---
_id: '1130'
abstract:
- lang: eng
text: "In this thesis we present a computer-aided programming approach to concurrency.
Our approach helps the programmer by automatically fixing concurrency-related
bugs, i.e. bugs that occur when the program is executed using an aggressive preemptive
scheduler, but not when using a non-preemptive (cooperative) scheduler. Bugs are
program behaviours that are incorrect w.r.t. a specification. We consider both
user-provided explicit specifications in the form of assertion\r\nstatements in
the code as well as an implicit specification. The implicit specification is inferred
from the non-preemptive behaviour. Let us consider sequences of calls that the
program makes to an external interface. The implicit specification requires that
any such sequence produced under a preemptive scheduler should be included in
the set of sequences produced under a non-preemptive scheduler. We consider several
semantics-preserving fixes that go beyond atomic sections typically explored in
the synchronisation synthesis literature. Our synthesis is able to place locks,
barriers and wait-signal statements and last, but not least reorder independent
statements. The latter may be useful if a thread is released to early, e.g., before
some initialisation is completed. We guarantee that our synthesis does not introduce
deadlocks and that the synchronisation inserted is optimal w.r.t. a given objective
function. We dub our solution trace-based synchronisation synthesis and it is
loosely based on counterexample-guided inductive synthesis (CEGIS). The synthesis
works by discovering a trace that is incorrect w.r.t. the specification and identifying
ordering constraints crucial to trigger the specification violation. Synchronisation
may be placed immediately (greedy approach) or delayed until all incorrect traces
are found (non-greedy approach). For the non-greedy approach we construct a set
of global constraints over synchronisation placements. Each model of the global
constraints set corresponds to a correctness-ensuring synchronisation placement.
The placement that is optimal w.r.t. the given objective function is chosen as
the synchronisation solution. We evaluate our approach on a number of realistic
(albeit simplified) Linux device-driver\r\nbenchmarks. The benchmarks are versions
of the drivers with known concurrency-related bugs. For the experiments with an
explicit specification we added assertions that would detect the bugs in the experiments.
Device drivers lend themselves to implicit specification, where the device and
the operating system are the external interfaces. Our experiments demonstrate
that our synthesis method is precise and efficient. We implemented objective functions
for coarse-grained and fine-grained locking and observed that different synchronisation
placements are produced for our experiments, favouring e.g. a minimal number of
synchronisation operations or maximum concurrency."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: Tarrach T. Automatic synthesis of synchronisation primitives for concurrent
programs. 2016. doi:10.15479/at:ista:1130
apa: Tarrach, T. (2016). Automatic synthesis of synchronisation primitives for
concurrent programs. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:1130
chicago: Tarrach, Thorsten. “Automatic Synthesis of Synchronisation Primitives for
Concurrent Programs.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/at:ista:1130.
ieee: T. Tarrach, “Automatic synthesis of synchronisation primitives for concurrent
programs,” Institute of Science and Technology Austria, 2016.
ista: Tarrach T. 2016. Automatic synthesis of synchronisation primitives for concurrent
programs. Institute of Science and Technology Austria.
mla: Tarrach, Thorsten. Automatic Synthesis of Synchronisation Primitives for
Concurrent Programs. Institute of Science and Technology Austria, 2016, doi:10.15479/at:ista:1130.
short: T. Tarrach, Automatic Synthesis of Synchronisation Primitives for Concurrent
Programs, Institute of Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:19Z
date_published: 2016-07-07T00:00:00Z
date_updated: 2023-09-07T11:57:01Z
day: '07'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ToHe
- _id: GradSch
doi: 10.15479/at:ista:1130
ec_funded: 1
file:
- access_level: open_access
checksum: 319a506831650327e85376db41fc1094
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:39:32Z
date_updated: 2021-02-22T11:39:32Z
file_id: '9179'
file_name: 2016_Tarrach_Thesis.pdf
file_size: 1523935
relation: main_file
success: 1
- access_level: closed
checksum: 39efcd789f0ad859ff15652cb7afc412
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-16T14:14:38Z
date_updated: 2021-11-17T13:46:55Z
file_id: '10296'
file_name: 2016_Tarrach_Thesispdfa.pdf
file_size: 1306068
relation: main_file
file_date_updated: 2021-11-17T13:46:55Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://thorstent.github.io/theses/phd_thorsten_tarrach.pdf
month: '07'
oa: 1
oa_version: Published Version
page: '151'
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6230'
related_material:
record:
- id: '1729'
relation: part_of_dissertation
status: public
- id: '2218'
relation: part_of_dissertation
status: public
- id: '2445'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
title: Automatic synthesis of synchronisation primitives for concurrent programs
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1131'
abstract:
- lang: eng
text: "Evolution of gene regulation is important for phenotypic evolution and diversity.
Sequence-specific binding of regulatory proteins is one of the key regulatory
mechanisms determining gene expression. Although there has been intense interest
in evolution of regulatory binding sites in the last decades, a theoretical understanding
is far from being complete. In this thesis, I aim at a better understanding of
the evolution of transcriptional regulatory binding sequences by using biophysical
and population genetic models.\r\nIn the first part of the thesis, I discuss how
to formulate the evolutionary dynamics of binding se- quences in a single isolated
binding site and in promoter/enhancer regions. I develop a theoretical framework
bridging between a thermodynamical model for transcription and a mutation-selection-drift
model for monomorphic populations. I mainly address the typical evolutionary rates,
and how they de- pend on biophysical parameters (e.g. binding length and specificity)
and population genetic parameters (e.g. population size and selection strength).\r\nIn
the second part of the thesis, I analyse empirical data for a better evolutionary
and biophysical understanding of sequence-specific binding of bacterial RNA polymerase.
First, I infer selection on regulatory and non-regulatory binding sites of RNA
polymerase in the E. coli K12 genome. Second, I infer the chemical potential of
RNA polymerase, an important but unknown physical parameter defining the threshold
energy for strong binding. Furthermore, I try to understand the relation between
the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial
isolates by constructing a simple but biophysically motivated gene expression
model. Lastly, I lay out a statistical framework to predict adaptive point mutations
in de novo promoter evolution in a selection experiment."
acknowledgement: This PhD thesis may not have been completed without the help and
care I received from some peo- ple during my PhD life. I am especially grateful
to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices
but also for their patience and support. I thank Calin Guet and Jonathan Bollback
for allowing me to “play around” in their labs and get some experience on experimental
evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and
sharing their experimental data with me. I thank Johannes Jaeger for reviewing my
thesis. I thank all members of Barton group (aka bartonians) for their feedback,
and all workers of IST Austria for making the best working conditions. Lastly, I
thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous
support and encouragement. I truly had a great chance of having right people around
me.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
citation:
ama: Tugrul M. Evolution of transcriptional regulatory sequences. 2016.
apa: Tugrul, M. (2016). Evolution of transcriptional regulatory sequences.
Institute of Science and Technology Austria.
chicago: Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute
of Science and Technology Austria, 2016.
ieee: M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute
of Science and Technology Austria, 2016.
ista: Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute
of Science and Technology Austria.
mla: Tugrul, Murat. Evolution of Transcriptional Regulatory Sequences. Institute
of Science and Technology Austria, 2016.
short: M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of
Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:19Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2025-05-28T11:57:04Z
day: '01'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
file:
- access_level: closed
checksum: 66cb61a59943e4fb7447c6a86be5ef51
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T08:53:52Z
date_updated: 2019-08-13T08:53:52Z
file_id: '6810'
file_name: Tugrul_thesis_w_signature_page.pdf
file_size: 3695257
relation: main_file
- access_level: open_access
checksum: 293e388d70563760f6b24c3e66283dda
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:45:20Z
date_updated: 2021-02-22T11:45:20Z
file_id: '9182'
file_name: 2016_Tugrul_Thesis.pdf
file_size: 3880811
relation: main_file
success: 1
file_date_updated: 2021-02-22T11:45:20Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '89'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6229'
related_material:
record:
- id: '5554'
relation: research_data
status: public
- id: '1666'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Evolution of transcriptional regulatory sequences
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1134'
abstract:
- lang: eng
text: 'Hybrid systems have both continuous and discrete dynamics and are useful
for modeling a variety of control systems, from air traffic control protocols
to robotic maneuvers and beyond. Recently, numerous powerful and scalable tools
for analyzing hybrid systems have emerged. Several of these tools implement automated
formal methods for mathematically proving a system meets a specification. This
tutorial session will present three recent hybrid systems tools: C2E2, HyST, and
TuLiP. C2E2 is a simulated-based verification tool for hybrid systems, and uses
validated numerical solvers and bloating of simulation traces to verify systems
meet specifications. HyST is a hybrid systems model transformation and translation
tool, and uses a canonical intermediate representation to support most of the
recent verification tools, as well as automated sound abstractions that simplify
verification of a given hybrid system. TuLiP is a controller synthesis tool for
hybrid systems, where given a temporal logic specification to be satisfied for
a system (plant) model, TuLiP will find a controller that meets a given specification.
© 2016 IEEE.'
article_number: '7587948'
author:
- first_name: Parasara
full_name: Duggirala, Parasara
last_name: Duggirala
- first_name: Chuchu
full_name: Fan, Chuchu
last_name: Fan
- first_name: Matthew
full_name: Potok, Matthew
last_name: Potok
- first_name: Bolun
full_name: Qi, Bolun
last_name: Qi
- first_name: Sayan
full_name: Mitra, Sayan
last_name: Mitra
- first_name: Mahesh
full_name: Viswanathan, Mahesh
last_name: Viswanathan
- first_name: Stanley
full_name: Bak, Stanley
last_name: Bak
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Taylor
full_name: Johnson, Taylor
last_name: Johnson
- first_name: Luan
full_name: Nguyen, Luan
last_name: Nguyen
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Andrew
full_name: Sogokon, Andrew
last_name: Sogokon
- first_name: Hoang
full_name: Tran, Hoang
last_name: Tran
- first_name: Weiming
full_name: Xiang, Weiming
last_name: Xiang
citation:
ama: 'Duggirala P, Fan C, Potok M, et al. Tutorial: Software tools for hybrid systems
verification transformation and synthesis C2E2 HyST and TuLiP. In: 2016 IEEE
Conference on Control Applications. IEEE; 2016. doi:10.1109/CCA.2016.7587948'
apa: 'Duggirala, P., Fan, C., Potok, M., Qi, B., Mitra, S., Viswanathan, M., … Xiang,
W. (2016). Tutorial: Software tools for hybrid systems verification transformation
and synthesis C2E2 HyST and TuLiP. In 2016 IEEE Conference on Control Applications.
Buenos Aires, Argentina : IEEE. https://doi.org/10.1109/CCA.2016.7587948'
chicago: 'Duggirala, Parasara, Chuchu Fan, Matthew Potok, Bolun Qi, Sayan Mitra,
Mahesh Viswanathan, Stanley Bak, et al. “Tutorial: Software Tools for Hybrid Systems
Verification Transformation and Synthesis C2E2 HyST and TuLiP.” In 2016 IEEE
Conference on Control Applications. IEEE, 2016. https://doi.org/10.1109/CCA.2016.7587948.'
ieee: 'P. Duggirala et al., “Tutorial: Software tools for hybrid systems
verification transformation and synthesis C2E2 HyST and TuLiP,” in 2016 IEEE
Conference on Control Applications, Buenos Aires, Argentina , 2016.'
ista: 'Duggirala P, Fan C, Potok M, Qi B, Mitra S, Viswanathan M, Bak S, Bogomolov
S, Johnson T, Nguyen L, Schilling C, Sogokon A, Tran H, Xiang W. 2016. Tutorial:
Software tools for hybrid systems verification transformation and synthesis C2E2
HyST and TuLiP. 2016 IEEE Conference on Control Applications. CCA: Control Applications
, 7587948.'
mla: 'Duggirala, Parasara, et al. “Tutorial: Software Tools for Hybrid Systems Verification
Transformation and Synthesis C2E2 HyST and TuLiP.” 2016 IEEE Conference on
Control Applications, 7587948, IEEE, 2016, doi:10.1109/CCA.2016.7587948.'
short: P. Duggirala, C. Fan, M. Potok, B. Qi, S. Mitra, M. Viswanathan, S. Bak,
S. Bogomolov, T. Johnson, L. Nguyen, C. Schilling, A. Sogokon, H. Tran, W. Xiang,
in:, 2016 IEEE Conference on Control Applications, IEEE, 2016.
conference:
end_date: 2016-09-22
location: 'Buenos Aires, Argentina '
name: 'CCA: Control Applications '
start_date: 2016-09-19
date_created: 2018-12-11T11:50:20Z
date_published: 2016-10-10T00:00:00Z
date_updated: 2021-01-12T06:48:32Z
day: '10'
department:
- _id: ToHe
doi: 10.1109/CCA.2016.7587948
language:
- iso: eng
month: '10'
oa_version: None
publication: 2016 IEEE Conference on Control Applications
publication_status: published
publisher: IEEE
publist_id: '6224'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Tutorial: Software tools for hybrid systems verification transformation and
synthesis C2E2 HyST and TuLiP'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1135'
abstract:
- lang: eng
text: 'Time-triggered (TT) switched networks are a deterministic communication infrastructure
used by real-time distributed embedded systems. These networks rely on the notion
of globally discretized time (i.e. time slots) and a static TT schedule that prescribes
which message is sent through which link at every time slot, such that all messages
reach their destination before a global timeout. These schedules are generated
offline, assuming a static network with fault-free links, and entrusting all error-handling
functions to the end user. Assuming the network is static is an over-optimistic
view, and indeed links tend to fail in practice. We study synthesis of TT schedules
on a network in which links fail over time and we assume the switches run a very
simple error-recovery protocol once they detect a crashed link. We address the
problem of finding a pk; qresistant schedule; namely, one that, assuming the switches
run a fixed error-recovery protocol, guarantees that the number of messages that
arrive at their destination by the timeout is at least no matter what sequence
of at most k links fail. Thus, we maintain the simplicity of the switches while
giving a guarantee on the number of messages that meet the timeout. We show how
a pk; q-resistant schedule can be obtained using a CEGAR-like approach: find a
schedule, decide whether it is pk; q-resistant, and if it is not, use the witnessing
fault sequence to generate a constraint that is added to the program. The newly
added constraint disallows the schedule to be regenerated in a future iteration
while also eliminating several other schedules that are not pk; q-resistant. We
illustrate the applicability of our approach using an SMT-based implementation.
© 2016 ACM.'
article_number: '26'
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shibashis
full_name: Guha, Shibashis
last_name: Guha
- first_name: Guillermo
full_name: Rodríguez Navas, Guillermo
last_name: Rodríguez Navas
citation:
ama: 'Avni G, Guha S, Rodríguez Navas G. Synthesizing time triggered schedules for
switched networks with faulty links. In: Proceedings of the 13th International
Conference on Embedded Software . ACM; 2016. doi:10.1145/2968478.2968499'
apa: 'Avni, G., Guha, S., & Rodríguez Navas, G. (2016). Synthesizing time triggered
schedules for switched networks with faulty links. In Proceedings of the 13th
International Conference on Embedded Software . Pittsburgh, PA, USA: ACM.
https://doi.org/10.1145/2968478.2968499'
chicago: Avni, Guy, Shibashis Guha, and Guillermo Rodríguez Navas. “Synthesizing
Time Triggered Schedules for Switched Networks with Faulty Links.” In Proceedings
of the 13th International Conference on Embedded Software . ACM, 2016. https://doi.org/10.1145/2968478.2968499.
ieee: G. Avni, S. Guha, and G. Rodríguez Navas, “Synthesizing time triggered schedules
for switched networks with faulty links,” in Proceedings of the 13th International
Conference on Embedded Software , Pittsburgh, PA, USA, 2016.
ista: 'Avni G, Guha S, Rodríguez Navas G. 2016. Synthesizing time triggered schedules
for switched networks with faulty links. Proceedings of the 13th International
Conference on Embedded Software . EMSOFT: Embedded Software , 26.'
mla: Avni, Guy, et al. “Synthesizing Time Triggered Schedules for Switched Networks
with Faulty Links.” Proceedings of the 13th International Conference on Embedded
Software , 26, ACM, 2016, doi:10.1145/2968478.2968499.
short: G. Avni, S. Guha, G. Rodríguez Navas, in:, Proceedings of the 13th International
Conference on Embedded Software , ACM, 2016.
conference:
end_date: 2016-10-07
location: Pittsburgh, PA, USA
name: 'EMSOFT: Embedded Software '
start_date: 2016-10-01
date_created: 2018-12-11T11:50:20Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2021-01-12T06:48:33Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/2968478.2968499
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:31Z
date_updated: 2018-12-12T10:09:31Z
file_id: '4755'
file_name: IST-2016-644-v1+1_emsoft-no-format.pdf
file_size: 279240
relation: main_file
file_date_updated: 2018-12-12T10:09:31Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 'Proceedings of the 13th International Conference on Embedded Software '
publication_status: published
publisher: ACM
publist_id: '6223'
pubrep_id: '644'
quality_controlled: '1'
scopus_import: 1
status: public
title: Synthesizing time triggered schedules for switched networks with faulty links
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1136'
abstract:
- lang: eng
text: We propose an interactive sculpting system for seamlessly editing pre-computed
animations of liquid, without the need for any resimulation. The input is a sequence
of meshes without correspondences representing the liquid surface over time. Our
method enables the efficient selection of consistent space-time parts of this
animation, such as moving waves or droplets, which we call space-time features.
Once selected, a feature can be copied, edited, or duplicated and then pasted
back anywhere in space and time in the same or in another liquid animation sequence.
Our method circumvents tedious user interactions by automatically computing the
spatial and temporal ranges of the selected feature. We also provide space-time
shape editing tools for non-uniform scaling, rotation, trajectory changes, and
temporal editing to locally speed up or slow down motion. Using our tools, the
user can edit and progressively refine any input simulation result, possibly using
a library of precomputed space-time features extracted from other animations.
In contrast to the trial-and-error loop usually required to edit animation results
through the tuning of indirect simulation parameters, our method gives the user
full control over the edited space-time behaviors. © 2016 Copyright held by the
owner/author(s).
acknowledgement: This work was partly supported by the starting grant BigSplash, as
well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2014-StG
638176 , and ERC-2011-ADG 20110209).
article_number: '2994261'
article_processing_charge: No
author:
- first_name: Pierre
full_name: Manteaux, Pierre
last_name: Manteaux
- first_name: Ulysse
full_name: Vimont, Ulysse
last_name: Vimont
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Damien
full_name: Rohmer, Damien
last_name: Rohmer
- first_name: Marie
full_name: Cani, Marie
last_name: Cani
citation:
ama: 'Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. Space-time sculpting of
liquid animation. In: Proceedings of the 9th International Conference on Motion
in Games . ACM; 2016. doi:10.1145/2994258.2994261'
apa: 'Manteaux, P., Vimont, U., Wojtan, C., Rohmer, D., & Cani, M. (2016). Space-time
sculpting of liquid animation. In Proceedings of the 9th International Conference
on Motion in Games . San Francisco, CA, USA: ACM. https://doi.org/10.1145/2994258.2994261'
chicago: Manteaux, Pierre, Ulysse Vimont, Chris Wojtan, Damien Rohmer, and Marie
Cani. “Space-Time Sculpting of Liquid Animation.” In Proceedings of the 9th
International Conference on Motion in Games . ACM, 2016. https://doi.org/10.1145/2994258.2994261.
ieee: P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, and M. Cani, “Space-time sculpting
of liquid animation,” in Proceedings of the 9th International Conference on
Motion in Games , San Francisco, CA, USA, 2016.
ista: 'Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. 2016. Space-time sculpting
of liquid animation. Proceedings of the 9th International Conference on Motion
in Games . MIG: Motion in Games, 2994261.'
mla: Manteaux, Pierre, et al. “Space-Time Sculpting of Liquid Animation.” Proceedings
of the 9th International Conference on Motion in Games , 2994261, ACM, 2016,
doi:10.1145/2994258.2994261.
short: P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, M. Cani, in:, Proceedings of
the 9th International Conference on Motion in Games , ACM, 2016.
conference:
end_date: 2016-10-12
location: San Francisco, CA, USA
name: 'MIG: Motion in Games'
start_date: 2016-10-10
date_created: 2018-12-11T11:50:20Z
date_published: 2016-10-10T00:00:00Z
date_updated: 2023-02-21T09:49:49Z
day: '10'
ddc:
- '004'
department:
- _id: ChWo
doi: 10.1145/2994258.2994261
ec_funded: 1
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.inria.fr/hal-01367181
month: '10'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: 'Proceedings of the 9th International Conference on Motion in Games '
publication_status: published
publisher: ACM
publist_id: '6222'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Space-time sculpting of liquid animation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1137'
abstract:
- lang: eng
text: RASGRP1 is an important guanine nucleotide exchange factor and activator of
the RAS-MAPK pathway following T cell antigen receptor (TCR) signaling. The consequences
of RASGRP1 mutations in humans are unknown. In a patient with recurrent bacterial
and viral infections, born to healthy consanguineous parents, we used homozygosity
mapping and exome sequencing to identify a biallelic stop-gain variant in RASGRP1.
This variant segregated perfectly with the disease and has not been reported in
genetic databases. RASGRP1 deficiency was associated in T cells and B cells with
decreased phosphorylation of the extracellular-signal-regulated serine kinase
ERK, which was restored following expression of wild-type RASGRP1. RASGRP1 deficiency
also resulted in defective proliferation, activation and motility of T cells and
B cells. RASGRP1-deficient natural killer (NK) cells exhibited impaired cytotoxicity
with defective granule convergence and actin accumulation. Interaction proteomics
identified the dynein light chain DYNLL1 as interacting with RASGRP1, which links
RASGRP1 to cytoskeletal dynamics. RASGRP1-deficient cells showed decreased activation
of the GTPase RhoA. Treatment with lenalidomide increased RhoA activity and reversed
the migration and activation defects of RASGRP1-deficient lymphocytes.
article_processing_charge: No
article_type: original
author:
- first_name: Elisabeth
full_name: Salzer, Elisabeth
last_name: Salzer
- first_name: Deniz
full_name: Çaǧdaş, Deniz
last_name: Çaǧdaş
- first_name: Miroslav
full_name: Hons, Miroslav
id: 4167FE56-F248-11E8-B48F-1D18A9856A87
last_name: Hons
orcid: 0000-0002-6625-3348
- first_name: Emily
full_name: Mace, Emily
last_name: Mace
- first_name: Wojciech
full_name: Garncarz, Wojciech
last_name: Garncarz
- first_name: Oezlem
full_name: Petronczki, Oezlem
last_name: Petronczki
- first_name: René
full_name: Platzer, René
last_name: Platzer
- first_name: Laurène
full_name: Pfajfer, Laurène
last_name: Pfajfer
- first_name: Ivan
full_name: Bilic, Ivan
last_name: Bilic
- first_name: Sol
full_name: Ban, Sol
last_name: Ban
- first_name: Katharina
full_name: Willmann, Katharina
last_name: Willmann
- first_name: Malini
full_name: Mukherjee, Malini
last_name: Mukherjee
- first_name: Verena
full_name: Supper, Verena
last_name: Supper
- first_name: Hsiangting
full_name: Hsu, Hsiangting
last_name: Hsu
- first_name: Pinaki
full_name: Banerjee, Pinaki
last_name: Banerjee
- first_name: Papiya
full_name: Sinha, Papiya
last_name: Sinha
- first_name: Fabienne
full_name: Mcclanahan, Fabienne
last_name: Mcclanahan
- first_name: Gerhard
full_name: Zlabinger, Gerhard
last_name: Zlabinger
- first_name: Winfried
full_name: Pickl, Winfried
last_name: Pickl
- first_name: John
full_name: Gribben, John
last_name: Gribben
- first_name: Hannes
full_name: Stockinger, Hannes
last_name: Stockinger
- first_name: Keiryn
full_name: Bennett, Keiryn
last_name: Bennett
- first_name: Johannes
full_name: Huppa, Johannes
last_name: Huppa
- first_name: Loï̈C
full_name: Dupré, Loï̈C
last_name: Dupré
- first_name: Özden
full_name: Sanal, Özden
last_name: Sanal
- first_name: Ulrich
full_name: Jäger, Ulrich
last_name: Jäger
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Ilhan
full_name: Tezcan, Ilhan
last_name: Tezcan
- first_name: Jordan
full_name: Orange, Jordan
last_name: Orange
- first_name: Kaan
full_name: Boztug, Kaan
last_name: Boztug
citation:
ama: Salzer E, Çaǧdaş D, Hons M, et al. RASGRP1 deficiency causes immunodeficiency
with impaired cytoskeletal dynamics. Nature Immunology. 2016;17(12):1352-1360.
doi:10.1038/ni.3575
apa: Salzer, E., Çaǧdaş, D., Hons, M., Mace, E., Garncarz, W., Petronczki, O., …
Boztug, K. (2016). RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal
dynamics. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/ni.3575
chicago: Salzer, Elisabeth, Deniz Çaǧdaş, Miroslav Hons, Emily Mace, Wojciech Garncarz,
Oezlem Petronczki, René Platzer, et al. “RASGRP1 Deficiency Causes Immunodeficiency
with Impaired Cytoskeletal Dynamics.” Nature Immunology. Nature Publishing
Group, 2016. https://doi.org/10.1038/ni.3575.
ieee: E. Salzer et al., “RASGRP1 deficiency causes immunodeficiency with
impaired cytoskeletal dynamics,” Nature Immunology, vol. 17, no. 12. Nature
Publishing Group, pp. 1352–1360, 2016.
ista: Salzer E, Çaǧdaş D, Hons M, Mace E, Garncarz W, Petronczki O, Platzer R, Pfajfer
L, Bilic I, Ban S, Willmann K, Mukherjee M, Supper V, Hsu H, Banerjee P, Sinha
P, Mcclanahan F, Zlabinger G, Pickl W, Gribben J, Stockinger H, Bennett K, Huppa
J, Dupré L, Sanal Ö, Jäger U, Sixt MK, Tezcan I, Orange J, Boztug K. 2016. RASGRP1
deficiency causes immunodeficiency with impaired cytoskeletal dynamics. Nature
Immunology. 17(12), 1352–1360.
mla: Salzer, Elisabeth, et al. “RASGRP1 Deficiency Causes Immunodeficiency with
Impaired Cytoskeletal Dynamics.” Nature Immunology, vol. 17, no. 12, Nature
Publishing Group, 2016, pp. 1352–60, doi:10.1038/ni.3575.
short: E. Salzer, D. Çaǧdaş, M. Hons, E. Mace, W. Garncarz, O. Petronczki, R. Platzer,
L. Pfajfer, I. Bilic, S. Ban, K. Willmann, M. Mukherjee, V. Supper, H. Hsu, P.
Banerjee, P. Sinha, F. Mcclanahan, G. Zlabinger, W. Pickl, J. Gribben, H. Stockinger,
K. Bennett, J. Huppa, L. Dupré, Ö. Sanal, U. Jäger, M.K. Sixt, I. Tezcan, J. Orange,
K. Boztug, Nature Immunology 17 (2016) 1352–1360.
date_created: 2018-12-11T11:50:21Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:48:33Z
day: '01'
department:
- _id: MiSi
doi: 10.1038/ni.3575
external_id:
pmid:
- '27776107'
intvolume: ' 17'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400263
month: '12'
oa: 1
oa_version: Submitted Version
page: 1352 - 1360
pmid: 1
publication: Nature Immunology
publication_status: published
publisher: Nature Publishing Group
publist_id: '6221'
quality_controlled: '1'
scopus_import: 1
status: public
title: RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1138'
abstract:
- lang: eng
text: Automata with monitor counters, where the transitions do not depend on counter
values, and nested weighted automata are two expressive automata-theoretic frameworks
for quantitative properties. For a well-studied and wide class of quantitative
functions, we establish that automata with monitor counters and nested weighted
automata are equivalent. We study for the first time such quantitative automata
under probabilistic semantics. We show that several problems that are undecidable
for the classical questions of emptiness and universality become decidable under
the probabilistic semantics. We present a complete picture of decidability for
such automata, and even an almost-complete picture of computational complexity,
for the probabilistic questions we consider. © 2016 ACM.
acknowledgement: This research was funded in part by the European Research Council
(ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF)
projects S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), FWF Grant No P23499-
N23, FWF NFN Grant No S114
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J. Quantitative automata under probabilistic
semantics. In: Proceedings of the 31st Annual ACM/IEEE Symposium. IEEE;
2016:76-85. doi:10.1145/2933575.2933588'
apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2016). Quantitative automata
under probabilistic semantics. In Proceedings of the 31st Annual ACM/IEEE Symposium
(pp. 76–85). New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2933588'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative
Automata under Probabilistic Semantics.” In Proceedings of the 31st Annual
ACM/IEEE Symposium, 76–85. IEEE, 2016. https://doi.org/10.1145/2933575.2933588.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative automata under
probabilistic semantics,” in Proceedings of the 31st Annual ACM/IEEE Symposium,
New York, NY, USA, 2016, pp. 76–85.
ista: 'Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative automata under probabilistic
semantics. Proceedings of the 31st Annual ACM/IEEE Symposium. LICS: Logic in Computer
Science, 76–85.'
mla: Chatterjee, Krishnendu, et al. “Quantitative Automata under Probabilistic Semantics.”
Proceedings of the 31st Annual ACM/IEEE Symposium, IEEE, 2016, pp. 76–85,
doi:10.1145/2933575.2933588.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings of the 31st Annual
ACM/IEEE Symposium, IEEE, 2016, pp. 76–85.
conference:
end_date: 2016-07-08
location: New York, NY, USA
name: 'LICS: Logic in Computer Science'
start_date: 2016-07-05
date_created: 2018-12-11T11:50:21Z
date_published: 2016-07-05T00:00:00Z
date_updated: 2021-01-12T06:48:34Z
day: '05'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1145/2933575.2933588
ec_funded: 1
external_id:
arxiv:
- '1604.06764'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.06764
month: '07'
oa: 1
oa_version: Preprint
page: 76 - 85
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Proceedings of the 31st Annual ACM/IEEE Symposium
publication_status: published
publisher: IEEE
publist_id: '6220'
quality_controlled: '1'
scopus_import: 1
status: public
title: Quantitative automata under probabilistic semantics
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1140'
abstract:
- lang: eng
text: 'Given a model of a system and an objective, the model-checking question asks
whether the model satisfies the objective. We study polynomial-time problems in
two classical models, graphs and Markov Decision Processes (MDPs), with respect
to several fundamental -regular objectives, e.g., Rabin and Streett objectives.
For many of these problems the best-known upper bounds are quadratic or cubic,
yet no super-linear lower bounds are known. In this work our contributions are
two-fold: First, we present several improved algorithms, and second, we present
the first conditional super-linear lower bounds based on widely believed assumptions
about the complexity of CNF-SAT and combinatorial Boolean matrix multiplication.
A separation result for two models with respect to an objective means a conditional
lower bound for one model that is strictly higher than the existing upper bound
for the other model, and similarly for two objectives with respect to a model.
Our results establish the following separation results: (1) A separation of models
(graphs and MDPs) for disjunctive queries of reachability and Büchi objectives.
(2) Two kinds of separations of objectives, both for graphs and MDPs, namely,
(2a) the separation of dual objectives such as Streett/Rabin objectives, and (2b)
the separation of conjunction and disjunction of multiple objectives of the same
type such as safety, Büchi, and coBüchi. In summary, our results establish the
first model and objective separation results for graphs and MDPs for various classical
-regular objectives. Quite strikingly, we establish conditional lower bounds for
the disjunction of objectives that are strictly higher than the existing upper
bounds for the conjunction of the same objectives. © 2016 ACM.'
acknowledgement: "K. C., M. H., and W. D. are partially supported by the
\ Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003.\r\nK.
C. is partially supported by the Austrian Science Fund (FWF)\r\nNFN Grant No S11407-N23
(RiSE/SHiNE) and an ERC Start grant\r\n(279307: Graph Games). For W. D., M. H.,
and V. L. the research\r\nleading to these results has received funding from the
European\r\nResearch Council under the European Union’s Seventh Framework\r\nProgramme
(FP/2007-2013) / ERC Grant Agreement no. 340506."
alternative_title:
- Proceedings Symposium on Logic in Computer Science
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Wolfgang
full_name: Dvoák, Wolfgang
last_name: Dvoák
- 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
citation:
ama: 'Chatterjee K, Dvoák W, Henzinger MH, Loitzenbauer V. Model and objective separation
with conditional lower bounds: disjunction is harder than conjunction. In: Proceedings
of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE;
2016:197-206. doi:10.1145/2933575.2935304'
apa: 'Chatterjee, K., Dvoák, W., Henzinger, M. H., & Loitzenbauer, V. (2016).
Model and objective separation with conditional lower bounds: disjunction is harder
than conjunction. In Proceedings of the 31st Annual ACM/IEEE Symposium on Logic
in Computer Science (pp. 197–206). New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2935304'
chicago: 'Chatterjee, Krishnendu, Wolfgang Dvoák, Monika H Henzinger, and Veronika
Loitzenbauer. “Model and Objective Separation with Conditional Lower Bounds: Disjunction
Is Harder than Conjunction.” In Proceedings of the 31st Annual ACM/IEEE Symposium
on Logic in Computer Science, 197–206. IEEE, 2016. https://doi.org/10.1145/2933575.2935304.'
ieee: 'K. Chatterjee, W. Dvoák, M. H. Henzinger, and V. Loitzenbauer, “Model and
objective separation with conditional lower bounds: disjunction is harder than
conjunction,” in Proceedings of the 31st Annual ACM/IEEE Symposium on Logic
in Computer Science, New York, NY, USA, 2016, pp. 197–206.'
ista: 'Chatterjee K, Dvoák W, Henzinger MH, Loitzenbauer V. 2016. Model and objective
separation with conditional lower bounds: disjunction is harder than conjunction.
Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science.
LICS: Logic in Computer Science, Proceedings Symposium on Logic in Computer Science,
, 197–206.'
mla: 'Chatterjee, Krishnendu, et al. “Model and Objective Separation with Conditional
Lower Bounds: Disjunction Is Harder than Conjunction.” Proceedings of the 31st
Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2016, pp. 197–206,
doi:10.1145/2933575.2935304.'
short: K. Chatterjee, W. Dvoák, M.H. Henzinger, V. Loitzenbauer, in:, Proceedings
of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2016,
pp. 197–206.
conference:
end_date: 2016-07-08
location: New York, NY, USA
name: 'LICS: Logic in Computer Science'
start_date: 2016-07-05
date_created: 2018-12-11T11:50:22Z
date_published: 2016-07-05T00:00:00Z
date_updated: 2025-06-02T08:53:44Z
day: '05'
department:
- _id: KrCh
doi: 10.1145/2933575.2935304
external_id:
arxiv:
- '1602.02670'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.02670
month: '07'
oa: 1
oa_version: Preprint
page: 197 - 206
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer
Science
publication_status: published
publisher: IEEE
publist_id: '6219'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Model and objective separation with conditional lower bounds: disjunction
is harder than conjunction'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1141'
abstract:
- lang: eng
text: In this paper we introduce the Multiobjective Optimization Hierarchic Genetic
Strategy with maturing (MO-mHGS), a meta-algorithm that performs evolutionary
optimization in a hierarchy of populations. The maturing mechanism improves growth
and reduces redundancy. The performance of MO-mHGS with selected state-of-the-art
multiobjective evolutionary algorithms as internal algorithms is analysed on benchmark
problems and their modifications for which single fitness evaluation time depends
on the solution accuracy. We compare the proposed algorithm with the Island Model
Genetic Algorithm as well as with single-deme methods, and discuss the impact
of internal algorithms on the MO-mHGS meta-algorithm. © 2016 Elsevier B.V.
acknowledgement: The work presented in this paper was partially supported by Polish
National Science Centre grant nos. DEC-2012/05/N/ST6/03433 and DEC-2011/03/B/ST6/01393.
Radosław Łazarz was supported by Polish National Science Centre grant no. DEC-2013/10/M/ST6/00531.
author:
- first_name: Radosław
full_name: Łazarz, Radosław
last_name: Łazarz
- first_name: Michał
full_name: Idzik, Michał
last_name: Idzik
- first_name: Konrad
full_name: Gądek, Konrad
last_name: Gądek
- first_name: Ewa P
full_name: Gajda-Zagorska, Ewa P
id: 47794CF0-F248-11E8-B48F-1D18A9856A87
last_name: Gajda-Zagorska
citation:
ama: Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. Hierarchic genetic strategy
with maturing as a generic tool for multiobjective optimization. Journal of
Computational Science. 2016;17(1):249-260. doi:10.1016/j.jocs.2016.03.004
apa: Łazarz, R., Idzik, M., Gądek, K., & Gajda-Zagorska, E. P. (2016). Hierarchic
genetic strategy with maturing as a generic tool for multiobjective optimization.
Journal of Computational Science. Elsevier. https://doi.org/10.1016/j.jocs.2016.03.004
chicago: Łazarz, Radosław, Michał Idzik, Konrad Gądek, and Ewa P Gajda-Zagorska.
“Hierarchic Genetic Strategy with Maturing as a Generic Tool for Multiobjective
Optimization.” Journal of Computational Science. Elsevier, 2016. https://doi.org/10.1016/j.jocs.2016.03.004.
ieee: R. Łazarz, M. Idzik, K. Gądek, and E. P. Gajda-Zagorska, “Hierarchic genetic
strategy with maturing as a generic tool for multiobjective optimization,” Journal
of Computational Science, vol. 17, no. 1. Elsevier, pp. 249–260, 2016.
ista: Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. 2016. Hierarchic genetic strategy
with maturing as a generic tool for multiobjective optimization. Journal of Computational
Science. 17(1), 249–260.
mla: Łazarz, Radosław, et al. “Hierarchic Genetic Strategy with Maturing as a Generic
Tool for Multiobjective Optimization.” Journal of Computational Science,
vol. 17, no. 1, Elsevier, 2016, pp. 249–60, doi:10.1016/j.jocs.2016.03.004.
short: R. Łazarz, M. Idzik, K. Gądek, E.P. Gajda-Zagorska, Journal of Computational
Science 17 (2016) 249–260.
date_created: 2018-12-11T11:50:22Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2021-01-12T06:48:35Z
day: '01'
department:
- _id: ChWo
doi: 10.1016/j.jocs.2016.03.004
intvolume: ' 17'
issue: '1'
language:
- iso: eng
month: '11'
oa_version: None
page: 249 - 260
publication: Journal of Computational Science
publication_status: published
publisher: Elsevier
publist_id: '6217'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hierarchic genetic strategy with maturing as a generic tool for multiobjective
optimization
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1142'
abstract:
- lang: eng
text: Hemolysis drives susceptibility to bacterial infections and predicts poor
outcome from sepsis. These detrimental effects are commonly considered to be a
consequence of heme-iron serving as a nutrient for bacteria. We employed a Gram-negative
sepsis model and found that elevated heme levels impaired the control of bacterial
proliferation independently of heme-iron acquisition by pathogens. Heme strongly
inhibited phagocytosis and the migration of human and mouse phagocytes by disrupting
actin cytoskeletal dynamics via activation of the GTP-binding Rho family protein
Cdc42 by the guanine nucleotide exchange factor DOCK8. A chemical screening approach
revealed that quinine effectively prevented heme effects on the cytoskeleton,
restored phagocytosis and improved survival in sepsis. These mechanistic insights
provide potential therapeutic targets for patients with sepsis or hemolytic disorders.
acknowledgement: 'Y. Fukui (Medical Institute of Bioregulation, Kyushu University)
and J. Stein (Theodor Kocher Institute, University of Bern) are acknowledged for
providing the DOCK8 deficient bone marrow. and H. Häcker (St. Judes Children''s
Research Hospital) for providing the ERHBD-HoxB8-encoding retroviral construct.
pSpCas9(BB)-2a-Puro (PX459) was a gift from F. Zhang (Massachusetts Institute of
Technology) (Addgene plasmid # 48139) and pGRG36 was a gift from N. Craig (Johns
Hopkins University School of Medicine) (Addgene plasmid # 16666). LifeAct-GFP-encoding
retrovirus was kindly provided by A. Leithner (Institute of Science and Technology
Austria). pSIM8 and TKC E. coli were gifts from D.L. Court (Center for Cancer Research,
National Cancer Institute). We acknowledge M. Gröger and S. Rauscher for excellent
technical support (Core imaging facility, Medical University of Vienna). We thank
D.P. Barlow and L.R. Cheever for critical reading of the manuscript. This work was
supported by the Austrian Academy of Sciences, the Science Fund of the Austrian
National Bank (14107) and the Austrian Science Fund FWF (I1620-B22) in the Infect-ERA
framework (to S.Knapp).'
author:
- first_name: Rui
full_name: Martins, Rui
last_name: Martins
- first_name: Julia
full_name: Maier, Julia
last_name: Maier
- first_name: Anna
full_name: Gorki, Anna
last_name: Gorki
- first_name: Kilian
full_name: Huber, Kilian
last_name: Huber
- first_name: Omar
full_name: Sharif, Omar
last_name: Sharif
- first_name: Philipp
full_name: Starkl, Philipp
last_name: Starkl
- first_name: Simona
full_name: Saluzzo, Simona
last_name: Saluzzo
- first_name: Federica
full_name: Quattrone, Federica
last_name: Quattrone
- first_name: Riem
full_name: Gawish, Riem
last_name: Gawish
- first_name: Karin
full_name: Lakovits, Karin
last_name: Lakovits
- first_name: Michael
full_name: Aichinger, Michael
last_name: Aichinger
- first_name: Branka
full_name: Radic Sarikas, Branka
last_name: Radic Sarikas
- first_name: Charles
full_name: Lardeau, Charles
last_name: Lardeau
- first_name: Anastasiya
full_name: Hladik, Anastasiya
last_name: Hladik
- first_name: Ana
full_name: Korosec, Ana
last_name: Korosec
- first_name: Markus
full_name: Brown, Markus
id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Kari
full_name: Vaahtomeri, Kari
id: 368EE576-F248-11E8-B48F-1D18A9856A87
last_name: Vaahtomeri
orcid: 0000-0001-7829-3518
- first_name: Michelle
full_name: Duggan, Michelle
id: 2EDEA62C-F248-11E8-B48F-1D18A9856A87
last_name: Duggan
- first_name: Dontscho
full_name: Kerjaschki, Dontscho
last_name: Kerjaschki
- first_name: Harald
full_name: Esterbauer, Harald
last_name: Esterbauer
- first_name: Jacques
full_name: Colinge, Jacques
last_name: Colinge
- first_name: Stephanie
full_name: Eisenbarth, Stephanie
last_name: Eisenbarth
- first_name: Thomas
full_name: Decker, Thomas
last_name: Decker
- first_name: Keiryn
full_name: Bennett, Keiryn
last_name: Bennett
- first_name: Stefan
full_name: Kubicek, Stefan
last_name: Kubicek
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Giulio
full_name: Superti Furga, Giulio
last_name: Superti Furga
- first_name: Sylvia
full_name: Knapp, Sylvia
last_name: Knapp
citation:
ama: Martins R, Maier J, Gorki A, et al. Heme drives hemolysis-induced susceptibility
to infection via disruption of phagocyte functions. Nature Immunology.
2016;17(12):1361-1372. doi:10.1038/ni.3590
apa: Martins, R., Maier, J., Gorki, A., Huber, K., Sharif, O., Starkl, P., … Knapp,
S. (2016). Heme drives hemolysis-induced susceptibility to infection via disruption
of phagocyte functions. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/ni.3590
chicago: Martins, Rui, Julia Maier, Anna Gorki, Kilian Huber, Omar Sharif, Philipp
Starkl, Simona Saluzzo, et al. “Heme Drives Hemolysis-Induced Susceptibility to
Infection via Disruption of Phagocyte Functions.” Nature Immunology. Nature
Publishing Group, 2016. https://doi.org/10.1038/ni.3590.
ieee: R. Martins et al., “Heme drives hemolysis-induced susceptibility to
infection via disruption of phagocyte functions,” Nature Immunology, vol.
17, no. 12. Nature Publishing Group, pp. 1361–1372, 2016.
ista: Martins R, Maier J, Gorki A, Huber K, Sharif O, Starkl P, Saluzzo S, Quattrone
F, Gawish R, Lakovits K, Aichinger M, Radic Sarikas B, Lardeau C, Hladik A, Korosec
A, Brown M, Vaahtomeri K, Duggan M, Kerjaschki D, Esterbauer H, Colinge J, Eisenbarth
S, Decker T, Bennett K, Kubicek S, Sixt MK, Superti Furga G, Knapp S. 2016. Heme
drives hemolysis-induced susceptibility to infection via disruption of phagocyte
functions. Nature Immunology. 17(12), 1361–1372.
mla: Martins, Rui, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection
via Disruption of Phagocyte Functions.” Nature Immunology, vol. 17, no.
12, Nature Publishing Group, 2016, pp. 1361–72, doi:10.1038/ni.3590.
short: R. Martins, J. Maier, A. Gorki, K. Huber, O. Sharif, P. Starkl, S. Saluzzo,
F. Quattrone, R. Gawish, K. Lakovits, M. Aichinger, B. Radic Sarikas, C. Lardeau,
A. Hladik, A. Korosec, M. Brown, K. Vaahtomeri, M. Duggan, D. Kerjaschki, H. Esterbauer,
J. Colinge, S. Eisenbarth, T. Decker, K. Bennett, S. Kubicek, M.K. Sixt, G. Superti
Furga, S. Knapp, Nature Immunology 17 (2016) 1361–1372.
date_created: 2018-12-11T11:50:22Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:48:36Z
day: '01'
department:
- _id: MiSi
- _id: PeJo
doi: 10.1038/ni.3590
intvolume: ' 17'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://ora.ox.ac.uk/objects/uuid:f53a464e-1e5b-4f08-a7d8-b6749b852b9d
month: '12'
oa: 1
oa_version: Submitted Version
page: 1361 - 1372
publication: Nature Immunology
publication_status: published
publisher: Nature Publishing Group
publist_id: '6216'
quality_controlled: '1'
scopus_import: 1
status: public
title: Heme drives hemolysis-induced susceptibility to infection via disruption of
phagocyte functions
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1143'
abstract:
- lang: eng
text: We study the ground state of a dilute Bose gas in a scaling limit where the
Gross-Pitaevskii functional emerges. This is a repulsive nonlinear Schrödinger
functional whose quartic term is proportional to the scattering length of the
interparticle interaction potential. We propose a new derivation of this limit
problem, with a method that bypasses some of the technical difficulties that previous
derivations had to face. The new method is based on a combination of Dyson\'s
lemma, the quantum de Finetti theorem and a second moment estimate for ground
states of the effective Dyson Hamiltonian. It applies equally well to the case
where magnetic fields or rotation are present.
author:
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
- first_name: Nicolas
full_name: Rougerie, Nicolas
last_name: Rougerie
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Nam P, Rougerie N, Seiringer R. Ground states of large bosonic systems: The
gross Pitaevskii limit revisited. Analysis and PDE. 2016;9(2):459-485.
doi:10.2140/apde.2016.9.459'
apa: 'Nam, P., Rougerie, N., & Seiringer, R. (2016). Ground states of large
bosonic systems: The gross Pitaevskii limit revisited. Analysis and PDE.
Mathematical Sciences Publishers. https://doi.org/10.2140/apde.2016.9.459'
chicago: 'Nam, Phan, Nicolas Rougerie, and Robert Seiringer. “Ground States of Large
Bosonic Systems: The Gross Pitaevskii Limit Revisited.” Analysis and PDE.
Mathematical Sciences Publishers, 2016. https://doi.org/10.2140/apde.2016.9.459.'
ieee: 'P. Nam, N. Rougerie, and R. Seiringer, “Ground states of large bosonic systems:
The gross Pitaevskii limit revisited,” Analysis and PDE, vol. 9, no. 2.
Mathematical Sciences Publishers, pp. 459–485, 2016.'
ista: 'Nam P, Rougerie N, Seiringer R. 2016. Ground states of large bosonic systems:
The gross Pitaevskii limit revisited. Analysis and PDE. 9(2), 459–485.'
mla: 'Nam, Phan, et al. “Ground States of Large Bosonic Systems: The Gross Pitaevskii
Limit Revisited.” Analysis and PDE, vol. 9, no. 2, Mathematical Sciences
Publishers, 2016, pp. 459–85, doi:10.2140/apde.2016.9.459.'
short: P. Nam, N. Rougerie, R. Seiringer, Analysis and PDE 9 (2016) 459–485.
date_created: 2018-12-11T11:50:23Z
date_published: 2016-03-24T00:00:00Z
date_updated: 2021-01-12T06:48:36Z
day: '24'
department:
- _id: RoSe
doi: 10.2140/apde.2016.9.459
ec_funded: 1
intvolume: ' 9'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1503.07061
month: '03'
oa: 1
oa_version: Preprint
page: 459 - 485
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Analysis and PDE
publication_status: published
publisher: Mathematical Sciences Publishers
publist_id: '6215'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Ground states of large bosonic systems: The gross Pitaevskii limit revisited'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2016'
...
---
_id: '1145'
abstract:
- lang: eng
text: Auxin directs plant ontogenesis via differential accumulation within tissues
depending largely on the activity of PIN proteins that mediate auxin efflux from
cells and its directional cell-to-cell transport. Regardless of the developmental
importance of PINs, the structure of these transporters is poorly characterized.
Here, we present experimental data concerning protein topology of plasma membrane-localized
PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters
combined with immunolocalization techniques, we mapped the membrane topology of
PINs and further cross-validated our results using available topology modeling
software. We delineated the topology of PIN1 with two transmembrane (TM) bundles
of five α-helices linked by a large intracellular loop and a C-terminus positioned
outside the cytoplasm. Using constraints derived from our experimental data, we
also provide an updated position of helical regions generating a verisimilitude
model of PIN1. Since the canonical long PINs show a high degree of conservation
in TM domains and auxin transport capacity has been demonstrated for Arabidopsis
representatives of this group, this empirically enhanced topological model of
PIN1 will be an important starting point for further studies on PIN structure–function
relationships. In addition, we have established protocols that can be used to
probe the topology of other plasma membrane proteins in plants. © 2016 The Authors
acknowledgement: This research has been financially supported by the Ministry of Education,
Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) (T.N.,
M.Z., M.P., J.H.), Czech Science Foundation (13-40637S [J.F., M.Z.], 13-39982S [J.H.]);
Research Foundation Flanders (Grant number FWO09/PDO/196) (S.V.) and the European
Research Council (project ERC-2011-StG-20101109-PSDP) (J.F.). We thank David G.
Robinson and Ranjan Swarup for sharing published material; Maria Šimášková, Mamoona
Khan, Eva Benková for technical assistance; and R. Tejos, J. Kleine-Vehn, and E.
Feraru for helpful discussions.
author:
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Markéta
full_name: Pernisová, Markéta
last_name: Pernisová
- first_name: Jan
full_name: Hejátko, Jan
last_name: Hejátko
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. Enquiry
into the topology of plasma membrane localized PIN auxin transport components.
Molecular Plant. 2016;9(11):1504-1519. doi:10.1016/j.molp.2016.08.010
apa: Nodzyński, T., Vanneste, S., Zwiewka, M., Pernisová, M., Hejátko, J., &
Friml, J. (2016). Enquiry into the topology of plasma membrane localized PIN auxin
transport components. Molecular Plant. Cell Press. https://doi.org/10.1016/j.molp.2016.08.010
chicago: Nodzyński, Tomasz, Steffen Vanneste, Marta Zwiewka, Markéta Pernisová,
Jan Hejátko, and Jiří Friml. “Enquiry into the Topology of Plasma Membrane Localized
PIN Auxin Transport Components.” Molecular Plant. Cell Press, 2016. https://doi.org/10.1016/j.molp.2016.08.010.
ieee: T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, and J. Friml,
“Enquiry into the topology of plasma membrane localized PIN auxin transport components,”
Molecular Plant, vol. 9, no. 11. Cell Press, pp. 1504–1519, 2016.
ista: Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. 2016.
Enquiry into the topology of plasma membrane localized PIN auxin transport components.
Molecular Plant. 9(11), 1504–1519.
mla: Nodzyński, Tomasz, et al. “Enquiry into the Topology of Plasma Membrane Localized
PIN Auxin Transport Components.” Molecular Plant, vol. 9, no. 11, Cell
Press, 2016, pp. 1504–19, doi:10.1016/j.molp.2016.08.010.
short: T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, J. Friml,
Molecular Plant 9 (2016) 1504–1519.
date_created: 2018-12-11T11:50:23Z
date_published: 2016-11-07T00:00:00Z
date_updated: 2021-01-12T06:48:37Z
day: '07'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1016/j.molp.2016.08.010
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:22Z
date_updated: 2018-12-12T10:13:22Z
file_id: '5004'
file_name: IST-2017-746-v1+1_1-s2.0-S1674205216301915-main.pdf
file_size: 5005876
relation: main_file
file_date_updated: 2018-12-12T10:13:22Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1504 - 1519
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Molecular Plant
publication_status: published
publisher: Cell Press
publist_id: '6213'
pubrep_id: '746'
quality_controlled: '1'
scopus_import: 1
status: public
title: Enquiry into the topology of plasma membrane localized PIN auxin transport
components
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2016'
...
---
_id: '1147'
abstract:
- lang: eng
text: Apical dominance is one of the fundamental developmental phenomena in plant
biology, which determines the overall architecture of aerial plant parts. Here
we show apex decapitation activated competition for dominance in adjacent upper
and lower axillary buds. A two-nodal-bud pea (Pisum sativum L.) was used as a
model system to monitor and assess auxin flow, auxin transport channels, and dormancy
and initiation status of axillary buds. Auxin flow was manipulated by lateral
stem wounds or chemically by auxin efflux inhibitors 2,3,5-triiodobenzoic acid
(TIBA), 1-N-naphtylphtalamic acid (NPA), or protein synthesis inhibitor cycloheximide
(CHX) treatments, which served to interfere with axillary bud competition. Redirecting
auxin flow to different points influenced which bud formed the outgrowing and
dominant shoot. The obtained results proved that competition between upper and
lower axillary buds as secondary auxin sources is based on the same auxin canalization
principle that operates between the shoot apex and axillary bud. © The Author(s)
2016.
acknowledgement: This research was carried out under the project CEITEC 2020 (LQ1601)
with financial support from the Ministry of Education, Youth and Sports of the Czech
Republic under the National Sustainability Programme II., supported by the project
“CEITEC–Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) and the
Agronomy faculty grant from Mendel University “IGA AF MENDELU” (IP 14/2013).
article_number: '35955'
author:
- first_name: Jozef
full_name: Balla, Jozef
last_name: Balla
- first_name: Zuzana
full_name: Medved'Ová, Zuzana
last_name: Medved'Ová
- first_name: Petr
full_name: Kalousek, Petr
last_name: Kalousek
- first_name: Natálie
full_name: Matiješčuková, Natálie
last_name: Matiješčuková
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Vilém
full_name: Reinöhl, Vilém
last_name: Reinöhl
- first_name: Stanislav
full_name: Procházka, Stanislav
last_name: Procházka
citation:
ama: Balla J, Medved’Ová Z, Kalousek P, et al. Auxin flow mediated competition between
axillary buds to restore apical dominance. Scientific Reports. 2016;6.
doi:10.1038/srep35955
apa: Balla, J., Medved’Ová, Z., Kalousek, P., Matiješčuková, N., Friml, J., Reinöhl,
V., & Procházka, S. (2016). Auxin flow mediated competition between axillary
buds to restore apical dominance. Scientific Reports. Nature Publishing
Group. https://doi.org/10.1038/srep35955
chicago: Balla, Jozef, Zuzana Medved’Ová, Petr Kalousek, Natálie Matiješčuková,
Jiří Friml, Vilém Reinöhl, and Stanislav Procházka. “Auxin Flow Mediated Competition
between Axillary Buds to Restore Apical Dominance.” Scientific Reports.
Nature Publishing Group, 2016. https://doi.org/10.1038/srep35955.
ieee: J. Balla et al., “Auxin flow mediated competition between axillary
buds to restore apical dominance,” Scientific Reports, vol. 6. Nature Publishing
Group, 2016.
ista: Balla J, Medved’Ová Z, Kalousek P, Matiješčuková N, Friml J, Reinöhl V, Procházka
S. 2016. Auxin flow mediated competition between axillary buds to restore apical
dominance. Scientific Reports. 6, 35955.
mla: Balla, Jozef, et al. “Auxin Flow Mediated Competition between Axillary Buds
to Restore Apical Dominance.” Scientific Reports, vol. 6, 35955, Nature
Publishing Group, 2016, doi:10.1038/srep35955.
short: J. Balla, Z. Medved’Ová, P. Kalousek, N. Matiješčuková, J. Friml, V. Reinöhl,
S. Procházka, Scientific Reports 6 (2016).
date_created: 2018-12-11T11:50:24Z
date_published: 2016-11-08T00:00:00Z
date_updated: 2021-01-12T06:48:38Z
day: '08'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1038/srep35955
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:28Z
date_updated: 2018-12-12T10:09:28Z
file_id: '4752'
file_name: IST-2017-745-v1+1_srep35955.pdf
file_size: 1587544
relation: main_file
file_date_updated: 2018-12-12T10:09:28Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6211'
pubrep_id: '745'
quality_controlled: '1'
scopus_import: 1
status: public
title: Auxin flow mediated competition between axillary buds to restore apical dominance
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1148'
abstract:
- lang: eng
text: Continuous-time Markov chain (CTMC) models have become a central tool for
understanding the dynamics of complex reaction networks and the importance of
stochasticity in the underlying biochemical processes. When such models are employed
to answer questions in applications, in order to ensure that the model provides
a sufficiently accurate representation of the real system, it is of vital importance
that the model parameters are inferred from real measured data. This, however,
is often a formidable task and all of the existing methods fail in one case or
the other, usually because the underlying CTMC model is high-dimensional and computationally
difficult to analyze. The parameter inference methods that tend to scale best
in the dimension of the CTMC are based on so-called moment closure approximations.
However, there exists a large number of different moment closure approximations
and it is typically hard to say a priori which of the approximations is the most
suitable for the inference procedure. Here, we propose a moment-based parameter
inference method that automatically chooses the most appropriate moment closure
method. Accordingly, contrary to existing methods, the user is not required to
be experienced in moment closure techniques. In addition to that, our method adaptively
changes the approximation during the parameter inference to ensure that always
the best approximation is used, even in cases where different approximations are
best in different regions of the parameter space. © 2016 Elsevier Ireland Ltd
acknowledgement: This work is based on the CMSB 2015 paper “Adaptive moment closure
for parameter inference of biochemical reaction networks” (Bogomolov et al., 2015).
The work was partly supported by the German Research Foundation (DFG) as part of
the Transregional Collaborative Research Center “Automatic Verification and Analysis
of Complex Systems” (SFB/TR 14 AVACS1), by the European Research Council (ERC) under
grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23
(RiSE) and Z211-N23 (Wittgenstein Award). J.R. acknowledges support from the People
Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme
(FP7/2007-2013) under REA grant agreement no. 291734.
author:
- first_name: Christian
full_name: Schilling, Christian
last_name: Schilling
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- 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: Andreas
full_name: Podelski, Andreas
last_name: Podelski
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
citation:
ama: Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. Adaptive moment
closure for parameter inference of biochemical reaction networks. Biosystems.
2016;149:15-25. doi:10.1016/j.biosystems.2016.07.005
apa: Schilling, C., Bogomolov, S., Henzinger, T. A., Podelski, A., & Ruess,
J. (2016). Adaptive moment closure for parameter inference of biochemical reaction
networks. Biosystems. Elsevier. https://doi.org/10.1016/j.biosystems.2016.07.005
chicago: Schilling, Christian, Sergiy Bogomolov, Thomas A Henzinger, Andreas Podelski,
and Jakob Ruess. “Adaptive Moment Closure for Parameter Inference of Biochemical
Reaction Networks.” Biosystems. Elsevier, 2016. https://doi.org/10.1016/j.biosystems.2016.07.005.
ieee: C. Schilling, S. Bogomolov, T. A. Henzinger, A. Podelski, and J. Ruess, “Adaptive
moment closure for parameter inference of biochemical reaction networks,” Biosystems,
vol. 149. Elsevier, pp. 15–25, 2016.
ista: Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. 2016. Adaptive
moment closure for parameter inference of biochemical reaction networks. Biosystems.
149, 15–25.
mla: Schilling, Christian, et al. “Adaptive Moment Closure for Parameter Inference
of Biochemical Reaction Networks.” Biosystems, vol. 149, Elsevier, 2016,
pp. 15–25, doi:10.1016/j.biosystems.2016.07.005.
short: C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems
149 (2016) 15–25.
date_created: 2018-12-11T11:50:24Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2023-02-23T10:08:46Z
day: '01'
department:
- _id: ToHe
- _id: GaTk
doi: 10.1016/j.biosystems.2016.07.005
ec_funded: 1
intvolume: ' 149'
language:
- iso: eng
month: '11'
oa_version: None
page: 15 - 25
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Biosystems
publication_status: published
publisher: Elsevier
publist_id: '6210'
quality_controlled: '1'
related_material:
record:
- id: '1658'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Adaptive moment closure for parameter inference of biochemical reaction networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 149
year: '2016'
...
---
_id: '1149'
abstract:
- lang: eng
text: 'We study the usefulness of two most prominent publicly available rigorous
ODE integrators: one provided by the CAPD group (capd.ii.uj.edu.pl), the other
based on the COSY Infinity project (cosyinfinity.org). Both integrators are capable
of handling entire sets of initial conditions and provide tight rigorous outer
enclosures of the images under a time-T map. We conduct extensive benchmark computations
using the well-known Lorenz system, and compare the computation time against the
final accuracy achieved. We also discuss the effect of a few technical parameters,
such as the order of the numerical integration method, the value of T, and the
phase space resolution. We conclude that COSY may provide more precise results
due to its ability of avoiding the variable dependency problem. However, the overall
cost of computations conducted using CAPD is typically lower, especially when
intervals of parameters are involved. Moreover, access to COSY is limited (registration
required) and the rigorous ODE integrators are not publicly available, while CAPD
is an open source free software project. Therefore, we recommend the latter integrator
for this kind of computations. Nevertheless, proper choice of the various integration
parameters turns out to be of even greater importance than the choice of the integrator
itself. © 2016 IMACS. Published by Elsevier B.V. All rights reserved.'
acknowledgement: "MG was partially supported by FAPESP grants 2013/07460-7 and 2010/00875-9,
and by CNPq grants 305860/2013-5 and 306453/2009-6, Brazil. The work of HK was partially
supported by Grant-in-Aid for Scientific Research (Nos.24654022, 25287029), Ministry
of Education, Science, Technology, Culture and Sports, Japan. KM was supported by
NSF grants NSF-DMS-0835621, 0915019, 1125174, 1248071, and contracts from AFOSR
and DARPA. TM was supported by Grant-in-Aid for JSPS Fellows No. 245312. A part
of the research of TM and HK was also supported by JST, CREST.\r\n\r\nResearch conducted
by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER)
through COMPETE – Programa Operacional Factores de Competitividade (POFC) and from
the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT)
in the framework of the research project FCOMP-01-0124-FEDER-010645 (Ref. FCT PTDC/MAT/098871/2008);
from the People Programme (Marie Curie Actions) of the European Union's Seventh
Framework Programme (FP7/2007-2013) under REA grant agreement No. 622033; and from
the same sources as HK.\r\n\r\nThe authors express their gratitude to the Department
of Mathematics of Kyoto University for making their server available for conducting
the computations described in the paper, and to the reviewers for helpful comments
that contributed towards increasing the quality of the paper."
author:
- first_name: Tomoyuki
full_name: Miyaji, Tomoyuki
last_name: Miyaji
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
- first_name: Marcio
full_name: Gameiro, Marcio
last_name: Gameiro
- first_name: Hiroshi
full_name: Kokubu, Hiroshi
last_name: Kokubu
- first_name: Konstantin
full_name: Mischaikow, Konstantin
last_name: Mischaikow
citation:
ama: Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. A study of rigorous
ODE integrators for multi scale set oriented computations. Applied Numerical
Mathematics. 2016;107:34-47. doi:10.1016/j.apnum.2016.04.005
apa: Miyaji, T., Pilarczyk, P., Gameiro, M., Kokubu, H., & Mischaikow, K. (2016).
A study of rigorous ODE integrators for multi scale set oriented computations.
Applied Numerical Mathematics. Elsevier. https://doi.org/10.1016/j.apnum.2016.04.005
chicago: Miyaji, Tomoyuki, Pawel Pilarczyk, Marcio Gameiro, Hiroshi Kokubu, and
Konstantin Mischaikow. “A Study of Rigorous ODE Integrators for Multi Scale Set
Oriented Computations.” Applied Numerical Mathematics. Elsevier, 2016.
https://doi.org/10.1016/j.apnum.2016.04.005.
ieee: T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, and K. Mischaikow, “A study
of rigorous ODE integrators for multi scale set oriented computations,” Applied
Numerical Mathematics, vol. 107. Elsevier, pp. 34–47, 2016.
ista: Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. 2016. A study of
rigorous ODE integrators for multi scale set oriented computations. Applied Numerical
Mathematics. 107, 34–47.
mla: Miyaji, Tomoyuki, et al. “A Study of Rigorous ODE Integrators for Multi Scale
Set Oriented Computations.” Applied Numerical Mathematics, vol. 107, Elsevier,
2016, pp. 34–47, doi:10.1016/j.apnum.2016.04.005.
short: T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, K. Mischaikow, Applied Numerical
Mathematics 107 (2016) 34–47.
date_created: 2018-12-11T11:50:25Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2021-01-12T06:48:38Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.apnum.2016.04.005
ec_funded: 1
intvolume: ' 107'
language:
- iso: eng
month: '09'
oa_version: None
page: 34 - 47
project:
- _id: 255F06BE-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '622033'
name: Persistent Homology - Images, Data and Maps
publication: Applied Numerical Mathematics
publication_status: published
publisher: Elsevier
publist_id: '6209'
quality_controlled: '1'
scopus_import: 1
status: public
title: A study of rigorous ODE integrators for multi scale set oriented computations
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 107
year: '2016'
...
---
_id: '1150'
abstract:
- lang: eng
text: When neutrophils infiltrate a site of inflammation, they have to stop at the
right place to exert their effector function. In this issue of Developmental Cell,
Wang et al. (2016) show that neutrophils sense reactive oxygen species via the
TRPM2 channel to arrest migration at their target site. © 2016 Elsevier Inc.
author:
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Renkawitz J, Sixt MK. A Radical Break Restraining Neutrophil Migration. Developmental
Cell. 2016;38(5):448-450. doi:10.1016/j.devcel.2016.08.017
apa: Renkawitz, J., & Sixt, M. K. (2016). A Radical Break Restraining Neutrophil
Migration. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2016.08.017
chicago: Renkawitz, Jörg, and Michael K Sixt. “A Radical Break Restraining Neutrophil
Migration.” Developmental Cell. Cell Press, 2016. https://doi.org/10.1016/j.devcel.2016.08.017.
ieee: J. Renkawitz and M. K. Sixt, “A Radical Break Restraining Neutrophil Migration,”
Developmental Cell, vol. 38, no. 5. Cell Press, pp. 448–450, 2016.
ista: Renkawitz J, Sixt MK. 2016. A Radical Break Restraining Neutrophil Migration.
Developmental Cell. 38(5), 448–450.
mla: Renkawitz, Jörg, and Michael K. Sixt. “A Radical Break Restraining Neutrophil
Migration.” Developmental Cell, vol. 38, no. 5, Cell Press, 2016, pp. 448–50,
doi:10.1016/j.devcel.2016.08.017.
short: J. Renkawitz, M.K. Sixt, Developmental Cell 38 (2016) 448–450.
date_created: 2018-12-11T11:50:25Z
date_published: 2016-09-12T00:00:00Z
date_updated: 2021-01-12T06:48:39Z
day: '12'
department:
- _id: MiSi
doi: 10.1016/j.devcel.2016.08.017
intvolume: ' 38'
issue: '5'
language:
- iso: eng
month: '09'
oa_version: None
page: 448 - 450
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '6208'
quality_controlled: '1'
scopus_import: 1
status: public
title: A Radical Break Restraining Neutrophil Migration
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2016'
...
---
_id: '1151'
abstract:
- lang: eng
text: Tissue patterning in multicellular organisms is the output of precise spatio–temporal
regulation of gene expression coupled with changes in hormone dynamics. In plants,
the hormone auxin regulates growth and development at every stage of a plant’s
life cycle. Auxin signaling occurs through binding of the auxin molecule to a
TIR1/AFB F-box ubiquitin ligase, allowing interaction with Aux/IAA transcriptional
repressor proteins. These are subsequently ubiquitinated and degraded via the
26S proteasome, leading to derepression of auxin response factors (ARFs). How
auxin is able to elicit such a diverse range of developmental responses through
a single signaling module has not yet been resolved. Here we present an alternative
auxin-sensing mechanism in which the ARF ARF3/ETTIN controls gene expression through
interactions with process-specific transcription factors. This noncanonical hormonesensing
mechanism exhibits strong preference for the naturally occurring auxin indole
3-acetic acid (IAA) and is important for coordinating growth and patterning in
diverse developmental contexts such as gynoecium morphogenesis, lateral root emergence,
ovule development, and primary branch formation. Disrupting this IAA-sensing ability
induces morphological aberrations with consequences for plant fitness. Therefore,
our findings introduce a novel transcription factor-based mechanism of hormone
perception in plants. © 2016 Simonini et al.
acknowledgement: "We thank Norwich Research Park Bioimaging, Grant Calder, Roy\r\nDunford,
Caroline Smith, Paul Thomas, and Mark Youles for\r\ntechnical support; Charlie Scutt,
Alejandro Ferrando, and George\r\nLomonossoff for plasmids; Toshiro Ito for seeds;
Brendan Davies\r\nand Barry Causier for the REGIA library; and Mark Buttner,\r\nSimona
Masiero, Fabio Rossi, Doris Wagner, and Jun Xiao for\r\nhelp and material. We are
also grateful to Stefano Bencivenga,\r\nMarie Brüser, Friederike Jantzen, Lukasz
Langowski, Xinran Li,\r\nand Nicola Stacey for discussions and helpful comments
on the\r\nmanuscript. This work was supported by grants BB/M004112/1\r\nand BB/I017232/1
(Crop Improvement Research Club) to L.Ø.\r\nfrom the Biotechnological and Biological
Sciences Research\r\nCouncil, and Institute Strategic Programme grant (BB/J004553/\r\n1)
to the John Innes Centre. S.S., J.D., and L.Ø conceived the ex-\r\nperiments. "
author:
- first_name: Sara
full_name: Simonini, Sara
last_name: Simonini
- first_name: Joyita
full_name: Deb, Joyita
last_name: Deb
- first_name: Laila
full_name: Moubayidin, Laila
last_name: Moubayidin
- first_name: Pauline
full_name: Stephenson, Pauline
last_name: Stephenson
- first_name: Manoj
full_name: Valluru, Manoj
last_name: Valluru
- first_name: Alejandra
full_name: Freire Rios, Alejandra
last_name: Freire Rios
- first_name: Karim
full_name: Sorefan, Karim
last_name: Sorefan
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Lars
full_name: Östergaard, Lars
last_name: Östergaard
citation:
ama: Simonini S, Deb J, Moubayidin L, et al. A noncanonical auxin sensing mechanism
is required for organ morphogenesis in arabidopsis. Genes and Development.
2016;30(20):2286-2296. doi:10.1101/gad.285361.116
apa: Simonini, S., Deb, J., Moubayidin, L., Stephenson, P., Valluru, M., Freire
Rios, A., … Östergaard, L. (2016). A noncanonical auxin sensing mechanism is required
for organ morphogenesis in arabidopsis. Genes and Development. Cold Spring
Harbor Laboratory Press. https://doi.org/10.1101/gad.285361.116
chicago: Simonini, Sara, Joyita Deb, Laila Moubayidin, Pauline Stephenson, Manoj
Valluru, Alejandra Freire Rios, Karim Sorefan, Dolf Weijers, Jiří Friml, and Lars
Östergaard. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis
in Arabidopsis.” Genes and Development. Cold Spring Harbor Laboratory Press,
2016. https://doi.org/10.1101/gad.285361.116.
ieee: S. Simonini et al., “A noncanonical auxin sensing mechanism is required
for organ morphogenesis in arabidopsis,” Genes and Development, vol. 30,
no. 20. Cold Spring Harbor Laboratory Press, pp. 2286–2296, 2016.
ista: Simonini S, Deb J, Moubayidin L, Stephenson P, Valluru M, Freire Rios A, Sorefan
K, Weijers D, Friml J, Östergaard L. 2016. A noncanonical auxin sensing mechanism
is required for organ morphogenesis in arabidopsis. Genes and Development. 30(20),
2286–2296.
mla: Simonini, Sara, et al. “A Noncanonical Auxin Sensing Mechanism Is Required
for Organ Morphogenesis in Arabidopsis.” Genes and Development, vol. 30,
no. 20, Cold Spring Harbor Laboratory Press, 2016, pp. 2286–96, doi:10.1101/gad.285361.116.
short: S. Simonini, J. Deb, L. Moubayidin, P. Stephenson, M. Valluru, A. Freire
Rios, K. Sorefan, D. Weijers, J. Friml, L. Östergaard, Genes and Development 30
(2016) 2286–2296.
date_created: 2018-12-11T11:50:25Z
date_published: 2016-10-15T00:00:00Z
date_updated: 2021-01-12T06:48:39Z
day: '15'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1101/gad.285361.116
external_id:
pmid:
- '27898393'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-25T09:32:55Z
date_updated: 2019-01-25T09:32:55Z
file_id: '5882'
file_name: 2016_GeneDev_Simonini.pdf
file_size: 1419263
relation: main_file
success: 1
file_date_updated: 2019-01-25T09:32:55Z
has_accepted_license: '1'
intvolume: ' 30'
issue: '20'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 2286 - 2296
pmid: 1
publication: Genes and Development
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '6207'
quality_controlled: '1'
scopus_import: 1
status: public
title: A noncanonical auxin sensing mechanism is required for organ morphogenesis
in arabidopsis
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: 30
year: '2016'
...
---
_id: '1153'
abstract:
- lang: eng
text: Differential cell growth enables flexible organ bending in the presence of
environmental signals such as light or gravity. A prominent example of the developmental
processes based on differential cell growth is the formation of the apical hook
that protects the fragile shoot apical meristem when it breaks through the soil
during germination. Here, we combined in silico and in vivo approaches to identify
a minimal mechanism producing auxin gradient-guided differential growth during
the establishment of the apical hook in the model plant Arabidopsis thaliana.
Computer simulation models based on experimental data demonstrate that asymmetric
expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus
convex (outer) side of the hook suffices to establish an auxin maximum in the
epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism
that translates this maximum into differential growth, and thus curvature, of
the apical hook. Through a combination of experimental and in silico computational
approaches, we have identified the individual contributions of differential cell
elongation and proliferation to defining the apical hook and reveal the role of
auxin-ethylene crosstalk in balancing these two processes. © 2016 American Society
of Plant Biologists. All rights reserved.
acknowledgement: "We thank Martine De Cock and Annick Bleys for help in preparing
the manuscript, Daniel Van Damme for sharing material and stimulating discussion,
and Rudiger Simon for support during revision of the manuscript.\r\nThis work was
supported by grants from the European Research Council (StartingIndependentResearchGrantERC-2007-Stg-207362-HCPO)and
the Czech Science Foundation (GACR CZ.1.07/2.3.00/20.0043) to E.B.\r\nand Natural
Sciences and Engineering Research Council of Canada Discovery Grant 2014-05325 to
P.P. K.W. acknowledges funding from a Human Frontier Science Program Long-Term Fellowship
(LT-000209-2014)."
author:
- first_name: Petra
full_name: Žádníková, Petra
last_name: Žádníková
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Anas
full_name: Abuzeineh, Anas
last_name: Abuzeineh
- first_name: Marçal
full_name: Gallemí, Marçal
last_name: Gallemí
- first_name: Dominique
full_name: Van Der Straeten, Dominique
last_name: Van Der Straeten
- first_name: Richard
full_name: Smith, Richard
last_name: Smith
- first_name: Dirk
full_name: Inze, Dirk
last_name: Inze
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Przemysław
full_name: Prusinkiewicz, Przemysław
last_name: Prusinkiewicz
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Žádníková P, Wabnik KT, Abuzeineh A, et al. A model of differential growth
guided apical hook formation in plants. Plant Cell. 2016;28(10):2464-2477.
doi:10.1105/tpc.15.00569
apa: Žádníková, P., Wabnik, K. T., Abuzeineh, A., Gallemí, M., Van Der Straeten,
D., Smith, R., … Benková, E. (2016). A model of differential growth guided apical
hook formation in plants. Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.15.00569
chicago: Žádníková, Petra, Krzysztof T Wabnik, Anas Abuzeineh, Marçal Gallemí, Dominique
Van Der Straeten, Richard Smith, Dirk Inze, Jiří Friml, Przemysław Prusinkiewicz,
and Eva Benková. “A Model of Differential Growth Guided Apical Hook Formation
in Plants.” Plant Cell. American Society of Plant Biologists, 2016. https://doi.org/10.1105/tpc.15.00569.
ieee: P. Žádníková et al., “A model of differential growth guided apical
hook formation in plants,” Plant Cell, vol. 28, no. 10. American Society
of Plant Biologists, pp. 2464–2477, 2016.
ista: Žádníková P, Wabnik KT, Abuzeineh A, Gallemí M, Van Der Straeten D, Smith
R, Inze D, Friml J, Prusinkiewicz P, Benková E. 2016. A model of differential
growth guided apical hook formation in plants. Plant Cell. 28(10), 2464–2477.
mla: Žádníková, Petra, et al. “A Model of Differential Growth Guided Apical Hook
Formation in Plants.” Plant Cell, vol. 28, no. 10, American Society of
Plant Biologists, 2016, pp. 2464–77, doi:10.1105/tpc.15.00569.
short: P. Žádníková, K.T. Wabnik, A. Abuzeineh, M. Gallemí, D. Van Der Straeten,
R. Smith, D. Inze, J. Friml, P. Prusinkiewicz, E. Benková, Plant Cell 28 (2016)
2464–2477.
date_created: 2018-12-11T11:50:26Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2021-01-12T06:48:40Z
day: '01'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1105/tpc.15.00569
ec_funded: 1
intvolume: ' 28'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/
month: '10'
oa: 1
oa_version: Submitted Version
page: 2464 - 2477
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6205'
quality_controlled: '1'
scopus_import: 1
status: public
title: A model of differential growth guided apical hook formation in plants
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2016'
...
---
_id: '1154'
abstract:
- lang: eng
text: "Cellular locomotion is a central hallmark of eukaryotic life. It is governed
by cell-extrinsic molecular factors, which can either emerge in the soluble phase
or as immobilized, often adhesive ligands. To encode for direction, every cue
must be present as a spatial or temporal gradient. Here, we developed a microfluidic
chamber that allows measurement of cell migration in combined response to surface
immobilized and soluble molecular gradients. As a proof of principle we study
the response of dendritic cells to their major guidance cues, chemokines. The
majority of data on chemokine gradient sensing is based on in vitro studies employing
soluble gradients. Despite evidence suggesting that in vivo chemokines are often
immobilized to sugar residues, limited information is available how cells respond
to immobilized chemokines. We tracked migration of dendritic cells towards immobilized
gradients of the chemokine CCL21 and varying superimposed soluble gradients of
CCL19. Differential migratory patterns illustrate the potential of our setup to
quantitatively study the competitive response to both types of gradients. Beyond
chemokines our approach is broadly applicable to alternative systems of chemo-
and haptotaxis such as cells migrating along gradients of adhesion receptor ligands
vs. any soluble cue. \r\n"
acknowledgement: 'This work was supported by the Swiss National Science Foundation
(Ambizione fellowship; PZ00P3-154733 to M.M.), the Swiss Multiple Sclerosis Society
(research support to M.M.), a fellowship from the Boehringer Ingelheim Fonds (BIF)
to J.S., the European Research Council (grant ERC GA 281556) and a START award from
the Austrian Science Foundation (FWF) to M.S. #BioimagingFacility'
article_number: '36440'
author:
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Veronika
full_name: Bierbaum, Veronika
id: 3FD04378-F248-11E8-B48F-1D18A9856A87
last_name: Bierbaum
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Tino
full_name: Frank, Tino
last_name: Frank
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Savaş
full_name: Tay, Savaş
last_name: Tay
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Matthias
full_name: Mehling, Matthias
id: 3C23B994-F248-11E8-B48F-1D18A9856A87
last_name: Mehling
orcid: 0000-0001-8599-1226
citation:
ama: Schwarz J, Bierbaum V, Merrin J, et al. A microfluidic device for measuring
cell migration towards substrate bound and soluble chemokine gradients. Scientific
Reports. 2016;6. doi:10.1038/srep36440
apa: Schwarz, J., Bierbaum, V., Merrin, J., Frank, T., Hauschild, R., Bollenbach,
M. T., … Mehling, M. (2016). A microfluidic device for measuring cell migration
towards substrate bound and soluble chemokine gradients. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/srep36440
chicago: Schwarz, Jan, Veronika Bierbaum, Jack Merrin, Tino Frank, Robert Hauschild,
Mark Tobias Bollenbach, Savaş Tay, Michael K Sixt, and Matthias Mehling. “A Microfluidic
Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine
Gradients.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep36440.
ieee: J. Schwarz et al., “A microfluidic device for measuring cell migration
towards substrate bound and soluble chemokine gradients,” Scientific Reports,
vol. 6. Nature Publishing Group, 2016.
ista: Schwarz J, Bierbaum V, Merrin J, Frank T, Hauschild R, Bollenbach MT, Tay
S, Sixt MK, Mehling M. 2016. A microfluidic device for measuring cell migration
towards substrate bound and soluble chemokine gradients. Scientific Reports. 6,
36440.
mla: Schwarz, Jan, et al. “A Microfluidic Device for Measuring Cell Migration towards
Substrate Bound and Soluble Chemokine Gradients.” Scientific Reports, vol.
6, 36440, Nature Publishing Group, 2016, doi:10.1038/srep36440.
short: J. Schwarz, V. Bierbaum, J. Merrin, T. Frank, R. Hauschild, M.T. Bollenbach,
S. Tay, M.K. Sixt, M. Mehling, Scientific Reports 6 (2016).
date_created: 2018-12-11T11:50:27Z
date_published: 2016-11-07T00:00:00Z
date_updated: 2021-01-12T06:48:41Z
day: '07'
ddc:
- '579'
department:
- _id: MiSi
- _id: NanoFab
- _id: Bio
- _id: ToBo
doi: 10.1038/srep36440
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:32Z
date_updated: 2018-12-12T10:09:32Z
file_id: '4756'
file_name: IST-2017-744-v1+1_srep36440.pdf
file_size: 2353456
relation: main_file
file_date_updated: 2018-12-12T10:09:32Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
- _id: 25A8E5EA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 564-B12
name: Cytoskeletal force generation and transduction of leukocytes (FWF)
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6204'
pubrep_id: '744'
quality_controlled: '1'
scopus_import: 1
status: public
title: A microfluidic device for measuring cell migration towards substrate bound
and soluble chemokine gradients
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1157'
abstract:
- lang: eng
text: We consider sample covariance matrices of the form Q = ( σ1/2X)(σ1/2X)∗, where
the sample X is an M ×N random matrix whose entries are real independent random
variables with variance 1/N and whereσ is an M × M positive-definite deterministic
matrix. We analyze the asymptotic fluctuations of the largest rescaled eigenvalue
of Q when both M and N tend to infinity with N/M →d ϵ (0,∞). For a large class
of populations σ in the sub-critical regime, we show that the distribution of
the largest rescaled eigenvalue of Q is given by the type-1 Tracy-Widom distribution
under the additional assumptions that (1) either the entries of X are i.i.d. Gaussians
or (2) that σ is diagonal and that the entries of X have a sub-exponential decay.
acknowledgement: "We thank Horng-Tzer Yau for numerous discussions and remarks. We
are grateful to Ben Adlam, Jinho Baik, Zhigang Bao, Paul Bourgade, László Erd ̋os,
Iain Johnstone and Antti Knowles for comments. We are also grate-\r\nful to the
anonymous referee for carefully reading our manuscript and suggesting several improvements."
author:
- first_name: Ji
full_name: Lee, Ji
last_name: Lee
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Lee J, Schnelli K. Tracy-widom distribution for the largest eigenvalue of real
sample covariance matrices with general population. Annals of Applied Probability.
2016;26(6):3786-3839. doi:10.1214/16-AAP1193
apa: Lee, J., & Schnelli, K. (2016). Tracy-widom distribution for the largest
eigenvalue of real sample covariance matrices with general population. Annals
of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AAP1193
chicago: Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest
Eigenvalue of Real Sample Covariance Matrices with General Population.” Annals
of Applied Probability. Institute of Mathematical Statistics, 2016. https://doi.org/10.1214/16-AAP1193.
ieee: J. Lee and K. Schnelli, “Tracy-widom distribution for the largest eigenvalue
of real sample covariance matrices with general population,” Annals of Applied
Probability, vol. 26, no. 6. Institute of Mathematical Statistics, pp. 3786–3839,
2016.
ista: Lee J, Schnelli K. 2016. Tracy-widom distribution for the largest eigenvalue
of real sample covariance matrices with general population. Annals of Applied
Probability. 26(6), 3786–3839.
mla: Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue
of Real Sample Covariance Matrices with General Population.” Annals of Applied
Probability, vol. 26, no. 6, Institute of Mathematical Statistics, 2016, pp.
3786–839, doi:10.1214/16-AAP1193.
short: J. Lee, K. Schnelli, Annals of Applied Probability 26 (2016) 3786–3839.
date_created: 2018-12-11T11:50:27Z
date_published: 2016-12-15T00:00:00Z
date_updated: 2021-01-12T06:48:43Z
day: '15'
department:
- _id: LaEr
doi: 10.1214/16-AAP1193
ec_funded: 1
intvolume: ' 26'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1409.4979
month: '12'
oa: 1
oa_version: Preprint
page: 3786 - 3839
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Annals of Applied Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '6201'
quality_controlled: '1'
scopus_import: 1
status: public
title: Tracy-widom distribution for the largest eigenvalue of real sample covariance
matrices with general population
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2016'
...