---
_id: '2862'
abstract:
- lang: eng
text: Motile cilia perform crucial functions during embryonic development and throughout
adult life. Development of organs containing motile cilia involves regulation
of cilia formation (ciliogenesis) and formation of a luminal space (lumenogenesis)
in which cilia generate fluid flows. Control of ciliogenesis and lumenogenesis
is not yet fully understood, and it remains unclear whether these processes are
coupled. In the zebrafish embryo, lethal giant larvae 2 (lgl2) is expressed prominently
in ciliated organs. Lgl proteins are involved in establishing cell polarity and
have been implicated in vesicle trafficking. Here, we identified a role for Lgl2
in development of ciliated epithelia in Kupffer's vesicle, which directs left-right
asymmetry of the embryo; the otic vesicles, which give rise to the inner ear;
and the pronephric ducts of the kidney. Using Kupffer's vesicle as a model ciliated
organ, we found that depletion of Lgl2 disrupted lumen formation and reduced cilia
number and length. Immunofluorescence and time-lapse imaging of Kupffer's vesicle
morphogenesis in Lgl2-deficient embryos suggested cell adhesion defects and revealed
loss of the adherens junction component E-cadherin at lateral membranes. Genetic
interaction experiments indicate that Lgl2 interacts with Rab11a to regulate E-cadherin
and mediate lumen formation that is uncoupled from cilia formation. These results
uncover new roles and interactions for Lgl2 that are crucial for both lumenogenesis
and ciliogenesis and indicate that these processes are genetically separable in
zebrafish.
acknowledgement: Deposited in PMC for release after 12 months. We thank members of
the Amack lab for helpful discussions and Mahendra Sonawane for donating reagents.
author:
- first_name: Hwee
full_name: Tay, Hwee
last_name: Tay
- first_name: Sabrina
full_name: Schulze, Sabrina
last_name: Schulze
- first_name: Julien
full_name: Compagnon, Julien
id: 2E3E0988-F248-11E8-B48F-1D18A9856A87
last_name: Compagnon
- first_name: Fiona
full_name: Foley, Fiona
last_name: Foley
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: H Joseph
full_name: Yost, H Joseph
last_name: Yost
- first_name: Salim
full_name: Abdelilah Seyfried, Salim
last_name: Abdelilah Seyfried
- first_name: Jeffrey
full_name: Amack, Jeffrey
last_name: Amack
citation:
ama: Tay H, Schulze S, Compagnon J, et al. Lethal giant larvae 2 regulates development
of the ciliated organ Kupffer’s vesicle. Development. 2013;140(7):1550-1559.
doi:10.1242/dev.087130
apa: Tay, H., Schulze, S., Compagnon, J., Foley, F., Heisenberg, C.-P. J., Yost,
H. J., … Amack, J. (2013). Lethal giant larvae 2 regulates development of the
ciliated organ Kupffer’s vesicle. Development. Company of Biologists. https://doi.org/10.1242/dev.087130
chicago: Tay, Hwee, Sabrina Schulze, Julien Compagnon, Fiona Foley, Carl-Philipp
J Heisenberg, H Joseph Yost, Salim Abdelilah Seyfried, and Jeffrey Amack. “Lethal
Giant Larvae 2 Regulates Development of the Ciliated Organ Kupffer’s Vesicle.”
Development. Company of Biologists, 2013. https://doi.org/10.1242/dev.087130.
ieee: H. Tay et al., “Lethal giant larvae 2 regulates development of the
ciliated organ Kupffer’s vesicle,” Development, vol. 140, no. 7. Company
of Biologists, pp. 1550–1559, 2013.
ista: Tay H, Schulze S, Compagnon J, Foley F, Heisenberg C-PJ, Yost HJ, Abdelilah
Seyfried S, Amack J. 2013. Lethal giant larvae 2 regulates development of the
ciliated organ Kupffer’s vesicle. Development. 140(7), 1550–1559.
mla: Tay, Hwee, et al. “Lethal Giant Larvae 2 Regulates Development of the Ciliated
Organ Kupffer’s Vesicle.” Development, vol. 140, no. 7, Company of Biologists,
2013, pp. 1550–59, doi:10.1242/dev.087130.
short: H. Tay, S. Schulze, J. Compagnon, F. Foley, C.-P.J. Heisenberg, H.J. Yost,
S. Abdelilah Seyfried, J. Amack, Development 140 (2013) 1550–1559.
date_created: 2018-12-11T11:59:59Z
date_published: 2013-04-01T00:00:00Z
date_updated: 2021-01-12T07:00:20Z
day: '01'
department:
- _id: CaHe
doi: 10.1242/dev.087130
external_id:
pmid:
- '23482490'
intvolume: ' 140'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596994/
month: '04'
oa: 1
oa_version: Submitted Version
page: 1550 - 1559
pmid: 1
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '3927'
quality_controlled: '1'
scopus_import: 1
status: public
title: Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s
vesicle
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 140
year: '2013'
...
---
_id: '2863'
abstract:
- lang: eng
text: Neural populations encode information about their stimulus in a collective
fashion, by joint activity patterns of spiking and silence. A full account of
this mapping from stimulus to neural activity is given by the conditional probability
distribution over neural codewords given the sensory input. For large populations,
direct sampling of these distributions is impossible, and so we must rely on constructing
appropriate models. We show here that in a population of 100 retinal ganglion
cells in the salamander retina responding to temporal white-noise stimuli, dependencies
between cells play an important encoding role. We introduce the stimulus-dependent
maximum entropy (SDME) model—a minimal extension of the canonical linear-nonlinear
model of a single neuron, to a pairwise-coupled neural population. We find that
the SDME model gives a more accurate account of single cell responses and in particular
significantly outperforms uncoupled models in reproducing the distributions of
population codewords emitted in response to a stimulus. We show how the SDME model,
in conjunction with static maximum entropy models of population vocabulary, can
be used to estimate information-theoretic quantities like average surprise and
information transmission in a neural population.
article_number: e1002922
author:
- first_name: Einat
full_name: Granot Atedgi, Einat
last_name: Granot Atedgi
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Ronen
full_name: Segev, Ronen
last_name: Segev
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
citation:
ama: Granot Atedgi E, Tkačik G, Segev R, Schneidman E. Stimulus-dependent maximum
entropy models of neural population codes. PLoS Computational Biology.
2013;9(3). doi:10.1371/journal.pcbi.1002922
apa: Granot Atedgi, E., Tkačik, G., Segev, R., & Schneidman, E. (2013). Stimulus-dependent
maximum entropy models of neural population codes. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1002922
chicago: Granot Atedgi, Einat, Gašper Tkačik, Ronen Segev, and Elad Schneidman.
“Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS
Computational Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1002922.
ieee: E. Granot Atedgi, G. Tkačik, R. Segev, and E. Schneidman, “Stimulus-dependent
maximum entropy models of neural population codes,” PLoS Computational Biology,
vol. 9, no. 3. Public Library of Science, 2013.
ista: Granot Atedgi E, Tkačik G, Segev R, Schneidman E. 2013. Stimulus-dependent
maximum entropy models of neural population codes. PLoS Computational Biology.
9(3), e1002922.
mla: Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of
Neural Population Codes.” PLoS Computational Biology, vol. 9, no. 3, e1002922,
Public Library of Science, 2013, doi:10.1371/journal.pcbi.1002922.
short: E. Granot Atedgi, G. Tkačik, R. Segev, E. Schneidman, PLoS Computational
Biology 9 (2013).
date_created: 2018-12-11T12:00:00Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2021-01-12T07:00:20Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1002922
file:
- access_level: open_access
checksum: 5a30876c193209fa05b26db71845dd16
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:45Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5099'
file_name: IST-2013-120-v1+1_journal.pcbi.1002922.pdf
file_size: 1548120
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '3926'
pubrep_id: '120'
quality_controlled: '1'
scopus_import: 1
status: public
title: Stimulus-dependent maximum entropy models of neural population codes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '2880'
abstract:
- lang: eng
text: Lateral root (LR) formation is initiated when pericycle cells accumulate auxin,
thereby acquiring founder cell (FC) status and triggering asymmetric cell divisions,
giving rise to a new primordium. How this auxin maximum in pericycle cells builds
up and remains focused is not understood. We report that the endodermis plays
an active role in the regulation of auxin accumulation and is instructive for
FCs to progress during the LR initiation (LRI) phase. We describe the functional
importance of a PIN3 (PIN-formed) auxin efflux carrier-dependent hormone reflux
pathway between overlaying endodermal and pericycle FCs. Disrupting this reflux
pathway causes dramatic defects in the progress of FCs towards the next initiation
phase. Our data identify an unexpected regulatory function for the endodermis
in LRI as part of the fine-tuning mechanism that appears to act as a check point
in LR organogenesis after FCs are specified.
author:
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Marleen
full_name: Vanstraelen, Marleen
last_name: Vanstraelen
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Ding
full_name: Zhaojun, Ding
last_name: Zhaojun
- first_name: Malcolm
full_name: Bennett, Malcolm
last_name: Bennett
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Marhavý P, Vanstraelen M, De Rybel B, et al. Auxin reflux between the endodermis
and pericycle promotes lateral root initiation. EMBO Journal. 2013;32(1):149-158.
doi:10.1038/emboj.2012.303
apa: Marhavý, P., Vanstraelen, M., De Rybel, B., Zhaojun, D., Bennett, M., Beeckman,
T., & Benková, E. (2013). Auxin reflux between the endodermis and pericycle
promotes lateral root initiation. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2012.303
chicago: Marhavý, Peter, Marleen Vanstraelen, Bert De Rybel, Ding Zhaojun, Malcolm
Bennett, Tom Beeckman, and Eva Benková. “Auxin Reflux between the Endodermis and
Pericycle Promotes Lateral Root Initiation.” EMBO Journal. Wiley-Blackwell,
2013. https://doi.org/10.1038/emboj.2012.303.
ieee: P. Marhavý et al., “Auxin reflux between the endodermis and pericycle
promotes lateral root initiation,” EMBO Journal, vol. 32, no. 1. Wiley-Blackwell,
pp. 149–158, 2013.
ista: Marhavý P, Vanstraelen M, De Rybel B, Zhaojun D, Bennett M, Beeckman T, Benková
E. 2013. Auxin reflux between the endodermis and pericycle promotes lateral root
initiation. EMBO Journal. 32(1), 149–158.
mla: Marhavý, Peter, et al. “Auxin Reflux between the Endodermis and Pericycle Promotes
Lateral Root Initiation.” EMBO Journal, vol. 32, no. 1, Wiley-Blackwell,
2013, pp. 149–58, doi:10.1038/emboj.2012.303.
short: P. Marhavý, M. Vanstraelen, B. De Rybel, D. Zhaojun, M. Bennett, T. Beeckman,
E. Benková, EMBO Journal 32 (2013) 149–158.
date_created: 2018-12-11T12:00:07Z
date_published: 2013-01-09T00:00:00Z
date_updated: 2021-01-12T07:00:27Z
day: '09'
department:
- _id: EvBe
doi: 10.1038/emboj.2012.303
ec_funded: 1
external_id:
pmid:
- '23178590'
intvolume: ' 32'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545298/
month: '01'
oa: 1
oa_version: Submitted Version
page: 149 - 158
pmid: 1
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3882'
quality_controlled: '1'
scopus_import: 1
status: public
title: Auxin reflux between the endodermis and pericycle promotes lateral root initiation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2013'
...
---
_id: '2881'
abstract:
- lang: eng
text: The puzzle piece-shaped Arabidopsis leaf pavement cells (PCs) with interdigitated
lobes and indents is a good model system to investigate the mechanisms that coordinate
cell polarity and shape formation within a tissue. Auxin has been shown to coordinate
the interdigitation by activating ROP GTPase-dependent signaling pathways. To
identify additional components or mechanisms, we screened for mutants with abnormal
PC morphogenesis and found that cytokinin signaling regulates the PC interdigitation
pattern. Reduction in cytokinin accumulation and defects in cytokinin signaling
(such as in ARR7-over-expressing lines, the ahk3cre1 cytokinin receptor mutant,
and the ahp12345 cytokinin signaling mutant) enhanced PC interdigitation, whereas
over-production of cytokinin and over-activation of cytokinin signaling in an
ARR20 over-expression line delayed or abolished PC interdigitation throughout
the cotyledon. Genetic and biochemical analyses suggest that cytokinin signaling
acts upstream of ROPs to suppress the formation of interdigitated pattern. Our
results provide novel mechanistic understanding of the pathways controlling PC
shape and uncover a new role for cytokinin signaling in cell morphogenesis.
acknowledgement: is work was supported by grants from the US National Institute of
General Medical Sciences (GM081451 and GM081451-03S2) to ZY. We thank National Science
Foundation grant (IOS-1147250) to GVR and MX. HL and DL were partially supported
by the Chinese Scholarship Council.
author:
- first_name: Hongjiang
full_name: Hongjiang Li
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
- first_name: Deshu
full_name: Lin, Deshu
last_name: Lin
- first_name: Mingzhang
full_name: Wen, Mingzhang
last_name: Wen
- first_name: Mingtang
full_name: Xie, Mingtang
last_name: Xie
- first_name: Jérôme
full_name: Duclercq, Jérôme
last_name: Duclercq
- first_name: Agnieszka
full_name: Bielach, Agnieszka
last_name: Bielach
- first_name: Jungmook
full_name: Kim, Jungmook
last_name: Kim
- first_name: G Venugopala
full_name: Reddy, G Venugopala
last_name: Reddy
- first_name: Jianru
full_name: Zuo, Jianru
last_name: Zuo
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Hongwei
full_name: Guo, Hongwei
last_name: Guo
- first_name: Zhenbiao
full_name: Yang, Zhenbiao
last_name: Yang
citation:
ama: Li H, Xu T, Lin D, et al. Cytokinin signaling regulates pavement cell morphogenesis
in Arabidopsis. Cell Research. 2013;23(2):290-299. doi:10.1038/cr.2012.146
apa: Li, H., Xu, T., Lin, D., Wen, M., Xie, M., Duclercq, J., … Yang, Z. (2013).
Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis. Cell
Research. Nature Publishing Group. https://doi.org/10.1038/cr.2012.146
chicago: Li, Hongjiang, Tongda Xu, Deshu Lin, Mingzhang Wen, Mingtang Xie, Jérôme
Duclercq, Agnieszka Bielach, et al. “Cytokinin Signaling Regulates Pavement Cell
Morphogenesis in Arabidopsis.” Cell Research. Nature Publishing Group,
2013. https://doi.org/10.1038/cr.2012.146.
ieee: H. Li et al., “Cytokinin signaling regulates pavement cell morphogenesis
in Arabidopsis,” Cell Research, vol. 23, no. 2. Nature Publishing Group,
pp. 290–299, 2013.
ista: Li H, Xu T, Lin D, Wen M, Xie M, Duclercq J, Bielach A, Kim J, Reddy GV, Zuo
J, Benková E, Friml J, Guo H, Yang Z. 2013. Cytokinin signaling regulates pavement
cell morphogenesis in Arabidopsis. Cell Research. 23(2), 290–299.
mla: Li, Hongjiang, et al. “Cytokinin Signaling Regulates Pavement Cell Morphogenesis
in Arabidopsis.” Cell Research, vol. 23, no. 2, Nature Publishing Group,
2013, pp. 290–99, doi:10.1038/cr.2012.146.
short: H. Li, T. Xu, D. Lin, M. Wen, M. Xie, J. Duclercq, A. Bielach, J. Kim, G.V.
Reddy, J. Zuo, E. Benková, J. Friml, H. Guo, Z. Yang, Cell Research 23 (2013)
290–299.
date_created: 2018-12-11T12:00:07Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2021-01-12T07:00:27Z
day: '01'
doi: 10.1038/cr.2012.146
extern: 1
intvolume: ' 23'
issue: '2'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567823/
month: '02'
oa: 1
page: 290 - 299
publication: Cell Research
publication_status: published
publisher: Nature Publishing Group
publist_id: '3881'
quality_controlled: 0
status: public
title: Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis
type: journal_article
volume: 23
year: '2013'
...
---
_id: '2882'
abstract:
- lang: eng
text: Gravitropic bending of plant organs is mediated by an asymmetric signaling
of the plant hormone auxin between the upper and lower side of the respective
organ. Here, we show that also another plant hormone, gibberellic acid (GA), shows
asymmetric action during gravitropic responses. Immunodetection using an antibody
against GA and monitoring GA signaling output by downstream degradation of DELLA
proteins revealed an asymmetric GA distribution and response with the maximum
at the lower side of gravistimulated roots. Genetic or pharmacological manipulation
of GA levels or response affects gravity-mediated auxin redistribution and root
bending response. The higher GA levels at the lower side of the root correlate
with increased amounts of PIN-FORMED2 (PIN2) auxin transporter at the plasma membrane.
The observed increase in PIN2 stability is caused by a specific GA effect on trafficking
of PIN proteins to lytic vacuoles that presumably occurs downstream of brefeldin
A-sensitive endosomes. Our results suggest that asymmetric auxin distribution
instructive for gravity-induced differential growth is consolidated by the asymmetric
action of GA that stabilizes the PIN-dependent auxin stream along the lower side
of gravistimulated roots.
author:
- first_name: Christian
full_name: Löfke, Christian
last_name: Löfke
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Ingo
full_name: Heilmann, Ingo
last_name: Heilmann
- first_name: Marc
full_name: Van Montagu, Marc
last_name: Van Montagu
- first_name: Thomas
full_name: Teichmann, Thomas
last_name: Teichmann
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Löfke C, Zwiewka M, Heilmann I, Van Montagu M, Teichmann T, Friml J. Asymmetric
gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters
during root gravitropism. PNAS. 2013;110(9):3627-3632. doi:10.1073/pnas.1300107110
apa: Löfke, C., Zwiewka, M., Heilmann, I., Van Montagu, M., Teichmann, T., &
Friml, J. (2013). Asymmetric gibberellin signaling regulates vacuolar trafficking
of PIN auxin transporters during root gravitropism. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.1300107110
chicago: Löfke, Christian, Marta Zwiewka, Ingo Heilmann, Marc Van Montagu, Thomas
Teichmann, and Jiří Friml. “Asymmetric Gibberellin Signaling Regulates Vacuolar
Trafficking of PIN Auxin Transporters during Root Gravitropism.” PNAS.
National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1300107110.
ieee: C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, and J. Friml,
“Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin
transporters during root gravitropism,” PNAS, vol. 110, no. 9. National
Academy of Sciences, pp. 3627–3632, 2013.
ista: Löfke C, Zwiewka M, Heilmann I, Van Montagu M, Teichmann T, Friml J. 2013.
Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters
during root gravitropism. PNAS. 110(9), 3627–3632.
mla: Löfke, Christian, et al. “Asymmetric Gibberellin Signaling Regulates Vacuolar
Trafficking of PIN Auxin Transporters during Root Gravitropism.” PNAS,
vol. 110, no. 9, National Academy of Sciences, 2013, pp. 3627–32, doi:10.1073/pnas.1300107110.
short: C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, J. Friml,
PNAS 110 (2013) 3627–3632.
date_created: 2018-12-11T12:00:07Z
date_published: 2013-02-26T00:00:00Z
date_updated: 2021-01-12T07:00:27Z
day: '26'
department:
- _id: JiFr
doi: 10.1073/pnas.1300107110
external_id:
pmid:
- '23391733'
intvolume: ' 110'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587205/
month: '02'
oa: 1
oa_version: Submitted Version
page: 3627 - 3632
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3879'
quality_controlled: '1'
scopus_import: 1
status: public
title: Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin
transporters during root gravitropism
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2883'
abstract:
- lang: eng
text: Plant architecture is influenced by the polar, cell-to-cell transport of auxin
that is primarily provided and regulated by plasma membrane efflux catalysts of
the PIN-FORMED and B family of ABC transporter (ABCB) classes. The latter were
shown to require the functionality of the FK506 binding protein42 TWISTED DWARF1
(TWD1), although underlying mechanisms are unclear. By genetic manipulation of
TWD1 expression, we show here that TWD1 affects shootward root auxin reflux and,
thus, downstream developmental traits, such as epidermal twisting and gravitropism
of the root. Using immunological assays, we demonstrate a predominant lateral,
mainly outward-facing, plasma membrane location for TWD1 in the root epidermis
characterized by the lateral marker ABC transporter G36/PLEIOTROPIC DRUG-RESISTANCE8/PENETRATION3.
At these epidermal plasma membrane domains, TWD1 colocalizes with nonpolar ABCB1.
In planta bioluminescence resonance energy transfer analysis was used to verify
specific ABC transporter B1 (ABCB1)-TWD1 interaction. Our data support a model
in which TWD1 promotes lateral ABCB-mediated auxin efflux via protein-protein
interaction at the plasma membrane, minimizing reflux from the root apoplast into
the cytoplasm.
acknowledgement: We would thank Vincent Vincenzetti and Laurence Charrier for excellent
technical assistance, A. von Arnim for the donation of BRET vectors, E. Spalding
for TWD1-CFP, TWD1-CFP/29-1-GFP/ER-YFP, and ABCB4-GFP lines, M. Palmgren for discussion
and support, and E. Martinoia for TT12 cDNA, support, and mentorship. Imaging data
were partially collected at the Center for Advanced Bioimaging, University of Copenhagen,
Denmark. This work was supported by grants from the Novartis Foundation (to M.G.),
from the Danish Research School for Biotechnology (to M.G. and A.S.), from the Forschungskredit
of the University of Zurich (to A.B.), from the Pool de Recherche of the University
of Fribourg (to M.G.), and from the Swiss National Funds (to M.G.). M.G. dedicates
this work to his father, who passed away during the resubmission process.
author:
- first_name: Bangjun
full_name: Wang, Bangjun
last_name: Wang
- first_name: Aurélien
full_name: Bailly, Aurélien
last_name: Bailly
- first_name: Marta
full_name: Zwiewk, Marta
last_name: Zwiewk
- first_name: Sina
full_name: Henrichs, Sina
last_name: Henrichs
- first_name: Elisa
full_name: Azzarello, Elisa
last_name: Azzarello
- first_name: Stefano
full_name: Mancuso, Stefano
last_name: Mancuso
- first_name: Masayoshi
full_name: Maeshima, Masayoshi
last_name: Maeshima
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Alexander
full_name: Schulz, Alexander
last_name: Schulz
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
citation:
ama: Wang B, Bailly A, Zwiewk M, et al. Arabidopsis TWISTED DWARF1 functionally
interacts with auxin exporter ABCB1 on the root plasma membrane. Plant Cell.
2013;25(1):202-214. doi:10.1105/tpc.112.105999
apa: Wang, B., Bailly, A., Zwiewk, M., Henrichs, S., Azzarello, E., Mancuso, S.,
… Geisler, M. (2013). Arabidopsis TWISTED DWARF1 functionally interacts with auxin
exporter ABCB1 on the root plasma membrane. Plant Cell. American Society
of Plant Biologists. https://doi.org/10.1105/tpc.112.105999
chicago: Wang, Bangjun, Aurélien Bailly, Marta Zwiewk, Sina Henrichs, Elisa Azzarello,
Stefano Mancuso, Masayoshi Maeshima, Jiří Friml, Alexander Schulz, and Markus
Geisler. “Arabidopsis TWISTED DWARF1 Functionally Interacts with Auxin Exporter
ABCB1 on the Root Plasma Membrane.” Plant Cell. American Society of Plant
Biologists, 2013. https://doi.org/10.1105/tpc.112.105999.
ieee: B. Wang et al., “Arabidopsis TWISTED DWARF1 functionally interacts
with auxin exporter ABCB1 on the root plasma membrane,” Plant Cell, vol.
25, no. 1. American Society of Plant Biologists, pp. 202–214, 2013.
ista: Wang B, Bailly A, Zwiewk M, Henrichs S, Azzarello E, Mancuso S, Maeshima M,
Friml J, Schulz A, Geisler M. 2013. Arabidopsis TWISTED DWARF1 functionally interacts
with auxin exporter ABCB1 on the root plasma membrane. Plant Cell. 25(1), 202–214.
mla: Wang, Bangjun, et al. “Arabidopsis TWISTED DWARF1 Functionally Interacts with
Auxin Exporter ABCB1 on the Root Plasma Membrane.” Plant Cell, vol. 25,
no. 1, American Society of Plant Biologists, 2013, pp. 202–14, doi:10.1105/tpc.112.105999.
short: B. Wang, A. Bailly, M. Zwiewk, S. Henrichs, E. Azzarello, S. Mancuso, M.
Maeshima, J. Friml, A. Schulz, M. Geisler, Plant Cell 25 (2013) 202–214.
date_created: 2018-12-11T12:00:08Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:28Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.112.105999
external_id:
pmid:
- '23321285'
intvolume: ' 25'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584535/
month: '01'
oa: 1
oa_version: Submitted Version
page: 202 - 214
pmid: 1
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3878'
quality_controlled: '1'
scopus_import: 1
status: public
title: Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1
on the root plasma membrane
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...
---
_id: '2886'
abstract:
- lang: eng
text: We focus on the realizability problem of Message Sequence Graphs (MSG), i.e.
the problem whether a given MSG specification is correctly distributable among
parallel components communicating via messages. This fundamental problem of MSG
is known to be undecidable. We introduce a well motivated restricted class of
MSG, so called controllable-choice MSG, and show that all its models are realizable
and moreover it is decidable whether a given MSG model is a member of this class.
In more detail, this class of MSG specifications admits a deadlock-free realization
by overloading existing messages with additional bounded control data. We also
show that the presented class is the largest known subclass of MSG that allows
for deadlock-free realization.
alternative_title:
- LNCS
author:
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Vojtěch
full_name: Řehák, Vojtěch
last_name: Řehák
citation:
ama: Chmelik M, Řehák V. Controllable-choice message sequence graphs. 2013;7721:118-130.
doi:10.1007/978-3-642-36046-6_12
apa: 'Chmelik, M., & Řehák, V. (2013). Controllable-choice message sequence
graphs. Presented at the MEMICS: Mathematical and Engineering Methods in Computer
Science, Znojmo, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-36046-6_12'
chicago: Chmelik, Martin, and Vojtěch Řehák. “Controllable-Choice Message Sequence
Graphs.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-36046-6_12.
ieee: M. Chmelik and V. Řehák, “Controllable-choice message sequence graphs,” vol.
7721. Springer, pp. 118–130, 2013.
ista: Chmelik M, Řehák V. 2013. Controllable-choice message sequence graphs. 7721,
118–130.
mla: Chmelik, Martin, and Vojtěch Řehák. Controllable-Choice Message Sequence
Graphs. Vol. 7721, Springer, 2013, pp. 118–30, doi:10.1007/978-3-642-36046-6_12.
short: M. Chmelik, V. Řehák, 7721 (2013) 118–130.
conference:
end_date: 2012-10-28
location: Znojmo, Czech Republic
name: 'MEMICS: Mathematical and Engineering Methods in Computer Science'
start_date: 2012-10-25
date_created: 2018-12-11T12:00:09Z
date_published: 2013-01-09T00:00:00Z
date_updated: 2020-08-11T10:09:52Z
day: '09'
department:
- _id: KrCh
doi: 10.1007/978-3-642-36046-6_12
ec_funded: 1
intvolume: ' 7721'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1209.4499
month: '01'
oa: 1
oa_version: Submitted Version
page: 118 - 130
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '3873'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Controllable-choice message sequence graphs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7721
year: '2013'
...
---
_id: '2887'
abstract:
- lang: eng
text: 'Root system growth and development is highly plastic and is influenced by
the surrounding environment. Roots frequently grow in heterogeneous environments
that include interactions from neighboring plants and physical impediments in
the rhizosphere. To investigate how planting density and physical objects affect
root system growth, we grew rice in a transparent gel system in close proximity
with another plant or a physical object. Root systems were imaged and reconstructed
in three dimensions. Root-root interaction strength was calculated using quantitative
metrics that characterize the extent towhich the reconstructed root systems overlap
each other. Surprisingly, we found the overlap of root systems of the same genotype
was significantly higher than that of root systems of different genotypes. Root
systems of the same genotype tended to grow toward each other but those of different
genotypes appeared to avoid each other. Shoot separation experiments excluded
the possibility of aerial interactions, suggesting root communication. Staggered
plantings indicated that interactions likely occur at root tips in close proximity.
Recognition of obstacles also occurred through root tips, but through physical
contact in a size-dependent manner. These results indicate that root systems use
two different forms of communication to recognize objects and alter root architecture:
root-root recognition, possibly mediated through root exudates, and root-object
recognition mediated by physical contact at the root tips. This finding suggests
that root tips act as local sensors that integrate rhizosphere information into
global root architectural changes.'
article_processing_charge: No
article_type: original
author:
- first_name: Suqin
full_name: Fang, Suqin
last_name: Fang
- first_name: Randy
full_name: Clark, Randy
last_name: Clark
- first_name: Ying
full_name: Zheng, Ying
last_name: Zheng
- first_name: Anjali
full_name: Iyer Pascuzzi, Anjali
last_name: Iyer Pascuzzi
- first_name: Joshua
full_name: Weitz, Joshua
last_name: Weitz
- first_name: Leon
full_name: Kochian, Leon
last_name: Kochian
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Hong
full_name: Liao, Hong
last_name: Liao
- first_name: Philip
full_name: Benfey, Philip
last_name: Benfey
citation:
ama: Fang S, Clark R, Zheng Y, et al. Genotypic recognition and spatial responses
by rice roots. PNAS. 2013;110(7):2670-2675. doi:10.1073/pnas.1222821110
apa: Fang, S., Clark, R., Zheng, Y., Iyer Pascuzzi, A., Weitz, J., Kochian, L.,
… Benfey, P. (2013). Genotypic recognition and spatial responses by rice roots.
PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1222821110
chicago: Fang, Suqin, Randy Clark, Ying Zheng, Anjali Iyer Pascuzzi, Joshua Weitz,
Leon Kochian, Herbert Edelsbrunner, Hong Liao, and Philip Benfey. “Genotypic Recognition
and Spatial Responses by Rice Roots.” PNAS. National Academy of Sciences,
2013. https://doi.org/10.1073/pnas.1222821110.
ieee: S. Fang et al., “Genotypic recognition and spatial responses by rice
roots,” PNAS, vol. 110, no. 7. National Academy of Sciences, pp. 2670–2675,
2013.
ista: Fang S, Clark R, Zheng Y, Iyer Pascuzzi A, Weitz J, Kochian L, Edelsbrunner
H, Liao H, Benfey P. 2013. Genotypic recognition and spatial responses by rice
roots. PNAS. 110(7), 2670–2675.
mla: Fang, Suqin, et al. “Genotypic Recognition and Spatial Responses by Rice Roots.”
PNAS, vol. 110, no. 7, National Academy of Sciences, 2013, pp. 2670–75,
doi:10.1073/pnas.1222821110.
short: S. Fang, R. Clark, Y. Zheng, A. Iyer Pascuzzi, J. Weitz, L. Kochian, H. Edelsbrunner,
H. Liao, P. Benfey, PNAS 110 (2013) 2670–2675.
date_created: 2018-12-11T12:00:09Z
date_published: 2013-02-12T00:00:00Z
date_updated: 2021-01-12T07:00:29Z
day: '12'
department:
- _id: HeEd
doi: 10.1073/pnas.1222821110
external_id:
pmid:
- '23362379'
intvolume: ' 110'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574932/
month: '02'
oa: 1
oa_version: Published Version
page: 2670 - 2675
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3872'
quality_controlled: '1'
scopus_import: 1
status: public
title: Genotypic recognition and spatial responses by rice roots
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2901'
abstract:
- lang: eng
text: ' We introduce the M-modes problem for graphical models: predicting the M
label configurations of highest probability that are at the same time local maxima
of the probability landscape. M-modes have multiple possible applications: because
they are intrinsically diverse, they provide a principled alternative to non-maximum
suppression techniques for structured prediction, they can act as codebook vectors
for quantizing the configuration space, or they can form component centers for
mixture model approximation. We present two algorithms for solving the M-modes
problem. The first algorithm solves the problem in polynomial time when the underlying
graphical model is a simple chain. The second algorithm solves the problem for
junction chains. In synthetic and real dataset, we demonstrate how M-modes can
improve the performance of prediction. We also use the generated modes as a tool
to understand the topography of the probability distribution of configurations,
for example with relation to the training set size and amount of noise in the
data. '
alternative_title:
- ' JMLR: W&CP'
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Zhu
full_name: Yan, Zhu
last_name: Yan
- first_name: Dimitris
full_name: Metaxas, Dimitris
last_name: Metaxas
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Chen C, Kolmogorov V, Yan Z, Metaxas D, Lampert C. Computing the M most probable
modes of a graphical model. In: Vol 31. JMLR; 2013:161-169.'
apa: 'Chen, C., Kolmogorov, V., Yan, Z., Metaxas, D., & Lampert, C. (2013).
Computing the M most probable modes of a graphical model (Vol. 31, pp. 161–169).
Presented at the AISTATS: Conference on Uncertainty in Artificial Intelligence,
Scottsdale, AZ, United States: JMLR.'
chicago: Chen, Chao, Vladimir Kolmogorov, Zhu Yan, Dimitris Metaxas, and Christoph
Lampert. “Computing the M Most Probable Modes of a Graphical Model,” 31:161–69.
JMLR, 2013.
ieee: 'C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, and C. Lampert, “Computing the
M most probable modes of a graphical model,” presented at the AISTATS: Conference
on Uncertainty in Artificial Intelligence, Scottsdale, AZ, United States, 2013,
vol. 31, pp. 161–169.'
ista: 'Chen C, Kolmogorov V, Yan Z, Metaxas D, Lampert C. 2013. Computing the M
most probable modes of a graphical model. AISTATS: Conference on Uncertainty
in Artificial Intelligence, JMLR: W&CP, vol. 31, 161–169.'
mla: Chen, Chao, et al. Computing the M Most Probable Modes of a Graphical Model.
Vol. 31, JMLR, 2013, pp. 161–69.
short: C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, C. Lampert, in:, JMLR, 2013,
pp. 161–169.
conference:
end_date: 2013-05-01
location: Scottsdale, AZ, United States
name: ' AISTATS: Conference on Uncertainty in Artificial Intelligence'
start_date: 2013-04-29
date_created: 2018-12-11T12:00:14Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:35Z
day: '01'
department:
- _id: HeEd
- _id: VlKo
- _id: ChLa
intvolume: ' 31'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://jmlr.org/proceedings/papers/v31/chen13a.html
month: '01'
oa: 1
oa_version: None
page: 161 - 169
publication_status: published
publisher: JMLR
publist_id: '3846'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computing the M most probable modes of a graphical model
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2013'
...
---
_id: '2906'
abstract:
- lang: eng
text: "Motivated by an application in cell biology, we describe an extension of
the kinetic data structures framework from Delaunay triangulations to fixed-radius
alpha complexes. Our algorithm is implemented\r\nusing CGAL, following the exact
geometric computation paradigm. We report on several\r\ntechniques to accelerate
the computation that turn our implementation applicable to the underlying biological\r\nproblem."
alternative_title:
- ALENEX
author:
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Kerber M, Edelsbrunner H. 3D kinetic alpha complexes and their implementation.
In: 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments.
Society of Industrial and Applied Mathematics; 2013:70-77. doi:10.1137/1.9781611972931.6'
apa: 'Kerber, M., & Edelsbrunner, H. (2013). 3D kinetic alpha complexes and
their implementation. In 2013 Proceedings of the 15th Workshop on Algorithm
Engineering and Experiments (pp. 70–77). New Orleans, LA, United States: Society
of Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611972931.6'
chicago: Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes
and Their Implementation.” In 2013 Proceedings of the 15th Workshop on Algorithm
Engineering and Experiments, 70–77. Society of Industrial and Applied Mathematics,
2013. https://doi.org/10.1137/1.9781611972931.6.
ieee: M. Kerber and H. Edelsbrunner, “3D kinetic alpha complexes and their implementation,”
in 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments,
New Orleans, LA, United States, 2013, pp. 70–77.
ista: 'Kerber M, Edelsbrunner H. 2013. 3D kinetic alpha complexes and their implementation.
2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments.
ALENEX: Algorithm Engineering and Experiments, ALENEX, , 70–77.'
mla: Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes and
Their Implementation.” 2013 Proceedings of the 15th Workshop on Algorithm Engineering
and Experiments, Society of Industrial and Applied Mathematics, 2013, pp.
70–77, doi:10.1137/1.9781611972931.6.
short: M. Kerber, H. Edelsbrunner, in:, 2013 Proceedings of the 15th Workshop on
Algorithm Engineering and Experiments, Society of Industrial and Applied Mathematics,
2013, pp. 70–77.
conference:
end_date: 2013-01-07
location: New Orleans, LA, United States
name: 'ALENEX: Algorithm Engineering and Experiments'
start_date: 2013-01-07
date_created: 2018-12-11T12:00:16Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:36Z
day: '01'
ddc:
- '500'
department:
- _id: HeEd
doi: 10.1137/1.9781611972931.6
file:
- access_level: open_access
checksum: a15a3ba22df9445731507f3e06c9fcee
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:57Z
date_updated: 2020-07-14T12:45:52Z
file_id: '4720'
file_name: IST-2016-547-v1+1_2013-P-08-MedusaII.pdf
file_size: 403013
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 70 - 77
publication: 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments
publication_status: published
publisher: Society of Industrial and Applied Mathematics
publist_id: '3841'
pubrep_id: '547'
quality_controlled: '1'
scopus_import: 1
status: public
title: 3D kinetic alpha complexes and their implementation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2907'
abstract:
- lang: eng
text: 'Sex and recombination are among the most striking features of the living
world, and they play a crucial role in allowing the evolution of complex adaptation.
The sharing of genomes through the sexual union of different individuals requires
elaborate behavioral and physiological adaptations. At the molecular level, the
alignment of two DNA double helices, followed by their precise cutting and rejoining,
is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary
consequences: distinct sexes, elaborate mating displays, selfish genetic elements,
and so on.'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Recombination and sex. In: The Princeton Guide to Evolution.
Princeton University Press; 2013:328-333.'
apa: Barton, N. H. (2013). Recombination and sex. In The Princeton Guide to Evolution
(pp. 328–333). Princeton University Press.
chicago: Barton, Nicholas H. “Recombination and Sex.” In The Princeton Guide
to Evolution, 328–33. Princeton University Press, 2013.
ieee: N. H. Barton, “Recombination and sex,” in The Princeton Guide to Evolution,
Princeton University Press, 2013, pp. 328–333.
ista: 'Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution.
, 328–333.'
mla: Barton, Nicholas H. “Recombination and Sex.” The Princeton Guide to Evolution,
Princeton University Press, 2013, pp. 328–33.
short: N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University
Press, 2013, pp. 328–333.
date_created: 2018-12-11T12:00:16Z
date_published: 2013-11-04T00:00:00Z
date_updated: 2021-01-12T07:00:37Z
day: '04'
ddc:
- '576'
department:
- _id: NiBa
file:
- access_level: open_access
checksum: 8332ca9cb40f7e66d1006b175ce36b60
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: system
date_created: 2018-12-12T10:16:47Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5237'
file_name: IST-2013-119-v1+1_IV.4_Recombination_and_Sex_Barton_1-13-13-e.docx
file_size: 79838
relation: main_file
- access_level: open_access
checksum: 849f418620fb78d6ba23bb4f488ee93f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:48Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5238'
file_name: IST-2017-119-v1+2_Barton_Recombination_Sex.pdf
file_size: 144131
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 328 - 333
publication: The Princeton Guide to Evolution
publication_identifier:
isbn:
- '9780691149776'
publication_status: published
publisher: Princeton University Press
publist_id: '3839'
pubrep_id: '119'
quality_controlled: '1'
status: public
title: Recombination and sex
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2908'
abstract:
- lang: eng
text: 'Hybridization is an almost inevitable component of speciation, and its study
can tell us much about that process. However, hybridization itself may have a
negligible influence on the origin of species: on the one hand, universally favoured
alleles spread readily across hybrid zones, whilst on the other, spatially heterogeneous
selection causes divergence despite gene flow. Thus, narrow hybrid zones or occasional
hybridisation may hardly affect the process of divergence.'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Does hybridisation influence speciation? . Journal of Evolutionary
Biology. 2013;26(2):267-269. doi:10.1111/jeb.12015
apa: Barton, N. H. (2013). Does hybridisation influence speciation? . Journal
of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/jeb.12015
chicago: Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal
of Evolutionary Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/jeb.12015.
ieee: N. H. Barton, “Does hybridisation influence speciation? ,” Journal of
Evolutionary Biology, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013.
ista: Barton NH. 2013. Does hybridisation influence speciation? . Journal of Evolutionary
Biology. 26(2), 267–269.
mla: Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal
of Evolutionary Biology, vol. 26, no. 2, Wiley-Blackwell, 2013, pp. 267–69,
doi:10.1111/jeb.12015.
short: N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269.
date_created: 2018-12-11T12:00:17Z
date_published: 2013-01-17T00:00:00Z
date_updated: 2021-01-12T07:00:37Z
day: '17'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/jeb.12015
file:
- access_level: open_access
checksum: 716e88714c3411cd0bd70928b14ea692
content_type: text/rtf
creator: system
date_created: 2018-12-12T10:09:38Z
date_updated: 2020-07-14T12:45:52Z
file_id: '4762'
file_name: IST-2013-111-v1+1_Hybridisation_and_speciation_revised.rtf
file_size: 13339
relation: main_file
- access_level: open_access
checksum: 957fd07c71c1b1eac2c65ae3311aca78
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:39Z
date_updated: 2020-07-14T12:45:52Z
file_id: '4763'
file_name: IST-2017-111-v1+2_Hybridisation_and_speciation_revised.pdf
file_size: 103437
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 26'
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 267 - 269
publication: Journal of Evolutionary Biology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3835'
pubrep_id: '111'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Does hybridisation influence speciation? '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2013'
...
---
_id: '2909'
abstract:
- lang: eng
text: "We survey a class of models for spatially structured populations\r\nwhich
we have called spatial Λ-Fleming–Viot processes. They arise from a flexible\r\nframework
for modelling in which the key innovation is that random genetic drift\r\nis driven
by a Poisson point process of spatial ‘events’. We demonstrate how this\r\novercomes
some of the obstructions to modelling populations which evolve in two-\r\n(and
higher-) dimensional spatial continua, how its predictions match phenomena\r\nobserved
in data and how it fits with classical models. Finally we outline some\r\ndirections
for future research."
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum.
Journal of Statistical Mechanics Theory and Experiment. 2013;2013(1). doi:10.1088/1742-5468/2013/01/P01002
apa: Barton, N. H., Etheridge, A., & Véber, A. (2013). Modelling evolution in
a spatial continuum. Journal of Statistical Mechanics Theory and Experiment.
IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2013/01/P01002
chicago: Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “Modelling Evolution
in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment.
IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/01/P01002.
ieee: N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial
continuum,” Journal of Statistical Mechanics Theory and Experiment, vol.
2013, no. 1. IOP Publishing Ltd., 2013.
ista: Barton NH, Etheridge A, Véber A. 2013. Modelling evolution in a spatial continuum.
Journal of Statistical Mechanics Theory and Experiment. 2013(1).
mla: Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” Journal
of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1, IOP Publishing
Ltd., 2013, doi:10.1088/1742-5468/2013/01/P01002.
short: N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory
and Experiment 2013 (2013).
date_created: 2018-12-11T12:00:17Z
date_published: 2013-01-16T00:00:00Z
date_updated: 2021-01-12T07:00:37Z
day: '16'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1088/1742-5468/2013/01/P01002
ec_funded: 1
file:
- access_level: open_access
checksum: ce8a4424385b3086138a1e054e16e0e3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:52Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5242'
file_name: IST-2016-557-v1+1_BEVrevised.pdf
file_size: 702583
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 2013'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Journal of Statistical Mechanics Theory and Experiment
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '3834'
pubrep_id: '557'
quality_controlled: '1'
scopus_import: 1
status: public
title: Modelling evolution in a spatial continuum
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2013
year: '2013'
...
---
_id: '2910'
abstract:
- lang: eng
text: "Coalescent simulation has become an indispensable tool in population genetics
and many complex evolutionary scenarios have been incorporated into the basic
algorithm. Despite many years of intense interest in spatial structure, however,
there are no available methods to simulate the ancestry of a sample of genes that
occupy a spatial continuum. This is mainly due to the severe technical problems
encountered by the classical model of isolation\r\nby distance. A recently introduced
model solves these technical problems and provides a solid theoretical basis for
the study of populations evolving in continuous space. We present a detailed algorithm
to simulate the coalescent process in this model, and provide an efficient implementation
of a generalised version of this algorithm as a freely available Python module."
author:
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: Kelleher J, Barton NH, Etheridge A. Coalescent simulation in continuous space.
Bioinformatics. 2013;29(7):955-956. doi:10.1093/bioinformatics/btt067
apa: Kelleher, J., Barton, N. H., & Etheridge, A. (2013). Coalescent simulation
in continuous space. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btt067
chicago: Kelleher, Jerome, Nicholas H Barton, and Alison Etheridge. “Coalescent
Simulation in Continuous Space.” Bioinformatics. Oxford University Press,
2013. https://doi.org/10.1093/bioinformatics/btt067.
ieee: J. Kelleher, N. H. Barton, and A. Etheridge, “Coalescent simulation in continuous
space,” Bioinformatics, vol. 29, no. 7. Oxford University Press, pp. 955–956,
2013.
ista: Kelleher J, Barton NH, Etheridge A. 2013. Coalescent simulation in continuous
space. Bioinformatics. 29(7), 955–956.
mla: Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space.” Bioinformatics,
vol. 29, no. 7, Oxford University Press, 2013, pp. 955–56, doi:10.1093/bioinformatics/btt067.
short: J. Kelleher, N.H. Barton, A. Etheridge, Bioinformatics 29 (2013) 955–956.
date_created: 2018-12-11T12:00:17Z
date_published: 2013-02-07T00:00:00Z
date_updated: 2021-01-12T07:00:38Z
day: '07'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/bioinformatics/btt067
ec_funded: 1
file:
- access_level: open_access
checksum: a3b54d7477fac923815ac082403d9bd0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:04Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5189'
file_name: IST-2016-556-v1+1_bioinformatics-2013.pdf
file_size: 170197
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 29'
issue: '7'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 955 - 956
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Bioinformatics
publication_status: published
publisher: Oxford University Press
publist_id: '3833'
pubrep_id: '556'
quality_controlled: '1'
scopus_import: 1
status: public
title: Coalescent simulation in continuous space
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2013'
...
---
_id: '2913'
abstract:
- lang: eng
text: 'The ability of an organism to distinguish between various stimuli is limited
by the structure and noise in the population code of its sensory neurons. Here
we infer a distance measure on the stimulus space directly from the recorded activity
of 100 neurons in the salamander retina. In contrast to previously used measures
of stimulus similarity, this "neural metric" tells us how distinguishable
a pair of stimulus clips is to the retina, based on the similarity between the
induced distributions of population responses. We show that the retinal distance
strongly deviates from Euclidean, or any static metric, yet has a simple structure:
we identify the stimulus features that the neural population is jointly sensitive
to, and show the support-vector-machine- like kernel function relating the stimulus
and neural response spaces. We show that the non-Euclidean nature of the retinal
distance has important consequences for neural decoding.'
article_number: '058104'
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Einat
full_name: Granot Atedgi, Einat
last_name: Granot Atedgi
- first_name: Ronen
full_name: Segev, Ronen
last_name: Segev
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
citation:
ama: 'Tkačik G, Granot Atedgi E, Segev R, Schneidman E. Retinal metric: a stimulus
distance measure derived from population neural responses. Physical Review
Letters. 2013;110(5). doi:10.1103/PhysRevLett.110.058104'
apa: 'Tkačik, G., Granot Atedgi, E., Segev, R., & Schneidman, E. (2013). Retinal
metric: a stimulus distance measure derived from population neural responses.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.058104'
chicago: 'Tkačik, Gašper, Einat Granot Atedgi, Ronen Segev, and Elad Schneidman.
“Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.”
Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.058104.'
ieee: 'G. Tkačik, E. Granot Atedgi, R. Segev, and E. Schneidman, “Retinal metric:
a stimulus distance measure derived from population neural responses,” Physical
Review Letters, vol. 110, no. 5. American Physical Society, 2013.'
ista: 'Tkačik G, Granot Atedgi E, Segev R, Schneidman E. 2013. Retinal metric: a
stimulus distance measure derived from population neural responses. Physical Review
Letters. 110(5), 058104.'
mla: 'Tkačik, Gašper, et al. “Retinal Metric: A Stimulus Distance Measure Derived
from Population Neural Responses.” Physical Review Letters, vol. 110, no.
5, 058104, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.058104.'
short: G. Tkačik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters
110 (2013).
date_created: 2018-12-11T12:00:18Z
date_published: 2013-01-28T00:00:00Z
date_updated: 2021-01-12T07:00:39Z
day: '28'
department:
- _id: GaTk
doi: 10.1103/PhysRevLett.110.058104
intvolume: ' 110'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1205.6598
month: '01'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '3830'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Retinal metric: a stimulus distance measure derived from population neural
responses'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2914'
abstract:
- lang: eng
text: The scale invariance of natural images suggests an analogy to the statistical
mechanics of physical systems at a critical point. Here we examine the distribution
of pixels in small image patches and show how to construct the corresponding thermodynamics.
We find evidence for criticality in a diverging specific heat, which corresponds
to large fluctuations in how "surprising" we find individual images,
and in the quantitative form of the entropy vs energy. We identify special image
configurations as local energy minima and show that average patches within each
basin are interpretable as lines and edges in all orientations.
acknowledgement: "This work was supported in part by NSF Grants No. IIS-0613435, No.
IBN-0344678, and No. PHY-0957573, by NIH Grant No. T32 MH065214, by the Human Frontier
Science Program, and by the Swartz Foundation.\r\nCC BY 3.0\r\n"
article_number: '018701'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Greg
full_name: Stephens, Greg
last_name: Stephens
- first_name: Thierry
full_name: Mora, Thierry
last_name: Mora
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: William
full_name: Bialek, William
last_name: Bialek
citation:
ama: Stephens G, Mora T, Tkačik G, Bialek W. Statistical thermodynamics of natural
images. Physical Review Letters. 2013;110(1). doi:10.1103/PhysRevLett.110.018701
apa: Stephens, G., Mora, T., Tkačik, G., & Bialek, W. (2013). Statistical thermodynamics
of natural images. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/PhysRevLett.110.018701
chicago: Stephens, Greg, Thierry Mora, Gašper Tkačik, and William Bialek. “Statistical
Thermodynamics of Natural Images.” Physical Review Letters. American Physical
Society, 2013. https://doi.org/10.1103/PhysRevLett.110.018701.
ieee: G. Stephens, T. Mora, G. Tkačik, and W. Bialek, “Statistical thermodynamics
of natural images,” Physical Review Letters, vol. 110, no. 1. American
Physical Society, 2013.
ista: Stephens G, Mora T, Tkačik G, Bialek W. 2013. Statistical thermodynamics of
natural images. Physical Review Letters. 110(1), 018701.
mla: Stephens, Greg, et al. “Statistical Thermodynamics of Natural Images.” Physical
Review Letters, vol. 110, no. 1, 018701, American Physical Society, 2013,
doi:10.1103/PhysRevLett.110.018701.
short: G. Stephens, T. Mora, G. Tkačik, W. Bialek, Physical Review Letters 110 (2013).
date_created: 2018-12-11T12:00:19Z
date_published: 2013-01-02T00:00:00Z
date_updated: 2023-09-04T11:47:51Z
day: '02'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.1103/PhysRevLett.110.018701
external_id:
arxiv:
- '0806.2694'
file:
- access_level: open_access
checksum: 72bfbc2094c4680e8a8a6bed668cd06d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:44Z
date_updated: 2020-07-14T12:45:53Z
file_id: '5366'
file_name: IST-2016-401-v1+1_1281.full.pdf
file_size: 416965
relation: main_file
file_date_updated: 2020-07-14T12:45:53Z
has_accepted_license: '1'
intvolume: ' 110'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '3829'
pubrep_id: '401'
quality_controlled: '1'
status: public
title: Statistical thermodynamics of natural images
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2919'
abstract:
- lang: eng
text: The distribution of the phytohormone auxin regulates many aspects of plant
development including growth response to gravity. Gravitropic root curvature involves
coordinated and asymmetric cell elongation between the lower and upper side of
the root, mediated by differential cellular auxin levels. The asymmetry in the
auxin distribution is established and maintained by a spatio-temporal regulation
of the PIN-FORMED (PIN) auxin transporter activity. We provide novel insights
into the complex regulation of PIN abundance and activity during root gravitropism.
We show that PIN2 turnover is differentially regulated on the upper and lower
side of gravistimulated roots by distinct but partially overlapping auxin feedback
mechanisms. In addition to regulating transcription and clathrin-mediated internalization,
auxin also controls PIN abundance at the plasma membrane by promoting their vacuolar
targeting and degradation. This effect of elevated auxin levels requires the activity
of SKP-Cullin-F-box TIR1/AFB (SCF TIR1/AFB)-dependent pathway. Importantly, also
suboptimal auxin levels mediate PIN degradation utilizing the same signalling
pathway. These feedback mechanisms are functionally important during gravitropic
response and ensure fine-tuning of auxin fluxes for maintaining as well as terminating
asymmetric growth.
author:
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Jürgen
full_name: Kleine Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Urszula
full_name: Kania, Urszula
id: 4AE5C486-F248-11E8-B48F-1D18A9856A87
last_name: Kania
- first_name: Wim
full_name: Grunewald, Wim
last_name: Grunewald
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Baster P, Robert S, Kleine Vehn J, et al. SCF^TIR1 AFB-auxin signalling regulates
PIN vacuolar trafficking and auxin fluxes during root gravitropism. EMBO Journal.
2013;32(2):260-274. doi:10.1038/emboj.2012.310
apa: Baster, P., Robert, S., Kleine Vehn, J., Vanneste, S., Kania, U., Grunewald,
W., … Friml, J. (2013). SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking
and auxin fluxes during root gravitropism. EMBO Journal. Wiley-Blackwell.
https://doi.org/10.1038/emboj.2012.310
chicago: Baster, Pawel, Stéphanie Robert, Jürgen Kleine Vehn, Steffen Vanneste,
Urszula Kania, Wim Grunewald, Bert De Rybel, Tom Beeckman, and Jiří Friml. “SCF^TIR1
AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during
Root Gravitropism.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2012.310.
ieee: P. Baster et al., “SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar
trafficking and auxin fluxes during root gravitropism,” EMBO Journal, vol.
32, no. 2. Wiley-Blackwell, pp. 260–274, 2013.
ista: Baster P, Robert S, Kleine Vehn J, Vanneste S, Kania U, Grunewald W, De Rybel
B, Beeckman T, Friml J. 2013. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar
trafficking and auxin fluxes during root gravitropism. EMBO Journal. 32(2), 260–274.
mla: Baster, Pawel, et al. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar
Trafficking and Auxin Fluxes during Root Gravitropism.” EMBO Journal, vol.
32, no. 2, Wiley-Blackwell, 2013, pp. 260–74, doi:10.1038/emboj.2012.310.
short: P. Baster, S. Robert, J. Kleine Vehn, S. Vanneste, U. Kania, W. Grunewald,
B. De Rybel, T. Beeckman, J. Friml, EMBO Journal 32 (2013) 260–274.
date_created: 2018-12-11T12:00:20Z
date_published: 2013-01-23T00:00:00Z
date_updated: 2021-01-12T07:00:41Z
day: '23'
department:
- _id: JiFr
doi: 10.1038/emboj.2012.310
external_id:
pmid:
- '23211744'
intvolume: ' 32'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553380/
month: '01'
oa: 1
oa_version: Submitted Version
page: 260 - 274
pmid: 1
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3818'
quality_controlled: '1'
scopus_import: 1
status: public
title: SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin
fluxes during root gravitropism
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2013'
...
---
_id: '2920'
abstract:
- lang: eng
text: Cell polarisation in development is a common and fundamental process underlying
embryo patterning and morphogenesis, and has been extensively studied over the
past years. Our current knowledge of cell polarisation in development is predominantly
based on studies that have analysed polarisation of single cells, such as eggs,
or cellular aggregates with a stable polarising interface, such as cultured epithelial
cells (St Johnston and Ahringer, 2010). However, in embryonic development, particularly
of vertebrates, cell polarisation processes often encompass large numbers of cells
that are placed within moving and proliferating tissues, and undergo mesenchymal-to-epithelial
transitions with a highly complex spatiotemporal choreography. How such intricate
cell polarisation processes in embryonic development are achieved has only started
to be analysed. By using live imaging of neurulation in the transparent zebrafish
embryo, Buckley et al (2012) now describe a novel polarisation strategy by which
cells assemble an apical domain in the part of their cell body that intersects
with the midline of the forming neural rod. This mechanism, along with the previously
described mirror-symmetric divisions (Tawk et al, 2007), is thought to trigger
formation of both neural rod midline and lumen.
author:
- first_name: Julien
full_name: Compagnon, Julien
id: 2E3E0988-F248-11E8-B48F-1D18A9856A87
last_name: Compagnon
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Compagnon J, Heisenberg C-PJ. Neurulation coordinating cell polarisation and
lumen formation. EMBO Journal. 2013;32(1):1-3. doi:10.1038/emboj.2012.325
apa: Compagnon, J., & Heisenberg, C.-P. J. (2013). Neurulation coordinating
cell polarisation and lumen formation. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2012.325
chicago: Compagnon, Julien, and Carl-Philipp J Heisenberg. “Neurulation Coordinating
Cell Polarisation and Lumen Formation.” EMBO Journal. Wiley-Blackwell,
2013. https://doi.org/10.1038/emboj.2012.325.
ieee: J. Compagnon and C.-P. J. Heisenberg, “Neurulation coordinating cell polarisation
and lumen formation,” EMBO Journal, vol. 32, no. 1. Wiley-Blackwell, pp.
1–3, 2013.
ista: Compagnon J, Heisenberg C-PJ. 2013. Neurulation coordinating cell polarisation
and lumen formation. EMBO Journal. 32(1), 1–3.
mla: Compagnon, Julien, and Carl-Philipp J. Heisenberg. “Neurulation Coordinating
Cell Polarisation and Lumen Formation.” EMBO Journal, vol. 32, no. 1, Wiley-Blackwell,
2013, pp. 1–3, doi:10.1038/emboj.2012.325.
short: J. Compagnon, C.-P.J. Heisenberg, EMBO Journal 32 (2013) 1–3.
date_created: 2018-12-11T12:00:20Z
date_published: 2013-01-09T00:00:00Z
date_updated: 2021-01-12T07:00:42Z
day: '09'
department:
- _id: CaHe
doi: 10.1038/emboj.2012.325
external_id:
pmid:
- '23211745'
intvolume: ' 32'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545307/
month: '01'
oa: 1
oa_version: Submitted Version
page: 1 - 3
pmid: 1
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3817'
quality_controlled: '1'
scopus_import: 1
status: public
title: Neurulation coordinating cell polarisation and lumen formation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2013'
...
---
_id: '2940'
abstract:
- lang: eng
text: "A chain rule for an entropy notion H(.) states that the entropy H(X) of a
variable X decreases by at most l if conditioned on an l-bit string A, i.e., H(X|A)>=
H(X)-l. More generally, it satisfies a chain rule for conditional entropy if H(X|Y,A)>=
H(X|Y)-l.\r\n\r\nAll natural information theoretic entropy notions we are aware
of (like Shannon or min-entropy) satisfy some kind of chain rule for conditional
entropy. Moreover, many computational entropy notions (like Yao entropy, unpredictability
entropy and several variants of HILL entropy) satisfy the chain rule for conditional
entropy, though here not only the quantity decreases by l, but also the quality
of the entropy decreases exponentially in l. However, for \r\nthe standard notion
of conditional HILL entropy (the computational equivalent of min-entropy) the
existence of such a rule was unknown so far.\r\n\r\nIn this paper, we prove that
for conditional HILL entropy no meaningful chain rule exists, assuming the existence
of one-way permutations: there exist distributions X,Y,A, where A is a distribution
over a single bit, but $H(X|Y)>>H(X|Y,A)$, even if we simultaneously allow
for a massive degradation in the quality of the entropy.\r\n\r\nThe idea underlying
our construction is based on a surprising connection between the chain rule for
HILL entropy and deniable encryption. "
alternative_title:
- LNCS
author:
- first_name: Stephan
full_name: Krenn, Stephan
id: 329FCCF0-F248-11E8-B48F-1D18A9856A87
last_name: Krenn
orcid: 0000-0003-2835-9093
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Akshay
full_name: Wadia, Akshay
last_name: Wadia
citation:
ama: 'Krenn S, Pietrzak KZ, Wadia A. A counterexample to the chain rule for conditional
HILL entropy, and what deniable encryption has to do with it. In: Sahai A, ed.
Vol 7785. Springer; 2013:23-39. doi:10.1007/978-3-642-36594-2_2'
apa: 'Krenn, S., Pietrzak, K. Z., & Wadia, A. (2013). A counterexample to the
chain rule for conditional HILL entropy, and what deniable encryption has to do
with it. In A. Sahai (Ed.) (Vol. 7785, pp. 23–39). Presented at the TCC: Theory
of Cryptography Conference, Tokyo, Japan: Springer. https://doi.org/10.1007/978-3-642-36594-2_2'
chicago: Krenn, Stephan, Krzysztof Z Pietrzak, and Akshay Wadia. “A Counterexample
to the Chain Rule for Conditional HILL Entropy, and What Deniable Encryption Has
to Do with It.” edited by Amit Sahai, 7785:23–39. Springer, 2013. https://doi.org/10.1007/978-3-642-36594-2_2.
ieee: 'S. Krenn, K. Z. Pietrzak, and A. Wadia, “A counterexample to the chain rule
for conditional HILL entropy, and what deniable encryption has to do with it,”
presented at the TCC: Theory of Cryptography Conference, Tokyo, Japan, 2013, vol.
7785, pp. 23–39.'
ista: 'Krenn S, Pietrzak KZ, Wadia A. 2013. A counterexample to the chain rule for
conditional HILL entropy, and what deniable encryption has to do with it. TCC:
Theory of Cryptography Conference, LNCS, vol. 7785, 23–39.'
mla: Krenn, Stephan, et al. A Counterexample to the Chain Rule for Conditional
HILL Entropy, and What Deniable Encryption Has to Do with It. Edited by Amit
Sahai, vol. 7785, Springer, 2013, pp. 23–39, doi:10.1007/978-3-642-36594-2_2.
short: S. Krenn, K.Z. Pietrzak, A. Wadia, in:, A. Sahai (Ed.), Springer, 2013, pp.
23–39.
conference:
end_date: 2013-03-06
location: Tokyo, Japan
name: 'TCC: Theory of Cryptography Conference'
start_date: 2013-03-03
date_created: 2018-12-11T12:00:27Z
date_published: 2013-01-29T00:00:00Z
date_updated: 2023-02-23T10:00:43Z
day: '29'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.1007/978-3-642-36594-2_2
ec_funded: 1
editor:
- first_name: Amit
full_name: Sahai, Amit
last_name: Sahai
file:
- access_level: open_access
checksum: beb0cc1c0579da2d2e84394230a5da78
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T14:11:11Z
date_updated: 2020-07-14T12:45:54Z
file_id: '5875'
file_name: 2013_LNCS_Krenn.pdf
file_size: 414823
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file_date_updated: 2020-07-14T12:45:54Z
has_accepted_license: '1'
intvolume: ' 7785'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 23 - 39
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '3795'
quality_controlled: '1'
related_material:
record:
- id: '1479'
relation: later_version
status: public
scopus_import: 1
status: public
title: A counterexample to the chain rule for conditional HILL entropy, and what deniable
encryption has to do with it
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7785
year: '2013'
...
---
_id: '2948'
abstract:
- lang: eng
text: 'Many visual datasets are traditionally used to analyze the performance of
different learning techniques. The evaluation is usually done within each dataset,
therefore it is questionable if such results are a reliable indicator of true
generalization ability. We propose here an algorithm to exploit the existing data
resources when learning on a new multiclass problem. Our main idea is to identify
an image representation that decomposes orthogonally into two subspaces: a part
specific to each dataset, and a part generic to, and therefore shared between,
all the considered source sets. This allows us to use the generic representation
as un-biased reference knowledge for a novel classification task. By casting the
method in the multi-view setting, we also make it possible to use different features
for different databases. We call the algorithm MUST, Multitask Unaligned Shared
knowledge Transfer. Through extensive experiments on five public datasets, we
show that MUST consistently improves the cross-datasets generalization performance.'
acknowledgement: This work was supported by the PASCAL 2 Network of Excellence (TT)
and by the Newton International Fellowship (NQ)
alternative_title:
- LNCS
author:
- first_name: Tatiana
full_name: Tommasi, Tatiana
last_name: Tommasi
- first_name: Novi
full_name: Quadrianto, Novi
last_name: Quadrianto
- first_name: Barbara
full_name: Caputo, Barbara
last_name: Caputo
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Tommasi T, Quadrianto N, Caputo B, Lampert C. Beyond dataset bias: Multi-task
unaligned shared knowledge transfer. 2013;7724:1-15. doi:10.1007/978-3-642-37331-2_1'
apa: 'Tommasi, T., Quadrianto, N., Caputo, B., & Lampert, C. (2013). Beyond
dataset bias: Multi-task unaligned shared knowledge transfer. Presented at the
ACCV: Asian Conference on Computer Vision, Daejeon, Korea: Springer. https://doi.org/10.1007/978-3-642-37331-2_1'
chicago: 'Tommasi, Tatiana, Novi Quadrianto, Barbara Caputo, and Christoph Lampert.
“Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer.” Lecture
Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-37331-2_1.'
ieee: 'T. Tommasi, N. Quadrianto, B. Caputo, and C. Lampert, “Beyond dataset bias:
Multi-task unaligned shared knowledge transfer,” vol. 7724. Springer, pp. 1–15,
2013.'
ista: 'Tommasi T, Quadrianto N, Caputo B, Lampert C. 2013. Beyond dataset bias:
Multi-task unaligned shared knowledge transfer. 7724, 1–15.'
mla: 'Tommasi, Tatiana, et al. Beyond Dataset Bias: Multi-Task Unaligned Shared
Knowledge Transfer. Vol. 7724, Springer, 2013, pp. 1–15, doi:10.1007/978-3-642-37331-2_1.'
short: T. Tommasi, N. Quadrianto, B. Caputo, C. Lampert, 7724 (2013) 1–15.
conference:
end_date: 2012-11-09
location: Daejeon, Korea
name: 'ACCV: Asian Conference on Computer Vision'
start_date: 2012-11-05
date_created: 2018-12-11T12:00:30Z
date_published: 2013-04-04T00:00:00Z
date_updated: 2020-08-11T10:09:54Z
day: '04'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.1007/978-3-642-37331-2_1
file:
- access_level: open_access
checksum: a0a7234a89e2192af655b0d0ae3bf445
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T14:03:11Z
date_updated: 2020-07-14T12:45:55Z
file_id: '5874'
file_name: 2012_ACCV_Tommasi.pdf
file_size: 1513620
relation: main_file
file_date_updated: 2020-07-14T12:45:55Z
has_accepted_license: '1'
intvolume: ' 7724'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 1 - 15
publication_status: published
publisher: Springer
publist_id: '3784'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: 'Beyond dataset bias: Multi-task unaligned shared knowledge transfer'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7724
year: '2013'
...