---
_id: '3055'
abstract:
- lang: eng
  text: 'ACAP-type ARF GTPase activating proteins (ARF-GAPs) regulate multiple cellular
    processes, including endocytosis, secretion, phagocytosis, cell adhesion and cell
    migration. However, the regulation of ACAP functions by other cellular proteins
    is poorly understood. We have reported previously that a plant ACAP, VAN3, plays
    a pivotal role in plant venation continuity. Here, we report on newly identified
    VAN3 regulators: the CVP2 (cotyledon vascular pattern 2) 5 PTase, which is considered
    to degrade IP3 and also to produce PtdIns(4)P from PtdIns(4,5)P2; and a PH domain-containing
    protein, VAB (VAN3 binding protein). Combinational mutations of both CVP2 and
    its closest homologue CVL1 (CVP2 like 1) phenocopied the strong allele of van3
    mutants, showing severe vascular continuity. The phenotype of double mutants between
    van3, cvp2 and vab suggested that VAN3, CVP2 and VAB function in vascular pattern
    formation in the same pathway. Localization analysis revealed that both CVP2 and
    VAB colocalize with VAN3 in the trans- Golgi network (TGN), supporting their functions
    in the same pathway. The subcellular localization of VAN3 was dependent on its
    PH domain, and mislocalization of VAN3 was induced in cvp2 or vab mutants. These
    results suggest that CVP2 and VAB cooperatively regulate the subcellular localization
    of VAN3 through the interaction between its PH domain and phosphoinositides and/or
    inositol phosphates. In addition, PtdIns(4)P, to which VAN3 binds preferentially,
    enhanced the ARF-GAP activity of VAN3, whereas IP3 inhibited it. These results
    suggest the existence of PtdIns(4)P and/or IP3-dependent subcellular targeting
    and regulation of VAN3 ACAP activity that governs plant vascular tissue continuity.'
author:
- first_name: Satoshi
  full_name: Naramoto, Satoshi
  last_name: Naramoto
- first_name: Shinichiro
  full_name: Sawa, Shinichiro
  last_name: Sawa
- first_name: Koji
  full_name: Koizumi, Koji
  last_name: Koizumi
- first_name: Tomohiro
  full_name: Uemura, Tomohiro
  last_name: Uemura
- first_name: Takashi
  full_name: Ueda, Takashi
  last_name: Ueda
- first_name: Jirí
  full_name: Jirí Friml
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Akihiko
  full_name: Nakano, Akihiko
  last_name: Nakano
- first_name: Hiroo
  full_name: Fukuda, Hiroo
  last_name: Fukuda
citation:
  ama: Naramoto S, Sawa S, Koizumi K, et al. Phosphoinositide-dependent regulation
    of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity
    in plants. <i>Development</i>. 2009;136(9):1529-1538. doi:<a href="https://doi.org/10.1242/dev.030098">10.1242/dev.030098</a>
  apa: Naramoto, S., Sawa, S., Koizumi, K., Uemura, T., Ueda, T., Friml, J., … Fukuda,
    H. (2009). Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization
    and activity essential for vascular tissue continuity in plants. <i>Development</i>.
    Company of Biologists. <a href="https://doi.org/10.1242/dev.030098">https://doi.org/10.1242/dev.030098</a>
  chicago: Naramoto, Satoshi, Shinichiro Sawa, Koji Koizumi, Tomohiro Uemura, Takashi
    Ueda, Jiří Friml, Akihiko Nakano, and Hiroo Fukuda. “Phosphoinositide-Dependent
    Regulation of VAN3 ARF-GAP Localization and Activity Essential for Vascular Tissue
    Continuity in Plants.” <i>Development</i>. Company of Biologists, 2009. <a href="https://doi.org/10.1242/dev.030098">https://doi.org/10.1242/dev.030098</a>.
  ieee: S. Naramoto <i>et al.</i>, “Phosphoinositide-dependent regulation of VAN3
    ARF-GAP localization and activity essential for vascular tissue continuity in
    plants,” <i>Development</i>, vol. 136, no. 9. Company of Biologists, pp. 1529–1538,
    2009.
  ista: Naramoto S, Sawa S, Koizumi K, Uemura T, Ueda T, Friml J, Nakano A, Fukuda
    H. 2009. Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and
    activity essential for vascular tissue continuity in plants. Development. 136(9),
    1529–1538.
  mla: Naramoto, Satoshi, et al. “Phosphoinositide-Dependent Regulation of VAN3 ARF-GAP
    Localization and Activity Essential for Vascular Tissue Continuity in Plants.”
    <i>Development</i>, vol. 136, no. 9, Company of Biologists, 2009, pp. 1529–38,
    doi:<a href="https://doi.org/10.1242/dev.030098">10.1242/dev.030098</a>.
  short: S. Naramoto, S. Sawa, K. Koizumi, T. Uemura, T. Ueda, J. Friml, A. Nakano,
    H. Fukuda, Development 136 (2009) 1529–1538.
date_created: 2018-12-11T12:01:06Z
date_published: 2009-05-01T00:00:00Z
date_updated: 2021-01-12T07:40:44Z
day: '01'
doi: 10.1242/dev.030098
extern: 1
intvolume: '       136'
issue: '9'
month: '05'
page: 1529 - 1538
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '3647'
quality_controlled: 0
status: public
title: Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity
  essential for vascular tissue continuity in plants
type: journal_article
volume: 136
year: '2009'
...
---
_id: '3056'
abstract:
- lang: eng
  text: Local hormone maxima are essential for the development of multicellular structures
    and organs. For example, steroid hormones accumulate in specific cell types of
    the animal fetus to induce sexual differentiation and concentration peaks of the
    plant hormone auxin direct organ initiation and mediate tissue patterning. Here
    we provide an example of a regulated local hormone minimum required during organogenesis.
    Our results demonstrate that formation of a local auxin minimum is necessary for
    specification of the valve margin separation layer where Arabidopsis fruit opening
    takes place. Consequently, ectopic production of auxin, specifically in valve
    margin cells, leads to a complete loss of proper cell fate determination. The
    valve margin identity factor INDEHISCENT (IND) is responsible for forming the
    auxin minimum by coordinating auxin efflux in separation-layer cells. We propose
    that the simplicity of formation and maintenance make local hormone minima particularly
    well suited to specify a small number of cells such as the stripes at the valve
    margins.
author:
- first_name: Karim
  full_name: Sorefan, Karim
  last_name: Sorefan
- first_name: Thomas
  full_name: Girin, Thomas
  last_name: Girin
- first_name: Sarah
  full_name: Liljegren, Sarah J
  last_name: Liljegren
- first_name: Karin
  full_name: Ljung, Karin
  last_name: Ljung
- first_name: Pedro
  full_name: Robles, Pedro
  last_name: Robles
- first_name: Carlos
  full_name: Galván-Ampudia, Carlos S
  last_name: Galván Ampudia
- first_name: Remko
  full_name: Offringa, Remko
  last_name: Offringa
- first_name: Jirí
  full_name: Jirí Friml
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Martin
  full_name: Yanofsky, Martin F
  last_name: Yanofsky
- first_name: Lars
  full_name: Østergaard, Lars
  last_name: Østergaard
citation:
  ama: Sorefan K, Girin T, Liljegren S, et al. A regulated auxin minimum is required
    for seed dispersal in Arabidopsis. <i>Nature</i>. 2009;459(7246):583-586. doi:<a
    href="https://doi.org/10.1038/nature07875">10.1038/nature07875</a>
  apa: Sorefan, K., Girin, T., Liljegren, S., Ljung, K., Robles, P., Galván Ampudia,
    C., … Østergaard, L. (2009). A regulated auxin minimum is required for seed dispersal
    in Arabidopsis. <i>Nature</i>. Nature Publishing Group. <a href="https://doi.org/10.1038/nature07875">https://doi.org/10.1038/nature07875</a>
  chicago: Sorefan, Karim, Thomas Girin, Sarah Liljegren, Karin Ljung, Pedro Robles,
    Carlos Galván Ampudia, Remko Offringa, Jiří Friml, Martin Yanofsky, and Lars Østergaard.
    “A Regulated Auxin Minimum Is Required for Seed Dispersal in Arabidopsis.” <i>Nature</i>.
    Nature Publishing Group, 2009. <a href="https://doi.org/10.1038/nature07875">https://doi.org/10.1038/nature07875</a>.
  ieee: K. Sorefan <i>et al.</i>, “A regulated auxin minimum is required for seed
    dispersal in Arabidopsis,” <i>Nature</i>, vol. 459, no. 7246. Nature Publishing
    Group, pp. 583–586, 2009.
  ista: Sorefan K, Girin T, Liljegren S, Ljung K, Robles P, Galván Ampudia C, Offringa
    R, Friml J, Yanofsky M, Østergaard L. 2009. A regulated auxin minimum is required
    for seed dispersal in Arabidopsis. Nature. 459(7246), 583–586.
  mla: Sorefan, Karim, et al. “A Regulated Auxin Minimum Is Required for Seed Dispersal
    in Arabidopsis.” <i>Nature</i>, vol. 459, no. 7246, Nature Publishing Group, 2009,
    pp. 583–86, doi:<a href="https://doi.org/10.1038/nature07875">10.1038/nature07875</a>.
  short: K. Sorefan, T. Girin, S. Liljegren, K. Ljung, P. Robles, C. Galván Ampudia,
    R. Offringa, J. Friml, M. Yanofsky, L. Østergaard, Nature 459 (2009) 583–586.
date_created: 2018-12-11T12:01:06Z
date_published: 2009-05-28T00:00:00Z
date_updated: 2021-01-12T07:40:44Z
day: '28'
doi: 10.1038/nature07875
extern: 1
intvolume: '       459'
issue: '7246'
month: '05'
page: 583 - 586
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '3646'
quality_controlled: 0
status: public
title: A regulated auxin minimum is required for seed dispersal in Arabidopsis
type: journal_article
volume: 459
year: '2009'
...
---
_id: '3057'
abstract:
- lang: eng
  text: The differential distribution of the plant signaling molecule auxin is required
    for many aspects of plant development. Local auxin maxima and gradients arise
    as a result of local auxin metabolism and, predominantly, from directional cell-to-cell
    transport. In this primer, we discuss how the coordinated activity of several
    auxin influx and efflux systems, which transport auxin across the plasma membrane,
    mediates directional auxin flow. This activity crucially contributes to the correct
    setting of developmental cues in embryogenesis, organogenesis, vascular tissue
    formation and directional growth in response to environmental stimuli.
author:
- first_name: Jan
  full_name: Petrášek, Jan
  last_name: Petrášek
- first_name: Jirí
  full_name: Friml, Jirí
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: Petrášek J, Friml J. Auxin transport routes in plant development. <i>Development</i>.
    2009;136(16):2675-2688. doi:<a href="https://doi.org/10.1242/dev.030353">10.1242/dev.030353</a>
  apa: Petrášek, J., &#38; Friml, J. (2009). Auxin transport routes in plant development.
    <i>Development</i>. Company of Biologists. <a href="https://doi.org/10.1242/dev.030353">https://doi.org/10.1242/dev.030353</a>
  chicago: Petrášek, Jan, and Jiří Friml. “Auxin Transport Routes in Plant Development.”
    <i>Development</i>. Company of Biologists, 2009. <a href="https://doi.org/10.1242/dev.030353">https://doi.org/10.1242/dev.030353</a>.
  ieee: J. Petrášek and J. Friml, “Auxin transport routes in plant development,” <i>Development</i>,
    vol. 136, no. 16. Company of Biologists, pp. 2675–2688, 2009.
  ista: Petrášek J, Friml J. 2009. Auxin transport routes in plant development. Development.
    136(16), 2675–2688.
  mla: Petrášek, Jan, and Jiří Friml. “Auxin Transport Routes in Plant Development.”
    <i>Development</i>, vol. 136, no. 16, Company of Biologists, 2009, pp. 2675–88,
    doi:<a href="https://doi.org/10.1242/dev.030353">10.1242/dev.030353</a>.
  short: J. Petrášek, J. Friml, Development 136 (2009) 2675–2688.
date_created: 2018-12-11T12:01:07Z
date_published: 2009-08-15T00:00:00Z
date_updated: 2021-01-12T07:40:45Z
day: '15'
doi: 10.1242/dev.030353
extern: '1'
external_id:
  pmid:
  - '    19633168'
intvolume: '       136'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pubmed/19633168
month: '08'
oa: 1
oa_version: Published Version
page: 2675 - 2688
pmid: 1
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '3644'
quality_controlled: '1'
status: public
title: Auxin transport routes in plant development
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2009'
...
---
_id: '3058'
abstract:
- lang: eng
  text: The plant signalling molecule auxin provides positional informa-tion in a
    variety of developmental processes by means of its differential distribution (gradients)
    within plant tissues. Thus, cellular auxin levels often determine the developmental
    output of auxin signalling. Conceptually, transmembrane transport and metabolic
    processes regulate the steady-state levels of auxin in any given cell2,3. In particular,
    PIN auxin-efflux-carrier-mediated, directional transport between cells is crucial
    for generating auxin gradients2,4,5. Here we show that Arabidopsis thaliana PIN5,
    an atypical member of the PIN gene family, encodes a functional auxin transporter
    that is required for auxin-mediated develop-ment. PIN5 does not have a direct
    role in cell-to-cell transport but regulates intracellular auxin homeostasis and
    metabolism. PIN5 localizes, unlike other characterized plasma membrane PIN proteins,
    to endoplasmic reticulum (ER), presumably medi-ating auxin flow from the cytosol
    to the lumen of the ER. The ER localization of other PIN5-like transporters (including
    the moss PIN) indicates that the diversification of PIN protein functions in mediating
    auxin homeostasis at the ER, and cell-to-cell auxin transport at the plasma membrane,
    represent an ancient event during the evolution of land plants.
author:
- first_name: Jozef
  full_name: Mravec, Jozef
  last_name: Mravec
- first_name: Petr
  full_name: Skůpa, Petr
  last_name: Skůpa
- first_name: Aurélien
  full_name: Bailly, Aurélien
  last_name: Bailly
- first_name: Klára
  full_name: Hoyerová, Klára
  last_name: Hoyerová
- first_name: Pavel
  full_name: Křeček, Pavel
  last_name: Křeček
- first_name: Agnieszka
  full_name: Bielach, Agnieszka
  last_name: Bielach
- first_name: Jan
  full_name: Petrášek, Jan
  last_name: Petrášek
- first_name: Jing
  full_name: Zhang, Jing
  last_name: Zhang
- first_name: Vassilena
  full_name: Gaykova, Vassilena
  last_name: Gaykova
- first_name: York
  full_name: Stierhof, York-Dieter
  last_name: Stierhof
- first_name: Petre
  full_name: Dobrev, Petre I
  last_name: Dobrev
- first_name: Kateřina
  full_name: Schwarzerová, Kateřina
  last_name: Schwarzerová
- first_name: Jakub
  full_name: Rolčík, Jakub
  last_name: Rolčík
- first_name: Daniela
  full_name: Seifertová, Daniela
  last_name: Seifertová
- first_name: Christian
  full_name: Luschnig, Christian
  last_name: Luschnig
- first_name: Eva
  full_name: Eva Benková
  id: 38F4F166-F248-11E8-B48F-1D18A9856A87
  last_name: Benková
  orcid: 0000-0002-8510-9739
- first_name: Eva
  full_name: Zažímalová, Eva
  last_name: Zažímalová
- first_name: Markus
  full_name: Geisler, Markus
  last_name: Geisler
- first_name: Jirí
  full_name: Jirí Friml
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: Mravec J, Skůpa P, Bailly A, et al. Subcellular homeostasis of phytohormone
    auxin is mediated by the ER localized PIN5 transporter. <i>Nature</i>. 2009;459(7250):1136-1140.
    doi:<a href="https://doi.org/10.1038/nature08066">10.1038/nature08066</a>
  apa: Mravec, J., Skůpa, P., Bailly, A., Hoyerová, K., Křeček, P., Bielach, A., …
    Friml, J. (2009). Subcellular homeostasis of phytohormone auxin is mediated by
    the ER localized PIN5 transporter. <i>Nature</i>. Nature Publishing Group. <a
    href="https://doi.org/10.1038/nature08066">https://doi.org/10.1038/nature08066</a>
  chicago: Mravec, Jozef, Petr Skůpa, Aurélien Bailly, Klára Hoyerová, Pavel Křeček,
    Agnieszka Bielach, Jan Petrášek, et al. “Subcellular Homeostasis of Phytohormone
    Auxin Is Mediated by the ER Localized PIN5 Transporter.” <i>Nature</i>. Nature
    Publishing Group, 2009. <a href="https://doi.org/10.1038/nature08066">https://doi.org/10.1038/nature08066</a>.
  ieee: J. Mravec <i>et al.</i>, “Subcellular homeostasis of phytohormone auxin is
    mediated by the ER localized PIN5 transporter,” <i>Nature</i>, vol. 459, no. 7250.
    Nature Publishing Group, pp. 1136–1140, 2009.
  ista: Mravec J, Skůpa P, Bailly A, Hoyerová K, Křeček P, Bielach A, Petrášek J,
    Zhang J, Gaykova V, Stierhof Y, Dobrev P, Schwarzerová K, Rolčík J, Seifertová
    D, Luschnig C, Benková E, Zažímalová E, Geisler M, Friml J. 2009. Subcellular
    homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter.
    Nature. 459(7250), 1136–1140.
  mla: Mravec, Jozef, et al. “Subcellular Homeostasis of Phytohormone Auxin Is Mediated
    by the ER Localized PIN5 Transporter.” <i>Nature</i>, vol. 459, no. 7250, Nature
    Publishing Group, 2009, pp. 1136–40, doi:<a href="https://doi.org/10.1038/nature08066">10.1038/nature08066</a>.
  short: J. Mravec, P. Skůpa, A. Bailly, K. Hoyerová, P. Křeček, A. Bielach, J. Petrášek,
    J. Zhang, V. Gaykova, Y. Stierhof, P. Dobrev, K. Schwarzerová, J. Rolčík, D. Seifertová,
    C. Luschnig, E. Benková, E. Zažímalová, M. Geisler, J. Friml, Nature 459 (2009)
    1136–1140.
date_created: 2018-12-11T12:01:07Z
date_published: 2009-06-25T00:00:00Z
date_updated: 2021-01-12T07:40:45Z
day: '25'
doi: 10.1038/nature08066
extern: 1
intvolume: '       459'
issue: '7250'
month: '06'
page: 1136 - 1140
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '3645'
quality_controlled: 0
status: public
title: Subcellular homeostasis of phytohormone auxin is mediated by the ER localized
  PIN5 transporter
type: journal_article
volume: 459
year: '2009'
...
---
_id: '3059'
abstract:
- lang: eng
  text: The phytohormone auxin plays a major role in embryonic and postembryonic plant
    development. The temporal and spatial distribution of auxin largely depends on
    the subcellular polar localization of members of the PIN-FORMED (PIN) auxin efflux
    carrier family. The Ser/Thr protein kinase PINOID (PID) catalyzes PIN phosphorylation
    and crucially contributes to the regulation of apical-basal PIN polarity. The
    GTP exchange factor on ADP-ribosylation factors (ARF-GEF), GNOM preferentially
    mediates PIN recycling at the basal side of the cell. Interference with GNOM activity
    leads to dynamic PIN transcytosis between different sides of the cell. Our genetic,
    pharmacological, and cell biological approaches illustrate that PID and GNOM influence
    PIN polarity and plant development in an antagonistic manner and that the PID-dependent
    PIN phosphorylation results in GNOM-independent polar PIN targeting. The data
    suggest that PID and the protein phosphatase 2A not only regulate the static PIN
    polarity, but also act antagonistically on the rate of GNOM-dependent polar PIN
    transcytosis. We propose a model that includes PID-dependent PIN phosphorylation
    at the plasma membrane and the subsequent sorting of PIN proteins to a GNOM-independent
    pathway for polarity alterations during developmental processes, such as lateral
    root formation and leaf vasculature development.
author:
- first_name: Jürgen
  full_name: Kleine-Vehn, Jürgen
  last_name: Kleine Vehn
- first_name: Fang
  full_name: Huang, Fang
  last_name: Huang
- first_name: Satoshi
  full_name: Naramoto, Satoshi
  last_name: Naramoto
- first_name: Jing
  full_name: Zhang, Jing
  last_name: Zhang
- first_name: Marta
  full_name: Michniewicz, Marta
  last_name: Michniewicz
- first_name: Remko
  full_name: Offringa, Remko
  last_name: Offringa
- first_name: Jirí
  full_name: Jirí Friml
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: Kleine Vehn J, Huang F, Naramoto S, et al. PIN auxin efflux carrier polarity
    is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking
    in arabidopsis. <i>Plant Cell</i>. 2009;21(12):3839-3849. doi:<a href="https://doi.org/10.1105/tpc.109.071639">10.1105/tpc.109.071639</a>
  apa: Kleine Vehn, J., Huang, F., Naramoto, S., Zhang, J., Michniewicz, M., Offringa,
    R., &#38; Friml, J. (2009). PIN auxin efflux carrier polarity is regulated by
    PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis.
    <i>Plant Cell</i>. American Society of Plant Biologists. <a href="https://doi.org/10.1105/tpc.109.071639">https://doi.org/10.1105/tpc.109.071639</a>
  chicago: Kleine Vehn, Jürgen, Fang Huang, Satoshi Naramoto, Jing Zhang, Marta Michniewicz,
    Remko Offringa, and Jiří Friml. “PIN Auxin Efflux Carrier Polarity Is Regulated
    by PINOID Kinase Mediated Recruitment into GNOM Independent Trafficking in Arabidopsis.”
    <i>Plant Cell</i>. American Society of Plant Biologists, 2009. <a href="https://doi.org/10.1105/tpc.109.071639">https://doi.org/10.1105/tpc.109.071639</a>.
  ieee: J. Kleine Vehn <i>et al.</i>, “PIN auxin efflux carrier polarity is regulated
    by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis,”
    <i>Plant Cell</i>, vol. 21, no. 12. American Society of Plant Biologists, pp.
    3839–3849, 2009.
  ista: Kleine Vehn J, Huang F, Naramoto S, Zhang J, Michniewicz M, Offringa R, Friml
    J. 2009. PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated
    recruitment into GNOM independent trafficking in arabidopsis. Plant Cell. 21(12),
    3839–3849.
  mla: Kleine Vehn, Jürgen, et al. “PIN Auxin Efflux Carrier Polarity Is Regulated
    by PINOID Kinase Mediated Recruitment into GNOM Independent Trafficking in Arabidopsis.”
    <i>Plant Cell</i>, vol. 21, no. 12, American Society of Plant Biologists, 2009,
    pp. 3839–49, doi:<a href="https://doi.org/10.1105/tpc.109.071639">10.1105/tpc.109.071639</a>.
  short: J. Kleine Vehn, F. Huang, S. Naramoto, J. Zhang, M. Michniewicz, R. Offringa,
    J. Friml, Plant Cell 21 (2009) 3839–3849.
date_created: 2018-12-11T12:01:07Z
date_published: 2009-12-01T00:00:00Z
date_updated: 2021-01-12T07:40:45Z
day: '01'
doi: 10.1105/tpc.109.071639
extern: 1
intvolume: '        21'
issue: '12'
month: '12'
page: 3839 - 3849
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3643'
quality_controlled: 0
status: public
title: PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment
  into GNOM independent trafficking in arabidopsis
type: journal_article
volume: 21
year: '2009'
...
---
_id: '3060'
article_type: letter_note
author:
- first_name: Karin
  full_name: Schumacher, Karin
  last_name: Schumacher
- first_name: Jirí
  full_name: Friml, Jirí
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: Schumacher K, Friml J. Cell biology. <i>Current Opinion in Plant Biology</i>.
    2009;12(6):651-652. doi:<a href="https://doi.org/10.1016/j.pbi.2009.10.009">10.1016/j.pbi.2009.10.009</a>
  apa: Schumacher, K., &#38; Friml, J. (2009). Cell biology. <i>Current Opinion in
    Plant Biology</i>. Elsevier. <a href="https://doi.org/10.1016/j.pbi.2009.10.009">https://doi.org/10.1016/j.pbi.2009.10.009</a>
  chicago: Schumacher, Karin, and Jiří Friml. “Cell Biology.” <i>Current Opinion in
    Plant Biology</i>. Elsevier, 2009. <a href="https://doi.org/10.1016/j.pbi.2009.10.009">https://doi.org/10.1016/j.pbi.2009.10.009</a>.
  ieee: K. Schumacher and J. Friml, “Cell biology,” <i>Current Opinion in Plant Biology</i>,
    vol. 12, no. 6. Elsevier, pp. 651–652, 2009.
  ista: Schumacher K, Friml J. 2009. Cell biology. Current Opinion in Plant Biology.
    12(6), 651–652.
  mla: Schumacher, Karin, and Jiří Friml. “Cell Biology.” <i>Current Opinion in Plant
    Biology</i>, vol. 12, no. 6, Elsevier, 2009, pp. 651–52, doi:<a href="https://doi.org/10.1016/j.pbi.2009.10.009">10.1016/j.pbi.2009.10.009</a>.
  short: K. Schumacher, J. Friml, Current Opinion in Plant Biology 12 (2009) 651–652.
date_created: 2018-12-11T12:01:08Z
date_published: 2009-12-01T00:00:00Z
date_updated: 2021-01-12T07:40:46Z
day: '01'
doi: 10.1016/j.pbi.2009.10.009
extern: '1'
intvolume: '        12'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 651 - 652
publication: Current Opinion in Plant Biology
publication_status: published
publisher: Elsevier
publist_id: '3641'
quality_controlled: '1'
status: public
title: Cell biology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2009'
...
---
_id: '3061'
abstract:
- lang: eng
  text: The PIN-FORMED (PIN) proteins are secondary transporters acting in the efflux
    of the plant signal molecule auxin from cells. They are asymmetrically localized
    within cells and their polarity determines the directionality of intercellular
    auxin flow. PIN genes are found exclusively in the genomes of multicellular plants
    and play an important role in regulating asymmetric auxin distribution in multiple
    developmental processes, including embryogenesis, organogenesis, tissue differentiation
    and tropic responses. All PIN proteins have a similar structure with amino- and
    carboxy-terminal hydrophobic, membrane-spanning domains separated by a central
    hydrophilic domain. The structure of the hydrophobic domains is well conserved.
    The hydrophilic domain is more divergent and it determines eight groups within
    the protein family. The activity of PIN proteins is regulated at multiple levels,
    including transcription, protein stability, subcellular localization and transport
    activity. Different endogenous and environmental signals can modulate PIN activity
    and thus modulate auxin-distribution-dependent development. A large group of PIN
    proteins, including the most ancient members known from mosses, localize to the
    endoplasmic reticulum and they regulate the subcellular compartmentalization of
    auxin and thus auxin metabolism. Further work is needed to establish the physiological
    importance of this unexpected mode of auxin homeostasis regulation. Furthermore,
    the evolution of PIN-based transport, PIN protein structure and more detailed
    biochemical characterization of the transport function are important topics for
    further studies.
author:
- first_name: Pavel
  full_name: Křeček, Pavel
  last_name: Křeček
- first_name: Petr
  full_name: Skůpa, Petr
  last_name: Skůpa
- first_name: Jiří
  full_name: Libus, Jiří
  last_name: Libus
- first_name: Satoshi
  full_name: Naramoto, Satoshi
  last_name: Naramoto
- first_name: Ricardo
  full_name: Tejos, Ricardo
  last_name: Tejos
- first_name: Jirí
  full_name: Friml, Jirí
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Eva
  full_name: Zažímalová, Eva
  last_name: Zažímalová
citation:
  ama: Křeček P, Skůpa P, Libus J, et al. The PIN-FORMED (PIN) protein family of auxin
    transporters. <i>Genome Biology</i>. 2009;10(12). doi:<a href="https://doi.org/10.1186/gb-2009-10-12-249">10.1186/gb-2009-10-12-249</a>
  apa: Křeček, P., Skůpa, P., Libus, J., Naramoto, S., Tejos, R., Friml, J., &#38;
    Zažímalová, E. (2009). The PIN-FORMED (PIN) protein family of auxin transporters.
    <i>Genome Biology</i>. BioMed Central. <a href="https://doi.org/10.1186/gb-2009-10-12-249">https://doi.org/10.1186/gb-2009-10-12-249</a>
  chicago: Křeček, Pavel, Petr Skůpa, Jiří Libus, Satoshi Naramoto, Ricardo Tejos,
    Jiří Friml, and Eva Zažímalová. “The PIN-FORMED (PIN) Protein Family of Auxin
    Transporters.” <i>Genome Biology</i>. BioMed Central, 2009. <a href="https://doi.org/10.1186/gb-2009-10-12-249">https://doi.org/10.1186/gb-2009-10-12-249</a>.
  ieee: P. Křeček <i>et al.</i>, “The PIN-FORMED (PIN) protein family of auxin transporters,”
    <i>Genome Biology</i>, vol. 10, no. 12. BioMed Central, 2009.
  ista: Křeček P, Skůpa P, Libus J, Naramoto S, Tejos R, Friml J, Zažímalová E. 2009.
    The PIN-FORMED (PIN) protein family of auxin transporters. Genome Biology. 10(12).
  mla: Křeček, Pavel, et al. “The PIN-FORMED (PIN) Protein Family of Auxin Transporters.”
    <i>Genome Biology</i>, vol. 10, no. 12, BioMed Central, 2009, doi:<a href="https://doi.org/10.1186/gb-2009-10-12-249">10.1186/gb-2009-10-12-249</a>.
  short: P. Křeček, P. Skůpa, J. Libus, S. Naramoto, R. Tejos, J. Friml, E. Zažímalová,
    Genome Biology 10 (2009).
date_created: 2018-12-11T12:01:08Z
date_published: 2009-12-29T00:00:00Z
date_updated: 2021-01-12T07:40:46Z
day: '29'
doi: 10.1186/gb-2009-10-12-249
extern: '1'
external_id:
  pmid:
  - '20053306'
intvolume: '        10'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812941/
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_status: published
publisher: BioMed Central
publist_id: '3640'
quality_controlled: '1'
status: public
title: The PIN-FORMED (PIN) protein family of auxin transporters
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2009'
...
---
_id: '3197'
abstract:
- lang: eng
  text: |-
    The problem of obtaining the maximum a posteriori estimate of a general discrete Markov random field (i.e., a Markov random field defined using a discrete set of labels) is known to be NP-hard. However, due to its central importance in many applications, several approximation algorithms have been proposed in the literature. In this paper, we present an analysis of three such algorithms based on convex relaxations: (i) LP-S: the linear programming (LP) relaxation proposed by Schlesinger (1976) for a special case and independently in Chekuri et al. (2001), Koster et al. (1998), and Wainwright et al. (2005) for the general case; (ii) QP-RL: the quadratic programming (QP) relaxation of Ravikumar and Lafferty (2006); and (iii) SOCP-MS: the second order cone programming (SOCP) relaxation first proposed by Muramatsu and Suzuki (2003) for two label problems and later extended by Kumar et al. (2006) for a general label set.

    We show that the SOCP-MS and the QP-RL relaxations are equivalent. Furthermore, we prove that despite the flexibility in the form of the constraints/objective function offered by QP and SOCP, the LP-S relaxation strictly dominates (i.e., provides a better approximation than) QP-RL and SOCP-MS. We generalize these results by defining a large class of SOCP (and equivalent QP) relaxations which is dominated by the LP-S relaxation. Based on these results we propose some novel SOCP relaxations which define constraints using random variables that form cycles or cliques in the graphical model representation of the random field. Using some examples we show that the new SOCP relaxations strictly dominate the previous approaches.
author:
- first_name: M Pawan
  full_name: Kumar, M Pawan
  last_name: Kumar
- first_name: Vladimir
  full_name: Vladimir Kolmogorov
  id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kolmogorov
- first_name: Philip
  full_name: Torr, Philip H
  last_name: Torr
citation:
  ama: Kumar MP, Kolmogorov V, Torr P. An analysis of convex relaxations for MAP estimation
    of discrete MRFs. <i>Journal of Machine Learning Research</i>. 2009;10:71-106.
  apa: Kumar, M. P., Kolmogorov, V., &#38; Torr, P. (2009). An analysis of convex
    relaxations for MAP estimation of discrete MRFs. <i>Journal of Machine Learning
    Research</i>. Microtome Publishing.
  chicago: Kumar, M Pawan, Vladimir Kolmogorov, and Philip Torr. “An Analysis of Convex
    Relaxations for MAP Estimation of Discrete MRFs.” <i>Journal of Machine Learning
    Research</i>. Microtome Publishing, 2009.
  ieee: M. P. Kumar, V. Kolmogorov, and P. Torr, “An analysis of convex relaxations
    for MAP estimation of discrete MRFs,” <i>Journal of Machine Learning Research</i>,
    vol. 10. Microtome Publishing, pp. 71–106, 2009.
  ista: Kumar MP, Kolmogorov V, Torr P. 2009. An analysis of convex relaxations for
    MAP estimation of discrete MRFs. Journal of Machine Learning Research. 10, 71–106.
  mla: Kumar, M. Pawan, et al. “An Analysis of Convex Relaxations for MAP Estimation
    of Discrete MRFs.” <i>Journal of Machine Learning Research</i>, vol. 10, Microtome
    Publishing, 2009, pp. 71–106.
  short: M.P. Kumar, V. Kolmogorov, P. Torr, Journal of Machine Learning Research
    10 (2009) 71–106.
date_created: 2018-12-11T12:01:57Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:44Z
day: '01'
extern: 1
intvolume: '        10'
main_file_link:
- open_access: '1'
  url: https://hal.inria.fr/hal-00773608
month: '01'
oa: 1
page: 71 - 106
publication: Journal of Machine Learning Research
publication_status: published
publisher: Microtome Publishing
publist_id: '3484'
quality_controlled: 0
status: public
title: An analysis of convex relaxations for MAP estimation of discrete MRFs
type: journal_article
volume: 10
year: '2009'
...
---
_id: '3199'
abstract:
- lang: eng
  text: Many interactive image segmentation approaches use an objective function which
    includes appearance models as an unknown variable. Since the resulting optimization
    problem is NP-hard the segmentation and appearance are typically optimized separately,
    in an EM-style fashion. One contribution of this paper is to express the objective
    function purely in terms of the unknown segmentation, using higher-order cliques.
    This formulation reveals an interesting bias of the model towards balanced segmentations.
    Furthermore, it enables us to develop a new dual decomposition optimization procedure,
    which provides additionally a lower bound. Hence, we are able to improve on existing
    optimizers, and verify that for a considerable number of real world examples we
    even achieve global optimality. This is important since we are able, for the first
    time, to analyze the deficiencies of the model. Another contribution is to establish
    a property of a particular dual decomposition approach which involves convex functions
    depending on foreground area. As a consequence, we show that the optimal decomposition
    for our problem can be computed efficiently via a parametric maxflow algorithm.
author:
- first_name: Sara
  full_name: Vicente, Sara
  last_name: Vicente
- first_name: Vladimir
  full_name: Vladimir Kolmogorov
  id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kolmogorov
- first_name: Carsten
  full_name: Rother, Carsten
  last_name: Rother
citation:
  ama: 'Vicente S, Kolmogorov V, Rother C. Joint optimization of segmentation and
    appearance models. In: IEEE; 2009:755-762. doi:<a href="https://doi.org/10.1109/ICCV.2009.5459287">10.1109/ICCV.2009.5459287</a>'
  apa: 'Vicente, S., Kolmogorov, V., &#38; Rother, C. (2009). Joint optimization of
    segmentation and appearance models (pp. 755–762). Presented at the ICCV: International
    Conference on Computer Vision, IEEE. <a href="https://doi.org/10.1109/ICCV.2009.5459287">https://doi.org/10.1109/ICCV.2009.5459287</a>'
  chicago: Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Joint Optimization
    of Segmentation and Appearance Models,” 755–62. IEEE, 2009. <a href="https://doi.org/10.1109/ICCV.2009.5459287">https://doi.org/10.1109/ICCV.2009.5459287</a>.
  ieee: 'S. Vicente, V. Kolmogorov, and C. Rother, “Joint optimization of segmentation
    and appearance models,” presented at the ICCV: International Conference on Computer
    Vision, 2009, pp. 755–762.'
  ista: 'Vicente S, Kolmogorov V, Rother C. 2009. Joint optimization of segmentation
    and appearance models. ICCV: International Conference on Computer Vision, 755–762.'
  mla: Vicente, Sara, et al. <i>Joint Optimization of Segmentation and Appearance
    Models</i>. IEEE, 2009, pp. 755–62, doi:<a href="https://doi.org/10.1109/ICCV.2009.5459287">10.1109/ICCV.2009.5459287</a>.
  short: S. Vicente, V. Kolmogorov, C. Rother, in:, IEEE, 2009, pp. 755–762.
conference:
  name: 'ICCV: International Conference on Computer Vision'
date_created: 2018-12-11T12:01:58Z
date_published: 2009-05-01T00:00:00Z
date_updated: 2021-01-12T07:41:44Z
day: '01'
doi: 10.1109/ICCV.2009.5459287
extern: 1
main_file_link:
- open_access: '0'
  url: http://www.robots.ox.ac.uk/~vgg/rg/papers/segmentationappearance.pdf
month: '05'
page: 755 - 762
publication_status: published
publisher: IEEE
publist_id: '3482'
quality_controlled: 0
status: public
title: Joint optimization of segmentation and appearance models
type: conference
year: '2009'
...
---
_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: '110'
abstract:
- lang: eng
  text: In order to better understand magnetic reconnection and particle acceleration
    in solar flares, we compare the RHESSI hard X-ray (HXR) footpoint motions of three
    flares with a detailed study of the corresponding topology given by a Magnetic
    Charge Topology model. We analyze the relationship between the footpoint motions
    and topological spine lines and find that the examined footpoint sources move
    along spine lines. We present a three-dimensional topological model in which this
    movement can be understood. As reconnection proceeds, flux is transferred between
    the reconnecting domains, causing the separator to move. The movement of the separator\'s
    chromospheric ends, identified with the HXR footpoints, is along those spine lines
    on which the separator ends.
acknowledgement: This work was supported by RHESSI funds from the University of California
  at Berkeley through a contract, SA1868-26308PG, with Montana State University. Funding
  for our Research Experience for Undergraduates (REU) students was provided by NSF
  grant ATM-0243923.
author:
- first_name: Angela
  full_name: Des Jardins, Angela
  last_name: Des Jardins
- first_name: Richard
  full_name: Canfield, Richard
  last_name: Canfield
- first_name: Dana
  full_name: Longcope, Dana
  last_name: Longcope
- first_name: Crystal
  full_name: Fordyce, Crystal
  last_name: Fordyce
- first_name: Scott R
  full_name: Waitukaitis, Scott R
  id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
  last_name: Waitukaitis
  orcid: 0000-0002-2299-3176
citation:
  ama: 'Des Jardins A, Canfield R, Longcope D, Fordyce C, Waitukaitis SR. Reconnection
    in three dimensions: The role of spines in three eruptive flares. <i>The Astrophysical
    Journal</i>. 2009;693(2):1628-1636. doi:<a href="https://doi.org/10.1088/0004-637X/693/2/1628">10.1088/0004-637X/693/2/1628</a>'
  apa: 'Des Jardins, A., Canfield, R., Longcope, D., Fordyce, C., &#38; Waitukaitis,
    S. R. (2009). Reconnection in three dimensions: The role of spines in three eruptive
    flares. <i>The Astrophysical Journal</i>. IOP Publishing Ltd. <a href="https://doi.org/10.1088/0004-637X/693/2/1628">https://doi.org/10.1088/0004-637X/693/2/1628</a>'
  chicago: 'Des Jardins, Angela, Richard Canfield, Dana Longcope, Crystal Fordyce,
    and Scott R Waitukaitis. “Reconnection in Three Dimensions: The Role of Spines
    in Three Eruptive Flares.” <i>The Astrophysical Journal</i>. IOP Publishing Ltd.,
    2009. <a href="https://doi.org/10.1088/0004-637X/693/2/1628">https://doi.org/10.1088/0004-637X/693/2/1628</a>.'
  ieee: 'A. Des Jardins, R. Canfield, D. Longcope, C. Fordyce, and S. R. Waitukaitis,
    “Reconnection in three dimensions: The role of spines in three eruptive flares,”
    <i>The Astrophysical Journal</i>, vol. 693, no. 2. IOP Publishing Ltd., pp. 1628–1636,
    2009.'
  ista: 'Des Jardins A, Canfield R, Longcope D, Fordyce C, Waitukaitis SR. 2009. Reconnection
    in three dimensions: The role of spines in three eruptive flares. The Astrophysical
    Journal. 693(2), 1628–1636.'
  mla: 'Des Jardins, Angela, et al. “Reconnection in Three Dimensions: The Role of
    Spines in Three Eruptive Flares.” <i>The Astrophysical Journal</i>, vol. 693,
    no. 2, IOP Publishing Ltd., 2009, pp. 1628–36, doi:<a href="https://doi.org/10.1088/0004-637X/693/2/1628">10.1088/0004-637X/693/2/1628</a>.'
  short: A. Des Jardins, R. Canfield, D. Longcope, C. Fordyce, S.R. Waitukaitis, The
    Astrophysical Journal 693 (2009) 1628–1636.
date_created: 2018-12-11T11:44:41Z
date_published: 2009-03-10T00:00:00Z
date_updated: 2021-01-12T06:48:16Z
day: '10'
doi: 10.1088/0004-637X/693/2/1628
extern: '1'
intvolume: '       693'
issue: '2'
language:
- iso: eng
month: '03'
oa_version: None
page: 1628 - 1636
publication: The Astrophysical Journal
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '7944'
quality_controlled: '1'
status: public
title: 'Reconnection in three dimensions: The role of spines in three eruptive flares'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 693
year: '2009'
...
---
_id: '111'
abstract:
- lang: eng
  text: Thin streams of liquid commonly break up into characteristic droplet patterns
    owing to the surface-tension-driven PlateauRayleigh instability 1-3. Very similar
    patterns are observed when initially uniform streams of dry granular material
    break up into clusters of grains4-6, even though flows of macroscopic particles
    are considered to lack surface tension7,8. Recent studies on freely falling granular
    streams tracked fluctuations in the stream profile9, but the clustering mechanism
    remained unresolved because the full evolution of the instability could not be
    observed. Here we demonstrate that the cluster formation is driven by minute,
    nanoNewton cohesive forces that arise from a combination of van der Waals interactions
    and capillary bridges between nanometre-scale surface asperities. Our experiments
    involve high-speed video imaging of the granular stream in the co-moving frame,
    control over the properties of the grain surfaces and the use of atomic force
    microscopy to measure grain-grain interactions. The cohesive forces that we measure
    correspond to an equivalent surface tension five orders of magnitude below that,
    of ordinary liquids. We find that, the shapes of these weakly cohesive, non-thermal
    clusters of macroscopic particles closely resemble droplets resulting from thermally
    induced rupture of liquid nanojets 10-12.
acknowledgement: This work was supported by NSF through its MRSEC programme and the
  Inter-American Materials Collaboration Chicago-Chile, and by the Keck Initiative
  for Ultrafast Imaging at the University of Chicago.
author:
- first_name: John
  full_name: Royer, John
  last_name: Royer
- first_name: Daniel
  full_name: Evans, Daniel
  last_name: Evans
- first_name: Loreto
  full_name: Oyarte, Loreto
  last_name: Oyarte
- first_name: Qiti
  full_name: Guo, Qiti
  last_name: Guo
- first_name: Eliot
  full_name: Kapit, Eliot
  last_name: Kapit
- first_name: Matthias
  full_name: Möbius, Matthias
  last_name: Möbius
- first_name: Scott R
  full_name: Waitukaitis, Scott R
  id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
  last_name: Waitukaitis
  orcid: 0000-0002-2299-3176
- first_name: Heinrich
  full_name: Jaeger, Heinrich
  last_name: Jaeger
citation:
  ama: Royer J, Evans D, Oyarte L, et al. High-speed tracking of rupture and clustering
    in freely falling granular streams. <i>Nature</i>. 2009;459(7250):1110-1113. doi:<a
    href="https://doi.org/10.1038/nature08115">10.1038/nature08115</a>
  apa: Royer, J., Evans, D., Oyarte, L., Guo, Q., Kapit, E., Möbius, M., … Jaeger,
    H. (2009). High-speed tracking of rupture and clustering in freely falling granular
    streams. <i>Nature</i>. Nature Publishing Group. <a href="https://doi.org/10.1038/nature08115">https://doi.org/10.1038/nature08115</a>
  chicago: Royer, John, Daniel Evans, Loreto Oyarte, Qiti Guo, Eliot Kapit, Matthias
    Möbius, Scott R Waitukaitis, and Heinrich Jaeger. “High-Speed Tracking of Rupture
    and Clustering in Freely Falling Granular Streams.” <i>Nature</i>. Nature Publishing
    Group, 2009. <a href="https://doi.org/10.1038/nature08115">https://doi.org/10.1038/nature08115</a>.
  ieee: J. Royer <i>et al.</i>, “High-speed tracking of rupture and clustering in
    freely falling granular streams,” <i>Nature</i>, vol. 459, no. 7250. Nature Publishing
    Group, pp. 1110–1113, 2009.
  ista: Royer J, Evans D, Oyarte L, Guo Q, Kapit E, Möbius M, Waitukaitis SR, Jaeger
    H. 2009. High-speed tracking of rupture and clustering in freely falling granular
    streams. Nature. 459(7250), 1110–1113.
  mla: Royer, John, et al. “High-Speed Tracking of Rupture and Clustering in Freely
    Falling Granular Streams.” <i>Nature</i>, vol. 459, no. 7250, Nature Publishing
    Group, 2009, pp. 1110–13, doi:<a href="https://doi.org/10.1038/nature08115">10.1038/nature08115</a>.
  short: J. Royer, D. Evans, L. Oyarte, Q. Guo, E. Kapit, M. Möbius, S.R. Waitukaitis,
    H. Jaeger, Nature 459 (2009) 1110–1113.
date_created: 2018-12-11T11:44:41Z
date_published: 2009-06-25T00:00:00Z
date_updated: 2021-01-12T06:48:21Z
day: '25'
doi: 10.1038/nature08115
extern: '1'
intvolume: '       459'
issue: '7250'
language:
- iso: eng
month: '06'
oa_version: None
page: 1110 - 1113
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '7943'
quality_controlled: '1'
status: public
title: High-speed tracking of rupture and clustering in freely falling granular streams
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 459
year: '2009'
...
