---
_id: '863'
abstract:
- lang: eng
text: The origins of neural systems remain unresolved. In contrast to other basal
metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived
muscular systems. These holoplanktonic predators also have sophisticated ciliated
locomotion, behaviour and distinct development. Here we present the draft genome
of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore
transcriptomes, and show that they are remarkably distinct from other animal genomes
in their content of neurogenic, immune and developmental genes. Our integrative
analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis
is supported by comparative analysis of multiple gene families, including the
apparent absence of HOX genes, canonical microRNA machinery, and reduced immune
complement in ctenophores. Although two distinct nervous systems are well recognized
in ctenophores, many bilaterian neuron-specific genes and genes of 'classical'
neurotransmitter pathways either are absent or, if present, are not expressed
in neurons. Our metabolomic and physiological data are consistent with the hypothesis
that ctenophore neural systems, and possibly muscle specification, evolved independently
from those in other animals.
acknowledgement: We thank Friday Harbor Laboratories for facilities during animal
collection and Marine Genomics apprenticeships (L.L.M., B.J.S.); E. Dabe, G. Winters,
J. Netherton, N. Churches and C. Bostwick for help with animal, tissue, in situ,
RNA and DNA assays; and X.-X. Tan, F. Lu and T. Tyazelova for sequencing. We thank
F. Nivens for videos and P. L. Williams for database support. This work was supported
by NSF (NSF-0744649 and NSF CNS-0821622 to L.L.M.; NSF CHE-1111705 to J.V.S.), NIH
(1R01GM097502, R01MH097062, R21RR025699 and 5R21DA030118 to L.L.M.; P30 DA018310
to J.V.S.; R01 AG029360 and 1S10RR027052 to E.I.R.), NASA NNX13AJ31G (to K.M.H.,
L.L.M. and K.M.K.), NSERC 458115 and 211598 (J.P.R.), University of Florida Opportunity
Funds/McKnight Brain Research and Florida Biodiversity Institute (L.L.M.), Rostock
Inc./A.V. Chikunov (E.I.R.), grant from Russian Federation Government 14.B25.31.0033
(Resolution No.220) (E.I.R.). F.A.K., I.S.P. and R.D. were supported by HHMI (55007424),
EMBO and MINECO (BFU2012-31329 and Sev-2012-0208). Contributions of AU Marine Biology
Program 117 and Molette laboratory 22.
author:
- first_name: Leonid
full_name: Moroz, Leonid L
last_name: Moroz
- first_name: Kevin
full_name: Kocot, Kevin M
last_name: Kocot
- first_name: Mathew
full_name: Citarella, Mathew R
last_name: Citarella
- first_name: Sohn
full_name: Dosung, Sohn
last_name: Dosung
- first_name: Tigran
full_name: Norekian, Tigran P
last_name: Norekian
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Anastasia
full_name: Grigorenko, Anastasia P
last_name: Grigorenko
- first_name: Christopher
full_name: Dailey, Christopher A
last_name: Dailey
- first_name: Eugene
full_name: Berezikov, Eugene
last_name: Berezikov
- first_name: Katherine
full_name: Buckley, Katherine M
last_name: Buckley
- first_name: Andrey
full_name: Ptitsyn, Andrey A
last_name: Ptitsyn
- first_name: Denis
full_name: Reshetov, Denis A
last_name: Reshetov
- first_name: Krishanu
full_name: Mukherjee, Krishanu
last_name: Mukherjee
- first_name: Tatiana
full_name: Moroz, Tatiana P
last_name: Moroz
- first_name: Yelena
full_name: Bobkova, Yelena V
last_name: Bobkova
- first_name: Fahong
full_name: Yu, Fahong
last_name: Yu
- first_name: Vladimir
full_name: Kapitonov, Vladimir V
last_name: Kapitonov
- first_name: Jerzy
full_name: Jurka, Jerzy W
last_name: Jurka
- first_name: Yuriy
full_name: Bobkov, Yuriy V
last_name: Bobkov
- first_name: Joshua
full_name: Swore, Joshua J
last_name: Swore
- first_name: David
full_name: Girardo, David O
last_name: Girardo
- first_name: Alexander
full_name: Fodor, Alexander
last_name: Fodor
- first_name: Fedor
full_name: Gusev, Fedor E
last_name: Gusev
- first_name: Rachel
full_name: Sanford, Rachel S
last_name: Sanford
- first_name: Rebecca
full_name: Bruders, Rebecca
last_name: Bruders
- first_name: Ellen
full_name: Kittler, Ellen L
last_name: Kittler
- first_name: Claudia
full_name: Mills, Claudia E
last_name: Mills
- first_name: Jonathan
full_name: Rast, Jonathan P
last_name: Rast
- first_name: Romain
full_name: Derelle, Romain
last_name: Derelle
- first_name: Victor
full_name: Solovyev, Victor
last_name: Solovyev
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Billie
full_name: Swalla, Billie J
last_name: Swalla
- first_name: Jonathan
full_name: Sweedler, Jonathan V
last_name: Sweedler
- first_name: Evgeny
full_name: Rogaev, Evgeny I
last_name: Rogaev
- first_name: Kenneth
full_name: Halanych, Kenneth M
last_name: Halanych
- first_name: Andrea
full_name: Kohn, Andrea B
last_name: Kohn
citation:
ama: Moroz L, Kocot K, Citarella M, et al. The ctenophore genome and the evolutionary
origins of neural systems. Nature. 2014;510(7503):109-114. doi:10.1038/nature13400
apa: Moroz, L., Kocot, K., Citarella, M., Dosung, S., Norekian, T., Povolotskaya,
I., … Kohn, A. (2014). The ctenophore genome and the evolutionary origins of neural
systems. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13400
chicago: Moroz, Leonid, Kevin Kocot, Mathew Citarella, Sohn Dosung, Tigran Norekian,
Inna Povolotskaya, Anastasia Grigorenko, et al. “The Ctenophore Genome and the
Evolutionary Origins of Neural Systems.” Nature. Nature Publishing Group,
2014. https://doi.org/10.1038/nature13400.
ieee: L. Moroz et al., “The ctenophore genome and the evolutionary origins
of neural systems,” Nature, vol. 510, no. 7503. Nature Publishing Group,
pp. 109–114, 2014.
ista: Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko
A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz
T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor
A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev
V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The
ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503),
109–114.
mla: Moroz, Leonid, et al. “The Ctenophore Genome and the Evolutionary Origins of
Neural Systems.” Nature, vol. 510, no. 7503, Nature Publishing Group, 2014,
pp. 109–14, doi:10.1038/nature13400.
short: L. Moroz, K. Kocot, M. Citarella, S. Dosung, T. Norekian, I. Povolotskaya,
A. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, A. Ptitsyn, D. Reshetov, K.
Mukherjee, T. Moroz, Y. Bobkova, F. Yu, V. Kapitonov, J. Jurka, Y. Bobkov, J.
Swore, D. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C.
Mills, J. Rast, R. Derelle, V. Solovyev, F. Kondrashov, B. Swalla, J. Sweedler,
E. Rogaev, K. Halanych, A. Kohn, Nature 510 (2014) 109–114.
date_created: 2018-12-11T11:48:54Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:21Z
day: '01'
doi: 10.1038/nature13400
extern: 1
intvolume: ' 510'
issue: '7503'
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '01'
page: 109 - 114
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6785'
quality_controlled: 0
status: public
title: The ctenophore genome and the evolutionary origins of neural systems
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
volume: 510
year: '2014'
...
---
_id: '865'
abstract:
- lang: eng
text: Research on existing drugs often discovers novel mechanisms of their action
and leads to the expansion of their therapeutic scope and subsequent remarketing.
The Wnt signaling pathway is of the immediate therapeutic relevance, as it plays
critical roles in cancer development and progression. However, drugs which disrupt
this pathway are unavailable despite the high demand. Here we report an attempt
to identify antagonists of the Wnt-FZD interaction among the library of the FDA-approved
drugs. We performed an in silico screening which brought up several potential
antagonists of the ligand-receptor interaction. 14 of these substances were tested
using the TopFlash luciferase reporter assay and four of them identified as active
and specific inhibitors of the Wnt3a-induced signaling. However, further analysis
through GTP-binding and β-catenin stabilization assays showed that the compounds
do not target the Wnt-FZD pair, but inhibit the signaling at downstream levels.
We further describe the previously unknown inhibitory activity of an anti-leprosy
drug clofazimine in the Wnt pathway and provide data demonstrating its efficiency
in suppressing growth of Wnt-dependent triple-negative breast cancer cells. These
data provide a basis for further investigations of the efficiency of clofazimine
in treatment of Wnt-dependent cancers.
author:
- first_name: Alexey
full_name: Koval, Alexey V
last_name: Koval
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Polina
full_name: Shichkova, Polina
last_name: Shichkova
- first_name: S
full_name: Khunderyakova, S
last_name: Khunderyakova
- first_name: Yury
full_name: Markov, Yury
last_name: Markov
- first_name: J
full_name: Panchenko, J
last_name: Panchenko
- first_name: A
full_name: Volodina, A
last_name: Volodina
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Vladimir
full_name: Katanaev, Vladimir L
last_name: Katanaev
citation:
ama: Koval A, Vlasov P, Shichkova P, et al. Anti leprosy drug clofazimine inhibits
growth of triple-negative breast cancer cells via inhibition of canonical Wnt
signaling. Biochemical Pharmacology. 2014;87(4):571-578. doi:10.1016/j.bcp.2013.12.007
apa: Koval, A., Vlasov, P., Shichkova, P., Khunderyakova, S., Markov, Y., Panchenko,
J., … Katanaev, V. (2014). Anti leprosy drug clofazimine inhibits growth of triple-negative
breast cancer cells via inhibition of canonical Wnt signaling. Biochemical
Pharmacology. Elsevier. https://doi.org/10.1016/j.bcp.2013.12.007
chicago: Koval, Alexey, Peter Vlasov, Polina Shichkova, S Khunderyakova, Yury Markov,
J Panchenko, A Volodina, Fyodor Kondrashov, and Vladimir Katanaev. “Anti Leprosy
Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition
of Canonical Wnt Signaling.” Biochemical Pharmacology. Elsevier, 2014.
https://doi.org/10.1016/j.bcp.2013.12.007.
ieee: A. Koval et al., “Anti leprosy drug clofazimine inhibits growth of
triple-negative breast cancer cells via inhibition of canonical Wnt signaling,”
Biochemical Pharmacology, vol. 87, no. 4. Elsevier, pp. 571–578, 2014.
ista: Koval A, Vlasov P, Shichkova P, Khunderyakova S, Markov Y, Panchenko J, Volodina
A, Kondrashov F, Katanaev V. 2014. Anti leprosy drug clofazimine inhibits growth
of triple-negative breast cancer cells via inhibition of canonical Wnt signaling.
Biochemical Pharmacology. 87(4), 571–578.
mla: Koval, Alexey, et al. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative
Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical
Pharmacology, vol. 87, no. 4, Elsevier, 2014, pp. 571–78, doi:10.1016/j.bcp.2013.12.007.
short: A. Koval, P. Vlasov, P. Shichkova, S. Khunderyakova, Y. Markov, J. Panchenko,
A. Volodina, F. Kondrashov, V. Katanaev, Biochemical Pharmacology 87 (2014) 571–578.
date_created: 2018-12-11T11:48:55Z
date_published: 2014-02-15T00:00:00Z
date_updated: 2021-01-12T08:20:24Z
day: '15'
doi: 10.1016/j.bcp.2013.12.007
extern: 1
intvolume: ' 87'
issue: '4'
month: '02'
page: 571 - 578
publication: Biochemical Pharmacology
publication_status: published
publisher: Elsevier
publist_id: '6782'
quality_controlled: 0
status: public
title: Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer
cells via inhibition of canonical Wnt signaling
type: journal_article
volume: 87
year: '2014'
...
---
_id: '892'
abstract:
- lang: eng
text: The study of molecular evolution is important because it reveals how protein
functions emerge and evolve. Recently, several types of studies indicated that
substitutions in molecular evolution occur in a compensatory manner, whereby the
occurrence of a substitution depends on the amino acid residues at other sites.
However, a molecular or structural basis behind the compensation often remains
obscure. Here, we review studies on the interface of structural biology and molecular
evolution that revealed novel aspects of compensatory evolution. In many cases
structural studies benefit from evolutionary data while structural data often
add a functional dimension to the study of molecular evolution.
acknowledgement: |
The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)’ and (BFU2012-31329), the European Union and the European Research Council grant (335980_EinME), RFBR (13-04-00253a), MCB RAS (01201358029) and MES RK Grants.
author:
- first_name: Dmitry
full_name: Ivankov, Dmitry N
last_name: Ivankov
- first_name: Alexei
full_name: Finkelstein, Alexei V
last_name: Finkelstein
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Ivankov D, Finkelstein A, Kondrashov F. A structural perspective of compensatory
evolution. Current Opinion in Structural Biology. 2014;26(1):104-112. doi:10.1016/j.sbi.2014.05.004
apa: Ivankov, D., Finkelstein, A., & Kondrashov, F. (2014). A structural perspective
of compensatory evolution. Current Opinion in Structural Biology. Elsevier.
https://doi.org/10.1016/j.sbi.2014.05.004
chicago: Ivankov, Dmitry, Alexei Finkelstein, and Fyodor Kondrashov. “A Structural
Perspective of Compensatory Evolution.” Current Opinion in Structural Biology.
Elsevier, 2014. https://doi.org/10.1016/j.sbi.2014.05.004.
ieee: D. Ivankov, A. Finkelstein, and F. Kondrashov, “A structural perspective of
compensatory evolution,” Current Opinion in Structural Biology, vol. 26,
no. 1. Elsevier, pp. 104–112, 2014.
ista: Ivankov D, Finkelstein A, Kondrashov F. 2014. A structural perspective of
compensatory evolution. Current Opinion in Structural Biology. 26(1), 104–112.
mla: Ivankov, Dmitry, et al. “A Structural Perspective of Compensatory Evolution.”
Current Opinion in Structural Biology, vol. 26, no. 1, Elsevier, 2014,
pp. 104–12, doi:10.1016/j.sbi.2014.05.004.
short: D. Ivankov, A. Finkelstein, F. Kondrashov, Current Opinion in Structural
Biology 26 (2014) 104–112.
date_created: 2018-12-11T11:49:03Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2021-01-12T08:21:21Z
day: '01'
doi: 10.1016/j.sbi.2014.05.004
extern: 1
intvolume: ' 26'
issue: '1'
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '06'
page: 104 - 112
publication: Current Opinion in Structural Biology
publication_status: published
publisher: Elsevier
publist_id: '6756'
quality_controlled: 0
status: public
title: A structural perspective of compensatory evolution
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
volume: 26
year: '2014'
...
---
_id: '1629'
abstract:
- lang: eng
text: We propose a method for propagating edit operations in 2D vector graphics,
based on geometric relationship functions. These functions quantify the geometric
relationship of a point to a polygon, such as the distance to the boundary or
the direction to the closest corner vertex. The level sets of the relationship
functions describe points with the same relationship to a polygon. For a given
query point, we first determine a set of relationships to local features, construct
all level sets for these relationships, and accumulate them. The maxima of the
resulting distribution are points with similar geometric relationships. We show
extensions to handle mirror symmetries, and discuss the use of relationship functions
as local coordinate systems. Our method can be applied, for example, to interactive
floorplan editing, and it is especially useful for large layouts, where individual
edits would be cumbersome. We demonstrate populating 2D layouts with tens to hundreds
of objects by propagating relatively few edit operations.
article_number: '15'
author:
- first_name: Paul
full_name: Guerrero, Paul
last_name: Guerrero
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Michael
full_name: Wimmer, Michael
last_name: Wimmer
- first_name: Peter
full_name: Wonka, Peter
last_name: Wonka
citation:
ama: Guerrero P, Jeschke S, Wimmer M, Wonka P. Edit propagation using geometric
relationship functions. ACM Transactions on Graphics. 2014;33(2). doi:10.1145/2591010
apa: Guerrero, P., Jeschke, S., Wimmer, M., & Wonka, P. (2014). Edit propagation
using geometric relationship functions. ACM Transactions on Graphics. ACM.
https://doi.org/10.1145/2591010
chicago: Guerrero, Paul, Stefan Jeschke, Michael Wimmer, and Peter Wonka. “Edit
Propagation Using Geometric Relationship Functions.” ACM Transactions on Graphics.
ACM, 2014. https://doi.org/10.1145/2591010.
ieee: P. Guerrero, S. Jeschke, M. Wimmer, and P. Wonka, “Edit propagation using
geometric relationship functions,” ACM Transactions on Graphics, vol. 33,
no. 2. ACM, 2014.
ista: Guerrero P, Jeschke S, Wimmer M, Wonka P. 2014. Edit propagation using geometric
relationship functions. ACM Transactions on Graphics. 33(2), 15.
mla: Guerrero, Paul, et al. “Edit Propagation Using Geometric Relationship Functions.”
ACM Transactions on Graphics, vol. 33, no. 2, 15, ACM, 2014, doi:10.1145/2591010.
short: P. Guerrero, S. Jeschke, M. Wimmer, P. Wonka, ACM Transactions on Graphics
33 (2014).
date_created: 2018-12-11T11:53:08Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2021-01-12T06:52:06Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2591010
file:
- access_level: open_access
checksum: 7f91e588a4e888610313b98271e6418e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:22Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4876'
file_name: IST-2016-577-v1+1_2014.TOG.Paul.EditingPropagation.final.pdf
file_size: 9832561
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 33'
issue: '2'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '5526'
pubrep_id: '577'
quality_controlled: '1'
status: public
title: Edit propagation using geometric relationship functions
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2014'
...
---
_id: '1643'
abstract:
- lang: eng
text: We extend the notion of verifiable random functions (VRF) to constrained VRFs,
which generalize the concept of constrained pseudorandom functions, put forward
by Boneh and Waters (Asiacrypt’13), and independently by Kiayias et al. (CCS’13)
and Boyle et al. (PKC’14), who call them delegatable PRFs and functional PRFs,
respectively. In a standard VRF the secret key sk allows one to evaluate a pseudorandom
function at any point of its domain; in addition, it enables computation of a
non-interactive proof that the function value was computed correctly. In a constrained
VRF from the key sk one can derive constrained keys skS for subsets S of the domain,
which allow computation of function values and proofs only at points in S. After
formally defining constrained VRFs, we derive instantiations from the multilinear-maps-based
constrained PRFs by Boneh and Waters, yielding a VRF with constrained keys for
any set that can be decided by a polynomial-size circuit. Our VRFs have the same
function values as the Boneh-Waters PRFs and are proved secure under the same
hardness assumption, showing that verifiability comes at no cost. Constrained
(functional) VRFs were stated as an open problem by Boyle et al.
alternative_title:
- LNCS
author:
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
citation:
ama: 'Fuchsbauer G. Constrained Verifiable Random Functions . In: Abdalla M, De
Prisco R, eds. SCN 2014. Vol 8642. Springer; 2014:95-114. doi:10.1007/978-3-319-10879-7_7'
apa: 'Fuchsbauer, G. (2014). Constrained Verifiable Random Functions . In M. Abdalla
& R. De Prisco (Eds.), SCN 2014 (Vol. 8642, pp. 95–114). Amalfi, Italy:
Springer. https://doi.org/10.1007/978-3-319-10879-7_7'
chicago: Fuchsbauer, Georg. “Constrained Verifiable Random Functions .” In SCN
2014, edited by Michel Abdalla and Roberto De Prisco, 8642:95–114. Springer,
2014. https://doi.org/10.1007/978-3-319-10879-7_7.
ieee: G. Fuchsbauer, “Constrained Verifiable Random Functions ,” in SCN 2014,
Amalfi, Italy, 2014, vol. 8642, pp. 95–114.
ista: 'Fuchsbauer G. 2014. Constrained Verifiable Random Functions . SCN 2014. SCN:
Security and Cryptography for Networks, LNCS, vol. 8642, 95–114.'
mla: Fuchsbauer, Georg. “Constrained Verifiable Random Functions .” SCN 2014,
edited by Michel Abdalla and Roberto De Prisco, vol. 8642, Springer, 2014, pp.
95–114, doi:10.1007/978-3-319-10879-7_7.
short: G. Fuchsbauer, in:, M. Abdalla, R. De Prisco (Eds.), SCN 2014, Springer,
2014, pp. 95–114.
conference:
end_date: 2014-09-05
location: Amalfi, Italy
name: 'SCN: Security and Cryptography for Networks'
start_date: 2014-09-03
date_created: 2018-12-11T11:53:13Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:12Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-319-10879-7_7
ec_funded: 1
editor:
- first_name: Michel
full_name: Abdalla, Michel
last_name: Abdalla
- first_name: Roberto
full_name: De Prisco, Roberto
last_name: De Prisco
intvolume: ' 8642'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprint.iacr.org/2014/537
month: '01'
oa: 1
oa_version: Submitted Version
page: 95 - 114
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: SCN 2014
publication_status: published
publisher: Springer
publist_id: '5509'
scopus_import: 1
status: public
title: 'Constrained Verifiable Random Functions '
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8642
year: '2014'
...
---
_id: '1702'
abstract:
- lang: eng
text: In this paper we present INTERHORN, a solver for recursion-free Horn clauses.
The main application domain of INTERHORN lies in solving interpolation problems
arising in software verification. We show how a range of interpolation problems,
including path, transition, nested, state/transition and well-founded interpolation
can be handled directly by INTERHORN. By detailing these interpolation problems
and their Horn clause representations, we hope to encourage the emergence of a
common back-end interpolation interface useful for diverse verification tools.
alternative_title:
- EPTCS
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Corneliu
full_name: Popeea, Corneliu
last_name: Popeea
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
citation:
ama: 'Gupta A, Popeea C, Rybalchenko A. Generalised interpolation by solving recursion
free-horn clauses. In: Electronic Proceedings in Theoretical Computer Science,
EPTCS. Vol 169. Open Publishing; 2014:31-38. doi:10.4204/EPTCS.169.5'
apa: 'Gupta, A., Popeea, C., & Rybalchenko, A. (2014). Generalised interpolation
by solving recursion free-horn clauses. In Electronic Proceedings in Theoretical
Computer Science, EPTCS (Vol. 169, pp. 31–38). Vienna, Austria: Open Publishing.
https://doi.org/10.4204/EPTCS.169.5'
chicago: Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Generalised
Interpolation by Solving Recursion Free-Horn Clauses.” In Electronic Proceedings
in Theoretical Computer Science, EPTCS, 169:31–38. Open Publishing, 2014.
https://doi.org/10.4204/EPTCS.169.5.
ieee: A. Gupta, C. Popeea, and A. Rybalchenko, “Generalised interpolation by solving
recursion free-horn clauses,” in Electronic Proceedings in Theoretical Computer
Science, EPTCS, Vienna, Austria, 2014, vol. 169, pp. 31–38.
ista: 'Gupta A, Popeea C, Rybalchenko A. 2014. Generalised interpolation by solving
recursion free-horn clauses. Electronic Proceedings in Theoretical Computer Science,
EPTCS. HCVS: Horn Clauses for Verification and Synthesis, EPTCS, vol. 169, 31–38.'
mla: Gupta, Ashutosh, et al. “Generalised Interpolation by Solving Recursion Free-Horn
Clauses.” Electronic Proceedings in Theoretical Computer Science, EPTCS,
vol. 169, Open Publishing, 2014, pp. 31–38, doi:10.4204/EPTCS.169.5.
short: A. Gupta, C. Popeea, A. Rybalchenko, in:, Electronic Proceedings in Theoretical
Computer Science, EPTCS, Open Publishing, 2014, pp. 31–38.
conference:
end_date: 2014-07-17
location: Vienna, Austria
name: 'HCVS: Horn Clauses for Verification and Synthesis'
start_date: 2014-07-17
date_created: 2018-12-11T11:53:33Z
date_published: 2014-12-02T00:00:00Z
date_updated: 2021-01-12T06:52:38Z
day: '02'
department:
- _id: ToHe
doi: 10.4204/EPTCS.169.5
intvolume: ' 169'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1303.7378v2
month: '12'
oa: 1
oa_version: Submitted Version
page: 31 - 38
publication: Electronic Proceedings in Theoretical Computer Science, EPTCS
publication_status: published
publisher: Open Publishing
publist_id: '5435'
quality_controlled: '1'
status: public
title: Generalised interpolation by solving recursion free-horn clauses
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 169
year: '2014'
...
---
_id: '1708'
abstract:
- lang: eng
text: It has been long argued that, because of inherent ambiguity and noise, the
brain needs to represent uncertainty in the form of probability distributions.
The neural encoding of such distributions remains however highly controversial.
Here we present a novel circuit model for representing multidimensional real-valued
distributions using a spike based spatio-temporal code. Our model combines the
computational advantages of the currently competing models for probabilistic codes
and exhibits realistic neural responses along a variety of classic measures. Furthermore,
the model highlights the challenges associated with interpreting neural activity
in relation to behavioral uncertainty and points to alternative population-level
approaches for the experimental validation of distributed representations.
author:
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
- first_name: Sophie
full_name: Denève, Sophie
last_name: Denève
citation:
ama: 'Savin C, Denève S. Spatio-temporal representations of uncertainty in spiking
neural networks. In: Vol 3. Neural Information Processing Systems; 2014:2024-2032.'
apa: 'Savin, C., & Denève, S. (2014). Spatio-temporal representations of uncertainty
in spiking neural networks (Vol. 3, pp. 2024–2032). Presented at the NIPS: Neural
Information Processing Systems, Montreal, Canada: Neural Information Processing
Systems.'
chicago: Savin, Cristina, and Sophie Denève. “Spatio-Temporal Representations of
Uncertainty in Spiking Neural Networks,” 3:2024–32. Neural Information Processing
Systems, 2014.
ieee: 'C. Savin and S. Denève, “Spatio-temporal representations of uncertainty in
spiking neural networks,” presented at the NIPS: Neural Information Processing
Systems, Montreal, Canada, 2014, vol. 3, no. January, pp. 2024–2032.'
ista: 'Savin C, Denève S. 2014. Spatio-temporal representations of uncertainty in
spiking neural networks. NIPS: Neural Information Processing Systems vol. 3, 2024–2032.'
mla: Savin, Cristina, and Sophie Denève. Spatio-Temporal Representations of Uncertainty
in Spiking Neural Networks. Vol. 3, no. January, Neural Information Processing
Systems, 2014, pp. 2024–32.
short: C. Savin, S. Denève, in:, Neural Information Processing Systems, 2014, pp.
2024–2032.
conference:
end_date: 2014-12-13
location: Montreal, Canada
name: 'NIPS: Neural Information Processing Systems'
start_date: 2014-12-08
date_created: 2018-12-11T11:53:35Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:40Z
day: '01'
department:
- _id: GaTk
intvolume: ' 3'
issue: January
language:
- iso: eng
main_file_link:
- url: http://papers.nips.cc/paper/5343-spatio-temporal-representations-of-uncertainty-in-spiking-neural-networks.pdf
month: '01'
oa_version: None
page: 2024 - 2032
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '5427'
quality_controlled: '1'
scopus_import: 1
status: public
title: Spatio-temporal representations of uncertainty in spiking neural networks
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2014'
...
---
_id: '1733'
abstract:
- lang: eng
text: The classical (boolean) notion of refinement for behavioral interfaces of
system components is the alternating refinement preorder. In this paper, we define
a distance for interfaces, called interface simulation distance. It makes the
alternating refinement preorder quantitative by, intuitively, tolerating errors
(while counting them) in the alternating simulation game. We show that the interface
simulation distance satisfies the triangle inequality, that the distance between
two interfaces does not increase under parallel composition with a third interface,
that the distance between two interfaces can be bounded from above and below by
distances between abstractions of the two interfaces, and how to synthesize an
interface from incompatible requirements. We illustrate the framework, and the
properties of the distances under composition of interfaces, with two case studies.
author:
- first_name: Pavol
full_name: Cerny, Pavol
last_name: Cerny
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
citation:
ama: Cerny P, Chmelik M, Henzinger TA, Radhakrishna A. Interface simulation distances.
Theoretical Computer Science. 2014;560(3):348-363. doi:10.1016/j.tcs.2014.08.019
apa: Cerny, P., Chmelik, M., Henzinger, T. A., & Radhakrishna, A. (2014). Interface
simulation distances. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2014.08.019
chicago: Cerny, Pavol, Martin Chmelik, Thomas A Henzinger, and Arjun Radhakrishna.
“Interface Simulation Distances.” Theoretical Computer Science. Elsevier,
2014. https://doi.org/10.1016/j.tcs.2014.08.019.
ieee: P. Cerny, M. Chmelik, T. A. Henzinger, and A. Radhakrishna, “Interface simulation
distances,” Theoretical Computer Science, vol. 560, no. 3. Elsevier, pp.
348–363, 2014.
ista: Cerny P, Chmelik M, Henzinger TA, Radhakrishna A. 2014. Interface simulation
distances. Theoretical Computer Science. 560(3), 348–363.
mla: Cerny, Pavol, et al. “Interface Simulation Distances.” Theoretical Computer
Science, vol. 560, no. 3, Elsevier, 2014, pp. 348–63, doi:10.1016/j.tcs.2014.08.019.
short: P. Cerny, M. Chmelik, T.A. Henzinger, A. Radhakrishna, Theoretical Computer
Science 560 (2014) 348–363.
date_created: 2018-12-11T11:53:43Z
date_published: 2014-12-04T00:00:00Z
date_updated: 2023-02-23T11:04:00Z
day: '04'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1016/j.tcs.2014.08.019
ec_funded: 1
intvolume: ' 560'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1210.2450
month: '12'
oa: 1
oa_version: Submitted Version
page: 348 - 363
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _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: Theoretical Computer Science
publication_status: published
publisher: Elsevier
publist_id: '5392'
quality_controlled: '1'
related_material:
record:
- id: '2916'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Interface simulation distances
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 560
year: '2014'
...
---
_id: '1761'
abstract:
- lang: eng
text: Metal silicides formed by means of thermal annealing processes are employed
as contact materials in microelectronics. Control of the structure of silicide/silicon
interfaces becomes a critical issue when the characteristic size of the device
is reduced below a few tens of nanometers. Here, we report on silicide clustering
occurring within the channel of PtSi/Si/PtSi Schottky-barrier transistors. This
phenomenon is investigated through atomistic simulations and low-temperature resonant-tunneling
spectroscopy. Our results provide evidence for the segregation of a PtSi cluster
with a diameter of a few nanometers from the silicide contact. The cluster acts
as a metallic quantum dot giving rise to distinct signatures of quantum transport
through its discrete energy states.
acknowledgement: This work was supported by the Agence Nationale de la Recherche and
by the EU through the ERC Starting Grant HybridNano
author:
- first_name: Massimo
full_name: Mongillo, Massimo
last_name: Mongillo
- first_name: Panayotis
full_name: Spathis, Panayotis N
last_name: Spathis
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Silvano
full_name: De Franceschi, Silvano
last_name: De Franceschi
- first_name: Pascal
full_name: Gentile, Pascal
last_name: Gentile
- first_name: Riccardo
full_name: Rurali, Riccardo
last_name: Rurali
- first_name: Xavier
full_name: Cartoixà, Xavier
last_name: Cartoixà
citation:
ama: Mongillo M, Spathis P, Katsaros G, et al. PtSi clustering in silicon probed
by transport spectroscopy. Physical Review X. 2014;3(4). doi:10.1103/PhysRevX.3.041025
apa: Mongillo, M., Spathis, P., Katsaros, G., De Franceschi, S., Gentile, P., Rurali,
R., & Cartoixà, X. (2014). PtSi clustering in silicon probed by transport
spectroscopy. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.3.041025
chicago: Mongillo, Massimo, Panayotis Spathis, Georgios Katsaros, Silvano De Franceschi,
Pascal Gentile, Riccardo Rurali, and Xavier Cartoixà. “PtSi Clustering in Silicon
Probed by Transport Spectroscopy.” Physical Review X. American Physical
Society, 2014. https://doi.org/10.1103/PhysRevX.3.041025.
ieee: M. Mongillo et al., “PtSi clustering in silicon probed by transport
spectroscopy,” Physical Review X, vol. 3, no. 4. American Physical Society,
2014.
ista: Mongillo M, Spathis P, Katsaros G, De Franceschi S, Gentile P, Rurali R, Cartoixà
X. 2014. PtSi clustering in silicon probed by transport spectroscopy. Physical
Review X. 3(4).
mla: Mongillo, Massimo, et al. “PtSi Clustering in Silicon Probed by Transport Spectroscopy.”
Physical Review X, vol. 3, no. 4, American Physical Society, 2014, doi:10.1103/PhysRevX.3.041025.
short: M. Mongillo, P. Spathis, G. Katsaros, S. De Franceschi, P. Gentile, R. Rurali,
X. Cartoixà, Physical Review X 3 (2014).
date_created: 2018-12-11T11:53:52Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:02Z
day: '01'
doi: 10.1103/PhysRevX.3.041025
extern: 1
intvolume: ' 3'
issue: '4'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1407.5413
month: '01'
oa: 1
publication: Physical Review X
publication_status: published
publisher: American Physical Society
publist_id: '5363'
quality_controlled: 0
status: public
title: PtSi clustering in silicon probed by transport spectroscopy
type: journal_article
volume: 3
year: '2014'
...
---
_id: '1791'
abstract:
- lang: eng
text: Acute gene inactivation using short hairpin RNA (shRNA, knockdown) in developing
brain is a powerful technique to study genetic function; however, discrepancies
between knockdown and knockout murine phenotypes have left unanswered questions.
For example, doublecortin (Dcx) knockdown but not knockout shows a neocortical
neuronal migration phenotype. Here we report that in utero electroporation of
shRNA, but not siRNA or miRNA, to Dcx demonstrates a migration phenotype in Dcx
knockouts akin to the effect in wild-type mice, suggestingshRNA-mediated off-target
toxicity. This effect wasnot limited to Dcx, as it was observed in Dclk1 knockouts,
as well as with a fraction of scrambled shRNAs, suggesting a sequence-dependent
but not sequence-specific effect. Profiling RNAs from electroporated cells showed
a defect in endogenous let7 miRNA levels, and disruption of let7 or Dicer recapitulated
the migration defect. The results suggest that shRNA-mediated knockdown can produce
untoward migration effects by altering endogenous miRNA pathways.
acknowledgement: This work was supported by the National Institutes of Health R01NS41537.
G.K. was supported by an EMBO Long Term Fellowship, S.L.B. by the A.P. Giannini
Fellowship, and A.G.F. by the Brain Behavior Research Foundation
author:
- first_name: Seungtae
full_name: Baek, SeungTae
last_name: Baek
- first_name: Géraldine
full_name: Kerjan, Géraldine
last_name: Kerjan
- first_name: Stephanie
full_name: Bielas, Stephanie L
last_name: Bielas
- first_name: Jieun
full_name: Lee, Jieun
last_name: Lee
- first_name: Ali
full_name: Fenstermaker, Ali G
last_name: Fenstermaker
- first_name: Gaia
full_name: Gaia Novarino
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Joseph
full_name: Gleeson, Joseph G
last_name: Gleeson
citation:
ama: Baek S, Kerjan G, Bielas S, et al. Off-target effect of doublecortin family
shRNA on neuronal migration associated with endogenous MicroRNA dysregulation.
Neuron. 2014;82(6):1255-1262. doi:10.1016/j.neuron.2014.04.036
apa: Baek, S., Kerjan, G., Bielas, S., Lee, J., Fenstermaker, A., Novarino, G.,
& Gleeson, J. (2014). Off-target effect of doublecortin family shRNA on neuronal
migration associated with endogenous MicroRNA dysregulation. Neuron. Elsevier.
https://doi.org/10.1016/j.neuron.2014.04.036
chicago: Baek, Seungtae, Géraldine Kerjan, Stephanie Bielas, Jieun Lee, Ali Fenstermaker,
Gaia Novarino, and Joseph Gleeson. “Off-Target Effect of Doublecortin Family ShRNA
on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron.
Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.036.
ieee: S. Baek et al., “Off-target effect of doublecortin family shRNA on
neuronal migration associated with endogenous MicroRNA dysregulation,” Neuron,
vol. 82, no. 6. Elsevier, pp. 1255–1262, 2014.
ista: Baek S, Kerjan G, Bielas S, Lee J, Fenstermaker A, Novarino G, Gleeson J.
2014. Off-target effect of doublecortin family shRNA on neuronal migration associated
with endogenous MicroRNA dysregulation. Neuron. 82(6), 1255–1262.
mla: Baek, Seungtae, et al. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal
Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron, vol.
82, no. 6, Elsevier, 2014, pp. 1255–62, doi:10.1016/j.neuron.2014.04.036.
short: S. Baek, G. Kerjan, S. Bielas, J. Lee, A. Fenstermaker, G. Novarino, J. Gleeson,
Neuron 82 (2014) 1255–1262.
date_created: 2018-12-11T11:54:01Z
date_published: 2014-06-18T00:00:00Z
date_updated: 2021-01-12T06:53:13Z
day: '18'
doi: 10.1016/j.neuron.2014.04.036
extern: 1
intvolume: ' 82'
issue: '6'
month: '06'
page: 1255 - 1262
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '5322'
quality_controlled: 0
status: public
title: Off-target effect of doublecortin family shRNA on neuronal migration associated
with endogenous MicroRNA dysregulation
type: journal_article
volume: 82
year: '2014'
...
---
_id: '1806'
abstract:
- lang: eng
text: The generation of asymmetry, at both cellular and tissue level, is one of
the most essential capabilities of all eukaryotic organisms. It mediates basically
all multicellular development ranging from embryogenesis and de novo organ formation
till responses to various environmental stimuli. In plants, the awe-inspiring
number of such processes is regulated by phytohormone auxin and its directional,
cell-to-cell transport. The mediators of this transport, PIN auxin transporters,
are asymmetrically localized at the plasma membrane, and this polar localization
determines the directionality of intercellular auxin flow. Thus, auxin transport
contributes crucially to the generation of local auxin gradients or maxima, which
instruct given cell to change its developmental program. Here, we introduce and
discuss the molecular components and cellular mechanisms regulating the generation
and maintenance of cellular PIN polarity, as the general hallmarks of cell polarity
in plants.
author:
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Baster P, Friml J. Auxin on the road navigated by cellular PIN polarity. In:
Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development.
Springer; 2014:143-170. doi:10.1007/978-3-7091-1526-8_8'
apa: Baster, P., & Friml, J. (2014). Auxin on the road navigated by cellular
PIN polarity. In E. Zažímalová, J. Petrášek, & E. Benková (Eds.), Auxin
and Its Role in Plant Development (pp. 143–170). Springer. https://doi.org/10.1007/978-3-7091-1526-8_8
chicago: Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular
PIN Polarity.” In Auxin and Its Role in Plant Development, edited by Eva
Zažímalová, Jan Petrášek, and Eva Benková, 143–70. Springer, 2014. https://doi.org/10.1007/978-3-7091-1526-8_8.
ieee: P. Baster and J. Friml, “Auxin on the road navigated by cellular PIN polarity,”
in Auxin and Its Role in Plant Development, E. Zažímalová, J. Petrášek,
and E. Benková, Eds. Springer, 2014, pp. 143–170.
ista: 'Baster P, Friml J. 2014.Auxin on the road navigated by cellular PIN polarity.
In: Auxin and Its Role in Plant Development. , 143–170.'
mla: Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN
Polarity.” Auxin and Its Role in Plant Development, edited by Eva Zažímalová
et al., Springer, 2014, pp. 143–70, doi:10.1007/978-3-7091-1526-8_8.
short: P. Baster, J. Friml, in:, E. Zažímalová, J. Petrášek, E. Benková (Eds.),
Auxin and Its Role in Plant Development, Springer, 2014, pp. 143–170.
date_created: 2018-12-11T11:54:07Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T06:53:19Z
day: '01'
department:
- _id: JiFr
doi: 10.1007/978-3-7091-1526-8_8
editor:
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
language:
- iso: eng
month: '04'
oa_version: None
page: 143 - 170
publication: Auxin and Its Role in Plant Development
publication_status: published
publisher: Springer
publist_id: '5304'
quality_controlled: '1'
scopus_import: 1
status: public
title: Auxin on the road navigated by cellular PIN polarity
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1816'
abstract:
- lang: eng
text: Watermarking techniques for vector graphics dislocate vertices in order to
embed imperceptible, yet detectable, statistical features into the input data.
The embedding process may result in a change of the topology of the input data,
e.g., by introducing self-intersections, which is undesirable or even disastrous
for many applications. In this paper we present a watermarking framework for two-dimensional
vector graphics that employs conventional watermarking techniques but still provides
the guarantee that the topology of the input data is preserved. The geometric
part of this framework computes so-called maximum perturbation regions (MPR) of
vertices. We propose two efficient algorithms to compute MPRs based on Voronoi
diagrams and constrained triangulations. Furthermore, we present two algorithms
to conditionally correct the watermarked data in order to increase the watermark
embedding capacity and still guarantee topological correctness. While we focus
on the watermarking of input formed by straight-line segments, one of our approaches
can also be extended to circular arcs. We conclude the paper by demonstrating
and analyzing the applicability of our framework in conjunction with two well-known
watermarking techniques.
acknowledgement: 'Work by Martin Held and Stefan Huber was supported by Austrian Science
Fund (FWF): L367-N15 and P25816-N15.'
author:
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Martin
full_name: Held, Martin
last_name: Held
- first_name: Peter
full_name: Meerwald, Peter
last_name: Meerwald
- first_name: Roland
full_name: Kwitt, Roland
last_name: Kwitt
citation:
ama: Huber S, Held M, Meerwald P, Kwitt R. Topology-preserving watermarking of vector
graphics. International Journal of Computational Geometry and Applications.
2014;24(1):61-86. doi:10.1142/S0218195914500034
apa: Huber, S., Held, M., Meerwald, P., & Kwitt, R. (2014). Topology-preserving
watermarking of vector graphics. International Journal of Computational Geometry
and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195914500034
chicago: Huber, Stefan, Martin Held, Peter Meerwald, and Roland Kwitt. “Topology-Preserving
Watermarking of Vector Graphics.” International Journal of Computational Geometry
and Applications. World Scientific Publishing, 2014. https://doi.org/10.1142/S0218195914500034.
ieee: S. Huber, M. Held, P. Meerwald, and R. Kwitt, “Topology-preserving watermarking
of vector graphics,” International Journal of Computational Geometry and Applications,
vol. 24, no. 1. World Scientific Publishing, pp. 61–86, 2014.
ista: Huber S, Held M, Meerwald P, Kwitt R. 2014. Topology-preserving watermarking
of vector graphics. International Journal of Computational Geometry and Applications.
24(1), 61–86.
mla: Huber, Stefan, et al. “Topology-Preserving Watermarking of Vector Graphics.”
International Journal of Computational Geometry and Applications, vol.
24, no. 1, World Scientific Publishing, 2014, pp. 61–86, doi:10.1142/S0218195914500034.
short: S. Huber, M. Held, P. Meerwald, R. Kwitt, International Journal of Computational
Geometry and Applications 24 (2014) 61–86.
date_created: 2018-12-11T11:54:10Z
date_published: 2014-03-16T00:00:00Z
date_updated: 2021-01-12T06:53:23Z
day: '16'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1142/S0218195914500034
file:
- access_level: open_access
checksum: be45c133ab4d43351260e21beaa8f4b1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:43Z
date_updated: 2020-07-14T12:45:17Z
file_id: '4704'
file_name: IST-2016-443-v1+1_S0218195914500034.pdf
file_size: 991734
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 24'
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 61 - 86
publication: International Journal of Computational Geometry and Applications
publication_status: published
publisher: World Scientific Publishing
publist_id: '5290'
pubrep_id: '443'
quality_controlled: '1'
scopus_import: 1
status: public
title: Topology-preserving watermarking of vector graphics
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2014'
...
---
_id: '1821'
abstract:
- lang: eng
text: We review recent progress towards a rigorous understanding of the Bogoliubov
approximation for bosonic quantum many-body systems. We focus, in particular,
on the excitation spectrum of a Bose gas in the mean-field (Hartree) limit. A
list of open problems will be discussed at the end.
article_number: '1.4881536'
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Seiringer R. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation.
Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4881536
apa: Seiringer, R. (2014). Bose gases, Bose-Einstein condensation, and the Bogoliubov
approximation. Journal of Mathematical Physics. American Institute of Physics.
https://doi.org/10.1063/1.4881536
chicago: Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov
Approximation.” Journal of Mathematical Physics. American Institute of
Physics, 2014. https://doi.org/10.1063/1.4881536.
ieee: R. Seiringer, “Bose gases, Bose-Einstein condensation, and the Bogoliubov
approximation,” Journal of Mathematical Physics, vol. 55, no. 7. American
Institute of Physics, 2014.
ista: Seiringer R. 2014. Bose gases, Bose-Einstein condensation, and the Bogoliubov
approximation. Journal of Mathematical Physics. 55(7), 1.4881536.
mla: Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov
Approximation.” Journal of Mathematical Physics, vol. 55, no. 7, 1.4881536,
American Institute of Physics, 2014, doi:10.1063/1.4881536.
short: R. Seiringer, Journal of Mathematical Physics 55 (2014).
date_created: 2018-12-11T11:54:11Z
date_published: 2014-06-26T00:00:00Z
date_updated: 2021-01-12T06:53:25Z
day: '26'
ddc:
- '510'
- '530'
department:
- _id: RoSe
doi: 10.1063/1.4881536
file:
- access_level: open_access
checksum: ed0efc93c10f1341155f0316af617b82
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:49Z
date_updated: 2020-07-14T12:45:17Z
file_id: '5172'
file_name: IST-2016-532-v1+1_J._Mathematical_Phys._2014_Seiringer.pdf
file_size: 269171
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 55'
issue: '7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication: Journal of Mathematical Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5285'
pubrep_id: '532'
quality_controlled: '1'
scopus_import: 1
status: public
title: Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2014'
...
---
_id: '1822'
article_number: '075101'
author:
- first_name: Vojkan
full_name: Jakšić, Vojkan
last_name: Jakšić
- first_name: Claude
full_name: Pillet, Claude
last_name: Pillet
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Jakšić V, Pillet C, Seiringer R. Introduction. Journal of Mathematical Physics.
2014;55(7). doi:10.1063/1.4884877
apa: Jakšić, V., Pillet, C., & Seiringer, R. (2014). Introduction. Journal
of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4884877
chicago: Jakšić, Vojkan, Claude Pillet, and Robert Seiringer. “Introduction.” Journal
of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4884877.
ieee: V. Jakšić, C. Pillet, and R. Seiringer, “Introduction,” Journal of Mathematical
Physics, vol. 55, no. 7. American Institute of Physics, 2014.
ista: Jakšić V, Pillet C, Seiringer R. 2014. Introduction. Journal of Mathematical
Physics. 55(7), 075101.
mla: Jakšić, Vojkan, et al. “Introduction.” Journal of Mathematical Physics,
vol. 55, no. 7, 075101, American Institute of Physics, 2014, doi:10.1063/1.4884877.
short: V. Jakšić, C. Pillet, R. Seiringer, Journal of Mathematical Physics 55 (2014).
date_created: 2018-12-11T11:54:12Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2021-01-12T06:53:25Z
day: '01'
department:
- _id: RoSe
doi: 10.1063/1.4884877
intvolume: ' 55'
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
publication: Journal of Mathematical Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5284'
quality_controlled: '1'
scopus_import: 1
status: public
title: Introduction
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2014'
...
---
_id: '1829'
abstract:
- lang: eng
text: Hitting and batting tasks, such as tennis forehands, ping-pong strokes, or
baseball batting, depend on predictions where the ball can be intercepted and
how it can properly be returned to the opponent. These predictions get more accurate
over time, hence the behaviors need to be continuously modified. As a result,
movement templates with a learned global shape need to be adapted during the execution
so that the racket reaches a target position and velocity that will return the
ball over to the other side of the net or court. It requires altering learned
movements to hit a varying target with the necessary velocity at a specific instant
in time. Such a task cannot be incorporated straightforwardly in most movement
representations suitable for learning. For example, the standard formulation of
the dynamical system based motor primitives (introduced by Ijspeert et al (2002b))
does not satisfy this property despite their flexibility which has allowed learning
tasks ranging from locomotion to kendama. In order to fulfill this requirement,
we reformulate the Ijspeert framework to incorporate the possibility of specifying
a desired hitting point and a desired hitting velocity while maintaining all advantages
of the original formulation.We show that the proposed movement template formulation
works well in two scenarios, i.e., for hitting a ball on a string with a table
tennis racket at a specified velocity and for returning balls launched by a ball
gun successfully over the net using forehand movements.
alternative_title:
- Springer Tracts in Advanced Robotics
author:
- first_name: Katharina
full_name: Muelling, Katharina
last_name: Muelling
- first_name: Oliver
full_name: Kroemer, Oliver
last_name: Kroemer
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
citation:
ama: 'Muelling K, Kroemer O, Lampert C, Schölkopf B. Movement templates for learning
of hitting and batting. In: Kober J, Peters J, eds. Learning Motor Skills.
Vol 97. From Algorithms to Robot Experiments. Springer; 2014:69-82. doi:10.1007/978-3-319-03194-1_3'
apa: Muelling, K., Kroemer, O., Lampert, C., & Schölkopf, B. (2014). Movement
templates for learning of hitting and batting. In J. Kober & J. Peters (Eds.),
Learning Motor Skills (Vol. 97, pp. 69–82). Springer. https://doi.org/10.1007/978-3-319-03194-1_3
chicago: Muelling, Katharina, Oliver Kroemer, Christoph Lampert, and Bernhard Schölkopf.
“Movement Templates for Learning of Hitting and Batting.” In Learning Motor
Skills, edited by Jens Kober and Jan Peters, 97:69–82. From Algorithms to
Robot Experiments. Springer, 2014. https://doi.org/10.1007/978-3-319-03194-1_3.
ieee: K. Muelling, O. Kroemer, C. Lampert, and B. Schölkopf, “Movement templates
for learning of hitting and batting,” in Learning Motor Skills, vol. 97,
J. Kober and J. Peters, Eds. Springer, 2014, pp. 69–82.
ista: 'Muelling K, Kroemer O, Lampert C, Schölkopf B. 2014.Movement templates for
learning of hitting and batting. In: Learning Motor Skills. Springer Tracts in
Advanced Robotics, vol. 97, 69–82.'
mla: Muelling, Katharina, et al. “Movement Templates for Learning of Hitting and
Batting.” Learning Motor Skills, edited by Jens Kober and Jan Peters, vol.
97, Springer, 2014, pp. 69–82, doi:10.1007/978-3-319-03194-1_3.
short: K. Muelling, O. Kroemer, C. Lampert, B. Schölkopf, in:, J. Kober, J. Peters
(Eds.), Learning Motor Skills, Springer, 2014, pp. 69–82.
date_created: 2018-12-11T11:54:14Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:28Z
day: '01'
department:
- _id: ChLa
doi: 10.1007/978-3-319-03194-1_3
editor:
- first_name: Jens
full_name: Kober, Jens
last_name: Kober
- first_name: Jan
full_name: Peters, Jan
last_name: Peters
intvolume: ' 97'
language:
- iso: eng
month: '01'
oa_version: None
page: 69 - 82
publication: Learning Motor Skills
publication_status: published
publisher: Springer
publist_id: '5274'
quality_controlled: '1'
scopus_import: 1
series_title: From Algorithms to Robot Experiments
status: public
title: Movement templates for learning of hitting and batting
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 97
year: '2014'
...
---
_id: '1842'
abstract:
- lang: eng
text: We prove polynomial upper bounds of geometric Ramsey numbers of pathwidth-2
outerplanar triangulations in both convex and general cases. We also prove that
the geometric Ramsey numbers of the ladder graph on 2n vertices are bounded by
O(n3) and O(n10), in the convex and general case, respectively. We then apply
similar methods to prove an (Formula presented.) upper bound on the Ramsey number
of a path with n ordered vertices.
acknowledgement: Marek Krčál was supported by the ERC Advanced Grant No. 267165.
author:
- first_name: Josef
full_name: Cibulka, Josef
last_name: Cibulka
- first_name: Pu
full_name: Gao, Pu
last_name: Gao
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
- first_name: Tomáš
full_name: Valla, Tomáš
last_name: Valla
- first_name: Pavel
full_name: Valtr, Pavel
last_name: Valtr
citation:
ama: Cibulka J, Gao P, Krcál M, Valla T, Valtr P. On the geometric ramsey number
of outerplanar graphs. Discrete & Computational Geometry. 2014;53(1):64-79.
doi:10.1007/s00454-014-9646-x
apa: Cibulka, J., Gao, P., Krcál, M., Valla, T., & Valtr, P. (2014). On the
geometric ramsey number of outerplanar graphs. Discrete & Computational
Geometry. Springer. https://doi.org/10.1007/s00454-014-9646-x
chicago: Cibulka, Josef, Pu Gao, Marek Krcál, Tomáš Valla, and Pavel Valtr. “On
the Geometric Ramsey Number of Outerplanar Graphs.” Discrete & Computational
Geometry. Springer, 2014. https://doi.org/10.1007/s00454-014-9646-x.
ieee: J. Cibulka, P. Gao, M. Krcál, T. Valla, and P. Valtr, “On the geometric ramsey
number of outerplanar graphs,” Discrete & Computational Geometry, vol.
53, no. 1. Springer, pp. 64–79, 2014.
ista: Cibulka J, Gao P, Krcál M, Valla T, Valtr P. 2014. On the geometric ramsey
number of outerplanar graphs. Discrete & Computational Geometry. 53(1), 64–79.
mla: Cibulka, Josef, et al. “On the Geometric Ramsey Number of Outerplanar Graphs.”
Discrete & Computational Geometry, vol. 53, no. 1, Springer, 2014,
pp. 64–79, doi:10.1007/s00454-014-9646-x.
short: J. Cibulka, P. Gao, M. Krcál, T. Valla, P. Valtr, Discrete & Computational
Geometry 53 (2014) 64–79.
date_created: 2018-12-11T11:54:18Z
date_published: 2014-11-14T00:00:00Z
date_updated: 2021-01-12T06:53:33Z
day: '14'
department:
- _id: UlWa
- _id: HeEd
doi: 10.1007/s00454-014-9646-x
intvolume: ' 53'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1310.7004
month: '11'
oa: 1
oa_version: Submitted Version
page: 64 - 79
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '5260'
scopus_import: 1
status: public
title: On the geometric ramsey number of outerplanar graphs
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2014'
...
---
_id: '1844'
abstract:
- lang: eng
text: 'Local protein interactions ("molecular context" effects) dictate
amino acid replacements and can be described in terms of site-specific, energetic
preferences for any different amino acid. It has been recently debated whether
these preferences remain approximately constant during evolution or whether, due
to coevolution of sites, they change strongly. Such research highlights an unresolved
and fundamental issue with far-reaching implications for phylogenetic analysis
and molecular evolution modeling. Here, we take advantage of the recent availability
of phenotypically supported laboratory resurrections of Precambrian thioredoxins
and β-lactamases to experimentally address the change of site-specific amino acid
preferences over long geological timescales. Extensive mutational analyses support
the notion that evolutionary adjustment to a new amino acid may occur, but to
a large extent this is insufficient to erase the primitive preference for amino
acid replacements. Generally, site-specific amino acid preferences appear to remain
conserved throughout evolutionary history despite local sequence divergence. We
show such preference conservation to be readily understandable in molecular terms
and we provide crystallographic evidence for an intriguing structural-switch mechanism:
Energetic preference for an ancestral amino acid in a modern protein can be linked
to reorganization upon mutation to the ancestral local structure around the mutated
site. Finally, we point out that site-specific preference conservation naturally
leads to one plausible evolutionary explanation for the existence of intragenic
global suppressor mutations.'
author:
- first_name: Valeria
full_name: Risso, Valeria
last_name: Risso
- first_name: Fadia
full_name: Manssour Triedo, Fadia
last_name: Manssour Triedo
- first_name: Asuncion
full_name: Delgado Delgado, Asuncion
last_name: Delgado Delgado
- first_name: Rocio
full_name: Arco, Rocio
last_name: Arco
- first_name: Alicia
full_name: Barroso Deljesús, Alicia
last_name: Barroso Deljesús
- first_name: Álvaro
full_name: Inglés Prieto, Álvaro
id: 2A9DB292-F248-11E8-B48F-1D18A9856A87
last_name: Inglés Prieto
orcid: 0000-0002-5409-8571
- first_name: Raquel
full_name: Godoy Ruiz, Raquel
last_name: Godoy Ruiz
- first_name: Josè
full_name: Gavira, Josè
last_name: Gavira
- first_name: Eric
full_name: Gaucher, Eric
last_name: Gaucher
- first_name: Beatriz
full_name: Ibarra Molero, Beatriz
last_name: Ibarra Molero
- first_name: Jose
full_name: Sánchez Ruiz, Jose
last_name: Sánchez Ruiz
citation:
ama: Risso V, Manssour Triedo F, Delgado Delgado A, et al. Mutational studies on
resurrected ancestral proteins reveal conservation of site-specific amino acid
preferences throughout evolutionary history. Molecular Biology and Evolution.
2014;32(2):440-455. doi:10.1093/molbev/msu312
apa: Risso, V., Manssour Triedo, F., Delgado Delgado, A., Arco, R., Barroso Deljesús,
A., Inglés Prieto, Á., … Sánchez Ruiz, J. (2014). Mutational studies on resurrected
ancestral proteins reveal conservation of site-specific amino acid preferences
throughout evolutionary history. Molecular Biology and Evolution. Oxford
University Press. https://doi.org/10.1093/molbev/msu312
chicago: Risso, Valeria, Fadia Manssour Triedo, Asuncion Delgado Delgado, Rocio
Arco, Alicia Barroso Deljesús, Álvaro Inglés Prieto, Raquel Godoy Ruiz, et al.
“Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific
Amino Acid Preferences throughout Evolutionary History.” Molecular Biology
and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu312.
ieee: V. Risso et al., “Mutational studies on resurrected ancestral proteins
reveal conservation of site-specific amino acid preferences throughout evolutionary
history,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University
Press, pp. 440–455, 2014.
ista: Risso V, Manssour Triedo F, Delgado Delgado A, Arco R, Barroso Deljesús A,
Inglés Prieto Á, Godoy Ruiz R, Gavira J, Gaucher E, Ibarra Molero B, Sánchez Ruiz
J. 2014. Mutational studies on resurrected ancestral proteins reveal conservation
of site-specific amino acid preferences throughout evolutionary history. Molecular
Biology and Evolution. 32(2), 440–455.
mla: Risso, Valeria, et al. “Mutational Studies on Resurrected Ancestral Proteins
Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary
History.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University
Press, 2014, pp. 440–55, doi:10.1093/molbev/msu312.
short: V. Risso, F. Manssour Triedo, A. Delgado Delgado, R. Arco, A. Barroso Deljesús,
Á. Inglés Prieto, R. Godoy Ruiz, J. Gavira, E. Gaucher, B. Ibarra Molero, J. Sánchez
Ruiz, Molecular Biology and Evolution 32 (2014) 440–455.
date_created: 2018-12-11T11:54:19Z
date_published: 2014-11-12T00:00:00Z
date_updated: 2021-01-12T06:53:34Z
day: '12'
ddc:
- '571'
department:
- _id: HaJa
doi: 10.1093/molbev/msu312
file:
- access_level: open_access
checksum: 06215318e66be8f3e0c33abb07e9d3da
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:56Z
date_updated: 2020-07-14T12:45:19Z
file_id: '5247'
file_name: IST-2016-430-v1+1_Mol_Biol_Evol-2015-Risso-440-55.pdf
file_size: 1545246
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 32'
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 440 - 455
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '5257'
pubrep_id: '430'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mutational studies on resurrected ancestral proteins reveal conservation of
site-specific amino acid preferences throughout evolutionary history
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2014'
...
---
_id: '1852'
abstract:
- lang: eng
text: To control morphogenesis, molecular regulatory networks have to interfere
with the mechanical properties of the individual cells of developing organs and
tissues, but how this is achieved is not well known. We study this issue here
in the shoot meristem of higher plants, a group of undifferentiated cells where
complex changes in growth rates and directions lead to the continuous formation
of new organs [1, 2]. Here, we show that the plant hormone auxin plays an important
role in this process via a dual, local effect on the extracellular matrix, the
cell wall, which determines cell shape. Our study reveals that auxin not only
causes a limited reduction in wall stiffness but also directly interferes with
wall anisotropy via the regulation of cortical microtubule dynamics. We further
show that to induce growth isotropy and organ outgrowth, auxin somehow interferes
with the cortical microtubule-ordering activity of a network of proteins, including
AUXIN BINDING PROTEIN 1 and KATANIN 1. Numerical simulations further indicate
that the induced isotropy is sufficient to amplify the effects of the relatively
minor changes in wall stiffness to promote organogenesis and the establishment
of new growth axes in a robust manner.
acknowledgement: 'This work was funded by grants from EraSysBio+ (iSAM) and ERC (Morphodynamics). '
author:
- first_name: Massimiliano
full_name: Sassi, Massimiliano
last_name: Sassi
- first_name: Olivier
full_name: Ali, Olivier
last_name: Ali
- first_name: Frédéric
full_name: Boudon, Frédéric
last_name: Boudon
- first_name: Gladys
full_name: Cloarec, Gladys
last_name: Cloarec
- first_name: Ursula
full_name: Abad, Ursula
last_name: Abad
- first_name: Coralie
full_name: Cellier, Coralie
last_name: Cellier
- first_name: Xu
full_name: Chen, Xu
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Benjamin
full_name: Gilles, Benjamin
last_name: Gilles
- first_name: Pascale
full_name: Milani, Pascale
last_name: Milani
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Teva
full_name: Vernoux, Teva
last_name: Vernoux
- first_name: Christophe
full_name: Godin, Christophe
last_name: Godin
- first_name: Olivier
full_name: Hamant, Olivier
last_name: Hamant
- first_name: Jan
full_name: Traas, Jan
last_name: Traas
citation:
ama: Sassi M, Ali O, Boudon F, et al. An auxin-mediated shift toward growth isotropy
promotes organ formation at the shoot meristem in Arabidopsis. Current Biology.
2014;24(19):2335-2342. doi:10.1016/j.cub.2014.08.036
apa: Sassi, M., Ali, O., Boudon, F., Cloarec, G., Abad, U., Cellier, C., … Traas,
J. (2014). An auxin-mediated shift toward growth isotropy promotes organ formation
at the shoot meristem in Arabidopsis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.08.036
chicago: Sassi, Massimiliano, Olivier Ali, Frédéric Boudon, Gladys Cloarec, Ursula
Abad, Coralie Cellier, Xu Chen, et al. “An Auxin-Mediated Shift toward Growth
Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current
Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.08.036.
ieee: M. Sassi et al., “An auxin-mediated shift toward growth isotropy promotes
organ formation at the shoot meristem in Arabidopsis,” Current Biology,
vol. 24, no. 19. Cell Press, pp. 2335–2342, 2014.
ista: Sassi M, Ali O, Boudon F, Cloarec G, Abad U, Cellier C, Chen X, Gilles B,
Milani P, Friml J, Vernoux T, Godin C, Hamant O, Traas J. 2014. An auxin-mediated
shift toward growth isotropy promotes organ formation at the shoot meristem in
Arabidopsis. Current Biology. 24(19), 2335–2342.
mla: Sassi, Massimiliano, et al. “An Auxin-Mediated Shift toward Growth Isotropy
Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current Biology,
vol. 24, no. 19, Cell Press, 2014, pp. 2335–42, doi:10.1016/j.cub.2014.08.036.
short: M. Sassi, O. Ali, F. Boudon, G. Cloarec, U. Abad, C. Cellier, X. Chen, B.
Gilles, P. Milani, J. Friml, T. Vernoux, C. Godin, O. Hamant, J. Traas, Current
Biology 24 (2014) 2335–2342.
date_created: 2018-12-11T11:54:22Z
date_published: 2014-10-06T00:00:00Z
date_updated: 2021-01-12T06:53:37Z
day: '06'
department:
- _id: JiFr
doi: 10.1016/j.cub.2014.08.036
intvolume: ' 24'
issue: '19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-01074821
month: '10'
oa: 1
oa_version: Submitted Version
page: 2335 - 2342
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '5248'
quality_controlled: '1'
scopus_import: 1
status: public
title: An auxin-mediated shift toward growth isotropy promotes organ formation at
the shoot meristem in Arabidopsis
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2014'
...
---
_id: '1853'
abstract:
- lang: eng
text: Wireless sensor networks (WSNs) composed of low-power, low-cost sensor nodes
are expected to form the backbone of future intelligent networks for a broad range
of civil, industrial and military applications. These sensor nodes are often deployed
through random spreading, and function in dynamic environments. Many applications
of WSNs such as pollution tracking, forest fire detection, and military surveillance
require knowledge of the location of constituent nodes. But the use of technologies
such as GPS on all nodes is prohibitive due to power and cost constraints. So,
the sensor nodes need to autonomously determine their locations. Most localization
techniques use anchor nodes with known locations to determine the position of
remaining nodes. Localization techniques have two conflicting requirements. On
one hand, an ideal localization technique should be computationally simple and
on the other hand, it must be resistant to attacks that compromise anchor nodes.
In this paper, we propose a computationally light-weight game theoretic secure
localization technique and demonstrate its effectiveness in comparison to existing
techniques.
author:
- first_name: Susmit
full_name: Jha, Susmit
last_name: Jha
- first_name: Stavros
full_name: Tripakis, Stavros
last_name: Tripakis
- first_name: Sanjit
full_name: Seshia, Sanjit
last_name: Seshia
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Jha S, Tripakis S, Seshia S, Chatterjee K. Game theoretic secure localization
in wireless sensor networks. In: IEEE; 2014:85-90. doi:10.1109/IOT.2014.7030120'
apa: 'Jha, S., Tripakis, S., Seshia, S., & Chatterjee, K. (2014). Game theoretic
secure localization in wireless sensor networks (pp. 85–90). Presented at the
IOT: Internet of Things, Cambridge, USA: IEEE. https://doi.org/10.1109/IOT.2014.7030120'
chicago: Jha, Susmit, Stavros Tripakis, Sanjit Seshia, and Krishnendu Chatterjee.
“Game Theoretic Secure Localization in Wireless Sensor Networks,” 85–90. IEEE,
2014. https://doi.org/10.1109/IOT.2014.7030120.
ieee: 'S. Jha, S. Tripakis, S. Seshia, and K. Chatterjee, “Game theoretic secure
localization in wireless sensor networks,” presented at the IOT: Internet of Things,
Cambridge, USA, 2014, pp. 85–90.'
ista: 'Jha S, Tripakis S, Seshia S, Chatterjee K. 2014. Game theoretic secure localization
in wireless sensor networks. IOT: Internet of Things, 85–90.'
mla: Jha, Susmit, et al. Game Theoretic Secure Localization in Wireless Sensor
Networks. IEEE, 2014, pp. 85–90, doi:10.1109/IOT.2014.7030120.
short: S. Jha, S. Tripakis, S. Seshia, K. Chatterjee, in:, IEEE, 2014, pp. 85–90.
conference:
end_date: 2014-10-08
location: Cambridge, USA
name: 'IOT: Internet of Things'
start_date: 2014-10-06
date_created: 2018-12-11T11:54:22Z
date_published: 2014-02-03T00:00:00Z
date_updated: 2021-01-12T06:53:38Z
day: '03'
department:
- _id: KrCh
doi: 10.1109/IOT.2014.7030120
language:
- iso: eng
month: '02'
oa_version: None
page: 85 - 90
publication_status: published
publisher: IEEE
publist_id: '5247'
quality_controlled: '1'
status: public
title: Game theoretic secure localization in wireless sensor networks
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1854'
abstract:
- lang: eng
text: In this paper, we present a method for non-rigid, partial shape matching in
vector graphics. Given a user-specified query region in a 2D shape, similar regions
are found, even if they are non-linearly distorted. Furthermore, a non-linear
mapping is established between the query regions and these matches, which allows
the automatic transfer of editing operations such as texturing. This is achieved
by a two-step approach. First, pointwise correspondences between the query region
and the whole shape are established. The transformation parameters of these correspondences
are registered in an appropriate transformation space. For transformations between
similar regions, these parameters form surfaces in transformation space, which
are extracted in the second step of our method. The extracted regions may be related
to the query region by a non-rigid transform, enabling non-rigid shape matching.
In this paper, we present a method for non-rigid, partial shape matching in vector
graphics. Given a user-specified query region in a 2D shape, similar regions are
found, even if they are non-linearly distorted. Furthermore, a non-linear mapping
is established between the query regions and these matches, which allows the automatic
transfer of editing operations such as texturing. This is achieved by a two-step
approach. First, pointwise correspondences between the query region and the whole
shape are established. The transformation parameters of these correspondences
are registered in an appropriate transformation space. For transformations between
similar regions, these parameters form surfaces in transformation space, which
are extracted in the second step of our method. The extracted regions may be related
to the query region by a non-rigid transform, enabling non-rigid shape matching.
author:
- first_name: Paul
full_name: Guerrero, Paul
last_name: Guerrero
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Michael
full_name: Wimmer, Michael
last_name: Wimmer
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
citation:
ama: Guerrero P, Auzinger T, Wimmer M, Jeschke S. Partial shape matching using transformation
parameter similarity. Computer Graphics Forum. 2014;34(1):239-252. doi:10.1111/cgf.12509
apa: Guerrero, P., Auzinger, T., Wimmer, M., & Jeschke, S. (2014). Partial shape
matching using transformation parameter similarity. Computer Graphics Forum.
Wiley. https://doi.org/10.1111/cgf.12509
chicago: Guerrero, Paul, Thomas Auzinger, Michael Wimmer, and Stefan Jeschke. “Partial
Shape Matching Using Transformation Parameter Similarity.” Computer Graphics
Forum. Wiley, 2014. https://doi.org/10.1111/cgf.12509.
ieee: P. Guerrero, T. Auzinger, M. Wimmer, and S. Jeschke, “Partial shape matching
using transformation parameter similarity,” Computer Graphics Forum, vol.
34, no. 1. Wiley, pp. 239–252, 2014.
ista: Guerrero P, Auzinger T, Wimmer M, Jeschke S. 2014. Partial shape matching
using transformation parameter similarity. Computer Graphics Forum. 34(1), 239–252.
mla: Guerrero, Paul, et al. “Partial Shape Matching Using Transformation Parameter
Similarity.” Computer Graphics Forum, vol. 34, no. 1, Wiley, 2014, pp.
239–52, doi:10.1111/cgf.12509.
short: P. Guerrero, T. Auzinger, M. Wimmer, S. Jeschke, Computer Graphics Forum
34 (2014) 239–252.
date_created: 2018-12-11T11:54:22Z
date_published: 2014-11-05T00:00:00Z
date_updated: 2021-01-12T06:53:38Z
day: '05'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1111/cgf.12509
file:
- access_level: open_access
checksum: 91946bfc509c77f5fd3151a3ff2b2c8f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:58Z
date_updated: 2020-07-14T12:45:19Z
file_id: '5182'
file_name: IST-2016-574-v1+1_Guerrero-2014-TPS-paper.pdf
file_size: 24817484
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 239 - 252
publication: Computer Graphics Forum
publication_status: published
publisher: Wiley
publist_id: '5246'
pubrep_id: '574'
quality_controlled: '1'
scopus_import: 1
status: public
title: Partial shape matching using transformation parameter similarity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2014'
...