>.'
  short: P. Dhonukshe, J. Kleine Vehn, J. Friml, Protoplasma 226 (2005) 67–73.
date_created: 2018-12-11T12:00:47Z
date_published: 2005-10-01T00:00:00Z
date_updated: 2021-01-12T07:40:22Z
day: '01'
doi: 10.1007/s00709-005-0104-8
extern: '1'
intvolume: '       226'
issue: 1-2
language:
- iso: eng
month: '10'
oa_version: None
page: 67 - 73
publication: Protoplasma
publication_status: published
publisher: Springer
publist_id: '3701'
quality_controlled: '1'
status: public
title: 'Cell polarity, auxin transport and cytoskeleton mediated division planes:
  Who comes first?'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 226
year: '2005'
...
---
_id: '3001'
abstract:
- lang: eng
  text: 'One of the mechanisms by which signalling molecules regulate cellular behaviour
    is modulating subcellular protein translocation. This mode of regulation is often
    based on specialized vesicle trafficking, termed constitutive cycling, which consists
    of repeated internalization and recycling of proteins to and from the plasma membrane.
    No such mechanism of hormone action has been shown in plants although several
    proteins, including the PIN auxin efflux facilitators, exhibit constitutive cycling.
    Here we show that a major regulator of plant development, auxin, inhibits endocytosis.
    This effect is specific to biologically active auxins and requires activity of
    the Calossin-like protein BIG. By inhibiting the internalization step of PIN constitutive
    cycling, auxin increases levels of PINs at the plasma membrane. Concomitantly,
    auxin promotes its own efflux from cells by a vesicle-trafficking-dependent mechanism.
    Furthermore, asymmetric auxin translocation during gravitropism is correlated
    with decreased PIN internalization. Our data imply a previously undescribed mode
    of plant hormone action: by modulating PIN protein trafficking, auxin regulates
    PIN abundance and activity at the cell surface, providing a mechanism for the
    feedback regulation of auxin transport.'
author:
- first_name: Tomasz
  full_name: Paciorek, Tomasz
  last_name: Paciorek
- first_name: Eva
  full_name: Zažímalová, Eva
  last_name: Zažímalová
- first_name: Nadia
  full_name: Ruthardt, Nadia
  last_name: Ruthardt
- first_name: Jan
  full_name: Petrášek, Jan
  last_name: Petrášek
- first_name: York
  full_name: Stierhof, York-Dieter
  last_name: Stierhof
- first_name: Jürgen
  full_name: Kleine-Vehn, Jürgen
  last_name: Kleine Vehn
- first_name: David
  full_name: Morris, David A
  last_name: Morris
- first_name: Neil
  full_name: Emans, Neil
  last_name: Emans
- first_name: Gerd
  full_name: Jürgens, Gerd
  last_name: Jürgens
- first_name: Niko
  full_name: Geldner, Niko
  last_name: Geldner
- first_name: Jirí
  full_name: Jirí Friml
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: Paciorek T, Zažímalová E, Ruthardt N, et al. Auxin inhibits endocytosis and
    promotes its own efflux from cells. <i>Nature</i>. 2005;435(7046):1251-1256. doi:<a
    href="https://doi.org/10.1038/nature03633">10.1038/nature03633</a>
  apa: Paciorek, T., Zažímalová, E., Ruthardt, N., Petrášek, J., Stierhof, Y., Kleine
    Vehn, J., … Friml, J. (2005). Auxin inhibits endocytosis and promotes its own
    efflux from cells. <i>Nature</i>. Nature Publishing Group. <a href="https://doi.org/10.1038/nature03633">https://doi.org/10.1038/nature03633</a>
  chicago: Paciorek, Tomasz, Eva Zažímalová, Nadia Ruthardt, Jan Petrášek, York Stierhof,
    Jürgen Kleine Vehn, David Morris, et al. “Auxin Inhibits Endocytosis and Promotes
    Its Own Efflux from Cells.” <i>Nature</i>. Nature Publishing Group, 2005. <a href="https://doi.org/10.1038/nature03633">https://doi.org/10.1038/nature03633</a>.
  ieee: T. Paciorek <i>et al.</i>, “Auxin inhibits endocytosis and promotes its own
    efflux from cells,” <i>Nature</i>, vol. 435, no. 7046. Nature Publishing Group,
    pp. 1251–1256, 2005.
  ista: Paciorek T, Zažímalová E, Ruthardt N, Petrášek J, Stierhof Y, Kleine Vehn
    J, Morris D, Emans N, Jürgens G, Geldner N, Friml J. 2005. Auxin inhibits endocytosis
    and promotes its own efflux from cells. Nature. 435(7046), 1251–1256.
  mla: Paciorek, Tomasz, et al. “Auxin Inhibits Endocytosis and Promotes Its Own Efflux
    from Cells.” <i>Nature</i>, vol. 435, no. 7046, Nature Publishing Group, 2005,
    pp. 1251–56, doi:<a href="https://doi.org/10.1038/nature03633">10.1038/nature03633</a>.
  short: T. Paciorek, E. Zažímalová, N. Ruthardt, J. Petrášek, Y. Stierhof, J. Kleine
    Vehn, D. Morris, N. Emans, G. Jürgens, N. Geldner, J. Friml, Nature 435 (2005)
    1251–1256.
date_created: 2018-12-11T12:00:47Z
date_published: 2005-06-30T00:00:00Z
date_updated: 2021-01-12T07:40:23Z
day: '30'
doi: 10.1038/nature03633
extern: 1
intvolume: '       435'
issue: '7046'
month: '06'
page: 1251 - 1256
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '3702'
quality_controlled: 0
status: public
title: Auxin inhibits endocytosis and promotes its own efflux from cells
type: journal_article
volume: 435
year: '2005'
...
---
_id: '3003'
abstract:
- lang: eng
  text: 'Plant development displays an exceptional plasticity and adaptability that
    involves the dynamic, asymmetric distribution of the phytohormone auxin. Polar
    auxin flow, which requires polarly localized transport facilitators of the PIN
    family, largely contributes to the establishment and maintenance of the auxin
    gradients. Functionally overlapping action of PIN proteins mediates multiple developmental
    processes, including embryo formation, organ development and tropisms. Here we
    show that PIN proteins exhibit synergistic interactions, which involve cross-regulation
    of PIN gene expression in pin mutants or plants with inhibited auxin transport.
    Auxin itself positively feeds back on PIN gene expression in a tissue-specific
    manner through an AUX/IAA-dependent signalling pathway. This regulatory switch
    is indicative of a mechanism by which the loss of a specific PIN protein is compensated
    for by auxin-dependent ectopic: expression of its homologues. The compensatory
    properties of the PIN-dependent transport network might enable the stabilization
    of auxin gradients and potentially contribute to the robustness of plant adaptive
    development.'
author:
- first_name: Anne
  full_name: Vieten, Anne
  last_name: Vieten
- first_name: Steffen
  full_name: Vanneste, Steffen
  last_name: Vanneste
- first_name: Justyna
  full_name: Wiśniewska, Justyna
  last_name: Wiśniewska
- first_name: Eva
  full_name: Eva Benková
  id: 38F4F166-F248-11E8-B48F-1D18A9856A87
  last_name: Benková
  orcid: 0000-0002-8510-9739
- first_name: René
  full_name: Benjamins, René
  last_name: Benjamins
- first_name: Tom
  full_name: Beeckman, Tom
  last_name: Beeckman
- first_name: Christian
  full_name: Luschnig, Christian
  last_name: Luschnig
- first_name: Jirí
  full_name: Jirí Friml
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: Vieten A, Vanneste S, Wiśniewska J, et al. Functional redundancy of PIN proteins
    is accompanied by auxin-dependent cross-regulation of PIN expression. <i>Development</i>.
    2005;132(20):4521-4531. doi:<a href="https://doi.org/10.1242/dev.02027">10.1242/dev.02027</a>
  apa: Vieten, A., Vanneste, S., Wiśniewska, J., Benková, E., Benjamins, R., Beeckman,
    T., … Friml, J. (2005). Functional redundancy of PIN proteins is accompanied by
    auxin-dependent cross-regulation of PIN expression. <i>Development</i>. Company
    of Biologists. <a href="https://doi.org/10.1242/dev.02027">https://doi.org/10.1242/dev.02027</a>
  chicago: Vieten, Anne, Steffen Vanneste, Justyna Wiśniewska, Eva Benková, René Benjamins,
    Tom Beeckman, Christian Luschnig, and Jiří Friml. “Functional Redundancy of PIN
    Proteins Is Accompanied by Auxin-Dependent Cross-Regulation of PIN Expression.”
    <i>Development</i>. Company of Biologists, 2005. <a href="https://doi.org/10.1242/dev.02027">https://doi.org/10.1242/dev.02027</a>.
  ieee: A. Vieten <i>et al.</i>, “Functional redundancy of PIN proteins is accompanied
    by auxin-dependent cross-regulation of PIN expression,” <i>Development</i>, vol.
    132, no. 20. Company of Biologists, pp. 4521–4531, 2005.
  ista: Vieten A, Vanneste S, Wiśniewska J, Benková E, Benjamins R, Beeckman T, Luschnig
    C, Friml J. 2005. Functional redundancy of PIN proteins is accompanied by auxin-dependent
    cross-regulation of PIN expression. Development. 132(20), 4521–4531.
  mla: Vieten, Anne, et al. “Functional Redundancy of PIN Proteins Is Accompanied
    by Auxin-Dependent Cross-Regulation of PIN Expression.” <i>Development</i>, vol.
    132, no. 20, Company of Biologists, 2005, pp. 4521–31, doi:<a href="https://doi.org/10.1242/dev.02027">10.1242/dev.02027</a>.
  short: A. Vieten, S. Vanneste, J. Wiśniewska, E. Benková, R. Benjamins, T. Beeckman,
    C. Luschnig, J. Friml, Development 132 (2005) 4521–4531.
date_created: 2018-12-11T12:00:48Z
date_published: 2005-10-01T00:00:00Z
date_updated: 2021-01-12T07:40:23Z
day: '01'
doi: 10.1242/dev.02027
extern: 1
intvolume: '       132'
issue: '20'
month: '10'
page: 4521 - 4531
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '3700'
quality_controlled: 0
status: public
title: Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation
  of PIN expression
type: journal_article
volume: 132
year: '2005'
...
---
_id: '3004'
abstract:
- lang: eng
  text: Molecular mechanisms of pattern formation in the plant embryo are not well
    understood. Recent molecular and cellular studies, in conjunction with earlier
    microsurgical, physiological, and genetic work, are now starting to define the
    outlines of a model where gradients of the signaling molecule auxin play a central
    role in embryo patterning. It is relatively clear how these gradients are established
    and interpreted, but how they are maintained is still unresolved. Here, we have
    studied the contributions of auxin biosynthesis, conjugation, and transport pathways
    to the maintenance of embryonic auxin gradients. Auxin homeostasis in the embryo
    was manipulated by region-specific conditional expression of indoleacetic acid-tryptophan
    monooxygenase or indoleacetic acid-lysine synthetase, bacterial enzymes for auxin
    biosynthesis or conjugation. Neither manipulation of auxin biosynthesis nor of
    auxin conjugation interfered with auxin gradients and patterning in the embryo.
    This result suggests a compensatory mechanism for buffering auxin gradients in
    the embryo. Chemical and genetic inhibition revealed that auxin transport activity,
    in particular that of the PIN-FORMED1 (PIN1) and PIN4 proteins, is a major factor
    in the maintenance of these gradients.
author:
- first_name: Dolf
  full_name: Weijers, Dolf
  last_name: Weijers
- first_name: Michael
  full_name: Sauer, Michael
  last_name: Sauer
- first_name: Olivier
  full_name: Meurette, Olivier
  last_name: Meurette
- first_name: Jirí
  full_name: Jirí Friml
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Karin
  full_name: Ljung, Karin
  last_name: Ljung
- first_name: Göran
  full_name: Sandberg, Göran
  last_name: Sandberg
- first_name: Paul
  full_name: Hooykaas, Paul
  last_name: Hooykaas
- first_name: Remko
  full_name: Offringa, Remko
  last_name: Offringa
citation:
  ama: Weijers D, Sauer M, Meurette O, et al. Maintenance of embryonic auxin distribution
    for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis.
    <i>Plant Cell</i>. 2005;17(9):2517-2526. doi:<a href="https://doi.org/10.1105/tpc.105.034637">10.1105/tpc.105.034637</a>
  apa: Weijers, D., Sauer, M., Meurette, O., Friml, J., Ljung, K., Sandberg, G., …
    Offringa, R. (2005). Maintenance of embryonic auxin distribution for apical basal
    patterning by PIN FORMED dependent auxin transport in Arabidopsis. <i>Plant Cell</i>.
    American Society of Plant Biologists. <a href="https://doi.org/10.1105/tpc.105.034637">https://doi.org/10.1105/tpc.105.034637</a>
  chicago: Weijers, Dolf, Michael Sauer, Olivier Meurette, Jiří Friml, Karin Ljung,
    Göran Sandberg, Paul Hooykaas, and Remko Offringa. “Maintenance of Embryonic Auxin
    Distribution for Apical Basal Patterning by PIN FORMED Dependent Auxin Transport
    in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2005.
    <a href="https://doi.org/10.1105/tpc.105.034637">https://doi.org/10.1105/tpc.105.034637</a>.
  ieee: D. Weijers <i>et al.</i>, “Maintenance of embryonic auxin distribution for
    apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis,”
    <i>Plant Cell</i>, vol. 17, no. 9. American Society of Plant Biologists, pp. 2517–2526,
    2005.
  ista: Weijers D, Sauer M, Meurette O, Friml J, Ljung K, Sandberg G, Hooykaas P,
    Offringa R. 2005. Maintenance of embryonic auxin distribution for apical basal
    patterning by PIN FORMED dependent auxin transport in Arabidopsis. Plant Cell.
    17(9), 2517–2526.
  mla: Weijers, Dolf, et al. “Maintenance of Embryonic Auxin Distribution for Apical
    Basal Patterning by PIN FORMED Dependent Auxin Transport in Arabidopsis.” <i>Plant
    Cell</i>, vol. 17, no. 9, American Society of Plant Biologists, 2005, pp. 2517–26,
    doi:<a href="https://doi.org/10.1105/tpc.105.034637">10.1105/tpc.105.034637</a>.
  short: D. Weijers, M. Sauer, O. Meurette, J. Friml, K. Ljung, G. Sandberg, P. Hooykaas,
    R. Offringa, Plant Cell 17 (2005) 2517–2526.
date_created: 2018-12-11T12:00:48Z
date_published: 2005-07-01T00:00:00Z
date_updated: 2021-01-12T07:40:24Z
day: '01'
doi: 10.1105/tpc.105.034637
extern: 1
intvolume: '        17'
issue: '9'
month: '07'
page: 2517 - 2526
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3698'
quality_controlled: 0
status: public
title: Maintenance of embryonic auxin distribution for apical basal patterning by
  PIN FORMED dependent auxin transport in Arabidopsis
type: journal_article
volume: 17
year: '2005'
...
---
_id: '3141'
abstract:
- lang: eng
  text: The two actin-related subunits of the Arp2/3 complex, Arp2 and Arp3, are proposed
    to form a pseudo actin dimer that nucleates actin polymerization. However, in
    the crystal structure of the inactive complex, they are too far apart to form
    such a nucleus. Here, we show using EM that yeast and bovine Arp2/3 complexes
    exist in a distribution among open, intermediate and closed conformations. The
    crystal structure docks well into the open conformation. The activator WASp binds
    at the cleft between Arp2 and Arp3, and all WASp-bound complexes are closed. The
    inhibitor coronin binds near the p35 subunit, and all coronin-bound complexes
    are open. Activating and loss-of-function mutations in the p35 subunit skew conformational
    distribution in opposite directions, closed and open, respectively. We conclude
    that WASp stabilizes p35-dependent closure of the complex, holding Arp2 and Arp3
    closer together to nucleate an actin filament.
author:
- first_name: Avital
  full_name: Rodal, Avital A
  last_name: Rodal
- first_name: Olga
  full_name: Sokolova, Olga
  last_name: Sokolova
- first_name: Deborah
  full_name: Robins, Deborah B
  last_name: Robins
- first_name: Karen
  full_name: Daugherty, Karen M
  last_name: Daugherty
- first_name: Simon
  full_name: Simon Hippenmeyer
  id: 37B36620-F248-11E8-B48F-1D18A9856A87
  last_name: Hippenmeyer
  orcid: 0000-0003-2279-1061
- first_name: Howard
  full_name: Riezman, Howard
  last_name: Riezman
- first_name: Nikolaus
  full_name: Grigorieff, Nikolaus
  last_name: Grigorieff
- first_name: Bruce
  full_name: Goode, Bruce L
  last_name: Goode
citation:
  ama: Rodal A, Sokolova O, Robins D, et al. Conformational changes in the Arp2 3
    complex leading to actin nucleation. <i>Nature Structural and Molecular Biology</i>.
    2005;12(1):26-31. doi:<a href="https://doi.org/10.1038/nsmb870">10.1038/nsmb870</a>
  apa: Rodal, A., Sokolova, O., Robins, D., Daugherty, K., Hippenmeyer, S., Riezman,
    H., … Goode, B. (2005). Conformational changes in the Arp2 3 complex leading to
    actin nucleation. <i>Nature Structural and Molecular Biology</i>. Nature Publishing
    Group. <a href="https://doi.org/10.1038/nsmb870">https://doi.org/10.1038/nsmb870</a>
  chicago: Rodal, Avital, Olga Sokolova, Deborah Robins, Karen Daugherty, Simon Hippenmeyer,
    Howard Riezman, Nikolaus Grigorieff, and Bruce Goode. “Conformational Changes
    in the Arp2 3 Complex Leading to Actin Nucleation.” <i>Nature Structural and Molecular
    Biology</i>. Nature Publishing Group, 2005. <a href="https://doi.org/10.1038/nsmb870">https://doi.org/10.1038/nsmb870</a>.
  ieee: A. Rodal <i>et al.</i>, “Conformational changes in the Arp2 3 complex leading
    to actin nucleation,” <i>Nature Structural and Molecular Biology</i>, vol. 12,
    no. 1. Nature Publishing Group, pp. 26–31, 2005.
  ista: Rodal A, Sokolova O, Robins D, Daugherty K, Hippenmeyer S, Riezman H, Grigorieff
    N, Goode B. 2005. Conformational changes in the Arp2 3 complex leading to actin
    nucleation. Nature Structural and Molecular Biology. 12(1), 26–31.
  mla: Rodal, Avital, et al. “Conformational Changes in the Arp2 3 Complex Leading
    to Actin Nucleation.” <i>Nature Structural and Molecular Biology</i>, vol. 12,
    no. 1, Nature Publishing Group, 2005, pp. 26–31, doi:<a href="https://doi.org/10.1038/nsmb870">10.1038/nsmb870</a>.
  short: A. Rodal, O. Sokolova, D. Robins, K. Daugherty, S. Hippenmeyer, H. Riezman,
    N. Grigorieff, B. Goode, Nature Structural and Molecular Biology 12 (2005) 26–31.
date_created: 2018-12-11T12:01:38Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:21Z
day: '01'
doi: 10.1038/nsmb870
extern: 1
intvolume: '        12'
issue: '1'
month: '01'
page: 26 - 31
publication: Nature Structural and Molecular Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3554'
quality_controlled: 0
status: public
title: Conformational changes in the Arp2 3 complex leading to actin nucleation
type: journal_article
volume: 12
year: '2005'
...
---
_id: '3143'
abstract:
- lang: eng
  text: Two ETS transcription factors of the Pea3 subfamily are induced in subpopulations
    of dorsal root ganglion (DRG) sensory and spinal motor neurons by target-derived
    factors. Their expression controls late aspects of neuronal differentiation such
    as target invasion and branching. Here, we show that the late onset of ETS gene
    expression is an essential requirement for normal sensory neuron differentiation.
    We provide genetic evidence in the mouse that precocious ETS expression in DRG
    sensory neurons perturbs axonal projections, the acquisition of terminal differentiation
    markers, and their dependence on neurotrophic support. Together, our findings
    indicate that DRG sensory neurons exhibit a temporal developmental switch that
    can be revealed by distinct responses to ETS transcription factor signaling at
    sequential steps of neuronal maturation.
author:
- first_name: Simon
  full_name: Simon Hippenmeyer
  id: 37B36620-F248-11E8-B48F-1D18A9856A87
  last_name: Hippenmeyer
  orcid: 0000-0003-2279-1061
- first_name: Eline
  full_name: Vrieseling, Eline
  last_name: Vrieseling
- first_name: Markus
  full_name: Sigrist, Markus
  last_name: Sigrist
- first_name: Thomas
  full_name: Portmann, Thomas
  last_name: Portmann
- first_name: Celia
  full_name: Laengle, Celia
  last_name: Laengle
- first_name: David
  full_name: Ladle, David R
  last_name: Ladle
- first_name: Silvia
  full_name: Arber, Silvia
  last_name: Arber
citation:
  ama: Hippenmeyer S, Vrieseling E, Sigrist M, et al. A developmental switch in the
    response of DRG neurons to ETS transcription factor signaling. <i>PLoS Biology</i>.
    2005;3(5):0878-0890. doi:<a href="https://doi.org/10.1371/journal.pbio.0030159">10.1371/journal.pbio.0030159</a>
  apa: Hippenmeyer, S., Vrieseling, E., Sigrist, M., Portmann, T., Laengle, C., Ladle,
    D., &#38; Arber, S. (2005). A developmental switch in the response of DRG neurons
    to ETS transcription factor signaling. <i>PLoS Biology</i>. Public Library of
    Science. <a href="https://doi.org/10.1371/journal.pbio.0030159">https://doi.org/10.1371/journal.pbio.0030159</a>
  chicago: Hippenmeyer, Simon, Eline Vrieseling, Markus Sigrist, Thomas Portmann,
    Celia Laengle, David Ladle, and Silvia Arber. “A Developmental Switch in the Response
    of DRG Neurons to ETS Transcription Factor Signaling.” <i>PLoS Biology</i>. Public
    Library of Science, 2005. <a href="https://doi.org/10.1371/journal.pbio.0030159">https://doi.org/10.1371/journal.pbio.0030159</a>.
  ieee: S. Hippenmeyer <i>et al.</i>, “A developmental switch in the response of DRG
    neurons to ETS transcription factor signaling,” <i>PLoS Biology</i>, vol. 3, no.
    5. Public Library of Science, pp. 0878–0890, 2005.
  ista: Hippenmeyer S, Vrieseling E, Sigrist M, Portmann T, Laengle C, Ladle D, Arber
    S. 2005. A developmental switch in the response of DRG neurons to ETS transcription
    factor signaling. PLoS Biology. 3(5), 0878–0890.
  mla: Hippenmeyer, Simon, et al. “A Developmental Switch in the Response of DRG Neurons
    to ETS Transcription Factor Signaling.” <i>PLoS Biology</i>, vol. 3, no. 5, Public
    Library of Science, 2005, pp. 0878–90, doi:<a href="https://doi.org/10.1371/journal.pbio.0030159">10.1371/journal.pbio.0030159</a>.
  short: S. Hippenmeyer, E. Vrieseling, M. Sigrist, T. Portmann, C. Laengle, D. Ladle,
    S. Arber, PLoS Biology 3 (2005) 0878–0890.
date_created: 2018-12-11T12:01:38Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T07:41:21Z
day: '01'
doi: 10.1371/journal.pbio.0030159
extern: 1
intvolume: '         3'
issue: '5'
license: https://creativecommons.org/licenses/by/4.0/
month: '05'
page: 0878 - 0890
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '3552'
quality_controlled: 0
status: public
title: A developmental switch in the response of DRG neurons to ETS transcription
  factor signaling
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: 3
year: '2005'
...
---
_id: '3175'
abstract:
- lang: eng
  text: This paper addresses the novel problem of automatically synthesizing an output
    image from a large collection of different input images. The synthesized image,
    called a digital tapestry, can be viewed as a visual summary or a virtual 'thumbnail'
    of all the images in the input collection. The problem of creating the tapestry
    is cast as a multi-class labeling problem such that each region in the tapestry
    is constructed from input image blocks that are salient and such that neighboring
    blocks satisfy spatial compatibility. This is formulated using a Markov Random
    Field and optimized via the graph cut based expansion move algorithm. The standard
    expansion move algorithm can only handle energies with metric terms, while our
    energy contains non-metric (soft and hard) constraints. Therefore we propose two
    novel contributions. First, we extend the expansion move algorithm for energy
    functions with non-metric hard constraints. Secondly, we modify it for functions
    with &quot;almost&quot; metric soft terms, and show that it gives good results
    in practice. The proposed framework was tested on several consumer photograph
    collections, and the results are presented.
author:
- first_name: Carsten
  full_name: Rother, Carsten
  last_name: Rother
- first_name: Sanjiv
  full_name: Kumar, Sanjiv
  last_name: Kumar
- first_name: Vladimir
  full_name: Vladimir Kolmogorov
  id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kolmogorov
- first_name: Andrew
  full_name: Blake, Andrew
  last_name: Blake
citation:
  ama: 'Rother C, Kumar S, Kolmogorov V, Blake A. Digital tapestry. In: Vol 1. IEEE;
    2005:589-596. doi:<a href="https://doi.org/10.1109/CVPR.2005.130">10.1109/CVPR.2005.130</a>'
  apa: 'Rother, C., Kumar, S., Kolmogorov, V., &#38; Blake, A. (2005). Digital tapestry
    (Vol. 1, pp. 589–596). Presented at the CVPR: Computer Vision and Pattern Recognition,
    IEEE. <a href="https://doi.org/10.1109/CVPR.2005.130">https://doi.org/10.1109/CVPR.2005.130</a>'
  chicago: Rother, Carsten, Sanjiv Kumar, Vladimir Kolmogorov, and Andrew Blake. “Digital
    Tapestry,” 1:589–96. IEEE, 2005. <a href="https://doi.org/10.1109/CVPR.2005.130">https://doi.org/10.1109/CVPR.2005.130</a>.
  ieee: 'C. Rother, S. Kumar, V. Kolmogorov, and A. Blake, “Digital tapestry,” presented
    at the CVPR: Computer Vision and Pattern Recognition, 2005, vol. 1, pp. 589–596.'
  ista: 'Rother C, Kumar S, Kolmogorov V, Blake A. 2005. Digital tapestry. CVPR: Computer
    Vision and Pattern Recognition vol. 1, 589–596.'
  mla: Rother, Carsten, et al. <i>Digital Tapestry</i>. Vol. 1, IEEE, 2005, pp. 589–96,
    doi:<a href="https://doi.org/10.1109/CVPR.2005.130">10.1109/CVPR.2005.130</a>.
  short: C. Rother, S. Kumar, V. Kolmogorov, A. Blake, in:, IEEE, 2005, pp. 589–596.
conference:
  name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:50Z
date_published: 2005-07-25T00:00:00Z
date_updated: 2021-01-12T07:41:35Z
day: '25'
doi: 10.1109/CVPR.2005.130
extern: 1
intvolume: '         1'
main_file_link:
- open_access: '0'
  url: http://research.microsoft.com/en-us/um/people/ablake/papers/ablake/rother_cvpr05.pdf
month: '07'
page: 589 - 596
publication_status: published
publisher: IEEE
publist_id: '3503'
quality_controlled: 0
status: public
title: Digital tapestry
type: conference
volume: 1
year: '2005'
...
---
_id: '3176'
abstract:
- lang: eng
  text: |
    This paper demonstrates the high quality, real-time segmentation techniques. We achieve real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, contrast and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, layered dynamic programming (LDP), solves stereo in an extended 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour model that is learned on the fly, and stereo disparities are obtained by dynamic programming. The second algorithm, layered graph cut (LGC), does not directly solve stereo. Instead the stereo match likelihood is marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar performance, substantially better than stereo or colour/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output.
author:
- first_name: Vladimir
  full_name: Vladimir Kolmogorov
  id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kolmogorov
- first_name: Antonio
  full_name: Criminisi, Antonio
  last_name: Criminisi
- first_name: Andrew
  full_name: Blake, Andrew
  last_name: Blake
- first_name: Geoffrey
  full_name: Cross, Geoffrey
  last_name: Cross
- first_name: Carsten
  full_name: Rother, Carsten
  last_name: Rother
citation:
  ama: 'Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Bi-layer segmentation
    of binocular stereo video. In: IEEE; 2005:1186-1186. doi:<a href="https://doi.org/10.1109/CVPR.2005.90">10.1109/CVPR.2005.90</a>'
  apa: 'Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., &#38; Rother, C. (2005).
    Bi-layer segmentation of binocular stereo video (pp. 1186–1186). Presented at
    the CVPR: Computer Vision and Pattern Recognition, IEEE. <a href="https://doi.org/10.1109/CVPR.2005.90">https://doi.org/10.1109/CVPR.2005.90</a>'
  chicago: Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross,
    and Carsten Rother. “Bi-Layer Segmentation of Binocular Stereo Video,” 1186–1186.
    IEEE, 2005. <a href="https://doi.org/10.1109/CVPR.2005.90">https://doi.org/10.1109/CVPR.2005.90</a>.
  ieee: 'V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Bi-layer
    segmentation of binocular stereo video,” presented at the CVPR: Computer Vision
    and Pattern Recognition, 2005, pp. 1186–1186.'
  ista: 'Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2005. Bi-layer segmentation
    of binocular stereo video. CVPR: Computer Vision and Pattern Recognition, 1186–1186.'
  mla: Kolmogorov, Vladimir, et al. <i>Bi-Layer Segmentation of Binocular Stereo Video</i>.
    IEEE, 2005, pp. 1186–1186, doi:<a href="https://doi.org/10.1109/CVPR.2005.90">10.1109/CVPR.2005.90</a>.
  short: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, in:, IEEE, 2005,
    pp. 1186–1186.
conference:
  name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:50Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:35Z
day: '01'
doi: 10.1109/CVPR.2005.90
extern: 1
month: '01'
page: 1186 - 1186
publication_status: published
publisher: IEEE
publist_id: '3504'
quality_controlled: 0
status: public
title: Bi-layer segmentation of binocular stereo video
type: conference
year: '2005'
...
---
_id: '3181'
abstract:
- lang: eng
  text: Tree-reweighted max-product (TRW) message passing [9] is a modified form of
    the ordinary max-product algorithm for attempting to find minimal energy configurations
    in Markov random field with cycles. For a TRW fixed point satisfying the strong
    tree agreement condition, the algorithm outputs a configuration that is provably
    optimal. In this paper, we focus on the case of binary variables with pairwise
    couplings, and establish stronger properties of TRW fixed points that satisfy
    only the milder condition of weak tree agreement (WTA). First, we demonstrate
    how it is possible to identify part of the optimal solution - i.e., a provably
    optimal solution for a subset of nodes - without knowing a complete solution.
    Second, we show that for submodular functions, a WTA fixed point always yields
    a globally optimal solution. We establish that for binary variables, any WTA fixed
    point always achieves the global maximum of the linear programming relaxation
    underlying the TRW method.
author:
- first_name: Vladimir
  full_name: Vladimir Kolmogorov
  id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kolmogorov
- first_name: Martin
  full_name: Wainwright, Martin J
  last_name: Wainwright
citation:
  ama: 'Kolmogorov V, Wainwright M. On the optimality of tree reweighted max product
    message passing. In: AUAI Press; 2005:316-323.'
  apa: 'Kolmogorov, V., &#38; Wainwright, M. (2005). On the optimality of tree reweighted
    max product message passing (pp. 316–323). Presented at the UAI: Uncertainty in
    Artificial Intelligence, AUAI Press.'
  chicago: Kolmogorov, Vladimir, and Martin Wainwright. “On the Optimality of Tree
    Reweighted Max Product Message Passing,” 316–23. AUAI Press, 2005.
  ieee: 'V. Kolmogorov and M. Wainwright, “On the optimality of tree reweighted max
    product message passing,” presented at the UAI: Uncertainty in Artificial Intelligence,
    2005, pp. 316–323.'
  ista: 'Kolmogorov V, Wainwright M. 2005. On the optimality of tree reweighted max
    product message passing. UAI: Uncertainty in Artificial Intelligence, 316–323.'
  mla: Kolmogorov, Vladimir, and Martin Wainwright. <i>On the Optimality of Tree Reweighted
    Max Product Message Passing</i>. AUAI Press, 2005, pp. 316–23.
  short: V. Kolmogorov, M. Wainwright, in:, AUAI Press, 2005, pp. 316–323.
conference:
  name: 'UAI: Uncertainty in Artificial Intelligence'
date_created: 2018-12-11T12:01:51Z
date_published: 2005-07-01T00:00:00Z
date_updated: 2021-01-12T07:41:38Z
day: '01'
extern: 1
main_file_link:
- open_access: '0'
  url: http://research.microsoft.com/pubs/67405/trw_opt_uai05.pdf
month: '07'
page: 316 - 323
publication_status: published
publisher: AUAI Press
publist_id: '3500'
quality_controlled: 0
status: public
title: On the optimality of tree reweighted max product message passing
type: conference
year: '2005'
...
---
_id: '3182'
abstract:
- lang: eng
  text: In the work of the authors (2003), we showed that graph cuts can find hypersurfaces
    of globally minimal length (or area) under any Riemannian metric. Here we show
    that graph cuts on directed regular grids can approximate a significantly more
    general class of continuous non-symmetric metrics. Using submodularity condition
    (Boros and Hammer, 2002 and Kolmogorov and Zabih, 2004), we obtain a tight characterization
    of graph-representable metrics. Such &quot;submodular&quot; metrics have an elegant
    geometric interpretation via hypersurface functionals combining length/area and
    flux. Practically speaking, we attend 'geo-cuts' algorithm to a wider class of
    geometrically motivated hypersurface functionals and show how to globally optimize
    any combination of length/area and flux of a given vector field. The concept of
    flux was recently introduced into computer vision by Vasilevskiy and Siddiqi (2002)
    but it was mainly studied within variational framework so far. We are first to
    show that flux can be integrated into graph cuts as well. Combining geometric
    concepts of flux and length/area within the global optimization framework of graph
    cuts allows principled discrete segmentation models and advances the slate of
    the art for the graph cuts methods in vision. In particular we address the &quot;shrinking&quot;
    problem of graph cuts, improve segmentation of long thin objects, and introduce
    useful shape constraints.
author:
- first_name: Vladimir
  full_name: Vladimir Kolmogorov
  id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kolmogorov
- first_name: Yuri
  full_name: Boykov, Yuri
  last_name: Boykov
citation:
  ama: 'Kolmogorov V, Boykov Y. What metrics can be approximated by geo cuts or global
    optimization of length area and flux. In: Vol 1. IEEE; 2005:564-571. doi:<a href="https://doi.org/10.1109/ICCV.2005.252">10.1109/ICCV.2005.252</a>'
  apa: 'Kolmogorov, V., &#38; Boykov, Y. (2005). What metrics can be approximated
    by geo cuts or global optimization of length area and flux (Vol. 1, pp. 564–571).
    Presented at the ICCV: International Conference on Computer Vision, IEEE. <a href="https://doi.org/10.1109/ICCV.2005.252">https://doi.org/10.1109/ICCV.2005.252</a>'
  chicago: Kolmogorov, Vladimir, and Yuri Boykov. “What Metrics Can Be Approximated
    by Geo Cuts or Global Optimization of Length Area and Flux,” 1:564–71. IEEE, 2005.
    <a href="https://doi.org/10.1109/ICCV.2005.252">https://doi.org/10.1109/ICCV.2005.252</a>.
  ieee: 'V. Kolmogorov and Y. Boykov, “What metrics can be approximated by geo cuts
    or global optimization of length area and flux,” presented at the ICCV: International
    Conference on Computer Vision, 2005, vol. 1, pp. 564–571.'
  ista: 'Kolmogorov V, Boykov Y. 2005. What metrics can be approximated by geo cuts
    or global optimization of length area and flux. ICCV: International Conference
    on Computer Vision vol. 1, 564–571.'
  mla: Kolmogorov, Vladimir, and Yuri Boykov. <i>What Metrics Can Be Approximated
    by Geo Cuts or Global Optimization of Length Area and Flux</i>. Vol. 1, IEEE,
    2005, pp. 564–71, doi:<a href="https://doi.org/10.1109/ICCV.2005.252">10.1109/ICCV.2005.252</a>.
  short: V. Kolmogorov, Y. Boykov, in:, IEEE, 2005, pp. 564–571.
conference:
  name: 'ICCV: International Conference on Computer Vision'
date_created: 2018-12-11T12:01:52Z
date_published: 2005-12-05T00:00:00Z
date_updated: 2021-01-12T07:41:38Z
day: '05'
doi: 10.1109/ICCV.2005.252
extern: 1
intvolume: '         1'
month: '12'
page: 564 - 571
publication_status: published
publisher: IEEE
publist_id: '3501'
quality_controlled: 0
status: public
title: What metrics can be approximated by geo cuts or global optimization of length
  area and flux
type: conference
volume: 1
year: '2005'
...
---
_id: '3183'
abstract:
- lang: eng
  text: This paper describes two algorithms capable of real-time segmentation of foreground
    from background layers in stereo video sequences. Automatic separation of layers
    from colour/contrast or from stereo alone is known to be error-prone. Here, colour,
    contrast and stereo matching information are fused to infer layers accurately
    and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves
    stereo in an extended 6-state space that represents both foreground/background
    layers and occluded regions. The stereo-match likelihood is then fused with a
    contrast-sensitive colour model that is learned on the fly, and stereo disparities
    are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC),
    does not directly solve stereo. Instead the stereo match likelihood is marginalised
    over foreground and background hypotheses, and fused with a contrast-sensitive
    colour model like the one used in LDP. Segmentation is solved efficiently by ternary
    graph cut. Both algorithms are evaluated with respect to ground truth data and
    found to have similar perfomance, substantially better than stereo or colour/contrast
    alone. However, their characteristics with respect to computational efficiency
    are rather different. The algorithms are demonstrated in the application of background
    substitution and shown to give good quality composite video output.
author:
- first_name: Vladimir
  full_name: Vladimir Kolmogorov
  id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kolmogorov
- first_name: Antonio
  full_name: Criminisi, Antonio
  last_name: Criminisi
- first_name: Andrew
  full_name: Blake, Andrew
  last_name: Blake
- first_name: Geoffrey
  full_name: Cross, Geoffrey
  last_name: Cross
- first_name: Carsten
  full_name: Rother, Carsten
  last_name: Rother
citation:
  ama: 'Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Bi-layer segmentation
    of binocular stereo video. In: Vol 2. IEEE; 2005:407-414. doi:<a href="https://doi.org/10.1109/CVPR.2005.91">10.1109/CVPR.2005.91</a>'
  apa: 'Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., &#38; Rother, C. (2005).
    Bi-layer segmentation of binocular stereo video (Vol. 2, pp. 407–414). Presented
    at the CVPR: Computer Vision and Pattern Recognition, IEEE. <a href="https://doi.org/10.1109/CVPR.2005.91">https://doi.org/10.1109/CVPR.2005.91</a>'
  chicago: Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross,
    and Carsten Rother. “Bi-Layer Segmentation of Binocular Stereo Video,” 2:407–14.
    IEEE, 2005. <a href="https://doi.org/10.1109/CVPR.2005.91">https://doi.org/10.1109/CVPR.2005.91</a>.
  ieee: 'V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Bi-layer
    segmentation of binocular stereo video,” presented at the CVPR: Computer Vision
    and Pattern Recognition, 2005, vol. 2, pp. 407–414.'
  ista: 'Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2005. Bi-layer segmentation
    of binocular stereo video. CVPR: Computer Vision and Pattern Recognition vol.
    2, 407–414.'
  mla: Kolmogorov, Vladimir, et al. <i>Bi-Layer Segmentation of Binocular Stereo Video</i>.
    Vol. 2, IEEE, 2005, pp. 407–14, doi:<a href="https://doi.org/10.1109/CVPR.2005.91">10.1109/CVPR.2005.91</a>.
  short: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, in:, IEEE, 2005,
    pp. 407–414.
conference:
  name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:52Z
date_published: 2005-07-25T00:00:00Z
date_updated: 2021-01-12T07:41:38Z
day: '25'
doi: 10.1109/CVPR.2005.91
extern: 1
intvolume: '         2'
main_file_link:
- open_access: '0'
  url: http://research.microsoft.com/pubs/67281/criminisi_cvpr2005.pdf
month: '07'
page: 407 - 414
publication_status: published
publisher: IEEE
publist_id: '3502'
quality_controlled: 0
status: public
title: Bi-layer segmentation of binocular stereo video
type: conference
volume: 2
year: '2005'
...
---
_id: '3211'
abstract:
- lang: eng
  text: We present an improved bound on the advantage of any q-query adversary at
    distinguishing between the CBC MAC over a random n-bit permutation and a random
    function outputting n bits. The result assumes that no message queried is a prefix
    of any other, as is the case when all messages to be MACed have the same length.
    We go on to give an improved analysis of the encrypted CBC MAC, where there is
    no restriction on queried messages. Letting m be the block length of the longest
    query, our bounds are about mq2/2n for the basic CBC MAC and mo(1)q2/2n for the
    encrypted CBC MAC, improving prior bounds of m2q2/2n. The new bounds translate
    into improved guarantees on the probability of forging these MACs.
acknowledgement: Pietrzak was supported by the Swiss National Science Foundation,
  project No. 200020-103847/1.
alternative_title:
- LNCS
author:
- first_name: Mihir
  full_name: Bellare, Mihir
  last_name: Bellare
- first_name: Krzysztof Z
  full_name: Krzysztof Pietrzak
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
- first_name: Phillip
  full_name: Rogaway, Phillip
  last_name: Rogaway
citation:
  ama: 'Bellare M, Pietrzak KZ, Rogaway P. Improved security analyses for CBC MACs.
    In: Vol 3621. Springer; 2005:527-545. doi:<a href="https://doi.org/10.1007/11535218_32">10.1007/11535218_32</a>'
  apa: 'Bellare, M., Pietrzak, K. Z., &#38; Rogaway, P. (2005). Improved security
    analyses for CBC MACs (Vol. 3621, pp. 527–545). Presented at the CRYPTO: International
    Cryptology Conference, Springer. <a href="https://doi.org/10.1007/11535218_32">https://doi.org/10.1007/11535218_32</a>'
  chicago: Bellare, Mihir, Krzysztof Z Pietrzak, and Phillip Rogaway. “Improved Security
    Analyses for CBC MACs,” 3621:527–45. Springer, 2005. <a href="https://doi.org/10.1007/11535218_32">https://doi.org/10.1007/11535218_32</a>.
  ieee: 'M. Bellare, K. Z. Pietrzak, and P. Rogaway, “Improved security analyses for
    CBC MACs,” presented at the CRYPTO: International Cryptology Conference, 2005,
    vol. 3621, pp. 527–545.'
  ista: 'Bellare M, Pietrzak KZ, Rogaway P. 2005. Improved security analyses for CBC
    MACs. CRYPTO: International Cryptology Conference, LNCS, vol. 3621, 527–545.'
  mla: Bellare, Mihir, et al. <i>Improved Security Analyses for CBC MACs</i>. Vol.
    3621, Springer, 2005, pp. 527–45, doi:<a href="https://doi.org/10.1007/11535218_32">10.1007/11535218_32</a>.
  short: M. Bellare, K.Z. Pietrzak, P. Rogaway, in:, Springer, 2005, pp. 527–545.
conference:
  name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:02Z
date_published: 2005-09-12T00:00:00Z
date_updated: 2021-01-12T07:41:50Z
day: '12'
doi: 10.1007/11535218_32
extern: 1
intvolume: '      3621'
month: '09'
page: 527 - 545
publication_status: published
publisher: Springer
publist_id: '3469'
quality_controlled: 0
status: public
title: Improved security analyses for CBC MACs
type: conference
volume: 3621
year: '2005'
...
---
_id: '3212'
abstract:
- lang: eng
  text: |-
    The Full-Domain Hash (FDH) signature scheme [3] forms one the most basic usages of random oracles. It works with a family F of trapdoor permutations (TDP), where the signature of m is computed as f−1(h(m)) (here f ∈R F and h is modelled as a random oracle). It is known to be existentially unforgeable for any TDP family F [3], although a much tighter security reduction is known for a restrictive class of TDP’s [10,14] — namely, those induced by a family of claw-free permutations (CFP) pairs. The latter result was shown [11] to match the best possible “black-box” security reduction in the random oracle model, irrespective of the TDP family F (e.g., RSA) one might use.
    In this work we investigate the question if it is possible to instantiate the random oracle h with a “real” family of hash functions H such that the corresponding schemes can be proven secure in the standard model, under some natural assumption on the family F. Our main result rules out the existence of such instantiations for any assumption on F which (1) is satisfied by a family of random permutations; and (2) does not allow the attacker to invert f ∈R F on an a-priori unbounded number of points. Moreover, this holds even if the choice of H can arbitrarily depend on f. As an immediate corollary, we rule out instantiating FDH based on general claw-free permutations, which shows that in order to prove the security of FDH in the standard model one must utilize significantly more structure on F than what is sufficient for the best proof of security in the random oracle model.
acknowledgement: Supported by NSF CAREER Award CCR-0133806 and TC Grant No.CCR-0311095.
  Supported by the Swiss National Science Foundation, project No. 200020-103847/1
alternative_title:
- LNCS
author:
- first_name: Yevgeniy
  full_name: Dodis, Yevgeniy
  last_name: Dodis
- first_name: Roberto
  full_name: Oliveira, Roberto
  last_name: Oliveira
- first_name: Krzysztof Z
  full_name: Krzysztof Pietrzak
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
citation:
  ama: 'Dodis Y, Oliveira R, Pietrzak KZ. On the generic insecurity of the full domain
    hash. In: Vol 3621. Springer; 2005:449-466. doi:<a href="https://doi.org/10.1007/11535218_27">10.1007/11535218_27</a>'
  apa: 'Dodis, Y., Oliveira, R., &#38; Pietrzak, K. Z. (2005). On the generic insecurity
    of the full domain hash (Vol. 3621, pp. 449–466). Presented at the CRYPTO: International
    Cryptology Conference, Springer. <a href="https://doi.org/10.1007/11535218_27">https://doi.org/10.1007/11535218_27</a>'
  chicago: Dodis, Yevgeniy, Roberto Oliveira, and Krzysztof Z Pietrzak. “On the Generic
    Insecurity of the Full Domain Hash,” 3621:449–66. Springer, 2005. <a href="https://doi.org/10.1007/11535218_27">https://doi.org/10.1007/11535218_27</a>.
  ieee: 'Y. Dodis, R. Oliveira, and K. Z. Pietrzak, “On the generic insecurity of
    the full domain hash,” presented at the CRYPTO: International Cryptology Conference,
    2005, vol. 3621, pp. 449–466.'
  ista: 'Dodis Y, Oliveira R, Pietrzak KZ. 2005. On the generic insecurity of the
    full domain hash. CRYPTO: International Cryptology Conference, LNCS, vol. 3621,
    449–466.'
  mla: Dodis, Yevgeniy, et al. <i>On the Generic Insecurity of the Full Domain Hash</i>.
    Vol. 3621, Springer, 2005, pp. 449–66, doi:<a href="https://doi.org/10.1007/11535218_27">10.1007/11535218_27</a>.
  short: Y. Dodis, R. Oliveira, K.Z. Pietrzak, in:, Springer, 2005, pp. 449–466.
conference:
  name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:03Z
date_published: 2005-09-12T00:00:00Z
date_updated: 2021-01-12T07:41:50Z
day: '12'
doi: 10.1007/11535218_27
extern: 1
intvolume: '      3621'
month: '09'
page: 449 - 466
publication_status: published
publisher: Springer
publist_id: '3470'
quality_controlled: 0
status: public
title: On the generic insecurity of the full domain hash
type: conference
volume: 3621
year: '2005'
...
---
_id: '3213'
abstract:
- lang: eng
  text: |-
    We study the question whether the sequential or parallel composition of two functions, each indistinguishable from a random function by non-adaptive distinguishers is secure against adaptive distinguishers. The sequential composition of F and G is the function G(F()), the parallel composition is F G where ⋆ is some group operation. It has been shown that composition indeed gives adaptive security in the information theoretic setting, but unfortunately the proof does not translate into the more interesting computational case.
    In this work we show that in the computational setting composition does not imply adaptive security: If there is a prime order cyclic group where the decisional Diffie-Hellman assumption holds, then there are functions F and G which are indistinguishable by non-adaptive polynomially time-bounded adversaries, but whose parallel composition can be completely broken (i.e. we recover the key) with only three adaptive queries. We give a similar result for sequential composition. Interestingly, we need a standard assumption from the asymmetric (aka. public-key) world to prove a negative result for symmetric (aka. private-key) systems.
acknowledgement: Supported by the Swiss National Science Foundation, project No. 200020-103847/1.
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
  full_name: Krzysztof Pietrzak
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
citation:
  ama: 'Pietrzak KZ. Composition does not imply adaptive security. In: Vol 3621. Springer;
    2005:55-65. doi:<a href="https://doi.org/10.1007/11535218_4">10.1007/11535218_4</a>'
  apa: 'Pietrzak, K. Z. (2005). Composition does not imply adaptive security (Vol.
    3621, pp. 55–65). Presented at the CRYPTO: International Cryptology Conference,
    Springer. <a href="https://doi.org/10.1007/11535218_4">https://doi.org/10.1007/11535218_4</a>'
  chicago: Pietrzak, Krzysztof Z. “Composition Does Not Imply Adaptive Security,”
    3621:55–65. Springer, 2005. <a href="https://doi.org/10.1007/11535218_4">https://doi.org/10.1007/11535218_4</a>.
  ieee: 'K. Z. Pietrzak, “Composition does not imply adaptive security,” presented
    at the CRYPTO: International Cryptology Conference, 2005, vol. 3621, pp. 55–65.'
  ista: 'Pietrzak KZ. 2005. Composition does not imply adaptive security. CRYPTO:
    International Cryptology Conference, LNCS, vol. 3621, 55–65.'
  mla: Pietrzak, Krzysztof Z. <i>Composition Does Not Imply Adaptive Security</i>.
    Vol. 3621, Springer, 2005, pp. 55–65, doi:<a href="https://doi.org/10.1007/11535218_4">10.1007/11535218_4</a>.
  short: K.Z. Pietrzak, in:, Springer, 2005, pp. 55–65.
conference:
  name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:03Z
date_published: 2005-09-12T00:00:00Z
date_updated: 2021-01-12T07:41:50Z
day: '12'
doi: 10.1007/11535218_4
extern: 1
intvolume: '      3621'
month: '09'
page: 55 - 65
publication_status: published
publisher: Springer
publist_id: '3468'
quality_controlled: 0
status: public
title: Composition does not imply adaptive security
type: conference
volume: 3621
year: '2005'
...
---
_id: '11120'
abstract:
- lang: eng
  text: The nuclear envelope (NE) is a highly specialized membrane that delineates
    the eukaryotic cell nucleus. It is composed of the inner and outer nuclear membranes,
    nuclear pore complexes (NPCs) and, in metazoa, the lamina. The NE not only regulates
    the trafficking of macromolecules between nucleoplasm and cytosol but also provides
    anchoring sites for chromatin and the cytoskeleton. Through these interactions,
    the NE helps position the nucleus within the cell and chromosomes within the nucleus,
    thereby regulating the expression of certain genes. The NE is not static, rather
    it is continuously remodeled during cell division. The most dramatic example of
    NE reorganization occurs during mitosis in metazoa when the NE undergoes a complete
    cycle of disassembly and reformation. Despite the importance of the NE for eukaryotic
    cell life, relatively little is known about its biogenesis or many of its functions.
    We thus are far from understanding the molecular etiology of a diverse group of
    NE-associated diseases.
article_processing_charge: No
article_type: original
author:
- first_name: Martin W
  full_name: HETZER, Martin W
  id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
  last_name: HETZER
  orcid: 0000-0002-2111-992X
- first_name: Tobias C.
  full_name: Walther, Tobias C.
  last_name: Walther
- first_name: Iain W.
  full_name: Mattaj, Iain W.
  last_name: Mattaj
citation:
  ama: 'Hetzer M, Walther TC, Mattaj IW. Pushing the envelope: Structure, function,
    and dynamics of the nuclear periphery. <i>Annual Review of Cell and Developmental
    Biology</i>. 2005;21:347-380. doi:<a href="https://doi.org/10.1146/annurev.cellbio.21.090704.151152">10.1146/annurev.cellbio.21.090704.151152</a>'
  apa: 'Hetzer, M., Walther, T. C., &#38; Mattaj, I. W. (2005). Pushing the envelope:
    Structure, function, and dynamics of the nuclear periphery. <i>Annual Review of
    Cell and Developmental Biology</i>. Annual Reviews. <a href="https://doi.org/10.1146/annurev.cellbio.21.090704.151152">https://doi.org/10.1146/annurev.cellbio.21.090704.151152</a>'
  chicago: 'Hetzer, Martin, Tobias C. Walther, and Iain W. Mattaj. “Pushing the Envelope:
    Structure, Function, and Dynamics of the Nuclear Periphery.” <i>Annual Review
    of Cell and Developmental Biology</i>. Annual Reviews, 2005. <a href="https://doi.org/10.1146/annurev.cellbio.21.090704.151152">https://doi.org/10.1146/annurev.cellbio.21.090704.151152</a>.'
  ieee: 'M. Hetzer, T. C. Walther, and I. W. Mattaj, “Pushing the envelope: Structure,
    function, and dynamics of the nuclear periphery,” <i>Annual Review of Cell and
    Developmental Biology</i>, vol. 21. Annual Reviews, pp. 347–380, 2005.'
  ista: 'Hetzer M, Walther TC, Mattaj IW. 2005. Pushing the envelope: Structure, function,
    and dynamics of the nuclear periphery. Annual Review of Cell and Developmental
    Biology. 21, 347–380.'
  mla: 'Hetzer, Martin, et al. “Pushing the Envelope: Structure, Function, and Dynamics
    of the Nuclear Periphery.” <i>Annual Review of Cell and Developmental Biology</i>,
    vol. 21, Annual Reviews, 2005, pp. 347–80, doi:<a href="https://doi.org/10.1146/annurev.cellbio.21.090704.151152">10.1146/annurev.cellbio.21.090704.151152</a>.'
  short: M. Hetzer, T.C. Walther, I.W. Mattaj, Annual Review of Cell and Developmental
    Biology 21 (2005) 347–380.
date_created: 2022-04-07T07:56:52Z
date_published: 2005-11-10T00:00:00Z
date_updated: 2022-07-18T08:57:34Z
day: '10'
doi: 10.1146/annurev.cellbio.21.090704.151152
extern: '1'
external_id:
  pmid:
  - '16212499'
intvolume: '        21'
keyword:
- Cell Biology
- Developmental Biology
language:
- iso: eng
month: '11'
oa_version: None
page: 347-380
pmid: 1
publication: Annual Review of Cell and Developmental Biology
publication_identifier:
  eissn:
  - 1530-8995
  issn:
  - 1081-0706
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Pushing the envelope: Structure, function, and dynamics of the nuclear periphery'
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 21
year: '2005'
...
---
_id: '11698'
abstract:
- lang: eng
  text: We give a short survey of the use of hyperlink analysis in web search engine
    ranking and sketch other applications of hyperlink analysis in the web space.
article_processing_charge: No
author:
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
citation:
  ama: 'Henzinger MH. Hyperlink analysis on the world wide web. In: <i>Proceedings
    of the 16th ACM Conference on Hypertext and Hypermedia</i>. Association for Computing
    Machinery; 2005:1-3. doi:<a href="https://doi.org/10.1145/1083356.1083357">10.1145/1083356.1083357</a>'
  apa: 'Henzinger, M. H. (2005). Hyperlink analysis on the world wide web. In <i>Proceedings
    of the 16th ACM conference on Hypertext and hypermedia</i> (pp. 1–3). Salzburg,
    Austria: Association for Computing Machinery. <a href="https://doi.org/10.1145/1083356.1083357">https://doi.org/10.1145/1083356.1083357</a>'
  chicago: Henzinger, Monika H. “Hyperlink Analysis on the World Wide Web.” In <i>Proceedings
    of the 16th ACM Conference on Hypertext and Hypermedia</i>, 1–3. Association for
    Computing Machinery, 2005. <a href="https://doi.org/10.1145/1083356.1083357">https://doi.org/10.1145/1083356.1083357</a>.
  ieee: M. H. Henzinger, “Hyperlink analysis on the world wide web,” in <i>Proceedings
    of the 16th ACM conference on Hypertext and hypermedia</i>, Salzburg, Austria,
    2005, pp. 1–3.
  ista: 'Henzinger MH. 2005. Hyperlink analysis on the world wide web. Proceedings
    of the 16th ACM conference on Hypertext and hypermedia. HYPERTEXT: Conference
    on Hypertext and Hypermedia, 1–3.'
  mla: Henzinger, Monika H. “Hyperlink Analysis on the World Wide Web.” <i>Proceedings
    of the 16th ACM Conference on Hypertext and Hypermedia</i>, Association for Computing
    Machinery, 2005, pp. 1–3, doi:<a href="https://doi.org/10.1145/1083356.1083357">10.1145/1083356.1083357</a>.
  short: M.H. Henzinger, in:, Proceedings of the 16th ACM Conference on Hypertext
    and Hypermedia, Association for Computing Machinery, 2005, pp. 1–3.
conference:
  end_date: 2005-09-09
  location: Salzburg, Austria
  name: 'HYPERTEXT: Conference on Hypertext and Hypermedia'
  start_date: 2005-09-06
date_created: 2022-07-29T10:47:23Z
date_published: 2005-09-06T00:00:00Z
date_updated: 2023-02-09T11:54:40Z
day: '06'
doi: 10.1145/1083356.1083357
extern: '1'
keyword:
- Hyperlink Analysis
- World Wide Web
language:
- iso: eng
month: '09'
oa_version: None
page: 1-3
publication: Proceedings of the 16th ACM conference on Hypertext and hypermedia
publication_identifier:
  isbn:
  - '9781595931689'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hyperlink analysis on the world wide web
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2005'
...
---
_id: '11763'
abstract:
- lang: eng
  text: "We present the first polylog-competitive online algorithm for the general
    multicast admission control and routing problem in the throughput model. The ratio
    of the number of requests accepted by the optimum offline algorithm to the expected
    number of requests accepted by our algorithm is O((log n + log log M)(log n +
    log M) log n), where M is the number of multicast groups and n is the number of
    nodes in the graph. We show that this is close to optimum by presenting an\r\nΩ(log
    n log M) lower bound on this ratio for any randomized online algorithm against
    an oblivious adversary, when M is much larger than the link capacities. Our lower
    bound applies even in the restricted case where the link capacities are much larger
    than bandwidth requested by a single multicast. We also present a simple proof
    showing that it is impossible to be competitive against an adaptive online adversary.\r\nAs
    in the previous online routing algorithms, our algorithm uses edge-costs when
    deciding on which is the best path to use. In contrast to the previous competitive
    algorithms in the throughput model, our cost is not a direct function of the edge
    load. The new cost definition allows us to decouple the effects of routing and
    admission decisions of different multicast groups."
article_processing_charge: No
article_type: original
author:
- first_name: Ashish
  full_name: Goel, Ashish
  last_name: Goel
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
- first_name: Serge
  full_name: Plotkin, Serge
  last_name: Plotkin
citation:
  ama: Goel A, Henzinger MH, Plotkin S. An online throughput-competitive algorithm
    for multicast routing and admission control. <i>Journal of Algorithms</i>. 2005;55(1):1-20.
    doi:<a href="https://doi.org/10.1016/j.jalgor.2004.11.001">10.1016/j.jalgor.2004.11.001</a>
  apa: Goel, A., Henzinger, M. H., &#38; Plotkin, S. (2005). An online throughput-competitive
    algorithm for multicast routing and admission control. <i>Journal of Algorithms</i>.
    Elsevier. <a href="https://doi.org/10.1016/j.jalgor.2004.11.001">https://doi.org/10.1016/j.jalgor.2004.11.001</a>
  chicago: Goel, Ashish, Monika H Henzinger, and Serge Plotkin. “An Online Throughput-Competitive
    Algorithm for Multicast Routing and Admission Control.” <i>Journal of Algorithms</i>.
    Elsevier, 2005. <a href="https://doi.org/10.1016/j.jalgor.2004.11.001">https://doi.org/10.1016/j.jalgor.2004.11.001</a>.
  ieee: A. Goel, M. H. Henzinger, and S. Plotkin, “An online throughput-competitive
    algorithm for multicast routing and admission control,” <i>Journal of Algorithms</i>,
    vol. 55, no. 1. Elsevier, pp. 1–20, 2005.
  ista: Goel A, Henzinger MH, Plotkin S. 2005. An online throughput-competitive algorithm
    for multicast routing and admission control. Journal of Algorithms. 55(1), 1–20.
  mla: Goel, Ashish, et al. “An Online Throughput-Competitive Algorithm for Multicast
    Routing and Admission Control.” <i>Journal of Algorithms</i>, vol. 55, no. 1,
    Elsevier, 2005, pp. 1–20, doi:<a href="https://doi.org/10.1016/j.jalgor.2004.11.001">10.1016/j.jalgor.2004.11.001</a>.
  short: A. Goel, M.H. Henzinger, S. Plotkin, Journal of Algorithms 55 (2005) 1–20.
date_created: 2022-08-08T12:03:00Z
date_published: 2005-04-01T00:00:00Z
date_updated: 2023-02-21T16:33:22Z
day: '01'
doi: 10.1016/j.jalgor.2004.11.001
extern: '1'
intvolume: '        55'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1016/j.jalgor.2004.11.001
month: '04'
oa: 1
oa_version: Published Version
page: 1-20
publication: Journal of Algorithms
publication_identifier:
  issn:
  - 0196-6774
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
  record:
  - id: '11926'
    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: An online throughput-competitive algorithm for multicast routing and admission
  control
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2005'
...
---
_id: '8028'
abstract:
- lang: eng
  text: 'Transmission of signals within the brain is essential for cognitive function,
    but it is not clear how neural circuits support reliable and accurate signal propagation
    over a sufficiently large dynamic range. Two modes of propagation have been studied:
    synfire chains, in which synchronous activity travels through feedforward layers
    of a neuronal network, and the propagation of fluctuations in firing rate across
    these layers. In both cases, a sufficient amount of noise, which was added to
    previous models from an external source, had to be included to support stable
    propagation. Sparse, randomly connected networks of spiking model neurons can
    generate chaotic patterns of activity. We investigate whether this activity, which
    is a more realistic noise source, is sufficient to allow for signal transmission.
    We find that, for rate-coded signals but not for synfire chains, such networks
    support robust and accurate signal reproduction through up to six layers if appropriate
    adjustments are made in synaptic strengths. We investigate the factors affecting
    transmission and show that multiple signals can propagate simultaneously along
    different pathways. Using this feature, we show how different types of logic gates
    can arise within the architecture of the random network through the strengthening
    of specific synapses.'
article_processing_charge: No
article_type: original
author:
- first_name: Tim P
  full_name: Vogels, Tim P
  id: CB6FF8D2-008F-11EA-8E08-2637E6697425
  last_name: Vogels
  orcid: 0000-0003-3295-6181
- first_name: L. F.
  full_name: Abbott, L. F.
  last_name: Abbott
citation:
  ama: Vogels TP, Abbott LF. Signal propagation and logic gating in networks of integrate-and-fire
    neurons. <i>Journal of Neuroscience</i>. 2005;25(46):10786-10795. doi:<a href="https://doi.org/10.1523/jneurosci.3508-05.2005">10.1523/jneurosci.3508-05.2005</a>
  apa: Vogels, T. P., &#38; Abbott, L. F. (2005). Signal propagation and logic gating
    in networks of integrate-and-fire neurons. <i>Journal of Neuroscience</i>. Society
    for Neuroscience. <a href="https://doi.org/10.1523/jneurosci.3508-05.2005">https://doi.org/10.1523/jneurosci.3508-05.2005</a>
  chicago: Vogels, Tim P, and L. F. Abbott. “Signal Propagation and Logic Gating in
    Networks of Integrate-and-Fire Neurons.” <i>Journal of Neuroscience</i>. Society
    for Neuroscience, 2005. <a href="https://doi.org/10.1523/jneurosci.3508-05.2005">https://doi.org/10.1523/jneurosci.3508-05.2005</a>.
  ieee: T. P. Vogels and L. F. Abbott, “Signal propagation and logic gating in networks
    of integrate-and-fire neurons,” <i>Journal of Neuroscience</i>, vol. 25, no. 46.
    Society for Neuroscience, pp. 10786–10795, 2005.
  ista: Vogels TP, Abbott LF. 2005. Signal propagation and logic gating in networks
    of integrate-and-fire neurons. Journal of Neuroscience. 25(46), 10786–10795.
  mla: Vogels, Tim P., and L. F. Abbott. “Signal Propagation and Logic Gating in Networks
    of Integrate-and-Fire Neurons.” <i>Journal of Neuroscience</i>, vol. 25, no. 46,
    Society for Neuroscience, 2005, pp. 10786–95, doi:<a href="https://doi.org/10.1523/jneurosci.3508-05.2005">10.1523/jneurosci.3508-05.2005</a>.
  short: T.P. Vogels, L.F. Abbott, Journal of Neuroscience 25 (2005) 10786–10795.
date_created: 2020-06-25T13:12:33Z
date_published: 2005-11-16T00:00:00Z
date_updated: 2021-01-12T08:16:37Z
day: '16'
doi: 10.1523/jneurosci.3508-05.2005
extern: '1'
external_id:
  pmid:
  - '16291952'
intvolume: '        25'
issue: '46'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6725859/
month: '11'
oa: 1
oa_version: Published Version
page: 10786-10795
pmid: 1
publication: Journal of Neuroscience
publication_identifier:
  issn:
  - 0270-6474
  - 1529-2401
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
status: public
title: Signal propagation and logic gating in networks of integrate-and-fire neurons
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 25
year: '2005'
...
---
_id: '8029'
abstract:
- lang: eng
  text: 'Neural network modeling is often concerned with stimulus-driven responses,
    but most of the activity in the brain is internally generated. Here, we review
    network models of internally generated activity, focusing on three types of network
    dynamics: (a) sustained responses to transient stimuli, which provide a model
    of working memory; (b) oscillatory network activity; and (c) chaotic activity,
    which models complex patterns of background spiking in cortical and other circuits.
    We also review propagation of stimulus-driven activity through spontaneously active
    networks. Exploring these aspects of neural network dynamics is critical for understanding
    how neural circuits produce cognitive function.'
article_processing_charge: No
article_type: review
author:
- first_name: Tim P
  full_name: Vogels, Tim P
  id: CB6FF8D2-008F-11EA-8E08-2637E6697425
  last_name: Vogels
  orcid: 0000-0003-3295-6181
- first_name: Kanaka
  full_name: Rajan, Kanaka
  last_name: Rajan
- first_name: L.F.
  full_name: Abbott, L.F.
  last_name: Abbott
citation:
  ama: Vogels TP, Rajan K, Abbott LF. Neural network dynamics. <i>Annual Review of
    Neuroscience</i>. 2005;28(1):357-376. doi:<a href="https://doi.org/10.1146/annurev.neuro.28.061604.135637">10.1146/annurev.neuro.28.061604.135637</a>
  apa: Vogels, T. P., Rajan, K., &#38; Abbott, L. F. (2005). Neural network dynamics.
    <i>Annual Review of Neuroscience</i>. Annual Reviews. <a href="https://doi.org/10.1146/annurev.neuro.28.061604.135637">https://doi.org/10.1146/annurev.neuro.28.061604.135637</a>
  chicago: Vogels, Tim P, Kanaka Rajan, and L.F. Abbott. “Neural Network Dynamics.”
    <i>Annual Review of Neuroscience</i>. Annual Reviews, 2005. <a href="https://doi.org/10.1146/annurev.neuro.28.061604.135637">https://doi.org/10.1146/annurev.neuro.28.061604.135637</a>.
  ieee: T. P. Vogels, K. Rajan, and L. F. Abbott, “Neural network dynamics,” <i>Annual
    Review of Neuroscience</i>, vol. 28, no. 1. Annual Reviews, pp. 357–376, 2005.
  ista: Vogels TP, Rajan K, Abbott LF. 2005. Neural network dynamics. Annual Review
    of Neuroscience. 28(1), 357–376.
  mla: Vogels, Tim P., et al. “Neural Network Dynamics.” <i>Annual Review of Neuroscience</i>,
    vol. 28, no. 1, Annual Reviews, 2005, pp. 357–76, doi:<a href="https://doi.org/10.1146/annurev.neuro.28.061604.135637">10.1146/annurev.neuro.28.061604.135637</a>.
  short: T.P. Vogels, K. Rajan, L.F. Abbott, Annual Review of Neuroscience 28 (2005)
    357–376.
date_created: 2020-06-25T13:13:11Z
date_published: 2005-07-21T00:00:00Z
date_updated: 2021-01-12T08:16:37Z
day: '21'
doi: 10.1146/annurev.neuro.28.061604.135637
extern: '1'
external_id:
  pmid:
  - '16022600'
intvolume: '        28'
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 357-376
pmid: 1
publication: Annual Review of Neuroscience
publication_identifier:
  issn:
  - 0147-006X
  - 1545-4126
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
status: public
title: Neural network dynamics
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 28
year: '2005'
...
