---
_id: '3158'
abstract:
- lang: eng
text: We describe here the development and characterization of a conditionally inducible
mouse model expressing Lifeact-GFP, a peptide that reports the dynamics of filamentous
actin. We have used this model to study platelets, megakaryocytes and melanoblasts
and we provide evidence that Lifeact-GFP is a useful reporter in these cell types
ex vivo. In the case of platelets and megakaryocytes, these cells are not transfectable
by traditional methods, so conditional activation of Lifeact allows the study
of actin dynamics in these cells live. We studied melanoblasts in native skin
explants from embryos, allowing the visualization of live actin dynamics during
cytokinesis and migration. Our study revealed that melanoblasts lacking the small
GTPase Rac1 show a delay in the formation of new pseudopodia following cytokinesis
that accounts for the previously reported cytokinesis delay in these cells. Thus,
through use of this mouse model, we were able to gain insights into the actin
dynamics of cells that could only previously be studied using fixed specimens
or following isolation from their native tissue environment.
author:
- first_name: Hannah
full_name: Schachtner, Hannah
last_name: Schachtner
- first_name: Ang
full_name: Li, Ang
last_name: Li
- first_name: David
full_name: Stevenson, David
last_name: Stevenson
- first_name: Simon
full_name: Calaminus, Simon
last_name: Calaminus
- first_name: Steven
full_name: Thomas, Steven
last_name: Thomas
- first_name: Steve
full_name: Watson, Steve
last_name: Watson
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Roland
full_name: Wedlich Söldner, Roland
last_name: Wedlich Söldner
- first_name: Douglas
full_name: Strathdee, Douglas
last_name: Strathdee
- first_name: Laura
full_name: Machesky, Laura
last_name: Machesky
citation:
ama: Schachtner H, Li A, Stevenson D, et al. Tissue inducible Lifeact expression
allows visualization of actin dynamics in vivo and ex vivo. European Journal
of Cell Biology. 2012;91(11-12):923-929. doi:10.1016/j.ejcb.2012.04.002
apa: Schachtner, H., Li, A., Stevenson, D., Calaminus, S., Thomas, S., Watson, S.,
… Machesky, L. (2012). Tissue inducible Lifeact expression allows visualization
of actin dynamics in vivo and ex vivo. European Journal of Cell Biology.
Elsevier. https://doi.org/10.1016/j.ejcb.2012.04.002
chicago: Schachtner, Hannah, Ang Li, David Stevenson, Simon Calaminus, Steven Thomas,
Steve Watson, Michael K Sixt, Roland Wedlich Söldner, Douglas Strathdee, and Laura
Machesky. “Tissue Inducible Lifeact Expression Allows Visualization of Actin Dynamics
in Vivo and Ex Vivo.” European Journal of Cell Biology. Elsevier, 2012.
https://doi.org/10.1016/j.ejcb.2012.04.002.
ieee: H. Schachtner et al., “Tissue inducible Lifeact expression allows visualization
of actin dynamics in vivo and ex vivo,” European Journal of Cell Biology,
vol. 91, no. 11–12. Elsevier, pp. 923–929, 2012.
ista: Schachtner H, Li A, Stevenson D, Calaminus S, Thomas S, Watson S, Sixt MK,
Wedlich Söldner R, Strathdee D, Machesky L. 2012. Tissue inducible Lifeact expression
allows visualization of actin dynamics in vivo and ex vivo. European Journal of
Cell Biology. 91(11–12), 923–929.
mla: Schachtner, Hannah, et al. “Tissue Inducible Lifeact Expression Allows Visualization
of Actin Dynamics in Vivo and Ex Vivo.” European Journal of Cell Biology,
vol. 91, no. 11–12, Elsevier, 2012, pp. 923–29, doi:10.1016/j.ejcb.2012.04.002.
short: H. Schachtner, A. Li, D. Stevenson, S. Calaminus, S. Thomas, S. Watson, M.K.
Sixt, R. Wedlich Söldner, D. Strathdee, L. Machesky, European Journal of Cell
Biology 91 (2012) 923–929.
date_created: 2018-12-11T12:01:44Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2021-01-12T07:41:27Z
day: '01'
department:
- _id: MiSi
doi: 10.1016/j.ejcb.2012.04.002
external_id:
pmid:
- '22658956'
intvolume: ' 91'
issue: 11-12
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930012/
month: '11'
oa: 1
oa_version: Submitted Version
page: 923 - 929
pmid: 1
publication: European Journal of Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '3534'
quality_controlled: '1'
scopus_import: 1
status: public
title: Tissue inducible Lifeact expression allows visualization of actin dynamics
in vivo and ex vivo
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2012'
...
---
_id: '3159'
abstract:
- lang: eng
text: The structure of hierarchical networks in biological and physical systems
has long been characterized using the Horton-Strahler ordering scheme. The scheme
assigns an integer order to each edge in the network based on the topology of
branching such that the order increases from distal parts of the network (e.g.,
mountain streams or capillaries) to the "root" of the network (e.g.,
the river outlet or the aorta). However, Horton-Strahler ordering cannot be applied
to networks with loops because they they create a contradiction in the edge ordering
in terms of which edge precedes another in the hierarchy. Here, we present a generalization
of the Horton-Strahler order to weighted planar reticular networks, where weights
are assumed to correlate with the importance of network edges, e.g., weights estimated
from edge widths may correlate to flow capacity. Our method assigns hierarchical
levels not only to edges of the network, but also to its loops, and classifies
the edges into reticular edges, which are responsible for loop formation, and
tree edges. In addition, we perform a detailed and rigorous theoretical analysis
of the sensitivity of the hierarchical levels to weight perturbations. In doing
so, we show that the ordering of the reticular edges is more robust to noise in
weight estimation than is the ordering of the tree edges. We discuss applications
of this generalized Horton-Strahler ordering to the study of leaf venation and
other biological networks.
acknowledgement: "his work was supported by the National Science Foundation Plant
Genome Research Program (grant 0820624 to H.E. and J.S.W.), the Defense Advanced
Projects Research Agency (grant HR0011-09-1-0055 to H.E. and J.S.W.), and the European
Science Foundation (under the Research Networking Programme on “Applied and Computational
Algebraic Topology” run by H.E.). Joshua S. Weitz, Ph.D., holds a Career Award at
the Scientific Interface from the Burroughs Wellcome Fund.\r\n\r\n\r\n\r\nDuring
preparation of this manuscript the authors became aware of a related work by Katifori
and Magnasco (arXiv:1110.1412v1), concurrently submitted and accepted for publication
in PLoS ONE."
article_number: e36715
author:
- first_name: Yuriy
full_name: Mileyko, Yuriy
last_name: Mileyko
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Charles
full_name: Price, Charles
last_name: Price
- first_name: Joshua
full_name: Weitz, Joshua
last_name: Weitz
citation:
ama: Mileyko Y, Edelsbrunner H, Price C, Weitz J. Hierarchical ordering of reticular
networks. PLoS One. 2012;7(6). doi:10.1371/journal.pone.0036715
apa: Mileyko, Y., Edelsbrunner, H., Price, C., & Weitz, J. (2012). Hierarchical
ordering of reticular networks. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0036715
chicago: Mileyko, Yuriy, Herbert Edelsbrunner, Charles Price, and Joshua Weitz.
“Hierarchical Ordering of Reticular Networks.” PLoS One. Public Library
of Science, 2012. https://doi.org/10.1371/journal.pone.0036715.
ieee: Y. Mileyko, H. Edelsbrunner, C. Price, and J. Weitz, “Hierarchical ordering
of reticular networks,” PLoS One, vol. 7, no. 6. Public Library of Science,
2012.
ista: Mileyko Y, Edelsbrunner H, Price C, Weitz J. 2012. Hierarchical ordering of
reticular networks. PLoS One. 7(6), e36715.
mla: Mileyko, Yuriy, et al. “Hierarchical Ordering of Reticular Networks.” PLoS
One, vol. 7, no. 6, e36715, Public Library of Science, 2012, doi:10.1371/journal.pone.0036715.
short: Y. Mileyko, H. Edelsbrunner, C. Price, J. Weitz, PLoS One 7 (2012).
date_created: 2018-12-11T12:01:44Z
date_published: 2012-06-06T00:00:00Z
date_updated: 2021-01-12T07:41:28Z
day: '06'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1371/journal.pone.0036715
file:
- access_level: open_access
checksum: 515a98ad72e470752f03f13663dcaff8
content_type: application/pdf
creator: kschuh
date_created: 2019-02-05T12:38:43Z
date_updated: 2020-07-14T12:46:01Z
file_id: '5922'
file_name: 2012_PLoS_Mileyko.PDF
file_size: 541583
relation: main_file
file_date_updated: 2020-07-14T12:46:01Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3530'
pubrep_id: '385'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hierarchical ordering of reticular networks
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: 7
year: '2012'
...
---
_id: '3160'
abstract:
- lang: eng
text: There is a long-running controversy about how early cell fate decisions are
made in the developing mammalian embryo. 1,2 In particular, it is controversial
when the first events that can predict the establishment of the pluripotent and
extra-embryonic lineages in the blastocyst of the pre-implantation embryo occur.
It has long been proposed that the position and polarity of cells at the 16- to
32-cell stage embryo influence their decision to either give rise to the pluripotent
cell lineage that eventually contributes to the inner cell mass (ICM), comprising
the primitive endoderm (PE) and the epiblast (EPI), or the extra-embryonic trophectoderm
(TE) surrounding the blastocoel. The positioning of cells in the embryo at this
developmental stage could largely be the result of random events, making this
a stochastic model of cell lineage allocation. Contrary to such a stochastic model,
some studies have detected putative differences in the lineage potential of individual
blastomeres before compaction, indicating that the first cell fate decisions may
occur as early as at the 4-cell stage. Using a non-invasive, quantitative in vivo
imaging assay to study the kinetic behavior of Oct4 (also known as POU5F1), a
key transcription factor (TF) controlling pre-implantation development in the
mouse embryo, 3-5 a recent study identifies Oct4 kinetics as a predictive measure
of cell lineage patterning in the early mouse embryo. 6 Here, we discuss the implications
of such molecular heterogeneities in early development and offer potential avenues
toward a mechanistic understanding of these observations, contributing to the
resolution of the controversy of developmental cell lineage allocation.
author:
- first_name: Periklis
full_name: Pantazis, Periklis
last_name: Pantazis
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Pantazis P, Bollenbach MT. Transcription factor kinetics and the emerging asymmetry
in the early mammalian embryo. Cell Cycle. 2012;11(11):2055-2058. doi:10.4161/cc.20118
apa: Pantazis, P., & Bollenbach, M. T. (2012). Transcription factor kinetics
and the emerging asymmetry in the early mammalian embryo. Cell Cycle. Taylor
and Francis. https://doi.org/10.4161/cc.20118
chicago: Pantazis, Periklis, and Mark Tobias Bollenbach. “Transcription Factor Kinetics
and the Emerging Asymmetry in the Early Mammalian Embryo.” Cell Cycle.
Taylor and Francis, 2012. https://doi.org/10.4161/cc.20118.
ieee: P. Pantazis and M. T. Bollenbach, “Transcription factor kinetics and the emerging
asymmetry in the early mammalian embryo,” Cell Cycle, vol. 11, no. 11.
Taylor and Francis, pp. 2055–2058, 2012.
ista: Pantazis P, Bollenbach MT. 2012. Transcription factor kinetics and the emerging
asymmetry in the early mammalian embryo. Cell Cycle. 11(11), 2055–2058.
mla: Pantazis, Periklis, and Mark Tobias Bollenbach. “Transcription Factor Kinetics
and the Emerging Asymmetry in the Early Mammalian Embryo.” Cell Cycle,
vol. 11, no. 11, Taylor and Francis, 2012, pp. 2055–58, doi:10.4161/cc.20118.
short: P. Pantazis, M.T. Bollenbach, Cell Cycle 11 (2012) 2055–2058.
date_created: 2018-12-11T12:01:44Z
date_published: 2012-06-01T00:00:00Z
date_updated: 2021-01-12T07:41:28Z
day: '01'
department:
- _id: ToBo
doi: 10.4161/cc.20118
intvolume: ' 11'
issue: '11'
language:
- iso: eng
month: '06'
oa_version: None
page: 2055 - 2058
publication: Cell Cycle
publication_status: published
publisher: Taylor and Francis
publist_id: '3531'
quality_controlled: '1'
scopus_import: 1
status: public
title: Transcription factor kinetics and the emerging asymmetry in the early mammalian
embryo
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2012'
...
---
_id: '3161'
abstract:
- lang: eng
text: 'Some inflammatory stimuli trigger activation of the NLRP3 inflammasome by
inducing efflux of cellular potassium. Loss of cellular potassium is known to
potently suppress protein synthesis, leading us to test whether the inhibition
of protein synthesis itself serves as an activating signal for the NLRP3 inflammasome.
Murine bone marrow-derived macrophages, either primed by LPS or unprimed, were
exposed to a panel of inhibitors of ribosomal function: ricin, cycloheximide,
puromycin, pactamycin, and anisomycin. Macrophages were also exposed to nigericin,
ATP, monosodium urate (MSU), and poly I:C. Synthesis of pro-IL-ß and release of
IL-1ß from cells in response to these agents was detected by immunoblotting and
ELISA. Release of intracellular potassium was measured by mass spectrometry. Inhibition
of translation by each of the tested translation inhibitors led to processing
of IL-1ß, which was released from cells. Processing and release of IL-1ß was reduced
or absent from cells deficient in NLRP3, ASC, or caspase-1, demonstrating the
role of the NLRP3 inflammasome. Despite the inability of these inhibitors to trigger
efflux of intracellular potassium, the addition of high extracellular potassium
suppressed activation of the NLRP3 inflammasome. MSU and double-stranded RNA,
which are known to activate the NLRP3 inflammasome, also substantially inhibited
protein translation, supporting a close association between inhibition of translation
and inflammasome activation. These data demonstrate that translational inhibition
itself constitutes a heretofore-unrecognized mechanism underlying IL-1ß dependent
inflammatory signaling and that other physical, chemical, or pathogen-associated
agents that impair translation may lead to IL-1ß-dependent inflammation through
activation of the NLRP3 inflammasome. For agents that inhibit translation through
decreased cellular potassium, the application of high extracellular potassium
restores protein translation and suppresses activation of the NLRP inflammasome.
For agents that inhibit translation through mechanisms that do not involve loss
of potassium, high extracellular potassium suppresses IL-1ß processing through
a mechanism that remains undefined.'
acknowledgement: "Supported by National Institutes of Health grants GM071338 (ML)
and AI059355 (BM).\r\nWe acknowledge the expertise of Dr. Martina Ralle in Department
of Biochemistry and Molecular Biology at OHSU for measurements of potassium using
inductively coupled plasma mass spectrometry."
article_number: e36044
author:
- first_name: Meghan
full_name: Vyleta, Meghan
id: 418901AA-F248-11E8-B48F-1D18A9856A87
last_name: Vyleta
- first_name: John
full_name: Wong, John
last_name: Wong
- first_name: Bruce
full_name: Magun, Bruce
last_name: Magun
citation:
ama: Vyleta M, Wong J, Magun B. Suppression of ribosomal function triggers innate
immune signaling through activation of the NLRP3 inflammasome. PLoS One.
2012;7(5). doi:10.1371/journal.pone.0036044
apa: Vyleta, M., Wong, J., & Magun, B. (2012). Suppression of ribosomal function
triggers innate immune signaling through activation of the NLRP3 inflammasome.
PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0036044
chicago: Vyleta, Meghan, John Wong, and Bruce Magun. “Suppression of Ribosomal Function
Triggers Innate Immune Signaling through Activation of the NLRP3 Inflammasome.”
PLoS One. Public Library of Science, 2012. https://doi.org/10.1371/journal.pone.0036044.
ieee: M. Vyleta, J. Wong, and B. Magun, “Suppression of ribosomal function triggers
innate immune signaling through activation of the NLRP3 inflammasome,” PLoS
One, vol. 7, no. 5. Public Library of Science, 2012.
ista: Vyleta M, Wong J, Magun B. 2012. Suppression of ribosomal function triggers
innate immune signaling through activation of the NLRP3 inflammasome. PLoS One.
7(5), e36044.
mla: Vyleta, Meghan, et al. “Suppression of Ribosomal Function Triggers Innate Immune
Signaling through Activation of the NLRP3 Inflammasome.” PLoS One, vol.
7, no. 5, e36044, Public Library of Science, 2012, doi:10.1371/journal.pone.0036044.
short: M. Vyleta, J. Wong, B. Magun, PLoS One 7 (2012).
date_created: 2018-12-11T12:01:45Z
date_published: 2012-05-14T00:00:00Z
date_updated: 2021-01-12T07:41:29Z
day: '14'
ddc:
- '610'
department:
- _id: SyCr
doi: 10.1371/journal.pone.0036044
file:
- access_level: open_access
checksum: 30cef37e27eaa467f6571b3640282010
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:30Z
date_updated: 2020-07-14T12:46:01Z
file_id: '5082'
file_name: IST-2012-97-v1+1_journal.pone.0036044.pdf
file_size: 2984012
relation: main_file
file_date_updated: 2020-07-14T12:46:01Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3526'
pubrep_id: '97'
quality_controlled: '1'
scopus_import: 1
status: public
title: Suppression of ribosomal function triggers innate immune signaling through
activation of the NLRP3 inflammasome
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: 7
year: '2012'
...
---
_id: '3162'
abstract:
- lang: eng
text: Given a dense-time real-valued signal and a parameterized temporal logic formula
with both magnitude and timing parameters, we compute the subset of the parameter
space that renders the formula satisfied by the trace. We provide two preliminary
implementations, one which follows the exact semantics and attempts to compute
the validity domain by quantifier elimination in linear arithmetics and one which
conducts adaptive search in the parameter space.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Eugene
full_name: Asarin, Eugene
last_name: Asarin
- first_name: Alexandre
full_name: Donzé, Alexandre
last_name: Donzé
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
citation:
ama: 'Asarin E, Donzé A, Maler O, Nickovic D. Parametric identification of temporal
properties. In: Vol 7186. Springer; 2012:147-160. doi:10.1007/978-3-642-29860-8_12'
apa: 'Asarin, E., Donzé, A., Maler, O., & Nickovic, D. (2012). Parametric identification
of temporal properties (Vol. 7186, pp. 147–160). Presented at the RV: Runtime
Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-642-29860-8_12'
chicago: Asarin, Eugene, Alexandre Donzé, Oded Maler, and Dejan Nickovic. “Parametric
Identification of Temporal Properties,” 7186:147–60. Springer, 2012. https://doi.org/10.1007/978-3-642-29860-8_12.
ieee: 'E. Asarin, A. Donzé, O. Maler, and D. Nickovic, “Parametric identification
of temporal properties,” presented at the RV: Runtime Verification, San Francisco,
CA, United States, 2012, vol. 7186, pp. 147–160.'
ista: 'Asarin E, Donzé A, Maler O, Nickovic D. 2012. Parametric identification of
temporal properties. RV: Runtime Verification, LNCS, vol. 7186, 147–160.'
mla: Asarin, Eugene, et al. Parametric Identification of Temporal Properties.
Vol. 7186, Springer, 2012, pp. 147–60, doi:10.1007/978-3-642-29860-8_12.
short: E. Asarin, A. Donzé, O. Maler, D. Nickovic, in:, Springer, 2012, pp. 147–160.
conference:
end_date: 2011-09-30
location: San Francisco, CA, United States
name: 'RV: Runtime Verification'
start_date: 2011-09-27
date_created: 2018-12-11T12:01:45Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:29Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-642-29860-8_12
file:
- access_level: open_access
checksum: ba4a75287008fc64b8fbf78a7476ec32
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T12:50:15Z
date_updated: 2020-07-14T12:46:01Z
file_id: '7862'
file_name: 2012_RV_Asarin.pdf
file_size: 374726
relation: main_file
file_date_updated: 2020-07-14T12:46:01Z
has_accepted_license: '1'
intvolume: ' 7186'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 147 - 160
publication_status: published
publisher: Springer
publist_id: '3525'
quality_controlled: '1'
scopus_import: 1
status: public
title: Parametric identification of temporal properties
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7186
year: '2012'
...
---
_id: '3164'
abstract:
- lang: eng
text: Overview of the Special Issue on structured prediction and inference.
author:
- first_name: Matthew
full_name: Blaschko, Matthew
last_name: Blaschko
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Blaschko M, Lampert C. Guest editorial: Special issue on structured prediction
and inference. International Journal of Computer Vision. 2012;99(3):257-258.
doi:10.1007/s11263-012-0530-y'
apa: 'Blaschko, M., & Lampert, C. (2012). Guest editorial: Special issue on
structured prediction and inference. International Journal of Computer Vision.
Springer. https://doi.org/10.1007/s11263-012-0530-y'
chicago: 'Blaschko, Matthew, and Christoph Lampert. “Guest Editorial: Special Issue
on Structured Prediction and Inference.” International Journal of Computer
Vision. Springer, 2012. https://doi.org/10.1007/s11263-012-0530-y.'
ieee: 'M. Blaschko and C. Lampert, “Guest editorial: Special issue on structured
prediction and inference,” International Journal of Computer Vision, vol.
99, no. 3. Springer, pp. 257–258, 2012.'
ista: 'Blaschko M, Lampert C. 2012. Guest editorial: Special issue on structured
prediction and inference. International Journal of Computer Vision. 99(3), 257–258.'
mla: 'Blaschko, Matthew, and Christoph Lampert. “Guest Editorial: Special Issue
on Structured Prediction and Inference.” International Journal of Computer
Vision, vol. 99, no. 3, Springer, 2012, pp. 257–58, doi:10.1007/s11263-012-0530-y.'
short: M. Blaschko, C. Lampert, International Journal of Computer Vision 99 (2012)
257–258.
date_created: 2018-12-11T12:01:46Z
date_published: 2012-09-01T00:00:00Z
date_updated: 2021-01-12T07:41:30Z
day: '01'
department:
- _id: ChLa
doi: 10.1007/s11263-012-0530-y
intvolume: ' 99'
issue: '3'
language:
- iso: eng
month: '09'
oa_version: None
page: 257 - 258
publication: International Journal of Computer Vision
publication_status: published
publisher: Springer
publist_id: '3521'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Guest editorial: Special issue on structured prediction and inference'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2012'
...
---
_id: '3165'
abstract:
- lang: eng
text: Computing the winning set for Büchi objectives in alternating games on graphs
is a central problem in computer aided verification with a large number of applications.
The long standing best known upper bound for solving the problem is Õ(n·m), where
n is the number of vertices and m is the number of edges in the graph. We are
the first to break the Õ(n·m) boundary by presenting a new technique that reduces
the running time to O(n 2). This bound also leads to O(n 2) time algorithms for
computing the set of almost-sure winning vertices for Büchi objectives (1) in
alternating games with probabilistic transitions (improving an earlier bound of
Õ(n·m)), (2) in concurrent graph games with constant actions (improving an earlier
bound of O(n 3)), and (3) in Markov decision processes (improving for m > n
4/3 an earlier bound of O(min(m 1.5, m·n 2/3)). We also show that the same technique
can be used to compute the maximal end-component decomposition of a graph in time
O(n 2), which is an improvement over earlier bounds for m > n 4/3. Finally,
we show how to maintain the winning set for Büchi objectives in alternating games
under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized
time per operation. This is the first dynamic algorithm for this problem.
acknowledgement: 'The research was supported by Austrian Science Fund (FWF) Grant
No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification, Vienna
Science and Technology Fund (WWTF) Grant ICT10-002, FWF NFN Grant No S11407-N23
(RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: 'Chatterjee K, Henzinger MH. An O(n2) time algorithm for alternating Büchi
games. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms.
SIAM; 2012:1386-1399. doi:10.1137/1.9781611973099.109'
apa: 'Chatterjee, K., & Henzinger, M. H. (2012). An O(n2) time algorithm for
alternating Büchi games. In Proceedings of the Annual ACM-SIAM Symposium on
Discrete Algorithms (pp. 1386–1399). Kyoto, Japan: SIAM. https://doi.org/10.1137/1.9781611973099.109'
chicago: Chatterjee, Krishnendu, and Monika H Henzinger. “An O(N2) Time Algorithm
for Alternating Büchi Games.” In Proceedings of the Annual ACM-SIAM Symposium
on Discrete Algorithms, 1386–99. SIAM, 2012. https://doi.org/10.1137/1.9781611973099.109.
ieee: K. Chatterjee and M. H. Henzinger, “An O(n2) time algorithm for alternating
Büchi games,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms,
Kyoto, Japan, 2012, pp. 1386–1399.
ista: 'Chatterjee K, Henzinger MH. 2012. An O(n2) time algorithm for alternating
Büchi games. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms.
SODA: Symposium on Discrete Algorithms, 1386–1399.'
mla: Chatterjee, Krishnendu, and Monika H. Henzinger. “An O(N2) Time Algorithm for
Alternating Büchi Games.” Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms, SIAM, 2012, pp. 1386–99, doi:10.1137/1.9781611973099.109.
short: K. Chatterjee, M.H. Henzinger, in:, Proceedings of the Annual ACM-SIAM Symposium
on Discrete Algorithms, SIAM, 2012, pp. 1386–1399.
conference:
end_date: 2012-01-19
location: Kyoto, Japan
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2012-01-17
date_created: 2018-12-11T12:01:46Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2025-06-02T08:53:48Z
day: '01'
department:
- _id: KrCh
doi: 10.1137/1.9781611973099.109
ec_funded: 1
external_id:
arxiv:
- '1109.5018'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1109.5018
month: '01'
oa: 1
oa_version: None
page: 1386 - 1399
project:
- _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: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms
publication_status: published
publisher: SIAM
publist_id: '3519'
pubrep_id: '15'
quality_controlled: '1'
related_material:
record:
- id: '5379'
relation: earlier_version
status: public
- id: '2141'
relation: later_version
status: public
status: public
title: An O(n2) time algorithm for alternating Büchi games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '3166'
abstract:
- lang: eng
text: 'There is evidence that the genetic code was established prior to the existence
of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms
had to rely on simple anaerobic bioenergetic processes. In this work I propose
that amino acid fermentation powered metabolism in the RNA world, and that this
was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were
used as carbon sources rather than as catalytic or structural elements. In modern
bacteria, amino acid fermentation is known as the Stickland reaction. This pathway
involves two amino acids: the first undergoes oxidative deamination, and the second
acts as an electron acceptor through reductive deamination. This redox reaction
results in two keto acids that are employed to synthesise ATP via substrate-level
phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some
bacteria of the genus Clostridium. Two other facts support Stickland fermentation
in the RNA world. First, several Stickland amino acid pairs are synthesised in
abiotic amino acid synthesis. This suggests that amino acids that could be used
as an energy substrate were freely available. Second, anticodons that have complementary
sequences often correspond to amino acids that form Stickland pairs. The main
hypothesis of this paper is that pairs of complementary proto-adapters were assigned
to Stickland amino acids pairs. There are signatures of this hypothesis in the
genetic code. Furthermore, it is argued that the proto-adapters formed double
strands that brought amino acid pairs into proximity to facilitate their mutual
redox reaction, structurally constraining the anticodon pairs that are assigned
to these amino acid pairs. Significance tests which randomise the code are performed
to study the extent of the variability of the energetic (ATP) yield. Random assignments
can lead to a substantial yield of ATP and maintain enough variability, thus selection
can act and refine the assignments into a proto-code that optimises the energetic
yield. Monte Carlo simulations are performed to evaluate the establishment of
these simple proto-codes, based on amino acid substitutions and codon swapping.
In all cases, donor amino acids are assigned to anticodons composed of U+G, and
have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to
the the remaining codons. These bioenergetic and structural constraints allow
for a metabolic role for amino acids before their co-option as catalyst cofactors.
Reviewers: this article was reviewed by Prof. William Martin, Prof. Eors Szathmary
(nominated by Dr. Gaspar Jekely) and Dr. Adam Kun (nominated by Dr. Sandor Pongor)'
acknowledgement: 'The author was supported by the ERC-2009-AdG Grant for project 250152
SELECTIONINFORMATION. '
article_number: '6'
author:
- first_name: Harold
full_name: Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
citation:
ama: de Vladar H. Amino acid fermentation at the origin of the genetic code. Biology
Direct. 2012;7. doi:10.1186/1745-6150-7-6
apa: de Vladar, H. (2012). Amino acid fermentation at the origin of the genetic
code. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-6
chicago: Vladar, Harold de. “Amino Acid Fermentation at the Origin of the Genetic
Code.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-6.
ieee: H. de Vladar, “Amino acid fermentation at the origin of the genetic code,”
Biology Direct, vol. 7. BioMed Central, 2012.
ista: de Vladar H. 2012. Amino acid fermentation at the origin of the genetic code.
Biology Direct. 7, 6.
mla: de Vladar, Harold. “Amino Acid Fermentation at the Origin of the Genetic Code.”
Biology Direct, vol. 7, 6, BioMed Central, 2012, doi:10.1186/1745-6150-7-6.
short: H. de Vladar, Biology Direct 7 (2012).
date_created: 2018-12-11T12:01:46Z
date_published: 2012-02-10T00:00:00Z
date_updated: 2021-01-12T07:41:31Z
day: '10'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1186/1745-6150-7-6
ec_funded: 1
file:
- access_level: open_access
checksum: e511e401e239ef608a7fd79b21a06d78
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:44Z
date_updated: 2020-07-14T12:46:02Z
file_id: '5166'
file_name: IST-2012-99-v1+1_1745-6150-7-6.pdf
file_size: 4099536
relation: main_file
file_date_updated: 2020-07-14T12:46:02Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '3518'
pubrep_id: '99'
quality_controlled: '1'
status: public
title: Amino acid fermentation at the origin of the genetic code
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: 7
year: '2012'
...
---
_id: '3167'
article_type: letter_note
author:
- first_name: Michele
full_name: Weber, Michele
id: 3A3FC708-F248-11E8-B48F-1D18A9856A87
last_name: Weber
citation:
ama: Weber M. NextGen speaks 13 . Science. 2012;336(6077):32-34. doi:10.1126/science.336.6077.32
apa: Weber, M. (2012). NextGen speaks 13 . Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.336.6077.32
chicago: Weber, Michele. “NextGen Speaks 13 .” Science. American Association
for the Advancement of Science, 2012. https://doi.org/10.1126/science.336.6077.32.
ieee: M. Weber, “NextGen speaks 13 ,” Science, vol. 336, no. 6077. American
Association for the Advancement of Science, pp. 32–34, 2012.
ista: Weber M. 2012. NextGen speaks 13 . Science. 336(6077), 32–34.
mla: Weber, Michele. “NextGen Speaks 13 .” Science, vol. 336, no. 6077, American
Association for the Advancement of Science, 2012, pp. 32–34, doi:10.1126/science.336.6077.32.
short: M. Weber, Science 336 (2012) 32–34.
date_created: 2018-12-11T12:01:47Z
date_published: 2012-04-06T00:00:00Z
date_updated: 2021-01-12T07:41:32Z
day: '06'
department:
- _id: MiSi
doi: 10.1126/science.336.6077.32
external_id:
pmid:
- '22491839'
intvolume: ' 336'
issue: '6077'
language:
- iso: eng
month: '04'
oa_version: None
page: 32-34
pmid: 1
popular_science: '1'
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '3516'
status: public
title: 'NextGen speaks 13 '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 336
year: '2012'
...
---
_id: '3168'
abstract:
- lang: eng
text: The induction of a signaling pathway is characterized by transient complex
formation and mutual posttranslational modification of proteins. To faithfully
capture this combinatorial process in a mathematical model is an important challenge
in systems biology. Exploiting the limited context on which most binding and modification
events are conditioned, attempts have been made to reduce the combinatorial complexity
by quotienting the reachable set of molecular species into species aggregates
while preserving the deterministic semantics of the thermodynamic limit. Recently,
we proposed a quotienting that also preserves the stochastic semantics and that
is complete in the sense that the semantics of individual species can be recovered
from the aggregate semantics. In this paper, we prove that this quotienting yields
a sufficient condition for weak lumpability (that is to say that the quotient
system is still Markovian for a given set of initial distributions) and that it
gives rise to a backward Markov bisimulation between the original and aggregated
transition system (which means that the conditional probability of being in a
given state in the original system knowing that we are in its equivalence class
is an invariant of the system). We illustrate the framework on a case study of
the epidermal growth factor (EGF)/insulin receptor crosstalk.
acknowledgement: "We would like to thank the anonymous reviewers for their comments
on the different versions of the paper. We would also like to thank Ferdinanda Camporesi
for her careful reading and the useful insights that she gave us about the paper.\r\nJérôme
Feret’s contribution was partially supported by the AbstractCell ANR-Chair of Excellence.
Heinz Koeppl’s research is supported by the Swiss National Science Foundation, grant
no. 200020-117975/1. Tatjana Petrov’s research is supported by SystemsX.ch (the
Swiss Initiative in Systems Biology)."
author:
- first_name: Jérôme
full_name: Feret, Jérôme
last_name: Feret
- 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: Heinz
full_name: Koeppl, Heinz
last_name: Koeppl
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule
based systems. Theoretical Computer Science. 2012;431:137-164. doi:10.1016/j.tcs.2011.12.059
apa: Feret, J., Henzinger, T. A., Koeppl, H., & Petrov, T. (2012). Lumpability
abstractions of rule based systems. Theoretical Computer Science. Elsevier.
https://doi.org/10.1016/j.tcs.2011.12.059
chicago: Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability
Abstractions of Rule Based Systems.” Theoretical Computer Science. Elsevier,
2012. https://doi.org/10.1016/j.tcs.2011.12.059.
ieee: J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions
of rule based systems,” Theoretical Computer Science, vol. 431. Elsevier,
pp. 137–164, 2012.
ista: Feret J, Henzinger TA, Koeppl H, Petrov T. 2012. Lumpability abstractions
of rule based systems. Theoretical Computer Science. 431, 137–164.
mla: Feret, Jérôme, et al. “Lumpability Abstractions of Rule Based Systems.” Theoretical
Computer Science, vol. 431, Elsevier, 2012, pp. 137–64, doi:10.1016/j.tcs.2011.12.059.
short: J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, Theoretical Computer Science
431 (2012) 137–164.
date_created: 2018-12-11T12:01:47Z
date_published: 2012-05-04T00:00:00Z
date_updated: 2023-02-23T11:39:40Z
day: '04'
department:
- _id: ToHe
doi: 10.1016/j.tcs.2011.12.059
intvolume: ' 431'
language:
- iso: eng
month: '05'
oa_version: None
page: 137 - 164
publication: Theoretical Computer Science
publication_status: published
publisher: Elsevier
publist_id: '3515'
pubrep_id: '73'
quality_controlled: '1'
related_material:
record:
- id: '3719'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Lumpability abstractions of rule based systems
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 431
year: '2012'
...
---
_id: '3242'
abstract:
- lang: eng
text: Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated
disease defences at the individual and colony level. An intriguing yet little
understood phenomenon is that social contact to pathogen-exposed individuals reduces
susceptibility of previously naive nestmates to this pathogen. We tested whether
such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium
anisopliae is based on active upregulation of the immune system of nestmates following
contact to an infectious individual or passive protection via transfer of immune
effectors among group members—that is, active versus passive immunisation. We
found no evidence for involvement of passive immunisation via transfer of antimicrobials
among colony members. Instead, intensive allogrooming behaviour between naive
and pathogen-exposed ants before fungal conidia firmly attached to their cuticle
suggested passage of the pathogen from the exposed individuals to their nestmates.
By tracing fluorescence-labelled conidia we indeed detected frequent pathogen
transfer to the nestmates, where they caused low-level infections as revealed
by growth of small numbers of fungal colony forming units from their dissected
body content. These infections rarely led to death, but instead promoted an enhanced
ability to inhibit fungal growth and an active upregulation of immune genes involved
in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there
was no upregulation of the gene cathepsin L, which is associated with antibacterial
and antiviral defences, and we found no increased antibacterial activity of nestmates
of fungus-exposed ants. This indicates that social immunisation after fungal exposure
is specific, similar to recent findings for individual-level immune priming in
invertebrates. Epidemiological modeling further suggests that active social immunisation
is adaptive, as it leads to faster elimination of the disease and lower death
rates than passive immunisation. Interestingly, humans have also utilised the
protective effect of low-level infections to fight smallpox by intentional transfer
of low pathogen doses (“variolation” or “inoculation”).
acknowledgement: Funding for this project was obtained by the German Research Foundation
DFG (http://www.dfg.de/en/index.jsp) as an Individual Research Grant (CR118/2-1
to SC) and the European Research Council (http://erc.europa.eu/) in form of two
ERC Starting Grants (ERC-2009-StG240371-SocialVaccines to SC and ERC-2010-StG259294-LatentCauses
to FJT). In addition, the Junge Akademie (Young Academy of the Berlin-Brandenburg
Academy of Sciences and Humanities and the National Academy of Sciences Leopoldina
(http://www.diejungeakademie.de/english/index.html) funded this joint Antnet project
of SC and FJT. The funders had no role in study design, data collection and analysis,
decision to publish, or preparation of the manuscript.
article_number: e1001300
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Meghan
full_name: Vyleta, Meghan
id: 418901AA-F248-11E8-B48F-1D18A9856A87
last_name: Vyleta
- first_name: Fabian
full_name: Theis, Fabian
last_name: Theis
- first_name: Miriam
full_name: Stock, Miriam
id: 42462816-F248-11E8-B48F-1D18A9856A87
last_name: Stock
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Martina
full_name: Klatt, Martina
id: E60F29C6-E9AE-11E9-AF6E-D190C7302F38
last_name: Klatt
- first_name: Verena
full_name: Drescher, Verena
last_name: Drescher
- first_name: Carsten
full_name: Marr, Carsten
last_name: Marr
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Konrad M, Vyleta M, Theis F, et al. Social transfer of pathogenic fungus promotes
active immunisation in ant colonies. PLoS Biology. 2012;10(4). doi:10.1371/journal.pbio.1001300
apa: Konrad, M., Vyleta, M., Theis, F., Stock, M., Tragust, S., Klatt, M., … Cremer,
S. (2012). Social transfer of pathogenic fungus promotes active immunisation in
ant colonies. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1001300
chicago: Konrad, Matthias, Meghan Vyleta, Fabian Theis, Miriam Stock, Simon Tragust,
Martina Klatt, Verena Drescher, Carsten Marr, Line V Ugelvig, and Sylvia Cremer.
“Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.”
PLoS Biology. Public Library of Science, 2012. https://doi.org/10.1371/journal.pbio.1001300.
ieee: M. Konrad et al., “Social transfer of pathogenic fungus promotes active
immunisation in ant colonies,” PLoS Biology, vol. 10, no. 4. Public Library
of Science, 2012.
ista: Konrad M, Vyleta M, Theis F, Stock M, Tragust S, Klatt M, Drescher V, Marr
C, Ugelvig LV, Cremer S. 2012. Social transfer of pathogenic fungus promotes active
immunisation in ant colonies. PLoS Biology. 10(4), e1001300.
mla: Konrad, Matthias, et al. “Social Transfer of Pathogenic Fungus Promotes Active
Immunisation in Ant Colonies.” PLoS Biology, vol. 10, no. 4, e1001300,
Public Library of Science, 2012, doi:10.1371/journal.pbio.1001300.
short: M. Konrad, M. Vyleta, F. Theis, M. Stock, S. Tragust, M. Klatt, V. Drescher,
C. Marr, L.V. Ugelvig, S. Cremer, PLoS Biology 10 (2012).
date_created: 2018-12-11T12:02:13Z
date_published: 2012-04-03T00:00:00Z
date_updated: 2023-02-23T14:07:11Z
day: '03'
ddc:
- '570'
- '579'
department:
- _id: SyCr
doi: 10.1371/journal.pbio.1001300
ec_funded: 1
file:
- access_level: open_access
checksum: 4ebacefd9fbab5c68adf829124115fd1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:28Z
date_updated: 2020-07-14T12:46:04Z
file_id: '4689'
file_name: IST-2012-96-v1+1_journal.pbio.1001300.pdf
file_size: 674228
relation: main_file
file_date_updated: 2020-07-14T12:46:04Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
- _id: 25E0E184-B435-11E9-9278-68D0E5697425
name: Antnet
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '3434'
pubrep_id: '96'
quality_controlled: '1'
related_material:
record:
- id: '9755'
relation: research_data
status: public
scopus_import: 1
status: public
title: Social transfer of pathogenic fungus promotes active immunisation in ant colonies
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2012'
...
---
_id: '3243'
abstract:
- lang: eng
text: 'Wie wandelt sich das Berufsbild in Wissenschaftlichen Bibliotheken? Patrick
Danowski gibt seine Einschätzung ab. '
article_processing_charge: No
article_type: letter_note
author:
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
citation:
ama: Danowski P. Zwischen Technologie und Information. Büchereiperspektiven.
2012;2012(1):11.
apa: Danowski, P. (2012). Zwischen Technologie und Information. Büchereiperspektiven.
Büchereiverband Österreichs.
chicago: Danowski, Patrick. “Zwischen Technologie und Information.” Büchereiperspektiven.
Büchereiverband Österreichs, 2012.
ieee: P. Danowski, “Zwischen Technologie und Information,” Büchereiperspektiven,
vol. 2012, no. 1. Büchereiverband Österreichs, p. 11, 2012.
ista: Danowski P. 2012. Zwischen Technologie und Information. Büchereiperspektiven.
2012(1), 11.
mla: Danowski, Patrick. “Zwischen Technologie und Information.” Büchereiperspektiven,
vol. 2012, no. 1, Büchereiverband Österreichs, 2012, p. 11.
short: P. Danowski, Büchereiperspektiven 2012 (2012) 11.
date_created: 2018-12-11T12:02:13Z
date_published: 2012-03-01T00:00:00Z
date_updated: 2023-10-16T10:40:18Z
day: '01'
department:
- _id: E-Lib
intvolume: ' 2012'
issue: '1'
language:
- iso: ger
main_file_link:
- open_access: '1'
url: https://www.bvoe.at/sites/default/files/2022-07/BP_1_12.pdf
month: '03'
oa: 1
oa_version: Published Version
page: '11'
popular_science: '1'
publication: Büchereiperspektiven
publication_identifier:
issn:
- 1607-7172
publication_status: published
publisher: Büchereiverband Österreichs
publist_id: '3433'
status: public
title: Zwischen Technologie und Information
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2012
year: '2012'
...
---
_id: '3244'
abstract:
- lang: eng
text: "Bibliothekare haben die Aufgabe, sich mit neuen Medienformen auseinanderzusetzen.\r\n"
article_processing_charge: No
article_type: letter_note
author:
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
citation:
ama: Danowski P. Die Zeit des Abwartens ist vorbei! BuB - Forum Bibliothek und
Information. 2012;64(4):284.
apa: Danowski, P. (2012). Die Zeit des Abwartens ist vorbei! BuB - Forum Bibliothek
und Information. Fachzeitschrift des BIB – Berufsverband Information Bibliothek.
chicago: Danowski, Patrick. “Die Zeit des Abwartens ist vorbei!” BuB - Forum
Bibliothek und Information. Fachzeitschrift des BIB – Berufsverband Information
Bibliothek, 2012.
ieee: P. Danowski, “Die Zeit des Abwartens ist vorbei!,” BuB - Forum Bibliothek
und Information, vol. 64, no. 4. Fachzeitschrift des BIB – Berufsverband Information
Bibliothek, p. 284, 2012.
ista: Danowski P. 2012. Die Zeit des Abwartens ist vorbei! BuB - Forum Bibliothek
und Information. 64(4), 284.
mla: Danowski, Patrick. “Die Zeit des Abwartens ist vorbei!” BuB - Forum Bibliothek
und Information, vol. 64, no. 4, Fachzeitschrift des BIB – Berufsverband Information
Bibliothek, 2012, p. 284.
short: P. Danowski, BuB - Forum Bibliothek und Information 64 (2012) 284.
date_created: 2018-12-11T12:02:13Z
date_published: 2012-04-15T00:00:00Z
date_updated: 2023-10-16T10:19:14Z
day: '15'
department:
- _id: E-Lib
intvolume: ' 64'
issue: '4'
language:
- iso: ger
main_file_link:
- open_access: '1'
url: https://www.b-u-b.de/fileadmin/archiv/imports/pdf_files/2012/bub_2012_04_284.pdf
month: '04'
oa: 1
oa_version: Published Version
page: '284'
popular_science: '1'
publication: BuB - Forum Bibliothek und Information
publication_identifier:
issn:
- 1869 -1137
publication_status: published
publisher: Fachzeitschrift des BIB – Berufsverband Information Bibliothek
publist_id: '3432'
status: public
title: Die Zeit des Abwartens ist vorbei!
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2012'
...
---
_id: '3245'
abstract:
- lang: eng
text: How cells orchestrate their behavior during collective migration is a long-standing
question. Using magnetic tweezers to apply mechanical stimuli to Xenopus mesendoderm
cells, Weber etal. (2012) now reveal, in this issue of Developmental Cell, a cadherin-mediated
mechanosensitive response that promotes cell polarization and movement persistence
during the collective mesendoderm migration in gastrulation.
author:
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- 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: Behrndt M, Heisenberg C-PJ. Spurred by resistance mechanosensation in collective
migration. Developmental Cell. 2012;22(1):3-4. doi:10.1016/j.devcel.2011.12.018
apa: Behrndt, M., & Heisenberg, C.-P. J. (2012). Spurred by resistance mechanosensation
in collective migration. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2011.12.018
chicago: Behrndt, Martin, and Carl-Philipp J Heisenberg. “Spurred by Resistance
Mechanosensation in Collective Migration.” Developmental Cell. Cell Press,
2012. https://doi.org/10.1016/j.devcel.2011.12.018.
ieee: M. Behrndt and C.-P. J. Heisenberg, “Spurred by resistance mechanosensation
in collective migration,” Developmental Cell, vol. 22, no. 1. Cell Press,
pp. 3–4, 2012.
ista: Behrndt M, Heisenberg C-PJ. 2012. Spurred by resistance mechanosensation in
collective migration. Developmental Cell. 22(1), 3–4.
mla: Behrndt, Martin, and Carl-Philipp J. Heisenberg. “Spurred by Resistance Mechanosensation
in Collective Migration.” Developmental Cell, vol. 22, no. 1, Cell Press,
2012, pp. 3–4, doi:10.1016/j.devcel.2011.12.018.
short: M. Behrndt, C.-P.J. Heisenberg, Developmental Cell 22 (2012) 3–4.
date_created: 2018-12-11T12:02:14Z
date_published: 2012-01-17T00:00:00Z
date_updated: 2021-01-12T07:42:05Z
day: '17'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2011.12.018
intvolume: ' 22'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 3 - 4
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '3426'
quality_controlled: '1'
scopus_import: 1
status: public
title: Spurred by resistance mechanosensation in collective migration
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2012'
...
---
_id: '3246'
abstract:
- lang: eng
text: Visualizing and analyzing shape changes at various scales, ranging from single
molecules to whole organisms, are essential for understanding complex morphogenetic
processes, such as early embryonic development. Embryo morphogenesis relies on
the interplay between different tissues, the properties of which are again determined
by the interaction between their constituent cells. Cell interactions, on the
other hand, are controlled by various molecules, such as signaling and adhesion
molecules, which in order to exert their functions need to be spatiotemporally
organized within and between the interacting cells. In this review, we will focus
on the role of cell adhesion functioning at different scales to organize cell,
tissue and embryo morphogenesis. We will specifically ask how the subcellular
distribution of adhesion molecules controls the formation of cell-cell contacts,
how cell-cell contacts determine tissue shape, and how tissue interactions regulate
embryo morphogenesis.
acknowledgement: This review comes from a themed issue on Cell structure and dynamics
Edited by Jason Swedlow and Gaudenz Danuser
author:
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- 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: Barone V, Heisenberg C-PJ. Cell adhesion in embryo morphogenesis. Current
Opinion in Cell Biology. 2012;24(1):148-153. doi:10.1016/j.ceb.2011.11.006
apa: Barone, V., & Heisenberg, C.-P. J. (2012). Cell adhesion in embryo morphogenesis.
Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2011.11.006
chicago: Barone, Vanessa, and Carl-Philipp J Heisenberg. “Cell Adhesion in Embryo
Morphogenesis.” Current Opinion in Cell Biology. Elsevier, 2012. https://doi.org/10.1016/j.ceb.2011.11.006.
ieee: V. Barone and C.-P. J. Heisenberg, “Cell adhesion in embryo morphogenesis,”
Current Opinion in Cell Biology, vol. 24, no. 1. Elsevier, pp. 148–153,
2012.
ista: Barone V, Heisenberg C-PJ. 2012. Cell adhesion in embryo morphogenesis. Current
Opinion in Cell Biology. 24(1), 148–153.
mla: Barone, Vanessa, and Carl-Philipp J. Heisenberg. “Cell Adhesion in Embryo Morphogenesis.”
Current Opinion in Cell Biology, vol. 24, no. 1, Elsevier, 2012, pp. 148–53,
doi:10.1016/j.ceb.2011.11.006.
short: V. Barone, C.-P.J. Heisenberg, Current Opinion in Cell Biology 24 (2012)
148–153.
date_created: 2018-12-11T12:02:14Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2023-09-07T12:05:08Z
day: '01'
department:
- _id: CaHe
doi: 10.1016/j.ceb.2011.11.006
intvolume: ' 24'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 148 - 153
publication: Current Opinion in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '3423'
quality_controlled: '1'
related_material:
record:
- id: '961'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Cell adhesion in embryo morphogenesis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2012'
...
---
_id: '3247'
abstract:
- lang: eng
text: The Brazilian Merganser is a very rare and threatened species that nowadays
inhabits only a few protected areas and their surroundings in the Brazilian territory.
In order to estimate the remaining genetic diversity and population structure
in this species, two mitochondrial genes were sequenced in 39 individuals belonging
to two populations and in one individual collected in Argentina in 1950. We found
a highly significant divergence between two major remaining populations of Mergus
octosetaceus, which suggests a historical population structure in this species.
Furthermore, two deeply divergent lineages were found in a single location, which
could due to current or historical secondary contact. Based on the available genetic
data, we point out future directions which would contribute to design strategies
for conservation and management of this threatened species.
acknowledgement: "The present study received grants from FAPEMIG, CNPq, Petrobras
Ambiental and Fundação O Boticário de Conservação da Natureza, and followed all
ethical guidelines and legal requirements of Brazil for sampling and studying an
endangered species.\r\nWe thank the Specialist Work Group for the Conservation of
Brazilian Merganser for valuable discussions and opinions on this manuscript. We
also thank all the staff from Instituto Terra Brasilis and Funatura (Vivian S. Braz
and Gislaine Disconzi) for collecting the samples at Serra da Canastra and Chapada
dos Veadeiros, respectively; Dario A. Lijtmaerand and Pablo Tubaro for providing
the samples from Argentina, Bradley C. Livezey for sending copies of his papers,
and Geoff M. Hilton and Paulo de Tarso Z. Antas for useful suggestions that greatly
improved this manuscript."
author:
- first_name: Sibelle
full_name: Vilaça, Sibelle
last_name: Vilaça
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Lívia
full_name: Lins, Lívia
last_name: Lins
- first_name: Fabrício
full_name: Santos, Fabrício
last_name: Santos
citation:
ama: Vilaça S, Fernandes Redondo RA, Lins L, Santos F. Remaining genetic diversity
in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. 2012;13(1):293-298.
doi:10.1007/s10592-011-0262-5
apa: Vilaça, S., Fernandes Redondo, R. A., Lins, L., & Santos, F. (2012). Remaining
genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation
Genetics. Springer. https://doi.org/10.1007/s10592-011-0262-5
chicago: Vilaça, Sibelle, Rodrigo A Fernandes Redondo, Lívia Lins, and Fabrício
Santos. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).”
Conservation Genetics. Springer, 2012. https://doi.org/10.1007/s10592-011-0262-5.
ieee: S. Vilaça, R. A. Fernandes Redondo, L. Lins, and F. Santos, “Remaining genetic
diversity in Brazilian Merganser (Mergus octosetaceus),” Conservation Genetics,
vol. 13, no. 1. Springer, pp. 293–298, 2012.
ista: Vilaça S, Fernandes Redondo RA, Lins L, Santos F. 2012. Remaining genetic
diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics.
13(1), 293–298.
mla: Vilaça, Sibelle, et al. “Remaining Genetic Diversity in Brazilian Merganser
(Mergus Octosetaceus).” Conservation Genetics, vol. 13, no. 1, Springer,
2012, pp. 293–98, doi:10.1007/s10592-011-0262-5.
short: S. Vilaça, R.A. Fernandes Redondo, L. Lins, F. Santos, Conservation Genetics
13 (2012) 293–298.
date_created: 2018-12-11T12:02:15Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2021-01-12T07:42:05Z
day: '01'
department:
- _id: JoBo
doi: 10.1007/s10592-011-0262-5
intvolume: ' 13'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 293 - 298
publication: Conservation Genetics
publication_status: published
publisher: Springer
publist_id: '3420'
quality_controlled: '1'
scopus_import: 1
status: public
title: Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2012'
...
---
_id: '3248'
abstract:
- lang: eng
text: We describe RTblob, a high speed vision system that detects objects in cluttered
scenes based on their color and shape at a speed of over 800 frames/s. Because
the system is available as open-source software and relies only on off-the-shelf
PC hardware components, it can provide the basis for multiple application scenarios.
As an illustrative example, we show how RTblob can be used in a robotic table
tennis scenario to estimate ball trajectories through 3D space simultaneously
from four cameras images at a speed of 200 Hz.
article_processing_charge: No
article_type: original
author:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Jan
full_name: Peters, Jan
last_name: Peters
citation:
ama: Lampert C, Peters J. Real-time detection of colored objects in multiple camera
streams with off-the-shelf hardware components. Journal of Real-Time Image
Processing. 2012;7(1):31-41. doi:10.1007/s11554-010-0168-3
apa: Lampert, C., & Peters, J. (2012). Real-time detection of colored objects
in multiple camera streams with off-the-shelf hardware components. Journal
of Real-Time Image Processing. Springer. https://doi.org/10.1007/s11554-010-0168-3
chicago: Lampert, Christoph, and Jan Peters. “Real-Time Detection of Colored Objects
in Multiple Camera Streams with off-the-Shelf Hardware Components.” Journal
of Real-Time Image Processing. Springer, 2012. https://doi.org/10.1007/s11554-010-0168-3.
ieee: C. Lampert and J. Peters, “Real-time detection of colored objects in multiple
camera streams with off-the-shelf hardware components,” Journal of Real-Time
Image Processing, vol. 7, no. 1. Springer, pp. 31–41, 2012.
ista: Lampert C, Peters J. 2012. Real-time detection of colored objects in multiple
camera streams with off-the-shelf hardware components. Journal of Real-Time Image
Processing. 7(1), 31–41.
mla: Lampert, Christoph, and Jan Peters. “Real-Time Detection of Colored Objects
in Multiple Camera Streams with off-the-Shelf Hardware Components.” Journal
of Real-Time Image Processing, vol. 7, no. 1, Springer, 2012, pp. 31–41, doi:10.1007/s11554-010-0168-3.
short: C. Lampert, J. Peters, Journal of Real-Time Image Processing 7 (2012) 31–41.
date_created: 2018-12-11T12:02:15Z
date_published: 2012-03-01T00:00:00Z
date_updated: 2022-05-24T08:05:40Z
day: '01'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.1007/s11554-010-0168-3
file:
- access_level: open_access
checksum: 241be47ea50e81a283bcf4c45b07e8cc
content_type: application/pdf
creator: kschuh
date_created: 2019-02-12T10:52:25Z
date_updated: 2020-07-14T12:46:04Z
file_id: '5958'
file_name: 2012_Springer_Lampert.pdf
file_size: 2933187
relation: main_file
file_date_updated: 2020-07-14T12:46:04Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 31 - 41
publication: Journal of Real-Time Image Processing
publication_identifier:
eissn:
- 1861-8219
issn:
- 1861-8200
publication_status: published
publisher: Springer
publist_id: '3417'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Real-time detection of colored objects in multiple camera streams with off-the-shelf
hardware components
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2012'
...
---
_id: '3249'
abstract:
- lang: eng
text: Boolean notions of correctness are formalized by preorders on systems. Quantitative
measures of correctness can be formalized by real-valued distance functions between
systems, where the distance between implementation and specification provides
a measure of "fit" or "desirability". We extend the simulation
preorder to the quantitative setting by making each player of a simulation game
pay a certain price for her choices. We use the resulting games with quantitative
objectives to define three different simulation distances. The correctness distance
measures how much the specification must be changed in order to be satisfied by
the implementation. The coverage distance measures how much the implementation
restricts the degrees of freedom offered by the specification. The robustness
distance measures how much a system can deviate from the implementation description
without violating the specification. We consider these distances for safety as
well as liveness specifications. The distances can be computed in polynomial time
for safety specifications, and for liveness specifications given by weak fairness
constraints. We show that the distance functions satisfy the triangle inequality,
that the distance between two systems does not increase under parallel composition
with a third system, and that the distance between two systems can be bounded
from above and below by distances between abstractions of the two systems. These
properties suggest that our simulation distances provide an appropriate basis
for a quantitative theory of discrete systems. We also demonstrate how the robustness
distance can be used to measure how many transmission errors are tolerated by
error correcting codes.
acknowledgement: This work was partially supported by the ERC Advanced Grant QUAREM,
the FWF NFN Grant S11402-N23 (RiSE), the European Union project COMBEST and the
European Network of Excellence Artist Design.
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- 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, Henzinger TA, Radhakrishna A. Simulation distances. Theoretical
Computer Science. 2012;413(1):21-35. doi:10.1016/j.tcs.2011.08.002
apa: Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2012). Simulation distances.
Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2011.08.002
chicago: Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Simulation Distances.”
Theoretical Computer Science. Elsevier, 2012. https://doi.org/10.1016/j.tcs.2011.08.002.
ieee: P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Simulation distances,” Theoretical
Computer Science, vol. 413, no. 1. Elsevier, pp. 21–35, 2012.
ista: Cerny P, Henzinger TA, Radhakrishna A. 2012. Simulation distances. Theoretical
Computer Science. 413(1), 21–35.
mla: Cerny, Pavol, et al. “Simulation Distances.” Theoretical Computer Science,
vol. 413, no. 1, Elsevier, 2012, pp. 21–35, doi:10.1016/j.tcs.2011.08.002.
short: P. Cerny, T.A. Henzinger, A. Radhakrishna, Theoretical Computer Science 413
(2012) 21–35.
date_created: 2018-12-11T12:02:15Z
date_published: 2012-01-06T00:00:00Z
date_updated: 2023-02-23T12:24:04Z
day: '06'
department:
- _id: ToHe
doi: 10.1016/j.tcs.2011.08.002
ec_funded: 1
intvolume: ' 413'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 21 - 35
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
publication: Theoretical Computer Science
publication_status: published
publisher: Elsevier
publist_id: '3408'
pubrep_id: '42'
quality_controlled: '1'
related_material:
record:
- id: '4393'
relation: earlier_version
status: public
- id: '5389'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Simulation distances
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 413
year: '2012'
...
---
_id: '3250'
abstract:
- lang: eng
text: The Learning Parity with Noise (LPN) problem has recently found many applications
in cryptography as the hardness assumption underlying the constructions of "provably
secure" cryptographic schemes like encryption or authentication protocols.
Being provably secure means that the scheme comes with a proof showing that the
existence of an efficient adversary against the scheme implies that the underlying
hardness assumption is wrong. LPN based schemes are appealing for theoretical
and practical reasons. On the theoretical side, LPN based schemes offer a very
strong security guarantee. The LPN problem is equivalent to the problem of decoding
random linear codes, a problem that has been extensively studied in the last half
century. The fastest known algorithms run in exponential time and unlike most
number-theoretic problems used in cryptography, the LPN problem does not succumb
to known quantum algorithms. On the practical side, LPN based schemes are often
extremely simple and efficient in terms of code-size as well as time and space
requirements. This makes them prime candidates for light-weight devices like RFID
tags, which are too weak to implement standard cryptographic primitives like the
AES block-cipher. This talk will be a gentle introduction to provable security
using simple LPN based schemes as examples. Starting from pseudorandom generators
and symmetric key encryption, over secret-key authentication protocols, and, if
time admits, touching on recent constructions of public-key identification, commitments
and zero-knowledge proofs.
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Pietrzak KZ. Cryptography from learning parity with noise. In: Vol 7147. Springer;
2012:99-114. doi:10.1007/978-3-642-27660-6_9'
apa: 'Pietrzak, K. Z. (2012). Cryptography from learning parity with noise (Vol.
7147, pp. 99–114). Presented at the SOFSEM: Current Trends in Theory and Practice
of Computer Science, Špindlerův Mlýn, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-27660-6_9'
chicago: Pietrzak, Krzysztof Z. “Cryptography from Learning Parity with Noise,”
7147:99–114. Springer, 2012. https://doi.org/10.1007/978-3-642-27660-6_9.
ieee: 'K. Z. Pietrzak, “Cryptography from learning parity with noise,” presented
at the SOFSEM: Current Trends in Theory and Practice of Computer Science, Špindlerův
Mlýn, Czech Republic, 2012, vol. 7147, pp. 99–114.'
ista: 'Pietrzak KZ. 2012. Cryptography from learning parity with noise. SOFSEM:
Current Trends in Theory and Practice of Computer Science, LNCS, vol. 7147, 99–114.'
mla: Pietrzak, Krzysztof Z. Cryptography from Learning Parity with Noise.
Vol. 7147, Springer, 2012, pp. 99–114, doi:10.1007/978-3-642-27660-6_9.
short: K.Z. Pietrzak, in:, Springer, 2012, pp. 99–114.
conference:
end_date: 2012-01-27
location: Špindlerův Mlýn, Czech Republic
name: 'SOFSEM: Current Trends in Theory and Practice of Computer Science'
start_date: 2012-01-21
date_created: 2018-12-11T12:02:15Z
date_published: 2012-02-19T00:00:00Z
date_updated: 2021-01-12T07:42:07Z
day: '19'
department:
- _id: KrPi
doi: 10.1007/978-3-642-27660-6_9
intvolume: ' 7147'
language:
- iso: eng
month: '02'
oa_version: None
page: 99 - 114
publication_status: published
publisher: Springer
publist_id: '3407'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cryptography from learning parity with noise
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7147
year: '2012'
...
---
_id: '3251'
abstract:
- lang: eng
text: Many infinite state systems can be seen as well-structured transition systems
(WSTS), i.e., systems equipped with a well-quasi-ordering on states that is also
a simulation relation. WSTS are an attractive target for formal analysis because
there exist generic algorithms that decide interesting verification problems for
this class. Among the most popular algorithms are acceleration-based forward analyses
for computing the covering set. Termination of these algorithms can only be guaranteed
for flattable WSTS. Yet, many WSTS of practical interest are not flattable and
the question whether any given WSTS is flattable is itself undecidable. We therefore
propose an analysis that computes the covering set and captures the essence of
acceleration-based algorithms, but sacrifices precision for guaranteed termination.
Our analysis is an abstract interpretation whose abstract domain builds on the
ideal completion of the well-quasi-ordered state space, and a widening operator
that mimics acceleration and controls the loss of precision of the analysis. We
present instances of our framework for various classes of WSTS. Our experience
with a prototype implementation indicates that, despite the inherent precision
loss, our analysis often computes the precise covering set of the analyzed system.
acknowledgement: This research was supported in part by the European Research Council
(ERC) Advanced Investigator Grant QUAREM and by the Austrian Science Fund (FWF)
project S11402-N23.
alternative_title:
- LNCS
author:
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Zufferey D, Wies T, Henzinger TA. Ideal abstractions for well structured transition
systems. In: Vol 7148. Springer; 2012:445-460. doi:10.1007/978-3-642-27940-9_29'
apa: 'Zufferey, D., Wies, T., & Henzinger, T. A. (2012). Ideal abstractions
for well structured transition systems (Vol. 7148, pp. 445–460). Presented at
the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia,
PA, USA: Springer. https://doi.org/10.1007/978-3-642-27940-9_29'
chicago: Zufferey, Damien, Thomas Wies, and Thomas A Henzinger. “Ideal Abstractions
for Well Structured Transition Systems,” 7148:445–60. Springer, 2012. https://doi.org/10.1007/978-3-642-27940-9_29.
ieee: 'D. Zufferey, T. Wies, and T. A. Henzinger, “Ideal abstractions for well structured
transition systems,” presented at the VMCAI: Verification, Model Checking and
Abstract Interpretation, Philadelphia, PA, USA, 2012, vol. 7148, pp. 445–460.'
ista: 'Zufferey D, Wies T, Henzinger TA. 2012. Ideal abstractions for well structured
transition systems. VMCAI: Verification, Model Checking and Abstract Interpretation,
LNCS, vol. 7148, 445–460.'
mla: Zufferey, Damien, et al. Ideal Abstractions for Well Structured Transition
Systems. Vol. 7148, Springer, 2012, pp. 445–60, doi:10.1007/978-3-642-27940-9_29.
short: D. Zufferey, T. Wies, T.A. Henzinger, in:, Springer, 2012, pp. 445–460.
conference:
end_date: 2012-01-24
location: Philadelphia, PA, USA
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2012-01-22
date_created: 2018-12-11T12:02:16Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2023-09-07T11:36:36Z
day: '01'
ddc:
- '000'
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-27940-9_29
ec_funded: 1
file:
- access_level: open_access
checksum: f2f0d55efa32309ad1fe65a5fcaad90c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:35Z
date_updated: 2020-07-14T12:46:05Z
file_id: '4759'
file_name: IST-2012-100-v1+1_Ideal_abstractions_for_well-structured_transition_systems.pdf
file_size: 217104
relation: main_file
file_date_updated: 2020-07-14T12:46:05Z
has_accepted_license: '1'
intvolume: ' 7148'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 445 - 460
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '3406'
pubrep_id: '100'
quality_controlled: '1'
related_material:
record:
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relation: dissertation_contains
status: public
status: public
title: Ideal abstractions for well structured transition systems
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7148
year: '2012'
...