---
_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
relation: main_file
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'
...
---
_id: '2973'
abstract:
- lang: eng
text: "Efficient zero-knowledge proofs of knowledge (ZK-PoK) are basic building
blocks of many practical cryptographic applications such as identification schemes,
group signatures, and secure multiparty computation. Currently, first applications
that critically rely on ZK-PoKs are being deployed in the real world. The most
prominent example is Direct Anonymous Attestation (DAA), which was adopted by
the Trusted Computing Group (TCG) and implemented as one of the functionalities
of the cryptographic Trusted Platform Module (TPM) chip.\n\nImplementing systems
using ZK-PoK turns out to be challenging, since ZK-PoK are, loosely speaking,
significantly more complex than standard crypto primitives, such as encryption
and signature schemes. As a result, implementation cycles of ZK-PoK are time-consuming
and error-prone, in particular for developers with minor or no cryptographic skills.
\n\nIn this paper we report on our ongoing and future research vision with the
goal to bring ZK-PoK to practice by making them accessible to crypto and security
engineers. To this end we are developing compilers and related tools that support
and partially automate the design, implementation, verification and secure implementation
of ZK-PoK protocols."
acknowledgement: This work is being performed within the FP7 EU project CACE (Computer
Aided Cryptography Engineering).
alternative_title:
- LNCS
author:
- first_name: Endre
full_name: Bangerter, Endre
last_name: Bangerter
- first_name: Stefania
full_name: Barzan, Stefania
last_name: Barzan
- first_name: Stephan
full_name: Stephan Krenn
id: 329FCCF0-F248-11E8-B48F-1D18A9856A87
last_name: Krenn
orcid: 0000-0003-2835-9093
- first_name: Ahmad
full_name: Sadeghi, Ahmad-Reza
last_name: Sadeghi
- first_name: Thomas
full_name: Schneider, Thomas
last_name: Schneider
- first_name: Joe
full_name: Tsay, Joe-Kai
last_name: Tsay
citation:
ama: 'Bangerter E, Barzan S, Krenn S, Sadeghi A, Schneider T, Tsay J. Bringing Zero-Knowledge
Proofs of Knowledge to Practice. In: Christianson B, Malcolm J, Matyas V, Roe
M, eds. Vol 7028. Springer; 2013:51-62. doi:10.1007/978-3-642-36213-2_9'
apa: 'Bangerter, E., Barzan, S., Krenn, S., Sadeghi, A., Schneider, T., & Tsay,
J. (2013). Bringing Zero-Knowledge Proofs of Knowledge to Practice. In B. Christianson,
J. Malcolm, V. Matyas, & M. Roe (Eds.) (Vol. 7028, pp. 51–62). Presented at
the SPW: Security Protocols Workshop, Springer. https://doi.org/10.1007/978-3-642-36213-2_9'
chicago: Bangerter, Endre, Stefania Barzan, Stephan Krenn, Ahmad Sadeghi, Thomas
Schneider, and Joe Tsay. “Bringing Zero-Knowledge Proofs of Knowledge to Practice.”
edited by Bruce Christianson, James Malcolm, Vashek Matyas, and Michael Roe, 7028:51–62.
Springer, 2013. https://doi.org/10.1007/978-3-642-36213-2_9.
ieee: 'E. Bangerter, S. Barzan, S. Krenn, A. Sadeghi, T. Schneider, and J. Tsay,
“Bringing Zero-Knowledge Proofs of Knowledge to Practice,” presented at the SPW:
Security Protocols Workshop, 2013, vol. 7028, pp. 51–62.'
ista: 'Bangerter E, Barzan S, Krenn S, Sadeghi A, Schneider T, Tsay J. 2013. Bringing
Zero-Knowledge Proofs of Knowledge to Practice. SPW: Security Protocols Workshop,
LNCS, vol. 7028, 51–62.'
mla: Bangerter, Endre, et al. Bringing Zero-Knowledge Proofs of Knowledge to
Practice. Edited by Bruce Christianson et al., vol. 7028, Springer, 2013,
pp. 51–62, doi:10.1007/978-3-642-36213-2_9.
short: E. Bangerter, S. Barzan, S. Krenn, A. Sadeghi, T. Schneider, J. Tsay, in:,
B. Christianson, J. Malcolm, V. Matyas, M. Roe (Eds.), Springer, 2013, pp. 51–62.
conference:
name: 'SPW: Security Protocols Workshop'
date_created: 2018-12-11T12:00:38Z
date_published: 2013-01-08T00:00:00Z
date_updated: 2021-01-12T07:40:10Z
day: '08'
doi: 10.1007/978-3-642-36213-2_9
editor:
- first_name: Bruce
full_name: Christianson, Bruce
last_name: Christianson
- first_name: James
full_name: Malcolm, James A.
last_name: Malcolm
- first_name: Vashek
full_name: Matyas, Vashek
last_name: Matyas
- first_name: Michael
full_name: Roe, Michael
last_name: Roe
extern: 1
intvolume: ' 7028'
main_file_link:
- open_access: '1'
url: http://eprint.iacr.org/2009/211.pdf
month: '01'
oa: 1
page: 51 - 62
publication_status: published
publisher: Springer
publist_id: '3732'
quality_controlled: 0
status: public
title: Bringing Zero-Knowledge Proofs of Knowledge to Practice
type: conference
volume: 7028
year: '2013'
...
---
_id: '3261'
abstract:
- lang: eng
text: Cells in a developing embryo have no direct way of "measuring" their
physical position. Through a variety of processes, however, the expression levels
of multiple genes come to be correlated with position, and these expression levels
thus form a code for "positional information." We show how to measure
this information, in bits, using the gap genes in the Drosophila embryo as an
example. Individual genes carry nearly two bits of information, twice as much
as expected if the expression patterns consisted only of on/off domains separated
by sharp boundaries. Taken together, four gap genes carry enough information to
define a cell's location with an error bar of ~1% along the anterior-posterior
axis of the embryo. This precision is nearly enough for each cell to have a unique
identity, which is the maximum information the system can use, and is nearly constant
along the length of the embryo. We argue that this constancy is a signature of
optimality in the transmission of information from primary morphogen inputs to
the output of the gap gene network.
author:
- first_name: Julien
full_name: Dubuis, Julien
last_name: Dubuis
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Eric
full_name: Wieschaus, Eric
last_name: Wieschaus
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
- first_name: William
full_name: Bialek, William
last_name: Bialek
citation:
ama: Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. Positional information,
in bits. PNAS. 2013;110(41):16301-16308. doi:10.1073/pnas.1315642110
apa: Dubuis, J., Tkačik, G., Wieschaus, E., Gregor, T., & Bialek, W. (2013).
Positional information, in bits. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1315642110
chicago: Dubuis, Julien, Gašper Tkačik, Eric Wieschaus, Thomas Gregor, and William
Bialek. “Positional Information, in Bits.” PNAS. National Academy of Sciences,
2013. https://doi.org/10.1073/pnas.1315642110.
ieee: J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, and W. Bialek, “Positional
information, in bits,” PNAS, vol. 110, no. 41. National Academy of Sciences,
pp. 16301–16308, 2013.
ista: Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. 2013. Positional information,
in bits. PNAS. 110(41), 16301–16308.
mla: Dubuis, Julien, et al. “Positional Information, in Bits.” PNAS, vol.
110, no. 41, National Academy of Sciences, 2013, pp. 16301–08, doi:10.1073/pnas.1315642110.
short: J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, W. Bialek, PNAS 110 (2013)
16301–16308.
date_created: 2018-12-11T12:02:19Z
date_published: 2013-10-08T00:00:00Z
date_updated: 2021-01-12T07:42:13Z
day: '08'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1073/pnas.1315642110
external_id:
pmid:
- '24089448'
file:
- access_level: open_access
checksum: ecd859fe52a562193027d428b5524a8d
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T13:53:23Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5873'
file_name: 2013_PNAS_Dubuis.pdf
file_size: 1670548
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
intvolume: ' 110'
issue: '41'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 16301 - 16308
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3387'
quality_controlled: '1'
scopus_import: 1
status: public
title: Positional information, in bits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '10895'
abstract:
- lang: eng
text: 'Due to their sessile lifestyles, plants need to deal with the limitations
and stresses imposed by the changing environment. Plants cope with these by a
remarkable developmental flexibility, which is embedded in their strategy to survive.
Plants can adjust their size, shape and number of organs, bend according to gravity
and light, and regenerate tissues that were damaged, utilizing a coordinating,
intercellular signal, the plant hormone, auxin. Another versatile signal is the
cation, Ca2+, which is a crucial second messenger for many rapid cellular processes
during responses to a wide range of endogenous and environmental signals, such
as hormones, light, drought stress and others. Auxin is a good candidate for one
of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling
is poorly understood. Here, we will provide an overview of possible developmental
and physiological roles, as well as mechanisms underlying the interconnection
of Ca2+ and auxin signaling. '
article_processing_charge: No
article_type: original
author:
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Vanneste S, Friml J. Calcium: The missing link in auxin action. Plants.
2013;2(4):650-675. doi:10.3390/plants2040650'
apa: 'Vanneste, S., & Friml, J. (2013). Calcium: The missing link in auxin action.
Plants. MDPI. https://doi.org/10.3390/plants2040650'
chicago: 'Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin
Action.” Plants. MDPI, 2013. https://doi.org/10.3390/plants2040650.'
ieee: 'S. Vanneste and J. Friml, “Calcium: The missing link in auxin action,” Plants,
vol. 2, no. 4. MDPI, pp. 650–675, 2013.'
ista: 'Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants.
2(4), 650–675.'
mla: 'Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.”
Plants, vol. 2, no. 4, MDPI, 2013, pp. 650–75, doi:10.3390/plants2040650.'
short: S. Vanneste, J. Friml, Plants 2 (2013) 650–675.
date_created: 2022-03-21T07:13:49Z
date_published: 2013-10-21T00:00:00Z
date_updated: 2022-03-21T12:15:29Z
day: '21'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3390/plants2040650
external_id:
pmid:
- '27137397'
file:
- access_level: open_access
checksum: fb4ff2e820e344e253c9197544610be6
content_type: application/pdf
creator: dernst
date_created: 2022-03-21T12:12:56Z
date_updated: 2022-03-21T12:12:56Z
file_id: '10916'
file_name: 2013_Plants_Vanneste.pdf
file_size: 670188
relation: main_file
success: 1
file_date_updated: 2022-03-21T12:12:56Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '4'
keyword:
- Plant Science
- Ecology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '10'
oa: 1
oa_version: Published Version
page: 650-675
pmid: 1
publication: Plants
publication_identifier:
issn:
- 2223-7747
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Calcium: The missing link in auxin action'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2013'
...
---
_id: '11085'
abstract:
- lang: eng
text: During mitotic exit, missegregated chromosomes can recruit their own nuclear
envelope (NE) to form micronuclei (MN). MN have reduced functioning compared to
primary nuclei in the same cell, although the two compartments appear to be structurally
comparable. Here we show that over 60% of MN undergo an irreversible loss of compartmentalization
during interphase due to NE collapse. This disruption of the MN, which is induced
by defects in nuclear lamina assembly, drastically reduces nuclear functions and
can trigger massive DNA damage. MN disruption is associated with chromatin compaction
and invasion of endoplasmic reticulum (ER) tubules into the chromatin. We identified
disrupted MN in both major subtypes of human non-small-cell lung cancer, suggesting
that disrupted MN could be a useful objective biomarker for genomic instability
in solid tumors. Our study shows that NE collapse is a key event underlying MN
dysfunction and establishes a link between aberrant NE organization and aneuploidy.
article_processing_charge: No
article_type: original
author:
- first_name: Emily M.
full_name: Hatch, Emily M.
last_name: Hatch
- first_name: Andrew H.
full_name: Fischer, Andrew H.
last_name: Fischer
- first_name: Thomas J.
full_name: Deerinck, Thomas J.
last_name: Deerinck
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. Catastrophic nuclear envelope
collapse in cancer cell micronuclei. Cell. 2013;154(1):47-60. doi:10.1016/j.cell.2013.06.007
apa: Hatch, E. M., Fischer, A. H., Deerinck, T. J., & Hetzer, M. (2013). Catastrophic
nuclear envelope collapse in cancer cell micronuclei. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.06.007
chicago: Hatch, Emily M., Andrew H. Fischer, Thomas J. Deerinck, and Martin Hetzer.
“Catastrophic Nuclear Envelope Collapse in Cancer Cell Micronuclei.” Cell.
Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.06.007.
ieee: E. M. Hatch, A. H. Fischer, T. J. Deerinck, and M. Hetzer, “Catastrophic nuclear
envelope collapse in cancer cell micronuclei,” Cell, vol. 154, no. 1. Elsevier,
pp. 47–60, 2013.
ista: Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. 2013. Catastrophic nuclear envelope
collapse in cancer cell micronuclei. Cell. 154(1), 47–60.
mla: Hatch, Emily M., et al. “Catastrophic Nuclear Envelope Collapse in Cancer Cell
Micronuclei.” Cell, vol. 154, no. 1, Elsevier, 2013, pp. 47–60, doi:10.1016/j.cell.2013.06.007.
short: E.M. Hatch, A.H. Fischer, T.J. Deerinck, M. Hetzer, Cell 154 (2013) 47–60.
date_created: 2022-04-07T07:50:51Z
date_published: 2013-07-03T00:00:00Z
date_updated: 2022-07-18T08:45:47Z
day: '03'
doi: 10.1016/j.cell.2013.06.007
extern: '1'
external_id:
pmid:
- '23827674'
intvolume: ' 154'
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2013.06.007
month: '07'
oa: 1
oa_version: Published Version
page: 47-60
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Catastrophic nuclear envelope collapse in cancer cell micronuclei
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 154
year: '2013'
...
---
_id: '11086'
abstract:
- lang: eng
text: Faithful execution of developmental gene expression programs occurs at multiple
levels and involves many different components such as transcription factors, histone-modification
enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins,
well known components that control nucleo-cytoplasmic trafficking, have wide-ranging
functions in developmental gene regulation that potentially extend beyond their
role in nuclear transport. Whether the unexpected role of nuclear pore proteins
in transcription regulation, which initially has been described in fungi and flies,
also applies to human cells is unknown. Here we show at a genome-wide level that
the nuclear pore protein NUP98 associates with developmentally regulated genes
active during human embryonic stem cell differentiation. Overexpression of a dominant
negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes.
In addition, we identify two modes of developmental gene regulation by NUP98 that
are differentiated by the spatial localization of NUP98 target genes. Genes in
the initial stage of developmental induction can associate with NUP98 that is
embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that
are highly induced can interact with NUP98 in the nuclear interior, away from
the nuclear pores. This work demonstrates for the first time that NUP98 dynamically
associates with the human genome during differentiation, revealing a role of a
nuclear pore protein in regulating developmental gene expression programs.
article_number: e1003308
article_processing_charge: No
article_type: original
author:
- first_name: Yun
full_name: Liang, Yun
last_name: Liang
- first_name: Tobias M.
full_name: Franks, Tobias M.
last_name: Franks
- first_name: Maria C.
full_name: Marchetto, Maria C.
last_name: Marchetto
- first_name: Fred H.
full_name: Gage, Fred H.
last_name: Gage
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. Dynamic association of
NUP98 with the human genome. PLoS Genetics. 2013;9(2). doi:10.1371/journal.pgen.1003308
apa: Liang, Y., Franks, T. M., Marchetto, M. C., Gage, F. H., & Hetzer, M. (2013).
Dynamic association of NUP98 with the human genome. PLoS Genetics. Public
Library of Science. https://doi.org/10.1371/journal.pgen.1003308
chicago: Liang, Yun, Tobias M. Franks, Maria C. Marchetto, Fred H. Gage, and Martin
Hetzer. “Dynamic Association of NUP98 with the Human Genome.” PLoS Genetics.
Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003308.
ieee: Y. Liang, T. M. Franks, M. C. Marchetto, F. H. Gage, and M. Hetzer, “Dynamic
association of NUP98 with the human genome,” PLoS Genetics, vol. 9, no.
2. Public Library of Science, 2013.
ista: Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. 2013. Dynamic association
of NUP98 with the human genome. PLoS Genetics. 9(2), e1003308.
mla: Liang, Yun, et al. “Dynamic Association of NUP98 with the Human Genome.” PLoS
Genetics, vol. 9, no. 2, e1003308, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003308.
short: Y. Liang, T.M. Franks, M.C. Marchetto, F.H. Gage, M. Hetzer, PLoS Genetics
9 (2013).
date_created: 2022-04-07T07:50:59Z
date_published: 2013-02-28T00:00:00Z
date_updated: 2022-07-18T08:45:58Z
day: '28'
doi: 10.1371/journal.pgen.1003308
extern: '1'
external_id:
pmid:
- '23468646'
intvolume: ' 9'
issue: '2'
keyword:
- Cancer Research
- Genetics (clinical)
- Genetics
- Molecular Biology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pgen.1003308
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic association of NUP98 with the human genome
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 9
year: '2013'
...
---
_id: '11087'
abstract:
- lang: eng
text: Intracellular proteins with long lifespans have recently been linked to age-dependent
defects, ranging from decreased fertility to the functional decline of neurons.
Why long-lived proteins exist in metabolically active cellular environments and
how they are maintained over time remains poorly understood. Here, we provide
a system-wide identification of proteins with exceptional lifespans in the rat
brain. These proteins are inefficiently replenished despite being translated robustly
throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence,
we found that nuclear pore complexes (NPCs) are maintained over a cell’s life
through slow but finite exchange of even its most stable subcomplexes. This maintenance
is limited, however, as some nucleoporin levels decrease during aging, providing
a rationale for the previously observed age-dependent deterioration of NPC function.
Our identification of a long-lived proteome reveals cellular components that are
at increased risk for damage accumulation, linking long-term protein persistence
to the cellular aging process.
article_processing_charge: No
article_type: original
author:
- first_name: Brandon H.
full_name: Toyama, Brandon H.
last_name: Toyama
- first_name: Jeffrey N.
full_name: Savas, Jeffrey N.
last_name: Savas
- first_name: Sung Kyu
full_name: Park, Sung Kyu
last_name: Park
- first_name: Michael S.
full_name: Harris, Michael S.
last_name: Harris
- first_name: Nicholas T.
full_name: Ingolia, Nicholas T.
last_name: Ingolia
- first_name: John R.
full_name: Yates, John R.
last_name: Yates
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Toyama BH, Savas JN, Park SK, et al. Identification of long-lived proteins
reveals exceptional stability of essential cellular structures. Cell. 2013;154(5):971-982.
doi:10.1016/j.cell.2013.07.037
apa: Toyama, B. H., Savas, J. N., Park, S. K., Harris, M. S., Ingolia, N. T., Yates,
J. R., & Hetzer, M. (2013). Identification of long-lived proteins reveals
exceptional stability of essential cellular structures. Cell. Elsevier.
https://doi.org/10.1016/j.cell.2013.07.037
chicago: Toyama, Brandon H., Jeffrey N. Savas, Sung Kyu Park, Michael S. Harris,
Nicholas T. Ingolia, John R. Yates, and Martin Hetzer. “Identification of Long-Lived
Proteins Reveals Exceptional Stability of Essential Cellular Structures.” Cell.
Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.07.037.
ieee: B. H. Toyama et al., “Identification of long-lived proteins reveals
exceptional stability of essential cellular structures,” Cell, vol. 154,
no. 5. Elsevier, pp. 971–982, 2013.
ista: Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, Yates JR, Hetzer M. 2013.
Identification of long-lived proteins reveals exceptional stability of essential
cellular structures. Cell. 154(5), 971–982.
mla: Toyama, Brandon H., et al. “Identification of Long-Lived Proteins Reveals Exceptional
Stability of Essential Cellular Structures.” Cell, vol. 154, no. 5, Elsevier,
2013, pp. 971–82, doi:10.1016/j.cell.2013.07.037.
short: B.H. Toyama, J.N. Savas, S.K. Park, M.S. Harris, N.T. Ingolia, J.R. Yates,
M. Hetzer, Cell 154 (2013) 971–982.
date_created: 2022-04-07T07:51:08Z
date_published: 2013-08-29T00:00:00Z
date_updated: 2022-07-18T08:50:47Z
day: '29'
doi: 10.1016/j.cell.2013.07.037
extern: '1'
external_id:
pmid:
- '23993091'
intvolume: ' 154'
issue: '5'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2013.07.037
month: '08'
oa: 1
oa_version: Published Version
page: 971-982
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Identification of long-lived proteins reveals exceptional stability of essential
cellular structures
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 154
year: '2013'
...
---
_id: '11088'
abstract:
- lang: eng
text: 'The crowded intracellular environment poses a formidable challenge to experimental
and theoretical analyses of intracellular transport mechanisms. Our measurements
of single-particle trajectories in cytoplasm and their random-walk interpretations
elucidate two of these mechanisms: molecular diffusion in crowded environments
and cytoskeletal transport along microtubules. We employed acousto-optic deflector
microscopy to map out the three-dimensional trajectories of microspheres migrating
in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM),
continuous time random walk, and fractional BM were alternatively used to represent
these trajectories. The comparison of the experimental and numerical data demonstrates
that cytoskeletal transport along microtubules and diffusion in the cytosolic
fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct
signatures. Among the three random-walk models used, continuous time random walk
provides the best representation of diffusion, whereas microtubular transport
is accurately modeled with fractional BM.'
article_processing_charge: No
article_type: original
author:
- first_name: Benjamin M.
full_name: Regner, Benjamin M.
last_name: Regner
- first_name: Dejan
full_name: Vučinić, Dejan
last_name: Vučinić
- first_name: Cristina
full_name: Domnisoru, Cristina
last_name: Domnisoru
- first_name: Thomas M.
full_name: Bartol, Thomas M.
last_name: Bartol
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Daniel M.
full_name: Tartakovsky, Daniel M.
last_name: Tartakovsky
- first_name: Terrence J.
full_name: Sejnowski, Terrence J.
last_name: Sejnowski
citation:
ama: Regner BM, Vučinić D, Domnisoru C, et al. Anomalous diffusion of single particles
in cytoplasm. Biophysical Journal. 2013;104(8):1652-1660. doi:10.1016/j.bpj.2013.01.049
apa: Regner, B. M., Vučinić, D., Domnisoru, C., Bartol, T. M., Hetzer, M., Tartakovsky,
D. M., & Sejnowski, T. J. (2013). Anomalous diffusion of single particles
in cytoplasm. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2013.01.049
chicago: Regner, Benjamin M., Dejan Vučinić, Cristina Domnisoru, Thomas M. Bartol,
Martin Hetzer, Daniel M. Tartakovsky, and Terrence J. Sejnowski. “Anomalous Diffusion
of Single Particles in Cytoplasm.” Biophysical Journal. Elsevier, 2013.
https://doi.org/10.1016/j.bpj.2013.01.049.
ieee: B. M. Regner et al., “Anomalous diffusion of single particles in cytoplasm,”
Biophysical Journal, vol. 104, no. 8. Elsevier, pp. 1652–1660, 2013.
ista: Regner BM, Vučinić D, Domnisoru C, Bartol TM, Hetzer M, Tartakovsky DM, Sejnowski
TJ. 2013. Anomalous diffusion of single particles in cytoplasm. Biophysical Journal.
104(8), 1652–1660.
mla: Regner, Benjamin M., et al. “Anomalous Diffusion of Single Particles in Cytoplasm.”
Biophysical Journal, vol. 104, no. 8, Elsevier, 2013, pp. 1652–60, doi:10.1016/j.bpj.2013.01.049.
short: B.M. Regner, D. Vučinić, C. Domnisoru, T.M. Bartol, M. Hetzer, D.M. Tartakovsky,
T.J. Sejnowski, Biophysical Journal 104 (2013) 1652–1660.
date_created: 2022-04-07T07:51:26Z
date_published: 2013-04-16T00:00:00Z
date_updated: 2022-07-18T08:51:01Z
day: '16'
doi: 10.1016/j.bpj.2013.01.049
extern: '1'
external_id:
pmid:
- '23601312'
intvolume: ' 104'
issue: '8'
keyword:
- Biophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.bpj.2013.01.049
month: '04'
oa: 1
oa_version: Published Version
page: 1652-1660
pmid: 1
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anomalous diffusion of single particles in cytoplasm
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 104
year: '2013'
...
---
_id: '11520'
abstract:
- lang: eng
text: We present the spatially resolved Hα dynamics of 16 star-forming galaxies
at z ∼ 0.81 using the new KMOS multi-object integral field spectrograph on the
ESO Very Large Telescope. These galaxies, selected using 1.18 μm narrowband imaging
from the 10 deg2 CFHT-HiZELS survey of the SA 22 hr field, are found in a ∼4 Mpc
overdensity of Hα emitters and likely reside in a group/intermediate environment,
but not a cluster. We confirm and identify a rich group of star-forming galaxies
at z = 0.813 ± 0.003, with 13 galaxies within 1000 km s−1 of each other, and seven
within a diameter of 3 Mpc. All of our galaxies are “typical” star-forming galaxies
at their redshift, 0.8 ± 0.4 SFR$^*_{z = 0.8}$, spanning a range of specific star
formation rates (sSFRs) of 0.2–1.1 Gyr−1 and have a median metallicity very close
to solar of 12 + log(O/H) = 8.62 ± 0.06. We measure the spatially resolved Hα
dynamics of the galaxies in our sample and show that 13 out of 16 galaxies can
be described by rotating disks and use the data to derive inclination corrected
rotation speeds of 50–275 km s−1. The fraction of disks within our sample is 75%
± 8%, consistent with previous results based on Hubble Space Telescope morphologies
of Hα-selected galaxies at z ∼ 1 and confirming that disks dominate the SFR density
at z ∼ 1. Our Hα galaxies are well fitted by the z ∼ 1–2 Tully–Fisher (TF) relation,
confirming the evolution seen in the zero point. Apart from having, on average,
higher stellar masses and lower sSFRs, our group galaxies at z = 0.81 present
the same mass–metallicity and TF relation as z ∼ 1 field galaxies and are all
disk galaxies.
acknowledgement: 'We thank the referee for many helpful comments and suggestions which
greatly improved the clarity and quality of this work. D.S. acknowledges financial
support from the Netherlands Organisation for Scientific research (NWO) through
a Veni fellowship and also funding from the European Community Seventh Framework
Programme (FP7/2007-2013) under grant agreement number RG226604 (OPTICON) which
allowed access to CFHT time (proposals: 11BO29 & 12AO19). A.M.S. gratefully acknowledges
an STFC Advanced Fellowship through grant number ST/H005234/1. I.R.S., J.P.S., and
R.G.B. acknowledge support from the UK Science and Technology Facilities Council
(STFC) under ST/I001573/1. I.R.S. acknowledges STFC (ST/J001422/1), the ERC Advanced
Investigator program DUSTYGAL and a Royal Society/Wolfson Merit Award. P.N.B. acknowledges
support from STFC. R.M.S. acknowledges support from the grant ST/1001573/1. The
data presented here are based on observations with the KMOS spectrograph on the
ESO/VLT under program 60.A-9460 and can be accessed through the ESO data archive.
The authors also wish to acknowledge the help from Michael Hilker in preparing the
KMOS observations.'
article_number: '139'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: D.
full_name: Sobral, D.
last_name: Sobral
- first_name: A. M.
full_name: Swinbank, A. M.
last_name: Swinbank
- first_name: J. P.
full_name: Stott, J. P.
last_name: Stott
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: R. G.
full_name: Bower, R. G.
last_name: Bower
- first_name: Ian
full_name: Smail, Ian
last_name: Smail
- first_name: P.
full_name: Best, P.
last_name: Best
- first_name: J. E.
full_name: Geach, J. E.
last_name: Geach
- first_name: R. M.
full_name: Sharples, R. M.
last_name: Sharples
citation:
ama: Sobral D, Swinbank AM, Stott JP, et al. The dynamics of z=0.8 H-alpha-selected
star-forming galaxies from KMOS/CF-HiZELS. The Astrophysical Journal. 2013;779(2).
doi:10.1088/0004-637x/779/2/139
apa: Sobral, D., Swinbank, A. M., Stott, J. P., Matthee, J. J., Bower, R. G., Smail,
I., … Sharples, R. M. (2013). The dynamics of z=0.8 H-alpha-selected star-forming
galaxies from KMOS/CF-HiZELS. The Astrophysical Journal. IOP Publishing.
https://doi.org/10.1088/0004-637x/779/2/139
chicago: Sobral, D., A. M. Swinbank, J. P. Stott, Jorryt J Matthee, R. G. Bower,
Ian Smail, P. Best, J. E. Geach, and R. M. Sharples. “The Dynamics of Z=0.8 H-Alpha-Selected
Star-Forming Galaxies from KMOS/CF-HiZELS.” The Astrophysical Journal.
IOP Publishing, 2013. https://doi.org/10.1088/0004-637x/779/2/139.
ieee: D. Sobral et al., “The dynamics of z=0.8 H-alpha-selected star-forming
galaxies from KMOS/CF-HiZELS,” The Astrophysical Journal, vol. 779, no.
2. IOP Publishing, 2013.
ista: Sobral D, Swinbank AM, Stott JP, Matthee JJ, Bower RG, Smail I, Best P, Geach
JE, Sharples RM. 2013. The dynamics of z=0.8 H-alpha-selected star-forming galaxies
from KMOS/CF-HiZELS. The Astrophysical Journal. 779(2), 139.
mla: Sobral, D., et al. “The Dynamics of Z=0.8 H-Alpha-Selected Star-Forming Galaxies
from KMOS/CF-HiZELS.” The Astrophysical Journal, vol. 779, no. 2, 139,
IOP Publishing, 2013, doi:10.1088/0004-637x/779/2/139.
short: D. Sobral, A.M. Swinbank, J.P. Stott, J.J. Matthee, R.G. Bower, I. Smail,
P. Best, J.E. Geach, R.M. Sharples, The Astrophysical Journal 779 (2013).
date_created: 2022-07-07T09:14:48Z
date_published: 2013-12-03T00:00:00Z
date_updated: 2022-08-18T10:43:07Z
day: '03'
doi: 10.1088/0004-637x/779/2/139
extern: '1'
external_id:
arxiv:
- '1310.3822'
intvolume: ' 779'
issue: '2'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: evolution – galaxies'
- high-redshift – galaxies
- starburst
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1310.3822
month: '12'
oa: 1
oa_version: Preprint
publication: The Astrophysical Journal
publication_identifier:
eissn:
- 1538-4357
issn:
- 0004-637X
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: The dynamics of z=0.8 H-alpha-selected star-forming galaxies from KMOS/CF-HiZELS
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 779
year: '2013'
...
---
_id: '11759'
abstract:
- lang: eng
text: Matching markets play a prominent role in economic theory. A prime example
of such a market is the sponsored search market. Here, as in other markets of
that kind, market equilibria correspond to feasible, envy free, and bidder optimal
outcomes. For settings without budgets such an outcome always exists and can be
computed in polynomial-time by the so-called Hungarian Method. Moreover, every
mechanism that computes such an outcome is incentive compatible. We show that
the Hungarian Method can be modified so that it finds a feasible, envy free, and
bidder optimal outcome for settings with budgets. We also show that in settings
with budgets no mechanism that computes such an outcome can be incentive compatible
for all inputs. For inputs in general position, however, the presented mechanism—as
any other mechanism that computes such an outcome for settings with budgets—is
incentive compatible.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Paul
full_name: Dütting, Paul
last_name: Dütting
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Ingmar
full_name: Weber, Ingmar
last_name: Weber
citation:
ama: Dütting P, Henzinger MH, Weber I. Sponsored search, market equilibria, and
the Hungarian Method. Information Processing Letters. 2013;113(3):67-73.
doi:10.1016/j.ipl.2012.11.006
apa: Dütting, P., Henzinger, M. H., & Weber, I. (2013). Sponsored search, market
equilibria, and the Hungarian Method. Information Processing Letters. Elsevier.
https://doi.org/10.1016/j.ipl.2012.11.006
chicago: Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “Sponsored Search,
Market Equilibria, and the Hungarian Method.” Information Processing Letters.
Elsevier, 2013. https://doi.org/10.1016/j.ipl.2012.11.006.
ieee: P. Dütting, M. H. Henzinger, and I. Weber, “Sponsored search, market equilibria,
and the Hungarian Method,” Information Processing Letters, vol. 113, no.
3. Elsevier, pp. 67–73, 2013.
ista: Dütting P, Henzinger MH, Weber I. 2013. Sponsored search, market equilibria,
and the Hungarian Method. Information Processing Letters. 113(3), 67–73.
mla: Dütting, Paul, et al. “Sponsored Search, Market Equilibria, and the Hungarian
Method.” Information Processing Letters, vol. 113, no. 3, Elsevier, 2013,
pp. 67–73, doi:10.1016/j.ipl.2012.11.006.
short: P. Dütting, M.H. Henzinger, I. Weber, Information Processing Letters 113
(2013) 67–73.
date_created: 2022-08-08T11:29:08Z
date_published: 2013-02-15T00:00:00Z
date_updated: 2022-09-12T09:36:15Z
day: '15'
doi: 10.1016/j.ipl.2012.11.006
extern: '1'
external_id:
arxiv:
- '0912.1934'
intvolume: ' 113'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0912.1934
month: '02'
oa: 1
oa_version: Preprint
page: 67-73
publication: Information Processing Letters
publication_identifier:
issn:
- 0020-0190
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sponsored search, market equilibria, and the Hungarian Method
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2013'
...
---
_id: '11791'
abstract:
- lang: eng
text: The focus of classic mechanism design has been on truthful direct-revelation
mechanisms. In the context of combinatorial auctions the truthful direct-revelation
mechanism that maximizes social welfare is the VCG mechanism. For many valuation
spaces computing the allocation and payments of the VCG mechanism, however, is
a computationally hard problem. We thus study the performance of the VCG mechanism
when bidders are forced to choose bids from a subspace of the valuation space
for which the VCG outcome can be computed efficiently. We prove improved upper
bounds on the welfare loss for restrictions to additive bids and upper and lower
bounds for restrictions to non-additive bids. These bounds show that the welfare
loss increases in expressiveness. All our bounds apply to equilibrium concepts
that can be computed in polynomial time as well as to learning outcomes.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Paul
full_name: Dütting, Paul
last_name: Dütting
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Martin
full_name: Starnberger, Martin
last_name: Starnberger
citation:
ama: 'Dütting P, Henzinger MH, Starnberger M. Valuation compressions in VCG-based
combinatorial auctions. In: 9th International Conference on Web and Internet
Economics. Vol 8289. Springer Nature; 2013:146–159. doi:10.1007/978-3-642-45046-4_13'
apa: 'Dütting, P., Henzinger, M. H., & Starnberger, M. (2013). Valuation compressions
in VCG-based combinatorial auctions. In 9th International Conference on Web
and Internet Economics (Vol. 8289, pp. 146–159). Cambridge, MA, USA: Springer
Nature. https://doi.org/10.1007/978-3-642-45046-4_13'
chicago: Dütting, Paul, Monika H Henzinger, and Martin Starnberger. “Valuation Compressions
in VCG-Based Combinatorial Auctions.” In 9th International Conference on Web
and Internet Economics, 8289:146–159. Springer Nature, 2013. https://doi.org/10.1007/978-3-642-45046-4_13.
ieee: P. Dütting, M. H. Henzinger, and M. Starnberger, “Valuation compressions in
VCG-based combinatorial auctions,” in 9th International Conference on Web and
Internet Economics, Cambridge, MA, USA, 2013, vol. 8289, pp. 146–159.
ista: 'Dütting P, Henzinger MH, Starnberger M. 2013. Valuation compressions in VCG-based
combinatorial auctions. 9th International Conference on Web and Internet Economics.
WINE: International Conference on Web and Internet Economics, LNCS, vol. 8289,
146–159.'
mla: Dütting, Paul, et al. “Valuation Compressions in VCG-Based Combinatorial Auctions.”
9th International Conference on Web and Internet Economics, vol. 8289,
Springer Nature, 2013, pp. 146–159, doi:10.1007/978-3-642-45046-4_13.
short: P. Dütting, M.H. Henzinger, M. Starnberger, in:, 9th International Conference
on Web and Internet Economics, Springer Nature, 2013, pp. 146–159.
conference:
end_date: 2013-12-14
location: Cambridge, MA, USA
name: 'WINE: International Conference on Web and Internet Economics'
start_date: 2013-12-01
date_created: 2022-08-11T11:05:14Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2023-02-13T11:20:42Z
day: '01'
doi: 10.1007/978-3-642-45046-4_13
extern: '1'
external_id:
arxiv:
- '1310.3153'
intvolume: ' 8289'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1310.3153
month: '12'
oa: 1
oa_version: Preprint
page: 146–159
publication: 9th International Conference on Web and Internet Economics
publication_identifier:
isbn:
- '9783642450457'
issn:
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Valuation compressions in VCG-based combinatorial auctions
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8289
year: '2013'
...
---
_id: '11792'
abstract:
- lang: eng
text: "We study the problem of maximizing a monotone submodular function with viability
constraints. This problem originates from computational biology, where we are
given a phylogenetic tree over a set of species and a directed graph, the so-called
food web, encoding viability constraints between these species. These food webs
usually have constant depth. The goal is to select a subset of k species that
satisfies the viability constraints and has maximal phylogenetic diversity. As
this problem is known to be NP-hard, we investigate approximation algorithm. We
present the first constant factor approximation algorithm if the depth is constant.
Its approximation ratio is (1−1\U0001D452√). This algorithm not only applies to
phylogenetic trees with viability constraints but for arbitrary monotone submodular
set functions with viability constraints. Second, we show that there is no (1 − 1/e + ε)-approximation
algorithm for our problem setting (even for additive functions) and that there
is no approximation algorithm for a slight extension of this setting."
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Wolfgang
full_name: Dvořák, Wolfgang
last_name: Dvořák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: David P.
full_name: Williamson, David P.
last_name: Williamson
citation:
ama: 'Dvořák W, Henzinger MH, Williamson DP. Maximizing a submodular function with
viability constraints. In: 21st Annual European Symposium on Algorithms.
Vol 8125. Springer Nature; 2013:409-420. doi:10.1007/978-3-642-40450-4_35'
apa: 'Dvořák, W., Henzinger, M. H., & Williamson, D. P. (2013). Maximizing a
submodular function with viability constraints. In 21st Annual European Symposium
on Algorithms (Vol. 8125, pp. 409–420). Sophia Antipolis, France: Springer
Nature. https://doi.org/10.1007/978-3-642-40450-4_35'
chicago: Dvořák, Wolfgang, Monika H Henzinger, and David P. Williamson. “Maximizing
a Submodular Function with Viability Constraints.” In 21st Annual European
Symposium on Algorithms, 8125:409–20. Springer Nature, 2013. https://doi.org/10.1007/978-3-642-40450-4_35.
ieee: W. Dvořák, M. H. Henzinger, and D. P. Williamson, “Maximizing a submodular
function with viability constraints,” in 21st Annual European Symposium on
Algorithms, Sophia Antipolis, France, 2013, vol. 8125, pp. 409–420.
ista: 'Dvořák W, Henzinger MH, Williamson DP. 2013. Maximizing a submodular function
with viability constraints. 21st Annual European Symposium on Algorithms. ESA:
European Symposium on Algorithms, LNCS, vol. 8125, 409–420.'
mla: Dvořák, Wolfgang, et al. “Maximizing a Submodular Function with Viability Constraints.”
21st Annual European Symposium on Algorithms, vol. 8125, Springer Nature,
2013, pp. 409–20, doi:10.1007/978-3-642-40450-4_35.
short: W. Dvořák, M.H. Henzinger, D.P. Williamson, in:, 21st Annual European Symposium
on Algorithms, Springer Nature, 2013, pp. 409–420.
conference:
end_date: 2013-09-04
location: Sophia Antipolis, France
name: 'ESA: European Symposium on Algorithms'
start_date: 2013-09-02
date_created: 2022-08-11T11:18:19Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2023-02-21T16:28:24Z
day: '01'
doi: 10.1007/978-3-642-40450-4_35
extern: '1'
external_id:
arxiv:
- '1611.05753'
intvolume: ' 8125'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1611.05753
month: '09'
oa: 1
oa_version: Preprint
page: 409 - 420
publication: 21st Annual European Symposium on Algorithms
publication_identifier:
isbn:
- '9783642404498'
issn:
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '11792'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Maximizing a submodular function with viability constraints
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8125
year: '2013'
...
---
_id: '11793'
abstract:
- lang: eng
text: "We study the problem of maintaining a breadth-first spanning tree (BFS tree)
in partially dynamic distributed networks modeling a sequence of either failures
or additions of communication links (but not both). We show (1 + ε)-approximation
algorithms whose amortized time (over some number of link changes) is sublinear
in D, the maximum diameter of the network. This breaks the Θ(D) time bound of
recomputing “from scratch”.\r\n\r\nOur technique also leads to a (1 + ε)-approximate
incremental algorithm for single-source shortest paths (SSSP) in the sequential
(usual RAM) model. Prior to our work, the state of the art was the classic exact
algorithm of [9] that is optimal under some assumptions [27]. Our result is the
first to show that, in the incremental setting, this bound can be beaten in certain
cases if a small approximation is allowed."
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Henzinger MH, Krinninger S, Nanongkai D. Sublinear-time maintenance of breadth-first
spanning tree in partially dynamic networks. In: 40th International Colloquium
on Automata, Languages, and Programming. Vol 7966. Springer Nature; 2013:607–619.
doi:10.1007/978-3-642-39212-2_53'
apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2013). Sublinear-time
maintenance of breadth-first spanning tree in partially dynamic networks. In 40th
International Colloquium on Automata, Languages, and Programming (Vol. 7966,
pp. 607–619). Riga, Latvia: Springer Nature. https://doi.org/10.1007/978-3-642-39212-2_53'
chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Sublinear-Time
Maintenance of Breadth-First Spanning Tree in Partially Dynamic Networks.” In
40th International Colloquium on Automata, Languages, and Programming,
7966:607–619. Springer Nature, 2013. https://doi.org/10.1007/978-3-642-39212-2_53.
ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Sublinear-time maintenance
of breadth-first spanning tree in partially dynamic networks,” in 40th International
Colloquium on Automata, Languages, and Programming, Riga, Latvia, 2013, vol.
7966, pp. 607–619.
ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2013. Sublinear-time maintenance
of breadth-first spanning tree in partially dynamic networks. 40th International
Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium
on Automata, Languages, and Programming, LNCS, vol. 7966, 607–619.'
mla: Henzinger, Monika H., et al. “Sublinear-Time Maintenance of Breadth-First Spanning
Tree in Partially Dynamic Networks.” 40th International Colloquium on Automata,
Languages, and Programming, vol. 7966, Springer Nature, 2013, pp. 607–619,
doi:10.1007/978-3-642-39212-2_53.
short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 40th International Colloquium
on Automata, Languages, and Programming, Springer Nature, 2013, pp. 607–619.
conference:
end_date: 2013-07-12
location: Riga, Latvia
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2013-07-08
date_created: 2022-08-11T11:25:13Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2023-02-21T16:28:26Z
day: '01'
doi: 10.1007/978-3-642-39212-2_53
extern: '1'
external_id:
arxiv:
- '1512.08147'
intvolume: ' 7966'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1512.08147
month: '07'
oa: 1
oa_version: Preprint
page: 607–619
publication: 40th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783642392115'
issn:
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '11793'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Sublinear-time maintenance of breadth-first spanning tree in partially dynamic
networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7966
year: '2013'
...
---
_id: '11856'
abstract:
- lang: eng
text: 'We study dynamic (1 + ϵ)-approximation algorithms for the all-pairs shortest
paths problem in unweighted undirected n-node m-edge graphs under edge deletions.
The fastest algorithm for this problem is a randomized algorithm with a total
update time of Ȏ(mn) and constant query time by Roditty and Zwick (FOCS 2004).
The fastest deterministic algorithm is from a 1981 paper by Even and Shiloach
(JACM 1981); it has a total update time of O(mn 2 ) and constant query time. We
improve these results as follows: (1) We present an algorithm with a total update
time of Ȏ(n 5/2 ) and constant query time that has an additive error of two in
addition to the 1 + ϵ multiplicative error. This beats the previous Ȏ(mn) time
when m = Ω(n 3/2 ). Note that the additive error is unavoidable since, even in
the static case, an O(n 3-δ )-time (a so-called truly sub cubic) combinatorial
algorithm with 1 + ϵ multiplicative error cannot have an additive error less than
2 - ϵ, unless we make a major breakthrough for Boolean matrix multiplication (Dor,
Halperin and Zwick FOCS 1996) and many other long-standing problems (Vassilevska
Williams and Williams FOCS 2010). The algorithm can also be turned into a (2 +
ϵ)-approximation algorithm (without an additive error) with the same time guarantees,
improving the recent (3 + ϵ)-approximation algorithm with Ȏ(n 5/2+O(1√(log n))
) running time of Bernstein and Roditty (SODA 2011) in terms of both approximation
and time guarantees. (2) We present a deterministic algorithm with a total update
time of Ȏ(mn) and a query time of O(log log n). The algorithm has a multiplicative
error of 1 + ϵ and gives the first improved deterministic algorithm since 1981.
It also answers an open question raised by Bernstein in his STOC 2013 paper. In
order to achieve our results, we introduce two new techniques: (1) A lazy Even-Shiloach
tree algorithm which maintains a bounded-distance shortest-paths tree on a certain
type of emulator called locally persevering emulator. (2) A derandomization technique
based on moving Even-Shiloach trees as a way to derandomize the standard random
set argument. These techniques might be of independent interest.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Henzinger MH, Krinninger S, Nanongkai D. Dynamic approximate all-pairs shortest
paths: Breaking the O(mn) barrier and derandomization. In: 54th Annual Symposium
on Foundations of Computer Science. Institute of Electrical and Electronics
Engineers; 2013:538-547. doi:10.1109/focs.2013.64'
apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2013). Dynamic approximate
all-pairs shortest paths: Breaking the O(mn) barrier and derandomization. In 54th
Annual Symposium on Foundations of Computer Science (pp. 538–547). Berkeley,
CA, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/focs.2013.64'
chicago: 'Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Dynamic
Approximate All-Pairs Shortest Paths: Breaking the O(Mn) Barrier and Derandomization.”
In 54th Annual Symposium on Foundations of Computer Science, 538–47. Institute
of Electrical and Electronics Engineers, 2013. https://doi.org/10.1109/focs.2013.64.'
ieee: 'M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Dynamic approximate all-pairs
shortest paths: Breaking the O(mn) barrier and derandomization,” in 54th Annual
Symposium on Foundations of Computer Science, Berkeley, CA, United States,
2013, pp. 538–547.'
ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2013. Dynamic approximate all-pairs
shortest paths: Breaking the O(mn) barrier and derandomization. 54th Annual Symposium
on Foundations of Computer Science. FOCS: Symposium on Foundations of Computer
Science, 538–547.'
mla: 'Henzinger, Monika H., et al. “Dynamic Approximate All-Pairs Shortest Paths:
Breaking the O(Mn) Barrier and Derandomization.” 54th Annual Symposium on Foundations
of Computer Science, Institute of Electrical and Electronics Engineers, 2013,
pp. 538–47, doi:10.1109/focs.2013.64.'
short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 54th Annual Symposium on
Foundations of Computer Science, Institute of Electrical and Electronics Engineers,
2013, pp. 538–547.
conference:
end_date: 2013-10-29
location: Berkeley, CA, United States
name: 'FOCS: Symposium on Foundations of Computer Science'
start_date: 2013-10-26
date_created: 2022-08-16T08:22:37Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2023-02-17T09:56:04Z
day: '01'
doi: 10.1109/focs.2013.64
extern: '1'
external_id:
arxiv:
- '1308.0776'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1308.0776
month: '10'
oa: 1
oa_version: Preprint
page: 538-547
publication: 54th Annual Symposium on Foundations of Computer Science
publication_identifier:
eisbn:
- 978-0-7695-5135-7
issn:
- 0272-5428
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and
derandomization'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '12198'
abstract:
- lang: eng
text: The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes
DNA demethylation before fertilization, but the targeting preferences, mechanism,
and biological significance of this process remain unclear. Here, we show that
active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for
all of the demethylation in the central cell and preferentially targets small,
AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative
cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation
of similar sequences, and lack of DEMETER in vegetative cells causes reduced small
RNA–directed DNA methylation of transposons in sperm. Our results demonstrate
that demethylation in companion cells reinforces transposon methylation in plant
gametes and likely contributes to stable silencing of transposable elements across
generations.
acknowledgement: We thank S. Harmer for assistance with the analysis of histone modifications,
the BioOptics team at the Vienna Biocenter Campus for sorting sperm and vegetative
cell nuclei, K. Slotkin for the LAT52p-amiRNA=GFP plasmid, and G. Drews for the
DD45p-GFP transgenic line. This work was partially funded by an NIH grant (GM69415)
to R.L.F., NSF grants (MCB-0918821 and IOS-1025890) to R.L.F. and D.Z., a Young
Investigator Grant from the Arnold and Mabel Beckman Foundation to D.Z., an Austrian
Science Fund (FWF) grant P21389-B03 to H.T., a Ruth L. Kirschstein NIH Predoctoral
Fellowship (GM093633) to C.A.I., a Fulbright Scholarship to J.A.R., a fellowship
from the Jane Coffin Childs Memorial Fund to A.Z., and a Robert and Colleen Haas
Scholarship to D.R. Sequencing data are deposited in GEO (GSE38935).
article_processing_charge: No
article_type: original
author:
- first_name: Christian A.
full_name: Ibarra, Christian A.
last_name: Ibarra
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Vera K.
full_name: Schoft, Vera K.
last_name: Schoft
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Rie
full_name: Uzawa, Rie
last_name: Uzawa
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Nina
full_name: Chumak, Nina
last_name: Chumak
- first_name: Adriana
full_name: Machlicova, Adriana
last_name: Machlicova
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Denisse
full_name: Rojas, Denisse
last_name: Rojas
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Hisashi
full_name: Tamaru, Hisashi
last_name: Tamaru
- first_name: Daniel
full_name: Zilberman, Daniel
last_name: Zilberman
citation:
ama: Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion
cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364.
doi:10.1126/science.1224839
apa: Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues,
J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells
reinforces transposon methylation in gametes. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.1224839
chicago: Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie
Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in
Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science.
American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839.
ieee: C. A. Ibarra et al., “Active DNA demethylation in plant companion cells
reinforces transposon methylation in gametes,” Science, vol. 337, no. 6100.
American Association for the Advancement of Science, pp. 1360–1364, 2012.
ista: Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A,
Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman
D. 2012. Active DNA demethylation in plant companion cells reinforces transposon
methylation in gametes. Science. 337(6100), 1360–1364.
mla: Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells
Reinforces Transposon Methylation in Gametes.” Science, vol. 337, no. 6100,
American Association for the Advancement of Science, 2012, pp. 1360–64, doi:10.1126/science.1224839.
short: C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues,
A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H.
Tamaru, D. Zilberman, Science 337 (2012) 1360–1364.
date_created: 2023-01-16T09:21:24Z
date_published: 2012-09-14T00:00:00Z
date_updated: 2023-10-16T09:27:26Z
day: '14'
department:
- _id: XiFe
doi: 10.1126/science.1224839
external_id:
pmid:
- '22984074'
intvolume: ' 337'
issue: '6100'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/
month: '09'
oa: 1
oa_version: Published Version
page: 1360-1364
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Active DNA demethylation in plant companion cells reinforces transposon methylation
in gametes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 337
year: '2012'
...
---
_id: '12644'
abstract:
- lang: eng
text: In the Dry Andes of central Chile, summer water resources originate mostly
from snowmelt and ice melt. We use the physically based, spatially distributed
hydrological model TOPKAPI to study the exchange between glaciers and climate
in the upper Aconcagua River Basin during the summer season and identify the model
parameters that are robust and transferable and those that are more dependent
on calibration. TOPKAPI has recently been adapted to incorporate an enhanced temperature
index approach for snow and ice melting. We suggest a calibration procedure that
allows calibration of parameters in three steps by separating parameters governing
distinct processes. We evaluate the parameters' transferability in time and in
space by applying the model at two spatial scales. TOPKAPI's ability to simulate
the relevant processes is tested against meteorological, ablation, and glacier
runoff data measured on Juncal Norte Glacier during two glacier ablation seasons.
The model was applied successfully to the climatic setting of the Dry Andes once
its parameters were recalibrated. We found a clear distinction between parameters
that are stable in time and those that need recalibration. The parameters of the
melt model are transferable from one season to the other, while the parameters
governing the extrapolation of meteorological input data and the routing of glacier
meltwater need recalibration from one season to the other. Sensitivity analysis
revealed that the model is most sensitive to the temperature lapse rate governing
the extrapolation of air temperature from point measurements to the glacier scale
and to the melt parameter that multiplies the shortwave radiation balance.
article_number: W03509
article_processing_charge: No
article_type: original
author:
- first_name: S.
full_name: Ragettli, S.
last_name: Ragettli
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: 'Ragettli S, Pellicciotti F. Calibration of a physically based, spatially distributed
hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological
processes to constrain model parameters. Water Resources Research. 2012;48(3).
doi:10.1029/2011wr010559'
apa: 'Ragettli, S., & Pellicciotti, F. (2012). Calibration of a physically based,
spatially distributed hydrological model in a glacierized basin: On the use of
knowledge from glaciometeorological processes to constrain model parameters. Water
Resources Research. American Geophysical Union. https://doi.org/10.1029/2011wr010559'
chicago: 'Ragettli, S., and Francesca Pellicciotti. “Calibration of a Physically
Based, Spatially Distributed Hydrological Model in a Glacierized Basin: On the
Use of Knowledge from Glaciometeorological Processes to Constrain Model Parameters.”
Water Resources Research. American Geophysical Union, 2012. https://doi.org/10.1029/2011wr010559.'
ieee: 'S. Ragettli and F. Pellicciotti, “Calibration of a physically based, spatially
distributed hydrological model in a glacierized basin: On the use of knowledge
from glaciometeorological processes to constrain model parameters,” Water Resources
Research, vol. 48, no. 3. American Geophysical Union, 2012.'
ista: 'Ragettli S, Pellicciotti F. 2012. Calibration of a physically based, spatially
distributed hydrological model in a glacierized basin: On the use of knowledge
from glaciometeorological processes to constrain model parameters. Water Resources
Research. 48(3), W03509.'
mla: 'Ragettli, S., and Francesca Pellicciotti. “Calibration of a Physically Based,
Spatially Distributed Hydrological Model in a Glacierized Basin: On the Use of
Knowledge from Glaciometeorological Processes to Constrain Model Parameters.”
Water Resources Research, vol. 48, no. 3, W03509, American Geophysical
Union, 2012, doi:10.1029/2011wr010559.'
short: S. Ragettli, F. Pellicciotti, Water Resources Research 48 (2012).
date_created: 2023-02-20T08:17:39Z
date_published: 2012-03-01T00:00:00Z
date_updated: 2023-02-21T09:38:36Z
day: '01'
doi: 10.1029/2011wr010559
extern: '1'
intvolume: ' 48'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1029/2011WR010559
month: '03'
oa: 1
oa_version: Published Version
publication: Water Resources Research
publication_identifier:
issn:
- 0043-1397
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Calibration of a physically based, spatially distributed hydrological model
in a glacierized basin: On the use of knowledge from glaciometeorological processes
to constrain model parameters'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2012'
...
---
_id: '12646'
abstract:
- lang: eng
text: Assessment of water resources from remote mountainous catchments plays a crucial
role for the development of rural areas in or in the vicinity of mountain ranges.
The scarcity of data, however, prevents the application of standard approaches
that are based on data-driven models. The Hindu Kush–Karakoram–Himalaya mountain
range is a crucial area in terms of water resources, but our understanding of
the response of its high-elevation catchments to a changing climate is hindered
by lack of hydro-meteorological and cryospheric data. Hydrological modeling is
challenging here because internal inconsistencies—such as an underestimation of
precipitation input that can be compensated for by an overestimation of meltwater—might
be hidden due to the complexity of feedback mechanisms that govern melt and runoff
generation in such basins. Data scarcity adds to this difficulty by preventing
the application of systematic calibration procedures that would allow identification
of the parameter set that could guarantee internal consistency in the simulation
of the single hydrological components. In this work, we use simulations from the
Hunza River Basin in the Karakoram region obtained with the hydrological model
TOPKAPI to quantify the predictive power of discharge and snow-cover data sets,
as well as the combination of both. We also show that short-term measurements
of meteorological variables such as radiative fluxes, wind speed, relative humidity,
and air temperature from glacio-meteorological experiments are crucial for a correct
parameterization of surface melt processes. They enable detailed simulations of
the energy fluxes governing glacier–atmosphere interaction and the resulting ablation
through energy-balance modeling. These simulations are used to derive calibrated
parameters for the simplified snow and glacier routines in TOPKAPI. We demonstrate
that such parameters are stable in space and time in similar climatic regions,
thus reducing the number of parameters requiring calibration.
article_processing_charge: No
article_type: original
author:
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Cyrill
full_name: Buergi, Cyrill
last_name: Buergi
- first_name: Walter Willem
full_name: Immerzeel, Walter Willem
last_name: Immerzeel
- first_name: Markus
full_name: Konz, Markus
last_name: Konz
- first_name: Arun B.
full_name: Shrestha, Arun B.
last_name: Shrestha
citation:
ama: 'Pellicciotti F, Buergi C, Immerzeel WW, Konz M, Shrestha AB. Challenges and
uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan
(HKH) basins: Suggestions for calibration strategies. Mountain Research and
Development. 2012;32(1):39-50. doi:10.1659/mrd-journal-d-11-00092.1'
apa: 'Pellicciotti, F., Buergi, C., Immerzeel, W. W., Konz, M., & Shrestha,
A. B. (2012). Challenges and uncertainties in hydrological modeling of remote
Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies.
Mountain Research and Development. International Mountain Society. https://doi.org/10.1659/mrd-journal-d-11-00092.1'
chicago: 'Pellicciotti, Francesca, Cyrill Buergi, Walter Willem Immerzeel, Markus
Konz, and Arun B. Shrestha. “Challenges and Uncertainties in Hydrological Modeling
of Remote Hindu Kush–Karakoram–Himalayan (HKH) Basins: Suggestions for Calibration
Strategies.” Mountain Research and Development. International Mountain
Society, 2012. https://doi.org/10.1659/mrd-journal-d-11-00092.1.'
ieee: 'F. Pellicciotti, C. Buergi, W. W. Immerzeel, M. Konz, and A. B. Shrestha,
“Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan
(HKH) basins: Suggestions for calibration strategies,” Mountain Research and
Development, vol. 32, no. 1. International Mountain Society, pp. 39–50, 2012.'
ista: 'Pellicciotti F, Buergi C, Immerzeel WW, Konz M, Shrestha AB. 2012. Challenges
and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan
(HKH) basins: Suggestions for calibration strategies. Mountain Research and Development.
32(1), 39–50.'
mla: 'Pellicciotti, Francesca, et al. “Challenges and Uncertainties in Hydrological
Modeling of Remote Hindu Kush–Karakoram–Himalayan (HKH) Basins: Suggestions for
Calibration Strategies.” Mountain Research and Development, vol. 32, no.
1, International Mountain Society, 2012, pp. 39–50, doi:10.1659/mrd-journal-d-11-00092.1.'
short: F. Pellicciotti, C. Buergi, W.W. Immerzeel, M. Konz, A.B. Shrestha, Mountain
Research and Development 32 (2012) 39–50.
date_created: 2023-02-20T08:17:47Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2023-02-21T09:31:54Z
day: '01'
doi: 10.1659/mrd-journal-d-11-00092.1
extern: '1'
intvolume: ' 32'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1659/MRD-JOURNAL-D-11-00092.1
month: '02'
oa: 1
oa_version: Published Version
page: 39-50
publication: Mountain Research and Development
publication_identifier:
eissn:
- 1994-7151
issn:
- 0276-4741
publication_status: published
publisher: International Mountain Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan
(HKH) basins: Suggestions for calibration strategies'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2012'
...