---
_id: '7225'
abstract:
- lang: eng
text: "This is a literature teaching resource review for biologically inspired microfluidics
courses\r\nor exploring the diverse applications of microfluidics. The structure
is around key papers and model\r\norganisms. While courses gradually change over
time, a focus remains on understanding how\r\nmicrofluidics has developed as well
as what it can and cannot do for researchers. As a primary\r\nstarting point,
we cover micro-fluid mechanics principles and microfabrication of devices. A variety\r\nof
applications are discussed using model prokaryotic and eukaryotic organisms from
the set\r\nof bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei),
yeast (Saccharomyces cerevisiae),\r\nslime molds (Physarum polycephalum), worms
(Caenorhabditis elegans), flies (Drosophila melangoster),\r\nplants (Arabidopsis
thaliana), and mouse immune cells (Mus musculus). Other engineering and\r\nbiochemical
methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics,\r\nbiotic
games, and diagnostics. While we have not yet reached the end-all lab on a chip,\r\nmicrofluidics
can still be used effectively for specific applications."
article_number: '109'
article_processing_charge: Yes
article_type: review
author:
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
citation:
ama: Merrin J. Frontiers in microfluidics, a teaching resource review. Bioengineering.
2019;6(4). doi:10.3390/bioengineering6040109
apa: Merrin, J. (2019). Frontiers in microfluidics, a teaching resource review.
Bioengineering. MDPI. https://doi.org/10.3390/bioengineering6040109
chicago: Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.”
Bioengineering. MDPI, 2019. https://doi.org/10.3390/bioengineering6040109.
ieee: J. Merrin, “Frontiers in microfluidics, a teaching resource review,” Bioengineering,
vol. 6, no. 4. MDPI, 2019.
ista: Merrin J. 2019. Frontiers in microfluidics, a teaching resource review. Bioengineering.
6(4), 109.
mla: Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering,
vol. 6, no. 4, 109, MDPI, 2019, doi:10.3390/bioengineering6040109.
short: J. Merrin, Bioengineering 6 (2019).
date_created: 2020-01-05T23:00:45Z
date_published: 2019-12-03T00:00:00Z
date_updated: 2023-09-06T14:52:49Z
day: '03'
ddc:
- '620'
department:
- _id: NanoFab
doi: 10.3390/bioengineering6040109
external_id:
isi:
- '000505590000024'
pmid:
- '31816954'
file:
- access_level: open_access
checksum: 80f1499e2a4caccdf3aa54b137fd99a0
content_type: application/pdf
creator: dernst
date_created: 2020-01-07T14:49:59Z
date_updated: 2020-07-14T12:47:54Z
file_id: '7243'
file_name: 2019_Bioengineering_Merrin.pdf
file_size: 2660780
relation: main_file
file_date_updated: 2020-07-14T12:47:54Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Bioengineering
publication_identifier:
eissn:
- '23065354'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Frontiers in microfluidics, a teaching resource review
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: 6
year: '2019'
...
---
_id: '7226'
article_number: '123504'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Vojkan
full_name: Jaksic, Vojkan
last_name: Jaksic
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Jaksic V, Seiringer R. Introduction to the Special Collection: International
Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics.
2019;60(12). doi:10.1063/1.5138135'
apa: 'Jaksic, V., & Seiringer, R. (2019). Introduction to the Special Collection:
International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical
Physics. AIP Publishing. https://doi.org/10.1063/1.5138135'
chicago: 'Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection:
International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical
Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5138135.'
ieee: 'V. Jaksic and R. Seiringer, “Introduction to the Special Collection: International
Congress on Mathematical Physics (ICMP) 2018,” Journal of Mathematical Physics,
vol. 60, no. 12. AIP Publishing, 2019.'
ista: 'Jaksic V, Seiringer R. 2019. Introduction to the Special Collection: International
Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics.
60(12), 123504.'
mla: 'Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection:
International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical
Physics, vol. 60, no. 12, 123504, AIP Publishing, 2019, doi:10.1063/1.5138135.'
short: V. Jaksic, R. Seiringer, Journal of Mathematical Physics 60 (2019).
date_created: 2020-01-05T23:00:46Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2024-02-28T13:01:45Z
day: '01'
ddc:
- '500'
department:
- _id: RoSe
doi: 10.1063/1.5138135
external_id:
isi:
- '000505529800002'
file:
- access_level: open_access
checksum: bbd12ad1999a9ad7ba4d3c6f2e579c22
content_type: application/pdf
creator: dernst
date_created: 2020-01-07T14:59:13Z
date_updated: 2020-07-14T12:47:54Z
file_id: '7244'
file_name: 2019_JournalMathPhysics_Jaksic.pdf
file_size: 1025015
relation: main_file
file_date_updated: 2020-07-14T12:47:54Z
has_accepted_license: '1'
intvolume: ' 60'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Journal of Mathematical Physics
publication_identifier:
issn:
- '00222488'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Introduction to the Special Collection: International Congress on Mathematical
Physics (ICMP) 2018'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2019'
...
---
_id: '7228'
abstract:
- lang: eng
text: "Traditional concurrent programming involves manipulating shared mutable state.
Alternatives to this programming style are communicating sequential processes
(CSP) and actor models, which share data via explicit communication. These models
have been known for almost half a century, and have recently had started to gain
significant traction among modern programming languages. The common abstraction
for communication between several processes is the channel. Although channels
are similar to producer-consumer data structures, they have different semantics
and support additional operations, such as the select expression. Despite their
growing popularity, most known implementations of channels use lock-based data
structures and can be rather inefficient.\r\n\r\nIn this paper, we present the
first efficient lock-free algorithm for implementing a communication channel for
CSP programming. We provide implementations and experimental results in the Kotlin
and Go programming languages. Our new algorithm outperforms existing implementations
on many workloads, while providing non-blocking progress guarantee. Our design
can serve as an example of how to construct general communication data structures
for CSP and actor models. "
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Roman
full_name: Elizarov, Roman
last_name: Elizarov
citation:
ama: 'Koval N, Alistarh D-A, Elizarov R. Scalable FIFO channels for programming
via communicating sequential processes. In: 25th Anniversary of Euro-Par.
Vol 11725. Springer Nature; 2019:317-333. doi:10.1007/978-3-030-29400-7_23'
apa: 'Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Scalable FIFO channels
for programming via communicating sequential processes. In 25th Anniversary
of Euro-Par (Vol. 11725, pp. 317–333). Göttingen, Germany: Springer Nature.
https://doi.org/10.1007/978-3-030-29400-7_23'
chicago: Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Scalable FIFO
Channels for Programming via Communicating Sequential Processes.” In 25th Anniversary
of Euro-Par, 11725:317–33. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29400-7_23.
ieee: N. Koval, D.-A. Alistarh, and R. Elizarov, “Scalable FIFO channels for programming
via communicating sequential processes,” in 25th Anniversary of Euro-Par,
Göttingen, Germany, 2019, vol. 11725, pp. 317–333.
ista: 'Koval N, Alistarh D-A, Elizarov R. 2019. Scalable FIFO channels for programming
via communicating sequential processes. 25th Anniversary of Euro-Par. Euro-Par:
European Conference on Parallel Processing, LNCS, vol. 11725, 317–333.'
mla: Koval, Nikita, et al. “Scalable FIFO Channels for Programming via Communicating
Sequential Processes.” 25th Anniversary of Euro-Par, vol. 11725, Springer
Nature, 2019, pp. 317–33, doi:10.1007/978-3-030-29400-7_23.
short: N. Koval, D.-A. Alistarh, R. Elizarov, in:, 25th Anniversary of Euro-Par,
Springer Nature, 2019, pp. 317–333.
conference:
end_date: 2019-08-30
location: Göttingen, Germany
name: 'Euro-Par: European Conference on Parallel Processing'
start_date: 2019-08-26
date_created: 2020-01-05T23:00:46Z
date_published: 2019-08-13T00:00:00Z
date_updated: 2023-09-06T14:53:59Z
day: '13'
department:
- _id: DaAl
doi: 10.1007/978-3-030-29400-7_23
external_id:
isi:
- '000851061400023'
intvolume: ' 11725'
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 317-333
publication: 25th Anniversary of Euro-Par
publication_identifier:
eissn:
- 1611-3349
isbn:
- 978-3-0302-9399-4
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scalable FIFO channels for programming via communicating sequential processes
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11725
year: '2019'
...
---
_id: '7230'
abstract:
- lang: eng
text: Simple drawings of graphs are those in which each pair of edges share at most
one point, either a common endpoint or a proper crossing. In this paper we study
the problem of extending a simple drawing D(G) of a graph G by inserting a set
of edges from the complement of G into D(G) such that the result is a simple drawing.
In the context of rectilinear drawings, the problem is trivial. For pseudolinear
drawings, the existence of such an extension follows from Levi’s enlargement lemma.
In contrast, we prove that deciding if a given set of edges can be inserted into
a simple drawing is NP-complete. Moreover, we show that the maximization version
of the problem is APX-hard. We also present a polynomial-time algorithm for deciding
whether one edge uv can be inserted into D(G) when {u,v} is a dominating set for
the graph G.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Alan M
full_name: Arroyo Guevara, Alan M
id: 3207FDC6-F248-11E8-B48F-1D18A9856A87
last_name: Arroyo Guevara
orcid: 0000-0003-2401-8670
- first_name: Martin
full_name: Derka, Martin
last_name: Derka
- first_name: Irene
full_name: Parada, Irene
last_name: Parada
citation:
ama: 'Arroyo Guevara AM, Derka M, Parada I. Extending simple drawings. In: 27th
International Symposium on Graph Drawing and Network Visualization. Vol 11904.
Springer Nature; 2019:230-243. doi:10.1007/978-3-030-35802-0_18'
apa: 'Arroyo Guevara, A. M., Derka, M., & Parada, I. (2019). Extending simple
drawings. In 27th International Symposium on Graph Drawing and Network Visualization
(Vol. 11904, pp. 230–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-35802-0_18'
chicago: Arroyo Guevara, Alan M, Martin Derka, and Irene Parada. “Extending Simple
Drawings.” In 27th International Symposium on Graph Drawing and Network Visualization,
11904:230–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-35802-0_18.
ieee: A. M. Arroyo Guevara, M. Derka, and I. Parada, “Extending simple drawings,”
in 27th International Symposium on Graph Drawing and Network Visualization,
Prague, Czech Republic, 2019, vol. 11904, pp. 230–243.
ista: 'Arroyo Guevara AM, Derka M, Parada I. 2019. Extending simple drawings. 27th
International Symposium on Graph Drawing and Network Visualization. GD: Graph
Drawing and Network Visualization, LNCS, vol. 11904, 230–243.'
mla: Arroyo Guevara, Alan M., et al. “Extending Simple Drawings.” 27th International
Symposium on Graph Drawing and Network Visualization, vol. 11904, Springer
Nature, 2019, pp. 230–43, doi:10.1007/978-3-030-35802-0_18.
short: A.M. Arroyo Guevara, M. Derka, I. Parada, in:, 27th International Symposium
on Graph Drawing and Network Visualization, Springer Nature, 2019, pp. 230–243.
conference:
end_date: 2019-09-20
location: Prague, Czech Republic
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2019-09-17
date_created: 2020-01-05T23:00:47Z
date_published: 2019-11-28T00:00:00Z
date_updated: 2023-09-06T14:56:00Z
day: '28'
department:
- _id: UlWa
doi: 10.1007/978-3-030-35802-0_18
ec_funded: 1
external_id:
arxiv:
- '1908.08129'
isi:
- '000612918800018'
intvolume: ' 11904'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1908.08129
month: '11'
oa: 1
oa_version: Preprint
page: 230-243
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 27th International Symposium on Graph Drawing and Network Visualization
publication_identifier:
eissn:
- 1611-3349
isbn:
- 978-3-0303-5801-3
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extending simple drawings
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11904
year: '2019'
...
---
_id: '7231'
abstract:
- lang: eng
text: Piecewise Barrier Tubes (PBT) is a new technique for flowpipe overapproximation
for nonlinear systems with polynomial dynamics, which leverages a combination
of barrier certificates. PBT has advantages over traditional time-step based methods
in dealing with those nonlinear dynamical systems in which there is a large difference
in speed between trajectories, producing an overapproximation that is time independent.
However, the existing approach for PBT is not efficient due to the application
of interval methods for enclosure-box computation, and it can only deal with continuous
dynamical systems without uncertainty. In this paper, we extend the approach with
the ability to handle both continuous and hybrid dynamical systems with uncertainty
that can reside in parameters and/or noise. We also improve the efficiency of
the method significantly, by avoiding the use of interval-based methods for the
enclosure-box computation without loosing soundness. We have developed a C++ prototype
implementing the proposed approach and we evaluate it on several benchmarks. The
experiments show that our approach is more efficient and precise than other methods
in the literature.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Yu
full_name: Jiang, Yu
last_name: Jiang
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Kong H, Bartocci E, Jiang Y, Henzinger TA. Piecewise robust barrier tubes
for nonlinear hybrid systems with uncertainty. In: 17th International Conference
on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature;
2019:123-141. doi:10.1007/978-3-030-29662-9_8'
apa: 'Kong, H., Bartocci, E., Jiang, Y., & Henzinger, T. A. (2019). Piecewise
robust barrier tubes for nonlinear hybrid systems with uncertainty. In 17th
International Conference on Formal Modeling and Analysis of Timed Systems
(Vol. 11750, pp. 123–141). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_8'
chicago: Kong, Hui, Ezio Bartocci, Yu Jiang, and Thomas A Henzinger. “Piecewise
Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” In 17th
International Conference on Formal Modeling and Analysis of Timed Systems,
11750:123–41. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_8.
ieee: H. Kong, E. Bartocci, Y. Jiang, and T. A. Henzinger, “Piecewise robust barrier
tubes for nonlinear hybrid systems with uncertainty,” in 17th International
Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The
Netherlands, 2019, vol. 11750, pp. 123–141.
ista: 'Kong H, Bartocci E, Jiang Y, Henzinger TA. 2019. Piecewise robust barrier
tubes for nonlinear hybrid systems with uncertainty. 17th International Conference
on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and
Analysis of Timed Systems, LNCS, vol. 11750, 123–141.'
mla: Kong, Hui, et al. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems
with Uncertainty.” 17th International Conference on Formal Modeling and Analysis
of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 123–41, doi:10.1007/978-3-030-29662-9_8.
short: H. Kong, E. Bartocci, Y. Jiang, T.A. Henzinger, in:, 17th International Conference
on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 123–141.
conference:
end_date: 2019-08-29
location: Amsterdam, The Netherlands
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
start_date: 2019-08-27
date_created: 2020-01-05T23:00:47Z
date_published: 2019-08-13T00:00:00Z
date_updated: 2023-09-06T14:55:15Z
day: '13'
department:
- _id: ToHe
doi: 10.1007/978-3-030-29662-9_8
external_id:
arxiv:
- '1907.11514'
isi:
- '000611677700008'
intvolume: ' 11750'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.11514
month: '08'
oa: 1
oa_version: Preprint
page: 123-141
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: The Wittgenstein Prize
publication: 17th International Conference on Formal Modeling and Analysis of Timed
Systems
publication_identifier:
eissn:
- 1611-3349
isbn:
- 978-3-0302-9661-2
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11750
year: '2019'
...
---
_id: '7232'
abstract:
- lang: eng
text: 'We present Mixed-time Signal Temporal Logic (STL−MX), a specification formalism
which extends STL by capturing the discrete/ continuous time duality found in
many cyber-physical systems (CPS), as well as mixed-signal electronic designs.
In STL−MX, properties of components with continuous dynamics are expressed in
STL, while specifications of components with discrete dynamics are written in
LTL. To combine the two layers, we evaluate formulas on two traces, discrete-
and continuous-time, and introduce two interface operators that map signals, properties
and their satisfaction signals across the two time domains. We show that STL-mx
has the expressive power of STL supplemented with an implicit T-periodic clock
signal. We develop and implement an algorithm for monitoring STL-mx formulas and
illustrate the approach using a mixed-signal example. '
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
citation:
ama: 'Ferrere T, Maler O, Nickovic D. Mixed-time signal temporal logic. In: 17th
International Conference on Formal Modeling and Analysis of Timed Systems.
Vol 11750. Springer Nature; 2019:59-75. doi:10.1007/978-3-030-29662-9_4'
apa: 'Ferrere, T., Maler, O., & Nickovic, D. (2019). Mixed-time signal temporal
logic. In 17th International Conference on Formal Modeling and Analysis of
Timed Systems (Vol. 11750, pp. 59–75). Amsterdam, The Netherlands: Springer
Nature. https://doi.org/10.1007/978-3-030-29662-9_4'
chicago: Ferrere, Thomas, Oded Maler, and Dejan Nickovic. “Mixed-Time Signal Temporal
Logic.” In 17th International Conference on Formal Modeling and Analysis of
Timed Systems, 11750:59–75. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_4.
ieee: T. Ferrere, O. Maler, and D. Nickovic, “Mixed-time signal temporal logic,”
in 17th International Conference on Formal Modeling and Analysis of Timed Systems,
Amsterdam, The Netherlands, 2019, vol. 11750, pp. 59–75.
ista: 'Ferrere T, Maler O, Nickovic D. 2019. Mixed-time signal temporal logic. 17th
International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS:
Formal Modeling and Anaysis of Timed Systems, LNCS, vol. 11750, 59–75.'
mla: Ferrere, Thomas, et al. “Mixed-Time Signal Temporal Logic.” 17th International
Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer
Nature, 2019, pp. 59–75, doi:10.1007/978-3-030-29662-9_4.
short: T. Ferrere, O. Maler, D. Nickovic, in:, 17th International Conference on
Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 59–75.
conference:
end_date: 2019-08-29
location: Amsterdam, The Netherlands
name: 'FORMATS: Formal Modeling and Anaysis of Timed Systems'
start_date: 2019-08-27
date_created: 2020-01-05T23:00:48Z
date_published: 2019-08-13T00:00:00Z
date_updated: 2023-09-06T14:57:17Z
day: '13'
department:
- _id: ToHe
doi: 10.1007/978-3-030-29662-9_4
external_id:
isi:
- '000611677700004'
intvolume: ' 11750'
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 59-75
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 17th International Conference on Formal Modeling and Analysis of Timed
Systems
publication_identifier:
eissn:
- 1611-3349
isbn:
- 978-3-0302-9661-2
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mixed-time signal temporal logic
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11750
year: '2019'
...
---
_id: '7233'
abstract:
- lang: eng
text: We demonstrate electro-optic frequency comb generation using a doubly resonant
system comprising a whispering gallery mode disk resonator made of lithium niobate
mounted inside a three dimensional copper cavity. We observe 180 sidebands centred
at 1550 nm.
article_number: NM2A.5
article_processing_charge: No
author:
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: Florian
full_name: Sedlmeir, Florian
last_name: Sedlmeir
- first_name: Gerd
full_name: Leuchs, Gerd
last_name: Leuchs
- first_name: Madhuri
full_name: Kumari, Madhuri
last_name: Kumari
- first_name: Harald G.L.
full_name: Schwefel, Harald G.L.
last_name: Schwefel
citation:
ama: 'Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. Resonant electro-optic
frequency comb generation in lithium niobate disk resonator inside a microwave
cavity. In: Nonlinear Optics, OSA Technical Digest. Optica Publishing
Group; 2019. doi:10.1364/NLO.2019.NM2A.5'
apa: 'Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kumari, M., & Schwefel,
H. G. L. (2019). Resonant electro-optic frequency comb generation in lithium niobate
disk resonator inside a microwave cavity. In Nonlinear Optics, OSA Technical
Digest. Waikoloa Beach, Hawaii (HI), United States: Optica Publishing Group.
https://doi.org/10.1364/NLO.2019.NM2A.5'
chicago: Rueda Sanchez, Alfredo R, Florian Sedlmeir, Gerd Leuchs, Madhuri Kumari,
and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb Generation in
Lithium Niobate Disk Resonator inside a Microwave Cavity.” In Nonlinear Optics,
OSA Technical Digest. Optica Publishing Group, 2019. https://doi.org/10.1364/NLO.2019.NM2A.5.
ieee: A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, and H. G. L. Schwefel,
“Resonant electro-optic frequency comb generation in lithium niobate disk resonator
inside a microwave cavity,” in Nonlinear Optics, OSA Technical Digest,
Waikoloa Beach, Hawaii (HI), United States, 2019.
ista: 'Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. 2019. Resonant
electro-optic frequency comb generation in lithium niobate disk resonator inside
a microwave cavity. Nonlinear Optics, OSA Technical Digest. NLO: Nonlinear Optics,
NM2A.5.'
mla: Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb Generation
in Lithium Niobate Disk Resonator inside a Microwave Cavity.” Nonlinear Optics,
OSA Technical Digest, NM2A.5, Optica Publishing Group, 2019, doi:10.1364/NLO.2019.NM2A.5.
short: A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, H.G.L. Schwefel, in:,
Nonlinear Optics, OSA Technical Digest, Optica Publishing Group, 2019.
conference:
end_date: 2019-07-19
location: Waikoloa Beach, Hawaii (HI), United States
name: 'NLO: Nonlinear Optics'
start_date: 2019-07-15
date_created: 2020-01-05T23:00:48Z
date_published: 2019-07-15T00:00:00Z
date_updated: 2023-10-17T12:14:46Z
day: '15'
department:
- _id: JoFi
doi: 10.1364/NLO.2019.NM2A.5
language:
- iso: eng
month: '07'
oa_version: None
publication: Nonlinear Optics, OSA Technical Digest
publication_identifier:
isbn:
- '9781557528209'
publication_status: published
publisher: Optica Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: Resonant electro-optic frequency comb generation in lithium niobate disk resonator
inside a microwave cavity
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '73'
abstract:
- lang: eng
text: We consider the space of probability measures on a discrete set X, endowed
with a dynamical optimal transport metric. Given two probability measures supported
in a subset Y⊆X, it is natural to ask whether they can be connected by a constant
speed geodesic with support in Y at all times. Our main result answers this question
affirmatively, under a suitable geometric condition on Y introduced in this paper.
The proof relies on an extension result for subsolutions to discrete Hamilton-Jacobi
equations, which is of independent interest.
article_number: '19'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Matthias
full_name: Erbar, Matthias
last_name: Erbar
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Melchior
full_name: Wirth, Melchior
last_name: Wirth
citation:
ama: Erbar M, Maas J, Wirth M. On the geometry of geodesics in discrete optimal
transport. Calculus of Variations and Partial Differential Equations. 2019;58(1).
doi:10.1007/s00526-018-1456-1
apa: Erbar, M., Maas, J., & Wirth, M. (2019). On the geometry of geodesics in
discrete optimal transport. Calculus of Variations and Partial Differential
Equations. Springer. https://doi.org/10.1007/s00526-018-1456-1
chicago: Erbar, Matthias, Jan Maas, and Melchior Wirth. “On the Geometry of Geodesics
in Discrete Optimal Transport.” Calculus of Variations and Partial Differential
Equations. Springer, 2019. https://doi.org/10.1007/s00526-018-1456-1.
ieee: M. Erbar, J. Maas, and M. Wirth, “On the geometry of geodesics in discrete
optimal transport,” Calculus of Variations and Partial Differential Equations,
vol. 58, no. 1. Springer, 2019.
ista: Erbar M, Maas J, Wirth M. 2019. On the geometry of geodesics in discrete optimal
transport. Calculus of Variations and Partial Differential Equations. 58(1), 19.
mla: Erbar, Matthias, et al. “On the Geometry of Geodesics in Discrete Optimal Transport.”
Calculus of Variations and Partial Differential Equations, vol. 58, no.
1, 19, Springer, 2019, doi:10.1007/s00526-018-1456-1.
short: M. Erbar, J. Maas, M. Wirth, Calculus of Variations and Partial Differential
Equations 58 (2019).
date_created: 2018-12-11T11:44:29Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2023-09-13T09:12:35Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s00526-018-1456-1
ec_funded: 1
external_id:
arxiv:
- '1805.06040'
isi:
- '000452849400001'
file:
- access_level: open_access
checksum: ba05ac2d69de4c58d2cd338b63512798
content_type: application/pdf
creator: dernst
date_created: 2019-01-28T15:37:11Z
date_updated: 2020-07-14T12:47:55Z
file_id: '5895'
file_name: 2018_Calculus_Erbar.pdf
file_size: 645565
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 58'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 260482E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: ' F06504'
name: Taming Complexity in Partial Di erential Systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Calculus of Variations and Partial Differential Equations
publication_identifier:
issn:
- '09442669'
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the geometry of geodesics in discrete optimal transport
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: 58
year: '2019'
...
---
_id: '7340'
abstract:
- lang: eng
text: Coupling of endoplasmic reticulum stress to dimerisation‑dependent activation
of the UPR transducer IRE1 is incompletely understood. Whilst the luminal co-chaperone
ERdj4 promotes a complex between the Hsp70 BiP and IRE1's stress-sensing luminal
domain (IRE1LD) that favours the latter's monomeric inactive state and loss of
ERdj4 de-represses IRE1, evidence linking these cellular and in vitro observations
is presently lacking. We report that enforced loading of endogenous BiP onto endogenous
IRE1α repressed UPR signalling in CHO cells and deletions in the IRE1α locus that
de-repressed the UPR in cells, encode flexible regions of IRE1LD that mediated
BiP‑induced monomerisation in vitro. Changes in the hydrogen exchange mass spectrometry
profile of IRE1LD induced by ERdj4 and BiP confirmed monomerisation and were consistent
with active destabilisation of the IRE1LD dimer. Together, these observations
support a competition model whereby waning ER stress passively partitions ERdj4
and BiP to IRE1LD to initiate active repression of UPR signalling.
acknowledgement: We thank the CIMR flow cytometry core facility team (Reiner Schulte,
Chiara Cossetti and Gabriela Grondys-Kotarba) for assistance with FACS, the Huntington
lab for access to the Octet machine, Steffen Preissler for advice on data interpretation,
Roman Kityk and Nicole Luebbehusen for help and advice with HX-MS experiments.
article_number: e50793
article_processing_charge: No
article_type: original
author:
- first_name: Niko Paresh
full_name: Amin-Wetzel, Niko Paresh
id: E95D3014-9D8C-11E9-9C80-D2F8E5697425
last_name: Amin-Wetzel
- first_name: Lisa
full_name: Neidhardt, Lisa
last_name: Neidhardt
- first_name: Yahui
full_name: Yan, Yahui
last_name: Yan
- first_name: Matthias P.
full_name: Mayer, Matthias P.
last_name: Mayer
- first_name: David
full_name: Ron, David
last_name: Ron
citation:
ama: Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. Unstructured regions in
IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression
of the UPR. eLife. 2019;8. doi:10.7554/eLife.50793
apa: Amin-Wetzel, N. P., Neidhardt, L., Yan, Y., Mayer, M. P., & Ron, D. (2019).
Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal
domain dimer and repression of the UPR. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.50793
chicago: Amin-Wetzel, Niko Paresh, Lisa Neidhardt, Yahui Yan, Matthias P. Mayer,
and David Ron. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation
of the Luminal Domain Dimer and Repression of the UPR.” ELife. eLife Sciences
Publications, 2019. https://doi.org/10.7554/eLife.50793.
ieee: N. P. Amin-Wetzel, L. Neidhardt, Y. Yan, M. P. Mayer, and D. Ron, “Unstructured
regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer
and repression of the UPR,” eLife, vol. 8. eLife Sciences Publications,
2019.
ista: Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. 2019. Unstructured regions
in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and
repression of the UPR. eLife. 8, e50793.
mla: Amin-Wetzel, Niko Paresh, et al. “Unstructured Regions in IRE1α Specify BiP-Mediated
Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife,
vol. 8, e50793, eLife Sciences Publications, 2019, doi:10.7554/eLife.50793.
short: N.P. Amin-Wetzel, L. Neidhardt, Y. Yan, M.P. Mayer, D. Ron, ELife 8 (2019).
date_created: 2020-01-19T23:00:39Z
date_published: 2019-12-24T00:00:00Z
date_updated: 2023-09-06T14:58:02Z
day: '24'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.7554/eLife.50793
external_id:
isi:
- '000512303700001'
pmid:
- '31873072'
file:
- access_level: open_access
checksum: 29fcbcd8c1fc7f11a596ed7f14ea1c82
content_type: application/pdf
creator: dernst
date_created: 2020-11-19T11:37:41Z
date_updated: 2020-11-19T11:37:41Z
file_id: '8777'
file_name: 2019_eLife_AminWetzel.pdf
file_size: 4817384
relation: main_file
success: 1
file_date_updated: 2020-11-19T11:37:41Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal
domain dimer and repression of the UPR
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: '2019'
...
---
_id: '7391'
abstract:
- lang: eng
text: Electron microscopy (EM) is a technology that enables visualization of single
proteins at a nanometer resolution. However, current protein analysis by EM mainly
relies on immunolabeling with gold-particle-conjugated antibodies, which is compromised
by large size of antibody, precluding precise detection of protein location in
biological samples. Here, we develop a specific chemical labeling method for EM
detection of proteins at single-molecular level. Rational design of α-helical
peptide tag and probe structure provided a complementary reaction pair that enabled
specific cysteine conjugation of the tag. The developed chemical labeling with
gold-nanoparticle-conjugated probe showed significantly higher labeling efficiency
and detectability of high-density clusters of tag-fused G protein-coupled receptors
in freeze-fracture replicas compared with immunogold labeling. Furthermore, in
ultrathin sections, the spatial resolution of the chemical labeling was significantly
higher than that of antibody-mediated labeling. These results demonstrate substantial
advantages of the chemical labeling approach for single protein visualization
by EM.
article_processing_charge: No
article_type: original
author:
- first_name: Shigekazu
full_name: Tabata, Shigekazu
id: 4427179E-F248-11E8-B48F-1D18A9856A87
last_name: Tabata
- first_name: Marijo
full_name: Jevtic, Marijo
id: 4BE3BC94-F248-11E8-B48F-1D18A9856A87
last_name: Jevtic
- first_name: Nobutaka
full_name: Kurashige, Nobutaka
last_name: Kurashige
- first_name: Hirokazu
full_name: Fuchida, Hirokazu
last_name: Fuchida
- first_name: Munetsugu
full_name: Kido, Munetsugu
last_name: Kido
- first_name: Kazushi
full_name: Tani, Kazushi
last_name: Tani
- first_name: Naoki
full_name: Zenmyo, Naoki
last_name: Zenmyo
- first_name: Shohei
full_name: Uchinomiya, Shohei
last_name: Uchinomiya
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Makoto
full_name: Itakura, Makoto
last_name: Itakura
- first_name: Itaru
full_name: Hamachi, Itaru
last_name: Hamachi
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Akio
full_name: Ojida, Akio
last_name: Ojida
citation:
ama: Tabata S, Jevtic M, Kurashige N, et al. Electron microscopic detection of single
membrane proteins by a specific chemical labeling. iScience. 2019;22(12):256-268.
doi:10.1016/j.isci.2019.11.025
apa: Tabata, S., Jevtic, M., Kurashige, N., Fuchida, H., Kido, M., Tani, K., … Ojida,
A. (2019). Electron microscopic detection of single membrane proteins by a specific
chemical labeling. IScience. Elsevier. https://doi.org/10.1016/j.isci.2019.11.025
chicago: Tabata, Shigekazu, Marijo Jevtic, Nobutaka Kurashige, Hirokazu Fuchida,
Munetsugu Kido, Kazushi Tani, Naoki Zenmyo, et al. “Electron Microscopic Detection
of Single Membrane Proteins by a Specific Chemical Labeling.” IScience.
Elsevier, 2019. https://doi.org/10.1016/j.isci.2019.11.025.
ieee: S. Tabata et al., “Electron microscopic detection of single membrane
proteins by a specific chemical labeling,” iScience, vol. 22, no. 12. Elsevier,
pp. 256–268, 2019.
ista: Tabata S, Jevtic M, Kurashige N, Fuchida H, Kido M, Tani K, Zenmyo N, Uchinomiya
S, Harada H, Itakura M, Hamachi I, Shigemoto R, Ojida A. 2019. Electron microscopic
detection of single membrane proteins by a specific chemical labeling. iScience.
22(12), 256–268.
mla: Tabata, Shigekazu, et al. “Electron Microscopic Detection of Single Membrane
Proteins by a Specific Chemical Labeling.” IScience, vol. 22, no. 12, Elsevier,
2019, pp. 256–68, doi:10.1016/j.isci.2019.11.025.
short: S. Tabata, M. Jevtic, N. Kurashige, H. Fuchida, M. Kido, K. Tani, N. Zenmyo,
S. Uchinomiya, H. Harada, M. Itakura, I. Hamachi, R. Shigemoto, A. Ojida, IScience
22 (2019) 256–268.
date_created: 2020-01-29T15:56:56Z
date_published: 2019-12-20T00:00:00Z
date_updated: 2024-03-25T23:30:07Z
day: '20'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1016/j.isci.2019.11.025
ec_funded: 1
external_id:
isi:
- :000504652000020
pmid:
- '31786521'
file:
- access_level: open_access
checksum: f3e90056a49f09b205b1c4f8c739ffd1
content_type: application/pdf
creator: dernst
date_created: 2020-02-04T10:48:36Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7448'
file_name: 2019_iScience_Tabata.pdf
file_size: 7197776
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 22'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 256-268
pmid: 1
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
- _id: 25CBA828-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '720270'
name: Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)
publication: iScience
publication_identifier:
issn:
- 2589-0042
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '11393'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Electron microscopic detection of single membrane proteins by a specific chemical
labeling
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: 22
year: '2019'
...
---
_id: '7393'
abstract:
- lang: eng
text: The study of parallel ecological divergence provides important clues to the
operation of natural selection. Parallel divergence often occurs in heterogeneous
environments with different kinds of environmental gradients in different locations,
but the genomic basis underlying this process is unknown. We investigated the
genomics of rapid parallel adaptation in the marine snail Littorina saxatilis
in response to two independent environmental axes (crab-predation versus wave-action
and low-shore versus high-shore). Using pooled whole-genome resequencing, we show
that sharing of genomic regions of high differentiation between environments is
generally low but increases at smaller spatial scales. We identify different shared
genomic regions of divergence for each environmental axis and show that most of
these regions overlap with candidate chromosomal inversions. Several inversion
regions are divergent and polymorphic across many localities. We argue that chromosomal
inversions could store shared variation that fuels rapid parallel adaptation to
heterogeneous environments, possibly as balanced polymorphism shared by adaptive
gene flow.
article_number: eaav9963
article_processing_charge: No
article_type: original
author:
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Tomas
full_name: Larsson, Tomas
last_name: Larsson
- first_name: Marina
full_name: Panova, Marina
last_name: Panova
- 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: 'Morales HE, Faria R, Johannesson K, et al. Genomic architecture of parallel
ecological divergence: Beyond a single environmental contrast. Science Advances.
2019;5(12). doi:10.1126/sciadv.aav9963'
apa: 'Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram,
A. M., & Butlin, R. K. (2019). Genomic architecture of parallel ecological
divergence: Beyond a single environmental contrast. Science Advances. AAAS.
https://doi.org/10.1126/sciadv.aav9963'
chicago: 'Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina
Panova, Anja M Westram, and Roger K. Butlin. “Genomic Architecture of Parallel
Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances.
AAAS, 2019. https://doi.org/10.1126/sciadv.aav9963.'
ieee: 'H. E. Morales et al., “Genomic architecture of parallel ecological
divergence: Beyond a single environmental contrast,” Science Advances,
vol. 5, no. 12. AAAS, 2019.'
ista: 'Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin
RK. 2019. Genomic architecture of parallel ecological divergence: Beyond a single
environmental contrast. Science Advances. 5(12), eaav9963.'
mla: 'Morales, Hernán E., et al. “Genomic Architecture of Parallel Ecological Divergence:
Beyond a Single Environmental Contrast.” Science Advances, vol. 5, no.
12, eaav9963, AAAS, 2019, doi:10.1126/sciadv.aav9963.'
short: H.E. Morales, R. Faria, K. Johannesson, T. Larsson, M. Panova, A.M. Westram,
R.K. Butlin, Science Advances 5 (2019).
date_created: 2020-01-29T15:58:27Z
date_published: 2019-12-04T00:00:00Z
date_updated: 2023-09-06T15:35:56Z
day: '04'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1126/sciadv.aav9963
ec_funded: 1
external_id:
isi:
- '000505069600008'
pmid:
- '31840052'
file:
- access_level: open_access
checksum: af99a5dcdc66c6d6102051faf3be48d8
content_type: application/pdf
creator: dernst
date_created: 2020-02-03T13:33:25Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7442'
file_name: 2019_ScienceAdvances_Morales.pdf
file_size: 1869449
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '12'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Genomic architecture of parallel ecological divergence: Beyond a single environmental
contrast'
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 5
year: '2019'
...
---
_id: '7394'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Yasin
full_name: Dagdas, Yasin
last_name: Dagdas
citation:
ama: 'Benková E, Dagdas Y. Editorial overview: Cell biology in the era of omics?
Current Opinion in Plant Biology. 2019;52(12):A1-A2. doi:10.1016/j.pbi.2019.11.002'
apa: 'Benková, E., & Dagdas, Y. (2019). Editorial overview: Cell biology in
the era of omics? Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2019.11.002'
chicago: 'Benková, Eva, and Yasin Dagdas. “Editorial Overview: Cell Biology in the
Era of Omics?” Current Opinion in Plant Biology. Elsevier, 2019. https://doi.org/10.1016/j.pbi.2019.11.002.'
ieee: 'E. Benková and Y. Dagdas, “Editorial overview: Cell biology in the era of
omics?,” Current Opinion in Plant Biology, vol. 52, no. 12. Elsevier, pp.
A1–A2, 2019.'
ista: 'Benková E, Dagdas Y. 2019. Editorial overview: Cell biology in the era of
omics? Current Opinion in Plant Biology. 52(12), A1–A2.'
mla: 'Benková, Eva, and Yasin Dagdas. “Editorial Overview: Cell Biology in the Era
of Omics?” Current Opinion in Plant Biology, vol. 52, no. 12, Elsevier,
2019, pp. A1–2, doi:10.1016/j.pbi.2019.11.002.'
short: E. Benková, Y. Dagdas, Current Opinion in Plant Biology 52 (2019) A1–A2.
date_created: 2020-01-29T16:00:07Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-09-07T14:56:55Z
day: '01'
department:
- _id: EvBe
doi: 10.1016/j.pbi.2019.11.002
external_id:
isi:
- '000502890600001'
pmid:
- '31787165'
intvolume: ' 52'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: A1-A2
pmid: 1
publication: Current Opinion in Plant Biology
publication_identifier:
issn:
- 1369-5266
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Editorial overview: Cell biology in the era of omics?'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 52
year: '2019'
...
---
_id: '7395'
abstract:
- lang: eng
text: The mitochondrial electron transport chain complexes are organized into supercomplexes
(SCs) of defined stoichiometry, which have been proposed to regulate electron
flux via substrate channeling. We demonstrate that CoQ trapping in the isolated
SC I+III2 limits complex (C)I turnover, arguing against channeling. The SC structure,
resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may
be rate limiting because of unequal access of CoQ to the active sites of CIII2.
CI shows a transition between “closed” and “open” conformations, accompanied by
the striking rotation of a key transmembrane helix. Furthermore, the state of
CI affects the conformational flexibility within CIII2, demonstrating crosstalk
between the enzymes. CoQ was identified at only three of the four binding sites
in CIII2, suggesting that interaction with CI disrupts CIII2 symmetry in a functionally
relevant manner. Together, these observations indicate a more nuanced functional
role for the SCs.
article_processing_charge: No
article_type: original
author:
- first_name: James A
full_name: Letts, James A
id: 322DA418-F248-11E8-B48F-1D18A9856A87
last_name: Letts
orcid: 0000-0002-9864-3586
- first_name: Karol
full_name: Fiedorczuk, Karol
id: 5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0
last_name: Fiedorczuk
- first_name: Gianluca
full_name: Degliesposti, Gianluca
last_name: Degliesposti
- first_name: Mark
full_name: Skehel, Mark
last_name: Skehel
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. Structures of
respiratory supercomplex I+III2 reveal functional and conformational crosstalk.
Molecular Cell. 2019;75(6):1131-1146.e6. doi:10.1016/j.molcel.2019.07.022
apa: Letts, J. A., Fiedorczuk, K., Degliesposti, G., Skehel, M., & Sazanov,
L. A. (2019). Structures of respiratory supercomplex I+III2 reveal functional
and conformational crosstalk. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2019.07.022
chicago: Letts, James A, Karol Fiedorczuk, Gianluca Degliesposti, Mark Skehel, and
Leonid A Sazanov. “Structures of Respiratory Supercomplex I+III2 Reveal Functional
and Conformational Crosstalk.” Molecular Cell. Cell Press, 2019. https://doi.org/10.1016/j.molcel.2019.07.022.
ieee: J. A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, and L. A. Sazanov,
“Structures of respiratory supercomplex I+III2 reveal functional and conformational
crosstalk,” Molecular Cell, vol. 75, no. 6. Cell Press, p. 1131–1146.e6,
2019.
ista: Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. 2019. Structures
of respiratory supercomplex I+III2 reveal functional and conformational crosstalk.
Molecular Cell. 75(6), 1131–1146.e6.
mla: Letts, James A., et al. “Structures of Respiratory Supercomplex I+III2 Reveal
Functional and Conformational Crosstalk.” Molecular Cell, vol. 75, no.
6, Cell Press, 2019, p. 1131–1146.e6, doi:10.1016/j.molcel.2019.07.022.
short: J.A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, L.A. Sazanov, Molecular
Cell 75 (2019) 1131–1146.e6.
date_created: 2020-01-29T16:02:33Z
date_published: 2019-09-19T00:00:00Z
date_updated: 2023-09-07T14:53:06Z
day: '19'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1016/j.molcel.2019.07.022
ec_funded: 1
external_id:
isi:
- '000486614200006'
pmid:
- '31492636'
file:
- access_level: open_access
checksum: 5202f53a237d6650ece038fbf13bdcea
content_type: application/pdf
creator: dernst
date_created: 2020-02-04T10:37:28Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7447'
file_name: 2019_MolecularCell_Letts.pdf
file_size: 9654895
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 75'
isi: 1
issue: '6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1131-1146.e6
pmid: 1
project:
- _id: 2590DB08-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '701309'
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
publication: Molecular Cell
publication_identifier:
issn:
- 1097-2765
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structures of respiratory supercomplex I+III2 reveal functional and conformational
crosstalk
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: 75
year: '2019'
...
---
_id: '7396'
abstract:
- lang: eng
text: The angular momentum of molecules, or, equivalently, their rotation in three-dimensional
space, is ideally suited for quantum control. Molecular angular momentum is naturally
quantized, time evolution is governed by a well-known Hamiltonian with only a
few accurately known parameters, and transitions between rotational levels can
be driven by external fields from various parts of the electromagnetic spectrum.
Control over the rotational motion can be exerted in one-, two-, and many-body
scenarios, thereby allowing one to probe Anderson localization, target stereoselectivity
of bimolecular reactions, or encode quantum information to name just a few examples.
The corresponding approaches to quantum control are pursued within separate, and
typically disjoint, subfields of physics, including ultrafast science, cold collisions,
ultracold gases, quantum information science, and condensed-matter physics. It
is the purpose of this review to present the various control phenomena, which
all rely on the same underlying physics, within a unified framework. To this end,
recall the Hamiltonian for free rotations, assuming the rigid rotor approximation
to be valid, and summarize the different ways for a rotor to interact with external
electromagnetic fields. These interactions can be exploited for control—from achieving
alignment, orientation, or laser cooling in a one-body framework, steering bimolecular
collisions, or realizing a quantum computer or quantum simulator in the many-body
setting.
article_number: '035005 '
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Christiane P.
full_name: Koch, Christiane P.
last_name: Koch
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Dominique
full_name: Sugny, Dominique
last_name: Sugny
citation:
ama: Koch CP, Lemeshko M, Sugny D. Quantum control of molecular rotation. Reviews
of Modern Physics. 2019;91(3). doi:10.1103/revmodphys.91.035005
apa: Koch, C. P., Lemeshko, M., & Sugny, D. (2019). Quantum control of molecular
rotation. Reviews of Modern Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.035005
chicago: Koch, Christiane P., Mikhail Lemeshko, and Dominique Sugny. “Quantum Control
of Molecular Rotation.” Reviews of Modern Physics. American Physical Society,
2019. https://doi.org/10.1103/revmodphys.91.035005.
ieee: C. P. Koch, M. Lemeshko, and D. Sugny, “Quantum control of molecular rotation,”
Reviews of Modern Physics, vol. 91, no. 3. American Physical Society, 2019.
ista: Koch CP, Lemeshko M, Sugny D. 2019. Quantum control of molecular rotation.
Reviews of Modern Physics. 91(3), 035005.
mla: Koch, Christiane P., et al. “Quantum Control of Molecular Rotation.” Reviews
of Modern Physics, vol. 91, no. 3, 035005, American Physical Society, 2019,
doi:10.1103/revmodphys.91.035005.
short: C.P. Koch, M. Lemeshko, D. Sugny, Reviews of Modern Physics 91 (2019).
date_created: 2020-01-29T16:04:19Z
date_published: 2019-09-18T00:00:00Z
date_updated: 2024-02-28T13:15:33Z
day: '18'
department:
- _id: MiLe
doi: 10.1103/revmodphys.91.035005
external_id:
arxiv:
- '1810.11338'
isi:
- '000486661700001'
intvolume: ' 91'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1810.11338
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Reviews of Modern Physics
publication_identifier:
eissn:
- 1539-0756
issn:
- 0034-6861
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum control of molecular rotation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2019'
...
---
_id: '7397'
abstract:
- lang: eng
text: Polymer additives can substantially reduce the drag of turbulent flows and
the upperlimit, the so called “maximum drag reduction” (MDR) asymptote is universal,
i.e. inde-pendent of the type of polymer and solvent used. Until recently, the
consensus was that,in this limit, flows are in a marginal state where only a minimal
level of turbulence activ-ity persists. Observations in direct numerical simulations
using minimal sized channelsappeared to support this view and reported long “hibernation” periods where turbu-lence
is marginalized. In simulations of pipe flow we find that, indeed, with increasingWeissenberg
number (Wi), turbulence expresses long periods of hibernation if the domainsize
is small. However, with increasing pipe length, the temporal hibernation continuouslyalters
to spatio-temporal intermittency and here the flow consists of turbulent puffs
sur-rounded by laminar flow. Moreover, upon an increase in Wi, the flow fully
relaminarises,in agreement with recent experiments. At even larger Wi, a different
instability is en-countered causing a drag increase towards MDR. Our findings
hence link earlier minimalflow unit simulations with recent experiments and confirm
that the addition of polymersinitially suppresses Newtonian turbulence and leads
to a reverse transition. The MDRstate on the other hand results from a separate
instability and the underlying dynamicscorresponds to the recently proposed state
of elasto-inertial-turbulence (EIT).
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: George H
full_name: Choueiri, George H
id: 448BD5BC-F248-11E8-B48F-1D18A9856A87
last_name: Choueiri
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Lopez Alonso JM, Choueiri GH, Hof B. Dynamics of viscoelastic pipe flow at
low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid
Mechanics. 2019;874:699-719. doi:10.1017/jfm.2019.486
apa: Lopez Alonso, J. M., Choueiri, G. H., & Hof, B. (2019). Dynamics of viscoelastic
pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal
of Fluid Mechanics. CUP. https://doi.org/10.1017/jfm.2019.486
chicago: Lopez Alonso, Jose M, George H Choueiri, and Björn Hof. “Dynamics of Viscoelastic
Pipe Flow at Low Reynolds Numbers in the Maximum Drag Reduction Limit.” Journal
of Fluid Mechanics. CUP, 2019. https://doi.org/10.1017/jfm.2019.486.
ieee: J. M. Lopez Alonso, G. H. Choueiri, and B. Hof, “Dynamics of viscoelastic
pipe flow at low Reynolds numbers in the maximum drag reduction limit,” Journal
of Fluid Mechanics, vol. 874. CUP, pp. 699–719, 2019.
ista: Lopez Alonso JM, Choueiri GH, Hof B. 2019. Dynamics of viscoelastic pipe flow
at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid
Mechanics. 874, 699–719.
mla: Lopez Alonso, Jose M., et al. “Dynamics of Viscoelastic Pipe Flow at Low Reynolds
Numbers in the Maximum Drag Reduction Limit.” Journal of Fluid Mechanics,
vol. 874, CUP, 2019, pp. 699–719, doi:10.1017/jfm.2019.486.
short: J.M. Lopez Alonso, G.H. Choueiri, B. Hof, Journal of Fluid Mechanics 874
(2019) 699–719.
date_created: 2020-01-29T16:05:19Z
date_published: 2019-09-10T00:00:00Z
date_updated: 2023-09-06T15:36:36Z
day: '10'
department:
- _id: BjHo
doi: 10.1017/jfm.2019.486
external_id:
arxiv:
- '1808.04080'
isi:
- '000475349900001'
intvolume: ' 874'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.04080
month: '09'
oa: 1
oa_version: Preprint
page: 699-719
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- 1469-7645
issn:
- 0022-1120
publication_status: published
publisher: CUP
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag
reduction limit
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 874
year: '2019'
...
---
_id: '7398'
abstract:
- lang: eng
text: 'Transporters of the solute carrier 6 (SLC6) family translocate their cognate
substrate together with Na+ and Cl−. Detailed kinetic models exist for the transporters
of GABA (GAT1/SLC6A1) and the monoamines dopamine (DAT/SLC6A3) and serotonin (SERT/SLC6A4).
Here, we posited that the transport cycle of individual SLC6 transporters reflects
the physiological requirements they operate under. We tested this hypothesis by
analyzing the transport cycle of glycine transporter 1 (GlyT1/SLC6A9) and glycine
transporter 2 (GlyT2/SLC6A5). GlyT2 is the only SLC6 family member known to translocate
glycine, Na+, and Cl− in a 1:3:1 stoichiometry. We analyzed partial reactions
in real time by electrophysiological recordings. Contrary to monoamine transporters,
both GlyTs were found to have a high transport capacity driven by rapid return
of the empty transporter after release of Cl− on the intracellular side. Rapid
cycling of both GlyTs was further supported by highly cooperative binding of cosubstrate
ions and substrate such that their forward transport mode was maintained even
under conditions of elevated intracellular Na+ or Cl−. The most important differences
in the transport cycle of GlyT1 and GlyT2 arose from the kinetics of charge movement
and the resulting voltage-dependent rate-limiting reactions: the kinetics of GlyT1
were governed by transition of the substrate-bound transporter from outward- to
inward-facing conformations, whereas the kinetics of GlyT2 were governed by Na+
binding (or a related conformational change). Kinetic modeling showed that the
kinetics of GlyT1 are ideally suited for supplying the extracellular glycine levels
required for NMDA receptor activation.'
article_processing_charge: No
article_type: original
author:
- first_name: Fatma Asli
full_name: Erdem, Fatma Asli
last_name: Erdem
- first_name: Marija
full_name: Ilic, Marija
last_name: Ilic
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Jakub
full_name: Gołacki, Jakub
last_name: Gołacki
- first_name: Gert
full_name: Lubec, Gert
last_name: Lubec
- first_name: Michael
full_name: Freissmuth, Michael
last_name: Freissmuth
- first_name: Walter
full_name: Sandtner, Walter
last_name: Sandtner
citation:
ama: Erdem FA, Ilic M, Koppensteiner P, et al. A comparison of the transport kinetics
of glycine transporter 1 and glycine transporter 2. The Journal of General
Physiology. 2019;151(8):1035-1050. doi:10.1085/jgp.201912318
apa: Erdem, F. A., Ilic, M., Koppensteiner, P., Gołacki, J., Lubec, G., Freissmuth,
M., & Sandtner, W. (2019). A comparison of the transport kinetics of glycine
transporter 1 and glycine transporter 2. The Journal of General Physiology.
Rockefeller University Press. https://doi.org/10.1085/jgp.201912318
chicago: Erdem, Fatma Asli, Marija Ilic, Peter Koppensteiner, Jakub Gołacki, Gert
Lubec, Michael Freissmuth, and Walter Sandtner. “A Comparison of the Transport
Kinetics of Glycine Transporter 1 and Glycine Transporter 2.” The Journal of
General Physiology. Rockefeller University Press, 2019. https://doi.org/10.1085/jgp.201912318.
ieee: F. A. Erdem et al., “A comparison of the transport kinetics of glycine
transporter 1 and glycine transporter 2,” The Journal of General Physiology,
vol. 151, no. 8. Rockefeller University Press, pp. 1035–1050, 2019.
ista: Erdem FA, Ilic M, Koppensteiner P, Gołacki J, Lubec G, Freissmuth M, Sandtner
W. 2019. A comparison of the transport kinetics of glycine transporter 1 and glycine
transporter 2. The Journal of General Physiology. 151(8), 1035–1050.
mla: Erdem, Fatma Asli, et al. “A Comparison of the Transport Kinetics of Glycine
Transporter 1 and Glycine Transporter 2.” The Journal of General Physiology,
vol. 151, no. 8, Rockefeller University Press, 2019, pp. 1035–50, doi:10.1085/jgp.201912318.
short: F.A. Erdem, M. Ilic, P. Koppensteiner, J. Gołacki, G. Lubec, M. Freissmuth,
W. Sandtner, The Journal of General Physiology 151 (2019) 1035–1050.
date_created: 2020-01-29T16:06:29Z
date_published: 2019-07-03T00:00:00Z
date_updated: 2023-09-07T14:52:23Z
day: '03'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1085/jgp.201912318
external_id:
isi:
- '000478792500008'
pmid:
- '31270129'
file:
- access_level: open_access
checksum: 5706b4ccd74ee3e50bf7ecb2a203df71
content_type: application/pdf
creator: dernst
date_created: 2020-02-05T07:20:32Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7450'
file_name: 2019_JGP_Erdem.pdf
file_size: 2641297
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 151'
isi: 1
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 1035-1050
pmid: 1
publication: The Journal of General Physiology
publication_identifier:
eissn:
- 1540-7748
issn:
- 0022-1295
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: A comparison of the transport kinetics of glycine transporter 1 and glycine
transporter 2
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 151
year: '2019'
...
---
_id: '7399'
abstract:
- lang: eng
text: Long non-coding (lnc) RNAs are numerous and found throughout the mammalian
genome, and many are thought to be involved in the regulation of gene expression.
However, the majority remain relatively uncharacterised and of uncertain function
making the use of model systems to uncover their mode of action valuable. Imprinted
lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted
genes on the same chromosome, making them one of the best characterized lncRNAs
for silencing distant genes in cis. In this study we examined silencing of the
distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster
in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted
genes by disrupting promoter-enhancer interactions by being transcribed through
the enhancer, which we called the enhancer interference hypothesis. Here we tested
this hypothesis by first using allele-specific chromosome conformation capture
(3C) to detect interactions between the Slc22a3 promoter and the locus of the
Airn lncRNA that silences it on the paternal chromosome. In agreement with the
model, we found interactions enriched on the maternal allele across the entire
Airn gene consistent with multiple enhancer-promoter interactions. Therefore,
to test the enhancer interference hypothesis we devised an approach to delete
the entire Airn gene. However, the deletion showed that there are no essential
enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating
that the Airn RNA rather than its transcription is responsible for silencing distant
imprinted genes. Furthermore, we found that silent imprinted genes were covered
with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose
an alternative hypothesis whereby the chromosome interactions may initially guide
the lncRNA to target imprinted promoters and recruit repressive chromatin, and
that these interactions are lost once silencing is established.
article_number: e1008268
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Andergassen, Daniel
last_name: Andergassen
- first_name: Markus
full_name: Muckenhuber, Markus
last_name: Muckenhuber
- first_name: Philipp C.
full_name: Bammer, Philipp C.
last_name: Bammer
- first_name: Tomasz M.
full_name: Kulinski, Tomasz M.
last_name: Kulinski
- first_name: Hans-Christian
full_name: Theussl, Hans-Christian
last_name: Theussl
- first_name: Takahiko
full_name: Shimizu, Takahiko
last_name: Shimizu
- first_name: Josef M.
full_name: Penninger, Josef M.
last_name: Penninger
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Quanah J.
full_name: Hudson, Quanah J.
last_name: Hudson
citation:
ama: Andergassen D, Muckenhuber M, Bammer PC, et al. The Airn lncRNA does not require
any DNA elements within its locus to silence distant imprinted genes. PLoS
Genetics. 2019;15(7). doi:10.1371/journal.pgen.1008268
apa: Andergassen, D., Muckenhuber, M., Bammer, P. C., Kulinski, T. M., Theussl,
H.-C., Shimizu, T., … Hudson, Q. J. (2019). The Airn lncRNA does not require any
DNA elements within its locus to silence distant imprinted genes. PLoS Genetics.
Public Library of Science. https://doi.org/10.1371/journal.pgen.1008268
chicago: Andergassen, Daniel, Markus Muckenhuber, Philipp C. Bammer, Tomasz M. Kulinski,
Hans-Christian Theussl, Takahiko Shimizu, Josef M. Penninger, Florian Pauler,
and Quanah J. Hudson. “The Airn LncRNA Does Not Require Any DNA Elements within
Its Locus to Silence Distant Imprinted Genes.” PLoS Genetics. Public Library
of Science, 2019. https://doi.org/10.1371/journal.pgen.1008268.
ieee: D. Andergassen et al., “The Airn lncRNA does not require any DNA elements
within its locus to silence distant imprinted genes,” PLoS Genetics, vol.
15, no. 7. Public Library of Science, 2019.
ista: Andergassen D, Muckenhuber M, Bammer PC, Kulinski TM, Theussl H-C, Shimizu
T, Penninger JM, Pauler F, Hudson QJ. 2019. The Airn lncRNA does not require any
DNA elements within its locus to silence distant imprinted genes. PLoS Genetics.
15(7), e1008268.
mla: Andergassen, Daniel, et al. “The Airn LncRNA Does Not Require Any DNA Elements
within Its Locus to Silence Distant Imprinted Genes.” PLoS Genetics, vol.
15, no. 7, e1008268, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008268.
short: D. Andergassen, M. Muckenhuber, P.C. Bammer, T.M. Kulinski, H.-C. Theussl,
T. Shimizu, J.M. Penninger, F. Pauler, Q.J. Hudson, PLoS Genetics 15 (2019).
date_created: 2020-01-29T16:14:07Z
date_published: 2019-07-22T00:00:00Z
date_updated: 2023-10-17T12:30:27Z
day: '22'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1371/journal.pgen.1008268
external_id:
isi:
- '000478689100025'
pmid:
- '31329595'
file:
- access_level: open_access
checksum: 2f51fc91e4a4199827adc51d432ad864
content_type: application/pdf
creator: dernst
date_created: 2020-02-04T10:11:55Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7446'
file_name: 2019_PlosGenetics_Andergassen.pdf
file_size: 2302307
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Airn lncRNA does not require any DNA elements within its locus to silence
distant imprinted genes
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: 15
year: '2019'
...
---
_id: '7400'
abstract:
- lang: eng
text: 'Suppressed recombination allows divergence between homologous sex chromosomes
and the functionality of their genes. Here, we reveal patterns of the earliest
stages of sex-chromosome evolution in the diploid dioecious herb Mercurialis annua
on the basis of cytological analysis, de novo genome assembly and annotation,
genetic mapping, exome resequencing of natural populations, and transcriptome
analysis. The genome assembly contained 34,105 expressed genes, of which 10,076
were assigned to linkage groups. Genetic mapping and exome resequencing of individuals
across the species range both identified the largest linkage group, LG1, as the
sex chromosome. Although the sex chromosomes of M. annua are karyotypically homomorphic,
we estimate that about one-third of the Y chromosome, containing 568 transcripts
and spanning 22.3 cM in the corresponding female map, has ceased recombining.
Nevertheless, we found limited evidence for Y-chromosome degeneration in terms
of gene loss and pseudogenization, and most X- and Y-linked genes appear to have
diverged in the period subsequent to speciation between M. annua and its sister
species M. huetii, which shares the same sex-determining region. Taken together,
our results suggest that the M. annua Y chromosome has at least two evolutionary
strata: a small old stratum shared with M. huetii, and a more recent larger stratum
that is probably unique to M. annua and that stopped recombining ∼1 MYA. Patterns
of gene expression within the nonrecombining region are consistent with the idea
that sexually antagonistic selection may have played a role in favoring suppressed
recombination.'
article_processing_charge: No
article_type: original
author:
- first_name: Paris
full_name: Veltsos, Paris
last_name: Veltsos
- first_name: Kate E.
full_name: Ridout, Kate E.
last_name: Ridout
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Santiago C.
full_name: González-Martínez, Santiago C.
last_name: González-Martínez
- first_name: Aline
full_name: Muyle, Aline
last_name: Muyle
- first_name: Olivier
full_name: Emery, Olivier
last_name: Emery
- first_name: Pasi
full_name: Rastas, Pasi
last_name: Rastas
- first_name: Vojtech
full_name: Hudzieczek, Vojtech
last_name: Hudzieczek
- first_name: Roman
full_name: Hobza, Roman
last_name: Hobza
- first_name: Boris
full_name: Vyskot, Boris
last_name: Vyskot
- first_name: Gabriel A. B.
full_name: Marais, Gabriel A. B.
last_name: Marais
- first_name: Dmitry A.
full_name: Filatov, Dmitry A.
last_name: Filatov
- first_name: John R.
full_name: Pannell, John R.
last_name: Pannell
citation:
ama: Veltsos P, Ridout KE, Toups MA, et al. Early sex-chromosome evolution in the
diploid dioecious plant Mercurialis annua. Genetics. 2019;212(3):815-835.
doi:10.1534/genetics.119.302045
apa: Veltsos, P., Ridout, K. E., Toups, M. A., González-Martínez, S. C., Muyle,
A., Emery, O., … Pannell, J. R. (2019). Early sex-chromosome evolution in the
diploid dioecious plant Mercurialis annua. Genetics. Genetics Society of
America. https://doi.org/10.1534/genetics.119.302045
chicago: Veltsos, Paris, Kate E. Ridout, Melissa A Toups, Santiago C. González-Martínez,
Aline Muyle, Olivier Emery, Pasi Rastas, et al. “Early Sex-Chromosome Evolution
in the Diploid Dioecious Plant Mercurialis Annua.” Genetics. Genetics Society
of America, 2019. https://doi.org/10.1534/genetics.119.302045.
ieee: P. Veltsos et al., “Early sex-chromosome evolution in the diploid dioecious
plant Mercurialis annua,” Genetics, vol. 212, no. 3. Genetics Society of
America, pp. 815–835, 2019.
ista: Veltsos P, Ridout KE, Toups MA, González-Martínez SC, Muyle A, Emery O, Rastas
P, Hudzieczek V, Hobza R, Vyskot B, Marais GAB, Filatov DA, Pannell JR. 2019.
Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua.
Genetics. 212(3), 815–835.
mla: Veltsos, Paris, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious
Plant Mercurialis Annua.” Genetics, vol. 212, no. 3, Genetics Society of
America, 2019, pp. 815–35, doi:10.1534/genetics.119.302045.
short: P. Veltsos, K.E. Ridout, M.A. Toups, S.C. González-Martínez, A. Muyle, O.
Emery, P. Rastas, V. Hudzieczek, R. Hobza, B. Vyskot, G.A.B. Marais, D.A. Filatov,
J.R. Pannell, Genetics 212 (2019) 815–835.
date_created: 2020-01-29T16:15:44Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-09-07T14:49:29Z
day: '01'
department:
- _id: BeVi
doi: 10.1534/genetics.119.302045
ec_funded: 1
external_id:
isi:
- '000474809300015'
pmid:
- '31113811'
intvolume: ' 212'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1534/genetics.119.302045
month: '07'
oa: 1
oa_version: Published Version
page: 815-835
pmid: 1
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genetics
publication_identifier:
eissn:
- 1943-2631
issn:
- 0016-6731
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
scopus_import: '1'
status: public
title: Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 212
year: '2019'
...
---
_id: '7401'
abstract:
- lang: eng
text: 'The genus g(G) of a graph G is the minimum g such that G has an embedding
on the orientable surface M_g of genus g. A drawing of a graph on a surface is
independently even if every pair of nonadjacent edges in the drawing crosses an
even number of times. The Z_2-genus of a graph G, denoted by g_0(G), is the minimum
g such that G has an independently even drawing on M_g. By a result of Battle,
Harary, Kodama and Youngs from 1962, the graph genus is additive over 2-connected
blocks. In 2013, Schaefer and Stefankovic proved that the Z_2-genus of a graph
is additive over 2-connected blocks as well, and asked whether this result can
be extended to so-called 2-amalgamations, as an analogue of results by Decker,
Glover, Huneke, and Stahl for the genus. We give the following partial answer.
If G=G_1 cup G_2, G_1 and G_2 intersect in two vertices u and v, and G-u-v has
k connected components (among which we count the edge uv if present), then |g_0(G)-(g_0(G_1)+g_0(G_2))|<=k+1.
For complete bipartite graphs K_{m,n}, with n >= m >= 3, we prove that g_0(K_{m,n})/g(K_{m,n})=1-O(1/n).
Similar results are proved also for the Euler Z_2-genus. We express the Z_2-genus
of a graph using the minimum rank of partial symmetric matrices over Z_2; a problem
that might be of independent interest. '
alternative_title:
- LIPIcs
article_number: '39'
article_processing_charge: No
arxiv: 1
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Jan
full_name: Kyncl, Jan
last_name: Kyncl
citation:
ama: 'Fulek R, Kyncl J. Z_2-Genus of graphs and minimum rank of partial symmetric
matrices. In: 35th International Symposium on Computational Geometry (SoCG
2019). Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.SOCG.2019.39'
apa: 'Fulek, R., & Kyncl, J. (2019). Z_2-Genus of graphs and minimum rank of
partial symmetric matrices. In 35th International Symposium on Computational
Geometry (SoCG 2019) (Vol. 129). Portland, OR, United States: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.39'
chicago: Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of
Partial Symmetric Matrices.” In 35th International Symposium on Computational
Geometry (SoCG 2019), Vol. 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2019. https://doi.org/10.4230/LIPICS.SOCG.2019.39.
ieee: R. Fulek and J. Kyncl, “Z_2-Genus of graphs and minimum rank of partial symmetric
matrices,” in 35th International Symposium on Computational Geometry (SoCG
2019), Portland, OR, United States, 2019, vol. 129.
ista: 'Fulek R, Kyncl J. 2019. Z_2-Genus of graphs and minimum rank of partial symmetric
matrices. 35th International Symposium on Computational Geometry (SoCG 2019).
SoCG: Symposium on Computational Geometry, LIPIcs, vol. 129, 39.'
mla: Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of Partial
Symmetric Matrices.” 35th International Symposium on Computational Geometry
(SoCG 2019), vol. 129, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2019, doi:10.4230/LIPICS.SOCG.2019.39.
short: R. Fulek, J. Kyncl, in:, 35th International Symposium on Computational Geometry
(SoCG 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.
conference:
end_date: 2019-06-21
location: Portland, OR, United States
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2019-06-18
date_created: 2020-01-29T16:17:05Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2021-01-12T08:13:24Z
day: '01'
ddc:
- '000'
department:
- _id: UlWa
doi: 10.4230/LIPICS.SOCG.2019.39
external_id:
arxiv:
- '1903.08637'
file:
- access_level: open_access
checksum: aac37b09118cc0ab58cf77129e691f8c
content_type: application/pdf
creator: dernst
date_created: 2020-02-04T09:14:31Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7445'
file_name: 2019_LIPIcs_Fulek.pdf
file_size: 628347
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 129'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication: 35th International Symposium on Computational Geometry (SoCG 2019)
publication_identifier:
isbn:
- 978-3-95977-104-7
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Z_2-Genus of graphs and minimum rank of partial symmetric matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2019'
...
---
_id: '7402'
abstract:
- lang: eng
text: Graph planning gives rise to fundamental algorithmic questions such as shortest
path, traveling salesman problem, etc. A classical problem in discrete planning
is to consider a weighted graph and construct a path that maximizes the sum of
weights for a given time horizon T. However, in many scenarios, the time horizon
is not fixed, but the stopping time is chosen according to some distribution such
that the expected stopping time is T. If the stopping time distribution is not
known, then to ensure robustness, the distribution is chosen by an adversary,
to represent the worst-case scenario. A stationary plan for every vertex always
chooses the same outgoing edge. For fixed horizon or fixed stopping-time distribution,
stationary plans are not sufficient for optimality. Quite surprisingly we show
that when an adversary chooses the stopping-time distribution with expected stopping
time T, then stationary plans are sufficient. While computing optimal stationary
plans for fixed horizon is NP-complete, we show that computing optimal stationary
plans under adversarial stopping-time distribution can be achieved in polynomial
time. Consequently, our polynomial-time algorithm for adversarial stopping time
also computes an optimal plan among all possible plans.
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: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: 'Chatterjee K, Doyen L. Graph planning with expected finite horizon. In: 34th
Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE; 2019:1-13. doi:10.1109/lics.2019.8785706'
apa: 'Chatterjee, K., & Doyen, L. (2019). Graph planning with expected finite
horizon. In 34th Annual ACM/IEEE Symposium on Logic in Computer Science
(pp. 1–13). Vancouver, BC, Canada: IEEE. https://doi.org/10.1109/lics.2019.8785706'
chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected
Finite Horizon.” In 34th Annual ACM/IEEE Symposium on Logic in Computer Science,
1–13. IEEE, 2019. https://doi.org/10.1109/lics.2019.8785706.
ieee: K. Chatterjee and L. Doyen, “Graph planning with expected finite horizon,”
in 34th Annual ACM/IEEE Symposium on Logic in Computer Science, Vancouver,
BC, Canada, 2019, pp. 1–13.
ista: 'Chatterjee K, Doyen L. 2019. Graph planning with expected finite horizon.
34th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on
Logic in Computer Science, 1–13.'
mla: Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite
Horizon.” 34th Annual ACM/IEEE Symposium on Logic in Computer Science,
IEEE, 2019, pp. 1–13, doi:10.1109/lics.2019.8785706.
short: K. Chatterjee, L. Doyen, in:, 34th Annual ACM/IEEE Symposium on Logic in
Computer Science, IEEE, 2019, pp. 1–13.
conference:
end_date: 2019-06-27
location: Vancouver, BC, Canada
name: 'LICS: Symposium on Logic in Computer Science'
start_date: 2019-06-24
date_created: 2020-01-29T16:18:33Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2025-07-14T09:09:54Z
day: '01'
department:
- _id: KrCh
doi: 10.1109/lics.2019.8785706
external_id:
arxiv:
- '1802.03642'
isi:
- '000805002800001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.03642
month: '06'
oa: 1
oa_version: Preprint
page: 1-13
publication: 34th Annual ACM/IEEE Symposium on Logic in Computer Science
publication_identifier:
isbn:
- '9781728136080'
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '11402'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Graph planning with expected finite horizon
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...