---
_id: '8793'
abstract:
- lang: eng
text: We study optimal election sequences for repeatedly selecting a (very) small
group of leaders among a set of participants (players) with publicly known unique
ids. In every time slot, every player has to select exactly one player that it
considers to be the current leader, oblivious to the selection of the other players,
but with the overarching goal of maximizing a given parameterized global (“social”)
payoff function in the limit. We consider a quite generic model, where the local
payoff achieved by a given player depends, weighted by some arbitrary but fixed
real parameter, on the number of different leaders chosen in a round, the number
of players that choose the given player as the leader, and whether the chosen
leader has changed w.r.t. the previous round or not. The social payoff can be
the maximum, average or minimum local payoff of the players. Possible applications
include quite diverse examples such as rotating coordinator-based distributed
algorithms and long-haul formation flying of social birds. Depending on the weights
and the particular social payoff, optimal sequences can be very different, from
simple round-robin where all players chose the same leader alternatingly every
time slot to very exotic patterns, where a small group of leaders (at most 2)
is elected in every time slot. Moreover, we study the question if and when a single
player would not benefit w.r.t. its local payoff when deviating from the given
optimal sequence, i.e., when our optimal sequences are Nash equilibria in the
restricted strategy space of oblivious strategies. As this is the case for many
parameterizations of our model, our results reveal that no punishment is needed
to make it rational for the players to optimize the social payoff.
acknowledgement: "We are grateful to Matthias Függer and Thomas Nowak for having raised
our interest in the problem studied in this paper.\r\nThis work has been supported
the Austrian Science Fund (FWF) projects S11405, S11407 (RiSE), and P28182 (ADynNet)."
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Zeiner, Martin
last_name: Zeiner
- first_name: Ulrich
full_name: Schmid, Ulrich
last_name: Schmid
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Zeiner M, Schmid U, Chatterjee K. Optimal strategies for selecting coordinators.
Discrete Applied Mathematics. 2021;289(1):392-415. doi:10.1016/j.dam.2020.10.022
apa: Zeiner, M., Schmid, U., & Chatterjee, K. (2021). Optimal strategies for
selecting coordinators. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2020.10.022
chicago: Zeiner, Martin, Ulrich Schmid, and Krishnendu Chatterjee. “Optimal Strategies
for Selecting Coordinators.” Discrete Applied Mathematics. Elsevier, 2021.
https://doi.org/10.1016/j.dam.2020.10.022.
ieee: M. Zeiner, U. Schmid, and K. Chatterjee, “Optimal strategies for selecting
coordinators,” Discrete Applied Mathematics, vol. 289, no. 1. Elsevier,
pp. 392–415, 2021.
ista: Zeiner M, Schmid U, Chatterjee K. 2021. Optimal strategies for selecting coordinators.
Discrete Applied Mathematics. 289(1), 392–415.
mla: Zeiner, Martin, et al. “Optimal Strategies for Selecting Coordinators.” Discrete
Applied Mathematics, vol. 289, no. 1, Elsevier, 2021, pp. 392–415, doi:10.1016/j.dam.2020.10.022.
short: M. Zeiner, U. Schmid, K. Chatterjee, Discrete Applied Mathematics 289 (2021)
392–415.
date_created: 2020-11-22T23:01:26Z
date_published: 2021-01-31T00:00:00Z
date_updated: 2023-08-04T11:12:41Z
day: '31'
ddc:
- '510'
department:
- _id: KrCh
doi: 10.1016/j.dam.2020.10.022
external_id:
isi:
- '000596823800035'
file:
- access_level: open_access
checksum: f1039ff5a2d6ca116720efdb84ee9d5e
content_type: application/pdf
creator: dernst
date_created: 2021-02-04T11:28:42Z
date_updated: 2021-02-04T11:28:42Z
file_id: '9089'
file_name: 2021_DiscreteApplMath_Zeiner.pdf
file_size: 652739
relation: main_file
success: 1
file_date_updated: 2021-02-04T11:28:42Z
has_accepted_license: '1'
intvolume: ' 289'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 392-415
project:
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: Discrete Applied Mathematics
publication_identifier:
issn:
- 0166218X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal strategies for selecting coordinators
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 289
year: '2021'
...
---
_id: '8816'
abstract:
- lang: eng
text: Area-dependent quantum field theory is a modification of two-dimensional topological
quantum field theory, where one equips each connected component of a bordism with
a positive real number—interpreted as area—which behaves additively under glueing.
As opposed to topological theories, in area-dependent theories the state spaces
can be infinite-dimensional. We introduce the notion of regularised Frobenius
algebras in Hilbert spaces and show that area-dependent theories are in one-to-one
correspondence to commutative regularised Frobenius algebras. We also provide
a state sum construction for area-dependent theories. Our main example is two-dimensional
Yang–Mills theory with compact gauge group, which we treat in detail.
acknowledgement: The authors thank Yuki Arano, Nils Carqueville, Alexei Davydov, Reiner
Lauterbach, Pau Enrique Moliner, Chris Heunen, André Henriques, Ehud Meir, Catherine
Meusburger, Gregor Schaumann, Richard Szabo and Stefan Wagner for helpful discussions
and comments. We also thank the referees for their detailed comments which significantly
improved the exposition of this paper. LS is supported by the DFG Research Training
Group 1670 “Mathematics Inspired by String Theory and Quantum Field Theory”. Open
access funding provided by Institute of Science and Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Ingo
full_name: Runkel, Ingo
last_name: Runkel
- first_name: Lorant
full_name: Szegedy, Lorant
id: 7943226E-220E-11EA-94C7-D59F3DDC885E
last_name: Szegedy
orcid: 0000-0003-2834-5054
citation:
ama: Runkel I, Szegedy L. Area-dependent quantum field theory. Communications
in Mathematical Physics. 2021;381(1):83–117. doi:10.1007/s00220-020-03902-1
apa: Runkel, I., & Szegedy, L. (2021). Area-dependent quantum field theory.
Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-020-03902-1
chicago: Runkel, Ingo, and Lorant Szegedy. “Area-Dependent Quantum Field Theory.”
Communications in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s00220-020-03902-1.
ieee: I. Runkel and L. Szegedy, “Area-dependent quantum field theory,” Communications
in Mathematical Physics, vol. 381, no. 1. Springer Nature, pp. 83–117, 2021.
ista: Runkel I, Szegedy L. 2021. Area-dependent quantum field theory. Communications
in Mathematical Physics. 381(1), 83–117.
mla: Runkel, Ingo, and Lorant Szegedy. “Area-Dependent Quantum Field Theory.” Communications
in Mathematical Physics, vol. 381, no. 1, Springer Nature, 2021, pp. 83–117,
doi:10.1007/s00220-020-03902-1.
short: I. Runkel, L. Szegedy, Communications in Mathematical Physics 381 (2021)
83–117.
date_created: 2020-11-29T23:01:17Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2023-08-04T11:13:35Z
day: '01'
ddc:
- '510'
department:
- _id: MiLe
doi: 10.1007/s00220-020-03902-1
external_id:
isi:
- '000591139000001'
file:
- access_level: open_access
checksum: 6f451f9c2b74bedbc30cf884a3e02670
content_type: application/pdf
creator: dernst
date_created: 2021-02-03T15:00:30Z
date_updated: 2021-02-03T15:00:30Z
file_id: '9081'
file_name: 2021_CommMathPhys_Runkel.pdf
file_size: 790526
relation: main_file
success: 1
file_date_updated: 2021-02-03T15:00:30Z
has_accepted_license: '1'
intvolume: ' 381'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 83–117
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- '14320916'
issn:
- '00103616'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Area-dependent quantum field theory
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 381
year: '2021'
...
---
_id: '8818'
abstract:
- lang: eng
text: The hippocampus has a major role in encoding and consolidating long-term memories,
and undergoes plastic changes during sleep1. These changes require precise homeostatic
control by subcortical neuromodulatory structures2. The underlying mechanisms
of this phenomenon, however, remain unknown. Here, using multi-structure recordings
in macaque monkeys, we show that the brainstem transiently modulates hippocampal
network events through phasic pontine waves known as pontogeniculooccipital waves
(PGO waves). Two physiologically distinct types of PGO wave appear to occur sequentially,
selectively influencing high-frequency ripples and low-frequency theta events,
respectively. The two types of PGO wave are associated with opposite hippocampal
spike-field coupling, prompting periods of high neural synchrony of neural populations
during periods of ripple and theta instances. The coupling between PGO waves and
ripples, classically associated with distinct sleep stages, supports the notion
that a global coordination mechanism of hippocampal sleep dynamics by cholinergic
pontine transients may promote systems and synaptic memory consolidation as well
as synaptic homeostasis.
acknowledgement: We thank O. Eschenko and M. Constantinou for providing feedback on
earlier versions of this work, and J. Werner and M. Schnabel for technical support
during the development of this study. This research was supported by the Max Planck
Society.
article_processing_charge: No
article_type: original
author:
- first_name: Juan F
full_name: Ramirez Villegas, Juan F
id: 44B06F76-F248-11E8-B48F-1D18A9856A87
last_name: Ramirez Villegas
- first_name: Michel
full_name: Besserve, Michel
last_name: Besserve
- first_name: Yusuke
full_name: Murayama, Yusuke
last_name: Murayama
- first_name: Henry C.
full_name: Evrard, Henry C.
last_name: Evrard
- first_name: Axel
full_name: Oeltermann, Axel
last_name: Oeltermann
- first_name: Nikos K.
full_name: Logothetis, Nikos K.
last_name: Logothetis
citation:
ama: Ramirez Villegas JF, Besserve M, Murayama Y, Evrard HC, Oeltermann A, Logothetis
NK. Coupling of hippocampal theta and ripples with pontogeniculooccipital waves.
Nature. 2021;589(7840):96-102. doi:10.1038/s41586-020-2914-4
apa: Ramirez Villegas, J. F., Besserve, M., Murayama, Y., Evrard, H. C., Oeltermann,
A., & Logothetis, N. K. (2021). Coupling of hippocampal theta and ripples
with pontogeniculooccipital waves. Nature. Springer Nature. https://doi.org/10.1038/s41586-020-2914-4
chicago: Ramirez Villegas, Juan F, Michel Besserve, Yusuke Murayama, Henry C. Evrard,
Axel Oeltermann, and Nikos K. Logothetis. “Coupling of Hippocampal Theta and Ripples
with Pontogeniculooccipital Waves.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-020-2914-4.
ieee: J. F. Ramirez Villegas, M. Besserve, Y. Murayama, H. C. Evrard, A. Oeltermann,
and N. K. Logothetis, “Coupling of hippocampal theta and ripples with pontogeniculooccipital
waves,” Nature, vol. 589, no. 7840. Springer Nature, pp. 96–102, 2021.
ista: Ramirez Villegas JF, Besserve M, Murayama Y, Evrard HC, Oeltermann A, Logothetis
NK. 2021. Coupling of hippocampal theta and ripples with pontogeniculooccipital
waves. Nature. 589(7840), 96–102.
mla: Ramirez Villegas, Juan F., et al. “Coupling of Hippocampal Theta and Ripples
with Pontogeniculooccipital Waves.” Nature, vol. 589, no. 7840, Springer
Nature, 2021, pp. 96–102, doi:10.1038/s41586-020-2914-4.
short: J.F. Ramirez Villegas, M. Besserve, Y. Murayama, H.C. Evrard, A. Oeltermann,
N.K. Logothetis, Nature 589 (2021) 96–102.
date_created: 2020-11-29T23:01:19Z
date_published: 2021-01-07T00:00:00Z
date_updated: 2023-08-04T11:13:08Z
day: '07'
department:
- _id: JoCs
doi: 10.1038/s41586-020-2914-4
external_id:
isi:
- '000591047800005'
pmid:
- '33208951'
intvolume: ' 589'
isi: 1
issue: '7840'
language:
- iso: eng
month: '01'
oa_version: None
page: 96-102
pmid: 1
publication: Nature
publication_identifier:
eissn:
- '14764687'
issn:
- '00280836'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-020-03068-9
scopus_import: '1'
status: public
title: Coupling of hippocampal theta and ripples with pontogeniculooccipital waves
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 589
year: '2021'
...
---
_id: '8773'
abstract:
- lang: eng
text: Let g be a complex semisimple Lie algebra. We give a classification of contravariant
forms on the nondegenerate Whittaker g-modules Y(χ,η) introduced by Kostant. We
prove that the set of all contravariant forms on Y(χ,η) forms a vector space whose
dimension is given by the cardinality of the Weyl group of g. We also describe
a procedure for parabolically inducing contravariant forms. As a corollary, we
deduce the existence of the Shapovalov form on a Verma module, and provide a formula
for the dimension of the space of contravariant forms on the degenerate Whittaker
modules M(χ,η) introduced by McDowell.
acknowledgement: "We would like to thank Peter Trapa for useful discussions, and Dragan
Milicic and Arun Ram for valuable feedback on the structure of the paper. The first
author acknowledges the support of the European Unions Horizon 2020 research and
innovation programme under the Marie Skodowska-Curie Grant Agreement No. 754411.
The second author is\r\nsupported by the National Science Foundation Award No. 1803059."
article_processing_charge: No
article_type: original
author:
- first_name: Adam
full_name: Brown, Adam
id: 70B7FDF6-608D-11E9-9333-8535E6697425
last_name: Brown
- first_name: Anna
full_name: Romanov, Anna
last_name: Romanov
citation:
ama: Brown A, Romanov A. Contravariant forms on Whittaker modules. Proceedings
of the American Mathematical Society. 2021;149(1):37-52. doi:10.1090/proc/15205
apa: Brown, A., & Romanov, A. (2021). Contravariant forms on Whittaker modules.
Proceedings of the American Mathematical Society. American Mathematical
Society. https://doi.org/10.1090/proc/15205
chicago: Brown, Adam, and Anna Romanov. “Contravariant Forms on Whittaker Modules.”
Proceedings of the American Mathematical Society. American Mathematical
Society, 2021. https://doi.org/10.1090/proc/15205.
ieee: A. Brown and A. Romanov, “Contravariant forms on Whittaker modules,” Proceedings
of the American Mathematical Society, vol. 149, no. 1. American Mathematical
Society, pp. 37–52, 2021.
ista: Brown A, Romanov A. 2021. Contravariant forms on Whittaker modules. Proceedings
of the American Mathematical Society. 149(1), 37–52.
mla: Brown, Adam, and Anna Romanov. “Contravariant Forms on Whittaker Modules.”
Proceedings of the American Mathematical Society, vol. 149, no. 1, American
Mathematical Society, 2021, pp. 37–52, doi:10.1090/proc/15205.
short: A. Brown, A. Romanov, Proceedings of the American Mathematical Society 149
(2021) 37–52.
date_created: 2020-11-19T10:17:40Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2023-08-04T11:11:47Z
day: '01'
department:
- _id: HeEd
doi: 10.1090/proc/15205
ec_funded: 1
external_id:
arxiv:
- '1910.08286'
isi:
- '000600416300004'
intvolume: ' 149'
isi: 1
issue: '1'
keyword:
- Applied Mathematics
- General Mathematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1910.08286
month: '01'
oa: 1
oa_version: Preprint
page: 37-52
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Proceedings of the American Mathematical Society
publication_identifier:
eissn:
- 1088-6826
issn:
- 0002-9939
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
status: public
title: Contravariant forms on Whittaker modules
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 149
year: '2021'
...
---
_id: '8792'
abstract:
- lang: eng
text: This paper is concerned with a non-isothermal Cahn-Hilliard model based on
a microforce balance. The model was derived by A. Miranville and G. Schimperna
starting from the two fundamental laws of Thermodynamics, following M. Gurtin's
two-scale approach. The main working assumptions are made on the behaviour of
the heat flux as the absolute temperature tends to zero and to infinity. A suitable
Ginzburg-Landau free energy is considered. Global-in-time existence for the initial-boundary
value problem associated to the entropy formulation and, in a subcase, also to
the weak formulation of the model is proved by deriving suitable a priori estimates
and by showing weak sequential stability of families of approximating solutions.
At last, some highlights are given regarding a possible approximation scheme compatible
with the a-priori estimates available for the system.
acknowledgement: G. Schimperna has been partially supported by GNAMPA (Gruppo Nazionale
per l'Analisi Matematica, la Probabilità e le loro Applicazioni) of INdAM (Istituto
Nazionale di Alta Matematica).
article_processing_charge: No
article_type: original
author:
- first_name: Alice
full_name: Marveggio, Alice
id: 25647992-AA84-11E9-9D75-8427E6697425
last_name: Marveggio
- first_name: Giulio
full_name: Schimperna, Giulio
last_name: Schimperna
citation:
ama: Marveggio A, Schimperna G. On a non-isothermal Cahn-Hilliard model based on
a microforce balance. Journal of Differential Equations. 2021;274(2):924-970.
doi:10.1016/j.jde.2020.10.030
apa: Marveggio, A., & Schimperna, G. (2021). On a non-isothermal Cahn-Hilliard
model based on a microforce balance. Journal of Differential Equations.
Elsevier. https://doi.org/10.1016/j.jde.2020.10.030
chicago: Marveggio, Alice, and Giulio Schimperna. “On a Non-Isothermal Cahn-Hilliard
Model Based on a Microforce Balance.” Journal of Differential Equations.
Elsevier, 2021. https://doi.org/10.1016/j.jde.2020.10.030.
ieee: A. Marveggio and G. Schimperna, “On a non-isothermal Cahn-Hilliard model based
on a microforce balance,” Journal of Differential Equations, vol. 274,
no. 2. Elsevier, pp. 924–970, 2021.
ista: Marveggio A, Schimperna G. 2021. On a non-isothermal Cahn-Hilliard model based
on a microforce balance. Journal of Differential Equations. 274(2), 924–970.
mla: Marveggio, Alice, and Giulio Schimperna. “On a Non-Isothermal Cahn-Hilliard
Model Based on a Microforce Balance.” Journal of Differential Equations,
vol. 274, no. 2, Elsevier, 2021, pp. 924–70, doi:10.1016/j.jde.2020.10.030.
short: A. Marveggio, G. Schimperna, Journal of Differential Equations 274 (2021)
924–970.
date_created: 2020-11-22T23:01:26Z
date_published: 2021-02-15T00:00:00Z
date_updated: 2023-08-04T11:12:16Z
day: '15'
department:
- _id: JuFi
doi: 10.1016/j.jde.2020.10.030
external_id:
arxiv:
- '2004.02618'
isi:
- '000600845300023'
intvolume: ' 274'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2004.02618
month: '02'
oa: 1
oa_version: Preprint
page: 924-970
publication: Journal of Differential Equations
publication_identifier:
eissn:
- '10902732'
issn:
- '00220396'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: On a non-isothermal Cahn-Hilliard model based on a microforce balance
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 274
year: '2021'
...
---
_id: '8912'
abstract:
- lang: eng
text: "For automata, synchronization, the problem of bringing an automaton to a
particular state regardless of its initial state, is important. It has several
applications in practice and is related to a fifty-year-old conjecture on the
length of the shortest synchronizing word. Although using shorter words increases
the effectiveness in practice, finding a shortest one (which is not necessarily
unique) is NP-hard. For this reason, there exist various heuristics in the literature.
However, high-quality heuristics such as SynchroP producing relatively shorter
sequences are very expensive and can take hours when the automaton has tens of
thousands of states. The SynchroP heuristic has been frequently used as a benchmark
to evaluate the performance of the new heuristics. In this work, we first improve
the runtime of SynchroP and its variants by using algorithmic techniques. We then
focus on adapting SynchroP for many-core architectures,\r\nand overall, we obtain
more than 1000× speedup on GPUs compared to naive sequential implementation that
has been frequently used as a benchmark to evaluate new heuristics in the literature.
We also propose two SynchroP variants and evaluate their performance."
acknowledgement: This work was supported by The Scientific and Technological Research
Council of Turkey (TUBITAK) [grant number 114E569]. This research was supported
in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).
We would like to thank the authors of (Roman & Szykula, 2015) for providing their
heuristics implementations, which we used to compare our SynchroP implementation
as given in Table 11.
article_number: '114203'
article_processing_charge: No
article_type: original
author:
- first_name: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
- first_name: Ömer Faruk
full_name: Altun, Ömer Faruk
last_name: Altun
- first_name: Kamil Tolga
full_name: Atam, Kamil Tolga
last_name: Atam
- first_name: Sertac
full_name: Karahoda, Sertac
last_name: Karahoda
- first_name: Kamer
full_name: Kaya, Kamer
last_name: Kaya
- first_name: Hüsnü
full_name: Yenigün, Hüsnü
last_name: Yenigün
citation:
ama: Sarac NE, Altun ÖF, Atam KT, Karahoda S, Kaya K, Yenigün H. Boosting expensive
synchronizing heuristics. Expert Systems with Applications. 2021;167(4).
doi:10.1016/j.eswa.2020.114203
apa: Sarac, N. E., Altun, Ö. F., Atam, K. T., Karahoda, S., Kaya, K., & Yenigün,
H. (2021). Boosting expensive synchronizing heuristics. Expert Systems with
Applications. Elsevier. https://doi.org/10.1016/j.eswa.2020.114203
chicago: Sarac, Naci E, Ömer Faruk Altun, Kamil Tolga Atam, Sertac Karahoda, Kamer
Kaya, and Hüsnü Yenigün. “Boosting Expensive Synchronizing Heuristics.” Expert
Systems with Applications. Elsevier, 2021. https://doi.org/10.1016/j.eswa.2020.114203.
ieee: N. E. Sarac, Ö. F. Altun, K. T. Atam, S. Karahoda, K. Kaya, and H. Yenigün,
“Boosting expensive synchronizing heuristics,” Expert Systems with Applications,
vol. 167, no. 4. Elsevier, 2021.
ista: Sarac NE, Altun ÖF, Atam KT, Karahoda S, Kaya K, Yenigün H. 2021. Boosting
expensive synchronizing heuristics. Expert Systems with Applications. 167(4),
114203.
mla: Sarac, Naci E., et al. “Boosting Expensive Synchronizing Heuristics.” Expert
Systems with Applications, vol. 167, no. 4, 114203, Elsevier, 2021, doi:10.1016/j.eswa.2020.114203.
short: N.E. Sarac, Ö.F. Altun, K.T. Atam, S. Karahoda, K. Kaya, H. Yenigün, Expert
Systems with Applications 167 (2021).
date_created: 2020-12-02T13:34:25Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2023-08-04T11:19:00Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1016/j.eswa.2020.114203
external_id:
isi:
- '000640531100038'
file:
- access_level: open_access
checksum: 600c2f81bc898a725bcfa7cf26ff4fed
content_type: application/pdf
creator: esarac
date_created: 2020-12-02T13:33:51Z
date_updated: 2020-12-02T13:33:51Z
file_id: '8913'
file_name: synchroPaperRevised.pdf
file_size: 634967
relation: main_file
file_date_updated: 2020-12-02T13:33:51Z
has_accepted_license: '1'
intvolume: ' 167'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Expert Systems with Applications
publication_identifier:
issn:
- '09574174'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Boosting expensive synchronizing heuristics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 167
year: '2021'
...
---
_id: '8928'
abstract:
- lang: eng
text: Domestication is a human‐induced selection process that imprints the genomes
of domesticated populations over a short evolutionary time scale and that occurs
in a given demographic context. Reconstructing historical gene flow, effective
population size changes and their timing is therefore of fundamental interest
to understand how plant demography and human selection jointly shape genomic divergence
during domestication. Yet, the comparison under a single statistical framework
of independent domestication histories across different crop species has been
little evaluated so far. Thus, it is unclear whether domestication leads to convergent
demographic changes that similarly affect crop genomes. To address this question,
we used existing and new transcriptome data on three crop species of Solanaceae
(eggplant, pepper and tomato), together with their close wild relatives. We fitted
twelve demographic models of increasing complexity on the unfolded joint allele
frequency spectrum for each wild/crop pair, and we found evidence for both shared
and species‐specific demographic processes between species. A convergent history
of domestication with gene flow was inferred for all three species, along with
evidence of strong reduction in the effective population size during the cultivation
stage of tomato and pepper. The absence of any reduction in size of the crop in
eggplant stands out from the classical view of the domestication process; as does
the existence of a “protracted period” of management before cultivation. Our results
also suggest divergent management strategies of modern cultivars among species
as their current demography substantially differs. Finally, the timing of domestication
is species‐specific and supported by the few historical records available.
acknowledgement: This work was supported by the EU Marie Curie Career Integration
grant (FP7‐PEOPLE‐2011‐CIG grant agreement PCIG10‐GA‐2011‐304164) attributed to
CS. SA was supported by a PhD fellowship from the French Région PACA and the Plant
Breeding division of INRA, in partnership with Gautier Semences. CF was supported
by an Austrian Science Foundation FWF grant (Project M 2463‐B29). Authors thank
Mathilde Causse and Beatriz Vicoso for their team leading. Thanks to the Italian
Eggplant Genome Consortium, which includes the DISAFA, Plant Genetics and Breeding
(University of Torino), the Biotechnology Department (University of Verona), the
CREA‐ORL in Montanaso Lombardo (LO) and the ENEA in Rome for providing access to
the eggplant genome reference. Thanks to CRB‐lég ( https://www6.paca.inra.fr/gafl_eng/Vegetables-GRC
) for managing and providing the genetic resources, to Marie‐Christine Daunay and
Alain Palloix (INRA UR1052) for assistance in choosing the biological material used,
to Muriel Latreille and Sylvain Santoni from the UMR AGAP (INRA Montpellier, France)
for their help with RNAseq library preparation, to Jean‐Paul Bouchet and Jacques
Lagnel (INRA UR1052) for their Bioinformatics assistance.
article_processing_charge: No
article_type: original
author:
- first_name: Stéphanie
full_name: Arnoux, Stéphanie
last_name: Arnoux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Christopher
full_name: Sauvage, Christopher
last_name: Sauvage
citation:
ama: Arnoux S, Fraisse C, Sauvage C. Genomic inference of complex domestication
histories in three Solanaceae species. Journal of Evolutionary Biology.
2021;34(2):270-283. doi:10.1111/jeb.13723
apa: Arnoux, S., Fraisse, C., & Sauvage, C. (2021). Genomic inference of complex
domestication histories in three Solanaceae species. Journal of Evolutionary
Biology. Wiley. https://doi.org/10.1111/jeb.13723
chicago: Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic
Inference of Complex Domestication Histories in Three Solanaceae Species.” Journal
of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13723.
ieee: S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication
histories in three Solanaceae species,” Journal of Evolutionary Biology,
vol. 34, no. 2. Wiley, pp. 270–283, 2021.
ista: Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication
histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2),
270–283.
mla: Arnoux, Stéphanie, et al. “Genomic Inference of Complex Domestication Histories
in Three Solanaceae Species.” Journal of Evolutionary Biology, vol. 34,
no. 2, Wiley, 2021, pp. 270–83, doi:10.1111/jeb.13723.
short: S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021)
270–283.
date_created: 2020-12-06T23:01:16Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2023-08-04T11:19:26Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/jeb.13723
external_id:
isi:
- '000587769700001'
pmid:
- '33107098'
intvolume: ' 34'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jeb.13723
month: '02'
oa: 1
oa_version: Published Version
page: 270-283
pmid: 1
project:
- _id: 2662AADE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02463
name: Sex chromosomes and species barriers
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- '14209101'
issn:
- 1010061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '13065'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Genomic inference of complex domestication histories in three Solanaceae species
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 34
year: '2021'
...
---
_id: '8992'
abstract:
- lang: eng
text: The phytohormone auxin plays a central role in shaping plant growth and development.
With decades of genetic and biochemical studies, numerous core molecular components
and their networks, underlying auxin biosynthesis, transport, and signaling, have
been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely
hydrolyzed by phosphatases, has been emerging to be a crucial type of post-translational
modification, regulating physiological and developmental auxin output at all levels.
In this review, we comprehensively discuss earlier and recent advances in our
understanding of genetics, biochemistry, and cell biology of the kinases and phosphatases
participating in auxin action. We provide insights into the mechanisms by which
reversible protein phosphorylation defines developmental auxin responses, discuss
current challenges, and provide our perspectives on future directions involving
the integration of the control of protein phosphorylation into the molecular auxin
network.
acknowledgement: This work was supported by the European Union’s Horizon 2020 Program
(ERC grant agreement no. 742985 to J.F.). S.T. was funded by a European Molecular
Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). C.L.
is supported by the Austrian Science Fund (FWF; P 31493).
article_processing_charge: No
article_type: original
author:
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Tan S, Luschnig C, Friml J. Pho-view of auxin: Reversible protein phosphorylation
in auxin biosynthesis, transport and signaling. Molecular Plant. 2021;14(1):151-165.
doi:10.1016/j.molp.2020.11.004'
apa: 'Tan, S., Luschnig, C., & Friml, J. (2021). Pho-view of auxin: Reversible
protein phosphorylation in auxin biosynthesis, transport and signaling. Molecular
Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.11.004'
chicago: 'Tan, Shutang, Christian Luschnig, and Jiří Friml. “Pho-View of Auxin:
Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling.”
Molecular Plant. Elsevier, 2021. https://doi.org/10.1016/j.molp.2020.11.004.'
ieee: 'S. Tan, C. Luschnig, and J. Friml, “Pho-view of auxin: Reversible protein
phosphorylation in auxin biosynthesis, transport and signaling,” Molecular
Plant, vol. 14, no. 1. Elsevier, pp. 151–165, 2021.'
ista: 'Tan S, Luschnig C, Friml J. 2021. Pho-view of auxin: Reversible protein phosphorylation
in auxin biosynthesis, transport and signaling. Molecular Plant. 14(1), 151–165.'
mla: 'Tan, Shutang, et al. “Pho-View of Auxin: Reversible Protein Phosphorylation
in Auxin Biosynthesis, Transport and Signaling.” Molecular Plant, vol.
14, no. 1, Elsevier, 2021, pp. 151–65, doi:10.1016/j.molp.2020.11.004.'
short: S. Tan, C. Luschnig, J. Friml, Molecular Plant 14 (2021) 151–165.
date_created: 2021-01-03T23:01:23Z
date_published: 2021-01-04T00:00:00Z
date_updated: 2023-08-04T11:21:13Z
day: '04'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.molp.2020.11.004
ec_funded: 1
external_id:
isi:
- '000605359400014'
pmid:
- '33186755'
file:
- access_level: open_access
checksum: 917e60e57092f22e16beac70b1775ea6
content_type: application/pdf
creator: dernst
date_created: 2021-01-07T14:03:53Z
date_updated: 2021-01-07T14:03:53Z
file_id: '8995'
file_name: 2020_MolecularPlant_Tan.pdf
file_size: 871088
relation: main_file
success: 1
file_date_updated: 2021-01-07T14:03:53Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 151-165
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 256FEF10-B435-11E9-9278-68D0E5697425
grant_number: 723-2015
name: Long Term Fellowship
publication: Molecular Plant
publication_identifier:
eissn:
- '17529867'
issn:
- '16742052'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis,
transport and signaling'
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2021'
...
---
_id: '8988'
abstract:
- lang: eng
text: The differentiation of cells depends on a precise control of their internal
organization, which is the result of a complex dynamic interplay between the cytoskeleton,
molecular motors, signaling molecules, and membranes. For example, in the developing
neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP]
with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite
branching by regulating the small GTPase ARF6. Together with the motor protein
KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol
(3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity.
However, what defines the function of ADAP1 and how its different roles are coordinated
are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions.
We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well
as PI(3,4)P2 act as stop signals for this transport instead of being transported.
We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity
to catalyze GTP hydrolysis by ARF6. Together, our results support a model for
the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters
high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates
from the motor to inactivate ARF6, promoting dendrite branching.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: EM-Fac
acknowledgement: "We thank Urban Bezeljak, Natalia Baranova, Mar Lopez-Pelegrin, Catarina
Alcarva, and Victoria Faas for sharing reagents and helpful discussions. We thank
Veronika Szentirmai for help with protein purifications. We thank Carrie Bernecky,
Sascha Martens, and the M.L. lab for comments on the manuscript. We thank the bioimaging
facility, the life science facility, and Armel Nicolas from the mass spec facility
at the Institute of Science and Technology (IST) Austria for technical support.
C.D. acknowledges funding from the IST fellowship program; this work was supported
by Human Frontier Science Program Young Investigator Grant\r\nRGY0083/2016. "
article_number: e2010054118
article_processing_charge: No
article_type: original
author:
- first_name: Christian F
full_name: Düllberg, Christian F
id: 459064DC-F248-11E8-B48F-1D18A9856A87
last_name: Düllberg
orcid: 0000-0001-6335-9748
- first_name: Albert
full_name: Auer, Albert
id: 3018E8C2-F248-11E8-B48F-1D18A9856A87
last_name: Auer
orcid: 0000-0002-3580-2906
- first_name: Nikola
full_name: Canigova, Nikola
id: 3795523E-F248-11E8-B48F-1D18A9856A87
last_name: Canigova
orcid: 0000-0002-8518-5926
- first_name: Katrin
full_name: Loibl, Katrin
id: 3760F32C-F248-11E8-B48F-1D18A9856A87
last_name: Loibl
orcid: 0000-0002-2429-7668
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. In vitro reconstitution
reveals phosphoinositides as cargo-release factors and activators of the ARF6
GAP ADAP1. PNAS. 2021;118(1). doi:10.1073/pnas.2010054118
apa: Düllberg, C. F., Auer, A., Canigova, N., Loibl, K., & Loose, M. (2021).
In vitro reconstitution reveals phosphoinositides as cargo-release factors and
activators of the ARF6 GAP ADAP1. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.2010054118
chicago: Düllberg, Christian F, Albert Auer, Nikola Canigova, Katrin Loibl, and
Martin Loose. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release
Factors and Activators of the ARF6 GAP ADAP1.” PNAS. National Academy of
Sciences, 2021. https://doi.org/10.1073/pnas.2010054118.
ieee: C. F. Düllberg, A. Auer, N. Canigova, K. Loibl, and M. Loose, “In vitro reconstitution
reveals phosphoinositides as cargo-release factors and activators of the ARF6
GAP ADAP1,” PNAS, vol. 118, no. 1. National Academy of Sciences, 2021.
ista: Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. 2021. In vitro reconstitution
reveals phosphoinositides as cargo-release factors and activators of the ARF6
GAP ADAP1. PNAS. 118(1), e2010054118.
mla: Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides
as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” PNAS, vol.
118, no. 1, e2010054118, National Academy of Sciences, 2021, doi:10.1073/pnas.2010054118.
short: C.F. Düllberg, A. Auer, N. Canigova, K. Loibl, M. Loose, PNAS 118 (2021).
date_created: 2021-01-03T23:01:23Z
date_published: 2021-01-05T00:00:00Z
date_updated: 2023-08-04T11:20:46Z
day: '05'
department:
- _id: MaLo
- _id: MiSi
doi: 10.1073/pnas.2010054118
external_id:
isi:
- '000607270100018'
pmid:
- '33443153'
intvolume: ' 118'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.2010054118
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2599F062-B435-11E9-9278-68D0E5697425
grant_number: RGY0083/2016
name: Reconstitution of cell polarity and axis determination in a cell-free system
publication: PNAS
publication_identifier:
eissn:
- '10916490'
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: In vitro reconstitution reveals phosphoinositides as cargo-release factors
and activators of the ARF6 GAP ADAP1
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...
---
_id: '8927'
abstract:
- lang: eng
text: The recent outbreak of coronavirus disease 2019 (COVID‐19), caused by the
Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) has resulted in a
world‐wide pandemic. Disseminated lung injury with the development of acute respiratory
distress syndrome (ARDS) is the main cause of mortality in COVID‐19. Although
liver failure does not seem to occur in the absence of pre‐existing liver disease,
hepatic involvement in COVID‐19 may correlate with overall disease severity and
serve as a prognostic factor for the development of ARDS. The spectrum of liver
injury in COVID‐19 may range from direct infection by SARS‐CoV‐2, indirect involvement
by systemic inflammation, hypoxic changes, iatrogenic causes such as drugs and
ventilation to exacerbation of underlying liver disease. This concise review discusses
the potential pathophysiological mechanisms for SARS‐CoV‐2 hepatic tropism as
well as acute and possibly long‐term liver injury in COVID‐19.
acknowledgement: This work was supported by grant F7310‐B21 from the Austrian Science
Foundation (to MT). We thank Jelena Remetic, Claudia D. Fuchs, Veronika Mlitz and
Daniel Steinacher, for their valuable input and discussion. Figure 1 and Figure
2 have been created with BioRender.com.
article_processing_charge: No
article_type: original
author:
- first_name: Alexander D.
full_name: Nardo, Alexander D.
last_name: Nardo
- first_name: Mathias
full_name: Schneeweiss-Gleixner, Mathias
last_name: Schneeweiss-Gleixner
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Emmanuel D.
full_name: Dixon, Emmanuel D.
last_name: Dixon
- first_name: Sigurd F.
full_name: Lax, Sigurd F.
last_name: Lax
- first_name: Michael
full_name: Trauner, Michael
last_name: Trauner
citation:
ama: Nardo AD, Schneeweiss-Gleixner M, Bakail MM, Dixon ED, Lax SF, Trauner M. Pathophysiological
mechanisms of liver injury in COVID-19. Liver International. 2021;41(1):20-32.
doi:10.1111/liv.14730
apa: Nardo, A. D., Schneeweiss-Gleixner, M., Bakail, M. M., Dixon, E. D., Lax, S.
F., & Trauner, M. (2021). Pathophysiological mechanisms of liver injury in
COVID-19. Liver International. Wiley. https://doi.org/10.1111/liv.14730
chicago: Nardo, Alexander D., Mathias Schneeweiss-Gleixner, May M Bakail, Emmanuel
D. Dixon, Sigurd F. Lax, and Michael Trauner. “Pathophysiological Mechanisms of
Liver Injury in COVID-19.” Liver International. Wiley, 2021. https://doi.org/10.1111/liv.14730.
ieee: A. D. Nardo, M. Schneeweiss-Gleixner, M. M. Bakail, E. D. Dixon, S. F. Lax,
and M. Trauner, “Pathophysiological mechanisms of liver injury in COVID-19,” Liver
International, vol. 41, no. 1. Wiley, pp. 20–32, 2021.
ista: Nardo AD, Schneeweiss-Gleixner M, Bakail MM, Dixon ED, Lax SF, Trauner M.
2021. Pathophysiological mechanisms of liver injury in COVID-19. Liver International.
41(1), 20–32.
mla: Nardo, Alexander D., et al. “Pathophysiological Mechanisms of Liver Injury
in COVID-19.” Liver International, vol. 41, no. 1, Wiley, 2021, pp. 20–32,
doi:10.1111/liv.14730.
short: A.D. Nardo, M. Schneeweiss-Gleixner, M.M. Bakail, E.D. Dixon, S.F. Lax, M.
Trauner, Liver International 41 (2021) 20–32.
date_created: 2020-12-06T23:01:16Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2023-08-04T11:19:51Z
day: '01'
ddc:
- '570'
department:
- _id: CampIT
doi: 10.1111/liv.14730
external_id:
isi:
- '000594239200001'
file:
- access_level: open_access
checksum: 6e4f21b77ef22c854e016240974fc473
content_type: application/pdf
creator: dernst
date_created: 2021-02-04T12:01:45Z
date_updated: 2021-02-04T12:01:45Z
file_id: '9091'
file_name: 2021_Liver_Nardo.pdf
file_size: 930414
relation: main_file
success: 1
file_date_updated: 2021-02-04T12:01:45Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 20-32
publication: Liver International
publication_identifier:
eissn:
- '14783231'
issn:
- '14783223'
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pathophysiological mechanisms of liver injury in COVID-19
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 41
year: '2021'
...
---
_id: '13356'
abstract:
- lang: eng
text: 'Self-assembly of nanoparticles can be mediated by polymers, but has so far
led almost exclusively to nanoparticle aggregates that are amorphous. Here, we
employed Coulombic interactions to generate a range of composite materials from
mixtures of charged nanoparticles and oppositely charged polymers. The assembly
behavior of these nanoparticle/polymer composites depends on their order of addition:
polymers added to nanoparticles give rise to stable aggregates, but nanoparticles
added to polymers disassemble the initially formed aggregates. The amorphous aggregates
were transformed into crystalline ones by transiently increasing the ionic strength
of the solution. The morphology of the resulting crystals depended on the length
of the polymer: short polymer chains mediated the self-assembly of nanoparticles
into strongly faceted crystals, whereas long chains led to pseudospherical nanoparticle/polymer
assemblies, within which the crystalline order of nanoparticles was retained.'
article_processing_charge: No
article_type: original
author:
- first_name: Tong
full_name: Bian, Tong
last_name: Bian
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Bian T, Klajn R. Morphology control in crystalline nanoparticle–polymer aggregates.
Annals of the New York Academy of Sciences. 2021;1505(1):191-201. doi:10.1111/nyas.14674
apa: Bian, T., & Klajn, R. (2021). Morphology control in crystalline nanoparticle–polymer
aggregates. Annals of the New York Academy of Sciences. Wiley. https://doi.org/10.1111/nyas.14674
chicago: Bian, Tong, and Rafal Klajn. “Morphology Control in Crystalline Nanoparticle–Polymer
Aggregates.” Annals of the New York Academy of Sciences. Wiley, 2021. https://doi.org/10.1111/nyas.14674.
ieee: T. Bian and R. Klajn, “Morphology control in crystalline nanoparticle–polymer
aggregates,” Annals of the New York Academy of Sciences, vol. 1505, no.
1. Wiley, pp. 191–201, 2021.
ista: Bian T, Klajn R. 2021. Morphology control in crystalline nanoparticle–polymer
aggregates. Annals of the New York Academy of Sciences. 1505(1), 191–201.
mla: Bian, Tong, and Rafal Klajn. “Morphology Control in Crystalline Nanoparticle–Polymer
Aggregates.” Annals of the New York Academy of Sciences, vol. 1505, no.
1, Wiley, 2021, pp. 191–201, doi:10.1111/nyas.14674.
short: T. Bian, R. Klajn, Annals of the New York Academy of Sciences 1505 (2021)
191–201.
date_created: 2023-08-01T09:33:39Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2023-08-07T10:01:10Z
day: '01'
ddc:
- '540'
doi: 10.1111/nyas.14674
extern: '1'
external_id:
pmid:
- '34427923'
intvolume: ' 1505'
issue: '1'
keyword:
- History and Philosophy of Science
- General Biochemistry
- Genetics and Molecular Biology
- General Neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/nyas.14674
month: '12'
oa: 1
oa_version: Published Version
page: 191-201
pmid: 1
publication: Annals of the New York Academy of Sciences
publication_identifier:
eissn:
- 1749-6632
issn:
- 0077-8923
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Morphology control in crystalline nanoparticle–polymer aggregates
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1505
year: '2021'
...
---
_id: '13359'
abstract:
- lang: eng
text: Dissipative self-assembly is ubiquitous in nature, where it gives rise to
complex structures and functions such as self-healing, homeostasis, and camouflage.
These phenomena are enabled by the continuous conversion of energy stored in chemical
fuels, such as ATP. Over the past decade, an increasing number of synthetic chemically
driven systems have been reported that mimic the features of their natural counterparts.
At the same time, it has been shown that dissipative self-assembly can also be
fueled by light; these optically fueled systems have been developed in parallel
to the chemically fueled ones. In this perspective, we critically compare these
two classes of systems. Despite the complementarity and fundamental differences
between these two modes of dissipative self-assembly, our analysis reveals that
multiple analogies exist between chemically and light-fueled systems. We hope
that these considerations will facilitate further development of the field of
dissipative self-assembly.
article_processing_charge: No
article_type: original
author:
- first_name: Maren
full_name: Weißenfels, Maren
last_name: Weißenfels
- first_name: Julius
full_name: Gemen, Julius
last_name: Gemen
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: 'Weißenfels M, Gemen J, Klajn R. Dissipative self-assembly: Fueling with chemicals
versus light. Chem. 2021;7(1):23-37. doi:10.1016/j.chempr.2020.11.025'
apa: 'Weißenfels, M., Gemen, J., & Klajn, R. (2021). Dissipative self-assembly:
Fueling with chemicals versus light. Chem. Elsevier. https://doi.org/10.1016/j.chempr.2020.11.025'
chicago: 'Weißenfels, Maren, Julius Gemen, and Rafal Klajn. “Dissipative Self-Assembly:
Fueling with Chemicals versus Light.” Chem. Elsevier, 2021. https://doi.org/10.1016/j.chempr.2020.11.025.'
ieee: 'M. Weißenfels, J. Gemen, and R. Klajn, “Dissipative self-assembly: Fueling
with chemicals versus light,” Chem, vol. 7, no. 1. Elsevier, pp. 23–37,
2021.'
ista: 'Weißenfels M, Gemen J, Klajn R. 2021. Dissipative self-assembly: Fueling
with chemicals versus light. Chem. 7(1), 23–37.'
mla: 'Weißenfels, Maren, et al. “Dissipative Self-Assembly: Fueling with Chemicals
versus Light.” Chem, vol. 7, no. 1, Elsevier, 2021, pp. 23–37, doi:10.1016/j.chempr.2020.11.025.'
short: M. Weißenfels, J. Gemen, R. Klajn, Chem 7 (2021) 23–37.
date_created: 2023-08-01T09:35:19Z
date_published: 2021-01-14T00:00:00Z
date_updated: 2023-08-07T10:04:28Z
day: '14'
doi: 10.1016/j.chempr.2020.11.025
extern: '1'
intvolume: ' 7'
issue: '1'
keyword:
- Materials Chemistry
- Biochemistry (medical)
- General Chemical Engineering
- Environmental Chemistry
- Biochemistry
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.chempr.2020.11.025
month: '01'
oa: 1
oa_version: Published Version
page: 23-37
publication: Chem
publication_identifier:
issn:
- 2451-9294
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Dissipative self-assembly: Fueling with chemicals versus light'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2021'
...
---
_id: '8966'
abstract:
- lang: eng
text: During development, a single cell is transformed into a highly complex organism
through progressive cell division, specification and rearrangement. An important
prerequisite for the emergence of patterns within the developing organism is to
establish asymmetries at various scales, ranging from individual cells to the
entire embryo, eventually giving rise to the different body structures. This becomes
especially apparent during gastrulation, when the earliest major lineage restriction
events lead to the formation of the different germ layers. Traditionally, the
unfolding of the developmental program from symmetry breaking to germ layer formation
has been studied by dissecting the contributions of different signaling pathways
and cellular rearrangements in the in vivo context of intact embryos. Recent efforts,
using the intrinsic capacity of embryonic stem cells to self-assemble and generate
embryo-like structures de novo, have opened new avenues for understanding the
many ways by which an embryo can be built and the influence of extrinsic factors
therein. Here, we discuss and compare divergent and conserved strategies leading
to germ layer formation in embryos as compared to in vitro systems, their upstream
molecular cascades and the role of extrinsic factors in this process.
acknowledgement: We thank Nicoletta Petridou, Diana Pinheiro, Cornelia Schwayer and
Stefania Tavano for feedback on the manuscript. Research in the Heisenberg lab is
supported by an ERC Advanced Grant (MECSPEC 742573) to C.-P.H. A.S. is a recipient
of a DOC Fellowship of the Austrian Academy of Science.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Schauer A, Heisenberg C-PJ. Reassembling gastrulation. Developmental Biology.
2021;474:71-81. doi:10.1016/j.ydbio.2020.12.014
apa: Schauer, A., & Heisenberg, C.-P. J. (2021). Reassembling gastrulation.
Developmental Biology. Elsevier. https://doi.org/10.1016/j.ydbio.2020.12.014
chicago: Schauer, Alexandra, and Carl-Philipp J Heisenberg. “Reassembling Gastrulation.”
Developmental Biology. Elsevier, 2021. https://doi.org/10.1016/j.ydbio.2020.12.014.
ieee: A. Schauer and C.-P. J. Heisenberg, “Reassembling gastrulation,” Developmental
Biology, vol. 474. Elsevier, pp. 71–81, 2021.
ista: Schauer A, Heisenberg C-PJ. 2021. Reassembling gastrulation. Developmental
Biology. 474, 71–81.
mla: Schauer, Alexandra, and Carl-Philipp J. Heisenberg. “Reassembling Gastrulation.”
Developmental Biology, vol. 474, Elsevier, 2021, pp. 71–81, doi:10.1016/j.ydbio.2020.12.014.
short: A. Schauer, C.-P.J. Heisenberg, Developmental Biology 474 (2021) 71–81.
date_created: 2020-12-22T09:53:34Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-07T13:30:01Z
day: '01'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1016/j.ydbio.2020.12.014
ec_funded: 1
external_id:
isi:
- '000639461800008'
file:
- access_level: open_access
checksum: fa2a5731fd16ab171b029f32f031c440
content_type: application/pdf
creator: kschuh
date_created: 2021-08-11T10:28:06Z
date_updated: 2021-08-11T10:28:06Z
file_id: '9880'
file_name: 2021_DevBiology_Schauer.pdf
file_size: 1440321
relation: main_file
success: 1
file_date_updated: 2021-08-11T10:28:06Z
has_accepted_license: '1'
intvolume: ' 474'
isi: 1
keyword:
- Developmental Biology
- Cell Biology
- Molecular Biology
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: 71-81
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 26B1E39C-B435-11E9-9278-68D0E5697425
grant_number: '25239'
name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues'
publication: Developmental Biology
publication_identifier:
issn:
- 0012-1606
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '12891'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Reassembling gastrulation
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 474
year: '2021'
...
---
_id: '8993'
abstract:
- lang: eng
text: N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar)
transport of the hormone auxin in plants. For decades, it has been a pivotal tool
in elucidating the unique polar auxin transport-based processes underlying plant
growth and development. Its exact mode of action has long been sought after and
is still being debated, with prevailing mechanistic schemes describing only indirect
connections between NPA and the main transporters responsible for directional
transport, namely PIN auxin exporters. Here we present data supporting a model
in which NPA associates with PINs in a more direct manner than hitherto postulated.
We show that NPA inhibits PIN activity in a heterologous oocyte system and that
expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to
specific saturable NPA binding. We thus propose that PINs are a bona fide NPA
target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent
auxin transport and a logical parsimonious explanation for the known physiological
effects of NPA on plant growth, as well as an alternative hypothesis to interpret
past and future results. We also introduce PIN dimerization and describe an effect
of NPA on this, suggesting that NPA binding could be exploited to gain insights
into structural aspects of PINs related to their transport mechanism.
acknowledgement: "This work was supported by Austrian Science Fund Grant FWF P21533-B20
(to L.A.); German Research Foundation Grant DFG HA3468/6-1 (to U.Z.H.); and European
Research Council Grant 742985 (to J.F.). We thank Herta Steinkellner and Alexandra
Castilho for N. benthamiana plants, Fabian Nagelreiter for statistical advice, Lanassa
Bassukas for help with [ɣ32P]-\r\nATP assays, and Josef Penninger for providing
access to mass spectrometry instruments at the Vienna BioCenter Core Facilities.
We thank PNAS reviewers for the many comments and suggestions that helped to improve
this manuscript."
article_number: e2020857118
article_processing_charge: No
article_type: original
author:
- first_name: Lindy
full_name: Abas, Lindy
last_name: Abas
- first_name: Martina
full_name: Kolb, Martina
last_name: Kolb
- first_name: Johannes
full_name: Stadlmann, Johannes
last_name: Stadlmann
- first_name: Dorina P.
full_name: Janacek, Dorina P.
last_name: Janacek
- first_name: Kristina
full_name: Lukic, Kristina
id: 2B04DB84-F248-11E8-B48F-1D18A9856A87
last_name: Lukic
orcid: 0000-0003-1581-881X
- first_name: Claus
full_name: Schwechheimer, Claus
last_name: Schwechheimer
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Lukas
full_name: Mach, Lukas
last_name: Mach
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Ulrich Z.
full_name: Hammes, Ulrich Z.
last_name: Hammes
citation:
ama: Abas L, Kolb M, Stadlmann J, et al. Naphthylphthalamic acid associates with
and inhibits PIN auxin transporters. PNAS. 2021;118(1). doi:10.1073/pnas.2020857118
apa: Abas, L., Kolb, M., Stadlmann, J., Janacek, D. P., Lukic, K., Schwechheimer,
C., … Hammes, U. Z. (2021). Naphthylphthalamic acid associates with and inhibits
PIN auxin transporters. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.2020857118
chicago: Abas, Lindy, Martina Kolb, Johannes Stadlmann, Dorina P. Janacek, Kristina
Lukic, Claus Schwechheimer, Leonid A Sazanov, Lukas Mach, Jiří Friml, and Ulrich
Z. Hammes. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.”
PNAS. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2020857118.
ieee: L. Abas et al., “Naphthylphthalamic acid associates with and inhibits
PIN auxin transporters,” PNAS, vol. 118, no. 1. National Academy of Sciences,
2021.
ista: Abas L, Kolb M, Stadlmann J, Janacek DP, Lukic K, Schwechheimer C, Sazanov
LA, Mach L, Friml J, Hammes UZ. 2021. Naphthylphthalamic acid associates with
and inhibits PIN auxin transporters. PNAS. 118(1), e2020857118.
mla: Abas, Lindy, et al. “Naphthylphthalamic Acid Associates with and Inhibits PIN
Auxin Transporters.” PNAS, vol. 118, no. 1, e2020857118, National Academy
of Sciences, 2021, doi:10.1073/pnas.2020857118.
short: L. Abas, M. Kolb, J. Stadlmann, D.P. Janacek, K. Lukic, C. Schwechheimer,
L.A. Sazanov, L. Mach, J. Friml, U.Z. Hammes, PNAS 118 (2021).
date_created: 2021-01-03T23:01:23Z
date_published: 2021-01-05T00:00:00Z
date_updated: 2023-08-07T13:29:23Z
day: '05'
department:
- _id: JiFr
- _id: LeSa
doi: 10.1073/pnas.2020857118
ec_funded: 1
external_id:
isi:
- '000607270100073'
pmid:
- '33443187'
intvolume: ' 118'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.2020857118
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: PNAS
publication_identifier:
eissn:
- '10916490'
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1073/pnas.2102232118
scopus_import: '1'
status: public
title: Naphthylphthalamic acid associates with and inhibits PIN auxin transporters
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...
---
_id: '8999'
abstract:
- lang: eng
text: "In many basic shear flows, such as pipe, Couette, and channel flow, turbulence
does not\r\narise from an instability of the laminar state, and both dynamical
states co-exist. With decreasing flow speed (i.e., decreasing Reynolds number)
the fraction of fluid in laminar motion increases while turbulence recedes and
eventually the entire flow relaminarizes. The first step towards understanding
the nature of this transition is to determine if the phase change is of either
first or second order. In the former case, the turbulent fraction would drop discontinuously
to zero as the Reynolds number decreases while in the latter the process would
be continuous. For Couette flow, the flow between two parallel plates, earlier
studies suggest a discontinuous scenario. In the present study we realize a Couette
flow between two concentric cylinders which allows studies to be carried out in
large aspect ratios and for extensive observation times. The presented measurements
show that the transition in this circular Couette geometry is continuous suggesting
that former studies were limited by finite size effects. A further characterization
of this transition, in particular its relation to the directed percolation universality
class, requires even larger system sizes than presently available. "
acknowledgement: "This research was funded by the Central Research Development Fund
of the University of\r\nBremen grant number ZF04B /2019/FB04 Avila_Kerstin (“Independent
Project for Postdocs”). Shreyas Jalikop is acknowledged for recording some of the
lifetime measurements\r\n"
article_number: '58'
article_processing_charge: No
article_type: original
author:
- first_name: Kerstin
full_name: Avila, Kerstin
id: fcf74381-53e1-11eb-a6dc-b0e2acf78757
last_name: Avila
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Avila K, Hof B. Second-order phase transition in counter-rotating taylor-couette
flow experiment. Entropy. 2021;23(1). doi:10.3390/e23010058
apa: Avila, K., & Hof, B. (2021). Second-order phase transition in counter-rotating
taylor-couette flow experiment. Entropy. MDPI. https://doi.org/10.3390/e23010058
chicago: Avila, Kerstin, and Björn Hof. “Second-Order Phase Transition in Counter-Rotating
Taylor-Couette Flow Experiment.” Entropy. MDPI, 2021. https://doi.org/10.3390/e23010058.
ieee: K. Avila and B. Hof, “Second-order phase transition in counter-rotating taylor-couette
flow experiment,” Entropy, vol. 23, no. 1. MDPI, 2021.
ista: Avila K, Hof B. 2021. Second-order phase transition in counter-rotating taylor-couette
flow experiment. Entropy. 23(1), 58.
mla: Avila, Kerstin, and Björn Hof. “Second-Order Phase Transition in Counter-Rotating
Taylor-Couette Flow Experiment.” Entropy, vol. 23, no. 1, 58, MDPI, 2021,
doi:10.3390/e23010058.
short: K. Avila, B. Hof, Entropy 23 (2021).
date_created: 2021-01-10T23:01:17Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2023-08-07T13:31:07Z
day: '01'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.3390/e23010058
external_id:
isi:
- '000610135400001'
pmid:
- '33396499'
file:
- access_level: open_access
checksum: 3ba3dd8b7eecff713b72c5e9ba30d626
content_type: application/pdf
creator: dernst
date_created: 2021-01-11T07:50:32Z
date_updated: 2021-01-11T07:50:32Z
file_id: '9003'
file_name: 2021_Entropy_Avila.pdf
file_size: 9456389
relation: main_file
success: 1
file_date_updated: 2021-01-11T07:50:32Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Entropy
publication_identifier:
eissn:
- 1099-4300
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Second-order phase transition in counter-rotating taylor-couette flow experiment
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 23
year: '2021'
...
---
_id: '9005'
abstract:
- lang: eng
text: Studies on the experimental realization of two-dimensional anyons in terms
of quasiparticles have been restricted, so far, to only anyons on the plane. It
is known, however, that the geometry and topology of space can have significant
effects on quantum statistics for particles moving on it. Here, we have undertaken
the first step toward realizing the emerging fractional statistics for particles
restricted to move on the sphere instead of on the plane. We show that such a
model arises naturally in the context of quantum impurity problems. In particular,
we demonstrate a setup in which the lowest-energy spectrum of two linear bosonic
or fermionic molecules immersed in a quantum many-particle environment can coincide
with the anyonic spectrum on the sphere. This paves the way toward the experimental
realization of anyons on the sphere using molecular impurities. Furthermore, since
a change in the alignment of the molecules corresponds to the exchange of the
particles on the sphere, such a realization reveals a novel type of exclusion
principle for molecular impurities, which could also be of use as a powerful technique
to measure the statistics parameter. Finally, our approach opens up a simple numerical
route to investigate the spectra of many anyons on the sphere. Accordingly, we
present the spectrum of two anyons on the sphere in the presence of a Dirac monopole
field.
acknowledgement: "We are grateful to A. Ghazaryan for valuable discussions and also
thank the anonymous referees for comments. D.L. acknowledges financial support from
the G¨oran Gustafsson Foundation (grant no. 1804) and LMU Munich. M.L. gratefully
acknowledges financial support\r\nby the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (grant agreements
No 801770)."
article_number: '015301'
article_processing_charge: No
article_type: original
author:
- first_name: Morris
full_name: Brooks, Morris
id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425
last_name: Brooks
orcid: 0000-0002-6249-0928
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: D.
full_name: Lundholm, D.
last_name: Lundholm
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
citation:
ama: Brooks M, Lemeshko M, Lundholm D, Yakaboylu E. Molecular impurities as a realization
of anyons on the two-sphere. Physical Review Letters. 2021;126(1). doi:10.1103/PhysRevLett.126.015301
apa: Brooks, M., Lemeshko, M., Lundholm, D., & Yakaboylu, E. (2021). Molecular
impurities as a realization of anyons on the two-sphere. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.126.015301
chicago: Brooks, Morris, Mikhail Lemeshko, D. Lundholm, and Enderalp Yakaboylu.
“Molecular Impurities as a Realization of Anyons on the Two-Sphere.” Physical
Review Letters. American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.126.015301.
ieee: M. Brooks, M. Lemeshko, D. Lundholm, and E. Yakaboylu, “Molecular impurities
as a realization of anyons on the two-sphere,” Physical Review Letters,
vol. 126, no. 1. American Physical Society, 2021.
ista: Brooks M, Lemeshko M, Lundholm D, Yakaboylu E. 2021. Molecular impurities
as a realization of anyons on the two-sphere. Physical Review Letters. 126(1),
015301.
mla: Brooks, Morris, et al. “Molecular Impurities as a Realization of Anyons on
the Two-Sphere.” Physical Review Letters, vol. 126, no. 1, 015301, American
Physical Society, 2021, doi:10.1103/PhysRevLett.126.015301.
short: M. Brooks, M. Lemeshko, D. Lundholm, E. Yakaboylu, Physical Review Letters
126 (2021).
date_created: 2021-01-17T23:01:10Z
date_published: 2021-01-08T00:00:00Z
date_updated: 2023-08-07T13:32:10Z
day: '08'
department:
- _id: MiLe
- _id: RoSe
doi: 10.1103/PhysRevLett.126.015301
ec_funded: 1
external_id:
arxiv:
- '2009.05948'
isi:
- '000606325000003'
intvolume: ' 126'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2009.05948
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/dancing-molecules-and-two-dimensional-particles/
record:
- id: '12390'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Molecular impurities as a realization of anyons on the two-sphere
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 126
year: '2021'
...
---
_id: '9009'
abstract:
- lang: eng
text: Recent advancements in live cell imaging technologies have identified the
phenomenon of intracellular propagation of late apoptotic events, such as cytochrome
c release and caspase activation. The mechanism, prevalence, and speed of apoptosis
propagation remain unclear. Additionally, no studies have demonstrated propagation
of the pro-apoptotic protein, BAX. To evaluate the role of BAX in intracellular
apoptotic propagation, we used high speed live-cell imaging to visualize fluorescently
tagged-BAX recruitment to mitochondria in four immortalized cell lines. We show
that propagation of mitochondrial BAX recruitment occurs in parallel to cytochrome
c and SMAC/Diablo release and is affected by cellular morphology, such that cells
with processes are more likely to exhibit propagation. The initiation of propagation
events is most prevalent in the distal tips of processes, while the rate of propagation
is influenced by the 2-dimensional width of the process. Propagation was rarely
observed in the cell soma, which exhibited near synchronous recruitment of BAX.
Propagation velocity is not affected by mitochondrial volume in segments of processes,
but is negatively affected by mitochondrial density. There was no evidence of
a propagating wave of increased levels of intracellular calcium ions. Alternatively,
we did observe a uniform increase in superoxide build-up in cellular mitochondria,
which was released as a propagating wave simultaneously with the propagating recruitment
of BAX to the mitochondrial outer membrane.
acknowledgement: This work was supported by National Institute of Health grants R01
EY030123, P30 EY016665, and T32 GM081061, an unrestricted research grant from Research
to Prevent Blindness, Inc., and the Frederick A. Davis Endowment from the Department
of Ophthalmology and Visual Sciences at the University of Wisconsin-Madison.
article_processing_charge: No
article_type: original
author:
- first_name: Joshua A.
full_name: Grosser, Joshua A.
last_name: Grosser
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Robert W.
full_name: Nickells, Robert W.
last_name: Nickells
citation:
ama: Grosser JA, Maes ME, Nickells RW. Characteristics of intracellular propagation
of mitochondrial BAX recruitment during apoptosis. Apoptosis. 2021;26(2):132-145.
doi:10.1007/s10495-020-01654-w
apa: Grosser, J. A., Maes, M. E., & Nickells, R. W. (2021). Characteristics
of intracellular propagation of mitochondrial BAX recruitment during apoptosis.
Apoptosis. Springer Nature. https://doi.org/10.1007/s10495-020-01654-w
chicago: Grosser, Joshua A., Margaret E Maes, and Robert W. Nickells. “Characteristics
of Intracellular Propagation of Mitochondrial BAX Recruitment during Apoptosis.”
Apoptosis. Springer Nature, 2021. https://doi.org/10.1007/s10495-020-01654-w.
ieee: J. A. Grosser, M. E. Maes, and R. W. Nickells, “Characteristics of intracellular
propagation of mitochondrial BAX recruitment during apoptosis,” Apoptosis,
vol. 26, no. 2. Springer Nature, pp. 132–145, 2021.
ista: Grosser JA, Maes ME, Nickells RW. 2021. Characteristics of intracellular propagation
of mitochondrial BAX recruitment during apoptosis. Apoptosis. 26(2), 132–145.
mla: Grosser, Joshua A., et al. “Characteristics of Intracellular Propagation of
Mitochondrial BAX Recruitment during Apoptosis.” Apoptosis, vol. 26, no.
2, Springer Nature, 2021, pp. 132–45, doi:10.1007/s10495-020-01654-w.
short: J.A. Grosser, M.E. Maes, R.W. Nickells, Apoptosis 26 (2021) 132–145.
date_created: 2021-01-17T23:01:11Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2023-08-07T13:32:40Z
day: '01'
department:
- _id: SaSi
doi: 10.1007/s10495-020-01654-w
external_id:
isi:
- '000606722600001'
pmid:
- '33426618'
intvolume: ' 26'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082518/
month: '02'
oa: 1
oa_version: Submitted Version
page: 132-145
pmid: 1
publication: Apoptosis
publication_identifier:
eissn:
- 1573-675X
issn:
- 1360-8185
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Characteristics of intracellular propagation of mitochondrial BAX recruitment
during apoptosis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 26
year: '2021'
...
---
_id: '9038'
abstract:
- lang: eng
text: 'Layered materials in which individual atomic layers are bonded by weak van
der Waals forces (vdW materials) constitute one of the most prominent platforms
for materials research. Particularly, polar vdW crystals, such as hexagonal boron
nitride (h-BN), alpha-molybdenum trioxide (α-MoO3) or alpha-vanadium pentoxide
(α-V2O5), have received significant attention in nano-optics, since they support
phonon polaritons (PhPs)―light coupled to lattice vibrations― with strong electromagnetic
confinement and low optical losses. Recently, correlative far- and near-field
studies of α-MoO3 have been demonstrated as an effective strategy to accurately
extract the permittivity of this material. Here, we use this accurately characterized
and low-loss polaritonic material to sense its local dielectric environment, namely
silica (SiO2), one of the most widespread substrates in nanotechnology. By studying
the propagation of PhPs on α-MoO3 flakes with different thicknesses laying on
SiO2 substrates via near-field microscopy (s-SNOM), we extract locally the infrared
permittivity of SiO2. Our work reveals PhPs nanoimaging as a versatile method
for the quantitative characterization of the local optical properties of dielectric
substrates, crucial for understanding and predicting the response of nanomaterials
and for the future scalability of integrated nanophotonic devices. '
acknowledgement: "P.A.-M. acknowledges financial support through JAE Intro program
from the Superior\r\nCouncil of Scientific Investigations and the Spanish Ministry
of Science and Innovation (grant number JAEINT_20_00589). G.Á.-P. and J.T.-G. acknowledge
financial support through the Severo Ochoa Program from the Government of the Principality
of Asturias (grant numbers PA-20-PF-BP19-053 and PA-18-PF-BP17-126, respectively).
J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government
of Spain (RYC2018-026196-I) and the Spanish Ministry of Science and Innovation (State
Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00).
P.A.-G. acknowledges support from the European Research Council under starting grant
no. 715496, 2DNANOPTICA and the Spanish Ministry of Science and Innovation (State
Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00)."
article_number: '120'
article_processing_charge: No
article_type: original
author:
- first_name: Patricia
full_name: Aguilar-Merino, Patricia
last_name: Aguilar-Merino
- first_name: Gonzalo
full_name: Álvarez-Pérez, Gonzalo
last_name: Álvarez-Pérez
- first_name: Javier
full_name: Taboada-Gutiérrez, Javier
last_name: Taboada-Gutiérrez
- first_name: Jiahua
full_name: Duan, Jiahua
last_name: Duan
- first_name: Ivan
full_name: Prieto Gonzalez, Ivan
id: 2A307FE2-F248-11E8-B48F-1D18A9856A87
last_name: Prieto Gonzalez
orcid: 0000-0002-7370-5357
- first_name: Luis Manuel
full_name: Álvarez-Prado, Luis Manuel
last_name: Álvarez-Prado
- first_name: Alexey Y.
full_name: Nikitin, Alexey Y.
last_name: Nikitin
- first_name: Javier
full_name: Martín-Sánchez, Javier
last_name: Martín-Sánchez
- first_name: Pablo
full_name: Alonso-González, Pablo
last_name: Alonso-González
citation:
ama: Aguilar-Merino P, Álvarez-Pérez G, Taboada-Gutiérrez J, et al. Extracting the
infrared permittivity of SiO2 substrates locally by near-field imaging of phonon
polaritons in a van der Waals crystal. Nanomaterials. 2021;11(1). doi:10.3390/nano11010120
apa: Aguilar-Merino, P., Álvarez-Pérez, G., Taboada-Gutiérrez, J., Duan, J., Prieto
Gonzalez, I., Álvarez-Prado, L. M., … Alonso-González, P. (2021). Extracting the
infrared permittivity of SiO2 substrates locally by near-field imaging of phonon
polaritons in a van der Waals crystal. Nanomaterials. MDPI. https://doi.org/10.3390/nano11010120
chicago: Aguilar-Merino, Patricia, Gonzalo Álvarez-Pérez, Javier Taboada-Gutiérrez,
Jiahua Duan, Ivan Prieto Gonzalez, Luis Manuel Álvarez-Prado, Alexey Y. Nikitin,
Javier Martín-Sánchez, and Pablo Alonso-González. “Extracting the Infrared Permittivity
of SiO2 Substrates Locally by Near-Field Imaging of Phonon Polaritons in a van
Der Waals Crystal.” Nanomaterials. MDPI, 2021. https://doi.org/10.3390/nano11010120.
ieee: P. Aguilar-Merino et al., “Extracting the infrared permittivity of
SiO2 substrates locally by near-field imaging of phonon polaritons in a van der
Waals crystal,” Nanomaterials, vol. 11, no. 1. MDPI, 2021.
ista: Aguilar-Merino P, Álvarez-Pérez G, Taboada-Gutiérrez J, Duan J, Prieto Gonzalez
I, Álvarez-Prado LM, Nikitin AY, Martín-Sánchez J, Alonso-González P. 2021. Extracting
the infrared permittivity of SiO2 substrates locally by near-field imaging of
phonon polaritons in a van der Waals crystal. Nanomaterials. 11(1), 120.
mla: Aguilar-Merino, Patricia, et al. “Extracting the Infrared Permittivity of SiO2
Substrates Locally by Near-Field Imaging of Phonon Polaritons in a van Der Waals
Crystal.” Nanomaterials, vol. 11, no. 1, 120, MDPI, 2021, doi:10.3390/nano11010120.
short: P. Aguilar-Merino, G. Álvarez-Pérez, J. Taboada-Gutiérrez, J. Duan, I. Prieto
Gonzalez, L.M. Álvarez-Prado, A.Y. Nikitin, J. Martín-Sánchez, P. Alonso-González,
Nanomaterials 11 (2021).
date_created: 2021-01-24T23:01:09Z
date_published: 2021-01-07T00:00:00Z
date_updated: 2023-08-07T13:35:50Z
day: '07'
ddc:
- '620'
department:
- _id: NanoFab
doi: 10.3390/nano11010120
external_id:
isi:
- '000610636600001'
pmid:
- '33430225'
file:
- access_level: open_access
checksum: 1edc13eeda83df5cd9fff9504727b1f5
content_type: application/pdf
creator: dernst
date_created: 2021-01-25T08:02:32Z
date_updated: 2021-01-25T08:02:32Z
file_id: '9042'
file_name: 2020_Nanomaterials_Aguilar_Merino.pdf
file_size: 2730267
relation: main_file
success: 1
file_date_updated: 2021-01-25T08:02:32Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nanomaterials
publication_identifier:
eissn:
- '20794991'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extracting the infrared permittivity of SiO2 substrates locally by near-field
imaging of phonon polaritons in a van der Waals crystal
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '9020'
abstract:
- lang: eng
text: 'We study dynamics and thermodynamics of ion transport in narrow, water-filled
channels, considered as effective 1D Coulomb systems. The long range nature of
the inter-ion interactions comes about due to the dielectric constants mismatch
between the water and the surrounding medium, confining the electric filed to
stay mostly within the water-filled channel. Statistical mechanics of such Coulomb
systems is dominated by entropic effects which may be accurately accounted for
by mapping onto an effective quantum mechanics. In presence of multivalent ions
the corresponding quantum mechanics appears to be non-Hermitian. In this review
we discuss a framework for semiclassical calculations for the effective non-Hermitian
Hamiltonians. Non-Hermiticity elevates WKB action integrals from the real line
to closed cycles on a complex Riemann surfaces where direct calculations are not
attainable. We circumvent this issue by applying tools from algebraic topology,
such as the Picard-Fuchs equation. We discuss how its solutions relate to the
thermodynamics and correlation functions of multivalent solutions within narrow,
water-filled channels. '
acknowledgement: "A.K. was supported by NSF grants DMR-2037654. T.G. acknowledges
funding from the Institute of Science and Technology (IST) Austria, and from the
European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie
Grant Agreement No. 754411.\r\nWe are indebted to Boris Shklovskii for introducing
us to the problem, and Alexander Gorsky and Peter Koroteev for introducing us to
the Picard-Fuchs methods. A very special thanks goes to Michael Janas for several
years of excellent collaboration on these topics. TG thanks Michael Kreshchuk for
introduction to the exact WKB method and great collaboration on related projects.
Figure 3 and Figure 4 are reproduced from Reference [25] with friendly permission
by the Russian Academy of Sciences. Figure 2, Figure 4, Figure 5, Figure 6, and
Figure 8 are reproduced from Reference [26] with friendly permission by IOP Publishing."
article_number: e23010125
article_processing_charge: Yes
article_type: original
author:
- first_name: Tobias
full_name: Gulden, Tobias
id: 1083E038-9F73-11E9-A4B5-532AE6697425
last_name: Gulden
orcid: 0000-0001-6814-7541
- first_name: Alex
full_name: Kamenev, Alex
last_name: Kamenev
citation:
ama: Gulden T, Kamenev A. Dynamics of ion channels via non-hermitian quantum mechanics.
Entropy. 2021;23(1). doi:10.3390/e23010125
apa: Gulden, T., & Kamenev, A. (2021). Dynamics of ion channels via non-hermitian
quantum mechanics. Entropy. MDPI. https://doi.org/10.3390/e23010125
chicago: Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian
Quantum Mechanics.” Entropy. MDPI, 2021. https://doi.org/10.3390/e23010125.
ieee: T. Gulden and A. Kamenev, “Dynamics of ion channels via non-hermitian quantum
mechanics,” Entropy, vol. 23, no. 1. MDPI, 2021.
ista: Gulden T, Kamenev A. 2021. Dynamics of ion channels via non-hermitian quantum
mechanics. Entropy. 23(1), e23010125.
mla: Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian
Quantum Mechanics.” Entropy, vol. 23, no. 1, e23010125, MDPI, 2021, doi:10.3390/e23010125.
short: T. Gulden, A. Kamenev, Entropy 23 (2021).
date_created: 2021-01-19T11:12:06Z
date_published: 2021-01-19T00:00:00Z
date_updated: 2023-08-07T13:34:18Z
day: '19'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.3390/e23010125
ec_funded: 1
external_id:
arxiv:
- '2012.01390'
isi:
- '000610122000001'
file:
- access_level: open_access
checksum: 6cd0e706156827c45c740534bd32c179
content_type: application/pdf
creator: tgulden
date_created: 2021-01-19T11:11:14Z
date_updated: 2021-01-19T11:11:14Z
file_id: '9021'
file_name: Final published paper.pdf
file_size: 981285
relation: main_file
file_date_updated: 2021-01-19T11:11:14Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Entropy
publication_identifier:
eissn:
- 1099-4300
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Dynamics of ion channels via non-hermitian quantum mechanics
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 23
year: '2021'
...
---
_id: '9037'
abstract:
- lang: eng
text: "We continue our study of ‘no‐dimension’ analogues of basic theorems in combinatorial
and convex geometry in Banach spaces. We generalize some results of the paper
(Adiprasito, Bárány and Mustafa, ‘Theorems of Carathéodory, Helly, and Tverberg
without dimension’, Proceedings of the Thirtieth Annual ACM‐SIAM Symposium on
Discrete Algorithms (Society for Industrial and Applied Mathematics, San Diego,
California, 2019) 2350–2360) and prove no‐dimension versions of the colored Tverberg
theorem, the selection lemma and the weak \U0001D700 ‐net theorem in Banach spaces
of type \U0001D45D>1 . To prove these results, we use the original ideas of Adiprasito,
Bárány and Mustafa for the Euclidean case, our no‐dimension version of the Radon
theorem and slightly modified version of the celebrated Maurey lemma."
acknowledgement: "I wish to thank Imre Bárány for bringing the problem to my attention.
I am grateful to Marton Naszódi and Igor Tsiutsiurupa for useful remarks and help
with the text.\r\nThe author acknowledges the financial support from the Ministry
of Educational and Science of the Russian Federation in the framework of MegaGrant
no 075‐15‐2019‐1926."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Grigory
full_name: Ivanov, Grigory
id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E
last_name: Ivanov
citation:
ama: Ivanov G. No-dimension Tverberg’s theorem and its corollaries in Banach spaces
of type p. Bulletin of the London Mathematical Society. 2021;53(2):631-641.
doi:10.1112/blms.12449
apa: Ivanov, G. (2021). No-dimension Tverberg’s theorem and its corollaries in Banach
spaces of type p. Bulletin of the London Mathematical Society. London Mathematical
Society. https://doi.org/10.1112/blms.12449
chicago: Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in
Banach Spaces of Type P.” Bulletin of the London Mathematical Society.
London Mathematical Society, 2021. https://doi.org/10.1112/blms.12449.
ieee: G. Ivanov, “No-dimension Tverberg’s theorem and its corollaries in Banach
spaces of type p,” Bulletin of the London Mathematical Society, vol. 53,
no. 2. London Mathematical Society, pp. 631–641, 2021.
ista: Ivanov G. 2021. No-dimension Tverberg’s theorem and its corollaries in Banach
spaces of type p. Bulletin of the London Mathematical Society. 53(2), 631–641.
mla: Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in Banach
Spaces of Type P.” Bulletin of the London Mathematical Society, vol. 53,
no. 2, London Mathematical Society, 2021, pp. 631–41, doi:10.1112/blms.12449.
short: G. Ivanov, Bulletin of the London Mathematical Society 53 (2021) 631–641.
date_created: 2021-01-24T23:01:08Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2023-08-07T13:35:20Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1112/blms.12449
external_id:
arxiv:
- '1912.08561'
isi:
- '000607265100001'
file:
- access_level: open_access
checksum: e6ceaa6470d835eb4c211cbdd38fdfd1
content_type: application/pdf
creator: kschuh
date_created: 2021-08-06T09:59:45Z
date_updated: 2021-08-06T09:59:45Z
file_id: '9796'
file_name: 2021_BLMS_Ivanov.pdf
file_size: 194550
relation: main_file
success: 1
file_date_updated: 2021-08-06T09:59:45Z
has_accepted_license: '1'
intvolume: ' 53'
isi: 1
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 631-641
publication: Bulletin of the London Mathematical Society
publication_identifier:
eissn:
- '14692120'
issn:
- '00246093'
publication_status: published
publisher: London Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: No-dimension Tverberg's theorem and its corollaries in Banach spaces of type
p
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 53
year: '2021'
...
---
_id: '9046'
acknowledgement: Our work was supported by the Swedish Research Council (grant 2017-01527)
to DIA
article_number: e1009172
article_processing_charge: No
article_type: original
author:
- first_name: Roderich
full_name: Römhild, Roderich
id: 68E56E44-62B0-11EA-B963-444F3DDC885E
last_name: Römhild
orcid: 0000-0001-9480-5261
- first_name: Dan I.
full_name: Andersson, Dan I.
last_name: Andersson
citation:
ama: Römhild R, Andersson DI. Mechanisms and therapeutic potential of collateral
sensitivity to antibiotics. PLoS Pathogens. 2021;17(1). doi:10.1371/journal.ppat.1009172
apa: Römhild, R., & Andersson, D. I. (2021). Mechanisms and therapeutic potential
of collateral sensitivity to antibiotics. PLoS Pathogens. Public Library
of Science. https://doi.org/10.1371/journal.ppat.1009172
chicago: Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential
of Collateral Sensitivity to Antibiotics.” PLoS Pathogens. Public Library
of Science, 2021. https://doi.org/10.1371/journal.ppat.1009172.
ieee: R. Römhild and D. I. Andersson, “Mechanisms and therapeutic potential of collateral
sensitivity to antibiotics,” PLoS Pathogens, vol. 17, no. 1. Public Library
of Science, 2021.
ista: Römhild R, Andersson DI. 2021. Mechanisms and therapeutic potential of collateral
sensitivity to antibiotics. PLoS Pathogens. 17(1), e1009172.
mla: Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential
of Collateral Sensitivity to Antibiotics.” PLoS Pathogens, vol. 17, no.
1, e1009172, Public Library of Science, 2021, doi:10.1371/journal.ppat.1009172.
short: R. Römhild, D.I. Andersson, PLoS Pathogens 17 (2021).
date_created: 2021-01-31T23:01:21Z
date_published: 2021-01-14T00:00:00Z
date_updated: 2023-08-07T13:36:55Z
day: '14'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1371/journal.ppat.1009172
external_id:
isi:
- '000610190400007'
pmid:
- '33444399'
file:
- access_level: open_access
checksum: d745d7f8fcbb9b95fea16a36f94dee31
content_type: application/pdf
creator: dernst
date_created: 2021-02-03T12:13:03Z
date_updated: 2021-02-03T12:13:03Z
file_id: '9070'
file_name: 2021_PlosPathogens_Roemhild.pdf
file_size: 570066
relation: main_file
success: 1
file_date_updated: 2021-02-03T12:13:03Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Pathogens
publication_identifier:
eissn:
- '15537374'
issn:
- '15537366'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanisms and therapeutic potential of collateral sensitivity to antibiotics
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2021'
...
---
_id: '9047'
abstract:
- lang: eng
text: This work analyzes the latency of the simplified successive cancellation (SSC)
decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It
is shown that, unlike conventional successive cancellation decoding, where latency
is linear in the block length, the latency of SSC decoding is sublinear. More
specifically, the latency of SSC decoding is O(N1−1/μ) , where N is the block
length and μ is the scaling exponent of the channel, which captures the speed
of convergence of the rate to capacity. Numerical results demonstrate the tightness
of the bound and show that most of the latency reduction arises from the parallel
decoding of subcodes of rate 0 or 1.
acknowledgement: M. Mondelli was partially supported by grants NSF DMS-1613091, CCF-1714305,
IIS-1741162, and ONR N00014-18-1-2729. S. A. Hashemi is supported by a Postdoctoral
Fellowship from the Natural Sciences and Engineering Research Council of Canada
(NSERC) and by Huawei. The authors would like to thank the anonymous reviewers for
their comments that helped improving the quality of the manuscript.
article_processing_charge: No
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: Seyyed Ali
full_name: Hashemi, Seyyed Ali
last_name: Hashemi
- first_name: John M.
full_name: Cioffi, John M.
last_name: Cioffi
- first_name: Andrea
full_name: Goldsmith, Andrea
last_name: Goldsmith
citation:
ama: Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. Sublinear latency for simplified
successive cancellation decoding of polar codes. IEEE Transactions on Wireless
Communications. 2021;20(1):18-27. doi:10.1109/TWC.2020.3022922
apa: Mondelli, M., Hashemi, S. A., Cioffi, J. M., & Goldsmith, A. (2021). Sublinear
latency for simplified successive cancellation decoding of polar codes. IEEE
Transactions on Wireless Communications. IEEE. https://doi.org/10.1109/TWC.2020.3022922
chicago: Mondelli, Marco, Seyyed Ali Hashemi, John M. Cioffi, and Andrea Goldsmith.
“Sublinear Latency for Simplified Successive Cancellation Decoding of Polar Codes.”
IEEE Transactions on Wireless Communications. IEEE, 2021. https://doi.org/10.1109/TWC.2020.3022922.
ieee: M. Mondelli, S. A. Hashemi, J. M. Cioffi, and A. Goldsmith, “Sublinear latency
for simplified successive cancellation decoding of polar codes,” IEEE Transactions
on Wireless Communications, vol. 20, no. 1. IEEE, pp. 18–27, 2021.
ista: Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. 2021. Sublinear latency for
simplified successive cancellation decoding of polar codes. IEEE Transactions
on Wireless Communications. 20(1), 18–27.
mla: Mondelli, Marco, et al. “Sublinear Latency for Simplified Successive Cancellation
Decoding of Polar Codes.” IEEE Transactions on Wireless Communications,
vol. 20, no. 1, IEEE, 2021, pp. 18–27, doi:10.1109/TWC.2020.3022922.
short: M. Mondelli, S.A. Hashemi, J.M. Cioffi, A. Goldsmith, IEEE Transactions on
Wireless Communications 20 (2021) 18–27.
date_created: 2021-01-31T23:01:21Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2023-08-07T13:36:25Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/TWC.2020.3022922
external_id:
arxiv:
- '1909.04892'
isi:
- '000607808800002'
intvolume: ' 20'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1909.04892
month: '01'
oa: 1
oa_version: Preprint
page: 18-27
publication: IEEE Transactions on Wireless Communications
publication_identifier:
eissn:
- '15582248'
issn:
- '15361276'
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '8536'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Sublinear latency for simplified successive cancellation decoding of polar
codes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 20
year: '2021'
...
---
_id: '9036'
abstract:
- lang: eng
text: In this short note, we prove that the square root of the quantum Jensen-Shannon
divergence is a true metric on the cone of positive matrices, and hence in particular
on the quantum state space.
acknowledgement: D. Virosztek was supported by the European Union's Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 846294,
and partially supported by the Hungarian National Research, Development and Innovation
Office (NKFIH) via grants no. K124152, and no. KH129601.
article_number: '107595'
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Virosztek, Daniel
id: 48DB45DA-F248-11E8-B48F-1D18A9856A87
last_name: Virosztek
orcid: 0000-0003-1109-5511
citation:
ama: Virosztek D. The metric property of the quantum Jensen-Shannon divergence.
Advances in Mathematics. 2021;380(3). doi:10.1016/j.aim.2021.107595
apa: Virosztek, D. (2021). The metric property of the quantum Jensen-Shannon divergence.
Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2021.107595
chicago: Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.”
Advances in Mathematics. Elsevier, 2021. https://doi.org/10.1016/j.aim.2021.107595.
ieee: D. Virosztek, “The metric property of the quantum Jensen-Shannon divergence,”
Advances in Mathematics, vol. 380, no. 3. Elsevier, 2021.
ista: Virosztek D. 2021. The metric property of the quantum Jensen-Shannon divergence.
Advances in Mathematics. 380(3), 107595.
mla: Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.”
Advances in Mathematics, vol. 380, no. 3, 107595, Elsevier, 2021, doi:10.1016/j.aim.2021.107595.
short: D. Virosztek, Advances in Mathematics 380 (2021).
date_created: 2021-01-22T17:55:17Z
date_published: 2021-03-26T00:00:00Z
date_updated: 2023-08-07T13:34:48Z
day: '26'
department:
- _id: LaEr
doi: 10.1016/j.aim.2021.107595
ec_funded: 1
external_id:
arxiv:
- '1910.10447'
isi:
- '000619676100035'
intvolume: ' 380'
isi: 1
issue: '3'
keyword:
- General Mathematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1910.10447
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 26A455A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '846294'
name: Geometric study of Wasserstein spaces and free probability
publication: Advances in Mathematics
publication_identifier:
issn:
- 0001-8708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: The metric property of the quantum Jensen-Shannon divergence
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 380
year: '2021'
...
---
_id: '9101'
abstract:
- lang: eng
text: 'Behavioral predispositions are innate tendencies of animals to behave in
a given way without the input of learning. They increase survival chances and,
due to environmental and ecological challenges, may vary substantially even between
closely related taxa. These differences are likely to be especially pronounced
in long-lived species like crocodilians. This order is particularly relevant for
comparative cognition due to its phylogenetic proximity to birds. Here we compared
early life behavioral predispositions in two Alligatoridae species. We exposed
American alligator and spectacled caiman hatchlings to three different novel situations:
a novel object, a novel environment that was open and a novel environment with
a shelter. This was then repeated a week later. During exposure to the novel environments,
alligators moved around more and explored a larger range of the arena than the
caimans. When exposed to the novel object, the alligators reduced the mean distance
to the novel object in the second phase, while the caimans further increased it,
indicating diametrically opposite ontogenetic development in behavioral predispositions.
Although all crocodilian hatchlings face comparable challenges, e.g., high predation
pressure, the effectiveness of parental protection might explain the observed
pattern. American alligators are apex predators capable of protecting their offspring
against most dangers, whereas adult spectacled caimans are frequently predated
themselves. Their distancing behavior might be related to increased predator avoidance
and also explain the success of invasive spectacled caimans in the natural habitats
of other crocodilians.'
acknowledgement: We thank Jamie Gilks and Terry Miles for their support at Crocodiles
of the World. We are grateful to the Department of Cognitive Biology, University
of Vienna for provision of working space and hardware. Finally, we would like to
thank Cliodhna Quigley, Rachael Harrison and Urs A. Reber for discussion. Open Access
funding provided by Lund University. This project was funded by the Marietta Blau
grant (BMFWF) to S. A. R.
article_processing_charge: No
article_type: original
author:
- first_name: Stephan A.
full_name: Reber, Stephan A.
last_name: Reber
- first_name: Jinook
full_name: Oh, Jinook
id: 403169A4-080F-11EA-9993-BF3F3DDC885E
last_name: Oh
orcid: 0000-0001-7425-2372
- first_name: Judith
full_name: Janisch, Judith
last_name: Janisch
- first_name: Colin
full_name: Stevenson, Colin
last_name: Stevenson
- first_name: Shaun
full_name: Foggett, Shaun
last_name: Foggett
- first_name: Anna
full_name: Wilkinson, Anna
last_name: Wilkinson
citation:
ama: Reber SA, Oh J, Janisch J, Stevenson C, Foggett S, Wilkinson A. Early life
differences in behavioral predispositions in two Alligatoridae species. Animal
Cognition. 2021;24(4):753-764. doi:10.1007/s10071-020-01461-5
apa: Reber, S. A., Oh, J., Janisch, J., Stevenson, C., Foggett, S., & Wilkinson,
A. (2021). Early life differences in behavioral predispositions in two Alligatoridae
species. Animal Cognition. Springer Nature. https://doi.org/10.1007/s10071-020-01461-5
chicago: Reber, Stephan A., Jinook Oh, Judith Janisch, Colin Stevenson, Shaun Foggett,
and Anna Wilkinson. “Early Life Differences in Behavioral Predispositions in Two
Alligatoridae Species.” Animal Cognition. Springer Nature, 2021. https://doi.org/10.1007/s10071-020-01461-5.
ieee: S. A. Reber, J. Oh, J. Janisch, C. Stevenson, S. Foggett, and A. Wilkinson,
“Early life differences in behavioral predispositions in two Alligatoridae species,”
Animal Cognition, vol. 24, no. 4. Springer Nature, pp. 753–764, 2021.
ista: Reber SA, Oh J, Janisch J, Stevenson C, Foggett S, Wilkinson A. 2021. Early
life differences in behavioral predispositions in two Alligatoridae species. Animal
Cognition. 24(4), 753–764.
mla: Reber, Stephan A., et al. “Early Life Differences in Behavioral Predispositions
in Two Alligatoridae Species.” Animal Cognition, vol. 24, no. 4, Springer
Nature, 2021, pp. 753–64, doi:10.1007/s10071-020-01461-5.
short: S.A. Reber, J. Oh, J. Janisch, C. Stevenson, S. Foggett, A. Wilkinson, Animal
Cognition 24 (2021) 753–764.
date_created: 2021-02-07T23:01:13Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-07T13:41:08Z
day: '01'
ddc:
- '590'
department:
- _id: SyCr
doi: 10.1007/s10071-020-01461-5
external_id:
isi:
- '000608382100001'
file:
- access_level: open_access
checksum: d9dfa0d1de6d684692b041d936dd858e
content_type: application/pdf
creator: dernst
date_created: 2021-02-09T07:40:14Z
date_updated: 2021-02-09T07:40:14Z
file_id: '9107'
file_name: 2021_AnimalCognition_Reber.pdf
file_size: 1117991
relation: main_file
success: 1
file_date_updated: 2021-02-09T07:40:14Z
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 753-764
publication: Animal Cognition
publication_identifier:
eissn:
- '14359456'
issn:
- '14359448'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Early life differences in behavioral predispositions in two Alligatoridae species
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 24
year: '2021'
...
---
_id: '9100'
abstract:
- lang: eng
text: 'Marine environments are inhabited by a broad representation of the tree of
life, yet our understanding of speciation in marine ecosystems is extremely limited
compared with terrestrial and freshwater environments. Developing a more comprehensive
picture of speciation in marine environments requires that we ''dive under the
surface'' by studying a wider range of taxa and ecosystems is necessary for a
more comprehensive picture of speciation. Although studying marine evolutionary
processes is often challenging, recent technological advances in different fields,
from maritime engineering to genomics, are making it increasingly possible to
study speciation of marine life forms across diverse ecosystems and taxa. Motivated
by recent research in the field, including the 14 contributions in this issue,
we highlight and discuss six axes of research that we think will deepen our understanding
of speciation in the marine realm: (a) study a broader range of marine environments
and organisms; (b) identify the reproductive barriers driving speciation between
marine taxa; (c) understand the role of different genomic architectures underlying
reproductive isolation; (d) infer the evolutionary history of divergence using
model‐based approaches; (e) study patterns of hybridization and introgression
between marine taxa; and (f) implement highly interdisciplinary, collaborative
research programmes. In outlining these goals, we hope to inspire researchers
to continue filling this critical knowledge gap surrounding the origins of marine
biodiversity.'
acknowledgement: "We would like to thank all the participants in the speciation symposium
of the Marine Evolution Conference in Sweden for the interesting discussions and
to all the contributors to this special\r\nissue. We thank Nicolas Bierne and Wolf
Blanckenhorn (reviewer and editor, respectively) for valuable suggestions during
the revision of the manuscript, and Roger K. Butlin and Anja M. Westram for very
helpful comments on a previous draft. We would also like to thank Wolf Blanckenhorn
and Nicola Cook, the Editor in Chief and the Managing Editor of the Journal of Evolutionary
Biology, respectively, for the encouragement and support in putting together this
special issue, and to all reviewers involved. RF was financed by the European Union's
Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie
Grant Agreement Number 706376 and is currently financed by the FEDER Funds through
the Operational Competitiveness Factors Program COMPETE and by National Funds through
the Foundation for Science and Technology (FCT) within the scope of the project
‘Hybrabbid' (PTDC/BIA-EVL/30628/2017-POCI-01-0145-FEDER-030628). KJ was funded by
the Swedish\r\nResearch Council, VR. SS was supported by NERC and ERC funding awarded
to Roger K. Butlin."
article_processing_charge: No
article_type: original
author:
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
citation:
ama: 'Faria R, Johannesson K, Stankowski S. Speciation in marine environments: Diving
under the surface. Journal of Evolutionary Biology. 2021;34(1):4-15. doi:10.1111/jeb.13756'
apa: 'Faria, R., Johannesson, K., & Stankowski, S. (2021). Speciation in marine
environments: Diving under the surface. Journal of Evolutionary Biology.
Wiley. https://doi.org/10.1111/jeb.13756'
chicago: 'Faria, Rui, Kerstin Johannesson, and Sean Stankowski. “Speciation in Marine
Environments: Diving under the Surface.” Journal of Evolutionary Biology.
Wiley, 2021. https://doi.org/10.1111/jeb.13756.'
ieee: 'R. Faria, K. Johannesson, and S. Stankowski, “Speciation in marine environments:
Diving under the surface,” Journal of Evolutionary Biology, vol. 34, no.
1. Wiley, pp. 4–15, 2021.'
ista: 'Faria R, Johannesson K, Stankowski S. 2021. Speciation in marine environments:
Diving under the surface. Journal of Evolutionary Biology. 34(1), 4–15.'
mla: 'Faria, Rui, et al. “Speciation in Marine Environments: Diving under the Surface.”
Journal of Evolutionary Biology, vol. 34, no. 1, Wiley, 2021, pp. 4–15,
doi:10.1111/jeb.13756.'
short: R. Faria, K. Johannesson, S. Stankowski, Journal of Evolutionary Biology
34 (2021) 4–15.
date_created: 2021-02-07T23:01:13Z
date_published: 2021-01-18T00:00:00Z
date_updated: 2023-08-07T13:42:08Z
day: '18'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.13756
external_id:
isi:
- '000608367500001'
file:
- access_level: open_access
checksum: 5755856a5368d4b4cdd6fad5ab27f4d1
content_type: application/pdf
creator: dernst
date_created: 2021-02-09T09:04:02Z
date_updated: 2021-02-09T09:04:02Z
file_id: '9108'
file_name: 2021_JourEvolBiology_Faria.pdf
file_size: 561340
relation: main_file
success: 1
file_date_updated: 2021-02-09T09:04:02Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 4-15
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- '14209101'
issn:
- 1010061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Speciation in marine environments: Diving under the surface'
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 34
year: '2021'
...
---
_id: '9093'
abstract:
- lang: eng
text: We employ the Gross-Pitaevskii equation to study acoustic emission generated
in a uniform Bose gas by a static impurity. The impurity excites a sound-wave
packet, which propagates through the gas. We calculate the shape of this wave
packet in the limit of long wave lengths, and argue that it is possible to extract
properties of the impurity by observing this shape. We illustrate here this possibility
for a Bose gas with a trapped impurity atom -- an example of a relevant experimental
setup. Presented results are general for all one-dimensional systems described
by the nonlinear Schrödinger equation and can also be used in nonatomic systems,
e.g., to analyze light propagation in nonlinear optical media. Finally, we calculate
the shape of the sound-wave packet for a three-dimensional Bose gas assuming a
spherically symmetric perturbation.
acknowledgement: "We acknowledge fruitful discussions with Dr. Simos Mistakidis regarding
beyond mean-field\r\neffects in our system. We also thank Prof. Maxim Olshanii for
valuable suggestions to improve\r\nthe manuscript.O.V.M acknowledges the support
from the National Science Foundation\r\nthrough grants No. PHY-1402249, No. PHY-1607221,
and No. PHY-1912542 and the\r\nBinational (US-Israel) Science Foundation through
grant No. 2015616, as well as by the Israel\r\nScience Foundation (grant No. 1287/17)
and from the German Aeronautics and Space Administration\r\n(DLR) through Grant
No. 50WM1957. This work has also received funding from\r\nthe DFG Project No.413495248
[VO 2437/1-1] and European Union’s Horizon 2020 research\r\nand innovation programme
under the Marie Skłodowska-Curie Grant Agreement No. 754411\r\n(A. G. V.)"
article_number: '025'
article_processing_charge: No
article_type: original
author:
- first_name: Oleksandr
full_name: Marchukov, Oleksandr
last_name: Marchukov
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Marchukov O, Volosniev A. Shape of a sound wave in a weakly-perturbed Bose
gas. SciPost Physics. 2021;10(2). doi:10.21468/scipostphys.10.2.025
apa: Marchukov, O., & Volosniev, A. (2021). Shape of a sound wave in a weakly-perturbed
Bose gas. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.10.2.025
chicago: Marchukov, Oleksandr, and Artem Volosniev. “Shape of a Sound Wave in a
Weakly-Perturbed Bose Gas.” SciPost Physics. SciPost Foundation, 2021.
https://doi.org/10.21468/scipostphys.10.2.025.
ieee: O. Marchukov and A. Volosniev, “Shape of a sound wave in a weakly-perturbed
Bose gas,” SciPost Physics, vol. 10, no. 2. SciPost Foundation, 2021.
ista: Marchukov O, Volosniev A. 2021. Shape of a sound wave in a weakly-perturbed
Bose gas. SciPost Physics. 10(2), 025.
mla: Marchukov, Oleksandr, and Artem Volosniev. “Shape of a Sound Wave in a Weakly-Perturbed
Bose Gas.” SciPost Physics, vol. 10, no. 2, 025, SciPost Foundation, 2021,
doi:10.21468/scipostphys.10.2.025.
short: O. Marchukov, A. Volosniev, SciPost Physics 10 (2021).
date_created: 2021-02-04T12:39:24Z
date_published: 2021-02-03T00:00:00Z
date_updated: 2023-08-07T13:39:37Z
day: '03'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.21468/scipostphys.10.2.025
ec_funded: 1
external_id:
arxiv:
- '2004.08075'
isi:
- '000646783100027'
file:
- access_level: open_access
checksum: 9fd614b7ab49999e7267874df2582f7e
content_type: application/pdf
creator: dernst
date_created: 2021-02-09T07:06:22Z
date_updated: 2021-02-09T07:06:22Z
file_id: '9105'
file_name: 2021_SciPostPhysics_Marchukov.pdf
file_size: 666512
relation: main_file
success: 1
file_date_updated: 2021-02-09T07:06:22Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: SciPost Physics
publication_identifier:
issn:
- 2542-4653
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
status: public
title: Shape of a sound wave in a weakly-perturbed Bose gas
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '8689'
abstract:
- lang: eng
text: 'This paper continues the discussion started in [CK19] concerning Arnold''s
legacy on classical KAM theory and (some of) its modern developments. We prove
a detailed and explicit `global'' Arnold''s KAM Theorem, which yields, in particular,
the Whitney conjugacy of a non{degenerate, real{analytic, nearly-integrable Hamiltonian
system to an integrable system on a closed, nowhere dense, positive measure subset
of the phase space. Detailed measure estimates on the Kolmogorov''s set are provided
in the case the phase space is: (A) a uniform neighbourhood of an arbitrary (bounded)
set times the d-torus and (B) a domain with C2 boundary times the d-torus. All
constants are explicitly given.'
article_processing_charge: No
article_type: original
author:
- first_name: Luigi
full_name: Chierchia, Luigi
last_name: Chierchia
- first_name: Edmond
full_name: Koudjinan, Edmond
id: 52DF3E68-AEFA-11EA-95A4-124A3DDC885E
last_name: Koudjinan
orcid: 0000-0003-2640-4049
citation:
ama: Chierchia L, Koudjinan E. V.I. Arnold’s “‘Global’” KAM theorem and geometric
measure estimates. Regular and Chaotic Dynamics. 2021;26(1):61-88. doi:10.1134/S1560354721010044
apa: Chierchia, L., & Koudjinan, E. (2021). V.I. Arnold’s “‘Global’” KAM theorem
and geometric measure estimates. Regular and Chaotic Dynamics. Springer
Nature. https://doi.org/10.1134/S1560354721010044
chicago: Chierchia, Luigi, and Edmond Koudjinan. “V.I. Arnold’s ‘“Global”’ KAM Theorem
and Geometric Measure Estimates.” Regular and Chaotic Dynamics. Springer
Nature, 2021. https://doi.org/10.1134/S1560354721010044.
ieee: L. Chierchia and E. Koudjinan, “V.I. Arnold’s ‘“Global”’ KAM theorem and geometric
measure estimates,” Regular and Chaotic Dynamics, vol. 26, no. 1. Springer
Nature, pp. 61–88, 2021.
ista: Chierchia L, Koudjinan E. 2021. V.I. Arnold’s ‘“Global”’ KAM theorem and geometric
measure estimates. Regular and Chaotic Dynamics. 26(1), 61–88.
mla: Chierchia, Luigi, and Edmond Koudjinan. “V.I. Arnold’s ‘“Global”’ KAM Theorem
and Geometric Measure Estimates.” Regular and Chaotic Dynamics, vol. 26,
no. 1, Springer Nature, 2021, pp. 61–88, doi:10.1134/S1560354721010044.
short: L. Chierchia, E. Koudjinan, Regular and Chaotic Dynamics 26 (2021) 61–88.
date_created: 2020-10-21T14:56:47Z
date_published: 2021-02-03T00:00:00Z
date_updated: 2023-08-07T13:37:27Z
day: '03'
ddc:
- '515'
department:
- _id: VaKa
doi: 10.1134/S1560354721010044
external_id:
arxiv:
- '2010.13243'
isi:
- '000614454700004'
intvolume: ' 26'
isi: 1
issue: '1'
keyword:
- Nearly{integrable Hamiltonian systems
- perturbation theory
- KAM Theory
- Arnold's scheme
- Kolmogorov's set
- primary invariant tori
- Lagrangian tori
- measure estimates
- small divisors
- integrability on nowhere dense sets
- Diophantine frequencies.
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2010.13243
month: '02'
oa: 1
oa_version: Preprint
page: 61-88
publication: Regular and Chaotic Dynamics
publication_identifier:
issn:
- 1560-3547
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: V.I. Arnold's ''Global'' KAM theorem and geometric measure estimates
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 26
year: '2021'
...
---
_id: '9099'
abstract:
- lang: eng
text: We show that on an Abelian variety over an algebraically closed field of positive
characteristic, the obstruction to lifting an automorphism to a field of characteristic
zero as a morphism vanishes if and only if it vanishes for lifting it as a derived
autoequivalence. We also compare the deformation space of these two types of deformations.
acknowledgement: I would like to thank Piotr Achinger, Daniel Huybrechts, Katrina
Honigs, Marcin Lara, and Maciek Zdanowicz for the mathematical discussions, Tamas
Hausel for hosting me in his research group at IST Austria, and the referees for
their valuable suggestions. This research has received funding from the European
Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie
Grant Agreement No. 754411.
article_processing_charge: No
article_type: original
author:
- first_name: Tanya K
full_name: Srivastava, Tanya K
id: 4D046628-F248-11E8-B48F-1D18A9856A87
last_name: Srivastava
citation:
ama: Srivastava TK. Lifting automorphisms on Abelian varieties as derived autoequivalences.
Archiv der Mathematik. 2021;116(5):515-527. doi:10.1007/s00013-020-01564-y
apa: Srivastava, T. K. (2021). Lifting automorphisms on Abelian varieties as derived
autoequivalences. Archiv Der Mathematik. Springer Nature. https://doi.org/10.1007/s00013-020-01564-y
chicago: Srivastava, Tanya K. “Lifting Automorphisms on Abelian Varieties as Derived
Autoequivalences.” Archiv Der Mathematik. Springer Nature, 2021. https://doi.org/10.1007/s00013-020-01564-y.
ieee: T. K. Srivastava, “Lifting automorphisms on Abelian varieties as derived autoequivalences,”
Archiv der Mathematik, vol. 116, no. 5. Springer Nature, pp. 515–527, 2021.
ista: Srivastava TK. 2021. Lifting automorphisms on Abelian varieties as derived
autoequivalences. Archiv der Mathematik. 116(5), 515–527.
mla: Srivastava, Tanya K. “Lifting Automorphisms on Abelian Varieties as Derived
Autoequivalences.” Archiv Der Mathematik, vol. 116, no. 5, Springer Nature,
2021, pp. 515–27, doi:10.1007/s00013-020-01564-y.
short: T.K. Srivastava, Archiv Der Mathematik 116 (2021) 515–527.
date_created: 2021-02-07T23:01:13Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2023-08-07T13:42:38Z
day: '01'
department:
- _id: TaHa
doi: 10.1007/s00013-020-01564-y
ec_funded: 1
external_id:
arxiv:
- '2001.07762'
isi:
- '000612580200001'
intvolume: ' 116'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2001.07762
month: '05'
oa: 1
oa_version: Preprint
page: 515-527
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Archiv der Mathematik
publication_identifier:
eissn:
- '14208938'
issn:
- 0003889X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lifting automorphisms on Abelian varieties as derived autoequivalences
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 116
year: '2021'
...
---
_id: '9098'
abstract:
- lang: eng
text: "We study properties of the volume of projections of the n-dimensional\r\ncross-polytope
$\\crosp^n = \\{ x \\in \\R^n \\mid |x_1| + \\dots + |x_n| \\leqslant 1\\}.$ We
prove that the projection of $\\crosp^n$ onto a k-dimensional coordinate subspace
has the maximum possible volume for k=2 and for k=3.\r\nWe obtain the exact lower
bound on the volume of such a projection onto a two-dimensional plane. Also, we
show that there exist local maxima which are not global ones for the volume of
a projection of $\\crosp^n$ onto a k-dimensional subspace for any n>k⩾2."
acknowledgement: Research was supported by the Russian Foundation for Basic Research,
project 18-01-00036A (Theorems 1.5 and 5.3) and by the Ministry of Education and
Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926
(Theorems 1.2 and 7.3).
article_number: '112312'
article_processing_charge: No
article_type: original
author:
- first_name: Grigory
full_name: Ivanov, Grigory
id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E
last_name: Ivanov
citation:
ama: Ivanov G. On the volume of projections of the cross-polytope. Discrete Mathematics.
2021;344(5). doi:10.1016/j.disc.2021.112312
apa: Ivanov, G. (2021). On the volume of projections of the cross-polytope. Discrete
Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2021.112312
chicago: Ivanov, Grigory. “On the Volume of Projections of the Cross-Polytope.”
Discrete Mathematics. Elsevier, 2021. https://doi.org/10.1016/j.disc.2021.112312.
ieee: G. Ivanov, “On the volume of projections of the cross-polytope,” Discrete
Mathematics, vol. 344, no. 5. Elsevier, 2021.
ista: Ivanov G. 2021. On the volume of projections of the cross-polytope. Discrete
Mathematics. 344(5), 112312.
mla: Ivanov, Grigory. “On the Volume of Projections of the Cross-Polytope.” Discrete
Mathematics, vol. 344, no. 5, 112312, Elsevier, 2021, doi:10.1016/j.disc.2021.112312.
short: G. Ivanov, Discrete Mathematics 344 (2021).
date_created: 2021-02-07T23:01:12Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2023-08-07T13:40:37Z
day: '01'
department:
- _id: UlWa
doi: 10.1016/j.disc.2021.112312
external_id:
arxiv:
- '1808.09165'
isi:
- '000633365200001'
intvolume: ' 344'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.09165
month: '05'
oa: 1
oa_version: Preprint
publication: Discrete Mathematics
publication_identifier:
issn:
- 0012365X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the volume of projections of the cross-polytope
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 344
year: '2021'
...
---
_id: '9188'
abstract:
- lang: eng
text: Genomic imprinting is an epigenetic mechanism that results in parental allele-specific
expression of ~1% of all genes in mouse and human. Imprinted genes are key developmental
regulators and play pivotal roles in many biological processes such as nutrient
transfer from the mother to offspring and neuronal development. Imprinted genes
are also involved in human disease, including neurodevelopmental disorders, and
often occur in clusters that are regulated by a common imprint control region
(ICR). In extra-embryonic tissues ICRs can act over large distances, with the
largest surrounding Igf2r spanning over 10 million base-pairs. Besides classical
imprinted expression that shows near exclusive maternal or paternal expression,
widespread biased imprinted expression has been identified mainly in brain. In
this review we discuss recent developments mapping cell type specific imprinted
expression in extra-embryonic tissues and neocortex in the mouse. We highlight
the advantages of using an inducible uniparental chromosome disomy (UPD) system
to generate cells carrying either two maternal or two paternal copies of a specific
chromosome to analyze the functional consequences of genomic imprinting. Mosaic
Analysis with Double Markers (MADM) allows fluorescent labeling and concomitant
induction of UPD sparsely in specific cell types, and thus to over-express or
suppress all imprinted genes on that chromosome. To illustrate the utility of
this technique, we explain how MADM-induced UPD revealed new insights about the
function of the well-studied Cdkn1c imprinted gene, and how MADM-induced UPDs
led to identification of highly cell type specific phenotypes related to perturbed
imprinted expression in the mouse neocortex. Finally, we give an outlook on how
MADM could be used to probe cell type specific imprinted expression in other tissues
in mouse, particularly in extra-embryonic tissues.
acknowledgement: We thank Melissa Stouffer for critically reading the manuscript.
This work was supported by IST Austria institutional funds; NÖ Forschung und Bildung
n[f + b] life science call grant (C13-002) to S.H. and the European Research Council
(ERC) under the European Union's Horizon 2020 research and innovation program (grant
agreement 725780 LinPro) to S.H.
article_number: '104986'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
- first_name: Quanah
full_name: Hudson, Quanah
last_name: Hudson
- first_name: Susanne
full_name: Laukoter, Susanne
id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87
last_name: Laukoter
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Pauler F, Hudson Q, Laukoter S, Hippenmeyer S. Inducible uniparental chromosome
disomy to probe genomic imprinting at single-cell level in brain and beyond. Neurochemistry
International. 2021;145(5). doi:10.1016/j.neuint.2021.104986
apa: Pauler, F., Hudson, Q., Laukoter, S., & Hippenmeyer, S. (2021). Inducible
uniparental chromosome disomy to probe genomic imprinting at single-cell level
in brain and beyond. Neurochemistry International. Elsevier. https://doi.org/10.1016/j.neuint.2021.104986
chicago: Pauler, Florian, Quanah Hudson, Susanne Laukoter, and Simon Hippenmeyer.
“Inducible Uniparental Chromosome Disomy to Probe Genomic Imprinting at Single-Cell
Level in Brain and Beyond.” Neurochemistry International. Elsevier, 2021.
https://doi.org/10.1016/j.neuint.2021.104986.
ieee: F. Pauler, Q. Hudson, S. Laukoter, and S. Hippenmeyer, “Inducible uniparental
chromosome disomy to probe genomic imprinting at single-cell level in brain and
beyond,” Neurochemistry International, vol. 145, no. 5. Elsevier, 2021.
ista: Pauler F, Hudson Q, Laukoter S, Hippenmeyer S. 2021. Inducible uniparental
chromosome disomy to probe genomic imprinting at single-cell level in brain and
beyond. Neurochemistry International. 145(5), 104986.
mla: Pauler, Florian, et al. “Inducible Uniparental Chromosome Disomy to Probe Genomic
Imprinting at Single-Cell Level in Brain and Beyond.” Neurochemistry International,
vol. 145, no. 5, 104986, Elsevier, 2021, doi:10.1016/j.neuint.2021.104986.
short: F. Pauler, Q. Hudson, S. Laukoter, S. Hippenmeyer, Neurochemistry International
145 (2021).
date_created: 2021-02-23T12:31:43Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2023-08-07T13:48:26Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.neuint.2021.104986
ec_funded: 1
external_id:
isi:
- '000635575000005'
pmid:
- '33600873'
file:
- access_level: open_access
checksum: c6d7a40089cd29e289f9b22e75768304
content_type: application/pdf
creator: kschuh
date_created: 2021-08-11T12:30:38Z
date_updated: 2021-08-11T12:30:38Z
file_id: '9883'
file_name: 2021_NCI_Pauler.pdf
file_size: 7083499
relation: main_file
success: 1
file_date_updated: 2021-08-11T12:30:38Z
has_accepted_license: '1'
intvolume: ' 145'
isi: 1
issue: '5'
keyword:
- Cell Biology
- Cellular and Molecular Neuroscience
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 25D92700-B435-11E9-9278-68D0E5697425
grant_number: LS13-002
name: Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain
publication: Neurochemistry International
publication_identifier:
issn:
- 0197-0186
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell
level in brain and beyond
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 145
year: '2021'
...
---
_id: '9158'
abstract:
- lang: eng
text: While several tools have been developed to study the ground state of many-body
quantum spin systems, the limitations of existing techniques call for the exploration
of new approaches. In this manuscript we develop an alternative analytical and
numerical framework for many-body quantum spin ground states, based on the disentanglement
formalism. In this approach, observables are exactly expressed as Gaussian-weighted
functional integrals over scalar fields. We identify the leading contribution
to these integrals, given by the saddle point of a suitable effective action.
Analytically, we develop a field-theoretical expansion of the functional integrals,
performed by means of appropriate Feynman rules. The expansion can be truncated
to a desired order to obtain analytical approximations to observables. Numerically,
we show that the disentanglement approach can be used to compute ground state
expectation values from classical stochastic processes. While the associated fluctuations
grow exponentially with imaginary time and the system size, this growth can be
mitigated by means of an importance sampling scheme based on knowledge of the
saddle point configuration. We illustrate the advantages and limitations of our
methods by considering the quantum Ising model in 1, 2 and 3 spatial dimensions.
Our analytical and numerical approaches are applicable to a broad class of systems,
bridging concepts from quantum lattice models, continuum field theory, and classical
stochastic processes.
acknowledgement: "S D N would like to thank M J Bhaseen, J Chalker, B Doyon, V Gritsev,
A Lamacraft,\r\nA Michailidis and M Serbyn for helpful feedback and stimulating
conversations. S D N\r\nacknowledges funding from the Institute of Science and Technology
(IST) Austria, and\r\nfrom the European Union’s Horizon 2020 research and innovation
program under the\r\nMarie Sk\blodowska-Curie Grant Agreement No. 754411. S D N
also acknowledges funding\r\nfrom the EPSRC Center for Doctoral Training in Cross-Disciplinary
Approaches to Non-\r\nEquilibrium Systems (CANES) under Grant EP/L015854/1. S D
N is grateful to IST\r\nAustria for providing open access funding."
article_number: '013101'
article_processing_charge: No
article_type: original
author:
- first_name: Stefano
full_name: De Nicola, Stefano
id: 42832B76-F248-11E8-B48F-1D18A9856A87
last_name: De Nicola
orcid: 0000-0002-4842-6671
citation:
ama: 'De Nicola S. Disentanglement approach to quantum spin ground states: Field
theory and stochastic simulation. Journal of Statistical Mechanics: Theory
and Experiment. 2021;2021(1). doi:10.1088/1742-5468/abc7c7'
apa: 'De Nicola, S. (2021). Disentanglement approach to quantum spin ground states:
Field theory and stochastic simulation. Journal of Statistical Mechanics: Theory
and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/abc7c7'
chicago: 'De Nicola, Stefano. “Disentanglement Approach to Quantum Spin Ground States:
Field Theory and Stochastic Simulation.” Journal of Statistical Mechanics:
Theory and Experiment. IOP Publishing, 2021. https://doi.org/10.1088/1742-5468/abc7c7.'
ieee: 'S. De Nicola, “Disentanglement approach to quantum spin ground states: Field
theory and stochastic simulation,” Journal of Statistical Mechanics: Theory
and Experiment, vol. 2021, no. 1. IOP Publishing, 2021.'
ista: 'De Nicola S. 2021. Disentanglement approach to quantum spin ground states:
Field theory and stochastic simulation. Journal of Statistical Mechanics: Theory
and Experiment. 2021(1), 013101.'
mla: 'De Nicola, Stefano. “Disentanglement Approach to Quantum Spin Ground States:
Field Theory and Stochastic Simulation.” Journal of Statistical Mechanics:
Theory and Experiment, vol. 2021, no. 1, 013101, IOP Publishing, 2021, doi:10.1088/1742-5468/abc7c7.'
short: 'S. De Nicola, Journal of Statistical Mechanics: Theory and Experiment 2021
(2021).'
date_created: 2021-02-17T17:48:46Z
date_published: 2021-01-05T00:00:00Z
date_updated: 2023-08-07T13:46:28Z
day: '05'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1088/1742-5468/abc7c7
ec_funded: 1
external_id:
isi:
- '000605080300001'
file:
- access_level: open_access
checksum: 64e2aae4837790db26e1dd1986c69c07
content_type: application/pdf
creator: dernst
date_created: 2021-02-19T14:04:40Z
date_updated: 2021-02-19T14:04:40Z
file_id: '9172'
file_name: 2021_JourStatMech_deNicola.pdf
file_size: 1693609
relation: main_file
success: 1
file_date_updated: 2021-02-19T14:04:40Z
has_accepted_license: '1'
intvolume: ' 2021'
isi: 1
issue: '1'
keyword:
- Statistics
- Probability and Uncertainty
- Statistics and Probability
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
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: 'Disentanglement approach to quantum spin ground states: Field theory and stochastic
simulation'
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 2021
year: '2021'
...
---
_id: '9118'
abstract:
- lang: eng
text: Cesium lead halides have intrinsically unstable crystal lattices and easily
transform within perovskite and nonperovskite structures. In this work, we explore
the conversion of the perovskite CsPbBr3 into Cs4PbBr6 in the presence of PbS
at 450 °C to produce doped nanocrystal-based composites with embedded Cs4PbBr6
nanoprecipitates. We show that PbBr2 is extracted from CsPbBr3 and diffuses into
the PbS lattice with a consequent increase in the concentration of free charge
carriers. This new doping strategy enables the adjustment of the density of charge
carriers between 1019 and 1020 cm–3, and it may serve as a general strategy for
doping other nanocrystal-based semiconductors.
acknowledgement: "M.C. has received funding from the European Union’s Horizon 2020
research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
No. 665385. ICN2\r\nacknowledges funding from Generalitat de Catalunya 2017 SGR
327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant No.
SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. This
project has received funding from the European Union’s Horizon 2020 research and
innovation programme under grant agreement No 823717 − ESTEEM3. M.V.K. acknowledges
the support by the European Research Council under the Horizon 2020 Framework Program
(ERC Consolidator Grant SCALEHALO\r\nGrant Agreement No. 819740) and by FET-OPEN
project no. 862656 (DROP-IT)."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Mariano
full_name: Calcabrini, Mariano
id: 45D7531A-F248-11E8-B48F-1D18A9856A87
last_name: Calcabrini
- first_name: Aziz
full_name: Genc, Aziz
last_name: Genc
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Tobias
full_name: Kleinhanns, Tobias
id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425
last_name: Kleinhanns
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Dmitry N.
full_name: Dirin, Dmitry N.
last_name: Dirin
- first_name: Quinten A.
full_name: Akkerman, Quinten A.
last_name: Akkerman
- first_name: Maksym V.
full_name: Kovalenko, Maksym V.
last_name: Kovalenko
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: Calcabrini M, Genc A, Liu Y, et al. Exploiting the lability of metal halide
perovskites for doping semiconductor nanocomposites. ACS Energy Letters.
2021;6(2):581-587. doi:10.1021/acsenergylett.0c02448
apa: Calcabrini, M., Genc, A., Liu, Y., Kleinhanns, T., Lee, S., Dirin, D. N., …
Ibáñez, M. (2021). Exploiting the lability of metal halide perovskites for doping
semiconductor nanocomposites. ACS Energy Letters. American Chemical Society.
https://doi.org/10.1021/acsenergylett.0c02448
chicago: Calcabrini, Mariano, Aziz Genc, Yu Liu, Tobias Kleinhanns, Seungho Lee,
Dmitry N. Dirin, Quinten A. Akkerman, Maksym V. Kovalenko, Jordi Arbiol, and Maria
Ibáñez. “Exploiting the Lability of Metal Halide Perovskites for Doping Semiconductor
Nanocomposites.” ACS Energy Letters. American Chemical Society, 2021. https://doi.org/10.1021/acsenergylett.0c02448.
ieee: M. Calcabrini et al., “Exploiting the lability of metal halide perovskites
for doping semiconductor nanocomposites,” ACS Energy Letters, vol. 6, no.
2. American Chemical Society, pp. 581–587, 2021.
ista: Calcabrini M, Genc A, Liu Y, Kleinhanns T, Lee S, Dirin DN, Akkerman QA, Kovalenko
MV, Arbiol J, Ibáñez M. 2021. Exploiting the lability of metal halide perovskites
for doping semiconductor nanocomposites. ACS Energy Letters. 6(2), 581–587.
mla: Calcabrini, Mariano, et al. “Exploiting the Lability of Metal Halide Perovskites
for Doping Semiconductor Nanocomposites.” ACS Energy Letters, vol. 6, no.
2, American Chemical Society, 2021, pp. 581–87, doi:10.1021/acsenergylett.0c02448.
short: M. Calcabrini, A. Genc, Y. Liu, T. Kleinhanns, S. Lee, D.N. Dirin, Q.A. Akkerman,
M.V. Kovalenko, J. Arbiol, M. Ibáñez, ACS Energy Letters 6 (2021) 581–587.
date_created: 2021-02-14T23:01:14Z
date_published: 2021-01-20T00:00:00Z
date_updated: 2023-08-07T13:46:00Z
day: '20'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1021/acsenergylett.0c02448
ec_funded: 1
external_id:
isi:
- '000619803400036'
file:
- access_level: open_access
checksum: 6fa7374bf8b95fdfe6e6c595322a6689
content_type: application/pdf
creator: dernst
date_created: 2021-02-17T07:36:52Z
date_updated: 2021-02-17T07:36:52Z
file_id: '9155'
file_name: 2021_ACSEnergyLetters_Calcabrini.pdf
file_size: 5071201
relation: main_file
success: 1
file_date_updated: 2021-02-17T07:36:52Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 581-587
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: ACS Energy Letters
publication_identifier:
eissn:
- 2380-8195
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
record:
- id: '12885'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Exploiting the lability of metal halide perovskites for doping semiconductor
nanocomposites
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 6
year: '2021'
...
---
_id: '9168'
abstract:
- lang: eng
text: Interspecific crossing experiments have shown that sex chromosomes play a
major role in reproductive isolation between many pairs of species. However, their
ability to act as reproductive barriers, which hamper interspecific genetic exchange,
has rarely been evaluated quantitatively compared to Autosomes. This genome-wide
limitation of gene flow is essential for understanding the complete separation
of species, and thus speciation. Here, we develop a mainland-island model of secondary
contact between hybridizing species of an XY (or ZW) sexual system. We obtain
theoretical predictions for the frequency of introgressed alleles, and the strength
of the barrier to neutral gene flow for the two types of chromosomes carrying
multiple interspecific barrier loci. Theoretical predictions are obtained for
scenarios where introgressed alleles are rare. We show that the same analytical
expressions apply for sex chromosomes and autosomes, but with different sex-averaged
effective parameters. The specific features of sex chromosomes (hemizygosity and
absence of recombination in the heterogametic sex) lead to reduced levels of introgression
on the X (or Z) compared to autosomes. This effect can be enhanced by certain
types of sex-biased forces, but it remains overall small (except when alleles
causing incompatibilities are recessive). We discuss these predictions in the
light of empirical data comprising model-based tests of introgression and cline
surveys in various biological systems.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "The computations were performed with the IST Austria High-Performance
Computing (HPC) Cluster and the Institut Français de Bioinformatique (IFB) Core
Cluster. We are grateful to Nick Barton and Beatriz Vicoso for critical comments
on the model and the manuscript. We also thank Brian Charlesworth, Stuart Baird,
and an anonymous reviewer for insightful comments.\r\nC.F. was supported by an Austrian
Science Foundation FWF grant (Project M 2463-B29)."
article_number: iyaa025
article_processing_charge: No
article_type: original
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
citation:
ama: 'Fraisse C, Sachdeva H. The rates of introgression and barriers to genetic
exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics.
2021;217(2). doi:10.1093/genetics/iyaa025'
apa: 'Fraisse, C., & Sachdeva, H. (2021). The rates of introgression and barriers
to genetic exchange between hybridizing species: Sex chromosomes vs autosomes.
Genetics. Genetics Society of America. https://doi.org/10.1093/genetics/iyaa025'
chicago: 'Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression
and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes
vs Autosomes.” Genetics. Genetics Society of America, 2021. https://doi.org/10.1093/genetics/iyaa025.'
ieee: 'C. Fraisse and H. Sachdeva, “The rates of introgression and barriers to genetic
exchange between hybridizing species: Sex chromosomes vs autosomes,” Genetics,
vol. 217, no. 2. Genetics Society of America, 2021.'
ista: 'Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic
exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics.
217(2), iyaa025.'
mla: 'Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and
Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.”
Genetics, vol. 217, no. 2, iyaa025, Genetics Society of America, 2021,
doi:10.1093/genetics/iyaa025.'
short: C. Fraisse, H. Sachdeva, Genetics 217 (2021).
date_created: 2021-02-18T14:41:30Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2023-08-07T13:47:01Z
day: '01'
department:
- _id: NiBa
doi: 10.1093/genetics/iyaa025
external_id:
isi:
- '000637218100005'
intvolume: ' 217'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/genetics/iyaa025
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 2662AADE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02463
name: Sex chromosomes and species barriers
publication: Genetics
publication_identifier:
issn:
- 1943-2631
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
status: public
title: 'The rates of introgression and barriers to genetic exchange between hybridizing
species: Sex chromosomes vs autosomes'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 217
year: '2021'
...
---
_id: '9113'
abstract:
- lang: eng
text: “Hydrogen economy” could enable a carbon-neutral sustainable energy chain.
However, issues with safety, storage, and transport of molecular hydrogen impede
its realization. Alcohols as liquid H2 carriers could be enablers, but state-of-the-art
reforming is difficult, requiring high temperatures >200 °C and pressures >25
bar, and the resulting H2 is carbonized beyond tolerance levels for direct use
in fuel cells. Here, we demonstrate ambient temperature and pressure alcohol reforming
in a fuel cell (ARFC) with a simultaneous electrical power output. The alcohol
is oxidized at the alkaline anode, where the resulting CO2 is sequestrated as
carbonate. Carbon-free H2 is liberated at the acidic cathode. The neutralization
energy between the alkaline anode and the acidic cathode drives the process, particularly
the unusually high entropy gain (1.27-fold ΔH). The significantly positive temperature
coefficient of the resulting electromotive force allows us to harvest a large
fraction of the output energy from the surrounding, achieving a thermodynamic
efficiency as high as 2.27. MoS2 as the cathode catalyst allows alcohol reforming
even under open-air conditions, a challenge that state-of-the-art alcohol reforming
failed to overcome. We further show reforming of a wide range of alcohols. The
ARFC offers an unprecedented route toward hydrogen economy as CO2 is simultaneously
captured and pure H2 produced at mild conditions.
acknowledgement: M.O.T. acknowledges DST/TMD/HFC/2 K18/58, DST-SERB, MHRD fast track,
and DST Nanomission forfinancialassistance. Z.M.B. acknowledges CSIR-SRF fellowship
fromMHRD, India. S.A.F. acknowledges support from IST Austria.
article_processing_charge: No
article_type: original
author:
- first_name: Zahid Manzoor
full_name: Manzoor Bhat, Zahid Manzoor
last_name: Manzoor Bhat
- first_name: Ravikumar
full_name: Thimmappa, Ravikumar
last_name: Thimmappa
- first_name: 'Neethu Christudas '
full_name: 'Dargily, Neethu Christudas '
last_name: Dargily
- first_name: 'Abdul '
full_name: 'Raafik, Abdul '
last_name: Raafik
- first_name: 'Alagar Raja '
full_name: 'Kottaichamy, Alagar Raja '
last_name: Kottaichamy
- first_name: 'Mruthyunjayachari Chattanahalli '
full_name: 'Devendrachari, Mruthyunjayachari Chattanahalli '
last_name: Devendrachari
- first_name: Mahesh
full_name: Itagi, Mahesh
last_name: Itagi
- first_name: Harish
full_name: ' Makri Nimbegondi Kotresh, Harish'
last_name: ' Makri Nimbegondi Kotresh'
- 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: 'Musthafa '
full_name: 'Ottakam Thotiyl, Musthafa '
last_name: Ottakam Thotiyl
citation:
ama: Manzoor Bhat ZM, Thimmappa R, Dargily NC, et al. Ambient condition alcohol
reforming to hydrogen with electricity output. ACS Sustainable Chemistry and
Engineering. 2021;9(8):3104-3111. doi:10.1021/acssuschemeng.0c07547
apa: Manzoor Bhat, Z. M., Thimmappa, R., Dargily, N. C., Raafik, A., Kottaichamy,
A. R., Devendrachari, M. C., … Ottakam Thotiyl, M. (2021). Ambient condition alcohol
reforming to hydrogen with electricity output. ACS Sustainable Chemistry and
Engineering. American Chemical Society. https://doi.org/10.1021/acssuschemeng.0c07547
chicago: Manzoor Bhat, Zahid Manzoor, Ravikumar Thimmappa, Neethu Christudas Dargily,
Abdul Raafik, Alagar Raja Kottaichamy, Mruthyunjayachari Chattanahalli Devendrachari,
Mahesh Itagi, Harish Makri Nimbegondi Kotresh, Stefan Alexander Freunberger,
and Musthafa Ottakam Thotiyl. “Ambient Condition Alcohol Reforming to Hydrogen
with Electricity Output.” ACS Sustainable Chemistry and Engineering. American
Chemical Society, 2021. https://doi.org/10.1021/acssuschemeng.0c07547.
ieee: Z. M. Manzoor Bhat et al., “Ambient condition alcohol reforming to
hydrogen with electricity output,” ACS Sustainable Chemistry and Engineering,
vol. 9, no. 8. American Chemical Society, pp. 3104–3111, 2021.
ista: Manzoor Bhat ZM, Thimmappa R, Dargily NC, Raafik A, Kottaichamy AR, Devendrachari
MC, Itagi M, Makri Nimbegondi Kotresh H, Freunberger SA, Ottakam Thotiyl M. 2021.
Ambient condition alcohol reforming to hydrogen with electricity output. ACS Sustainable
Chemistry and Engineering. 9(8), 3104–3111.
mla: Manzoor Bhat, Zahid Manzoor, et al. “Ambient Condition Alcohol Reforming to
Hydrogen with Electricity Output.” ACS Sustainable Chemistry and Engineering,
vol. 9, no. 8, American Chemical Society, 2021, pp. 3104–11, doi:10.1021/acssuschemeng.0c07547.
short: Z.M. Manzoor Bhat, R. Thimmappa, N.C. Dargily, A. Raafik, A.R. Kottaichamy,
M.C. Devendrachari, M. Itagi, H. Makri Nimbegondi Kotresh, S.A. Freunberger,
M. Ottakam Thotiyl, ACS Sustainable Chemistry and Engineering 9 (2021) 3104–3111.
date_created: 2021-02-12T09:20:18Z
date_published: 2021-02-11T00:00:00Z
date_updated: 2023-08-07T13:43:19Z
day: '11'
department:
- _id: StFr
doi: 10.1021/acssuschemeng.0c07547
external_id:
isi:
- '000625460400010'
intvolume: ' 9'
isi: 1
issue: '8'
language:
- iso: eng
month: '02'
oa_version: None
page: 3104-3111
publication: ACS Sustainable Chemistry and Engineering
publication_identifier:
eissn:
- 2168-0485
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ambient condition alcohol reforming to hydrogen with electricity output
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2021'
...
---
_id: '9119'
abstract:
- lang: eng
text: 'We present DILS, a deployable statistical analysis platform for conducting
demographic inferences with linked selection from population genomic data using
an Approximate Bayesian Computation framework. DILS takes as input single‐population
or two‐population data sets (multilocus fasta sequences) and performs three types
of analyses in a hierarchical manner, identifying: (a) the best demographic model
to study the importance of gene flow and population size change on the genetic
patterns of polymorphism and divergence, (b) the best genomic model to determine
whether the effective size Ne and migration rate N, m are heterogeneously distributed
along the genome (implying linked selection) and (c) loci in genomic regions most
associated with barriers to gene flow. Also available via a Web interface, an
objective of DILS is to facilitate collaborative research in speciation genomics.
Here, we show the performance and limitations of DILS by using simulations and
finally apply the method to published data on a divergence continuum composed
by 28 pairs of Mytilus mussel populations/species.'
article_processing_charge: No
article_type: original
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Iva
full_name: Popovic, Iva
last_name: Popovic
- first_name: Clément
full_name: Mazoyer, Clément
last_name: Mazoyer
- first_name: Bruno
full_name: Spataro, Bruno
last_name: Spataro
- first_name: Stéphane
full_name: Delmotte, Stéphane
last_name: Delmotte
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Étienne
full_name: Loire, Étienne
last_name: Loire
- first_name: Alexis
full_name: Simon, Alexis
last_name: Simon
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Laurent
full_name: Duret, Laurent
last_name: Duret
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
- first_name: Xavier
full_name: Vekemans, Xavier
last_name: Vekemans
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
citation:
ama: 'Fraisse C, Popovic I, Mazoyer C, et al. DILS: Demographic inferences with
linked selection by using ABC. Molecular Ecology Resources. 2021;21:2629-2644.
doi:10.1111/1755-0998.13323'
apa: 'Fraisse, C., Popovic, I., Mazoyer, C., Spataro, B., Delmotte, S., Romiguier,
J., … Roux, C. (2021). DILS: Demographic inferences with linked selection by using
ABC. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13323'
chicago: 'Fraisse, Christelle, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stéphane
Delmotte, Jonathan Romiguier, Étienne Loire, et al. “DILS: Demographic Inferences
with Linked Selection by Using ABC.” Molecular Ecology Resources. Wiley,
2021. https://doi.org/10.1111/1755-0998.13323.'
ieee: 'C. Fraisse et al., “DILS: Demographic inferences with linked selection
by using ABC,” Molecular Ecology Resources, vol. 21. Wiley, pp. 2629–2644,
2021.'
ista: 'Fraisse C, Popovic I, Mazoyer C, Spataro B, Delmotte S, Romiguier J, Loire
É, Simon A, Galtier N, Duret L, Bierne N, Vekemans X, Roux C. 2021. DILS: Demographic
inferences with linked selection by using ABC. Molecular Ecology Resources. 21,
2629–2644.'
mla: 'Fraisse, Christelle, et al. “DILS: Demographic Inferences with Linked Selection
by Using ABC.” Molecular Ecology Resources, vol. 21, Wiley, 2021, pp. 2629–44,
doi:10.1111/1755-0998.13323.'
short: C. Fraisse, I. Popovic, C. Mazoyer, B. Spataro, S. Delmotte, J. Romiguier,
É. Loire, A. Simon, N. Galtier, L. Duret, N. Bierne, X. Vekemans, C. Roux, Molecular
Ecology Resources 21 (2021) 2629–2644.
date_created: 2021-02-14T23:01:14Z
date_published: 2021-01-15T00:00:00Z
date_updated: 2023-08-07T13:45:18Z
day: '15'
department:
- _id: NiBa
doi: 10.1111/1755-0998.13323
external_id:
isi:
- '000614183100001'
intvolume: ' 21'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2020.06.15.151597v2
month: '01'
oa: 1
oa_version: Preprint
page: 2629-2644
publication: Molecular Ecology Resources
publication_identifier:
eissn:
- '17550998'
issn:
- 1755098X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'DILS: Demographic inferences with linked selection by using ABC'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 21
year: '2021'
...
---
_id: '9173'
abstract:
- lang: eng
text: We show that Hilbert schemes of points on supersingular Enriques surface in
characteristic 2, Hilbn(X), for n ≥ 2 are simply connected, symplectic varieties
but are not irreducible symplectic as the hodge number h2,0 > 1, even though a
supersingular Enriques surface is an irreducible symplectic variety. These are
the classes of varieties which appear only in characteristic 2 and they show that
the hodge number formula for G¨ottsche-Soergel does not hold over haracteristic
2. It also gives examples of varieties with trivial canonical class which are
neither irreducible symplectic nor Calabi-Yau, thereby showing that there are
strictly more classes of simply connected varieties with trivial canonical class
in characteristic 2 than over C as given by Beauville-Bogolomov decomposition
theorem.
acknowledgement: I would like to thank M. Zdanwociz for various mathematical discussions
which lead to this article, Tamas Hausel for hosting me in his research group at
IST Austria and the anonymous referee for their helpful suggestions and comments.
This research has received funding from the European Union's Horizon 2020 Marie
Sklodowska-Curie Actions Grant No. 754411 and Institue of Science and Technology
Austria IST-PLUS Grant No. 754411.
article_number: '102957'
article_processing_charge: No
article_type: original
author:
- first_name: Tanya K
full_name: Srivastava, Tanya K
id: 4D046628-F248-11E8-B48F-1D18A9856A87
last_name: Srivastava
citation:
ama: Srivastava TK. Pathologies of the Hilbert scheme of points of a supersingular
Enriques surface. Bulletin des Sciences Mathematiques. 2021;167(03). doi:10.1016/j.bulsci.2021.102957
apa: Srivastava, T. K. (2021). Pathologies of the Hilbert scheme of points of a
supersingular Enriques surface. Bulletin Des Sciences Mathematiques. Elsevier.
https://doi.org/10.1016/j.bulsci.2021.102957
chicago: Srivastava, Tanya K. “Pathologies of the Hilbert Scheme of Points of a
Supersingular Enriques Surface.” Bulletin Des Sciences Mathematiques. Elsevier,
2021. https://doi.org/10.1016/j.bulsci.2021.102957.
ieee: T. K. Srivastava, “Pathologies of the Hilbert scheme of points of a supersingular
Enriques surface,” Bulletin des Sciences Mathematiques, vol. 167, no. 03.
Elsevier, 2021.
ista: Srivastava TK. 2021. Pathologies of the Hilbert scheme of points of a supersingular
Enriques surface. Bulletin des Sciences Mathematiques. 167(03), 102957.
mla: Srivastava, Tanya K. “Pathologies of the Hilbert Scheme of Points of a Supersingular
Enriques Surface.” Bulletin Des Sciences Mathematiques, vol. 167, no. 03,
102957, Elsevier, 2021, doi:10.1016/j.bulsci.2021.102957.
short: T.K. Srivastava, Bulletin Des Sciences Mathematiques 167 (2021).
date_created: 2021-02-21T23:01:20Z
date_published: 2021-03-01T00:00:00Z
date_updated: 2023-08-07T13:47:48Z
day: '01'
department:
- _id: TaHa
doi: 10.1016/j.bulsci.2021.102957
ec_funded: 1
external_id:
arxiv:
- '2010.08976'
isi:
- '000623881600009'
intvolume: ' 167'
isi: 1
issue: '03'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2010.08976
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Bulletin des Sciences Mathematiques
publication_identifier:
issn:
- 0007-4497
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pathologies of the Hilbert scheme of points of a supersingular Enriques surface
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 167
year: '2021'
...
---
_id: '9200'
abstract:
- lang: eng
text: Formal design of embedded and cyber-physical systems relies on mathematical
modeling. In this paper, we consider the model class of hybrid automata whose
dynamics are defined by affine differential equations. Given a set of time-series
data, we present an algorithmic approach to synthesize a hybrid automaton exhibiting
behavior that is close to the data, up to a specified precision, and changes in
synchrony with the data. A fundamental problem in our synthesis algorithm is to
check membership of a time series in a hybrid automaton. Our solution integrates
reachability and optimization techniques for affine dynamical systems to obtain
both a sufficient and a necessary condition for membership, combined in a refinement
framework. The algorithm processes one time series at a time and hence can be
interrupted, provide an intermediate result, and be resumed. We report experimental
results demonstrating the applicability of our synthesis approach.
acknowledgement: This research was supported in part by the Austrian Science Fund
(FWF) under grant Z211-N23 (Wittgenstein Award) and the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
No. 754411.
article_processing_charge: No
author:
- first_name: Miriam
full_name: Garcia Soto, Miriam
id: 4B3207F6-F248-11E8-B48F-1D18A9856A87
last_name: Garcia Soto
orcid: 0000-0003-2936-5719
- 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: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
citation:
ama: 'Garcia Soto M, Henzinger TA, Schilling C. Synthesis of hybrid automata with
affine dynamics from time-series data. In: HSCC ’21: Proceedings of the 24th
International Conference on Hybrid Systems: Computation and Control. Association
for Computing Machinery; 2021:2102.12734. doi:10.1145/3447928.3456704'
apa: 'Garcia Soto, M., Henzinger, T. A., & Schilling, C. (2021). Synthesis of
hybrid automata with affine dynamics from time-series data. In HSCC ’21: Proceedings
of the 24th International Conference on Hybrid Systems: Computation and Control
(p. 2102.12734). Nashville, TN, United States: Association for Computing Machinery.
https://doi.org/10.1145/3447928.3456704'
chicago: 'Garcia Soto, Miriam, Thomas A Henzinger, and Christian Schilling. “Synthesis
of Hybrid Automata with Affine Dynamics from Time-Series Data.” In HSCC ’21:
Proceedings of the 24th International Conference on Hybrid Systems: Computation
and Control, 2102.12734. Association for Computing Machinery, 2021. https://doi.org/10.1145/3447928.3456704.'
ieee: 'M. Garcia Soto, T. A. Henzinger, and C. Schilling, “Synthesis of hybrid automata
with affine dynamics from time-series data,” in HSCC ’21: Proceedings of the
24th International Conference on Hybrid Systems: Computation and Control,
Nashville, TN, United States, 2021, p. 2102.12734.'
ista: 'Garcia Soto M, Henzinger TA, Schilling C. 2021. Synthesis of hybrid automata
with affine dynamics from time-series data. HSCC ’21: Proceedings of the 24th
International Conference on Hybrid Systems: Computation and Control. HSCC: International
Conference on Hybrid Systems Computation and Control, 2102.12734.'
mla: 'Garcia Soto, Miriam, et al. “Synthesis of Hybrid Automata with Affine Dynamics
from Time-Series Data.” HSCC ’21: Proceedings of the 24th International Conference
on Hybrid Systems: Computation and Control, Association for Computing Machinery,
2021, p. 2102.12734, doi:10.1145/3447928.3456704.'
short: 'M. Garcia Soto, T.A. Henzinger, C. Schilling, in:, HSCC ’21: Proceedings
of the 24th International Conference on Hybrid Systems: Computation and Control,
Association for Computing Machinery, 2021, p. 2102.12734.'
conference:
end_date: 2021-05-21
location: Nashville, TN, United States
name: 'HSCC: International Conference on Hybrid Systems Computation and Control'
start_date: 2021-05-19
date_created: 2021-02-26T16:30:39Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2023-08-07T13:49:33Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/3447928.3456704
ec_funded: 1
external_id:
arxiv:
- '2102.12734'
isi:
- '000932821700028'
file:
- access_level: open_access
checksum: 4c1202c1abf71384c3ee6fea88c2f80e
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T13:53:22Z
date_updated: 2021-05-25T13:53:22Z
file_id: '9424'
file_name: 2021_HSCC_Soto.pdf
file_size: 1474786
relation: main_file
success: 1
file_date_updated: 2021-05-25T13:53:22Z
has_accepted_license: '1'
isi: 1
keyword:
- hybrid automaton
- membership
- system identification
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '2102.12734'
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 'HSCC ''21: Proceedings of the 24th International Conference on Hybrid
Systems: Computation and Control'
publication_identifier:
isbn:
- '9781450383394'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synthesis of hybrid automata with affine dynamics from time-series data
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9205'
abstract:
- lang: eng
text: Cryo-EM grid preparation is an important bottleneck in protein structure determination,
especially for membrane proteins, typically requiring screening of a large number
of conditions. We systematically investigated the effects of buffer components,
blotting conditions and grid types on the outcome of grid preparation of five
different membrane protein samples. Aggregation was the most common type of problem
which was addressed by changing detergents, salt concentration or reconstitution
of proteins into nanodiscs or amphipols. We show that the optimal concentration
of detergent is between 0.05 and 0.4% and that the presence of a low concentration
of detergent with a high critical micellar concentration protects the proteins
from denaturation at the air-water interface. Furthermore, we discuss the strategies
for achieving an adequate ice thickness, particle coverage and orientation distribution
on free ice and on support films. Our findings provide a clear roadmap for comprehensive
screening of conditions for cryo-EM grid preparation of membrane proteins.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: We thank the Electron Microscopy Facilities at the Institute of Science
and Technology Austria and at the Vienna Biocenter for providing access and training
for the electron microscopes. This project has received funding from the European
Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement no. 665385 .
article_number: '102139'
article_processing_charge: No
article_type: original
author:
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
- first_name: Julia
full_name: Steiner, Julia
id: 3BB67EB0-F248-11E8-B48F-1D18A9856A87
last_name: Steiner
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Kampjut D, Steiner J, Sazanov LA. Cryo-EM grid optimization for membrane proteins.
iScience. 2021;24(3). doi:10.1016/j.isci.2021.102139
apa: Kampjut, D., Steiner, J., & Sazanov, L. A. (2021). Cryo-EM grid optimization
for membrane proteins. IScience. Elsevier. https://doi.org/10.1016/j.isci.2021.102139
chicago: Kampjut, Domen, Julia Steiner, and Leonid A Sazanov. “Cryo-EM Grid Optimization
for Membrane Proteins.” IScience. Elsevier, 2021. https://doi.org/10.1016/j.isci.2021.102139.
ieee: D. Kampjut, J. Steiner, and L. A. Sazanov, “Cryo-EM grid optimization for
membrane proteins,” iScience, vol. 24, no. 3. Elsevier, 2021.
ista: Kampjut D, Steiner J, Sazanov LA. 2021. Cryo-EM grid optimization for membrane
proteins. iScience. 24(3), 102139.
mla: Kampjut, Domen, et al. “Cryo-EM Grid Optimization for Membrane Proteins.” IScience,
vol. 24, no. 3, 102139, Elsevier, 2021, doi:10.1016/j.isci.2021.102139.
short: D. Kampjut, J. Steiner, L.A. Sazanov, IScience 24 (2021).
date_created: 2021-02-28T23:01:24Z
date_published: 2021-03-19T00:00:00Z
date_updated: 2023-08-07T13:54:06Z
day: '19'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1016/j.isci.2021.102139
ec_funded: 1
external_id:
isi:
- '000631646000012'
pmid:
- '33665558'
file:
- access_level: open_access
checksum: 50585447386fe5842f07ab9b3a66e7e9
content_type: application/pdf
creator: dernst
date_created: 2021-03-03T07:38:14Z
date_updated: 2021-03-03T07:38:14Z
file_id: '9219'
file_name: 2021_iScience_Kampjut.pdf
file_size: 7431411
relation: main_file
success: 1
file_date_updated: 2021-03-03T07:38:14Z
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: iScience
publication_identifier:
eissn:
- '25890042'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cryo-EM grid optimization for membrane proteins
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 24
year: '2021'
...
---
_id: '9207'
abstract:
- lang: eng
text: "In this paper we experimentally study the transitional range of Reynolds
numbers in\r\nplane Couette–Poiseuille flow, focusing our attention on the localized
turbulent structures\r\ntriggered by a strong impulsive jet and the large-scale
flow generated around these\r\nstructures. We present a detailed investigation
of the large-scale flow and show how\r\nits amplitude depends on Reynolds number
and amplitude perturbation. In addition,\r\nwe characterize the initial dynamics
of the localized turbulent spot, which includes the\r\ncoupling between the small
and large scales, as well as the dependence of the advection\r\nspeed on the large-scale
flow generated around the spot. Finally, we provide the first\r\nexperimental
measurements of the large-scale flow around an oblique turbulent band."
acknowledgement: "We thank Y. Duguet, S. Gomé, G. Lemoult, T. Liu, B. Semin and L.S.
Tuckerman for\r\nfruitful discussions. \r\nThis work was supported by a grant, TRANSFLOW,
provided by the Agence Nationale de\r\nla Recherche (ANR). A.M.P. was partially
supported by the French Embassy in Russia (I.I. Mechnikov scholarship) and by the
Russian Science Foundation (project no. 18-79-00189). L.K. was partially supported
by the European Union’s Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie grant agreement no. 754411."
article_number: A24
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lukasz
full_name: Klotz, Lukasz
id: 2C9AF1C2-F248-11E8-B48F-1D18A9856A87
last_name: Klotz
orcid: 0000-0003-1740-7635
- first_name: A. M.
full_name: Pavlenko, A. M.
last_name: Pavlenko
- first_name: J. E.
full_name: Wesfreid, J. E.
last_name: Wesfreid
citation:
ama: 'Klotz L, Pavlenko AM, Wesfreid JE. Experimental measurements in plane Couette-Poiseuille
flow: Dynamics of the large- and small-scale flow. Journal of Fluid Mechanics.
2021;912. doi:10.1017/jfm.2020.1089'
apa: 'Klotz, L., Pavlenko, A. M., & Wesfreid, J. E. (2021). Experimental measurements
in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow.
Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2020.1089'
chicago: 'Klotz, Lukasz, A. M. Pavlenko, and J. E. Wesfreid. “Experimental Measurements
in Plane Couette-Poiseuille Flow: Dynamics of the Large- and Small-Scale Flow.”
Journal of Fluid Mechanics. Cambridge University Press, 2021. https://doi.org/10.1017/jfm.2020.1089.'
ieee: 'L. Klotz, A. M. Pavlenko, and J. E. Wesfreid, “Experimental measurements
in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow,”
Journal of Fluid Mechanics, vol. 912. Cambridge University Press, 2021.'
ista: 'Klotz L, Pavlenko AM, Wesfreid JE. 2021. Experimental measurements in plane
Couette-Poiseuille flow: Dynamics of the large- and small-scale flow. Journal
of Fluid Mechanics. 912, A24.'
mla: 'Klotz, Lukasz, et al. “Experimental Measurements in Plane Couette-Poiseuille
Flow: Dynamics of the Large- and Small-Scale Flow.” Journal of Fluid Mechanics,
vol. 912, A24, Cambridge University Press, 2021, doi:10.1017/jfm.2020.1089.'
short: L. Klotz, A.M. Pavlenko, J.E. Wesfreid, Journal of Fluid Mechanics 912 (2021).
date_created: 2021-02-28T23:01:25Z
date_published: 2021-02-15T00:00:00Z
date_updated: 2023-08-07T13:55:40Z
day: '15'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1017/jfm.2020.1089
ec_funded: 1
external_id:
isi:
- '000618034400001'
file:
- access_level: open_access
checksum: b8020d6338667673e34fde0608913dd2
content_type: application/pdf
creator: dernst
date_created: 2021-03-03T09:49:34Z
date_updated: 2021-03-03T09:49:34Z
file_id: '9220'
file_name: 2021_JourFluidMechanics_Klotz.pdf
file_size: 4124471
relation: main_file
success: 1
file_date_updated: 2021-03-03T09:49:34Z
has_accepted_license: '1'
intvolume: ' 912'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- 1469-7645
issn:
- 0022-1120
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the
large- and small-scale flow'
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 912
year: '2021'
...
---
_id: '9206'
abstract:
- lang: eng
text: 'The precise engineering of thermoelectric materials using nanocrystals as
their building blocks has proven to be an excellent strategy to increase energy
conversion efficiency. Here we present a synthetic route to produce Sb-doped PbS
colloidal nanoparticles. These nanoparticles are then consolidated into nanocrystalline
PbS:Sb using spark plasma sintering. We demonstrate that the introduction of Sb
significantly influences the size, geometry, crystal lattice and especially the
carrier concentration of PbS. The increase of charge carrier concentration achieved
with the introduction of Sb translates into an increase of the electrical and
thermal conductivities and a decrease of the Seebeck coefficient. Overall, PbS:Sb
nanomaterial were characterized by two-fold higher thermoelectric figures of merit
than undoped PbS. '
acknowledgement: "This work was supported by European Regional Development Funds and
the Framework 7\r\nprogram under project UNION (FP7-NMP 310250). GSN acknowledges
support from the US National Science Foundation under grant No. DMR-1748188. DC
acknowledges support from COLCIENCIAS under project 120480863414. "
article_number: '853'
article_processing_charge: No
article_type: original
author:
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Kaya
full_name: Wei, Kaya
last_name: Wei
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Yu
full_name: Zhang, Yu
last_name: Zhang
- first_name: Mengyao
full_name: Li, Mengyao
last_name: Li
- first_name: Aziz
full_name: Genç, Aziz
last_name: Genç
- first_name: Taisiia
full_name: Berestok, Taisiia
last_name: Berestok
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: George S.
full_name: Nolas, George S.
last_name: Nolas
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Cadavid D, Wei K, Liu Y, et al. Synthesis, bottom up assembly and thermoelectric
properties of Sb-doped PbS nanocrystal building blocks. Materials. 2021;14(4).
doi:10.3390/ma14040853
apa: Cadavid, D., Wei, K., Liu, Y., Zhang, Y., Li, M., Genç, A., … Cabot, A. (2021).
Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal
building blocks. Materials. MDPI. https://doi.org/10.3390/ma14040853
chicago: Cadavid, Doris, Kaya Wei, Yu Liu, Yu Zhang, Mengyao Li, Aziz Genç, Taisiia
Berestok, et al. “Synthesis, Bottom up Assembly and Thermoelectric Properties
of Sb-Doped PbS Nanocrystal Building Blocks.” Materials. MDPI, 2021. https://doi.org/10.3390/ma14040853.
ieee: D. Cadavid et al., “Synthesis, bottom up assembly and thermoelectric
properties of Sb-doped PbS nanocrystal building blocks,” Materials, vol.
14, no. 4. MDPI, 2021.
ista: Cadavid D, Wei K, Liu Y, Zhang Y, Li M, Genç A, Berestok T, Ibáñez M, Shavel
A, Nolas GS, Cabot A. 2021. Synthesis, bottom up assembly and thermoelectric properties
of Sb-doped PbS nanocrystal building blocks. Materials. 14(4), 853.
mla: Cadavid, Doris, et al. “Synthesis, Bottom up Assembly and Thermoelectric Properties
of Sb-Doped PbS Nanocrystal Building Blocks.” Materials, vol. 14, no. 4,
853, MDPI, 2021, doi:10.3390/ma14040853.
short: D. Cadavid, K. Wei, Y. Liu, Y. Zhang, M. Li, A. Genç, T. Berestok, M. Ibáñez,
A. Shavel, G.S. Nolas, A. Cabot, Materials 14 (2021).
date_created: 2021-02-28T23:01:24Z
date_published: 2021-02-10T00:00:00Z
date_updated: 2023-08-07T13:50:03Z
day: '10'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.3390/ma14040853
external_id:
isi:
- '000624094100001'
file:
- access_level: open_access
checksum: 76d6c7f97b810ce504ab151c9bf3524e
content_type: application/pdf
creator: dernst
date_created: 2021-03-03T07:32:01Z
date_updated: 2021-03-03T07:32:01Z
file_id: '9218'
file_name: 2021_Materials_Cadavid.pdf
file_size: 2722517
relation: main_file
success: 1
file_date_updated: 2021-03-03T07:32:01Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Materials
publication_identifier:
eissn:
- 1996-1944
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS
nanocrystal building blocks
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2021'
...
---
_id: '9226'
abstract:
- lang: eng
text: 'Half a century after Lewis Wolpert''s seminal conceptual advance on how cellular
fates distribute in space, we provide a brief historical perspective on how the
concept of positional information emerged and influenced the field of developmental
biology and beyond. We focus on a modern interpretation of this concept in terms
of information theory, largely centered on its application to cell specification
in the early Drosophila embryo. We argue that a true physical variable (position)
is encoded in local concentrations of patterning molecules, that this mapping
is stochastic, and that the processes by which positions and corresponding cell
fates are determined based on these concentrations need to take such stochasticity
into account. With this approach, we shift the focus from biological mechanisms,
molecules, genes and pathways to quantitative systems-level questions: where does
positional information reside, how it is transformed and accessed during development,
and what fundamental limits it is subject to?'
acknowledgement: This work was supported in part by the National Science Foundation,
through the Center for the Physics of Biological Function (PHY-1734030), by the
National Institutes of Health (R01GM097275) and by the Fonds zur Förderung der wissenschaftlichen
Forschung (FWF P28844). Deposited in PMC for release after 12 months.
article_number: dev176065
article_processing_charge: No
article_type: original
author:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
citation:
ama: Tkačik G, Gregor T. The many bits of positional information. Development.
2021;148(2). doi:10.1242/dev.176065
apa: Tkačik, G., & Gregor, T. (2021). The many bits of positional information.
Development. The Company of Biologists. https://doi.org/10.1242/dev.176065
chicago: Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.”
Development. The Company of Biologists, 2021. https://doi.org/10.1242/dev.176065.
ieee: G. Tkačik and T. Gregor, “The many bits of positional information,” Development,
vol. 148, no. 2. The Company of Biologists, 2021.
ista: Tkačik G, Gregor T. 2021. The many bits of positional information. Development.
148(2), dev176065.
mla: Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.”
Development, vol. 148, no. 2, dev176065, The Company of Biologists, 2021,
doi:10.1242/dev.176065.
short: G. Tkačik, T. Gregor, Development 148 (2021).
date_created: 2021-03-07T23:01:25Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2023-08-07T13:57:30Z
day: '01'
department:
- _id: GaTk
doi: 10.1242/dev.176065
external_id:
isi:
- '000613906000007'
pmid:
- '33526425'
intvolume: ' 148'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1242/dev.176065
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Development
publication_identifier:
eissn:
- 1477-9129
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: The many bits of positional information
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 148
year: '2021'
...
---
_id: '9240'
abstract:
- lang: eng
text: A stochastic PDE, describing mesoscopic fluctuations in systems of weakly
interacting inertial particles of finite volume, is proposed and analysed in any
finite dimension . It is a regularised and inertial version of the Dean–Kawasaki
model. A high-probability well-posedness theory for this model is developed. This
theory improves significantly on the spatial scaling restrictions imposed in an
earlier work of the same authors, which applied only to significantly larger particles
in one dimension. The well-posedness theory now applies in d-dimensions when the
particle-width ϵ is proportional to for and N is the number of particles. This
scaling is optimal in a certain Sobolev norm. Key tools of the analysis are fractional
Sobolev spaces, sharp bounds on Bessel functions, separability of the regularisation
in the d-spatial dimensions, and use of the Faà di Bruno's formula.
acknowledgement: All authors thank the anonymous referee for his/her careful reading
of the manuscript and valuable suggestions. This paper was motivated by stimulating
discussions at the First Berlin–Leipzig Workshop on Fluctuating Hydrodynamics in
August 2019 with Ana Djurdjevac, Rupert Klein and Ralf Kornhuber. JZ gratefully
acknowledges funding by a Royal Society Wolfson Research Merit Award. FC gratefully
acknowledges funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement No. 754411.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Federico
full_name: Cornalba, Federico
id: 2CEB641C-A400-11E9-A717-D712E6697425
last_name: Cornalba
- first_name: Tony
full_name: Shardlow, Tony
last_name: Shardlow
- first_name: Johannes
full_name: Zimmer, Johannes
last_name: Zimmer
citation:
ama: Cornalba F, Shardlow T, Zimmer J. Well-posedness for a regularised inertial
Dean–Kawasaki model for slender particles in several space dimensions. Journal
of Differential Equations. 2021;284(5):253-283. doi:10.1016/j.jde.2021.02.048
apa: Cornalba, F., Shardlow, T., & Zimmer, J. (2021). Well-posedness for a regularised
inertial Dean–Kawasaki model for slender particles in several space dimensions.
Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2021.02.048
chicago: Cornalba, Federico, Tony Shardlow, and Johannes Zimmer. “Well-Posedness
for a Regularised Inertial Dean–Kawasaki Model for Slender Particles in Several
Space Dimensions.” Journal of Differential Equations. Elsevier, 2021. https://doi.org/10.1016/j.jde.2021.02.048.
ieee: F. Cornalba, T. Shardlow, and J. Zimmer, “Well-posedness for a regularised
inertial Dean–Kawasaki model for slender particles in several space dimensions,”
Journal of Differential Equations, vol. 284, no. 5. Elsevier, pp. 253–283,
2021.
ista: Cornalba F, Shardlow T, Zimmer J. 2021. Well-posedness for a regularised inertial
Dean–Kawasaki model for slender particles in several space dimensions. Journal
of Differential Equations. 284(5), 253–283.
mla: Cornalba, Federico, et al. “Well-Posedness for a Regularised Inertial Dean–Kawasaki
Model for Slender Particles in Several Space Dimensions.” Journal of Differential
Equations, vol. 284, no. 5, Elsevier, 2021, pp. 253–83, doi:10.1016/j.jde.2021.02.048.
short: F. Cornalba, T. Shardlow, J. Zimmer, Journal of Differential Equations 284
(2021) 253–283.
date_created: 2021-03-14T23:01:32Z
date_published: 2021-05-25T00:00:00Z
date_updated: 2023-08-07T14:08:05Z
day: '25'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1016/j.jde.2021.02.048
ec_funded: 1
external_id:
isi:
- '000634823300010'
file:
- access_level: open_access
checksum: c630b691fb9e716b02aa6103a9794ec8
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T07:18:01Z
date_updated: 2021-03-22T07:18:01Z
file_id: '9267'
file_name: 2021_JourDiffEquations_Cornalba.pdf
file_size: 473310
relation: main_file
success: 1
file_date_updated: 2021-03-22T07:18:01Z
has_accepted_license: '1'
intvolume: ' 284'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 253-283
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Differential Equations
publication_identifier:
eissn:
- 1090-2732
issn:
- 0022-0396
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles
in several space dimensions
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 284
year: '2021'
...
---
_id: '9253'
abstract:
- lang: eng
text: In March 2020, the Austrian government introduced a widespread lock-down in
response to the COVID-19 pandemic. Based on subjective impressions and anecdotal
evidence, Austrian public and private life came to a sudden halt. Here we assess
the effect of the lock-down quantitatively for all regions in Austria and present
an analysis of daily changes of human mobility throughout Austria using near-real-time
anonymized mobile phone data. We describe an efficient data aggregation pipeline
and analyze the mobility by quantifying mobile-phone traffic at specific point
of interests (POIs), analyzing individual trajectories and investigating the cluster
structure of the origin-destination graph. We found a reduction of commuters at
Viennese metro stations of over 80% and the number of devices with a radius of
gyration of less than 500 m almost doubled. The results of studying crowd-movement
behavior highlight considerable changes in the structure of mobility networks,
revealed by a higher modularity and an increase from 12 to 20 detected communities.
We demonstrate the relevance of mobility data for epidemiological studies by showing
a significant correlation of the outflow from the town of Ischgl (an early COVID-19
hotspot) and the reported COVID-19 cases with an 8-day time lag. This research
indicates that mobile phone usage data permits the moment-by-moment quantification
of mobility behavior for a whole country. We emphasize the need to improve the
availability of such data in anonymized form to empower rapid response to combat
COVID-19 and future pandemics.
article_processing_charge: No
author:
- first_name: Georg
full_name: Heiler, Georg
last_name: Heiler
- first_name: Tobias
full_name: Reisch, Tobias
last_name: Reisch
- first_name: Jan
full_name: Hurt, Jan
last_name: Hurt
- first_name: Mohammad
full_name: Forghani, Mohammad
last_name: Forghani
- first_name: Aida
full_name: Omani, Aida
last_name: Omani
- first_name: Allan
full_name: Hanbury, Allan
last_name: Hanbury
- first_name: Farid
full_name: Karimipour, Farid
id: 2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425
last_name: Karimipour
orcid: 0000-0001-6746-4174
citation:
ama: 'Heiler G, Reisch T, Hurt J, et al. Country-wide mobility changes observed
using mobile phone data during COVID-19 pandemic. In: 2020 IEEE International
Conference on Big Data. IEEE; 2021:3123-3132. doi:10.1109/bigdata50022.2020.9378374'
apa: 'Heiler, G., Reisch, T., Hurt, J., Forghani, M., Omani, A., Hanbury, A., &
Karimipour, F. (2021). Country-wide mobility changes observed using mobile phone
data during COVID-19 pandemic. In 2020 IEEE International Conference on Big
Data (pp. 3123–3132). Atlanta, GA, United States: IEEE. https://doi.org/10.1109/bigdata50022.2020.9378374'
chicago: Heiler, Georg, Tobias Reisch, Jan Hurt, Mohammad Forghani, Aida Omani,
Allan Hanbury, and Farid Karimipour. “Country-Wide Mobility Changes Observed Using
Mobile Phone Data during COVID-19 Pandemic.” In 2020 IEEE International Conference
on Big Data, 3123–32. IEEE, 2021. https://doi.org/10.1109/bigdata50022.2020.9378374.
ieee: G. Heiler et al., “Country-wide mobility changes observed using mobile
phone data during COVID-19 pandemic,” in 2020 IEEE International Conference
on Big Data, Atlanta, GA, United States, 2021, pp. 3123–3132.
ista: 'Heiler G, Reisch T, Hurt J, Forghani M, Omani A, Hanbury A, Karimipour F.
2021. Country-wide mobility changes observed using mobile phone data during COVID-19
pandemic. 2020 IEEE International Conference on Big Data. Big Data: International
Conference on Big Data, 3123–3132.'
mla: Heiler, Georg, et al. “Country-Wide Mobility Changes Observed Using Mobile
Phone Data during COVID-19 Pandemic.” 2020 IEEE International Conference on
Big Data, IEEE, 2021, pp. 3123–32, doi:10.1109/bigdata50022.2020.9378374.
short: G. Heiler, T. Reisch, J. Hurt, M. Forghani, A. Omani, A. Hanbury, F. Karimipour,
in:, 2020 IEEE International Conference on Big Data, IEEE, 2021, pp. 3123–3132.
conference:
end_date: 2020-12-13
location: Atlanta, GA, United States
name: 'Big Data: International Conference on Big Data'
start_date: 2020-12-10
date_created: 2021-03-21T11:34:07Z
date_published: 2021-03-19T00:00:00Z
date_updated: 2023-08-07T14:00:13Z
day: '19'
department:
- _id: HeEd
doi: 10.1109/bigdata50022.2020.9378374
external_id:
arxiv:
- '2008.10064'
isi:
- '000662554703032'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2008.10064
month: '03'
oa: 1
oa_version: Preprint
page: 3123-3132
publication: 2020 IEEE International Conference on Big Data
publication_identifier:
isbn:
- '9781728162515'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Country-wide mobility changes observed using mobile phone data during COVID-19
pandemic
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9228'
abstract:
- lang: eng
text: Legacy conferences are costly and time consuming, and exclude scientists lacking
various resources or abilities. During the 2020 pandemic, we created an online
conference platform, Neuromatch Conferences (NMC), aimed at developing technological
and cultural changes to make conferences more democratic, scalable, and accessible.
We discuss the lessons we learned.
acknowledgement: We thank all of our volunteers from the NMC conferences (list of
names in the appendix). We also thank the NSF for support from 1734220 to B.W.,
and DARPA for support to T.A.
article_processing_charge: No
article_type: original
author:
- first_name: Titipat
full_name: Achakulvisut, Titipat
last_name: Achakulvisut
- first_name: Tulakan
full_name: Ruangrong, Tulakan
last_name: Ruangrong
- first_name: Patrick
full_name: Mineault, Patrick
last_name: Mineault
- 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: Megan A.K.
full_name: Peters, Megan A.K.
last_name: Peters
- first_name: Panayiota
full_name: Poirazi, Panayiota
last_name: Poirazi
- first_name: Christopher
full_name: Rozell, Christopher
last_name: Rozell
- first_name: Brad
full_name: Wyble, Brad
last_name: Wyble
- first_name: Dan F.M.
full_name: Goodman, Dan F.M.
last_name: Goodman
- first_name: Konrad Paul
full_name: Kording, Konrad Paul
last_name: Kording
citation:
ama: 'Achakulvisut T, Ruangrong T, Mineault P, et al. Towards democratizing and
automating online conferences: Lessons from the Neuromatch Conferences. Trends
in Cognitive Sciences. 2021;25(4):265-268. doi:10.1016/j.tics.2021.01.007'
apa: 'Achakulvisut, T., Ruangrong, T., Mineault, P., Vogels, T. P., Peters, M. A.
K., Poirazi, P., … Kording, K. P. (2021). Towards democratizing and automating
online conferences: Lessons from the Neuromatch Conferences. Trends in Cognitive
Sciences. Elsevier. https://doi.org/10.1016/j.tics.2021.01.007'
chicago: 'Achakulvisut, Titipat, Tulakan Ruangrong, Patrick Mineault, Tim P Vogels,
Megan A.K. Peters, Panayiota Poirazi, Christopher Rozell, Brad Wyble, Dan F.M.
Goodman, and Konrad Paul Kording. “Towards Democratizing and Automating Online
Conferences: Lessons from the Neuromatch Conferences.” Trends in Cognitive
Sciences. Elsevier, 2021. https://doi.org/10.1016/j.tics.2021.01.007.'
ieee: 'T. Achakulvisut et al., “Towards democratizing and automating online
conferences: Lessons from the Neuromatch Conferences,” Trends in Cognitive
Sciences, vol. 25, no. 4. Elsevier, pp. 265–268, 2021.'
ista: 'Achakulvisut T, Ruangrong T, Mineault P, Vogels TP, Peters MAK, Poirazi P,
Rozell C, Wyble B, Goodman DFM, Kording KP. 2021. Towards democratizing and automating
online conferences: Lessons from the Neuromatch Conferences. Trends in Cognitive
Sciences. 25(4), 265–268.'
mla: 'Achakulvisut, Titipat, et al. “Towards Democratizing and Automating Online
Conferences: Lessons from the Neuromatch Conferences.” Trends in Cognitive
Sciences, vol. 25, no. 4, Elsevier, 2021, pp. 265–68, doi:10.1016/j.tics.2021.01.007.'
short: T. Achakulvisut, T. Ruangrong, P. Mineault, T.P. Vogels, M.A.K. Peters, P.
Poirazi, C. Rozell, B. Wyble, D.F.M. Goodman, K.P. Kording, Trends in Cognitive
Sciences 25 (2021) 265–268.
date_created: 2021-03-07T23:01:25Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2023-08-07T13:59:07Z
day: '01'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1016/j.tics.2021.01.007
external_id:
isi:
- '000627418000001'
pmid:
- '33608214'
file:
- access_level: open_access
checksum: 87e39ea7bd266b976e8631b66979214d
content_type: application/pdf
creator: dernst
date_created: 2022-05-27T07:31:24Z
date_updated: 2022-05-27T07:31:24Z
file_id: '11415'
file_name: 2021_TrendsCognitiveSciences_Achakulvisut.pdf
file_size: 380720
relation: main_file
success: 1
file_date_updated: 2022-05-27T07:31:24Z
has_accepted_license: '1'
intvolume: ' 25'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 265-268
pmid: 1
publication: Trends in Cognitive Sciences
publication_identifier:
eissn:
- 1879-307X
issn:
- 1364-6613
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Towards democratizing and automating online conferences: Lessons from the
Neuromatch Conferences'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 25
year: '2021'
...
---
_id: '9224'
abstract:
- lang: eng
text: We re-examine attempts to study the many-body localization transition using
measures that are physically natural on the ergodic/quantum chaotic regime of
the phase diagram. Using simple scaling arguments and an analysis of various models
for which rigorous results are available, we find that these measures can be particularly
adversely affected by the strong finite-size effects observed in nearly all numerical
studies of many-body localization. This severely impacts their utility in probing
the transition and the localized phase. In light of this analysis, we discuss
a recent study (Šuntajs et al., 2020) of the behaviour of the Thouless energy
and level repulsion in disordered spin chains, and its implications for the question
of whether MBL is a true phase of matter.
article_number: '168415'
article_processing_charge: No
article_type: original
author:
- first_name: D. A.
full_name: Abanin, D. A.
last_name: Abanin
- first_name: J. H.
full_name: Bardarson, J. H.
last_name: Bardarson
- first_name: G.
full_name: De Tomasi, G.
last_name: De Tomasi
- first_name: S.
full_name: Gopalakrishnan, S.
last_name: Gopalakrishnan
- first_name: V.
full_name: Khemani, V.
last_name: Khemani
- first_name: S. A.
full_name: Parameswaran, S. A.
last_name: Parameswaran
- first_name: F.
full_name: Pollmann, F.
last_name: Pollmann
- first_name: A. C.
full_name: Potter, A. C.
last_name: Potter
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: R.
full_name: Vasseur, R.
last_name: Vasseur
citation:
ama: 'Abanin DA, Bardarson JH, De Tomasi G, et al. Distinguishing localization from
chaos: Challenges in finite-size systems. Annals of Physics. 2021;427(4).
doi:10.1016/j.aop.2021.168415'
apa: 'Abanin, D. A., Bardarson, J. H., De Tomasi, G., Gopalakrishnan, S., Khemani,
V., Parameswaran, S. A., … Vasseur, R. (2021). Distinguishing localization from
chaos: Challenges in finite-size systems. Annals of Physics. Elsevier.
https://doi.org/10.1016/j.aop.2021.168415'
chicago: 'Abanin, D. A., J. H. Bardarson, G. De Tomasi, S. Gopalakrishnan, V. Khemani,
S. A. Parameswaran, F. Pollmann, A. C. Potter, Maksym Serbyn, and R. Vasseur.
“Distinguishing Localization from Chaos: Challenges in Finite-Size Systems.” Annals
of Physics. Elsevier, 2021. https://doi.org/10.1016/j.aop.2021.168415.'
ieee: 'D. A. Abanin et al., “Distinguishing localization from chaos: Challenges
in finite-size systems,” Annals of Physics, vol. 427, no. 4. Elsevier,
2021.'
ista: 'Abanin DA, Bardarson JH, De Tomasi G, Gopalakrishnan S, Khemani V, Parameswaran
SA, Pollmann F, Potter AC, Serbyn M, Vasseur R. 2021. Distinguishing localization
from chaos: Challenges in finite-size systems. Annals of Physics. 427(4), 168415.'
mla: 'Abanin, D. A., et al. “Distinguishing Localization from Chaos: Challenges
in Finite-Size Systems.” Annals of Physics, vol. 427, no. 4, 168415, Elsevier,
2021, doi:10.1016/j.aop.2021.168415.'
short: D.A. Abanin, J.H. Bardarson, G. De Tomasi, S. Gopalakrishnan, V. Khemani,
S.A. Parameswaran, F. Pollmann, A.C. Potter, M. Serbyn, R. Vasseur, Annals of
Physics 427 (2021).
date_created: 2021-03-07T23:01:25Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2023-08-07T13:58:30Z
day: '01'
department:
- _id: MaSe
doi: 10.1016/j.aop.2021.168415
external_id:
arxiv:
- '1911.04501'
isi:
- '000634879800007'
intvolume: ' 427'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1911.04501
month: '04'
oa: 1
oa_version: Preprint
publication: Annals of Physics
publication_identifier:
eissn:
- 1096035X
issn:
- '00034916'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Distinguishing localization from chaos: Challenges in finite-size systems'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 427
year: '2021'
...
---
_id: '9239'
abstract:
- lang: eng
text: 'A graph game proceeds as follows: two players move a token through a graph
to produce a finite or infinite path, which determines the payoff of the game.
We study bidding games in which in each turn, an auction determines which player
moves the token. Bidding games were largely studied in combination with two variants
of first-price auctions called “Richman” and “poorman” bidding. We study taxman
bidding, which span the spectrum between the two. The game is parameterized by
a constant : portion τ of the winning bid is paid to the other player, and portion to
the bank. While finite-duration (reachability) taxman games have been studied
before, we present, for the first time, results on infinite-duration taxman games:
we unify, generalize, and simplify previous equivalences between bidding games
and a class of stochastic games called random-turn games.'
article_processing_charge: No
article_type: original
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- 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: Đorđe
full_name: Žikelić, Đorđe
last_name: Žikelić
citation:
ama: Avni G, Henzinger TA, Žikelić Đ. Bidding mechanisms in graph games. Journal
of Computer and System Sciences. 2021;119(8):133-144. doi:10.1016/j.jcss.2021.02.008
apa: Avni, G., Henzinger, T. A., & Žikelić, Đ. (2021). Bidding mechanisms in
graph games. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2021.02.008
chicago: Avni, Guy, Thomas A Henzinger, and Đorđe Žikelić. “Bidding Mechanisms in
Graph Games.” Journal of Computer and System Sciences. Elsevier, 2021.
https://doi.org/10.1016/j.jcss.2021.02.008.
ieee: G. Avni, T. A. Henzinger, and Đ. Žikelić, “Bidding mechanisms in graph games,”
Journal of Computer and System Sciences, vol. 119, no. 8. Elsevier, pp.
133–144, 2021.
ista: Avni G, Henzinger TA, Žikelić Đ. 2021. Bidding mechanisms in graph games.
Journal of Computer and System Sciences. 119(8), 133–144.
mla: Avni, Guy, et al. “Bidding Mechanisms in Graph Games.” Journal of Computer
and System Sciences, vol. 119, no. 8, Elsevier, 2021, pp. 133–44, doi:10.1016/j.jcss.2021.02.008.
short: G. Avni, T.A. Henzinger, Đ. Žikelić, Journal of Computer and System Sciences
119 (2021) 133–144.
date_created: 2021-03-14T23:01:32Z
date_published: 2021-03-03T00:00:00Z
date_updated: 2023-08-07T14:08:34Z
day: '03'
department:
- _id: ToHe
doi: 10.1016/j.jcss.2021.02.008
external_id:
arxiv:
- '1905.03835'
isi:
- '000634149800009'
intvolume: ' 119'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1905.03835
month: '03'
oa: 1
oa_version: Preprint
page: 133-144
publication: Journal of Computer and System Sciences
publication_identifier:
eissn:
- 1090-2724
issn:
- 0022-0000
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '6884'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Bidding mechanisms in graph games
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 119
year: '2021'
...
---
_id: '9244'
abstract:
- lang: eng
text: 'Organ function depends on tissues adopting the correct architecture. However,
insights into organ architecture are currently hampered by an absence of standardized
quantitative 3D analysis. We aimed to develop a robust technology to visualize,
digitalize, and segment the architecture of two tubular systems in 3D: double
resin casting micro computed tomography (DUCT). As proof of principle, we applied
DUCT to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), characterized
by intrahepatic bile duct paucity, that can spontaneously generate a biliary system
in adulthood. DUCT identified increased central biliary branching and peripheral
bile duct tortuosity as two compensatory processes occurring in distinct regions
of Jag1Ndr/Ndr liver, leading to full reconstitution of wild-type biliary volume
and phenotypic recovery. DUCT is thus a powerful new technology for 3D analysis,
which can reveal novel phenotypes and provide a standardized method of defining
liver architecture in mouse models.'
acknowledgement: "Work in ERA lab is supported by the Swedish Research Council, the
Center of Innovative Medicine (CIMED) Grant, Karolinska Institutet, and the Heart
and Lung Foundation, and\r\nthe Daniel Alagille Award from the European Association
for the Study of the Liver. One project in ERA lab is funded by ModeRNA, unrelated
to this project. The funders have no role in the design or interpretation of the
work. SH has been supported by a KI-MU PhD student program, and by a Wera Ekstro¨m
Foundation Scholarship. We are grateful for support from Tornspiran foundation to
NVH. JK: This research was carried out under the project CEITEC 2020 (LQ1601) with
financial support from the Ministry of Education, Youth and Sports of the Czech
Republic under the National Sustainability Programme II and CzechNanoLab Research
Infrastructure supported by MEYS CR (LM2018110) . UL: The financial support from
the Swedish Research Council and ICMC (Integrated CardioMetabolic Center) is acknowledged.
JJ: The work was supported by the Grant Agency of Masaryk University (project no.
MUNI/A/1565/2018). We thank Kari Huppert and Stacey Huppert for their expertise
and help regarding bile duct cannulation and their laboratory hospitality. We also
thank Nadja Schultz and Charlotte L Mattsson for their help with common bile duct
cannulation. We thank Daniel Holl for his help with trachea cannulation. We thank
Nikos Papadogiannakis for his assistance with mild Alagille biopsy samples and discussion.
We thank Karolinska Biomedicum Imaging Core, especially Shigeaki Kanatani for his
help with image analysis. We thank Jan Masek and Carolina Gutierrez for their scientific
input in manuscript writing. We thank Peter Ranefall and the BioImage Informatics
(SciLife national facility) for their help writing parts of the MATLAB pipeline.\r\nThe
TROMA-III antibody developed by Rolf Kemler was obtained from the Developmental
Studies Hybridoma (DSHB) Bank developed under the auspices of NICHD and maintained
by The University of Iowa, Department of Biological Sciences, Iowa City, IA52242.
We thank Goncalo M Brito for all illustrations. This work was supported by the European
Union (European Research Council Starting grant 851288 to E.H.)."
article_number: e60916
article_processing_charge: No
article_type: original
author:
- first_name: Simona
full_name: Hankeova, Simona
last_name: Hankeova
- first_name: Jakub
full_name: Salplachta, Jakub
last_name: Salplachta
- first_name: Tomas
full_name: Zikmund, Tomas
last_name: Zikmund
- first_name: Michaela
full_name: Kavkova, Michaela
last_name: Kavkova
- first_name: Noémi
full_name: Van Hul, Noémi
last_name: Van Hul
- first_name: Adam
full_name: Brinek, Adam
last_name: Brinek
- first_name: Veronika
full_name: Smekalova, Veronika
last_name: Smekalova
- first_name: Jakub
full_name: Laznovsky, Jakub
last_name: Laznovsky
- first_name: Feven
full_name: Dawit, Feven
last_name: Dawit
- first_name: Josef
full_name: Jaros, Josef
last_name: Jaros
- first_name: Vítězslav
full_name: Bryja, Vítězslav
last_name: Bryja
- first_name: Urban
full_name: Lendahl, Urban
last_name: Lendahl
- first_name: Ewa
full_name: Ellis, Ewa
last_name: Ellis
- first_name: Antal
full_name: Nemeth, Antal
last_name: Nemeth
- first_name: Björn
full_name: Fischler, Björn
last_name: Fischler
- 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: Jozef
full_name: Kaiser, Jozef
last_name: Kaiser
- first_name: Emma Rachel
full_name: Andersson, Emma Rachel
last_name: Andersson
citation:
ama: Hankeova S, Salplachta J, Zikmund T, et al. DUCT reveals architectural mechanisms
contributing to bile duct recovery in a mouse model for alagille syndrome. eLife.
2021;10. doi:10.7554/eLife.60916
apa: Hankeova, S., Salplachta, J., Zikmund, T., Kavkova, M., Van Hul, N., Brinek,
A., … Andersson, E. R. (2021). DUCT reveals architectural mechanisms contributing
to bile duct recovery in a mouse model for alagille syndrome. ELife. eLife
Sciences Publications. https://doi.org/10.7554/eLife.60916
chicago: Hankeova, Simona, Jakub Salplachta, Tomas Zikmund, Michaela Kavkova, Noémi
Van Hul, Adam Brinek, Veronika Smekalova, et al. “DUCT Reveals Architectural Mechanisms
Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” ELife.
eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.60916.
ieee: S. Hankeova et al., “DUCT reveals architectural mechanisms contributing
to bile duct recovery in a mouse model for alagille syndrome,” eLife, vol.
10. eLife Sciences Publications, 2021.
ista: Hankeova S, Salplachta J, Zikmund T, Kavkova M, Van Hul N, Brinek A, Smekalova
V, Laznovsky J, Dawit F, Jaros J, Bryja V, Lendahl U, Ellis E, Nemeth A, Fischler
B, Hannezo EB, Kaiser J, Andersson ER. 2021. DUCT reveals architectural mechanisms
contributing to bile duct recovery in a mouse model for alagille syndrome. eLife.
10, e60916.
mla: Hankeova, Simona, et al. “DUCT Reveals Architectural Mechanisms Contributing
to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” ELife, vol.
10, e60916, eLife Sciences Publications, 2021, doi:10.7554/eLife.60916.
short: S. Hankeova, J. Salplachta, T. Zikmund, M. Kavkova, N. Van Hul, A. Brinek,
V. Smekalova, J. Laznovsky, F. Dawit, J. Jaros, V. Bryja, U. Lendahl, E. Ellis,
A. Nemeth, B. Fischler, E.B. Hannezo, J. Kaiser, E.R. Andersson, ELife 10 (2021).
date_created: 2021-03-14T23:01:34Z
date_published: 2021-02-26T00:00:00Z
date_updated: 2023-08-07T14:12:54Z
day: '26'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.7554/eLife.60916
ec_funded: 1
external_id:
isi:
- '000625357100001'
pmid:
- '33635272'
file:
- access_level: open_access
checksum: 20ccf4dfe46c48cf986794c8bf4fd1cb
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T08:50:33Z
date_updated: 2021-03-22T08:50:33Z
file_id: '9271'
file_name: 2021_eLife_Hankeova.pdf
file_size: 9259690
relation: main_file
success: 1
file_date_updated: 2021-03-22T08:50:33Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: DUCT reveals architectural mechanisms contributing to bile duct recovery in
a mouse model for alagille syndrome
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '9241'
abstract:
- lang: eng
text: 'Volumetric light transport is a pervasive physical phenomenon, and therefore
its accurate simulation is important for a broad array of disciplines. While suitable
mathematical models for computing the transport are now available, obtaining the
necessary material parameters needed to drive such simulations is a challenging
task: direct measurements of these parameters from material samples are seldom
possible. Building on the inverse scattering paradigm, we present a novel measurement
approach which indirectly infers the transport parameters from extrinsic observations
of multiple-scattered radiance. The novelty of the proposed approach lies in replacing
structured illumination with a structured reflector bonded to the sample, and
a robust fitting procedure that largely compensates for potential systematic errors
in the calibration of the setup. We show the feasibility of our approach by validating
simulations of complex 3D compositions of the measured materials against physical
prints, using photo-polymer resins. As presented in this paper, our technique
yields colorspace data suitable for accurate appearance reproduction in the area
of 3D printing. Beyond that, and without fundamental changes to the basic measurement
methodology, it could equally well be used to obtain spectral measurements that
are useful for other application areas.'
acknowledgement: "H2020 Marie Skłodowska-Curie Actions (642841); European Research
Council (715767); Grantová Agentura České Republiky (16-08111S, 16-18964S); Univerzita
Karlova v Praze (SVV-2017-260452); Engineering and Physical Sciences Research Council
(EP/K023578/1).\r\nWe are grateful to Stratasys Ltd. for access to the voxel-level
print interface of the J750\r\nmachine."
article_processing_charge: No
article_type: original
author:
- first_name: Oskar
full_name: Elek, Oskar
last_name: Elek
- first_name: Ran
full_name: Zhang, Ran
id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0002-3808-281X
- first_name: Denis
full_name: Sumin, Denis
last_name: Sumin
- first_name: Karol
full_name: Myszkowski, Karol
last_name: Myszkowski
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Alexander
full_name: Wilkie, Alexander
last_name: Wilkie
- first_name: Jaroslav
full_name: Křivánek, Jaroslav
last_name: Křivánek
- first_name: Tim
full_name: Weyrich, Tim
last_name: Weyrich
citation:
ama: Elek O, Zhang R, Sumin D, et al. Robust and practical measurement of volume
transport parameters in solid photo-polymer materials for 3D printing. Optics
Express. 2021;29(5):7568-7588. doi:10.1364/OE.406095
apa: Elek, O., Zhang, R., Sumin, D., Myszkowski, K., Bickel, B., Wilkie, A., … Weyrich,
T. (2021). Robust and practical measurement of volume transport parameters in
solid photo-polymer materials for 3D printing. Optics Express. The Optical
Society. https://doi.org/10.1364/OE.406095
chicago: Elek, Oskar, Ran Zhang, Denis Sumin, Karol Myszkowski, Bernd Bickel, Alexander
Wilkie, Jaroslav Křivánek, and Tim Weyrich. “Robust and Practical Measurement
of Volume Transport Parameters in Solid Photo-Polymer Materials for 3D Printing.”
Optics Express. The Optical Society, 2021. https://doi.org/10.1364/OE.406095.
ieee: O. Elek et al., “Robust and practical measurement of volume transport
parameters in solid photo-polymer materials for 3D printing,” Optics Express,
vol. 29, no. 5. The Optical Society, pp. 7568–7588, 2021.
ista: Elek O, Zhang R, Sumin D, Myszkowski K, Bickel B, Wilkie A, Křivánek J, Weyrich
T. 2021. Robust and practical measurement of volume transport parameters in solid
photo-polymer materials for 3D printing. Optics Express. 29(5), 7568–7588.
mla: Elek, Oskar, et al. “Robust and Practical Measurement of Volume Transport Parameters
in Solid Photo-Polymer Materials for 3D Printing.” Optics Express, vol.
29, no. 5, The Optical Society, 2021, pp. 7568–88, doi:10.1364/OE.406095.
short: O. Elek, R. Zhang, D. Sumin, K. Myszkowski, B. Bickel, A. Wilkie, J. Křivánek,
T. Weyrich, Optics Express 29 (2021) 7568–7588.
date_created: 2021-03-14T23:01:33Z
date_published: 2021-03-01T00:00:00Z
date_updated: 2023-08-07T14:11:57Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1364/OE.406095
ec_funded: 1
external_id:
isi:
- '000624968100103'
file:
- access_level: open_access
checksum: a9697ad83136c19ad87e46aa2db63cfd
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T08:15:28Z
date_updated: 2021-03-22T08:15:28Z
file_id: '9269'
file_name: 2021_OpticsExpress_Elek.pdf
file_size: 10873700
relation: main_file
success: 1
file_date_updated: 2021-03-22T08:15:28Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '5'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 7568-7588
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: Optics Express
publication_identifier:
eissn:
- 1094-4087
publication_status: published
publisher: The Optical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Robust and practical measurement of volume transport parameters in solid photo-polymer
materials for 3D printing
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 29
year: '2021'
...
---
_id: '9243'
abstract:
- lang: eng
text: Peptidoglycan is an essential component of the bacterial cell envelope that
surrounds the cytoplasmic membrane to protect the cell from osmotic lysis. Important
antibiotics such as β-lactams and glycopeptides target peptidoglycan biosynthesis.
Class A penicillin-binding proteins (PBPs) are bifunctional membrane-bound peptidoglycan
synthases that polymerize glycan chains and connect adjacent stem peptides by
transpeptidation. How these enzymes work in their physiological membrane environment
is poorly understood. Here, we developed a novel Förster resonance energy transfer-based
assay to follow in real time both reactions of class A PBPs reconstituted in liposomes
or supported lipid bilayers and applied this assay with PBP1B homologues from
Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii in the presence
or absence of their cognate lipoprotein activator. Our assay will allow unravelling
the mechanisms of peptidoglycan synthesis in a lipid-bilayer environment and can
be further developed to be used for high-throughput screening for new antimicrobials.
acknowledgement: 'We thank Alexander Egan (Newcastle University) for purified proteins
LpoB(sol) and LpoPPa(sol), Federico Corona (Newcastle University) for purified MepM,
and Oliver Birkholz and Jacob Piehler (Department of Biology and Center of Cellular
Nanoanalytics, University of Osnabru¨ ck) for their help with PBP1B reconstitution
into polymer-SLBs and initial guidance on single particle tracking. We also acknowledge
Christian P Richter and Changjiang You (Department of Biology and Center of Cellular
Nanoanalytics, University of Osnabru¨ ck) for providing SLIMfast software and tris-DODA-NTA
reagent, respectively. This work was funded by the BBSRC grant BB/R017409/1 (to
WV), the European Research Council through grant ERC-2015-StG-679239 (to ML), and
long-term fellowships HFSP LT 000824/2016-L4 and EMBO ALTF 1163–2015 (to NB). '
article_number: 1-32
article_processing_charge: No
article_type: original
author:
- first_name: Víctor M.
full_name: Hernández-Rocamora, Víctor M.
last_name: Hernández-Rocamora
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Katharina
full_name: Peters, Katharina
last_name: Peters
- first_name: Eefjan
full_name: Breukink, Eefjan
last_name: Breukink
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Waldemar
full_name: Vollmer, Waldemar
last_name: Vollmer
citation:
ama: Hernández-Rocamora VM, Baranova NS, Peters K, Breukink E, Loose M, Vollmer
W. Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin
binding proteins. eLife. 2021;10. doi:10.7554/eLife.61525
apa: Hernández-Rocamora, V. M., Baranova, N. S., Peters, K., Breukink, E., Loose,
M., & Vollmer, W. (2021). Real time monitoring of peptidoglycan synthesis
by membrane-reconstituted penicillin binding proteins. ELife. eLife Sciences
Publications. https://doi.org/10.7554/eLife.61525
chicago: Hernández-Rocamora, Víctor M., Natalia S. Baranova, Katharina Peters, Eefjan
Breukink, Martin Loose, and Waldemar Vollmer. “Real Time Monitoring of Peptidoglycan
Synthesis by Membrane-Reconstituted Penicillin Binding Proteins.” ELife.
eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.61525.
ieee: V. M. Hernández-Rocamora, N. S. Baranova, K. Peters, E. Breukink, M. Loose,
and W. Vollmer, “Real time monitoring of peptidoglycan synthesis by membrane-reconstituted
penicillin binding proteins,” eLife, vol. 10. eLife Sciences Publications,
2021.
ista: Hernández-Rocamora VM, Baranova NS, Peters K, Breukink E, Loose M, Vollmer
W. 2021. Real time monitoring of peptidoglycan synthesis by membrane-reconstituted
penicillin binding proteins. eLife. 10, 1–32.
mla: Hernández-Rocamora, Víctor M., et al. “Real Time Monitoring of Peptidoglycan
Synthesis by Membrane-Reconstituted Penicillin Binding Proteins.” ELife,
vol. 10, 1–32, eLife Sciences Publications, 2021, doi:10.7554/eLife.61525.
short: V.M. Hernández-Rocamora, N.S. Baranova, K. Peters, E. Breukink, M. Loose,
W. Vollmer, ELife 10 (2021).
date_created: 2021-03-14T23:01:33Z
date_published: 2021-02-24T00:00:00Z
date_updated: 2023-08-07T14:10:50Z
day: '24'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.7554/eLife.61525
ec_funded: 1
external_id:
isi:
- '000627596400001'
file:
- access_level: open_access
checksum: 79897a09bfecd9914d39c4aea2841855
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T07:36:08Z
date_updated: 2021-03-22T07:36:08Z
file_id: '9268'
file_name: 2021_eLife_HernandezRocamora.pdf
file_size: 2314698
relation: main_file
success: 1
file_date_updated: 2021-03-22T07:36:08Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: 2596EAB6-B435-11E9-9278-68D0E5697425
grant_number: ALTF 2015-1163
name: Synthesis of bacterial cell wall
- _id: 259B655A-B435-11E9-9278-68D0E5697425
grant_number: LT000824/2016
name: Reconstitution of bacterial cell wall sythesis
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin
binding proteins
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '9246'
abstract:
- lang: eng
text: We consider the Fröhlich Hamiltonian in a mean-field limit where many bosonic
particles weakly couple to the quantized phonon field. For large particle numbers
and a suitably small coupling, we show that the dynamics of the system is approximately
described by the Landau–Pekar equations. These describe a Bose–Einstein condensate
interacting with a classical polarization field, whose dynamics is effected by
the condensate, i.e., the back-reaction of the phonons that are created by the
particles during the time evolution is of leading order.
acknowledgement: "Financial support by the European Research Council (ERC) under the\r\nEuropean
Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo 694227;
N.L and R.S.), the SNSF Eccellenza Project PCEFP2 181153 (N.L) and the\r\nDeutsche
Forschungsgemeinschaft (DFG) through the Research TrainingGroup 1838: Spectral\r\nTheory
and Dynamics of Quantum Systems (D.M.) is gratefully acknowledged. N.L.\r\ngratefully
acknowledges support from the NCCRSwissMAP and would like to thank Simone\r\nRademacher
and Benjamin Schlein for interesting discussions about the time-evolution of\r\nthe
polaron at strong coupling. D.M. thanks Marcel Griesemer and Andreas Wünsch for\r\nextensive
discussions about the Fröhlich polaron."
article_processing_charge: No
article_type: original
author:
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Leopold NK, Mitrouskas DJ, Seiringer R. Derivation of the Landau–Pekar equations
in a many-body mean-field limit. Archive for Rational Mechanics and Analysis.
2021;240:383-417. doi:10.1007/s00205-021-01616-9
apa: Leopold, N. K., Mitrouskas, D. J., & Seiringer, R. (2021). Derivation of
the Landau–Pekar equations in a many-body mean-field limit. Archive for Rational
Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01616-9
chicago: Leopold, Nikolai K, David Johannes Mitrouskas, and Robert Seiringer. “Derivation
of the Landau–Pekar Equations in a Many-Body Mean-Field Limit.” Archive for
Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01616-9.
ieee: N. K. Leopold, D. J. Mitrouskas, and R. Seiringer, “Derivation of the Landau–Pekar
equations in a many-body mean-field limit,” Archive for Rational Mechanics
and Analysis, vol. 240. Springer Nature, pp. 383–417, 2021.
ista: Leopold NK, Mitrouskas DJ, Seiringer R. 2021. Derivation of the Landau–Pekar
equations in a many-body mean-field limit. Archive for Rational Mechanics and
Analysis. 240, 383–417.
mla: Leopold, Nikolai K., et al. “Derivation of the Landau–Pekar Equations in a
Many-Body Mean-Field Limit.” Archive for Rational Mechanics and Analysis,
vol. 240, Springer Nature, 2021, pp. 383–417, doi:10.1007/s00205-021-01616-9.
short: N.K. Leopold, D.J. Mitrouskas, R. Seiringer, Archive for Rational Mechanics
and Analysis 240 (2021) 383–417.
date_created: 2021-03-14T23:01:34Z
date_published: 2021-02-26T00:00:00Z
date_updated: 2023-08-07T14:12:27Z
day: '26'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s00205-021-01616-9
ec_funded: 1
external_id:
arxiv:
- '2001.03993'
isi:
- '000622226200001'
file:
- access_level: open_access
checksum: 23449e44dc5132501a5c86e70638800f
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T08:31:29Z
date_updated: 2021-03-22T08:31:29Z
file_id: '9270'
file_name: 2021_ArchRationalMechAnal_Leopold.pdf
file_size: 558006
relation: main_file
success: 1
file_date_updated: 2021-03-22T08:31:29Z
has_accepted_license: '1'
intvolume: ' 240'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 383-417
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
eissn:
- '14320673'
issn:
- '00039527'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Derivation of the Landau–Pekar equations in a many-body mean-field limit
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 240
year: '2021'
...
---
_id: '9256'
abstract:
- lang: eng
text: We consider the ferromagnetic quantum Heisenberg model in one dimension, for
any spin S≥1/2. We give upper and lower bounds on the free energy, proving that
at low temperature it is asymptotically equal to the one of an ideal Bose gas
of magnons, as predicted by the spin-wave approximation. The trial state used
in the upper bound yields an analogous estimate also in the case of two spatial
dimensions, which is believed to be sharp at low temperature.
acknowledgement: "The work of MN was supported by the National Science Centre (NCN)
Project Nr. 2016/21/D/ST1/02430. The work of RS was supported by the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant Agreement No. 694227).\r\nOpen access funding provided by Institute of Science
and Technology (IST Austria)."
article_number: '31'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Marcin M
full_name: Napiórkowski, Marcin M
id: 4197AD04-F248-11E8-B48F-1D18A9856A87
last_name: Napiórkowski
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Napiórkowski MM, Seiringer R. Free energy asymptotics of the quantum Heisenberg
spin chain. Letters in Mathematical Physics. 2021;111(2). doi:10.1007/s11005-021-01375-4
apa: Napiórkowski, M. M., & Seiringer, R. (2021). Free energy asymptotics of
the quantum Heisenberg spin chain. Letters in Mathematical Physics. Springer
Nature. https://doi.org/10.1007/s11005-021-01375-4
chicago: Napiórkowski, Marcin M, and Robert Seiringer. “Free Energy Asymptotics
of the Quantum Heisenberg Spin Chain.” Letters in Mathematical Physics.
Springer Nature, 2021. https://doi.org/10.1007/s11005-021-01375-4.
ieee: M. M. Napiórkowski and R. Seiringer, “Free energy asymptotics of the quantum
Heisenberg spin chain,” Letters in Mathematical Physics, vol. 111, no.
2. Springer Nature, 2021.
ista: Napiórkowski MM, Seiringer R. 2021. Free energy asymptotics of the quantum
Heisenberg spin chain. Letters in Mathematical Physics. 111(2), 31.
mla: Napiórkowski, Marcin M., and Robert Seiringer. “Free Energy Asymptotics of
the Quantum Heisenberg Spin Chain.” Letters in Mathematical Physics, vol.
111, no. 2, 31, Springer Nature, 2021, doi:10.1007/s11005-021-01375-4.
short: M.M. Napiórkowski, R. Seiringer, Letters in Mathematical Physics 111 (2021).
date_created: 2021-03-21T23:01:19Z
date_published: 2021-03-09T00:00:00Z
date_updated: 2023-08-07T14:17:00Z
day: '09'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s11005-021-01375-4
external_id:
isi:
- '000626837400001'
file:
- access_level: open_access
checksum: 687fef1525789c0950de90468dd81604
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T11:01:09Z
date_updated: 2021-03-22T11:01:09Z
file_id: '9273'
file_name: 2021_LettersMathPhysics_Napiorkowski.pdf
file_size: 397962
relation: main_file
success: 1
file_date_updated: 2021-03-22T11:01:09Z
has_accepted_license: '1'
intvolume: ' 111'
isi: 1
issue: '2'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Letters in Mathematical Physics
publication_identifier:
eissn:
- '15730530'
issn:
- '03779017'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Free energy asymptotics of the quantum Heisenberg spin chain
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 111
year: '2021'
...
---
_id: '9242'
abstract:
- lang: eng
text: In the recent years important experimental advances in resonant electro-optic
modulators as high-efficiency sources for coherent frequency combs and as devices
for quantum information transfer have been realized, where strong optical and
microwave mode coupling were achieved. These features suggest electro-optic-based
devices as candidates for entangled optical frequency comb sources. In the present
work, I study the generation of entangled optical frequency combs in millimeter-sized
resonant electro-optic modulators. These devices profit from the experimentally
proven advantages such as nearly constant optical free spectral ranges over several
gigahertz, and high optical and microwave quality factors. The generation of frequency
multiplexed quantum channels with spectral bandwidth in the MHz range for conservative
parameter values paves the way towards novel uses in long-distance hybrid quantum
networks, quantum key distribution, enhanced optical metrology, and quantum computing.
acknowledgement: "I thank Prof. Shabir Barzanjeh and Dr. Ulrich Vogl for the fruitful
discussions.\r\n"
article_number: '023708'
article_processing_charge: No
article_type: original
author:
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
citation:
ama: Rueda Sanchez AR. Frequency-multiplexed hybrid optical entangled source based
on the Pockels effect. Physical Review A. 2021;103(2). doi:10.1103/PhysRevA.103.023708
apa: Rueda Sanchez, A. R. (2021). Frequency-multiplexed hybrid optical entangled
source based on the Pockels effect. Physical Review A. American Physical
Society. https://doi.org/10.1103/PhysRevA.103.023708
chicago: Rueda Sanchez, Alfredo R. “Frequency-Multiplexed Hybrid Optical Entangled
Source Based on the Pockels Effect.” Physical Review A. American Physical
Society, 2021. https://doi.org/10.1103/PhysRevA.103.023708.
ieee: A. R. Rueda Sanchez, “Frequency-multiplexed hybrid optical entangled source
based on the Pockels effect,” Physical Review A, vol. 103, no. 2. American
Physical Society, 2021.
ista: Rueda Sanchez AR. 2021. Frequency-multiplexed hybrid optical entangled source
based on the Pockels effect. Physical Review A. 103(2), 023708.
mla: Rueda Sanchez, Alfredo R. “Frequency-Multiplexed Hybrid Optical Entangled Source
Based on the Pockels Effect.” Physical Review A, vol. 103, no. 2, 023708,
American Physical Society, 2021, doi:10.1103/PhysRevA.103.023708.
short: A.R. Rueda Sanchez, Physical Review A 103 (2021).
date_created: 2021-03-14T23:01:33Z
date_published: 2021-02-11T00:00:00Z
date_updated: 2023-08-07T14:11:18Z
day: '11'
department:
- _id: JoFi
doi: 10.1103/PhysRevA.103.023708
external_id:
arxiv:
- '2010.05356'
isi:
- '000617037900013'
intvolume: ' 103'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2010.05356
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Frequency-multiplexed hybrid optical entangled source based on the Pockels
effect
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 103
year: '2021'
...
---
_id: '9257'
abstract:
- lang: eng
text: 'The inverse problem of designing component interactions to target emergent
structure is fundamental to numerous applications in biotechnology, materials
science, and statistical physics. Equally important is the inverse problem of
designing emergent kinetics, but this has received considerably less attention.
Using recent advances in automatic differentiation, we show how kinetic pathways
can be precisely designed by directly differentiating through statistical physics
models, namely free energy calculations and molecular dynamics simulations. We
consider two systems that are crucial to our understanding of structural self-assembly:
bulk crystallization and small nanoclusters. In each case, we are able to assemble
precise dynamical features. Using gradient information, we manipulate interactions
among constituent particles to tune the rate at which these systems yield specific
structures of interest. Moreover, we use this approach to learn nontrivial features
about the high-dimensional design space, allowing us to accurately predict when
multiple kinetic features can be simultaneously and independently controlled.
These results provide a concrete and generalizable foundation for studying nonstructural
self-assembly, including kinetic properties as well as other complex emergent
properties, in a vast array of systems.'
acknowledgement: We thank Agnese Curatolo, Megan Engel, Ofer Kimchi, Seong Ho Pahng,
and Roy Frostig for helpful discussions. This material is based on work supported
by NSF Graduate Research Fellowship Grant DGE1745303. This research was funded by
NSF Grant DMS-1715477, Materials Research Science and Engineering Centers Grant
DMR-1420570, and Office of Naval Research Grant N00014-17-1-3029. M.P.B. is an investigator
of the Simons Foundation.
article_number: e2024083118
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Ella M.
full_name: King, Ella M.
last_name: King
- first_name: Samuel S.
full_name: Schoenholz, Samuel S.
last_name: Schoenholz
- first_name: Ekin D.
full_name: Cubuk, Ekin D.
last_name: Cubuk
- first_name: Michael P.
full_name: Brenner, Michael P.
last_name: Brenner
citation:
ama: Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. Designing self-assembling
kinetics with differentiable statistical physics models. Proceedings of the
National Academy of Sciences. 2021;118(10). doi:10.1073/pnas.2024083118
apa: Goodrich, C. P., King, E. M., Schoenholz, S. S., Cubuk, E. D., & Brenner,
M. P. (2021). Designing self-assembling kinetics with differentiable statistical
physics models. Proceedings of the National Academy of Sciences. National
Academy of Sciences. https://doi.org/10.1073/pnas.2024083118
chicago: Goodrich, Carl Peter, Ella M. King, Samuel S. Schoenholz, Ekin D. Cubuk,
and Michael P. Brenner. “Designing Self-Assembling Kinetics with Differentiable
Statistical Physics Models.” Proceedings of the National Academy of Sciences.
National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2024083118.
ieee: C. P. Goodrich, E. M. King, S. S. Schoenholz, E. D. Cubuk, and M. P. Brenner,
“Designing self-assembling kinetics with differentiable statistical physics models,”
Proceedings of the National Academy of Sciences, vol. 118, no. 10. National
Academy of Sciences, 2021.
ista: Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. 2021. Designing
self-assembling kinetics with differentiable statistical physics models. Proceedings
of the National Academy of Sciences. 118(10), e2024083118.
mla: Goodrich, Carl Peter, et al. “Designing Self-Assembling Kinetics with Differentiable
Statistical Physics Models.” Proceedings of the National Academy of Sciences,
vol. 118, no. 10, e2024083118, National Academy of Sciences, 2021, doi:10.1073/pnas.2024083118.
short: C.P. Goodrich, E.M. King, S.S. Schoenholz, E.D. Cubuk, M.P. Brenner, Proceedings
of the National Academy of Sciences 118 (2021).
date_created: 2021-03-21T23:01:20Z
date_published: 2021-03-09T00:00:00Z
date_updated: 2023-08-07T14:19:34Z
day: '09'
ddc:
- '530'
department:
- _id: CaGo
doi: 10.1073/pnas.2024083118
external_id:
isi:
- '000627429100097'
pmid:
- '33653960'
file:
- access_level: open_access
checksum: 5be8da2b1c0757feb1057f1a515cf9e0
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T12:23:54Z
date_updated: 2021-03-22T12:23:54Z
file_id: '9278'
file_name: 2021_PNAS_Goodrich.pdf
file_size: 1047954
relation: main_file
success: 1
file_date_updated: 2021-03-22T12:23:54Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '10'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Designing self-assembling kinetics with differentiable statistical physics
models
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...
---
_id: '9262'
abstract:
- lang: eng
text: Sequence-specific oligomers with predictable folding patterns, i.e., foldamers,
provide new opportunities to mimic α-helical peptides and design inhibitors of
protein-protein interactions. One major hurdle of this strategy is to retain the
correct orientation of key side chains involved in protein surface recognition.
Here, we show that the structural plasticity of a foldamer backbone may notably
contribute to the required spatial adjustment for optimal interaction with the
protein surface. By using oligoureas as α helix mimics, we designed a foldamer/peptide
hybrid inhibitor of histone chaperone ASF1, a key regulator of chromatin dynamics.
The crystal structure of its complex with ASF1 reveals a notable plasticity of
the urea backbone, which adapts to the ASF1 surface to maintain the same binding
interface. One additional benefit of generating ASF1 ligands with nonpeptide oligourea
segments is the resistance to proteolysis in human plasma, which was highly improved
compared to the cognate α-helical peptide.
acknowledgement: 'We thank the Synchrotron SOLEIL, the European Synchrotron Radiation
Facility (ESRF), and the French Infrastructure for Integrated Structural Biology
(FRISBI) ANR-10-INBS-05. We are particularly grateful to A. Clavier and A. Campalans
for help in setting up and performing the cell penetration assays. Funding: Research
was funded by the French Centre National de Recherche Scientifique (CNRS), the Commissariat
à l’Energie Atomique (CEA), University of Bordeaux, University Paris-Saclay, and
the Synchrotron Soleil. The project was supported by the ANR 2007 BREAKABOUND (JC-07-216078),
2011 BIPBIP (ANR-10-BINF-0003), 2012 CHAPINHIB (ANR-12-BSV5-0022-01), 2015 CHIPSET
(ANR-15-CE11-008-01), 2015 HIMPP2I (ANR-15-CE07-0010), and the program labeled by
the ARC foundation 2016 PGA1*20160203953). M.B. was supported by Canceropole (Paris,
France) and a grant for young researchers from La Ligue contre le Cancer. J.M. was
supported by La Ligue contre le Cancer.'
article_number: eabd9153
article_processing_charge: No
article_type: original
author:
- first_name: Johanne
full_name: Mbianda, Johanne
last_name: Mbianda
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Christophe
full_name: André, Christophe
last_name: André
- first_name: Gwenaëlle
full_name: Moal, Gwenaëlle
last_name: Moal
- first_name: Marie E.
full_name: Perrin, Marie E.
last_name: Perrin
- first_name: Guillaume
full_name: Pinna, Guillaume
last_name: Pinna
- first_name: Raphaël
full_name: Guerois, Raphaël
last_name: Guerois
- first_name: Francois
full_name: Becher, Francois
last_name: Becher
- first_name: Pierre
full_name: Legrand, Pierre
last_name: Legrand
- first_name: Seydou
full_name: Traoré, Seydou
last_name: Traoré
- first_name: Céline
full_name: Douat, Céline
last_name: Douat
- first_name: Gilles
full_name: Guichard, Gilles
last_name: Guichard
- first_name: Françoise
full_name: Ochsenbein, Françoise
last_name: Ochsenbein
citation:
ama: Mbianda J, Bakail MM, André C, et al. Optimal anchoring of a foldamer inhibitor
of ASF1 histone chaperone through backbone plasticity. Science Advances.
2021;7(12). doi:10.1126/sciadv.abd9153
apa: Mbianda, J., Bakail, M. M., André, C., Moal, G., Perrin, M. E., Pinna, G.,
… Ochsenbein, F. (2021). Optimal anchoring of a foldamer inhibitor of ASF1 histone
chaperone through backbone plasticity. Science Advances. American Association
for the Advancement of Science. https://doi.org/10.1126/sciadv.abd9153
chicago: Mbianda, Johanne, May M Bakail, Christophe André, Gwenaëlle Moal, Marie
E. Perrin, Guillaume Pinna, Raphaël Guerois, et al. “Optimal Anchoring of a Foldamer
Inhibitor of ASF1 Histone Chaperone through Backbone Plasticity.” Science Advances.
American Association for the Advancement of Science, 2021. https://doi.org/10.1126/sciadv.abd9153.
ieee: J. Mbianda et al., “Optimal anchoring of a foldamer inhibitor of ASF1
histone chaperone through backbone plasticity,” Science Advances, vol.
7, no. 12. American Association for the Advancement of Science, 2021.
ista: Mbianda J, Bakail MM, André C, Moal G, Perrin ME, Pinna G, Guerois R, Becher
F, Legrand P, Traoré S, Douat C, Guichard G, Ochsenbein F. 2021. Optimal anchoring
of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity.
Science Advances. 7(12), eabd9153.
mla: Mbianda, Johanne, et al. “Optimal Anchoring of a Foldamer Inhibitor of ASF1
Histone Chaperone through Backbone Plasticity.” Science Advances, vol.
7, no. 12, eabd9153, American Association for the Advancement of Science, 2021,
doi:10.1126/sciadv.abd9153.
short: J. Mbianda, M.M. Bakail, C. André, G. Moal, M.E. Perrin, G. Pinna, R. Guerois,
F. Becher, P. Legrand, S. Traoré, C. Douat, G. Guichard, F. Ochsenbein, Science
Advances 7 (2021).
date_created: 2021-03-22T07:14:03Z
date_published: 2021-03-19T00:00:00Z
date_updated: 2023-08-07T14:20:26Z
day: '19'
ddc:
- '570'
department:
- _id: CampIT
doi: 10.1126/sciadv.abd9153
external_id:
isi:
- '000633443000011'
pmid:
- '33741589'
file:
- access_level: open_access
checksum: 737624cd0e630ffa7c52797a690500e3
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T12:49:00Z
date_updated: 2021-03-22T12:49:00Z
file_id: '9280'
file_name: 2021_ScienceAdv_Mbianda.pdf
file_size: 837156
relation: main_file
success: 1
file_date_updated: 2021-03-22T12:49:00Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '12'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
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: Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through
backbone plasticity
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 7
year: '2021'
...
---
_id: '9259'
abstract:
- lang: eng
text: Gradients of chemokines and growth factors guide migrating cells and morphogenetic
processes. Migration of antigen-presenting dendritic cells from the interstitium
into the lymphatic system is dependent on chemokine CCL21, which is secreted by
endothelial cells of the lymphatic capillary, binds heparan sulfates and forms
gradients decaying into the interstitium. Despite the importance of CCL21 gradients,
and chemokine gradients in general, the mechanisms of gradient formation are unclear.
Studies on fibroblast growth factors have shown that limited diffusion is crucial
for gradient formation. Here, we used the mouse dermis as a model tissue to address
the necessity of CCL21 anchoring to lymphatic capillary heparan sulfates in the
formation of interstitial CCL21 gradients. Surprisingly, the absence of lymphatic
endothelial heparan sulfates resulted only in a modest decrease of CCL21 levels
at the lymphatic capillaries and did neither affect interstitial CCL21 gradient
shape nor dendritic cell migration toward lymphatic capillaries. Thus, heparan
sulfates at the level of the lymphatic endothelium are dispensable for the formation
of a functional CCL21 gradient.
acknowledgement: "This work was supported by Sigrid Juselius fellowship (KV), University
of Helsinki 3-year research grant (KV), Academy of Finland Research fellow funding
(315710, to KV), the European Research Council (ERC CoG 724373 to MS), and by the
Austrian Science foundation (FWF) (Y564-B12 START award to MS).\r\nTaija Mäkinen
is acknowledged for providing Prox1CreERT2 transgenic mice and Yu Yamaguchi for
providing the conditional Ext1 mouse strain."
article_number: '630002'
article_processing_charge: No
article_type: original
author:
- first_name: Kari
full_name: Vaahtomeri, Kari
id: 368EE576-F248-11E8-B48F-1D18A9856A87
last_name: Vaahtomeri
orcid: 0000-0001-7829-3518
- first_name: Christine
full_name: Moussion, Christine
id: 3356F664-F248-11E8-B48F-1D18A9856A87
last_name: Moussion
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Vaahtomeri K, Moussion C, Hauschild R, Sixt MK. Shape and function of interstitial
chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic
endothelium. Frontiers in Immunology. 2021;12. doi:10.3389/fimmu.2021.630002
apa: Vaahtomeri, K., Moussion, C., Hauschild, R., & Sixt, M. K. (2021). Shape
and function of interstitial chemokine CCL21 gradients are independent of heparan
sulfates produced by lymphatic endothelium. Frontiers in Immunology. Frontiers.
https://doi.org/10.3389/fimmu.2021.630002
chicago: Vaahtomeri, Kari, Christine Moussion, Robert Hauschild, and Michael K Sixt.
“Shape and Function of Interstitial Chemokine CCL21 Gradients Are Independent
of Heparan Sulfates Produced by Lymphatic Endothelium.” Frontiers in Immunology.
Frontiers, 2021. https://doi.org/10.3389/fimmu.2021.630002.
ieee: K. Vaahtomeri, C. Moussion, R. Hauschild, and M. K. Sixt, “Shape and function
of interstitial chemokine CCL21 gradients are independent of heparan sulfates
produced by lymphatic endothelium,” Frontiers in Immunology, vol. 12. Frontiers,
2021.
ista: Vaahtomeri K, Moussion C, Hauschild R, Sixt MK. 2021. Shape and function of
interstitial chemokine CCL21 gradients are independent of heparan sulfates produced
by lymphatic endothelium. Frontiers in Immunology. 12, 630002.
mla: Vaahtomeri, Kari, et al. “Shape and Function of Interstitial Chemokine CCL21
Gradients Are Independent of Heparan Sulfates Produced by Lymphatic Endothelium.”
Frontiers in Immunology, vol. 12, 630002, Frontiers, 2021, doi:10.3389/fimmu.2021.630002.
short: K. Vaahtomeri, C. Moussion, R. Hauschild, M.K. Sixt, Frontiers in Immunology
12 (2021).
date_created: 2021-03-21T23:01:20Z
date_published: 2021-02-25T00:00:00Z
date_updated: 2023-08-07T14:18:26Z
day: '25'
ddc:
- '570'
department:
- _id: MiSi
- _id: Bio
doi: 10.3389/fimmu.2021.630002
ec_funded: 1
external_id:
isi:
- '000627134400001'
pmid:
- '33717158'
file:
- access_level: open_access
checksum: 663f5a48375e42afa4bfef58d42ec186
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T12:08:26Z
date_updated: 2021-03-22T12:08:26Z
file_id: '9277'
file_name: 2021_FrontiersImmumo_Vaahtomeri.pdf
file_size: 3740146
relation: main_file
success: 1
file_date_updated: 2021-03-22T12:08:26Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
- _id: 25A8E5EA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 564-B12
name: Cytoskeletal force generation and force transduction of migrating leukocytes
publication: Frontiers in Immunology
publication_identifier:
eissn:
- 1664-3224
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Shape and function of interstitial chemokine CCL21 gradients are independent
of heparan sulfates produced by lymphatic endothelium
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9254'
abstract:
- lang: eng
text: 'Auxin is a key regulator of plant growth and development. Local auxin biosynthesis
and intercellular transport generates regional gradients in the root that are
instructive for processes such as specification of developmental zones that maintain
root growth and tropic responses. Here we present a toolbox to study auxin-mediated
root development that features: (i) the ability to control auxin synthesis with
high spatio-temporal resolution and (ii) single-cell nucleus tracking and morphokinetic
analysis infrastructure. Integration of these two features enables cutting-edge
analysis of root development at single-cell resolution based on morphokinetic
parameters under normal growth conditions and during cell-type-specific induction
of auxin biosynthesis. We show directional auxin flow in the root and refine the
contributions of key players in this process. In addition, we determine the quantitative
kinetics of Arabidopsis root meristem skewing, which depends on local auxin gradients
but does not require PIN2 and AUX1 auxin transporter activities. Beyond the mechanistic
insights into root development, the tools developed here will enable biologists
to study kinetics and morphology of various critical processes at the single cell-level
in whole organisms.'
acknowledgement: This work was supported by grants from the Israel Science Foundation
(2378/19 to E.S.), the Joint NSFC-ISF Research Grant (3419/20 to E.S. and Z.D.),
the Human Frontier Science Program (HFSP—LIY000540/2020 to E.S.), the European Research
Council Starting Grant (757683- RobustHormoneTrans to E.S.), PBC postdoctoral fellowships
(to Y.H. and M.O.), NIH (GM114660 to Y.Z.), Breast Cancer Research Foundation (BCRF
to I.T.).
article_number: '1657'
article_processing_charge: No
article_type: original
author:
- first_name: Yangjie
full_name: Hu, Yangjie
last_name: Hu
- first_name: Moutasem
full_name: Omary, Moutasem
last_name: Omary
- first_name: Yun
full_name: Hu, Yun
last_name: Hu
- first_name: Ohad
full_name: Doron, Ohad
last_name: Doron
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
- first_name: Qingguo
full_name: Chen, Qingguo
last_name: Chen
- first_name: Or
full_name: Megides, Or
last_name: Megides
- first_name: Ori
full_name: Chekli, Ori
last_name: Chekli
- first_name: Zhaojun
full_name: Ding, Zhaojun
last_name: Ding
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Yunde
full_name: Zhao, Yunde
last_name: Zhao
- first_name: Ilan
full_name: Tsarfaty, Ilan
last_name: Tsarfaty
- first_name: Eilon
full_name: Shani, Eilon
last_name: Shani
citation:
ama: Hu Y, Omary M, Hu Y, et al. Cell kinetics of auxin transport and activity in
Arabidopsis root growth and skewing. Nature Communications. 2021;12. doi:10.1038/s41467-021-21802-3
apa: Hu, Y., Omary, M., Hu, Y., Doron, O., Hörmayer, L., Chen, Q., … Shani, E. (2021).
Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-21802-3
chicago: Hu, Yangjie, Moutasem Omary, Yun Hu, Ohad Doron, Lukas Hörmayer, Qingguo
Chen, Or Megides, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis
Root Growth and Skewing.” Nature Communications. Springer Nature, 2021.
https://doi.org/10.1038/s41467-021-21802-3.
ieee: Y. Hu et al., “Cell kinetics of auxin transport and activity in Arabidopsis
root growth and skewing,” Nature Communications, vol. 12. Springer Nature,
2021.
ista: Hu Y, Omary M, Hu Y, Doron O, Hörmayer L, Chen Q, Megides O, Chekli O, Ding
Z, Friml J, Zhao Y, Tsarfaty I, Shani E. 2021. Cell kinetics of auxin transport
and activity in Arabidopsis root growth and skewing. Nature Communications. 12,
1657.
mla: Hu, Yangjie, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis
Root Growth and Skewing.” Nature Communications, vol. 12, 1657, Springer
Nature, 2021, doi:10.1038/s41467-021-21802-3.
short: Y. Hu, M. Omary, Y. Hu, O. Doron, L. Hörmayer, Q. Chen, O. Megides, O. Chekli,
Z. Ding, J. Friml, Y. Zhao, I. Tsarfaty, E. Shani, Nature Communications 12 (2021).
date_created: 2021-03-21T23:01:19Z
date_published: 2021-03-12T00:00:00Z
date_updated: 2023-08-07T14:17:55Z
day: '12'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41467-021-21802-3
external_id:
isi:
- '000630419400048'
pmid:
- '33712581'
file:
- access_level: open_access
checksum: e1022f3aee349853ded2b2b3e092362d
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T11:18:58Z
date_updated: 2021-03-22T11:18:58Z
file_id: '9275'
file_name: 2021_NatureComm_Hu.pdf
file_size: 8602096
relation: main_file
success: 1
file_date_updated: 2021-03-22T11:18:58Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell kinetics of auxin transport and activity in Arabidopsis root growth and
skewing
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9255'
abstract:
- lang: eng
text: Our ability to trust that a random number is truly random is essential for
fields as diverse as cryptography and fundamental tests of quantum mechanics.
Existing solutions both come with drawbacks—device-independent quantum random
number generators (QRNGs) are highly impractical and standard semi-device-independent
QRNGs are limited to a specific physical implementation and level of trust. Here
we propose a framework for semi-device-independent randomness certification, using
a source of trusted vacuum in the form of a signal shutter. It employs a flexible
set of assumptions and levels of trust, allowing it to be applied in a wide range
of physical scenarios involving both quantum and classical entropy sources. We
experimentally demonstrate our protocol with a photonic setup and generate secure
random bits under three different assumptions with varying degrees of security
and resulting data rates.
acknowledgement: We would like to thank Robert Fickler for discussions about the experimental
realization and Marek Sýs for running the NIST randomness test on the data we acquired
in the experiment. We would like to thank Ugo Zanforlin, Gerald Buller, Daniel White,
and Cristian Bonato for their help with the experiment. M. Pivoluska, M. Plesch,
and M.M. acknowledge Czech-Austrian project MultiQUEST (I3053-N27 and GF17-33780L).
M. Pivoluska and M. Plesch additionally acknowledge the support of VEGA project
2/0136/19. M.F. acknowledges support from the Polish NCN grant Sonata UMO-2014/14/E/ST2/00020,
the European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation program ERC AdG CERQUTE (grant agreement No 834266), the State Research
Agency (AEI) TRANQI (PID2019-106888GB-I00/10.13039/501100011033), the Government
of Spain (FIS2020-TRANQI; Severo Ochoa CEX2019-000910-S), Fundació Cellex, Fundació
Mir-Puig, and Generalitat de Catalunya (CERCA, AGAUR). M.M., W.M., N.H.V., and C.F.
acknowledge support from the QuantERA ERA-NET Co-fund (FWF Project I3773-N36) and
the UK Engineering and Physical Sciences Research Council (EPSRC) (EP/P024114/1).
article_number: '50'
article_processing_charge: No
article_type: original
author:
- first_name: Matej
full_name: Pivoluska, Matej
last_name: Pivoluska
- first_name: Martin
full_name: Plesch, Martin
last_name: Plesch
- first_name: Máté
full_name: Farkas, Máté
last_name: Farkas
- first_name: Natalia
full_name: Ruzickova, Natalia
id: D2761128-D73D-11E9-A1BF-BA0DE6697425
last_name: Ruzickova
- first_name: Clara
full_name: Flegel, Clara
last_name: Flegel
- first_name: Natalia Herrera
full_name: Valencia, Natalia Herrera
last_name: Valencia
- first_name: Will
full_name: Mccutcheon, Will
last_name: Mccutcheon
- first_name: Mehul
full_name: Malik, Mehul
last_name: Malik
- first_name: Edgar A.
full_name: Aguilar, Edgar A.
last_name: Aguilar
citation:
ama: Pivoluska M, Plesch M, Farkas M, et al. Semi-device-independent random number
generation with flexible assumptions. npj Quantum Information. 2021;7.
doi:10.1038/s41534-021-00387-1
apa: Pivoluska, M., Plesch, M., Farkas, M., Ruzickova, N., Flegel, C., Valencia,
N. H., … Aguilar, E. A. (2021). Semi-device-independent random number generation
with flexible assumptions. Npj Quantum Information. Springer Nature. https://doi.org/10.1038/s41534-021-00387-1
chicago: Pivoluska, Matej, Martin Plesch, Máté Farkas, Natalia Ruzickova, Clara
Flegel, Natalia Herrera Valencia, Will Mccutcheon, Mehul Malik, and Edgar A. Aguilar.
“Semi-Device-Independent Random Number Generation with Flexible Assumptions.”
Npj Quantum Information. Springer Nature, 2021. https://doi.org/10.1038/s41534-021-00387-1.
ieee: M. Pivoluska et al., “Semi-device-independent random number generation
with flexible assumptions,” npj Quantum Information, vol. 7. Springer Nature,
2021.
ista: Pivoluska M, Plesch M, Farkas M, Ruzickova N, Flegel C, Valencia NH, Mccutcheon
W, Malik M, Aguilar EA. 2021. Semi-device-independent random number generation
with flexible assumptions. npj Quantum Information. 7, 50.
mla: Pivoluska, Matej, et al. “Semi-Device-Independent Random Number Generation
with Flexible Assumptions.” Npj Quantum Information, vol. 7, 50, Springer
Nature, 2021, doi:10.1038/s41534-021-00387-1.
short: M. Pivoluska, M. Plesch, M. Farkas, N. Ruzickova, C. Flegel, N.H. Valencia,
W. Mccutcheon, M. Malik, E.A. Aguilar, Npj Quantum Information 7 (2021).
date_created: 2021-03-21T23:01:19Z
date_published: 2021-03-15T00:00:00Z
date_updated: 2023-08-07T14:17:26Z
day: '15'
ddc:
- '530'
department:
- _id: FyKo
doi: 10.1038/s41534-021-00387-1
external_id:
isi:
- '000629173100001'
file:
- access_level: open_access
checksum: 26d3f2a2c8c8fa8c1002028326b45f64
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T11:09:34Z
date_updated: 2021-03-22T11:09:34Z
file_id: '9274'
file_name: 2021_NPJQuantumInformation_Pivoluska.pdf
file_size: 1360271
relation: main_file
success: 1
file_date_updated: 2021-03-22T11:09:34Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: npj Quantum Information
publication_identifier:
eissn:
- 2056-6387
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Semi-device-independent random number generation with flexible assumptions
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 7
year: '2021'
...
---
_id: '9260'
abstract:
- lang: eng
text: We study the density of rational points on a higher-dimensional orbifold (Pn−1,Δ)
when Δ is a Q-divisor involving hyperplanes. This allows us to address a question
of Tanimoto about whether the set of rational points on such an orbifold constitutes
a thin set. Our approach relies on the Hardy–Littlewood circle method to first
study an asymptotic version of Waring’s problem for mixed powers. In doing so
we make crucial use of the recent resolution of the main conjecture in Vinogradov’s
mean value theorem, due to Bourgain–Demeter–Guth and Wooley.
acknowledgement: While working on this paper the authors were both supported by EPSRC
grant EP/P026710/1, and the second author received additional support from the NWO
Veni Grant 016.Veni.192.047. Thanks are due to Marta Pieropan, Arne Smeets and Sho
Tanimoto for useful conversations related to this topic, and to the anonymous referee
for numerous helpful suggestions.
article_processing_charge: No
article_type: original
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Shuntaro
full_name: Yamagishi, Shuntaro
last_name: Yamagishi
citation:
ama: Browning TD, Yamagishi S. Arithmetic of higher-dimensional orbifolds and a
mixed Waring problem. Mathematische Zeitschrift. 2021;299:1071–1101. doi:10.1007/s00209-021-02695-w
apa: Browning, T. D., & Yamagishi, S. (2021). Arithmetic of higher-dimensional
orbifolds and a mixed Waring problem. Mathematische Zeitschrift. Springer
Nature. https://doi.org/10.1007/s00209-021-02695-w
chicago: Browning, Timothy D, and Shuntaro Yamagishi. “Arithmetic of Higher-Dimensional
Orbifolds and a Mixed Waring Problem.” Mathematische Zeitschrift. Springer
Nature, 2021. https://doi.org/10.1007/s00209-021-02695-w.
ieee: T. D. Browning and S. Yamagishi, “Arithmetic of higher-dimensional orbifolds
and a mixed Waring problem,” Mathematische Zeitschrift, vol. 299. Springer
Nature, pp. 1071–1101, 2021.
ista: Browning TD, Yamagishi S. 2021. Arithmetic of higher-dimensional orbifolds
and a mixed Waring problem. Mathematische Zeitschrift. 299, 1071–1101.
mla: Browning, Timothy D., and Shuntaro Yamagishi. “Arithmetic of Higher-Dimensional
Orbifolds and a Mixed Waring Problem.” Mathematische Zeitschrift, vol.
299, Springer Nature, 2021, pp. 1071–1101, doi:10.1007/s00209-021-02695-w.
short: T.D. Browning, S. Yamagishi, Mathematische Zeitschrift 299 (2021) 1071–1101.
date_created: 2021-03-21T23:01:21Z
date_published: 2021-03-05T00:00:00Z
date_updated: 2023-08-07T14:20:00Z
day: '05'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.1007/s00209-021-02695-w
external_id:
isi:
- '000625573800002'
file:
- access_level: open_access
checksum: 8ed9f49568806894744096dbbca0ad7b
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T12:41:26Z
date_updated: 2021-03-22T12:41:26Z
file_id: '9279'
file_name: 2021_MathZeitschrift_Browning.pdf
file_size: 492685
relation: main_file
success: 1
file_date_updated: 2021-03-22T12:41:26Z
has_accepted_license: '1'
intvolume: ' 299'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1071–1101
project:
- _id: 26A8D266-B435-11E9-9278-68D0E5697425
grant_number: EP-P026710-2
name: Between rational and integral points
publication: Mathematische Zeitschrift
publication_identifier:
eissn:
- 1432-1823
issn:
- 0025-5874
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arithmetic of higher-dimensional orbifolds and a mixed Waring problem
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 299
year: '2021'
...
---
_id: '9258'
acknowledgement: 'We thank S. van der Walt and K. Marchuk for discussion during development.
This project was funded by Packard Fellowship and Chan Zuckerberg Biohub Investigator
Awards to L.W.; STROBE: A NSF Science and Technology Center; an NSF Graduate Research
Fellowship awarded to H.P.; a Berkeley Institute for Data Science/UCSF Bakar Computational
Health Sciences Institute Fellowship awarded to H.P. with support from the Koret
Foundation, the Gordon and Betty Moore Foundation, and the Alfred P. Sloan Foundation
to the University of California, Berkeley. K.W.E., B.L. and M.T. were funded by
the Chan Zuckerberg Initiative and NIH grant P41GM135019.'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Henry
full_name: Pinkard, Henry
last_name: Pinkard
- first_name: Nico
full_name: Stuurman, Nico
last_name: Stuurman
- first_name: Ivan E.
full_name: Ivanov, Ivan E.
last_name: Ivanov
- first_name: Nicholas M.
full_name: Anthony, Nicholas M.
last_name: Anthony
- first_name: Wei
full_name: Ouyang, Wei
last_name: Ouyang
- first_name: Bin
full_name: Li, Bin
last_name: Li
- first_name: Bin
full_name: Yang, Bin
last_name: Yang
- first_name: Mark A.
full_name: Tsuchida, Mark A.
last_name: Tsuchida
- first_name: Bryant
full_name: Chhun, Bryant
last_name: Chhun
- first_name: Grace
full_name: Zhang, Grace
last_name: Zhang
- first_name: Ryan
full_name: Mei, Ryan
last_name: Mei
- first_name: Michael
full_name: Anderson, Michael
last_name: Anderson
- first_name: Douglas P.
full_name: Shepherd, Douglas P.
last_name: Shepherd
- first_name: Ian
full_name: Hunt-Isaak, Ian
last_name: Hunt-Isaak
- first_name: Raymond L.
full_name: Dunn, Raymond L.
last_name: Dunn
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
- first_name: Saul
full_name: Kato, Saul
last_name: Kato
- first_name: Loïc A.
full_name: Royer, Loïc A.
last_name: Royer
- first_name: Jay R.
full_name: Thiagarajah, Jay R.
last_name: Thiagarajah
- first_name: Kevin W.
full_name: Eliceiri, Kevin W.
last_name: Eliceiri
- first_name: Emma
full_name: Lundberg, Emma
last_name: Lundberg
- first_name: Shalin B.
full_name: Mehta, Shalin B.
last_name: Mehta
- first_name: Laura
full_name: Waller, Laura
last_name: Waller
citation:
ama: 'Pinkard H, Stuurman N, Ivanov IE, et al. Pycro-Manager: Open-source software
for customized and reproducible microscope control. Nature Methods. 2021;18(3):226-228.
doi:10.1038/s41592-021-01087-6'
apa: 'Pinkard, H., Stuurman, N., Ivanov, I. E., Anthony, N. M., Ouyang, W., Li,
B., … Waller, L. (2021). Pycro-Manager: Open-source software for customized and
reproducible microscope control. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-021-01087-6'
chicago: 'Pinkard, Henry, Nico Stuurman, Ivan E. Ivanov, Nicholas M. Anthony, Wei
Ouyang, Bin Li, Bin Yang, et al. “Pycro-Manager: Open-Source Software for Customized
and Reproducible Microscope Control.” Nature Methods. Springer Nature,
2021. https://doi.org/10.1038/s41592-021-01087-6.'
ieee: 'H. Pinkard et al., “Pycro-Manager: Open-source software for customized
and reproducible microscope control,” Nature Methods, vol. 18, no. 3. Springer
Nature, pp. 226–228, 2021.'
ista: 'Pinkard H, Stuurman N, Ivanov IE, Anthony NM, Ouyang W, Li B, Yang B, Tsuchida
MA, Chhun B, Zhang G, Mei R, Anderson M, Shepherd DP, Hunt-Isaak I, Dunn RL, Jahr
W, Kato S, Royer LA, Thiagarajah JR, Eliceiri KW, Lundberg E, Mehta SB, Waller
L. 2021. Pycro-Manager: Open-source software for customized and reproducible microscope
control. Nature Methods. 18(3), 226–228.'
mla: 'Pinkard, Henry, et al. “Pycro-Manager: Open-Source Software for Customized
and Reproducible Microscope Control.” Nature Methods, vol. 18, no. 3, Springer
Nature, 2021, pp. 226–28, doi:10.1038/s41592-021-01087-6.'
short: H. Pinkard, N. Stuurman, I.E. Ivanov, N.M. Anthony, W. Ouyang, B. Li, B.
Yang, M.A. Tsuchida, B. Chhun, G. Zhang, R. Mei, M. Anderson, D.P. Shepherd, I.
Hunt-Isaak, R.L. Dunn, W. Jahr, S. Kato, L.A. Royer, J.R. Thiagarajah, K.W. Eliceiri,
E. Lundberg, S.B. Mehta, L. Waller, Nature Methods 18 (2021) 226–228.
date_created: 2021-03-21T23:01:20Z
date_published: 2021-03-01T00:00:00Z
date_updated: 2023-08-07T14:19:08Z
day: '01'
department:
- _id: JoDa
doi: 10.1038/s41592-021-01087-6
external_id:
isi:
- '000625600600007'
pmid:
- '33674797'
intvolume: ' 18'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41592-021-01087-6
month: '03'
oa: 1
oa_version: Published Version
page: 226-228
pmid: 1
publication: Nature Methods
publication_identifier:
eissn:
- 1548-7105
issn:
- 1548-7091
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Pycro-Manager: Open-source software for customized and reproducible microscope
control'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2021'
...
---
_id: '9306'
abstract:
- lang: eng
text: Assemblies of actin and its regulators underlie the dynamic morphology of
all eukaryotic cells. To understand how actin regulatory proteins work together
to generate actin-rich structures such as filopodia, we analyzed the localization
of diverse actin regulators within filopodia in Drosophila embryos and in a complementary
in vitro system of filopodia-like structures (FLSs). We found that the composition
of the regulatory protein complex where actin is incorporated (the filopodial
tip complex) is remarkably heterogeneous both in vivo and in vitro. Our data reveal
that different pairs of proteins correlate with each other and with actin bundle
length, suggesting the presence of functional subcomplexes. This is consistent
with a theoretical framework where three or more redundant subcomplexes join the
tip complex stochastically, with any two being sufficient to drive filopodia formation.
We provide an explanation for the observed heterogeneity and suggest that a mechanism
based on multiple components allows stereotypical filopodial dynamics to arise
from diverse upstream signaling pathways.
acknowledgement: "This work was supported by European Research Council grant 281971,
Wellcome Trust Research Career Development Fellowship WT095829AIA and Wellcome Trust
Senior Research\r\nFellowship 219482/Z/19/Z to J.L. Gallop, a Wellcome Trust Senior
Investigator Award 098357 to B.D. Simons, and an Austrian Science Fund grant (P31639)
to E. Hannezo. We acknowledge\r\ncore funding by the Wellcome Trust (092096) and
Cancer Research UK (C6946/A14492). U. Dobramysl was supported by a Wellcome Trust
Junior Interdisciplinary Fellowship grant\r\n(105602/Z/14/Z) and a Herchel Smith
Postdoctoral Fellowship. H. Shimo was supported by a Funai Foundation Overseas scholarship."
article_number: e202003052
article_processing_charge: No
article_type: original
author:
- first_name: Ulrich
full_name: Dobramysl, Ulrich
last_name: Dobramysl
- first_name: Iris Katharina
full_name: Jarsch, Iris Katharina
last_name: Jarsch
- first_name: Yoshiko
full_name: Inoue, Yoshiko
last_name: Inoue
- first_name: Hanae
full_name: Shimo, Hanae
last_name: Shimo
- first_name: Benjamin
full_name: Richier, Benjamin
last_name: Richier
- first_name: Jonathan R.
full_name: Gadsby, Jonathan R.
last_name: Gadsby
- first_name: Julia
full_name: Mason, Julia
last_name: Mason
- first_name: Alicja
full_name: Szałapak, Alicja
last_name: Szałapak
- first_name: Pantelis Savvas
full_name: Ioannou, Pantelis Savvas
last_name: Ioannou
- first_name: Guilherme Pereira
full_name: Correia, Guilherme Pereira
last_name: Correia
- first_name: Astrid
full_name: Walrant, Astrid
last_name: Walrant
- first_name: Richard
full_name: Butler, Richard
last_name: Butler
- 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: Benjamin D.
full_name: Simons, Benjamin D.
last_name: Simons
- first_name: Jennifer L.
full_name: Gallop, Jennifer L.
last_name: Gallop
citation:
ama: Dobramysl U, Jarsch IK, Inoue Y, et al. Stochastic combinations of actin regulatory
proteins are sufficient to drive filopodia formation. Journal of Cell Biology.
2021;220(4). doi:10.1083/jcb.202003052
apa: Dobramysl, U., Jarsch, I. K., Inoue, Y., Shimo, H., Richier, B., Gadsby, J.
R., … Gallop, J. L. (2021). Stochastic combinations of actin regulatory proteins
are sufficient to drive filopodia formation. Journal of Cell Biology. Rockefeller
University Press. https://doi.org/10.1083/jcb.202003052
chicago: Dobramysl, Ulrich, Iris Katharina Jarsch, Yoshiko Inoue, Hanae Shimo, Benjamin
Richier, Jonathan R. Gadsby, Julia Mason, et al. “Stochastic Combinations of Actin
Regulatory Proteins Are Sufficient to Drive Filopodia Formation.” Journal of
Cell Biology. Rockefeller University Press, 2021. https://doi.org/10.1083/jcb.202003052.
ieee: U. Dobramysl et al., “Stochastic combinations of actin regulatory proteins
are sufficient to drive filopodia formation,” Journal of Cell Biology,
vol. 220, no. 4. Rockefeller University Press, 2021.
ista: Dobramysl U, Jarsch IK, Inoue Y, Shimo H, Richier B, Gadsby JR, Mason J, Szałapak
A, Ioannou PS, Correia GP, Walrant A, Butler R, Hannezo EB, Simons BD, Gallop
JL. 2021. Stochastic combinations of actin regulatory proteins are sufficient
to drive filopodia formation. Journal of Cell Biology. 220(4), e202003052.
mla: Dobramysl, Ulrich, et al. “Stochastic Combinations of Actin Regulatory Proteins
Are Sufficient to Drive Filopodia Formation.” Journal of Cell Biology,
vol. 220, no. 4, e202003052, Rockefeller University Press, 2021, doi:10.1083/jcb.202003052.
short: U. Dobramysl, I.K. Jarsch, Y. Inoue, H. Shimo, B. Richier, J.R. Gadsby, J.
Mason, A. Szałapak, P.S. Ioannou, G.P. Correia, A. Walrant, R. Butler, E.B. Hannezo,
B.D. Simons, J.L. Gallop, Journal of Cell Biology 220 (2021).
date_created: 2021-04-04T22:01:21Z
date_published: 2021-03-19T00:00:00Z
date_updated: 2023-08-07T14:32:28Z
day: '19'
ddc:
- '576'
department:
- _id: EdHa
doi: 10.1083/jcb.202003052
external_id:
isi:
- '000663160600002'
pmid:
- '33740033'
file:
- access_level: open_access
checksum: 4739ffd90f2c7e05ac5b00f057c58aa2
content_type: application/pdf
creator: dernst
date_created: 2021-04-06T10:39:08Z
date_updated: 2021-04-06T10:39:08Z
file_id: '9310'
file_name: 2021_JCB_Dobramysl.pdf
file_size: 9019720
relation: main_file
success: 1
file_date_updated: 2021-04-06T10:39:08Z
has_accepted_license: '1'
intvolume: ' 220'
isi: 1
issue: '4'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 268294B6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31639
name: Active mechano-chemical description of the cell cytoskeleton
publication: Journal of Cell Biology
publication_identifier:
eissn:
- '15408140'
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stochastic combinations of actin regulatory proteins are sufficient to drive
filopodia formation
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 220
year: '2021'
...
---
_id: '9307'
abstract:
- lang: eng
text: We establish finite time extinction with probability one for weak solutions
of the Cauchy–Dirichlet problem for the 1D stochastic porous medium equation with
Stratonovich transport noise and compactly supported smooth initial datum. Heuristically,
this is expected to hold because Brownian motion has average spread rate O(t12)
whereas the support of solutions to the deterministic PME grows only with rate
O(t1m+1). The rigorous proof relies on a contraction principle up to time-dependent
shift for Wong–Zakai type approximations, the transformation to a deterministic
PME with two copies of a Brownian path as the lateral boundary, and techniques
from the theory of viscosity solutions.
acknowledgement: This project has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
No. 665385 . I am very grateful to M. Gerencsér and J. Maas for proposing this problem
as well as helpful discussions. Special thanks go to F. Cornalba for suggesting
the additional κ-truncation in Proposition 5. I am also indebted to an anonymous
referee for pointing out a gap in a previous version of the proof of Lemma 9 (concerning
the treatment of the noise term). The issue is resolved in this version.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Sebastian
full_name: Hensel, Sebastian
id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87
last_name: Hensel
orcid: 0000-0001-7252-8072
citation:
ama: 'Hensel S. Finite time extinction for the 1D stochastic porous medium equation
with transport noise. Stochastics and Partial Differential Equations: Analysis
and Computations. 2021;9:892–939. doi:10.1007/s40072-021-00188-9'
apa: 'Hensel, S. (2021). Finite time extinction for the 1D stochastic porous medium
equation with transport noise. Stochastics and Partial Differential Equations:
Analysis and Computations. Springer Nature. https://doi.org/10.1007/s40072-021-00188-9'
chicago: 'Hensel, Sebastian. “Finite Time Extinction for the 1D Stochastic Porous
Medium Equation with Transport Noise.” Stochastics and Partial Differential
Equations: Analysis and Computations. Springer Nature, 2021. https://doi.org/10.1007/s40072-021-00188-9.'
ieee: 'S. Hensel, “Finite time extinction for the 1D stochastic porous medium equation
with transport noise,” Stochastics and Partial Differential Equations: Analysis
and Computations, vol. 9. Springer Nature, pp. 892–939, 2021.'
ista: 'Hensel S. 2021. Finite time extinction for the 1D stochastic porous medium
equation with transport noise. Stochastics and Partial Differential Equations:
Analysis and Computations. 9, 892–939.'
mla: 'Hensel, Sebastian. “Finite Time Extinction for the 1D Stochastic Porous Medium
Equation with Transport Noise.” Stochastics and Partial Differential Equations:
Analysis and Computations, vol. 9, Springer Nature, 2021, pp. 892–939, doi:10.1007/s40072-021-00188-9.'
short: 'S. Hensel, Stochastics and Partial Differential Equations: Analysis and
Computations 9 (2021) 892–939.'
date_created: 2021-04-04T22:01:21Z
date_published: 2021-03-21T00:00:00Z
date_updated: 2023-08-07T14:31:59Z
day: '21'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s40072-021-00188-9
ec_funded: 1
external_id:
isi:
- '000631001700001'
file:
- access_level: open_access
checksum: 6529b609c9209861720ffa4685111bc6
content_type: application/pdf
creator: dernst
date_created: 2021-04-06T09:31:28Z
date_updated: 2021-04-06T09:31:28Z
file_id: '9309'
file_name: 2021_StochPartDiffEquation_Hensel.pdf
file_size: 727005
relation: main_file
success: 1
file_date_updated: 2021-04-06T09:31:28Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 892–939
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: 'Stochastics and Partial Differential Equations: Analysis and Computations'
publication_identifier:
eissn:
- 2194-041X
issn:
- 2194-0401
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Finite time extinction for the 1D stochastic porous medium equation with transport
noise
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2021'
...
---
_id: '9297'
abstract:
- lang: eng
text: 'We report the results of an experimental investigation into the decay of
turbulence in plane Couette–Poiseuille flow using ‘quench’ experiments where the
flow laminarises after a sudden reduction in Reynolds number Re. Specifically,
we study the velocity field in the streamwise–spanwise plane. We show that the
spanwise velocity containing rolls decays faster than the streamwise velocity,
which displays elongated regions of higher or lower velocity called streaks. At
final Reynolds numbers above 425, the decay of streaks displays two stages: first
a slow decay when rolls are present and secondly a more rapid decay of streaks
alone. The difference in behaviour results from the regeneration of streaks by
rolls, called the lift-up effect. We define the turbulent fraction as the portion
of the flow containing turbulence and this is estimated by thresholding the spanwise
velocity component. It decreases linearly with time in the whole range of final
Re. The corresponding decay slope increases linearly with final Re. The extrapolated
value at which this decay slope vanishes is Reaz≈656±10, close to Reg≈670 at which
turbulence is self-sustained. The decay of the energy computed from the spanwise
velocity component is found to be exponential. The corresponding decay rate increases
linearly with Re, with an extrapolated vanishing value at ReAz≈688±10. This value
is also close to the value at which the turbulence is self-sustained, showing
that valuable information on the transition can be obtained over a wide range
of Re.'
acknowledgement: "We gratefully acknowledge Joran Rolland, Yohann Duguet, Romain Monchaux,
S´ebastien Gom´e, Laurette Tuckerman, Dwight Barkley, Olivier Dauchot and Sabine
Bottin for fruitful discussions. We thank Xavier Benoit-Gonin, Amaury Fourgeaud,
Thierry Darnige, Olivier Brouard and Justine Laurent for technical help. This work
has benefited from the ANR TransFlow, and by starting grants obtained by B.S. from
CNRS (INSIS) and ESPCI. T.M. was\r\nsupported by a Joliot visiting professorship
grant from ESPCI."
article_number: A65
article_processing_charge: No
article_type: original
author:
- first_name: T.
full_name: Liu, T.
last_name: Liu
- first_name: B.
full_name: Semin, B.
last_name: Semin
- first_name: Lukasz
full_name: Klotz, Lukasz
id: 2C9AF1C2-F248-11E8-B48F-1D18A9856A87
last_name: Klotz
orcid: 0000-0003-1740-7635
- first_name: R.
full_name: Godoy-Diana, R.
last_name: Godoy-Diana
- first_name: J. E.
full_name: Wesfreid, J. E.
last_name: Wesfreid
- first_name: T.
full_name: Mullin, T.
last_name: Mullin
citation:
ama: Liu T, Semin B, Klotz L, Godoy-Diana R, Wesfreid JE, Mullin T. Decay of streaks
and rolls in plane Couette-Poiseuille flow. Journal of Fluid Mechanics.
2021;915. doi:10.1017/jfm.2021.89
apa: Liu, T., Semin, B., Klotz, L., Godoy-Diana, R., Wesfreid, J. E., & Mullin,
T. (2021). Decay of streaks and rolls in plane Couette-Poiseuille flow. Journal
of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2021.89
chicago: Liu, T., B. Semin, Lukasz Klotz, R. Godoy-Diana, J. E. Wesfreid, and T.
Mullin. “Decay of Streaks and Rolls in Plane Couette-Poiseuille Flow.” Journal
of Fluid Mechanics. Cambridge University Press, 2021. https://doi.org/10.1017/jfm.2021.89.
ieee: T. Liu, B. Semin, L. Klotz, R. Godoy-Diana, J. E. Wesfreid, and T. Mullin,
“Decay of streaks and rolls in plane Couette-Poiseuille flow,” Journal of Fluid
Mechanics, vol. 915. Cambridge University Press, 2021.
ista: Liu T, Semin B, Klotz L, Godoy-Diana R, Wesfreid JE, Mullin T. 2021. Decay
of streaks and rolls in plane Couette-Poiseuille flow. Journal of Fluid Mechanics.
915, A65.
mla: Liu, T., et al. “Decay of Streaks and Rolls in Plane Couette-Poiseuille Flow.”
Journal of Fluid Mechanics, vol. 915, A65, Cambridge University Press,
2021, doi:10.1017/jfm.2021.89.
short: T. Liu, B. Semin, L. Klotz, R. Godoy-Diana, J.E. Wesfreid, T. Mullin, Journal
of Fluid Mechanics 915 (2021).
date_created: 2021-03-28T22:01:42Z
date_published: 2021-03-17T00:00:00Z
date_updated: 2023-08-07T14:30:11Z
day: '17'
department:
- _id: BjHo
doi: 10.1017/jfm.2021.89
external_id:
arxiv:
- '2008.08851'
isi:
- '000629677500001'
intvolume: ' 915'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2008.08851
month: '03'
oa: 1
oa_version: Preprint
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- 1469-7645
issn:
- 0022-1120
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Decay of streaks and rolls in plane Couette-Poiseuille flow
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 915
year: '2021'
...
---
_id: '9295'
abstract:
- lang: eng
text: "Hill's Conjecture states that the crossing number cr(\U0001D43E\U0001D45B)
\ of the complete graph \U0001D43E\U0001D45B in the plane (equivalently, the
sphere) is 14⌊\U0001D45B2⌋⌊\U0001D45B−12⌋⌊\U0001D45B−22⌋⌊\U0001D45B−32⌋=\U0001D45B4/64+\U0001D442(\U0001D45B3)
. Moon proved that the expected number of crossings in a spherical drawing in
which the points are randomly distributed and joined by geodesics is precisely
\ \U0001D45B4/64+\U0001D442(\U0001D45B3) , thus matching asymptotically the conjectured
value of cr(\U0001D43E\U0001D45B) . Let cr\U0001D443(\U0001D43A) denote the
crossing number of a graph \U0001D43A in the projective plane. Recently, Elkies
proved that the expected number of crossings in a naturally defined random projective
plane drawing of \U0001D43E\U0001D45B is (\U0001D45B4/8\U0001D70B2)+\U0001D442(\U0001D45B3)
. In analogy with the relation of Moon's result to Hill's conjecture, Elkies asked
if lim\U0001D45B→∞ cr\U0001D443(\U0001D43E\U0001D45B)/\U0001D45B4=1/8\U0001D70B2
. We construct drawings of \U0001D43E\U0001D45B in the projective plane that
disprove this."
acknowledgement: "We thank two reviewers for their corrections and suggestions on
the original version of this\r\npaper. This project has received funding from NSERC
Grant 50503-10940-500 and from the European Union’s Horizon 2020 research and innovation
programme under the Marie SkłodowskaCurie grant agreement No 754411, IST, Klosterneuburg,
Austria."
article_processing_charge: No
article_type: original
author:
- first_name: Alan M
full_name: Arroyo Guevara, Alan M
id: 3207FDC6-F248-11E8-B48F-1D18A9856A87
last_name: Arroyo Guevara
orcid: 0000-0003-2401-8670
- first_name: Dan
full_name: Mcquillan, Dan
last_name: Mcquillan
- first_name: R. Bruce
full_name: Richter, R. Bruce
last_name: Richter
- first_name: Gelasio
full_name: Salazar, Gelasio
last_name: Salazar
- first_name: Matthew
full_name: Sullivan, Matthew
last_name: Sullivan
citation:
ama: Arroyo Guevara AM, Mcquillan D, Richter RB, Salazar G, Sullivan M. Drawings
of complete graphs in the projective plane. Journal of Graph Theory. 2021;97(3):426-440.
doi:10.1002/jgt.22665
apa: Arroyo Guevara, A. M., Mcquillan, D., Richter, R. B., Salazar, G., & Sullivan,
M. (2021). Drawings of complete graphs in the projective plane. Journal of
Graph Theory. Wiley. https://doi.org/10.1002/jgt.22665
chicago: Arroyo Guevara, Alan M, Dan Mcquillan, R. Bruce Richter, Gelasio Salazar,
and Matthew Sullivan. “Drawings of Complete Graphs in the Projective Plane.” Journal
of Graph Theory. Wiley, 2021. https://doi.org/10.1002/jgt.22665.
ieee: A. M. Arroyo Guevara, D. Mcquillan, R. B. Richter, G. Salazar, and M. Sullivan,
“Drawings of complete graphs in the projective plane,” Journal of Graph Theory,
vol. 97, no. 3. Wiley, pp. 426–440, 2021.
ista: Arroyo Guevara AM, Mcquillan D, Richter RB, Salazar G, Sullivan M. 2021. Drawings
of complete graphs in the projective plane. Journal of Graph Theory. 97(3), 426–440.
mla: Arroyo Guevara, Alan M., et al. “Drawings of Complete Graphs in the Projective
Plane.” Journal of Graph Theory, vol. 97, no. 3, Wiley, 2021, pp. 426–40,
doi:10.1002/jgt.22665.
short: A.M. Arroyo Guevara, D. Mcquillan, R.B. Richter, G. Salazar, M. Sullivan,
Journal of Graph Theory 97 (2021) 426–440.
date_created: 2021-03-28T22:01:41Z
date_published: 2021-03-23T00:00:00Z
date_updated: 2023-08-07T14:26:15Z
day: '23'
department:
- _id: UlWa
doi: 10.1002/jgt.22665
ec_funded: 1
external_id:
arxiv:
- '2002.02287'
isi:
- '000631693200001'
intvolume: ' 97'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2002.02287
month: '03'
oa: 1
oa_version: Preprint
page: 426-440
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Graph Theory
publication_identifier:
eissn:
- 1097-0118
issn:
- 0364-9024
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Drawings of complete graphs in the projective plane
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 97
year: '2021'
...
---
_id: '9294'
abstract:
- lang: eng
text: In this issue of Developmental Cell, Doyle and colleagues identify periodic
anterior contraction as a characteristic feature of fibroblasts and mesenchymal
cancer cells embedded in 3D collagen gels. This contractile mechanism generates
a matrix prestrain required for crawling in fibrous 3D environments.
article_processing_charge: No
article_type: original
author:
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Gärtner FR, Sixt MK. Engaging the front wheels to drive through fibrous terrain.
Developmental Cell. 2021;56(6):723-725. doi:10.1016/j.devcel.2021.03.002
apa: Gärtner, F. R., & Sixt, M. K. (2021). Engaging the front wheels to drive
through fibrous terrain. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2021.03.002
chicago: Gärtner, Florian R, and Michael K Sixt. “Engaging the Front Wheels to Drive
through Fibrous Terrain.” Developmental Cell. Elsevier, 2021. https://doi.org/10.1016/j.devcel.2021.03.002.
ieee: F. R. Gärtner and M. K. Sixt, “Engaging the front wheels to drive through
fibrous terrain,” Developmental Cell, vol. 56, no. 6. Elsevier, pp. 723–725,
2021.
ista: Gärtner FR, Sixt MK. 2021. Engaging the front wheels to drive through fibrous
terrain. Developmental Cell. 56(6), 723–725.
mla: Gärtner, Florian R., and Michael K. Sixt. “Engaging the Front Wheels to Drive
through Fibrous Terrain.” Developmental Cell, vol. 56, no. 6, Elsevier,
2021, pp. 723–25, doi:10.1016/j.devcel.2021.03.002.
short: F.R. Gärtner, M.K. Sixt, Developmental Cell 56 (2021) 723–725.
date_created: 2021-03-28T22:01:41Z
date_published: 2021-03-22T00:00:00Z
date_updated: 2023-08-07T14:26:47Z
day: '22'
department:
- _id: MiSi
doi: 10.1016/j.devcel.2021.03.002
external_id:
isi:
- '000631681200004'
pmid:
- '33756118'
intvolume: ' 56'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2021.03.002
month: '03'
oa: 1
oa_version: Published Version
page: 723-725
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- '18781551'
issn:
- '15345807'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Engaging the front wheels to drive through fibrous terrain
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 56
year: '2021'
...
---
_id: '9329'
abstract:
- lang: eng
text: "Background: To understand information coding in single neurons, it is necessary
to analyze subthreshold synaptic events, action potentials (APs), and their interrelation
in different behavioral states. However, detecting excitatory postsynaptic potentials
(EPSPs) or currents (EPSCs) in behaving animals remains challenging, because of
unfavorable signal-to-noise ratio, high frequency, fluctuating amplitude, and
variable time course of synaptic events.\r\nNew method: We developed a method
for synaptic event detection, termed MOD (Machine-learning Optimal-filtering Detection-procedure),
which combines concepts of supervised machine learning and optimal Wiener filtering.
Experts were asked to manually score short epochs of data. The algorithm was trained
to obtain the optimal filter coefficients of a Wiener filter and the optimal detection
threshold. Scored and unscored data were then processed with the optimal filter,
and events were detected as peaks above threshold.\r\nResults: We challenged MOD
with EPSP traces in vivo in mice during spatial navigation and EPSC traces in
vitro in slices under conditions of enhanced transmitter release. The area under
the curve (AUC) of the receiver operating characteristics (ROC) curve was, on
average, 0.894 for in vivo and 0.969 for in vitro data sets, indicating high detection
accuracy and efficiency.\r\nComparison with existing methods: When benchmarked
using a (1 − AUC)−1 metric, MOD outperformed previous methods (template-fit, deconvolution,
and Bayesian methods) by an average factor of 3.13 for in vivo data sets, but
showed comparable (template-fit, deconvolution) or higher (Bayesian) computational
efficacy.\r\nConclusions: MOD may become an important new tool for large-scale,
real-time analysis of synaptic activity."
acknowledged_ssus:
- _id: SSU
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement number 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen
Forschung (Z 312-B27, Wittgenstein award to P.J.). We thank Drs. Jozsef Csicsvari,
Christoph Lampert, and Federico Stella for critically reading previous manuscript
versions. We are also grateful to Drs. Josh Merel and Ben Shababo for their help
with applying the Bayesian detection method to our data. We also thank Florian Marr
for technical assistance, Eleftheria Kralli-Beller for manuscript editing, and the
Scientific Service Units of IST Austria for efficient support.
article_number: '109125'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: 'Zhang X, Schlögl A, Vandael DH, Jonas PM. MOD: A novel machine-learning optimal-filtering
method for accurate and efficient detection of subthreshold synaptic events in
vivo. Journal of Neuroscience Methods. 2021;357(6). doi:10.1016/j.jneumeth.2021.109125'
apa: 'Zhang, X., Schlögl, A., Vandael, D. H., & Jonas, P. M. (2021). MOD: A
novel machine-learning optimal-filtering method for accurate and efficient detection
of subthreshold synaptic events in vivo. Journal of Neuroscience Methods.
Elsevier. https://doi.org/10.1016/j.jneumeth.2021.109125'
chicago: 'Zhang, Xiaomin, Alois Schlögl, David H Vandael, and Peter M Jonas. “MOD:
A Novel Machine-Learning Optimal-Filtering Method for Accurate and Efficient Detection
of Subthreshold Synaptic Events in Vivo.” Journal of Neuroscience Methods.
Elsevier, 2021. https://doi.org/10.1016/j.jneumeth.2021.109125.'
ieee: 'X. Zhang, A. Schlögl, D. H. Vandael, and P. M. Jonas, “MOD: A novel machine-learning
optimal-filtering method for accurate and efficient detection of subthreshold
synaptic events in vivo,” Journal of Neuroscience Methods, vol. 357, no.
6. Elsevier, 2021.'
ista: 'Zhang X, Schlögl A, Vandael DH, Jonas PM. 2021. MOD: A novel machine-learning
optimal-filtering method for accurate and efficient detection of subthreshold
synaptic events in vivo. Journal of Neuroscience Methods. 357(6), 109125.'
mla: 'Zhang, Xiaomin, et al. “MOD: A Novel Machine-Learning Optimal-Filtering Method
for Accurate and Efficient Detection of Subthreshold Synaptic Events in Vivo.”
Journal of Neuroscience Methods, vol. 357, no. 6, 109125, Elsevier, 2021,
doi:10.1016/j.jneumeth.2021.109125.'
short: X. Zhang, A. Schlögl, D.H. Vandael, P.M. Jonas, Journal of Neuroscience Methods
357 (2021).
date_created: 2021-04-18T22:01:39Z
date_published: 2021-03-09T00:00:00Z
date_updated: 2023-08-07T14:36:14Z
day: '09'
ddc:
- '570'
department:
- _id: PeJo
- _id: ScienComp
doi: 10.1016/j.jneumeth.2021.109125
ec_funded: 1
external_id:
isi:
- '000661088500005'
file:
- access_level: open_access
checksum: 2a5800d91b96d08b525e17319dcd5e44
content_type: application/pdf
creator: dernst
date_created: 2021-04-19T08:30:22Z
date_updated: 2021-04-19T08:30:22Z
file_id: '9339'
file_name: 2021_JourNeuroscienceMeth_Zhang.pdf
file_size: 6924738
relation: main_file
success: 1
file_date_updated: 2021-04-19T08:30:22Z
has_accepted_license: '1'
intvolume: ' 357'
isi: 1
issue: '6'
language:
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month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
publication: Journal of Neuroscience Methods
publication_identifier:
eissn:
- 1872-678X
issn:
- 0165-0270
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'MOD: A novel machine-learning optimal-filtering method for accurate and efficient
detection of subthreshold synaptic events in vivo'
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 357
year: '2021'
...
---
_id: '9316'
abstract:
- lang: eng
text: Embryo morphogenesis is impacted by dynamic changes in tissue material properties,
which have been proposed to occur via processes akin to phase transitions (PTs).
Here, we show that rigidity percolation provides a simple and robust theoretical
framework to predict material/structural PTs of embryonic tissues from local cell
connectivity. By using percolation theory, combined with directly monitoring dynamic
changes in tissue rheology and cell contact mechanics, we demonstrate that the
zebrafish blastoderm undergoes a genuine rigidity PT, brought about by a small
reduction in adhesion-dependent cell connectivity below a critical value. We quantitatively
predict and experimentally verify hallmarks of PTs, including power-law exponents
and associated discontinuities of macroscopic observables. Finally, we show that
this uniform PT depends on blastoderm cells undergoing meta-synchronous divisions
causing random and, consequently, uniform changes in cell connectivity. Collectively,
our theoretical and experimental findings reveal the structural basis of material
PTs in an organismal context.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: We thank Carl Goodrich and the members of the Heisenberg and Hannezo
groups, in particular Reka Korei, for help, technical advice, and discussions; and
the Bioimaging and zebrafish facilities of the IST Austria for continuous support.
This work was supported by the Elise Richter Program of Austrian Science Fund (FWF)
to N.I.P. ( V 736-B26 ) and the European Union (European Research Council Advanced
Grant 742573 to C.-P.H. and European Research Council Starting Grant 851288 to E.H.).
article_processing_charge: No
article_type: original
author:
- first_name: Nicoletta
full_name: Petridou, Nicoletta
id: 2A003F6C-F248-11E8-B48F-1D18A9856A87
last_name: Petridou
orcid: 0000-0002-8451-1195
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. Rigidity percolation
uncovers a structural basis for embryonic tissue phase transitions. Cell.
2021;184(7):1914-1928.e19. doi:10.1016/j.cell.2021.02.017
apa: Petridou, N., Corominas-Murtra, B., Heisenberg, C.-P. J., & Hannezo, E.
B. (2021). Rigidity percolation uncovers a structural basis for embryonic tissue
phase transitions. Cell. Elsevier. https://doi.org/10.1016/j.cell.2021.02.017
chicago: Petridou, Nicoletta, Bernat Corominas-Murtra, Carl-Philipp J Heisenberg,
and Edouard B Hannezo. “Rigidity Percolation Uncovers a Structural Basis for Embryonic
Tissue Phase Transitions.” Cell. Elsevier, 2021. https://doi.org/10.1016/j.cell.2021.02.017.
ieee: N. Petridou, B. Corominas-Murtra, C.-P. J. Heisenberg, and E. B. Hannezo,
“Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions,”
Cell, vol. 184, no. 7. Elsevier, p. 1914–1928.e19, 2021.
ista: Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. 2021. Rigidity
percolation uncovers a structural basis for embryonic tissue phase transitions.
Cell. 184(7), 1914–1928.e19.
mla: Petridou, Nicoletta, et al. “Rigidity Percolation Uncovers a Structural Basis
for Embryonic Tissue Phase Transitions.” Cell, vol. 184, no. 7, Elsevier,
2021, p. 1914–1928.e19, doi:10.1016/j.cell.2021.02.017.
short: N. Petridou, B. Corominas-Murtra, C.-P.J. Heisenberg, E.B. Hannezo, Cell
184 (2021) 1914–1928.e19.
date_created: 2021-04-11T22:01:14Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2023-08-07T14:33:59Z
day: '01'
ddc:
- '570'
department:
- _id: CaHe
- _id: EdHa
doi: 10.1016/j.cell.2021.02.017
ec_funded: 1
external_id:
isi:
- '000636734000022'
pmid:
- '33730596'
file:
- access_level: open_access
checksum: 1e5295fbd9c2a459173ec45a0e8a7c2e
content_type: application/pdf
creator: cziletti
date_created: 2021-06-08T10:04:10Z
date_updated: 2021-06-08T10:04:10Z
file_id: '9534'
file_name: 2021_Cell_Petridou.pdf
file_size: 11405875
relation: main_file
success: 1
file_date_updated: 2021-06-08T10:04:10Z
has_accepted_license: '1'
intvolume: ' 184'
isi: 1
issue: '7'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1914-1928.e19
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 2693FD8C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: V00736
name: Tissue material properties in embryonic development
publication: Cell
publication_identifier:
eissn:
- '10974172'
issn:
- '00928674'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/embryonic-tissue-undergoes-phase-transition/
scopus_import: '1'
status: public
title: Rigidity percolation uncovers a structural basis for embryonic tissue phase
transitions
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 184
year: '2021'
...
---
_id: '9317'
abstract:
- lang: eng
text: Given a locally finite X⊆Rd and a radius r≥0, the k-fold cover of X and r
consists of all points in Rd that have k or more points of X within distance r.
We consider two filtrations—one in scale obtained by fixing k and increasing r,
and the other in depth obtained by fixing r and decreasing k—and we compute the
persistence diagrams of both. While standard methods suffice for the filtration
in scale, we need novel geometric and topological concepts for the filtration
in depth. In particular, we introduce a rhomboid tiling in Rd+1 whose horizontal
integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module
of Delaunay mosaics that is isomorphic to the persistence module of the multi-covers.
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant Agreement No. 78818 Alpha), and by the DFG Collaborative Research Center
TRR 109, ‘Discretization in Geometry and Dynamics’, through Grant No. I02979-N35
of the Austrian Science Fund (FWF)\r\nOpen Access funding provided by the Institute
of Science and Technology (IST Austria)."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
citation:
ama: Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. Discrete
and Computational Geometry. 2021;65:1296–1313. doi:10.1007/s00454-021-00281-9
apa: Edelsbrunner, H., & Osang, G. F. (2021). The multi-cover persistence of
Euclidean balls. Discrete and Computational Geometry. Springer Nature.
https://doi.org/10.1007/s00454-021-00281-9
chicago: Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence
of Euclidean Balls.” Discrete and Computational Geometry. Springer Nature,
2021. https://doi.org/10.1007/s00454-021-00281-9.
ieee: H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean
balls,” Discrete and Computational Geometry, vol. 65. Springer Nature,
pp. 1296–1313, 2021.
ista: Edelsbrunner H, Osang GF. 2021. The multi-cover persistence of Euclidean balls.
Discrete and Computational Geometry. 65, 1296–1313.
mla: Edelsbrunner, Herbert, and Georg F. Osang. “The Multi-Cover Persistence of
Euclidean Balls.” Discrete and Computational Geometry, vol. 65, Springer
Nature, 2021, pp. 1296–1313, doi:10.1007/s00454-021-00281-9.
short: H. Edelsbrunner, G.F. Osang, Discrete and Computational Geometry 65 (2021)
1296–1313.
date_created: 2021-04-11T22:01:15Z
date_published: 2021-03-31T00:00:00Z
date_updated: 2023-08-07T14:35:44Z
day: '31'
ddc:
- '516'
department:
- _id: HeEd
doi: 10.1007/s00454-021-00281-9
ec_funded: 1
external_id:
isi:
- '000635460400001'
file:
- access_level: open_access
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content_type: application/pdf
creator: cchlebak
date_created: 2021-12-01T10:56:53Z
date_updated: 2021-12-01T10:56:53Z
file_id: '10394'
file_name: 2021_DisCompGeo_Edelsbrunner_Osang.pdf
file_size: 677704
relation: main_file
success: 1
file_date_updated: 2021-12-01T10:56:53Z
has_accepted_license: '1'
intvolume: ' 65'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1296–1313
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '187'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: The multi-cover persistence of Euclidean balls
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 65
year: '2021'
...
---
_id: '9318'
abstract:
- lang: eng
text: We consider a system of N bosons in the mean-field scaling regime for a class
of interactions including the repulsive Coulomb potential. We derive an asymptotic
expansion of the low-energy eigenstates and the corresponding energies, which
provides corrections to Bogoliubov theory to any order in 1/N.
acknowledgement: The first author gratefully acknowledges funding from the European
Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie
Grant Agreement No. 754411. The third author was supported by the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant Agreement No. 694227).
article_number: e28
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lea
full_name: Bossmann, Lea
id: A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425
last_name: Bossmann
orcid: 0000-0002-6854-1343
- first_name: Sören P
full_name: Petrat, Sören P
id: 40AC02DC-F248-11E8-B48F-1D18A9856A87
last_name: Petrat
orcid: 0000-0002-9166-5889
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Bossmann L, Petrat SP, Seiringer R. Asymptotic expansion of low-energy excitations
for weakly interacting bosons. Forum of Mathematics, Sigma. 2021;9. doi:10.1017/fms.2021.22
apa: Bossmann, L., Petrat, S. P., & Seiringer, R. (2021). Asymptotic expansion
of low-energy excitations for weakly interacting bosons. Forum of Mathematics,
Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2021.22
chicago: Bossmann, Lea, Sören P Petrat, and Robert Seiringer. “Asymptotic Expansion
of Low-Energy Excitations for Weakly Interacting Bosons.” Forum of Mathematics,
Sigma. Cambridge University Press, 2021. https://doi.org/10.1017/fms.2021.22.
ieee: L. Bossmann, S. P. Petrat, and R. Seiringer, “Asymptotic expansion of low-energy
excitations for weakly interacting bosons,” Forum of Mathematics, Sigma,
vol. 9. Cambridge University Press, 2021.
ista: Bossmann L, Petrat SP, Seiringer R. 2021. Asymptotic expansion of low-energy
excitations for weakly interacting bosons. Forum of Mathematics, Sigma. 9, e28.
mla: Bossmann, Lea, et al. “Asymptotic Expansion of Low-Energy Excitations for Weakly
Interacting Bosons.” Forum of Mathematics, Sigma, vol. 9, e28, Cambridge
University Press, 2021, doi:10.1017/fms.2021.22.
short: L. Bossmann, S.P. Petrat, R. Seiringer, Forum of Mathematics, Sigma 9 (2021).
date_created: 2021-04-11T22:01:15Z
date_published: 2021-03-26T00:00:00Z
date_updated: 2023-08-07T14:35:06Z
day: '26'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1017/fms.2021.22
ec_funded: 1
external_id:
isi:
- '000634006900001'
file:
- access_level: open_access
checksum: 17a3e6786d1e930cf0c14a880a6d7e92
content_type: application/pdf
creator: dernst
date_created: 2021-04-12T07:15:58Z
date_updated: 2021-04-12T07:15:58Z
file_id: '9319'
file_name: 2021_ForumMath_Bossmann.pdf
file_size: 883851
relation: main_file
success: 1
file_date_updated: 2021-04-12T07:15:58Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Forum of Mathematics, Sigma
publication_identifier:
eissn:
- '20505094'
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Asymptotic expansion of low-energy excitations for weakly interacting bosons
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2021'
...
---
_id: '9331'
abstract:
- lang: eng
text: 'Quantum entanglement has been generated and verified in cold-atom experiments
and used to make atom-interferometric measurements below the shot-noise limit.
However, current state-of-the-art cold-atom devices exploit separable (i.e., unentangled)
atomic states. This perspective piece asks the question: can entanglement usefully
improve cold-atom sensors, in the sense that it gives new sensing capabilities
unachievable with current state-of-the-art devices? We briefly review the state-of-the-art
in precision cold-atom sensing, focusing on clocks and inertial sensors, identifying
the potential benefits entanglement could bring to these devices, and the challenges
that need to be overcome to realize these benefits. We survey demonstrated methods
of generating metrologically useful entanglement in cold-atom systems, note their
relative strengths and weaknesses, and assess their prospects for near-to-medium
term quantum-enhanced cold-atom sensing.'
acknowledgement: We acknowledge fruitful discussions with John Close, Chris Freier,
Kyle Hardman, Joseph Hope, and Paul Wigley, and insightful suggestions made by Franck
Pereira dos Santos on behalf of the Atom Interferometry and Inertial Sensors team
at SYRTE. S.S.S. was supported by an Australian Research Council Discovery Early
Career Researcher Award (DECRA), Project No. DE200100495. O.H. was supported by
IST Austria.
article_number: '140501'
article_processing_charge: No
article_type: original
author:
- first_name: Stuart S.
full_name: Szigeti, Stuart S.
last_name: Szigeti
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Simon A.
full_name: Haine, Simon A.
last_name: Haine
citation:
ama: 'Szigeti SS, Hosten O, Haine SA. Improving cold-atom sensors with quantum entanglement:
Prospects and challenges. Applied Physics Letters. 2021;118(14). doi:10.1063/5.0050235'
apa: 'Szigeti, S. S., Hosten, O., & Haine, S. A. (2021). Improving cold-atom
sensors with quantum entanglement: Prospects and challenges. Applied Physics
Letters. AIP Publishing. https://doi.org/10.1063/5.0050235'
chicago: 'Szigeti, Stuart S., Onur Hosten, and Simon A. Haine. “Improving Cold-Atom
Sensors with Quantum Entanglement: Prospects and Challenges.” Applied Physics
Letters. AIP Publishing, 2021. https://doi.org/10.1063/5.0050235.'
ieee: 'S. S. Szigeti, O. Hosten, and S. A. Haine, “Improving cold-atom sensors with
quantum entanglement: Prospects and challenges,” Applied Physics Letters,
vol. 118, no. 14. AIP Publishing, 2021.'
ista: 'Szigeti SS, Hosten O, Haine SA. 2021. Improving cold-atom sensors with quantum
entanglement: Prospects and challenges. Applied Physics Letters. 118(14), 140501.'
mla: 'Szigeti, Stuart S., et al. “Improving Cold-Atom Sensors with Quantum Entanglement:
Prospects and Challenges.” Applied Physics Letters, vol. 118, no. 14, 140501,
AIP Publishing, 2021, doi:10.1063/5.0050235.'
short: S.S. Szigeti, O. Hosten, S.A. Haine, Applied Physics Letters 118 (2021).
date_created: 2021-04-18T22:01:40Z
date_published: 2021-04-07T00:00:00Z
date_updated: 2023-08-07T14:36:42Z
day: '07'
department:
- _id: OnHo
doi: 10.1063/5.0050235
external_id:
arxiv:
- '2010.09168'
isi:
- '000637702100001'
intvolume: ' 118'
isi: 1
issue: '14'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2010.09168
month: '04'
oa: 1
oa_version: Preprint
publication: Applied Physics Letters
publication_identifier:
issn:
- '00036951'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Improving cold-atom sensors with quantum entanglement: Prospects and challenges'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...
---
_id: '9330'
abstract:
- lang: eng
text: In nerve cells the genes encoding for α2δ subunits of voltage-gated calcium
channels have been linked to synaptic functions and neurological disease. Here
we show that α2δ subunits are essential for the formation and organization of
glutamatergic synapses. Using a cellular α2δ subunit triple-knockout/knockdown
model, we demonstrate a failure in presynaptic differentiation evidenced by defective
presynaptic calcium channel clustering and calcium influx, smaller presynaptic
active zones, and a strongly reduced accumulation of presynaptic vesicle-associated
proteins (synapsin and vGLUT). The presynaptic defect is associated with the downscaling
of postsynaptic AMPA receptors and the postsynaptic density. The role of α2δ isoforms
as synaptic organizers is highly redundant, as each individual α2δ isoform can
rescue presynaptic calcium channel trafficking and expression of synaptic proteins.
Moreover, α2δ-2 and α2δ-3 with mutated metal ion-dependent adhesion sites can
fully rescue presynaptic synapsin expression but only partially calcium channel
trafficking, suggesting that the regulatory role of α2δ subunits is independent
from its role as a calcium channel subunit. Our findings influence the current
view on excitatory synapse formation. First, our study suggests that postsynaptic
differentiation is secondary to presynaptic differentiation. Second, the dependence
of presynaptic differentiation on α2δ implicates α2δ subunits as potential nucleation
points for the organization of synapses. Finally, our results suggest that α2δ
subunits act as transsynaptic organizers of glutamatergic synapses, thereby aligning
the synaptic active zone with the postsynaptic density.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "We thank Arnold Schwartz for providing α2δ-1 knockout mice; Ariane
Benedetti, Sabine Baumgartner, Sandra Demetz, and Irene Mahlknecht for technical
support; Nadine Ortner and Andreas Lieb for electrophysiological experiments; the
team of the Electron Microscopy Facility at the Institute of Science and Technology
Austria for technical support related to ultrastructural analysis; Hermann Dietrich
and Anja Beierfuß and her team for animal care; Jutta Engel and Jörg Striessnig
for critical discussions; and Bruno Benedetti and Bernhard Flucher for critical
discussions and reading the manuscript. This study was supported by Austrian Science
Fund Grants P24079, F44060, F44150, and DOC30-B30 (to G.J.O.) and T855 (to M.C.),
European Research Council Grant AdG 694539 (to R.S.), Deutsche Forschungsgemeinschaft\r\nGrant
SFB1348-TP A03 (to M.M.), and Interdisziplinäre Zentrum für Klinische Forschung
Münster Grant Mi3/004/19 (to M.M.). This work is part of the PhD theses of C.L.S.,
S.M.G., and C.A."
article_processing_charge: No
article_type: original
author:
- first_name: Clemens L.
full_name: Schöpf, Clemens L.
last_name: Schöpf
- first_name: Cornelia
full_name: Ablinger, Cornelia
last_name: Ablinger
- first_name: Stefanie M.
full_name: Geisler, Stefanie M.
last_name: Geisler
- first_name: Ruslan I.
full_name: Stanika, Ruslan I.
last_name: Stanika
- first_name: Marta
full_name: Campiglio, Marta
last_name: Campiglio
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Benedikt
full_name: Nimmervoll, Benedikt
last_name: Nimmervoll
- first_name: Bettina
full_name: Schlick, Bettina
last_name: Schlick
- first_name: Johannes
full_name: Brockhaus, Johannes
last_name: Brockhaus
- first_name: Markus
full_name: Missler, Markus
last_name: Missler
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Gerald J.
full_name: Obermair, Gerald J.
last_name: Obermair
citation:
ama: Schöpf CL, Ablinger C, Geisler SM, et al. Presynaptic α2δ subunits are key
organizers of glutamatergic synapses. PNAS. 2021;118(14). doi:10.1073/pnas.1920827118
apa: Schöpf, C. L., Ablinger, C., Geisler, S. M., Stanika, R. I., Campiglio, M.,
Kaufmann, W., … Obermair, G. J. (2021). Presynaptic α2δ subunits are key organizers
of glutamatergic synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1920827118
chicago: Schöpf, Clemens L., Cornelia Ablinger, Stefanie M. Geisler, Ruslan I. Stanika,
Marta Campiglio, Walter Kaufmann, Benedikt Nimmervoll, et al. “Presynaptic Α2δ
Subunits Are Key Organizers of Glutamatergic Synapses.” PNAS. National
Academy of Sciences, 2021. https://doi.org/10.1073/pnas.1920827118.
ieee: C. L. Schöpf et al., “Presynaptic α2δ subunits are key organizers of
glutamatergic synapses,” PNAS, vol. 118, no. 14. National Academy of Sciences,
2021.
ista: Schöpf CL, Ablinger C, Geisler SM, Stanika RI, Campiglio M, Kaufmann W, Nimmervoll
B, Schlick B, Brockhaus J, Missler M, Shigemoto R, Obermair GJ. 2021. Presynaptic
α2δ subunits are key organizers of glutamatergic synapses. PNAS. 118(14).
mla: Schöpf, Clemens L., et al. “Presynaptic Α2δ Subunits Are Key Organizers of
Glutamatergic Synapses.” PNAS, vol. 118, no. 14, National Academy of Sciences,
2021, doi:10.1073/pnas.1920827118.
short: C.L. Schöpf, C. Ablinger, S.M. Geisler, R.I. Stanika, M. Campiglio, W. Kaufmann,
B. Nimmervoll, B. Schlick, J. Brockhaus, M. Missler, R. Shigemoto, G.J. Obermair,
PNAS 118 (2021).
date_created: 2021-04-18T22:01:40Z
date_published: 2021-04-06T00:00:00Z
date_updated: 2023-08-08T13:08:47Z
day: '06'
ddc:
- '570'
department:
- _id: EM-Fac
- _id: RySh
doi: 10.1073/pnas.1920827118
ec_funded: 1
external_id:
isi:
- '000637398300002'
file:
- access_level: open_access
checksum: dd014f68ae9d7d8d8fc4139a24e04506
content_type: application/pdf
creator: dernst
date_created: 2021-04-19T10:10:56Z
date_updated: 2021-04-19T10:10:56Z
file_id: '9340'
file_name: 2021_PNAS_Schoepf.pdf
file_size: 2603911
relation: main_file
success: 1
file_date_updated: 2021-04-19T10:10:56Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '14'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
publication: PNAS
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Presynaptic α2δ subunits are key organizers of glutamatergic synapses
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...
---
_id: '9332'
abstract:
- lang: eng
text: Lateral root (LR) formation is an example of a plant post-embryonic organogenesis
event. LRs are issued from non-dividing cells entering consecutive steps of formative
divisions, proliferation and elongation. The chromatin remodeling protein PICKLE
(PKL) negatively regulates auxin-mediated LR formation through a mechanism that
is not yet known. Here we show that PKL interacts with RETINOBLASTOMA-RELATED
1 (RBR1) to repress the LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) promoter activity.
Since LBD16 function is required for the formative division of LR founder cells,
repression mediated by the PKL–RBR1 complex negatively regulates formative division
and LR formation. Inhibition of LR formation by PKL–RBR1 is counteracted by auxin,
indicating that, in addition to auxin-mediated transcriptional responses, the
fine-tuned process of LR formation is also controlled at the chromatin level in
an auxin-signaling dependent manner.
acknowledgement: "This research was supported by a postdoctoral fellowship of the
Carl Tryggers Foundation (to K.Ö.) and by grants from Vetenskapsrådet (Nr.: 621-2004-2921
to L.B.) and VINNOVA (to L.B. and S.R.).\r\nWe thank Frederic Berger, Hidehiro Fukaki,
Malcolm Bennett, Claudia Köhler, Jiri Friml for providing pRBR1::RBR1-RFP, ssl2-1,
slr-1, pPKL::PKL-GFP seeds and the DR5 expressing vector, respectively. Authors
are grateful to Hayashi Kenichiro for providing the auxinol compound and to Rishi
Bhalerao for stimulating discussions. The technical help of Adeline Rigal and Thomas
Vain with the auxinol experiments is much appreciated."
article_number: '3862'
article_processing_charge: No
article_type: original
author:
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: Pál
full_name: Miskolczi, Pál
last_name: Miskolczi
- first_name: Peter
full_name: Marhavý, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavý
orcid: 0000-0001-5227-5741
- first_name: Alfredo
full_name: Cruz-Ramírez, Alfredo
last_name: Cruz-Ramírez
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: László
full_name: Bakó, László
last_name: Bakó
citation:
ama: Ötvös K, Miskolczi P, Marhavý P, et al. Pickle recruits retinoblastoma related
1 to control lateral root formation in arabidopsis. International Journal of
Molecular Sciences. 2021;22(8). doi:10.3390/ijms22083862
apa: Ötvös, K., Miskolczi, P., Marhavý, P., Cruz-Ramírez, A., Benková, E., Robert,
S., & Bakó, L. (2021). Pickle recruits retinoblastoma related 1 to control
lateral root formation in arabidopsis. International Journal of Molecular Sciences.
MDPI. https://doi.org/10.3390/ijms22083862
chicago: Ötvös, Krisztina, Pál Miskolczi, Peter Marhavý, Alfredo Cruz-Ramírez, Eva
Benková, Stéphanie Robert, and László Bakó. “Pickle Recruits Retinoblastoma Related
1 to Control Lateral Root Formation in Arabidopsis.” International Journal
of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22083862.
ieee: K. Ötvös et al., “Pickle recruits retinoblastoma related 1 to control
lateral root formation in arabidopsis,” International Journal of Molecular
Sciences, vol. 22, no. 8. MDPI, 2021.
ista: Ötvös K, Miskolczi P, Marhavý P, Cruz-Ramírez A, Benková E, Robert S, Bakó
L. 2021. Pickle recruits retinoblastoma related 1 to control lateral root formation
in arabidopsis. International Journal of Molecular Sciences. 22(8), 3862.
mla: Ötvös, Krisztina, et al. “Pickle Recruits Retinoblastoma Related 1 to Control
Lateral Root Formation in Arabidopsis.” International Journal of Molecular
Sciences, vol. 22, no. 8, 3862, MDPI, 2021, doi:10.3390/ijms22083862.
short: K. Ötvös, P. Miskolczi, P. Marhavý, A. Cruz-Ramírez, E. Benková, S. Robert,
L. Bakó, International Journal of Molecular Sciences 22 (2021).
date_created: 2021-04-18T22:01:41Z
date_published: 2021-04-08T00:00:00Z
date_updated: 2023-08-08T13:09:58Z
day: '08'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.3390/ijms22083862
external_id:
isi:
- '000644394800001'
file:
- access_level: open_access
checksum: 26ada2531ad1f9c01a1664de0431f1fe
content_type: application/pdf
creator: dernst
date_created: 2021-04-19T10:54:55Z
date_updated: 2021-04-19T10:54:55Z
file_id: '9342'
file_name: 2021_JourMolecularScience_Oetvoes.pdf
file_size: 2769717
relation: main_file
success: 1
file_date_updated: 2021-04-19T10:54:55Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '8'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- 1422-0067
issn:
- 1661-6596
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pickle recruits retinoblastoma related 1 to control lateral root formation
in arabidopsis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 22
year: '2021'
...
---
_id: '9333'
abstract:
- lang: eng
text: We revise a previous result about the Fröhlich dynamics in the strong coupling
limit obtained in Griesemer (Rev Math Phys 29(10):1750030, 2017). In the latter
it was shown that the Fröhlich time evolution applied to the initial state φ0⊗ξα,
where φ0 is the electron ground state of the Pekar energy functional and ξα the
associated coherent state of the phonons, can be approximated by a global phase
for times small compared to α2. In the present note we prove that a similar approximation
holds for t=O(α2) if one includes a nontrivial effective dynamics for the phonons
that is generated by an operator proportional to α−2 and quadratic in creation
and annihilation operators. Our result implies that the electron ground state
remains close to its initial state for times of order α2, while the phonon fluctuations
around the coherent state ξα can be described by a time-dependent Bogoliubov transformation.
acknowledgement: 'I thank Marcel Griesemer for many interesting discussions about
the Fröhlich polaron and also for valuable comments on this manuscript. Helpful
discussions with Nikolai Leopold and Robert Seiringer are also gratefully acknowledged.
This work was partially supported by the Deutsche Forschungsgemeinschaft (DFG) through
the Research Training Group 1838: Spectral Theory and Dynamics of Quantum Systems.
Open Access funding enabled and organized by Projekt DEAL.'
article_number: '45'
article_processing_charge: No
article_type: original
author:
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
citation:
ama: Mitrouskas DJ. A note on the Fröhlich dynamics in the strong coupling limit.
Letters in Mathematical Physics. 2021;111. doi:10.1007/s11005-021-01380-7
apa: Mitrouskas, D. J. (2021). A note on the Fröhlich dynamics in the strong coupling
limit. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-021-01380-7
chicago: Mitrouskas, David Johannes. “A Note on the Fröhlich Dynamics in the Strong
Coupling Limit.” Letters in Mathematical Physics. Springer Nature, 2021.
https://doi.org/10.1007/s11005-021-01380-7.
ieee: D. J. Mitrouskas, “A note on the Fröhlich dynamics in the strong coupling
limit,” Letters in Mathematical Physics, vol. 111. Springer Nature, 2021.
ista: Mitrouskas DJ. 2021. A note on the Fröhlich dynamics in the strong coupling
limit. Letters in Mathematical Physics. 111, 45.
mla: Mitrouskas, David Johannes. “A Note on the Fröhlich Dynamics in the Strong
Coupling Limit.” Letters in Mathematical Physics, vol. 111, 45, Springer
Nature, 2021, doi:10.1007/s11005-021-01380-7.
short: D.J. Mitrouskas, Letters in Mathematical Physics 111 (2021).
date_created: 2021-04-18T22:01:41Z
date_published: 2021-04-05T00:00:00Z
date_updated: 2023-08-08T13:09:28Z
day: '05'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s11005-021-01380-7
external_id:
isi:
- '000637359300002'
file:
- access_level: open_access
checksum: be56c0845a43c0c5c772ee0b5053f7d7
content_type: application/pdf
creator: dernst
date_created: 2021-04-19T10:40:01Z
date_updated: 2021-04-19T10:40:01Z
file_id: '9341'
file_name: 2021_LettersMathPhysics_Mitrouskas.pdf
file_size: 438084
relation: main_file
success: 1
file_date_updated: 2021-04-19T10:40:01Z
has_accepted_license: '1'
intvolume: ' 111'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Letters in Mathematical Physics
publication_identifier:
eissn:
- '15730530'
issn:
- '03779017'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A note on the Fröhlich dynamics in the strong coupling limit
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 111
year: '2021'
...
---
_id: '9335'
abstract:
- lang: eng
text: 'Various degenerate diffusion equations exhibit a waiting time phenomenon:
depending on the “flatness” of the compactly supported initial datum at the boundary
of the support, the support of the solution may not expand for a certain amount
of time. We show that this phenomenon is captured by particular Lagrangian discretizations
of the porous medium and the thin film equations, and we obtain sufficient criteria
for the occurrence of waiting times that are consistent with the known ones for
the original PDEs. For the spatially discrete solution, the waiting time phenomenon
refers to a deviation of the edge of support from its original position by a quantity
comparable to the mesh width, over a mesh-independent time interval. Our proof
is based on estimates on the fluid velocity in Lagrangian coordinates. Combining
weighted entropy estimates with an iteration technique à la Stampacchia leads
to upper bounds on free boundary propagation. Numerical simulations show that
the phenomenon is already clearly visible for relatively coarse discretizations.'
acknowledgement: This research was supported by the DFG Collaborative Research Center
TRR 109, “Discretization in Geometry and Dynamics”.
article_processing_charge: No
article_type: original
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Daniel
full_name: Matthes, Daniel
last_name: Matthes
citation:
ama: Fischer JL, Matthes D. The waiting time phenomenon in spatially discretized
porous medium and thin film equations. SIAM Journal on Numerical Analysis.
2021;59(1):60-87. doi:10.1137/19M1300017
apa: Fischer, J. L., & Matthes, D. (2021). The waiting time phenomenon in spatially
discretized porous medium and thin film equations. SIAM Journal on Numerical
Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1300017
chicago: Fischer, Julian L, and Daniel Matthes. “The Waiting Time Phenomenon in
Spatially Discretized Porous Medium and Thin Film Equations.” SIAM Journal
on Numerical Analysis. Society for Industrial and Applied Mathematics, 2021.
https://doi.org/10.1137/19M1300017.
ieee: J. L. Fischer and D. Matthes, “The waiting time phenomenon in spatially discretized
porous medium and thin film equations,” SIAM Journal on Numerical Analysis,
vol. 59, no. 1. Society for Industrial and Applied Mathematics, pp. 60–87, 2021.
ista: Fischer JL, Matthes D. 2021. The waiting time phenomenon in spatially discretized
porous medium and thin film equations. SIAM Journal on Numerical Analysis. 59(1),
60–87.
mla: Fischer, Julian L., and Daniel Matthes. “The Waiting Time Phenomenon in Spatially
Discretized Porous Medium and Thin Film Equations.” SIAM Journal on Numerical
Analysis, vol. 59, no. 1, Society for Industrial and Applied Mathematics,
2021, pp. 60–87, doi:10.1137/19M1300017.
short: J.L. Fischer, D. Matthes, SIAM Journal on Numerical Analysis 59 (2021) 60–87.
date_created: 2021-04-18T22:01:42Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2023-08-08T13:10:40Z
day: '01'
department:
- _id: JuFi
doi: 10.1137/19M1300017
external_id:
arxiv:
- '1911.04185'
isi:
- '000625044600003'
intvolume: ' 59'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1911.04185
month: '01'
oa: 1
oa_version: Preprint
page: 60-87
publication: SIAM Journal on Numerical Analysis
publication_identifier:
issn:
- 0036-1429
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: The waiting time phenomenon in spatially discretized porous medium and thin
film equations
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 59
year: '2021'
...
---
_id: '9349'
abstract:
- lang: eng
text: 'The way in which interactions between mechanics and biochemistry lead to
the emergence of complex cell and tissue organization is an old question that
has recently attracted renewed interest from biologists, physicists, mathematicians
and computer scientists. Rapid advances in optical physics, microscopy and computational
image analysis have greatly enhanced our ability to observe and quantify spatiotemporal
patterns of signalling, force generation, deformation, and flow in living cells
and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation
are allowing us to perturb the underlying machinery that generates these patterns
in increasingly sophisticated ways. Rapid advances in theory and computing have
made it possible to construct predictive models that describe how cell and tissue
organization and dynamics emerge from the local coupling of biochemistry and mechanics.
Together, these advances have opened up a wealth of new opportunities to explore
how mechanochemical patterning shapes organismal development. In this roadmap,
we present a series of forward-looking case studies on mechanochemical patterning
in development, written by scientists working at the interface between the physical
and biological sciences, and covering a wide range of spatial and temporal scales,
organisms, and modes of development. Together, these contributions highlight the
many ways in which the dynamic coupling of mechanics and biochemistry shapes biological
dynamics: from mechanoenzymes that sense force to tune their activity and motor
output, to collectives of cells in tissues that flow and redistribute biochemical
signals during development.'
acknowledgement: The AK group is supported by IST Austria and by the ERC under European
Union Horizon 2020 research and innovation programme Grant 680037. Apologies to
those whose work could not be mentioned due to limited space. We thank all my lab
members, both past and present, for stimulating discussion. This work was funded
by a Singapore Ministry of Education Tier 3 Grant, MOE2016-T3-1-005. We thank Francis
Corson for continuous discussion and collaboration contributing to these views and
for figure 4(A). PC is sponsored by the Institut Pasteur and the European Union's
Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie
Grant Agreement No. 665807. Research in JG's laboratory is funded by the European
Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC
Grant Agreement No. 337635, Institut Pasteur, CNRS, Cercle FSER, Fondation pour
la Recherche Medicale, the Vallee Foundation and the ANR-19-CE-13-0024 Grant. We
thank Erez Braun and Alex Mogilner for comments on the manuscript and Niv Ierushalmi
for help with figure 5. This project has received funding from the European Union's
Horizon 2020 research and innovation programme under Grant Agreement No. ERC-2018-COG
Grant 819174-HydraMechanics awarded to KK. EH thanks all lab members, as well as
Pierre Recho, Tsuyoshi Hirashima, Diana Pinheiro and Carl-Philip Heisenberg, for
fruitful discussions on these topics—and apologize for not being able to cite many
very relevant publications due to the strict 10-reference limit. EH acknowledges
the support of Austrian Science Fund (FWF) (P 31639) and the European Research Council
under the European Union's Horizon 2020 Research and Innovation Programme Grant
Agreements (851288). The authors acknowledge the inspiring scientists whose work
could not be cited in this perspective due to space constraints; the members of
the Gartner Lab for helpful discussions; the Barbara and Gerson Bakar Foundation,
the Chan Zuckerberg Biohub Investigators Programme, the National Institute of Health,
and the Centre for Cellular Construction, an NSF Science and Technology Centre.
The Minc laboratory is currently funded by the CNRS and the European Research Council
(CoG Forcaster No. 647073). Research in the lab of J-LM is supported by the Institut
Curie, the Centre National de la Recherche Scientifique (CNRS), the Institut National
de la Santé Et de la Recherche Médicale (INSERM), and is funded by grants from the
ATIP-Avenir programme, the Fondation Schlumberger pour l'Éducation et la Recherche
via the Fondation pour la Recherche Médicale, the European Research Council Starting
Grant ERC-2017-StG 757557, the European Molecular Biology Organization Young Investigator
programme (EMBO YIP), the INSERM transversal programme Human Development Cell Atlas
(HuDeCA), Paris Sciences Lettres (PSL) 'nouvelle équipe' and QLife (17-CONV-0005)
grants and Labex DEEP (ANR-11-LABX-0044) which are part of the IDEX PSL (ANR-10-IDEX-0001-02).
We acknowledge useful discussions with Massimo Vergassola, Sebastian Streichan and
my lab members. Work in my laboratory on Drosophila embryogenesis is partly supported
by NIH-R01GM122936. The authors acknowledge the support by a grant from the European
Research Council (Grant No. 682161). Lenne group is funded by a grant from the 'Investissements
d'Avenir' French Government programme managed by the French National Research Agency
(ANR-16-CONV-0001) and by the Excellence Initiative of Aix-Marseille University—A*MIDEX,
and ANR projects MechaResp (ANR-17-CE13-0032) and AdGastrulo (ANR-19-CE13-0022).
article_number: '041501'
article_processing_charge: No
article_type: original
author:
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full_name: Lenne, Pierre François
last_name: Lenne
- first_name: Edwin
full_name: Munro, Edwin
last_name: Munro
- first_name: Idse
full_name: Heemskerk, Idse
last_name: Heemskerk
- first_name: Aryeh
full_name: Warmflash, Aryeh
last_name: Warmflash
- first_name: Laura
full_name: Bocanegra, Laura
id: 4896F754-F248-11E8-B48F-1D18A9856A87
last_name: Bocanegra
- first_name: Kasumi
full_name: Kishi, Kasumi
id: 3065DFC4-F248-11E8-B48F-1D18A9856A87
last_name: Kishi
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Yuchen
full_name: Long, Yuchen
last_name: Long
- first_name: Antoine
full_name: Fruleux, Antoine
last_name: Fruleux
- first_name: Arezki
full_name: Boudaoud, Arezki
last_name: Boudaoud
- first_name: Timothy E.
full_name: Saunders, Timothy E.
last_name: Saunders
- first_name: Paolo
full_name: Caldarelli, Paolo
last_name: Caldarelli
- first_name: Arthur
full_name: Michaut, Arthur
last_name: Michaut
- first_name: Jerome
full_name: Gros, Jerome
last_name: Gros
- first_name: Yonit
full_name: Maroudas-Sacks, Yonit
last_name: Maroudas-Sacks
- first_name: Kinneret
full_name: Keren, Kinneret
last_name: Keren
- 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: Zev J.
full_name: Gartner, Zev J.
last_name: Gartner
- first_name: Benjamin
full_name: Stormo, Benjamin
last_name: Stormo
- first_name: Amy
full_name: Gladfelter, Amy
last_name: Gladfelter
- first_name: Alan
full_name: Rodrigues, Alan
last_name: Rodrigues
- first_name: Amy
full_name: Shyer, Amy
last_name: Shyer
- first_name: Nicolas
full_name: Minc, Nicolas
last_name: Minc
- first_name: Jean Léon
full_name: Maître, Jean Léon
last_name: Maître
- first_name: Stefano
full_name: Di Talia, Stefano
last_name: Di Talia
- first_name: Bassma
full_name: Khamaisi, Bassma
last_name: Khamaisi
- first_name: David
full_name: Sprinzak, David
last_name: Sprinzak
- first_name: Sham
full_name: Tlili, Sham
last_name: Tlili
citation:
ama: Lenne PF, Munro E, Heemskerk I, et al. Roadmap for the multiscale coupling
of biochemical and mechanical signals during development. Physical biology.
2021;18(4). doi:10.1088/1478-3975/abd0db
apa: Lenne, P. F., Munro, E., Heemskerk, I., Warmflash, A., Bocanegra, L., Kishi,
K., … Tlili, S. (2021). Roadmap for the multiscale coupling of biochemical and
mechanical signals during development. Physical Biology. IOP Publishing.
https://doi.org/10.1088/1478-3975/abd0db
chicago: Lenne, Pierre François, Edwin Munro, Idse Heemskerk, Aryeh Warmflash, Laura
Bocanegra, Kasumi Kishi, Anna Kicheva, et al. “Roadmap for the Multiscale Coupling
of Biochemical and Mechanical Signals during Development.” Physical Biology.
IOP Publishing, 2021. https://doi.org/10.1088/1478-3975/abd0db.
ieee: P. F. Lenne et al., “Roadmap for the multiscale coupling of biochemical
and mechanical signals during development,” Physical biology, vol. 18,
no. 4. IOP Publishing, 2021.
ista: Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra L, Kishi K, Kicheva
A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J,
Maroudas-Sacks Y, Keren K, Hannezo EB, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues
A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. 2021.
Roadmap for the multiscale coupling of biochemical and mechanical signals during
development. Physical biology. 18(4), 041501.
mla: Lenne, Pierre François, et al. “Roadmap for the Multiscale Coupling of Biochemical
and Mechanical Signals during Development.” Physical Biology, vol. 18,
no. 4, 041501, IOP Publishing, 2021, doi:10.1088/1478-3975/abd0db.
short: P.F. Lenne, E. Munro, I. Heemskerk, A. Warmflash, L. Bocanegra, K. Kishi,
A. Kicheva, Y. Long, A. Fruleux, A. Boudaoud, T.E. Saunders, P. Caldarelli, A.
Michaut, J. Gros, Y. Maroudas-Sacks, K. Keren, E.B. Hannezo, Z.J. Gartner, B.
Stormo, A. Gladfelter, A. Rodrigues, A. Shyer, N. Minc, J.L. Maître, S. Di Talia,
B. Khamaisi, D. Sprinzak, S. Tlili, Physical Biology 18 (2021).
date_created: 2021-04-25T22:01:29Z
date_published: 2021-04-14T00:00:00Z
date_updated: 2023-08-08T13:15:46Z
day: '14'
ddc:
- '570'
department:
- _id: AnKi
- _id: EdHa
doi: 10.1088/1478-3975/abd0db
ec_funded: 1
external_id:
isi:
- '000640396400001'
pmid:
- '33276350'
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oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
- _id: 268294B6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31639
name: Active mechano-chemical description of the cell cytoskeleton
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Physical biology
publication_identifier:
eissn:
- 1478-3975
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
related_material:
record:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Roadmap for the multiscale coupling of biochemical and mechanical signals during
development
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2021'
...
---
_id: '9334'
abstract:
- lang: eng
text: 'Polaritons with directional in-plane propagation and ultralow losses in van
der Waals (vdW) crystals promise unprecedented manipulation of light at the nanoscale.
However, these polaritons present a crucial limitation: their directional propagation
is intrinsically determined by the crystal structure of the host material, imposing
forbidden directions of propagation. Here, we demonstrate that directional polaritons
(in-plane hyperbolic phonon polaritons) in a vdW crystal (α-phase molybdenum trioxide)
can be directed along forbidden directions by inducing an optical topological
transition, which emerges when the slab is placed on a substrate with a given
negative permittivity (4H–silicon carbide). By visualizing the transition in real
space, we observe exotic polaritonic states between mutually orthogonal hyperbolic
regimes, which unveil the topological origin of the transition: a gap opening
in the dispersion. This work provides insights into optical topological transitions
in vdW crystals, which introduce a route to direct light at the nanoscale.'
acknowledgement: 'G.Á.-P. and J.T.-G. acknowledge support through the Severo Ochoa
Program from the government of the Principality of Asturias (grant nos. PA20-PF-BP19-053
and PA-18-PF-BP17-126, respectively). K.V.V. and V.S.V. acknowledge the Ministry
of Science and Higher Education of the Russian Federation (no. 0714-2020-0002).
J. M.-S. acknowledges financial support through the Ramón y Cajal Program from the
government of Spain and FSE (RYC2018-026196-I). A.Y.N. acknowledges the Spanish
Ministry of Science, Innovation and Universities (national project no. MAT201788358-C3-3-R),
and the Basque Department of Education (PIBA-2020-1-0014). P.A.-G. acknowledges
support from the European Research Council under starting grant no. 715496, 2DNANOPTICA. '
article_number: eabf2690
article_processing_charge: No
article_type: original
author:
- first_name: J.
full_name: Duan, J.
last_name: Duan
- first_name: G.
full_name: Álvarez-Pérez, G.
last_name: Álvarez-Pérez
- first_name: K. V.
full_name: Voronin, K. V.
last_name: Voronin
- first_name: Ivan
full_name: Prieto Gonzalez, Ivan
id: 2A307FE2-F248-11E8-B48F-1D18A9856A87
last_name: Prieto Gonzalez
orcid: 0000-0002-7370-5357
- first_name: J.
full_name: Taboada-Gutiérrez, J.
last_name: Taboada-Gutiérrez
- first_name: V. S.
full_name: Volkov, V. S.
last_name: Volkov
- first_name: J.
full_name: Martín-Sánchez, J.
last_name: Martín-Sánchez
- first_name: A. Y.
full_name: Nikitin, A. Y.
last_name: Nikitin
- first_name: P.
full_name: Alonso-González, P.
last_name: Alonso-González
citation:
ama: Duan J, Álvarez-Pérez G, Voronin KV, et al. Enabling propagation of anisotropic
polaritons along forbidden directions via a topological transition. Science
Advances. 2021;7(14). doi:10.1126/sciadv.abf2690
apa: Duan, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., Taboada-Gutiérrez,
J., Volkov, V. S., … Alonso-González, P. (2021). Enabling propagation of anisotropic
polaritons along forbidden directions via a topological transition. Science
Advances. AAAS. https://doi.org/10.1126/sciadv.abf2690
chicago: Duan, J., G. Álvarez-Pérez, K. V. Voronin, Ivan Prieto Gonzalez, J. Taboada-Gutiérrez,
V. S. Volkov, J. Martín-Sánchez, A. Y. Nikitin, and P. Alonso-González. “Enabling
Propagation of Anisotropic Polaritons along Forbidden Directions via a Topological
Transition.” Science Advances. AAAS, 2021. https://doi.org/10.1126/sciadv.abf2690.
ieee: J. Duan et al., “Enabling propagation of anisotropic polaritons along
forbidden directions via a topological transition,” Science Advances, vol.
7, no. 14. AAAS, 2021.
ista: Duan J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Taboada-Gutiérrez
J, Volkov VS, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2021. Enabling
propagation of anisotropic polaritons along forbidden directions via a topological
transition. Science Advances. 7(14), eabf2690.
mla: Duan, J., et al. “Enabling Propagation of Anisotropic Polaritons along Forbidden
Directions via a Topological Transition.” Science Advances, vol. 7, no.
14, eabf2690, AAAS, 2021, doi:10.1126/sciadv.abf2690.
short: J. Duan, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, J. Taboada-Gutiérrez,
V.S. Volkov, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Science Advances
7 (2021).
date_created: 2021-04-18T22:01:42Z
date_published: 2021-04-02T00:00:00Z
date_updated: 2023-08-08T13:11:31Z
day: '02'
ddc:
- '530'
department:
- _id: NanoFab
doi: 10.1126/sciadv.abf2690
external_id:
isi:
- '000636455600027'
pmid:
- '33811076'
file:
- access_level: open_access
checksum: 4b383d4a1d484a71bbc64ecf401bbdbb
content_type: application/pdf
creator: dernst
date_created: 2021-04-19T11:17:29Z
date_updated: 2021-04-19T11:17:29Z
file_id: '9343'
file_name: 2021_ScienceAdv_Duan.pdf
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relation: main_file
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has_accepted_license: '1'
intvolume: ' 7'
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issue: '14'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Science Advances
publication_identifier:
eissn:
- '23752548'
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Enabling propagation of anisotropic polaritons along forbidden directions via
a topological transition
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 7
year: '2021'
...
---
_id: '9351'
abstract:
- lang: eng
text: 'We consider the many-body quantum evolution of a factorized initial data,
in the mean-field regime. We show that fluctuations around the limiting Hartree
dynamics satisfy large deviation estimates that are consistent with central limit
theorems that have been established in the last years. '
acknowledgement: The authors gratefully acknowledge Gérard Ben Arous for suggesting
this kind of result. K.L.K. was partially supported by NSF CAREER Award DMS-125479
and a Simons Sabbatical Fellowship. S.R. acknowledges funding from the European
Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 754411. B. S. gratefully acknowledges partial support from the
NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical
and energetic properties of Bose–Einstein condensates” and from the European Research
Council through the ERC-AdG CLaQS. Funding Open access funding provided by Institute
of Science and Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Kay
full_name: Kirkpatrick, Kay
last_name: Kirkpatrick
- first_name: Simone Anna Elvira
full_name: Rademacher, Simone Anna Elvira
id: 856966FE-A408-11E9-977E-802DE6697425
last_name: Rademacher
orcid: 0000-0001-5059-4466
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
citation:
ama: Kirkpatrick K, Rademacher SAE, Schlein B. A large deviation principle in many-body
quantum dynamics. Annales Henri Poincare. 2021;22:2595-2618. doi:10.1007/s00023-021-01044-1
apa: Kirkpatrick, K., Rademacher, S. A. E., & Schlein, B. (2021). A large deviation
principle in many-body quantum dynamics. Annales Henri Poincare. Springer
Nature. https://doi.org/10.1007/s00023-021-01044-1
chicago: Kirkpatrick, Kay, Simone Anna Elvira Rademacher, and Benjamin Schlein.
“A Large Deviation Principle in Many-Body Quantum Dynamics.” Annales Henri
Poincare. Springer Nature, 2021. https://doi.org/10.1007/s00023-021-01044-1.
ieee: K. Kirkpatrick, S. A. E. Rademacher, and B. Schlein, “A large deviation principle
in many-body quantum dynamics,” Annales Henri Poincare, vol. 22. Springer
Nature, pp. 2595–2618, 2021.
ista: Kirkpatrick K, Rademacher SAE, Schlein B. 2021. A large deviation principle
in many-body quantum dynamics. Annales Henri Poincare. 22, 2595–2618.
mla: Kirkpatrick, Kay, et al. “A Large Deviation Principle in Many-Body Quantum
Dynamics.” Annales Henri Poincare, vol. 22, Springer Nature, 2021, pp.
2595–618, doi:10.1007/s00023-021-01044-1.
short: K. Kirkpatrick, S.A.E. Rademacher, B. Schlein, Annales Henri Poincare 22
(2021) 2595–2618.
date_created: 2021-04-25T22:01:30Z
date_published: 2021-04-08T00:00:00Z
date_updated: 2023-08-08T13:14:40Z
day: '08'
ddc:
- '530'
department:
- _id: RoSe
doi: 10.1007/s00023-021-01044-1
ec_funded: 1
external_id:
arxiv:
- '2010.13754'
isi:
- '000638022600001'
file:
- access_level: open_access
checksum: 1a0fb963f2f415ba470881a794f20eb6
content_type: application/pdf
creator: cchlebak
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date_updated: 2021-10-15T11:15:40Z
file_id: '10143'
file_name: 2021_Annales_Kirkpatrick.pdf
file_size: 522669
relation: main_file
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file_date_updated: 2021-10-15T11:15:40Z
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isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 2595-2618
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Annales Henri Poincare
publication_identifier:
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A large deviation principle in many-body quantum dynamics
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 22
year: '2021'
...
---
_id: '9336'
abstract:
- lang: eng
text: Mentorship is experience and/or knowledge‐based guidance. Mentors support,
sponsor and advocate for mentees. Having one or more mentors when you seek advice
can significantly influence and improve your research endeavours, well‐being and
career development. Positive mentee–mentor relationships are vital for maintaining
work–life balance and success in careers. Early‐career researchers (ECRs), in
particular, can benefit from mentorship to navigate challenges in academic and
nonacademic life and careers. Yet, strategies for selecting mentors and maintaining
interactions with them are often underdiscussed within research environments.
In this Words of Advice, we provide recommendations for ECRs to seek and manage
mentorship interactions. Our article draws from our experiences as ECRs and published
work, to provide suggestions for mentees to proactively promote beneficial mentorship
interactions. The recommended practices highlight the importance of identifying
mentorship needs, planning and selecting multiple and diverse mentors, setting
goals, and maintaining constructive, and mutually beneficial working relationships
with mentors.
acknowledgement: The authors thank Nicholas Asby of the University of Chicago for
valuable comments on an earlier version of this work. A.P.S. was partially supported
by the NARSAD Young Investigator Grant 27705. S.J.H was supported by the National
Institutes of Health grant R35GM133732.
alternative_title:
- Words of Advice
article_processing_charge: No
article_type: original
author:
- first_name: Sarvenaz
full_name: Sarabipour, Sarvenaz
last_name: Sarabipour
- first_name: Sarah J.
full_name: Hainer, Sarah J.
last_name: Hainer
- first_name: Feyza N
full_name: Arslan, Feyza N
id: 49DA7910-F248-11E8-B48F-1D18A9856A87
last_name: Arslan
orcid: 0000-0001-5809-9566
- first_name: Charlotte M.
full_name: De Winde, Charlotte M.
last_name: De Winde
- first_name: Emily
full_name: Furlong, Emily
last_name: Furlong
- first_name: Natalia
full_name: Bielczyk, Natalia
last_name: Bielczyk
- first_name: Nafisa M.
full_name: Jadavji, Nafisa M.
last_name: Jadavji
- first_name: Aparna P.
full_name: Shah, Aparna P.
last_name: Shah
- first_name: Sejal
full_name: Davla, Sejal
last_name: Davla
citation:
ama: Sarabipour S, Hainer SJ, Arslan FN, et al. Building and sustaining mentor interactions
as a mentee. FEBS Journal. 2021. doi:10.1111/febs.15823
apa: Sarabipour, S., Hainer, S. J., Arslan, F. N., De Winde, C. M., Furlong, E.,
Bielczyk, N., … Davla, S. (2021). Building and sustaining mentor interactions
as a mentee. FEBS Journal. Wiley. https://doi.org/10.1111/febs.15823
chicago: Sarabipour, Sarvenaz, Sarah J. Hainer, Feyza N Arslan, Charlotte M. De
Winde, Emily Furlong, Natalia Bielczyk, Nafisa M. Jadavji, Aparna P. Shah, and
Sejal Davla. “Building and Sustaining Mentor Interactions as a Mentee.” FEBS
Journal. Wiley, 2021. https://doi.org/10.1111/febs.15823.
ieee: S. Sarabipour et al., “Building and sustaining mentor interactions
as a mentee,” FEBS Journal. Wiley, 2021.
ista: Sarabipour S, Hainer SJ, Arslan FN, De Winde CM, Furlong E, Bielczyk N, Jadavji
NM, Shah AP, Davla S. 2021. Building and sustaining mentor interactions as a mentee.
FEBS Journal.
mla: Sarabipour, Sarvenaz, et al. “Building and Sustaining Mentor Interactions as
a Mentee.” FEBS Journal, Wiley, 2021, doi:10.1111/febs.15823.
short: S. Sarabipour, S.J. Hainer, F.N. Arslan, C.M. De Winde, E. Furlong, N. Bielczyk,
N.M. Jadavji, A.P. Shah, S. Davla, FEBS Journal (2021).
date_created: 2021-04-18T22:01:43Z
date_published: 2021-04-05T00:00:00Z
date_updated: 2023-08-08T13:12:55Z
day: '05'
department:
- _id: CaHe
doi: 10.1111/febs.15823
external_id:
isi:
- '000636678800001'
pmid:
- '33818917'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/febs.15823
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: FEBS Journal
publication_identifier:
eissn:
- 1742-4658
issn:
- 1742-464X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Building and sustaining mentor interactions as a mentee
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9350'
abstract:
- lang: eng
text: Intercellular adhesion is the key to multicellularity, and its malfunction
plays an important role in various developmental and disease-related processes.
Although it has been intensively studied by both biologists and physicists, a
commonly accepted definition of cell-cell adhesion is still being debated. Cell-cell
adhesion has been described at the molecular scale as a function of adhesion receptors
controlling binding affinity, at the cellular scale as resistance to detachment
forces or modulation of surface tension, and at the tissue scale as a regulator
of cellular rearrangements and morphogenesis. In this review, we aim to summarize
and discuss recent advances in the molecular, cellular, and theoretical description
of cell-cell adhesion, ranging from biomimetic models to the complexity of cells
and tissues in an organismal context. In particular, we will focus on cadherin-mediated
cell-cell adhesion and the role of adhesion signaling and mechanosensation therein,
two processes central for understanding the biological and physical basis of cell-cell
adhesion.
acknowledgement: T.S. acknowledges funding by the research program “The Active Matter
Physics of Collective Metastasis,” which is financed by the Dutch Research Council
(NWO).
article_processing_charge: No
article_type: original
author:
- first_name: Feyza N
full_name: Arslan, Feyza N
id: 49DA7910-F248-11E8-B48F-1D18A9856A87
last_name: Arslan
orcid: 0000-0001-5809-9566
- first_name: Julia
full_name: Eckert, Julia
last_name: Eckert
- first_name: Thomas
full_name: Schmidt, Thomas
last_name: Schmidt
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: 'Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. Holding it together: when
cadherin meets cadherin. Biophysical Journal. 2021;120:4182-4192. doi:10.1016/j.bpj.2021.03.025'
apa: 'Arslan, F. N., Eckert, J., Schmidt, T., & Heisenberg, C.-P. J. (2021).
Holding it together: when cadherin meets cadherin. Biophysical Journal.
Biophysical Society. https://doi.org/10.1016/j.bpj.2021.03.025'
chicago: 'Arslan, Feyza N, Julia Eckert, Thomas Schmidt, and Carl-Philipp J Heisenberg.
“Holding It Together: When Cadherin Meets Cadherin.” Biophysical Journal.
Biophysical Society, 2021. https://doi.org/10.1016/j.bpj.2021.03.025.'
ieee: 'F. N. Arslan, J. Eckert, T. Schmidt, and C.-P. J. Heisenberg, “Holding it
together: when cadherin meets cadherin,” Biophysical Journal, vol. 120.
Biophysical Society, pp. 4182–4192, 2021.'
ista: 'Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. 2021. Holding it together:
when cadherin meets cadherin. Biophysical Journal. 120, 4182–4192.'
mla: 'Arslan, Feyza N., et al. “Holding It Together: When Cadherin Meets Cadherin.”
Biophysical Journal, vol. 120, Biophysical Society, 2021, pp. 4182–92,
doi:10.1016/j.bpj.2021.03.025.'
short: F.N. Arslan, J. Eckert, T. Schmidt, C.-P.J. Heisenberg, Biophysical Journal
120 (2021) 4182–4192.
date_created: 2021-04-25T22:01:30Z
date_published: 2021-10-05T00:00:00Z
date_updated: 2023-08-08T13:14:10Z
day: '05'
department:
- _id: CaHe
doi: 10.1016/j.bpj.2021.03.025
external_id:
isi:
- '000704646900006'
pmid:
- '33794149'
intvolume: ' 120'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://scholarlypublications.universiteitleiden.nl/access/item%3A3251048/view
month: '10'
oa: 1
oa_version: Published Version
page: 4182-4192
pmid: 1
publication: Biophysical Journal
publication_identifier:
eissn:
- 1542-0086
issn:
- 0006-3495
publication_status: published
publisher: Biophysical Society
quality_controlled: '1'
related_material:
record:
- id: '12368'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Holding it together: when cadherin meets cadherin'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 120
year: '2021'
...
---
_id: '9348'
abstract:
- lang: eng
text: We consider the stochastic quantization of a quartic double-well energy functional
in the semiclassical regime and derive optimal asymptotics for the exponentially
small splitting of the ground state energy. Our result provides an infinite-dimensional
version of some sharp tunneling estimates known in finite dimensions for semiclassical
Witten Laplacians in degree zero. From a stochastic point of view it proves that
the L2 spectral gap of the stochastic one-dimensional Allen-Cahn equation in finite
volume satisfies a Kramers-type formula in the limit of vanishing noise. We work
with finite-dimensional lattice approximations and establish semiclassical estimates
which are uniform in the dimension. Our key estimate shows that the constant separating
the two exponentially small eigenvalues from the rest of the spectrum can be taken
independently of the dimension.
acknowledgement: GDG gratefully acknowledges the financial support of HIM Bonn in
the framework of the 2019 Junior Trimester Programs “Kinetic Theory” and “Randomness,
PDEs and Nonlinear Fluctuations” and the hospitality at the University of Rome La
Sapienza during his frequent visits.
article_number: '109029'
article_processing_charge: No
article_type: original
author:
- first_name: Morris
full_name: Brooks, Morris
id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425
last_name: Brooks
orcid: 0000-0002-6249-0928
- first_name: Giacomo
full_name: Di Gesù, Giacomo
last_name: Di Gesù
citation:
ama: Brooks M, Di Gesù G. Sharp tunneling estimates for a double-well model in infinite
dimension. Journal of Functional Analysis. 2021;281(3). doi:10.1016/j.jfa.2021.109029
apa: Brooks, M., & Di Gesù, G. (2021). Sharp tunneling estimates for a double-well
model in infinite dimension. Journal of Functional Analysis. Elsevier.
https://doi.org/10.1016/j.jfa.2021.109029
chicago: Brooks, Morris, and Giacomo Di Gesù. “Sharp Tunneling Estimates for a Double-Well
Model in Infinite Dimension.” Journal of Functional Analysis. Elsevier,
2021. https://doi.org/10.1016/j.jfa.2021.109029.
ieee: M. Brooks and G. Di Gesù, “Sharp tunneling estimates for a double-well model
in infinite dimension,” Journal of Functional Analysis, vol. 281, no. 3.
Elsevier, 2021.
ista: Brooks M, Di Gesù G. 2021. Sharp tunneling estimates for a double-well model
in infinite dimension. Journal of Functional Analysis. 281(3), 109029.
mla: Brooks, Morris, and Giacomo Di Gesù. “Sharp Tunneling Estimates for a Double-Well
Model in Infinite Dimension.” Journal of Functional Analysis, vol. 281,
no. 3, 109029, Elsevier, 2021, doi:10.1016/j.jfa.2021.109029.
short: M. Brooks, G. Di Gesù, Journal of Functional Analysis 281 (2021).
date_created: 2021-04-25T22:01:29Z
date_published: 2021-04-07T00:00:00Z
date_updated: 2023-08-08T13:15:11Z
day: '07'
department:
- _id: RoSe
doi: 10.1016/j.jfa.2021.109029
external_id:
arxiv:
- '1911.03187'
isi:
- '000644702800005'
intvolume: ' 281'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1911.03187
month: '04'
oa: 1
oa_version: Preprint
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sharp tunneling estimates for a double-well model in infinite dimension
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 281
year: '2021'
...
---
_id: '9352'
abstract:
- lang: eng
text: This paper provides an a priori error analysis of a localized orthogonal decomposition
method for the numerical stochastic homogenization of a model random diffusion
problem. If the uniformly elliptic and bounded random coefficient field of the
model problem is stationary and satisfies a quantitative decorrelation assumption
in the form of the spectral gap inequality, then the expected $L^2$ error of the
method can be estimated, up to logarithmic factors, by $H+(\varepsilon/H)^{d/2}$,
$\varepsilon$ being the small correlation length of the random coefficient and
$H$ the width of the coarse finite element mesh that determines the spatial resolution.
The proof bridges recent results of numerical homogenization and quantitative
stochastic homogenization.
acknowledgement: 'This work was initiated while the authors enjoyed the kind hospitality
of the Hausdorff Institute for Mathematics in Bonn during the trimester program
Multiscale Problems: Algorithms, Numerical Analysis, and Computation. D. Peterseim
would like to acknowledge the kind hospitality of the Erwin Schrödinger International
Institute for Mathematics and Physics (ESI), where parts of this research were
developed under the frame of the thematic program Numerical Analysis of Complex
PDE Models in the Sciences.'
article_processing_charge: No
article_type: original
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Dietmar
full_name: Gallistl, Dietmar
last_name: Gallistl
- first_name: Dietmar
full_name: Peterseim, Dietmar
last_name: Peterseim
citation:
ama: Fischer JL, Gallistl D, Peterseim D. A priori error analysis of a numerical
stochastic homogenization method. SIAM Journal on Numerical Analysis. 2021;59(2):660-674.
doi:10.1137/19M1308992
apa: Fischer, J. L., Gallistl, D., & Peterseim, D. (2021). A priori error analysis
of a numerical stochastic homogenization method. SIAM Journal on Numerical
Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1308992
chicago: Fischer, Julian L, Dietmar Gallistl, and Dietmar Peterseim. “A Priori Error
Analysis of a Numerical Stochastic Homogenization Method.” SIAM Journal on
Numerical Analysis. Society for Industrial and Applied Mathematics, 2021.
https://doi.org/10.1137/19M1308992.
ieee: J. L. Fischer, D. Gallistl, and D. Peterseim, “A priori error analysis of
a numerical stochastic homogenization method,” SIAM Journal on Numerical Analysis,
vol. 59, no. 2. Society for Industrial and Applied Mathematics, pp. 660–674, 2021.
ista: Fischer JL, Gallistl D, Peterseim D. 2021. A priori error analysis of a numerical
stochastic homogenization method. SIAM Journal on Numerical Analysis. 59(2), 660–674.
mla: Fischer, Julian L., et al. “A Priori Error Analysis of a Numerical Stochastic
Homogenization Method.” SIAM Journal on Numerical Analysis, vol. 59, no.
2, Society for Industrial and Applied Mathematics, 2021, pp. 660–74, doi:10.1137/19M1308992.
short: J.L. Fischer, D. Gallistl, D. Peterseim, SIAM Journal on Numerical Analysis
59 (2021) 660–674.
date_created: 2021-04-25T22:01:31Z
date_published: 2021-03-09T00:00:00Z
date_updated: 2023-08-08T13:13:37Z
day: '09'
department:
- _id: JuFi
doi: 10.1137/19M1308992
external_id:
arxiv:
- '1912.11646'
isi:
- '000646030400003'
intvolume: ' 59'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.11646
month: '03'
oa: 1
oa_version: Preprint
page: 660-674
publication: SIAM Journal on Numerical Analysis
publication_identifier:
issn:
- 0036-1429
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: A priori error analysis of a numerical stochastic homogenization method
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 59
year: '2021'
...
---
_id: '9363'
abstract:
- lang: eng
text: Optogenetics has been harnessed to shed new mechanistic light on current and
future therapeutic strategies. This has been to date achieved by the regulation
of ion flow and electrical signals in neuronal cells and neural circuits that
are known to be affected by disease. In contrast, the optogenetic delivery of
trophic biochemical signals, which support cell survival and are implicated in
degenerative disorders, has never been demonstrated in an animal model of disease.
Here, we reengineered the human and Drosophila melanogaster REarranged during
Transfection (hRET and dRET) receptors to be activated by light, creating one-component
optogenetic tools termed Opto-hRET and Opto-dRET. Upon blue light stimulation,
these receptors robustly induced the MAPK/ERK proliferative signaling pathway
in cultured cells. In PINK1B9 flies that exhibit loss of PTEN-induced putative
kinase 1 (PINK1), a kinase associated with familial Parkinson’s disease (PD),
light activation of Opto-dRET suppressed mitochondrial defects, tissue degeneration
and behavioral deficits. In human cells with PINK1 loss-of-function, mitochondrial
fragmentation was rescued using Opto-dRET via the PI3K/NF-кB pathway. Our results
demonstrate that a light-activated receptor can ameliorate disease hallmarks in
a genetic model of PD. The optogenetic delivery of trophic signals is cell type-specific
and reversible and thus has the potential to inspire novel strategies towards
a spatio-temporal regulation of tissue repair.
acknowledgement: We thank R. Cagan, A. Whitworth and J. Nagpal for fly lines and advice,
S. Herlitze for provision of a tissue culture illuminator, and Verian Bader for
help with statistical analysis.
article_processing_charge: No
author:
- first_name: Álvaro
full_name: Inglés Prieto, Álvaro
id: 2A9DB292-F248-11E8-B48F-1D18A9856A87
last_name: Inglés Prieto
orcid: 0000-0002-5409-8571
- first_name: Nikolas
full_name: Furthmann, Nikolas
last_name: Furthmann
- first_name: Samuel H.
full_name: Crossman, Samuel H.
last_name: Crossman
- first_name: Alexandra Madelaine
full_name: Tichy, Alexandra Madelaine
last_name: Tichy
- first_name: Nina
full_name: Hoyer, Nina
last_name: Hoyer
- first_name: Meike
full_name: Petersen, Meike
last_name: Petersen
- first_name: Vanessa
full_name: Zheden, Vanessa
id: 39C5A68A-F248-11E8-B48F-1D18A9856A87
last_name: Zheden
- first_name: Julia
full_name: Bicher, Julia
id: 3CCBB46E-F248-11E8-B48F-1D18A9856A87
last_name: Bicher
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Peter
full_name: Soba, Peter
last_name: Soba
- first_name: Konstanze F.
full_name: Winklhofer, Konstanze F.
last_name: Winklhofer
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Inglés Prieto Á, Furthmann N, Crossman SH, et al. Optogenetic delivery of trophic
signals in a genetic model of Parkinson’s disease. PLoS genetics. 2021;17(4):e1009479.
doi:10.1371/journal.pgen.1009479
apa: Inglés Prieto, Á., Furthmann, N., Crossman, S. H., Tichy, A. M., Hoyer, N.,
Petersen, M., … Janovjak, H. L. (2021). Optogenetic delivery of trophic signals
in a genetic model of Parkinson’s disease. PLoS Genetics. Public Library
of Science. https://doi.org/10.1371/journal.pgen.1009479
chicago: Inglés Prieto, Álvaro, Nikolas Furthmann, Samuel H. Crossman, Alexandra
Madelaine Tichy, Nina Hoyer, Meike Petersen, Vanessa Zheden, et al. “Optogenetic
Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” PLoS
Genetics. Public Library of Science, 2021. https://doi.org/10.1371/journal.pgen.1009479.
ieee: Á. Inglés Prieto et al., “Optogenetic delivery of trophic signals in
a genetic model of Parkinson’s disease,” PLoS genetics, vol. 17, no. 4.
Public Library of Science, p. e1009479, 2021.
ista: Inglés Prieto Á, Furthmann N, Crossman SH, Tichy AM, Hoyer N, Petersen M,
Zheden V, Bicher J, Gschaider-Reichhart E, György A, Siekhaus DE, Soba P, Winklhofer
KF, Janovjak HL. 2021. Optogenetic delivery of trophic signals in a genetic model
of Parkinson’s disease. PLoS genetics. 17(4), e1009479.
mla: Inglés Prieto, Álvaro, et al. “Optogenetic Delivery of Trophic Signals in a
Genetic Model of Parkinson’s Disease.” PLoS Genetics, vol. 17, no. 4, Public
Library of Science, 2021, p. e1009479, doi:10.1371/journal.pgen.1009479.
short: Á. Inglés Prieto, N. Furthmann, S.H. Crossman, A.M. Tichy, N. Hoyer, M. Petersen,
V. Zheden, J. Bicher, E. Gschaider-Reichhart, A. György, D.E. Siekhaus, P. Soba,
K.F. Winklhofer, H.L. Janovjak, PLoS Genetics 17 (2021) e1009479.
date_created: 2021-05-02T22:01:29Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2023-08-08T13:17:47Z
day: '01'
ddc:
- '570'
department:
- _id: EM-Fac
- _id: LoSw
- _id: DaSi
doi: 10.1371/journal.pgen.1009479
external_id:
isi:
- '000640606700001'
file:
- access_level: open_access
checksum: 82a74668f863e8dfb22fdd4f845c92ce
content_type: application/pdf
creator: kschuh
date_created: 2021-05-04T09:05:27Z
date_updated: 2021-05-04T09:05:27Z
file_id: '9369'
file_name: 2021_PLOS_Ingles-Prieto.pdf
file_size: 3072764
relation: main_file
success: 1
file_date_updated: 2021-05-04T09:05:27Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: e1009479
publication: PLoS genetics
publication_identifier:
eissn:
- '15537404'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2021'
...
---
_id: '9380'
abstract:
- lang: eng
text: Shigella are pathogens originating within the Escherichia lineage but frequently
classified as a separate genus. Shigella genomes contain numerous insertion sequences
(ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous
recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess
the contribution of genomic rearrangements to Shigella evolution. We found that
Shigella experienced exceptionally high rates of intragenomic rearrangements and
had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic
E. coli. The high rearrangement rate resulted in independent disruption of syntenic
regions and parallel rearrangements in different Shigella lineages. Specifically,
we identified two types of chromosomally encoded E3 ubiquitin-protein ligases
acquired independently by all Shigella strains that also showed a high level of
sequence conservation in the promoter and further in the 5′-intergenic region.
In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic
E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli,
we found a rate of genome rearrangements comparable to those in other E. coli
and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These
data indicate that the accumulation of ISs influenced many aspects of genome evolution
and played an important role in the evolution of intracellular pathogens. Our
research demonstrates the power of comparative genomics-based on synteny block
composition and an important role of non-coding regions in the evolution of genomic
islands.
acknowledgement: We thank Fyodor Kondrashov for valuable advice and manuscript proofreading.
We also thank Alla Mikheenko for assistance with Circos.
article_number: '628622'
article_processing_charge: No
article_type: original
author:
- first_name: Zaira
full_name: Seferbekova, Zaira
last_name: Seferbekova
- first_name: Alexey
full_name: Zabelkin, Alexey
last_name: Zabelkin
- first_name: Yulia
full_name: Yakovleva, Yulia
last_name: Yakovleva
- first_name: Robert
full_name: Afasizhev, Robert
last_name: Afasizhev
- first_name: Natalia O.
full_name: Dranenko, Natalia O.
last_name: Dranenko
- first_name: Nikita
full_name: Alexeev, Nikita
last_name: Alexeev
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
citation:
ama: Seferbekova Z, Zabelkin A, Yakovleva Y, et al. High rates of genome rearrangements
and pathogenicity of Shigella spp. Frontiers in Microbiology. 2021;12.
doi:10.3389/fmicb.2021.628622
apa: Seferbekova, Z., Zabelkin, A., Yakovleva, Y., Afasizhev, R., Dranenko, N. O.,
Alexeev, N., … Bochkareva, O. (2021). High rates of genome rearrangements and
pathogenicity of Shigella spp. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2021.628622
chicago: Seferbekova, Zaira, Alexey Zabelkin, Yulia Yakovleva, Robert Afasizhev,
Natalia O. Dranenko, Nikita Alexeev, Mikhail S. Gelfand, and Olga Bochkareva.
“High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” Frontiers
in Microbiology. Frontiers, 2021. https://doi.org/10.3389/fmicb.2021.628622.
ieee: Z. Seferbekova et al., “High rates of genome rearrangements and pathogenicity
of Shigella spp,” Frontiers in Microbiology, vol. 12. Frontiers, 2021.
ista: Seferbekova Z, Zabelkin A, Yakovleva Y, Afasizhev R, Dranenko NO, Alexeev
N, Gelfand MS, Bochkareva O. 2021. High rates of genome rearrangements and pathogenicity
of Shigella spp. Frontiers in Microbiology. 12, 628622.
mla: Seferbekova, Zaira, et al. “High Rates of Genome Rearrangements and Pathogenicity
of Shigella Spp.” Frontiers in Microbiology, vol. 12, 628622, Frontiers,
2021, doi:10.3389/fmicb.2021.628622.
short: Z. Seferbekova, A. Zabelkin, Y. Yakovleva, R. Afasizhev, N.O. Dranenko, N.
Alexeev, M.S. Gelfand, O. Bochkareva, Frontiers in Microbiology 12 (2021).
date_created: 2021-05-09T22:01:38Z
date_published: 2021-04-12T00:00:00Z
date_updated: 2023-08-08T13:30:39Z
day: '12'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.3389/fmicb.2021.628622
ec_funded: 1
external_id:
isi:
- '000643713300001'
file:
- access_level: open_access
checksum: 2f856543add59273a482a7f326fc0400
content_type: application/pdf
creator: kschuh
date_created: 2021-05-11T13:05:52Z
date_updated: 2021-05-11T13:05:52Z
file_id: '9384'
file_name: 2021_Frontiers_Microbiology_Seferbekova.pdf
file_size: 14362316
relation: main_file
success: 1
file_date_updated: 2021-05-11T13:05:52Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Frontiers in Microbiology
publication_identifier:
eissn:
- 1664-302X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: High rates of genome rearrangements and pathogenicity of Shigella spp
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9359'
abstract:
- lang: eng
text: "We prove that the factorization homologies of a scheme with coefficients
in truncated polynomial algebras compute the cohomologies of its generalized configuration
spaces. Using Koszul duality between commutative algebras and Lie algebras, we
obtain new expressions for the cohomologies of the latter. As a consequence, we
obtain a uniform and conceptual approach for treating homological stability, homological
densities, and arithmetic densities of generalized configuration spaces. Our results
categorify, generalize, and in fact provide a conceptual understanding of the
coincidences appearing in the work of Farb--Wolfson--Wood. Our computation of
the stable homological densities also yields rational homotopy types, answering
a question posed by Vakil--Wood. Our approach hinges on the study of homological
stability of cohomological Chevalley complexes, which is of independent interest.\r\n"
acknowledgement: "This paper owes an obvious intellectual debt to the illuminating
treatments of factorization homology by J.\r\nFrancis, D. Gaitsgory, and J. Lurie
in [GL,G1, FG]. The author would like to thank B. Farb and J. Wolfson for\r\nbringing
the question of explaining coincidences in homological densities to his attention.
Moreover, the author\r\nthanks J. Wolfson for many helpful conversations on the
subject, O. Randal-Williams for many comments which\r\ngreatly help improve the
exposition, and G. C. Drummond-Cole for many useful conversations on L∞-algebras.\r\nFinally,
the author is grateful to the anonymous referee for carefully reading the manuscript
and for providing\r\nnumerous comments which greatly helped improve the clarity
and precision of the exposition.\r\nThis work is supported by the Advanced Grant
“Arithmetic and Physics of Higgs moduli spaces” No. 320593 of\r\nthe European Research
Council and the Lise Meitner fellowship “Algebro-Geometric Applications of Factorization\r\nHomology,”
Austrian Science Fund (FWF): M 2751."
article_processing_charge: No
article_type: original
author:
- first_name: Quoc P
full_name: Ho, Quoc P
id: 3DD82E3C-F248-11E8-B48F-1D18A9856A87
last_name: Ho
citation:
ama: Ho QP. Homological stability and densities of generalized configuration spaces.
Geometry & Topology. 2021;25(2):813-912. doi:10.2140/gt.2021.25.813
apa: Ho, Q. P. (2021). Homological stability and densities of generalized configuration
spaces. Geometry & Topology. Mathematical Sciences Publishers. https://doi.org/10.2140/gt.2021.25.813
chicago: Ho, Quoc P. “Homological Stability and Densities of Generalized Configuration
Spaces.” Geometry & Topology. Mathematical Sciences Publishers, 2021.
https://doi.org/10.2140/gt.2021.25.813.
ieee: Q. P. Ho, “Homological stability and densities of generalized configuration
spaces,” Geometry & Topology, vol. 25, no. 2. Mathematical Sciences
Publishers, pp. 813–912, 2021.
ista: Ho QP. 2021. Homological stability and densities of generalized configuration
spaces. Geometry & Topology. 25(2), 813–912.
mla: Ho, Quoc P. “Homological Stability and Densities of Generalized Configuration
Spaces.” Geometry & Topology, vol. 25, no. 2, Mathematical Sciences
Publishers, 2021, pp. 813–912, doi:10.2140/gt.2021.25.813.
short: Q.P. Ho, Geometry & Topology 25 (2021) 813–912.
date_created: 2021-05-02T06:59:33Z
date_published: 2021-04-27T00:00:00Z
date_updated: 2023-08-08T13:28:59Z
day: '27'
ddc:
- '514'
- '516'
- '512'
department:
- _id: TaHa
doi: 10.2140/gt.2021.25.813
ec_funded: 1
external_id:
arxiv:
- '1802.07948'
isi:
- '000682738600005'
file:
- access_level: open_access
checksum: 643a8d2d6f06f0888dcd7503f55d0920
content_type: application/pdf
creator: qho
date_created: 2021-05-03T06:54:06Z
date_updated: 2021-05-03T06:54:06Z
file_id: '9366'
file_name: densities.pdf
file_size: 479268
relation: main_file
success: 1
file_date_updated: 2021-05-03T06:54:06Z
has_accepted_license: '1'
intvolume: ' 25'
isi: 1
issue: '2'
keyword:
- Generalized configuration spaces
- homological stability
- homological densities
- chiral algebras
- chiral homology
- factorization algebras
- Koszul duality
- Ran space
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 813-912
project:
- _id: 25E549F4-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '320593'
name: Arithmetic and physics of Higgs moduli spaces
- _id: 26B96266-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02751
name: Algebro-Geometric Applications of Factorization Homology
publication: Geometry & Topology
publication_identifier:
issn:
- 1364-0380
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
status: public
title: Homological stability and densities of generalized configuration spaces
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 25
year: '2021'
...
---
_id: '9361'
abstract:
- lang: eng
text: The multimeric matrix (M) protein of clinically relevant paramyxoviruses orchestrates
assembly and budding activity of viral particles at the plasma membrane (PM).
We identified within the canine distemper virus (CDV) M protein two microdomains,
potentially assuming α-helix structures, which are essential for membrane budding
activity. Remarkably, while two rationally designed microdomain M mutants (E89R,
microdomain 1 and L239D, microdomain 2) preserved proper folding, dimerization,
interaction with the nucleocapsid protein, localization at and deformation of
the PM, the virus-like particle formation, as well as production of infectious
virions (as monitored using a membrane budding-complementation system), were,
in sharp contrast, strongly impaired. Of major importance, raster image correlation
spectroscopy (RICS) revealed that both microdomains contributed to finely tune
M protein mobility specifically at the PM. Collectively, our data highlighted
the cornerstone membrane budding-priming activity of two spatially discrete M
microdomains, potentially by coordinating the assembly of productive higher oligomers
at the PM.
acknowledgement: This work was supported by the Swiss National Science Foundation
(referencenumber 310030_173185 to P. P.).
article_number: e01024-20
article_processing_charge: No
author:
- first_name: Matthieu
full_name: Gast, Matthieu
last_name: Gast
- first_name: Nicole P.
full_name: Kadzioch, Nicole P.
last_name: Kadzioch
- first_name: Doreen
full_name: Milius, Doreen
id: 384050BC-F248-11E8-B48F-1D18A9856A87
last_name: Milius
- first_name: Francesco
full_name: Origgi, Francesco
last_name: Origgi
- first_name: Philippe
full_name: Plattet, Philippe
last_name: Plattet
citation:
ama: Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. Oligomerization and cell
egress controlled by two microdomains of canine distemper virus matrix protein.
mSphere. 2021;6(2). doi:10.1128/mSphere.01024-20
apa: Gast, M., Kadzioch, N. P., Milius, D., Origgi, F., & Plattet, P. (2021).
Oligomerization and cell egress controlled by two microdomains of canine distemper
virus matrix protein. MSphere. American Society for Microbiology. https://doi.org/10.1128/mSphere.01024-20
chicago: Gast, Matthieu, Nicole P. Kadzioch, Doreen Milius, Francesco Origgi, and
Philippe Plattet. “Oligomerization and Cell Egress Controlled by Two Microdomains
of Canine Distemper Virus Matrix Protein.” MSphere. American Society for
Microbiology, 2021. https://doi.org/10.1128/mSphere.01024-20.
ieee: M. Gast, N. P. Kadzioch, D. Milius, F. Origgi, and P. Plattet, “Oligomerization
and cell egress controlled by two microdomains of canine distemper virus matrix
protein,” mSphere, vol. 6, no. 2. American Society for Microbiology, 2021.
ista: Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. 2021. Oligomerization
and cell egress controlled by two microdomains of canine distemper virus matrix
protein. mSphere. 6(2), e01024-20.
mla: Gast, Matthieu, et al. “Oligomerization and Cell Egress Controlled by Two Microdomains
of Canine Distemper Virus Matrix Protein.” MSphere, vol. 6, no. 2, e01024-20,
American Society for Microbiology, 2021, doi:10.1128/mSphere.01024-20.
short: M. Gast, N.P. Kadzioch, D. Milius, F. Origgi, P. Plattet, MSphere 6 (2021).
date_created: 2021-05-02T22:01:28Z
date_published: 2021-04-14T00:00:00Z
date_updated: 2023-08-08T13:26:12Z
day: '14'
ddc:
- '570'
department:
- _id: Bio
doi: 10.1128/mSphere.01024-20
external_id:
isi:
- '000663823400025'
pmid:
- '33853875'
file:
- access_level: open_access
checksum: 310748d140c8838335c1314431095898
content_type: application/pdf
creator: kschuh
date_created: 2021-05-04T12:41:38Z
date_updated: 2021-05-04T12:41:38Z
file_id: '9370'
file_name: 2021_mSphere_Gast.pdf
file_size: 3379349
relation: main_file
success: 1
file_date_updated: 2021-05-04T12:41:38Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: mSphere
publication_identifier:
eissn:
- '23795042'
publication_status: published
publisher: American Society for Microbiology
quality_controlled: '1'
scopus_import: '1'
status: public
title: Oligomerization and cell egress controlled by two microdomains of canine distemper
virus matrix protein
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 6
year: '2021'
...
---
_id: '9376'
abstract:
- lang: eng
text: This paper presents a method for designing planar multistable compliant structures.
Given a sequence of desired stable states and the corresponding poses of the structure,
we identify the topology and geometric realization of a mechanism—consisting of
bars and joints—that is able to physically reproduce the desired multistable behavior.
In order to solve this problem efficiently, we build on insights from minimally
rigid graph theory to identify simple but effective topologies for the mechanism.
We then optimize its geometric parameters, such as joint positions and bar lengths,
to obtain correct transitions between the given poses. Simultaneously, we ensure
adequate stability of each pose based on an effective approximate error metric
related to the elastic energy Hessian of the bars in the mechanism. As demonstrated
by our results, we obtain functional multistable mechanisms of manageable complexity
that can be fabricated using 3D printing. Further, we evaluated the effectiveness
of our method on a large number of examples in the simulation and fabricated several
physical prototypes.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: 'We would like to thank everyone who contributed to this paper, the
authors of artworks for all the examples, including @macrovec-tor_official and Wikimedia
for the FLAG semaphore, and @pikisuper-star for the FIGURINE. The photos of iconic
poses in the teaser were supplied by (from left to right): Mike Hewitt/Olympics
Day 8 - Athletics/Gettty Images, Oneinchpunch/Basketball player training on acourt
in New york city/Shutterstock, and Andrew Redington/TigerWoods/Getty Images. We
also want to express our gratitude to Christian Hafner for insightful discussions,
the IST Austria machine shop SSU, all proof-readers, and anonymous reviewers. This
project has received funding from the European Union’s Horizon 2020 research and
innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841
(DISTRO), and under the European Research Council grant agreement No 715767 (MATERIALIZABLE).'
article_number: '186'
article_processing_charge: No
article_type: original
author:
- first_name: Ran
full_name: Zhang, Ran
id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0002-3808-281X
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Zhang R, Auzinger T, Bickel B. Computational design of planar multistable compliant
structures. ACM Transactions on Graphics. 2021;40(5). doi:10.1145/3453477
apa: Zhang, R., Auzinger, T., & Bickel, B. (2021). Computational design of planar
multistable compliant structures. ACM Transactions on Graphics. Association
for Computing Machinery. https://doi.org/10.1145/3453477
chicago: Zhang, Ran, Thomas Auzinger, and Bernd Bickel. “Computational Design of
Planar Multistable Compliant Structures.” ACM Transactions on Graphics.
Association for Computing Machinery, 2021. https://doi.org/10.1145/3453477.
ieee: R. Zhang, T. Auzinger, and B. Bickel, “Computational design of planar multistable
compliant structures,” ACM Transactions on Graphics, vol. 40, no. 5. Association
for Computing Machinery, 2021.
ista: Zhang R, Auzinger T, Bickel B. 2021. Computational design of planar multistable
compliant structures. ACM Transactions on Graphics. 40(5), 186.
mla: Zhang, Ran, et al. “Computational Design of Planar Multistable Compliant Structures.”
ACM Transactions on Graphics, vol. 40, no. 5, 186, Association for Computing
Machinery, 2021, doi:10.1145/3453477.
short: R. Zhang, T. Auzinger, B. Bickel, ACM Transactions on Graphics 40 (2021).
date_created: 2021-05-08T17:37:08Z
date_published: 2021-10-08T00:00:00Z
date_updated: 2023-08-08T13:31:38Z
day: '08'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3453477
ec_funded: 1
external_id:
isi:
- '000752079300003'
file:
- access_level: open_access
checksum: 8564b3118457d4c8939a8ef2b1a2f16c
content_type: application/pdf
creator: bbickel
date_created: 2021-05-08T17:36:59Z
date_updated: 2021-05-08T17:36:59Z
file_id: '9377'
file_name: Multistable-authorversion.pdf
file_size: 18926557
relation: main_file
- access_level: open_access
checksum: 3b6e874e30bfa1bfc3ad3498710145a1
content_type: video/mp4
creator: bbickel
date_created: 2021-05-08T17:38:22Z
date_updated: 2021-05-08T17:38:22Z
file_id: '9378'
file_name: multistable-video.mp4
file_size: 76542901
relation: main_file
success: 1
- access_level: open_access
checksum: 20dc3bc42e1a912a5b0247c116772098
content_type: application/pdf
creator: bbickel
date_created: 2021-12-17T08:13:51Z
date_updated: 2021-12-17T08:13:51Z
description: This document provides additional results and analyzes the robustness
and limitations of our approach.
file_id: '10562'
file_name: multistable-supplementary material.pdf
file_size: 3367072
relation: supplementary_material
title: Supplementary Material for “Computational Design of Planar Multistable Compliant
Structures”
file_date_updated: 2021-12-17T08:13:51Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '5'
keyword:
- multistability
- mechanism
- computational design
- rigidity
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: Computational design of planar multistable compliant structures
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...
---
_id: '9375'
abstract:
- lang: eng
text: Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes
and linkage are central to genetics and underpin virtually all genetic and selection
analysis. And yet, genomic data often lack haplotype information, due to constraints
in sequencing technologies. Here we present “haplotagging”, a simple, low-cost
linked-read sequencing technique that allows sequencing of hundreds of individuals
while retaining linkage information. We apply haplotagging to construct megabase-size
haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene),
which form overlapping hybrid zones across an elevational gradient in Ecuador.
Haplotagging identifies loci controlling distinctive high- and lowland wing color
patterns. Divergent haplotypes are found at the same major loci in both species,
while chromosome rearrangements show no parallelism. Remarkably, in both species
the geographic clines for the major wing pattern loci are displaced by 18 km,
leading to the rise of a novel hybrid morph in the centre of the hybrid zone.
We propose that shared warning signalling (Müllerian mimicry) may couple the cline
shifts seen in both species, and facilitate the parallel co-emergence of a novel
hybrid morph in both co-mimetic species. Our results show the power of efficient
haplotyping methods when combined with large-scale sequencing data from natural
populations.
acknowledgement: 'We thank Felicity Jones for input into experimental design, helpful
discussion and improving the manuscript. We thank the Rolian, Jiggins, Chan and
Jones Labs members for support, insightful scientific discussion and improving the
manuscript. We thank the Rolian lab members, the Animal Resource Centre staff at
the University of Calgary, and Caroline Schmid and Ann-Katrin Geysel at the Friedrich
Miescher Laboratory for animal husbandry. We thank Christa Lanz, Rebecca Schwab
and Ilja Bezrukov for assistance with high-throughput sequencing and associated
data processing; Andre Noll and the MPI Tübingen IT team for computational support.
We thank Ben Haller and Richard Durbin for helpful discussions. We thank David M.
Kingsley for thoughtful input that has greatly improved our manuscript. J.I.M. is
supported by a Research Fellowship from St. John’s College, Cambridge. A.D. was
supported by a European Research Council Consolidator Grant (No. 617279 “EvolRecombAdapt”,
P/I Felicity Jones). C.R. is supported by Discovery Grant #4181932 from the Natural
Sciences and Engineering Research Council of Canada and by the Faculty of Veterinary
Medicine at the University of Calgary. C.D.J. is supported by a BBSRC grant BB/R007500
and a European Research Council Advanced Grant (No. 339873 “SpeciationGenetics”).
M.K. and Y.F.C. are supported by the Max Planck Society and a European Research
Council Starting Grant (No. 639096 “HybridMiX”).'
article_number: e2015005118
article_processing_charge: No
article_type: original
author:
- first_name: Joana I.
full_name: Meier, Joana I.
last_name: Meier
- first_name: Patricio A.
full_name: Salazar, Patricio A.
last_name: Salazar
- first_name: Marek
full_name: Kučka, Marek
last_name: Kučka
- first_name: Robert William
full_name: Davies, Robert William
last_name: Davies
- first_name: Andreea
full_name: Dréau, Andreea
last_name: Dréau
- first_name: Ismael
full_name: Aldás, Ismael
last_name: Aldás
- first_name: Olivia Box
full_name: Power, Olivia Box
last_name: Power
- first_name: Nicola J.
full_name: Nadeau, Nicola J.
last_name: Nadeau
- first_name: Jon R.
full_name: Bridle, Jon R.
last_name: Bridle
- first_name: Campbell
full_name: Rolian, Campbell
last_name: Rolian
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: W. Owen
full_name: McMillan, W. Owen
last_name: McMillan
- first_name: Chris D.
full_name: Jiggins, Chris D.
last_name: Jiggins
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
citation:
ama: Meier JI, Salazar PA, Kučka M, et al. Haplotype tagging reveals parallel formation
of hybrid races in two butterfly species. PNAS. 2021;118(25). doi:10.1073/pnas.2015005118
apa: Meier, J. I., Salazar, P. A., Kučka, M., Davies, R. W., Dréau, A., Aldás, I.,
… Chan, Y. F. (2021). Haplotype tagging reveals parallel formation of hybrid races
in two butterfly species. PNAS. Proceedings of the National Academy of
Sciences. https://doi.org/10.1073/pnas.2015005118
chicago: Meier, Joana I., Patricio A. Salazar, Marek Kučka, Robert William Davies,
Andreea Dréau, Ismael Aldás, Olivia Box Power, et al. “Haplotype Tagging Reveals
Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS. Proceedings
of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2015005118.
ieee: J. I. Meier et al., “Haplotype tagging reveals parallel formation of
hybrid races in two butterfly species,” PNAS, vol. 118, no. 25. Proceedings
of the National Academy of Sciences, 2021.
ista: Meier JI, Salazar PA, Kučka M, Davies RW, Dréau A, Aldás I, Power OB, Nadeau
NJ, Bridle JR, Rolian C, Barton NH, McMillan WO, Jiggins CD, Chan YF. 2021. Haplotype
tagging reveals parallel formation of hybrid races in two butterfly species. PNAS.
118(25), e2015005118.
mla: Meier, Joana I., et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid
Races in Two Butterfly Species.” PNAS, vol. 118, no. 25, e2015005118, Proceedings
of the National Academy of Sciences, 2021, doi:10.1073/pnas.2015005118.
short: J.I. Meier, P.A. Salazar, M. Kučka, R.W. Davies, A. Dréau, I. Aldás, O.B.
Power, N.J. Nadeau, J.R. Bridle, C. Rolian, N.H. Barton, W.O. McMillan, C.D. Jiggins,
Y.F. Chan, PNAS 118 (2021).
date_created: 2021-05-07T17:10:21Z
date_published: 2021-06-21T00:00:00Z
date_updated: 2023-08-08T13:33:09Z
day: '21'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1073/pnas.2015005118
external_id:
isi:
- '000671755600001'
pmid:
- '34155138'
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pmid: 1
publication: PNAS
publication_identifier:
eissn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Haplotype tagging reveals parallel formation of hybrid races in two butterfly
species
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...
---
_id: '9394'
abstract:
- lang: eng
text: 'Chromosomal inversions have long been recognized for their role in local
adaptation. By suppressing recombination in heterozygous individuals, they can
maintain coadapted gene complexes and protect them from homogenizing effects of
gene flow. However, to fully understand their importance for local adaptation
we need to know their influence on phenotypes under divergent selection. For this,
the marine snail Littorina saxatilis provides an ideal study system. Divergent
ecotypes adapted to wave action and crab predation occur in close proximity on
intertidal shores with gene flow between them. Here, we used F2 individuals obtained
from crosses between the ecotypes to test for associations between genomic regions
and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape,
shell thickness, and behavior. We show that most of these traits are influenced
by two previously detected inversion regions that are divergent between ecotypes.
We thus gain a better understanding of one important underlying mechanism responsible
for the rapid and repeated formation of ecotypes: divergent selection acting on
inversions. We also found that some inversions contributed to more than one trait
suggesting that they may contain several loci involved in adaptation, consistent
with the hypothesis that suppression of recombination within inversions facilitates
differentiation in the presence of gene flow.'
acknowledgement: 'We are very grateful to Irena Senčić for technical assistance and
to Michelle Kortyna and Sean Holland at the Center for Anchored Phylogenomics for
assistance with data collection. RKB was funded by the Natural Environment Research
Council and by the European Research Council. KJ was funded by the Swedish Research
Councils VR and Formas (Linnaeus Grant: 217‐2008‐1719). JL was funded by a studentship
from the Leverhulme Centre for Advanced Biological Modelling. AMW was funded by
the European Union''s Horizon 2020 research and innovation program under Marie Skłodowska‐Curie
Grant agreement no. 797747. RF was funded by the European Union''s Horizon 2020
research and innovation programme under the Marie Sklodowska‐Curie Grant agreement
No. 706376 and by FEDER Funds through the Operational Competitiveness Factors Program—COMPETE
and by National Funds through FCT—Foundation for Science and Technology within the
scope of the project “Hybrabbid” (PTDC/BIA‐EVL/30628/2017‐ POCI‐01‐0145‐FEDER‐030628).
We are grateful to other members of the Littorina research group for helpful discussions.
We thank Claire Mérot and an anonymous referee for insightful comments on an earlier
version. '
article_processing_charge: No
article_type: original
author:
- first_name: Eva L.
full_name: Koch, Eva L.
last_name: Koch
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Jenny
full_name: Larsson, Jenny
last_name: Larsson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Alan R.
full_name: Lemmon, Alan R.
last_name: Lemmon
- first_name: E. Moriarty
full_name: Lemmon, E. Moriarty
last_name: Lemmon
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Koch EL, Morales HE, Larsson J, et al. Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis. Evolution
Letters. 2021;5(3):196-213. doi:10.1002/evl3.227
apa: Koch, E. L., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon,
A. R., … Butlin, R. K. (2021). Genetic variation for adaptive traits is associated
with polymorphic inversions in Littorina saxatilis. Evolution Letters.
Wiley. https://doi.org/10.1002/evl3.227
chicago: Koch, Eva L., Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria,
Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin.
“Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions
in Littorina Saxatilis.” Evolution Letters. Wiley, 2021. https://doi.org/10.1002/evl3.227.
ieee: E. L. Koch et al., “Genetic variation for adaptive traits is associated
with polymorphic inversions in Littorina saxatilis,” Evolution Letters,
vol. 5, no. 3. Wiley, pp. 196–213, 2021.
ista: Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM,
Johannesson K, Butlin RK. 2021. Genetic variation for adaptive traits is associated
with polymorphic inversions in Littorina saxatilis. Evolution Letters. 5(3), 196–213.
mla: Koch, Eva L., et al. “Genetic Variation for Adaptive Traits Is Associated with
Polymorphic Inversions in Littorina Saxatilis.” Evolution Letters, vol.
5, no. 3, Wiley, 2021, pp. 196–213, doi:10.1002/evl3.227.
short: E.L. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon,
E.M. Lemmon, K. Johannesson, R.K. Butlin, Evolution Letters 5 (2021) 196–213.
date_created: 2021-05-16T22:01:47Z
date_published: 2021-05-07T00:00:00Z
date_updated: 2023-08-08T13:34:08Z
day: '07'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/evl3.227
ec_funded: 1
external_id:
isi:
- '000647846200001'
file:
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checksum: 023b1608e311f0fda30593ba3d0a4e0b
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-15T08:26:02Z
date_updated: 2021-10-15T08:26:02Z
file_id: '10142'
file_name: 2021_EvolutionLetters_Koch.pdf
file_size: 3021108
relation: main_file
success: 1
file_date_updated: 2021-10-15T08:26:02Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '3'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 196-213
project:
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: Evolution Letters
publication_identifier:
eissn:
- 2056-3744
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '12987'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Genetic variation for adaptive traits is associated with polymorphic inversions
in Littorina saxatilis
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2021'
...
---
_id: '9381'
abstract:
- lang: eng
text: 'A game of rock-paper-scissors is an interesting example of an interaction
where none of the pure strategies strictly dominates all others, leading to a
cyclic pattern. In this work, we consider an unstable version of rock-paper-scissors
dynamics and allow individuals to make behavioural mistakes during the strategy
execution. We show that such an assumption can break a cyclic relationship leading
to a stable equilibrium emerging with only one strategy surviving. We consider
two cases: completely random mistakes when individuals have no bias towards any
strategy and a general form of mistakes. Then, we determine conditions for a strategy
to dominate all other strategies. However, given that individuals who adopt a
dominating strategy are still prone to behavioural mistakes in the observed behaviour,
we may still observe extinct strategies. That is, behavioural mistakes in strategy
execution stabilise evolutionary dynamics leading to an evolutionary stable and,
potentially, mixed co-existence equilibrium.'
acknowledgement: Authors would like to thank Christian Hilbe and Martin Nowak for
their inspiring and very helpful feedback on the manuscript.
article_number: e1008523
article_processing_charge: No
article_type: original
author:
- first_name: Maria
full_name: Kleshnina, Maria
id: 4E21749C-F248-11E8-B48F-1D18A9856A87
last_name: Kleshnina
- first_name: Sabrina S.
full_name: Streipert, Sabrina S.
last_name: Streipert
- first_name: Jerzy A.
full_name: Filar, Jerzy A.
last_name: Filar
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Kleshnina M, Streipert SS, Filar JA, Chatterjee K. Mistakes can stabilise the
dynamics of rock-paper-scissors games. PLoS Computational Biology. 2021;17(4).
doi:10.1371/journal.pcbi.1008523
apa: Kleshnina, M., Streipert, S. S., Filar, J. A., & Chatterjee, K. (2021).
Mistakes can stabilise the dynamics of rock-paper-scissors games. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008523
chicago: Kleshnina, Maria, Sabrina S. Streipert, Jerzy A. Filar, and Krishnendu
Chatterjee. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors Games.”
PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008523.
ieee: M. Kleshnina, S. S. Streipert, J. A. Filar, and K. Chatterjee, “Mistakes can
stabilise the dynamics of rock-paper-scissors games,” PLoS Computational Biology,
vol. 17, no. 4. Public Library of Science, 2021.
ista: Kleshnina M, Streipert SS, Filar JA, Chatterjee K. 2021. Mistakes can stabilise
the dynamics of rock-paper-scissors games. PLoS Computational Biology. 17(4),
e1008523.
mla: Kleshnina, Maria, et al. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors
Games.” PLoS Computational Biology, vol. 17, no. 4, e1008523, Public Library
of Science, 2021, doi:10.1371/journal.pcbi.1008523.
short: M. Kleshnina, S.S. Streipert, J.A. Filar, K. Chatterjee, PLoS Computational
Biology 17 (2021).
date_created: 2021-05-09T22:01:38Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2023-08-08T13:31:08Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1008523
ec_funded: 1
external_id:
isi:
- '000639711200001'
file:
- access_level: open_access
checksum: a94ebe0c4116f5047eaa6029e54d2dac
content_type: application/pdf
creator: kschuh
date_created: 2021-05-11T13:50:06Z
date_updated: 2021-05-11T13:50:06Z
file_id: '9385'
file_name: 2021_pcbi_Kleshnina.pdf
file_size: 1323820
relation: main_file
success: 1
file_date_updated: 2021-05-11T13:50:06Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: PLoS Computational Biology
publication_identifier:
eissn:
- '15537358'
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mistakes can stabilise the dynamics of rock-paper-scissors games
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2021'
...
---
_id: '9392'
abstract:
- lang: eng
text: 'Humans conceptualize the diversity of life by classifying individuals into
types we call ‘species’1. The species we recognize influence political and financial
decisions and guide our understanding of how units of diversity evolve and interact.
Although the idea of species may seem intuitive, a debate about the best way to
define them has raged even before Darwin2. So much energy has been devoted to
the so-called ‘species problem’ that no amount of discourse will ever likely solve
it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete
understanding of how much researchers actually disagree and the factors that cause
them to think differently1,2. To address this, we used a survey to quantify the
species problem for the first time. The results indicate that the disagreement
is extensive: two randomly chosen respondents will most likely disagree on the
nature of species. The probability of disagreement is not predicted by researcher
experience or broad study system, but tended to be lower among researchers with
similar focus, training and who study the same organism. Should we see this diversity
of perspectives as a problem? We argue that we should not.'
acknowledgement: We thank Christopher Cooney, Martin Garlovsky, Anja M. Westram, Carina
Baskett, Stefanie Belohlavy, Michal Hledik, Arka Pal, Nicholas H. Barton, Roger
K. Butlin and members of the University of Sheffield Speciation Journal Club for
feedback on draft survey questions and/or comments on a draft manuscript. Three
anonymous reviewers gave thoughtful feedback that improved the manuscript. We thank
Ahmad Nadeem, who was paid to build the Shiny app. We are especially grateful to
everyone who took part in the survey. Ethical approval for the survey was obtained
through the University of Sheffield Ethics Review Procedure (Application 029768).
S.S. was supported by a NERC grant awarded to Roger K. Butlin.
article_processing_charge: No
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
citation:
ama: Stankowski S, Ravinet M. Quantifying the use of species concepts. Current
Biology. 2021;31(9):R428-R429. doi:10.1016/j.cub.2021.03.060
apa: Stankowski, S., & Ravinet, M. (2021). Quantifying the use of species concepts.
Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2021.03.060
chicago: Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.”
Current Biology. Cell Press, 2021. https://doi.org/10.1016/j.cub.2021.03.060.
ieee: S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” Current
Biology, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021.
ista: Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current
Biology. 31(9), R428–R429.
mla: Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.”
Current Biology, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:10.1016/j.cub.2021.03.060.
short: S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429.
date_created: 2021-05-16T22:01:46Z
date_published: 2021-05-10T00:00:00Z
date_updated: 2023-08-08T13:34:38Z
day: '10'
department:
- _id: NiBa
doi: 10.1016/j.cub.2021.03.060
external_id:
isi:
- '000654741200004'
pmid:
- '33974865'
intvolume: ' 31'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2021.03.060
month: '05'
oa: 1
oa_version: Published Version
page: R428-R429
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- '18790445'
issn:
- '09609822'
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantifying the use of species concepts
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 31
year: '2021'
...
---
_id: '9387'
abstract:
- lang: eng
text: We report the complete analysis of a deterministic model of deleterious mutations
and negative selection against them at two haploid loci without recombination.
As long as mutation is a weaker force than selection, mutant alleles remain rare
at the only stable equilibrium, and otherwise, a variety of dynamics are possible.
If the mutation-free genotype is absent, generally the only stable equilibrium
is the one that corresponds to fixation of the mutant allele at the locus where
it is less deleterious. This result suggests that fixation of a deleterious allele
that follows a click of the Muller’s ratchet is governed by natural selection,
instead of random drift.
acknowledgement: This work was supported by the Russian Science Foundation grant N
16-14-10173.
article_number: '110729'
article_processing_charge: No
article_type: original
author:
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- first_name: Tatiana Yu.
full_name: Neretina, Tatiana Yu.
last_name: Neretina
- first_name: Alexey S.
full_name: Kondrashov, Alexey S.
last_name: Kondrashov
citation:
ama: Khudiakova K, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection
balance and Muller’s ratchet. Journal of Theoretical Biology. 2021;524.
doi:10.1016/j.jtbi.2021.110729
apa: Khudiakova, K., Neretina, T. Y., & Kondrashov, A. S. (2021). Two linked
loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical
Biology. Elsevier . https://doi.org/10.1016/j.jtbi.2021.110729
chicago: Khudiakova, Kseniia, Tatiana Yu. Neretina, and Alexey S. Kondrashov. “Two
Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” Journal
of Theoretical Biology. Elsevier , 2021. https://doi.org/10.1016/j.jtbi.2021.110729.
ieee: K. Khudiakova, T. Y. Neretina, and A. S. Kondrashov, “Two linked loci under
mutation-selection balance and Muller’s ratchet,” Journal of Theoretical Biology,
vol. 524. Elsevier , 2021.
ista: Khudiakova K, Neretina TY, Kondrashov AS. 2021. Two linked loci under mutation-selection
balance and Muller’s ratchet. Journal of Theoretical Biology. 524, 110729.
mla: Khudiakova, Kseniia, et al. “Two Linked Loci under Mutation-Selection Balance
and Muller’s Ratchet.” Journal of Theoretical Biology, vol. 524, 110729,
Elsevier , 2021, doi:10.1016/j.jtbi.2021.110729.
short: K. Khudiakova, T.Y. Neretina, A.S. Kondrashov, Journal of Theoretical Biology
524 (2021).
date_created: 2021-05-12T05:58:42Z
date_published: 2021-04-24T00:00:00Z
date_updated: 2023-08-08T13:32:40Z
day: '24'
department:
- _id: GradSch
doi: 10.1016/j.jtbi.2021.110729
external_id:
isi:
- '000659161500002'
intvolume: ' 524'
isi: 1
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- Modelling and Simulation
- Statistics and Probability
- General Immunology and Microbiology
- Applied Mathematics
- General Agricultural and Biological Sciences
- General Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/477489v1
month: '04'
oa: 1
oa_version: Preprint
publication: Journal of Theoretical Biology
publication_identifier:
issn:
- 0022-5193
publication_status: published
publisher: 'Elsevier '
quality_controlled: '1'
status: public
title: Two linked loci under mutation-selection balance and Muller’s ratchet
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 524
year: '2021'
...
---
_id: '12987'
abstract:
- lang: eng
text: Chromosomal inversion polymorphisms, segments of chromosomes that are flipped
in orientation and occur in reversed order in some individuals, have long been
recognized to play an important role in local adaptation. They can reduce recombination
in heterozygous individuals and thus help to maintain sets of locally adapted
alleles. In a wide range of organisms, populations adapted to different habitats
differ in frequency of inversion arrangements. However, getting a full understanding
of the importance of inversions for adaptation requires confirmation of their
influence on traits under divergent selection. Here, we studied a marine snail,
Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab
predation. These two types occur in close proximity on different parts of the
shore. Gene flow between them exists in contact zones. However, they exhibit strong
phenotypic divergence in several traits under habitat-specific selection, including
size, shape and behaviour. We used crosses between these ecotypes to identify
genomic regions that explain variation in these traits by using QTL analysis and
variance partitioning across linkage groups. We could show that previously detected
inversion regions contribute to adaptive divergence. Some inversions influenced
multiple traits suggesting that they contain sets of locally adaptive alleles.
Our study also identified regions without known inversions that are important
for phenotypic divergence. Thus, we provide a more complete overview of the importance
of inversions in relation to the remaining genome.
article_processing_charge: No
author:
- first_name: Eva
full_name: Koch, Eva
last_name: Koch
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Jenny
full_name: Larsson, Jenny
last_name: Larsson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Alan R.
full_name: Lemmon, Alan R.
last_name: Lemmon
- first_name: E. Moriarty
full_name: Lemmon, E. Moriarty
last_name: Lemmon
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive
traits is associated with polymorphic inversions in Littorina saxatilis. 2021.
doi:10.5061/DRYAD.ZGMSBCCB4'
apa: 'Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon,
A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4'
chicago: 'Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria,
Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin.
“Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic
Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.'
ieee: 'E. Koch et al., “Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.'
ista: 'Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM,
Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.'
mla: 'Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated
with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4.'
short: E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M.
Lemmon, K. Johannesson, R.K. Butlin, (2021).
date_created: 2023-05-16T12:34:09Z
date_published: 2021-04-10T00:00:00Z
date_updated: 2023-08-08T13:34:07Z
day: '10'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.ZGMSBCCB4
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.zgmsbccb4
month: '04'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9394'
relation: used_in_publication
status: public
status: public
title: 'Data from: Genetic variation for adaptive traits is associated with polymorphic
inversions in Littorina saxatilis'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9408'
abstract:
- lang: eng
text: We present a computational design system that assists users to model, optimize,
and fabricate quad-robots with soft skins. Our system addresses the challenging
task of predicting their physical behavior by fully integrating the multibody
dynamics of the mechanical skeleton and the elastic behavior of the soft skin.
The developed motion control strategy uses an alternating optimization scheme
to avoid expensive full space time-optimization, interleaving space-time optimization
for the skeleton, and frame-by-frame optimization for the full dynamics. The output
are motor torques to drive the robot to achieve a user prescribed motion trajectory.
We also provide a collection of convenient engineering tools and empirical manufacturing
guidance to support the fabrication of the designed quad-robot. We validate the
feasibility of designs generated with our system through physics simulations and
with a physically-fabricated prototype.
acknowledgement: The authors would like to thank anonymous reviewers for their constructive
comments. Weiwei Xu is partially supported by Zhejiang Lab. Yin Yang is partially
spported by NSF under Grant Nos. CHS 1845024 and 1717972. Weiwei Xu and Hujun Bao
are supported by Fundamental Research Funds for the Central Universities. This project
has received funding from the European Research Council (ERC) under the European
Unions Horizon 2020 research and innovation programme (Grant agreement No 715767).
article_number: 2881-2895
article_processing_charge: No
author:
- first_name: Xudong
full_name: Feng, Xudong
last_name: Feng
- first_name: Jiafeng
full_name: Liu, Jiafeng
last_name: Liu
- first_name: Huamin
full_name: Wang, Huamin
last_name: Wang
- first_name: Yin
full_name: Yang, Yin
last_name: Yang
- first_name: Hujun
full_name: Bao, Hujun
last_name: Bao
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Weiwei
full_name: Xu, Weiwei
last_name: Xu
citation:
ama: Feng X, Liu J, Wang H, et al. Computational design of skinned Quad-Robots.
IEEE Transactions on Visualization and Computer Graphics. 2021;27(6). doi:10.1109/TVCG.2019.2957218
apa: Feng, X., Liu, J., Wang, H., Yang, Y., Bao, H., Bickel, B., & Xu, W. (2021).
Computational design of skinned Quad-Robots. IEEE Transactions on Visualization
and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2019.2957218
chicago: Feng, Xudong, Jiafeng Liu, Huamin Wang, Yin Yang, Hujun Bao, Bernd Bickel,
and Weiwei Xu. “Computational Design of Skinned Quad-Robots.” IEEE Transactions
on Visualization and Computer Graphics. IEEE, 2021. https://doi.org/10.1109/TVCG.2019.2957218.
ieee: X. Feng et al., “Computational design of skinned Quad-Robots,” IEEE
Transactions on Visualization and Computer Graphics, vol. 27, no. 6. IEEE,
2021.
ista: Feng X, Liu J, Wang H, Yang Y, Bao H, Bickel B, Xu W. 2021. Computational
design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer
Graphics. 27(6), 2881–2895.
mla: Feng, Xudong, et al. “Computational Design of Skinned Quad-Robots.” IEEE
Transactions on Visualization and Computer Graphics, vol. 27, no. 6, 2881–2895,
IEEE, 2021, doi:10.1109/TVCG.2019.2957218.
short: X. Feng, J. Liu, H. Wang, Y. Yang, H. Bao, B. Bickel, W. Xu, IEEE Transactions
on Visualization and Computer Graphics 27 (2021).
date_created: 2021-05-23T22:01:42Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-08T13:45:46Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1109/TVCG.2019.2957218
ec_funded: 1
external_id:
isi:
- '000649620700009'
pmid:
- '31804937'
file:
- access_level: open_access
checksum: a78e6ac94e33ade4ffaea66943d5f7dc
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T15:08:49Z
date_updated: 2021-05-25T15:08:49Z
file_id: '9427'
file_name: 2021_TVCG_Feng.pdf
file_size: 6183002
relation: main_file
success: 1
file_date_updated: 2021-05-25T15:08:49Z
has_accepted_license: '1'
intvolume: ' 27'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: IEEE Transactions on Visualization and Computer Graphics
publication_identifier:
eissn:
- '10772626'
issn:
- '19410506'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computational design of skinned Quad-Robots
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 27
year: '2021'
...
---
_id: '9410'
abstract:
- lang: eng
text: Antibiotic concentrations vary dramatically in the body and the environment.
Hence, understanding the dynamics of resistance evolution along antibiotic concentration
gradients is critical for predicting and slowing the emergence and spread of resistance.
While it has been shown that increasing the concentration of an antibiotic slows
resistance evolution, how adaptation to one antibiotic concentration correlates
with fitness at other points along the gradient has not received much attention.
Here, we selected populations of Escherichia coli at several points along a concentration
gradient for three different antibiotics, asking how rapidly resistance evolved
and whether populations became specialized to the antibiotic concentration they
were selected on. Populations selected at higher concentrations evolved resistance
more slowly but exhibited equal or higher fitness across the whole gradient. Populations
selected at lower concentrations evolved resistance rapidly, but overall fitness
in the presence of antibiotics was lower. However, these populations readily adapted
to higher concentrations upon subsequent selection. Our results indicate that
resistance management strategies must account not only for the rates of resistance
evolution but also for the fitness of evolved strains.
acknowledgement: We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton,
Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall,
Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and
Michael Whitlock for insightful support.
article_number: '20200913'
article_processing_charge: No
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Hildegard
full_name: Uecker, Hildegard
id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
last_name: Uecker
orcid: 0000-0001-9435-2813
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
citation:
ama: Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic
concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913
apa: Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points
along antibiotic concentration gradients. Biology Letters. Royal Society
of London. https://doi.org/10.1098/rsbl.2020.0913
chicago: Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different
Points along Antibiotic Concentration Gradients.” Biology Letters. Royal
Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913.
ieee: M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along
antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal
Society of London, 2021.
ista: Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic
concentration gradients. Biology letters. 17(5), 20200913.
mla: Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration
Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of
London, 2021, doi:10.1098/rsbl.2020.0913.
short: M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).
date_created: 2021-05-23T22:01:43Z
date_published: 2021-05-12T00:00:00Z
date_updated: 2023-08-08T13:44:35Z
day: '12'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1098/rsbl.2020.0913
ec_funded: 1
external_id:
isi:
- '000651501400001'
pmid:
- ' 33975485'
file:
- access_level: open_access
checksum: 9c13c1f5af7609c97c741f11d293188a
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T14:09:03Z
date_updated: 2021-05-25T14:09:03Z
file_id: '9425'
file_name: 2021_BiologyLetters_Lagator.pdf
file_size: 726759
relation: main_file
success: 1
file_date_updated: 2021-05-25T14:09:03Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Biology letters
publication_identifier:
eissn:
- 1744957X
publication_status: published
publisher: Royal Society of London
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adaptation at different points along antibiotic concentration gradients
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2021'
...
---
_id: '9412'
abstract:
- lang: eng
text: We extend our recent result [22] on the central limit theorem for the linear
eigenvalue statistics of non-Hermitian matrices X with independent, identically
distributed complex entries to the real symmetry class. We find that the expectation
and variance substantially differ from their complex counterparts, reflecting
(i) the special spectral symmetry of real matrices onto the real axis; and (ii)
the fact that real i.i.d. matrices have many real eigenvalues. Our result generalizes
the previously known special cases where either the test function is analytic
[49] or the first four moments of the matrix elements match the real Gaussian
[59, 44]. The key element of the proof is the analysis of several weakly dependent
Dyson Brownian motions (DBMs). The conceptual novelty of the real case compared
with [22] is that the correlation structure of the stochastic differentials in
each individual DBM is non-trivial, potentially even jeopardising its well-posedness.
article_number: '24'
article_processing_charge: No
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. Fluctuation around the circular law for
random matrices with real entries. Electronic Journal of Probability. 2021;26.
doi:10.1214/21-EJP591
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Fluctuation around
the circular law for random matrices with real entries. Electronic Journal
of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/21-EJP591
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Fluctuation
around the Circular Law for Random Matrices with Real Entries.” Electronic
Journal of Probability. Institute of Mathematical Statistics, 2021. https://doi.org/10.1214/21-EJP591.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Fluctuation around the circular
law for random matrices with real entries,” Electronic Journal of Probability,
vol. 26. Institute of Mathematical Statistics, 2021.
ista: Cipolloni G, Erdös L, Schröder DJ. 2021. Fluctuation around the circular law
for random matrices with real entries. Electronic Journal of Probability. 26,
24.
mla: Cipolloni, Giorgio, et al. “Fluctuation around the Circular Law for Random
Matrices with Real Entries.” Electronic Journal of Probability, vol. 26,
24, Institute of Mathematical Statistics, 2021, doi:10.1214/21-EJP591.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability
26 (2021).
date_created: 2021-05-23T22:01:44Z
date_published: 2021-03-23T00:00:00Z
date_updated: 2023-08-08T13:39:19Z
day: '23'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1214/21-EJP591
ec_funded: 1
external_id:
arxiv:
- '2002.02438'
isi:
- '000641855600001'
file:
- access_level: open_access
checksum: 864ab003ad4cffea783f65aa8c2ba69f
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T13:24:19Z
date_updated: 2021-05-25T13:24:19Z
file_id: '9423'
file_name: 2021_EJP_Cipolloni.pdf
file_size: 865148
relation: main_file
success: 1
file_date_updated: 2021-05-25T13:24:19Z
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Electronic Journal of Probability
publication_identifier:
eissn:
- '10836489'
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fluctuation around the circular law for random matrices with real entries
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 26
year: '2021'
...
---
_id: '9407'
abstract:
- lang: eng
text: 'High impact epidemics constitute one of the largest threats humanity is facing
in the 21st century. In the absence of pharmaceutical interventions, physical
distancing together with testing, contact tracing and quarantining are crucial
in slowing down epidemic dynamics. Yet, here we show that if testing capacities
are limited, containment may fail dramatically because such combined countermeasures
drastically change the rules of the epidemic transition: Instead of continuous,
the response to countermeasures becomes discontinuous. Rather than following the
conventional exponential growth, the outbreak that is initially strongly suppressed
eventually accelerates and scales faster than exponential during an explosive
growth period. As a consequence, containment measures either suffice to stop the
outbreak at low total case numbers or fail catastrophically if marginally too
weak, thus implying large uncertainties in reliably estimating overall epidemic
dynamics, both during initial phases and during second wave scenarios.'
acknowledgement: The authors thank Malte Schröder for valuable discussions and creating
the scale-free network topologies. B.H. thanks Mukund Vasudevan for helpful discussion.
The research by M.T. was supported by the Deutsche Forschungsgemeinschaft (DFG,
German Research Foundation) under Germany´s Excellence Strategy–EXC-2068–390729961–Cluster
of Excellence Physics of Life of TU Dresden.
article_number: '2586'
article_processing_charge: No
article_type: original
author:
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Marc
full_name: Timme, Marc
last_name: Timme
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Scarselli D, Budanur NB, Timme M, Hof B. Discontinuous epidemic transition
due to limited testing. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-22725-9
apa: Scarselli, D., Budanur, N. B., Timme, M., & Hof, B. (2021). Discontinuous
epidemic transition due to limited testing. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-021-22725-9
chicago: Scarselli, Davide, Nazmi B Budanur, Marc Timme, and Björn Hof. “Discontinuous
Epidemic Transition Due to Limited Testing.” Nature Communications. Springer
Nature, 2021. https://doi.org/10.1038/s41467-021-22725-9.
ieee: D. Scarselli, N. B. Budanur, M. Timme, and B. Hof, “Discontinuous epidemic
transition due to limited testing,” Nature Communications, vol. 12, no.
1. Springer Nature, 2021.
ista: Scarselli D, Budanur NB, Timme M, Hof B. 2021. Discontinuous epidemic transition
due to limited testing. Nature Communications. 12(1), 2586.
mla: Scarselli, Davide, et al. “Discontinuous Epidemic Transition Due to Limited
Testing.” Nature Communications, vol. 12, no. 1, 2586, Springer Nature,
2021, doi:10.1038/s41467-021-22725-9.
short: D. Scarselli, N.B. Budanur, M. Timme, B. Hof, Nature Communications 12 (2021).
date_created: 2021-05-23T22:01:42Z
date_published: 2021-05-10T00:00:00Z
date_updated: 2023-08-08T13:45:13Z
day: '10'
ddc:
- '570'
department:
- _id: BjHo
doi: 10.1038/s41467-021-22725-9
external_id:
isi:
- '000687305500044'
file:
- access_level: open_access
checksum: fe26c1b8a7da1ae07a6c03f80ff06ea1
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T14:18:40Z
date_updated: 2021-05-25T14:18:40Z
file_id: '9426'
file_name: 2021_NatureCommunications_Scarselli.pdf
file_size: 1176573
relation: main_file
success: 1
file_date_updated: 2021-05-25T14:18:40Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/smashing-the-covid-curve/
scopus_import: '1'
status: public
title: Discontinuous epidemic transition due to limited testing
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9411'
abstract:
- lang: eng
text: The dynamics of a triangular magnetocapillary swimmer is studied using the
lattice Boltzmann method. We extend on our previous work, which deals with the
self-assembly and a specific type of the swimmer motion characterized by the swimmer’s
maximum velocity centred around the particle’s inverse viscous time. Here, we
identify additional regimes of motion. First, modifying the ratio of surface tension
and magnetic forces allows to study the swimmer propagation in the regime of significantly
lower frequencies mainly defined by the strength of the magnetocapillary potential.
Second, introducing a constant magnetic contribution in each of the particles
in addition to their magnetic moment induced by external fields leads to another
regime characterized by strong in-plane swimmer reorientations that resemble experimental
observations.
acknowledgement: This work was financially supported by the DFG Priority Programme
SPP 1726 “Microswimmers–From Single Particle Motion to Collective Behaviour” (HA
4382/5-1). We further acknowledge the Jülich Supercomputing Centre (JSC) and the
High Performance Computing Centre Stuttgart (HLRS) for the allocation of computing
time.
article_number: '59'
article_processing_charge: No
author:
- first_name: Alexander
full_name: Sukhov, Alexander
last_name: Sukhov
- first_name: Maxime
full_name: Hubert, Maxime
last_name: Hubert
- first_name: Galien M
full_name: Grosjean, Galien M
id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425
last_name: Grosjean
orcid: 0000-0001-5154-417X
- first_name: Oleg
full_name: Trosman, Oleg
last_name: Trosman
- first_name: Sebastian
full_name: Ziegler, Sebastian
last_name: Ziegler
- first_name: Ylona
full_name: Collard, Ylona
last_name: Collard
- first_name: Nicolas
full_name: Vandewalle, Nicolas
last_name: Vandewalle
- first_name: Ana Sunčana
full_name: Smith, Ana Sunčana
last_name: Smith
- first_name: Jens
full_name: Harting, Jens
last_name: Harting
citation:
ama: Sukhov A, Hubert M, Grosjean GM, et al. Regimes of motion of magnetocapillary
swimmers. European Physical Journal E. 2021;44(4). doi:10.1140/epje/s10189-021-00065-2
apa: Sukhov, A., Hubert, M., Grosjean, G. M., Trosman, O., Ziegler, S., Collard,
Y., … Harting, J. (2021). Regimes of motion of magnetocapillary swimmers. European
Physical Journal E. Springer. https://doi.org/10.1140/epje/s10189-021-00065-2
chicago: Sukhov, Alexander, Maxime Hubert, Galien M Grosjean, Oleg Trosman, Sebastian
Ziegler, Ylona Collard, Nicolas Vandewalle, Ana Sunčana Smith, and Jens Harting.
“Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal
E. Springer, 2021. https://doi.org/10.1140/epje/s10189-021-00065-2.
ieee: A. Sukhov et al., “Regimes of motion of magnetocapillary swimmers,”
European Physical Journal E, vol. 44, no. 4. Springer, 2021.
ista: Sukhov A, Hubert M, Grosjean GM, Trosman O, Ziegler S, Collard Y, Vandewalle
N, Smith AS, Harting J. 2021. Regimes of motion of magnetocapillary swimmers.
European Physical Journal E. 44(4), 59.
mla: Sukhov, Alexander, et al. “Regimes of Motion of Magnetocapillary Swimmers.”
European Physical Journal E, vol. 44, no. 4, 59, Springer, 2021, doi:10.1140/epje/s10189-021-00065-2.
short: A. Sukhov, M. Hubert, G.M. Grosjean, O. Trosman, S. Ziegler, Y. Collard,
N. Vandewalle, A.S. Smith, J. Harting, European Physical Journal E 44 (2021).
date_created: 2021-05-23T22:01:44Z
date_published: 2021-04-24T00:00:00Z
date_updated: 2023-08-08T13:36:28Z
day: '24'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1140/epje/s10189-021-00065-2
external_id:
isi:
- '000643251300001'
file:
- access_level: open_access
checksum: 0ef342d011afbe3c5cb058fda9a3f395
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T11:32:14Z
date_updated: 2021-05-25T11:32:14Z
file_id: '9422'
file_name: 2021_EPJE_Sukhov.pdf
file_size: 2507870
relation: main_file
success: 1
file_date_updated: 2021-05-25T11:32:14Z
has_accepted_license: '1'
intvolume: ' 44'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: European Physical Journal E
publication_identifier:
eissn:
- 1292895X
issn:
- '12928941'
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Regimes of motion of magnetocapillary swimmers
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 44
year: '2021'
...
---
_id: '9414'
abstract:
- lang: eng
text: Microtubule plus-end depolymerization rate is a potentially important target
of physiological regulation, but it has been challenging to measure, so its role
in spatial organization is poorly understood. Here we apply a method for tracking
plus ends based on time difference imaging to measure depolymerization rates in
large interphase asters growing in Xenopus egg extract. We observed strong spatial
regulation of depolymerization rates, which were higher in the aster interior
compared with the periphery, and much less regulation of polymerization or catastrophe
rates. We interpret these data in terms of a limiting component model, where aster
growth results in lower levels of soluble tubulin and microtubule-associated proteins
(MAPs) in the interior cytosol compared with that at the periphery. The steady-state
polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the
aster interior. We propose that the limiting component for microtubule assembly
is a MAP that inhibits depolymerization, and that egg asters are tuned to low
microtubule density.
acknowledgement: The authors thank the members of Mitchison, Brugués, and Jay Gatlin
groups (University of Wyoming) for discussions. We thank Heino Andreas (MPI-CBG)
for frog maintenance. We thank Nikon for microscopy support at Marine Biological
Laboratory (MBL). K.I. was supported by fellowships from the Honjo International
Scholarship Foundation and Center of Systems Biology Dresden. F.D. was supported
by the DIGGS-BB fellowship provided by the German Research Foundation (DFG). P.C.
is supported by a Boehringer Ingelheim Fonds PhD fellowship. J.F.P. was supported
by a fellowship from the Fannie and John Hertz Foundation. M.L.’s research is supported
by European Research Council (ERC) Grant no. ERC-2015-StG-679239. J.B.’s research
is supported by the Human Frontiers Science Program (CDA00074/2014). T.J.M.’s research
is supported by National Institutes of Health Grant no. R35GM131753.
article_processing_charge: No
article_type: original
author:
- first_name: Keisuke
full_name: Ishihara, Keisuke
last_name: Ishihara
- first_name: Franziska
full_name: Decker, Franziska
last_name: Decker
- first_name: Paulo R
full_name: Dos Santos Caldas, Paulo R
id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87
last_name: Dos Santos Caldas
orcid: 0000-0001-6730-4461
- first_name: James F.
full_name: Pelletier, James F.
last_name: Pelletier
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Jan
full_name: Brugués, Jan
last_name: Brugués
- first_name: Timothy J.
full_name: Mitchison, Timothy J.
last_name: Mitchison
citation:
ama: Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule
depolymerization in large asters. Molecular Biology of the Cell. 2021;32(9):869-879.
doi:10.1091/MBC.E20-11-0723
apa: Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose,
M., Brugués, J., & Mitchison, T. J. (2021). Spatial variation of microtubule
depolymerization in large asters. Molecular Biology of the Cell. American
Society for Cell Biology. https://doi.org/10.1091/MBC.E20-11-0723
chicago: Ishihara, Keisuke, Franziska Decker, Paulo R Dos Santos Caldas, James F.
Pelletier, Martin Loose, Jan Brugués, and Timothy J. Mitchison. “Spatial Variation
of Microtubule Depolymerization in Large Asters.” Molecular Biology of the
Cell. American Society for Cell Biology, 2021. https://doi.org/10.1091/MBC.E20-11-0723.
ieee: K. Ishihara et al., “Spatial variation of microtubule depolymerization
in large asters,” Molecular Biology of the Cell, vol. 32, no. 9. American
Society for Cell Biology, pp. 869–879, 2021.
ista: Ishihara K, Decker F, Dos Santos Caldas PR, Pelletier JF, Loose M, Brugués
J, Mitchison TJ. 2021. Spatial variation of microtubule depolymerization in large
asters. Molecular Biology of the Cell. 32(9), 869–879.
mla: Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization
in Large Asters.” Molecular Biology of the Cell, vol. 32, no. 9, American
Society for Cell Biology, 2021, pp. 869–79, doi:10.1091/MBC.E20-11-0723.
short: K. Ishihara, F. Decker, P.R. Dos Santos Caldas, J.F. Pelletier, M. Loose,
J. Brugués, T.J. Mitchison, Molecular Biology of the Cell 32 (2021) 869–879.
date_created: 2021-05-23T22:01:45Z
date_published: 2021-04-19T00:00:00Z
date_updated: 2023-08-08T13:36:02Z
day: '19'
department:
- _id: MaLo
doi: 10.1091/MBC.E20-11-0723
ec_funded: 1
external_id:
isi:
- '000641574700005'
intvolume: ' 32'
isi: 1
issue: '9'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/3.0/
main_file_link:
- open_access: '1'
url: https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723
month: '04'
oa: 1
oa_version: Published Version
page: 869-879
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: 260D98C8-B435-11E9-9278-68D0E5697425
name: Reconstitution of Bacterial Cell Division Using Purified Components
publication: Molecular Biology of the Cell
publication_identifier:
eissn:
- 1939-4586
issn:
- 1059-1524
publication_status: published
publisher: American Society for Cell Biology
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spatial variation of microtubule depolymerization in large asters
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA
3.0)
short: CC BY-NC-SA (3.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 32
year: '2021'
...
---
_id: '9356'
abstract:
- lang: eng
text: 'In runtime verification, a monitor watches a trace of a system and, if possible,
decides after observing each finite prefix whether or not the unknown infinite
trace satisfies a given specification. We generalize the theory of runtime verification
to monitors that attempt to estimate numerical values of quantitative trace properties
(instead of attempting to conclude boolean values of trace specifications), such
as maximal or average response time along a trace. Quantitative monitors are approximate:
with every finite prefix, they can improve their estimate of the infinite trace''s
unknown property value. Consequently, quantitative monitors can be compared with
regard to a precision-cost trade-off: better approximations of the property value
require more monitor resources, such as states (in the case of finite-state monitors)
or registers, and additional resources yield better approximations. We introduce
a formal framework for quantitative and approximate monitoring, show how it conservatively
generalizes the classical boolean setting for monitoring, and give several precision-cost
trade-offs for monitors. For example, we prove that there are quantitative properties
for which every additional register improves monitoring precision.'
acknowledgement: We thank the anonymous reviewers for their helpful comments. This
research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23
(Wittgenstein Award).
article_number: '9470547'
article_processing_charge: No
author:
- 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: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
citation:
ama: 'Henzinger TA, Sarac NE. Quantitative and approximate monitoring. In: Proceedings
of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute
of Electrical and Electronics Engineers; 2021. doi:10.1109/LICS52264.2021.9470547'
apa: 'Henzinger, T. A., & Sarac, N. E. (2021). Quantitative and approximate
monitoring. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in
Computer Science. Online: Institute of Electrical and Electronics Engineers.
https://doi.org/10.1109/LICS52264.2021.9470547'
chicago: Henzinger, Thomas A, and Naci E Sarac. “Quantitative and Approximate Monitoring.”
In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science.
Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470547.
ieee: T. A. Henzinger and N. E. Sarac, “Quantitative and approximate monitoring,”
in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science,
Online, 2021.
ista: 'Henzinger TA, Sarac NE. 2021. Quantitative and approximate monitoring. Proceedings
of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium
on Logic in Computer Science, 9470547.'
mla: Henzinger, Thomas A., and Naci E. Sarac. “Quantitative and Approximate Monitoring.”
Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science,
9470547, Institute of Electrical and Electronics Engineers, 2021, doi:10.1109/LICS52264.2021.9470547.
short: T.A. Henzinger, N.E. Sarac, in:, Proceedings of the 36th Annual ACM/IEEE
Symposium on Logic in Computer Science, Institute of Electrical and Electronics
Engineers, 2021.
conference:
end_date: 2021-07-02
location: Online
name: 'LICS: Symposium on Logic in Computer Science'
start_date: 2021-06-29
date_created: 2021-04-30T17:30:47Z
date_published: 2021-06-29T00:00:00Z
date_updated: 2023-08-08T13:52:56Z
day: '29'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.1109/LICS52264.2021.9470547
external_id:
arxiv:
- '2105.08353'
isi:
- '000947350400021'
file:
- access_level: open_access
checksum: 6e4cba3f72775f479c5b1b75d1a4a0c4
content_type: application/pdf
creator: esarac
date_created: 2021-06-16T08:23:54Z
date_updated: 2021-06-16T08:23:54Z
file_id: '9557'
file_name: qam.pdf
file_size: 641990
relation: main_file
success: 1
file_date_updated: 2021-06-16T08:23:54Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer
Science
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantitative and approximate monitoring
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9439'
abstract:
- lang: eng
text: The ability to adapt to changes in stimulus statistics is a hallmark of sensory
systems. Here, we developed a theoretical framework that can account for the dynamics
of adaptation from an information processing perspective. We use this framework
to optimize and analyze adaptive sensory codes, and we show that codes optimized
for stationary environments can suffer from prolonged periods of poor performance
when the environment changes. To mitigate the adversarial effects of these environmental
changes, sensory systems must navigate tradeoffs between the ability to accurately
encode incoming stimuli and the ability to rapidly detect and adapt to changes
in the distribution of these stimuli. We derive families of codes that balance
these objectives, and we demonstrate their close match to experimentally observed
neural dynamics during mean and variance adaptation. Our results provide a unifying
perspective on adaptation across a range of sensory systems, environments, and
sensory tasks.
acknowledgement: We thank D. Kastner and T. Münch for generously providing figures
from their work. We also thank V. Jayaraman, M. Noorman, T. Ma, and K. Krishnamurthy
for useful discussions and feedback on the manuscript. W.F.M. was funded by the
European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie
Grant Agreement No. 754411. A.M.H. was supported by the Howard Hughes Medical Institute.
article_processing_charge: No
article_type: original
author:
- first_name: Wiktor F
full_name: Mlynarski, Wiktor F
id: 358A453A-F248-11E8-B48F-1D18A9856A87
last_name: Mlynarski
- first_name: Ann M.
full_name: Hermundstad, Ann M.
last_name: Hermundstad
citation:
ama: Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature
Neuroscience. 2021;24:998-1009. doi:10.1038/s41593-021-00846-0
apa: Mlynarski, W. F., & Hermundstad, A. M. (2021). Efficient and adaptive sensory
codes. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-021-00846-0
chicago: Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory
Codes.” Nature Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00846-0.
ieee: W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,”
Nature Neuroscience, vol. 24. Springer Nature, pp. 998–1009, 2021.
ista: Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes.
Nature Neuroscience. 24, 998–1009.
mla: Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory
Codes.” Nature Neuroscience, vol. 24, Springer Nature, 2021, pp. 998–1009,
doi:10.1038/s41593-021-00846-0.
short: W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.
date_created: 2021-05-30T22:01:24Z
date_published: 2021-05-20T00:00:00Z
date_updated: 2023-08-08T13:51:14Z
day: '20'
department:
- _id: GaTk
doi: 10.1038/s41593-021-00846-0
ec_funded: 1
external_id:
isi:
- '000652577300003'
intvolume: ' 24'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/669200 '
month: '05'
oa: 1
oa_version: Preprint
page: 998-1009
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature Neuroscience
publication_identifier:
eissn:
- 1546-1726
issn:
- 1097-6256
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient and adaptive sensory codes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 24
year: '2021'
...
---
_id: '9443'
abstract:
- lang: eng
text: Endoplasmic reticulum–plasma membrane contact sites (ER–PM CS) play fundamental
roles in all eukaryotic cells. Arabidopsis thaliana mutants lacking the ER–PM
protein tether synaptotagmin1 (SYT1) exhibit decreased PM integrity under multiple
abiotic stresses, such as freezing, high salt, osmotic stress, and mechanical
damage. Here, we show that, together with SYT1, the stress-induced SYT3 is an
ER–PM tether that also functions in maintaining PM integrity. The ER–PM CS localization
of SYT1 and SYT3 is dependent on PM phosphatidylinositol-4-phosphate and is regulated
by abiotic stress. Lipidomic analysis revealed that cold stress increased the
accumulation of diacylglycerol at the PM in a syt1/3 double mutant relative to
wild-type while the levels of most glycerolipid species remain unchanged. In addition,
the SYT1-green fluorescent protein fusion preferentially binds diacylglycerol
in vivo with little affinity for polar glycerolipids. Our work uncovers a SYT-dependent
mechanism of stress adaptation counteracting the detrimental accumulation of diacylglycerol
at the PM produced during episodes of abiotic stress.
acknowledgement: "We would also like to thank Lothar Willmitzer for the lipidomic
analysis at the Max Planck Institute of Molecular Plant Physiology (Potsdam, Germany).
We thank Manuela Vega from SCI for her technical assistance in image analysis. We
thank John R. Pearson and the Bionand Nanoimaging Unit, F. David Navas Fernández
and the SCAI Imaging Facility and The Plant Cell Biology facility at the Shanghai
Center for Plant Stress Biology for assistance with confocal microscopy. The FaFAH1
clone was a gift from Iraida Amaya Saavedra (IFAPA-Centro de Churriana, Málaga,
Spain). The AHA3 antibody against the H+-ATPase was a gift from Ramón Serrano Salom
(Instituto de Biología Molecular y Celular de Plantas, Valencia, Spain). The MAP-mTU2-SAC1
construct was provided by Yvon Jaillais (Laboratoire Reproduction et Développement
des Plantes, Univ Lyon, France). The pGWB5 from the pGWB vector series, was provided
by Tsuyoshi Nakagawa (Department of Molecular and Functional Genomics, Shimane University).
We thank Plan Propio from the University of Málaga for financial support.\r\nFunding"
article_processing_charge: No
article_type: original
author:
- first_name: N
full_name: Ruiz-Lopez, N
last_name: Ruiz-Lopez
- first_name: J
full_name: Pérez-Sancho, J
last_name: Pérez-Sancho
- first_name: A
full_name: Esteban Del Valle, A
last_name: Esteban Del Valle
- first_name: RP
full_name: Haslam, RP
last_name: Haslam
- first_name: S
full_name: Vanneste, S
last_name: Vanneste
- first_name: R
full_name: Catalá, R
last_name: Catalá
- first_name: C
full_name: Perea-Resa, C
last_name: Perea-Resa
- first_name: D
full_name: Van Damme, D
last_name: Van Damme
- first_name: S
full_name: García-Hernández, S
last_name: García-Hernández
- first_name: A
full_name: Albert, A
last_name: Albert
- first_name: J
full_name: Vallarino, J
last_name: Vallarino
- first_name: J
full_name: Lin, J
last_name: Lin
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: AP
full_name: Macho, AP
last_name: Macho
- first_name: J
full_name: Salinas, J
last_name: Salinas
- first_name: A
full_name: Rosado, A
last_name: Rosado
- first_name: JA
full_name: Napier, JA
last_name: Napier
- first_name: V
full_name: Amorim-Silva, V
last_name: Amorim-Silva
- first_name: MA
full_name: Botella, MA
last_name: Botella
citation:
ama: Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, et al. Synaptotagmins at
the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol
homeostasis during abiotic stress. Plant Cell. 2021;33(7):2431-2453. doi:10.1093/plcell/koab122
apa: Ruiz-Lopez, N., Pérez-Sancho, J., Esteban Del Valle, A., Haslam, R., Vanneste,
S., Catalá, R., … Botella, M. (2021). Synaptotagmins at the endoplasmic reticulum-plasma
membrane contact sites maintain diacylglycerol homeostasis during abiotic stress.
Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab122
chicago: Ruiz-Lopez, N, J Pérez-Sancho, A Esteban Del Valle, RP Haslam, S Vanneste,
R Catalá, C Perea-Resa, et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma
Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.”
Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab122.
ieee: N. Ruiz-Lopez et al., “Synaptotagmins at the endoplasmic reticulum-plasma
membrane contact sites maintain diacylglycerol homeostasis during abiotic stress,”
Plant Cell, vol. 33, no. 7. American Society of Plant Biologists, pp. 2431–2453,
2021.
ista: Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, Haslam R, Vanneste S, Catalá
R, Perea-Resa C, Van Damme D, García-Hernández S, Albert A, Vallarino J, Lin J,
Friml J, Macho A, Salinas J, Rosado A, Napier J, Amorim-Silva V, Botella M. 2021.
Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain
diacylglycerol homeostasis during abiotic stress. Plant Cell. 33(7), 2431–2453.
mla: Ruiz-Lopez, N., et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma
Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.”
Plant Cell, vol. 33, no. 7, American Society of Plant Biologists, 2021,
pp. 2431–53, doi:10.1093/plcell/koab122.
short: N. Ruiz-Lopez, J. Pérez-Sancho, A. Esteban Del Valle, R. Haslam, S. Vanneste,
R. Catalá, C. Perea-Resa, D. Van Damme, S. García-Hernández, A. Albert, J. Vallarino,
J. Lin, J. Friml, A. Macho, J. Salinas, A. Rosado, J. Napier, V. Amorim-Silva,
M. Botella, Plant Cell 33 (2021) 2431–2453.
date_created: 2021-06-02T13:13:58Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-08T13:54:32Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1093/plcell/koab122
ec_funded: 1
external_id:
isi:
- '000703938100026'
pmid:
- '33944955'
file:
- access_level: open_access
checksum: 22d596678d00310d793611864a6d0fcd
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-14T13:36:38Z
date_updated: 2021-10-14T13:36:38Z
file_id: '10141'
file_name: 2021_PlantCell_RuizLopez.pdf
file_size: 2952028
relation: main_file
success: 1
file_date_updated: 2021-10-14T13:36:38Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 2431-2453
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Plant Cell
publication_identifier:
eissn:
- 1532-298x
issn:
- 1040-4651
publication_status: published
publisher: American Society of Plant Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain
diacylglycerol homeostasis during abiotic stress
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 33
year: '2021'
...