---
_id: '7007'
abstract:
- lang: eng
text: 'We consider the primitive relay channel, where the source sends a message
to the relay and to the destination, and the relay helps the communication by
transmitting an additional message to the destination via a separate channel.
Two well-known coding techniques have been introduced for this setting: decode-and-forward
and compress-and-forward. In decode-and-forward, the relay completely decodes
the message and sends some information to the destination; in compress-and-forward,
the relay does not decode, and it sends a compressed version of the received signal
to the destination using Wyner–Ziv coding. In this paper, we present a novel coding
paradigm that provides an improved achievable rate for the primitive relay channel.
The idea is to combine compress-and-forward and decode-and-forward via a chaining
construction. We transmit over pairs of blocks: in the first block, we use compress-and-forward;
and, in the second block, we use decode-and-forward. More specifically, in the
first block, the relay does not decode, it compresses the received signal via
Wyner–Ziv, and it sends only part of the compression to the destination. In the
second block, the relay completely decodes the message, it sends some information
to the destination, and it also sends the remaining part of the compression coming
from the first block. By doing so, we are able to strictly outperform both compress-and-forward
and decode-and-forward. Note that the proposed coding scheme can be implemented
with polar codes. As such, it has the typical attractive properties of polar coding
schemes, namely, quasi-linear encoding and decoding complexity, and error probability
that decays at super-polynomial speed. As a running example, we take into account
the special case of the erasure relay channel, and we provide a comparison between
the rates achievable by our proposed scheme and the existing upper and lower bounds.'
article_number: '218'
article_type: original
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: S. Hamed
full_name: Hassani, S. Hamed
last_name: Hassani
- first_name: Rüdiger
full_name: Urbanke, Rüdiger
last_name: Urbanke
citation:
ama: Mondelli M, Hassani SH, Urbanke R. A new coding paradigm for the primitive
relay channel. Algorithms. 2019;12(10). doi:10.3390/a12100218
apa: Mondelli, M., Hassani, S. H., & Urbanke, R. (2019). A new coding paradigm
for the primitive relay channel. Algorithms. MDPI. https://doi.org/10.3390/a12100218
chicago: Mondelli, Marco, S. Hamed Hassani, and Rüdiger Urbanke. “A New Coding Paradigm
for the Primitive Relay Channel.” Algorithms. MDPI, 2019. https://doi.org/10.3390/a12100218.
ieee: M. Mondelli, S. H. Hassani, and R. Urbanke, “A new coding paradigm for the
primitive relay channel,” Algorithms, vol. 12, no. 10. MDPI, 2019.
ista: Mondelli M, Hassani SH, Urbanke R. 2019. A new coding paradigm for the primitive
relay channel. Algorithms. 12(10), 218.
mla: Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.”
Algorithms, vol. 12, no. 10, 218, MDPI, 2019, doi:10.3390/a12100218.
short: M. Mondelli, S.H. Hassani, R. Urbanke, Algorithms 12 (2019).
date_created: 2019-11-12T14:46:19Z
date_published: 2019-10-18T00:00:00Z
date_updated: 2023-02-23T12:49:28Z
day: '18'
ddc:
- '510'
department:
- _id: MaMo
doi: 10.3390/a12100218
external_id:
arxiv:
- '1801.03153'
file:
- access_level: open_access
checksum: 267756d8f9db572f496cd1663c89d59a
content_type: application/pdf
creator: dernst
date_created: 2019-11-12T14:48:45Z
date_updated: 2020-07-14T12:47:47Z
file_id: '7008'
file_name: 2019_Algorithms_Mondelli.pdf
file_size: 696791
relation: main_file
file_date_updated: 2020-07-14T12:47:47Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '10'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '10'
oa: 1
oa_version: Published Version
publication: Algorithms
publication_identifier:
issn:
- 1999-4893
publication_status: published
publisher: MDPI
quality_controlled: '1'
related_material:
record:
- id: '6675'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: A new coding paradigm for the primitive relay channel
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: 12
year: '2019'
...
---
_id: '7035'
abstract:
- lang: eng
text: 'The aim of this short note is to expound one particular issue that was discussed
during the talk [10] given at the symposium ”Researches on isometries as preserver
problems and related topics” at Kyoto RIMS. That is, the role of Dirac masses
by describing the isometry group of various metric spaces of probability measures. This article is of survey character, and it does not contain any essentially new
results.From an isometric point of view, in some cases, metric spaces of measures
are similar to C(K)-type function spaces. Similarity means here that their isometries are driven by some nice transformations
of the underlying space. Of course, it depends on the particular choice of the metric how nice these
transformations should be. Sometimes, as we will see, being a homeomorphism is
enough to generate an isometry. But sometimes we need more: the transformation
must preserve the underlying distance as well. Statements claiming that isometries
in questions are necessarily induced by homeomorphisms are called Banach-Stone-type
results, while results asserting that the underlying transformation is necessarily
an isometry are termed as isometric rigidity results.As Dirac masses can be considered as building bricks of the set of all Borel measures, a natural
question arises:Is it enough to understand how an isometry acts on the set of
Dirac masses? Does this action extend uniquely to all measures?In what follows,
we will thoroughly investigate this question.'
article_processing_charge: No
author:
- first_name: Gyorgy Pal
full_name: Geher, Gyorgy Pal
last_name: Geher
- first_name: Tamas
full_name: Titkos, Tamas
last_name: Titkos
- first_name: Daniel
full_name: Virosztek, Daniel
id: 48DB45DA-F248-11E8-B48F-1D18A9856A87
last_name: Virosztek
orcid: 0000-0003-1109-5511
citation:
ama: 'Geher GP, Titkos T, Virosztek D. Dirac masses and isometric rigidity. In:
Kyoto RIMS Kôkyûroku. Vol 2125. Research Institute for Mathematical Sciences,
Kyoto University; 2019:34-41.'
apa: 'Geher, G. P., Titkos, T., & Virosztek, D. (2019). Dirac masses and isometric
rigidity. In Kyoto RIMS Kôkyûroku (Vol. 2125, pp. 34–41). Kyoto, Japan:
Research Institute for Mathematical Sciences, Kyoto University.'
chicago: Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Dirac Masses and
Isometric Rigidity.” In Kyoto RIMS Kôkyûroku, 2125:34–41. Research Institute
for Mathematical Sciences, Kyoto University, 2019.
ieee: G. P. Geher, T. Titkos, and D. Virosztek, “Dirac masses and isometric rigidity,”
in Kyoto RIMS Kôkyûroku, Kyoto, Japan, 2019, vol. 2125, pp. 34–41.
ista: Geher GP, Titkos T, Virosztek D. 2019. Dirac masses and isometric rigidity.
Kyoto RIMS Kôkyûroku. Research on isometries as preserver problems and related
topics vol. 2125, 34–41.
mla: Geher, Gyorgy Pal, et al. “Dirac Masses and Isometric Rigidity.” Kyoto RIMS
Kôkyûroku, vol. 2125, Research Institute for Mathematical Sciences, Kyoto
University, 2019, pp. 34–41.
short: G.P. Geher, T. Titkos, D. Virosztek, in:, Kyoto RIMS Kôkyûroku, Research
Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41.
conference:
end_date: 2019-01-30
location: Kyoto, Japan
name: Research on isometries as preserver problems and related topics
start_date: 2019-01-28
date_created: 2019-11-18T15:39:53Z
date_published: 2019-01-30T00:00:00Z
date_updated: 2021-01-12T08:11:33Z
day: '30'
department:
- _id: LaEr
intvolume: ' 2125'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.kurims.kyoto-u.ac.jp/~kyodo/kokyuroku/contents/2125.html
month: '01'
oa: 1
oa_version: Submitted Version
page: 34-41
publication: Kyoto RIMS Kôkyûroku
publication_status: published
publisher: Research Institute for Mathematical Sciences, Kyoto University
quality_controlled: '1'
status: public
title: Dirac masses and isometric rigidity
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2125
year: '2019'
...
---
_id: '7055'
abstract:
- lang: eng
text: A recent class of topological nodal-line semimetals with the general formula
MSiX (M = Zr, Hf and X = S, Se, Te) has attracted much experimental and theoretical
interest due to their properties, particularly their large magnetoresistances
and high carrier mobilities. The plateletlike nature of the MSiX crystals and
their extremely low residual resistivities make measurements of the resistivity
along the [001] direction extremely challenging. To accomplish such measurements,
microstructures of single crystals were prepared using focused ion beam techniques.
Microstructures prepared in this manner have very well-defined geometries and
maintain their high crystal quality, verified by the observations of quantum oscillations.
We present magnetoresistance and quantum oscillation data for currents applied
along both [001] and [100] in ZrSiS and ZrSiSe, which are consistent with the
nontrivial topology of the Dirac line-node, as determined by a measured π Berry
phase. Surprisingly, we find that, despite the three dimensional nature of both
the Fermi surfaces of ZrSiS and ZrSiSe, both the resistivity anisotropy under
applied magnetic fields and the in-plane angular dependent magnetoresistance differ
considerably between the two compounds. Finally, we discuss the role microstructuring
can play in the study of these materials and our ability to make these microstructures
free-standing.
article_number: '101116'
article_processing_charge: No
article_type: original
author:
- first_name: Kent R.
full_name: Shirer, Kent R.
last_name: Shirer
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: Tino
full_name: Zimmerling, Tino
last_name: Zimmerling
- first_name: Maja D.
full_name: Bachmann, Maja D.
last_name: Bachmann
- first_name: Markus
full_name: König, Markus
last_name: König
- first_name: Philip J. W.
full_name: Moll, Philip J. W.
last_name: Moll
- first_name: Leslie
full_name: Schoop, Leslie
last_name: Schoop
- first_name: Andrew P.
full_name: Mackenzie, Andrew P.
last_name: Mackenzie
citation:
ama: Shirer KR, Modic KA, Zimmerling T, et al. Out-of-plane transport in ZrSiS and
ZrSiSe microstructures. APL Materials. 2019;7(10). doi:10.1063/1.5124568
apa: Shirer, K. R., Modic, K. A., Zimmerling, T., Bachmann, M. D., König, M., Moll,
P. J. W., … Mackenzie, A. P. (2019). Out-of-plane transport in ZrSiS and ZrSiSe
microstructures. APL Materials. AIP. https://doi.org/10.1063/1.5124568
chicago: Shirer, Kent R., Kimberly A Modic, Tino Zimmerling, Maja D. Bachmann, Markus
König, Philip J. W. Moll, Leslie Schoop, and Andrew P. Mackenzie. “Out-of-Plane
Transport in ZrSiS and ZrSiSe Microstructures.” APL Materials. AIP, 2019.
https://doi.org/10.1063/1.5124568.
ieee: K. R. Shirer et al., “Out-of-plane transport in ZrSiS and ZrSiSe microstructures,”
APL Materials, vol. 7, no. 10. AIP, 2019.
ista: Shirer KR, Modic KA, Zimmerling T, Bachmann MD, König M, Moll PJW, Schoop
L, Mackenzie AP. 2019. Out-of-plane transport in ZrSiS and ZrSiSe microstructures.
APL Materials. 7(10), 101116.
mla: Shirer, Kent R., et al. “Out-of-Plane Transport in ZrSiS and ZrSiSe Microstructures.”
APL Materials, vol. 7, no. 10, 101116, AIP, 2019, doi:10.1063/1.5124568.
short: K.R. Shirer, K.A. Modic, T. Zimmerling, M.D. Bachmann, M. König, P.J.W. Moll,
L. Schoop, A.P. Mackenzie, APL Materials 7 (2019).
date_created: 2019-11-19T12:52:43Z
date_published: 2019-10-17T00:00:00Z
date_updated: 2021-01-12T08:11:35Z
day: '17'
ddc:
- '530'
doi: 10.1063/1.5124568
extern: '1'
file:
- access_level: open_access
checksum: 142fe7b3e37d8e916071743bb194360d
content_type: application/pdf
creator: dernst
date_created: 2019-11-20T12:27:01Z
date_updated: 2020-07-14T12:47:48Z
file_id: '7087'
file_name: 2019_APL_Shirer.pdf
file_size: 2453220
relation: main_file
file_date_updated: 2020-07-14T12:47:48Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: APL Materials
publication_identifier:
issn:
- 2166-532X
publication_status: published
publisher: AIP
quality_controlled: '1'
status: public
title: Out-of-plane transport in ZrSiS and ZrSiSe microstructures
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: 7
year: '2019'
...
---
_id: '7057'
abstract:
- lang: eng
text: We present a high magnetic field study of NbP—a member of the monopnictide
Weyl semimetal (WSM) family. While the monoarsenides (NbAs and TaAs) have topologically
distinct left and right-handed Weyl fermi surfaces, NbP is argued to be “topologically
trivial” due to the fact that all pairs of Weyl nodes are encompassed by a single
Fermi surface. We use torque magnetometry to measure the magnetic response of
NbP up to 60 tesla and uncover a Berry paramagnetic response, characteristic of
the topological Weyl nodes, across the entire field range. At the quantum limit
B* (≈32 T), τ/B experiences a change in slope when the chemical potential enters
the last Landau level. Our calculations confirm that this magnetic response arises
from band topology of the Weyl pocket, even though the Fermi surface encompasses
both Weyl nodes at zero magnetic field. We also find that the magnetic field pulls
the chemical potential to the chiral n = 0 Landau level in the quantum limit,
providing a disorder-free way of accessing chiral Weyl fermions in systems that
are “not quite” WSMs in zero magnetic field.
article_number: '2095'
article_processing_charge: No
article_type: original
author:
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: Tobias
full_name: Meng, Tobias
last_name: Meng
- first_name: Filip
full_name: Ronning, Filip
last_name: Ronning
- first_name: Eric D.
full_name: Bauer, Eric D.
last_name: Bauer
- first_name: Philip J. W.
full_name: Moll, Philip J. W.
last_name: Moll
- first_name: B. J.
full_name: Ramshaw, B. J.
last_name: Ramshaw
citation:
ama: Modic KA, Meng T, Ronning F, Bauer ED, Moll PJW, Ramshaw BJ. Thermodynamic
signatures of Weyl fermions in NbP. Scientific Reports. 2019;9(1). doi:10.1038/s41598-018-38161-7
apa: Modic, K. A., Meng, T., Ronning, F., Bauer, E. D., Moll, P. J. W., & Ramshaw,
B. J. (2019). Thermodynamic signatures of Weyl fermions in NbP. Scientific
Reports. Springer Nature. https://doi.org/10.1038/s41598-018-38161-7
chicago: Modic, Kimberly A, Tobias Meng, Filip Ronning, Eric D. Bauer, Philip J.
W. Moll, and B. J. Ramshaw. “Thermodynamic Signatures of Weyl Fermions in NbP.”
Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-018-38161-7.
ieee: K. A. Modic, T. Meng, F. Ronning, E. D. Bauer, P. J. W. Moll, and B. J. Ramshaw,
“Thermodynamic signatures of Weyl fermions in NbP,” Scientific Reports,
vol. 9, no. 1. Springer Nature, 2019.
ista: Modic KA, Meng T, Ronning F, Bauer ED, Moll PJW, Ramshaw BJ. 2019. Thermodynamic
signatures of Weyl fermions in NbP. Scientific Reports. 9(1), 2095.
mla: Modic, Kimberly A., et al. “Thermodynamic Signatures of Weyl Fermions in NbP.”
Scientific Reports, vol. 9, no. 1, 2095, Springer Nature, 2019, doi:10.1038/s41598-018-38161-7.
short: K.A. Modic, T. Meng, F. Ronning, E.D. Bauer, P.J.W. Moll, B.J. Ramshaw, Scientific
Reports 9 (2019).
date_created: 2019-11-19T13:00:35Z
date_published: 2019-02-14T00:00:00Z
date_updated: 2021-01-12T08:11:36Z
day: '14'
ddc:
- '530'
doi: 10.1038/s41598-018-38161-7
extern: '1'
file:
- access_level: open_access
checksum: 3b5a7b316e1ff22aa0f89e8d1f1ace91
content_type: application/pdf
creator: dernst
date_created: 2019-11-20T12:24:13Z
date_updated: 2020-07-14T12:47:48Z
file_id: '7086'
file_name: 2019_ScientificReports_Modic.pdf
file_size: 3256400
relation: main_file
file_date_updated: 2020-07-14T12:47:48Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Thermodynamic signatures of Weyl fermions in NbP
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: 9
year: '2019'
...
---
_id: '7056'
abstract:
- lang: eng
text: "In the Ca1−x La x FeAs2 (1 1 2) family of pnictide superconductors, we have
investigated a highly overdoped composition (x = 0.56), prepared by a high-pressure,
high-temperature synthesis. Magnetic measurements show an antiferromagnetic transition
at T N = 120 K, well above the one at lower doping (0.15 < x < 0.27).\r\n\r\nBelow
the onset of long-range magnetic order at T N, the electrical resistivity is strongly
reduced and is dominated by electron–electron interactions, as evident from its
temperature dependence. The Seebeck coefficient shows a clear metallic behavior
as in narrow band conductors. The temperature dependence of the Hall coefficient
and the violation of Kohler's rule agree with the multiband character of the material.
No superconductivity was observed down to 1.8 K. The success of the high-pressure
synthesis encourages further investigations of the so far only partially explored
phase diagram in this family of Iron-based high temperature superconductors.\r\n"
article_number: '485705'
article_processing_charge: No
article_type: original
author:
- first_name: Edoardo
full_name: Martino, Edoardo
last_name: Martino
- first_name: Maja D
full_name: Bachmann, Maja D
last_name: Bachmann
- first_name: Lidia
full_name: Rossi, Lidia
last_name: Rossi
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: Ivica
full_name: Zivkovic, Ivica
last_name: Zivkovic
- first_name: Henrik M
full_name: Rønnow, Henrik M
last_name: Rønnow
- first_name: Philip J W
full_name: Moll, Philip J W
last_name: Moll
- first_name: Ana
full_name: Akrap, Ana
last_name: Akrap
- first_name: László
full_name: Forró, László
last_name: Forró
- first_name: Sergiy
full_name: Katrych, Sergiy
last_name: Katrych
citation:
ama: 'Martino E, Bachmann MD, Rossi L, et al. Persistent antiferromagnetic order
in heavily overdoped Ca1−x La x FeAs2. Journal of Physics: Condensed Matter.
2019;31(48). doi:10.1088/1361-648x/ab3b43'
apa: 'Martino, E., Bachmann, M. D., Rossi, L., Modic, K. A., Zivkovic, I., Rønnow,
H. M., … Katrych, S. (2019). Persistent antiferromagnetic order in heavily overdoped
Ca1−x La x FeAs2. Journal of Physics: Condensed Matter. IOP Publishing.
https://doi.org/10.1088/1361-648x/ab3b43'
chicago: 'Martino, Edoardo, Maja D Bachmann, Lidia Rossi, Kimberly A Modic, Ivica
Zivkovic, Henrik M Rønnow, Philip J W Moll, Ana Akrap, László Forró, and Sergiy
Katrych. “Persistent Antiferromagnetic Order in Heavily Overdoped Ca1−x La x FeAs2.”
Journal of Physics: Condensed Matter. IOP Publishing, 2019. https://doi.org/10.1088/1361-648x/ab3b43.'
ieee: 'E. Martino et al., “Persistent antiferromagnetic order in heavily
overdoped Ca1−x La x FeAs2,” Journal of Physics: Condensed Matter, vol.
31, no. 48. IOP Publishing, 2019.'
ista: 'Martino E, Bachmann MD, Rossi L, Modic KA, Zivkovic I, Rønnow HM, Moll PJW,
Akrap A, Forró L, Katrych S. 2019. Persistent antiferromagnetic order in heavily
overdoped Ca1−x La x FeAs2. Journal of Physics: Condensed Matter. 31(48), 485705.'
mla: 'Martino, Edoardo, et al. “Persistent Antiferromagnetic Order in Heavily Overdoped
Ca1−x La x FeAs2.” Journal of Physics: Condensed Matter, vol. 31, no. 48,
485705, IOP Publishing, 2019, doi:10.1088/1361-648x/ab3b43.'
short: 'E. Martino, M.D. Bachmann, L. Rossi, K.A. Modic, I. Zivkovic, H.M. Rønnow,
P.J.W. Moll, A. Akrap, L. Forró, S. Katrych, Journal of Physics: Condensed Matter
31 (2019).'
date_created: 2019-11-19T12:56:17Z
date_published: 2019-09-03T00:00:00Z
date_updated: 2021-01-12T08:11:35Z
day: '03'
doi: 10.1088/1361-648x/ab3b43
extern: '1'
external_id:
arxiv:
- '1905.08640'
intvolume: ' 31'
issue: '48'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1905.08640
month: '09'
oa: 1
oa_version: Preprint
publication: 'Journal of Physics: Condensed Matter'
publication_identifier:
eissn:
- 1361-648X
issn:
- 0953-8984
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
status: public
title: Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2019'
...
---
_id: '7082'
abstract:
- lang: eng
text: Although crystals of strongly correlated metals exhibit a diverse set of electronic
ground states, few approaches exist for spatially modulating their properties.
In this study, we demonstrate disorder-free control, on the micrometer scale,
over the superconducting state in samples of the heavy-fermion superconductor
CeIrIn5. We pattern crystals by focused ion beam milling to tailor the boundary
conditions for the elastic deformation upon thermal contraction during cooling.
The resulting nonuniform strain fields induce complex patterns of superconductivity,
owing to the strong dependence of the transition temperature on the strength and
direction of strain. These results showcase a generic approach to manipulating
electronic order on micrometer length scales in strongly correlated matter without
compromising the cleanliness, stoichiometry, or mean free path.
article_processing_charge: No
article_type: original
author:
- first_name: Maja D.
full_name: Bachmann, Maja D.
last_name: Bachmann
- first_name: G. M.
full_name: Ferguson, G. M.
last_name: Ferguson
- first_name: Florian
full_name: Theuss, Florian
last_name: Theuss
- first_name: Tobias
full_name: Meng, Tobias
last_name: Meng
- first_name: Carsten
full_name: Putzke, Carsten
last_name: Putzke
- first_name: Toni
full_name: Helm, Toni
last_name: Helm
- first_name: K. R.
full_name: Shirer, K. R.
last_name: Shirer
- first_name: You-Sheng
full_name: Li, You-Sheng
last_name: Li
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: Michael
full_name: Nicklas, Michael
last_name: Nicklas
- first_name: Markus
full_name: König, Markus
last_name: König
- first_name: D.
full_name: Low, D.
last_name: Low
- first_name: Sayak
full_name: Ghosh, Sayak
last_name: Ghosh
- first_name: Andrew P.
full_name: Mackenzie, Andrew P.
last_name: Mackenzie
- first_name: Frank
full_name: Arnold, Frank
last_name: Arnold
- first_name: Elena
full_name: Hassinger, Elena
last_name: Hassinger
- first_name: Ross D.
full_name: McDonald, Ross D.
last_name: McDonald
- first_name: Laurel E.
full_name: Winter, Laurel E.
last_name: Winter
- first_name: Eric D.
full_name: Bauer, Eric D.
last_name: Bauer
- first_name: Filip
full_name: Ronning, Filip
last_name: Ronning
- first_name: B. J.
full_name: Ramshaw, B. J.
last_name: Ramshaw
- first_name: Katja C.
full_name: Nowack, Katja C.
last_name: Nowack
- first_name: Philip J. W.
full_name: Moll, Philip J. W.
last_name: Moll
citation:
ama: Bachmann MD, Ferguson GM, Theuss F, et al. Spatial control of heavy-fermion
superconductivity in CeIrIn5. Science. 2019;366(6462):221-226. doi:10.1126/science.aao6640
apa: Bachmann, M. D., Ferguson, G. M., Theuss, F., Meng, T., Putzke, C., Helm, T.,
… Moll, P. J. W. (2019). Spatial control of heavy-fermion superconductivity in
CeIrIn5. Science. AAAS. https://doi.org/10.1126/science.aao6640
chicago: Bachmann, Maja D., G. M. Ferguson, Florian Theuss, Tobias Meng, Carsten
Putzke, Toni Helm, K. R. Shirer, et al. “Spatial Control of Heavy-Fermion Superconductivity
in CeIrIn5.” Science. AAAS, 2019. https://doi.org/10.1126/science.aao6640.
ieee: M. D. Bachmann et al., “Spatial control of heavy-fermion superconductivity
in CeIrIn5,” Science, vol. 366, no. 6462. AAAS, pp. 221–226, 2019.
ista: Bachmann MD, Ferguson GM, Theuss F, Meng T, Putzke C, Helm T, Shirer KR, Li
Y-S, Modic KA, Nicklas M, König M, Low D, Ghosh S, Mackenzie AP, Arnold F, Hassinger
E, McDonald RD, Winter LE, Bauer ED, Ronning F, Ramshaw BJ, Nowack KC, Moll PJW.
2019. Spatial control of heavy-fermion superconductivity in CeIrIn5. Science.
366(6462), 221–226.
mla: Bachmann, Maja D., et al. “Spatial Control of Heavy-Fermion Superconductivity
in CeIrIn5.” Science, vol. 366, no. 6462, AAAS, 2019, pp. 221–26, doi:10.1126/science.aao6640.
short: M.D. Bachmann, G.M. Ferguson, F. Theuss, T. Meng, C. Putzke, T. Helm, K.R.
Shirer, Y.-S. Li, K.A. Modic, M. Nicklas, M. König, D. Low, S. Ghosh, A.P. Mackenzie,
F. Arnold, E. Hassinger, R.D. McDonald, L.E. Winter, E.D. Bauer, F. Ronning, B.J.
Ramshaw, K.C. Nowack, P.J.W. Moll, Science 366 (2019) 221–226.
date_created: 2019-11-19T13:55:58Z
date_published: 2019-10-11T00:00:00Z
date_updated: 2021-01-12T08:11:46Z
day: '11'
doi: 10.1126/science.aao6640
extern: '1'
intvolume: ' 366'
issue: '6462'
language:
- iso: eng
month: '10'
oa_version: None
page: 221-226
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
status: public
title: Spatial control of heavy-fermion superconductivity in CeIrIn5
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 366
year: '2019'
...
---
_id: '7128'
abstract:
- lang: eng
text: Loss of functional cardiomyocytes is a major determinant of heart failure
after myocardial infarction. Previous high throughput screening studies have identified
a few microRNAs (miRNAs) that can induce cardiomyocyte proliferation and stimulate
cardiac regeneration in mice. Here, we show that all of the most effective of
these miRNAs activate nuclear localization of the master transcriptional cofactor
Yes-associated protein (YAP) and induce expression of YAP-responsive genes. In
particular, miR-199a-3p directly targets two mRNAs coding for proteins impinging
on the Hippo pathway, the upstream YAP inhibitory kinase TAOK1, and the E3 ubiquitin
ligase β-TrCP, which leads to YAP degradation. Several of the pro-proliferative
miRNAs (including miR-199a-3p) also inhibit filamentous actin depolymerization
by targeting Cofilin2, a process that by itself activates YAP nuclear translocation.
Thus, activation of YAP and modulation of the actin cytoskeleton are major components
of the pro-proliferative action of miR-199a-3p and other miRNAs that induce cardiomyocyte
proliferation.
article_processing_charge: Yes
article_type: original
author:
- first_name: Consuelo
full_name: Torrini, Consuelo
last_name: Torrini
- first_name: Ryan J
full_name: Cubero, Ryan J
id: 850B2E12-9CD4-11E9-837F-E719E6697425
last_name: Cubero
orcid: 0000-0003-0002-1867
- first_name: Ellen
full_name: Dirkx, Ellen
last_name: Dirkx
- first_name: Luca
full_name: Braga, Luca
last_name: Braga
- first_name: Hashim
full_name: Ali, Hashim
last_name: Ali
- first_name: Giulia
full_name: Prosdocimo, Giulia
last_name: Prosdocimo
- first_name: Maria Ines
full_name: Gutierrez, Maria Ines
last_name: Gutierrez
- first_name: Chiara
full_name: Collesi, Chiara
last_name: Collesi
- first_name: Danilo
full_name: Licastro, Danilo
last_name: Licastro
- first_name: Lorena
full_name: Zentilin, Lorena
last_name: Zentilin
- first_name: Miguel
full_name: Mano, Miguel
last_name: Mano
- first_name: Serena
full_name: Zacchigna, Serena
last_name: Zacchigna
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Matteo
full_name: Marsili, Matteo
last_name: Marsili
- first_name: Areejit
full_name: Samal, Areejit
last_name: Samal
- first_name: Mauro
full_name: Giacca, Mauro
last_name: Giacca
citation:
ama: Torrini C, Cubero RJ, Dirkx E, et al. Common regulatory pathways mediate activity
of microRNAs inducing cardiomyocyte proliferation. Cell Reports. 2019;27(9):2759-2771.e5.
doi:10.1016/j.celrep.2019.05.005
apa: Torrini, C., Cubero, R. J., Dirkx, E., Braga, L., Ali, H., Prosdocimo, G.,
… Giacca, M. (2019). Common regulatory pathways mediate activity of microRNAs
inducing cardiomyocyte proliferation. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2019.05.005
chicago: Torrini, Consuelo, Ryan J Cubero, Ellen Dirkx, Luca Braga, Hashim Ali,
Giulia Prosdocimo, Maria Ines Gutierrez, et al. “Common Regulatory Pathways Mediate
Activity of MicroRNAs Inducing Cardiomyocyte Proliferation.” Cell Reports.
Elsevier, 2019. https://doi.org/10.1016/j.celrep.2019.05.005.
ieee: C. Torrini et al., “Common regulatory pathways mediate activity of
microRNAs inducing cardiomyocyte proliferation,” Cell Reports, vol. 27,
no. 9. Elsevier, p. 2759–2771.e5, 2019.
ista: Torrini C, Cubero RJ, Dirkx E, Braga L, Ali H, Prosdocimo G, Gutierrez MI,
Collesi C, Licastro D, Zentilin L, Mano M, Zacchigna S, Vendruscolo M, Marsili
M, Samal A, Giacca M. 2019. Common regulatory pathways mediate activity of microRNAs
inducing cardiomyocyte proliferation. Cell Reports. 27(9), 2759–2771.e5.
mla: Torrini, Consuelo, et al. “Common Regulatory Pathways Mediate Activity of MicroRNAs
Inducing Cardiomyocyte Proliferation.” Cell Reports, vol. 27, no. 9, Elsevier,
2019, p. 2759–2771.e5, doi:10.1016/j.celrep.2019.05.005.
short: C. Torrini, R.J. Cubero, E. Dirkx, L. Braga, H. Ali, G. Prosdocimo, M.I.
Gutierrez, C. Collesi, D. Licastro, L. Zentilin, M. Mano, S. Zacchigna, M. Vendruscolo,
M. Marsili, A. Samal, M. Giacca, Cell Reports 27 (2019) 2759–2771.e5.
date_created: 2019-11-26T22:30:07Z
date_published: 2019-05-28T00:00:00Z
date_updated: 2021-01-12T08:11:56Z
day: '28'
ddc:
- '576'
doi: 10.1016/j.celrep.2019.05.005
extern: '1'
external_id:
pmid:
- '31141697'
file:
- access_level: open_access
checksum: c5d855d07263bfec718673385d0ea2d7
content_type: application/pdf
creator: rcubero
date_created: 2019-11-26T22:30:43Z
date_updated: 2020-07-14T12:47:50Z
file_id: '7129'
file_name: torrini_cellreports_2019.pdf
file_size: 4650750
relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
intvolume: ' 27'
issue: '9'
keyword:
- cardiomyocyte
- cell cycle
- Cofilin2
- cytoskeleton
- Hippo
- microRNA
- regeneration
- YAP
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: 2759-2771.e5
pmid: 1
publication: Cell Reports
publication_identifier:
issn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte
proliferation
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: 27
year: '2019'
...
---
_id: '7130'
abstract:
- lang: eng
text: "We show that statistical criticality, i.e. the occurrence of power law frequency
distributions, arises in samples that are maximally informative about the underlying
generating process. In order to reach this conclusion, we first identify the frequency
with which different outcomes occur in a sample, as the variable carrying useful
information on the generative process. The entropy of the frequency, that we call
relevance, provides an upper bound to the number of informative bits. This differs
from the entropy of the data, that we take as a measure of resolution. Samples
that maximise relevance at a given resolution—that we call maximally informative
samples—exhibit statistical criticality. In particular, Zipf's law arises at the
optimal trade-off between resolution (i.e. compression) and relevance. As a byproduct,
we derive a bound of the maximal number of parameters that can be estimated from
a dataset, in the absence of prior knowledge on the generative model.\r\n\r\nFurthermore,
we relate criticality to the statistical properties of the representation of the
data generating process. We show that, as a consequence of the concentration property
of the asymptotic equipartition property, representations that are maximally informative
about the data generating process are characterised by an exponential distribution
of energy levels. This arises from a principle of minimal entropy, that is conjugate
of the maximum entropy principle in statistical mechanics. This explains why statistical
criticality requires no parameter fine tuning in maximally informative samples."
acknowledgement: We acknowledge interesting discussions with M Abbott, E Aurell, J
Barbier, R Monasson, T Mora, I Nemenman, N Tishby and R Zecchina. This research
was supported by the Kavli Foundation and the Centre of Excellence scheme of the
Research Council of Norway (Centre for Neural Computation) (RJC and YR), by the
Basic Science Research Program through the National Research Foundation of Korea
(NRF), funded by the Ministry of Education (2016R1D1A1B03932264) (JJ), and, in part,
by the ICTP through the OEA-AC-98 (JS).
article_number: '063402'
article_processing_charge: No
article_type: original
author:
- first_name: Ryan J
full_name: Cubero, Ryan J
id: 850B2E12-9CD4-11E9-837F-E719E6697425
last_name: Cubero
orcid: 0000-0003-0002-1867
- first_name: Junghyo
full_name: Jo, Junghyo
last_name: Jo
- first_name: Matteo
full_name: Marsili, Matteo
last_name: Marsili
- first_name: Yasser
full_name: Roudi, Yasser
last_name: Roudi
- first_name: Juyong
full_name: Song, Juyong
last_name: Song
citation:
ama: 'Cubero RJ, Jo J, Marsili M, Roudi Y, Song J. Statistical criticality arises
in most informative representations. Journal of Statistical Mechanics: Theory
and Experiment. 2019;2019(6). doi:10.1088/1742-5468/ab16c8'
apa: 'Cubero, R. J., Jo, J., Marsili, M., Roudi, Y., & Song, J. (2019). Statistical
criticality arises in most informative representations. Journal of Statistical
Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/ab16c8'
chicago: 'Cubero, Ryan J, Junghyo Jo, Matteo Marsili, Yasser Roudi, and Juyong Song.
“Statistical Criticality Arises in Most Informative Representations.” Journal
of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2019. https://doi.org/10.1088/1742-5468/ab16c8.'
ieee: 'R. J. Cubero, J. Jo, M. Marsili, Y. Roudi, and J. Song, “Statistical criticality
arises in most informative representations,” Journal of Statistical Mechanics:
Theory and Experiment, vol. 2019, no. 6. IOP Publishing, 2019.'
ista: 'Cubero RJ, Jo J, Marsili M, Roudi Y, Song J. 2019. Statistical criticality
arises in most informative representations. Journal of Statistical Mechanics:
Theory and Experiment. 2019(6), 063402.'
mla: 'Cubero, Ryan J., et al. “Statistical Criticality Arises in Most Informative
Representations.” Journal of Statistical Mechanics: Theory and Experiment,
vol. 2019, no. 6, 063402, IOP Publishing, 2019, doi:10.1088/1742-5468/ab16c8.'
short: 'R.J. Cubero, J. Jo, M. Marsili, Y. Roudi, J. Song, Journal of Statistical
Mechanics: Theory and Experiment 2019 (2019).'
date_created: 2019-11-26T22:36:09Z
date_published: 2019-06-17T00:00:00Z
date_updated: 2021-01-12T08:11:57Z
day: '17'
doi: 10.1088/1742-5468/ab16c8
extern: '1'
external_id:
arxiv:
- '1808.00249'
intvolume: ' 2019'
issue: '6'
keyword:
- optimization under uncertainty
- source coding
- large deviation
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.00249
month: '06'
oa: 1
oa_version: Preprint
publication: 'Journal of Statistical Mechanics: Theory and Experiment'
publication_identifier:
issn:
- 1742-5468
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
status: public
title: Statistical criticality arises in most informative representations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2019
year: '2019'
...
---
_id: '7150'
abstract:
- lang: eng
text: "In this work, we use algebraic methods for studying distance computation
and subgraph detection tasks in the congested clique model. Specifically, we adapt
parallel matrix multiplication implementations to the congested clique, obtaining
an O(n1−2/ω) round matrix multiplication algorithm, where ω<2.3728639 is the exponent
of matrix multiplication. In conjunction with known techniques from centralised
algorithmics, this gives significant improvements over previous best upper bounds
in the congested clique model. The highlight results include:\r\n\r\n1. triangle
and 4-cycle counting in O(n0.158) rounds, improving upon the O(n1/3) algorithm
of Dolev et al. [DISC 2012],\r\n2. a (1+o(1))-approximation of all-pairs shortest
paths in O(n0.158) rounds, improving upon the O~(n1/2)-round (2+o(1))-approximation
algorithm given by Nanongkai [STOC 2014], and\r\n 3. computing the girth in O(n0.158)
rounds, which is the first non-trivial solution in this model.\r\n \r\nIn addition,
we present a novel constant-round combinatorial algorithm for detecting 4-cycles."
article_processing_charge: No
article_type: original
author:
- first_name: Keren
full_name: Censor-Hillel, Keren
last_name: Censor-Hillel
- first_name: Petteri
full_name: Kaski, Petteri
last_name: Kaski
- first_name: Janne
full_name: Korhonen, Janne
id: C5402D42-15BC-11E9-A202-CA2BE6697425
last_name: Korhonen
- first_name: Christoph
full_name: Lenzen, Christoph
last_name: Lenzen
- first_name: Ami
full_name: Paz, Ami
last_name: Paz
- first_name: Jukka
full_name: Suomela, Jukka
last_name: Suomela
citation:
ama: Censor-Hillel K, Kaski P, Korhonen J, Lenzen C, Paz A, Suomela J. Algebraic
methods in the congested clique. Distributed Computing. 2019;32(6):461-478.
doi:10.1007/s00446-016-0270-2
apa: Censor-Hillel, K., Kaski, P., Korhonen, J., Lenzen, C., Paz, A., & Suomela,
J. (2019). Algebraic methods in the congested clique. Distributed Computing.
Springer Nature. https://doi.org/10.1007/s00446-016-0270-2
chicago: Censor-Hillel, Keren, Petteri Kaski, Janne Korhonen, Christoph Lenzen,
Ami Paz, and Jukka Suomela. “Algebraic Methods in the Congested Clique.” Distributed
Computing. Springer Nature, 2019. https://doi.org/10.1007/s00446-016-0270-2.
ieee: K. Censor-Hillel, P. Kaski, J. Korhonen, C. Lenzen, A. Paz, and J. Suomela,
“Algebraic methods in the congested clique,” Distributed Computing, vol.
32, no. 6. Springer Nature, pp. 461–478, 2019.
ista: Censor-Hillel K, Kaski P, Korhonen J, Lenzen C, Paz A, Suomela J. 2019. Algebraic
methods in the congested clique. Distributed Computing. 32(6), 461–478.
mla: Censor-Hillel, Keren, et al. “Algebraic Methods in the Congested Clique.” Distributed
Computing, vol. 32, no. 6, Springer Nature, 2019, pp. 461–78, doi:10.1007/s00446-016-0270-2.
short: K. Censor-Hillel, P. Kaski, J. Korhonen, C. Lenzen, A. Paz, J. Suomela, Distributed
Computing 32 (2019) 461–478.
date_created: 2019-12-05T09:49:49Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2021-01-12T08:12:05Z
day: '01'
doi: 10.1007/s00446-016-0270-2
extern: '1'
external_id:
arxiv:
- '1503.04963'
intvolume: ' 32'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1503.04963
month: '12'
oa: 1
oa_version: Preprint
page: 461-478
publication: Distributed Computing
publication_identifier:
issn:
- 0178-2770
- 1432-0452
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Algebraic methods in the congested clique
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2019'
...
---
_id: '7171'
abstract:
- lang: ger
text: "Wissen Sie, was sich hinter künstlicher Intelligenz und maschinellem Lernen
verbirgt? \r\nDieses Sachbuch erklärt Ihnen leicht verständlich und ohne komplizierte
Formeln die grundlegenden Methoden und Vorgehensweisen des maschinellen Lernens.
Mathematisches Vorwissen ist dafür nicht nötig. Kurzweilig und informativ illustriert
Lisa, die Protagonistin des Buches, diese anhand von Alltagssituationen. \r\nEin
Buch für alle, die in Diskussionen über Chancen und Risiken der aktuellen Entwicklung
der künstlichen Intelligenz und des maschinellen Lernens mit Faktenwissen punkten
möchten. Auch für Schülerinnen und Schüler geeignet!"
article_processing_charge: No
citation:
ama: 'Kersting K, Lampert C, Rothkopf C, eds. Wie Maschinen Lernen: Künstliche
Intelligenz Verständlich Erklärt. 1st ed. Wiesbaden: Springer Nature; 2019.
doi:10.1007/978-3-658-26763-6'
apa: 'Kersting, K., Lampert, C., & Rothkopf, C. (Eds.). (2019). Wie Maschinen
Lernen: Künstliche Intelligenz Verständlich Erklärt (1st ed.). Wiesbaden:
Springer Nature. https://doi.org/10.1007/978-3-658-26763-6'
chicago: 'Kersting, Kristian, Christoph Lampert, and Constantin Rothkopf, eds. Wie
Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed. Wiesbaden:
Springer Nature, 2019. https://doi.org/10.1007/978-3-658-26763-6.'
ieee: 'K. Kersting, C. Lampert, and C. Rothkopf, Eds., Wie Maschinen Lernen:
Künstliche Intelligenz Verständlich Erklärt, 1st ed. Wiesbaden: Springer Nature,
2019.'
ista: 'Kersting K, Lampert C, Rothkopf C eds. 2019. Wie Maschinen Lernen: Künstliche
Intelligenz Verständlich Erklärt 1st ed., Wiesbaden: Springer Nature, XIV, 245p.'
mla: 'Kersting, Kristian, et al., editors. Wie Maschinen Lernen: Künstliche Intelligenz
Verständlich Erklärt. 1st ed., Springer Nature, 2019, doi:10.1007/978-3-658-26763-6.'
short: 'K. Kersting, C. Lampert, C. Rothkopf, eds., Wie Maschinen Lernen: Künstliche
Intelligenz Verständlich Erklärt, 1st ed., Springer Nature, Wiesbaden, 2019.'
date_created: 2019-12-11T14:15:56Z
date_published: 2019-10-30T00:00:00Z
date_updated: 2021-12-22T14:40:58Z
day: '30'
department:
- _id: ChLa
doi: 10.1007/978-3-658-26763-6
edition: '1'
editor:
- first_name: Kristian
full_name: Kersting, Kristian
last_name: Kersting
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Constantin
full_name: Rothkopf, Constantin
last_name: Rothkopf
language:
- iso: ger
month: '10'
oa_version: None
page: XIV, 245
place: Wiesbaden
publication_identifier:
eisbn:
- 978-3-658-26763-6
isbn:
- 978-3-658-26762-9
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/book-release-how-machines-learn/
status: public
title: 'Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt'
type: book_editor
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2019'
...
---
_id: '7275'
abstract:
- lang: eng
text: Aprotic alkali metal–oxygen batteries require reversible formation of metal
superoxide or peroxide on cycling. Severe parasitic reactions cause poor rechargeability,
efficiency, and cycle life and have been shown to be caused by singlet oxygen
(1O2) that forms at all stages of cycling. However, its formation mechanism remains
unclear. We show that disproportionation of superoxide, the product or intermediate
on discharge and charge, to peroxide and oxygen is responsible for 1O2 formation.
While the overall reaction is driven by the stability of peroxide and thus favored
by stronger Lewis acidic cations such as Li+, the 1O2 fraction is enhanced by
weak Lewis acids such as organic cations. Concurrently, the metal peroxide yield
drops with increasing 1O2. The results explain a major parasitic pathway during
cell cycling and the growing severity in K–, Na–, and Li–O2 cells based on the
growing propensity for disproportionation. High capacities and rates with peroxides
are now realized to require solution processes, which form peroxide or release
O2via disproportionation. The results therefore establish the central dilemma
that disproportionation is required for high capacity but also responsible for
irreversible reactions. Highly reversible cell operation requires hence finding
reaction routes that avoid disproportionation.
article_processing_charge: No
article_type: original
author:
- first_name: Eléonore
full_name: Mourad, Eléonore
last_name: Mourad
- first_name: Yann K.
full_name: Petit, Yann K.
last_name: Petit
- first_name: Riccardo
full_name: Spezia, Riccardo
last_name: Spezia
- first_name: Aleksej
full_name: Samojlov, Aleksej
last_name: Samojlov
- first_name: Francesco F.
full_name: Summa, Francesco F.
last_name: Summa
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
- first_name: Christian
full_name: Leypold, Christian
last_name: Leypold
- first_name: Nika
full_name: Mahne, Nika
last_name: Mahne
- first_name: Christian
full_name: Slugovc, Christian
last_name: Slugovc
- first_name: Olivier
full_name: Fontaine, Olivier
last_name: Fontaine
- first_name: Sergio
full_name: Brutti, Sergio
last_name: Brutti
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Mourad E, Petit YK, Spezia R, et al. Singlet oxygen from cation driven superoxide
disproportionation and consequences for aprotic metal–O2 batteries. Energy
& Environmental Science. 2019;12(8):2559-2568. doi:10.1039/c9ee01453e
apa: Mourad, E., Petit, Y. K., Spezia, R., Samojlov, A., Summa, F. F., Prehal, C.,
… Freunberger, S. A. (2019). Singlet oxygen from cation driven superoxide disproportionation
and consequences for aprotic metal–O2 batteries. Energy & Environmental
Science. RSC. https://doi.org/10.1039/c9ee01453e
chicago: Mourad, Eléonore, Yann K. Petit, Riccardo Spezia, Aleksej Samojlov, Francesco
F. Summa, Christian Prehal, Christian Leypold, et al. “Singlet Oxygen from Cation
Driven Superoxide Disproportionation and Consequences for Aprotic Metal–O2 Batteries.”
Energy & Environmental Science. RSC, 2019. https://doi.org/10.1039/c9ee01453e.
ieee: E. Mourad et al., “Singlet oxygen from cation driven superoxide disproportionation
and consequences for aprotic metal–O2 batteries,” Energy & Environmental
Science, vol. 12, no. 8. RSC, pp. 2559–2568, 2019.
ista: Mourad E, Petit YK, Spezia R, Samojlov A, Summa FF, Prehal C, Leypold C, Mahne
N, Slugovc C, Fontaine O, Brutti S, Freunberger SA. 2019. Singlet oxygen from
cation driven superoxide disproportionation and consequences for aprotic metal–O2
batteries. Energy & Environmental Science. 12(8), 2559–2568.
mla: Mourad, Eléonore, et al. “Singlet Oxygen from Cation Driven Superoxide Disproportionation
and Consequences for Aprotic Metal–O2 Batteries.” Energy & Environmental
Science, vol. 12, no. 8, RSC, 2019, pp. 2559–68, doi:10.1039/c9ee01453e.
short: E. Mourad, Y.K. Petit, R. Spezia, A. Samojlov, F.F. Summa, C. Prehal, C.
Leypold, N. Mahne, C. Slugovc, O. Fontaine, S. Brutti, S.A. Freunberger, Energy
& Environmental Science 12 (2019) 2559–2568.
date_created: 2020-01-15T07:18:04Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2021-01-12T08:12:41Z
day: '01'
ddc:
- '530'
- '541'
- '540'
doi: 10.1039/c9ee01453e
extern: '1'
file:
- access_level: open_access
checksum: 94d4cfb2ab0b4c90ef76a7f3cc811feb
content_type: application/pdf
creator: dernst
date_created: 2020-01-30T16:11:05Z
date_updated: 2020-07-14T12:47:55Z
file_id: '7424'
file_name: 2019_EnergyEnvironScienc_Mourad.pdf
file_size: 2888027
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: 2559-2568
publication: Energy & Environmental Science
publication_identifier:
issn:
- 1754-5692
- 1754-5706
publication_status: published
publisher: RSC
quality_controlled: '1'
status: public
title: Singlet oxygen from cation driven superoxide disproportionation and consequences
for aprotic metal–O2 batteries
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2019'
...
---
_id: '7280'
abstract:
- lang: eng
text: Non-aqueous lithium-oxygen batteries cycle by forming lithium peroxide during
discharge and oxidizing it during recharge. The significant problem of oxidizing
the solid insulating lithium peroxide can greatly be facilitated by incorporating
redox mediators that shuttle electron-holes between the porous substrate and lithium
peroxide. Redox mediator stability is thus key for energy efficiency, reversibility,
and cycle life. However, the gradual deactivation of redox mediators during repeated
cycling has not conclusively been explained. Here, we show that organic redox
mediators are predominantly decomposed by singlet oxygen that forms during cycling.
Their reaction with superoxide, previously assumed to mainly trigger their degradation,
peroxide, and dioxygen, is orders of magnitude slower in comparison. The reduced
form of the mediator is markedly more reactive towards singlet oxygen than the
oxidized form, from which we derive reaction mechanisms supported by density functional
theory calculations. Redox mediators must thus be designed for stability against
singlet oxygen.
article_number: '1380'
article_processing_charge: No
article_type: original
author:
- first_name: Won-Jin
full_name: Kwak, Won-Jin
last_name: Kwak
- first_name: Hun
full_name: Kim, Hun
last_name: Kim
- first_name: Yann K.
full_name: Petit, Yann K.
last_name: Petit
- first_name: Christian
full_name: Leypold, Christian
last_name: Leypold
- first_name: Trung Thien
full_name: Nguyen, Trung Thien
last_name: Nguyen
- first_name: Nika
full_name: Mahne, Nika
last_name: Mahne
- first_name: Paul
full_name: Redfern, Paul
last_name: Redfern
- first_name: Larry A.
full_name: Curtiss, Larry A.
last_name: Curtiss
- first_name: Hun-Gi
full_name: Jung, Hun-Gi
last_name: Jung
- first_name: Sergey M.
full_name: Borisov, Sergey M.
last_name: Borisov
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Yang-Kook
full_name: Sun, Yang-Kook
last_name: Sun
citation:
ama: Kwak W-J, Kim H, Petit YK, et al. Deactivation of redox mediators in lithium-oxygen
batteries by singlet oxygen. Nature Communications. 2019;10. doi:10.1038/s41467-019-09399-0
apa: Kwak, W.-J., Kim, H., Petit, Y. K., Leypold, C., Nguyen, T. T., Mahne, N.,
… Sun, Y.-K. (2019). Deactivation of redox mediators in lithium-oxygen batteries
by singlet oxygen. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09399-0
chicago: Kwak, Won-Jin, Hun Kim, Yann K. Petit, Christian Leypold, Trung Thien Nguyen,
Nika Mahne, Paul Redfern, et al. “Deactivation of Redox Mediators in Lithium-Oxygen
Batteries by Singlet Oxygen.” Nature Communications. Springer Nature, 2019.
https://doi.org/10.1038/s41467-019-09399-0.
ieee: W.-J. Kwak et al., “Deactivation of redox mediators in lithium-oxygen
batteries by singlet oxygen,” Nature Communications, vol. 10. Springer
Nature, 2019.
ista: Kwak W-J, Kim H, Petit YK, Leypold C, Nguyen TT, Mahne N, Redfern P, Curtiss
LA, Jung H-G, Borisov SM, Freunberger SA, Sun Y-K. 2019. Deactivation of redox
mediators in lithium-oxygen batteries by singlet oxygen. Nature Communications.
10, 1380.
mla: Kwak, Won-Jin, et al. “Deactivation of Redox Mediators in Lithium-Oxygen Batteries
by Singlet Oxygen.” Nature Communications, vol. 10, 1380, Springer Nature,
2019, doi:10.1038/s41467-019-09399-0.
short: W.-J. Kwak, H. Kim, Y.K. Petit, C. Leypold, T.T. Nguyen, N. Mahne, P. Redfern,
L.A. Curtiss, H.-G. Jung, S.M. Borisov, S.A. Freunberger, Y.-K. Sun, Nature Communications
10 (2019).
date_created: 2020-01-15T12:12:26Z
date_published: 2019-03-26T00:00:00Z
date_updated: 2021-01-12T08:12:44Z
day: '26'
ddc:
- '540'
doi: 10.1038/s41467-019-09399-0
extern: '1'
file:
- access_level: open_access
checksum: 123dd33e7f26761c82c74e10811a1e4d
content_type: application/pdf
creator: dernst
date_created: 2020-01-22T15:58:54Z
date_updated: 2020-07-14T12:47:55Z
file_id: '7355'
file_name: 2019_NatureComm_Kwak.pdf
file_size: 1003676
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 10'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen
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: 10
year: '2019'
...
---
_id: '7276'
abstract:
- lang: eng
text: Singlet oxygen (1O2) causes a major fraction of the parasitic chemistry during
the cycling of non‐aqueous alkali metal‐O2 batteries and also contributes to interfacial
reactivity of transition‐metal oxide intercalation compounds. We introduce DABCOnium,
the mono alkylated form of 1,4‐diazabicyclo[2.2.2]octane (DABCO), as an efficient
1O2 quencher with an unusually high oxidative stability of ca. 4.2 V vs. Li/Li+.
Previous quenchers are strongly Lewis basic amines with too low oxidative stability.
DABCOnium is an ionic liquid, non‐volatile, highly soluble in the electrolyte,
stable against superoxide and peroxide, and compatible with lithium metal. The
electrochemical stability covers the required range for metal–O2 batteries and
greatly reduces 1O2 related parasitic chemistry as demonstrated for the Li–O2
cell.
article_processing_charge: No
article_type: original
author:
- first_name: Yann K.
full_name: Petit, Yann K.
last_name: Petit
- first_name: Christian
full_name: Leypold, Christian
last_name: Leypold
- first_name: Nika
full_name: Mahne, Nika
last_name: Mahne
- first_name: Eléonore
full_name: Mourad, Eléonore
last_name: Mourad
- first_name: Lukas
full_name: Schafzahl, Lukas
last_name: Schafzahl
- first_name: Christian
full_name: Slugovc, Christian
last_name: Slugovc
- first_name: Sergey M.
full_name: Borisov, Sergey M.
last_name: Borisov
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: 'Petit YK, Leypold C, Mahne N, et al. DABCOnium: An efficient and high-voltage
stable singlet oxygen quencher for metal-O2 cells. Angewandte Chemie International
Edition. 2019;58(20):6535-6539. doi:10.1002/anie.201901869'
apa: 'Petit, Y. K., Leypold, C., Mahne, N., Mourad, E., Schafzahl, L., Slugovc,
C., … Freunberger, S. A. (2019). DABCOnium: An efficient and high-voltage stable
singlet oxygen quencher for metal-O2 cells. Angewandte Chemie International
Edition. Wiley. https://doi.org/10.1002/anie.201901869'
chicago: 'Petit, Yann K., Christian Leypold, Nika Mahne, Eléonore Mourad, Lukas
Schafzahl, Christian Slugovc, Sergey M. Borisov, and Stefan Alexander Freunberger.
“DABCOnium: An Efficient and High-Voltage Stable Singlet Oxygen Quencher for Metal-O2
Cells.” Angewandte Chemie International Edition. Wiley, 2019. https://doi.org/10.1002/anie.201901869.'
ieee: 'Y. K. Petit et al., “DABCOnium: An efficient and high-voltage stable
singlet oxygen quencher for metal-O2 cells,” Angewandte Chemie International
Edition, vol. 58, no. 20. Wiley, pp. 6535–6539, 2019.'
ista: 'Petit YK, Leypold C, Mahne N, Mourad E, Schafzahl L, Slugovc C, Borisov SM,
Freunberger SA. 2019. DABCOnium: An efficient and high-voltage stable singlet
oxygen quencher for metal-O2 cells. Angewandte Chemie International Edition. 58(20),
6535–6539.'
mla: 'Petit, Yann K., et al. “DABCOnium: An Efficient and High-Voltage Stable Singlet
Oxygen Quencher for Metal-O2 Cells.” Angewandte Chemie International Edition,
vol. 58, no. 20, Wiley, 2019, pp. 6535–39, doi:10.1002/anie.201901869.'
short: Y.K. Petit, C. Leypold, N. Mahne, E. Mourad, L. Schafzahl, C. Slugovc, S.M.
Borisov, S.A. Freunberger, Angewandte Chemie International Edition 58 (2019) 6535–6539.
date_created: 2020-01-15T07:19:27Z
date_published: 2019-05-13T00:00:00Z
date_updated: 2021-01-12T08:12:42Z
day: '13'
ddc:
- '540'
doi: 10.1002/anie.201901869
extern: '1'
file:
- access_level: open_access
checksum: 9620b6a511a910d7abe1f26c42dc7f83
content_type: application/pdf
creator: dernst
date_created: 2020-01-22T16:16:54Z
date_updated: 2020-07-14T12:47:55Z
file_id: '7356'
file_name: 2019_AngewChemie_Petit.pdf
file_size: 952737
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 58'
issue: '20'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 6535-6539
publication: Angewandte Chemie International Edition
publication_identifier:
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: 'DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for
metal-O2 cells'
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: 58
year: '2019'
...
---
_id: '7281'
abstract:
- lang: eng
text: Li–O2 batteries are plagued by side reactions that cause poor rechargeability
and efficiency. These reactions were recently revealed to be predominantly caused
by singlet oxygen, which can be neutralized by chemical traps or physical quenchers.
However, traps are irreversibly consumed and thus only active for a limited time,
and so far identified quenchers lack oxidative stability to be suitable for typically
required recharge potentials. Thus, reducing the charge potential within the stability
limit of the quencher and/or finding more stable quenchers is required. Here,
we show that dimethylphenazine as a redox mediator decreases the charge potential
well within the stability limit of the quencher 1,4-diazabicyclo[2.2.2]octane.
The quencher can thus mitigate the parasitic reactions without being oxidatively
decomposed. At the same time the quencher protects the redox mediator from singlet
oxygen attack. The mutual conservation of the redox mediator and the quencher
is rational for stable and effective Li–O2 batteries.
article_processing_charge: No
article_type: original
author:
- first_name: Won-Jin
full_name: Kwak, Won-Jin
last_name: Kwak
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Hun
full_name: Kim, Hun
last_name: Kim
- first_name: Jiwon
full_name: Park, Jiwon
last_name: Park
- first_name: Trung Thien
full_name: Nguyen, Trung Thien
last_name: Nguyen
- first_name: Hun-Gi
full_name: Jung, Hun-Gi
last_name: Jung
- first_name: Hye Ryung
full_name: Byon, Hye Ryung
last_name: Byon
- first_name: Yang-Kook
full_name: Sun, Yang-Kook
last_name: Sun
citation:
ama: Kwak W-J, Freunberger SA, Kim H, et al. Mutual conservation of redox mediator
and singlet oxygen quencher in Lithium–Oxygen batteries. ACS Catalysis.
2019;9(11):9914-9922. doi:10.1021/acscatal.9b01337
apa: Kwak, W.-J., Freunberger, S. A., Kim, H., Park, J., Nguyen, T. T., Jung, H.-G.,
… Sun, Y.-K. (2019). Mutual conservation of redox mediator and singlet oxygen
quencher in Lithium–Oxygen batteries. ACS Catalysis. ACS. https://doi.org/10.1021/acscatal.9b01337
chicago: Kwak, Won-Jin, Stefan Alexander Freunberger, Hun Kim, Jiwon Park, Trung
Thien Nguyen, Hun-Gi Jung, Hye Ryung Byon, and Yang-Kook Sun. “Mutual Conservation
of Redox Mediator and Singlet Oxygen Quencher in Lithium–Oxygen Batteries.” ACS
Catalysis. ACS, 2019. https://doi.org/10.1021/acscatal.9b01337.
ieee: W.-J. Kwak et al., “Mutual conservation of redox mediator and singlet
oxygen quencher in Lithium–Oxygen batteries,” ACS Catalysis, vol. 9, no.
11. ACS, pp. 9914–9922, 2019.
ista: Kwak W-J, Freunberger SA, Kim H, Park J, Nguyen TT, Jung H-G, Byon HR, Sun
Y-K. 2019. Mutual conservation of redox mediator and singlet oxygen quencher in
Lithium–Oxygen batteries. ACS Catalysis. 9(11), 9914–9922.
mla: Kwak, Won-Jin, et al. “Mutual Conservation of Redox Mediator and Singlet Oxygen
Quencher in Lithium–Oxygen Batteries.” ACS Catalysis, vol. 9, no. 11, ACS,
2019, pp. 9914–22, doi:10.1021/acscatal.9b01337.
short: W.-J. Kwak, S.A. Freunberger, H. Kim, J. Park, T.T. Nguyen, H.-G. Jung, H.R.
Byon, Y.-K. Sun, ACS Catalysis 9 (2019) 9914–9922.
date_created: 2020-01-15T12:12:40Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2021-01-12T08:12:44Z
day: '01'
ddc:
- '540'
doi: 10.1021/acscatal.9b01337
extern: '1'
file:
- access_level: open_access
checksum: bbaebfe5ff0bcab6235821ba3460b7de
content_type: application/pdf
creator: sfreunbe
date_created: 2020-06-29T15:19:30Z
date_updated: 2020-07-14T12:47:55Z
file_id: '8053'
file_name: Revised Manuscript.pdf
file_size: 1199086
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 9914-9922
publication: ACS Catalysis
publication_identifier:
issn:
- 2155-5435
publication_status: published
publisher: ACS
quality_controlled: '1'
status: public
title: Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen
batteries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2019'
...
---
_id: '7282'
abstract:
- lang: eng
text: Interphases that form on the anode surface of lithium-ion batteries are critical
for performance and lifetime, but are poorly understood. Now, a decade-old misconception
regarding a main component of the interphase has been revealed, which could potentially
lead to improved devices.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Freunberger SA. Interphase identity crisis. Nature Chemistry. 2019;11(9):761-763.
doi:10.1038/s41557-019-0311-0
apa: Freunberger, S. A. (2019). Interphase identity crisis. Nature Chemistry.
Springer Nature. https://doi.org/10.1038/s41557-019-0311-0
chicago: Freunberger, Stefan Alexander. “Interphase Identity Crisis.” Nature
Chemistry. Springer Nature, 2019. https://doi.org/10.1038/s41557-019-0311-0.
ieee: S. A. Freunberger, “Interphase identity crisis,” Nature Chemistry,
vol. 11, no. 9. Springer Nature, pp. 761–763, 2019.
ista: Freunberger SA. 2019. Interphase identity crisis. Nature Chemistry. 11(9),
761–763.
mla: Freunberger, Stefan Alexander. “Interphase Identity Crisis.” Nature Chemistry,
vol. 11, no. 9, Springer Nature, 2019, pp. 761–63, doi:10.1038/s41557-019-0311-0.
short: S.A. Freunberger, Nature Chemistry 11 (2019) 761–763.
date_created: 2020-01-15T12:12:53Z
date_published: 2019-08-19T00:00:00Z
date_updated: 2021-01-12T08:12:44Z
day: '19'
ddc:
- '540'
- '547'
doi: 10.1038/s41557-019-0311-0
extern: '1'
file:
- access_level: open_access
checksum: 76806cff3d5b62f846499a8617cee7ef
content_type: application/pdf
creator: sfreunbe
date_created: 2020-06-29T15:38:21Z
date_updated: 2020-07-14T12:47:55Z
file_id: '8054'
file_name: Freunberger on Eichhorn.pdf
file_size: 286805
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '9'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 761-763
publication: Nature Chemistry
publication_identifier:
issn:
- 1755-4330
- 1755-4349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Interphase identity crisis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2019'
...
---
_id: '7283'
abstract:
- lang: eng
text: Potassium–air batteries, which suffer from oxygen cathode and potassium metal
anode degradation, can be cycled thousands of times when an organic anode replaces
the metal.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Yann K.
full_name: Petit, Yann K.
last_name: Petit
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Petit YK, Freunberger SA. Thousands of cycles. Nature Materials. 2019;18(4):301-302.
doi:10.1038/s41563-019-0313-8
apa: Petit, Y. K., & Freunberger, S. A. (2019). Thousands of cycles. Nature
Materials. Springer Nature. https://doi.org/10.1038/s41563-019-0313-8
chicago: Petit, Yann K., and Stefan Alexander Freunberger. “Thousands of Cycles.”
Nature Materials. Springer Nature, 2019. https://doi.org/10.1038/s41563-019-0313-8.
ieee: Y. K. Petit and S. A. Freunberger, “Thousands of cycles,” Nature Materials,
vol. 18, no. 4. Springer Nature, pp. 301–302, 2019.
ista: Petit YK, Freunberger SA. 2019. Thousands of cycles. Nature Materials. 18(4),
301–302.
mla: Petit, Yann K., and Stefan Alexander Freunberger. “Thousands of Cycles.” Nature
Materials, vol. 18, no. 4, Springer Nature, 2019, pp. 301–02, doi:10.1038/s41563-019-0313-8.
short: Y.K. Petit, S.A. Freunberger, Nature Materials 18 (2019) 301–302.
date_created: 2020-01-15T12:13:05Z
date_published: 2019-03-20T00:00:00Z
date_updated: 2021-01-12T08:12:45Z
day: '20'
ddc:
- '540'
- '541'
doi: 10.1038/s41563-019-0313-8
extern: '1'
file:
- access_level: open_access
checksum: 4c9a0314327028a22dd902bc109b8798
content_type: application/pdf
creator: sfreunbe
date_created: 2020-06-29T16:26:54Z
date_updated: 2020-07-14T12:47:55Z
file_id: '8059'
file_name: NaV_final.pdf
file_size: 398123
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '4'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 301-302
publication: Nature Materials
publication_identifier:
issn:
- 1476-1122
- 1476-4660
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Thousands of cycles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2019'
...
---
_id: '7284'
abstract:
- lang: eng
text: In this issue of Joule, Dongmin Im and coworkers from Samsung in South Korea
describe a prototype lithium-O2 battery that reaches ∼700 Wh kg–1 and ∼600 Wh
L–1 on the cell level. They cut all components to the minimum to reach this value.
Difficulties filling the pores with discharge product and inhomogeneous cell utilization
turn out to limit the achievable energy. Their work underlines the importance
of reporting performance with respect to full cell weight and volume.
article_processing_charge: No
article_type: review
author:
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Prehal C, Freunberger SA. Li-O2 cell-scale energy densities. Joule.
2019;3(2):321-323. doi:10.1016/j.joule.2019.01.020
apa: Prehal, C., & Freunberger, S. A. (2019). Li-O2 cell-scale energy densities.
Joule. Elsevier. https://doi.org/10.1016/j.joule.2019.01.020
chicago: Prehal, Christian, and Stefan Alexander Freunberger. “Li-O2 Cell-Scale
Energy Densities.” Joule. Elsevier, 2019. https://doi.org/10.1016/j.joule.2019.01.020.
ieee: C. Prehal and S. A. Freunberger, “Li-O2 cell-scale energy densities,” Joule,
vol. 3, no. 2. Elsevier, pp. 321–323, 2019.
ista: Prehal C, Freunberger SA. 2019. Li-O2 cell-scale energy densities. Joule.
3(2), 321–323.
mla: Prehal, Christian, and Stefan Alexander Freunberger. “Li-O2 Cell-Scale Energy
Densities.” Joule, vol. 3, no. 2, Elsevier, 2019, pp. 321–23, doi:10.1016/j.joule.2019.01.020.
short: C. Prehal, S.A. Freunberger, Joule 3 (2019) 321–323.
date_created: 2020-01-15T12:13:15Z
date_published: 2019-02-20T00:00:00Z
date_updated: 2021-01-12T08:12:45Z
day: '20'
doi: 10.1016/j.joule.2019.01.020
extern: '1'
intvolume: ' 3'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.doi.org/10.1016/j.joule.2019.01.020
month: '02'
oa: 1
oa_version: Published Version
page: 321-323
publication: Joule
publication_identifier:
issn:
- 2542-4351
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Li-O2 cell-scale energy densities
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2019'
...
---
_id: '7358'
abstract:
- lang: eng
text: Telencephalic organoids generated from human pluripotent stem cells (hPSCs)
are emerging as an effective system to study the distinct features of the developing
human brain and the underlying causes of many neurological disorders. While progress
in organoid technology has been steadily advancing, many challenges remain including
rampant batch-to-batch and cell line-to-cell line variability and irreproducibility.
Here, we demonstrate that a major contributor to successful cortical organoid
production is the manner in which hPSCs are maintained prior to differentiation.
Optimal results were achieved using fibroblast-feeder-supported hPSCs compared
to feeder-independent cells, related to differences in their transcriptomic states.
Feeder-supported hPSCs display elevated activation of diverse TGFβ superfamily
signaling pathways and increased expression of genes associated with naïve pluripotency.
We further identify combinations of TGFβ-related growth factors that are necessary
and together sufficient to impart broad telencephalic organoid competency to feeder-free
hPSCs and enable reproducible formation of brain structures suitable for disease
modeling.
article_processing_charge: No
author:
- first_name: Momoko
full_name: Watanabe, Momoko
last_name: Watanabe
- first_name: Jillian R.
full_name: Haney, Jillian R.
last_name: Haney
- first_name: Neda
full_name: Vishlaghi, Neda
last_name: Vishlaghi
- first_name: Felix
full_name: Turcios, Felix
last_name: Turcios
- first_name: Jessie E.
full_name: Buth, Jessie E.
last_name: Buth
- first_name: Wen
full_name: Gu, Wen
last_name: Gu
- first_name: Amanda J.
full_name: Collier, Amanda J.
last_name: Collier
- first_name: Osvaldo
full_name: Miranda, Osvaldo
id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425
last_name: Miranda
orcid: 0000-0001-6618-6889
- first_name: Di
full_name: Chen, Di
last_name: Chen
- first_name: Shan
full_name: Sabri, Shan
last_name: Sabri
- first_name: Amander T.
full_name: Clark, Amander T.
last_name: Clark
- first_name: Kathrin
full_name: Plath, Kathrin
last_name: Plath
- first_name: Heather R.
full_name: Christofk, Heather R.
last_name: Christofk
- first_name: Michael J.
full_name: Gandal, Michael J.
last_name: Gandal
- first_name: Bennett G.
full_name: Novitch, Bennett G.
last_name: Novitch
citation:
ama: Watanabe M, Haney JR, Vishlaghi N, et al. TGFβ superfamily signaling regulates
the state of human stem cell pluripotency and competency to create telencephalic
organoids. bioRxiv. 2019. doi:10.1101/2019.12.13.875773
apa: Watanabe, M., Haney, J. R., Vishlaghi, N., Turcios, F., Buth, J. E., Gu, W.,
… Novitch, B. G. (2019). TGFβ superfamily signaling regulates the state of human
stem cell pluripotency and competency to create telencephalic organoids. bioRxiv.
Cold Spring Harbor Laboratory. https://doi.org/10.1101/2019.12.13.875773
chicago: Watanabe, Momoko, Jillian R. Haney, Neda Vishlaghi, Felix Turcios, Jessie
E. Buth, Wen Gu, Amanda J. Collier, et al. “TGFβ Superfamily Signaling Regulates
the State of Human Stem Cell Pluripotency and Competency to Create Telencephalic
Organoids.” BioRxiv. Cold Spring Harbor Laboratory, 2019. https://doi.org/10.1101/2019.12.13.875773.
ieee: M. Watanabe et al., “TGFβ superfamily signaling regulates the state
of human stem cell pluripotency and competency to create telencephalic organoids,”
bioRxiv. Cold Spring Harbor Laboratory, 2019.
ista: Watanabe M, Haney JR, Vishlaghi N, Turcios F, Buth JE, Gu W, Collier AJ, Miranda
O, Chen D, Sabri S, Clark AT, Plath K, Christofk HR, Gandal MJ, Novitch BG. 2019.
TGFβ superfamily signaling regulates the state of human stem cell pluripotency
and competency to create telencephalic organoids. bioRxiv, 10.1101/2019.12.13.875773.
mla: Watanabe, Momoko, et al. “TGFβ Superfamily Signaling Regulates the State of
Human Stem Cell Pluripotency and Competency to Create Telencephalic Organoids.”
BioRxiv, Cold Spring Harbor Laboratory, 2019, doi:10.1101/2019.12.13.875773.
short: M. Watanabe, J.R. Haney, N. Vishlaghi, F. Turcios, J.E. Buth, W. Gu, A.J.
Collier, O. Miranda, D. Chen, S. Sabri, A.T. Clark, K. Plath, H.R. Christofk,
M.J. Gandal, B.G. Novitch, BioRxiv (2019).
date_created: 2020-01-23T09:53:40Z
date_published: 2019-12-13T00:00:00Z
date_updated: 2022-06-17T08:03:32Z
day: '13'
doi: 10.1101/2019.12.13.875773
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2019.12.13.875773
month: '12'
oa: 1
oa_version: Preprint
page: '75'
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
status: public
title: TGFβ superfamily signaling regulates the state of human stem cell pluripotency
and competency to create telencephalic organoids
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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
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: '7453'
abstract:
- lang: eng
text: We illustrate the ingredients of the state-of-the-art of model-based approach
for the formal design and verification of cyber-physical systems. To capture the
interaction between a discrete controller and its continuously evolving environment,
we use the formal models of timed and hybrid automata. We explain the steps of
modeling and verification in the tools Uppaal and SpaceEx using a case study based
on a dual-chamber implantable pacemaker monitoring a human heart. We show how
to design a model as a composition of components, how to construct models at varying
levels of detail, how to establish that one model is an abstraction of another,
how to specify correctness requirements using temporal logic, and how to verify
that a model satisfies a logical requirement.
acknowledgement: This research was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award). This
research has received funding from the Sino-Danish Basic Research Centre, IDEA4CPS,
funded by the Danish National Research Foundation and the National Science Foundation,
China, the Innovation Fund Denmark centre DiCyPS, as well as the ERC Advanced Grant
LASSO.
alternative_title:
- Lecture Notes in Computer Science
article_processing_charge: No
author:
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Kim G.
full_name: Larsen, Kim G.
last_name: Larsen
- first_name: Marius
full_name: Mikučionis, Marius
last_name: Mikučionis
citation:
ama: 'Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. Continuous-time
models for system design and analysis. In: Steffen B, Woeginger G, eds. Computing
and Software Science. Vol 10000. LNCS. Springer Nature; 2019:452-477. doi:10.1007/978-3-319-91908-9_22'
apa: Alur, R., Giacobbe, M., Henzinger, T. A., Larsen, K. G., & Mikučionis,
M. (2019). Continuous-time models for system design and analysis. In B. Steffen
& G. Woeginger (Eds.), Computing and Software Science (Vol. 10000,
pp. 452–477). Springer Nature. https://doi.org/10.1007/978-3-319-91908-9_22
chicago: Alur, Rajeev, Mirco Giacobbe, Thomas A Henzinger, Kim G. Larsen, and Marius
Mikučionis. “Continuous-Time Models for System Design and Analysis.” In Computing
and Software Science, edited by Bernhard Steffen and Gerhard Woeginger, 10000:452–77.
LNCS. Springer Nature, 2019. https://doi.org/10.1007/978-3-319-91908-9_22.
ieee: R. Alur, M. Giacobbe, T. A. Henzinger, K. G. Larsen, and M. Mikučionis, “Continuous-time
models for system design and analysis,” in Computing and Software Science,
vol. 10000, B. Steffen and G. Woeginger, Eds. Springer Nature, 2019, pp. 452–477.
ista: 'Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. 2019.Continuous-time
models for system design and analysis. In: Computing and Software Science. Lecture
Notes in Computer Science, vol. 10000, 452–477.'
mla: Alur, Rajeev, et al. “Continuous-Time Models for System Design and Analysis.”
Computing and Software Science, edited by Bernhard Steffen and Gerhard
Woeginger, vol. 10000, Springer Nature, 2019, pp. 452–77, doi:10.1007/978-3-319-91908-9_22.
short: R. Alur, M. Giacobbe, T.A. Henzinger, K.G. Larsen, M. Mikučionis, in:, B.
Steffen, G. Woeginger (Eds.), Computing and Software Science, Springer Nature,
2019, pp. 452–477.
date_created: 2020-02-05T10:51:44Z
date_published: 2019-10-05T00:00:00Z
date_updated: 2022-09-06T08:25:52Z
day: '05'
department:
- _id: ToHe
doi: 10.1007/978-3-319-91908-9_22
editor:
- first_name: Bernhard
full_name: Steffen, Bernhard
last_name: Steffen
- first_name: Gerhard
full_name: Woeginger, Gerhard
last_name: Woeginger
intvolume: ' 10000'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/978-3-319-91908-9_22
month: '10'
oa: 1
oa_version: Published Version
page: 452-477
project:
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Computing and Software Science
publication_identifier:
eisbn:
- '9783319919089'
eissn:
- 0302-9743
isbn:
- '9783319919072'
issn:
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: Continuous-time models for system design and analysis
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10000
year: '2019'
...
---
_id: '7459'
abstract:
- lang: eng
text: We report the fabrication of BaTiO3-Ni magnetoelectric nanocomposites comprising
of BaTiO3 nanotubes surrounded by Ni matrix. BaTiO3 nanotubes obtained from the
hydrothermal transformation of TiO2 have both inner and outer surfaces, which
facilitates greater magnetoelectric coupling with the surrounding Ni matrix. The
magnetoelectric coupling was studied by measuring the piezoelectric behavior in
the presence of an in-plane direct magnetic field. A higher magnetoelectric voltage
coefficient of 110 mV/cm·Oe was obtained, because of better coupling between Ni
and BaTiO3 through the walls of the nanotubes. Such nanocomposite developed directly
on Ti substrate may lead to efficient fabrication of magnetoelectric devices.
article_processing_charge: No
article_type: original
author:
- first_name: Samba Siva
full_name: Vadla, Samba Siva
last_name: Vadla
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Subish
full_name: John, Subish
last_name: John
- first_name: Gabriel
full_name: Caruntu, Gabriel
last_name: Caruntu
- first_name: Somnath C.
full_name: Roy, Somnath C.
last_name: Roy
citation:
ama: Vadla SS, Costanzo T, John S, Caruntu G, Roy SC. Local probing of magnetoelectric
coupling in BaTiO3-Ni 1–3 composites. Scripta Materialia. 2019;159:33-36.
doi:10.1016/j.scriptamat.2018.09.003
apa: Vadla, S. S., Costanzo, T., John, S., Caruntu, G., & Roy, S. C. (2019).
Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites. Scripta
Materialia. Elsevier. https://doi.org/10.1016/j.scriptamat.2018.09.003
chicago: Vadla, Samba Siva, Tommaso Costanzo, Subish John, Gabriel Caruntu, and
Somnath C. Roy. “Local Probing of Magnetoelectric Coupling in BaTiO3-Ni 1–3 Composites.”
Scripta Materialia. Elsevier, 2019. https://doi.org/10.1016/j.scriptamat.2018.09.003.
ieee: S. S. Vadla, T. Costanzo, S. John, G. Caruntu, and S. C. Roy, “Local probing
of magnetoelectric coupling in BaTiO3-Ni 1–3 composites,” Scripta Materialia,
vol. 159. Elsevier, pp. 33–36, 2019.
ista: Vadla SS, Costanzo T, John S, Caruntu G, Roy SC. 2019. Local probing of magnetoelectric
coupling in BaTiO3-Ni 1–3 composites. Scripta Materialia. 159, 33–36.
mla: Vadla, Samba Siva, et al. “Local Probing of Magnetoelectric Coupling in BaTiO3-Ni
1–3 Composites.” Scripta Materialia, vol. 159, Elsevier, 2019, pp. 33–36,
doi:10.1016/j.scriptamat.2018.09.003.
short: S.S. Vadla, T. Costanzo, S. John, G. Caruntu, S.C. Roy, Scripta Materialia
159 (2019) 33–36.
date_created: 2020-02-05T14:19:17Z
date_published: 2019-01-15T00:00:00Z
date_updated: 2023-02-23T13:08:31Z
day: '15'
doi: 10.1016/j.scriptamat.2018.09.003
extern: '1'
intvolume: ' 159'
language:
- iso: eng
month: '01'
oa_version: None
page: 33-36
publication: Scripta Materialia
publication_identifier:
issn:
- 1359-6462
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 159
year: '2019'
...
---
_id: '7476'
abstract:
- lang: eng
text: The sebaceous gland (SG) is an essential component of the skin, and SG dysfunction
is debilitating1,2. Yet, the cellular bases for its origin, development and subsequent
maintenance remain poorly understood. Here, we apply large-scale quantitative
fate mapping to define the patterns of cell fate behaviour during SG development
and maintenance. We show that the SG develops from a defined number of lineage-restricted
progenitors that undergo a programme of independent and stochastic cell fate decisions.
Following an expansion phase, equipotent progenitors transition into a phase of
homeostatic turnover, which is correlated with changes in the mechanical properties
of the stroma and spatial restrictions on gland size. Expression of the oncogene
KrasG12D results in a release from these constraints and unbridled gland expansion.
Quantitative clonal fate analysis reveals that, during this phase, the primary
effect of the Kras oncogene is to drive a constant fate bias with little effect
on cell division rates. These findings provide insight into the developmental
programme of the SG, as well as the mechanisms that drive tumour progression and
gland dysfunction.
article_processing_charge: No
article_type: original
author:
- first_name: Marianne Stemann
full_name: Andersen, Marianne Stemann
last_name: Andersen
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Svetlana
full_name: Ulyanchenko, Svetlana
last_name: Ulyanchenko
- first_name: Soline
full_name: Estrach, Soline
last_name: Estrach
- first_name: Yasuko
full_name: Antoku, Yasuko
last_name: Antoku
- first_name: Sabrina
full_name: Pisano, Sabrina
last_name: Pisano
- first_name: Kim E.
full_name: Boonekamp, Kim E.
last_name: Boonekamp
- first_name: Sarah
full_name: Sendrup, Sarah
last_name: Sendrup
- first_name: Martti
full_name: Maimets, Martti
last_name: Maimets
- first_name: Marianne Terndrup
full_name: Pedersen, Marianne Terndrup
last_name: Pedersen
- first_name: Jens V.
full_name: Johansen, Jens V.
last_name: Johansen
- first_name: Ditte L.
full_name: Clement, Ditte L.
last_name: Clement
- first_name: Chloe C.
full_name: Feral, Chloe C.
last_name: Feral
- first_name: Benjamin D.
full_name: Simons, Benjamin D.
last_name: Simons
- first_name: Kim B.
full_name: Jensen, Kim B.
last_name: Jensen
citation:
ama: Andersen MS, Hannezo EB, Ulyanchenko S, et al. Tracing the cellular dynamics
of sebaceous gland development in normal and perturbed states. Nature Cell
Biology. 2019;21(8):924-932. doi:10.1038/s41556-019-0362-x
apa: Andersen, M. S., Hannezo, E. B., Ulyanchenko, S., Estrach, S., Antoku, Y.,
Pisano, S., … Jensen, K. B. (2019). Tracing the cellular dynamics of sebaceous
gland development in normal and perturbed states. Nature Cell Biology.
Springer Nature. https://doi.org/10.1038/s41556-019-0362-x
chicago: Andersen, Marianne Stemann, Edouard B Hannezo, Svetlana Ulyanchenko, Soline
Estrach, Yasuko Antoku, Sabrina Pisano, Kim E. Boonekamp, et al. “Tracing the
Cellular Dynamics of Sebaceous Gland Development in Normal and Perturbed States.”
Nature Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0362-x.
ieee: M. S. Andersen et al., “Tracing the cellular dynamics of sebaceous
gland development in normal and perturbed states,” Nature Cell Biology,
vol. 21, no. 8. Springer Nature, pp. 924–932, 2019.
ista: Andersen MS, Hannezo EB, Ulyanchenko S, Estrach S, Antoku Y, Pisano S, Boonekamp
KE, Sendrup S, Maimets M, Pedersen MT, Johansen JV, Clement DL, Feral CC, Simons
BD, Jensen KB. 2019. Tracing the cellular dynamics of sebaceous gland development
in normal and perturbed states. Nature Cell Biology. 21(8), 924–932.
mla: Andersen, Marianne Stemann, et al. “Tracing the Cellular Dynamics of Sebaceous
Gland Development in Normal and Perturbed States.” Nature Cell Biology,
vol. 21, no. 8, Springer Nature, 2019, pp. 924–32, doi:10.1038/s41556-019-0362-x.
short: M.S. Andersen, E.B. Hannezo, S. Ulyanchenko, S. Estrach, Y. Antoku, S. Pisano,
K.E. Boonekamp, S. Sendrup, M. Maimets, M.T. Pedersen, J.V. Johansen, D.L. Clement,
C.C. Feral, B.D. Simons, K.B. Jensen, Nature Cell Biology 21 (2019) 924–932.
date_created: 2020-02-11T08:43:49Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2021-01-12T08:13:47Z
day: '01'
doi: 10.1038/s41556-019-0362-x
extern: '1'
external_id:
pmid:
- '31358966'
intvolume: ' 21'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978139/
month: '08'
oa: 1
oa_version: Submitted Version
page: 924-932
pmid: 1
publication: Nature Cell Biology
publication_identifier:
issn:
- 1465-7392
- 1476-4679
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Tracing the cellular dynamics of sebaceous gland development in normal and
perturbed states
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2019'
...
---
_id: '7548'
abstract:
- lang: eng
text: Although the aggregation of the amyloid-β peptide (Aβ) into amyloid fibrils
is a well-established hallmark of Alzheimer’s disease, the complex mechanisms
linking this process to neurodegeneration are still incompletely understood. The
nematode worm C. elegans is a valuable model organism through which to study these
mechanisms because of its simple nervous system and its relatively short lifespan.
Standard Aβ-based C. elegans models of Alzheimer’s disease are designed to study
the toxic effects of the overexpression of Aβ in the muscle or nervous systems.
However, the wide variety of effects associated with the tissue-level overexpression
of Aβ makes it difficult to single out and study specific cellular mechanisms
related to the onset of Alzheimer’s disease. Here, to better understand how to
investigate the early events affecting neuronal signalling, we created a C. elegans
model expressing Aβ42, the 42-residue form of Aβ, from a single-copy gene insertion
in just one pair of glutamatergic sensory neurons, the BAG neurons. In behavioural
assays, we found that the Aβ42-expressing animals displayed a subtle modulation
of the response to CO2, compared to controls. Ca2+ imaging revealed that the BAG
neurons in young Aβ42-expressing nematodes were activated more strongly than in
control animals, and that neuronal activation remained intact until old age. Taken
together, our results suggest that Aβ42-expression in this very subtle model of
AD is sufficient to modulate the behavioural response but not strong enough to
generate significant neurotoxicity, suggesting that slightly more aggressive perturbations
will enable effectively studies of the links between the modulation of a physiological
response and its associated neurotoxicity.
article_number: e0217746
article_processing_charge: No
article_type: original
author:
- first_name: Tessa
full_name: Sinnige, Tessa
last_name: Sinnige
- first_name: Prashanth
full_name: Ciryam, Prashanth
last_name: Ciryam
- first_name: Samuel
full_name: Casford, Samuel
last_name: Casford
- first_name: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
citation:
ama: Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. Expression
of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates
the associated behavioural response. PLOS ONE. 2019;14(5). doi:10.1371/journal.pone.0217746
apa: Sinnige, T., Ciryam, P., Casford, S., Dobson, C. M., de Bono, M., & Vendruscolo,
M. (2019). Expression of the amyloid-β peptide in a single pair of C. elegans
sensory neurons modulates the associated behavioural response. PLOS ONE.
Public Library of Science. https://doi.org/10.1371/journal.pone.0217746
chicago: Sinnige, Tessa, Prashanth Ciryam, Samuel Casford, Christopher M. Dobson,
Mario de Bono, and Michele Vendruscolo. “Expression of the Amyloid-β Peptide in
a Single Pair of C. Elegans Sensory Neurons Modulates the Associated Behavioural
Response.” PLOS ONE. Public Library of Science, 2019. https://doi.org/10.1371/journal.pone.0217746.
ieee: T. Sinnige, P. Ciryam, S. Casford, C. M. Dobson, M. de Bono, and M. Vendruscolo,
“Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons
modulates the associated behavioural response,” PLOS ONE, vol. 14, no.
5. Public Library of Science, 2019.
ista: Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. 2019.
Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons
modulates the associated behavioural response. PLOS ONE. 14(5), e0217746.
mla: Sinnige, Tessa, et al. “Expression of the Amyloid-β Peptide in a Single Pair
of C. Elegans Sensory Neurons Modulates the Associated Behavioural Response.”
PLOS ONE, vol. 14, no. 5, e0217746, Public Library of Science, 2019, doi:10.1371/journal.pone.0217746.
short: T. Sinnige, P. Ciryam, S. Casford, C.M. Dobson, M. de Bono, M. Vendruscolo,
PLOS ONE 14 (2019).
date_created: 2020-02-28T10:45:13Z
date_published: 2019-05-31T00:00:00Z
date_updated: 2021-01-12T08:14:08Z
day: '31'
doi: 10.1371/journal.pone.0217746
extern: '1'
intvolume: ' 14'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: Published Version
publication: PLOS ONE
publication_identifier:
issn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
status: public
title: Expression of the amyloid-β peptide in a single pair of C. elegans sensory
neurons modulates the associated behavioural response
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2019'
...
---
_id: '7547'
abstract:
- lang: eng
text: The BH3-only family of proteins is key for initiating apoptosis in a variety
of contexts, and may also contribute to non-apoptotic cellular processes. Historically,
the nematode Caenorhabditis elegans has provided a powerful system for studying
and identifying conserved regulators of BH3-only proteins. In C. elegans, the
BH3-only protein egl-1 is expressed during development to cell-autonomously trigger
most developmental cell deaths. Here we provide evidence that egl-1 is also transcribed
after development in the sensory neuron pair URX without inducing apoptosis. We
used genetic screening and epistasis analysis to determine that its transcription
is regulated in URX by neuronal activity and/or in parallel by orthologs of Protein
Kinase G and the Salt-Inducible Kinase family. Because several BH3-only family
proteins are also expressed in the adult nervous system of mammals, we suggest
that studying egl-1 expression in URX may shed light on mechanisms that regulate
conserved family members in higher organisms.
article_processing_charge: No
article_type: original
author:
- first_name: Jesse
full_name: Cohn, Jesse
last_name: Cohn
- first_name: Vivek
full_name: Dwivedi, Vivek
last_name: Dwivedi
- first_name: Giulio
full_name: Valperga, Giulio
last_name: Valperga
- first_name: Nicole
full_name: Zarate, Nicole
last_name: Zarate
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: H. Robert
full_name: Horvitz, H. Robert
last_name: Horvitz
- first_name: Jonathan T.
full_name: Pierce, Jonathan T.
last_name: Pierce
citation:
ama: 'Cohn J, Dwivedi V, Valperga G, et al. Activity-dependent regulation of the
proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans.
G3: Genes, Genomes, Genetics. 2019;9(11):3703-3714. doi:10.1534/g3.119.400654'
apa: 'Cohn, J., Dwivedi, V., Valperga, G., Zarate, N., de Bono, M., Horvitz, H.
R., & Pierce, J. T. (2019). Activity-dependent regulation of the proapoptotic
BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. G3:
Genes, Genomes, Genetics. Genetics Society of America. https://doi.org/10.1534/g3.119.400654'
chicago: 'Cohn, Jesse, Vivek Dwivedi, Giulio Valperga, Nicole Zarate, Mario de Bono,
H. Robert Horvitz, and Jonathan T. Pierce. “Activity-Dependent Regulation of the
Proapoptotic BH3-Only Gene Egl-1 in a Living Neuron Pair in Caenorhabditis Elegans.”
G3: Genes, Genomes, Genetics. Genetics Society of America, 2019. https://doi.org/10.1534/g3.119.400654.'
ieee: 'J. Cohn et al., “Activity-dependent regulation of the proapoptotic
BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans,” G3:
Genes, Genomes, Genetics, vol. 9, no. 11. Genetics Society of America, pp.
3703–3714, 2019.'
ista: 'Cohn J, Dwivedi V, Valperga G, Zarate N, de Bono M, Horvitz HR, Pierce JT.
2019. Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in
a living neuron pair in Caenorhabditis elegans. G3: Genes, Genomes, Genetics.
9(11), 3703–3714.'
mla: 'Cohn, Jesse, et al. “Activity-Dependent Regulation of the Proapoptotic BH3-Only
Gene Egl-1 in a Living Neuron Pair in Caenorhabditis Elegans.” G3: Genes, Genomes,
Genetics, vol. 9, no. 11, Genetics Society of America, 2019, pp. 3703–14,
doi:10.1534/g3.119.400654.'
short: 'J. Cohn, V. Dwivedi, G. Valperga, N. Zarate, M. de Bono, H.R. Horvitz, J.T.
Pierce, G3: Genes, Genomes, Genetics 9 (2019) 3703–3714.'
date_created: 2020-02-28T10:44:27Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2021-01-12T08:14:07Z
day: '01'
doi: 10.1534/g3.119.400654
extern: '1'
external_id:
pmid:
- '31519744'
intvolume: ' 9'
issue: '11'
language:
- iso: eng
month: '11'
oa_version: Published Version
page: 3703-3714
pmid: 1
publication: 'G3: Genes, Genomes, Genetics'
publication_identifier:
issn:
- 2160-1836
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
status: public
title: Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a
living neuron pair in Caenorhabditis elegans
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2019'
...
---
_id: '7550'
abstract:
- lang: eng
text: 'We consider an optimal control problem for an abstract nonlinear dissipative
evolution equation. The differential constraint is penalized by augmenting the
target functional by a nonnegative global-in-time functional which is null-minimized
in the evolution equation is satisfied. Different variational settings are presented,
leading to the convergence of the penalization method for gradient flows, noncyclic
and semimonotone flows, doubly nonlinear evolutions, and GENERIC systems. '
acknowledgement: This work is supported by Vienna Science and Technology Fund (WWTF)
through Project MA14-009 and by the Austrian Science Fund (FWF) projects F 65 and
I 2375.
article_processing_charge: No
article_type: original
author:
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
- first_name: Ulisse
full_name: Stefanelli, Ulisse
last_name: Stefanelli
citation:
ama: Portinale L, Stefanelli U. Penalization via global functionals of optimal-control
problems for dissipative evolution. Advances in Mathematical Sciences and Applications.
2019;28(2):425-447.
apa: Portinale, L., & Stefanelli, U. (2019). Penalization via global functionals
of optimal-control problems for dissipative evolution. Advances in Mathematical
Sciences and Applications. Gakko Tosho.
chicago: Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals
of Optimal-Control Problems for Dissipative Evolution.” Advances in Mathematical
Sciences and Applications. Gakko Tosho, 2019.
ieee: L. Portinale and U. Stefanelli, “Penalization via global functionals of optimal-control
problems for dissipative evolution,” Advances in Mathematical Sciences and
Applications, vol. 28, no. 2. Gakko Tosho, pp. 425–447, 2019.
ista: Portinale L, Stefanelli U. 2019. Penalization via global functionals of optimal-control
problems for dissipative evolution. Advances in Mathematical Sciences and Applications.
28(2), 425–447.
mla: Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals
of Optimal-Control Problems for Dissipative Evolution.” Advances in Mathematical
Sciences and Applications, vol. 28, no. 2, Gakko Tosho, 2019, pp. 425–47.
short: L. Portinale, U. Stefanelli, Advances in Mathematical Sciences and Applications
28 (2019) 425–447.
date_created: 2020-02-28T10:54:41Z
date_published: 2019-10-22T00:00:00Z
date_updated: 2022-06-17T07:52:41Z
day: '22'
department:
- _id: JaMa
external_id:
arxiv:
- '1910.10050'
intvolume: ' 28'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1910.10050'
month: '10'
oa: 1
oa_version: Preprint
page: 425-447
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: Advances in Mathematical Sciences and Applications
publication_identifier:
issn:
- 1343-4373
publication_status: published
publisher: Gakko Tosho
quality_controlled: '1'
status: public
title: Penalization via global functionals of optimal-control problems for dissipative
evolution
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2019'
...
---
_id: '7552'
abstract:
- lang: eng
text: 'There is increasing evidence that protein binding to specific sites along
DNA can activate the reading out of genetic information without coming into direct
physical contact with the gene. There also is evidence that these distant but
interacting sites are embedded in a liquid droplet of proteins which condenses
out of the surrounding solution. We argue that droplet-mediated interactions can
account for crucial features of gene regulation only if the droplet is poised
at a non-generic point in its phase diagram. We explore a minimal model that embodies
this idea, show that this model has a natural mechanism for self-tuning, and suggest
direct experimental tests. '
article_processing_charge: No
author:
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation.
arXiv:191208579.
apa: Bialek, W., Gregor, T., & Tkačik, G. (n.d.). Action at a distance in transcriptional
regulation. arXiv:1912.08579. ArXiv.
chicago: Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance
in Transcriptional Regulation.” ArXiv:1912.08579. ArXiv, n.d.
ieee: W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional
regulation,” arXiv:1912.08579. ArXiv.
ista: Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation.
arXiv:1912.08579, .
mla: Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.”
ArXiv:1912.08579, ArXiv.
short: W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.).
date_created: 2020-02-28T10:57:08Z
date_published: 2019-12-18T00:00:00Z
date_updated: 2021-01-12T08:14:09Z
day: '18'
department:
- _id: GaTk
external_id:
arxiv:
- '1912.08579'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.08579
month: '12'
oa: 1
oa_version: Preprint
page: '5'
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: arXiv:1912.08579
publication_status: submitted
publisher: ArXiv
status: public
title: Action at a distance in transcriptional regulation
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7576'
abstract:
- lang: eng
text: We present the results of a friendly competition for formal verification of
continuous and hybrid systems with nonlinear continuous dynamics. The friendly
competition took place as part of the workshop Applied Verification for Continuous
and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex,
Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are
applied to solve reachability analysis problems on four benchmark problems, one
of them with hybrid dynamics. We do not rank the tools based on the results, but
show the current status and discover the potential advantages of different tools.
article_processing_charge: No
author:
- first_name: Fabian
full_name: Immler, Fabian
last_name: Immler
- first_name: Matthias
full_name: Althoff, Matthias
last_name: Althoff
- first_name: Luis
full_name: Benet, Luis
last_name: Benet
- first_name: Alexandre
full_name: Chapoutot, Alexandre
last_name: Chapoutot
- first_name: Xin
full_name: Chen, Xin
last_name: Chen
- first_name: Marcelo
full_name: Forets, Marcelo
last_name: Forets
- first_name: Luca
full_name: Geretti, Luca
last_name: Geretti
- first_name: Niklas
full_name: Kochdumper, Niklas
last_name: Kochdumper
- first_name: David P.
full_name: Sanders, David P.
last_name: Sanders
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
citation:
ama: 'Immler F, Althoff M, Benet L, et al. ARCH-COMP19 Category Report: Continuous
and hybrid systems with nonlinear dynamics. In: EPiC Series in Computing.
Vol 61. EasyChair Publications; 2019:41-61. doi:10.29007/m75b'
apa: 'Immler, F., Althoff, M., Benet, L., Chapoutot, A., Chen, X., Forets, M., …
Schilling, C. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems
with nonlinear dynamics. In EPiC Series in Computing (Vol. 61, pp. 41–61).
Montreal, Canada: EasyChair Publications. https://doi.org/10.29007/m75b'
chicago: 'Immler, Fabian, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin
Chen, Marcelo Forets, Luca Geretti, Niklas Kochdumper, David P. Sanders, and Christian
Schilling. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear
Dynamics.” In EPiC Series in Computing, 61:41–61. EasyChair Publications,
2019. https://doi.org/10.29007/m75b.'
ieee: 'F. Immler et al., “ARCH-COMP19 Category Report: Continuous and hybrid
systems with nonlinear dynamics,” in EPiC Series in Computing, Montreal,
Canada, 2019, vol. 61, pp. 41–61.'
ista: 'Immler F, Althoff M, Benet L, Chapoutot A, Chen X, Forets M, Geretti L, Kochdumper
N, Sanders DP, Schilling C. 2019. ARCH-COMP19 Category Report: Continuous and
hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International
Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 41–61.'
mla: 'Immler, Fabian, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid
Systems with Nonlinear Dynamics.” EPiC Series in Computing, vol. 61, EasyChair
Publications, 2019, pp. 41–61, doi:10.29007/m75b.'
short: F. Immler, M. Althoff, L. Benet, A. Chapoutot, X. Chen, M. Forets, L. Geretti,
N. Kochdumper, D.P. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair
Publications, 2019, pp. 41–61.
conference:
end_date: 2019-04-15
location: Montreal, Canada
name: 'ARCH: International Workshop on Applied Verification on Continuous and Hybrid
Systems'
start_date: 2019-04-15
date_created: 2020-03-08T23:00:49Z
date_published: 2019-05-25T00:00:00Z
date_updated: 2021-01-12T08:14:17Z
day: '25'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.29007/m75b
file:
- access_level: open_access
checksum: 9138977a06fcd6a95976eb4bca875f0c
content_type: application/pdf
creator: dernst
date_created: 2020-03-24T07:36:36Z
date_updated: 2020-07-14T12:48:00Z
file_id: '7617'
file_name: 2019_ARCH19_Immler.pdf
file_size: 1934830
relation: main_file
file_date_updated: 2020-07-14T12:48:00Z
has_accepted_license: '1'
intvolume: ' 61'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 41-61
publication: EPiC Series in Computing
publication_identifier:
eissn:
- '23987340'
publication_status: published
publisher: EasyChair Publications
quality_controlled: '1'
scopus_import: 1
status: public
title: 'ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear
dynamics'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2019'
...
---
_id: '7627'
abstract:
- lang: eng
text: 'Electrodepositing insulating and insoluble Li2O2 is the key process during discharge of aprotic Li-O2
batteries and determines rate, capacity, and reversibility. Current understanding states that the
partition between surface adsorbed and solvated LiO2 governs whether Li2O2 grows as surface film,
leading to low capacity even at low rates, or in solution, leading to particles
and high capacities. Here we show that Li2O2 forms to the widest extent as particles
via solution mediated LiO2 disproportionation. We describe a unified Li2O2 growth model that conclusively explains capacity limitations across the
whole range of electrolytes. Deciding for particle morphology, achievable rate
and capacities are species mobilities, electrode specific surface area (determining true areal rate) and the concentration
distribution of associated LiO2 in solution. Provided that species mobilities
and surface are high, high, capacities are possible even with low-donor-number
electrolytes, previously considered prototypical for low capacity via surface growth. The tools for these insights are microscopy, hydrodynamic
voltammetry, a numerical reaction model, and in situ small/wide angle X-ray scattering
(SAXS/WAXS). Combined with sophisticated data analysis, SAXS allows retrieving
rich quantitative information from complex multi-phase systems. On a wider perspective,
this SAXS method is a powerful in situ metrology with atomic to sub-micron resolution to study mechanisms in complex electrochemical systems and
beyond. '
article_processing_charge: No
author:
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
- first_name: Aleksej
full_name: Samojlov, Aleksej
last_name: Samojlov
- first_name: Manfred
full_name: Nachtnebel, Manfred
last_name: Nachtnebel
- first_name: Manfred
full_name: Kriechbaum, Manfred
last_name: Kriechbaum
- first_name: Heinz
full_name: Amenitsch, Heinz
last_name: Amenitsch
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Prehal C, Samojlov A, Nachtnebel M, Kriechbaum M, Amenitsch H, Freunberger
SA. A revised O2 reduction model in Li-O2 batteries as revealed by in situ small
angle X-ray scattering.
apa: Prehal, C., Samojlov, A., Nachtnebel, M., Kriechbaum, M., Amenitsch, H., &
Freunberger, S. A. (n.d.). A revised O2 reduction model in Li-O2 batteries as
revealed by in situ small angle X-ray scattering. ChemRxiv.
chicago: Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Manfred Kriechbaum,
Heinz Amenitsch, and Stefan Alexander Freunberger. “A Revised O2 Reduction Model
in Li-O2 Batteries as Revealed by in Situ Small Angle X-Ray Scattering.” ChemRxiv,
n.d.
ieee: C. Prehal, A. Samojlov, M. Nachtnebel, M. Kriechbaum, H. Amenitsch, and S.
A. Freunberger, “A revised O2 reduction model in Li-O2 batteries as revealed by
in situ small angle X-ray scattering.” ChemRxiv.
ista: Prehal C, Samojlov A, Nachtnebel M, Kriechbaum M, Amenitsch H, Freunberger
SA. A revised O2 reduction model in Li-O2 batteries as revealed by in situ small
angle X-ray scattering.
mla: Prehal, Christian, et al. A Revised O2 Reduction Model in Li-O2 Batteries
as Revealed by in Situ Small Angle X-Ray Scattering. ChemRxiv.
short: C. Prehal, A. Samojlov, M. Nachtnebel, M. Kriechbaum, H. Amenitsch, S.A.
Freunberger, (n.d.).
date_created: 2020-04-01T10:10:21Z
date_published: 2019-12-26T00:00:00Z
date_updated: 2020-04-06T10:36:21Z
day: '26'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.26434/chemrxiv.11447775.v1
month: '12'
oa: 1
oa_version: Preprint
page: '50'
publication_status: submitted
publisher: ChemRxiv
status: public
title: A revised O2 reduction model in Li-O2 batteries as revealed by in situ small
angle X-ray scattering
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7710'
abstract:
- lang: eng
text: 'The number of human genomes being genotyped or sequenced increases exponentially
and efficient haplotype estimation methods able to handle this amount of data
are now required. Here we present a method, SHAPEIT4, which substantially improves
upon other methods to process large genotype and high coverage sequencing datasets.
It notably exhibits sub-linear running times with sample size, provides highly
accurate haplotypes and allows integrating external phasing information such as
large reference panels of haplotypes, collections of pre-phased variants and long
sequencing reads. We provide SHAPEIT4 in an open source format and demonstrate
its performance in terms of accuracy and running times on two gold standard datasets:
the UK Biobank data and the Genome In A Bottle.'
article_number: '5436'
article_processing_charge: No
article_type: original
author:
- first_name: Olivier
full_name: Delaneau, Olivier
last_name: Delaneau
- first_name: Jean-François
full_name: Zagury, Jean-François
last_name: Zagury
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Jonathan L.
full_name: Marchini, Jonathan L.
last_name: Marchini
- first_name: Emmanouil T.
full_name: Dermitzakis, Emmanouil T.
last_name: Dermitzakis
citation:
ama: Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. Accurate,
scalable and integrative haplotype estimation. Nature Communications. 2019;10.
doi:10.1038/s41467-019-13225-y
apa: Delaneau, O., Zagury, J.-F., Robinson, M. R., Marchini, J. L., & Dermitzakis,
E. T. (2019). Accurate, scalable and integrative haplotype estimation. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13225-y
chicago: Delaneau, Olivier, Jean-François Zagury, Matthew Richard Robinson, Jonathan
L. Marchini, and Emmanouil T. Dermitzakis. “Accurate, Scalable and Integrative
Haplotype Estimation.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13225-y.
ieee: O. Delaneau, J.-F. Zagury, M. R. Robinson, J. L. Marchini, and E. T. Dermitzakis,
“Accurate, scalable and integrative haplotype estimation,” Nature Communications,
vol. 10. Springer Nature, 2019.
ista: Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. 2019. Accurate,
scalable and integrative haplotype estimation. Nature Communications. 10, 5436.
mla: Delaneau, Olivier, et al. “Accurate, Scalable and Integrative Haplotype Estimation.”
Nature Communications, vol. 10, 5436, Springer Nature, 2019, doi:10.1038/s41467-019-13225-y.
short: O. Delaneau, J.-F. Zagury, M.R. Robinson, J.L. Marchini, E.T. Dermitzakis,
Nature Communications 10 (2019).
date_created: 2020-04-30T10:40:32Z
date_published: 2019-11-28T00:00:00Z
date_updated: 2021-01-12T08:15:01Z
day: '28'
doi: 10.1038/s41467-019-13225-y
extern: '1'
intvolume: ' 10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-019-13225-y
month: '11'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Accurate, scalable and integrative haplotype estimation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2019'
...
---
_id: '7711'
abstract:
- lang: eng
text: The nature and extent of mitochondrial DNA variation in a population and how
it affects traits is poorly understood. Here we resequence the mitochondrial genomes
of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that
stratify along 12 mitochondrial haplotypes. We identify 1,845 cases of mitonuclear
allelic imbalances, thus implying that mitochondrial haplotypes are reflected
in the nuclear genome. However, no major fitness effects are associated with mitonuclear
imbalance, suggesting that such imbalances reflect population structure at the
mitochondrial level rather than genomic incompatibilities. Although mitochondrial
haplotypes have no direct impact on mitochondrial respiration, some haplotypes
are associated with stress- and metabolism-related phenotypes, including food
intake in males. Finally, through reciprocal swapping of mitochondrial genomes,
we demonstrate that a mitochondrial haplotype associated with high food intake
can rescue a low food intake phenotype. Together, our findings provide new insight
into population structure at the mitochondrial level and point to the importance
of incorporating mitochondrial haplotypes in genotype–phenotype relationship studies.
article_processing_charge: No
article_type: original
author:
- first_name: Roel P. J.
full_name: Bevers, Roel P. J.
last_name: Bevers
- first_name: Maria
full_name: Litovchenko, Maria
last_name: Litovchenko
- first_name: Adamandia
full_name: Kapopoulou, Adamandia
last_name: Kapopoulou
- first_name: Virginie S.
full_name: Braman, Virginie S.
last_name: Braman
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Johan
full_name: Auwerx, Johan
last_name: Auwerx
- first_name: Brian
full_name: Hollis, Brian
last_name: Hollis
- first_name: Bart
full_name: Deplancke, Bart
last_name: Deplancke
citation:
ama: Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Mitochondrial haplotypes affect
metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism.
2019;1(12):1226-1242. doi:10.1038/s42255-019-0147-3
apa: Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson,
M. R., Auwerx, J., … Deplancke, B. (2019). Mitochondrial haplotypes affect metabolic
phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism.
Springer Nature. https://doi.org/10.1038/s42255-019-0147-3
chicago: Bevers, Roel P. J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S.
Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke.
“Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic
Reference Panel.” Nature Metabolism. Springer Nature, 2019. https://doi.org/10.1038/s42255-019-0147-3.
ieee: R. P. J. Bevers et al., “Mitochondrial haplotypes affect metabolic
phenotypes in the Drosophila Genetic Reference Panel,” Nature Metabolism,
vol. 1, no. 12. Springer Nature, pp. 1226–1242, 2019.
ista: Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J,
Hollis B, Deplancke B. 2019. Mitochondrial haplotypes affect metabolic phenotypes
in the Drosophila Genetic Reference Panel. Nature Metabolism. 1(12), 1226–1242.
mla: Bevers, Roel P. J., et al. “Mitochondrial Haplotypes Affect Metabolic Phenotypes
in the Drosophila Genetic Reference Panel.” Nature Metabolism, vol. 1,
no. 12, Springer Nature, 2019, pp. 1226–42, doi:10.1038/s42255-019-0147-3.
short: R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson,
J. Auwerx, B. Hollis, B. Deplancke, Nature Metabolism 1 (2019) 1226–1242.
date_created: 2020-04-30T10:40:56Z
date_published: 2019-12-09T00:00:00Z
date_updated: 2021-01-12T08:15:01Z
day: '09'
doi: 10.1038/s42255-019-0147-3
extern: '1'
intvolume: ' 1'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 1226-1242
publication: Nature Metabolism
publication_identifier:
issn:
- 2522-5812
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s42255-020-0202-0
status: public
title: Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic
Reference Panel
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2019'
...
---
_id: '7782'
abstract:
- lang: eng
text: As genome-wide association studies (GWAS) increased in size, numerous gene-environment
interactions (GxE) have been discovered, many of which however explore only one
environment at a time and may suffer from statistical artefacts leading to biased
interaction estimates. Here we propose a maximum likelihood method to estimate
the contribution of GxE to complex traits taking into account all interacting
environmental variables at the same time, without the need to measure any. This
is possible because GxE induces fluctuations in the conditional trait variance,
the extent of which depends on the strength of GxE. The approach can be applied
to continuous outcomes and for single SNPs or genetic risk scores (GRS). Extensive
simulations demonstrated that our method yields unbiased interaction estimates
and excellent confidence interval coverage. We also offer a strategy to distinguish
specific GxE from general heteroscedasticity (scale effects). Applying our method
to 32 complex traits in the UK Biobank reveals that for body mass index (BMI)
the GRSxE explains an additional 1.9% variance on top of the 5.2% GRS contribution.
However, this interaction is not specific to the GRS and holds for any variable
similarly correlated with BMI. On the contrary, the GRSxE interaction effect for
leg impedance Embedded Image is significantly (P < 10−56) larger than it would
be expected for a similarly correlated variable Embedded Image. We showed that
our method could robustly detect the global contribution of GxE to complex traits,
which turned out to be substantial for certain obesity measures.
article_processing_charge: No
author:
- first_name: Jonathan
full_name: Sulc, Jonathan
last_name: Sulc
- first_name: Ninon
full_name: Mounier, Ninon
last_name: Mounier
- first_name: Felix
full_name: Günther, Felix
last_name: Günther
- first_name: Thomas
full_name: Winkler, Thomas
last_name: Winkler
- first_name: Andrew R.
full_name: Wood, Andrew R.
last_name: Wood
- first_name: Timothy M.
full_name: Frayling, Timothy M.
last_name: Frayling
- first_name: Iris M.
full_name: Heid, Iris M.
last_name: Heid
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Zoltán
full_name: Kutalik, Zoltán
last_name: Kutalik
citation:
ama: 'Sulc J, Mounier N, Günther F, et al. Maximum likelihood method quantifies
the overall contribution of gene-environment interaction to continuous traits:
An application to complex traits in the UK Biobank. bioRxiv. 2019.'
apa: 'Sulc, J., Mounier, N., Günther, F., Winkler, T., Wood, A. R., Frayling, T.
M., … Kutalik, Z. (2019). Maximum likelihood method quantifies the overall contribution
of gene-environment interaction to continuous traits: An application to complex
traits in the UK Biobank. bioRxiv. Cold Spring Harbor Laboratory.'
chicago: 'Sulc, Jonathan, Ninon Mounier, Felix Günther, Thomas Winkler, Andrew R.
Wood, Timothy M. Frayling, Iris M. Heid, Matthew Richard Robinson, and Zoltán
Kutalik. “Maximum Likelihood Method Quantifies the Overall Contribution of Gene-Environment
Interaction to Continuous Traits: An Application to Complex Traits in the UK Biobank.”
BioRxiv. Cold Spring Harbor Laboratory, 2019.'
ieee: 'J. Sulc et al., “Maximum likelihood method quantifies the overall
contribution of gene-environment interaction to continuous traits: An application
to complex traits in the UK Biobank,” bioRxiv. Cold Spring Harbor Laboratory,
2019.'
ista: 'Sulc J, Mounier N, Günther F, Winkler T, Wood AR, Frayling TM, Heid IM, Robinson
MR, Kutalik Z. 2019. Maximum likelihood method quantifies the overall contribution
of gene-environment interaction to continuous traits: An application to complex
traits in the UK Biobank. bioRxiv, .'
mla: 'Sulc, Jonathan, et al. “Maximum Likelihood Method Quantifies the Overall Contribution
of Gene-Environment Interaction to Continuous Traits: An Application to Complex
Traits in the UK Biobank.” BioRxiv, Cold Spring Harbor Laboratory, 2019.'
short: J. Sulc, N. Mounier, F. Günther, T. Winkler, A.R. Wood, T.M. Frayling, I.M.
Heid, M.R. Robinson, Z. Kutalik, BioRxiv (2019).
date_created: 2020-04-30T13:04:26Z
date_published: 2019-06-14T00:00:00Z
date_updated: 2021-01-12T08:15:30Z
day: '14'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/632380 '
month: '06'
oa: 1
oa_version: Preprint
page: '20'
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
status: public
title: 'Maximum likelihood method quantifies the overall contribution of gene-environment
interaction to continuous traits: An application to complex traits in the UK Biobank'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '8013'
article_number: e1007049
article_processing_charge: No
article_type: original
author:
- first_name: Christopher B.
full_name: Currin, Christopher B.
last_name: Currin
- first_name: Phumlani N.
full_name: Khoza, Phumlani N.
last_name: Khoza
- first_name: Alexander D.
full_name: Antrobus, Alexander D.
last_name: Antrobus
- first_name: Peter E.
full_name: Latham, Peter E.
last_name: Latham
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Joseph V.
full_name: Raimondo, Joseph V.
last_name: Raimondo
citation:
ama: 'Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. Think:
Theory for Africa. PLOS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007049'
apa: 'Currin, C. B., Khoza, P. N., Antrobus, A. D., Latham, P. E., Vogels, T. P.,
& Raimondo, J. V. (2019). Think: Theory for Africa. PLOS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007049'
chicago: 'Currin, Christopher B., Phumlani N. Khoza, Alexander D. Antrobus, Peter
E. Latham, Tim P Vogels, and Joseph V. Raimondo. “Think: Theory for Africa.” PLOS
Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007049.'
ieee: 'C. B. Currin, P. N. Khoza, A. D. Antrobus, P. E. Latham, T. P. Vogels, and
J. V. Raimondo, “Think: Theory for Africa,” PLOS Computational Biology,
vol. 15, no. 7. Public Library of Science, 2019.'
ista: 'Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. 2019.
Think: Theory for Africa. PLOS Computational Biology. 15(7), e1007049.'
mla: 'Currin, Christopher B., et al. “Think: Theory for Africa.” PLOS Computational
Biology, vol. 15, no. 7, e1007049, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007049.'
short: C.B. Currin, P.N. Khoza, A.D. Antrobus, P.E. Latham, T.P. Vogels, J.V. Raimondo,
PLOS Computational Biology 15 (2019).
date_created: 2020-06-25T12:50:39Z
date_published: 2019-07-11T00:00:00Z
date_updated: 2021-01-12T08:16:31Z
day: '11'
ddc:
- '570'
doi: 10.1371/journal.pcbi.1007049
extern: '1'
external_id:
pmid:
- '31295253'
file:
- access_level: open_access
checksum: 723bdfb6ee5c747cbbb32baf01d17fad
content_type: application/pdf
creator: cziletti
date_created: 2020-07-02T12:22:57Z
date_updated: 2020-07-14T12:48:08Z
file_id: '8079'
file_name: 2019_PlosCompBio_Currin.pdf
file_size: 773969
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
status: public
title: 'Think: Theory for Africa'
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 15
year: '2019'
...
---
_id: '8014'
abstract:
- lang: eng
text: 'Working memory, the ability to keep recently accessed information available
for immediate manipulation, has been proposed to rely on two mechanisms that appear
difficult to reconcile: self-sustained neural firing, or the opposite—activity-silent
synaptic traces. Here we review and contrast models of these two mechanisms, and
then show that both phenomena can co-exist within a unified system in which neurons
hold information in both activity and synapses. Rapid plasticity in flexibly-coding
neurons allows features to be bound together into objects, with an important emergent
property being the focus of attention. One memory item is held by persistent activity
in an attended or “focused” state, and is thus remembered better than other items.
Other, previously attended items can remain in memory but in the background, encoded
in activity-silent synaptic traces. This dual functional architecture provides
a unified common mechanism accounting for a diversity of perplexing attention
and memory effects that have been hitherto difficult to explain in a single theoretical
framework.'
article_processing_charge: No
article_type: original
author:
- first_name: Sanjay G.
full_name: Manohar, Sanjay G.
last_name: Manohar
- first_name: Nahid
full_name: Zokaei, Nahid
last_name: Zokaei
- first_name: Sean J.
full_name: Fallon, Sean J.
last_name: Fallon
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Masud
full_name: Husain, Masud
last_name: Husain
citation:
ama: Manohar SG, Zokaei N, Fallon SJ, Vogels TP, Husain M. Neural mechanisms of
attending to items in working memory. Neuroscience and Biobehavioral Reviews.
2019;101:1-12. doi:10.1016/j.neubiorev.2019.03.017
apa: Manohar, S. G., Zokaei, N., Fallon, S. J., Vogels, T. P., & Husain, M.
(2019). Neural mechanisms of attending to items in working memory. Neuroscience
and Biobehavioral Reviews. Elsevier . https://doi.org/10.1016/j.neubiorev.2019.03.017
chicago: Manohar, Sanjay G., Nahid Zokaei, Sean J. Fallon, Tim P Vogels, and Masud
Husain. “Neural Mechanisms of Attending to Items in Working Memory.” Neuroscience
and Biobehavioral Reviews. Elsevier , 2019. https://doi.org/10.1016/j.neubiorev.2019.03.017.
ieee: S. G. Manohar, N. Zokaei, S. J. Fallon, T. P. Vogels, and M. Husain, “Neural
mechanisms of attending to items in working memory,” Neuroscience and Biobehavioral
Reviews, vol. 101. Elsevier , pp. 1–12, 2019.
ista: Manohar SG, Zokaei N, Fallon SJ, Vogels TP, Husain M. 2019. Neural mechanisms
of attending to items in working memory. Neuroscience and Biobehavioral Reviews.
101, 1–12.
mla: Manohar, Sanjay G., et al. “Neural Mechanisms of Attending to Items in Working
Memory.” Neuroscience and Biobehavioral Reviews, vol. 101, Elsevier , 2019,
pp. 1–12, doi:10.1016/j.neubiorev.2019.03.017.
short: S.G. Manohar, N. Zokaei, S.J. Fallon, T.P. Vogels, M. Husain, Neuroscience
and Biobehavioral Reviews 101 (2019) 1–12.
date_created: 2020-06-25T12:52:13Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2021-01-12T08:16:31Z
day: '01'
ddc:
- '570'
doi: 10.1016/j.neubiorev.2019.03.017
extern: '1'
external_id:
pmid:
- '30922977'
file:
- access_level: open_access
checksum: 7b972e3d6f7bb3122c8c5648f44e60ca
content_type: application/pdf
creator: cziletti
date_created: 2020-07-02T13:17:52Z
date_updated: 2020-07-14T12:48:08Z
file_id: '8080'
file_name: 2019_NeurosBiobehavRev_Manohar.pdf
file_size: 1754418
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
intvolume: ' 101'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/233007 '
month: '06'
oa: 1
oa_version: Published Version
page: 1-12
pmid: 1
publication: Neuroscience and Biobehavioral Reviews
publication_identifier:
issn:
- 0149-7634
publication_status: published
publisher: 'Elsevier '
quality_controlled: '1'
status: public
title: Neural mechanisms of attending to items in working memory
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 101
year: '2019'
...
---
_id: '8175'
abstract:
- lang: eng
text: We study edge asymptotics of poissonized Plancherel-type measures on skew
Young diagrams (integer partitions). These measures can be seen as generalizations
of those studied by Baik--Deift--Johansson and Baik--Rains in resolving Ulam's
problem on longest increasing subsequences of random permutations and the last
passage percolation (corner growth) discrete versions thereof. Moreover they interpolate
between said measures and the uniform measure on partitions. In the new KPZ-like
1/3 exponent edge scaling limit with logarithmic corrections, we find new probability
distributions generalizing the classical Tracy--Widom GUE, GOE and GSE distributions
from the theory of random matrices.
acknowledgement: "D.B. is especially grateful to Patrik Ferrari for suggesting simplifications
in Section 3 and\r\nto Alessandra Occelli for suggesting the name for the models
of Section 2.\r\n"
article_number: '34'
article_processing_charge: No
author:
- first_name: Dan
full_name: Betea, Dan
last_name: Betea
- first_name: Jérémie
full_name: Bouttier, Jérémie
last_name: Bouttier
- first_name: Peter
full_name: Nejjar, Peter
id: 4BF426E2-F248-11E8-B48F-1D18A9856A87
last_name: Nejjar
- first_name: Mirjana
full_name: Vuletíc, Mirjana
last_name: Vuletíc
citation:
ama: 'Betea D, Bouttier J, Nejjar P, Vuletíc M. New edge asymptotics of skew Young
diagrams via free boundaries. In: Proceedings on the 31st International Conference
on Formal Power Series and Algebraic Combinatorics. Formal Power Series and
Algebraic Combinatorics; 2019.'
apa: 'Betea, D., Bouttier, J., Nejjar, P., & Vuletíc, M. (2019). New edge asymptotics
of skew Young diagrams via free boundaries. In Proceedings on the 31st International
Conference on Formal Power Series and Algebraic Combinatorics. Ljubljana,
Slovenia: Formal Power Series and Algebraic Combinatorics.'
chicago: Betea, Dan, Jérémie Bouttier, Peter Nejjar, and Mirjana Vuletíc. “New Edge
Asymptotics of Skew Young Diagrams via Free Boundaries.” In Proceedings on
the 31st International Conference on Formal Power Series and Algebraic Combinatorics.
Formal Power Series and Algebraic Combinatorics, 2019.
ieee: D. Betea, J. Bouttier, P. Nejjar, and M. Vuletíc, “New edge asymptotics of
skew Young diagrams via free boundaries,” in Proceedings on the 31st International
Conference on Formal Power Series and Algebraic Combinatorics, Ljubljana,
Slovenia, 2019.
ista: 'Betea D, Bouttier J, Nejjar P, Vuletíc M. 2019. New edge asymptotics of skew
Young diagrams via free boundaries. Proceedings on the 31st International Conference
on Formal Power Series and Algebraic Combinatorics. FPSAC: International Conference
on Formal Power Series and Algebraic Combinatorics, 34.'
mla: Betea, Dan, et al. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.”
Proceedings on the 31st International Conference on Formal Power Series and
Algebraic Combinatorics, 34, Formal Power Series and Algebraic Combinatorics,
2019.
short: D. Betea, J. Bouttier, P. Nejjar, M. Vuletíc, in:, Proceedings on the 31st
International Conference on Formal Power Series and Algebraic Combinatorics, Formal
Power Series and Algebraic Combinatorics, 2019.
conference:
end_date: 2019-07-05
location: Ljubljana, Slovenia
name: 'FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics'
start_date: 2019-07-01
date_created: 2020-07-26T22:01:04Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2021-01-12T08:17:18Z
day: '01'
department:
- _id: LaEr
ec_funded: 1
external_id:
arxiv:
- '1902.08750'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.08750
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Proceedings on the 31st International Conference on Formal Power Series
and Algebraic Combinatorics
publication_status: published
publisher: Formal Power Series and Algebraic Combinatorics
quality_controlled: '1'
scopus_import: '1'
status: public
title: New edge asymptotics of skew Young diagrams via free boundaries
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '8228'
abstract:
- lang: eng
text: "Background: Atopics have a lower risk for malignancies, and IgE targeted
to tumors is superior to IgG in fighting cancer. Whether IgE-mediated innate or
adaptive immune surveillance can confer protection against tumors remains unclear.\r\nObjective:
We aimed to investigate the effects of active and passive immunotherapy to the
tumor-associated antigen HER-2 in three murine models differing in Epsilon-B-cell-receptor
expression affecting the levels of expressed IgE.\r\nMethods: We compared the
levels of several serum specific anti-HER-2 antibodies (IgE, IgG1, IgG2a, IgG2b,
IgA) and the survival rates in low-IgE ΔM1M2 mice lacking the transmembrane/cytoplasmic
domain of Epsilon-B-cell-receptors expressing reduced IgE levels, high-IgE KN1
mice expressing chimeric Epsilon-Gamma1-B-cell receptors with 4-6-fold elevated
serum IgE levels, and wild type (WT) BALB/c. Prior engrafting mice with D2F2/E2
mammary tumors overexpressing HER-2, mice were vaccinated with HER-2 or vehicle
control PBS using the Th2-adjuvant Al(OH)3 (active immunotherapy), or treated
with the murine anti-HER-2 IgG1 antibody 4D5 (passive immunotherapy).\r\nResults:
Overall, among the three strains of mice, HER-2 vaccination induced significantly
higher levels of HER-2 specific IgE and IgG1 in high-IgE KN1, while low-IgE ΔM1M2
mice had higher IgG2a levels. HER-2 vaccination and passive immunotherapy prolonged
the survival in tumor-grafted WT and low-IgE ΔM1M2 strains compared with treatment
controls; active vaccination provided the highest benefit. Notably, untreated
high-IgE KN1 mice displayed the longest survival of all strains, which could not
be further extended by active or passive immunotherapy.\r\nConclusion: Active
and passive immunotherapies prolong survival in wild type and low-IgE ΔM1M2 mice
engrafted with mammary tumors. High-IgE KN1 mice have an innate survival benefit
following tumor challenge."
article_number: '100044'
article_processing_charge: No
article_type: original
author:
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
orcid: 0000-0002-8701-2412
- first_name: Gertrude
full_name: Achatz-Straussberger, Gertrude
last_name: Achatz-Straussberger
- first_name: Anna
full_name: Bentley-Lukschal, Anna
last_name: Bentley-Lukschal
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Gernot
full_name: Achatz, Gernot
last_name: Achatz
- first_name: Sophia N.
full_name: Karagiannis, Sophia N.
last_name: Karagiannis
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: 'Singer J, Achatz-Straussberger G, Bentley-Lukschal A, et al. AllergoOncology:
High innate IgE levels are decisive for the survival of cancer-bearing mice. World
Allergy Organization Journal. 2019;12(7). doi:10.1016/j.waojou.2019.100044'
apa: 'Singer, J., Achatz-Straussberger, G., Bentley-Lukschal, A., Singer, J., Achatz,
G., Karagiannis, S. N., & Jensen-Jarolim, E. (2019). AllergoOncology: High
innate IgE levels are decisive for the survival of cancer-bearing mice. World
Allergy Organization Journal. Elsevier. https://doi.org/10.1016/j.waojou.2019.100044'
chicago: 'Singer, Josef, Gertrude Achatz-Straussberger, Anna Bentley-Lukschal, Judit
Singer, Gernot Achatz, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology:
High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.”
World Allergy Organization Journal. Elsevier, 2019. https://doi.org/10.1016/j.waojou.2019.100044.'
ieee: 'J. Singer et al., “AllergoOncology: High innate IgE levels are decisive
for the survival of cancer-bearing mice,” World Allergy Organization Journal,
vol. 12, no. 7. Elsevier, 2019.'
ista: 'Singer J, Achatz-Straussberger G, Bentley-Lukschal A, Singer J, Achatz G,
Karagiannis SN, Jensen-Jarolim E. 2019. AllergoOncology: High innate IgE levels
are decisive for the survival of cancer-bearing mice. World Allergy Organization
Journal. 12(7), 100044.'
mla: 'Singer, Josef, et al. “AllergoOncology: High Innate IgE Levels Are Decisive
for the Survival of Cancer-Bearing Mice.” World Allergy Organization Journal,
vol. 12, no. 7, 100044, Elsevier, 2019, doi:10.1016/j.waojou.2019.100044.'
short: J. Singer, G. Achatz-Straussberger, A. Bentley-Lukschal, J. Singer, G. Achatz,
S.N. Karagiannis, E. Jensen-Jarolim, World Allergy Organization Journal 12 (2019).
date_created: 2020-08-10T11:50:54Z
date_published: 2019-07-29T00:00:00Z
date_updated: 2021-01-12T08:17:36Z
day: '29'
doi: 10.1016/j.waojou.2019.100044
extern: '1'
intvolume: ' 12'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.waojou.2019.100044
month: '07'
oa: 1
oa_version: Published Version
publication: World Allergy Organization Journal
publication_identifier:
issn:
- 1939-4551
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing
mice'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2019'
...
---
_id: '8229'
abstract:
- lang: eng
text: Food proteins may get nitrated by various exogenous or endogenous mechanisms.
As individuals might get recurrently exposed to nitrated proteins via daily diet,
we aimed to investigate the effect of repeatedly ingested nitrated food proteins
on the subsequent immune response in non-allergic and allergic mice using the
milk allergen beta-lactoglobulin (BLG) as model food protein in a mouse model.
Evaluating the presence of nitrated proteins in food, we could detect 3-nitrotyrosine
(3-NT) in extracts of different foods and in stomach content extracts of non-allergic
mice under physiological conditions. Chemically nitrated BLG (BLGn) exhibited
enhanced susceptibility to degradation in simulated gastric fluid experiments
compared to untreated BLG (BLGu). Gavage of BLGn to non-allergic animals increased
interferon-γ and interleukin-10 release of stimulated spleen cells and led to
the formation of BLG-specific serum IgA. Allergic mice receiving three oral gavages
of BLGn had higher levels of mouse mast cell protease-1 (mMCP-1) compared to allergic
mice receiving BLGu. Regardless of the preceding immune status, non-allergic or
allergic, repeatedly ingested nitrated food proteins seem to considerably influence
the subsequent immune response.
article_number: '2463'
article_processing_charge: No
article_type: original
author:
- first_name: Anna S.
full_name: Ondracek, Anna S.
last_name: Ondracek
orcid: 0000-0001-7625-3651
- first_name: Denise
full_name: Heiden, Denise
last_name: Heiden
- first_name: Gertie J.
full_name: Oostingh, Gertie J.
last_name: Oostingh
- first_name: Elisabeth
full_name: Fuerst, Elisabeth
last_name: Fuerst
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Cornelia
full_name: Bergmayr, Cornelia
last_name: Bergmayr
- first_name: Johanna
full_name: Rohrhofer, Johanna
last_name: Rohrhofer
orcid: 0000-0002-2783-2099
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
orcid: 0000-0003-4019-5765
- first_name: Albert
full_name: Duschl, Albert
last_name: Duschl
orcid: 0000-0002-7034-9860
- first_name: Eva
full_name: Untersmayr, Eva
last_name: Untersmayr
orcid: 0000-0002-1963-499X
citation:
ama: Ondracek AS, Heiden D, Oostingh GJ, et al. Immune effects of the nitrated food
allergen beta-lactoglobulin in an experimental food allergy model. Nutrients.
2019;11(10). doi:10.3390/nu11102463
apa: Ondracek, A. S., Heiden, D., Oostingh, G. J., Fuerst, E., Singer, J., Bergmayr,
C., … Untersmayr, E. (2019). Immune effects of the nitrated food allergen beta-lactoglobulin
in an experimental food allergy model. Nutrients. MDPI. https://doi.org/10.3390/nu11102463
chicago: Ondracek, Anna S., Denise Heiden, Gertie J. Oostingh, Elisabeth Fuerst,
Judit Singer, Cornelia Bergmayr, Johanna Rohrhofer, Erika Jensen-Jarolim, Albert
Duschl, and Eva Untersmayr. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin
in an Experimental Food Allergy Model.” Nutrients. MDPI, 2019. https://doi.org/10.3390/nu11102463.
ieee: A. S. Ondracek et al., “Immune effects of the nitrated food allergen
beta-lactoglobulin in an experimental food allergy model,” Nutrients, vol.
11, no. 10. MDPI, 2019.
ista: Ondracek AS, Heiden D, Oostingh GJ, Fuerst E, Singer J, Bergmayr C, Rohrhofer
J, Jensen-Jarolim E, Duschl A, Untersmayr E. 2019. Immune effects of the nitrated
food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients.
11(10), 2463.
mla: Ondracek, Anna S., et al. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin
in an Experimental Food Allergy Model.” Nutrients, vol. 11, no. 10, 2463,
MDPI, 2019, doi:10.3390/nu11102463.
short: A.S. Ondracek, D. Heiden, G.J. Oostingh, E. Fuerst, J. Singer, C. Bergmayr,
J. Rohrhofer, E. Jensen-Jarolim, A. Duschl, E. Untersmayr, Nutrients 11 (2019).
date_created: 2020-08-10T11:51:04Z
date_published: 2019-10-15T00:00:00Z
date_updated: 2021-01-12T08:17:36Z
day: '15'
doi: 10.3390/nu11102463
extern: '1'
intvolume: ' 11'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3390/nu11102463
month: '10'
oa: 1
oa_version: Published Version
publication: Nutrients
publication_identifier:
issn:
- 2072-6643
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental
food allergy model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2019'
...
---
_id: '8227'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Kristina M.
full_name: Ilieva, Kristina M.
last_name: Ilieva
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Heather J.
full_name: Bax, Heather J.
last_name: Bax
- first_name: Silvia
full_name: Crescioli, Silvia
last_name: Crescioli
- first_name: Laura
full_name: Montero‐Morales, Laura
last_name: Montero‐Morales
- first_name: Silvia
full_name: Mele, Silvia
last_name: Mele
- first_name: Heng Sheng
full_name: Sow, Heng Sheng
last_name: Sow
- first_name: Chara
full_name: Stavraka, Chara
last_name: Stavraka
- first_name: Debra H.
full_name: Josephs, Debra H.
last_name: Josephs
- first_name: James F.
full_name: Spicer, James F.
last_name: Spicer
- first_name: Herta
full_name: Steinkellner, Herta
last_name: Steinkellner
orcid: 0000-0003-4823-1505
- first_name: Erika
full_name: Jensen‐Jarolim, Erika
last_name: Jensen‐Jarolim
orcid: 0000-0003-4019-5765
- first_name: Andrew N. J.
full_name: Tutt, Andrew N. J.
last_name: Tutt
orcid: 0000-0001-8715-2901
- first_name: Sophia N.
full_name: Karagiannis, Sophia N.
last_name: Karagiannis
orcid: 0000-0002-4100-7810
citation:
ama: 'Ilieva KM, Singer J, Bax HJ, et al. AllergoOncology: Expression platform development
and functional profiling of an anti‐HER2 IgE antibody. Allergy. 2019;74(10):1985-1989.
doi:10.1111/all.13818'
apa: 'Ilieva, K. M., Singer, J., Bax, H. J., Crescioli, S., Montero‐Morales, L.,
Mele, S., … Karagiannis, S. N. (2019). AllergoOncology: Expression platform development
and functional profiling of an anti‐HER2 IgE antibody. Allergy. Wiley.
https://doi.org/10.1111/all.13818'
chicago: 'Ilieva, Kristina M., Judit Singer, Heather J. Bax, Silvia Crescioli, Laura
Montero‐Morales, Silvia Mele, Heng Sheng Sow, et al. “AllergoOncology: Expression
Platform Development and Functional Profiling of an Anti‐HER2 IgE Antibody.” Allergy.
Wiley, 2019. https://doi.org/10.1111/all.13818.'
ieee: 'K. M. Ilieva et al., “AllergoOncology: Expression platform development
and functional profiling of an anti‐HER2 IgE antibody,” Allergy, vol. 74,
no. 10. Wiley, pp. 1985–1989, 2019.'
ista: 'Ilieva KM, Singer J, Bax HJ, Crescioli S, Montero‐Morales L, Mele S, Sow
HS, Stavraka C, Josephs DH, Spicer JF, Steinkellner H, Jensen‐Jarolim E, Tutt
ANJ, Karagiannis SN. 2019. AllergoOncology: Expression platform development and
functional profiling of an anti‐HER2 IgE antibody. Allergy. 74(10), 1985–1989.'
mla: 'Ilieva, Kristina M., et al. “AllergoOncology: Expression Platform Development
and Functional Profiling of an Anti‐HER2 IgE Antibody.” Allergy, vol. 74,
no. 10, Wiley, 2019, pp. 1985–89, doi:10.1111/all.13818.'
short: K.M. Ilieva, J. Singer, H.J. Bax, S. Crescioli, L. Montero‐Morales, S. Mele,
H.S. Sow, C. Stavraka, D.H. Josephs, J.F. Spicer, H. Steinkellner, E. Jensen‐Jarolim,
A.N.J. Tutt, S.N. Karagiannis, Allergy 74 (2019) 1985–1989.
date_created: 2020-08-10T11:50:42Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2021-01-12T08:17:35Z
day: '01'
doi: 10.1111/all.13818
extern: '1'
intvolume: ' 74'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/all.13818
month: '10'
oa: 1
oa_version: Published Version
page: 1985-1989
publication: Allergy
publication_identifier:
issn:
- 0105-4538
- 1398-9995
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: 'AllergoOncology: Expression platform development and functional profiling
of an anti‐HER2 IgE antibody'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2019'
...
---
_id: '8263'
abstract:
- lang: eng
text: "Background: The genus Streptococcus comprises pathogens that strongly influence
the health of humans and animals. Genome sequencing of multiple Streptococcus
strains demonstrated high variability in gene content and order even in closely
related strains of the same species and created a newly emerged object for genomic
analysis, the pan-genome. Here we analysed the genome evolution of 25 strains
of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of
Streptococcus pneumoniae.\r\n\r\nResults: Fractions of the pan-genome, unique,
periphery, and universal genes differ in size, functional composition, the level
of nucleotide substitutions, and predisposition to horizontal gene transfer and
genomic rearrangements. The density of substitutions in intergenic regions appears
to be correlated with selection acting on adjacent genes, implying that more conserved
genes tend to have more conserved regulatory regions.\r\nThe total pan-genome
of the genus is open, but only due to strain-specific genes, whereas other pan-genome
fractions reach saturation. We have identified the set of genes with phylogenies
inconsistent with species and non-conserved location in the chromosome; these
genes are rare in at least one species and have likely experienced recent horizontal
transfer between species. The strain-specific fraction is enriched with mobile
elements and hypothetical proteins, but also contains a number of candidate virulence-related
genes, so it may have a strong impact on adaptability and pathogenicity.\r\nMapping
the rearrangements to the phylogenetic tree revealed large parallel inversions
in all species. A parallel inversion of length 15 kB with breakpoints formed by
genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to
replacement of gene fragments that likely indicates the action of an antigen variation
mechanism.\r\n\r\nConclusions: Members of genus Streptococcus have a highly dynamic,
open pan-genome, that potentially confers them with the ability to adapt to changing
environmental conditions, i.e. antibiotic resistance or transmission between different
hosts. Hence, integrated analysis of all aspects of genome evolution is important
for the identification of potential pathogens and design of drugs and vaccines."
article_number: '83'
article_processing_charge: No
article_type: original
author:
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
orcid: 0000-0003-0120-9319
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Anna A.
full_name: Karan, Anna A.
last_name: Karan
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: 'Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. Micro-evolution of three
Streptococcus species: Selection, antigenic variation, and horizontal gene inflow.
BMC Evolutionary Biology. 2019;19. doi:10.1186/s12862-019-1403-6'
apa: 'Shelyakin, P. V., Bochkareva, O., Karan, A. A., & Gelfand, M. S. (2019).
Micro-evolution of three Streptococcus species: Selection, antigenic variation,
and horizontal gene inflow. BMC Evolutionary Biology. Springer Nature.
https://doi.org/10.1186/s12862-019-1403-6'
chicago: 'Shelyakin, Pavel V., Olga Bochkareva, Anna A. Karan, and Mikhail S. Gelfand.
“Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation,
and Horizontal Gene Inflow.” BMC Evolutionary Biology. Springer Nature,
2019. https://doi.org/10.1186/s12862-019-1403-6.'
ieee: 'P. V. Shelyakin, O. Bochkareva, A. A. Karan, and M. S. Gelfand, “Micro-evolution
of three Streptococcus species: Selection, antigenic variation, and horizontal
gene inflow,” BMC Evolutionary Biology, vol. 19. Springer Nature, 2019.'
ista: 'Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. 2019. Micro-evolution of
three Streptococcus species: Selection, antigenic variation, and horizontal gene
inflow. BMC Evolutionary Biology. 19, 83.'
mla: 'Shelyakin, Pavel V., et al. “Micro-Evolution of Three Streptococcus Species:
Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary
Biology, vol. 19, 83, Springer Nature, 2019, doi:10.1186/s12862-019-1403-6.'
short: P.V. Shelyakin, O. Bochkareva, A.A. Karan, M.S. Gelfand, BMC Evolutionary
Biology 19 (2019).
date_created: 2020-08-15T11:04:07Z
date_published: 2019-03-27T00:00:00Z
date_updated: 2023-02-23T13:28:54Z
day: '27'
doi: 10.1186/s12862-019-1403-6
extern: '1'
intvolume: ' 19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/s12862-019-1403-6
month: '03'
oa: 1
oa_version: Published Version
publication: BMC Evolutionary Biology
publication_identifier:
issn:
- 1471-2148
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Micro-evolution of three Streptococcus species: Selection, antigenic variation,
and horizontal gene inflow'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2019'
...
---
_id: '8296'
abstract:
- lang: eng
text: While showing great promise, smart contracts are difficult to program correctly,
as they need a deep understanding of cryptography and distributed algorithms,
and offer limited functionality, as they have to be deterministic and cannot operate
on secret data. In this paper we present Protean, a general-purpose decentralized
computing platform that addresses these limitations by moving from a monolithic
execution model, where all participating nodes store all the state and execute
every computation, to a modular execution-model. Protean employs secure specialized
modules, called functional units, for building decentralized applications that
are currently insecure or impossible to implement with smart contracts. Each functional
unit is a distributed system that provides a special-purpose functionality by
exposing atomic transactions to the smart-contract developer. Combining these
transactions into arbitrarily-defined workflows, developers can build a larger
class of decentralized applications, such as provably-secure and fair lotteries
or e-voting.
article_processing_charge: No
author:
- first_name: Enis Ceyhun
full_name: Alp, Enis Ceyhun
last_name: Alp
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Georgia
full_name: Fragkouli, Georgia
last_name: Fragkouli
- first_name: Bryan
full_name: Ford, Bryan
last_name: Ford
citation:
ama: 'Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. Rethinking general-purpose
decentralized computing. In: Proceedings of the Workshop on Hot Topics in Operating
Systems. ACM; 2019:105-112. doi:10.1145/3317550.3321448'
apa: 'Alp, E. C., Kokoris Kogias, E., Fragkouli, G., & Ford, B. (2019). Rethinking
general-purpose decentralized computing. In Proceedings of the Workshop on
Hot Topics in Operating Systems (pp. 105–112). Bertinoro, Italy: ACM. https://doi.org/10.1145/3317550.3321448'
chicago: Alp, Enis Ceyhun, Eleftherios Kokoris Kogias, Georgia Fragkouli, and Bryan
Ford. “Rethinking General-Purpose Decentralized Computing.” In Proceedings
of the Workshop on Hot Topics in Operating Systems, 105–12. ACM, 2019. https://doi.org/10.1145/3317550.3321448.
ieee: E. C. Alp, E. Kokoris Kogias, G. Fragkouli, and B. Ford, “Rethinking general-purpose
decentralized computing,” in Proceedings of the Workshop on Hot Topics in Operating
Systems, Bertinoro, Italy, 2019, pp. 105–112.
ista: 'Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. 2019. Rethinking general-purpose
decentralized computing. Proceedings of the Workshop on Hot Topics in Operating
Systems. HotOS: Workshop on Hot Topics in Operating Systems, 105–112.'
mla: Alp, Enis Ceyhun, et al. “Rethinking General-Purpose Decentralized Computing.”
Proceedings of the Workshop on Hot Topics in Operating Systems, ACM, 2019,
pp. 105–12, doi:10.1145/3317550.3321448.
short: E.C. Alp, E. Kokoris Kogias, G. Fragkouli, B. Ford, in:, Proceedings of the
Workshop on Hot Topics in Operating Systems, ACM, 2019, pp. 105–112.
conference:
end_date: 2019-05-15
location: Bertinoro, Italy
name: 'HotOS: Workshop on Hot Topics in Operating Systems'
start_date: 2019-05-13
date_created: 2020-08-26T11:45:45Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2021-01-12T08:17:56Z
day: '01'
doi: 10.1145/3317550.3321448
extern: '1'
language:
- iso: eng
month: '05'
oa_version: None
page: 105-112
publication: Proceedings of the Workshop on Hot Topics in Operating Systems
publication_identifier:
isbn:
- '9781450367271'
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rethinking general-purpose decentralized computing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '8304'
abstract:
- lang: eng
text: "Enabling secure communication across distributed systems is usually studied
under the assumption of trust between the different systems and an external adversary
trying to compromise the messages. With the appearance of distributed ledgers
or blockchains, numerous protocols have emerged, which attempt to achieve trustless
communication between distrusting ledgers and participants. Cross-chain communication
(CCC) thereby plays a fundamental role in cryptocurrency exchanges, sharding,
bootstrapping of new and feature-extension of existing distributed ledgers. Unfortunately,
existing proposals are designed ad-hoc for specific use-cases, making it hard
to gain confidence on their correctness and composability.\r\nWe provide the first
systematic exposition of protocols for CCC. First, we formalize the underlying
research problem and show that CCC is impossible without a trusted third party,
contrary to common beliefs in the blockchain community. We then develop a framework
to evaluate existing and to design new cross-chain protocols. The framework is
based on the use case, the trust model, and the security assumptions of interlinked
blockchains. Finally, we identify security and privacy challenges faced by protocols
in the cross-chain setting.\r\nThis Systematization of Knowledge (SoK) offers
a comprehensive guide for designing protocols bridging the numerous distributed
ledgers available today. It aims to facilitate clearer communication between academia
and industry in the field."
article_number: 2019/1128
article_processing_charge: No
author:
- first_name: Alexei
full_name: Zamyatin, Alexei
last_name: Zamyatin
- first_name: Mustafa
full_name: Al-Bassam, Mustafa
last_name: Al-Bassam
- first_name: Dionysis
full_name: Zindros, Dionysis
last_name: Zindros
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Pedro
full_name: Moreno-Sanchez, Pedro
last_name: Moreno-Sanchez
- first_name: Aggelos
full_name: Kiayias, Aggelos
last_name: Kiayias
- first_name: William J.
full_name: Knottenbelt, William J.
last_name: Knottenbelt
citation:
ama: 'Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed
ledgers. Cryptology ePrint Archive.'
apa: 'Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez,
P., Kiayias, A., & Knottenbelt, W. J. (n.d.). SoK: Communication across distributed
ledgers. Cryptology ePrint Archive.'
chicago: 'Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris
Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK:
Communication across Distributed Ledgers.” Cryptology EPrint Archive, n.d.'
ieee: 'A. Zamyatin et al., “SoK: Communication across distributed ledgers,”
Cryptology ePrint Archive. .'
ista: 'Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias
A, Knottenbelt WJ. SoK: Communication across distributed ledgers. Cryptology ePrint
Archive, 2019/1128.'
mla: 'Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.”
Cryptology EPrint Archive, 2019/1128.'
short: A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez,
A. Kiayias, W.J. Knottenbelt, Cryptology EPrint Archive (n.d.).
date_created: 2020-08-26T12:16:38Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2021-09-24T12:08:14Z
day: '01'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://eprint.iacr.org/2019/1128 '
month: '10'
oa: 1
oa_version: Preprint
publication: Cryptology ePrint Archive
publication_status: submitted
status: public
title: 'SoK: Communication across distributed ledgers'
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2019'
...
---
_id: '8303'
abstract:
- lang: eng
text: 'ByzCoin, a promising alternative of Bitcoin, is a scalable consensus protocol
used as a building block of many research and enterprise-level decentralized systems.
In this paper, we show that ByzCoin is unsuitable for deployment in an anopen,
adversarial network and instead introduceMOTOR. MOTORis designed as a secure,
robust, and scalable consensus suitable for permissionless sharded blockchains.
MOTORachieves these properties by making four key design choices: (a) it prioritizes
robustness in adversarial environments while maintaining adequate scalability,
(b) it employees provably correct cryptography that resists DoS attacks from individual
nodes, (c) it deploys unpredictable rotating leaders to defend against mildly-adaptive
adversaries and prevents censorship, and (d) it creates an incentive compatible
reward mechanism. These choices are materialized as (a) a “rotating subleader”
communication pattern that balances the scalability needs with the robustness
requirements under failures, (b) deployment of provable secure BLS multi-signatures,
(c) use of deterministic thresh-old signatures as a source of randomness and (d)
careful design of the reward allocation mechanism. We have implemented MOTORand
compare it withByzCoin. We show that MOTORcan scale similar to ByzCoin with an
at most2xoverhead whereas it maintains good performance even under high-percentage
of faults, unlike ByzCoin.'
article_number: 2019/676
article_processing_charge: No
author:
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
citation:
ama: Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers.
Cryptology ePrint Archive.
apa: Kokoris Kogias, E. (n.d.). Robust and scalable consensus for sharded distributed
ledgers. Cryptology ePrint Archive.
chicago: Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded
Distributed Ledgers.” Cryptology EPrint Archive, n.d.
ieee: E. Kokoris Kogias, “Robust and scalable consensus for sharded distributed
ledgers,” Cryptology ePrint Archive. .
ista: Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers.
Cryptology ePrint Archive, 2019/676.
mla: Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed
Ledgers.” Cryptology EPrint Archive, 2019/676.
short: E. Kokoris Kogias, Cryptology EPrint Archive (n.d.).
date_created: 2020-08-26T12:13:56Z
date_published: 2019-06-06T00:00:00Z
date_updated: 2021-09-24T12:07:11Z
day: '06'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2019/676
month: '06'
oa: 1
oa_version: Preprint
publication: Cryptology ePrint Archive
publication_status: submitted
status: public
title: Robust and scalable consensus for sharded distributed ledgers
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2019'
...
---
_id: '8311'
abstract:
- lang: eng
text: 'One of the core promises of blockchain technology is that of enabling trustworthy
data dissemination in a trustless environment. What current blockchain systems
deliver, however, is slow dissemination of public data, rendering blockchain technology
unusable in settings where latency, transaction capacity, or data confidentiality
are important. In this thesis we focus on providing solutions on two of the most
pressing problems blockchain technology currently faces: scalability and data
confidentiality. To address the scalability issue, we present OMNILEDGER, a novel
scale-out distributed ledger that preserves long-term security under permissionless
operation. It ensures security and correctness by using a bias-resistant public-randomness
protocol for choosing large, statistically representative shards that process
transactions, and by introducing an efficient cross-shard commit protocol that
atomically handles transactions affecting multiple shards. To enable secure sharing
of confidential data we present CALYPSO, the first fully decentralized, auditable
access-control framework for secure blockchain-based data sharing which builds
upon two abstractions. First, on-chain secrets enable collective management of
(verifiably shared) secrets under a Byzantine adversary where an access-control
blockchain enforces user-specific access rules and a secret-management cothority
administers encrypted data. Second, skipchain-based identity and access management
enables efficient administration of dynamic, sovereign identities and access policies
and, in particular, permits clients to maintain long-term relationships with respect
to evolving user identities thanks to the trust-delegating forward links of skipchains.
In order to build OMNILEDGER and CALYPSO, we first build a set of tools for efficient
decentralization, which are presented in Part II of this dissertation. These tools
can be used in decentralized and distributed systems to achieve (1) scalable consensus
(BYZCOIN), (2) bias- resistant distributed randomness creations (RANDHOUND), and
(3) relationship-keeping between independently updating communication endpoints
(SKIPCHAINIAC). Although we use this tools in the scope off this thesis, they
can be (and already have been) used in a far wider scope.'
article_processing_charge: No
author:
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
citation:
ama: Kokoris Kogias E. Secure, confidential blockchains providing high throughput
and low latency. 2019. doi:10.5075/epfl-thesis-7101
apa: Kokoris Kogias, E. (2019). Secure, confidential blockchains providing high
throughput and low latency. École Polytechnique Fédérale de Lausanne. https://doi.org/10.5075/epfl-thesis-7101
chicago: Kokoris Kogias, Eleftherios. “Secure, Confidential Blockchains Providing
High Throughput and Low Latency.” École Polytechnique Fédérale de Lausanne, 2019.
https://doi.org/10.5075/epfl-thesis-7101.
ieee: E. Kokoris Kogias, “Secure, confidential blockchains providing high throughput
and low latency,” École Polytechnique Fédérale de Lausanne, 2019.
ista: Kokoris Kogias E. 2019. Secure, confidential blockchains providing high throughput
and low latency. École Polytechnique Fédérale de Lausanne.
mla: Kokoris Kogias, Eleftherios. Secure, Confidential Blockchains Providing
High Throughput and Low Latency. École Polytechnique Fédérale de Lausanne,
2019, doi:10.5075/epfl-thesis-7101.
short: E. Kokoris Kogias, Secure, Confidential Blockchains Providing High Throughput
and Low Latency, École Polytechnique Fédérale de Lausanne, 2019.
date_created: 2020-08-27T11:22:24Z
date_published: 2019-09-27T00:00:00Z
date_updated: 2021-12-20T15:30:47Z
day: '27'
degree_awarded: PhD
doi: 10.5075/epfl-thesis-7101
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.doi.org/10.5075/epfl-thesis-7101
month: '09'
oa: 1
oa_version: Published Version
page: '244'
publication_status: published
publisher: École Polytechnique Fédérale de Lausanne
status: public
supervisor:
- first_name: Bryan Alexander
full_name: Ford, Bryan Alexander
last_name: Ford
title: Secure, confidential blockchains providing high throughput and low latency
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2019'
...
---
_id: '8314'
abstract:
- lang: eng
text: "Off-chain protocols (channels) are a promising solution to the scalability
and privacy challenges of blockchain payments. Current proposals, however, require
synchrony assumptions to preserve the safety of a channel, leaking to an adversary
the exact amount of time needed to control the network for a successful attack.
In this paper, we introduce Brick, the first payment channel that remains secure
under network asynchrony and concurrently provides correct incentives. The core
idea is to incorporate the conflict resolution process within the channel by introducing
a rational committee of external parties, called Wardens. Hence, if a party wants
to close a channel unilaterally, it can only get the committee's approval for
the last valid state. Brick provides sub-second latency because it does not employ
heavy-weight consensus. Instead,\r\nBrick uses consistent broadcast to announce
updates and close the channel, a light-weight abstraction that is powerful enough
to preserve safety and liveness to any rational parties. Furthermore, we consider
permissioned blockchains, where the additional property of auditability might
be desired for regulatory purposes. We introduce Brick+, an off-chain construction
that provides auditability on top of Brick without conflicting with its privacy
guarantees. We formally define the properties our payment channel construction
should fulfill, and prove that both Brick and Brick+ satisfy them. We also design
incentives for Brick such that honest and rational behavior aligns. Finally, we
provide a reference implementation of the smart contracts in Solidity."
article_number: '1905.11360'
article_processing_charge: No
author:
- first_name: Georgia
full_name: Avarikioti, Georgia
last_name: Avarikioti
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Roger
full_name: Wattenhofer, Roger
last_name: Wattenhofer
- first_name: Dionysis
full_name: Zindros, Dionysis
last_name: Zindros
citation:
ama: 'Avarikioti G, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous
payment channels. arXiv.'
apa: 'Avarikioti, G., Kokoris Kogias, E., Wattenhofer, R., & Zindros, D. (n.d.).
Brick: Asynchronous payment channels. arXiv.'
chicago: 'Avarikioti, Georgia, Eleftherios Kokoris Kogias, Roger Wattenhofer, and
Dionysis Zindros. “Brick: Asynchronous Payment Channels.” ArXiv, n.d.'
ieee: 'G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick:
Asynchronous payment channels,” arXiv. .'
ista: 'Avarikioti G, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous
payment channels. arXiv, 1905.11360.'
mla: 'Avarikioti, Georgia, et al. “Brick: Asynchronous Payment Channels.” ArXiv,
1905.11360.'
short: G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, ArXiv (n.d.).
date_created: 2020-08-27T11:36:54Z
date_published: 2019-05-27T00:00:00Z
date_updated: 2021-01-12T08:18:04Z
day: '27'
extern: '1'
external_id:
arxiv:
- '1905.11360'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1905.11360
month: '05'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: 'Brick: Asynchronous payment channels'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '8315'
abstract:
- lang: eng
text: "Sharding distributed ledgers is the most promising on-chain solution for
scaling blockchain technology. In this work, we define and analyze the properties
a sharded distributed ledger should fulfill. More specifically, we show that a
sharded blockchain cannot be scalable under a fully adaptive adversary, but it
can scale up to $O(n/\\log n)$ under an epoch-adaptive adversary. This is possible
only if the distributed ledger creates succinct proofs of the valid state updates
at the end of each epoch. Our model builds upon and extends the Bitcoin backbone
protocol by defining consistency and\r\nscalability. Consistency encompasses the
need for atomic execution of cross-shard transactions to preserve safety, whereas
scalability encapsulates the speedup a sharded system can gain in comparison to
a non-sharded system. In\r\norder to show the power of our framework, we analyze
the most prominent sharded blockchains and either prove their correctness (OmniLedger,
RapidChain) under our model or pinpoint where they fail to balance the consistency
and\r\nscalability requirements (Elastico, Monoxide). "
article_number: '1910.10434'
article_processing_charge: No
author:
- first_name: Georgia
full_name: Avarikioti, Georgia
last_name: Avarikioti
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Roger
full_name: Wattenhofer, Roger
last_name: Wattenhofer
citation:
ama: 'Avarikioti G, Kokoris Kogias E, Wattenhofer R. Divide and scale: Formalization
of distributed ledger sharding protocols. arXiv.'
apa: 'Avarikioti, G., Kokoris Kogias, E., & Wattenhofer, R. (n.d.). Divide and
scale: Formalization of distributed ledger sharding protocols. arXiv.'
chicago: 'Avarikioti, Georgia, Eleftherios Kokoris Kogias, and Roger Wattenhofer.
“Divide and Scale: Formalization of Distributed Ledger Sharding Protocols.” ArXiv,
n.d.'
ieee: 'G. Avarikioti, E. Kokoris Kogias, and R. Wattenhofer, “Divide and scale:
Formalization of distributed ledger sharding protocols,” arXiv. .'
ista: 'Avarikioti G, Kokoris Kogias E, Wattenhofer R. Divide and scale: Formalization
of distributed ledger sharding protocols. arXiv, 1910.10434.'
mla: 'Avarikioti, Georgia, et al. “Divide and Scale: Formalization of Distributed
Ledger Sharding Protocols.” ArXiv, 1910.10434.'
short: G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, ArXiv (n.d.).
date_created: 2020-08-27T11:37:43Z
date_published: 2019-10-23T00:00:00Z
date_updated: 2021-01-12T08:18:05Z
day: '23'
extern: '1'
external_id:
arxiv:
- '1910.10434'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1910.10434
month: '10'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: 'Divide and scale: Formalization of distributed ledger sharding protocols'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '8313'
abstract:
- lang: eng
text: The present invention concerns a computer-implemented method for secure data
exchange between a sender (A) and a recipient (B), wherein the method is performed
by the sender (A) and comprises encrypting data using a symmetric key k, creating
a write transaction T W , wherein the write transaction T W comprises information
usable to derive the symmetric key k and an access policy identifying the recipient
(B) as being allowed to decrypt the encrypted data, providing the recipient (B)
access to the encrypted data, and sending the write transaction T W to a first
group of servers (AC) for being stored in a blockchain data structure maintained
by the first group of servers (AC).
applicant:
- 'École Polytechnique Fédérale De Lausanne '
article_processing_charge: No
author:
- first_name: Bryan
full_name: Ford, Bryan
last_name: Ford
- first_name: Linus
full_name: Gasser, Linus
last_name: Gasser
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Philipp
full_name: Janovic, Philipp
last_name: Janovic
citation:
ama: Ford B, Gasser L, Kokoris Kogias E, Janovic P. Methods and systems for secure
data exchange. 2019.
apa: Ford, B., Gasser, L., Kokoris Kogias, E., & Janovic, P. (2019). Methods
and systems for secure data exchange.
chicago: Ford, Bryan, Linus Gasser, Eleftherios Kokoris Kogias, and Philipp Janovic.
“Methods and Systems for Secure Data Exchange,” 2019.
ieee: B. Ford, L. Gasser, E. Kokoris Kogias, and P. Janovic, “Methods and systems
for secure data exchange.” 2019.
ista: Ford B, Gasser L, Kokoris Kogias E, Janovic P. 2019. Methods and systems for
secure data exchange.
mla: Ford, Bryan, et al. Methods and Systems for Secure Data Exchange. 2019.
short: B. Ford, L. Gasser, E. Kokoris Kogias, P. Janovic, (2019).
date_created: 2020-08-27T11:24:44Z
date_published: 2019-08-22T00:00:00Z
date_updated: 2022-01-05T14:00:32Z
day: '22'
extern: '1'
ipc: G06F21/62 ; H04L9/08 ; H04L9/32
ipn: WO2019158209 (A1)
main_file_link:
- open_access: '1'
url: https://patents.google.com/patent/WO2019158209A1
month: '08'
oa: 1
oa_version: Published Version
publication_date: 2019-08-22
status: public
title: Methods and systems for secure data exchange
type: patent
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2019'
...
---
_id: '8405'
abstract:
- lang: eng
text: Atomic-resolution structure determination is crucial for understanding protein
function. Cryo-EM and NMR spectroscopy both provide structural information, but
currently cryo-EM does not routinely give access to atomic-level structural data,
and, generally, NMR structure determination is restricted to small (<30 kDa) proteins.
We introduce an integrated structure determination approach that simultaneously
uses NMR and EM data to overcome the limits of each of these methods. The approach
enables structure determination of the 468 kDa large dodecameric aminopeptidase
TET2 to a precision and accuracy below 1 Å by combining secondary-structure information
obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large
subunits, distance restraints from backbone amides and ILV methyl groups, and
a 4.1 Å resolution EM map. The resulting structure exceeds current standards of
NMR and EM structure determination in terms of molecular weight and precision.
Importantly, the approach is successful even in cases where only medium-resolution
cryo-EM data are available.
article_number: '2697'
article_processing_charge: No
article_type: original
author:
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Leandro F.
full_name: Estrozi, Leandro F.
last_name: Estrozi
- first_name: Charles D.
full_name: Schwieters, Charles D.
last_name: Schwieters
- first_name: Gregory
full_name: Effantin, Gregory
last_name: Effantin
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Remy
full_name: Sounier, Remy
last_name: Sounier
- first_name: Astrid C.
full_name: Sivertsen, Astrid C.
last_name: Sivertsen
- first_name: Elena
full_name: Schmidt, Elena
last_name: Schmidt
- first_name: Rime
full_name: Kerfah, Rime
last_name: Kerfah
- first_name: Guillaume
full_name: Mas, Guillaume
last_name: Mas
- first_name: Jacques-Philippe
full_name: Colletier, Jacques-Philippe
last_name: Colletier
- first_name: Peter
full_name: Güntert, Peter
last_name: Güntert
- first_name: Adrien
full_name: Favier, Adrien
last_name: Favier
- first_name: Guy
full_name: Schoehn, Guy
last_name: Schoehn
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Jerome
full_name: Boisbouvier, Jerome
last_name: Boisbouvier
citation:
ama: Gauto DF, Estrozi LF, Schwieters CD, et al. Integrated NMR and cryo-EM atomic-resolution
structure determination of a half-megadalton enzyme complex. Nature Communications.
2019;10. doi:10.1038/s41467-019-10490-9
apa: Gauto, D. F., Estrozi, L. F., Schwieters, C. D., Effantin, G., Macek, P., Sounier,
R., … Boisbouvier, J. (2019). Integrated NMR and cryo-EM atomic-resolution structure
determination of a half-megadalton enzyme complex. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-019-10490-9
chicago: Gauto, Diego F., Leandro F. Estrozi, Charles D. Schwieters, Gregory Effantin,
Pavel Macek, Remy Sounier, Astrid C. Sivertsen, et al. “Integrated NMR and Cryo-EM
Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.”
Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-10490-9.
ieee: D. F. Gauto et al., “Integrated NMR and cryo-EM atomic-resolution structure
determination of a half-megadalton enzyme complex,” Nature Communications,
vol. 10. Springer Nature, 2019.
ista: Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen
AC, Schmidt E, Kerfah R, Mas G, Colletier J-P, Güntert P, Favier A, Schoehn G,
Schanda P, Boisbouvier J. 2019. Integrated NMR and cryo-EM atomic-resolution structure
determination of a half-megadalton enzyme complex. Nature Communications. 10,
2697.
mla: Gauto, Diego F., et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure
Determination of a Half-Megadalton Enzyme Complex.” Nature Communications,
vol. 10, 2697, Springer Nature, 2019, doi:10.1038/s41467-019-10490-9.
short: D.F. Gauto, L.F. Estrozi, C.D. Schwieters, G. Effantin, P. Macek, R. Sounier,
A.C. Sivertsen, E. Schmidt, R. Kerfah, G. Mas, J.-P. Colletier, P. Güntert, A.
Favier, G. Schoehn, P. Schanda, J. Boisbouvier, Nature Communications 10 (2019).
date_created: 2020-09-17T10:28:25Z
date_published: 2019-06-19T00:00:00Z
date_updated: 2021-01-12T08:19:03Z
day: '19'
doi: 10.1038/s41467-019-10490-9
extern: '1'
external_id:
pmid:
- '31217444'
intvolume: ' 10'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-019-10490-9
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton
enzyme complex
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2019'
...
---
_id: '8406'
abstract:
- lang: eng
text: Coordinated conformational transitions in oligomeric enzymatic complexes modulate
function in response to substrates and play a crucial role in enzyme inhibition
and activation. Caseinolytic protease (ClpP) is a tetradecameric complex, which
has emerged as a drug target against multiple pathogenic bacteria. Activation
of different ClpPs by inhibitors has been independently reported from drug development
efforts, but no rationale for inhibitor-induced activation has been hitherto proposed.
Using an integrated approach that includes x-ray crystallography, solid- and solution-state
nuclear magnetic resonance, molecular dynamics simulations, and isothermal titration
calorimetry, we show that the proteasome inhibitor bortezomib binds to the ClpP
active-site serine, mimicking a peptide substrate, and induces a concerted allosteric
activation of the complex. The bortezomib-activated conformation also exhibits
a higher affinity for its cognate unfoldase ClpX. We propose a universal allosteric
mechanism, where substrate binding to a single subunit locks ClpP into an active
conformation optimized for chaperone association and protein processive degradation.
article_number: eaaw3818
article_processing_charge: No
article_type: original
author:
- first_name: Jan
full_name: Felix, Jan
last_name: Felix
- first_name: Katharina
full_name: Weinhäupl, Katharina
last_name: Weinhäupl
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
- first_name: François
full_name: Dehez, François
last_name: Dehez
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Cecile
full_name: Morlot, Cecile
last_name: Morlot
- first_name: Olga
full_name: Abian, Olga
last_name: Abian
- first_name: Irina
full_name: Gutsche, Irina
last_name: Gutsche
- first_name: Adrian
full_name: Velazquez-Campoy, Adrian
last_name: Velazquez-Campoy
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Hugo
full_name: Fraga, Hugo
last_name: Fraga
citation:
ama: Felix J, Weinhäupl K, Chipot C, et al. Mechanism of the allosteric activation
of the ClpP protease machinery by substrates and active-site inhibitors. Science
Advances. 2019;5(9). doi:10.1126/sciadv.aaw3818
apa: Felix, J., Weinhäupl, K., Chipot, C., Dehez, F., Hessel, A., Gauto, D. F.,
… Fraga, H. (2019). Mechanism of the allosteric activation of the ClpP protease
machinery by substrates and active-site inhibitors. Science Advances. American
Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw3818
chicago: Felix, Jan, Katharina Weinhäupl, Christophe Chipot, François Dehez, Audrey
Hessel, Diego F. Gauto, Cecile Morlot, et al. “Mechanism of the Allosteric Activation
of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” Science
Advances. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/sciadv.aaw3818.
ieee: J. Felix et al., “Mechanism of the allosteric activation of the ClpP
protease machinery by substrates and active-site inhibitors,” Science Advances,
vol. 5, no. 9. American Association for the Advancement of Science, 2019.
ista: Felix J, Weinhäupl K, Chipot C, Dehez F, Hessel A, Gauto DF, Morlot C, Abian
O, Gutsche I, Velazquez-Campoy A, Schanda P, Fraga H. 2019. Mechanism of the allosteric
activation of the ClpP protease machinery by substrates and active-site inhibitors.
Science Advances. 5(9), eaaw3818.
mla: Felix, Jan, et al. “Mechanism of the Allosteric Activation of the ClpP Protease
Machinery by Substrates and Active-Site Inhibitors.” Science Advances,
vol. 5, no. 9, eaaw3818, American Association for the Advancement of Science,
2019, doi:10.1126/sciadv.aaw3818.
short: J. Felix, K. Weinhäupl, C. Chipot, F. Dehez, A. Hessel, D.F. Gauto, C. Morlot,
O. Abian, I. Gutsche, A. Velazquez-Campoy, P. Schanda, H. Fraga, Science Advances
5 (2019).
date_created: 2020-09-17T10:28:36Z
date_published: 2019-09-04T00:00:00Z
date_updated: 2021-01-12T08:19:03Z
day: '04'
doi: 10.1126/sciadv.aaw3818
extern: '1'
intvolume: ' 5'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.1126/sciadv.aaw3818'
month: '09'
oa: 1
oa_version: Published Version
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
status: public
title: Mechanism of the allosteric activation of the ClpP protease machinery by substrates
and active-site inhibitors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2019'
...
---
_id: '8413'
abstract:
- lang: eng
text: NMR relaxation dispersion methods provide a holistic way to observe microsecond
time-scale protein backbone motion both in solution and in the solid state. Different
nuclei (1H and 15N) and different relaxation dispersion techniques (Bloch–McConnell
and near-rotary-resonance) give complementary information about the amplitudes
and time scales of the conformational dynamics and provide comprehensive insights
into the mechanistic details of the structural rearrangements. In this paper,
we exemplify the benefits of the combination of various solution- and solid-state
relaxation dispersion methods on a microcrystalline protein (α-spectrin SH3 domain),
for which we are able to identify and model the functionally relevant conformational
rearrangements around the ligand recognition loop occurring on multiple microsecond
time scales. The observed loop motions suggest that the SH3 domain exists in a
binding-competent conformation in dynamic equilibrium with a sterically impaired
ground-state conformation both in solution and in crystalline form. This inherent
plasticity between the interconverting macrostates is compatible with a conformational-preselection
model and provides new insights into the recognition mechanisms of SH3 domains.
article_processing_charge: No
article_type: original
author:
- first_name: Petra
full_name: Rovó, Petra
last_name: Rovó
- first_name: Colin A.
full_name: Smith, Colin A.
last_name: Smith
- first_name: Diego
full_name: Gauto, Diego
last_name: Gauto
- first_name: Bert L.
full_name: de Groot, Bert L.
last_name: de Groot
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Rasmus
full_name: Linser, Rasmus
last_name: Linser
citation:
ama: Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. Mechanistic insights
into microsecond time-scale motion of solid proteins using complementary 15N and
1H relaxation dispersion techniques. Journal of the American Chemical Society.
2019;141(2):858-869. doi:10.1021/jacs.8b09258
apa: Rovó, P., Smith, C. A., Gauto, D., de Groot, B. L., Schanda, P., & Linser,
R. (2019). Mechanistic insights into microsecond time-scale motion of solid proteins
using complementary 15N and 1H relaxation dispersion techniques. Journal of
the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.8b09258
chicago: Rovó, Petra, Colin A. Smith, Diego Gauto, Bert L. de Groot, Paul Schanda,
and Rasmus Linser. “Mechanistic Insights into Microsecond Time-Scale Motion of
Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.”
Journal of the American Chemical Society. American Chemical Society, 2019.
https://doi.org/10.1021/jacs.8b09258.
ieee: P. Rovó, C. A. Smith, D. Gauto, B. L. de Groot, P. Schanda, and R. Linser,
“Mechanistic insights into microsecond time-scale motion of solid proteins using
complementary 15N and 1H relaxation dispersion techniques,” Journal of the
American Chemical Society, vol. 141, no. 2. American Chemical Society, pp.
858–869, 2019.
ista: Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. 2019. Mechanistic
insights into microsecond time-scale motion of solid proteins using complementary
15N and 1H relaxation dispersion techniques. Journal of the American Chemical
Society. 141(2), 858–869.
mla: Rovó, Petra, et al. “Mechanistic Insights into Microsecond Time-Scale Motion
of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.”
Journal of the American Chemical Society, vol. 141, no. 2, American Chemical
Society, 2019, pp. 858–69, doi:10.1021/jacs.8b09258.
short: P. Rovó, C.A. Smith, D. Gauto, B.L. de Groot, P. Schanda, R. Linser, Journal
of the American Chemical Society 141 (2019) 858–869.
date_created: 2020-09-17T10:29:50Z
date_published: 2019-01-08T00:00:00Z
date_updated: 2021-01-12T08:19:07Z
day: '08'
doi: 10.1021/jacs.8b09258
extern: '1'
external_id:
pmid:
- '30620186'
intvolume: ' 141'
issue: '2'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '01'
oa_version: Submitted Version
page: 858-869
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Mechanistic insights into microsecond time-scale motion of solid proteins using
complementary 15N and 1H relaxation dispersion techniques
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 141
year: '2019'
...
---
_id: '8412'
abstract:
- lang: eng
text: Microsecond to millisecond timescale backbone dynamics of the amyloid core
residues in Y145Stop human prion protein (PrP) fibrils were investigated by using
15N rotating frame (R1ρ) relaxation dispersion solid‐state nuclear magnetic resonance
spectroscopy over a wide range of spin‐lock fields. Numerical simulations enabled
the experimental relaxation dispersion profiles for most of the fibril core residues
to be modelled by using a two‐state exchange process with a common exchange rate
of 1000 s−1, corresponding to protein backbone motion on the timescale of 1 ms,
and an excited‐state population of 2 %. We also found that the relaxation dispersion
profiles for several amino acids positioned near the edges of the most structured
regions of the amyloid core were better modelled by assuming somewhat higher excited‐state
populations (∼5–15 %) and faster exchange rate constants, corresponding to protein
backbone motions on the timescale of ∼100–300 μs. The slow backbone dynamics of
the core residues were evaluated in the context of the structural model of human
Y145Stop PrP amyloid.
article_processing_charge: No
article_type: original
author:
- first_name: Matthew D.
full_name: Shannon, Matthew D.
last_name: Shannon
- first_name: Theint
full_name: Theint, Theint
last_name: Theint
- first_name: Dwaipayan
full_name: Mukhopadhyay, Dwaipayan
last_name: Mukhopadhyay
- first_name: Krystyna
full_name: Surewicz, Krystyna
last_name: Surewicz
- first_name: Witold K.
full_name: Surewicz, Witold K.
last_name: Surewicz
- first_name: Dominique
full_name: Marion, Dominique
last_name: Marion
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Christopher P.
full_name: Jaroniec, Christopher P.
last_name: Jaroniec
citation:
ama: Shannon MD, Theint T, Mukhopadhyay D, et al. Conformational dynamics in the
core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR.
ChemPhysChem. 2019;20(2):311-317. doi:10.1002/cphc.201800779
apa: Shannon, M. D., Theint, T., Mukhopadhyay, D., Surewicz, K., Surewicz, W. K.,
Marion, D., … Jaroniec, C. P. (2019). Conformational dynamics in the core of human
Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem.
Wiley. https://doi.org/10.1002/cphc.201800779
chicago: Shannon, Matthew D., Theint Theint, Dwaipayan Mukhopadhyay, Krystyna Surewicz,
Witold K. Surewicz, Dominique Marion, Paul Schanda, and Christopher P. Jaroniec.
“Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed
by Relaxation Dispersion NMR.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201800779.
ieee: M. D. Shannon et al., “Conformational dynamics in the core of human
Y145Stop prion protein amyloid probed by relaxation dispersion NMR,” ChemPhysChem,
vol. 20, no. 2. Wiley, pp. 311–317, 2019.
ista: Shannon MD, Theint T, Mukhopadhyay D, Surewicz K, Surewicz WK, Marion D, Schanda
P, Jaroniec CP. 2019. Conformational dynamics in the core of human Y145Stop prion
protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. 20(2), 311–317.
mla: Shannon, Matthew D., et al. “Conformational Dynamics in the Core of Human Y145Stop
Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” ChemPhysChem,
vol. 20, no. 2, Wiley, 2019, pp. 311–17, doi:10.1002/cphc.201800779.
short: M.D. Shannon, T. Theint, D. Mukhopadhyay, K. Surewicz, W.K. Surewicz, D.
Marion, P. Schanda, C.P. Jaroniec, ChemPhysChem 20 (2019) 311–317.
date_created: 2020-09-17T10:29:43Z
date_published: 2019-01-21T00:00:00Z
date_updated: 2021-01-12T08:19:06Z
day: '21'
doi: 10.1002/cphc.201800779
extern: '1'
external_id:
pmid:
- '30276945'
intvolume: ' 20'
issue: '2'
keyword:
- Physical and Theoretical Chemistry
- Atomic and Molecular Physics
- and Optics
language:
- iso: eng
month: '01'
oa_version: Submitted Version
page: 311-317
pmid: 1
publication: ChemPhysChem
publication_identifier:
issn:
- 1439-4235
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Conformational dynamics in the core of human Y145Stop prion protein amyloid
probed by relaxation dispersion NMR
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2019'
...
---
_id: '8411'
abstract:
- lang: eng
text: 'Studying protein dynamics on microsecond‐to‐millisecond (μs‐ms) time scales
can provide important insight into protein function. In magic‐angle‐spinning (MAS)
NMR, μs dynamics can be visualized by R1p rotating‐frame relaxation dispersion
experiments in different regimes of radio‐frequency field strengths: at low RF
field strength, isotropic‐chemical‐shift fluctuation leads to “Bloch‐McConnell‐type”
relaxation dispersion, while when the RF field approaches rotary resonance conditions
bond angle fluctuations manifest as increased R1p rate constants (“Near‐Rotary‐Resonance
Relaxation Dispersion”, NERRD). Here we explore the joint analysis of both regimes
to gain comprehensive insight into motion in terms of geometric amplitudes, chemical‐shift
changes, populations and exchange kinetics. We use a numerical simulation procedure
to illustrate these effects and the potential of extracting exchange parameters,
and apply the methodology to the study of a previously described conformational
exchange process in microcrystalline ubiquitin.'
article_processing_charge: No
article_type: original
author:
- first_name: Dominique
full_name: Marion, Dominique
last_name: Marion
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Karine
full_name: Giandoreggio-Barranco, Karine
last_name: Giandoreggio-Barranco
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. Microsecond
protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion
MAS NMR. ChemPhysChem. 2019;20(2):276-284. doi:10.1002/cphc.201800935
apa: Marion, D., Gauto, D. F., Ayala, I., Giandoreggio-Barranco, K., & Schanda,
P. (2019). Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance
R1p relaxation-dispersion MAS NMR. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201800935
chicago: Marion, Dominique, Diego F. Gauto, Isabel Ayala, Karine Giandoreggio-Barranco,
and Paul Schanda. “Microsecond Protein Dynamics from Combined Bloch-McConnell
and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” ChemPhysChem.
Wiley, 2019. https://doi.org/10.1002/cphc.201800935.
ieee: D. Marion, D. F. Gauto, I. Ayala, K. Giandoreggio-Barranco, and P. Schanda,
“Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance
R1p relaxation-dispersion MAS NMR,” ChemPhysChem, vol. 20, no. 2. Wiley,
pp. 276–284, 2019.
ista: Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. 2019. Microsecond
protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion
MAS NMR. ChemPhysChem. 20(2), 276–284.
mla: Marion, Dominique, et al. “Microsecond Protein Dynamics from Combined Bloch-McConnell
and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” ChemPhysChem,
vol. 20, no. 2, Wiley, 2019, pp. 276–84, doi:10.1002/cphc.201800935.
short: D. Marion, D.F. Gauto, I. Ayala, K. Giandoreggio-Barranco, P. Schanda, ChemPhysChem
20 (2019) 276–284.
date_created: 2020-09-17T10:29:36Z
date_published: 2019-01-21T00:00:00Z
date_updated: 2021-01-12T08:19:06Z
day: '21'
doi: 10.1002/cphc.201800935
extern: '1'
external_id:
pmid:
- '30444575'
intvolume: ' 20'
issue: '2'
keyword:
- Physical and Theoretical Chemistry
- Atomic and Molecular Physics
- and Optics
language:
- iso: eng
month: '01'
oa_version: Submitted Version
page: 276-284
pmid: 1
publication: ChemPhysChem
publication_identifier:
issn:
- 1439-4235
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance
R1p relaxation-dispersion MAS NMR
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2019'
...