---
_id: '14'
abstract:
- lang: eng
text: The intercellular transport of auxin is driven by PIN-formed (PIN) auxin efflux
carriers. PINs are localized at the plasma membrane (PM) and on constitutively
recycling endomembrane vesicles. Therefore, PINs can mediate auxin transport either
by direct translocation across the PM or by pumping auxin into secretory vesicles
(SVs), leading to its secretory release upon fusion with the PM. Which of these
two mechanisms dominates is a matter of debate. Here, we addressed the issue with
a mathematical modeling approach. We demonstrate that the efficiency of secretory
transport depends on SV size, half-life of PINs on the PM, pH, exocytosis frequency
and PIN density. 3D structured illumination microscopy (SIM) was used to determine
PIN density on the PM. Combining this data with published values of the other
parameters, we show that the transport activity of PINs in SVs would have to be
at least 1000× greater than on the PM in order to produce a comparable macroscopic
auxin transport. If both transport mechanisms operated simultaneously and PINs
were equally active on SVs and PM, the contribution of secretion to the total
auxin flux would be negligible. In conclusion, while secretory vesicle-mediated
transport of auxin is an intriguing and theoretically possible model, it is unlikely
to be a major mechanism of auxin transport inplanta.
acknowledgement: 'European Research Council (ERC): 742985 to Jiri Friml; M.A. was
supported by the Austrian Science Fund (FWF) (M2379-B28); AJ was supported by the
Austria Science Fund (FWF): I03630 to Jiri Friml.'
article_processing_charge: No
article_type: original
author:
- first_name: Sander
full_name: Hille, Sander
last_name: Hille
- first_name: Maria
full_name: Akhmanova, Maria
id: 3425EC26-F248-11E8-B48F-1D18A9856A87
last_name: Akhmanova
orcid: 0000-0003-1522-3162
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. Relative contribution
of PIN-containing secretory vesicles and plasma membrane PINs to the directed
auxin transport: Theoretical estimation. International Journal of Molecular
Sciences. 2018;19(11). doi:10.3390/ijms19113566'
apa: 'Hille, S., Akhmanova, M., Glanc, M., Johnson, A. J., & Friml, J. (2018).
Relative contribution of PIN-containing secretory vesicles and plasma membrane
PINs to the directed auxin transport: Theoretical estimation. International
Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms19113566'
chicago: 'Hille, Sander, Maria Akhmanova, Matous Glanc, Alexander J Johnson, and
Jiří Friml. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma
Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International
Journal of Molecular Sciences. MDPI, 2018. https://doi.org/10.3390/ijms19113566.'
ieee: 'S. Hille, M. Akhmanova, M. Glanc, A. J. Johnson, and J. Friml, “Relative
contribution of PIN-containing secretory vesicles and plasma membrane PINs to
the directed auxin transport: Theoretical estimation,” International Journal
of Molecular Sciences, vol. 19, no. 11. MDPI, 2018.'
ista: 'Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. 2018. Relative contribution
of PIN-containing secretory vesicles and plasma membrane PINs to the directed
auxin transport: Theoretical estimation. International Journal of Molecular Sciences.
19(11).'
mla: 'Hille, Sander, et al. “Relative Contribution of PIN-Containing Secretory Vesicles
and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.”
International Journal of Molecular Sciences, vol. 19, no. 11, MDPI, 2018,
doi:10.3390/ijms19113566.'
short: S. Hille, M. Akhmanova, M. Glanc, A.J. Johnson, J. Friml, International Journal
of Molecular Sciences 19 (2018).
date_created: 2018-12-11T11:44:09Z
date_published: 2018-11-12T00:00:00Z
date_updated: 2023-09-18T08:09:32Z
day: '12'
ddc:
- '580'
department:
- _id: DaSi
- _id: JiFr
doi: 10.3390/ijms19113566
ec_funded: 1
external_id:
isi:
- '000451528500282'
file:
- access_level: open_access
checksum: e4b59c2599b0ca26ebf5b8434bcde94a
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:04:11Z
date_updated: 2020-07-14T12:44:50Z
file_id: '5719'
file_name: 2018_IJMS_Hille.pdf
file_size: 2200593
relation: main_file
file_date_updated: 2020-07-14T12:44:50Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '11'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- 1422-0067
publication_status: published
publisher: MDPI
publist_id: '8042'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Relative contribution of PIN-containing secretory vesicles and plasma membrane
PINs to the directed auxin transport: Theoretical estimation'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 19
year: '2018'
...
---
_id: '140'
abstract:
- lang: eng
text: Reachability analysis is difficult for hybrid automata with affine differential
equations, because the reach set needs to be approximated. Promising abstraction
techniques usually employ interval methods or template polyhedra. Interval methods
account for dense time and guarantee soundness, and there are interval-based tools
that overapproximate affine flowpipes. But interval methods impose bounded and
rigid shapes, which make refinement expensive and fixpoint detection difficult.
Template polyhedra, on the other hand, can be adapted flexibly and can be unbounded,
but sound template refinement for unbounded reachability analysis has been implemented
only for systems with piecewise constant dynamics. We capitalize on the advantages
of both techniques, combining interval arithmetic and template polyhedra, using
the former to abstract time and the latter to abstract space. During a CEGAR loop,
whenever a spurious error trajectory is found, we compute additional space constraints
and split time intervals, and use these space-time interpolants to eliminate the
counterexample. Space-time interpolation offers a lazy, flexible framework for
increasing precision while guaranteeing soundness, both for error avoidance and
fixpoint detection. To the best of out knowledge, this is the first abstraction
refinement scheme for the reachability analysis over unbounded and dense time
of affine hybrid systems, which is both sound and automatic. We demonstrate the
effectiveness of our algorithm with several benchmark examples, which cannot be
handled by other tools.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- 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: 'Frehse G, Giacobbe M, Henzinger TA. Space-time interpolants. In: Vol 10981.
Springer; 2018:468-486. doi:10.1007/978-3-319-96145-3_25'
apa: 'Frehse, G., Giacobbe, M., & Henzinger, T. A. (2018). Space-time interpolants
(Vol. 10981, pp. 468–486). Presented at the CAV: Computer Aided Verification,
Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96145-3_25'
chicago: Frehse, Goran, Mirco Giacobbe, and Thomas A Henzinger. “Space-Time Interpolants,”
10981:468–86. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_25.
ieee: 'G. Frehse, M. Giacobbe, and T. A. Henzinger, “Space-time interpolants,” presented
at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981,
pp. 468–486.'
ista: 'Frehse G, Giacobbe M, Henzinger TA. 2018. Space-time interpolants. CAV: Computer
Aided Verification, LNCS, vol. 10981, 468–486.'
mla: Frehse, Goran, et al. Space-Time Interpolants. Vol. 10981, Springer,
2018, pp. 468–86, doi:10.1007/978-3-319-96145-3_25.
short: G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2018, pp. 468–486.
conference:
end_date: 2018-07-17
location: Oxford, United Kingdom
name: 'CAV: Computer Aided Verification'
start_date: 2018-07-14
date_created: 2018-12-11T11:44:50Z
date_published: 2018-07-18T00:00:00Z
date_updated: 2023-09-19T09:30:43Z
day: '18'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-319-96145-3_25
external_id:
isi:
- '000491481600025'
file:
- access_level: open_access
checksum: 6dca832f575d6b3f0ea9dff56f579142
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:53Z
date_updated: 2020-07-14T12:44:50Z
file_id: '5310'
file_name: IST-2018-1010-v1+1_space-time_interpolants.pdf
file_size: 563710
relation: main_file
file_date_updated: 2020-07-14T12:44:50Z
has_accepted_license: '1'
intvolume: ' 10981'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 468 - 486
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '7783'
pubrep_id: '1010'
quality_controlled: '1'
related_material:
record:
- id: '6894'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Space-time interpolants
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: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10981
year: '2018'
...
---
_id: '141'
abstract:
- lang: eng
text: 'Given a model and a specification, the fundamental model-checking problem
asks for algorithmic verification of whether the model satisfies the specification.
We consider graphs and Markov decision processes (MDPs), which are fundamental
models for reactive systems. One of the very basic specifications that arise in
verification of reactive systems is the strong fairness (aka Streett) objective.
Given different types of requests and corresponding grants, the objective requires
that for each type, if the request event happens infinitely often, then the corresponding
grant event must also happen infinitely often. All ω -regular objectives can be
expressed as Streett objectives and hence they are canonical in verification.
To handle the state-space explosion, symbolic algorithms are required that operate
on a succinct implicit representation of the system rather than explicitly accessing
the system. While explicit algorithms for graphs and MDPs with Streett objectives
have been widely studied, there has been no improvement of the basic symbolic
algorithms. The worst-case numbers of symbolic steps required for the basic symbolic
algorithms are as follows: quadratic for graphs and cubic for MDPs. In this work
we present the first sub-quadratic symbolic algorithm for graphs with Streett
objectives, and our algorithm is sub-quadratic even for MDPs. Based on our algorithmic
insights we present an implementation of the new symbolic approach and show that
it improves the existing approach on several academic benchmark examples.'
acknowledgement: 'Acknowledgements. K. C. and M. H. are partially supported by the
Vienna Science and Technology Fund (WWTF) grant ICT15-003. K. C. is partially supported
by the Austrian Science Fund (FWF): S11407-N23 (RiSE/SHiNE), and an ERC Start Grant
(279307: Graph Games). V. T. is partially supported by the European Union’s Horizon
2020 research and innovation programme under the Marie Sk lodowska-Curie Grant Agreement
No. 665385.'
alternative_title:
- LNCS
article_processing_charge: No
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: Veronika
full_name: Loitzenbauer, Veronika
last_name: Loitzenbauer
- first_name: Simin
full_name: Oraee, Simin
last_name: Oraee
- first_name: Viktor
full_name: Toman, Viktor
id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87
last_name: Toman
orcid: 0000-0001-9036-063X
citation:
ama: 'Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. Symbolic algorithms
for graphs and Markov decision processes with fairness objectives. In: Vol 10982.
Springer; 2018:178-197. doi:10.1007/978-3-319-96142-2_13'
apa: 'Chatterjee, K., Henzinger, M. H., Loitzenbauer, V., Oraee, S., & Toman,
V. (2018). Symbolic algorithms for graphs and Markov decision processes with fairness
objectives (Vol. 10982, pp. 178–197). Presented at the CAV: Computer Aided Verification,
Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96142-2_13'
chicago: Chatterjee, Krishnendu, Monika H Henzinger, Veronika Loitzenbauer, Simin
Oraee, and Viktor Toman. “Symbolic Algorithms for Graphs and Markov Decision Processes
with Fairness Objectives,” 10982:178–97. Springer, 2018. https://doi.org/10.1007/978-3-319-96142-2_13.
ieee: 'K. Chatterjee, M. H. Henzinger, V. Loitzenbauer, S. Oraee, and V. Toman,
“Symbolic algorithms for graphs and Markov decision processes with fairness objectives,”
presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018,
vol. 10982, pp. 178–197.'
ista: 'Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. 2018. Symbolic
algorithms for graphs and Markov decision processes with fairness objectives.
CAV: Computer Aided Verification, LNCS, vol. 10982, 178–197.'
mla: Chatterjee, Krishnendu, et al. Symbolic Algorithms for Graphs and Markov
Decision Processes with Fairness Objectives. Vol. 10982, Springer, 2018, pp.
178–97, doi:10.1007/978-3-319-96142-2_13.
short: K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, S. Oraee, V. Toman, in:,
Springer, 2018, pp. 178–197.
conference:
end_date: 2018-07-17
location: Oxford, United Kingdom
name: 'CAV: Computer Aided Verification'
start_date: 2018-07-14
date_created: 2018-12-11T11:44:51Z
date_published: 2018-07-18T00:00:00Z
date_updated: 2025-07-14T09:10:15Z
day: '18'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-319-96142-2_13
ec_funded: 1
external_id:
isi:
- '000491469700013'
file:
- access_level: open_access
checksum: 1a6ffa4febe8bb8ac28be3adb3eafebc
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T08:52:38Z
date_updated: 2020-07-14T12:44:53Z
file_id: '5737'
file_name: 2018_LNCS_Chatterjee.pdf
file_size: 675606
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 10982'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 178-197
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_status: published
publisher: Springer
publist_id: '7782'
quality_controlled: '1'
related_material:
record:
- id: '10199'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Symbolic algorithms for graphs and Markov decision processes with fairness
objectives
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: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10982
year: '2018'
...
---
_id: '142'
abstract:
- lang: eng
text: We address the problem of analyzing the reachable set of a polynomial nonlinear
continuous system by over-approximating the flowpipe of its dynamics. The common
approach to tackle this problem is to perform a numerical integration over a given
time horizon based on Taylor expansion and interval arithmetic. However, this
method results to be very conservative when there is a large difference in speed
between trajectories as time progresses. In this paper, we propose to use combinations
of barrier functions, which we call piecewise barrier tube (PBT), to over-approximate
flowpipe. The basic idea of PBT is that for each segment of a flowpipe, a coarse
box which is big enough to contain the segment is constructed using sampled simulation
and then in the box we compute by linear programming a set of barrier functions
(called barrier tube or BT for short) which work together to form a tube surrounding
the flowpipe. The benefit of using PBT is that (1) BT is independent of time and
hence can avoid being stretched and deformed by time; and (2) a small number of
BTs can form a tight over-approximation for the flowpipe, which means that the
computation required to decide whether the BTs intersect the unsafe set can be
reduced significantly. We implemented a prototype called PBTS in C++. Experiments
on some benchmark systems show that our approach is effective.
acknowledgement: 'Austrian Science Fund FWF: S11402-N23, S11405-N23, Z211-N32'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- 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: 'Kong H, Bartocci E, Henzinger TA. Reachable set over-approximation for nonlinear
systems using piecewise barrier tubes. In: Vol 10981. Springer; 2018:449-467.
doi:10.1007/978-3-319-96145-3_24'
apa: 'Kong, H., Bartocci, E., & Henzinger, T. A. (2018). Reachable set over-approximation
for nonlinear systems using piecewise barrier tubes (Vol. 10981, pp. 449–467).
Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer.
https://doi.org/10.1007/978-3-319-96145-3_24'
chicago: Kong, Hui, Ezio Bartocci, and Thomas A Henzinger. “Reachable Set Over-Approximation
for Nonlinear Systems Using Piecewise Barrier Tubes,” 10981:449–67. Springer,
2018. https://doi.org/10.1007/978-3-319-96145-3_24.
ieee: 'H. Kong, E. Bartocci, and T. A. Henzinger, “Reachable set over-approximation
for nonlinear systems using piecewise barrier tubes,” presented at the CAV: Computer
Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 449–467.'
ista: 'Kong H, Bartocci E, Henzinger TA. 2018. Reachable set over-approximation
for nonlinear systems using piecewise barrier tubes. CAV: Computer Aided Verification,
LNCS, vol. 10981, 449–467.'
mla: Kong, Hui, et al. Reachable Set Over-Approximation for Nonlinear Systems
Using Piecewise Barrier Tubes. Vol. 10981, Springer, 2018, pp. 449–67, doi:10.1007/978-3-319-96145-3_24.
short: H. Kong, E. Bartocci, T.A. Henzinger, in:, Springer, 2018, pp. 449–467.
conference:
end_date: 2018-07-17
location: Oxford, United Kingdom
name: 'CAV: Computer Aided Verification'
start_date: 2018-07-14
date_created: 2018-12-11T11:44:51Z
date_published: 2018-07-18T00:00:00Z
date_updated: 2023-09-15T12:12:08Z
day: '18'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-96145-3_24
external_id:
isi:
- '000491481600024'
file:
- access_level: open_access
checksum: fd95e8026deacef3dc752a733bb9355f
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T15:57:06Z
date_updated: 2020-07-14T12:44:53Z
file_id: '5718'
file_name: 2018_LNCS_Kong.pdf
file_size: 5591566
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 10981'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 449 - 467
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_status: published
publisher: Springer
publist_id: '7781'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reachable set over-approximation for nonlinear systems using piecewise barrier
tubes
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: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10981
year: '2018'
...
---
_id: '143'
abstract:
- lang: eng
text: 'Vector Addition Systems with States (VASS) provide a well-known and fundamental
model for the analysis of concurrent processes, parameterized systems, and are
also used as abstract models of programs in resource bound analysis. In this paper
we study the problem of obtaining asymptotic bounds on the termination time of
a given VASS. In particular, we focus on the practically important case of obtaining
polynomial bounds on termination time. Our main contributions are as follows:
First, we present a polynomial-time algorithm for deciding whether a given VASS
has a linear asymptotic complexity. We also show that if the complexity of a VASS
is not linear, it is at least quadratic. Second, we classify VASS according to
quantitative properties of their cycles. We show that certain singularities in
these properties are the key reason for non-polynomial asymptotic complexity of
VASS. In absence of singularities, we show that the asymptotic complexity is always
polynomial and of the form Θ(nk), for some integer k d, where d is the dimension
of the VASS. We present a polynomial-time algorithm computing the optimal k. For
general VASS, the same algorithm, which is based on a complete technique for the
construction of ranking functions in VASS, produces a valid lower bound, i.e.,
a k such that the termination complexity is (nk). Our results are based on new
insights into the geometry of VASS dynamics, which hold the potential for further
applicability to VASS analysis.'
alternative_title:
- ACM/IEEE Symposium on Logic in Computer Science
article_processing_charge: No
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Antonín
full_name: Kučera, Antonín
last_name: Kučera
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
- first_name: Dominik
full_name: Velan, Dominik
last_name: Velan
- first_name: Florian
full_name: Zuleger, Florian
last_name: Zuleger
citation:
ama: 'Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. Efficient
algorithms for asymptotic bounds on termination time in VASS. In: Vol F138033.
IEEE; 2018:185-194. doi:10.1145/3209108.3209191'
apa: 'Brázdil, T., Chatterjee, K., Kučera, A., Novotný, P., Velan, D., & Zuleger,
F. (2018). Efficient algorithms for asymptotic bounds on termination time in VASS
(Vol. F138033, pp. 185–194). Presented at the LICS: Logic in Computer Science,
Oxford, United Kingdom: IEEE. https://doi.org/10.1145/3209108.3209191'
chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Antonín Kučera, Petr Novotný, Dominik
Velan, and Florian Zuleger. “Efficient Algorithms for Asymptotic Bounds on Termination
Time in VASS,” F138033:185–94. IEEE, 2018. https://doi.org/10.1145/3209108.3209191.
ieee: 'T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, and F. Zuleger,
“Efficient algorithms for asymptotic bounds on termination time in VASS,” presented
at the LICS: Logic in Computer Science, Oxford, United Kingdom, 2018, vol. F138033,
pp. 185–194.'
ista: 'Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. 2018. Efficient
algorithms for asymptotic bounds on termination time in VASS. LICS: Logic in Computer
Science, ACM/IEEE Symposium on Logic in Computer Science, vol. F138033, 185–194.'
mla: Brázdil, Tomáš, et al. Efficient Algorithms for Asymptotic Bounds on Termination
Time in VASS. Vol. F138033, IEEE, 2018, pp. 185–94, doi:10.1145/3209108.3209191.
short: T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:,
IEEE, 2018, pp. 185–194.
conference:
end_date: 2018-07-12
location: Oxford, United Kingdom
name: 'LICS: Logic in Computer Science'
start_date: 2018-07-09
date_created: 2018-12-11T11:44:51Z
date_published: 2018-07-09T00:00:00Z
date_updated: 2025-06-02T08:53:48Z
day: '09'
department:
- _id: KrCh
doi: 10.1145/3209108.3209191
ec_funded: 1
external_id:
isi:
- '000545262800020'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.10985
month: '07'
oa: 1
oa_version: Preprint
page: 185 - 194
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_identifier:
isbn:
- 978-1-4503-5583-4
publication_status: published
publisher: IEEE
publist_id: '7780'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient algorithms for asymptotic bounds on termination time in VASS
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: F138033
year: '2018'
...
---
_id: '144'
abstract:
- lang: eng
text: The task of a monitor is to watch, at run-time, the execution of a reactive
system, and signal the occurrence of a safety violation in the observed sequence
of events. While finite-state monitors have been studied extensively, in practice,
monitoring software also makes use of unbounded memory. We define a model of automata
equipped with integer-valued registers which can execute only a bounded number
of instructions between consecutive events, and thus can form the theoretical
basis for the study of infinite-state monitors. We classify these register monitors
according to the number k of available registers, and the type of register instructions.
In stark contrast to the theory of computability for register machines, we prove
that for every k 1, monitors with k + 1 counters (with instruction set 〈+1, =〉)
are strictly more expressive than monitors with k counters. We also show that
adder monitors (with instruction set 〈1, +, =〉) are strictly more expressive than
counter monitors, but are complete for monitoring all computable safety -languages
for k = 6. Real-time monitors are further required to signal the occurrence of
a safety violation as soon as it occurs. The expressiveness hierarchy for counter
monitors carries over to real-time monitors. We then show that 2 adders cannot
simulate 3 counters in real-time. Finally, we show that real-time adder monitors
with inequalities are as expressive as real-time Turing machines.
alternative_title:
- ACM/IEEE Symposium on Logic in Computer Science
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ege
full_name: Saraç, Ege
last_name: Saraç
citation:
ama: 'Ferrere T, Henzinger TA, Saraç E. A theory of register monitors. In: Vol Part
F138033. IEEE; 2018:394-403. doi:10.1145/3209108.3209194'
apa: 'Ferrere, T., Henzinger, T. A., & Saraç, E. (2018). A theory of register
monitors (Vol. Part F138033, pp. 394–403). Presented at the LICS: Logic in Computer
Science, Oxford, UK: IEEE. https://doi.org/10.1145/3209108.3209194'
chicago: Ferrere, Thomas, Thomas A Henzinger, and Ege Saraç. “A Theory of Register
Monitors,” Part F138033:394–403. IEEE, 2018. https://doi.org/10.1145/3209108.3209194.
ieee: 'T. Ferrere, T. A. Henzinger, and E. Saraç, “A theory of register monitors,”
presented at the LICS: Logic in Computer Science, Oxford, UK, 2018, vol. Part
F138033, pp. 394–403.'
ista: 'Ferrere T, Henzinger TA, Saraç E. 2018. A theory of register monitors. LICS:
Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol.
Part F138033, 394–403.'
mla: Ferrere, Thomas, et al. A Theory of Register Monitors. Vol. Part F138033,
IEEE, 2018, pp. 394–403, doi:10.1145/3209108.3209194.
short: T. Ferrere, T.A. Henzinger, E. Saraç, in:, IEEE, 2018, pp. 394–403.
conference:
end_date: 2018-07-12
location: Oxford, UK
name: 'LICS: Logic in Computer Science'
start_date: 2018-07-09
date_created: 2018-12-11T11:44:52Z
date_published: 2018-07-09T00:00:00Z
date_updated: 2023-09-08T11:49:13Z
day: '09'
department:
- _id: ToHe
doi: 10.1145/3209108.3209194
external_id:
isi:
- '000545262800041'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 394 - 403
publication_status: published
publisher: IEEE
publist_id: '7779'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A theory of register monitors
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: Part F138033
year: '2018'
...
---
_id: '145'
abstract:
- lang: eng
text: Aged proteins can become hazardous to cellular function, by accumulating molecular
damage. This implies that cells should preferentially rely on newly produced ones.
We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic
transmission. We found that newly synthesized vesicle proteins were incorporated
in the actively recycling pool of vesicles responsible for all neurotransmitter
release during physiological activity. We observed this for the calcium sensor
Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion
protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization
by secondary ion mass spectrometry enabled us to query the entire protein makeup
of the actively recycling vesicles, which we found to be younger than that of
non-recycling vesicles. The young vesicle proteins remained in use for up to ~
24 h, during which they participated in recycling a few hundred times. They were
afterward reluctant to release and were degraded after an additional ~ 24–48 h.
We suggest that the recycling pool of synaptic vesicles relies on newly synthesized
proteins, while the inactive reserve pool contains older proteins.
acknowledgement: We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We
thank Erwin Neher for help with the development of the mathematical model of the
synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore
Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner
for providing the illustrations of synaptic vesicle and protein dynamics. We thank
Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the
manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate
School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is
a recipient of long-term fellowships from the European Molecular Biology Organization
(ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013).
The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG
NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence
Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05,
and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the
German Federal Ministry of Education and Research (03F0626A).
article_number: e98044
article_processing_charge: No
article_type: original
author:
- first_name: Sven M
full_name: Truckenbrodt, Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- first_name: Abhiyan
full_name: Viplav, Abhiyan
last_name: Viplav
- first_name: Sebsatian
full_name: Jähne, Sebsatian
last_name: Jähne
- first_name: Angela
full_name: Vogts, Angela
last_name: Vogts
- first_name: Annette
full_name: Denker, Annette
last_name: Denker
- first_name: Hanna
full_name: Wildhagen, Hanna
last_name: Wildhagen
- first_name: Eugenio
full_name: Fornasiero, Eugenio
last_name: Fornasiero
- first_name: Silvio
full_name: Rizzoli, Silvio
last_name: Rizzoli
citation:
ama: Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle
proteins are preferentially used in synaptic transmission. The EMBO Journal.
2018;37(15). doi:10.15252/embj.201798044
apa: Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen,
H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially
used in synaptic transmission. The EMBO Journal. Wiley. https://doi.org/10.15252/embj.201798044
chicago: Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette
Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced
Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The
EMBO Journal. Wiley, 2018. https://doi.org/10.15252/embj.201798044.
ieee: S. M. Truckenbrodt et al., “Newly produced synaptic vesicle proteins
are preferentially used in synaptic transmission,” The EMBO Journal, vol.
37, no. 15. Wiley, 2018.
ista: Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero
E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially
used in synaptic transmission. The EMBO Journal. 37(15), e98044.
mla: Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are
Preferentially Used in Synaptic Transmission.” The EMBO Journal, vol. 37,
no. 15, e98044, Wiley, 2018, doi:10.15252/embj.201798044.
short: S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen,
E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018).
date_created: 2018-12-11T11:44:52Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-13T09:02:48Z
day: '01'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.15252/embj.201798044
external_id:
isi:
- '000440416900005'
pmid:
- '29950309'
file:
- access_level: open_access
checksum: a540feb6c9af6aefc78de531461a8835
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:17:29Z
date_updated: 2020-07-14T12:44:56Z
file_id: '5710'
file_name: 2018_EMBO_Truckenbrodt.pdf
file_size: 2846470
relation: main_file
file_date_updated: 2020-07-14T12:44:56Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: The EMBO Journal
publication_identifier:
issn:
- 0261-4189
publication_status: published
publisher: Wiley
publist_id: '7778'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Newly produced synaptic vesicle proteins are preferentially used in synaptic
transmission
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '146'
abstract:
- lang: eng
text: The root cap protects the stem cell niche of angiosperm roots from damage.
In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are
regularly lost through programmed cell death, while the outermost layer of the
root cap covering the tip is repeatedly sloughed. Efficient coordination with
stem cells producing new layers is needed to maintain a constant size of the cap.
We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2
(HSL2), mediating such communication. Live imaging over several days characterized
this process from initial fractures in LRC cell files to full separation of a
layer. Enhanced expression of IDL1 in the separating root cap layers resulted
in increased frequency of sloughing, balanced with generation of new layers in
a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to
the transcription factors BEARSKIN1/2 and genes associated with programmed cell
death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation
and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the
homeostatic balance between stem cell division and sloughing activity.
article_processing_charge: No
article_type: original
author:
- first_name: Chun Lin
full_name: Shi, Chun Lin
last_name: Shi
- 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: Ullrich
full_name: Herrmann, Ullrich
last_name: Herrmann
- first_name: Mari
full_name: Wildhagen, Mari
last_name: Wildhagen
- first_name: Ivan
full_name: Kulik, Ivan
id: F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB
last_name: Kulik
- first_name: Andreas
full_name: Kopf, Andreas
last_name: Kopf
- first_name: Takashi
full_name: Ishida, Takashi
last_name: Ishida
- first_name: Vilde
full_name: Olsson, Vilde
last_name: Olsson
- first_name: Mari Kristine
full_name: Anker, Mari Kristine
last_name: Anker
- first_name: Markus
full_name: Albert, Markus
last_name: Albert
- first_name: Melinka A
full_name: Butenko, Melinka A
last_name: Butenko
- first_name: Georg
full_name: Felix, Georg
last_name: Felix
- first_name: Shinichiro
full_name: Sawa, Shinichiro
last_name: Sawa
- first_name: Manfred
full_name: Claassen, Manfred
last_name: Claassen
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Reidunn B
full_name: Aalen, Reidunn B
last_name: Aalen
citation:
ama: Shi CL, von Wangenheim D, Herrmann U, et al. The dynamics of root cap sloughing
in Arabidopsis is regulated by peptide signalling. Nature Plants. 2018;4(8):596-604.
doi:10.1038/s41477-018-0212-z
apa: Shi, C. L., von Wangenheim, D., Herrmann, U., Wildhagen, M., Kulik, I., Kopf,
A., … Aalen, R. B. (2018). The dynamics of root cap sloughing in Arabidopsis is
regulated by peptide signalling. Nature Plants. Nature Publishing Group.
https://doi.org/10.1038/s41477-018-0212-z
chicago: Shi, Chun Lin, Daniel von Wangenheim, Ullrich Herrmann, Mari Wildhagen,
Ivan Kulik, Andreas Kopf, Takashi Ishida, et al. “The Dynamics of Root Cap Sloughing
in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants. Nature
Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0212-z.
ieee: C. L. Shi et al., “The dynamics of root cap sloughing in Arabidopsis
is regulated by peptide signalling,” Nature Plants, vol. 4, no. 8. Nature
Publishing Group, pp. 596–604, 2018.
ista: Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida
T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml
J, Aalen RB. 2018. The dynamics of root cap sloughing in Arabidopsis is regulated
by peptide signalling. Nature Plants. 4(8), 596–604.
mla: Shi, Chun Lin, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is
Regulated by Peptide Signalling.” Nature Plants, vol. 4, no. 8, Nature
Publishing Group, 2018, pp. 596–604, doi:10.1038/s41477-018-0212-z.
short: C.L. Shi, D. von Wangenheim, U. Herrmann, M. Wildhagen, I. Kulik, A. Kopf,
T. Ishida, V. Olsson, M.K. Anker, M. Albert, M.A. Butenko, G. Felix, S. Sawa,
M. Claassen, J. Friml, R.B. Aalen, Nature Plants 4 (2018) 596–604.
date_created: 2018-12-11T11:44:52Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2023-09-19T10:08:45Z
day: '30'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41477-018-0212-z
external_id:
isi:
- '000443861300016'
pmid:
- '30061750'
file:
- access_level: open_access
checksum: da33101c76ee1b2dc5ab28fd2ccba9d0
content_type: application/pdf
creator: dernst
date_created: 2019-11-18T16:24:07Z
date_updated: 2020-07-14T12:44:56Z
file_id: '7043'
file_name: 2018_NaturePlants_Shi.pdf
file_size: 226829
relation: main_file
file_date_updated: 2020-07-14T12:44:56Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 596 - 604
pmid: 1
publication: Nature Plants
publication_status: published
publisher: Nature Publishing Group
publist_id: '7777'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-process-in-root-development-discovered/
scopus_import: '1'
status: public
title: The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 4
year: '2018'
...
---
_id: '147'
abstract:
- lang: eng
text: The trafficking of subcellular cargos in eukaryotic cells crucially depends
on vesicle budding, a process mediated by ARF-GEFs (ADP-ribosylation factor guanine
nucleotide exchange factors). In plants, ARF-GEFs play essential roles in endocytosis,
vacuolar trafficking, recycling, secretion, and polar trafficking. Moreover, they
are important for plant development, mainly through controlling the polar subcellular
localization of PIN-FORMED (PIN) transporters of the plant hormone auxin. Here,
using a chemical genetics screen in Arabidopsis thaliana, we identified Endosidin
4 (ES4), an inhibitor of eukaryotic ARF-GEFs. ES4 acts similarly to and synergistically
with the established ARF-GEF inhibitor Brefeldin A and has broad effects on intracellular
trafficking, including endocytosis, exocytosis, and vacuolar targeting. Additionally,
Arabidopsis and yeast (Sacharomyces cerevisiae) mutants defective in ARF-GEF show
altered sensitivity to ES4. ES4 interferes with the activation-based membrane
association of the ARF1 GTPases, but not of their mutant variants that are activated
independently of ARF-GEF activity. Biochemical approaches and docking simulations
confirmed that ES4 specifically targets the SEC7 domain-containing ARF-GEFs. These
observations collectively identify ES4 as a chemical tool enabling the study of
ARF-GEF-mediated processes, including ARF-GEF-mediated plant development.
acknowledgement: We thank Gerd Jürgens, Sandra Richter, and Sheng Yang He for providing
antibodies; Maciek Adamowski, Fernando Aniento, Sebastian Bednarek, Nico Callewaert,
Matyás Fendrych, Elena Feraru, and Mugurel I. Feraru for helpful suggestions; Siamsa
Doyle for critical reading of the manuscript and helpful comments and suggestions;
and Stephanie Smith and Martine De Cock for help in editing and language corrections.
We acknowledge the core facility Cellular Imaging of CEITEC supported by the Czech-BioImaging
large RI project (LM2015062 funded by MEYS CR) for their support with obtaining
scientific data presented in this article. Plant Sciences Core Facility of CEITEC
Masaryk University is gratefully acknowledged for obtaining part of the scientific
data presented in this article. We acknowledge support from the Fondation pour la
Recherche Médicale and from the Institut National du Cancer (J.C.). The research
leading to these results was funded by the European Research Council under the European
Union's 7th Framework Program (FP7/2007-2013)/ERC grant agreement numbers 282300
and 742985 and the Czech Science Foundation GAČR (GA18-26981S; J.F.); Ministry of
Education, Youth, and Sports/MEYS of the Czech Republic under the Project CEITEC
2020 (LQ1601; T.N.); the China Science Council for a predoctoral fellowship (Q.L.);
a joint research project within the framework of cooperation between the Research
Foundation-Flanders and the Bulgarian Academy of Sciences (VS.025.13N; K.M. and
E.R.); Vetenskapsrådet and Vinnova (Verket för Innovationssystem; S.R.), Knut och
Alice Wallenbergs Stiftelse via “Shapesystem” Grant 2012.0050 (S.R.), Kempe stiftelserna
(P.G.), Tryggers CTS410 (P.G.).
article_processing_charge: No
article_type: original
author:
- first_name: Urszula
full_name: Kania, Urszula
id: 4AE5C486-F248-11E8-B48F-1D18A9856A87
last_name: Kania
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Qing
full_name: Lu, Qing
last_name: Lu
- first_name: Glenn R
full_name: Hicks, Glenn R
last_name: Hicks
- first_name: Wim
full_name: Nerinckx, Wim
last_name: Nerinckx
- first_name: Kiril
full_name: Mishev, Kiril
last_name: Mishev
- first_name: Francois
full_name: Peurois, Francois
last_name: Peurois
- first_name: Jacqueline
full_name: Cherfils, Jacqueline
last_name: Cherfils
- first_name: Rycke Riet Maria
full_name: De, Rycke Riet Maria
last_name: De
- first_name: Peter
full_name: Grones, Peter
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Kania U, Nodzyński T, Lu Q, et al. The inhibitor Endosidin 4 targets SEC7 domain-type
ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes.
The Plant Cell. 2018;30(10):2553-2572. doi:10.1105/tpc.18.00127
apa: Kania, U., Nodzyński, T., Lu, Q., Hicks, G. R., Nerinckx, W., Mishev, K., …
Friml, J. (2018). The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase
exchange factors and interferes with sub cellular trafficking in eukaryotes. The
Plant Cell. Oxford University Press. https://doi.org/10.1105/tpc.18.00127
chicago: Kania, Urszula, Tomasz Nodzyński, Qing Lu, Glenn R Hicks, Wim Nerinckx,
Kiril Mishev, Francois Peurois, et al. “The Inhibitor Endosidin 4 Targets SEC7
Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking
in Eukaryotes.” The Plant Cell. Oxford University Press, 2018. https://doi.org/10.1105/tpc.18.00127.
ieee: U. Kania et al., “The inhibitor Endosidin 4 targets SEC7 domain-type
ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes,”
The Plant Cell, vol. 30, no. 10. Oxford University Press, pp. 2553–2572,
2018.
ista: Kania U, Nodzyński T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils
J, De RRM, Grones P, Robert S, Russinova E, Friml J. 2018. The inhibitor Endosidin
4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub
cellular trafficking in eukaryotes. The Plant Cell. 30(10), 2553–2572.
mla: Kania, Urszula, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type
ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.”
The Plant Cell, vol. 30, no. 10, Oxford University Press, 2018, pp. 2553–72,
doi:10.1105/tpc.18.00127.
short: U. Kania, T. Nodzyński, Q. Lu, G.R. Hicks, W. Nerinckx, K. Mishev, F. Peurois,
J. Cherfils, R.R.M. De, P. Grones, S. Robert, E. Russinova, J. Friml, The Plant
Cell 30 (2018) 2553–2572.
date_created: 2018-12-11T11:44:52Z
date_published: 2018-11-12T00:00:00Z
date_updated: 2025-05-07T11:12:30Z
day: '12'
department:
- _id: JiFr
doi: 10.1105/tpc.18.00127
ec_funded: 1
external_id:
isi:
- '000450000500023'
pmid:
- '30018156'
intvolume: ' 30'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1105/tpc.18.00127
month: '11'
oa: 1
oa_version: Published Version
page: 2553 - 2572
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: The Plant Cell
publication_identifier:
issn:
- 1040-4651
publication_status: published
publisher: Oxford University Press
publist_id: '7776'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors
and interferes with sub cellular trafficking in eukaryotes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 30
year: '2018'
...
---
_id: '539'
abstract:
- lang: eng
text: The whole life cycle of plants as well as their responses to environmental
stimuli is governed by a complex network of hormonal regulations. A number of
studies have demonstrated an essential role of both auxin and cytokinin in the
regulation of many aspects of plant growth and development including embryogenesis,
postembryonic organogenic processes such as root, and shoot branching, root and
shoot apical meristem activity and phyllotaxis. Over the last decades essential
knowledge on the key molecular factors and pathways that spatio-temporally define
auxin and cytokinin activities in the plant body has accumulated. However, how
both hormonal pathways are interconnected by a complex network of interactions
and feedback circuits that determines the final outcome of the individual hormone
actions is still largely unknown. Root system architecture establishment and in
particular formation of lateral organs is prime example of developmental process
at whose regulation both auxin and cytokinin pathways converge. To dissect convergence
points and pathways that tightly balance auxin - cytokinin antagonistic activities
that determine the root branching pattern transcriptome profiling was applied.
Genome wide expression analyses of the xylem pole pericycle, a tissue giving rise
to lateral roots, led to identification of genes that are highly responsive to
combinatorial auxin and cytokinin treatments and play an essential function in
the auxin-cytokinin regulated root branching. SYNERGISTIC AUXIN CYTOKININ 1 (SYAC1)
gene, which encodes for a protein of unknown function, was detected among the
top candidate genes of which expression was synergistically up-regulated by simultaneous
hormonal treatment. Plants with modulated SYAC1 activity exhibit severe defects
in the root system establishment and attenuate developmental responses to both
auxin and cytokinin. To explore the biological function of the SYAC1, we employed
different strategies including expression pattern analysis, subcellular localization
and phenotypic analyses of the syac1 loss-of-function and gain-of-function transgenic
lines along with the identification of the SYAC1 interaction partners. Detailed
functional characterization revealed that SYAC1 acts as a developmentally specific
regulator of the secretory pathway to control deposition of cell wall components
and thereby rapidly fine tune elongation growth.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Andrej
full_name: Hurny, Andrej
id: 4DC4AF46-F248-11E8-B48F-1D18A9856A87
last_name: Hurny
orcid: 0000-0003-3638-1426
citation:
ama: Hurny A. Identification and characterization of novel auxin-cytokinin cross-talk
components. 2018. doi:10.15479/AT:ISTA:th_930
apa: Hurny, A. (2018). Identification and characterization of novel auxin-cytokinin
cross-talk components. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_930
chicago: Hurny, Andrej. “Identification and Characterization of Novel Auxin-Cytokinin
Cross-Talk Components.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_930.
ieee: A. Hurny, “Identification and characterization of novel auxin-cytokinin cross-talk
components,” Institute of Science and Technology Austria, 2018.
ista: Hurny A. 2018. Identification and characterization of novel auxin-cytokinin
cross-talk components. Institute of Science and Technology Austria.
mla: Hurny, Andrej. Identification and Characterization of Novel Auxin-Cytokinin
Cross-Talk Components. Institute of Science and Technology Austria, 2018,
doi:10.15479/AT:ISTA:th_930.
short: A. Hurny, Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk
Components, Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:47:03Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-07T12:41:06Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: EvBe
doi: 10.15479/AT:ISTA:th_930
file:
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checksum: 0c9d6d1c80d9857e6e545213467bbcb2
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date_created: 2019-04-05T09:37:56Z
date_updated: 2020-12-02T23:30:08Z
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file_id: '6226'
file_name: 2018_Hurny_thesis_source.docx
file_size: 28112114
relation: source_file
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checksum: ecbe481a1413d270bd501b872c7ed54f
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creator: dernst
date_created: 2019-04-05T09:37:55Z
date_updated: 2020-12-02T09:52:16Z
embargo: 2019-07-10
file_id: '6227'
file_name: 2018_Hurny_thesis.pdf
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file_date_updated: 2020-12-02T23:30:08Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '147'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7277'
pubrep_id: '930'
related_material:
record:
- id: '1024'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: Identification and characterization of novel auxin-cytokinin cross-talk components
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '54'
abstract:
- lang: eng
text: During epithelial tissue development, repair, and homeostasis, adherens junctions
(AJs) ensure intercellular adhesion and tissue integrity while allowing for cell
and tissue dynamics. Mechanical forces play critical roles in AJs’ composition
and dynamics. Recent findings highlight that beyond a well-established role in
reinforcing cell-cell adhesion, AJ mechanosensitivity promotes junctional remodeling
and polarization, thereby regulating critical processes such as cell intercalation,
division, and collective migration. Here, we provide an integrated view of mechanosensing
mechanisms that regulate cell-cell contact composition, geometry, and integrity
under tension and highlight pivotal roles for mechanosensitive AJ remodeling in
preserving epithelial integrity and sustaining tissue dynamics.
acknowledgement: Research in the Bellaïche laboratory is supported by the European
Research Council (ERC Advanced, TiMoprh, 340784), the Fondation ARC pour la Recherche
sur le Cancer (SL220130607097), the Agence Nationale de la Recherche (ANR lLabex
DEEP; 11-LBX-0044, ANR-10-IDEX-0001-02), the Centre National de la Recherche Scientifique,
the Institut National de la Santé et de la Recherche Médicale, and Institut Curie
and PSL Research University funding or grants.
article_processing_charge: No
article_type: review
author:
- first_name: Diana C
full_name: Nunes Pinheiro, Diana C
id: 2E839F16-F248-11E8-B48F-1D18A9856A87
last_name: Nunes Pinheiro
orcid: 0000-0003-4333-7503
- first_name: Yohanns
full_name: Bellaïche, Yohanns
last_name: Bellaïche
citation:
ama: Nunes Pinheiro DC, Bellaïche Y. Mechanical force-driven adherents junction
remodeling and epithelial dynamics. Developmental Cell. 2018;47(1):3-19.
doi:10.1016/j.devcel.2018.09.014
apa: Nunes Pinheiro, D. C., & Bellaïche, Y. (2018). Mechanical force-driven
adherents junction remodeling and epithelial dynamics. Developmental Cell.
Cell Press. https://doi.org/10.1016/j.devcel.2018.09.014
chicago: Nunes Pinheiro, Diana C, and Yohanns Bellaïche. “Mechanical Force-Driven
Adherents Junction Remodeling and Epithelial Dynamics.” Developmental Cell.
Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.09.014.
ieee: D. C. Nunes Pinheiro and Y. Bellaïche, “Mechanical force-driven adherents
junction remodeling and epithelial dynamics,” Developmental Cell, vol.
47, no. 1. Cell Press, pp. 3–19, 2018.
ista: Nunes Pinheiro DC, Bellaïche Y. 2018. Mechanical force-driven adherents junction
remodeling and epithelial dynamics. Developmental Cell. 47(1), 3–19.
mla: Nunes Pinheiro, Diana C., and Yohanns Bellaïche. “Mechanical Force-Driven Adherents
Junction Remodeling and Epithelial Dynamics.” Developmental Cell, vol.
47, no. 1, Cell Press, 2018, pp. 3–19, doi:10.1016/j.devcel.2018.09.014.
short: D.C. Nunes Pinheiro, Y. Bellaïche, Developmental Cell 47 (2018) 3–19.
date_created: 2018-12-11T11:44:23Z
date_published: 2018-10-08T00:00:00Z
date_updated: 2023-09-13T08:54:38Z
day: '08'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2018.09.014
external_id:
isi:
- '000446579900002'
intvolume: ' 47'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- url: https://doi.org/10.1016/j.devcel.2018.09.014
month: '10'
oa_version: Published Version
page: 3 - 19
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '8000'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanical force-driven adherents junction remodeling and epithelial dynamics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 47
year: '2018'
...
---
_id: '542'
abstract:
- lang: eng
text: The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a
model for autosomal segregation distortion for close to a century, but several
questions remain regarding its biology and evolutionary history. A recently published
set of population genomics resources for wild mice includes several individuals
heterozygous for the t-haplotype, which we use to characterize this selfish element
at the genomic and transcriptomic level. Our results show that large sections
of the t-haplotype have been replaced by standard homologous sequences, possibly
due to occasional events of recombination, and that this complicates the inference
of its history. As expected for a long genomic segment of very low recombination,
the t-haplotype carries an excess of fixed nonsynonymous mutations compared to
the standard chromosome. This excess is stronger for regions that have not undergone
recent recombination, suggesting that occasional gene flow between the t and the
standard chromosome may provide a mechanism to regenerate coding sequences that
have accumulated deleterious mutations. Finally, we find that t-complex genes
with altered expression largely overlap with deleted or amplified regions, and
that carrying a t-haplotype alters the testis expression of genes outside of the
t-complex, providing new leads into the pathways involved in the biology of this
segregation distorter.
article_processing_charge: No
article_type: original
author:
- first_name: Réka K
full_name: Kelemen, Réka K
id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87
last_name: Kelemen
orcid: 0000-0002-8489-9281
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Kelemen RK, Vicoso B. Complex history and differentiation patterns of the t-haplotype,
a mouse meiotic driver. Genetics. 2018;208(1):365-375. doi:10.1534/genetics.117.300513
apa: Kelemen, R. K., & Vicoso, B. (2018). Complex history and differentiation
patterns of the t-haplotype, a mouse meiotic driver. Genetics. Genetics
Society of America. https://doi.org/10.1534/genetics.117.300513
chicago: Kelemen, Réka K, and Beatriz Vicoso. “Complex History and Differentiation
Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics. Genetics
Society of America, 2018. https://doi.org/10.1534/genetics.117.300513.
ieee: R. K. Kelemen and B. Vicoso, “Complex history and differentiation patterns
of the t-haplotype, a mouse meiotic driver,” Genetics, vol. 208, no. 1.
Genetics Society of America, pp. 365–375, 2018.
ista: Kelemen RK, Vicoso B. 2018. Complex history and differentiation patterns of
the t-haplotype, a mouse meiotic driver. Genetics. 208(1), 365–375.
mla: Kelemen, Réka K., and Beatriz Vicoso. “Complex History and Differentiation
Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics, vol. 208,
no. 1, Genetics Society of America, 2018, pp. 365–75, doi:10.1534/genetics.117.300513.
short: R.K. Kelemen, B. Vicoso, Genetics 208 (2018) 365–375.
date_created: 2018-12-11T11:47:04Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2024-02-21T13:48:27Z
day: '01'
ddc:
- '576'
department:
- _id: BeVi
doi: 10.1534/genetics.117.300513
ec_funded: 1
external_id:
isi:
- '000419356300024'
file:
- access_level: open_access
checksum: 2123845e7031a0cf043905be160f9e69
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:14Z
date_updated: 2020-07-14T12:46:50Z
file_id: '5132'
file_name: IST-2018-1058-v1+1_365.full__1_.pdf
file_size: 1311661
relation: main_file
file_date_updated: 2020-07-14T12:46:50Z
has_accepted_license: '1'
intvolume: ' 208'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 365 - 375
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '7274'
pubrep_id: '1058'
quality_controlled: '1'
related_material:
record:
- id: '5571'
relation: popular_science
status: public
- id: '5572'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Complex history and differentiation patterns of the t-haplotype, a mouse meiotic
driver
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 208
year: '2018'
...
---
_id: '543'
abstract:
- lang: eng
text: A central goal in theoretical neuroscience is to predict the response properties
of sensory neurons from first principles. To this end, “efficient coding” posits
that sensory neurons encode maximal information about their inputs given internal
constraints. There exist, however, many variants of efficient coding (e.g., redundancy
reduction, different formulations of predictive coding, robust coding, sparse
coding, etc.), differing in their regimes of applicability, in the relevance of
signals to be encoded, and in the choice of constraints. It is unclear how these
types of efficient coding relate or what is expected when different coding objectives
are combined. Here we present a unified framework that encompasses previously
proposed efficient coding models and extends to unique regimes. We show that optimizing
neural responses to encode predictive information can lead them to either correlate
or decorrelate their inputs, depending on the stimulus statistics; in contrast,
at low noise, efficiently encoding the past always predicts decorrelation. Later,
we investigate coding of naturalistic movies and show that qualitatively different
types of visual motion tuning and levels of response sparsity are predicted, depending
on whether the objective is to recover the past or predict the future. Our approach
promises a way to explain the observed diversity of sensory neural responses,
as due to multiple functional goals and constraints fulfilled by different cell
types and/or circuits.
article_processing_charge: No
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive,
and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115
apa: Chalk, M. J., Marre, O., & Tkačik, G. (2018). Toward a unified theory of
efficient, predictive, and sparse coding. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1711114115
chicago: Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory
of Efficient, Predictive, and Sparse Coding.” PNAS. National Academy of
Sciences, 2018. https://doi.org/10.1073/pnas.1711114115.
ieee: M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient,
predictive, and sparse coding,” PNAS, vol. 115, no. 1. National Academy
of Sciences, pp. 186–191, 2018.
ista: Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive,
and sparse coding. PNAS. 115(1), 186–191.
mla: Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive,
and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences,
2018, pp. 186–91, doi:10.1073/pnas.1711114115.
short: M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191.
date_created: 2018-12-11T11:47:04Z
date_published: 2018-01-02T00:00:00Z
date_updated: 2023-09-19T10:16:35Z
day: '02'
department:
- _id: GaTk
doi: 10.1073/pnas.1711114115
external_id:
isi:
- '000419128700049'
intvolume: ' 115'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/152660 '
month: '01'
oa: 1
oa_version: Submitted Version
page: 186 - 191
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '7273'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward a unified theory of efficient, predictive, and sparse coding
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '544'
abstract:
- lang: eng
text: Drosophila melanogaster plasmatocytes, the phagocytic cells among hemocytes,
are essential for immune responses, but also play key roles from early development
to death through their interactions with other cell types. They regulate homeostasis
and signaling during development, stem cell proliferation, metabolism, cancer,
wound responses and aging, displaying intriguing molecular and functional conservation
with vertebrate macrophages. Given the relative ease of genetics in Drosophila
compared to vertebrates, tools permitting visualization and genetic manipulation
of plasmatocytes and surrounding tissues independently at all stages would greatly
aid in fully understanding these processes, but are lacking. Here we describe
a comprehensive set of transgenic lines that allow this. These include extremely
brightly fluorescing mCherry-based lines that allow GAL4-independent visualization
of plasmatocyte nuclei, cytoplasm or actin cytoskeleton from embryonic Stage 8
through adulthood in both live and fixed samples even as heterozygotes, greatly
facilitating screening. These lines allow live visualization and tracking of embryonic
plasmatocytes, as well as larval plasmatocytes residing at the body wall or flowing
with the surrounding hemolymph. With confocal imaging, interactions of plasmatocytes
and inner tissues can be seen in live or fixed embryos, larvae and adults. They
permit efficient GAL4-independent FACS analysis/sorting of plasmatocytes throughout
life. To facilitate genetic analysis of reciprocal signaling, we have also made
a plasmatocyte-expressing QF2 line that in combination with extant GAL4 drivers
allows independent genetic manipulation of both plasmatocytes and surrounding
tissues, and a GAL80 line that blocks GAL4 drivers from affecting plasmatocytes,
both of which function from the early embryo to the adult.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: ' A. Ratheesh also by Marie Curie IIF GA-2012-32950BB:DICJI, Marko
Roblek by the provincial government of Lower Austria, K. Valoskova and S. Wachner
by DOC Fellowships from the Austrian Academy of Sciences, '
article_processing_charge: No
author:
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Marko
full_name: Roblek, Marko
id: 3047D808-F248-11E8-B48F-1D18A9856A87
last_name: Roblek
orcid: 0000-0001-9588-1389
- first_name: Aparna
full_name: Ratheesh, Aparna
id: 2F064CFE-F248-11E8-B48F-1D18A9856A87
last_name: Ratheesh
orcid: 0000-0001-7190-0776
- first_name: Katarina
full_name: Valosková, Katarina
id: 46F146FC-F248-11E8-B48F-1D18A9856A87
last_name: Valosková
- first_name: Vera
full_name: Belyaeva, Vera
id: 47F080FE-F248-11E8-B48F-1D18A9856A87
last_name: Belyaeva
- first_name: Stephanie
full_name: Wachner, Stephanie
id: 2A95E7B0-F248-11E8-B48F-1D18A9856A87
last_name: Wachner
- first_name: Yutaka
full_name: Matsubayashi, Yutaka
last_name: Matsubayashi
- first_name: Besaiz
full_name: Sanchez Sanchez, Besaiz
last_name: Sanchez Sanchez
- first_name: Brian
full_name: Stramer, Brian
last_name: Stramer
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
citation:
ama: 'György A, Roblek M, Ratheesh A, et al. Tools allowing independent visualization
and genetic manipulation of Drosophila melanogaster macrophages and surrounding
tissues. G3: Genes, Genomes, Genetics. 2018;8(3):845-857. doi:10.1534/g3.117.300452'
apa: 'György, A., Roblek, M., Ratheesh, A., Valosková, K., Belyaeva, V., Wachner,
S., … Siekhaus, D. E. (2018). Tools allowing independent visualization and genetic
manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3:
Genes, Genomes, Genetics. Genetics Society of America. https://doi.org/10.1534/g3.117.300452'
chicago: 'György, Attila, Marko Roblek, Aparna Ratheesh, Katarina Valosková, Vera
Belyaeva, Stephanie Wachner, Yutaka Matsubayashi, Besaiz Sanchez Sanchez, Brian
Stramer, and Daria E Siekhaus. “Tools Allowing Independent Visualization and Genetic
Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.”
G3: Genes, Genomes, Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/g3.117.300452.'
ieee: 'A. György et al., “Tools allowing independent visualization and genetic
manipulation of Drosophila melanogaster macrophages and surrounding tissues,”
G3: Genes, Genomes, Genetics, vol. 8, no. 3. Genetics Society of America,
pp. 845–857, 2018.'
ista: 'György A, Roblek M, Ratheesh A, Valosková K, Belyaeva V, Wachner S, Matsubayashi
Y, Sanchez Sanchez B, Stramer B, Siekhaus DE. 2018. Tools allowing independent
visualization and genetic manipulation of Drosophila melanogaster macrophages
and surrounding tissues. G3: Genes, Genomes, Genetics. 8(3), 845–857.'
mla: 'György, Attila, et al. “Tools Allowing Independent Visualization and Genetic
Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.”
G3: Genes, Genomes, Genetics, vol. 8, no. 3, Genetics Society of America,
2018, pp. 845–57, doi:10.1534/g3.117.300452.'
short: 'A. György, M. Roblek, A. Ratheesh, K. Valosková, V. Belyaeva, S. Wachner,
Y. Matsubayashi, B. Sanchez Sanchez, B. Stramer, D.E. Siekhaus, G3: Genes, Genomes,
Genetics 8 (2018) 845–857.'
date_created: 2018-12-11T11:47:05Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2024-03-25T23:30:15Z
day: '01'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.1534/g3.117.300452
ec_funded: 1
external_id:
isi:
- '000426693300011'
file:
- access_level: open_access
checksum: 7d9d28b915159078a4ca7add568010e8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:48Z
date_updated: 2020-07-14T12:46:56Z
file_id: '4905'
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file_size: 2251222
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file_date_updated: 2020-07-14T12:46:56Z
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intvolume: ' 8'
isi: 1
issue: '3'
language:
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month: '03'
oa: 1
oa_version: Published Version
page: 845 - 857
project:
- _id: 253B6E48-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29638
name: Drosophila TNFa´s Funktion in Immunzellen
- _id: 253B6E48-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29638
name: The role of Drosophila TNF alpha in immune cell invasion
- _id: 2637E9C0-B435-11E9-9278-68D0E5697425
grant_number: 'LSC16-021 '
name: Investigating the role of the novel major superfamily facilitator transporter
family member MFSD1 in metastasis
- _id: 2536F660-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
publication: 'G3: Genes, Genomes, Genetics'
publication_status: published
publisher: Genetics Society of America
publist_id: '7271'
pubrep_id: '990'
quality_controlled: '1'
related_material:
record:
- id: '6530'
relation: research_paper
- id: '6543'
relation: research_paper
- id: '11193'
relation: dissertation_contains
status: public
- id: '6546'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Tools allowing independent visualization and genetic manipulation of Drosophila
melanogaster macrophages and surrounding tissues
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2018'
...
---
_id: '5457'
abstract:
- lang: eng
text: "We consider the problem of expected cost analysis over nondeterministic probabilistic
programs, which aims at automated methods for analyzing the resource-usage of
such programs. Previous approaches for this problem could only handle nonnegative
bounded costs. However, in many scenarios, such as queuing networks or analysis
of cryptocurrency protocols, both positive and negative costs are necessary and
the costs are unbounded as well.\r\n\r\nIn this work, we present a sound and efficient
approach to obtain polynomial bounds on the expected accumulated cost of nondeterministic
probabilistic programs. Our approach can handle (a) general positive and negative
costs with bounded updates in variables; and (b) nonnegative costs with general
updates to variables. We show that several natural examples which could not be
handled by previous approaches are captured in our framework.\r\n\r\nMoreover,
our approach leads to an efficient polynomial-time algorithm, while no previous
approach for cost analysis of probabilistic programs could guarantee polynomial
runtime. Finally, we show the effectiveness of our approach by presenting experimental
results on a variety of programs, motivated by real-world applications, for which
we efficiently synthesize tight resource-usage bounds."
alternative_title:
- IST Austria Technical Report
author:
- first_name: '1'
full_name: Anonymous, 1
last_name: Anonymous
- first_name: '2'
full_name: Anonymous, 2
last_name: Anonymous
- first_name: '3'
full_name: Anonymous, 3
last_name: Anonymous
- first_name: '4'
full_name: Anonymous, 4
last_name: Anonymous
- first_name: '5'
full_name: Anonymous, 5
last_name: Anonymous
- first_name: '6'
full_name: Anonymous, 6
last_name: Anonymous
citation:
ama: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous
6. Cost Analysis of Nondeterministic Probabilistic Programs. IST Austria;
2018.
apa: Anonymous, 1, Anonymous, 2, Anonymous, 3, Anonymous, 4, Anonymous, 5, &
Anonymous, 6. (2018). Cost analysis of nondeterministic probabilistic programs.
IST Austria.
chicago: Anonymous, 1, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6
Anonymous. Cost Analysis of Nondeterministic Probabilistic Programs. IST
Austria, 2018.
ieee: 1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6 Anonymous,
Cost analysis of nondeterministic probabilistic programs. IST Austria,
2018.
ista: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous
6. 2018. Cost analysis of nondeterministic probabilistic programs, IST Austria,
27p.
mla: Anonymous, 1, et al. Cost Analysis of Nondeterministic Probabilistic Programs.
IST Austria, 2018.
short: 1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, 6 Anonymous,
Cost Analysis of Nondeterministic Probabilistic Programs, IST Austria, 2018.
date_created: 2018-12-12T11:39:26Z
date_published: 2018-11-11T00:00:00Z
date_updated: 2025-06-02T08:53:45Z
day: '11'
ddc:
- '000'
file:
- access_level: open_access
checksum: ba3adafd36fe200385ccda583063b9eb
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:32Z
date_updated: 2020-07-14T12:47:00Z
file_id: '5493'
file_name: IST-2018-1066-v1+1_techreport.pdf
file_size: 4202966
relation: main_file
- access_level: closed
checksum: 6cf3a19164bb8e5048a9c8c84dfd9fa3
content_type: text/plain
creator: dernst
date_created: 2019-05-10T13:22:12Z
date_updated: 2020-07-14T12:47:00Z
file_id: '6402'
file_name: authors-names.txt
file_size: 322
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '27'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '1066'
related_material:
record:
- id: '6175'
relation: later_version
status: public
scopus_import: 1
status: public
title: Cost analysis of nondeterministic probabilistic programs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '546'
abstract:
- lang: eng
text: The precise control of neural stem cell (NSC) proliferation and differentiation
is crucial for the development and function of the human brain. Here, we review
the emerging links between the alteration of embryonic and adult neurogenesis
and the etiology of neuropsychiatric disorders (NPDs) such as autism spectrum
disorders (ASDs) and schizophrenia (SCZ), as well as the advances in stem cell-based
modeling and the novel therapeutic targets derived from these studies.
article_processing_charge: No
author:
- first_name: Roberto
full_name: Sacco, Roberto
id: 42C9F57E-F248-11E8-B48F-1D18A9856A87
last_name: Sacco
- first_name: Emanuele
full_name: Cacci, Emanuele
last_name: Cacci
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Sacco R, Cacci E, Novarino G. Neural stem cells in neuropsychiatric disorders.
Current Opinion in Neurobiology. 2018;48(2):131-138. doi:10.1016/j.conb.2017.12.005
apa: Sacco, R., Cacci, E., & Novarino, G. (2018). Neural stem cells in neuropsychiatric
disorders. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2017.12.005
chicago: Sacco, Roberto, Emanuele Cacci, and Gaia Novarino. “Neural Stem Cells in
Neuropsychiatric Disorders.” Current Opinion in Neurobiology. Elsevier,
2018. https://doi.org/10.1016/j.conb.2017.12.005.
ieee: R. Sacco, E. Cacci, and G. Novarino, “Neural stem cells in neuropsychiatric
disorders,” Current Opinion in Neurobiology, vol. 48, no. 2. Elsevier,
pp. 131–138, 2018.
ista: Sacco R, Cacci E, Novarino G. 2018. Neural stem cells in neuropsychiatric
disorders. Current Opinion in Neurobiology. 48(2), 131–138.
mla: Sacco, Roberto, et al. “Neural Stem Cells in Neuropsychiatric Disorders.” Current
Opinion in Neurobiology, vol. 48, no. 2, Elsevier, 2018, pp. 131–38, doi:10.1016/j.conb.2017.12.005.
short: R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018)
131–138.
date_created: 2018-12-11T11:47:06Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2023-09-13T09:01:56Z
day: '01'
department:
- _id: GaNo
doi: 10.1016/j.conb.2017.12.005
external_id:
isi:
- '000427101600018'
intvolume: ' 48'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 131 - 138
publication: Current Opinion in Neurobiology
publication_status: published
publisher: Elsevier
publist_id: '7268'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neural stem cells in neuropsychiatric disorders
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 48
year: '2018'
...
---
_id: '55'
abstract:
- lang: eng
text: Many animals use antimicrobials to prevent or cure disease [1,2]. For example,
some animals will ingest plants with medicinal properties, both prophylactically
to prevent infection and therapeutically to self-medicate when sick. Antimicrobial
substances are also used as topical disinfectants, to prevent infection, protect
offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees,
wasps and termites) build nests in environments with a high abundance and diversity
of pathogenic microorganisms — such as soil and rotting wood — and colonies are
often densely crowded, creating conditions that favour disease outbreaks. Consequently,
social insects have evolved collective disease defences to protect their colonies
from epidemics. These traits can be seen as functionally analogous to the immune
system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials
to prevent and eradicate infections, and to keep the brood and nest clean. However,
these antimicrobial compounds can be harmful to the insects themselves, and it
is unknown how colonies prevent collateral damage when using them. Here, we demonstrate
that antimicrobial acids, produced by workers to disinfect the colony, are harmful
to the delicate pupal brood stage, but that the pupae are protected from the acids
by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial
poison to sanitize contaminated nestmates and brood. Here, Pull et al show that
they also prophylactically sanitise their colonies, and that the silk cocoon serves
as a barrier to protect developing pupae, thus preventing collateral damage during
nest sanitation.
article_processing_charge: No
article_type: original
author:
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Sina
full_name: Metzler, Sina
id: 48204546-F248-11E8-B48F-1D18A9856A87
last_name: Metzler
orcid: 0000-0002-9547-2494
- first_name: Elisabeth
full_name: Naderlinger, Elisabeth
id: 31757262-F248-11E8-B48F-1D18A9856A87
last_name: Naderlinger
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Pull C, Metzler S, Naderlinger E, Cremer S. Protection against the lethal side
effects of social immunity in ants. Current Biology. 2018;28(19):R1139-R1140.
doi:10.1016/j.cub.2018.08.063
apa: Pull, C., Metzler, S., Naderlinger, E., & Cremer, S. (2018). Protection
against the lethal side effects of social immunity in ants. Current Biology.
Cell Press. https://doi.org/10.1016/j.cub.2018.08.063
chicago: Pull, Christopher, Sina Metzler, Elisabeth Naderlinger, and Sylvia Cremer.
“Protection against the Lethal Side Effects of Social Immunity in Ants.” Current
Biology. Cell Press, 2018. https://doi.org/10.1016/j.cub.2018.08.063.
ieee: C. Pull, S. Metzler, E. Naderlinger, and S. Cremer, “Protection against the
lethal side effects of social immunity in ants,” Current Biology, vol.
28, no. 19. Cell Press, pp. R1139–R1140, 2018.
ista: Pull C, Metzler S, Naderlinger E, Cremer S. 2018. Protection against the lethal
side effects of social immunity in ants. Current Biology. 28(19), R1139–R1140.
mla: Pull, Christopher, et al. “Protection against the Lethal Side Effects of Social
Immunity in Ants.” Current Biology, vol. 28, no. 19, Cell Press, 2018,
pp. R1139–40, doi:10.1016/j.cub.2018.08.063.
short: C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018)
R1139–R1140.
date_created: 2018-12-11T11:44:23Z
date_published: 2018-10-08T00:00:00Z
date_updated: 2023-09-15T12:06:46Z
day: '08'
department:
- _id: SyCr
doi: 10.1016/j.cub.2018.08.063
external_id:
isi:
- '000446693400008'
intvolume: ' 28'
isi: 1
issue: '19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2018.08.063
month: '10'
oa: 1
oa_version: Published Version
page: R1139 - R1140
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '7999'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protection against the lethal side effects of social immunity in ants
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 28
year: '2018'
...
---
_id: '554'
abstract:
- lang: eng
text: We analyse the canonical Bogoliubov free energy functional in three dimensions
at low temperatures in the dilute limit. We prove existence of a first-order phase
transition and, in the limit (Formula presented.), we determine the critical temperature
to be (Formula presented.) to leading order. Here, (Formula presented.) is the
critical temperature of the free Bose gas, ρ is the density of the gas and a is
the scattering length of the pair-interaction potential V. We also prove asymptotic
expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula
in the limit (Formula presented.).
arxiv: 1
author:
- first_name: Marcin M
full_name: Napiórkowski, Marcin M
id: 4197AD04-F248-11E8-B48F-1D18A9856A87
last_name: Napiórkowski
- first_name: Robin
full_name: Reuvers, Robin
last_name: Reuvers
- first_name: Jan
full_name: Solovej, Jan
last_name: Solovej
citation:
ama: 'Napiórkowski MM, Reuvers R, Solovej J. The Bogoliubov free energy functional
II: The dilute Limit. Communications in Mathematical Physics. 2018;360(1):347-403.
doi:10.1007/s00220-017-3064-x'
apa: 'Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). The Bogoliubov
free energy functional II: The dilute Limit. Communications in Mathematical
Physics. Springer. https://doi.org/10.1007/s00220-017-3064-x'
chicago: 'Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “The Bogoliubov
Free Energy Functional II: The Dilute Limit.” Communications in Mathematical
Physics. Springer, 2018. https://doi.org/10.1007/s00220-017-3064-x.'
ieee: 'M. M. Napiórkowski, R. Reuvers, and J. Solovej, “The Bogoliubov free energy
functional II: The dilute Limit,” Communications in Mathematical Physics,
vol. 360, no. 1. Springer, pp. 347–403, 2018.'
ista: 'Napiórkowski MM, Reuvers R, Solovej J. 2018. The Bogoliubov free energy functional
II: The dilute Limit. Communications in Mathematical Physics. 360(1), 347–403.'
mla: 'Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional II:
The Dilute Limit.” Communications in Mathematical Physics, vol. 360, no.
1, Springer, 2018, pp. 347–403, doi:10.1007/s00220-017-3064-x.'
short: M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical
Physics 360 (2018) 347–403.
date_created: 2018-12-11T11:47:09Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2021-01-12T08:02:35Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00220-017-3064-x
external_id:
arxiv:
- '1511.05953'
intvolume: ' 360'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.05953
month: '05'
oa: 1
oa_version: Submitted Version
page: 347-403
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Communications in Mathematical Physics
publication_identifier:
issn:
- '00103616'
publication_status: published
publisher: Springer
publist_id: '7260'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The Bogoliubov free energy functional II: The dilute Limit'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 360
year: '2018'
...
---
_id: '555'
abstract:
- lang: eng
text: Conventional wisdom has it that proteins fold and assemble into definite structures,
and that this defines their function. Glycosaminoglycans (GAGs) are different.
In most cases the structures they form have a low degree of order, even when interacting
with proteins. Here, we discuss how physical features common to all GAGs — hydrophilicity,
charge, linearity and semi-flexibility — underpin the overall properties of GAG-rich
matrices. By integrating soft matter physics concepts (e.g. polymer brushes and
phase separation) with our molecular understanding of GAG–protein interactions,
we can better comprehend how GAG-rich matrices assemble, what their properties
are, and how they function. Taking perineuronal nets (PNNs) — a GAG-rich matrix
enveloping neurons — as a relevant example, we propose that microphase separation
determines the holey PNN anatomy that is pivotal to PNN functions.
acknowledgement: "This work was supported by the European Research Council [Starting
Grant 306435 ‘JELLY’; to RPR], the Spanish Ministry of Competitiveness and Innovation
[MAT2014-54867-R, to RPR], the EPSRC Centre for Doctoral Training in Tissue Engineering
and Regenerative Medicine — Innovation in Medical and Biological Engineering [EP/L014823/1,
to JCFK], the Royal Society [RG160410, to JCFK], Wings for Life [WFL-UK-008/15,
to JCFK] and the European Union, the Operational Programme Research, Development
and Education in the framework of the project ‘Centre of Reconstructive Neuroscience’
[CZ.02.1.01/0.0./0.0/15_003/0000419, to JCFK]. AJD would like to thank Arthritis
Research UK [16539, 19489] and the MRC [76445, G0900538] for funding his work on
GAG–protein interactions.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Ralf
full_name: Richter, Ralf
last_name: Richter
- first_name: Natalia
full_name: Baranova, Natalia
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Anthony
full_name: Day, Anthony
last_name: Day
- first_name: Jessica
full_name: Kwok, Jessica
last_name: Kwok
citation:
ama: 'Richter R, Baranova NS, Day A, Kwok J. Glycosaminoglycans in extracellular
matrix organisation: Are concepts from soft matter physics key to understanding
the formation of perineuronal nets? Current Opinion in Structural Biology.
2018;50:65-74. doi:10.1016/j.sbi.2017.12.002'
apa: 'Richter, R., Baranova, N. S., Day, A., & Kwok, J. (2018). Glycosaminoglycans
in extracellular matrix organisation: Are concepts from soft matter physics key
to understanding the formation of perineuronal nets? Current Opinion in Structural
Biology. Elsevier. https://doi.org/10.1016/j.sbi.2017.12.002'
chicago: 'Richter, Ralf, Natalia S. Baranova, Anthony Day, and Jessica Kwok. “Glycosaminoglycans
in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key
to Understanding the Formation of Perineuronal Nets?” Current Opinion in Structural
Biology. Elsevier, 2018. https://doi.org/10.1016/j.sbi.2017.12.002.'
ieee: 'R. Richter, N. S. Baranova, A. Day, and J. Kwok, “Glycosaminoglycans in extracellular
matrix organisation: Are concepts from soft matter physics key to understanding
the formation of perineuronal nets?,” Current Opinion in Structural Biology,
vol. 50. Elsevier, pp. 65–74, 2018.'
ista: 'Richter R, Baranova NS, Day A, Kwok J. 2018. Glycosaminoglycans in extracellular
matrix organisation: Are concepts from soft matter physics key to understanding
the formation of perineuronal nets? Current Opinion in Structural Biology. 50,
65–74.'
mla: 'Richter, Ralf, et al. “Glycosaminoglycans in Extracellular Matrix Organisation:
Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal
Nets?” Current Opinion in Structural Biology, vol. 50, Elsevier, 2018,
pp. 65–74, doi:10.1016/j.sbi.2017.12.002.'
short: R. Richter, N.S. Baranova, A. Day, J. Kwok, Current Opinion in Structural
Biology 50 (2018) 65–74.
date_created: 2018-12-11T11:47:09Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-11T14:07:03Z
day: '01'
department:
- _id: MaLo
doi: 10.1016/j.sbi.2017.12.002
external_id:
isi:
- '000443661300011'
intvolume: ' 50'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprints.whiterose.ac.uk/125524/
month: '06'
oa: 1
oa_version: Submitted Version
page: 65 - 74
publication: Current Opinion in Structural Biology
publication_status: published
publisher: Elsevier
publist_id: '7259'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Glycosaminoglycans in extracellular matrix organisation: Are concepts from
soft matter physics key to understanding the formation of perineuronal nets?'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 50
year: '2018'
...
---
_id: '556'
abstract:
- lang: eng
text: 'We investigate the free boundary Schur process, a variant of the Schur process
introduced by Okounkov and Reshetikhin, where we allow the first and the last
partitions to be arbitrary (instead of empty in the original setting). The pfaffian
Schur process, previously studied by several authors, is recovered when just one
of the boundary partitions is left free. We compute the correlation functions
of the process in all generality via the free fermion formalism, which we extend
with the thorough treatment of “free boundary states.” For the case of one free
boundary, our approach yields a new proof that the process is pfaffian. For the
case of two free boundaries, we find that the process is not pfaffian, but a closely
related process is. We also study three different applications of the Schur process
with one free boundary: fluctuations of symmetrized last passage percolation models,
limit shapes and processes for symmetric plane partitions and for plane overpartitions.'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Dan
full_name: Betea, Dan
last_name: Betea
- first_name: Jeremie
full_name: Bouttier, Jeremie
last_name: Bouttier
- first_name: Peter
full_name: Nejjar, Peter
id: 4BF426E2-F248-11E8-B48F-1D18A9856A87
last_name: Nejjar
- first_name: Mirjana
full_name: Vuletic, Mirjana
last_name: Vuletic
citation:
ama: Betea D, Bouttier J, Nejjar P, Vuletic M. The free boundary Schur process and
applications I. Annales Henri Poincare. 2018;19(12):3663-3742. doi:10.1007/s00023-018-0723-1
apa: Betea, D., Bouttier, J., Nejjar, P., & Vuletic, M. (2018). The free boundary
Schur process and applications I. Annales Henri Poincare. Springer Nature.
https://doi.org/10.1007/s00023-018-0723-1
chicago: Betea, Dan, Jeremie Bouttier, Peter Nejjar, and Mirjana Vuletic. “The Free
Boundary Schur Process and Applications I.” Annales Henri Poincare. Springer
Nature, 2018. https://doi.org/10.1007/s00023-018-0723-1.
ieee: D. Betea, J. Bouttier, P. Nejjar, and M. Vuletic, “The free boundary Schur
process and applications I,” Annales Henri Poincare, vol. 19, no. 12. Springer
Nature, pp. 3663–3742, 2018.
ista: Betea D, Bouttier J, Nejjar P, Vuletic M. 2018. The free boundary Schur process
and applications I. Annales Henri Poincare. 19(12), 3663–3742.
mla: Betea, Dan, et al. “The Free Boundary Schur Process and Applications I.” Annales
Henri Poincare, vol. 19, no. 12, Springer Nature, 2018, pp. 3663–742, doi:10.1007/s00023-018-0723-1.
short: D. Betea, J. Bouttier, P. Nejjar, M. Vuletic, Annales Henri Poincare 19 (2018)
3663–3742.
date_created: 2018-12-11T11:47:09Z
date_published: 2018-11-13T00:00:00Z
date_updated: 2024-02-20T10:48:17Z
day: '13'
ddc:
- '500'
department:
- _id: LaEr
- _id: JaMa
doi: 10.1007/s00023-018-0723-1
ec_funded: 1
external_id:
arxiv:
- '1704.05809'
file:
- access_level: open_access
checksum: 0c38abe73569b7166b7487ad5d23cc68
content_type: application/pdf
creator: dernst
date_created: 2019-01-21T15:18:55Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5866'
file_name: 2018_Annales_Betea.pdf
file_size: 3084674
relation: main_file
file_date_updated: 2020-07-14T12:47:03Z
has_accepted_license: '1'
intvolume: ' 19'
issue: '12'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 3663-3742
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Annales Henri Poincare
publication_identifier:
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
publist_id: '7258'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The free boundary Schur process and applications I
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: 19
year: '2018'
...