---
_id: '7360'
abstract:
- lang: eng
text: Inflammation, which is a highly regulated host response against danger signals,
may be harmful if it is excessive and deregulated. Ideally, anti-inflammatory
therapy should autonomously commence as soon as possible after the onset of inflammation,
should be controllable by a physician, and should not systemically block beneficial
immune response in the long term. We describe a genetically encoded anti-inflammatory
mammalian cell device based on a modular engineered genetic circuit comprising
a sensor, an amplifier, a “thresholder” to restrict activation of a positive-feedback
loop, a combination of advanced clinically used biopharmaceutical proteins, and
orthogonal regulatory elements that linked modules into the functional device.
This genetic circuit was autonomously activated by inflammatory signals, including
endogenous cecal ligation and puncture (CLP)-induced inflammation in mice and
serum from a systemic juvenile idiopathic arthritis (sIJA) patient, and could
be reset externally by a chemical signal. The microencapsulated anti-inflammatory
device significantly reduced the pathology in dextran sodium sulfate (DSS)-induced
acute murine colitis, demonstrating a synthetic immunological approach for autonomous
anti-inflammatory therapy.
article_processing_charge: No
article_type: original
author:
- first_name: Anže
full_name: Smole, Anže
last_name: Smole
- first_name: Duško
full_name: Lainšček, Duško
last_name: Lainšček
- first_name: Urban
full_name: Bezeljak, Urban
id: 2A58201A-F248-11E8-B48F-1D18A9856A87
last_name: Bezeljak
orcid: 0000-0003-1365-5631
- first_name: Simon
full_name: Horvat, Simon
last_name: Horvat
- first_name: Roman
full_name: Jerala, Roman
last_name: Jerala
citation:
ama: Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. A synthetic mammalian
therapeutic gene circuit for sensing and suppressing inflammation. Molecular
Therapy. 2017;25(1):102-119. doi:10.1016/j.ymthe.2016.10.005
apa: Smole, A., Lainšček, D., Bezeljak, U., Horvat, S., & Jerala, R. (2017).
A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation.
Molecular Therapy. Elsevier. https://doi.org/10.1016/j.ymthe.2016.10.005
chicago: Smole, Anže, Duško Lainšček, Urban Bezeljak, Simon Horvat, and Roman Jerala.
“A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.”
Molecular Therapy. Elsevier, 2017. https://doi.org/10.1016/j.ymthe.2016.10.005.
ieee: A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, and R. Jerala, “A synthetic
mammalian therapeutic gene circuit for sensing and suppressing inflammation,”
Molecular Therapy, vol. 25, no. 1. Elsevier, pp. 102–119, 2017.
ista: Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. 2017. A synthetic mammalian
therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy.
25(1), 102–119.
mla: Smole, Anže, et al. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing
and Suppressing Inflammation.” Molecular Therapy, vol. 25, no. 1, Elsevier,
2017, pp. 102–19, doi:10.1016/j.ymthe.2016.10.005.
short: A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, R. Jerala, Molecular Therapy
25 (2017) 102–119.
date_created: 2020-01-25T15:55:39Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:13:14Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1016/j.ymthe.2016.10.005
external_id:
pmid:
- '28129106'
file:
- access_level: open_access
checksum: ea8b1b28606dd1edab7379ba4fa3641f
content_type: application/pdf
creator: dernst
date_created: 2020-03-03T10:55:13Z
date_updated: 2020-07-14T12:47:56Z
file_id: '7561'
file_name: 2017_MolecularTherapy_Smole.pdf
file_size: 3404806
relation: main_file
file_date_updated: 2020-07-14T12:47:56Z
has_accepted_license: '1'
intvolume: ' 25'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 102-119
pmid: 1
publication: Molecular Therapy
publication_identifier:
issn:
- 1525-0016
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: A synthetic mammalian therapeutic gene circuit for sensing and suppressing
inflammation
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2017'
...
---
_id: '750'
abstract:
- lang: eng
text: Modern communication technologies allow first responders to contact thousands
of potential volunteers simultaneously for support during a crisis or disaster
event. However, such volunteer efforts must be well coordinated and monitored,
in order to offer an effective relief to the professionals. In this paper we extend
earlier work on optimally assigning volunteers to selected landmark locations.
In particular, we emphasize the aspect that obtaining good assignments requires
not only advanced computational tools, but also a realistic measure of distance
between volunteers and landmarks. Specifically, we propose the use of the Open
Street Map (OSM) driving distance instead of he previously used flight distance.
We find the OSM driving distance to be better aligned with the interests of volunteers
and first responders. Furthermore, we show that relying on the flying distance
leads to a substantial underestimation of the number of required volunteers, causing
negative side effects in case of an actual crisis situation.
author:
- first_name: Jasmin
full_name: Pielorz, Jasmin
id: 49BC895A-F248-11E8-B48F-1D18A9856A87
last_name: Pielorz
- first_name: Matthias
full_name: Prandtstetter, Matthias
last_name: Prandtstetter
- first_name: Markus
full_name: Straub, Markus
last_name: Straub
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Pielorz J, Prandtstetter M, Straub M, Lampert C. Optimal geospatial volunteer
allocation needs realistic distances. In: 2017 IEEE International Conference
on Big Data. IEEE; 2017:3760-3763. doi:10.1109/BigData.2017.8258375'
apa: 'Pielorz, J., Prandtstetter, M., Straub, M., & Lampert, C. (2017). Optimal
geospatial volunteer allocation needs realistic distances. In 2017 IEEE International
Conference on Big Data (pp. 3760–3763). Boston, MA, United States: IEEE. https://doi.org/10.1109/BigData.2017.8258375'
chicago: Pielorz, Jasmin, Matthias Prandtstetter, Markus Straub, and Christoph Lampert.
“Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” In 2017
IEEE International Conference on Big Data, 3760–63. IEEE, 2017. https://doi.org/10.1109/BigData.2017.8258375.
ieee: J. Pielorz, M. Prandtstetter, M. Straub, and C. Lampert, “Optimal geospatial
volunteer allocation needs realistic distances,” in 2017 IEEE International
Conference on Big Data, Boston, MA, United States, 2017, pp. 3760–3763.
ista: Pielorz J, Prandtstetter M, Straub M, Lampert C. 2017. Optimal geospatial
volunteer allocation needs realistic distances. 2017 IEEE International Conference
on Big Data. Big Data, 3760–3763.
mla: Pielorz, Jasmin, et al. “Optimal Geospatial Volunteer Allocation Needs Realistic
Distances.” 2017 IEEE International Conference on Big Data, IEEE, 2017,
pp. 3760–63, doi:10.1109/BigData.2017.8258375.
short: J. Pielorz, M. Prandtstetter, M. Straub, C. Lampert, in:, 2017 IEEE International
Conference on Big Data, IEEE, 2017, pp. 3760–3763.
conference:
end_date: 2017-12-14
location: Boston, MA, United States
name: Big Data
start_date: 2017-12-11
date_created: 2018-12-11T11:48:18Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:13:55Z
day: '01'
department:
- _id: ChLa
doi: 10.1109/BigData.2017.8258375
language:
- iso: eng
month: '12'
oa_version: None
page: 3760 - 3763
publication: 2017 IEEE International Conference on Big Data
publication_identifier:
isbn:
- 978-153862714-3
publication_status: published
publisher: IEEE
publist_id: '6906'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optimal geospatial volunteer allocation needs realistic distances
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '795'
abstract:
- lang: eng
text: 'We introduce a common generalization of the strong Hanani–Tutte theorem and
the weak Hanani–Tutte theorem: if a graph G has a drawing D in the plane where
every pair of independent edges crosses an even number of times, then G has a
planar drawing preserving the rotation of each vertex whose incident edges cross
each other evenly in D. The theorem is implicit in the proof of the strong Hanani–Tutte
theorem by Pelsmajer, Schaefer and Štefankovič. We give a new, somewhat simpler
proof.'
article_number: P3.18
article_processing_charge: No
article_type: original
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: Kynčl, Jan
last_name: Kynčl
- first_name: Dömötör
full_name: Pálvölgyi, Dömötör
last_name: Pálvölgyi
citation:
ama: Fulek R, Kynčl J, Pálvölgyi D. Unified Hanani Tutte theorem. Electronic
Journal of Combinatorics. 2017;24(3). doi:10.37236/6663
apa: Fulek, R., Kynčl, J., & Pálvölgyi, D. (2017). Unified Hanani Tutte theorem.
Electronic Journal of Combinatorics. International Press. https://doi.org/10.37236/6663
chicago: Fulek, Radoslav, Jan Kynčl, and Dömötör Pálvölgyi. “Unified Hanani Tutte
Theorem.” Electronic Journal of Combinatorics. International Press, 2017.
https://doi.org/10.37236/6663.
ieee: R. Fulek, J. Kynčl, and D. Pálvölgyi, “Unified Hanani Tutte theorem,” Electronic
Journal of Combinatorics, vol. 24, no. 3. International Press, 2017.
ista: Fulek R, Kynčl J, Pálvölgyi D. 2017. Unified Hanani Tutte theorem. Electronic
Journal of Combinatorics. 24(3), P3.18.
mla: Fulek, Radoslav, et al. “Unified Hanani Tutte Theorem.” Electronic Journal
of Combinatorics, vol. 24, no. 3, P3.18, International Press, 2017, doi:10.37236/6663.
short: R. Fulek, J. Kynčl, D. Pálvölgyi, Electronic Journal of Combinatorics 24
(2017).
date_created: 2018-12-11T11:48:32Z
date_published: 2017-07-28T00:00:00Z
date_updated: 2022-03-18T12:58:53Z
day: '28'
ddc:
- '000'
department:
- _id: UlWa
doi: 10.37236/6663
ec_funded: 1
file:
- access_level: open_access
checksum: ef320cff0f062051e858f929be6a3581
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T14:04:08Z
date_updated: 2020-07-14T12:48:06Z
file_id: '5853'
file_name: 2017_ElectrCombi_Fulek.pdf
file_size: 236944
relation: main_file
file_date_updated: 2020-07-14T12:48:06Z
has_accepted_license: '1'
intvolume: ' 24'
issue: '3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Electronic Journal of Combinatorics
publication_identifier:
issn:
- '10778926'
publication_status: published
publisher: International Press
publist_id: '6859'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unified Hanani Tutte theorem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2017'
...
---
_id: '797'
abstract:
- lang: ger
text: Phasenübergänge helfen beim Verständnis von Vielteilchensystemen in der Festkörperphysik
und Fluiddynamik bis hin zur Teilchenphysik. Unserer internationalen Kollaboration
ist es gelungen, einen neuartigen Phasenübergang in einem Quantensystem zu beobachten
[1]. In einem Mikrowellenresonator konnte erstmals die spontane Zustandsänderung
von undurchsichtig zu transparent nachgewiesen werden.
article_processing_charge: No
article_type: original
author:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Fink JM. Photonenblockade aufgelöst. Physik in unserer Zeit. 2017;48(3):111-113.
doi:10.1002/piuz.201770305
apa: Fink, J. M. (2017). Photonenblockade aufgelöst. Physik in Unserer Zeit.
Wiley. https://doi.org/10.1002/piuz.201770305
chicago: Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit.
Wiley, 2017. https://doi.org/10.1002/piuz.201770305.
ieee: J. M. Fink, “Photonenblockade aufgelöst,” Physik in unserer Zeit, vol.
48, no. 3. Wiley, pp. 111–113, 2017.
ista: Fink JM. 2017. Photonenblockade aufgelöst. Physik in unserer Zeit. 48(3),
111–113.
mla: Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit,
vol. 48, no. 3, Wiley, 2017, pp. 111–13, doi:10.1002/piuz.201770305.
short: J.M. Fink, Physik in Unserer Zeit 48 (2017) 111–113.
date_created: 2018-12-11T11:48:33Z
date_published: 2017-05-01T00:00:00Z
date_updated: 2022-03-24T09:16:20Z
day: '01'
department:
- _id: JoFi
doi: 10.1002/piuz.201770305
intvolume: ' 48'
issue: '3'
language:
- iso: eng
month: '05'
oa_version: None
page: 111 - 113
publication: Physik in unserer Zeit
publication_status: published
publisher: Wiley
publist_id: '6856'
quality_controlled: '1'
status: public
title: Photonenblockade aufgelöst
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2017'
...
---
_id: '807'
abstract:
- lang: eng
text: 'On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries
and the publisher Springer took its effect: this deal covers accessing the licensed
content on the one hand, and publishing open access on the other hand. More than
1000 papers by Austrian authors were published open access at Springer in the
first year alone. The working group "Springer Compact Evaluierung" made
the data for these articles available via the platform OpenAPC and would like
to use this opportunity to give a short account of what this publishing agreement
actually entails and the working group intends to do.'
author:
- first_name: Magdalena
full_name: Andrae, Magdalena
last_name: Andrae
- first_name: Márton
full_name: Villányi, Márton
id: 3FFCCD3A-F248-11E8-B48F-1D18A9856A87
last_name: Villányi
orcid: 0000-0001-8126-0426
citation:
ama: Andrae M, Villányi M. Der Springer Compact-Deal – Ein erster Einblick in die
Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer
Bibliothekarinnen und Bibliothekare. 2017;70(2):274-280. doi:10.31263/voebm.v70i2.1898
apa: Andrae, M., & Villányi, M. (2017). Der Springer Compact-Deal – Ein erster
Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen Der
Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1898
chicago: Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein
Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB,
2017. https://doi.org/10.31263/voebm.v70i2.1898.
ieee: M. Andrae and M. Villányi, “Der Springer Compact-Deal – Ein erster Einblick
in die Evaluierung einer Offsetting-Vereinbarung,” Mitteilungen der Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare, vol. 70, no. 2. VÖB,
pp. 274–280, 2017.
ista: Andrae M, Villányi M. 2017. Der Springer Compact-Deal – Ein erster Einblick
in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 274–280.
mla: Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster
Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der
Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 70,
no. 2, VÖB, 2017, pp. 274–80, doi:10.31263/voebm.v70i2.1898.
short: M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen
Und Bibliothekare 70 (2017) 274–280.
date_created: 2018-12-11T11:48:36Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:16:45Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.31263/voebm.v70i2.1898
file:
- access_level: open_access
checksum: 558c18bcf5580d87dd371ec626d52075
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T13:39:26Z
date_updated: 2020-07-14T12:48:09Z
file_id: '5851'
file_name: 2017_VOEB_Andrae.pdf
file_size: 125065
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
intvolume: ' 70'
issue: '2'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 274 - 280
popular_science: '1'
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
publication_identifier:
issn:
- '10222588'
publication_status: published
publisher: VÖB
publist_id: '6843'
scopus_import: 1
status: public
title: Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 70
year: '2017'
...
---
_id: '825'
abstract:
- lang: eng
text: What data is needed about data? Describing the process to answer this question
for the institutional data repository IST DataRep.
author:
- first_name: Barbara
full_name: Petritsch, Barbara
id: 406048EC-F248-11E8-B48F-1D18A9856A87
last_name: Petritsch
orcid: 0000-0003-2724-4614
citation:
ama: Petritsch B. Metadata for research data in practice. Mitteilungen der Vereinigung
Österreichischer Bibliothekarinnen & Bibliothekare. 2017;70(2):200-207.
doi:10.31263/voebm.v70i2.1678
apa: Petritsch, B. (2017). Metadata for research data in practice. Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB.
https://doi.org/10.31263/voebm.v70i2.1678
chicago: Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB,
2017. https://doi.org/10.31263/voebm.v70i2.1678.
ieee: B. Petritsch, “Metadata for research data in practice,” Mitteilungen der
Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70,
no. 2. VÖB, pp. 200–207, 2017.
ista: Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der
Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 70(2), 200–207.
mla: Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol.
70, no. 2, VÖB, 2017, pp. 200–07, doi:10.31263/voebm.v70i2.1678.
short: B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen
& Bibliothekare 70 (2017) 200–207.
date_created: 2018-12-11T11:48:42Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:17:44Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.31263/voebm.v70i2.1678
file:
- access_level: open_access
checksum: 7c4544d07efa2c2add8612b489abb4e2
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T13:32:17Z
date_updated: 2020-07-14T12:48:11Z
file_id: '5850'
file_name: 2017_VOEB_Petritsch.pdf
file_size: 7843975
relation: main_file
file_date_updated: 2020-07-14T12:48:11Z
has_accepted_license: '1'
intvolume: ' 70'
issue: '2'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 200 - 207
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare
publication_identifier:
issn:
- '10222588'
publication_status: published
publisher: VÖB
publist_id: '6823'
scopus_import: 1
status: public
title: Metadata for research data in practice
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: 70
year: '2017'
...
---
_id: '957'
abstract:
- lang: eng
text: Small molecule biosensors based on Forster resonance energy transfer (FRET)
enable small molecule signaling to be monitored with high spatial and temporal
resolution in complex cellular environments. FRET sensors can be constructed by
fusing a pair of fluorescent proteins to a suitable recognition domain, such as
a member of the solute-binding protein (SBP) superfamily. However, naturally occurring
SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability,
which may preclude imaging under physiological conditions, or because the positions
of their N- and C-termini may be suboptimal for fusion of fluorescent proteins,
which may limit the dynamic range of the resulting sensors. Here, we show how
these problems can be overcome using ancestral protein reconstruction and circular
permutation. Ancestral protein reconstruction, used as a protein engineering strategy,
leverages phylogenetic information to improve the thermostability of proteins,
while circular permutation enables the termini of an SBP to be repositioned to
maximize the dynamic range of the resulting FRET sensor. We also provide a protocol
for cloning the engineered SBPs into FRET sensor constructs using Golden Gate
assembly and discuss considerations for in situ characterization of the FRET sensors.
alternative_title:
- Methods in Molecular Biology
author:
- first_name: Ben
full_name: Clifton, Ben
last_name: Clifton
- first_name: Jason
full_name: Whitfield, Jason
last_name: Whitfield
- first_name: Inmaculada
full_name: Sanchez Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez Romero
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: 'Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction
and circular permutation for improving the stability and dynamic range of FRET
sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic
Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5'
apa: Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C.,
Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and
circular permutation for improving the stability and dynamic range of FRET sensors.
In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer.
https://doi.org/10.1007/978-1-4939-6940-1_5
chicago: Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde,
Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein
Reconstruction and Circular Permutation for Improving the Stability and Dynamic
Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor
Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5.
ieee: B. Clifton et al., “Ancestral protein reconstruction and circular permutation
for improving the stability and dynamic range of FRET sensors,” in Synthetic
Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.
ista: 'Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak
HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation
for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein
Switches. Methods in Molecular Biology, vol. 1596, 71–87.'
mla: Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation
for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein
Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5.
short: B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L.
Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer,
2017, pp. 71–87.
date_created: 2018-12-11T11:49:24Z
date_published: 2017-03-15T00:00:00Z
date_updated: 2021-01-12T08:22:13Z
day: '15'
department:
- _id: HaJa
doi: 10.1007/978-1-4939-6940-1_5
editor:
- first_name: Viktor
full_name: Stein, Viktor
last_name: Stein
intvolume: ' 1596'
language:
- iso: eng
month: '03'
oa_version: None
page: 71 - 87
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors (HFSP Young Investigator)
publication: Synthetic Protein Switches
publication_identifier:
issn:
- '10643745'
publication_status: published
publisher: Springer
publist_id: '6451'
quality_controlled: '1'
scopus_import: 1
series_title: Synthetic Protein Switches
status: public
title: Ancestral protein reconstruction and circular permutation for improving the
stability and dynamic range of FRET sensors
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 1596
year: '2017'
...
---
_id: '963'
abstract:
- lang: eng
text: 'Network games are widely used as a model for selfish resource-allocation
problems. In the classical model, each player selects a path connecting her source
and target vertex. The cost of traversing an edge depends on the number of players
that traverse it. Thus, it abstracts the fact that different users may use a resource
at different times and for different durations, which plays an important role
in defining the costs of the users in reality. For example, when transmitting
packets in a communication network, routing traffic in a road network, or processing
a task in a production system, the traversal of the network involves an inherent
delay, and so sharing and congestion of resources crucially depends on time. We
study timed network games , which add a time component to network games. Each
vertex v in the network is associated with a cost function, mapping the load on
v to the price that a player pays for staying in v for one time unit with this
load. In addition, each edge has a guard, describing time intervals in which the
edge can be traversed, forcing the players to spend time on vertices. Unlike earlier
work that add a time component to network games, the time in our model is continuous
and cannot be discretized. In particular, players have uncountably many strategies,
and a game may have uncountably many pure Nash equilibria. We study properties
of timed network games with cost-sharing or congestion cost functions: their stability,
equilibrium inefficiency, and complexity. In particular, we show that the answer
to the question whether we can restrict attention to boundary strategies, namely
ones in which edges are traversed only at the boundaries of guards, is mixed. '
alternative_title:
- LIPIcs
article_number: '37'
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shibashis
full_name: Guha, Shibashis
last_name: Guha
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: 'Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37'
apa: 'Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks
(Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science
(SG), Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37'
chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with
Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37.
ieee: 'G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented
at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark,
2017, vol. 83.'
ista: 'Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS:
Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 37.'
mla: Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37.
short: G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2017.
conference:
end_date: 2017-08-25
location: Aalborg, Denmark
name: 'MFCS: Mathematical Foundations of Computer Science (SG)'
start_date: 2017-08-21
date_created: 2018-12-11T11:49:26Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-02-23T12:35:50Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.MFCS.2017.37
file:
- access_level: open_access
checksum: f55eaf7f3c36ea07801112acfedd17d5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:10Z
date_updated: 2020-07-14T12:48:18Z
file_id: '5059'
file_name: IST-2017-829-v1+1_mfcs-cr.pdf
file_size: 369730
relation: main_file
file_date_updated: 2020-07-14T12:48:18Z
has_accepted_license: '1'
intvolume: ' 83'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication_identifier:
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6438'
pubrep_id: '829'
quality_controlled: '1'
related_material:
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relation: later_version
status: public
scopus_import: 1
status: public
title: Timed network games with clocks
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: 83
year: '2017'
...
---
_id: '9709'
abstract:
- lang: eng
text: Across the nervous system, certain population spiking patterns are observed
far more frequently than others. A hypothesis about this structure is that these
collective activity patterns function as population codewords–collective modes–carrying
information distinct from that of any single cell. We investigate this phenomenon
in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop
a novel statistical model that decomposes the population response into modes;
it predicts the distribution of spiking activity in the ganglion cell population
with high accuracy. We found that the modes represent localized features of the
visual stimulus that are distinct from the features represented by single neurons.
Modes form clusters of activity states that are readily discriminated from one
another. When we repeated the same visual stimulus, we found that the same mode
was robustly elicited. These results suggest that retinal ganglion cells’ collective
signaling is endowed with a form of error-correcting code–a principle that may
hold in brain areas beyond retina.
article_processing_charge: No
author:
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Mark
full_name: Ioffe, Mark
last_name: Ioffe
- first_name: Adrianna
full_name: Loback, Adrianna
last_name: Loback
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust
modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc'
apa: 'Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M.
(2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc'
chicago: 'Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik,
and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.”
Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc.'
ieee: 'J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data
from: Error-robust modes of the retinal population code.” Dryad, 2017.'
ista: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from:
Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc.'
mla: 'Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population
Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.'
short: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).
date_created: 2021-07-23T11:34:34Z
date_published: 2017-10-18T00:00:00Z
date_updated: 2023-02-21T16:34:41Z
day: '18'
department:
- _id: GaTk
doi: 10.5061/dryad.1f1rc
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.1f1rc
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1197'
relation: used_in_publication
status: public
status: public
title: 'Data from: Error-robust modes of the retinal population code'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '541'
abstract:
- lang: eng
text: 'While we have good understanding of bacterial metabolism at the population
level, we know little about the metabolic behavior of individual cells: do single
cells in clonal populations sometimes specialize on different metabolic pathways?
Such metabolic specialization could be driven by stochastic gene expression and
could provide individual cells with growth benefits of specialization. We measured
the degree of phenotypic specialization in two parallel metabolic pathways, the
assimilation of glucose and arabinose. We grew Escherichia coli in chemostats,
and used isotope-labeled sugars in combination with nanometer-scale secondary
ion mass spectrometry and mathematical modeling to quantify sugar assimilation
at the single-cell level. We found large variation in metabolic activities between
single cells, both in absolute assimilation and in the degree to which individual
cells specialize in the assimilation of different sugars. Analysis of transcriptional
reporters indicated that this variation was at least partially based on cell-to-cell
variation in gene expression. Metabolic differences between cells in clonal populations
could potentially reduce metabolic incompatibilities between different pathways,
and increase the rate at which parallel reactions can be performed.'
article_number: e1007122
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Frank
full_name: Schreiber, Frank
last_name: Schreiber
- first_name: Alma
full_name: Dal Co, Alma
last_name: Dal Co
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Sten
full_name: Littmann, Sten
last_name: Littmann
- first_name: Marcel
full_name: Kuypers, Marcel
last_name: Kuypers
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Nikolic N, Schreiber F, Dal Co A, et al. Cell-to-cell variation and specialization
in sugar metabolism in clonal bacterial populations. PLoS Genetics. 2017;13(12).
doi:10.1371/journal.pgen.1007122
apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann,
S., … Ackermann, M. (2017). Cell-to-cell variation and specialization in sugar
metabolism in clonal bacterial populations. PLoS Genetics. Public Library
of Science. https://doi.org/10.1371/journal.pgen.1007122
chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller,
Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and
Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics.
Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.
ieee: N. Nikolic et al., “Cell-to-cell variation and specialization in sugar
metabolism in clonal bacterial populations,” PLoS Genetics, vol. 13, no.
12. Public Library of Science, 2017.
ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers
M, Ackermann M. 2017. Cell-to-cell variation and specialization in sugar metabolism
in clonal bacterial populations. PLoS Genetics. 13(12), e1007122.
mla: Nikolic, Nela, et al. “Cell-to-Cell Variation and Specialization in Sugar Metabolism
in Clonal Bacterial Populations.” PLoS Genetics, vol. 13, no. 12, e1007122,
Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.
short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann,
M. Kuypers, M. Ackermann, PLoS Genetics 13 (2017).
date_created: 2018-12-11T11:47:04Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-02-23T14:10:34Z
day: '18'
ddc:
- '576'
- '579'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1007122
ec_funded: 1
file:
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checksum: 22426d9382f21554bad5fa5967afcfd0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:35Z
date_updated: 2020-07-14T12:46:46Z
file_id: '5088'
file_name: IST-2018-959-v1+1_2017_Nikolic_Cell-to-cell.pdf
file_size: 1308475
relation: main_file
file_date_updated: 2020-07-14T12:46:46Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PLoS Genetics
publication_identifier:
issn:
- '15537390'
publication_status: published
publisher: Public Library of Science
publist_id: '7275'
pubrep_id: '959'
quality_controlled: '1'
related_material:
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status: public
- id: '9845'
relation: research_data
status: public
- id: '9846'
relation: research_data
status: public
scopus_import: 1
status: public
title: Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial
populations
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: 13
year: '2017'
...