---
_id: '2830'
author:
- first_name: Christine
full_name: Moussion, Christine
id: 3356F664-F248-11E8-B48F-1D18A9856A87
last_name: Moussion
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Moussion C, Sixt MK. A conduit to amplify innate immunity. Immunity.
2013;38(5):853-854. doi:10.1016/j.immuni.2013.05.005
apa: Moussion, C., & Sixt, M. K. (2013). A conduit to amplify innate immunity.
Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2013.05.005
chicago: Moussion, Christine, and Michael K Sixt. “A Conduit to Amplify Innate Immunity.”
Immunity. Cell Press, 2013. https://doi.org/10.1016/j.immuni.2013.05.005.
ieee: C. Moussion and M. K. Sixt, “A conduit to amplify innate immunity,” Immunity,
vol. 38, no. 5. Cell Press, pp. 853–854, 2013.
ista: Moussion C, Sixt MK. 2013. A conduit to amplify innate immunity. Immunity.
38(5), 853–854.
mla: Moussion, Christine, and Michael K. Sixt. “A Conduit to Amplify Innate Immunity.”
Immunity, vol. 38, no. 5, Cell Press, 2013, pp. 853–54, doi:10.1016/j.immuni.2013.05.005.
short: C. Moussion, M.K. Sixt, Immunity 38 (2013) 853–854.
date_created: 2018-12-11T11:59:49Z
date_published: 2013-05-23T00:00:00Z
date_updated: 2021-01-12T07:00:01Z
day: '23'
department:
- _id: MiSi
doi: 10.1016/j.immuni.2013.05.005
intvolume: ' 38'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 853 - 854
publication: Immunity
publication_status: published
publisher: Cell Press
publist_id: '3969'
quality_controlled: '1'
scopus_import: 1
status: public
title: A conduit to amplify innate immunity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2013'
...
---
_id: '2831'
abstract:
- lang: eng
text: 'We consider Markov decision processes (MDPs) with Büchi (liveness) objectives.
We consider the problem of computing the set of almost-sure winning states from
where the objective can be ensured with probability 1. Our contributions are as
follows: First, we present the first subquadratic symbolic algorithm to compute
the almost-sure winning set for MDPs with Büchi objectives; our algorithm takes
O(n · √ m) symbolic steps as compared to the previous known algorithm that takes
O(n 2) symbolic steps, where n is the number of states and m is the number of
edges of the MDP. In practice MDPs have constant out-degree, and then our symbolic
algorithm takes O(n · √ n) symbolic steps, as compared to the previous known O(n
2) symbolic steps algorithm. Second, we present a new algorithm, namely win-lose
algorithm, with the following two properties: (a) the algorithm iteratively computes
subsets of the almost-sure winning set and its complement, as compared to all
previous algorithms that discover the almost-sure winning set upon termination;
and (b) requires O(n · √ K) symbolic steps, where K is the maximal number of edges
of strongly connected components (scc''s) of the MDP. The win-lose algorithm requires
symbolic computation of scc''s. Third, we improve the algorithm for symbolic scc
computation; the previous known algorithm takes linear symbolic steps, and our
new algorithm improves the constants associated with the linear number of steps.
In the worst case the previous known algorithm takes 5×n symbolic steps, whereas
our new algorithm takes 4×n symbolic steps.'
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
- first_name: Manas
full_name: Joglekar, Manas
last_name: Joglekar
- first_name: Nisarg
full_name: Shah, Nisarg
last_name: Shah
citation:
ama: Chatterjee K, Henzinger MH, Joglekar M, Shah N. Symbolic algorithms for qualitative
analysis of Markov decision processes with Büchi objectives. Formal Methods
in System Design. 2013;42(3):301-327. doi:10.1007/s10703-012-0180-2
apa: Chatterjee, K., Henzinger, M. H., Joglekar, M., & Shah, N. (2013). Symbolic
algorithms for qualitative analysis of Markov decision processes with Büchi objectives.
Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-012-0180-2
chicago: Chatterjee, Krishnendu, Monika H Henzinger, Manas Joglekar, and Nisarg
Shah. “Symbolic Algorithms for Qualitative Analysis of Markov Decision Processes
with Büchi Objectives.” Formal Methods in System Design. Springer, 2013.
https://doi.org/10.1007/s10703-012-0180-2.
ieee: K. Chatterjee, M. H. Henzinger, M. Joglekar, and N. Shah, “Symbolic algorithms
for qualitative analysis of Markov decision processes with Büchi objectives,”
Formal Methods in System Design, vol. 42, no. 3. Springer, pp. 301–327,
2013.
ista: Chatterjee K, Henzinger MH, Joglekar M, Shah N. 2013. Symbolic algorithms
for qualitative analysis of Markov decision processes with Büchi objectives. Formal
Methods in System Design. 42(3), 301–327.
mla: Chatterjee, Krishnendu, et al. “Symbolic Algorithms for Qualitative Analysis
of Markov Decision Processes with Büchi Objectives.” Formal Methods in System
Design, vol. 42, no. 3, Springer, 2013, pp. 301–27, doi:10.1007/s10703-012-0180-2.
short: K. Chatterjee, M.H. Henzinger, M. Joglekar, N. Shah, Formal Methods in System
Design 42 (2013) 301–327.
date_created: 2018-12-11T11:59:49Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2023-02-23T11:23:04Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/s10703-012-0180-2
ec_funded: 1
external_id:
arxiv:
- '1104.3348'
intvolume: ' 42'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1104.3348
month: '06'
oa: 1
oa_version: Preprint
page: 301 - 327
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Formal Methods in System Design
publication_status: published
publisher: Springer
publist_id: '3968'
quality_controlled: '1'
related_material:
record:
- id: '3342'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Symbolic algorithms for qualitative analysis of Markov decision processes with
Büchi objectives
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 42
year: '2013'
...
---
_id: '2832'
abstract:
- lang: eng
text: PIN-FORMED (PIN) proteins localize asymmetrically at the plasma membrane and
mediate intercellular polar transport of the plant hormone auxin that is crucial
for a multitude of developmental processes in plants. PIN localization is under
extensive control by environmental or developmental cues, but mechanisms regulating
PIN localization are not fully understood. Here we show that early endosomal components
ARF GEF BEN1 and newly identified Sec1/Munc18 family protein BEN2 are involved
in distinct steps of early endosomal trafficking. BEN1 and BEN2 are collectively
required for polar PIN localization, for their dynamic repolarization, and consequently
for auxin activity gradient formation and auxin-related developmental processes
including embryonic patterning, organogenesis, and vasculature venation patterning.
These results show that early endosomal trafficking is crucial for cell polarity
and auxin-dependent regulation of plant architecture.
article_number: e1003540
author:
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
- first_name: Saeko
full_name: Kitakura, Saeko
last_name: Kitakura
- first_name: Hana
full_name: Rakusová, Hana
last_name: Rakusová
- first_name: Tomohiro
full_name: Uemura, Tomohiro
last_name: Uemura
- first_name: Mugurel
full_name: Feraru, Mugurel
last_name: Feraru
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Tatsuo
full_name: Kakimoto, Tatsuo
last_name: Kakimoto
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Tanaka H, Kitakura S, Rakusová H, et al. Cell polarity and patterning by PIN
trafficking through early endosomal compartments in arabidopsis thaliana. PLoS
Genetics. 2013;9(5). doi:10.1371/journal.pgen.1003540
apa: Tanaka, H., Kitakura, S., Rakusová, H., Uemura, T., Feraru, M., De Rycke, R.,
… Friml, J. (2013). Cell polarity and patterning by PIN trafficking through early
endosomal compartments in arabidopsis thaliana. PLoS Genetics. Public Library
of Science. https://doi.org/10.1371/journal.pgen.1003540
chicago: Tanaka, Hirokazu, Saeko Kitakura, Hana Rakusová, Tomohiro Uemura, Mugurel
Feraru, Riet De Rycke, Stéphanie Robert, Tatsuo Kakimoto, and Jiří Friml. “Cell
Polarity and Patterning by PIN Trafficking through Early Endosomal Compartments
in Arabidopsis Thaliana.” PLoS Genetics. Public Library of Science, 2013.
https://doi.org/10.1371/journal.pgen.1003540.
ieee: H. Tanaka et al., “Cell polarity and patterning by PIN trafficking
through early endosomal compartments in arabidopsis thaliana,” PLoS Genetics,
vol. 9, no. 5. Public Library of Science, 2013.
ista: Tanaka H, Kitakura S, Rakusová H, Uemura T, Feraru M, De Rycke R, Robert S,
Kakimoto T, Friml J. 2013. Cell polarity and patterning by PIN trafficking through
early endosomal compartments in arabidopsis thaliana. PLoS Genetics. 9(5), e1003540.
mla: Tanaka, Hirokazu, et al. “Cell Polarity and Patterning by PIN Trafficking through
Early Endosomal Compartments in Arabidopsis Thaliana.” PLoS Genetics, vol.
9, no. 5, e1003540, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003540.
short: H. Tanaka, S. Kitakura, H. Rakusová, T. Uemura, M. Feraru, R. De Rycke, S.
Robert, T. Kakimoto, J. Friml, PLoS Genetics 9 (2013).
date_created: 2018-12-11T11:59:50Z
date_published: 2013-05-05T00:00:00Z
date_updated: 2021-01-12T07:00:03Z
day: '05'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1371/journal.pgen.1003540
ec_funded: 1
file:
- access_level: open_access
checksum: 050237d6c53e8d1601b26808ee1dd6d8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:39Z
date_updated: 2020-07-14T12:45:50Z
file_id: '4957'
file_name: IST-2016-411-v1+1_journal.pgen.1003540.pdf
file_size: 3813091
relation: main_file
file_date_updated: 2020-07-14T12:45:50Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '3967'
pubrep_id: '411'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cell polarity and patterning by PIN trafficking through early endosomal compartments
in arabidopsis thaliana
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '2833'
abstract:
- lang: eng
text: During development, mechanical forces cause changes in size, shape, number,
position, and gene expression of cells. They are therefore integral to any morphogenetic
processes. Force generation by actin-myosin networks and force transmission through
adhesive complexes are two self-organizing phenomena driving tissue morphogenesis.
Coordination and integration of forces by long-range force transmission and mechanosensing
of cells within tissues produce large-scale tissue shape changes. Extrinsic mechanical
forces also control tissue patterning by modulating cell fate specification and
differentiation. Thus, the interplay between tissue mechanics and biochemical
signaling orchestrates tissue morphogenesis and patterning in development.
acknowledgement: C.-P.H. is supported by the Institute of Science and Technology Austria
and grants from the Deutsche Forschungsgemeinschaft (DFG) and Fonds zur Förderung
der wissenschaftlichen Forschung (FWF).
author:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Yohanns
full_name: Bellaïche, Yohanns
last_name: Bellaïche
citation:
ama: Heisenberg C-PJ, Bellaïche Y. Forces in tissue morphogenesis and patterning.
Cell. 2013;153(5):948-962. doi:10.1016/j.cell.2013.05.008
apa: Heisenberg, C.-P. J., & Bellaïche, Y. (2013). Forces in tissue morphogenesis
and patterning. Cell. Cell Press. https://doi.org/10.1016/j.cell.2013.05.008
chicago: Heisenberg, Carl-Philipp J, and Yohanns Bellaïche. “Forces in Tissue Morphogenesis
and Patterning.” Cell. Cell Press, 2013. https://doi.org/10.1016/j.cell.2013.05.008.
ieee: C.-P. J. Heisenberg and Y. Bellaïche, “Forces in tissue morphogenesis and
patterning,” Cell, vol. 153, no. 5. Cell Press, pp. 948–962, 2013.
ista: Heisenberg C-PJ, Bellaïche Y. 2013. Forces in tissue morphogenesis and patterning.
Cell. 153(5), 948–962.
mla: Heisenberg, Carl-Philipp J., and Yohanns Bellaïche. “Forces in Tissue Morphogenesis
and Patterning.” Cell, vol. 153, no. 5, Cell Press, 2013, pp. 948–62, doi:10.1016/j.cell.2013.05.008.
short: C.-P.J. Heisenberg, Y. Bellaïche, Cell 153 (2013) 948–962.
date_created: 2018-12-11T11:59:50Z
date_published: 2013-05-23T00:00:00Z
date_updated: 2021-01-12T07:00:04Z
day: '23'
department:
- _id: CaHe
doi: 10.1016/j.cell.2013.05.008
intvolume: ' 153'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 948 - 962
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3966'
quality_controlled: '1'
scopus_import: 1
status: public
title: Forces in tissue morphogenesis and patterning
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 153
year: '2013'
...
---
_id: '2834'
abstract:
- lang: eng
text: Although the equations governing fluid flow are well known, there are no analytical
expressions that describe the complexity of turbulent motion. A recent proposition
is that in analogy to low dimensional chaotic systems, turbulence is organized
around unstable solutions of the governing equations which provide the building
blocks of the disordered dynamics. We report the discovery of periodic solutions
which just like intermittent turbulence are spatially localized and show that
turbulent transients arise from one such solution branch.
article_number: '224502'
arxiv: 1
author:
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
- first_name: Fernando
full_name: Mellibovsky, Fernando
last_name: Mellibovsky
- first_name: Nicolas
full_name: Roland, Nicolas
last_name: Roland
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Avila M, Mellibovsky F, Roland N, Hof B. Streamwise-localized solutions at
the onset of turbulence in pipe flow. Physical Review Letters. 2013;110(22).
doi:10.1103/PhysRevLett.110.224502
apa: Avila, M., Mellibovsky, F., Roland, N., & Hof, B. (2013). Streamwise-localized
solutions at the onset of turbulence in pipe flow. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.110.224502
chicago: Avila, Marc, Fernando Mellibovsky, Nicolas Roland, and Björn Hof. “Streamwise-Localized
Solutions at the Onset of Turbulence in Pipe Flow.” Physical Review Letters.
American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.224502.
ieee: M. Avila, F. Mellibovsky, N. Roland, and B. Hof, “Streamwise-localized solutions
at the onset of turbulence in pipe flow,” Physical Review Letters, vol.
110, no. 22. American Physical Society, 2013.
ista: Avila M, Mellibovsky F, Roland N, Hof B. 2013. Streamwise-localized solutions
at the onset of turbulence in pipe flow. Physical Review Letters. 110(22), 224502.
mla: Avila, Marc, et al. “Streamwise-Localized Solutions at the Onset of Turbulence
in Pipe Flow.” Physical Review Letters, vol. 110, no. 22, 224502, American
Physical Society, 2013, doi:10.1103/PhysRevLett.110.224502.
short: M. Avila, F. Mellibovsky, N. Roland, B. Hof, Physical Review Letters 110
(2013).
date_created: 2018-12-11T11:59:50Z
date_published: 2013-05-29T00:00:00Z
date_updated: 2021-01-12T07:00:05Z
day: '29'
department:
- _id: BjHo
doi: 10.1103/PhysRevLett.110.224502
ec_funded: 1
external_id:
arxiv:
- '1212.0230'
intvolume: ' 110'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1212.0230
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '3965'
quality_controlled: '1'
scopus_import: 1
status: public
title: Streamwise-localized solutions at the onset of turbulence in pipe flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2835'
abstract:
- lang: eng
text: The phytohormone auxin regulates virtually every aspect of plant development.
To identify new genes involved in auxin activity, a genetic screen was performed
for Arabidopsis (Arabidopsis thaliana) mutants with altered expression of the
auxin-responsive reporter DR5rev:GFP. One of the mutants recovered in the screen,
designated as weak auxin response3 (wxr3), exhibits much lower DR5rev:GFP expression
when treated with the synthetic auxin 2,4-dichlorophenoxyacetic acid and displays
severe defects in root development. The wxr3 mutant decreases polar auxin transport
and results in a disruption of the asymmetric auxin distribution. The levels of
the auxin transporters AUXIN1 and PIN-FORMED are dramatically reduced in the wxr3
root tip. Molecular analyses demonstrate that WXR3 is ROOT ULTRAVIOLET B-SENSITIVE1
(RUS1), a member of the conserved Domain of Unknown Function647 protein family
found in diverse eukaryotic organisms. Our data suggest that RUS1/WXR3 plays an
essential role in the regulation of polar auxin transport by maintaining the proper
level of auxin transporters on the plasma membrane.
author:
- first_name: Hong
full_name: Yu, Hong
last_name: Yu
- first_name: Michael
full_name: Karampelias, Michael
last_name: Karampelias
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Wendy
full_name: Peer, Wendy
last_name: Peer
- first_name: Ranjan
full_name: Swarup, Ranjan
last_name: Swarup
- first_name: Songqing
full_name: Ye, Songqing
last_name: Ye
- first_name: Lei
full_name: Ge, Lei
last_name: Ge
- first_name: Jerry
full_name: Cohen, Jerry
last_name: Cohen
- first_name: Angus
full_name: Murphy, Angus
last_name: Murphy
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Mark
full_name: Estelle, Mark
last_name: Estelle
citation:
ama: Yu H, Karampelias M, Robert S, et al. Root ultraviolet b-sensitive1/weak auxin
response3 is essential for polar auxin transport in arabidopsis. Plant Physiology.
2013;162(2):965-976. doi:10.1104/pp.113.217018
apa: Yu, H., Karampelias, M., Robert, S., Peer, W., Swarup, R., Ye, S., … Estelle,
M. (2013). Root ultraviolet b-sensitive1/weak auxin response3 is essential for
polar auxin transport in arabidopsis. Plant Physiology. American Society
of Plant Biologists. https://doi.org/10.1104/pp.113.217018
chicago: Yu, Hong, Michael Karampelias, Stéphanie Robert, Wendy Peer, Ranjan Swarup,
Songqing Ye, Lei Ge, et al. “Root Ultraviolet B-Sensitive1/Weak Auxin Response3
Is Essential for Polar Auxin Transport in Arabidopsis.” Plant Physiology.
American Society of Plant Biologists, 2013. https://doi.org/10.1104/pp.113.217018.
ieee: H. Yu et al., “Root ultraviolet b-sensitive1/weak auxin response3 is
essential for polar auxin transport in arabidopsis,” Plant Physiology,
vol. 162, no. 2. American Society of Plant Biologists, pp. 965–976, 2013.
ista: Yu H, Karampelias M, Robert S, Peer W, Swarup R, Ye S, Ge L, Cohen J, Murphy
A, Friml J, Estelle M. 2013. Root ultraviolet b-sensitive1/weak auxin response3
is essential for polar auxin transport in arabidopsis. Plant Physiology. 162(2),
965–976.
mla: Yu, Hong, et al. “Root Ultraviolet B-Sensitive1/Weak Auxin Response3 Is Essential
for Polar Auxin Transport in Arabidopsis.” Plant Physiology, vol. 162,
no. 2, American Society of Plant Biologists, 2013, pp. 965–76, doi:10.1104/pp.113.217018.
short: H. Yu, M. Karampelias, S. Robert, W. Peer, R. Swarup, S. Ye, L. Ge, J. Cohen,
A. Murphy, J. Friml, M. Estelle, Plant Physiology 162 (2013) 965–976.
date_created: 2018-12-11T11:59:51Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2021-01-12T07:00:05Z
day: '01'
department:
- _id: JiFr
doi: 10.1104/pp.113.217018
external_id:
pmid:
- '23580592'
intvolume: ' 162'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668084/
month: '06'
oa: 1
oa_version: Submitted Version
page: 965 - 976
pmid: 1
publication: Plant Physiology
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3964'
quality_controlled: '1'
scopus_import: 1
status: public
title: Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin
transport in arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 162
year: '2013'
...
---
_id: '2836'
abstract:
- lang: eng
text: 'We study the automatic synthesis of fair non-repudiation protocols, a class
of fair exchange protocols, used for digital contract signing. First, we show
how to specify the objectives of the participating agents and the trusted third
party as path formulas in linear temporal logic and prove that the satisfaction
of these objectives imply fairness; a property required of fair exchange protocols.
We then show that weak (co-operative) co-synthesis and classical (strictly competitive)
co-synthesis fail, whereas assume-guarantee synthesis (AGS) succeeds. We demonstrate
the success of AGS as follows: (a) any solution of AGS is attack-free; no subset
of participants can violate the objectives of the other participants; (b) the
Asokan-Shoup-Waidner certified mail protocol that has known vulnerabilities is
not a solution of AGS; (c) the Kremer-Markowitch non-repudiation protocol is a
solution of AGS; and (d) AGS presents a new and symmetric fair non-repudiation
protocol that is attack-free. To our knowledge this is the first application of
synthesis to fair non-repudiation protocols, and our results show how synthesis
can both automatically discover vulnerabilities in protocols and generate correct
protocols. The solution to AGS can be computed efficiently as the secure equilibrium
solution of three-player graph games. '
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: Vishwanath
full_name: Raman, Vishwanath
last_name: Raman
citation:
ama: Chatterjee K, Raman V. Assume-guarantee synthesis for digital contract signing.
Formal Aspects of Computing. 2013;26(4):825-859. doi:10.1007/s00165-013-0283-6
apa: Chatterjee, K., & Raman, V. (2013). Assume-guarantee synthesis for digital
contract signing. Formal Aspects of Computing. Springer. https://doi.org/10.1007/s00165-013-0283-6
chicago: Chatterjee, Krishnendu, and Vishwanath Raman. “Assume-Guarantee Synthesis
for Digital Contract Signing.” Formal Aspects of Computing. Springer, 2013.
https://doi.org/10.1007/s00165-013-0283-6.
ieee: K. Chatterjee and V. Raman, “Assume-guarantee synthesis for digital contract
signing,” Formal Aspects of Computing, vol. 26, no. 4. Springer, pp. 825–859,
2013.
ista: Chatterjee K, Raman V. 2013. Assume-guarantee synthesis for digital contract
signing. Formal Aspects of Computing. 26(4), 825–859.
mla: Chatterjee, Krishnendu, and Vishwanath Raman. “Assume-Guarantee Synthesis for
Digital Contract Signing.” Formal Aspects of Computing, vol. 26, no. 4,
Springer, 2013, pp. 825–59, doi:10.1007/s00165-013-0283-6.
short: K. Chatterjee, V. Raman, Formal Aspects of Computing 26 (2013) 825–859.
date_created: 2018-12-11T11:59:51Z
date_published: 2013-07-04T00:00:00Z
date_updated: 2021-01-12T07:00:06Z
day: '04'
department:
- _id: KrCh
doi: 10.1007/s00165-013-0283-6
ec_funded: 1
external_id:
arxiv:
- '1004.2697'
intvolume: ' 26'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1004.2697
month: '07'
oa: 1
oa_version: Preprint
page: 825 - 859
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Formal Aspects of Computing
publication_status: published
publisher: Springer
publist_id: '3963'
quality_controlled: '1'
scopus_import: 1
status: public
title: Assume-guarantee synthesis for digital contract signing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2013'
...
---
_id: '2837'
abstract:
- lang: eng
text: We consider a general class of N × N random matrices whose entries hij are
independent up to a symmetry constraint, but not necessarily identically distributed.
Our main result is a local semicircle law which improves previous results [17]
both in the bulk and at the edge. The error bounds are given in terms of the basic
small parameter of the model, maxi,j E|hij|2. As a consequence, we prove the universality
of the local n-point correlation functions in the bulk spectrum for a class of
matrices whose entries do not have comparable variances, including random band
matrices with band width W ≫N1-εn with some εn > 0 and with a negligible mean-field
component. In addition, we provide a coherent and pedagogical proof of the local
semicircle law, streamlining and strengthening previous arguments from [17, 19,
6].
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Antti
full_name: Knowles, Antti
last_name: Knowles
- first_name: Horng
full_name: Yau, Horng
last_name: Yau
- first_name: Jun
full_name: Yin, Jun
last_name: Yin
citation:
ama: Erdös L, Knowles A, Yau H, Yin J. The local semicircle law for a general class
of random matrices. Electronic Journal of Probability. 2013;18(59):1-58.
doi:10.1214/EJP.v18-2473
apa: Erdös, L., Knowles, A., Yau, H., & Yin, J. (2013). The local semicircle
law for a general class of random matrices. Electronic Journal of Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/EJP.v18-2473
chicago: Erdös, László, Antti Knowles, Horng Yau, and Jun Yin. “The Local Semicircle
Law for a General Class of Random Matrices.” Electronic Journal of Probability.
Institute of Mathematical Statistics, 2013. https://doi.org/10.1214/EJP.v18-2473.
ieee: L. Erdös, A. Knowles, H. Yau, and J. Yin, “The local semicircle law for a
general class of random matrices,” Electronic Journal of Probability, vol.
18, no. 59. Institute of Mathematical Statistics, pp. 1–58, 2013.
ista: Erdös L, Knowles A, Yau H, Yin J. 2013. The local semicircle law for a general
class of random matrices. Electronic Journal of Probability. 18(59), 1–58.
mla: Erdös, László, et al. “The Local Semicircle Law for a General Class of Random
Matrices.” Electronic Journal of Probability, vol. 18, no. 59, Institute
of Mathematical Statistics, 2013, pp. 1–58, doi:10.1214/EJP.v18-2473.
short: L. Erdös, A. Knowles, H. Yau, J. Yin, Electronic Journal of Probability 18
(2013) 1–58.
date_created: 2018-12-11T11:59:51Z
date_published: 2013-05-29T00:00:00Z
date_updated: 2021-01-12T07:00:06Z
day: '29'
ddc:
- '530'
department:
- _id: LaEr
doi: 10.1214/EJP.v18-2473
file:
- access_level: open_access
checksum: aac9e52a00cb2f5149dc9e362b5ccf44
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:46Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5169'
file_name: IST-2016-406-v1+1_2473-13759-1-PB.pdf
file_size: 651497
relation: main_file
file_date_updated: 2020-07-14T12:45:50Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '59'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1-58
publication: Electronic Journal of Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '3962'
pubrep_id: '406'
quality_controlled: '1'
scopus_import: 1
status: public
title: The local semicircle law for a general class of random matrices
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: 18
year: '2013'
...
---
_id: '2838'
abstract:
- lang: eng
text: Individuals with Down syndrome (DS) present important motor deficits that
derive from altered motor development of infants and young children. DYRK1A, a
candidate gene for DS abnormalities has been implicated in motor function due
to its expression in motor nuclei in the adult brain, and its overexpression in
DS mouse models leads to hyperactivity and altered motor learning. However, its
precise role in the adult motor system, or its possible involvement in postnatal
locomotor development has not yet been clarified. During the postnatal period
we observed time-specific expression of Dyrk1A in discrete subsets of brainstem
nuclei and spinal cord motor neurons. Interestingly, we describe for the first
time the presence of Dyrk1A in the presynaptic terminal of the neuromuscular junctions
and its axonal transport from the facial nucleus, suggesting a function for Dyrk1A
in these structures. Relevant to DS, Dyrk1A overexpression in transgenic mice
(TgDyrk1A) produces motor developmental alterations possibly contributing to DS
motor phenotypes and modifies the numbers of motor cholinergic neurons, suggesting
that the kinase may have a role in the development of the brainstem and spinal
cord motor system.
article_number: e54285
author:
- first_name: Gloria
full_name: Arquè Fuste, Gloria
id: 3CF33908-F248-11E8-B48F-1D18A9856A87
last_name: Arquè Fuste
- first_name: Anna
full_name: Casanovas, Anna
last_name: Casanovas
- first_name: Mara
full_name: Dierssen, Mara
last_name: Dierssen
citation:
ama: 'Arquè Fuste G, Casanovas A, Dierssen M. Dyrk1A is dynamically expressed on
subsets of motor neurons and in the neuromuscular junction: Possible role in Down
syndrome. PLoS One. 2013;8(1). doi:10.1371/journal.pone.0054285'
apa: 'Arquè Fuste, G., Casanovas, A., & Dierssen, M. (2013). Dyrk1A is dynamically
expressed on subsets of motor neurons and in the neuromuscular junction: Possible
role in Down syndrome. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0054285'
chicago: 'Arquè Fuste, Gloria, Anna Casanovas, and Mara Dierssen. “Dyrk1A Is Dynamically
Expressed on Subsets of Motor Neurons and in the Neuromuscular Junction: Possible
Role in Down Syndrome.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0054285.'
ieee: 'G. Arquè Fuste, A. Casanovas, and M. Dierssen, “Dyrk1A is dynamically expressed
on subsets of motor neurons and in the neuromuscular junction: Possible role in
Down syndrome,” PLoS One, vol. 8, no. 1. Public Library of Science, 2013.'
ista: 'Arquè Fuste G, Casanovas A, Dierssen M. 2013. Dyrk1A is dynamically expressed
on subsets of motor neurons and in the neuromuscular junction: Possible role in
Down syndrome. PLoS One. 8(1), e54285.'
mla: 'Arquè Fuste, Gloria, et al. “Dyrk1A Is Dynamically Expressed on Subsets of
Motor Neurons and in the Neuromuscular Junction: Possible Role in Down Syndrome.”
PLoS One, vol. 8, no. 1, e54285, Public Library of Science, 2013, doi:10.1371/journal.pone.0054285.'
short: G. Arquè Fuste, A. Casanovas, M. Dierssen, PLoS One 8 (2013).
date_created: 2018-12-11T11:59:52Z
date_published: 2013-01-16T00:00:00Z
date_updated: 2021-01-12T07:00:07Z
day: '16'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1371/journal.pone.0054285
file:
- access_level: open_access
checksum: 512733b21419574a45f10cabef3d7f81
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:38Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5160'
file_name: IST-2016-407-v1+1_journal.pone.0054285.pdf
file_size: 4795977
relation: main_file
file_date_updated: 2020-07-14T12:45:50Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3960'
pubrep_id: '407'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular
junction: Possible role in Down syndrome'
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: 8
year: '2013'
...
---
_id: '2839'
abstract:
- lang: eng
text: Directional guidance of cells via gradients of chemokines is considered crucial
for embryonic development, cancer dissemination, and immune responses. Nevertheless,
the concept still lacks direct experimental confirmation in vivo. Here, we identify
endogenous gradients of the chemokine CCL21 within mouse skin and show that they
guide dendritic cells toward lymphatic vessels. Quantitative imaging reveals depots
of CCL21 within lymphatic endothelial cells and steeply decaying gradients within
the perilymphatic interstitium. These gradients match the migratory patterns of
the dendritic cells, which directionally approach vessels from a distance of up
to 90-micrometers. Interstitial CCL21 is immobilized to heparan sulfates, and
its experimental delocalization or swamping the endogenous gradients abolishes
directed migration. These findings functionally establish the concept of haptotaxis,
directed migration along immobilized gradients, in tissues.
acknowledgement: We thank M. Frank for technical assistance and S. Cremer, P. Schmalhorst,
and E. Kiermaier for critical reading of the manuscript. This work was supported
by a Humboldt Foundation postdoctoral fellowship (to M.W.), the German Research
Foundation (Si1323 1,2 to M.S.), the Human Frontier Science Program (HFSP RGP0058/2011
to M.S.), the European Research Council (ERC StG 281556 to M.S.), and the Swiss
National Science Foundation (31003A 127474 to D.F.L., 130488 to S.A.L.).
article_processing_charge: No
article_type: original
author:
- first_name: Michele
full_name: Weber, Michele
id: 3A3FC708-F248-11E8-B48F-1D18A9856A87
last_name: Weber
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Christine
full_name: Moussion, Christine
id: 3356F664-F248-11E8-B48F-1D18A9856A87
last_name: Moussion
- first_name: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Daniel
full_name: Legler, Daniel
last_name: Legler
- first_name: Sanjiv
full_name: Luther, Sanjiv
last_name: Luther
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Weber M, Hauschild R, Schwarz J, et al. Interstitial dendritic cell guidance
by haptotactic chemokine gradients. Science. 2013;339(6117):328-332. doi:10.1126/science.1228456
apa: Weber, M., Hauschild, R., Schwarz, J., Moussion, C., de Vries, I., Legler,
D., … Sixt, M. K. (2013). Interstitial dendritic cell guidance by haptotactic
chemokine gradients. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1228456
chicago: Weber, Michele, Robert Hauschild, Jan Schwarz, Christine Moussion, Ingrid
de Vries, Daniel Legler, Sanjiv Luther, Mark Tobias Bollenbach, and Michael K
Sixt. “Interstitial Dendritic Cell Guidance by Haptotactic Chemokine Gradients.”
Science. American Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1228456.
ieee: M. Weber et al., “Interstitial dendritic cell guidance by haptotactic
chemokine gradients,” Science, vol. 339, no. 6117. American Association
for the Advancement of Science, pp. 328–332, 2013.
ista: Weber M, Hauschild R, Schwarz J, Moussion C, de Vries I, Legler D, Luther
S, Bollenbach MT, Sixt MK. 2013. Interstitial dendritic cell guidance by haptotactic
chemokine gradients. Science. 339(6117), 328–332.
mla: Weber, Michele, et al. “Interstitial Dendritic Cell Guidance by Haptotactic
Chemokine Gradients.” Science, vol. 339, no. 6117, American Association
for the Advancement of Science, 2013, pp. 328–32, doi:10.1126/science.1228456.
short: M. Weber, R. Hauschild, J. Schwarz, C. Moussion, I. de Vries, D. Legler,
S. Luther, M.T. Bollenbach, M.K. Sixt, Science 339 (2013) 328–332.
date_created: 2018-12-11T11:59:52Z
date_published: 2013-01-18T00:00:00Z
date_updated: 2022-06-10T10:21:40Z
day: '18'
department:
- _id: MiSi
- _id: Bio
doi: 10.1126/science.1228456
ec_funded: 1
intvolume: ' 339'
issue: '6117'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://kops.uni-konstanz.de/bitstream/123456789/26341/2/Weber_263418.pdf
month: '01'
oa: 1
oa_version: Published Version
page: 328 - 332
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
- _id: 25ABD200-B435-11E9-9278-68D0E5697425
grant_number: RGP0058/2011
name: 'Cell migration in complex environments: from in vivo experiments to theoretical
models'
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '3959'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interstitial dendritic cell guidance by haptotactic chemokine gradients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 339
year: '2013'
...
---
_id: '2840'
abstract:
- lang: eng
text: It is known that the entorhinal cortex plays a crucial role in spatial cognition
in rodents. Neuroanatomical and electrophysiological data suggest that there is
a functional distinction between 2 subregions within the entorhinal cortex, the
medial entorhinal cortex (MEC), and the lateral entorhinal cortex (LEC). Rats
with MEC or LEC lesions were trained in 2 navigation tasks requiring allothetic
(water maze task) or idiothetic (path integration) information processing and
2-object exploration tasks allowing testing of spatial and nonspatial processing
of intramaze objects. MEC lesions mildly affected place navigation in the water
maze and produced a path integration deficit. They also altered the processing
of spatial information in both exploration tasks while sparing the processing
of nonspatial information. LEC lesions did not affect navigation abilities in
both the water maze and the path integration tasks. They altered spatial and nonspatial
processing in the object exploration task but not in the one-trial recognition
task. Overall, these results indicate that the MEC is important for spatial processing
and path integration. The LEC has some influence on both spatial and nonspatial
processes, suggesting that the 2 kinds of information interact at the level of
the EC.
author:
- first_name: Tiffany
full_name: Van Cauter, Tiffany
last_name: Van Cauter
- first_name: Jeremy
full_name: Camon, Jeremy
last_name: Camon
- first_name: Alice
full_name: Alvernhe, Alice
id: 467FB3D4-F248-11E8-B48F-1D18A9856A87
last_name: Alvernhe
- first_name: Coralie
full_name: Elduayen, Coralie
last_name: Elduayen
- first_name: Francesca
full_name: Sargolini, Francesca
last_name: Sargolini
- first_name: Étienne
full_name: Save, Étienne
last_name: Save
citation:
ama: Van Cauter T, Camon J, Alvernhe A, Elduayen C, Sargolini F, Save É. Distinct
roles of medial and lateral entorhinal cortex in spatial cognition. Cerebral
Cortex. 2013;23(2):451-459. doi:10.1093/cercor/bhs033
apa: Van Cauter, T., Camon, J., Alvernhe, A., Elduayen, C., Sargolini, F., &
Save, É. (2013). Distinct roles of medial and lateral entorhinal cortex in spatial
cognition. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bhs033
chicago: Van Cauter, Tiffany, Jeremy Camon, Alice Alvernhe, Coralie Elduayen, Francesca
Sargolini, and Étienne Save. “Distinct Roles of Medial and Lateral Entorhinal
Cortex in Spatial Cognition.” Cerebral Cortex. Oxford University Press,
2013. https://doi.org/10.1093/cercor/bhs033.
ieee: T. Van Cauter, J. Camon, A. Alvernhe, C. Elduayen, F. Sargolini, and É. Save,
“Distinct roles of medial and lateral entorhinal cortex in spatial cognition,”
Cerebral Cortex, vol. 23, no. 2. Oxford University Press, pp. 451–459,
2013.
ista: Van Cauter T, Camon J, Alvernhe A, Elduayen C, Sargolini F, Save É. 2013.
Distinct roles of medial and lateral entorhinal cortex in spatial cognition. Cerebral
Cortex. 23(2), 451–459.
mla: Van Cauter, Tiffany, et al. “Distinct Roles of Medial and Lateral Entorhinal
Cortex in Spatial Cognition.” Cerebral Cortex, vol. 23, no. 2, Oxford University
Press, 2013, pp. 451–59, doi:10.1093/cercor/bhs033.
short: T. Van Cauter, J. Camon, A. Alvernhe, C. Elduayen, F. Sargolini, É. Save,
Cerebral Cortex 23 (2013) 451–459.
date_created: 2018-12-11T11:59:52Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2021-01-12T07:00:08Z
day: '01'
department:
- _id: JoCs
doi: 10.1093/cercor/bhs033
intvolume: ' 23'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 451 - 459
publication: Cerebral Cortex
publication_status: published
publisher: Oxford University Press
publist_id: '3958'
quality_controlled: '1'
scopus_import: 1
status: public
title: Distinct roles of medial and lateral entorhinal cortex in spatial cognition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2013'
...
---
_id: '2841'
abstract:
- lang: eng
text: In zebrafish early development, blastoderm cells undergo extensive radial
intercalations, triggering the spreading of the blastoderm over the yolk cell
and thereby initiating embryonic body axis formation. Now reporting in Developmental
Cell, Song et al. (2013) demonstrate a critical function for EGF-dependent E-cadherin
endocytosis in promoting blastoderm cell intercalations.
author:
- first_name: Hitoshi
full_name: Morita, Hitoshi
id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87
last_name: Morita
- 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: 'Morita H, Heisenberg C-PJ. Holding on and letting go: Cadherin turnover in
cell intercalation. Developmental Cell. 2013;24(6):567-569. doi:10.1016/j.devcel.2013.03.007'
apa: 'Morita, H., & Heisenberg, C.-P. J. (2013). Holding on and letting go:
Cadherin turnover in cell intercalation. Developmental Cell. Cell Press.
https://doi.org/10.1016/j.devcel.2013.03.007'
chicago: 'Morita, Hitoshi, and Carl-Philipp J Heisenberg. “Holding on and Letting
Go: Cadherin Turnover in Cell Intercalation.” Developmental Cell. Cell
Press, 2013. https://doi.org/10.1016/j.devcel.2013.03.007.'
ieee: 'H. Morita and C.-P. J. Heisenberg, “Holding on and letting go: Cadherin turnover
in cell intercalation,” Developmental Cell, vol. 24, no. 6. Cell Press,
pp. 567–569, 2013.'
ista: 'Morita H, Heisenberg C-PJ. 2013. Holding on and letting go: Cadherin turnover
in cell intercalation. Developmental Cell. 24(6), 567–569.'
mla: 'Morita, Hitoshi, and Carl-Philipp J. Heisenberg. “Holding on and Letting Go:
Cadherin Turnover in Cell Intercalation.” Developmental Cell, vol. 24,
no. 6, Cell Press, 2013, pp. 567–69, doi:10.1016/j.devcel.2013.03.007.'
short: H. Morita, C.-P.J. Heisenberg, Developmental Cell 24 (2013) 567–569.
date_created: 2018-12-11T11:59:52Z
date_published: 2013-05-25T00:00:00Z
date_updated: 2021-01-12T07:00:09Z
day: '25'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2013.03.007
intvolume: ' 24'
issue: '6'
language:
- iso: eng
month: '05'
oa_version: None
page: 567 - 569
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '3956'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Holding on and letting go: Cadherin turnover in cell intercalation'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2013'
...
---
_id: '2842'
abstract:
- lang: eng
text: 'We outline two approaches to inference of neighbourhood size, N, and dispersal
rate, σ2, based on either allele frequencies or on the lengths of sequence blocks
that are shared between genomes. Over intermediate timescales (10-100 generations,
say), populations that live in two dimensions approach a quasi-equilibrium that
is independent of both their local structure and their deeper history. Over such
scales, the standardised covariance of allele frequencies (i.e. pairwise FS T)
falls with the logarithm of distance, and depends only on neighbourhood size,
N, and a ''local scale'', κ; the rate of gene flow, σ2, cannot be inferred. We
show how spatial correlations can be accounted for, assuming a Gaussian distribution
of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively,
inferences can be based on the distribution of the lengths of sequence that are
identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about
intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood
size, the distribution of long blocks is given directly by the classical Wright-Malécot
formula; this relationship can be used to infer both N and σ2. With small neighbourhood
size, there is an appreciable chance that recombinant lineages will coalesce back
before escaping into the distant past. For this case, we show that if genomes
are sampled from some distance apart, then the distribution of lengths of blocks
that are identical in state is geometric, with a mean that depends on N and σ2.'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: 'Barton NH, Etheridge A, Kelleher J, Véber A. Inference in two dimensions:
Allele frequencies versus lengths of shared sequence blocks. Theoretical Population
Biology. 2013;87(1):105-119. doi:10.1016/j.tpb.2013.03.001'
apa: 'Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Inference
in two dimensions: Allele frequencies versus lengths of shared sequence blocks.
Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2013.03.001'
chicago: 'Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber.
“Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence
Blocks.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2013.03.001.'
ieee: 'N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Inference in two
dimensions: Allele frequencies versus lengths of shared sequence blocks,” Theoretical
Population Biology, vol. 87, no. 1. Elsevier, pp. 105–119, 2013.'
ista: 'Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Inference in two dimensions:
Allele frequencies versus lengths of shared sequence blocks. Theoretical Population
Biology. 87(1), 105–119.'
mla: 'Barton, Nicholas H., et al. “Inference in Two Dimensions: Allele Frequencies
versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology,
vol. 87, no. 1, Elsevier, 2013, pp. 105–19, doi:10.1016/j.tpb.2013.03.001.'
short: N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population
Biology 87 (2013) 105–119.
date_created: 2018-12-11T11:59:53Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T07:00:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2013.03.001
ec_funded: 1
file:
- access_level: open_access
checksum: 9bf9d9a6fd03dd9df50906891f393bf8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:33Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5288'
file_name: IST-2016-558-v1+1_inference_revised3101NB.pdf
file_size: 1554712
relation: main_file
- access_level: open_access
checksum: 2bceddb76edacd0cd5fad73051e2a928
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:34Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5289'
file_name: IST-2016-558-v1+2_inference_revised3101NBApp.pdf
file_size: 822964
relation: main_file
file_date_updated: 2020-07-14T12:45:50Z
has_accepted_license: '1'
intvolume: ' 87'
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 105 - 119
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Theoretical Population Biology
publication_status: published
publisher: Elsevier
publist_id: '3953'
pubrep_id: '558'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Inference in two dimensions: Allele frequencies versus lengths of shared sequence
blocks'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2013'
...
---
_id: '2843'
abstract:
- lang: eng
text: 'Mathematical objects can be measured unambiguously, but not so objects from
our physical world. Even the total length of tubelike shapes has its difficulties.
We introduce a combination of geometric, probabilistic, and topological methods
to design a stable length estimate for tube-like shapes; that is: one that is
insensitive to small shape changes.'
alternative_title:
- LNCS
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: 'Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes.
In: 17th IAPR International Conference on Discrete Geometry for Computer Imagery.
Vol 7749. Springer; 2013:XV-XIX. doi:10.1007/978-3-642-37067-0'
apa: 'Edelsbrunner, H., & Pausinger, F. (2013). Stable length estimates of tube-like
shapes. In 17th IAPR International Conference on Discrete Geometry for Computer
Imagery (Vol. 7749, pp. XV–XIX). Seville, Spain: Springer. https://doi.org/10.1007/978-3-642-37067-0'
chicago: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates
of Tube-like Shapes.” In 17th IAPR International Conference on Discrete Geometry
for Computer Imagery, 7749:XV–XIX. Springer, 2013. https://doi.org/10.1007/978-3-642-37067-0.
ieee: H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,”
in 17th IAPR International Conference on Discrete Geometry for Computer Imagery,
Seville, Spain, 2013, vol. 7749, pp. XV–XIX.
ista: 'Edelsbrunner H, Pausinger F. 2013. Stable length estimates of tube-like shapes.
17th IAPR International Conference on Discrete Geometry for Computer Imagery.
DGCI: Discrete Geometry for Computer Imagery, LNCS, vol. 7749, XV–XIX.'
mla: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like
Shapes.” 17th IAPR International Conference on Discrete Geometry for Computer
Imagery, vol. 7749, Springer, 2013, pp. XV–XIX, doi:10.1007/978-3-642-37067-0.
short: H. Edelsbrunner, F. Pausinger, in:, 17th IAPR International Conference on
Discrete Geometry for Computer Imagery, Springer, 2013, pp. XV–XIX.
conference:
end_date: 2013-03-22
location: Seville, Spain
name: 'DGCI: Discrete Geometry for Computer Imagery'
start_date: 2013-03-20
date_created: 2018-12-11T11:59:53Z
date_published: 2013-02-21T00:00:00Z
date_updated: 2023-02-23T10:35:00Z
day: '21'
department:
- _id: HeEd
doi: 10.1007/978-3-642-37067-0
intvolume: ' 7749'
language:
- iso: eng
month: '02'
oa_version: None
page: XV - XIX
publication: 17th IAPR International Conference on Discrete Geometry for Computer
Imagery
publication_status: published
publisher: Springer
publist_id: '3952'
quality_controlled: '1'
related_material:
record:
- id: '2255'
relation: later_version
status: public
scopus_import: 1
status: public
title: Stable length estimates of tube-like shapes
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7749
year: '2013'
...
---
_id: '2844'
abstract:
- lang: eng
text: As soon as a seed germinates, plant growth relates to gravity to ensure that
the root penetrates the soil and the shoot expands aerially. Whereas mechanisms
of positive and negative orthogravitropism of primary roots and shoots are relatively
well understood [1-3], lateral organs often show more complex growth behavior
[4]. Lateral roots (LRs) seemingly suppress positive gravitropic growth and show
a defined gravitropic set-point angle (GSA) that allows radial expansion of the
root system (plagiotropism) [3, 4]. Despite its eminent importance for root architecture,
it so far remains completely unknown how lateral organs partially suppress positive
orthogravitropism. Here we show that the phytohormone auxin steers GSA formation
and limits positive orthogravitropism in LR. Low and high auxin levels/signaling
lead to radial or axial root systems, respectively. At a cellular level, it is
the auxin transport-dependent regulation of asymmetric growth in the elongation
zone that determines GSA. Our data suggest that strong repression of PIN4/PIN7
and transient PIN3 expression limit auxin redistribution in young LR columella
cells. We conclude that PIN activity, by temporally limiting the asymmetric auxin
fluxes in the tip of LRs, induces transient, differential growth responses in
the elongation zone and, consequently, controls root architecture.
author:
- first_name: Michel
full_name: Rosquete, Michel
last_name: Rosquete
- first_name: Daniel
full_name: Von Wangenheim, Daniel
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Elke
full_name: Barbez, Elke
last_name: Barbez
- first_name: Ernst
full_name: Stelzer, Ernst
last_name: Stelzer
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Alexis
full_name: Maizel, Alexis
last_name: Maizel
- first_name: Jürgen
full_name: Kleine Vehn, Jürgen
last_name: Kleine Vehn
citation:
ama: Rosquete M, von Wangenheim D, Marhavý P, et al. An auxin transport mechanism
restricts positive orthogravitropism in lateral roots. Current Biology.
2013;23(9):817-822. doi:10.1016/j.cub.2013.03.064
apa: Rosquete, M., von Wangenheim, D., Marhavý, P., Barbez, E., Stelzer, E., Benková,
E., … Kleine Vehn, J. (2013). An auxin transport mechanism restricts positive
orthogravitropism in lateral roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.03.064
chicago: Rosquete, Michel, Daniel von Wangenheim, Peter Marhavý, Elke Barbez, Ernst
Stelzer, Eva Benková, Alexis Maizel, and Jürgen Kleine Vehn. “An Auxin Transport
Mechanism Restricts Positive Orthogravitropism in Lateral Roots.” Current Biology.
Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.03.064.
ieee: M. Rosquete et al., “An auxin transport mechanism restricts positive
orthogravitropism in lateral roots,” Current Biology, vol. 23, no. 9. Cell
Press, pp. 817–822, 2013.
ista: Rosquete M, von Wangenheim D, Marhavý P, Barbez E, Stelzer E, Benková E, Maizel
A, Kleine Vehn J. 2013. An auxin transport mechanism restricts positive orthogravitropism
in lateral roots. Current Biology. 23(9), 817–822.
mla: Rosquete, Michel, et al. “An Auxin Transport Mechanism Restricts Positive Orthogravitropism
in Lateral Roots.” Current Biology, vol. 23, no. 9, Cell Press, 2013, pp.
817–22, doi:10.1016/j.cub.2013.03.064.
short: M. Rosquete, D. von Wangenheim, P. Marhavý, E. Barbez, E. Stelzer, E. Benková,
A. Maizel, J. Kleine Vehn, Current Biology 23 (2013) 817–822.
date_created: 2018-12-11T11:59:53Z
date_published: 2013-05-06T00:00:00Z
date_updated: 2021-01-12T07:00:10Z
day: '06'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1016/j.cub.2013.03.064
ec_funded: 1
intvolume: ' 23'
issue: '9'
language:
- iso: eng
month: '05'
oa_version: None
page: 817 - 822
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '3950'
quality_controlled: '1'
scopus_import: 1
status: public
title: An auxin transport mechanism restricts positive orthogravitropism in lateral
roots
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2013'
...
---
_id: '2845'
abstract:
- lang: eng
text: At synapses formed between dissociated neurons, about half of all synaptic
vesicles are refractory to evoked release, forming the so-called "resting
pool." Here, we use optical measurements of vesicular pH to study developmental
changes in pool partitioning and vesicle cycling in cultured hippocampal slices.
Two-photon imaging of a genetically encoded two-color release sensor (ratio-sypHy)
allowed us to perform calibrated measurements at individual Schaffer collateral
boutons. Mature boutons released a large fraction of their vesicles during simulated
place field activity, and vesicle retrieval rates were 7-fold higher compared
to immature boutons. Saturating stimulation mobilized essentially all vesicles
at mature synapses. Resting pool formation and a concomitant reduction in evoked
release was induced by chronic depolarization but not by acute inhibition of the
protein phosphatase calcineurin. We conclude that synapses in CA1 undergo a prominent
refinement of vesicle use during early postnatal development that is not recapitulated
in dissociated neuronal culture.
author:
- first_name: Tobias
full_name: Rose, Tobias
last_name: Rose
- first_name: Philipp
full_name: Schönenberger, Philipp
id: 3B9D816C-F248-11E8-B48F-1D18A9856A87
last_name: Schönenberger
- first_name: Karel
full_name: Jezek, Karel
last_name: Jezek
- first_name: Thomas
full_name: Oertner, Thomas
last_name: Oertner
citation:
ama: Rose T, Schönenberger P, Jezek K, Oertner T. Developmental refinement of vesicle
cycling at Schaffer collateral synapses. Neuron. 2013;77(6):1109-1121.
doi:10.1016/j.neuron.2013.01.021
apa: Rose, T., Schönenberger, P., Jezek, K., & Oertner, T. (2013). Developmental
refinement of vesicle cycling at Schaffer collateral synapses. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2013.01.021
chicago: Rose, Tobias, Philipp Schönenberger, Karel Jezek, and Thomas Oertner. “Developmental
Refinement of Vesicle Cycling at Schaffer Collateral Synapses.” Neuron.
Elsevier, 2013. https://doi.org/10.1016/j.neuron.2013.01.021.
ieee: T. Rose, P. Schönenberger, K. Jezek, and T. Oertner, “Developmental refinement
of vesicle cycling at Schaffer collateral synapses,” Neuron, vol. 77, no.
6. Elsevier, pp. 1109–1121, 2013.
ista: Rose T, Schönenberger P, Jezek K, Oertner T. 2013. Developmental refinement
of vesicle cycling at Schaffer collateral synapses. Neuron. 77(6), 1109–1121.
mla: Rose, Tobias, et al. “Developmental Refinement of Vesicle Cycling at Schaffer
Collateral Synapses.” Neuron, vol. 77, no. 6, Elsevier, 2013, pp. 1109–21,
doi:10.1016/j.neuron.2013.01.021.
short: T. Rose, P. Schönenberger, K. Jezek, T. Oertner, Neuron 77 (2013) 1109–1121.
date_created: 2018-12-11T11:59:54Z
date_published: 2013-03-20T00:00:00Z
date_updated: 2021-01-12T07:00:11Z
day: '20'
department:
- _id: JoCs
doi: 10.1016/j.neuron.2013.01.021
intvolume: ' 77'
issue: '6'
language:
- iso: eng
month: '03'
oa_version: None
page: 1109 - 1121
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '3949'
quality_controlled: '1'
scopus_import: 1
status: public
title: Developmental refinement of vesicle cycling at Schaffer collateral synapses
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2013'
...
---
_id: '2846'
abstract:
- lang: eng
text: The Red Queen hypothesis proposes that coevolving parasites select for outcrossing
in the host. Outcrossing relies on males, which often show lower immune investment
due to, for example, sexual selection. Here, we demonstrate that such sex differences
in immunity interfere with parasite-mediated selection for outcrossing. Two independent
coevolution experiments with Caenorhabditis elegans and its microparasite Bacillus
thuringiensis produced decreased yet stable frequencies of outcrossing male hosts.
A subsequent systematic analysis verified that male C. elegans suffered from a
direct selective disadvantage under parasite pressure (i.e. lower resistance,
decreased sexual activity, increased escape behaviour), which can reduce outcrossing
and thus male frequencies. At the same time, males offered an indirect selective
benefit, because male-mediated outcrossing increased offspring resistance, thus
favouring male persistence in the evolving populations. As sex differences in
immunity are widespread, such interference of opposing selective constraints is
likely of central importance during host adaptation to a coevolving parasite.
article_processing_charge: No
author:
- first_name: Leila
full_name: El Masri, Leila
id: 349A6E66-F248-11E8-B48F-1D18A9856A87
last_name: El Masri
- first_name: Rebecca
full_name: Schulte, Rebecca
last_name: Schulte
- first_name: Nadine
full_name: Timmermeyer, Nadine
last_name: Timmermeyer
- first_name: Stefanie
full_name: Thanisch, Stefanie
last_name: Thanisch
- first_name: Lena
full_name: Crummenerl, Lena
last_name: Crummenerl
- first_name: Gunther
full_name: Jansen, Gunther
last_name: Jansen
- first_name: Nico
full_name: Michiels, Nico
last_name: Michiels
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
citation:
ama: El Masri L, Schulte R, Timmermeyer N, et al. Sex differences in host defence
interfere with parasite-mediated selection for outcrossing during host-parasite
coevolution. Ecology Letters. 2013;16(4):461-468. doi:10.1111/ele.12068
apa: El Masri, L., Schulte, R., Timmermeyer, N., Thanisch, S., Crummenerl, L., Jansen,
G., … Schulenburg, H. (2013). Sex differences in host defence interfere with parasite-mediated
selection for outcrossing during host-parasite coevolution. Ecology Letters.
Wiley-Blackwell. https://doi.org/10.1111/ele.12068
chicago: El Masri, Leila, Rebecca Schulte, Nadine Timmermeyer, Stefanie Thanisch,
Lena Crummenerl, Gunther Jansen, Nico Michiels, and Hinrich Schulenburg. “Sex
Differences in Host Defence Interfere with Parasite-Mediated Selection for Outcrossing
during Host-Parasite Coevolution.” Ecology Letters. Wiley-Blackwell, 2013.
https://doi.org/10.1111/ele.12068.
ieee: L. El Masri et al., “Sex differences in host defence interfere with
parasite-mediated selection for outcrossing during host-parasite coevolution,”
Ecology Letters, vol. 16, no. 4. Wiley-Blackwell, pp. 461–468, 2013.
ista: El Masri L, Schulte R, Timmermeyer N, Thanisch S, Crummenerl L, Jansen G,
Michiels N, Schulenburg H. 2013. Sex differences in host defence interfere with
parasite-mediated selection for outcrossing during host-parasite coevolution.
Ecology Letters. 16(4), 461–468.
mla: El Masri, Leila, et al. “Sex Differences in Host Defence Interfere with Parasite-Mediated
Selection for Outcrossing during Host-Parasite Coevolution.” Ecology Letters,
vol. 16, no. 4, Wiley-Blackwell, 2013, pp. 461–68, doi:10.1111/ele.12068.
short: L. El Masri, R. Schulte, N. Timmermeyer, S. Thanisch, L. Crummenerl, G. Jansen,
N. Michiels, H. Schulenburg, Ecology Letters 16 (2013) 461–468.
date_created: 2018-12-11T11:59:54Z
date_published: 2013-04-04T00:00:00Z
date_updated: 2022-08-25T14:51:57Z
day: '04'
ddc:
- '570'
doi: 10.1111/ele.12068
extern: '1'
file:
- access_level: open_access
checksum: aa7db788f7da7d7f102539a249ebce50
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:52Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5176'
file_name: IST-2016-404-v1+1_ele12068.pdf
file_size: 763731
relation: main_file
file_date_updated: 2020-07-14T12:45:50Z
has_accepted_license: '1'
intvolume: ' 16'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 461 - 468
publication: Ecology Letters
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3948'
pubrep_id: '404'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sex differences in host defence interfere with parasite-mediated selection
for outcrossing during host-parasite coevolution
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: 16
year: '2013'
...
---
_id: '2847'
abstract:
- lang: eng
text: Depth-Bounded Systems form an expressive class of well-structured transition
systems. They can model a wide range of concurrent infinite-state systems including
those with dynamic thread creation, dynamically changing communication topology,
and complex shared heap structures. We present the first method to automatically
prove fair termination of depth-bounded systems. Our method uses a numerical abstraction
of the system, which we obtain by systematically augmenting an over-approximation
of the system’s reachable states with a finite set of counters. This numerical
abstraction can be analyzed with existing termination provers. What makes our
approach unique is the way in which it exploits the well-structuredness of the
analyzed system. We have implemented our work in a prototype tool and used it
to automatically prove liveness properties of complex concurrent systems, including
nonblocking algorithms such as Treiber’s stack and several distributed processes.
Many of these examples are beyond the scope of termination analyses that are based
on traditional counter abstractions.
alternative_title:
- LNCS
author:
- first_name: Kshitij
full_name: Bansal, Kshitij
last_name: Bansal
- first_name: Eric
full_name: Koskinen, Eric
last_name: Koskinen
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: Bansal K, Koskinen E, Wies T, Zufferey D. Structural Counter Abstraction. Piterman
N, Smolka S, eds. 2013;7795:62-77. doi:10.1007/978-3-642-36742-7_5
apa: 'Bansal, K., Koskinen, E., Wies, T., & Zufferey, D. (2013). Structural
Counter Abstraction. (N. Piterman & S. Smolka, Eds.). Presented at the TACAS:
Tools and Algorithms for the Construction and Analysis of Systems, Rome, Italy:
Springer. https://doi.org/10.1007/978-3-642-36742-7_5'
chicago: Bansal, Kshitij, Eric Koskinen, Thomas Wies, and Damien Zufferey. “Structural
Counter Abstraction.” Edited by Nir Piterman and Scott Smolka. Lecture Notes in
Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-36742-7_5.
ieee: K. Bansal, E. Koskinen, T. Wies, and D. Zufferey, “Structural Counter Abstraction,”
vol. 7795. Springer, pp. 62–77, 2013.
ista: Bansal K, Koskinen E, Wies T, Zufferey D. 2013. Structural Counter Abstraction
(eds. N. Piterman & S. Smolka). 7795, 62–77.
mla: Bansal, Kshitij, et al. Structural Counter Abstraction. Edited by Nir
Piterman and Scott Smolka, vol. 7795, Springer, 2013, pp. 62–77, doi:10.1007/978-3-642-36742-7_5.
short: K. Bansal, E. Koskinen, T. Wies, D. Zufferey, 7795 (2013) 62–77.
conference:
end_date: 2013-03-24
location: Rome, Italy
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2013-03-16
date_created: 2018-12-11T11:59:54Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2023-09-07T11:36:36Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-642-36742-7_5
ec_funded: 1
editor:
- first_name: Nir
full_name: Piterman, Nir
last_name: Piterman
- first_name: Scott
full_name: Smolka, Scott
last_name: Smolka
intvolume: ' 7795'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arise.or.at/pubpdf/Structural_Counter_Abstraction.pdf
month: '03'
oa: 1
oa_version: Submitted Version
page: 62 - 77
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: '3947'
quality_controlled: '1'
related_material:
record:
- id: '1405'
relation: dissertation_contains
status: public
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Structural Counter Abstraction
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7795
year: '2013'
...
---
_id: '2850'
abstract:
- lang: eng
text: "Recent work emphasizes that the maximum entropy principle provides a bridge
between statistical mechanics models for collective behavior in neural networks
and experiments on networks of real neurons. Most of this work has focused on
capturing the measured correlations among pairs of neurons. Here we suggest an
alternative, constructing models that are consistent with the distribution of
global network activity, i.e. the probability that K out of N cells in the network
generate action potentials in the same small time bin. The inverse problem that
we need to solve in constructing the model is analytically tractable, and provides
a natural 'thermodynamics' for the network in the limit of large N. We analyze
the responses of neurons in a small patch of the retina to naturalistic stimuli,
and find that the implied thermodynamics is very close to an unusual critical
point, in which the entropy (in proper units) is exactly equal to the energy.
© 2013 IOP Publishing Ltd and SISSA Medialab srl.\r\n"
acknowledgement: "his work was supported in part by NSF Grants IIS-0613435 and PHY-0957573,
by NIH Grants R01 EY14196 and P50 GM071508, by the Fannie and John Hertz Foundation,
by the Human Frontiers Science Program, by the Swartz Foundation, and by the WM
Keck Foundation.\r\n"
article_number: P03011
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Thierry
full_name: Mora, Thierry
last_name: Mora
- first_name: Dario
full_name: Amodei, Dario
last_name: Amodei
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
- first_name: William
full_name: Bialek, William
last_name: Bialek
citation:
ama: Tkačik G, Marre O, Mora T, Amodei D, Berry M, Bialek W. The simplest maximum
entropy model for collective behavior in a neural network. Journal of Statistical
Mechanics Theory and Experiment. 2013;2013(3). doi:10.1088/1742-5468/2013/03/P03011
apa: Tkačik, G., Marre, O., Mora, T., Amodei, D., Berry, M., & Bialek, W. (2013).
The simplest maximum entropy model for collective behavior in a neural network.
Journal of Statistical Mechanics Theory and Experiment. IOP Publishing
Ltd. https://doi.org/10.1088/1742-5468/2013/03/P03011
chicago: Tkačik, Gašper, Olivier Marre, Thierry Mora, Dario Amodei, Michael Berry,
and William Bialek. “The Simplest Maximum Entropy Model for Collective Behavior
in a Neural Network.” Journal of Statistical Mechanics Theory and Experiment.
IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/03/P03011.
ieee: G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, and W. Bialek, “The simplest
maximum entropy model for collective behavior in a neural network,” Journal
of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3. IOP Publishing
Ltd., 2013.
ista: Tkačik G, Marre O, Mora T, Amodei D, Berry M, Bialek W. 2013. The simplest
maximum entropy model for collective behavior in a neural network. Journal of
Statistical Mechanics Theory and Experiment. 2013(3), P03011.
mla: Tkačik, Gašper, et al. “The Simplest Maximum Entropy Model for Collective Behavior
in a Neural Network.” Journal of Statistical Mechanics Theory and Experiment,
vol. 2013, no. 3, P03011, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03011.
short: G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, W. Bialek, Journal of
Statistical Mechanics Theory and Experiment 2013 (2013).
date_created: 2018-12-11T11:59:55Z
date_published: 2013-03-12T00:00:00Z
date_updated: 2021-01-12T07:00:14Z
day: '12'
department:
- _id: GaTk
doi: 10.1088/1742-5468/2013/03/P03011
external_id:
arxiv:
- '1207.6319'
intvolume: ' 2013'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1207.6319
month: '03'
oa: 1
oa_version: Preprint
publication: Journal of Statistical Mechanics Theory and Experiment
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '3942'
quality_controlled: '1'
scopus_import: 1
status: public
title: The simplest maximum entropy model for collective behavior in a neural network
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2013
year: '2013'
...
---
_id: '2851'
abstract:
- lang: eng
text: The number of possible activity patterns in a population of neurons grows
exponentially with the size of the population. Typical experiments explore only
a tiny fraction of the large space of possible activity patterns in the case of
populations with more than 10 or 20 neurons. It is thus impossible, in this undersampled
regime, to estimate the probabilities with which most of the activity patterns
occur. As a result, the corresponding entropy - which is a measure of the computational
power of the neural population - cannot be estimated directly. We propose a simple
scheme for estimating the entropy in the undersampled regime, which bounds its
value from both below and above. The lower bound is the usual 'naive' entropy
of the experimental frequencies. The upper bound results from a hybrid approximation
of the entropy which makes use of the naive estimate, a maximum entropy fit, and
a coverage adjustment. We apply our simple scheme to artificial data, in order
to check their accuracy; we also compare its performance to those of several previously
defined entropy estimators. We then apply it to actual measurements of neural
activity in populations with up to 100 cells. Finally, we discuss the similarities
and differences between the proposed simple estimation scheme and various earlier
methods. © 2013 IOP Publishing Ltd and SISSA Medialab srl.
article_number: P03015
author:
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Julien
full_name: Dubuis, Julien
last_name: Dubuis
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Ravá
full_name: Da Silveira, Ravá
last_name: Da Silveira
citation:
ama: Berry M, Tkačik G, Dubuis J, Marre O, Da Silveira R. A simple method for estimating
the entropy of neural activity. Journal of Statistical Mechanics Theory and
Experiment. 2013;2013(3). doi:10.1088/1742-5468/2013/03/P03015
apa: Berry, M., Tkačik, G., Dubuis, J., Marre, O., & Da Silveira, R. (2013).
A simple method for estimating the entropy of neural activity. Journal of Statistical
Mechanics Theory and Experiment. IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2013/03/P03015
chicago: Berry, Michael, Gašper Tkačik, Julien Dubuis, Olivier Marre, and Ravá Da
Silveira. “A Simple Method for Estimating the Entropy of Neural Activity.” Journal
of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2013.
https://doi.org/10.1088/1742-5468/2013/03/P03015.
ieee: M. Berry, G. Tkačik, J. Dubuis, O. Marre, and R. Da Silveira, “A simple method
for estimating the entropy of neural activity,” Journal of Statistical Mechanics
Theory and Experiment, vol. 2013, no. 3. IOP Publishing Ltd., 2013.
ista: Berry M, Tkačik G, Dubuis J, Marre O, Da Silveira R. 2013. A simple method
for estimating the entropy of neural activity. Journal of Statistical Mechanics
Theory and Experiment. 2013(3), P03015.
mla: Berry, Michael, et al. “A Simple Method for Estimating the Entropy of Neural
Activity.” Journal of Statistical Mechanics Theory and Experiment, vol.
2013, no. 3, P03015, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03015.
short: M. Berry, G. Tkačik, J. Dubuis, O. Marre, R. Da Silveira, Journal of Statistical
Mechanics Theory and Experiment 2013 (2013).
date_created: 2018-12-11T11:59:56Z
date_published: 2013-03-12T00:00:00Z
date_updated: 2021-01-12T07:00:14Z
day: '12'
department:
- _id: GaTk
doi: 10.1088/1742-5468/2013/03/P03015
intvolume: ' 2013'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
publication: Journal of Statistical Mechanics Theory and Experiment
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '3941'
quality_controlled: '1'
scopus_import: 1
status: public
title: A simple method for estimating the entropy of neural activity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2013
year: '2013'
...