---
_id: '2826'
abstract:
- lang: eng
text: Myopia, or near-sightedness, is an ocular refractive error of unfocused image
quality in front of the retinal plane. Individuals with high-grade myopia (dioptric
power greater than -6.00) are predisposed to ocular morbidities such as glaucoma,
retinal detachment, and myopic maculopathy. Nonsyndromic, high-grade myopia is
highly heritable, and to date multiple gene loci have been reported. We performed
exome sequencing in 4 individuals from an 11-member family of European descent
from the United States. Affected individuals had a mean dioptric spherical equivalent
of -22.00 sphere. A premature stop codon mutation c.157C>T (p.Gln53*) cosegregating
with disease was discovered within SCO2 that maps to chromosome 22q13.33. Subsequent
analyses identified three additional mutations in three highly myopic unrelated
individuals (c.341G>A, c.418G>A, and c.776C>T). To determine differential
gene expression in a developmental mouse model, we induced myopia by applying
a -15.00D lens over one eye. Messenger RNA levels of SCO2 were significantly downregulated
in myopic mouse retinae. Immunohistochemistry in mouse eyes confirmed SCO2 protein
localization in retina, retinal pigment epithelium, and sclera. SCO2 encodes for
a copper homeostasis protein influential in mitochondrial cytochrome c oxidase
activity. Copper deficiencies have been linked with photoreceptor loss and myopia
with increased scleral wall elasticity. Retinal thinning has been reported with
an SC02 variant. Human mutation identification with support from an induced myopic
animal provides biological insights of myopic development.
author:
- first_name: Khanh
full_name: Tran Viet, Khanh
last_name: Tran Viet
- first_name: Caldwell
full_name: Powell, Caldwell
last_name: Powell
- first_name: Veluchamy
full_name: Barathi, Veluchamy
last_name: Barathi
- first_name: Thomas
full_name: Klemm, Thomas
last_name: Klemm
- first_name: Sebastian
full_name: Maurer Stroh, Sebastian
last_name: Maurer Stroh
- first_name: Vachiranee
full_name: Limviphuvadh, Vachiranee
last_name: Limviphuvadh
- first_name: Vincent
full_name: Soler, Vincent
last_name: Soler
- first_name: Candice
full_name: Ho, Candice
last_name: Ho
- first_name: Tammy
full_name: Yanovitch, Tammy
last_name: Yanovitch
- first_name: Georg
full_name: Schneider, Georg
id: 329095A0-F248-11E8-B48F-1D18A9856A87
last_name: Schneider
- first_name: Yi
full_name: Li, Yi
last_name: Li
- first_name: Erica
full_name: Nading, Erica
last_name: Nading
- first_name: Ravikanth
full_name: Metlapally, Ravikanth
last_name: Metlapally
- first_name: Seang
full_name: Saw, Seang
last_name: Saw
- first_name: Liang
full_name: Goh, Liang
last_name: Goh
- first_name: Steve
full_name: Rozen, Steve
last_name: Rozen
- first_name: Terri
full_name: Young, Terri
last_name: Young
citation:
ama: Tran Viet K, Powell C, Barathi V, et al. Mutations in SCO2 are associated with
autosomal-dominant high-grade myopia. American Journal of Human Genetics.
2013;92(5):820-826. doi:10.1016/j.ajhg.2013.04.005
apa: Tran Viet, K., Powell, C., Barathi, V., Klemm, T., Maurer Stroh, S., Limviphuvadh,
V., … Young, T. (2013). Mutations in SCO2 are associated with autosomal-dominant
high-grade myopia. American Journal of Human Genetics. Cell Press. https://doi.org/10.1016/j.ajhg.2013.04.005
chicago: Tran Viet, Khanh, Caldwell Powell, Veluchamy Barathi, Thomas Klemm, Sebastian
Maurer Stroh, Vachiranee Limviphuvadh, Vincent Soler, et al. “Mutations in SCO2
Are Associated with Autosomal-Dominant High-Grade Myopia.” American Journal
of Human Genetics. Cell Press, 2013. https://doi.org/10.1016/j.ajhg.2013.04.005.
ieee: K. Tran Viet et al., “Mutations in SCO2 are associated with autosomal-dominant
high-grade myopia,” American Journal of Human Genetics, vol. 92, no. 5.
Cell Press, pp. 820–826, 2013.
ista: Tran Viet K, Powell C, Barathi V, Klemm T, Maurer Stroh S, Limviphuvadh V,
Soler V, Ho C, Yanovitch T, Schneider G, Li Y, Nading E, Metlapally R, Saw S,
Goh L, Rozen S, Young T. 2013. Mutations in SCO2 are associated with autosomal-dominant
high-grade myopia. American Journal of Human Genetics. 92(5), 820–826.
mla: Tran Viet, Khanh, et al. “Mutations in SCO2 Are Associated with Autosomal-Dominant
High-Grade Myopia.” American Journal of Human Genetics, vol. 92, no. 5,
Cell Press, 2013, pp. 820–26, doi:10.1016/j.ajhg.2013.04.005.
short: K. Tran Viet, C. Powell, V. Barathi, T. Klemm, S. Maurer Stroh, V. Limviphuvadh,
V. Soler, C. Ho, T. Yanovitch, G. Schneider, Y. Li, E. Nading, R. Metlapally,
S. Saw, L. Goh, S. Rozen, T. Young, American Journal of Human Genetics 92 (2013)
820–826.
date_created: 2018-12-11T11:59:48Z
date_published: 2013-05-02T00:00:00Z
date_updated: 2021-01-12T06:59:59Z
day: '02'
department:
- _id: MD
doi: 10.1016/j.ajhg.2013.04.005
external_id:
pmid:
- '23643385'
intvolume: ' 92'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644634/
month: '05'
oa: 1
oa_version: Submitted Version
page: 820 - 826
pmid: 1
publication: American Journal of Human Genetics
publication_status: published
publisher: Cell Press
publist_id: '3974'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mutations in SCO2 are associated with autosomal-dominant high-grade myopia
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 92
year: '2013'
...
---
_id: '2827'
abstract:
- lang: eng
text: Removal of cargos from the cell surface via endocytosis is an efficient mechanism
to regulate activities of plasma membrane (PM)-resident proteins, such as receptors
or transporters. Salicylic acid (SA) is an important plant hormone that is traditionally
associated with pathogen defense. Here, we describe an unanticipated effect of
SA on subcellular endocytic cycling of proteins. Both exogenous treatments and
endogenously enhanced SA levels repressed endocytosis of different PM proteins.
The SA effect on endocytosis did not involve transcription or known components
of the SA signaling pathway for transcriptional regulation. SA likely targets
an endocytic mechanism that involves the coat protein clathrin, because SA interfered
with the clathrin incidence at the PM and clathrin-deficient mutants were less
sensitive to the impact of SA on the auxin distribution and root bending during
the gravitropic response. By contrast, SA did not affect the ligand-induced endocytosis
of the FLAGELLIN SENSING2 (FLS2) receptor during pathogen responses. Our data
suggest that the established SA impact on transcription in plant immunity and
the nontranscriptional effect of SA on clathrin-mediated endocytosis are independent
mechanisms by which SA regulates distinct aspects of plant physiology.
author:
- first_name: Yunlong
full_name: Du, Yunlong
last_name: Du
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Martina
full_name: Beck, Martina
last_name: Beck
- first_name: Ellie
full_name: Himschoot, Ellie
last_name: Himschoot
- first_name: Hongjiang
full_name: Li, Hongjiang
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Silke
full_name: Robatzek, Silke
last_name: Robatzek
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Du Y, Tejos R, Beck M, et al. Salicylic acid interferes with clathrin-mediated
endocytic protein trafficking. PNAS. 2013;110(19):7946-7951. doi:10.1073/pnas.1220205110
apa: Du, Y., Tejos, R., Beck, M., Himschoot, E., Li, H., Robatzek, S., … Friml,
J. (2013). Salicylic acid interferes with clathrin-mediated endocytic protein
trafficking. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1220205110
chicago: Du, Yunlong, Ricardo Tejos, Martina Beck, Ellie Himschoot, Hongjiang Li,
Silke Robatzek, Steffen Vanneste, and Jiří Friml. “Salicylic Acid Interferes with
Clathrin-Mediated Endocytic Protein Trafficking.” PNAS. National Academy
of Sciences, 2013. https://doi.org/10.1073/pnas.1220205110.
ieee: Y. Du et al., “Salicylic acid interferes with clathrin-mediated endocytic
protein trafficking,” PNAS, vol. 110, no. 19. National Academy of Sciences,
pp. 7946–7951, 2013.
ista: Du Y, Tejos R, Beck M, Himschoot E, Li H, Robatzek S, Vanneste S, Friml J.
2013. Salicylic acid interferes with clathrin-mediated endocytic protein trafficking.
PNAS. 110(19), 7946–7951.
mla: Du, Yunlong, et al. “Salicylic Acid Interferes with Clathrin-Mediated Endocytic
Protein Trafficking.” PNAS, vol. 110, no. 19, National Academy of Sciences,
2013, pp. 7946–51, doi:10.1073/pnas.1220205110.
short: Y. Du, R. Tejos, M. Beck, E. Himschoot, H. Li, S. Robatzek, S. Vanneste,
J. Friml, PNAS 110 (2013) 7946–7951.
date_created: 2018-12-11T11:59:48Z
date_published: 2013-05-07T00:00:00Z
date_updated: 2021-01-12T06:59:59Z
day: '07'
department:
- _id: JiFr
doi: 10.1073/pnas.1220205110
external_id:
pmid:
- '23613581'
intvolume: ' 110'
issue: '19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3651428/
month: '05'
oa: 1
oa_version: Submitted Version
page: 7946 - 7951
pmid: 1
project:
- _id: 2574781E-B435-11E9-9278-68D0E5697425
name: Koerber Prize 2010
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3972'
quality_controlled: '1'
scopus_import: 1
status: public
title: Salicylic acid interferes with clathrin-mediated endocytic protein trafficking
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2828'
abstract:
- lang: eng
text: 'We study the complexity of valued constraint satisfaction problems (VCSPs)
parametrized by a constraint language, a fixed set of cost functions over a finite
domain. An instance of the problem is specified by a sum of cost functions from
the language and the goal is to minimize the sum. Under the unique games conjecture,
the approximability of finite-valued VCSPs is well understood, see Raghavendra
[2008]. However, there is no characterization of finite-valued VCSPs, let alone
general-valued VCSPs, that can be solved exactly in polynomial time, thus giving
insights from a combinatorial optimization perspective. We consider the case of
languages containing all possible unary cost functions. In the case of languages
consisting of only {0, ∞}-valued cost functions (i.e., relations), such languages
have been called conservative and studied by Bulatov [2003, 2011] and recently
by Barto [2011]. Since we study valued languages, we call a language conservative
if it contains all finite-valued unary cost functions. The computational complexity
of conservative valued languages has been studied by Cohen et al. [2006] for languages
over Boolean domains, by Deineko et al. [2008] for {0, 1}-valued languages (a.k.a
Max-CSP), and by Takhanov [2010a] for {0, ∞}-valued languages containing all finite-valued
unary cost functions (a.k.a. Min-Cost-Hom). We prove a Schaefer-like dichotomy
theorem for conservative valued languages: if all cost functions in the language
satisfy a certain condition (specified by a complementary combination of STP and
MJN multimor-phisms), then any instance can be solved in polynomial time (via
a new algorithm developed in this article), otherwise the language is NP-hard.
This is the first complete complexity classification of general-valued constraint
languages over non-Boolean domains. It is a common phenomenon that complexity
classifications of problems over non-Boolean domains are significantly harder
than the Boolean cases. The polynomial-time algorithm we present for the tractable
cases is a generalization of the submodular minimization problem and a result
of Cohen et al. [2008]. Our results generalize previous results by Takhanov [2010a]
and (a subset of results) by Cohen et al. [2006] and Deineko et al. [2008]. Moreover,
our results do not rely on any computer-assisted search as in Deineko et al. [2008],
and provide a powerful tool for proving hardness of finite-valued and general-valued
languages.'
article_number: '10'
arxiv: 1
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Stanislav
full_name: Živný, Stanislav
last_name: Živný
citation:
ama: Kolmogorov V, Živný S. The complexity of conservative valued CSPs. Journal
of the ACM. 2013;60(2). doi:10.1145/2450142.2450146
apa: Kolmogorov, V., & Živný, S. (2013). The complexity of conservative valued
CSPs. Journal of the ACM. ACM. https://doi.org/10.1145/2450142.2450146
chicago: Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative
Valued CSPs.” Journal of the ACM. ACM, 2013. https://doi.org/10.1145/2450142.2450146.
ieee: V. Kolmogorov and S. Živný, “The complexity of conservative valued CSPs,”
Journal of the ACM, vol. 60, no. 2. ACM, 2013.
ista: Kolmogorov V, Živný S. 2013. The complexity of conservative valued CSPs. Journal
of the ACM. 60(2), 10.
mla: Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative
Valued CSPs.” Journal of the ACM, vol. 60, no. 2, 10, ACM, 2013, doi:10.1145/2450142.2450146.
short: V. Kolmogorov, S. Živný, Journal of the ACM 60 (2013).
date_created: 2018-12-11T11:59:48Z
date_published: 2013-04-02T00:00:00Z
date_updated: 2021-01-12T07:00:00Z
day: '02'
department:
- _id: VlKo
doi: 10.1145/2450142.2450146
external_id:
arxiv:
- '1110.2809'
intvolume: ' 60'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1110.2809
month: '04'
oa: 1
oa_version: Preprint
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '3971'
quality_controlled: '1'
scopus_import: 1
status: public
title: The complexity of conservative valued CSPs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2013'
...
---
_id: '2829'
abstract:
- lang: eng
text: Laminar-turbulent intermittency is intrinsic to the transitional regime of
a wide range of fluid flows including pipe, channel, boundary layer, and Couette
flow. In the latter turbulent spots can grow and form continuous stripes, yet
in the stripe-normal direction they remain interspersed by laminar fluid. We carry
out direct numerical simulations in a long narrow domain and observe that individual
turbulent stripes are transient. In agreement with recent observations in pipe
flow, we find that turbulence becomes sustained at a distinct critical point once
the spatial proliferation outweighs the inherent decaying process. By resolving
the asymptotic size distributions close to criticality we can for the first time
demonstrate scale invariance at the onset of turbulence.
article_number: '204502'
arxiv: 1
author:
- first_name: Liang
full_name: Shi, Liang
id: 374A3F1A-F248-11E8-B48F-1D18A9856A87
last_name: Shi
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Shi L, Avila M, Hof B. Scale invariance at the onset of turbulence in couette
flow. Physical Review Letters. 2013;110(20). doi:10.1103/PhysRevLett.110.204502
apa: Shi, L., Avila, M., & Hof, B. (2013). Scale invariance at the onset of
turbulence in couette flow. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/PhysRevLett.110.204502
chicago: Shi, Liang, Marc Avila, and Björn Hof. “Scale Invariance at the Onset of
Turbulence in Couette Flow.” Physical Review Letters. American Physical
Society, 2013. https://doi.org/10.1103/PhysRevLett.110.204502.
ieee: L. Shi, M. Avila, and B. Hof, “Scale invariance at the onset of turbulence
in couette flow,” Physical Review Letters, vol. 110, no. 20. American Physical
Society, 2013.
ista: Shi L, Avila M, Hof B. 2013. Scale invariance at the onset of turbulence in
couette flow. Physical Review Letters. 110(20), 204502.
mla: Shi, Liang, et al. “Scale Invariance at the Onset of Turbulence in Couette
Flow.” Physical Review Letters, vol. 110, no. 20, 204502, American Physical
Society, 2013, doi:10.1103/PhysRevLett.110.204502.
short: L. Shi, M. Avila, B. Hof, Physical Review Letters 110 (2013).
date_created: 2018-12-11T11:59:49Z
date_published: 2013-05-13T00:00:00Z
date_updated: 2021-01-12T07:00:00Z
day: '13'
department:
- _id: BjHo
doi: 10.1103/PhysRevLett.110.204502
ec_funded: 1
external_id:
arxiv:
- '1304.5446'
intvolume: ' 110'
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1304.5446
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
- _id: 2511D90C-B435-11E9-9278-68D0E5697425
grant_number: SFB 963 TP A8
name: Astrophysical instability of currents and turbulences
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '3970'
quality_controlled: '1'
scopus_import: 1
status: public
title: Scale invariance at the onset of turbulence in couette flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
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
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: '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: '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: '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: '2853'
abstract:
- lang: eng
text: High relatedness among interacting individuals has generally been considered
a precondition for the evolution of altruism. However, kin-selection theory also
predicts the evolution of altruism when relatedness is low, as long as the cost
of the altruistic act is minor compared with its benefit. Here, we demonstrate
evidence for a low-cost altruistic act in bacteria. We investigated Escherichia
coli responding to the attack of an obligately lytic phage by committing suicide
in order to prevent parasite transmission to nearby relatives. We found that bacterial
suicide provides large benefits to survivors at marginal costs to committers.
The cost of suicide was low, because infected cells are moribund, rapidly dying
upon phage infection, such that no more opportunity for reproduction remains.
As a consequence of its marginal cost, host suicide was selectively favoured even
when relatedness between committers and survivors approached zero. Altogether,
our findings demonstrate that low-cost suicide can evolve with ease, represents
an effective host-defence strategy, and seems to be widespread among microbes.
Moreover, low-cost suicide might also occur in higher organisms as exemplified
by infected social insect workers leaving the colony to die in isolation.
article_processing_charge: No
article_type: original
author:
- first_name: Dominik
full_name: Refardt, Dominik
last_name: Refardt
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Rolf
full_name: Kümmerli, Rolf
last_name: Kümmerli
citation:
ama: 'Refardt D, Bergmiller T, Kümmerli R. Altruism can evolve when relatedness
is low: Evidence from bacteria committing suicide upon phage infection. Proceedings
of the Royal Society of London Series B Biological Sciences. 2013;280(1759).
doi:10.1098/rspb.2012.3035'
apa: 'Refardt, D., Bergmiller, T., & Kümmerli, R. (2013). Altruism can evolve
when relatedness is low: Evidence from bacteria committing suicide upon phage
infection. Proceedings of the Royal Society of London Series B Biological Sciences.
The Royal Society. https://doi.org/10.1098/rspb.2012.3035'
chicago: 'Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Altruism Can
Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon
Phage Infection.” Proceedings of the Royal Society of London Series B Biological
Sciences. The Royal Society, 2013. https://doi.org/10.1098/rspb.2012.3035.'
ieee: 'D. Refardt, T. Bergmiller, and R. Kümmerli, “Altruism can evolve when relatedness
is low: Evidence from bacteria committing suicide upon phage infection,” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 280, no.
1759. The Royal Society, 2013.'
ista: 'Refardt D, Bergmiller T, Kümmerli R. 2013. Altruism can evolve when relatedness
is low: Evidence from bacteria committing suicide upon phage infection. Proceedings
of the Royal Society of London Series B Biological Sciences. 280(1759).'
mla: 'Refardt, Dominik, et al. “Altruism Can Evolve When Relatedness Is Low: Evidence
from Bacteria Committing Suicide upon Phage Infection.” Proceedings of the
Royal Society of London Series B Biological Sciences, vol. 280, no. 1759,
The Royal Society, 2013, doi:10.1098/rspb.2012.3035.'
short: D. Refardt, T. Bergmiller, R. Kümmerli, Proceedings of the Royal Society
of London Series B Biological Sciences 280 (2013).
date_created: 2018-12-11T11:59:56Z
date_published: 2013-05-22T00:00:00Z
date_updated: 2023-10-18T06:43:23Z
day: '22'
department:
- _id: CaGu
doi: 10.1098/rspb.2012.3035
external_id:
pmid:
- '23516238'
intvolume: ' 280'
issue: '1759'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619501/
month: '05'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_identifier:
eissn:
- 1471-2954
publication_status: published
publisher: The Royal Society
publist_id: '3939'
quality_controlled: '1'
related_material:
record:
- id: '9751'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Altruism can evolve when relatedness is low: Evidence from bacteria committing
suicide upon phage infection'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 280
year: '2013'
...
---
_id: '2854'
abstract:
- lang: eng
text: We consider concurrent games played on graphs. At every round of a game, each
player simultaneously and independently selects a move; the moves jointly determine
the transition to a successor state. Two basic objectives are the safety objective
to stay forever in a given set of states, and its dual, the reachability objective
to reach a given set of states. First, we present a simple proof of the fact that
in concurrent reachability games, for all ε>0, memoryless ε-optimal strategies
exist. A memoryless strategy is independent of the history of plays, and an ε-optimal
strategy achieves the objective with probability within ε of the value of the
game. In contrast to previous proofs of this fact, our proof is more elementary
and more combinatorial. Second, we present a strategy-improvement (a.k.a. policy-iteration)
algorithm for concurrent games with reachability objectives. Finally, we present
a strategy-improvement algorithm for turn-based stochastic games (where each player
selects moves in turns) with safety objectives. Our algorithms yield sequences
of player-1 strategies which ensure probabilities of winning that converge monotonically
(from below) to the value of the game. © 2012 Elsevier Inc.
acknowledgement: This work was partially supported in part by the NSF grants CCR-0132780,
CNS-0720884, CCR-0225610, by the Swiss National Science Foundation, ERC Start Grant
Graph Games (Project No. 279307), FWF NFN Grant S11407-N23 (RiSE), and a Microsoft
faculty fellows
article_processing_charge: No
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Luca
full_name: De Alfaro, Luca
last_name: De Alfaro
- 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: Chatterjee K, De Alfaro L, Henzinger TA. Strategy improvement for concurrent
reachability and turn based stochastic safety games. Journal of Computer and
System Sciences. 2013;79(5):640-657. doi:10.1016/j.jcss.2012.12.001
apa: Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2013). Strategy improvement
for concurrent reachability and turn based stochastic safety games. Journal
of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2012.12.001
chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Strategy
Improvement for Concurrent Reachability and Turn Based Stochastic Safety Games.”
Journal of Computer and System Sciences. Elsevier, 2013. https://doi.org/10.1016/j.jcss.2012.12.001.
ieee: K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Strategy improvement for
concurrent reachability and turn based stochastic safety games,” Journal of
Computer and System Sciences, vol. 79, no. 5. Elsevier, pp. 640–657, 2013.
ista: Chatterjee K, De Alfaro L, Henzinger TA. 2013. Strategy improvement for concurrent
reachability and turn based stochastic safety games. Journal of Computer and System
Sciences. 79(5), 640–657.
mla: Chatterjee, Krishnendu, et al. “Strategy Improvement for Concurrent Reachability
and Turn Based Stochastic Safety Games.” Journal of Computer and System Sciences,
vol. 79, no. 5, Elsevier, 2013, pp. 640–57, doi:10.1016/j.jcss.2012.12.001.
short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, Journal of Computer and System
Sciences 79 (2013) 640–657.
date_created: 2018-12-11T11:59:57Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T07:00:16Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1016/j.jcss.2012.12.001
ec_funded: 1
file:
- access_level: open_access
checksum: 6d3ee12cceb946a0abe69594b6a22409
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:48Z
date_updated: 2020-07-14T12:45:51Z
file_id: '5370'
file_name: IST-2015-388-v1+1_1-s2.0-S0022000012001778-main.pdf
file_size: 425488
relation: main_file
file_date_updated: 2020-07-14T12:45:51Z
has_accepted_license: '1'
intvolume: ' 79'
issue: '5'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 640 - 657
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Journal of Computer and System Sciences
publication_status: published
publisher: Elsevier
publist_id: '3938'
pubrep_id: '388'
quality_controlled: '1'
scopus_import: 1
status: public
title: Strategy improvement for concurrent reachability and turn based stochastic
safety games
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 79
year: '2013'
...
---
_id: '2855'
abstract:
- lang: eng
text: Genomic imprinting leads to preferred expression of either the maternal or
paternal alleles of a subset of genes. Imprinting is essential for mammalian development,
and its deregulation causes many diseases. However, the functional relevance of
imprinting at the cellular level is poorly understood for most imprinted genes.
We used mosaic analysis with double markers (MADM) in mice to create uniparental
disomies (UPDs) and to visualize imprinting effects with single-cell resolution.
Although chromosome 12 UPD did not produce detectable phenotypes, chromosome 7
UPD caused highly significant paternal growth dominance in the liver and lung,
but not in the brain or heart. A single gene on chromosome 7, encoding the secreted
insulin-like growth factor 2 (IGF2), accounts for most of the paternal dominance
effect. Mosaic analyses implied additional imprinted loci on chromosome 7 acting
cell autonomously to transmit the IGF2 signal. Our study reveals chromosome- and
cell-type specificity of genomic imprinting effects.
author:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Randy
full_name: Johnson, Randy
last_name: Johnson
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
citation:
ama: Hippenmeyer S, Johnson R, Luo L. Mosaic analysis with double markers reveals
cell type specific paternal growth dominance. Cell Reports. 2013;3(3):960-967.
doi:10.1016/j.celrep.2013.02.002
apa: Hippenmeyer, S., Johnson, R., & Luo, L. (2013). Mosaic analysis with double
markers reveals cell type specific paternal growth dominance. Cell Reports.
Cell Press. https://doi.org/10.1016/j.celrep.2013.02.002
chicago: Hippenmeyer, Simon, Randy Johnson, and Liqun Luo. “Mosaic Analysis with
Double Markers Reveals Cell Type Specific Paternal Growth Dominance.” Cell
Reports. Cell Press, 2013. https://doi.org/10.1016/j.celrep.2013.02.002.
ieee: S. Hippenmeyer, R. Johnson, and L. Luo, “Mosaic analysis with double markers
reveals cell type specific paternal growth dominance,” Cell Reports, vol.
3, no. 3. Cell Press, pp. 960–967, 2013.
ista: Hippenmeyer S, Johnson R, Luo L. 2013. Mosaic analysis with double markers
reveals cell type specific paternal growth dominance. Cell Reports. 3(3), 960–967.
mla: Hippenmeyer, Simon, et al. “Mosaic Analysis with Double Markers Reveals Cell
Type Specific Paternal Growth Dominance.” Cell Reports, vol. 3, no. 3,
Cell Press, 2013, pp. 960–67, doi:10.1016/j.celrep.2013.02.002.
short: S. Hippenmeyer, R. Johnson, L. Luo, Cell Reports 3 (2013) 960–967.
date_created: 2018-12-11T11:59:57Z
date_published: 2013-03-28T00:00:00Z
date_updated: 2021-01-12T07:00:16Z
day: '28'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.celrep.2013.02.002
file:
- access_level: open_access
checksum: 6e977b918e81384cd571ec5a9d812289
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:20Z
date_updated: 2020-07-14T12:45:51Z
file_id: '5274'
file_name: IST-2016-405-v1+1_1-s2.0-S2211124713000612-main.pdf
file_size: 1907211
relation: main_file
file_date_updated: 2020-07-14T12:45:51Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 960 - 967
publication: Cell Reports
publication_status: published
publisher: Cell Press
publist_id: '3937'
pubrep_id: '405'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mosaic analysis with double markers reveals cell type specific paternal growth
dominance
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2013'
...
---
_id: '2856'
abstract:
- lang: eng
text: 'G protein–coupled receptors (GPCRs), the largest family of membrane signaling
proteins, respond to neurotransmitters, hormones and small environmental molecules.
The neuronal function of many GPCRs has been difficult to resolve because of an
inability to gate them with subtype specificity, spatial precision, speed and
reversibility. To address this, we developed an approach for opto-chemical engineering
of native GPCRs. We applied this to the metabotropic glutamate receptors (mGluRs)
to generate light-agonized and light-antagonized mGluRs (LimGluRs). The light-agonized
LimGluR2, on which we focused, was fast, bistable and supported multiple rounds
of on/off switching. Light gated two of the primary neuronal functions of mGluR2:
suppression of excitability and inhibition of neurotransmitter release. We found
that the light-antagonized tool LimGluR2-block was able to manipulate negative
feedback of synaptically released glutamate on transmitter release. We generalized
the optical control to two additional family members: mGluR3 and mGluR6. This
system worked in rodent brain slices and in zebrafish in vivo, where we found
that mGluR2 modulated the threshold for escape behavior. These light-gated mGluRs
pave the way for determining the roles of mGluRs in synaptic plasticity, memory
and disease.'
acknowledgement: National Science Foundation grants CHE-0233882 and CHE-0840505 (to
the College of Chemistry at the University of California, Berkeley), a postdoctoral
fellowship of the European Molecular Biology Organization (H.J.)
author:
- first_name: Joshua
full_name: Levitz, Joshua
last_name: Levitz
- first_name: Carlos
full_name: Pantoja, Carlos
last_name: Pantoja
- first_name: Benjamin
full_name: Gaub, Benjamin
last_name: Gaub
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Andreas
full_name: Reiner, Andreas
last_name: Reiner
- first_name: Adam
full_name: Hoagland, Adam
last_name: Hoagland
- first_name: David
full_name: Schoppik, David
last_name: Schoppik
- first_name: Brian
full_name: Kane, Brian
last_name: Kane
- first_name: Philipp
full_name: Stawski, Philipp
last_name: Stawski
- first_name: Alexander
full_name: Schier, Alexander
last_name: Schier
- first_name: Dirk
full_name: Trauner, Dirk
last_name: Trauner
- first_name: Ehud
full_name: Isacoff, Ehud
last_name: Isacoff
citation:
ama: Levitz J, Pantoja C, Gaub B, et al. Optical control of metabotropic glutamate
receptors. Nature Neuroscience. 2013;16:507-516. doi:10.1038/nn.3346
apa: Levitz, J., Pantoja, C., Gaub, B., Janovjak, H. L., Reiner, A., Hoagland, A.,
… Isacoff, E. (2013). Optical control of metabotropic glutamate receptors. Nature
Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3346
chicago: Levitz, Joshua, Carlos Pantoja, Benjamin Gaub, Harald L Janovjak, Andreas
Reiner, Adam Hoagland, David Schoppik, et al. “Optical Control of Metabotropic
Glutamate Receptors.” Nature Neuroscience. Nature Publishing Group, 2013.
https://doi.org/10.1038/nn.3346.
ieee: J. Levitz et al., “Optical control of metabotropic glutamate receptors,”
Nature Neuroscience, vol. 16. Nature Publishing Group, pp. 507–516, 2013.
ista: Levitz J, Pantoja C, Gaub B, Janovjak HL, Reiner A, Hoagland A, Schoppik D,
Kane B, Stawski P, Schier A, Trauner D, Isacoff E. 2013. Optical control of metabotropic
glutamate receptors. Nature Neuroscience. 16, 507–516.
mla: Levitz, Joshua, et al. “Optical Control of Metabotropic Glutamate Receptors.”
Nature Neuroscience, vol. 16, Nature Publishing Group, 2013, pp. 507–16,
doi:10.1038/nn.3346.
short: J. Levitz, C. Pantoja, B. Gaub, H.L. Janovjak, A. Reiner, A. Hoagland, D.
Schoppik, B. Kane, P. Stawski, A. Schier, D. Trauner, E. Isacoff, Nature Neuroscience
16 (2013) 507–516.
date_created: 2018-12-11T11:59:57Z
date_published: 2013-03-03T00:00:00Z
date_updated: 2021-01-12T07:00:16Z
day: '03'
department:
- _id: HaJa
doi: 10.1038/nn.3346
external_id:
pmid:
- '23455609'
intvolume: ' 16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681425/
month: '03'
oa: 1
oa_version: Submitted Version
page: 507 - 516
pmid: 1
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '3936'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optical control of metabotropic glutamate receptors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2013'
...