---
_id: '79'
abstract:
- lang: eng
text: 'Markov Decision Processes (MDPs) are a popular class of models suitable for
solving control decision problems in probabilistic reactive systems. We consider
parametric MDPs (pMDPs) that include parameters in some of the transition probabilities
to account for stochastic uncertainties of the environment such as noise or input
disturbances. We study pMDPs with reachability objectives where the parameter
values are unknown and impossible to measure directly during execution, but there
is a probability distribution known over the parameter values. We study for the
first time computing parameter-independent strategies that are expectation optimal,
i.e., optimize the expected reachability probability under the probability distribution
over the parameters. We present an encoding of our problem to partially observable
MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies
in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating
(repeated) learner model; a series of benchmarks of varying configurations of
a robot moving on a grid; and a consensus protocol.'
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Sebastian
full_name: Arming, Sebastian
last_name: Arming
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Joost P
full_name: Katoen, Joost P
id: 4524F760-F248-11E8-B48F-1D18A9856A87
last_name: Katoen
- first_name: Ana
full_name: Sokolova, Ana
last_name: Sokolova
citation:
ama: 'Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. Parameter-independent
strategies for pMDPs via POMDPs. In: Vol 11024. Springer; 2018:53-70. doi:10.1007/978-3-319-99154-2_4'
apa: 'Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., & Sokolova, A.
(2018). Parameter-independent strategies for pMDPs via POMDPs (Vol. 11024, pp.
53–70). Presented at the QEST: Quantitative Evaluation of Systems, Beijing, China:
Springer. https://doi.org/10.1007/978-3-319-99154-2_4'
chicago: Arming, Sebastian, Ezio Bartocci, Krishnendu Chatterjee, Joost P Katoen,
and Ana Sokolova. “Parameter-Independent Strategies for PMDPs via POMDPs,” 11024:53–70.
Springer, 2018. https://doi.org/10.1007/978-3-319-99154-2_4.
ieee: 'S. Arming, E. Bartocci, K. Chatterjee, J. P. Katoen, and A. Sokolova, “Parameter-independent
strategies for pMDPs via POMDPs,” presented at the QEST: Quantitative Evaluation
of Systems, Beijing, China, 2018, vol. 11024, pp. 53–70.'
ista: 'Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. 2018. Parameter-independent
strategies for pMDPs via POMDPs. QEST: Quantitative Evaluation of Systems, LNCS,
vol. 11024, 53–70.'
mla: Arming, Sebastian, et al. Parameter-Independent Strategies for PMDPs via
POMDPs. Vol. 11024, Springer, 2018, pp. 53–70, doi:10.1007/978-3-319-99154-2_4.
short: S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer,
2018, pp. 53–70.
conference:
end_date: 2018-09-07
location: Beijing, China
name: 'QEST: Quantitative Evaluation of Systems'
start_date: 2018-09-04
date_created: 2018-12-11T11:44:31Z
date_published: 2018-08-15T00:00:00Z
date_updated: 2023-09-13T09:38:28Z
day: '15'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-99154-2_4
external_id:
arxiv:
- '1806.05126'
isi:
- '000548912200004'
intvolume: ' 11024'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.05126
month: '08'
oa: 1
oa_version: Preprint
page: 53-70
publication_status: published
publisher: Springer
publist_id: '7975'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Parameter-independent strategies for pMDPs via POMDPs
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11024
year: '2018'
...
---
_id: '806'
abstract:
- lang: eng
text: Social insect colonies have evolved many collectively performed adaptations
that reduce the impact of infectious disease and that are expected to maximize
their fitness. This colony-level protection is termed social immunity, and it
enhances the health and survival of the colony. In this review, we address how
social immunity emerges from its mechanistic components to produce colony-level
disease avoidance, resistance, and tolerance. To understand the evolutionary causes
and consequences of social immunity, we highlight the need for studies that evaluate
the effects of social immunity on colony fitness. We discuss the role that host
life history and ecology have on predicted eco-evolutionary dynamics, which differ
among the social insect lineages. Throughout the review, we highlight current
gaps in our knowledge and promising avenues for future research, which we hope
will bring us closer to an integrated understanding of socio-eco-evo-immunology.
article_processing_charge: No
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
citation:
ama: 'Cremer S, Pull C, Fürst M. Social immunity: Emergence and evolution of colony-level
disease protection. Annual Review of Entomology. 2018;63:105-123. doi:10.1146/annurev-ento-020117-043110'
apa: 'Cremer, S., Pull, C., & Fürst, M. (2018). Social immunity: Emergence and
evolution of colony-level disease protection. Annual Review of Entomology.
Annual Reviews. https://doi.org/10.1146/annurev-ento-020117-043110'
chicago: 'Cremer, Sylvia, Christopher Pull, and Matthias Fürst. “Social Immunity:
Emergence and Evolution of Colony-Level Disease Protection.” Annual Review
of Entomology. Annual Reviews, 2018. https://doi.org/10.1146/annurev-ento-020117-043110.'
ieee: 'S. Cremer, C. Pull, and M. Fürst, “Social immunity: Emergence and evolution
of colony-level disease protection,” Annual Review of Entomology, vol.
63. Annual Reviews, pp. 105–123, 2018.'
ista: 'Cremer S, Pull C, Fürst M. 2018. Social immunity: Emergence and evolution
of colony-level disease protection. Annual Review of Entomology. 63, 105–123.'
mla: 'Cremer, Sylvia, et al. “Social Immunity: Emergence and Evolution of Colony-Level
Disease Protection.” Annual Review of Entomology, vol. 63, Annual Reviews,
2018, pp. 105–23, doi:10.1146/annurev-ento-020117-043110.'
short: S. Cremer, C. Pull, M. Fürst, Annual Review of Entomology 63 (2018) 105–123.
corr_author: '1'
date_created: 2018-12-11T11:48:36Z
date_published: 2018-01-07T00:00:00Z
date_updated: 2026-04-08T14:19:10Z
day: '07'
department:
- _id: SyCr
doi: 10.1146/annurev-ento-020117-043110
external_id:
isi:
- '000424633700008'
intvolume: ' 63'
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
page: 105 - 123
publication: Annual Review of Entomology
publication_identifier:
issn:
- 1545-4487
publication_status: published
publisher: Annual Reviews
publist_id: '6844'
quality_controlled: '1'
related_material:
record:
- id: '819'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Social immunity: Emergence and evolution of colony-level disease protection'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 63
year: '2018'
...
---
_id: '81'
abstract:
- lang: eng
text: We solve the offline monitoring problem for timed propositional temporal logic
(TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider
extends linear temporal logic (LTL) with clock variables and reset quantifiers,
providing a mechanism to specify real-time constraints. We first describe a general
monitoring algorithm based on an exhaustive computation of the set of satisfying
clock assignments as a finite union of zones. We then propose a specialized monitoring
algorithm for the one-variable case using a partition of the time domain based
on the notion of region equivalence, whose complexity is linear in the length
of the signal, thereby generalizing a known result regarding the monitoring of
metric temporal logic (MTL). The region and zone representations of time constraints
are known from timed automata verification and can also be used in the discrete-time
case. Our prototype implementation appears to outperform previous discrete-time
implementations of TPTL monitoring,
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Adrian
full_name: Elgyütt, Adrian
id: 4A2E9DBA-F248-11E8-B48F-1D18A9856A87
last_name: Elgyütt
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables.
In: Vol 11022. Springer; 2018:53-70. doi:10.1007/978-3-030-00151-3_4'
apa: 'Elgyütt, A., Ferrere, T., & Henzinger, T. A. (2018). Monitoring temporal
logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS:
Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_4'
chicago: Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal
Logic with Clock Variables,” 11022:53–70. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_4.
ieee: 'A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with
clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed
Systems, Beijing, China, 2018, vol. 11022, pp. 53–70.'
ista: 'Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with
clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS,
vol. 11022, 53–70.'
mla: Elgyütt, Adrian, et al. Monitoring Temporal Logic with Clock Variables.
Vol. 11022, Springer, 2018, pp. 53–70, doi:10.1007/978-3-030-00151-3_4.
short: A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70.
conference:
end_date: 2018-09-06
location: Beijing, China
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
start_date: 2018-09-04
date_created: 2018-12-11T11:44:31Z
date_published: 2018-08-26T00:00:00Z
date_updated: 2025-04-15T06:26:03Z
day: '26'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-00151-3_4
external_id:
isi:
- '000884993200004'
file:
- access_level: open_access
checksum: e5d81c9b50a6bd9d8a2c16953aad7e23
content_type: application/pdf
creator: dernst
date_created: 2020-10-09T06:24:21Z
date_updated: 2020-10-09T06:24:21Z
file_id: '8638'
file_name: 2018_LNCS_Elgyuett.pdf
file_size: 537219
relation: main_file
success: 1
file_date_updated: 2020-10-09T06:24:21Z
has_accepted_license: '1'
intvolume: ' 11022'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 53 - 70
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication_status: published
publisher: Springer
publist_id: '7973'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monitoring temporal logic with clock variables
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11022
year: '2018'
...
---
_id: '82'
abstract:
- lang: eng
text: In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage,
bacterial cells resistant to the phage commonly emerge and become the dominant
population of bacteria. Following the ascent of resistant mutants, the densities
of bacteria in these simple communities become limited by resources rather than
the phage. Despite the evolution of resistant hosts, upon which the phage cannot
replicate, the lytic phage population is most commonly maintained in an apparently
stable state with the resistant bacteria. Several mechanisms have been put forward
to account for this result. Here we report the results of population dynamic/evolution
experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli
in serial transfer cultures. We show that, following the ascent of λVIR-resistant
bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal
media and in all cases in nutrient-rich broth. Using mathematical models and experiments,
we show that the dominant mechanism responsible for maintenance of λVIRin these
resource-limited populations dominated by resistant E. coli is a high rate of
either phenotypic or genetic transition from resistance to susceptibility—a hitherto
undemonstrated mechanism we term "leaky resistance." We discuss the
implications of leaky resistance to our understanding of the conditions for the
maintenance of phage in populations of bacteria—their “existence conditions.”.
article_number: '2005971'
article_processing_charge: Yes
author:
- first_name: Waqas
full_name: Chaudhry, Waqas
last_name: Chaudhry
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Nilang
full_name: Shah, Nilang
last_name: Shah
- first_name: Howard
full_name: Weiss, Howard
last_name: Weiss
- first_name: Ingrid
full_name: Mccall, Ingrid
last_name: Mccall
- first_name: Justin
full_name: Meyer, Justin
last_name: Meyer
- first_name: Animesh
full_name: Gupta, Animesh
last_name: Gupta
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Bruce
full_name: Levin, Bruce
last_name: Levin
citation:
ama: Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for
the existence of lytic bacteriophage. PLoS Biology. 2018;16(8). doi:10.1371/journal.pbio.2005971
apa: Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin,
B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971
chicago: Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall,
Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance
and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology.
Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.
ieee: W. Chaudhry et al., “Leaky resistance and the conditions for the existence
of lytic bacteriophage,” PLoS Biology, vol. 16, no. 8. Public Library of
Science, 2018.
ista: Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC,
Levin B. 2018. Leaky resistance and the conditions for the existence of lytic
bacteriophage. PLoS Biology. 16(8), 2005971.
mla: Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence
of Lytic Bacteriophage.” PLoS Biology, vol. 16, no. 8, 2005971, Public
Library of Science, 2018, doi:10.1371/journal.pbio.2005971.
short: W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta,
C.C. Guet, B. Levin, PLoS Biology 16 (2018).
date_created: 2018-12-11T11:44:32Z
date_published: 2018-08-16T00:00:00Z
date_updated: 2023-09-13T08:45:41Z
day: '16'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1371/journal.pbio.2005971
external_id:
isi:
- '000443383300024'
file:
- access_level: open_access
checksum: 527076f78265cd4ea192cd1569851587
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:55:31Z
date_updated: 2020-07-14T12:48:10Z
file_id: '5706'
file_name: 2018_Plos_Chaudhry.pdf
file_size: 4007095
relation: main_file
file_date_updated: 2020-07-14T12:48:10Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '7972'
quality_controlled: '1'
related_material:
record:
- id: '9810'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Leaky resistance and the conditions for the existence of lytic bacteriophage
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 16
year: '2018'
...
---
_id: '85'
abstract:
- lang: eng
text: Concurrent accesses to shared data structures must be synchronized to avoid
data races. Coarse-grained synchronization, which locks the entire data structure,
is easy to implement but does not scale. Fine-grained synchronization can scale
well, but can be hard to reason about. Hand-over-hand locking, in which operations
are pipelined as they traverse the data structure, combines fine-grained synchronization
with ease of use. However, the traditional implementation suffers from inherent
overheads. This paper introduces snapshot-based synchronization (SBS), a novel
hand-over-hand locking mechanism. SBS decouples the synchronization state from
the data, significantly improving cache utilization. Further, it relies on guarantees
provided by pipelining to minimize synchronization that requires cross-thread
communication. Snapshot-based synchronization thus scales much better than traditional
hand-over-hand locking, while maintaining the same ease of use.
acknowledgement: Trevor Brown was supported in part by the ISF (grants 2005/17 & 1749/14)
and by a NSERC post-doctoral fellowship.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Eran
full_name: Gilad, Eran
last_name: Gilad
- first_name: Trevor A
full_name: Brown, Trevor A
id: 3569F0A0-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Mark
full_name: Oskin, Mark
last_name: Oskin
- first_name: Yoav
full_name: Etsion, Yoav
last_name: Etsion
citation:
ama: 'Gilad E, Brown TA, Oskin M, Etsion Y. Snapshot based synchronization: A fast
replacement for Hand-over-Hand locking. In: Vol 11014. Springer; 2018:465-479.
doi:10.1007/978-3-319-96983-1_33'
apa: 'Gilad, E., Brown, T. A., Oskin, M., & Etsion, Y. (2018). Snapshot based
synchronization: A fast replacement for Hand-over-Hand locking (Vol. 11014, pp.
465–479). Presented at the Euro-Par: European Conference on Parallel Processing,
Turin, Italy: Springer. https://doi.org/10.1007/978-3-319-96983-1_33'
chicago: 'Gilad, Eran, Trevor A Brown, Mark Oskin, and Yoav Etsion. “Snapshot Based
Synchronization: A Fast Replacement for Hand-over-Hand Locking,” 11014:465–79.
Springer, 2018. https://doi.org/10.1007/978-3-319-96983-1_33.'
ieee: 'E. Gilad, T. A. Brown, M. Oskin, and Y. Etsion, “Snapshot based synchronization:
A fast replacement for Hand-over-Hand locking,” presented at the Euro-Par: European
Conference on Parallel Processing, Turin, Italy, 2018, vol. 11014, pp. 465–479.'
ista: 'Gilad E, Brown TA, Oskin M, Etsion Y. 2018. Snapshot based synchronization:
A fast replacement for Hand-over-Hand locking. Euro-Par: European Conference on
Parallel Processing, LNCS, vol. 11014, 465–479.'
mla: 'Gilad, Eran, et al. Snapshot Based Synchronization: A Fast Replacement
for Hand-over-Hand Locking. Vol. 11014, Springer, 2018, pp. 465–79, doi:10.1007/978-3-319-96983-1_33.'
short: E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479.
conference:
end_date: 2018-08-31
location: Turin, Italy
name: 'Euro-Par: European Conference on Parallel Processing'
start_date: 2018-08-27
date_created: 2018-12-11T11:44:33Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2026-04-16T09:53:41Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1007/978-3-319-96983-1_33
external_id:
isi:
- '000851042300031'
file:
- access_level: open_access
checksum: 13a3f250be8878405e791b53c19722ad
content_type: application/pdf
creator: dernst
date_created: 2019-02-12T07:40:40Z
date_updated: 2020-07-14T12:48:14Z
file_id: '5954'
file_name: 2018_Brown.pdf
file_size: 665372
relation: main_file
file_date_updated: 2020-07-14T12:48:14Z
has_accepted_license: '1'
intvolume: ' 11014'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Preprint
page: 465 - 479
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication_identifier:
issn:
- 0302-9743
publication_status: published
publisher: Springer
publist_id: '7969'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Snapshot based synchronization: A fast replacement for Hand-over-Hand locking'
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 11014
year: '2018'
...
---
_id: '86'
abstract:
- lang: eng
text: Responsiveness—the requirement that every request to a system be eventually
handled—is one of the fundamental liveness properties of a reactive system. Average
response time is a quantitative measure for the responsiveness requirement used
commonly in performance evaluation. We show how average response time can be computed
on state-transition graphs, on Markov chains, and on game graphs. In all three
cases, we give polynomial-time algorithms.
acknowledgement: 'This research was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein
Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund
(WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland
under grant 2014/15/D/ST6/04543.'
alternative_title:
- LNCS
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. Computing average response time. In: Lohstroh
M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer;
2018:143-161. doi:10.1007/978-3-319-95246-8_9'
apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average
response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles
of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average
Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia
Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,”
in Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani,
Eds. Springer, 2018, pp. 143–161.
ista: 'Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time.
In: Principles of Modeling. LNCS, vol. 10760, 143–161.'
mla: Chatterjee, Krishnendu, et al. “Computing Average Response Time.” Principles
of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018,
pp. 143–61, doi:10.1007/978-3-319-95246-8_9.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani
(Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.
date_created: 2018-12-11T11:44:33Z
date_published: 2018-07-20T00:00:00Z
date_updated: 2025-04-15T06:26:15Z
day: '20'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-95246-8_9
ec_funded: 1
editor:
- first_name: Marten
full_name: Lohstroh, Marten
last_name: Lohstroh
- first_name: Patricia
full_name: Derler, Patricia
last_name: Derler
- first_name: Marjan
full_name: Sirjani, Marjan
last_name: Sirjani
file:
- access_level: open_access
checksum: 9995c6ce6957333baf616fc4f20be597
content_type: application/pdf
creator: dernst
date_created: 2019-11-19T08:22:18Z
date_updated: 2020-07-14T12:48:14Z
file_id: '7053'
file_name: 2018_PrinciplesModeling_Chatterjee.pdf
file_size: 516307
relation: main_file
file_date_updated: 2020-07-14T12:48:14Z
has_accepted_license: '1'
intvolume: ' 10760'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 143 - 161
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
- _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: Principles of Modeling
publication_status: published
publisher: Springer
publist_id: '7968'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computing average response time
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10760
year: '2018'
...
---
_id: '8618'
abstract:
- lang: eng
text: The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT
nanoscopy have been developed from fluorescent proteins of the GFP superfamily.
These proteins are bright, but exhibit several drawbacks such as relatively large
size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore,
RSFPs from other origins with improved properties need to be explored. Here, we
report the development of two RSFPs based on the LOV domain of the photoreceptor
protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by
association with the abundant cellular cofactor flavin mononucleotide (FMN). Under
illumination with blue and ultraviolet light, they undergo a photocycle, making
these proteins inherently photoswitchable. Our first improved variant, rsLOV1,
can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy
of living cells with a resolution of down to 50 nm. In addition to their smaller
size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability
at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and
off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date.
Therefore, LOV-domain-based RSFPs have potential for applications where the switching
speed of GFP-based proteins is limiting.
article_number: '2724'
article_processing_charge: No
article_type: original
author:
- first_name: Carola
full_name: Gregor, Carola
last_name: Gregor
- first_name: Sven C.
full_name: Sidenstein, Sven C.
last_name: Sidenstein
- first_name: Martin
full_name: Andresen, Martin
last_name: Andresen
- first_name: Steffen J.
full_name: Sahl, Steffen J.
last_name: Sahl
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Stefan W.
full_name: Hell, Stefan W.
last_name: Hell
citation:
ama: Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. Novel reversibly
switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from
the bacterial photoreceptor YtvA. Scientific Reports. 2018;8. doi:10.1038/s41598-018-19947-1
apa: Gregor, C., Sidenstein, S. C., Andresen, M., Sahl, S. J., Danzl, J. G., &
Hell, S. W. (2018). Novel reversibly switchable fluorescent proteins for RESOLFT
and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific
Reports. Springer Nature. https://doi.org/10.1038/s41598-018-19947-1
chicago: Gregor, Carola, Sven C. Sidenstein, Martin Andresen, Steffen J. Sahl, Johann
G Danzl, and Stefan W. Hell. “Novel Reversibly Switchable Fluorescent Proteins
for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.”
Scientific Reports. Springer Nature, 2018. https://doi.org/10.1038/s41598-018-19947-1.
ieee: C. Gregor, S. C. Sidenstein, M. Andresen, S. J. Sahl, J. G. Danzl, and S.
W. Hell, “Novel reversibly switchable fluorescent proteins for RESOLFT and STED
nanoscopy engineered from the bacterial photoreceptor YtvA,” Scientific Reports,
vol. 8. Springer Nature, 2018.
ista: Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. 2018. Novel
reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered
from the bacterial photoreceptor YtvA. Scientific Reports. 8, 2724.
mla: Gregor, Carola, et al. “Novel Reversibly Switchable Fluorescent Proteins for
RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.”
Scientific Reports, vol. 8, 2724, Springer Nature, 2018, doi:10.1038/s41598-018-19947-1.
short: C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell,
Scientific Reports 8 (2018).
date_created: 2020-10-06T16:33:37Z
date_published: 2018-02-09T00:00:00Z
date_updated: 2024-10-21T06:02:43Z
day: '09'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.1038/s41598-018-19947-1
external_id:
isi:
- '000424630400037'
pmid:
- '29426833'
file:
- access_level: open_access
checksum: e642080fcbde9584c63544f587c74f03
content_type: application/pdf
creator: dernst
date_created: 2020-10-06T16:35:16Z
date_updated: 2020-10-06T16:35:16Z
file_id: '8619'
file_name: 2018_ScientificReports_Gregor.pdf
file_size: 2818077
relation: main_file
success: 1
file_date_updated: 2020-10-06T16:35:16Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
keyword:
- Multidisciplinary
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy
engineered from the bacterial photoreceptor YtvA
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2018'
...
---
_id: '87'
abstract:
- lang: eng
text: Using the geodesic distance on the n-dimensional sphere, we study the expected
radius function of the Delaunay mosaic of a random set of points. Specifically,
we consider the partition of the mosaic into intervals of the radius function
and determine the expected number of intervals whose radii are less than or equal
to a given threshold. We find that the expectations are essentially the same as
for the Poisson–Delaunay mosaic in n-dimensional Euclidean space. Assuming the
points are not contained in a hemisphere, the Delaunay mosaic is isomorphic to
the boundary complex of the convex hull in Rn+1, so we also get the expected number
of faces of a random inscribed polytope. As proved in Antonelli et al. [Adv. in
Appl. Probab. 9–12 (1977–1980)], an orthant section of the n-sphere is isometric
to the standard n-simplex equipped with the Fisher information metric. It follows
that the latter space has similar stochastic properties as the n-dimensional Euclidean
space. Our results are therefore relevant in information geometry and in population
genetics.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Anton
full_name: Nikitenko, Anton
id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87
last_name: Nikitenko
orcid: 0000-0002-0659-3201
citation:
ama: Edelsbrunner H, Nikitenko A. Random inscribed polytopes have similar radius
functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 2018;28(5):3215-3238.
doi:10.1214/18-AAP1389
apa: Edelsbrunner, H., & Nikitenko, A. (2018). Random inscribed polytopes have
similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/18-AAP1389
chicago: Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes
Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied
Probability. Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/18-AAP1389.
ieee: H. Edelsbrunner and A. Nikitenko, “Random inscribed polytopes have similar
radius functions as Poisson-Delaunay mosaics,” Annals of Applied Probability,
vol. 28, no. 5. Institute of Mathematical Statistics, pp. 3215–3238, 2018.
ista: Edelsbrunner H, Nikitenko A. 2018. Random inscribed polytopes have similar
radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 28(5),
3215–3238.
mla: Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have
Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability,
vol. 28, no. 5, Institute of Mathematical Statistics, 2018, pp. 3215–38, doi:10.1214/18-AAP1389.
short: H. Edelsbrunner, A. Nikitenko, Annals of Applied Probability 28 (2018) 3215–3238.
date_created: 2018-12-11T11:44:33Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2026-04-08T14:19:30Z
day: '01'
department:
- _id: HeEd
doi: 10.1214/18-AAP1389
external_id:
arxiv:
- '1705.02870'
isi:
- '000442893500018'
intvolume: ' 28'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.02870
month: '10'
oa: 1
oa_version: Preprint
page: 3215 - 3238
project:
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Annals of Applied Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '7967'
quality_controlled: '1'
related_material:
record:
- id: '6287'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Random inscribed polytopes have similar radius functions as Poisson-Delaunay
mosaics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 28
year: '2018'
...
---
_id: '913'
abstract:
- lang: eng
text: Coordinated cell polarization in developing tissues is a recurrent theme in
multicellular organisms. In plants, a directional distribution of the plant hormone
auxin is at the core of many developmental programs. A feedback regulation of
auxin on the polarized localization of PIN auxin transporters in individual cells
has been proposed as a self-organizing mechanism for coordinated tissue polarization,
but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport
remain unknown. We performed a microarray-based approach to find regulators of
the auxin-induced PIN relocation in the Arabidopsis thaliana root. We identified
a subset of a family of phosphatidylinositol transfer proteins (PITP), the PATELLINs
(PATL). Here, we show that PATLs are expressed in partially overlapping cells
types in different tissues going through mitosis or initiating differentiation
programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis
embryos, primary roots, lateral root primordia, and developing stomata. Higher
order patl mutants display reduced PIN1 repolarization in response to auxin, shorter
root apical meristem, and drastic defects in embryo and seedling development.
This suggests PATLs redundantly play a crucial role in polarity and patterning
in Arabidopsis.
article_number: jcs.204198
article_processing_charge: No
author:
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Cecilia
full_name: Rodríguez Furlán, Cecilia
last_name: Rodríguez Furlán
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Lorena
full_name: Norambuena, Lorena
last_name: Norambuena
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. PATELLINS
are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis
thaliana. Journal of Cell Science. 2018;131(2). doi:10.1242/jcs.204198
apa: Tejos, R., Rodríguez Furlán, C., Adamowski, M., Sauer, M., Norambuena, L.,
& Friml, J. (2018). PATELLINS are regulators of auxin mediated PIN1 relocation
and plant development in Arabidopsis thaliana. Journal of Cell Science.
Company of Biologists. https://doi.org/10.1242/jcs.204198
chicago: Tejos, Ricardo, Cecilia Rodríguez Furlán, Maciek Adamowski, Michael Sauer,
Lorena Norambuena, and Jiří Friml. “PATELLINS Are Regulators of Auxin Mediated
PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” Journal of
Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.204198.
ieee: R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, and
J. Friml, “PATELLINS are regulators of auxin mediated PIN1 relocation and plant
development in Arabidopsis thaliana,” Journal of Cell Science, vol. 131,
no. 2. Company of Biologists, 2018.
ista: Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J.
2018. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development
in Arabidopsis thaliana. Journal of Cell Science. 131(2), jcs. 204198.
mla: Tejos, Ricardo, et al. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation
and Plant Development in Arabidopsis Thaliana.” Journal of Cell Science,
vol. 131, no. 2, jcs. 204198, Company of Biologists, 2018, doi:10.1242/jcs.204198.
short: R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, J.
Friml, Journal of Cell Science 131 (2018).
corr_author: '1'
date_created: 2018-12-11T11:49:10Z
date_published: 2018-01-29T00:00:00Z
date_updated: 2025-07-10T12:01:38Z
day: '29'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1242/jcs.204198
ec_funded: 1
external_id:
isi:
- '000424842400019'
file:
- access_level: open_access
checksum: bf156c20a4f117b4b932370d54cbac8c
content_type: application/pdf
creator: dernst
date_created: 2019-04-12T08:46:32Z
date_updated: 2020-07-14T12:48:15Z
file_id: '6299'
file_name: 2017_adamowski_PATELLINS_are.pdf
file_size: 14925985
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 131'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Journal of Cell Science
publication_identifier:
issn:
- 0021-9533
publication_status: published
publisher: Company of Biologists
publist_id: '6530'
pubrep_id: '988'
quality_controlled: '1'
scopus_import: '1'
status: public
title: PATELLINS are regulators of auxin mediated PIN1 relocation and plant development
in Arabidopsis thaliana
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2018'
...
---
_id: '9229'
alternative_title:
- Molecular and cellular neuroscience
article_processing_charge: No
article_type: letter_note
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera
Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001
apa: Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology.
Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod.
https://doi.org/10.20388/omp2018.00s1.001
chicago: Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.”
Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod,
2018. https://doi.org/10.20388/omp2018.00s1.001.
ieee: J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,”
Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University
of Nizhny Novgorod, p. 11, 2018.
ista: Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology.
Opera Medica et Physiologica. 4(S1), 11.
mla: Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.”
Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University
of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001.
short: J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.
date_created: 2021-03-07T23:01:25Z
date_published: 2018-06-30T00:00:00Z
date_updated: 2026-06-18T19:43:22Z
day: '30'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.20388/omp2018.00s1.001
intvolume: ' 4'
issue: S1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://operamedphys.org/content/molecular-and-cellular-neuroscience
month: '06'
oa: 1
oa_version: Published Version
page: '11'
publication: Opera Medica et Physiologica
publication_identifier:
eissn:
- 2500-2295
issn:
- 2500-2287
publication_status: published
publisher: Lobachevsky State University of Nizhny Novgorod
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diffraction-unlimited optical imaging for synaptic physiology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2018'
...
---
_id: '9471'
abstract:
- lang: eng
text: The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation
and is required for endosperm genomic imprinting and embryo viability. Targets
of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons
and at the boundaries of large transposons, but how DME interacts with these diverse
chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1)
subunit of the chromatin remodeler FACT (facilitates chromatin transactions),
was previously shown to be involved in the DME-dependent regulation of genomic
imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction
between DME and chromatin, we focused on the activity of the two FACT subunits,
SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found
that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of
target sites, the first being euchromatic and accessible to DME, but the second,
representing over half of DME targets, requiring the action of FACT for DME-mediated
DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets
are GC-rich heterochromatin domains with high nucleosome occupancy enriched with
H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated
linker histone H1 specifically mediates the requirement for FACT at a subset of
DME-target loci. Overall, our results demonstrate that FACT is required for DME
targeting by facilitating its access to heterochromatin.
article_processing_charge: No
article_type: original
author:
- first_name: Jennifer M.
full_name: Frost, Jennifer M.
last_name: Frost
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Guen Tae
full_name: Park, Guen Tae
last_name: Park
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Miyuki
full_name: Nakamura, Miyuki
last_name: Nakamura
- first_name: Samuel J. H.
full_name: Lin, Samuel J. H.
last_name: Lin
- first_name: Hyunjin
full_name: Yoo, Hyunjin
last_name: Yoo
- first_name: Jaemyung
full_name: Choi, Jaemyung
last_name: Choi
- first_name: Yoko
full_name: Ikeda, Yoko
last_name: Ikeda
- first_name: Tetsu
full_name: Kinoshita, Tetsu
last_name: Kinoshita
- first_name: Yeonhee
full_name: Choi, Yeonhee
last_name: Choi
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis. Proceedings of the National
Academy of Sciences. 2018;115(20):E4720-E4729. doi:10.1073/pnas.1713333115
apa: Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S.
J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis. Proceedings of the National
Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1713333115
chicago: Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki
Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for
DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713333115.
ieee: J. M. Frost et al., “FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis,” Proceedings of the
National Academy of Sciences, vol. 115, no. 20. National Academy of Sciences,
pp. E4720–E4729, 2018.
ista: Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J,
Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required
for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings
of the National Academy of Sciences. 115(20), E4720–E4729.
mla: Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation
at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the
National Academy of Sciences, vol. 115, no. 20, National Academy of Sciences,
2018, pp. E4720–29, doi:10.1073/pnas.1713333115.
short: J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H.
Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings
of the National Academy of Sciences 115 (2018) E4720–E4729.
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text: Table S1. Genes with highest betweenness. Table S2. Local and Master regulators
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- first_name: Maude
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adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295339.v1'
chicago: 'Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler,
Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of
Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary
Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295339.v1.'
ieee: 'J. Higareda Almaraz et al., “Additional file 1: Of Norepinephrine
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adipocytes.” Springer Nature, 2018.'
ista: 'Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig
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regulatory network response in primary human white adipocytes, Springer Nature,
10.6084/m9.figshare.7295339.v1.'
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Springer Nature, 2018, doi:10.6084/m9.figshare.7295339.v1.'
short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S.
Herzig, M. Scheideler, (2018).
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---
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abstract:
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text: Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb).
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author:
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full_name: Higareda Almaraz, Juan
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apa: 'Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T.,
Herzig, S., & Scheideler, M. (2018). Additional file 3: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295369.v1'
chicago: 'Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler,
Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of
Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary
Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295369.v1.'
ieee: 'J. Higareda Almaraz et al., “Additional file 3: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
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regulatory network response in primary human white adipocytes, Springer Nature,
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an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.
Springer Nature, 2018, doi:10.6084/m9.figshare.7295369.v1.'
short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S.
Herzig, M. Scheideler, (2018).
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department:
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doi: 10.6084/m9.figshare.7295369.v1
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doi:10.1371/journal.pbio.2005971.s008
apa: Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin,
B. (2018). Numerical data used in figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971.s008
chicago: Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall,
Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used
in Figures.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.s008.
ieee: W. Chaudhry et al., “Numerical data used in figures.” Public Library
of Science, 2018.
ista: Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC,
Levin B. 2018. Numerical data used in figures, Public Library of Science, 10.1371/journal.pbio.2005971.s008.
mla: Chaudhry, Waqas, et al. Numerical Data Used in Figures. Public Library
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short: W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta,
C.C. Guet, B. Levin, (2018).
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---
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tables. (XLSX 50Â kb)
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full_name: Zapata, Luis
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M. (2018). Additional file 1: Of negative selection in tumor genome evolution
acts on essential cellular functions and the immunopeptidome. Springer Nature.
https://doi.org/10.6084/m9.figshare.6401390.v1'
chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski,
and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome
Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer
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ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer,
“Additional file 1: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome.” Springer Nature, 2018.'
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Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.'
short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer,
(2018).
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---
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abstract:
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text: This document contains the full list of genes with their respective significance
and dN/dS values. (TXT 4499Â kb)
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author:
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last_name: Zapata
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apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer,
M. (2018). Additional file 2: Of negative selection in tumor genome evolution
acts on essential cellular functions and the immunopeptidome. Springer Nature.
https://doi.org/10.6084/m9.figshare.6401414.v1'
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and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome
Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer
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“Additional file 2: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome.” Springer Nature, 2018.'
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Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.'
short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer,
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---
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text: 'File S1 contains figures that clarify the following features: (i) effect
of population size on the average number/frequency of SI classes, (ii) changes
in the minimal completeness deficit in time for a single class, and (iii) diversification
diagrams for all studied pathways, including the summary figure for k = 8. File
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chicago: Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and
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---
_id: '9831'
abstract:
- lang: eng
text: 'Implementation of the inference method in Matlab, including three applications
of the method: The first one for the model of ant motion, the second one for bacterial
chemotaxis, and the third one for the motion of fish.'
article_processing_charge: No
author:
- first_name: Katarína
full_name: Bod’Ová, Katarína
last_name: Bod’Ová
- first_name: Gabriel
full_name: Mitchell, Gabriel
id: 315BCD80-F248-11E8-B48F-1D18A9856A87
last_name: Mitchell
- first_name: Roy
full_name: Harpaz, Roy
last_name: Harpaz
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of
the inference method in Matlab. 2018. doi:10.1371/journal.pone.0193049.s001
apa: Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018).
Implementation of the inference method in Matlab. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049.s001
chicago: Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper
Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of
Science, 2018. https://doi.org/10.1371/journal.pone.0193049.s001.
ieee: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation
of the inference method in Matlab.” Public Library of Science, 2018.
ista: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation
of the inference method in Matlab, Public Library of Science, 10.1371/journal.pone.0193049.s001.
mla: Bod’Ová, Katarína, et al. Implementation of the Inference Method in Matlab.
Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.s001.
short: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).
date_created: 2021-08-09T07:01:24Z
date_published: 2018-03-07T00:00:00Z
date_updated: 2025-04-15T06:44:30Z
day: '07'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0193049.s001
month: '03'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '406'
relation: used_in_publication
status: public
status: public
title: Implementation of the inference method in Matlab
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9837'
abstract:
- lang: eng
text: Both classical and recent studies suggest that chromosomal inversion polymorphisms
are important in adaptation and speciation. However, biases in discovery and reporting
of inversions make it difficult to assess their prevalence and biological importance.
Here, we use an approach based on linkage disequilibrium among markers genotyped
for samples collected across a transect between contrasting habitats to detect
chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in
a single locality for the coastal marine snail, Littorina saxatilis. Patterns
of diversity in the field and of recombination in controlled crosses provide strong
evidence that at least the majority of these rearrangements are inversions. Most
show clinal changes in frequency between habitats, suggestive of divergent selection,
but only one appears to be fixed for different arrangements in the two habitats.
Consistent with widespread evidence for balancing selection on inversion polymorphisms,
we argue that a combination of heterosis and divergent selection can explain the
observed patterns and should be considered in other systems spanning environmental
gradients.
article_processing_charge: No
author:
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Pragya
full_name: Chaube, Pragya
last_name: Chaube
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Tomas
full_name: Larsson, Tomas
last_name: Larsson
- first_name: Alan R.
full_name: Lemmon, Alan R.
last_name: Lemmon
- first_name: Emily M.
full_name: Lemmon, Emily M.
last_name: Lemmon
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Marina
full_name: Panova, Marina
last_name: Panova
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements
in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113'
apa: 'Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon,
E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements
in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113'
chicago: 'Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon,
Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements
in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.'
ieee: 'R. Faria et al., “Data from: Multiple chromosomal rearrangements in
a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.'
ista: 'Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović
M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from:
Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis
ecotypes, Dryad, 10.5061/dryad.72cg113.'
mla: 'Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a
Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113.'
short: R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon,
M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin,
(2018).
date_created: 2021-08-09T12:46:39Z
date_published: 2018-10-09T00:00:00Z
date_updated: 2023-08-24T14:50:26Z
day: '09'
department:
- _id: NiBa
doi: 10.5061/dryad.72cg113
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.72cg113
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '6095'
relation: used_in_publication
status: public
status: public
title: 'Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina
saxatilis ecotypes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9838'
abstract:
- lang: eng
text: 'Facial shape is the basis for facial recognition and categorization. Facial
features reflect the underlying geometry of the skeletal structures. Here we reveal
that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped
by signals generated by neural structures: brain and olfactory epithelium. Brain-derived
Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal
capsule, whereas the formation of a capsule roof is controlled by signals from
the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned
out to be important for shaping membranous facial bones during development. This
suggests that conserved neurosensory structures could benefit from protection
and have evolved signals inducing cranial cartilages encasing them. Experiments
with mutant mice revealed that the genomic regulatory regions controlling production
of SHH in the nervous system contribute to facial cartilage morphogenesis, which
might be a mechanism responsible for the adaptive evolution of animal faces and
snouts.'
article_processing_charge: No
author:
- first_name: Marketa
full_name: Kaucka, Marketa
last_name: Kaucka
- first_name: Julian
full_name: Petersen, Julian
last_name: Petersen
- first_name: Marketa
full_name: Tesarova, Marketa
last_name: Tesarova
- first_name: Bara
full_name: Szarowska, Bara
last_name: Szarowska
- first_name: Maria Eleni
full_name: Kastriti, Maria Eleni
last_name: Kastriti
- first_name: Meng
full_name: Xie, Meng
last_name: Xie
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Karl
full_name: Annusver, Karl
last_name: Annusver
- first_name: Maria
full_name: Kasper, Maria
last_name: Kasper
- first_name: Orsolya
full_name: Symmons, Orsolya
last_name: Symmons
- first_name: Leslie
full_name: Pan, Leslie
last_name: Pan
- first_name: Francois
full_name: Spitz, Francois
last_name: Spitz
- first_name: Jozef
full_name: Kaiser, Jozef
last_name: Kaiser
- first_name: Maria
full_name: Hovorakova, Maria
last_name: Hovorakova
- first_name: Tomas
full_name: Zikmund, Tomas
last_name: Zikmund
- first_name: Kazunori
full_name: Sunadome, Kazunori
last_name: Sunadome
- first_name: Michael P
full_name: Matise, Michael P
last_name: Matise
- first_name: Hui
full_name: Wang, Hui
last_name: Wang
- first_name: Ulrika
full_name: Marklund, Ulrika
last_name: Marklund
- first_name: Hind
full_name: Abdo, Hind
last_name: Abdo
- first_name: Patrik
full_name: Ernfors, Patrik
last_name: Ernfors
- first_name: Pascal
full_name: Maire, Pascal
last_name: Maire
- first_name: Maud
full_name: Wurmser, Maud
last_name: Wurmser
- first_name: Andrei S
full_name: Chagin, Andrei S
last_name: Chagin
- first_name: Kaj
full_name: Fried, Kaj
last_name: Fried
- first_name: Igor
full_name: Adameyko, Igor
last_name: Adameyko
citation:
ama: 'Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain
and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.
2018. doi:10.5061/dryad.f1s76f2'
apa: 'Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie,
M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium
control shaping of the mammalian nasal capsule cartilage. Dryad. https://doi.org/10.5061/dryad.f1s76f2'
chicago: 'Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria
Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain
and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.”
Dryad, 2018. https://doi.org/10.5061/dryad.f1s76f2.'
ieee: 'M. Kaucka et al., “Data from: Signals from the brain and olfactory
epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.'
ista: 'Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva
A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund
T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser
M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and
olfactory epithelium control shaping of the mammalian nasal capsule cartilage,
Dryad, 10.5061/dryad.f1s76f2.'
mla: 'Kaucka, Marketa, et al. Data from: Signals from the Brain and Olfactory
Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage. Dryad,
2018, doi:10.5061/dryad.f1s76f2.'
short: M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie,
A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M.
Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo,
P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018).
date_created: 2021-08-09T12:54:35Z
date_published: 2018-06-14T00:00:00Z
date_updated: 2025-04-14T13:02:22Z
day: '14'
department:
- _id: AnKi
doi: 10.5061/dryad.f1s76f2
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.f1s76f2
month: '06'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '162'
relation: used_in_publication
status: public
status: public
title: 'Data from: Signals from the brain and olfactory epithelium control shaping
of the mammalian nasal capsule cartilage'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...