---
_id: '1127'
abstract:
- lang: eng
text: "Plant hormone auxin and its transport between cells belong to the most important\r\nmechanisms
controlling plant development. Auxin itself could change localization of PINs
and\r\nthereby control direction of its own flow. We performed an expression profiling
experiment\r\nin Arabidopsis roots to identify potential regulators of PIN polarity
which are transcriptionally\r\nregulated by auxin signalling. We identified several
novel regulators and performed a detailed\r\ncharacterization of the transcription
factor WRKY23 (At2g47260) and its role in auxin\r\nfeedback on PIN polarity. Gain-of-function
and dominant-negative mutants revealed that\r\nWRKY23 plays a crucial role in
mediating the auxin effect on PIN polarity. In concordance,\r\ntypical polar auxin
transport processes such as gravitropism and leaf vascular pattern\r\nformation
were disturbed by interfering with WRKY23 function.\r\nIn order to identify direct
targets of WRKY23, we performed consequential expression\r\nprofiling experiments
using a WRKY23 inducible gain-of-function line and dominant-negative\r\nWRKY23
line that is defunct in PIN re-arrangement. Among several genes mostly related
to\r\nthe groups of cell wall and defense process regulators, we identified LYSINE-HISTIDINE\r\nTRANSPORTER
1 (LHT1; At5g40780), a small amino acid permease gene from the amino\r\nacid/auxin
permease family (AAAP), we present its detailed characterisation in auxin feedback\r\non
PIN repolarization, identified its transcriptional regulation, we propose a potential\r\nmechanism
of its action. Moreover, we identified also a member of receptor-like protein\r\nkinase
LRR-RLK (LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN KINASE PROTEIN 1;\r\nLRRK1;
At1g05700), which also affects auxin-dependent PIN re-arrangement. We described\r\nits
transcriptional behaviour, subcellular localization. Based on global expression
data, we\r\ntried to identify ligand responsible for mechanism of signalling and
suggest signalling partner\r\nand interactors. Additionally, we described role
of novel phytohormone group, strigolactone,\r\nin auxin-dependent PIN re-arrangement,
that could be a fundament for future studies in this\r\nfield.\r\nOur results
provide first insights into an auxin transcriptional network targeting PIN\r\nlocalization
and thus regulating plant development. We highlighted WRKY23 transcriptional\r\nnetwork
and characterised its mediatory role in plant development. We identified direct\r\neffectors
of this network, LHT1 and LRRK1, and describe their roles in PIN re-arrangement
and\r\nPIN-dependent auxin transport processes."
acknowledgement: I would like to first acknowledge my supervisor Jiří Friml for support,
kind advice and patience. It was a pleasure to be a part of your lab, Jiří. I will
remember the atmosphere present in auxin lab at VIB in Ghent and at IST in Klosterneuburg
forever. I would like to thank all past and present lab members for the friendship
and friendly and scientific environment in the groups. It was so nice to cooperate
with you, guys. There was always someone who helped me with experiments, troubleshoot
issues coming from our work etc. At this place, I would like to thank especially
to Gergo Molnár. I’m happy (and lucky) that I have met him; he naturally became
my tutor and guide through my PhD. From no one else during my entire professional
career, I’ve learned that much.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Tomas
full_name: Prat, Tomas
id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87
last_name: Prat
citation:
ama: Prat T. Identification of novel regulators of PIN polarity and development
of novel auxin sensor. 2017.
apa: Prat, T. (2017). Identification of novel regulators of PIN polarity and
development of novel auxin sensor. Institute of Science and Technology Austria.
chicago: Prat, Tomas. “Identification of Novel Regulators of PIN Polarity and Development
of Novel Auxin Sensor.” Institute of Science and Technology Austria, 2017.
ieee: T. Prat, “Identification of novel regulators of PIN polarity and development
of novel auxin sensor,” Institute of Science and Technology Austria, 2017.
ista: Prat T. 2017. Identification of novel regulators of PIN polarity and development
of novel auxin sensor. Institute of Science and Technology Austria.
mla: Prat, Tomas. Identification of Novel Regulators of PIN Polarity and Development
of Novel Auxin Sensor. Institute of Science and Technology Austria, 2017.
short: T. Prat, Identification of Novel Regulators of PIN Polarity and Development
of Novel Auxin Sensor, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:50:17Z
date_published: 2017-01-12T00:00:00Z
date_updated: 2023-09-19T10:39:33Z
day: '12'
ddc:
- '580'
degree_awarded: PhD
department:
- _id: JiFr
file:
- access_level: closed
checksum: d192c7c6c5ea32c8432437286dc4909e
content_type: application/pdf
creator: dernst
date_created: 2019-04-05T08:45:14Z
date_updated: 2019-04-05T08:45:14Z
file_id: '6209'
file_name: IST_Austria_Thesis_Tomáš_Prát.pdf
file_size: 10285946
relation: main_file
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checksum: bab18b52cf98145926042d8ed99fdb3b
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:52:56Z
date_updated: 2021-02-22T11:52:56Z
file_id: '9185'
file_name: 2017_Thesis_Prat.pdf
file_size: 9802991
relation: main_file
success: 1
file_date_updated: 2021-02-22T11:52:56Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '131'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6233'
related_material:
record:
- id: '449'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Identification of novel regulators of PIN polarity and development of novel
auxin sensor
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '2016'
abstract:
- lang: eng
text: The Ising model is one of the simplest and most famous models of interacting
systems. It was originally proposed to model ferromagnetic interactions in statistical
physics and is now widely used to model spatial processes in many areas such as
ecology, sociology, and genetics, usually without testing its goodness-of-fit.
Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model.
The theory of Markov bases has been developed in algebraic statistics for exact
goodness-of-fit testing using a Monte Carlo approach. However, this beautiful
theory has fallen short of its promise for applications, because finding a Markov
basis is usually computationally intractable. We develop a Monte Carlo method
for exact goodness-of-fit testing for the Ising model which avoids computing a
Markov basis and also leads to a better connectivity of the Markov chain and hence
to a faster convergence. We show how this method can be applied to analyze the
spatial organization of receptors on the cell membrane.
article_processing_charge: No
author:
- first_name: Abraham
full_name: Martin Del Campo Sanchez, Abraham
last_name: Martin Del Campo Sanchez
- first_name: Sarah A
full_name: Cepeda Humerez, Sarah A
id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
last_name: Cepeda Humerez
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit
testing for the Ising model. Scandinavian Journal of Statistics. 2017;44(2):285-306.
doi:10.1111/sjos.12251
apa: Martin Del Campo Sanchez, A., Cepeda Humerez, S. A., & Uhler, C. (2017).
Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of
Statistics. Wiley-Blackwell. https://doi.org/10.1111/sjos.12251
chicago: Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline
Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.” Scandinavian Journal
of Statistics. Wiley-Blackwell, 2017. https://doi.org/10.1111/sjos.12251.
ieee: A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit
testing for the Ising model,” Scandinavian Journal of Statistics, vol.
44, no. 2. Wiley-Blackwell, pp. 285–306, 2017.
ista: Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit
testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306.
mla: Martin Del Campo Sanchez, Abraham, et al. “Exact Goodness-of-Fit Testing for
the Ising Model.” Scandinavian Journal of Statistics, vol. 44, no. 2, Wiley-Blackwell,
2017, pp. 285–306, doi:10.1111/sjos.12251.
short: A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian
Journal of Statistics 44 (2017) 285–306.
date_created: 2018-12-11T11:55:13Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-19T15:13:27Z
day: '01'
department:
- _id: GaTk
doi: 10.1111/sjos.12251
external_id:
arxiv:
- '1410.1242'
isi:
- '000400985000001'
intvolume: ' 44'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.1242
month: '06'
oa: 1
oa_version: Preprint
page: 285 - 306
publication: Scandinavian Journal of Statistics
publication_identifier:
issn:
- '03036898'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5060'
quality_controlled: '1'
related_material:
record:
- id: '6473'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Exact goodness-of-fit testing for the Ising model
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 44
year: '2017'
...
---
_id: '1528'
abstract:
- lang: eng
text: 'We consider N×N Hermitian random matrices H consisting of blocks of size
M≥N6/7. The matrix elements are i.i.d. within the blocks, close to a Gaussian
in the four moment matching sense, but their distribution varies from block to
block to form a block-band structure, with an essential band width M. We show
that the entries of the Green’s function G(z)=(H−z)−1 satisfy the local semicircle
law with spectral parameter z=E+iη down to the real axis for any η≫N−1, using
a combination of the supersymmetry method inspired by Shcherbina (J Stat Phys
155(3): 466–499, 2014) and the Green’s function comparison strategy. Previous
estimates were valid only for η≫M−1. The new estimate also implies that the eigenvectors
in the middle of the spectrum are fully delocalized.'
acknowledgement: "Z. Bao was supported by ERC Advanced Grant RANMAT No. 338804; L.
Erdős was partially supported by ERC Advanced Grant RANMAT No. 338804.\r\nOpen access
funding provided by Institute of Science and Technology (IST Austria). The authors
are very grateful to the anonymous referees for careful reading and valuable comments,
which helped to improve the organization."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
citation:
ama: Bao Z, Erdös L. Delocalization for a class of random block band matrices. Probability
Theory and Related Fields. 2017;167(3-4):673-776. doi:10.1007/s00440-015-0692-y
apa: Bao, Z., & Erdös, L. (2017). Delocalization for a class of random block
band matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-015-0692-y
chicago: Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block
Band Matrices.” Probability Theory and Related Fields. Springer, 2017.
https://doi.org/10.1007/s00440-015-0692-y.
ieee: Z. Bao and L. Erdös, “Delocalization for a class of random block band matrices,”
Probability Theory and Related Fields, vol. 167, no. 3–4. Springer, pp.
673–776, 2017.
ista: Bao Z, Erdös L. 2017. Delocalization for a class of random block band matrices.
Probability Theory and Related Fields. 167(3–4), 673–776.
mla: Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block
Band Matrices.” Probability Theory and Related Fields, vol. 167, no. 3–4,
Springer, 2017, pp. 673–776, doi:10.1007/s00440-015-0692-y.
short: Z. Bao, L. Erdös, Probability Theory and Related Fields 167 (2017) 673–776.
date_created: 2018-12-11T11:52:32Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2023-09-20T09:42:12Z
day: '01'
ddc:
- '530'
department:
- _id: LaEr
doi: 10.1007/s00440-015-0692-y
ec_funded: 1
external_id:
isi:
- '000398842700004'
file:
- access_level: open_access
checksum: 67afa85ff1e220cbc1f9f477a828513c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:05Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4665'
file_name: IST-2016-489-v1+1_s00440-015-0692-y.pdf
file_size: 1615755
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 167'
isi: 1
issue: 3-4
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 673 - 776
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Probability Theory and Related Fields
publication_identifier:
issn:
- '01788051'
publication_status: published
publisher: Springer
publist_id: '5644'
pubrep_id: '489'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Delocalization for a class of random block band matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 167
year: '2017'
...
---
_id: '1433'
abstract:
- lang: eng
text: Phat is an open-source C. ++ library for the computation of persistent homology
by matrix reduction, targeted towards developers of software for topological data
analysis. We aim for a simple generic design that decouples algorithms from data
structures without sacrificing efficiency or user-friendliness. We provide numerous
different reduction strategies as well as data types to store and manipulate the
boundary matrix. We compare the different combinations through extensive experimental
evaluation and identify optimization techniques that work well in practical situations.
We also compare our software with various other publicly available libraries for
persistent homology.
article_processing_charge: No
article_type: original
author:
- first_name: Ulrich
full_name: Bauer, Ulrich
last_name: Bauer
- first_name: Michael
full_name: Kerber, Michael
last_name: Kerber
- first_name: Jan
full_name: Reininghaus, Jan
last_name: Reininghaus
- first_name: Hubert
full_name: Wagner, Hubert
id: 379CA8B8-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
citation:
ama: Bauer U, Kerber M, Reininghaus J, Wagner H. Phat - Persistent homology algorithms
toolbox. Journal of Symbolic Computation. 2017;78:76-90. doi:10.1016/j.jsc.2016.03.008
apa: Bauer, U., Kerber, M., Reininghaus, J., & Wagner, H. (2017). Phat - Persistent
homology algorithms toolbox. Journal of Symbolic Computation. Academic
Press. https://doi.org/10.1016/j.jsc.2016.03.008
chicago: Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “Phat
- Persistent Homology Algorithms Toolbox.” Journal of Symbolic Computation.
Academic Press, 2017. https://doi.org/10.1016/j.jsc.2016.03.008.
ieee: U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “Phat - Persistent homology
algorithms toolbox,” Journal of Symbolic Computation, vol. 78. Academic
Press, pp. 76–90, 2017.
ista: Bauer U, Kerber M, Reininghaus J, Wagner H. 2017. Phat - Persistent homology
algorithms toolbox. Journal of Symbolic Computation. 78, 76–90.
mla: Bauer, Ulrich, et al. “Phat - Persistent Homology Algorithms Toolbox.” Journal
of Symbolic Computation, vol. 78, Academic Press, 2017, pp. 76–90, doi:10.1016/j.jsc.2016.03.008.
short: U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, Journal of Symbolic Computation
78 (2017) 76–90.
date_created: 2018-12-11T11:51:59Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T09:42:40Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.jsc.2016.03.008
ec_funded: 1
external_id:
isi:
- '000384396000005'
intvolume: ' 78'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.jsc.2016.03.008
month: '01'
oa: 1
oa_version: Published Version
page: 76 - 90
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Journal of Symbolic Computation
publication_identifier:
issn:
- ' 07477171'
publication_status: published
publisher: Academic Press
publist_id: '5765'
quality_controlled: '1'
related_material:
record:
- id: '10894'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Phat - Persistent homology algorithms toolbox
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 78
year: '2017'
...
---
_id: '1407'
abstract:
- lang: eng
text: We consider the problem of computing the set of initial states of a dynamical
system such that there exists a control strategy to ensure that the trajectories
satisfy a temporal logic specification with probability 1 (almost-surely). We
focus on discrete-time, stochastic linear dynamics and specifications given as
formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over
linear predicates in the states of the system. We propose a solution based on
iterative abstraction-refinement, and turn-based 2-player probabilistic games.
While the theoretical guarantee of our algorithm after any finite number of iterations
is only a partial solution, we show that if our algorithm terminates, then the
result is the set of all satisfying initial states. Moreover, for any (partial)
solution our algorithm synthesizes witness control strategies to ensure almost-sure
satisfaction of the temporal logic specification. While the proposed algorithm
guarantees progress and soundness in every iteration, it is computationally demanding.
We offer an alternative, more efficient solution for the reachability properties
that decomposes the problem into a series of smaller problems of the same type.
All algorithms are demonstrated on an illustrative case study.
article_processing_charge: No
author:
- first_name: Mária
full_name: Svoreňová, Mária
last_name: Svoreňová
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ivana
full_name: Cěrná, Ivana
last_name: Cěrná
- first_name: Cǎlin
full_name: Belta, Cǎlin
last_name: Belta
citation:
ama: 'Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal
logic control for stochastic linear systems using abstraction refinement of probabilistic
games. Nonlinear Analysis: Hybrid Systems. 2017;23(2):230-253. doi:10.1016/j.nahs.2016.04.006'
apa: 'Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., &
Belta, C. (2017). Temporal logic control for stochastic linear systems using abstraction
refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems.
Elsevier. https://doi.org/10.1016/j.nahs.2016.04.006'
chicago: 'Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee,
Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems
Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid
Systems. Elsevier, 2017. https://doi.org/10.1016/j.nahs.2016.04.006.'
ieee: 'M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta,
“Temporal logic control for stochastic linear systems using abstraction refinement
of probabilistic games,” Nonlinear Analysis: Hybrid Systems, vol. 23, no.
2. Elsevier, pp. 230–253, 2017.'
ista: 'Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2017.
Temporal logic control for stochastic linear systems using abstraction refinement
of probabilistic games. Nonlinear Analysis: Hybrid Systems. 23(2), 230–253.'
mla: 'Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems
Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid
Systems, vol. 23, no. 2, Elsevier, 2017, pp. 230–53, doi:10.1016/j.nahs.2016.04.006.'
short: 'M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta,
Nonlinear Analysis: Hybrid Systems 23 (2017) 230–253.'
date_created: 2018-12-11T11:51:50Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T09:43:09Z
day: '01'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1016/j.nahs.2016.04.006
ec_funded: 1
external_id:
arxiv:
- '1410.5387'
isi:
- '000390637000014'
intvolume: ' 23'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.5387
month: '02'
oa: 1
oa_version: Preprint
page: 230 - 253
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: 'Nonlinear Analysis: Hybrid Systems'
publication_status: published
publisher: Elsevier
publist_id: '5800'
quality_controlled: '1'
related_material:
record:
- id: '1689'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Temporal logic control for stochastic linear systems using abstraction refinement
of probabilistic games
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 23
year: '2017'
...
---
_id: '1367'
abstract:
- lang: eng
text: One of the major challenges in physically based modelling is making simulations
efficient. Adaptive models provide an essential solution to these efficiency goals.
These models are able to self-adapt in space and time, attempting to provide the
best possible compromise between accuracy and speed. This survey reviews the adaptive
solutions proposed so far in computer graphics. Models are classified according
to the strategy they use for adaptation, from time-stepping and freezing techniques
to geometric adaptivity in the form of structured grids, meshes and particles.
Applications range from fluids, through deformable bodies, to articulated solids.
acknowledgement: This work was partly supported by the starting grants ADAPT and BigSplash,
as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2012-StG_20111012,
ERC-2014-StG_638176 and ERC-2011-ADG_20110209).
article_processing_charge: No
author:
- first_name: Pierre
full_name: Manteaux, Pierre
last_name: Manteaux
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Rahul
full_name: Narain, Rahul
last_name: Narain
- first_name: Stéphane
full_name: Redon, Stéphane
last_name: Redon
- first_name: François
full_name: Faure, François
last_name: Faure
- first_name: Marie
full_name: Cani, Marie
last_name: Cani
citation:
ama: Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. Adaptive physically
based models in computer graphics. Computer Graphics Forum. 2017;36(6):312-337.
doi:10.1111/cgf.12941
apa: Manteaux, P., Wojtan, C., Narain, R., Redon, S., Faure, F., & Cani, M.
(2017). Adaptive physically based models in computer graphics. Computer Graphics
Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12941
chicago: Manteaux, Pierre, Chris Wojtan, Rahul Narain, Stéphane Redon, François
Faure, and Marie Cani. “Adaptive Physically Based Models in Computer Graphics.”
Computer Graphics Forum. Wiley-Blackwell, 2017. https://doi.org/10.1111/cgf.12941.
ieee: P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, and M. Cani, “Adaptive
physically based models in computer graphics,” Computer Graphics Forum,
vol. 36, no. 6. Wiley-Blackwell, pp. 312–337, 2017.
ista: Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. 2017. Adaptive physically
based models in computer graphics. Computer Graphics Forum. 36(6), 312–337.
mla: Manteaux, Pierre, et al. “Adaptive Physically Based Models in Computer Graphics.”
Computer Graphics Forum, vol. 36, no. 6, Wiley-Blackwell, 2017, pp. 312–37,
doi:10.1111/cgf.12941.
short: P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, M. Cani, Computer
Graphics Forum 36 (2017) 312–337.
date_created: 2018-12-11T11:51:37Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-09-20T11:05:36Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1111/cgf.12941
external_id:
isi:
- '000408634200019'
file:
- access_level: open_access
checksum: 7676e9a9ead6d58c3000988c97deb2ef
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:21Z
date_updated: 2020-07-14T12:44:47Z
file_id: '5208'
file_name: IST-2016-634-v1+1_starAdaptivity-cgf.pdf
file_size: 1434439
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 312 - 337
publication: Computer Graphics Forum
publication_identifier:
issn:
- '01677055'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5873'
pubrep_id: '634'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adaptive physically based models in computer graphics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 36
year: '2017'
...
---
_id: '1338'
abstract:
- lang: eng
text: We present a computer-aided programming approach to concurrency. The approach
allows programmers to program assuming a friendly, non-preemptive scheduler, and
our synthesis procedure inserts synchronization to ensure that the final program
works even with a preemptive scheduler. The correctness specification is implicit,
inferred from the non-preemptive behavior. Let us consider sequences of calls
that the program makes to an external interface. The specification requires that
any such sequence produced under a preemptive scheduler should be included in
the set of sequences produced under a non-preemptive scheduler. We guarantee that
our synthesis does not introduce deadlocks and that the synchronization inserted
is optimal w.r.t. a given objective function. The solution is based on a finitary
abstraction, an algorithm for bounded language inclusion modulo an independence
relation, and generation of a set of global constraints over synchronization placements.
Each model of the global constraints set corresponds to a correctness-ensuring
synchronization placement. The placement that is optimal w.r.t. the given objective
function is chosen as the synchronization solution. We apply the approach to device-driver
programming, where the driver threads call the software interface of the device
and the API provided by the operating system. Our experiments demonstrate that
our synthesis method is precise and efficient. The implicit specification helped
us find one concurrency bug previously missed when model-checking using an explicit,
user-provided specification. We implemented objective functions for coarse-grained
and fine-grained locking and observed that different synchronization placements
are produced for our experiments, favoring a minimal number of synchronization
operations or maximum concurrency, respectively.
article_processing_charge: No
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Edmund
full_name: Clarke, Edmund
last_name: Clarke
- 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: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Leonid
full_name: Ryzhyk, Leonid
last_name: Ryzhyk
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling
using synchronization synthesis. Formal Methods in System Design. 2017;50(2-3):97-139.
doi:10.1007/s10703-016-0256-5
apa: Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta,
R., & Tarrach, T. (2017). From non-preemptive to preemptive scheduling using
synchronization synthesis. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-016-0256-5
chicago: Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid
Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive
Scheduling Using Synchronization Synthesis.” Formal Methods in System Design.
Springer, 2017. https://doi.org/10.1007/s10703-016-0256-5.
ieee: P. Cerny et al., “From non-preemptive to preemptive scheduling using
synchronization synthesis,” Formal Methods in System Design, vol. 50, no.
2–3. Springer, pp. 97–139, 2017.
ista: Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach
T. 2017. From non-preemptive to preemptive scheduling using synchronization synthesis.
Formal Methods in System Design. 50(2–3), 97–139.
mla: Cerny, Pavol, et al. “From Non-Preemptive to Preemptive Scheduling Using Synchronization
Synthesis.” Formal Methods in System Design, vol. 50, no. 2–3, Springer,
2017, pp. 97–139, doi:10.1007/s10703-016-0256-5.
short: P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta,
T. Tarrach, Formal Methods in System Design 50 (2017) 97–139.
date_created: 2018-12-11T11:51:27Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T11:13:51Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/s10703-016-0256-5
ec_funded: 1
external_id:
isi:
- '000399888900001'
file:
- access_level: open_access
checksum: 1163dfd997e8212c789525d4178b1653
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:05Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4985'
file_name: IST-2016-656-v1+1_s10703-016-0256-5.pdf
file_size: 1416170
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 50'
isi: 1
issue: 2-3
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 97 - 139
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Formal Methods in System Design
publication_status: published
publisher: Springer
publist_id: '5929'
pubrep_id: '656'
quality_controlled: '1'
related_material:
record:
- id: '1729'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: From non-preemptive to preemptive scheduling using synchronization synthesis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 50
year: '2017'
...
---
_id: '1351'
abstract:
- lang: eng
text: The behaviour of gene regulatory networks (GRNs) is typically analysed using
simulation-based statistical testing-like methods. In this paper, we demonstrate
that we can replace this approach by a formal verification-like method that gives
higher assurance and scalability. We focus on Wagner’s weighted GRN model with
varying weights, which is used in evolutionary biology. In the model, weight parameters
represent the gene interaction strength that may change due to genetic mutations.
For a property of interest, we synthesise the constraints over the parameter space
that represent the set of GRNs satisfying the property. We experimentally show
that our parameter synthesis procedure computes the mutational robustness of GRNs—an
important problem of interest in evolutionary biology—more efficiently than the
classical simulation method. We specify the property in linear temporal logic.
We employ symbolic bounded model checking and SMT solving to compute the space
of GRNs that satisfy the property, which amounts to synthesizing a set of linear
constraints on the weights.
article_processing_charge: No
author:
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- 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: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking
the evolution of gene regulatory networks. Acta Informatica. 2017;54(8):765-787.
doi:10.1007/s00236-016-0278-x
apa: Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov,
T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica.
Springer. https://doi.org/10.1007/s00236-016-0278-x
chicago: Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago
Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.”
Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-016-0278-x.
ieee: M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov,
“Model checking the evolution of gene regulatory networks,” Acta Informatica,
vol. 54, no. 8. Springer, pp. 765–787, 2017.
ista: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model
checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.
mla: Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.”
Acta Informatica, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:10.1007/s00236-016-0278-x.
short: M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta
Informatica 54 (2017) 765–787.
date_created: 2018-12-11T11:51:32Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-09-20T11:06:03Z
day: '01'
ddc:
- '006'
- '576'
department:
- _id: ToHe
- _id: CaGu
- _id: NiBa
doi: 10.1007/s00236-016-0278-x
ec_funded: 1
external_id:
isi:
- '000414343200003'
file:
- access_level: open_access
checksum: 4e661d9135d7f8c342e8e258dee76f3e
content_type: application/pdf
creator: dernst
date_created: 2019-01-17T15:57:29Z
date_updated: 2020-07-14T12:44:46Z
file_id: '5841'
file_name: 2017_ActaInformatica_Giacobbe.pdf
file_size: 755241
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 54'
isi: 1
issue: '8'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 765 - 787
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Acta Informatica
publication_identifier:
issn:
- '00015903'
publication_status: published
publisher: Springer
publist_id: '5898'
pubrep_id: '649'
quality_controlled: '1'
related_material:
record:
- id: '1835'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Model checking the evolution of gene regulatory networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 54
year: '2017'
...
---
_id: '1336'
abstract:
- lang: eng
text: Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired
by natural evolution. In recent years the field of evolutionary computation has
developed a rigorous analytical theory to analyse the runtimes of EAs on many
illustrative problems. Here we apply this theory to a simple model of natural
evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the
time between occurrences of new mutations is much longer than the time it takes
for a mutated genotype to take over the population. In this situation, the population
only contains copies of one genotype and evolution can be modelled as a stochastic
process evolving one genotype by means of mutation and selection between the resident
and the mutated genotype. The probability of accepting the mutated genotype then
depends on the change in fitness. We study this process, SSWM, from an algorithmic
perspective, quantifying its expected optimisation time for various parameters
and investigating differences to a similar evolutionary algorithm, the well-known
(1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at
crossing fitness valleys and study an example where SSWM outperforms the (1+1)
EA by taking advantage of information on the fitness gradient.
article_processing_charge: No
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Jorge
full_name: Pérez Heredia, Jorge
last_name: Pérez Heredia
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison
of natural and artificial evolution. Algorithmica. 2017;78(2):681-713.
doi:10.1007/s00453-016-0212-1
apa: Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2017). Towards
a runtime comparison of natural and artificial evolution. Algorithmica.
Springer. https://doi.org/10.1007/s00453-016-0212-1
chicago: Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova.
“Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica.
Springer, 2017. https://doi.org/10.1007/s00453-016-0212-1.
ieee: T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime
comparison of natural and artificial evolution,” Algorithmica, vol. 78,
no. 2. Springer, pp. 681–713, 2017.
ista: Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime
comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.
mla: Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial
Evolution.” Algorithmica, vol. 78, no. 2, Springer, 2017, pp. 681–713,
doi:10.1007/s00453-016-0212-1.
short: T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017)
681–713.
date_created: 2018-12-11T11:51:27Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T11:14:42Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1007/s00453-016-0212-1
ec_funded: 1
external_id:
isi:
- '000400379500013'
file:
- access_level: open_access
checksum: 7873f665a0c598ac747c908f34cb14b9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:19Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4805'
file_name: IST-2016-658-v1+1_s00453-016-0212-1.pdf
file_size: 710206
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 78'
isi: 1
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 681 - 713
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Algorithmica
publication_identifier:
issn:
- '01784617'
publication_status: published
publisher: Springer
publist_id: '5931'
pubrep_id: '658'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Towards a runtime comparison of natural and artificial evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 78
year: '2017'
...
---
_id: '1337'
abstract:
- lang: eng
text: We consider the local eigenvalue distribution of large self-adjoint N×N random
matrices H=H∗ with centered independent entries. In contrast to previous works
the matrix of variances sij=\mathbbmE|hij|2 is not assumed to be stochastic. Hence
the density of states is not the Wigner semicircle law. Its possible shapes are
described in the companion paper (Ajanki et al. in Quadratic Vector Equations
on the Complex Upper Half Plane. arXiv:1506.05095). We show that as N grows, the
resolvent, G(z)=(H−z)−1, converges to a diagonal matrix, diag(m(z)), where m(z)=(m1(z),…,mN(z))
solves the vector equation −1/mi(z)=z+∑jsijmj(z) that has been analyzed in Ajanki
et al. (Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095).
We prove a local law down to the smallest spectral resolution scale, and bulk
universality for both real symmetric and complex hermitian symmetry classes.
acknowledgement: 'Open access funding provided by Institute of Science and Technology
(IST Austria). '
article_processing_charge: Yes (via OA deal)
author:
- first_name: Oskari H
full_name: Ajanki, Oskari H
id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87
last_name: Ajanki
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: Ajanki OH, Erdös L, Krüger TH. Universality for general Wigner-type matrices.
Probability Theory and Related Fields. 2017;169(3-4):667-727. doi:10.1007/s00440-016-0740-2
apa: Ajanki, O. H., Erdös, L., & Krüger, T. H. (2017). Universality for general
Wigner-type matrices. Probability Theory and Related Fields. Springer.
https://doi.org/10.1007/s00440-016-0740-2
chicago: Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Universality for
General Wigner-Type Matrices.” Probability Theory and Related Fields. Springer,
2017. https://doi.org/10.1007/s00440-016-0740-2.
ieee: O. H. Ajanki, L. Erdös, and T. H. Krüger, “Universality for general Wigner-type
matrices,” Probability Theory and Related Fields, vol. 169, no. 3–4. Springer,
pp. 667–727, 2017.
ista: Ajanki OH, Erdös L, Krüger TH. 2017. Universality for general Wigner-type
matrices. Probability Theory and Related Fields. 169(3–4), 667–727.
mla: Ajanki, Oskari H., et al. “Universality for General Wigner-Type Matrices.”
Probability Theory and Related Fields, vol. 169, no. 3–4, Springer, 2017,
pp. 667–727, doi:10.1007/s00440-016-0740-2.
short: O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields
169 (2017) 667–727.
date_created: 2018-12-11T11:51:27Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-09-20T11:14:17Z
day: '01'
ddc:
- '510'
- '530'
department:
- _id: LaEr
doi: 10.1007/s00440-016-0740-2
ec_funded: 1
external_id:
isi:
- '000414358400002'
file:
- access_level: open_access
checksum: 29f5a72c3f91e408aeb9e78344973803
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:25Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4686'
file_name: IST-2017-657-v1+2_s00440-016-0740-2.pdf
file_size: 988843
relation: main_file
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has_accepted_license: '1'
intvolume: ' 169'
isi: 1
issue: 3-4
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 667 - 727
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Probability Theory and Related Fields
publication_identifier:
issn:
- '01788051'
publication_status: published
publisher: Springer
publist_id: '5930'
pubrep_id: '657'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Universality for general Wigner-type matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 169
year: '2017'
...
---
_id: '1294'
abstract:
- lang: eng
text: We study controller synthesis problems for finite-state Markov decision processes,
where the objective is to optimize the expected mean-payoff performance and stability
(also known as variability in the literature). We argue that the basic notion
of expressing the stability using the statistical variance of the mean payoff
is sometimes insufficient, and propose an alternative definition. We show that
a strategy ensuring both the expected mean payoff and the variance below given
bounds requires randomization and memory, under both the above definitions. We
then show that the problem of finding such a strategy can be expressed as a set
of constraints.
article_processing_charge: No
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Vojtěch
full_name: Forejt, Vojtěch
last_name: Forejt
- first_name: Antonín
full_name: Kučera, Antonín
last_name: Kučera
citation:
ama: Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability
in Markov decision processes. Journal of Computer and System Sciences.
2017;84:144-170. doi:10.1016/j.jcss.2016.09.009
apa: Brázdil, T., Chatterjee, K., Forejt, V., & Kučera, A. (2017). Trading performance
for stability in Markov decision processes. Journal of Computer and System
Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2016.09.009
chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera.
“Trading Performance for Stability in Markov Decision Processes.” Journal of
Computer and System Sciences. Elsevier, 2017. https://doi.org/10.1016/j.jcss.2016.09.009.
ieee: T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance
for stability in Markov decision processes,” Journal of Computer and System
Sciences, vol. 84. Elsevier, pp. 144–170, 2017.
ista: Brázdil T, Chatterjee K, Forejt V, Kučera A. 2017. Trading performance for
stability in Markov decision processes. Journal of Computer and System Sciences.
84, 144–170.
mla: Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision
Processes.” Journal of Computer and System Sciences, vol. 84, Elsevier,
2017, pp. 144–70, doi:10.1016/j.jcss.2016.09.009.
short: T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, Journal of Computer and
System Sciences 84 (2017) 144–170.
date_created: 2018-12-11T11:51:12Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2023-09-20T11:15:31Z
day: '01'
ddc:
- '004'
- '006'
department:
- _id: KrCh
doi: 10.1016/j.jcss.2016.09.009
ec_funded: 1
external_id:
isi:
- '000388430000011'
file:
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checksum: 91271b23cf884d7c06d33bef0cd623b1
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creator: system
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date_updated: 2020-07-14T12:44:42Z
file_id: '4885'
file_name: IST-2016-717-v1+1_1-s2.0-S0022000016300897-main.pdf
file_size: 708657
relation: main_file
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intvolume: ' 84'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 144 - 170
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Journal of Computer and System Sciences
publication_status: published
publisher: Elsevier
publist_id: '6009'
pubrep_id: '717'
quality_controlled: '1'
related_material:
record:
- id: '2305'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Trading performance for stability in Markov decision processes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 84
year: '2017'
...
---
_id: '1228'
abstract:
- lang: eng
text: Since 2006, reprogrammed cells have increasingly been used as a biomedical
research technique in addition to neuro-psychiatric methods. These rapidly evolving
techniques allow for the generation of neuronal sub-populations, and have sparked
interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic
and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder
(BPD). This review provides a summary of 19 publications on reprogrammed adult
somatic cells derived from patients with SCZ, and five publications using this
technique in patients with BPD. As both disorders are complex and heterogeneous,
there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations
of dopaminergic transmission in vitro are sparse, despite the great explanatory
power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations
of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental
alterations. Some studies also report on the efficacy of medicinal compounds to
revert alterations observed in cellular models. However, due to the paucity of
replication studies, no comprehensive conclusions can be drawn from studies using
reprogrammed cells at the present time. In the future, findings from cell culture
methods need to be integrated with clinical, epidemiological, pharmacological
and imaging data in order to generate a more comprehensive picture of SCZ and
BPD.
acknowledgement: This work was supported by grants of the Austrian Science Fund (FWF)
P23585B09 to M.W. and F3506 to H.H.S. and the “Wiener Wissenschafts-, Forschungs-
und Technologiefonds” (Vienna Science and Technology Fund; WWTF) CS15-033 to M.W.
article_processing_charge: No
article_type: review
author:
- first_name: Ulrich
full_name: Sauerzopf, Ulrich
last_name: Sauerzopf
- first_name: Roberto
full_name: Sacco, Roberto
id: 42C9F57E-F248-11E8-B48F-1D18A9856A87
last_name: Sacco
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Marco
full_name: Niello, Marco
last_name: Niello
- first_name: Ana
full_name: Weidenauer, Ana
last_name: Weidenauer
- first_name: Nicole
full_name: Praschak Rieder, Nicole
last_name: Praschak Rieder
- first_name: Harald
full_name: Sitte, Harald
last_name: Sitte
- first_name: Matthaeus
full_name: Willeit, Matthaeus
last_name: Willeit
citation:
ama: Sauerzopf U, Sacco R, Novarino G, et al. Are reprogrammed cells a useful tool
for studying dopamine dysfunction in psychotic disorders? A review of the current
evidence. European Journal of Neuroscience. 2017;45(1):45-57. doi:10.1111/ejn.13418
apa: Sauerzopf, U., Sacco, R., Novarino, G., Niello, M., Weidenauer, A., Praschak
Rieder, N., … Willeit, M. (2017). Are reprogrammed cells a useful tool for studying
dopamine dysfunction in psychotic disorders? A review of the current evidence.
European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1111/ejn.13418
chicago: Sauerzopf, Ulrich, Roberto Sacco, Gaia Novarino, Marco Niello, Ana Weidenauer,
Nicole Praschak Rieder, Harald Sitte, and Matthaeus Willeit. “Are Reprogrammed
Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders?
A Review of the Current Evidence.” European Journal of Neuroscience. Wiley-Blackwell,
2017. https://doi.org/10.1111/ejn.13418.
ieee: U. Sauerzopf et al., “Are reprogrammed cells a useful tool for studying
dopamine dysfunction in psychotic disorders? A review of the current evidence,”
European Journal of Neuroscience, vol. 45, no. 1. Wiley-Blackwell, pp.
45–57, 2017.
ista: Sauerzopf U, Sacco R, Novarino G, Niello M, Weidenauer A, Praschak Rieder
N, Sitte H, Willeit M. 2017. Are reprogrammed cells a useful tool for studying
dopamine dysfunction in psychotic disorders? A review of the current evidence.
European Journal of Neuroscience. 45(1), 45–57.
mla: Sauerzopf, Ulrich, et al. “Are Reprogrammed Cells a Useful Tool for Studying
Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.”
European Journal of Neuroscience, vol. 45, no. 1, Wiley-Blackwell, 2017,
pp. 45–57, doi:10.1111/ejn.13418.
short: U. Sauerzopf, R. Sacco, G. Novarino, M. Niello, A. Weidenauer, N. Praschak
Rieder, H. Sitte, M. Willeit, European Journal of Neuroscience 45 (2017) 45–57.
date_created: 2018-12-11T11:50:50Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:16:01Z
day: '01'
ddc:
- '616'
department:
- _id: GaNo
doi: 10.1111/ejn.13418
external_id:
isi:
- '000392487100005'
pmid:
- '27690184'
file:
- access_level: open_access
checksum: c572cf02be8fbb7020cfcfb892182e4c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:48Z
date_updated: 2020-07-14T12:44:39Z
file_id: '4838'
file_name: IST-2017-738-v1+1_Sauerzopf_et_al-2017-European_Journal_of_Neuroscience.pdf
file_size: 169145
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 45'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 45 - 57
pmid: 1
publication: European Journal of Neuroscience
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6106'
pubrep_id: '738'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic
disorders? A review of the current evidence
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 45
year: '2017'
...
---
_id: '1213'
abstract:
- lang: eng
text: Bacterial cytokinesis is commonly initiated by the Z-ring, a dynamic cytoskeletal
structure that assembles at the site of division. Its primary component is FtsZ,
a tubulin-like GTPase, that like its eukaryotic relative forms protein filaments
in the presence of GTP. Since the discovery of the Z-ring 25 years ago, various
models for the role of FtsZ have been suggested. However, important information
about the architecture and dynamics of FtsZ filaments during cytokinesis is still
missing. One reason for this lack of knowledge has been the small size of bacteria,
which has made it difficult to resolve the orientation and dynamics of individual
FtsZ filaments in the Z-ring. While superresolution microscopy experiments have
helped to gain more information about the organization of the Z-ring in the dividing
cell, they were not yet able to elucidate a mechanism of how FtsZ filaments reorganize
during assembly and disassembly of the Z-ring. In this chapter, we explain how
to use an in vitro reconstitution approach to investigate the self-organization
of FtsZ filaments recruited to a biomimetic lipid bilayer by its membrane anchor
FtsA. We show how to perform single-molecule experiments to study the behavior
of individual FtsZ monomers during the constant reorganization of the FtsZ-FtsA
filament network. We describe how to analyze the dynamics of single molecules
and explain why this information can help to shed light onto possible mechanism
of Z-ring constriction. We believe that similar experimental approaches will be
useful to study the mechanism of membrane-based polymerization of other cytoskeletal
systems, not only from prokaryotic but also eukaryotic origin.
acknowledged_ssus:
- _id: Bio
acknowledgement: Natalia Baranova is supported by an EMBO Long-Term Fellowship (EMBO
ALTF 1163-2015) and Martin Loose by an ERC Starting Grant (ERCStG-2015-SelfOrganiCell).
alternative_title:
- Methods in Cell Biology
article_processing_charge: No
author:
- first_name: Natalia
full_name: Baranova, Natalia
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: 'Baranova NS, Loose M. Single-molecule measurements to study polymerization
dynamics of FtsZ-FtsA copolymers. In: Echard A, ed. Cytokinesis. Vol 137.
Academic Press; 2017:355-370. doi:10.1016/bs.mcb.2016.03.036'
apa: Baranova, N. S., & Loose, M. (2017). Single-molecule measurements to study
polymerization dynamics of FtsZ-FtsA copolymers. In A. Echard (Ed.), Cytokinesis
(Vol. 137, pp. 355–370). Academic Press. https://doi.org/10.1016/bs.mcb.2016.03.036
chicago: Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to
Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” In Cytokinesis,
edited by Arnaud Echard, 137:355–70. Academic Press, 2017. https://doi.org/10.1016/bs.mcb.2016.03.036.
ieee: N. S. Baranova and M. Loose, “Single-molecule measurements to study polymerization
dynamics of FtsZ-FtsA copolymers,” in Cytokinesis, vol. 137, A. Echard,
Ed. Academic Press, 2017, pp. 355–370.
ista: 'Baranova NS, Loose M. 2017.Single-molecule measurements to study polymerization
dynamics of FtsZ-FtsA copolymers. In: Cytokinesis. Methods in Cell Biology, vol.
137, 355–370.'
mla: Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study
Polymerization Dynamics of FtsZ-FtsA Copolymers.” Cytokinesis, edited by
Arnaud Echard, vol. 137, Academic Press, 2017, pp. 355–70, doi:10.1016/bs.mcb.2016.03.036.
short: N.S. Baranova, M. Loose, in:, A. Echard (Ed.), Cytokinesis, Academic Press,
2017, pp. 355–370.
date_created: 2018-12-11T11:50:45Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-09-20T11:16:30Z
day: '01'
department:
- _id: MaLo
doi: 10.1016/bs.mcb.2016.03.036
ec_funded: 1
editor:
- first_name: 'Arnaud '
full_name: 'Echard, Arnaud '
last_name: Echard
external_id:
isi:
- '000403542900022'
intvolume: ' 137'
isi: 1
language:
- iso: eng
month: '12'
oa_version: None
page: 355 - 370
project:
- _id: 2596EAB6-B435-11E9-9278-68D0E5697425
grant_number: ALTF 2015-1163
name: Synthesis of bacterial cell wall
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Cytokinesis
publication_identifier:
issn:
- 0091679X
publication_status: published
publisher: Academic Press
publist_id: '6134'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA
copolymers
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 137
year: '2017'
...
---
_id: '1198'
abstract:
- lang: eng
text: We consider a model of fermions interacting via point interactions, defined
via a certain weighted Dirichlet form. While for two particles the interaction
corresponds to infinite scattering length, the presence of further particles effectively
decreases the interaction strength. We show that the model becomes trivial in
the thermodynamic limit, in the sense that the free energy density at any given
particle density and temperature agrees with the corresponding expression for
non-interacting particles.
acknowledgement: 'Open access funding provided by Institute of Science and Technology
(IST Austria). '
article_processing_charge: Yes (via OA deal)
author:
- first_name: Thomas
full_name: Moser, Thomas
id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87
last_name: Moser
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Moser T, Seiringer R. Triviality of a model of particles with point interactions
in the thermodynamic limit. Letters in Mathematical Physics. 2017;107(3):533-552.
doi:10.1007/s11005-016-0915-x
apa: Moser, T., & Seiringer, R. (2017). Triviality of a model of particles with
point interactions in the thermodynamic limit. Letters in Mathematical Physics.
Springer. https://doi.org/10.1007/s11005-016-0915-x
chicago: Moser, Thomas, and Robert Seiringer. “Triviality of a Model of Particles
with Point Interactions in the Thermodynamic Limit.” Letters in Mathematical
Physics. Springer, 2017. https://doi.org/10.1007/s11005-016-0915-x.
ieee: T. Moser and R. Seiringer, “Triviality of a model of particles with point
interactions in the thermodynamic limit,” Letters in Mathematical Physics,
vol. 107, no. 3. Springer, pp. 533–552, 2017.
ista: Moser T, Seiringer R. 2017. Triviality of a model of particles with point
interactions in the thermodynamic limit. Letters in Mathematical Physics. 107(3),
533–552.
mla: Moser, Thomas, and Robert Seiringer. “Triviality of a Model of Particles with
Point Interactions in the Thermodynamic Limit.” Letters in Mathematical Physics,
vol. 107, no. 3, Springer, 2017, pp. 533–52, doi:10.1007/s11005-016-0915-x.
short: T. Moser, R. Seiringer, Letters in Mathematical Physics 107 (2017) 533–552.
date_created: 2018-12-11T11:50:40Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2023-09-20T11:18:13Z
day: '01'
ddc:
- '510'
- '539'
department:
- _id: RoSe
doi: 10.1007/s11005-016-0915-x
external_id:
isi:
- '000394280200007'
file:
- access_level: open_access
checksum: c0c835def162c1bc52f978fad26e3c2f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:40Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5296'
file_name: IST-2016-723-v1+1_s11005-016-0915-x.pdf
file_size: 587207
relation: main_file
file_date_updated: 2020-07-14T12:44:38Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: ' 533 - 552'
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Letters in Mathematical Physics
publication_identifier:
issn:
- '03779017'
publication_status: published
publisher: Springer
publist_id: '6152'
pubrep_id: '723'
quality_controlled: '1'
related_material:
record:
- id: '52'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Triviality of a model of particles with point interactions in the thermodynamic
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 107
year: '2017'
...
---
_id: '1207'
abstract:
- lang: eng
text: The eigenvalue distribution of the sum of two large Hermitian matrices, when
one of them is conjugated by a Haar distributed unitary matrix, is asymptotically
given by the free convolution of their spectral distributions. We prove that this
convergence also holds locally in the bulk of the spectrum, down to the optimal
scales larger than the eigenvalue spacing. The corresponding eigenvectors are
fully delocalized. Similar results hold for the sum of two real symmetric matrices,
when one is conjugated by Haar orthogonal matrix.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Bao Z, Erdös L, Schnelli K. Local law of addition of random matrices on optimal
scale. Communications in Mathematical Physics. 2017;349(3):947-990. doi:10.1007/s00220-016-2805-6
apa: Bao, Z., Erdös, L., & Schnelli, K. (2017). Local law of addition of random
matrices on optimal scale. Communications in Mathematical Physics. Springer.
https://doi.org/10.1007/s00220-016-2805-6
chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Law of Addition
of Random Matrices on Optimal Scale.” Communications in Mathematical Physics.
Springer, 2017. https://doi.org/10.1007/s00220-016-2805-6.
ieee: Z. Bao, L. Erdös, and K. Schnelli, “Local law of addition of random matrices
on optimal scale,” Communications in Mathematical Physics, vol. 349, no.
3. Springer, pp. 947–990, 2017.
ista: Bao Z, Erdös L, Schnelli K. 2017. Local law of addition of random matrices
on optimal scale. Communications in Mathematical Physics. 349(3), 947–990.
mla: Bao, Zhigang, et al. “Local Law of Addition of Random Matrices on Optimal Scale.”
Communications in Mathematical Physics, vol. 349, no. 3, Springer, 2017,
pp. 947–90, doi:10.1007/s00220-016-2805-6.
short: Z. Bao, L. Erdös, K. Schnelli, Communications in Mathematical Physics 349
(2017) 947–990.
date_created: 2018-12-11T11:50:43Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T11:16:57Z
day: '01'
ddc:
- '530'
department:
- _id: LaEr
doi: 10.1007/s00220-016-2805-6
ec_funded: 1
external_id:
isi:
- '000393696700005'
file:
- access_level: open_access
checksum: ddff79154c3daf27237de5383b1264a9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:47Z
date_updated: 2020-07-14T12:44:39Z
file_id: '5102'
file_name: IST-2016-722-v1+1_s00220-016-2805-6.pdf
file_size: 1033743
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 349'
isi: 1
issue: '3'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 947 - 990
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Communications in Mathematical Physics
publication_identifier:
issn:
- '00103616'
publication_status: published
publisher: Springer
publist_id: '6141'
pubrep_id: '722'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local law of addition of random matrices on optimal scale
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 349
year: '2017'
...
---
_id: '1196'
abstract:
- lang: eng
text: 'We define the . model-measuring problem: given a model . M and specification
. ϕ, what is the maximal distance . ρ such that all models . M'' within distance
. ρ from . M satisfy (or violate) . ϕ. The model-measuring problem presupposes
a distance function on models. We concentrate on . automatic distance functions,
which are defined by weighted automata. The model-measuring problem subsumes several
generalizations of the classical model-checking problem, in particular, quantitative
model-checking problems that measure the degree of satisfaction of a specification;
robustness problems that measure how much a model can be perturbed without violating
the specification; and parameter synthesis for hybrid systems. We show that for
automatic distance functions, and (a) . ω-regular linear-time, (b) . ω-regular
branching-time, and (c) hybrid specifications, the model-measuring problem can
be solved.We use automata-theoretic model-checking methods for model measuring,
replacing the emptiness question for word, tree, and hybrid automata by the .
optimal-value question for the weighted versions of these automata. For automata
over words and trees, we consider weighted automata that accumulate weights by
maximizing, summing, discounting, and limit averaging. For hybrid automata, we
consider monotonic (parametric) hybrid automata, a hybrid counterpart of (discrete)
weighted automata.We give several examples of using the model-measuring problem
to compute various notions of robustness and quantitative satisfaction for temporal
specifications. Further, we propose the modeling framework for model measuring
to ease the specification and reduce the likelihood of errors in modeling.Finally,
we present a variant of the model-measuring problem, called the . model-repair
problem. The model-repair problem applies to models that do not satisfy the specification;
it can be used to derive restrictions, under which the model satisfies the specification,
i.e., to repair the model.'
acknowledgement: "This research was supported in part by the European Research Council
(ERC) under grant 267989 (QUAREM), by the Austrian Science Fund1 (FWF) under grants
S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the National Science
Centre (NCN), Poland under grant 2014/15/D/ST6/04543.\r\nA Technical Report of this
article is available via: https://repository.ist.ac.at/171/"
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: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Henzinger TA, Otop J. Model measuring for discrete and hybrid systems. Nonlinear
Analysis: Hybrid Systems. 2017;23:166-190. doi:10.1016/j.nahs.2016.09.001'
apa: 'Henzinger, T. A., & Otop, J. (2017). Model measuring for discrete and
hybrid systems. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2016.09.001'
chicago: 'Henzinger, Thomas A, and Jan Otop. “Model Measuring for Discrete and Hybrid
Systems.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2017. https://doi.org/10.1016/j.nahs.2016.09.001.'
ieee: 'T. A. Henzinger and J. Otop, “Model measuring for discrete and hybrid systems,”
Nonlinear Analysis: Hybrid Systems, vol. 23. Elsevier, pp. 166–190, 2017.'
ista: 'Henzinger TA, Otop J. 2017. Model measuring for discrete and hybrid systems.
Nonlinear Analysis: Hybrid Systems. 23, 166–190.'
mla: 'Henzinger, Thomas A., and Jan Otop. “Model Measuring for Discrete and Hybrid
Systems.” Nonlinear Analysis: Hybrid Systems, vol. 23, Elsevier, 2017,
pp. 166–90, doi:10.1016/j.nahs.2016.09.001.'
short: 'T.A. Henzinger, J. Otop, Nonlinear Analysis: Hybrid Systems 23 (2017) 166–190.'
date_created: 2018-12-11T11:50:39Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T11:18:50Z
day: '01'
department:
- _id: ToHe
doi: 10.1016/j.nahs.2016.09.001
ec_funded: 1
external_id:
isi:
- '000390637000011'
intvolume: ' 23'
isi: 1
language:
- iso: eng
month: '02'
oa_version: None
page: 166 - 190
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 'Nonlinear Analysis: Hybrid Systems'
publication_status: published
publisher: Elsevier
publist_id: '6154'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Model measuring for discrete and hybrid systems
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 23
year: '2017'
...
---
_id: '1199'
abstract:
- lang: eng
text: Much of quantitative genetics is based on the ‘infinitesimal model’, under
which selection has a negligible effect on the genetic variance. This is typically
justified by assuming a very large number of loci with additive effects. However,
it applies even when genes interact, provided that the number of loci is large
enough that selection on each of them is weak relative to random drift. In the
long term, directional selection will change allele frequencies, but even then,
the effects of epistasis on the ultimate change in trait mean due to selection
may be modest. Stabilising selection can maintain many traits close to their optima,
even when the underlying alleles are weakly selected. However, the number of traits
that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this
is hard to reconcile with the apparent complexity of many organisms. Just as for
the mutation load, this limit can be evaded by a particular form of negative epistasis.
A more robust limit is set by the variance in reproductive success. This suggests
that selection accumulates information most efficiently in the infinitesimal regime,
when selection on individual alleles is weak, and comparable with random drift.
A review of evidence on selection strength suggests that although most variance
in fitness may be because of alleles with large Nes, substantial amounts of adaptation
may be because of alleles in the infinitesimal regime, in which epistasis has
modest effects.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. How does epistasis influence the response to selection? Heredity.
2017;118:96-109. doi:10.1038/hdy.2016.109
apa: Barton, N. H. (2017). How does epistasis influence the response to selection?
Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2016.109
chicago: Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?”
Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2016.109.
ieee: N. H. Barton, “How does epistasis influence the response to selection?,” Heredity,
vol. 118. Nature Publishing Group, pp. 96–109, 2017.
ista: Barton NH. 2017. How does epistasis influence the response to selection? Heredity.
118, 96–109.
mla: Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?”
Heredity, vol. 118, Nature Publishing Group, 2017, pp. 96–109, doi:10.1038/hdy.2016.109.
short: N.H. Barton, Heredity 118 (2017) 96–109.
date_created: 2018-12-11T11:50:40Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:17:47Z
day: '01'
department:
- _id: NiBa
doi: 10.1038/hdy.2016.109
ec_funded: 1
external_id:
isi:
- '000392229100011'
intvolume: ' 118'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176114/
month: '01'
oa: 1
oa_version: Submitted Version
page: 96 - 109
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Heredity
publication_status: published
publisher: Nature Publishing Group
publist_id: '6151'
quality_controlled: '1'
related_material:
record:
- id: '9710'
relation: research_data
status: public
scopus_import: '1'
status: public
title: How does epistasis influence the response to selection?
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 118
year: '2017'
...
---
_id: '1208'
abstract:
- lang: eng
text: We study parameter estimation in linear Gaussian covariance models, which
are p-dimensional Gaussian models with linear constraints on the covariance matrix.
Maximum likelihood estimation for this class of models leads to a non-convex optimization
problem which typically has many local maxima. Using recent results on the asymptotic
distribution of extreme eigenvalues of the Wishart distribution, we provide sufficient
conditions for any hill climbing method to converge to the global maximum. Although
we are primarily interested in the case in which n≫p, the proofs of our results
utilize large sample asymptotic theory under the scheme n/p→γ>1. Remarkably,
our numerical simulations indicate that our results remain valid for p as small
as 2. An important consequence of this analysis is that, for sample sizes n≃14p,
maximum likelihood estimation for linear Gaussian covariance models behaves as
if it were a convex optimization problem. © 2016 The Royal Statistical Society
and Blackwell Publishing Ltd.
article_processing_charge: No
author:
- first_name: Piotr
full_name: Zwiernik, Piotr
last_name: Zwiernik
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Donald
full_name: Richards, Donald
last_name: Richards
citation:
ama: 'Zwiernik P, Uhler C, Richards D. Maximum likelihood estimation for linear
Gaussian covariance models. Journal of the Royal Statistical Society Series
B: Statistical Methodology. 2017;79(4):1269-1292. doi:10.1111/rssb.12217'
apa: 'Zwiernik, P., Uhler, C., & Richards, D. (2017). Maximum likelihood estimation
for linear Gaussian covariance models. Journal of the Royal Statistical Society.
Series B: Statistical Methodology. Wiley-Blackwell. https://doi.org/10.1111/rssb.12217'
chicago: 'Zwiernik, Piotr, Caroline Uhler, and Donald Richards. “Maximum Likelihood
Estimation for Linear Gaussian Covariance Models.” Journal of the Royal Statistical
Society. Series B: Statistical Methodology. Wiley-Blackwell, 2017. https://doi.org/10.1111/rssb.12217.'
ieee: 'P. Zwiernik, C. Uhler, and D. Richards, “Maximum likelihood estimation for
linear Gaussian covariance models,” Journal of the Royal Statistical Society.
Series B: Statistical Methodology, vol. 79, no. 4. Wiley-Blackwell, pp. 1269–1292,
2017.'
ista: 'Zwiernik P, Uhler C, Richards D. 2017. Maximum likelihood estimation for
linear Gaussian covariance models. Journal of the Royal Statistical Society. Series
B: Statistical Methodology. 79(4), 1269–1292.'
mla: 'Zwiernik, Piotr, et al. “Maximum Likelihood Estimation for Linear Gaussian
Covariance Models.” Journal of the Royal Statistical Society. Series B: Statistical
Methodology, vol. 79, no. 4, Wiley-Blackwell, 2017, pp. 1269–92, doi:10.1111/rssb.12217.'
short: 'P. Zwiernik, C. Uhler, D. Richards, Journal of the Royal Statistical Society.
Series B: Statistical Methodology 79 (2017) 1269–1292.'
date_created: 2018-12-11T11:50:43Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-09-20T11:17:21Z
day: '01'
department:
- _id: CaUh
doi: 10.1111/rssb.12217
external_id:
isi:
- '000411712300012'
intvolume: ' 79'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1408.5604
month: '09'
oa: 1
oa_version: Submitted Version
page: 1269 - 1292
project:
- _id: 2530CA10-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 903-N35
name: 'Gaussian Graphical Models: Theory and Applications'
publication: 'Journal of the Royal Statistical Society. Series B: Statistical Methodology'
publication_identifier:
issn:
- '13697412'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6142'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Maximum likelihood estimation for linear Gaussian covariance models
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 79
year: '2017'
...
---
_id: '1174'
abstract:
- lang: eng
text: Security of cryptographic applications is typically defined by security games.
The adversary, within certain resources, cannot win with probability much better
than 0 (for unpredictability applications, like one-way functions) or much better
than 1/2 (indistinguishability applications for instance encryption schemes).
In so called squared-friendly applications the winning probability of the adversary,
for different values of the application secret randomness, is not only close to
0 or 1/2 on average, but also concentrated in the sense that its second central
moment is small. The class of squared-friendly applications, which contains all
unpredictability applications and many indistinguishability applications, is particularly
important for key derivation. Barak et al. observed that for square-friendly applications
one can beat the "RT-bound", extracting secure keys with significantly
smaller entropy loss. In turn Dodis and Yu showed that in squared-friendly applications
one can directly use a "weak" key, which has only high entropy, as a
secure key. In this paper we give sharp lower bounds on square security assuming
security for "weak" keys. We show that any application which is either
(a) secure with weak keys or (b) allows for entropy savings for keys derived by
universal hashing, must be square-friendly. Quantitatively, our lower bounds match
the positive results of Dodis and Yu and Barak et al. (TCC\'13, CRYPTO\'11) Hence,
they can be understood as a general characterization of squared-friendly applications.
While the positive results on squared-friendly applications where derived by one
clever application of the Cauchy-Schwarz Inequality, for tight lower bounds we
need more machinery. In our approach we use convex optimization techniques and
some theory of circular matrices.
alternative_title:
- LIPIcs
article_number: '57'
article_processing_charge: No
author:
- first_name: Maciej
full_name: Skórski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skórski
citation:
ama: 'Skórski M. Lower bounds on key derivation for square-friendly applications.
In: Vol 66. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.STACS.2017.57'
apa: 'Skórski, M. (2017). Lower bounds on key derivation for square-friendly applications
(Vol. 66). Presented at the STACS: Symposium on Theoretical Aspects of Computer
Science, Hannover, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.STACS.2017.57'
chicago: Skórski, Maciej. “Lower Bounds on Key Derivation for Square-Friendly Applications,”
Vol. 66. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.STACS.2017.57.
ieee: 'M. Skórski, “Lower bounds on key derivation for square-friendly applications,”
presented at the STACS: Symposium on Theoretical Aspects of Computer Science,
Hannover, Germany, 2017, vol. 66.'
ista: 'Skórski M. 2017. Lower bounds on key derivation for square-friendly applications.
STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 66,
57.'
mla: Skórski, Maciej. Lower Bounds on Key Derivation for Square-Friendly Applications.
Vol. 66, 57, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.STACS.2017.57.
short: M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.
conference:
end_date: 2017-03-11
location: Hannover, Germany
name: 'STACS: Symposium on Theoretical Aspects of Computer Science'
start_date: 2017-03-08
date_created: 2018-12-11T11:50:32Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2023-09-20T11:23:15Z
day: '01'
department:
- _id: KrPi
doi: 10.4230/LIPIcs.STACS.2017.57
ec_funded: 1
external_id:
isi:
- '000521077300057'
intvolume: ' 66'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://drops.dagstuhl.de/opus/volltexte/2017/6976
month: '03'
oa: 1
oa_version: Submitted Version
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6180'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lower bounds on key derivation for square-friendly applications
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 66
year: '2017'
...
---
_id: '1176'
abstract:
- lang: eng
text: The algorithm Argon2i-B of Biryukov, Dinu and Khovratovich is currently being
considered by the IRTF (Internet Research Task Force) as a new de-facto standard
for password hashing. An older version (Argon2i-A) of the same algorithm was chosen
as the winner of the recent Password Hashing Competition. An important competitor
to Argon2i-B is the recently introduced Balloon Hashing (BH) algorithm of Corrigan-Gibs,
Boneh and Schechter. A key security desiderata for any such algorithm is that
evaluating it (even using a custom device) requires a large amount of memory amortized
across multiple instances. Alwen and Blocki (CRYPTO 2016) introduced a class of
theoretical attacks against Argon2i-A and BH. While these attacks yield large
asymptotic reductions in the amount of memory, it was not, a priori, clear if
(1) they can be extended to the newer Argon2i-B, (2) the attacks are effective
on any algorithm for practical parameter ranges (e.g., 1GB of memory) and (3)
if they can be effectively instantiated against any algorithm under realistic
hardware constrains. In this work we answer all three of these questions in the
affirmative for all three algorithms. This is also the first work to analyze the
security of Argon2i-B. In more detail, we extend the theoretical attacks of Alwen
and Blocki (CRYPTO 2016) to the recent Argon2i-B proposal demonstrating severe
asymptotic deficiencies in its security. Next we introduce several novel heuristics
for improving the attack's concrete memory efficiency even when on-chip memory
bandwidth is bounded. We then simulate our attacks on randomly sampled Argon2i-A,
Argon2i-B and BH instances and measure the resulting memory consumption for various
practical parameter ranges and for a variety of upperbounds on the amount of parallelism
available to the attacker. Finally we describe, implement, and test a new heuristic
for applying the Alwen-Blocki attack to functions employing a technique developed
by Corrigan-Gibs et al. for improving concrete security of memory-hard functions.
We analyze the collected data and show the effects various parameters have on
the memory consumption of the attack. In particular, we can draw several interesting
conclusions about the level of security provided by these functions. · For the
Alwen-Blocki attack to fail against practical memory parameters, Argon2i-B must
be instantiated with more than 10 passes on memory - beyond the "paranoid" parameter
setting in the current IRTF proposal. · The technique of Corrigan-Gibs for improving
security can also be overcome by the Alwen-Blocki attack under realistic hardware
constraints. · On a positive note, both the asymptotic and concrete security of
Argon2i-B seem to improve on that of Argon2i-A.
article_number: '7961977'
article_processing_charge: No
author:
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Jeremiah
full_name: Blocki, Jeremiah
last_name: Blocki
citation:
ama: 'Alwen JF, Blocki J. Towards practical attacks on Argon2i and balloon hashing.
In: IEEE; 2017. doi:10.1109/EuroSP.2017.47'
apa: 'Alwen, J. F., & Blocki, J. (2017). Towards practical attacks on Argon2i
and balloon hashing. Presented at the EuroS&P: European Symposium on Security
and Privacy, Paris, France: IEEE. https://doi.org/10.1109/EuroSP.2017.47'
chicago: Alwen, Joel F, and Jeremiah Blocki. “Towards Practical Attacks on Argon2i
and Balloon Hashing.” IEEE, 2017. https://doi.org/10.1109/EuroSP.2017.47.
ieee: 'J. F. Alwen and J. Blocki, “Towards practical attacks on Argon2i and balloon
hashing,” presented at the EuroS&P: European Symposium on Security and Privacy,
Paris, France, 2017.'
ista: 'Alwen JF, Blocki J. 2017. Towards practical attacks on Argon2i and balloon
hashing. EuroS&P: European Symposium on Security and Privacy, 7961977.'
mla: Alwen, Joel F., and Jeremiah Blocki. Towards Practical Attacks on Argon2i
and Balloon Hashing. 7961977, IEEE, 2017, doi:10.1109/EuroSP.2017.47.
short: J.F. Alwen, J. Blocki, in:, IEEE, 2017.
conference:
end_date: 2017-04-28
location: Paris, France
name: 'EuroS&P: European Symposium on Security and Privacy'
start_date: 2017-04-26
date_created: 2018-12-11T11:50:33Z
date_published: 2017-07-03T00:00:00Z
date_updated: 2023-09-20T11:22:25Z
day: '03'
department:
- _id: KrPi
doi: 10.1109/EuroSP.2017.47
external_id:
isi:
- '000424197300011'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/759
month: '07'
oa: 1
oa_version: Submitted Version
publication_identifier:
isbn:
- 978-150905761-0
publication_status: published
publisher: IEEE
publist_id: '6178'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Towards practical attacks on Argon2i and balloon hashing
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '1187'
abstract:
- lang: eng
text: We construct efficient authentication protocols and message authentication
codes (MACs) whose security can be reduced to the learning parity with noise (LPN)
problem. Despite a large body of work—starting with the (Formula presented.) protocol
of Hopper and Blum in 2001—until now it was not even known how to construct an
efficient authentication protocol from LPN which is secure against man-in-the-middle
attacks. A MAC implies such a (two-round) protocol.
article_processing_charge: No
article_type: original
author:
- first_name: Eike
full_name: Kiltz, Eike
last_name: Kiltz
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Daniele
full_name: Venturi, Daniele
last_name: Venturi
- first_name: David
full_name: Cash, David
last_name: Cash
- first_name: Abhishek
full_name: Jain, Abhishek
last_name: Jain
citation:
ama: Kiltz E, Pietrzak KZ, Venturi D, Cash D, Jain A. Efficient authentication from
hard learning problems. Journal of Cryptology. 2017;30(4):1238-1275. doi:10.1007/s00145-016-9247-3
apa: Kiltz, E., Pietrzak, K. Z., Venturi, D., Cash, D., & Jain, A. (2017). Efficient
authentication from hard learning problems. Journal of Cryptology. Springer.
https://doi.org/10.1007/s00145-016-9247-3
chicago: Kiltz, Eike, Krzysztof Z Pietrzak, Daniele Venturi, David Cash, and Abhishek
Jain. “Efficient Authentication from Hard Learning Problems.” Journal of Cryptology.
Springer, 2017. https://doi.org/10.1007/s00145-016-9247-3.
ieee: E. Kiltz, K. Z. Pietrzak, D. Venturi, D. Cash, and A. Jain, “Efficient authentication
from hard learning problems,” Journal of Cryptology, vol. 30, no. 4. Springer,
pp. 1238–1275, 2017.
ista: Kiltz E, Pietrzak KZ, Venturi D, Cash D, Jain A. 2017. Efficient authentication
from hard learning problems. Journal of Cryptology. 30(4), 1238–1275.
mla: Kiltz, Eike, et al. “Efficient Authentication from Hard Learning Problems.”
Journal of Cryptology, vol. 30, no. 4, Springer, 2017, pp. 1238–75, doi:10.1007/s00145-016-9247-3.
short: E. Kiltz, K.Z. Pietrzak, D. Venturi, D. Cash, A. Jain, Journal of Cryptology
30 (2017) 1238–1275.
date_created: 2018-12-11T11:50:37Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2023-09-20T11:20:58Z
day: '01'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.1007/s00145-016-9247-3
ec_funded: 1
external_id:
isi:
- '000410788600007'
file:
- access_level: open_access
checksum: c647520d115b772a1682fc06fa273eb1
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T16:30:17Z
date_updated: 2020-07-14T12:44:37Z
file_id: '7843'
file_name: 2017_JournalCrypto_Kiltz.pdf
file_size: 516959
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 1238 - 1275
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: Journal of Cryptology
publication_status: published
publisher: Springer
publist_id: '6166'
quality_controlled: '1'
related_material:
record:
- id: '3238'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Efficient authentication from hard learning problems
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 30
year: '2017'
...
---
_id: '1192'
abstract:
- lang: eng
text: The main result of this paper is a generalization of the classical blossom
algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean
CSPs where each variable appears in exactly two constraints (we call it edge CSP)
and all constraints are even Δ-matroid relations (represented by lists of tuples).
As a consequence of this, we settle the complexity classification of planar Boolean
CSPs started by Dvorak and Kupec. Knowing that edge CSP is tractable for even
Δ-matroid constraints allows us to extend the tractability result to a larger
class of Δ-matroids that includes many classes that were known to be tractable
before, namely co-independent, compact, local and binary.
article_processing_charge: No
author:
- first_name: Alexandr
full_name: Kazda, Alexandr
id: 3B32BAA8-F248-11E8-B48F-1D18A9856A87
last_name: Kazda
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: 'Kazda A, Kolmogorov V, Rolinek M. Even delta-matroids and the complexity of
planar Boolean CSPs. In: SIAM; 2017:307-326. doi:10.1137/1.9781611974782.20'
apa: 'Kazda, A., Kolmogorov, V., & Rolinek, M. (2017). Even delta-matroids and
the complexity of planar Boolean CSPs (pp. 307–326). Presented at the SODA: Symposium
on Discrete Algorithms, Barcelona, Spain: SIAM. https://doi.org/10.1137/1.9781611974782.20'
chicago: Kazda, Alexandr, Vladimir Kolmogorov, and Michal Rolinek. “Even Delta-Matroids
and the Complexity of Planar Boolean CSPs,” 307–26. SIAM, 2017. https://doi.org/10.1137/1.9781611974782.20.
ieee: 'A. Kazda, V. Kolmogorov, and M. Rolinek, “Even delta-matroids and the complexity
of planar Boolean CSPs,” presented at the SODA: Symposium on Discrete Algorithms,
Barcelona, Spain, 2017, pp. 307–326.'
ista: 'Kazda A, Kolmogorov V, Rolinek M. 2017. Even delta-matroids and the complexity
of planar Boolean CSPs. SODA: Symposium on Discrete Algorithms, 307–326.'
mla: Kazda, Alexandr, et al. Even Delta-Matroids and the Complexity of Planar
Boolean CSPs. SIAM, 2017, pp. 307–26, doi:10.1137/1.9781611974782.20.
short: A. Kazda, V. Kolmogorov, M. Rolinek, in:, SIAM, 2017, pp. 307–326.
conference:
end_date: 2017-01019
location: Barcelona, Spain
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2017-01-16
date_created: 2018-12-11T11:50:38Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:20:26Z
day: '01'
department:
- _id: VlKo
doi: 10.1137/1.9781611974782.20
ec_funded: 1
external_id:
isi:
- '000426965800020'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.03124
month: '01'
oa: 1
oa_version: Submitted Version
page: 307 - 326
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_identifier:
isbn:
- 978-161197478-2
publication_status: published
publisher: SIAM
publist_id: '6159'
quality_controlled: '1'
related_material:
record:
- id: '6032'
relation: later_version
status: public
status: public
title: Even delta-matroids and the complexity of planar Boolean CSPs
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '1180'
abstract:
- lang: eng
text: In this article we define an algebraic vertex of a generalized polyhedron
and show that the set of algebraic vertices is the smallest set of points needed
to define the polyhedron. We prove that the indicator function of a generalized
polytope P is a linear combination of indicator functions of simplices whose vertices
are algebraic vertices of P. We also show that the indicator function of any generalized
polyhedron is a linear combination, with integer coefficients, of indicator functions
of cones with apices at algebraic vertices and line-cones. The concept of an algebraic
vertex is closely related to the Fourier–Laplace transform. We show that a point
v is an algebraic vertex of a generalized polyhedron P if and only if the tangent
cone of P, at v, has non-zero Fourier–Laplace transform.
article_processing_charge: No
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Imre
full_name: Bárány, Imre
last_name: Bárány
- first_name: Sinai
full_name: Robins, Sinai
last_name: Robins
citation:
ama: Akopyan A, Bárány I, Robins S. Algebraic vertices of non-convex polyhedra.
Advances in Mathematics. 2017;308:627-644. doi:10.1016/j.aim.2016.12.026
apa: Akopyan, A., Bárány, I., & Robins, S. (2017). Algebraic vertices of non-convex
polyhedra. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2016.12.026
chicago: Akopyan, Arseniy, Imre Bárány, and Sinai Robins. “Algebraic Vertices of
Non-Convex Polyhedra.” Advances in Mathematics. Academic Press, 2017. https://doi.org/10.1016/j.aim.2016.12.026.
ieee: A. Akopyan, I. Bárány, and S. Robins, “Algebraic vertices of non-convex polyhedra,”
Advances in Mathematics, vol. 308. Academic Press, pp. 627–644, 2017.
ista: Akopyan A, Bárány I, Robins S. 2017. Algebraic vertices of non-convex polyhedra.
Advances in Mathematics. 308, 627–644.
mla: Akopyan, Arseniy, et al. “Algebraic Vertices of Non-Convex Polyhedra.” Advances
in Mathematics, vol. 308, Academic Press, 2017, pp. 627–44, doi:10.1016/j.aim.2016.12.026.
short: A. Akopyan, I. Bárány, S. Robins, Advances in Mathematics 308 (2017) 627–644.
date_created: 2018-12-11T11:50:34Z
date_published: 2017-02-21T00:00:00Z
date_updated: 2023-09-20T11:21:27Z
day: '21'
department:
- _id: HeEd
doi: 10.1016/j.aim.2016.12.026
ec_funded: 1
external_id:
isi:
- '000409292900015'
intvolume: ' 308'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1508.07594
month: '02'
oa: 1
oa_version: Submitted Version
page: 627 - 644
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Advances in Mathematics
publication_identifier:
issn:
- '00018708'
publication_status: published
publisher: Academic Press
publist_id: '6173'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Algebraic vertices of non-convex polyhedra
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 308
year: '2017'
...
---
_id: '1159'
abstract:
- lang: eng
text: Auxin steers numerous physiological processes in plants, making the tight
control of its endogenous levels and spatiotemporal distribution a necessity.
This regulation is achieved by different mechanisms, including auxin biosynthesis,
metabolic conversions, degradation, and transport. Here, we introduce cis-cinnamic
acid (c-CA) as a novel and unique addition to a small group of endogenous molecules
affecting in planta auxin concentrations. c-CA is the photo-isomerization product
of the phenylpropanoid pathway intermediate trans-CA (t-CA). When grown on c-CA-containing
medium, an evolutionary diverse set of plant species were shown to exhibit phenotypes
characteristic for high auxin levels, including inhibition of primary root growth,
induction of root hairs, and promotion of adventitious and lateral rooting. By
molecular docking and receptor binding assays, we showed that c-CA itself is neither
an auxin nor an anti-auxin, and auxin profiling data revealed that c-CA does not
significantly interfere with auxin biosynthesis. Single cell-based auxin accumulation
assays showed that c-CA, and not t-CA, is a potent inhibitor of auxin efflux.
Auxin signaling reporters detected changes in spatiotemporal distribution of the
auxin response along the root of c-CA-treated plants, and long-distance auxin
transport assays showed no inhibition of rootward auxin transport. Overall, these
results suggest that the phenotypes of c-CA-treated plants are the consequence
of a local change in auxin accumulation, induced by the inhibition of auxin efflux.
This work reveals a novel mechanism how plants may regulate auxin levels and adds
a novel, naturally occurring molecule to the chemical toolbox for the studies
of auxin homeostasis.
article_processing_charge: No
article_type: original
author:
- first_name: Ward
full_name: Steenackers, Ward
last_name: Steenackers
- first_name: Petr
full_name: Klíma, Petr
last_name: Klíma
- first_name: Mussa
full_name: Quareshy, Mussa
last_name: Quareshy
- first_name: Igor
full_name: Cesarino, Igor
last_name: Cesarino
- first_name: Robert
full_name: Kumpf, Robert
last_name: Kumpf
- first_name: Sander
full_name: Corneillie, Sander
last_name: Corneillie
- first_name: Pedro
full_name: Araújo, Pedro
last_name: Araújo
- first_name: Tom
full_name: Viaene, Tom
last_name: Viaene
- first_name: Geert
full_name: Goeminne, Geert
last_name: Goeminne
- first_name: Moritz
full_name: Nowack, Moritz
last_name: Nowack
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Joshua
full_name: Blakeslee, Joshua
last_name: Blakeslee
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Richard
full_name: Napier, Richard
last_name: Napier
- first_name: Wout
full_name: Boerjan, Wout
last_name: Boerjan
- first_name: Bartel
full_name: Vanholme, Bartel
last_name: Vanholme
citation:
ama: Steenackers W, Klíma P, Quareshy M, et al. Cis-cinnamic acid is a novel natural
auxin efflux inhibitor that promotes lateral root formation. Plant Physiology.
2017;173(1):552-565. doi:10.1104/pp.16.00943
apa: Steenackers, W., Klíma, P., Quareshy, M., Cesarino, I., Kumpf, R., Corneillie,
S., … Vanholme, B. (2017). Cis-cinnamic acid is a novel natural auxin efflux inhibitor
that promotes lateral root formation. Plant Physiology. American Society
of Plant Biologists. https://doi.org/10.1104/pp.16.00943
chicago: Steenackers, Ward, Petr Klíma, Mussa Quareshy, Igor Cesarino, Robert Kumpf,
Sander Corneillie, Pedro Araújo, et al. “Cis-Cinnamic Acid Is a Novel Natural
Auxin Efflux Inhibitor That Promotes Lateral Root Formation.” Plant Physiology.
American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.00943.
ieee: W. Steenackers et al., “Cis-cinnamic acid is a novel natural auxin
efflux inhibitor that promotes lateral root formation,” Plant Physiology,
vol. 173, no. 1. American Society of Plant Biologists, pp. 552–565, 2017.
ista: Steenackers W, Klíma P, Quareshy M, Cesarino I, Kumpf R, Corneillie S, Araújo
P, Viaene T, Goeminne G, Nowack M, Ljung K, Friml J, Blakeslee J, Novák O, Zažímalová
E, Napier R, Boerjan W, Vanholme B. 2017. Cis-cinnamic acid is a novel natural
auxin efflux inhibitor that promotes lateral root formation. Plant Physiology.
173(1), 552–565.
mla: Steenackers, Ward, et al. “Cis-Cinnamic Acid Is a Novel Natural Auxin Efflux
Inhibitor That Promotes Lateral Root Formation.” Plant Physiology, vol.
173, no. 1, American Society of Plant Biologists, 2017, pp. 552–65, doi:10.1104/pp.16.00943.
short: W. Steenackers, P. Klíma, M. Quareshy, I. Cesarino, R. Kumpf, S. Corneillie,
P. Araújo, T. Viaene, G. Goeminne, M. Nowack, K. Ljung, J. Friml, J. Blakeslee,
O. Novák, E. Zažímalová, R. Napier, W. Boerjan, B. Vanholme, Plant Physiology
173 (2017) 552–565.
date_created: 2018-12-11T11:50:28Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:29:17Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1104/pp.16.00943
ec_funded: 1
external_id:
isi:
- '000394135800041'
pmid:
- '27837086'
file:
- access_level: open_access
checksum: fd4d1cfe7ed70e54bb12ae3881f3fb91
content_type: application/pdf
creator: dernst
date_created: 2019-11-18T16:12:25Z
date_updated: 2020-07-14T12:44:36Z
file_id: '7040'
file_name: 2016_PlantPhysi_Steenackers.pdf
file_size: 4109142
relation: main_file
file_date_updated: 2020-07-14T12:44:36Z
has_accepted_license: '1'
intvolume: ' 173'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 552 - 565
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Plant Physiology
publication_identifier:
issn:
- 0032-0889
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6199'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral
root formation
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 173
year: '2017'
...
---
_id: '1169'
abstract:
- lang: eng
text: Dispersal is a crucial factor in natural evolution, since it determines the
habitat experienced by any population and defines the spatial scale of interactions
between individuals. There is compelling evidence for systematic differences in
dispersal characteristics within the same population, i.e., genotype-dependent
dispersal. The consequences of genotype-dependent dispersal on other evolutionary
phenomena, however, are poorly understood. In this article we investigate the
effect of genotype-dependent dispersal on spatial gene frequency patterns, using
a generalization of the classical diffusion model of selection and dispersal.
Dispersal is characterized by the variance of dispersal (diffusion coefficient)
and the mean displacement (directional advection term). We demonstrate that genotype-dependent
dispersal may change the qualitative behavior of Fisher waves, which change from
being “pulled” to being “pushed” wave fronts as the discrepancy in dispersal between
genotypes increases. The speed of any wave is partitioned into components due
to selection, genotype-dependent variance of dispersal, and genotype-dependent
mean displacement. We apply our findings to wave fronts maintained by selection
against heterozygotes. Furthermore, we identify a benefit of increased variance
of dispersal, quantify its effect on the speed of the wave, and discuss the implications
for the evolution of dispersal strategies.
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
- first_name: Richard
full_name: Kollár, Richard
last_name: Kollár
citation:
ama: Novak S, Kollár R. Spatial gene frequency waves under genotype dependent dispersal.
Genetics. 2017;205(1):367-374. doi:10.1534/genetics.116.193946
apa: Novak, S., & Kollár, R. (2017). Spatial gene frequency waves under genotype
dependent dispersal. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.193946
chicago: Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under
Genotype Dependent Dispersal.” Genetics. Genetics Society of America, 2017.
https://doi.org/10.1534/genetics.116.193946.
ieee: S. Novak and R. Kollár, “Spatial gene frequency waves under genotype dependent
dispersal,” Genetics, vol. 205, no. 1. Genetics Society of America, pp.
367–374, 2017.
ista: Novak S, Kollár R. 2017. Spatial gene frequency waves under genotype dependent
dispersal. Genetics. 205(1), 367–374.
mla: Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype
Dependent Dispersal.” Genetics, vol. 205, no. 1, Genetics Society of America,
2017, pp. 367–74, doi:10.1534/genetics.116.193946.
short: S. Novak, R. Kollár, Genetics 205 (2017) 367–374.
date_created: 2018-12-11T11:50:31Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:24:21Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1534/genetics.116.193946
ec_funded: 1
external_id:
isi:
- '000393677300025'
file:
- access_level: open_access
checksum: 7c8ab79cda1f92760bbbbe0f53175bfc
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:43Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4833'
file_name: IST-2016-727-v1+1_SFC_Genetics_final.pdf
file_size: 361500
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 205'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 367 - 374
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
publist_id: '6188'
pubrep_id: '727'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spatial gene frequency waves under genotype dependent dispersal
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 205
year: '2017'
...
---
_id: '1160'
abstract:
- lang: eng
text: 'We investigate fundamental nonlinear dynamics of ferrofluidic Taylor-Couette
flow - flow confined be-tween two concentric independently rotating cylinders
- consider small aspect ratio by solving the ferro-hydrodynamical equations, carrying
out systematic bifurcation analysis. Without magnetic field, we find steady flow
patterns, previously observed with a simple fluid, such as those containing normal
one- or two vortex cells, as well as anomalous one-cell and twin-cell flow states.
However, when a symmetry-breaking transverse magnetic field is present, all flow
states exhibit stimulated, finite two-fold mode. Various bifurcations between
steady and unsteady states can occur, corresponding to the transitions between
the two-cell and one-cell states. While unsteady, axially oscillating flow states
can arise, we also detect the emergence of new unsteady flow states. In particular,
we uncover two new states: one contains only the azimuthally oscillating solution
in the configuration of the twin-cell flow state, and an-other a rotating flow
state. Topologically, these flow states are a limit cycle and a quasiperiodic
solution on a two-torus, respectively. Emergence of new flow states in addition
to observed ones with classical fluid, indicates that richer but potentially more
controllable dynamics in ferrofluidic flows, as such flow states depend on the
external magnetic field.'
article_number: '40012'
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Altmeyer, Sebastian
id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87
last_name: Altmeyer
orcid: 0000-0001-5964-0203
- first_name: Younghae
full_name: Do, Younghae
last_name: Do
- first_name: Ying
full_name: Lai, Ying
last_name: Lai
citation:
ama: Altmeyer S, Do Y, Lai Y. Dynamics of ferrofluidic flow in the Taylor-Couette
system with a small aspect ratio. Scientific Reports. 2017;7. doi:10.1038/srep40012
apa: Altmeyer, S., Do, Y., & Lai, Y. (2017). Dynamics of ferrofluidic flow in
the Taylor-Couette system with a small aspect ratio. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/srep40012
chicago: Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Dynamics of Ferrofluidic
Flow in the Taylor-Couette System with a Small Aspect Ratio.” Scientific Reports.
Nature Publishing Group, 2017. https://doi.org/10.1038/srep40012.
ieee: S. Altmeyer, Y. Do, and Y. Lai, “Dynamics of ferrofluidic flow in the Taylor-Couette
system with a small aspect ratio,” Scientific Reports, vol. 7. Nature Publishing
Group, 2017.
ista: Altmeyer S, Do Y, Lai Y. 2017. Dynamics of ferrofluidic flow in the Taylor-Couette
system with a small aspect ratio. Scientific Reports. 7, 40012.
mla: Altmeyer, Sebastian, et al. “Dynamics of Ferrofluidic Flow in the Taylor-Couette
System with a Small Aspect Ratio.” Scientific Reports, vol. 7, 40012, Nature
Publishing Group, 2017, doi:10.1038/srep40012.
short: S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 7 (2017).
date_created: 2018-12-11T11:50:28Z
date_published: 2017-01-06T00:00:00Z
date_updated: 2023-09-20T11:28:49Z
day: '06'
ddc:
- '532'
department:
- _id: BjHo
doi: 10.1038/srep40012
external_id:
isi:
- '000391269700001'
file:
- access_level: open_access
checksum: 694aa70399444570825099c1a7ec91f2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:16Z
date_updated: 2020-07-14T12:44:36Z
file_id: '4802'
file_name: IST-2017-743-v1+1_srep40012.pdf
file_size: 4546835
relation: main_file
file_date_updated: 2020-07-14T12:44:36Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_identifier:
issn:
- '20452322'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6198'
pubrep_id: '743'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect
ratio
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2017'
...
---
_id: '1162'
abstract:
- lang: eng
text: Selected universal experimental properties of high-temperature superconducting
(HTS) cuprates have been singled out in the last decade. One of the pivotal challenges
in this field is the designation of a consistent interpretation framework within
which we can describe quantitatively the universal features of those systems.
Here we analyze in a detailed manner the principal experimental data and compare
them quantitatively with the approach based on a single-band model of strongly
correlated electrons supplemented with strong antiferromagnetic (super)exchange
interaction (the so-called t−J−U model). The model rationale is provided by estimating
its microscopic parameters on the basis of the three-band approach for the Cu-O
plane. We use our original full Gutzwiller wave-function solution by going beyond
the renormalized mean-field theory (RMFT) in a systematic manner. Our approach
reproduces very well the observed hole doping (δ) dependence of the kinetic-energy
gain in the superconducting phase, one of the principal non-Bardeen-Cooper-Schrieffer
features of the cuprates. The calculated Fermi velocity in the nodal direction
is practically δ-independent and its universal value agrees very well with that
determined experimentally. Also, a weak doping dependence of the Fermi wave vector
leads to an almost constant value of the effective mass in a pure superconducting
phase which is both observed in experiment and reproduced within our approach.
An assessment of the currently used models (t−J, Hubbard) is carried out and the
results of the canonical RMFT as a zeroth-order solution are provided for comparison
to illustrate the necessity of the introduced higher-order contributions.
article_number: '024506'
article_processing_charge: No
author:
- first_name: Jozef
full_name: Spałek, Jozef
last_name: Spałek
- first_name: Michał
full_name: Zegrodnik, Michał
last_name: Zegrodnik
- first_name: Jan
full_name: Kaczmarczyk, Jan
id: 46C405DE-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarczyk
orcid: 0000-0002-1629-3675
citation:
ama: Spałek J, Zegrodnik M, Kaczmarczyk J. Universal properties of high temperature
superconductors from real space pairing t-J-U model and its quantitative comparison
with experiment. Physical Review B - Condensed Matter and Materials Physics.
2017;95(2). doi:10.1103/PhysRevB.95.024506
apa: Spałek, J., Zegrodnik, M., & Kaczmarczyk, J. (2017). Universal properties
of high temperature superconductors from real space pairing t-J-U model and its
quantitative comparison with experiment. Physical Review B - Condensed Matter
and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.95.024506
chicago: Spałek, Jozef, Michał Zegrodnik, and Jan Kaczmarczyk. “Universal Properties
of High Temperature Superconductors from Real Space Pairing T-J-U Model and Its
Quantitative Comparison with Experiment.” Physical Review B - Condensed Matter
and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.95.024506.
ieee: J. Spałek, M. Zegrodnik, and J. Kaczmarczyk, “Universal properties of high
temperature superconductors from real space pairing t-J-U model and its quantitative
comparison with experiment,” Physical Review B - Condensed Matter and Materials
Physics, vol. 95, no. 2. American Physical Society, 2017.
ista: Spałek J, Zegrodnik M, Kaczmarczyk J. 2017. Universal properties of high temperature
superconductors from real space pairing t-J-U model and its quantitative comparison
with experiment. Physical Review B - Condensed Matter and Materials Physics. 95(2),
024506.
mla: Spałek, Jozef, et al. “Universal Properties of High Temperature Superconductors
from Real Space Pairing T-J-U Model and Its Quantitative Comparison with Experiment.”
Physical Review B - Condensed Matter and Materials Physics, vol. 95, no.
2, 024506, American Physical Society, 2017, doi:10.1103/PhysRevB.95.024506.
short: J. Spałek, M. Zegrodnik, J. Kaczmarczyk, Physical Review B - Condensed Matter
and Materials Physics 95 (2017).
date_created: 2018-12-11T11:50:29Z
date_published: 2017-01-13T00:00:00Z
date_updated: 2023-09-20T11:25:56Z
day: '13'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.95.024506
ec_funded: 1
external_id:
isi:
- '000391852800006'
intvolume: ' 95'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.03247
month: '01'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review B - Condensed Matter and Materials Physics
publication_identifier:
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
publist_id: '6195'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Universal properties of high temperature superconductors from real space pairing
t-J-U model and its quantitative comparison with experiment
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 95
year: '2017'
...
---
_id: '1152'
abstract:
- lang: eng
text: We propose a new memetic strategy that can solve the multi-physics, complex
inverse problems, formulated as the multi-objective optimization ones, in which
objectives are misfits between the measured and simulated states of various governing
processes. The multi-deme structure of the strategy allows for both, intensive,
relatively cheap exploration with a moderate accuracy and more accurate search
many regions of Pareto set in parallel. The special type of selection operator
prefers the coherent alternative solutions, eliminating artifacts appearing in
the particular processes. The additional accuracy increment is obtained by the
parallel convex searches applied to the local scalarizations of the misfit vector.
The strategy is dedicated for solving ill-conditioned problems, for which inverting
the single physical process can lead to the ambiguous results. The skill of the
selection in artifact elimination is shown on the benchmark problem, while the
whole strategy was applied for identification of oil deposits, where the misfits
are related to various frequencies of the magnetic and electric waves of the magnetotelluric
measurements. 2016 Elsevier B.V.
article_processing_charge: No
author:
- first_name: Ewa P
full_name: Gajda-Zagorska, Ewa P
id: 47794CF0-F248-11E8-B48F-1D18A9856A87
last_name: Gajda-Zagorska
- first_name: Robert
full_name: Schaefer, Robert
last_name: Schaefer
- first_name: Maciej
full_name: Smołka, Maciej
last_name: Smołka
- first_name: David
full_name: Pardo, David
last_name: Pardo
- first_name: Julen
full_name: Alvarez Aramberri, Julen
last_name: Alvarez Aramberri
citation:
ama: Gajda-Zagorska EP, Schaefer R, Smołka M, Pardo D, Alvarez Aramberri J. A multi
objective memetic inverse solver reinforced by local optimization methods. Journal
of Computational Science. 2017;18:85-94. doi:10.1016/j.jocs.2016.06.007
apa: Gajda-Zagorska, E. P., Schaefer, R., Smołka, M., Pardo, D., & Alvarez Aramberri,
J. (2017). A multi objective memetic inverse solver reinforced by local optimization
methods. Journal of Computational Science. Elsevier. https://doi.org/10.1016/j.jocs.2016.06.007
chicago: Gajda-Zagorska, Ewa P, Robert Schaefer, Maciej Smołka, David Pardo, and
Julen Alvarez Aramberri. “A Multi Objective Memetic Inverse Solver Reinforced
by Local Optimization Methods.” Journal of Computational Science. Elsevier,
2017. https://doi.org/10.1016/j.jocs.2016.06.007.
ieee: E. P. Gajda-Zagorska, R. Schaefer, M. Smołka, D. Pardo, and J. Alvarez Aramberri,
“A multi objective memetic inverse solver reinforced by local optimization methods,”
Journal of Computational Science, vol. 18. Elsevier, pp. 85–94, 2017.
ista: Gajda-Zagorska EP, Schaefer R, Smołka M, Pardo D, Alvarez Aramberri J. 2017.
A multi objective memetic inverse solver reinforced by local optimization methods.
Journal of Computational Science. 18, 85–94.
mla: Gajda-Zagorska, Ewa P., et al. “A Multi Objective Memetic Inverse Solver Reinforced
by Local Optimization Methods.” Journal of Computational Science, vol.
18, Elsevier, 2017, pp. 85–94, doi:10.1016/j.jocs.2016.06.007.
short: E.P. Gajda-Zagorska, R. Schaefer, M. Smołka, D. Pardo, J. Alvarez Aramberri,
Journal of Computational Science 18 (2017) 85–94.
date_created: 2018-12-11T11:50:26Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:29:44Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1016/j.jocs.2016.06.007
external_id:
isi:
- '000393528700009'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T08:43:16Z
date_updated: 2019-01-18T08:43:16Z
file_id: '5842'
file_name: 2016_jocs_ewa.pdf
file_size: 1083911
relation: main_file
success: 1
file_date_updated: 2019-01-18T08:43:16Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 85 - 94
publication: Journal of Computational Science
publication_identifier:
issn:
- '18777503'
publication_status: published
publisher: Elsevier
publist_id: '6206'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A multi objective memetic inverse solver reinforced by local optimization methods
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 18
year: '2017'
...
---
_id: '1168'
abstract:
- lang: eng
text: Optimum experimental design theory has recently been extended for parameter
estimation in copula models. The use of these models allows one to gain in flexibility
by considering the model parameter set split into marginal and dependence parameters.
However, this separation also leads to the natural issue of estimating only a
subset of all model parameters. In this work, we treat this problem with the application
of the (Formula presented.)-optimality to copula models. First, we provide an
extension of the corresponding equivalence theory. Then, we analyze a wide range
of flexible copula models to highlight the usefulness of (Formula presented.)-optimality
in many possible scenarios. Finally, we discuss how the usage of the introduced
design criterion also relates to the more general issue of copula selection and
optimal design for model discrimination.
acknowledgement: 'This work has been supported by the project ANR-2011-IS01-001-01
“DESIRE” and Austrian Science Fund (FWF) I833-N18. Open access funding is provided
by the Austrian Science Fund (FWF). '
article_processing_charge: No
author:
- first_name: Elisa
full_name: Perrone, Elisa
id: 2A5F8724-F248-11E8-B48F-1D18A9856A87
last_name: Perrone
orcid: 0000-0003-0370-9835
- first_name: Andreas
full_name: Rappold, Andreas
last_name: Rappold
- first_name: Werner
full_name: Müller, Werner
last_name: Müller
citation:
ama: Perrone E, Rappold A, Müller W. D inf s optimality in copula models. Statistical
Methods and Applications. 2017;26(3):403-418. doi:10.1007/s10260-016-0375-6
apa: Perrone, E., Rappold, A., & Müller, W. (2017). D inf s optimality in copula
models. Statistical Methods and Applications. Springer. https://doi.org/10.1007/s10260-016-0375-6
chicago: Perrone, Elisa, Andreas Rappold, and Werner Müller. “D Inf s Optimality
in Copula Models.” Statistical Methods and Applications. Springer, 2017.
https://doi.org/10.1007/s10260-016-0375-6.
ieee: E. Perrone, A. Rappold, and W. Müller, “D inf s optimality in copula models,”
Statistical Methods and Applications, vol. 26, no. 3. Springer, pp. 403–418,
2017.
ista: Perrone E, Rappold A, Müller W. 2017. D inf s optimality in copula models.
Statistical Methods and Applications. 26(3), 403–418.
mla: Perrone, Elisa, et al. “D Inf s Optimality in Copula Models.” Statistical
Methods and Applications, vol. 26, no. 3, Springer, 2017, pp. 403–18, doi:10.1007/s10260-016-0375-6.
short: E. Perrone, A. Rappold, W. Müller, Statistical Methods and Applications 26
(2017) 403–418.
date_created: 2018-12-11T11:50:31Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2023-09-20T11:25:09Z
day: '01'
ddc:
- '519'
department:
- _id: CaUh
doi: 10.1007/s10260-016-0375-6
external_id:
isi:
- '000407973200004'
file:
- access_level: open_access
checksum: 0b2d1b647ca96e9ef13a14b8b6775e0f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:13Z
date_updated: 2020-07-14T12:44:37Z
file_id: '5199'
file_name: IST-2017-739-v1+2_10260_2016_375_MOESM1_ESM.pdf
file_size: 56664
relation: main_file
- access_level: open_access
checksum: 3321ef34e02e28acfc427f77cf32812a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:14Z
date_updated: 2020-07-14T12:44:37Z
file_id: '5200'
file_name: IST-2017-739-v1+3_s10260-016-0375-6.pdf
file_size: 688953
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
issue: '3'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 403 - 418
publication: Statistical Methods and Applications
publication_status: published
publisher: Springer
publist_id: '6189'
pubrep_id: '739'
quality_controlled: '1'
scopus_import: '1'
status: public
title: D inf s optimality in copula models
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 26
year: '2017'
...
---
_id: '1163'
abstract:
- lang: eng
text: 'We investigate the effect of the electron-hole (e-h) symmetry breaking on
d-wave superconductivity induced by non-local effects of correlations in the generalized
Hubbard model. The symmetry breaking is introduced in a two-fold manner: by the
next-to-nearest neighbor hopping of electrons and by the charge-bond interaction
- the off-diagonal term of the Coulomb potential. Both terms lead to a pronounced
asymmetry of the superconducting order parameter. The next-to-nearest neighbor
hopping enhances superconductivity for h-doping, while diminishes it for e-doping.
The charge-bond interaction alone leads to the opposite effect and, additionally,
to the kinetic-energy gain upon condensation in the underdoped regime. With both
terms included, with similar amplitudes, the height of the superconducting dome
and the critical doping remain in favor of h-doping. The influence of the charge-bond
interaction on deviations from symmetry of the shape of the gap at the Fermi surface
in the momentum space is briefly discussed.'
article_number: '085604'
article_processing_charge: No
author:
- first_name: Marcin
full_name: Wysokiński, Marcin
last_name: Wysokiński
- first_name: Jan
full_name: Kaczmarczyk, Jan
id: 46C405DE-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarczyk
orcid: 0000-0002-1629-3675
citation:
ama: 'Wysokiński M, Kaczmarczyk J. Unconventional superconductivity in generalized
Hubbard model role of electron–hole symmetry breaking terms. Journal of Physics:
Condensed Matter. 2017;29(8). doi:10.1088/1361-648X/aa532f'
apa: 'Wysokiński, M., & Kaczmarczyk, J. (2017). Unconventional superconductivity
in generalized Hubbard model role of electron–hole symmetry breaking terms. Journal
of Physics: Condensed Matter. IOP Publishing Ltd. https://doi.org/10.1088/1361-648X/aa532f'
chicago: 'Wysokiński, Marcin, and Jan Kaczmarczyk. “Unconventional Superconductivity
in Generalized Hubbard Model Role of Electron–Hole Symmetry Breaking Terms.” Journal
of Physics: Condensed Matter. IOP Publishing Ltd., 2017. https://doi.org/10.1088/1361-648X/aa532f.'
ieee: 'M. Wysokiński and J. Kaczmarczyk, “Unconventional superconductivity in generalized
Hubbard model role of electron–hole symmetry breaking terms,” Journal of Physics:
Condensed Matter, vol. 29, no. 8. IOP Publishing Ltd., 2017.'
ista: 'Wysokiński M, Kaczmarczyk J. 2017. Unconventional superconductivity in generalized
Hubbard model role of electron–hole symmetry breaking terms. Journal of Physics:
Condensed Matter. 29(8), 085604.'
mla: 'Wysokiński, Marcin, and Jan Kaczmarczyk. “Unconventional Superconductivity
in Generalized Hubbard Model Role of Electron–Hole Symmetry Breaking Terms.” Journal
of Physics: Condensed Matter, vol. 29, no. 8, 085604, IOP Publishing Ltd.,
2017, doi:10.1088/1361-648X/aa532f.'
short: 'M. Wysokiński, J. Kaczmarczyk, Journal of Physics: Condensed Matter 29 (2017).'
date_created: 2018-12-11T11:50:29Z
date_published: 2017-01-16T00:00:00Z
date_updated: 2023-09-20T11:25:32Z
day: '16'
department:
- _id: MiLe
doi: 10.1088/1361-648X/aa532f
ec_funded: 1
external_id:
isi:
- '000393955500001'
intvolume: ' 29'
isi: 1
issue: '8'
language:
- iso: eng
month: '01'
oa_version: None
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: 'Journal of Physics: Condensed Matter'
publication_identifier:
issn:
- '09538984'
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '6194'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unconventional superconductivity in generalized Hubbard model role of electron–hole
symmetry breaking terms
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 29
year: '2017'
...
---
_id: '1173'
abstract:
- lang: eng
text: We introduce the Voronoi functional of a triangulation of a finite set of
points in the Euclidean plane and prove that among all geometric triangulations
of the point set, the Delaunay triangulation maximizes the functional. This result
neither extends to topological triangulations in the plane nor to geometric triangulations
in three and higher dimensions.
acknowledgement: This research is partially supported by the Russian Government under
the Mega Project 11.G34.31.0053, by the Toposys project FP7-ICT-318493-STREP, by
ESF under the ACAT Research Network Programme, by RFBR grant 11-01-00735, and by
NSF grants DMS-1101688, DMS-1400876.
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Alexey
full_name: Glazyrin, Alexey
last_name: Glazyrin
- first_name: Oleg
full_name: Musin, Oleg
last_name: Musin
- first_name: Anton
full_name: Nikitenko, Anton
id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87
last_name: Nikitenko
orcid: 0000-0002-0659-3201
citation:
ama: Edelsbrunner H, Glazyrin A, Musin O, Nikitenko A. The Voronoi functional is
maximized by the Delaunay triangulation in the plane. Combinatorica. 2017;37(5):887-910.
doi:10.1007/s00493-016-3308-y
apa: Edelsbrunner, H., Glazyrin, A., Musin, O., & Nikitenko, A. (2017). The
Voronoi functional is maximized by the Delaunay triangulation in the plane. Combinatorica.
Springer. https://doi.org/10.1007/s00493-016-3308-y
chicago: Edelsbrunner, Herbert, Alexey Glazyrin, Oleg Musin, and Anton Nikitenko.
“The Voronoi Functional Is Maximized by the Delaunay Triangulation in the Plane.”
Combinatorica. Springer, 2017. https://doi.org/10.1007/s00493-016-3308-y.
ieee: H. Edelsbrunner, A. Glazyrin, O. Musin, and A. Nikitenko, “The Voronoi functional
is maximized by the Delaunay triangulation in the plane,” Combinatorica,
vol. 37, no. 5. Springer, pp. 887–910, 2017.
ista: Edelsbrunner H, Glazyrin A, Musin O, Nikitenko A. 2017. The Voronoi functional
is maximized by the Delaunay triangulation in the plane. Combinatorica. 37(5),
887–910.
mla: Edelsbrunner, Herbert, et al. “The Voronoi Functional Is Maximized by the Delaunay
Triangulation in the Plane.” Combinatorica, vol. 37, no. 5, Springer, 2017,
pp. 887–910, doi:10.1007/s00493-016-3308-y.
short: H. Edelsbrunner, A. Glazyrin, O. Musin, A. Nikitenko, Combinatorica 37 (2017)
887–910.
date_created: 2018-12-11T11:50:32Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2023-09-20T11:23:53Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00493-016-3308-y
ec_funded: 1
external_id:
isi:
- '000418056000005'
intvolume: ' 37'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1411.6337
month: '10'
oa: 1
oa_version: Submitted Version
page: 887 - 910
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Combinatorica
publication_identifier:
issn:
- '02099683'
publication_status: published
publisher: Springer
publist_id: '6182'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Voronoi functional is maximized by the Delaunay triangulation in the plane
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2017'
...
---
_id: '1161'
abstract:
- lang: eng
text: Coordinated changes of cell shape are often the result of the excitable, wave-like
dynamics of the actin cytoskeleton. New work shows that, in migrating cells, protrusion
waves arise from mechanochemical crosstalk between adhesion sites, membrane tension
and the actin protrusive machinery.
article_processing_charge: No
author:
- first_name: Jan
full_name: Müller, Jan
id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D
last_name: Müller
- 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: 'Müller J, Sixt MK. Cell migration: Making the waves. Current Biology.
2017;27(1):R24-R25. doi:10.1016/j.cub.2016.11.035'
apa: 'Müller, J., & Sixt, M. K. (2017). Cell migration: Making the waves. Current
Biology. Cell Press. https://doi.org/10.1016/j.cub.2016.11.035'
chicago: 'Müller, Jan, and Michael K Sixt. “Cell Migration: Making the Waves.” Current
Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2016.11.035.'
ieee: 'J. Müller and M. K. Sixt, “Cell migration: Making the waves,” Current
Biology, vol. 27, no. 1. Cell Press, pp. R24–R25, 2017.'
ista: 'Müller J, Sixt MK. 2017. Cell migration: Making the waves. Current Biology.
27(1), R24–R25.'
mla: 'Müller, Jan, and Michael K. Sixt. “Cell Migration: Making the Waves.” Current
Biology, vol. 27, no. 1, Cell Press, 2017, pp. R24–25, doi:10.1016/j.cub.2016.11.035.'
short: J. Müller, M.K. Sixt, Current Biology 27 (2017) R24–R25.
date_created: 2018-12-11T11:50:29Z
date_published: 2017-01-09T00:00:00Z
date_updated: 2023-09-20T11:28:19Z
day: '09'
department:
- _id: MiSi
doi: 10.1016/j.cub.2016.11.035
external_id:
isi:
- '000391902500010'
intvolume: ' 27'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: R24 - R25
publication: Current Biology
publication_identifier:
issn:
- '09609822'
publication_status: published
publisher: Cell Press
publist_id: '6197'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Cell migration: Making the waves'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 27
year: '2017'
...
---
_id: '1116'
abstract:
- lang: eng
text: "Time-triggered switched networks are a deterministic communication infrastructure
used by real-time distributed embedded systems. Due to the criticality of the
applications running over them, developers need to ensure that end-to-end communication
is dependable and predictable. Traditional approaches assume static networks that
are not flexible to changes caused by reconfigurations or, more importantly, faults,
which are dealt with in the application using redundancy. We adopt the concept
of handling faults in the switches from non-real-time networks while maintaining
the required predictability. \r\n\r\nWe study a class of forwarding schemes that
can handle various types of failures. We consider probabilistic failures. We study
a class of forwarding schemes that can handle various types of failures. We consider
probabilistic failures. For a given network with a forwarding scheme and a constant
ℓ, we compute the {\\em score} of the scheme, namely the probability (induced
by faults) that at least ℓ messages arrive on time. We reduce the scoring problem
to a reachability problem on a Markov chain with a "product-like" structure.
Its special structure allows us to reason about it symbolically, and reduce the
scoring problem to #SAT. Our solution is generic and can be adapted to different
networks and other contexts. Also, we show the computational complexity of the
scoring problem is #P-complete, and we study methods to estimate the score. We
evaluate the effectiveness of our techniques with an implementation. "
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shubham
full_name: Goel, Shubham
last_name: Goel
- 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: Guillermo
full_name: Rodríguez Navas, Guillermo
last_name: Rodríguez Navas
citation:
ama: 'Avni G, Goel S, Henzinger TA, Rodríguez Navas G. Computing scores of forwarding
schemes in switched networks with probabilistic faults. In: Vol 10206. Springer;
2017:169-187. doi:10.1007/978-3-662-54580-5_10'
apa: 'Avni, G., Goel, S., Henzinger, T. A., & Rodríguez Navas, G. (2017). Computing
scores of forwarding schemes in switched networks with probabilistic faults (Vol.
10206, pp. 169–187). Presented at the TACAS: Tools and Algorithms for the Construction
and Analysis of Systems, Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54580-5_10'
chicago: Avni, Guy, Shubham Goel, Thomas A Henzinger, and Guillermo Rodríguez Navas.
“Computing Scores of Forwarding Schemes in Switched Networks with Probabilistic
Faults,” 10206:169–87. Springer, 2017. https://doi.org/10.1007/978-3-662-54580-5_10.
ieee: 'G. Avni, S. Goel, T. A. Henzinger, and G. Rodríguez Navas, “Computing scores
of forwarding schemes in switched networks with probabilistic faults,” presented
at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems,
Uppsala, Sweden, 2017, vol. 10206, pp. 169–187.'
ista: 'Avni G, Goel S, Henzinger TA, Rodríguez Navas G. 2017. Computing scores of
forwarding schemes in switched networks with probabilistic faults. TACAS: Tools
and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10206,
169–187.'
mla: Avni, Guy, et al. Computing Scores of Forwarding Schemes in Switched Networks
with Probabilistic Faults. Vol. 10206, Springer, 2017, pp. 169–87, doi:10.1007/978-3-662-54580-5_10.
short: G. Avni, S. Goel, T.A. Henzinger, G. Rodríguez Navas, in:, Springer, 2017,
pp. 169–187.
conference:
end_date: 2017-04-29
location: Uppsala, Sweden
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2017-04-22
date_created: 2018-12-11T11:50:14Z
date_published: 2017-03-31T00:00:00Z
date_updated: 2023-09-20T11:32:43Z
day: '31'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-662-54580-5_10
external_id:
isi:
- '000440733400010'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:37Z
date_updated: 2018-12-12T10:08:37Z
file_id: '4698'
file_name: IST-2017-758-v1+1_tacas-cr.pdf
file_size: 321800
relation: main_file
file_date_updated: 2018-12-12T10:08:37Z
has_accepted_license: '1'
intvolume: ' 10206'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 169 - 187
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '6246'
pubrep_id: '758'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computing scores of forwarding schemes in switched networks with probabilistic
faults
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10206
year: '2017'
...
---
_id: '1118'
abstract:
- lang: eng
text: Sharp wave-ripple (SWR) oscillations play a key role in memory consolidation
during non-rapid eye movement sleep, immobility, and consummatory behavior. However,
whether temporally modulated synaptic excitation or inhibition underlies the ripples
is controversial. To address this question, we performed simultaneous recordings
of excitatory and inhibitory postsynaptic currents (EPSCs and IPSCs) and local
field potentials (LFPs) in the CA1 region of awake mice in vivo. During SWRs,
inhibition dominated over excitation, with a peak conductance ratio of 4.1 ± 0.5.
Furthermore, the amplitude of SWR-associated IPSCs was positively correlated with
SWR magnitude, whereas that of EPSCs was not. Finally, phase analysis indicated
that IPSCs were phase-locked to individual ripple cycles, whereas EPSCs were uniformly
distributed in phase space. Optogenetic inhibition indicated that PV+ interneurons
provided a major contribution to SWR-associated IPSCs. Thus, phasic inhibition,
but not excitation, shapes SWR oscillations in the hippocampal CA1 region in vivo.
acknowledged_ssus:
- _id: M-Shop
- _id: ScienComp
- _id: PreCl
article_processing_charge: No
author:
- first_name: Jian
full_name: Gan, Jian
id: 3614E438-F248-11E8-B48F-1D18A9856A87
last_name: Gan
- first_name: Shih-Ming
full_name: Weng, Shih-Ming
id: 2F9C5AC8-F248-11E8-B48F-1D18A9856A87
last_name: Weng
- first_name: Alejandro
full_name: Pernia-Andrade, Alejandro
id: 36963E98-F248-11E8-B48F-1D18A9856A87
last_name: Pernia-Andrade
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- 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: Gan J, Weng S-M, Pernia-Andrade A, Csicsvari JL, Jonas PM. Phase-locked inhibition,
but not excitation, underlies hippocampal ripple oscillations in awake mice in
vivo. Neuron. 2017;93(2):308-314. doi:10.1016/j.neuron.2016.12.018
apa: Gan, J., Weng, S.-M., Pernia-Andrade, A., Csicsvari, J. L., & Jonas, P.
M. (2017). Phase-locked inhibition, but not excitation, underlies hippocampal
ripple oscillations in awake mice in vivo. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2016.12.018
chicago: Gan, Jian, Shih-Ming Weng, Alejandro Pernia-Andrade, Jozsef L Csicsvari,
and Peter M Jonas. “Phase-Locked Inhibition, but Not Excitation, Underlies Hippocampal
Ripple Oscillations in Awake Mice in Vivo.” Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2016.12.018.
ieee: J. Gan, S.-M. Weng, A. Pernia-Andrade, J. L. Csicsvari, and P. M. Jonas, “Phase-locked
inhibition, but not excitation, underlies hippocampal ripple oscillations in awake
mice in vivo,” Neuron, vol. 93, no. 2. Elsevier, pp. 308–314, 2017.
ista: Gan J, Weng S-M, Pernia-Andrade A, Csicsvari JL, Jonas PM. 2017. Phase-locked
inhibition, but not excitation, underlies hippocampal ripple oscillations in awake
mice in vivo. Neuron. 93(2), 308–314.
mla: Gan, Jian, et al. “Phase-Locked Inhibition, but Not Excitation, Underlies Hippocampal
Ripple Oscillations in Awake Mice in Vivo.” Neuron, vol. 93, no. 2, Elsevier,
2017, pp. 308–14, doi:10.1016/j.neuron.2016.12.018.
short: J. Gan, S.-M. Weng, A. Pernia-Andrade, J.L. Csicsvari, P.M. Jonas, Neuron
93 (2017) 308–314.
date_created: 2018-12-11T11:50:15Z
date_published: 2017-01-18T00:00:00Z
date_updated: 2023-09-20T11:31:48Z
day: '18'
ddc:
- '571'
department:
- _id: PeJo
- _id: JoCs
doi: 10.1016/j.neuron.2016.12.018
ec_funded: 1
external_id:
isi:
- '000396428200010'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:56Z
date_updated: 2018-12-12T10:08:56Z
file_id: '4719'
file_name: IST-2017-752-v1+1_1-s2.0-S0896627316309606-main.pdf
file_size: 2738950
relation: main_file
file_date_updated: 2018-12-12T10:08:56Z
has_accepted_license: '1'
intvolume: ' 93'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 308 - 314
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '6244'
pubrep_id: '752'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations
in awake mice in vivo
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 93
year: '2017'
...
---
_id: '1117'
abstract:
- lang: eng
text: 'GABAergic synapses in brain circuits generate inhibitory output signals with
submillisecond latency and temporal precision. Whether the molecular identity
of the release sensor contributes to these signaling properties remains unclear.
Here, we examined the Ca^2+ sensor of exocytosis at GABAergic basket cell (BC)
to Purkinje cell (PC) synapses in cerebellum. Immunolabeling suggested that BC
terminals selectively expressed synaptotagmin 2 (Syt2), whereas synaptotagmin
1 (Syt1) was enriched in excitatory terminals. Genetic elimination of Syt2 reduced
action potential-evoked release to ∼10%, identifying Syt2 as the major Ca^2+ sensor
at BC-PC synapses. Differential adenovirus-mediated rescue revealed that Syt2
triggered release with shorter latency and higher temporal precision and mediated
faster vesicle pool replenishment than Syt1. Furthermore, deletion of Syt2 severely
reduced and delayed disynaptic inhibition following parallel fiber stimulation.
Thus, the selective use of Syt2 as release sensor at BC-PC synapses ensures fast
and efficient feedforward inhibition in cerebellar microcircuits. #bioimagingfacility-author'
acknowledged_ssus:
- _id: Bio
- _id: PreCl
article_processing_charge: No
author:
- first_name: Chong
full_name: Chen, Chong
id: 3DFD581A-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Itaru
full_name: Arai, Itaru
id: 32A73F6C-F248-11E8-B48F-1D18A9856A87
last_name: Arai
- first_name: Rachel
full_name: Satterield, Rachel
last_name: Satterield
- first_name: Samuel
full_name: Young, Samuel
last_name: Young
- 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: Chen C, Arai itaru, Satterield R, Young S, Jonas PM. Synaptotagmin 2 is the
fast Ca2+ sensor at a central inhibitory synapse. Cell Reports. 2017;18(3):723-736.
doi:10.1016/j.celrep.2016.12.067
apa: Chen, C., Arai, itaru, Satterield, R., Young, S., & Jonas, P. M. (2017).
Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse. Cell
Reports. Cell Press. https://doi.org/10.1016/j.celrep.2016.12.067
chicago: Chen, Chong, itaru Arai, Rachel Satterield, Samuel Young, and Peter M Jonas.
“Synaptotagmin 2 Is the Fast Ca2+ Sensor at a Central Inhibitory Synapse.” Cell
Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2016.12.067.
ieee: C. Chen, itaru Arai, R. Satterield, S. Young, and P. M. Jonas, “Synaptotagmin
2 is the fast Ca2+ sensor at a central inhibitory synapse,” Cell Reports,
vol. 18, no. 3. Cell Press, pp. 723–736, 2017.
ista: Chen C, Arai itaru, Satterield R, Young S, Jonas PM. 2017. Synaptotagmin
2 is the fast Ca2+ sensor at a central inhibitory synapse. Cell Reports. 18(3),
723–736.
mla: Chen, Chong, et al. “Synaptotagmin 2 Is the Fast Ca2+ Sensor at a Central Inhibitory
Synapse.” Cell Reports, vol. 18, no. 3, Cell Press, 2017, pp. 723–36, doi:10.1016/j.celrep.2016.12.067.
short: C. Chen, itaru Arai, R. Satterield, S. Young, P.M. Jonas, Cell Reports 18
(2017) 723–736.
date_created: 2018-12-11T11:50:14Z
date_published: 2017-01-17T00:00:00Z
date_updated: 2023-09-20T11:32:15Z
day: '17'
ddc:
- '571'
department:
- _id: PeJo
doi: 10.1016/j.celrep.2016.12.067
ec_funded: 1
external_id:
isi:
- '000396470600013'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:09Z
date_updated: 2018-12-12T10:16:09Z
file_id: '5195'
file_name: IST-2017-751-v1+1_1-s2.0-S2211124716317740-main.pdf
file_size: 4427591
relation: main_file
file_date_updated: 2018-12-12T10:16:09Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '3'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 723 - 736
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: Cell Reports
publication_identifier:
issn:
- '22111247'
publication_status: published
publisher: Cell Press
publist_id: '6245'
pubrep_id: '751'
quality_controlled: '1'
related_material:
record:
- id: '324'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 18
year: '2017'
...
---
_id: '1132'
abstract:
- lang: eng
text: The hippocampus is thought to initiate systems-wide mnemonic processes through
the reactivation of previously acquired spatial and episodic memory traces, which
can recruit the entorhinal cortex as a first stage of memory redistribution to
other brain areas. Hippocampal reactivation occurs during sharp wave-ripples,
in which synchronous network firing encodes sequences of places.We investigated
the coordination of this replay by recording assembly activity simultaneously
in the CA1 region of the hippocampus and superficial layers of the medial entorhinal
cortex. We found that entorhinal cell assemblies can replay trajectories independently
of the hippocampus and sharp wave-ripples. This suggests that the hippocampus
is not the sole initiator of spatial and episodic memory trace reactivation. Memory
systems involved in these processes may include nonhierarchical, parallel components.
article_processing_charge: No
author:
- first_name: Joseph
full_name: O'Neill, Joseph
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Charlotte
full_name: Boccara, Charlotte
id: 3FC06552-F248-11E8-B48F-1D18A9856A87
last_name: Boccara
orcid: 0000-0001-7237-5109
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Philipp
full_name: Schönenberger, Philipp
id: 3B9D816C-F248-11E8-B48F-1D18A9856A87
last_name: Schönenberger
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: O’Neill J, Boccara CN, Stella F, Schönenberger P, Csicsvari JL. Superficial
layers of the medial entorhinal cortex replay independently of the hippocampus.
Science. 2017;355(6321):184-188. doi:10.1126/science.aag2787
apa: O’Neill, J., Boccara, C. N., Stella, F., Schönenberger, P., & Csicsvari,
J. L. (2017). Superficial layers of the medial entorhinal cortex replay independently
of the hippocampus. Science. American Association for the Advancement of
Science. https://doi.org/10.1126/science.aag2787
chicago: O’Neill, Joseph, Charlotte N. Boccara, Federico Stella, Philipp Schönenberger,
and Jozsef L Csicsvari. “Superficial Layers of the Medial Entorhinal Cortex Replay
Independently of the Hippocampus.” Science. American Association for the
Advancement of Science, 2017. https://doi.org/10.1126/science.aag2787.
ieee: J. O’Neill, C. N. Boccara, F. Stella, P. Schönenberger, and J. L. Csicsvari,
“Superficial layers of the medial entorhinal cortex replay independently of the
hippocampus,” Science, vol. 355, no. 6321. American Association for the
Advancement of Science, pp. 184–188, 2017.
ista: O’Neill J, Boccara CN, Stella F, Schönenberger P, Csicsvari JL. 2017. Superficial
layers of the medial entorhinal cortex replay independently of the hippocampus.
Science. 355(6321), 184–188.
mla: O’Neill, Joseph, et al. “Superficial Layers of the Medial Entorhinal Cortex
Replay Independently of the Hippocampus.” Science, vol. 355, no. 6321,
American Association for the Advancement of Science, 2017, pp. 184–88, doi:10.1126/science.aag2787.
short: J. O’Neill, C.N. Boccara, F. Stella, P. Schönenberger, J.L. Csicsvari, Science
355 (2017) 184–188.
date_created: 2018-12-11T11:50:19Z
date_published: 2017-01-13T00:00:00Z
date_updated: 2023-09-20T11:30:35Z
day: '13'
ddc:
- '571'
department:
- _id: JoCs
doi: 10.1126/science.aag2787
ec_funded: 1
external_id:
isi:
- '000391743700044'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:22Z
date_updated: 2018-12-12T10:10:22Z
file_id: '4809'
file_name: IST-2018-976-v1+1_2017Preprint_ONeill_Superficial_layers.pdf
file_size: 3761201
relation: main_file
file_date_updated: 2018-12-12T10:10:22Z
has_accepted_license: '1'
intvolume: ' 355'
isi: 1
issue: '6321'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 184 - 188
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
publication: Science
publication_identifier:
issn:
- '00368075'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6226'
pubrep_id: '976'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Superficial layers of the medial entorhinal cortex replay independently of
the hippocampus
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 355
year: '2017'
...
---
_id: '1120'
abstract:
- lang: eng
text: 'The existence of a self-localization transition in the polaron problem has
been under an active debate ever since Landau suggested it 83 years ago. Here
we reveal the self-localization transition for the rotational analogue of the
polaron -- the angulon quasiparticle. We show that, unlike for the polarons, self-localization
of angulons occurs at finite impurity-bath coupling already at the mean-field
level. The transition is accompanied by the spherical-symmetry breaking of the
angulon ground state and a discontinuity in the first derivative of the ground-state
energy. Moreover, the type of the symmetry breaking is dictated by the symmetry
of the microscopic impurity-bath interaction, which leads to a number of distinct
self-localized states. The predicted effects can potentially be addressed in experiments
on cold molecules trapped in superfluid helium droplets and ultracold quantum
gases, as well as on electronic excitations in solids and Bose-Einstein condensates. '
article_number: '033608'
article_processing_charge: No
author:
- first_name: Xiang
full_name: Li, Xiang
id: 4B7E523C-F248-11E8-B48F-1D18A9856A87
last_name: Li
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Li X, Seiringer R, Lemeshko M. Angular self-localization of impurities rotating
in a bosonic bath. Physical Review A. 2017;95(3). doi:10.1103/PhysRevA.95.033608
apa: Li, X., Seiringer, R., & Lemeshko, M. (2017). Angular self-localization
of impurities rotating in a bosonic bath. Physical Review A. American Physical
Society. https://doi.org/10.1103/PhysRevA.95.033608
chicago: Li, Xiang, Robert Seiringer, and Mikhail Lemeshko. “Angular Self-Localization
of Impurities Rotating in a Bosonic Bath.” Physical Review A. American
Physical Society, 2017. https://doi.org/10.1103/PhysRevA.95.033608.
ieee: X. Li, R. Seiringer, and M. Lemeshko, “Angular self-localization of impurities
rotating in a bosonic bath,” Physical Review A, vol. 95, no. 3. American
Physical Society, 2017.
ista: Li X, Seiringer R, Lemeshko M. 2017. Angular self-localization of impurities
rotating in a bosonic bath. Physical Review A. 95(3), 033608.
mla: Li, Xiang, et al. “Angular Self-Localization of Impurities Rotating in a Bosonic
Bath.” Physical Review A, vol. 95, no. 3, 033608, American Physical Society,
2017, doi:10.1103/PhysRevA.95.033608.
short: X. Li, R. Seiringer, M. Lemeshko, Physical Review A 95 (2017).
date_created: 2018-12-11T11:50:15Z
date_published: 2017-03-06T00:00:00Z
date_updated: 2023-09-20T11:30:58Z
day: '06'
department:
- _id: MiLe
- _id: RoSe
doi: 10.1103/PhysRevA.95.033608
ec_funded: 1
external_id:
isi:
- '000395981900009'
intvolume: ' 95'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.04908
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review A
publication_identifier:
issn:
- '24699926'
publication_status: published
publisher: American Physical Society
publist_id: '6242'
quality_controlled: '1'
related_material:
record:
- id: '8958'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Angular self-localization of impurities rotating in a bosonic bath
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 95
year: '2017'
...
---
_id: '1133'
abstract:
- lang: eng
text: 'It is a common knowledge that an effective interaction of a quantum impurity
with an electromagnetic field can be screened by surrounding charge carriers,
whether mobile or static. Here we demonstrate that very strong, "anomalous" screening
can take place in the presence of a neutral, weakly polarizable environment, due
to an exchange of orbital angular momentum between the impurity and the bath.
Furthermore, we show that it is possible to generalize all phenomena related to
isolated impurities in an external field to the case when a many-body environment
is present, by casting the problem in terms of the angulon quasiparticle. As a
result, the relevant observables such as the effective Rabi frequency, geometric
phase, and impurity spatial alignment are straightforward to evaluate in terms
of a single parameter: the angular-momentum-dependent screening factor.'
article_number: '085302'
article_processing_charge: No
author:
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Yakaboylu E, Lemeshko M. Anomalous screening of quantum impurities by a neutral
environment. Physical Review Letters. 2017;118(8). doi:10.1103/PhysRevLett.118.085302
apa: Yakaboylu, E., & Lemeshko, M. (2017). Anomalous screening of quantum impurities
by a neutral environment. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/PhysRevLett.118.085302
chicago: Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anomalous Screening of Quantum
Impurities by a Neutral Environment.” Physical Review Letters. American
Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.085302.
ieee: E. Yakaboylu and M. Lemeshko, “Anomalous screening of quantum impurities by
a neutral environment,” Physical Review Letters, vol. 118, no. 8. American
Physical Society, 2017.
ista: Yakaboylu E, Lemeshko M. 2017. Anomalous screening of quantum impurities by
a neutral environment. Physical Review Letters. 118(8), 085302.
mla: Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anomalous Screening of Quantum
Impurities by a Neutral Environment.” Physical Review Letters, vol. 118,
no. 8, 085302, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.085302.
short: E. Yakaboylu, M. Lemeshko, Physical Review Letters 118 (2017).
date_created: 2018-12-11T11:50:19Z
date_published: 2017-02-22T00:00:00Z
date_updated: 2023-09-20T11:30:08Z
day: '22'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.118.085302
ec_funded: 1
external_id:
isi:
- '000394667600003'
intvolume: ' 118'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1612.02820
month: '02'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review Letters
publication_identifier:
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
publist_id: '6225'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anomalous screening of quantum impurities by a neutral environment
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 118
year: '2017'
...
---
_id: '1119'
abstract:
- lang: eng
text: Understanding the behavior of molecules interacting with superfluid helium
represents a formidable challenge and, in general, requires approaches relying
on large-scale numerical simulations. Here we demonstrate that experimental data
collected over the last 20 years provide evidence that molecules immersed in superfluid
helium form recently-predicted angulon quasiparticles [Phys. Rev. Lett. 114, 203001
(2015)]. Most importantly, casting the many-body problem in terms of angulons
amounts to a drastic simplification and yields effective molecular moments of
inertia as straightforward analytic solutions of a simple microscopic Hamiltonian.
The outcome of the angulon theory is in good agreement with experiment for a broad
range of molecular impurities, from heavy to medium-mass to light species. These
results pave the way to understanding molecular rotation in liquid and crystalline
phases in terms of the angulon quasiparticle.
article_number: '095301'
article_processing_charge: No
author:
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Lemeshko M. Quasiparticle approach to molecules interacting with quantum solvents.
Physical Review Letters. 2017;118(9). doi:10.1103/PhysRevLett.118.095301
apa: Lemeshko, M. (2017). Quasiparticle approach to molecules interacting with quantum
solvents. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.095301
chicago: Lemeshko, Mikhail. “Quasiparticle Approach to Molecules Interacting with
Quantum Solvents.” Physical Review Letters. American Physical Society,
2017. https://doi.org/10.1103/PhysRevLett.118.095301.
ieee: M. Lemeshko, “Quasiparticle approach to molecules interacting with quantum
solvents,” Physical Review Letters, vol. 118, no. 9. American Physical
Society, 2017.
ista: Lemeshko M. 2017. Quasiparticle approach to molecules interacting with quantum
solvents. Physical Review Letters. 118(9), 095301.
mla: Lemeshko, Mikhail. “Quasiparticle Approach to Molecules Interacting with Quantum
Solvents.” Physical Review Letters, vol. 118, no. 9, 095301, American Physical
Society, 2017, doi:10.1103/PhysRevLett.118.095301.
short: M. Lemeshko, Physical Review Letters 118 (2017).
date_created: 2018-12-11T11:50:15Z
date_published: 2017-02-27T00:00:00Z
date_updated: 2023-09-20T11:31:22Z
day: '27'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.118.095301
external_id:
isi:
- '000404769200006'
intvolume: ' 118'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.01604
month: '02'
oa: 1
oa_version: Submitted Version
project:
- _id: 25636330-B435-11E9-9278-68D0E5697425
grant_number: 11-NSF-1070
name: ROOTS Genome-wide Analysis of Root Traits
publication: Physical Review Letters
publication_identifier:
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
publist_id: '6243'
quality_controlled: '1'
status: public
title: Quasiparticle approach to molecules interacting with quantum solvents
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 118
year: '2017'
...
---
_id: '1110'
abstract:
- lang: eng
text: The phytohormone auxin is a major determinant and regulatory component important
for plant development. Auxin transport between cells is mediated by a complex
system of transporters such as AUX1/LAX, PIN, and ABCB proteins, and their localization
and activity is thought to be influenced by phosphatases and kinases. Flavonols
have been shown to alter auxin transport activity and changes in flavonol accumulation
in the Arabidopsis thaliana rol1-2 mutant cause defects in auxin transport and
seedling development. A new mutation in ROOTS CURL IN NPA 1 (RCN1), encoding a
regulatory subunit of the phosphatase PP2A, was found to suppress the growth defects
of rol1-2 without changing the flavonol content. rol1-2 rcn1-3 double mutants
show wild type-like auxin transport activity while levels of free auxin are not
affected by rcn1-3. In the rol1-2 mutant, PIN2 shows a flavonol-induced basal-to-apical
shift in polar localization which is reversed in the rol1-2 rcn1-3 to basal localization.
In vivo analysis of PINOID action, a kinase known to influence PIN protein localization
in a PP2A-antagonistic manner, revealed a negative impact of flavonols on PINOID
activity. Together, these data suggest that flavonols affect auxin transport by
modifying the antagonistic kinase/phosphatase equilibrium.
acknowledgement: European Research Council (project ERC-2011-StG-20101109-PSDP), European
Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation (GA13-40637S)
[JF].
article_number: '41906'
article_processing_charge: No
author:
- first_name: Benjamin
full_name: Kuhn, Benjamin
last_name: Kuhn
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Sanae
full_name: Errafi, Sanae
last_name: Errafi
- first_name: Rahel
full_name: Bucher, Rahel
last_name: Bucher
- first_name: Shibu
full_name: Gupta, Shibu
last_name: Gupta
- first_name: Bibek
full_name: Aryal, Bibek
last_name: Aryal
- first_name: Petre
full_name: Dobrev, Petre
last_name: Dobrev
- first_name: Laurent
full_name: Bigler, Laurent
last_name: Bigler
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Christoph
full_name: Ringli, Christoph
last_name: Ringli
citation:
ama: Kuhn B, Nodzyński T, Errafi S, et al. Flavonol-induced changes in PIN2 polarity
and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase
activity. Scientific Reports. 2017;7. doi:10.1038/srep41906
apa: Kuhn, B., Nodzyński, T., Errafi, S., Bucher, R., Gupta, S., Aryal, B., … Ringli,
C. (2017). Flavonol-induced changes in PIN2 polarity and auxin transport in the
Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific
Reports. Nature Publishing Group. https://doi.org/10.1038/srep41906
chicago: Kuhn, Benjamin, Tomasz Nodzyński, Sanae Errafi, Rahel Bucher, Shibu Gupta,
Bibek Aryal, Petre Dobrev, et al. “Flavonol-Induced Changes in PIN2 Polarity and
Auxin Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase
Activity.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep41906.
ieee: B. Kuhn et al., “Flavonol-induced changes in PIN2 polarity and auxin
transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity,”
Scientific Reports, vol. 7. Nature Publishing Group, 2017.
ista: Kuhn B, Nodzyński T, Errafi S, Bucher R, Gupta S, Aryal B, Dobrev P, Bigler
L, Geisler M, Zažímalová E, Friml J, Ringli C. 2017. Flavonol-induced changes
in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant
require phosphatase activity. Scientific Reports. 7, 41906.
mla: Kuhn, Benjamin, et al. “Flavonol-Induced Changes in PIN2 Polarity and Auxin
Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase Activity.”
Scientific Reports, vol. 7, 41906, Nature Publishing Group, 2017, doi:10.1038/srep41906.
short: B. Kuhn, T. Nodzyński, S. Errafi, R. Bucher, S. Gupta, B. Aryal, P. Dobrev,
L. Bigler, M. Geisler, E. Zažímalová, J. Friml, C. Ringli, Scientific Reports
7 (2017).
date_created: 2018-12-11T11:50:12Z
date_published: 2017-02-06T00:00:00Z
date_updated: 2023-09-20T11:35:35Z
day: '06'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1038/srep41906
ec_funded: 1
external_id:
isi:
- '000393367600001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:09Z
date_updated: 2018-12-12T10:18:09Z
file_id: '5328'
file_name: IST-2017-803-v1+1_srep41906.pdf
file_size: 1654496
relation: main_file
file_date_updated: 2018-12-12T10:18:09Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Scientific Reports
publication_identifier:
issn:
- '20452322'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6258'
pubrep_id: '803'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis
thaliana rol1-2 mutant require phosphatase activity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2017'
...
---
_id: '1104'
abstract:
- lang: eng
text: In the early visual system, cells of the same type perform the same computation
in different places of the visual field. How these cells code together a complex
visual scene is unclear. A common assumption is that cells of a single-type extract
a single-stimulus feature to form a feature map, but this has rarely been observed
directly. Using large-scale recordings in the rat retina, we show that a homogeneous
population of fast OFF ganglion cells simultaneously encodes two radically different
features of a visual scene. Cells close to a moving object code quasilinearly
for its position, while distant cells remain largely invariant to the object's
position and, instead, respond nonlinearly to changes in the object's speed. We
develop a quantitative model that accounts for this effect and identify a disinhibitory
circuit that mediates it. Ganglion cells of a single type thus do not code for
one, but two features simultaneously. This richer, flexible neural map might also
be present in other sensory systems.
article_number: '1964'
article_processing_charge: No
author:
- first_name: Stephane
full_name: Deny, Stephane
last_name: Deny
- first_name: Ulisse
full_name: Ferrari, Ulisse
last_name: Ferrari
- first_name: Emilie
full_name: Mace, Emilie
last_name: Mace
- first_name: Pierre
full_name: Yger, Pierre
last_name: Yger
- first_name: Romain
full_name: Caplette, Romain
last_name: Caplette
- first_name: Serge
full_name: Picaud, Serge
last_name: Picaud
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
citation:
ama: Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion
cells of a single type. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-02159-y
apa: Deny, S., Ferrari, U., Mace, E., Yger, P., Caplette, R., Picaud, S., … Marre,
O. (2017). Multiplexed computations in retinal ganglion cells of a single type.
Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-02159-y
chicago: Deny, Stephane, Ulisse Ferrari, Emilie Mace, Pierre Yger, Romain Caplette,
Serge Picaud, Gašper Tkačik, and Olivier Marre. “Multiplexed Computations in Retinal
Ganglion Cells of a Single Type.” Nature Communications. Nature Publishing
Group, 2017. https://doi.org/10.1038/s41467-017-02159-y.
ieee: S. Deny et al., “Multiplexed computations in retinal ganglion cells
of a single type,” Nature Communications, vol. 8, no. 1. Nature Publishing
Group, 2017.
ista: Deny S, Ferrari U, Mace E, Yger P, Caplette R, Picaud S, Tkačik G, Marre O.
2017. Multiplexed computations in retinal ganglion cells of a single type. Nature
Communications. 8(1), 1964.
mla: Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells
of a Single Type.” Nature Communications, vol. 8, no. 1, 1964, Nature Publishing
Group, 2017, doi:10.1038/s41467-017-02159-y.
short: S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkačik,
O. Marre, Nature Communications 8 (2017).
date_created: 2018-12-11T11:50:10Z
date_published: 2017-12-06T00:00:00Z
date_updated: 2023-09-20T11:41:19Z
day: '06'
ddc:
- '571'
department:
- _id: GaTk
doi: 10.1038/s41467-017-02159-y
ec_funded: 1
external_id:
isi:
- '000417241200004'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:06Z
date_updated: 2018-12-12T10:16:06Z
file_id: '5191'
file_name: IST-2018-921-v1+1_s41467-017-02159-y.pdf
file_size: 2872887
relation: main_file
file_date_updated: 2018-12-12T10:16:06Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25CD3DD2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '604102'
name: Localization of ion channels and receptors by two and three-dimensional immunoelectron
microscopic approaches
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6266'
pubrep_id: '921'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multiplexed computations in retinal ganglion cells of a single type
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '1114'
abstract:
- lang: eng
text: Nonequilibrium phase transitions exist in damped-driven open quantum systems
when the continuous tuning of an external parameter leads to a transition between
two robust steady states. In second-order transitions this change is abrupt at
a critical point, whereas in first-order transitions the two phases can coexist
in a critical hysteresis domain. Here, we report the observation of a first-order
dissipative quantum phase transition in a driven circuit quantum electrodynamics
system. It takes place when the photon blockade of the driven cavity-atom system
is broken by increasing the drive power. The observed experimental signature is
a bimodal phase space distribution with varying weights controlled by the drive
strength. Our measurements show an improved stabilization of the classical attractors
up to the millisecond range when the size of the quantum system is increased from
one to three artificial atoms. The formation of such robust pointer states could
be used for new quantum measurement schemes or to investigate multiphoton phases
of finite-size, nonlinear, open quantum systems.
article_number: '011012'
article_processing_charge: Yes
author:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: András
full_name: Dombi, András
last_name: Dombi
- first_name: András
full_name: Vukics, András
last_name: Vukics
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
- first_name: Peter
full_name: Domokos, Peter
last_name: Domokos
citation:
ama: Fink JM, Dombi A, Vukics A, Wallraff A, Domokos P. Observation of the photon
blockade breakdown phase transition. Physical Review X. 2017;7(1). doi:10.1103/PhysRevX.7.011012
apa: Fink, J. M., Dombi, A., Vukics, A., Wallraff, A., & Domokos, P. (2017).
Observation of the photon blockade breakdown phase transition. Physical Review
X. American Physical Society. https://doi.org/10.1103/PhysRevX.7.011012
chicago: Fink, Johannes M, András Dombi, András Vukics, Andreas Wallraff, and Peter
Domokos. “Observation of the Photon Blockade Breakdown Phase Transition.” Physical
Review X. American Physical Society, 2017. https://doi.org/10.1103/PhysRevX.7.011012.
ieee: J. M. Fink, A. Dombi, A. Vukics, A. Wallraff, and P. Domokos, “Observation
of the photon blockade breakdown phase transition,” Physical Review X,
vol. 7, no. 1. American Physical Society, 2017.
ista: Fink JM, Dombi A, Vukics A, Wallraff A, Domokos P. 2017. Observation of the
photon blockade breakdown phase transition. Physical Review X. 7(1), 011012.
mla: Fink, Johannes M., et al. “Observation of the Photon Blockade Breakdown Phase
Transition.” Physical Review X, vol. 7, no. 1, 011012, American Physical
Society, 2017, doi:10.1103/PhysRevX.7.011012.
short: J.M. Fink, A. Dombi, A. Vukics, A. Wallraff, P. Domokos, Physical Review
X 7 (2017).
date_created: 2018-12-11T11:50:13Z
date_published: 2017-01-31T00:00:00Z
date_updated: 2023-09-20T11:33:07Z
day: '31'
ddc:
- '539'
department:
- _id: JoFi
doi: 10.1103/PhysRevX.7.011012
external_id:
isi:
- '000397450500001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:52Z
date_updated: 2018-12-12T10:12:52Z
file_id: '4972'
file_name: IST-2017-753-v1+1_PhysRevX.7.011012.pdf
file_size: 1172926
relation: main_file
file_date_updated: 2018-12-12T10:12:52Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Physical Review X
publication_identifier:
issn:
- '21603308'
publication_status: published
publisher: American Physical Society
publist_id: '6252'
pubrep_id: '753'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Observation of the photon blockade breakdown phase transition
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2017'
...
---
_id: '1111'
abstract:
- lang: eng
text: Adaptation depends critically on the effects of new mutations and their dependency
on the genetic background in which they occur. These two factors can be summarized
by the fitness landscape. However, it would require testing all mutations in all
backgrounds, making the definition and analysis of fitness landscapes mostly inaccessible.
Instead of postulating a particular fitness landscape, we address this problem
by considering general classes of landscapes and calculating an upper limit for
the time it takes for a population to reach a fitness peak, circumventing the
need to have full knowledge about the fitness landscape. We analyze populations
in the weak-mutation regime and characterize the conditions that enable them to
quickly reach the fitness peak as a function of the number of sites under selection.
We show that for additive landscapes there is a critical selection strength enabling
populations to reach high-fitness genotypes, regardless of the distribution of
effects. This threshold scales with the number of sites under selection, effectively
setting a limit to adaptation, and results from the inevitable increase in deleterious
mutational pressure as the population adapts in a space of discrete genotypes.
Furthermore, we show that for the class of all unimodal landscapes this condition
is sufficient but not necessary for rapid adaptation, as in some highly epistatic
landscapes the critical strength does not depend on the number of sites under
selection; effectively removing this barrier to adaptation.
article_processing_charge: No
article_type: original
author:
- first_name: Jorge
full_name: Heredia, Jorge
last_name: Heredia
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Heredia J, Trubenova B, Sudholt D, Paixao T. Selection limits to adaptive walks
on correlated landscapes. Genetics. 2017;205(2):803-825. doi:10.1534/genetics.116.189340
apa: Heredia, J., Trubenova, B., Sudholt, D., & Paixao, T. (2017). Selection
limits to adaptive walks on correlated landscapes. Genetics. Genetics Society
of America. https://doi.org/10.1534/genetics.116.189340
chicago: Heredia, Jorge, Barbora Trubenova, Dirk Sudholt, and Tiago Paixao. “Selection
Limits to Adaptive Walks on Correlated Landscapes.” Genetics. Genetics
Society of America, 2017. https://doi.org/10.1534/genetics.116.189340.
ieee: J. Heredia, B. Trubenova, D. Sudholt, and T. Paixao, “Selection limits to
adaptive walks on correlated landscapes,” Genetics, vol. 205, no. 2. Genetics
Society of America, pp. 803–825, 2017.
ista: Heredia J, Trubenova B, Sudholt D, Paixao T. 2017. Selection limits to adaptive
walks on correlated landscapes. Genetics. 205(2), 803–825.
mla: Heredia, Jorge, et al. “Selection Limits to Adaptive Walks on Correlated Landscapes.”
Genetics, vol. 205, no. 2, Genetics Society of America, 2017, pp. 803–25,
doi:10.1534/genetics.116.189340.
short: J. Heredia, B. Trubenova, D. Sudholt, T. Paixao, Genetics 205 (2017) 803–825.
date_created: 2018-12-11T11:50:12Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T11:35:03Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.116.189340
ec_funded: 1
external_id:
isi:
- '000394144900025'
pmid:
- '27881471'
intvolume: ' 205'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1534/genetics.116.189340
month: '02'
oa: 1
oa_version: Published Version
page: 803 - 825
pmid: 1
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
publist_id: '6256'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Selection limits to adaptive walks on correlated landscapes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 205
year: '2017'
...
---
_id: '1109'
abstract:
- lang: eng
text: 'Rotation of molecules embedded in He nanodroplets is explored by a combination
of fs laser-induced alignment experiments and angulon quasiparticle theory. We
demonstrate that at low fluence of the fs alignment pulse, the molecule and its
solvation shell can be set into coherent collective rotation lasting long enough
to form revivals. With increasing fluence, however, the revivals disappear --
instead, rotational dynamics as rapid as for an isolated molecule is observed
during the first few picoseconds. Classical calculations trace this phenomenon
to transient decoupling of the molecule from its He shell. Our results open novel
opportunities for studying non-equilibrium solute-solvent dynamics and quantum
thermalization. '
article_number: '203203'
article_processing_charge: No
author:
- first_name: Benjamin
full_name: Shepperson, Benjamin
last_name: Shepperson
- first_name: Anders
full_name: Søndergaard, Anders
last_name: Søndergaard
- first_name: Lars
full_name: Christiansen, Lars
last_name: Christiansen
- first_name: Jan
full_name: Kaczmarczyk, Jan
id: 46C405DE-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarczyk
orcid: 0000-0002-1629-3675
- first_name: Robert
full_name: Zillich, Robert
last_name: Zillich
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Henrik
full_name: Stapelfeldt, Henrik
last_name: Stapelfeldt
citation:
ama: 'Shepperson B, Søndergaard A, Christiansen L, et al. Laser-induced rotation
of iodine molecules in helium nanodroplets: Revivals and breaking-free. Physical
Review Letters. 2017;118(20). doi:10.1103/PhysRevLett.118.203203'
apa: 'Shepperson, B., Søndergaard, A., Christiansen, L., Kaczmarczyk, J., Zillich,
R., Lemeshko, M., & Stapelfeldt, H. (2017). Laser-induced rotation of iodine
molecules in helium nanodroplets: Revivals and breaking-free. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.203203'
chicago: 'Shepperson, Benjamin, Anders Søndergaard, Lars Christiansen, Jan Kaczmarczyk,
Robert Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Laser-Induced Rotation
of Iodine Molecules in Helium Nanodroplets: Revivals and Breaking-Free.” Physical
Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.203203.'
ieee: 'B. Shepperson et al., “Laser-induced rotation of iodine molecules
in helium nanodroplets: Revivals and breaking-free,” Physical Review Letters,
vol. 118, no. 20. American Physical Society, 2017.'
ista: 'Shepperson B, Søndergaard A, Christiansen L, Kaczmarczyk J, Zillich R, Lemeshko
M, Stapelfeldt H. 2017. Laser-induced rotation of iodine molecules in helium nanodroplets:
Revivals and breaking-free. Physical Review Letters. 118(20), 203203.'
mla: 'Shepperson, Benjamin, et al. “Laser-Induced Rotation of Iodine Molecules in
Helium Nanodroplets: Revivals and Breaking-Free.” Physical Review Letters,
vol. 118, no. 20, 203203, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.203203.'
short: B. Shepperson, A. Søndergaard, L. Christiansen, J. Kaczmarczyk, R. Zillich,
M. Lemeshko, H. Stapelfeldt, Physical Review Letters 118 (2017).
date_created: 2018-12-11T11:50:12Z
date_published: 2017-05-19T00:00:00Z
date_updated: 2023-09-20T11:36:17Z
day: '19'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.118.203203
external_id:
isi:
- '000401664000005'
intvolume: ' 118'
isi: 1
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.01977
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6260'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals
and breaking-free'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 118
year: '2017'
...
---
_id: '1087'
abstract:
- lang: eng
text: Using extensive direct numerical simulations, the dynamics of laminar-turbulent
fronts in pipe flow is investigated for Reynolds numbers between and 5500. We
here investigate the physical distinction between the fronts of weak and strong
slugs both by analysing the turbulent kinetic energy budget and by comparing the
downstream front motion to the advection speed of bulk turbulent structures. Our
study shows that weak downstream fronts travel slower than turbulent structures
in the bulk and correspond to decaying turbulence at the front. At the downstream
front speed becomes faster than the advection speed, marking the onset of strong
fronts. In contrast to weak fronts, turbulent eddies are generated at strong fronts
by feeding on the downstream laminar flow. Our study also suggests that temporal
fluctuations of production and dissipation at the downstream laminar-turbulent
front drive the dynamical switches between the two types of front observed up
to.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Baofang
full_name: Song, Baofang
last_name: Song
- first_name: Dwight
full_name: Barkley, Dwight
last_name: Barkley
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Song B, Barkley D, Hof B, Avila M. Speed and structure of turbulent fronts
in pipe flow. Journal of Fluid Mechanics. 2017;813:1045-1059. doi:10.1017/jfm.2017.14
apa: Song, B., Barkley, D., Hof, B., & Avila, M. (2017). Speed and structure
of turbulent fronts in pipe flow. Journal of Fluid Mechanics. Cambridge
University Press. https://doi.org/10.1017/jfm.2017.14
chicago: Song, Baofang, Dwight Barkley, Björn Hof, and Marc Avila. “Speed and Structure
of Turbulent Fronts in Pipe Flow.” Journal of Fluid Mechanics. Cambridge
University Press, 2017. https://doi.org/10.1017/jfm.2017.14.
ieee: B. Song, D. Barkley, B. Hof, and M. Avila, “Speed and structure of turbulent
fronts in pipe flow,” Journal of Fluid Mechanics, vol. 813. Cambridge University
Press, pp. 1045–1059, 2017.
ista: Song B, Barkley D, Hof B, Avila M. 2017. Speed and structure of turbulent
fronts in pipe flow. Journal of Fluid Mechanics. 813, 1045–1059.
mla: Song, Baofang, et al. “Speed and Structure of Turbulent Fronts in Pipe Flow.”
Journal of Fluid Mechanics, vol. 813, Cambridge University Press, 2017,
pp. 1045–59, doi:10.1017/jfm.2017.14.
short: B. Song, D. Barkley, B. Hof, M. Avila, Journal of Fluid Mechanics 813 (2017)
1045–1059.
date_created: 2018-12-11T11:50:04Z
date_published: 2017-02-25T00:00:00Z
date_updated: 2023-09-20T11:47:22Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2017.14
ec_funded: 1
external_id:
isi:
- '000394376400044'
intvolume: ' 813'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1603.04077
month: '02'
oa: 1
oa_version: Submitted Version
page: 1045 - 1059
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Journal of Fluid Mechanics
publication_identifier:
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
publist_id: '6290'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Speed and structure of turbulent fronts in pipe flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 813
year: '2017'
...
---
_id: '1089'
abstract:
- lang: eng
text: We discuss properties of distributions that are multivariate totally positive
of order two (MTP2) related to conditional independence. In particular, we show
that any independence model generated by an MTP2 distribution is a compositional
semigraphoid which is upward-stable and singleton-transitive. In addition, we
prove that any MTP2 distribution satisfying an appropriate support condition is
faithful to its concentration graph. Finally, we analyze factorization properties
of MTP2 distributions and discuss ways of constructing MTP2 distributions; in
particular we give conditions on the log-linear parameters of a discrete distribution
which ensure MTP2 and characterize conditional Gaussian distributions which satisfy
MTP2.
article_processing_charge: No
author:
- first_name: Shaun
full_name: Fallat, Shaun
last_name: Fallat
- first_name: Steffen
full_name: Lauritzen, Steffen
last_name: Lauritzen
- first_name: Kayvan
full_name: Sadeghi, Kayvan
last_name: Sadeghi
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Nanny
full_name: Wermuth, Nanny
last_name: Wermuth
- first_name: Piotr
full_name: Zwiernik, Piotr
last_name: Zwiernik
citation:
ama: Fallat S, Lauritzen S, Sadeghi K, Uhler C, Wermuth N, Zwiernik P. Total positivity
in Markov structures. Annals of Statistics. 2017;45(3):1152-1184. doi:10.1214/16-AOS1478
apa: Fallat, S., Lauritzen, S., Sadeghi, K., Uhler, C., Wermuth, N., & Zwiernik,
P. (2017). Total positivity in Markov structures. Annals of Statistics.
Institute of Mathematical Statistics. https://doi.org/10.1214/16-AOS1478
chicago: Fallat, Shaun, Steffen Lauritzen, Kayvan Sadeghi, Caroline Uhler, Nanny
Wermuth, and Piotr Zwiernik. “Total Positivity in Markov Structures.” Annals
of Statistics. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-AOS1478.
ieee: S. Fallat, S. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth, and P. Zwiernik,
“Total positivity in Markov structures,” Annals of Statistics, vol. 45,
no. 3. Institute of Mathematical Statistics, pp. 1152–1184, 2017.
ista: Fallat S, Lauritzen S, Sadeghi K, Uhler C, Wermuth N, Zwiernik P. 2017. Total
positivity in Markov structures. Annals of Statistics. 45(3), 1152–1184.
mla: Fallat, Shaun, et al. “Total Positivity in Markov Structures.” Annals of
Statistics, vol. 45, no. 3, Institute of Mathematical Statistics, 2017, pp.
1152–84, doi:10.1214/16-AOS1478.
short: S. Fallat, S. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth, P. Zwiernik, Annals
of Statistics 45 (2017) 1152–1184.
date_created: 2018-12-11T11:50:05Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T11:46:53Z
day: '01'
department:
- _id: CaUh
doi: 10.1214/16-AOS1478
external_id:
isi:
- '000404395900008'
intvolume: ' 45'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1510.01290
month: '06'
oa: 1
oa_version: Submitted Version
page: 1152 - 1184
project:
- _id: 2530CA10-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 903-N35
name: 'Gaussian Graphical Models: Theory and Applications'
publication: Annals of Statistics
publication_identifier:
issn:
- '00905364'
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '6288'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Total positivity in Markov structures
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 45
year: '2017'
...
---
_id: '1080'
abstract:
- lang: eng
text: Reconstructing the evolutionary history of metastases is critical for understanding
their basic biological principles and has profound clinical implications. Genome-wide
sequencing data has enabled modern phylogenomic methods to accurately dissect
subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented
depth. However, existing methods are not designed to infer metastatic seeding
patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny
of metastases and map subclones to their anatomic locations. Treeomics infers
comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers.
Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing
artifacts; 7% of variants were misclassified by conventional statistical methods.
These artifacts can skew phylogenies by creating illusory tumour heterogeneity
among distinct samples. In silico benchmarking on simulated tumour phylogenies
across a wide range of sample purities (15–95%) and sequencing depths (25-800
× ) demonstrates the accuracy of Treeomics compared with existing methods.
article_number: '14114'
article_processing_charge: No
author:
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Alvin
full_name: Makohon Moore, Alvin
last_name: Makohon Moore
- first_name: Jeffrey
full_name: Gerold, Jeffrey
last_name: Gerold
- first_name: Ivana
full_name: Božić, Ivana
last_name: Božić
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Christine
full_name: Iacobuzio Donahue, Christine
last_name: Iacobuzio Donahue
- first_name: Bert
full_name: Vogelstein, Bert
last_name: Vogelstein
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Reiter J, Makohon Moore A, Gerold J, et al. Reconstructing metastatic seeding
patterns of human cancers. Nature Communications. 2017;8. doi:10.1038/ncomms14114
apa: Reiter, J., Makohon Moore, A., Gerold, J., Božić, I., Chatterjee, K., Iacobuzio
Donahue, C., … Nowak, M. (2017). Reconstructing metastatic seeding patterns of
human cancers. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14114
chicago: Reiter, Johannes, Alvin Makohon Moore, Jeffrey Gerold, Ivana Božić, Krishnendu
Chatterjee, Christine Iacobuzio Donahue, Bert Vogelstein, and Martin Nowak. “Reconstructing
Metastatic Seeding Patterns of Human Cancers.” Nature Communications. Nature
Publishing Group, 2017. https://doi.org/10.1038/ncomms14114.
ieee: J. Reiter et al., “Reconstructing metastatic seeding patterns of human
cancers,” Nature Communications, vol. 8. Nature Publishing Group, 2017.
ista: Reiter J, Makohon Moore A, Gerold J, Božić I, Chatterjee K, Iacobuzio Donahue
C, Vogelstein B, Nowak M. 2017. Reconstructing metastatic seeding patterns of
human cancers. Nature Communications. 8, 14114.
mla: Reiter, Johannes, et al. “Reconstructing Metastatic Seeding Patterns of Human
Cancers.” Nature Communications, vol. 8, 14114, Nature Publishing Group,
2017, doi:10.1038/ncomms14114.
short: J. Reiter, A. Makohon Moore, J. Gerold, I. Božić, K. Chatterjee, C. Iacobuzio
Donahue, B. Vogelstein, M. Nowak, Nature Communications 8 (2017).
date_created: 2018-12-11T11:50:02Z
date_published: 2017-01-31T00:00:00Z
date_updated: 2023-09-20T11:55:31Z
day: '31'
ddc:
- '004'
- '006'
department:
- _id: KrCh
doi: 10.1038/ncomms14114
ec_funded: 1
external_id:
isi:
- '000393096600001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:15Z
date_updated: 2018-12-12T10:15:15Z
file_id: '5133'
file_name: IST-2017-786-v1+1_ncomms14114.pdf
file_size: 897050
relation: main_file
file_date_updated: 2018-12-12T10:15:15Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6301'
pubrep_id: '786'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reconstructing metastatic seeding patterns of human cancers
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '1085'
abstract:
- lang: eng
text: Sex chromosomes evolve once recombination is halted between a homologous pair
of chromosomes. The dominant model of sex chromosome evolution posits that recombination
is suppressed between emerging X and Y chromosomes in order to resolve sexual
conflict. Here we test this model using whole genome and transcriptome resequencing
data in the guppy, a model for sexual selection with many Y-linked colour traits.
We show that although the nascent Y chromosome encompasses nearly half of the
linkage group, there has been no perceptible degradation of Y chromosome gene
content or activity. Using replicate wild populations with differing levels of
sexually antagonistic selection for colour, we also show that sexual selection
leads to greater expansion of the non-recombining region and increased Y chromosome
divergence. These results provide empirical support for longstanding models of
sex chromosome catalysis, and suggest an important role for sexual selection and
sexual conflict in genome evolution.
article_number: '14251'
article_processing_charge: No
author:
- first_name: Alison
full_name: Wright, Alison
last_name: Wright
- first_name: Iulia
full_name: Darolti, Iulia
last_name: Darolti
- first_name: Natasha
full_name: Bloch, Natasha
last_name: Bloch
- first_name: Vicencio
full_name: Oostra, Vicencio
last_name: Oostra
- first_name: Benjamin
full_name: Sandkam, Benjamin
last_name: Sandkam
- first_name: Séverine
full_name: Buechel, Séverine
last_name: Buechel
- first_name: Niclas
full_name: Kolm, Niclas
last_name: Kolm
- first_name: Felix
full_name: Breden, Felix
last_name: Breden
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Judith
full_name: Mank, Judith
last_name: Mank
citation:
ama: Wright A, Darolti I, Bloch N, et al. Convergent recombination suppression suggests
role of sexual selection in guppy sex chromosome formation. Nature Communications.
2017;8. doi:10.1038/ncomms14251
apa: Wright, A., Darolti, I., Bloch, N., Oostra, V., Sandkam, B., Buechel, S., …
Mank, J. (2017). Convergent recombination suppression suggests role of sexual
selection in guppy sex chromosome formation. Nature Communications. Nature
Publishing Group. https://doi.org/10.1038/ncomms14251
chicago: Wright, Alison, Iulia Darolti, Natasha Bloch, Vicencio Oostra, Benjamin
Sandkam, Séverine Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith
Mank. “Convergent Recombination Suppression Suggests Role of Sexual Selection
in Guppy Sex Chromosome Formation.” Nature Communications. Nature Publishing
Group, 2017. https://doi.org/10.1038/ncomms14251.
ieee: A. Wright et al., “Convergent recombination suppression suggests role
of sexual selection in guppy sex chromosome formation,” Nature Communications,
vol. 8. Nature Publishing Group, 2017.
ista: Wright A, Darolti I, Bloch N, Oostra V, Sandkam B, Buechel S, Kolm N, Breden
F, Vicoso B, Mank J. 2017. Convergent recombination suppression suggests role
of sexual selection in guppy sex chromosome formation. Nature Communications.
8, 14251.
mla: Wright, Alison, et al. “Convergent Recombination Suppression Suggests Role
of Sexual Selection in Guppy Sex Chromosome Formation.” Nature Communications,
vol. 8, 14251, Nature Publishing Group, 2017, doi:10.1038/ncomms14251.
short: A. Wright, I. Darolti, N. Bloch, V. Oostra, B. Sandkam, S. Buechel, N. Kolm,
F. Breden, B. Vicoso, J. Mank, Nature Communications 8 (2017).
date_created: 2018-12-11T11:50:04Z
date_published: 2017-01-31T00:00:00Z
date_updated: 2023-09-20T11:48:16Z
day: '31'
ddc:
- '570'
- '576'
department:
- _id: BeVi
doi: 10.1038/ncomms14251
external_id:
isi:
- '000392953700001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:22Z
date_updated: 2018-12-12T10:15:22Z
file_id: '5141'
file_name: IST-2017-791-v1+1_ncomms14251.pdf
file_size: 955256
relation: main_file
file_date_updated: 2018-12-12T10:15:22Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6292'
pubrep_id: '791'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convergent recombination suppression suggests role of sexual selection in guppy
sex chromosome 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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '1084'
abstract:
- lang: eng
text: 'BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis
controlling the response to antimicrobial peptides. In the presence of extracellular
bacitracin and nisin, respectively, the two response regulators (RRs) bind their
target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target
gene expression and ultimately antibiotic resistance. Despite high sequence similarity
between the RRs BceR and PsdR and their known binding sites, no cross-regulation
has been observed between them. We therefore investigated the specificity determinants
of PbceA and PpsdA that ensure the insulation of these two paralogous pathways
at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the
regulatory regions within these two promoters contain three important elements:
in addition to the known (main) binding site, we identified a linker region and
a secondary binding site that are crucial for functionality. Initial binding to
the high-affinity, low-specificity main binding site is a prerequisite for the
subsequent highly specific binding of a second RR dimer to the low-affinity secondary
binding site. In addition to this hierarchical cooperative binding, discrimination
requires a competition of the two RRs for their respective binding site mediated
by only slight differences in binding affinities.'
article_processing_charge: No
author:
- first_name: Chong
full_name: Fang, Chong
last_name: Fang
- first_name: Anna A
full_name: Nagy-Staron, Anna A
id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87
last_name: Nagy-Staron
orcid: 0000-0002-1391-8377
- first_name: Martin
full_name: Grafe, Martin
last_name: Grafe
- first_name: Ralf
full_name: Heermann, Ralf
last_name: Heermann
- first_name: Kirsten
full_name: Jung, Kirsten
last_name: Jung
- first_name: Susanne
full_name: Gebhard, Susanne
last_name: Gebhard
- first_name: Thorsten
full_name: Mascher, Thorsten
last_name: Mascher
citation:
ama: Fang C, Nagy-Staron AA, Grafe M, et al. Insulation and wiring specificity of
BceR like response regulators and their target promoters in Bacillus subtilis.
Molecular Microbiology. 2017;104(1):16-31. doi:10.1111/mmi.13597
apa: Fang, C., Nagy-Staron, A. A., Grafe, M., Heermann, R., Jung, K., Gebhard, S.,
& Mascher, T. (2017). Insulation and wiring specificity of BceR like response
regulators and their target promoters in Bacillus subtilis. Molecular Microbiology.
Wiley-Blackwell. https://doi.org/10.1111/mmi.13597
chicago: Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung,
Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR
like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular
Microbiology. Wiley-Blackwell, 2017. https://doi.org/10.1111/mmi.13597.
ieee: C. Fang et al., “Insulation and wiring specificity of BceR like response
regulators and their target promoters in Bacillus subtilis,” Molecular Microbiology,
vol. 104, no. 1. Wiley-Blackwell, pp. 16–31, 2017.
ista: Fang C, Nagy-Staron AA, Grafe M, Heermann R, Jung K, Gebhard S, Mascher T.
2017. Insulation and wiring specificity of BceR like response regulators and their
target promoters in Bacillus subtilis. Molecular Microbiology. 104(1), 16–31.
mla: Fang, Chong, et al. “Insulation and Wiring Specificity of BceR like Response
Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology,
vol. 104, no. 1, Wiley-Blackwell, 2017, pp. 16–31, doi:10.1111/mmi.13597.
short: C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T.
Mascher, Molecular Microbiology 104 (2017) 16–31.
date_created: 2018-12-11T11:50:03Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2023-09-20T11:48:43Z
day: '01'
department:
- _id: CaGu
doi: 10.1111/mmi.13597
external_id:
isi:
- '000398059200002'
intvolume: ' 104'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa_version: None
page: 16 - 31
publication: Molecular Microbiology
publication_identifier:
issn:
- ' 0950382X'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6294'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Insulation and wiring specificity of BceR like response regulators and their
target promoters in Bacillus subtilis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 104
year: '2017'
...
---
_id: '1079'
abstract:
- lang: eng
text: We study the ionization problem in the Thomas-Fermi-Dirac-von Weizsäcker theory
for atoms and molecules. We prove the nonexistence of minimizers for the energy
functional when the number of electrons is large and the total nuclear charge
is small. This nonexistence result also applies to external potentials decaying
faster than the Coulomb potential. In the case of arbitrary nuclear charges, we
obtain the nonexistence of stable minimizers and radial minimizers.
article_number: '6'
article_processing_charge: No
author:
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
- first_name: Hanne
full_name: Van Den Bosch, Hanne
last_name: Van Den Bosch
citation:
ama: Nam P, Van Den Bosch H. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory
with small nuclear charges. Mathematical Physics, Analysis and Geometry.
2017;20(2). doi:10.1007/s11040-017-9238-0
apa: Nam, P., & Van Den Bosch, H. (2017). Nonexistence in Thomas Fermi-Dirac-von
Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis
and Geometry. Springer. https://doi.org/10.1007/s11040-017-9238-0
chicago: Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von
Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis
and Geometry. Springer, 2017. https://doi.org/10.1007/s11040-017-9238-0.
ieee: P. Nam and H. Van Den Bosch, “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker
theory with small nuclear charges,” Mathematical Physics, Analysis and Geometry,
vol. 20, no. 2. Springer, 2017.
ista: Nam P, Van Den Bosch H. 2017. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker
theory with small nuclear charges. Mathematical Physics, Analysis and Geometry.
20(2), 6.
mla: Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von
Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis
and Geometry, vol. 20, no. 2, 6, Springer, 2017, doi:10.1007/s11040-017-9238-0.
short: P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20
(2017).
date_created: 2018-12-11T11:50:02Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T11:53:35Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s11040-017-9238-0
external_id:
isi:
- '000401270000004'
intvolume: ' 20'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1603.07368
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Mathematical Physics, Analysis and Geometry
publication_identifier:
issn:
- '13850172'
publication_status: published
publisher: Springer
publist_id: '6300'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear
charges
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 20
year: '2017'
...
---
_id: '1077'
abstract:
- lang: eng
text: Viral capsids are structurally constrained by interactions among the amino
acids (AAs) of their constituent proteins. Therefore, epistasis is expected to
evolve among physically interacting sites and to influence the rates of substitution.
To study the evolution of epistasis, we focused on the major structural protein
of the fX174 phage family by first reconstructing the ancestral protein sequences
of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction
differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each
ancestral haplotype and the extant species, we estimated, in silico, the distribution
of free energies and epistasis of the capsid structure. We found that free energy
has not significantly increased but epistasis has. We decomposed epistasis up
to fifth order and found that higher-order epistasis sometimes compensates pairwise
interactions making the free energy seem additive. The dN/dS ratio is low, suggesting
strong purifying selection, and that structure is under stabilizing selection.
We synthesized phages carrying ancestral haplotypes of the coat protein gene and
measured their fitness experimentally. Our findings indicate that stabilizing
mutations can have higher fitness, and that fitness optima do not necessarily
coincide with energy minima.
article_number: '20160139'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Harold
full_name: Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
- first_name: Tomasz
full_name: Włodarski, Tomasz
last_name: Włodarski
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay
between structure, energy and epistasis in the coat protein of the ϕX174 phage
family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139
apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J.
P. (2017). Evolutionary interplay between structure, energy and epistasis in the
coat protein of the ϕX174 phage family. Journal of the Royal Society Interface.
Royal Society of London. https://doi.org/10.1098/rsif.2016.0139
chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan
P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in
the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface.
Royal Society of London, 2017. https://doi.org/10.1098/rsif.2016.0139.
ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family,” Journal of the Royal Society Interface, vol. 14, no. 126.
Royal Society of London, 2017.
ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family. Journal of the Royal Society Interface. 14(126), 20160139.
mla: Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure,
Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal
of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society
of London, 2017, doi:10.1098/rsif.2016.0139.
short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal
of the Royal Society Interface 14 (2017).
date_created: 2018-12-11T11:50:01Z
date_published: 2017-01-04T00:00:00Z
date_updated: 2023-09-20T11:56:34Z
day: '04'
ddc:
- '570'
department:
- _id: NiBa
- _id: JoBo
doi: 10.1098/rsif.2016.0139
ec_funded: 1
external_id:
isi:
- '000393380400001'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:14:02Z
date_updated: 2019-01-18T09:14:02Z
file_id: '5843'
file_name: 2017_JRSI_Redondo.pdf
file_size: 1092015
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:14:02Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '126'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: Journal of the Royal Society Interface
publication_identifier:
issn:
- '17425689'
publication_status: published
publisher: Royal Society of London
publist_id: '6303'
quality_controlled: '1'
related_material:
record:
- id: '9864'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Evolutionary interplay between structure, energy and epistasis in the coat
protein of the ϕX174 phage family
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2017'
...
---
_id: '1067'
abstract:
- lang: eng
text: Embryo morphogenesis relies on highly coordinated movements of different tissues.
However, remarkably little is known about how tissues coordinate their movements
to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements
first become apparent during “doming,” when the blastoderm begins to spread over
the yolk sac, a process involving coordinated epithelial surface cell layer expansion
and mesenchymal deep cell intercalations. Here, we find that active surface cell
expansion represents the key process coordinating tissue movements during doming.
By using a combination of theory and experiments, we show that epithelial surface
cells not only trigger blastoderm expansion by reducing tissue surface tension,
but also drive blastoderm thinning by inducing tissue contraction through radial
deep cell intercalations. Thus, coordinated tissue expansion and thinning during
doming relies on surface cells simultaneously controlling tissue surface tension
and radial tissue contraction.
acknowledged_ssus:
- _id: PreCl
article_processing_charge: No
author:
- first_name: Hitoshi
full_name: Morita, Hitoshi
id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87
last_name: Morita
- first_name: Silvia
full_name: Grigolon, Silvia
last_name: Grigolon
- first_name: Martin
full_name: Bock, Martin
last_name: Bock
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Guillaume
full_name: Salbreux, Guillaume
last_name: Salbreux
- 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: Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. The physical
basis of coordinated tissue spreading in zebrafish gastrulation. Developmental
Cell. 2017;40(4):354-366. doi:10.1016/j.devcel.2017.01.010
apa: Morita, H., Grigolon, S., Bock, M., Krens, G., Salbreux, G., & Heisenberg,
C.-P. J. (2017). The physical basis of coordinated tissue spreading in zebrafish
gastrulation. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2017.01.010
chicago: Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume
Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue
Spreading in Zebrafish Gastrulation.” Developmental Cell. Cell Press, 2017.
https://doi.org/10.1016/j.devcel.2017.01.010.
ieee: H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, and C.-P. J. Heisenberg,
“The physical basis of coordinated tissue spreading in zebrafish gastrulation,”
Developmental Cell, vol. 40, no. 4. Cell Press, pp. 354–366, 2017.
ista: Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. 2017.
The physical basis of coordinated tissue spreading in zebrafish gastrulation.
Developmental Cell. 40(4), 354–366.
mla: Morita, Hitoshi, et al. “The Physical Basis of Coordinated Tissue Spreading
in Zebrafish Gastrulation.” Developmental Cell, vol. 40, no. 4, Cell Press,
2017, pp. 354–66, doi:10.1016/j.devcel.2017.01.010.
short: H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg,
Developmental Cell 40 (2017) 354–366.
date_created: 2018-12-11T11:49:58Z
date_published: 2017-02-27T00:00:00Z
date_updated: 2023-09-20T12:06:27Z
day: '27'
ddc:
- '572'
- '597'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2017.01.010
ec_funded: 1
external_id:
isi:
- '000395368300007'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:57Z
date_updated: 2018-12-12T10:10:57Z
file_id: '4849'
file_name: IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf
file_size: 6866187
relation: main_file
file_date_updated: 2018-12-12T10:10:57Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 354 - 366
project:
- _id: 2524F500-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '201439'
name: Developing High-Throughput Bioassays for Human Cancers in Zebrafish
publication: Developmental Cell
publication_identifier:
issn:
- '15345807'
publication_status: published
publisher: Cell Press
publist_id: '6320'
pubrep_id: '869'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The physical basis of coordinated tissue spreading in zebrafish gastrulation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 40
year: '2017'
...
---
_id: '1074'
abstract:
- lang: eng
text: Recently it has become feasible to detect long blocks of nearly identical
sequence shared between pairs of genomes. These IBD blocks are direct traces of
recent coalescence events and, as such, contain ample signal to infer recent demography.
Here, we examine sharing of such blocks in two-dimensional populations with local
migration. Using a diffusion approximation to trace genetic ancestry, we derive
analytical formulae for patterns of isolation by distance of IBD blocks, which
can also incorporate recent population density changes. We introduce an inference
scheme that uses a composite likelihood approach to fit these formulae. We then
extensively evaluate our theory and inference method on a range of scenarios using
simulated data. We first validate the diffusion approximation by showing that
the theoretical results closely match the simulated block sharing patterns. We
then demonstrate that our inference scheme can accurately and robustly infer dispersal
rate and effective density, as well as bounds on recent dynamics of population
density. To demonstrate an application, we use our estimation scheme to explore
the fit of a diffusion model to Eastern European samples in the POPRES data set.
We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last
centuries, combined with accelerating population growth, can explain the observed
exponential decay of block sharing with increasing pairwise sample distance.
article_processing_charge: No
author:
- first_name: Harald
full_name: Ringbauer, Harald
id: 417FCFF4-F248-11E8-B48F-1D18A9856A87
last_name: Ringbauer
orcid: 0000-0002-4884-9682
- first_name: Graham
full_name: Coop, Graham
last_name: Coop
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation
by distance of long shared sequence blocks. Genetics. 2017;205(3):1335-1351.
doi:10.1534/genetics.116.196220
apa: Ringbauer, H., Coop, G., & Barton, N. H. (2017). Inferring recent demography
from isolation by distance of long shared sequence blocks. Genetics. Genetics
Society of America. https://doi.org/10.1534/genetics.116.196220
chicago: Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent
Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics.
Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.196220.
ieee: H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from
isolation by distance of long shared sequence blocks,” Genetics, vol. 205,
no. 3. Genetics Society of America, pp. 1335–1351, 2017.
ista: Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation
by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.
mla: Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance
of Long Shared Sequence Blocks.” Genetics, vol. 205, no. 3, Genetics Society
of America, 2017, pp. 1335–51, doi:10.1534/genetics.116.196220.
short: H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.
date_created: 2018-12-11T11:50:00Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2023-09-20T12:00:56Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.116.196220
ec_funded: 1
external_id:
isi:
- '000395807200023'
intvolume: ' 205'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.biorxiv.org/content/early/2016/09/23/076810
month: '03'
oa: 1
oa_version: Preprint
page: 1335 - 1351
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
publist_id: '6307'
quality_controlled: '1'
related_material:
record:
- id: '200'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Inferring recent demography from isolation by distance of long shared sequence
blocks
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 205
year: '2017'
...
---
_id: '1076'
abstract:
- lang: eng
text: Signatures of the Coulomb corrections in the photoelectron momentum distribution
during laser-induced ionization of atoms or ions in tunneling and multiphoton
regimes are investigated analytically in the case of a one-dimensional problem.
A high-order Coulomb-corrected strong-field approximation is applied, where the
exact continuum state in the S matrix is approximated by the eikonal Coulomb-Volkov
state including the second-order corrections to the eikonal. Although without
high-order corrections our theory coincides with the known analytical R-matrix
(ARM) theory, we propose a simplified procedure for the matrix element derivation.
Rather than matching the eikonal Coulomb-Volkov wave function with the bound state
as in the ARM theory to remove the Coulomb singularity, we calculate the matrix
element via the saddle-point integration method by time as well as by coordinate,
and in this way avoiding the Coulomb singularity. The momentum shift in the photoelectron
momentum distribution with respect to the ARM theory due to high-order corrections
is analyzed for tunneling and multiphoton regimes. The relation of the quantum
corrections to the tunneling delay time is discussed.
article_number: '023403'
article_processing_charge: No
author:
- first_name: Michael
full_name: Klaiber, Michael
last_name: Klaiber
- first_name: Jiří
full_name: Daněk, Jiří
last_name: Daněk
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Karen
full_name: Hatsagortsyan, Karen
last_name: Hatsagortsyan
- first_name: Christoph
full_name: Keitel, Christoph
last_name: Keitel
citation:
ama: Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. Strong-field ionization
via a high-order Coulomb-corrected strong-field approximation. Physical Review
A - Atomic, Molecular, and Optical Physics. 2017;95(2). doi:10.1103/PhysRevA.95.023403
apa: Klaiber, M., Daněk, J., Yakaboylu, E., Hatsagortsyan, K., & Keitel, C.
(2017). Strong-field ionization via a high-order Coulomb-corrected strong-field
approximation. Physical Review A - Atomic, Molecular, and Optical Physics.
American Physical Society. https://doi.org/10.1103/PhysRevA.95.023403
chicago: Klaiber, Michael, Jiří Daněk, Enderalp Yakaboylu, Karen Hatsagortsyan,
and Christoph Keitel. “Strong-Field Ionization via a High-Order Coulomb-Corrected
Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical
Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevA.95.023403.
ieee: M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, and C. Keitel, “Strong-field
ionization via a high-order Coulomb-corrected strong-field approximation,”
Physical Review A - Atomic, Molecular, and Optical Physics, vol. 95, no. 2.
American Physical Society, 2017.
ista: Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. 2017. Strong-field
ionization via a high-order Coulomb-corrected strong-field approximation. Physical
Review A - Atomic, Molecular, and Optical Physics. 95(2), 023403.
mla: Klaiber, Michael, et al. “Strong-Field Ionization via a High-Order Coulomb-Corrected
Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical
Physics, vol. 95, no. 2, 023403, American Physical Society, 2017, doi:10.1103/PhysRevA.95.023403.
short: M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, C. Keitel, Physical
Review A - Atomic, Molecular, and Optical Physics 95 (2017).
date_created: 2018-12-11T11:50:01Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T11:57:23Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.95.023403
ec_funded: 1
external_id:
isi:
- '000400571700011'
intvolume: ' 95'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.07018
month: '02'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Physical Review A - Atomic, Molecular, and Optical Physics'
publication_identifier:
issn:
- '24699926'
publication_status: published
publisher: American Physical Society
publist_id: '6305'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strong-field ionization via a high-order Coulomb-corrected strong-field approximation
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 95
year: '2017'
...
---
_id: '1072'
abstract:
- lang: eng
text: Given a finite set of points in Rn and a radius parameter, we study the Čech,
Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized
discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel
sets of generalized discrete Morse functions, we prove that the four complexes
are simple-homotopy equivalent by a sequence of simplicial collapses, which are
explicitly described by a single discrete gradient field.
acknowledgement: This research has been supported by the EU project Toposys(FP7-ICT-318493-STREP),
by ESF under the ACAT Research Network Programme, by the Russian Government under
mega project 11.G34.31.0053, and by the DFG Collaborative Research Center SFB/TRR
109 “Discretization in Geometry and Dynamics”.
article_processing_charge: No
article_type: original
author:
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. Transactions
of the American Mathematical Society. 2017;369(5):3741-3762. doi:10.1090/tran/6991
apa: Bauer, U., & Edelsbrunner, H. (2017). The Morse theory of Čech and delaunay
complexes. Transactions of the American Mathematical Society. American
Mathematical Society. https://doi.org/10.1090/tran/6991
chicago: Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and
Delaunay Complexes.” Transactions of the American Mathematical Society.
American Mathematical Society, 2017. https://doi.org/10.1090/tran/6991.
ieee: U. Bauer and H. Edelsbrunner, “The Morse theory of Čech and delaunay complexes,”
Transactions of the American Mathematical Society, vol. 369, no. 5. American
Mathematical Society, pp. 3741–3762, 2017.
ista: Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes.
Transactions of the American Mathematical Society. 369(5), 3741–3762.
mla: Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay
Complexes.” Transactions of the American Mathematical Society, vol. 369,
no. 5, American Mathematical Society, 2017, pp. 3741–62, doi:10.1090/tran/6991.
short: U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society
369 (2017) 3741–3762.
date_created: 2018-12-11T11:49:59Z
date_published: 2017-05-01T00:00:00Z
date_updated: 2023-09-20T12:05:56Z
day: '01'
department:
- _id: HeEd
doi: 10.1090/tran/6991
ec_funded: 1
external_id:
arxiv:
- '1312.1231'
isi:
- '000398030400024'
intvolume: ' 369'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1312.1231
month: '05'
oa: 1
oa_version: Preprint
page: 3741 - 3762
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Transactions of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '6311'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Morse theory of Čech and delaunay complexes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 369
year: '2017'
...
---
_id: '1073'
abstract:
- lang: eng
text: Let X and Y be finite simplicial sets (e.g. finite simplicial complexes),
both equipped with a free simplicial action of a finite group G. Assuming that
Y is d-connected and dimX≤2d, for some d≥1, we provide an algorithm that computes
the set of all equivariant homotopy classes of equivariant continuous maps |X|→|Y|;
the existence of such a map can be decided even for dimX≤2d+1. This yields the
first algorithm for deciding topological embeddability of a k-dimensional finite
simplicial complex into Rn under the condition k≤23n−1. More generally, we present
an algorithm that, given a lifting-extension problem satisfying an appropriate
stability assumption, computes the set of all homotopy classes of solutions. This
result is new even in the non-equivariant situation.
article_processing_charge: No
author:
- first_name: Martin
full_name: Čadek, Martin
last_name: Čadek
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
- first_name: Lukáš
full_name: Vokřínek, Lukáš
last_name: Vokřínek
citation:
ama: Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension
problem. Discrete & Computational Geometry. 2017;54(4):915-965. doi:10.1007/s00454-016-9855-6
apa: Čadek, M., Krcál, M., & Vokřínek, L. (2017). Algorithmic solvability of
the lifting extension problem. Discrete & Computational Geometry. Springer.
https://doi.org/10.1007/s00454-016-9855-6
chicago: Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability
of the Lifting Extension Problem.” Discrete & Computational Geometry.
Springer, 2017. https://doi.org/10.1007/s00454-016-9855-6.
ieee: M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting
extension problem,” Discrete & Computational Geometry, vol. 54, no.
4. Springer, pp. 915–965, 2017.
ista: Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting
extension problem. Discrete & Computational Geometry. 54(4), 915–965.
mla: Čadek, Martin, et al. “Algorithmic Solvability of the Lifting Extension Problem.”
Discrete & Computational Geometry, vol. 54, no. 4, Springer, 2017,
pp. 915–65, doi:10.1007/s00454-016-9855-6.
short: M. Čadek, M. Krcál, L. Vokřínek, Discrete & Computational Geometry 54
(2017) 915–965.
date_created: 2018-12-11T11:50:00Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T12:01:28Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s00454-016-9855-6
external_id:
isi:
- '000400072700008'
intvolume: ' 54'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1307.6444
month: '06'
oa: 1
oa_version: Submitted Version
page: 915 - 965
publication: Discrete & Computational Geometry
publication_identifier:
issn:
- '01795376'
publication_status: published
publisher: Springer
publist_id: '6309'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Algorithmic solvability of the lifting extension problem
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 54
year: '2017'
...
---
_id: '1065'
abstract:
- lang: eng
text: 'We consider the problem of reachability in pushdown graphs. We study the
problem for pushdown graphs with constant treewidth. Even for pushdown graphs
with treewidth 1, for the reachability problem we establish the following: (i)
the problem is PTIME-complete, and (ii) any subcubic algorithm for the problem
would contradict the k-clique conjecture and imply faster combinatorial algorithms
for cliques in graphs.'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
citation:
ama: Chatterjee K, Osang GF. Pushdown reachability with constant treewidth. Information
Processing Letters. 2017;122:25-29. doi:10.1016/j.ipl.2017.02.003
apa: Chatterjee, K., & Osang, G. F. (2017). Pushdown reachability with constant
treewidth. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2017.02.003
chicago: Chatterjee, Krishnendu, and Georg F Osang. “Pushdown Reachability with
Constant Treewidth.” Information Processing Letters. Elsevier, 2017. https://doi.org/10.1016/j.ipl.2017.02.003.
ieee: K. Chatterjee and G. F. Osang, “Pushdown reachability with constant treewidth,”
Information Processing Letters, vol. 122. Elsevier, pp. 25–29, 2017.
ista: Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth.
Information Processing Letters. 122, 25–29.
mla: Chatterjee, Krishnendu, and Georg F. Osang. “Pushdown Reachability with Constant
Treewidth.” Information Processing Letters, vol. 122, Elsevier, 2017, pp.
25–29, doi:10.1016/j.ipl.2017.02.003.
short: K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29.
date_created: 2018-12-11T11:49:57Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T12:08:18Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
- _id: HeEd
doi: 10.1016/j.ipl.2017.02.003
ec_funded: 1
external_id:
isi:
- '000399506600005'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:17Z
date_updated: 2019-10-15T07:44:51Z
file_id: '4998'
file_name: IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf
file_size: 247657
relation: main_file
file_date_updated: 2019-10-15T07:44:51Z
has_accepted_license: '1'
intvolume: ' 122'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 25 - 29
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Information Processing Letters
publication_identifier:
issn:
- '00200190'
publication_status: published
publisher: Elsevier
publist_id: '6323'
pubrep_id: '991'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pushdown reachability with constant treewidth
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 122
year: '2017'
...
---
_id: '1063'
abstract:
- lang: eng
text: Severe environmental change can drive a population extinct unless the population
adapts in time to the new conditions (“evolutionary rescue”). How does biparental
sexual reproduction influence the chances of population persistence compared to
clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele
model for adaptation in diploid species, where rescue is contingent on the establishment
of the mutant homozygote. Reproduction can occur by random mating, selfing, or
clonally. Random mating generates and destroys the rescue mutant; selfing is efficient
at generating it but at the same time depletes the heterozygote, which can lead
to a low mutant frequency in the standing genetic variation. Due to these (and
other) antagonistic effects, we find a nontrivial dependence of population survival
on the rate of sex/selfing, which is strongly influenced by the dominance coefficient
of the mutation before and after the environmental change. Importantly, since
mating with the wild‐type breaks the mutant homozygote up, a slow decay of the
wild‐type population size can impede rescue in randomly mating populations.
article_processing_charge: No
author:
- first_name: Hildegard
full_name: Uecker, Hildegard
id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
last_name: Uecker
orcid: 0000-0001-9435-2813
citation:
ama: Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations.
Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191
apa: Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal
populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191
chicago: Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and
Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191.
ieee: H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,”
Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.
ista: Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal
populations. Evolution. 71(4), 845–858.
mla: Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal
Populations.” Evolution, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58,
doi:10.1111/evo.13191.
short: H. Uecker, Evolution 71 (2017) 845–858.
date_created: 2018-12-11T11:49:57Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2023-09-20T12:10:32Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/evo.13191
ec_funded: 1
external_id:
isi:
- '000398545200003'
intvolume: ' 71'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://biorxiv.org/content/early/2016/10/14/081042
month: '04'
oa: 1
oa_version: Submitted Version
page: 845 - 858
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution
publication_identifier:
issn:
- '00143820'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6327'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionary rescue in randomly mating, selfing, and clonal populations
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 71
year: '2017'
...
---
_id: '1066'
abstract:
- lang: eng
text: "Simulation is an attractive alternative to language inclusion for automata
as it is an under-approximation of language inclusion, but usually has much lower
complexity. Simulation has also been extended in two orthogonal directions, namely,
(1) fair simulation, for simulation over specified set of infinite runs; and (2)
quantitative simulation, for simulation between weighted automata. While fair
trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial
time. For weighted automata, the (quantitative) language inclusion problem is
undecidable in general, whereas the (quantitative) simulation reduces to quantitative
games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we
study (quantitative) simulation for weighted automata with Büchi acceptance conditions,
i.e., we generalize fair simulation from non-weighted automata to weighted automata.
We show that imposing Büchi acceptance conditions on weighted automata changes
many fundamental properties of the simulation games, yet they still admit pseudo-polynomial
time algorithms."
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative fair simulation
games. Information and Computation. 2017;254(2):143-166. doi:10.1016/j.ic.2016.10.006
apa: Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2017). Quantitative
fair simulation games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2016.10.006
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner.
“Quantitative Fair Simulation Games.” Information and Computation. Elsevier,
2017. https://doi.org/10.1016/j.ic.2016.10.006.
ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair
simulation games,” Information and Computation, vol. 254, no. 2. Elsevier,
pp. 143–166, 2017.
ista: Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation
games. Information and Computation. 254(2), 143–166.
mla: Chatterjee, Krishnendu, et al. “Quantitative Fair Simulation Games.” Information
and Computation, vol. 254, no. 2, Elsevier, 2017, pp. 143–66, doi:10.1016/j.ic.2016.10.006.
short: K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation
254 (2017) 143–166.
date_created: 2018-12-11T11:49:58Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T12:07:48Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1016/j.ic.2016.10.006
ec_funded: 1
external_id:
isi:
- '000402025600002'
intvolume: ' 254'
isi: 1
issue: '2'
language:
- iso: eng
month: '06'
oa_version: None
page: 143 - 166
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Information and Computation
publication_status: published
publisher: Elsevier
publist_id: '6322'
quality_controlled: '1'
related_material:
record:
- id: '5428'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Quantitative fair simulation games
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 254
year: '2017'
...
---
_id: '1023'
abstract:
- lang: eng
text: We consider products of independent square non-Hermitian random matrices.
More precisely, let X1,…, Xn be independent N × N random matrices with independent
entries (real or complex with independent real and imaginary parts) with zero
mean and variance 1/N. Soshnikov-O’Rourke [19] and Götze-Tikhomirov [15] showed
that the empirical spectral distribution of the product of n random matrices with
iid entries converges to (equation found). We prove that if the entries of the
matrices X1,…, Xn are independent (but not necessarily identically distributed)
and satisfy uniform subexponential decay condition, then in the bulk the convergence
of the ESD of X1,…, Xn to (0.1) holds up to the scale N–1/2+ε.
article_number: '22'
article_processing_charge: No
author:
- first_name: Yuriy
full_name: Nemish, Yuriy
id: 4D902E6A-F248-11E8-B48F-1D18A9856A87
last_name: Nemish
orcid: 0000-0002-7327-856X
citation:
ama: Nemish Y. Local law for the product of independent non-Hermitian random matrices
with independent entries. Electronic Journal of Probability. 2017;22. doi:10.1214/17-EJP38
apa: Nemish, Y. (2017). Local law for the product of independent non-Hermitian random
matrices with independent entries. Electronic Journal of Probability. Institute
of Mathematical Statistics. https://doi.org/10.1214/17-EJP38
chicago: Nemish, Yuriy. “Local Law for the Product of Independent Non-Hermitian
Random Matrices with Independent Entries.” Electronic Journal of Probability.
Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/17-EJP38.
ieee: Y. Nemish, “Local law for the product of independent non-Hermitian random
matrices with independent entries,” Electronic Journal of Probability,
vol. 22. Institute of Mathematical Statistics, 2017.
ista: Nemish Y. 2017. Local law for the product of independent non-Hermitian random
matrices with independent entries. Electronic Journal of Probability. 22, 22.
mla: Nemish, Yuriy. “Local Law for the Product of Independent Non-Hermitian Random
Matrices with Independent Entries.” Electronic Journal of Probability,
vol. 22, 22, Institute of Mathematical Statistics, 2017, doi:10.1214/17-EJP38.
short: Y. Nemish, Electronic Journal of Probability 22 (2017).
date_created: 2018-12-11T11:49:44Z
date_published: 2017-02-06T00:00:00Z
date_updated: 2023-09-22T09:27:51Z
day: '06'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1214/17-EJP38
external_id:
isi:
- '000396611900022'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:29Z
date_updated: 2018-12-12T10:15:29Z
file_id: '5149'
file_name: IST-2017-802-v1+1_euclid.ejp.1487991681.pdf
file_size: 742275
relation: main_file
file_date_updated: 2018-12-12T10:15:29Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Electronic Journal of Probability
publication_identifier:
issn:
- '10836489'
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '6370'
pubrep_id: '802'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local law for the product of independent non-Hermitian random matrices with
independent 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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 22
year: '2017'
...
---
_id: '1022'
abstract:
- lang: eng
text: We introduce a multiscale topological description of the Megaparsec web-like
cosmic matter distribution. Betti numbers and topological persistence offer a
powerful means of describing the rich connectivity structure of the cosmic web
and of its multiscale arrangement of matter and galaxies. Emanating from algebraic
topology and Morse theory, Betti numbers and persistence diagrams represent an
extension and deepening of the cosmologically familiar topological genus measure
and the related geometric Minkowski functionals. In addition to a description
of the mathematical background, this study presents the computational procedure
for computing Betti numbers and persistence diagrams for density field filtrations.
The field may be computed starting from a discrete spatial distribution of galaxies
or simulation particles. The main emphasis of this study concerns an extensive
and systematic exploration of the imprint of different web-like morphologies and
different levels of multiscale clustering in the corresponding computed Betti
numbers and persistence diagrams. To this end, we use Voronoi clustering models
as templates for a rich variety of web-like configurations and the fractal-like
Soneira-Peebles models exemplify a range of multiscale configurations. We have
identified the clear imprint of cluster nodes, filaments, walls, and voids in
persistence diagrams, along with that of the nested hierarchy of structures in
multiscale point distributions. We conclude by outlining the potential of persistent
topology for understanding the connectivity structure of the cosmic web, in large
simulations of cosmic structure formation and in the challenging context of the
observed galaxy distribution in large galaxy surveys.
acknowledgement: Part of this work has been supported by the 7th Framework Programme
for Research of the European Commission, under FETOpen grant number 255827 (CGL
Computational Geometry Learning) and ERC advanced grant, URSAT (Understanding Random
Systems via Algebraic Topology) number 320422.
article_processing_charge: No
author:
- first_name: Pratyush
full_name: Pranav, Pratyush
last_name: Pranav
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Rien
full_name: Van De Weygaert, Rien
last_name: Van De Weygaert
- first_name: Gert
full_name: Vegter, Gert
last_name: Vegter
- first_name: Michael
full_name: Kerber, Michael
last_name: Kerber
- first_name: Bernard
full_name: Jones, Bernard
last_name: Jones
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: Pranav P, Edelsbrunner H, Van De Weygaert R, et al. The topology of the cosmic
web in terms of persistent Betti numbers. Monthly Notices of the Royal Astronomical
Society. 2017;465(4):4281-4310. doi:10.1093/mnras/stw2862
apa: Pranav, P., Edelsbrunner, H., Van De Weygaert, R., Vegter, G., Kerber, M.,
Jones, B., & Wintraecken, M. (2017). The topology of the cosmic web in terms
of persistent Betti numbers. Monthly Notices of the Royal Astronomical Society.
Oxford University Press. https://doi.org/10.1093/mnras/stw2862
chicago: Pranav, Pratyush, Herbert Edelsbrunner, Rien Van De Weygaert, Gert Vegter,
Michael Kerber, Bernard Jones, and Mathijs Wintraecken. “The Topology of the Cosmic
Web in Terms of Persistent Betti Numbers.” Monthly Notices of the Royal Astronomical
Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stw2862.
ieee: P. Pranav et al., “The topology of the cosmic web in terms of persistent
Betti numbers,” Monthly Notices of the Royal Astronomical Society, vol.
465, no. 4. Oxford University Press, pp. 4281–4310, 2017.
ista: Pranav P, Edelsbrunner H, Van De Weygaert R, Vegter G, Kerber M, Jones B,
Wintraecken M. 2017. The topology of the cosmic web in terms of persistent Betti
numbers. Monthly Notices of the Royal Astronomical Society. 465(4), 4281–4310.
mla: Pranav, Pratyush, et al. “The Topology of the Cosmic Web in Terms of Persistent
Betti Numbers.” Monthly Notices of the Royal Astronomical Society, vol.
465, no. 4, Oxford University Press, 2017, pp. 4281–310, doi:10.1093/mnras/stw2862.
short: P. Pranav, H. Edelsbrunner, R. Van De Weygaert, G. Vegter, M. Kerber, B.
Jones, M. Wintraecken, Monthly Notices of the Royal Astronomical Society 465 (2017)
4281–4310.
date_created: 2018-12-11T11:49:44Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-22T09:40:55Z
day: '01'
department:
- _id: HeEd
doi: 10.1093/mnras/stw2862
external_id:
isi:
- '000395170200039'
intvolume: ' 465'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.04519
month: '01'
oa: 1
oa_version: Submitted Version
page: 4281 - 4310
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
issn:
- '00358711'
publication_status: published
publisher: Oxford University Press
publist_id: '6373'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The topology of the cosmic web in terms of persistent Betti numbers
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 465
year: '2017'
...
---
_id: '1026'
abstract:
- lang: eng
text: The optogenetic revolution enabled spatially-precise and temporally-precise
control over protein function, signaling pathway activation, and animal behavior
with tremendous success in the dissection of signaling networks and neural circuits.
Very recently, optogenetic methods have been paired with optical reporters in
novel drug screening platforms. In these all-optical platforms, light remotely
activated ion channels and kinases thereby obviating the use of electrophysiology
or reagents. Consequences were remarkable operational simplicity, throughput,
and cost-effectiveness that culminated in the identification of new drug candidates.
These blueprints for all-optical assays also revealed potential pitfalls and inspire
all-optical variants of other screens, such as those that aim at better understanding
dynamic drug action or orphan protein function.
acknowledgement: This work was supported by grants of the European Union Seventh Framework
Programme (CIG-303564), the Human Frontier Science Program (RGY0084_2012), and the
Austrian Science Fund FWF (W1232 MolecularDrugTargets).
article_processing_charge: No
article_type: original
author:
- first_name: Viviana
full_name: Agus, Viviana
last_name: Agus
- 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: 'Agus V, Janovjak HL. Optogenetic methods in drug screening: Technologies and
applications. Current Opinion in Biotechnology. 2017;48:8-14. doi:10.1016/j.copbio.2017.02.006'
apa: 'Agus, V., & Janovjak, H. L. (2017). Optogenetic methods in drug screening:
Technologies and applications. Current Opinion in Biotechnology. Elsevier.
https://doi.org/10.1016/j.copbio.2017.02.006'
chicago: 'Agus, Viviana, and Harald L Janovjak. “Optogenetic Methods in Drug Screening:
Technologies and Applications.” Current Opinion in Biotechnology. Elsevier,
2017. https://doi.org/10.1016/j.copbio.2017.02.006.'
ieee: 'V. Agus and H. L. Janovjak, “Optogenetic methods in drug screening: Technologies
and applications,” Current Opinion in Biotechnology, vol. 48. Elsevier,
pp. 8–14, 2017.'
ista: 'Agus V, Janovjak HL. 2017. Optogenetic methods in drug screening: Technologies
and applications. Current Opinion in Biotechnology. 48, 8–14.'
mla: 'Agus, Viviana, and Harald L. Janovjak. “Optogenetic Methods in Drug Screening:
Technologies and Applications.” Current Opinion in Biotechnology, vol.
48, Elsevier, 2017, pp. 8–14, doi:10.1016/j.copbio.2017.02.006.'
short: V. Agus, H.L. Janovjak, Current Opinion in Biotechnology 48 (2017) 8–14.
date_created: 2018-12-11T11:49:45Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-09-22T09:26:06Z
day: '01'
department:
- _id: HaJa
doi: 10.1016/j.copbio.2017.02.006
ec_funded: 1
external_id:
isi:
- '000418313200003'
intvolume: ' 48'
isi: 1
language:
- iso: eng
month: '12'
oa_version: None
page: 8 - 14
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors (HFSP Young Investigator)
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
- _id: 255A6082-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Current Opinion in Biotechnology
publication_identifier:
issn:
- '09581669'
publication_status: published
publisher: Elsevier
publist_id: '6365'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Optogenetic methods in drug screening: Technologies and applications'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 48
year: '2017'
...
---
_id: '1020'
abstract:
- lang: eng
text: Cellulose is the most abundant biopolymer on Earth. Cellulose fibers, such
as the one extracted form cotton or woodpulp, have been used by humankind for
hundreds of years to make textiles and paper. Here we show how, by engineering
light-matter interaction, we can optimize light scattering using exclusively cellulose
nanocrystals. The produced material is sustainable, biocompatible, and when compared
to ordinary microfiber-based paper, it shows enhanced scattering strength (×4),
yielding a transport mean free path as low as 3.5 μm in the visible light range.
The experimental results are in a good agreement with the theoretical predictions
obtained with a diffusive model for light propagation.
acknowledgement: This research was funded by the EPSRC (EP/M027961/1), the Leverhulme
Trust (RPG-2014-238), Royal Society (RG140457), the BBSRC David Phillips fellowship
(BB/K014617/1), and the European Research Council (ERC-2014-STG H2020 639088). All
data created during this research are provided in full in the results section and
Supporting Information. They are openly available from figshare and can be accessed
at ref 30.
article_processing_charge: No
author:
- first_name: Soraya
full_name: Caixeiro, Soraya
last_name: Caixeiro
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Olimpia
full_name: Onelli, Olimpia
last_name: Onelli
- first_name: Silvia
full_name: Vignolini, Silvia
last_name: Vignolini
- first_name: Riccardo
full_name: Sapienza, Riccardo
last_name: Sapienza
citation:
ama: Caixeiro S, Peruzzo M, Onelli O, Vignolini S, Sapienza R. Disordered cellulose
based nanostructures for enhanced light scattering. ACS Applied Materials and
Interfaces. 2017;9(9):7885-7890. doi:10.1021/acsami.6b15986
apa: Caixeiro, S., Peruzzo, M., Onelli, O., Vignolini, S., & Sapienza, R. (2017).
Disordered cellulose based nanostructures for enhanced light scattering. ACS
Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.6b15986
chicago: Caixeiro, Soraya, Matilda Peruzzo, Olimpia Onelli, Silvia Vignolini, and
Riccardo Sapienza. “Disordered Cellulose Based Nanostructures for Enhanced Light
Scattering.” ACS Applied Materials and Interfaces. American Chemical Society,
2017. https://doi.org/10.1021/acsami.6b15986.
ieee: S. Caixeiro, M. Peruzzo, O. Onelli, S. Vignolini, and R. Sapienza, “Disordered
cellulose based nanostructures for enhanced light scattering,” ACS Applied
Materials and Interfaces, vol. 9, no. 9. American Chemical Society, pp. 7885–7890,
2017.
ista: Caixeiro S, Peruzzo M, Onelli O, Vignolini S, Sapienza R. 2017. Disordered
cellulose based nanostructures for enhanced light scattering. ACS Applied Materials
and Interfaces. 9(9), 7885–7890.
mla: Caixeiro, Soraya, et al. “Disordered Cellulose Based Nanostructures for Enhanced
Light Scattering.” ACS Applied Materials and Interfaces, vol. 9, no. 9,
American Chemical Society, 2017, pp. 7885–90, doi:10.1021/acsami.6b15986.
short: S. Caixeiro, M. Peruzzo, O. Onelli, S. Vignolini, R. Sapienza, ACS Applied
Materials and Interfaces 9 (2017) 7885–7890.
date_created: 2018-12-11T11:49:44Z
date_published: 2017-03-08T00:00:00Z
date_updated: 2023-09-22T09:40:14Z
day: '08'
department:
- _id: JoFi
doi: 10.1021/acsami.6b15986
external_id:
isi:
- '000396186000002'
intvolume: ' 9'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.01415
month: '03'
oa: 1
oa_version: Submitted Version
page: 7885 - 7890
publication: ACS Applied Materials and Interfaces
publication_identifier:
issn:
- '19448244'
publication_status: published
publisher: American Chemical Society
publist_id: '6372'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Disordered cellulose based nanostructures for enhanced light scattering
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 9
year: '2017'
...
---
_id: '1021'
abstract:
- lang: eng
text: Most flows in nature and engineering are turbulent because of their large
velocities and spatial scales. Laboratory experiments on rotating quasi-Keplerian
flows, for which the angular velocity decreases radially but the angular momentum
increases, are however laminar at Reynolds numbers exceeding one million. This
is in apparent contradiction to direct numerical simulations showing that in these
experiments turbulence transition is triggered by the axial boundaries. We here
show numerically that as the Reynolds number increases, turbulence becomes progressively
confined to the boundary layers and the flow in the bulk fully relaminarizes.
Our findings support that turbulence is unlikely to occur in isothermal constant-density
quasi-Keplerian flows.
article_processing_charge: No
author:
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Lopez Alonso JM, Avila M. Boundary layer turbulence in experiments on quasi
Keplerian flows. Journal of Fluid Mechanics. 2017;817:21-34. doi:10.1017/jfm.2017.109
apa: Lopez Alonso, J. M., & Avila, M. (2017). Boundary layer turbulence in experiments
on quasi Keplerian flows. Journal of Fluid Mechanics. Cambridge University
Press. https://doi.org/10.1017/jfm.2017.109
chicago: Lopez Alonso, Jose M, and Marc Avila. “Boundary Layer Turbulence in Experiments
on Quasi Keplerian Flows.” Journal of Fluid Mechanics. Cambridge University
Press, 2017. https://doi.org/10.1017/jfm.2017.109.
ieee: J. M. Lopez Alonso and M. Avila, “Boundary layer turbulence in experiments
on quasi Keplerian flows,” Journal of Fluid Mechanics, vol. 817. Cambridge
University Press, pp. 21–34, 2017.
ista: Lopez Alonso JM, Avila M. 2017. Boundary layer turbulence in experiments on
quasi Keplerian flows. Journal of Fluid Mechanics. 817, 21–34.
mla: Lopez Alonso, Jose M., and Marc Avila. “Boundary Layer Turbulence in Experiments
on Quasi Keplerian Flows.” Journal of Fluid Mechanics, vol. 817, Cambridge
University Press, 2017, pp. 21–34, doi:10.1017/jfm.2017.109.
short: J.M. Lopez Alonso, M. Avila, Journal of Fluid Mechanics 817 (2017) 21–34.
date_created: 2018-12-11T11:49:44Z
date_published: 2017-04-25T00:00:00Z
date_updated: 2023-09-22T09:39:46Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2017.109
external_id:
isi:
- '000398179100006'
intvolume: ' 817'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.05527
month: '04'
oa: 1
oa_version: Submitted Version
page: 21 - 34
project:
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
publication: Journal of Fluid Mechanics
publication_identifier:
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
publist_id: '6371'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Boundary layer turbulence in experiments on quasi Keplerian flows
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 817
year: '2017'
...
---
_id: '1025'
abstract:
- lang: eng
text: Many organ surfaces are covered by a protective epithelial-cell layer. It
emerges that such layers are maintained by cell stretching that triggers cell
division mediated by the force-sensitive ion-channel protein Piezo1. See Letter
p.118
article_processing_charge: No
author:
- 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: 'Heisenberg C-PJ. Cell biology: Stretched divisions. Nature. 2017;543(7643):43-44.
doi:10.1038/nature21502'
apa: 'Heisenberg, C.-P. J. (2017). Cell biology: Stretched divisions. Nature.
Nature Publishing Group. https://doi.org/10.1038/nature21502'
chicago: 'Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature.
Nature Publishing Group, 2017. https://doi.org/10.1038/nature21502.'
ieee: 'C.-P. J. Heisenberg, “Cell biology: Stretched divisions,” Nature,
vol. 543, no. 7643. Nature Publishing Group, pp. 43–44, 2017.'
ista: 'Heisenberg C-PJ. 2017. Cell biology: Stretched divisions. Nature. 543(7643),
43–44.'
mla: 'Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature,
vol. 543, no. 7643, Nature Publishing Group, 2017, pp. 43–44, doi:10.1038/nature21502.'
short: C.-P.J. Heisenberg, Nature 543 (2017) 43–44.
date_created: 2018-12-11T11:49:45Z
date_published: 2017-03-02T00:00:00Z
date_updated: 2023-09-22T09:26:59Z
day: '02'
department:
- _id: CaHe
doi: 10.1038/nature21502
external_id:
isi:
- '000395671500025'
intvolume: ' 543'
isi: 1
issue: '7643'
language:
- iso: eng
month: '03'
oa_version: None
page: 43 - 44
publication: Nature
publication_identifier:
issn:
- '00280836'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6367'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Cell biology: Stretched divisions'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 543
year: '2017'
...
---
_id: '1017'
abstract:
- lang: eng
text: The development of the vertebrate central nervous system is reliant on a complex
cascade of biological processes that include mitotic division, relocation of migrating
neurons, and the extension of dendritic and axonal processes. Each of these cellular
events requires the diverse functional repertoire of the microtubule cytoskeleton
for the generation of forces, assembly of macromolecular complexes and transport
of molecules and organelles. The tubulins are a multi-gene family that encode
for the constituents of microtubules, and have been implicated in a spectrum of
neurological disorders. Evidence is building that different tubulins tune the
functional properties of the microtubule cytoskeleton dependent on the cell type,
developmental profile and subcellular localisation. Here we review of the origins
of the functional specification of the tubulin gene family in the developing brain
at a transcriptional, translational, and post-transcriptional level. We remind
the reader that tubulins are not just loading controls for your average Western
blot.
article_processing_charge: No
author:
- first_name: Martin
full_name: Breuss, Martin
last_name: Breuss
- first_name: Ines
full_name: Leca, Ines
last_name: Leca
- first_name: Thomas
full_name: Gstrein, Thomas
last_name: Gstrein
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: David
full_name: Keays, David
last_name: Keays
citation:
ama: 'Breuss M, Leca I, Gstrein T, Hansen AH, Keays D. Tubulins and brain development:
The origins of functional specification. Molecular and Cellular Neuroscience.
2017;84:58-67. doi:10.1016/j.mcn.2017.03.002'
apa: 'Breuss, M., Leca, I., Gstrein, T., Hansen, A. H., & Keays, D. (2017).
Tubulins and brain development: The origins of functional specification. Molecular
and Cellular Neuroscience. Academic Press. https://doi.org/10.1016/j.mcn.2017.03.002'
chicago: 'Breuss, Martin, Ines Leca, Thomas Gstrein, Andi H Hansen, and David Keays.
“Tubulins and Brain Development: The Origins of Functional Specification.” Molecular
and Cellular Neuroscience. Academic Press, 2017. https://doi.org/10.1016/j.mcn.2017.03.002.'
ieee: 'M. Breuss, I. Leca, T. Gstrein, A. H. Hansen, and D. Keays, “Tubulins and
brain development: The origins of functional specification,” Molecular and
Cellular Neuroscience, vol. 84. Academic Press, pp. 58–67, 2017.'
ista: 'Breuss M, Leca I, Gstrein T, Hansen AH, Keays D. 2017. Tubulins and brain
development: The origins of functional specification. Molecular and Cellular Neuroscience.
84, 58–67.'
mla: 'Breuss, Martin, et al. “Tubulins and Brain Development: The Origins of Functional
Specification.” Molecular and Cellular Neuroscience, vol. 84, Academic
Press, 2017, pp. 58–67, doi:10.1016/j.mcn.2017.03.002.'
short: M. Breuss, I. Leca, T. Gstrein, A.H. Hansen, D. Keays, Molecular and Cellular
Neuroscience 84 (2017) 58–67.
date_created: 2018-12-11T11:49:42Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2023-09-22T09:42:15Z
day: '01'
ddc:
- '571'
department:
- _id: SiHi
doi: 10.1016/j.mcn.2017.03.002
external_id:
isi:
- '000415140700007'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:19Z
date_updated: 2018-12-12T10:09:19Z
file_id: '4742'
file_name: IST-2017-806-v1+2_1-s2.0-S1044743116302500-main_1_.pdf
file_size: 1436377
relation: main_file
file_date_updated: 2018-12-12T10:09:19Z
has_accepted_license: '1'
intvolume: ' 84'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: 58 - 67
publication: Molecular and Cellular Neuroscience
publication_identifier:
issn:
- '10447431'
publication_status: published
publisher: Academic Press
publist_id: '6377'
pubrep_id: '806'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Tubulins and brain development: The origins of functional specification'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 84
year: '2017'
...
---
_id: '1015'
abstract:
- lang: eng
text: 'Vortices are commonly observed in the context of classical hydrodynamics:
from whirlpools after stirring the coffee in a cup to a violent atmospheric phenomenon
such as a tornado, all classical vortices are characterized by an arbitrary circulation
value of the local velocity field. On the other hand the appearance of vortices
with quantized circulation represents one of the fundamental signatures of macroscopic
quantum phenomena. In two-dimensional superfluids quantized vortices play a key
role in determining finite-temperature properties, as the superfluid phase and
the normal state are separated by a vortex unbinding transition, the Berezinskii-Kosterlitz-Thouless
transition. Very recent experiments with two-dimensional superfluid fermions motivate
the present work: we present theoretical results based on the renormalization
group showing that the universal jump of the superfluid density and the critical
temperature crucially depend on the interaction strength, providing a strong benchmark
for forthcoming investigations.'
article_number: '45702'
article_processing_charge: No
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Luca
full_name: Salasnich, Luca
last_name: Salasnich
citation:
ama: Bighin G, Salasnich L. Vortices and antivortices in two-dimensional ultracold
Fermi gases. Scientific Reports. 2017;7. doi:10.1038/srep45702
apa: Bighin, G., & Salasnich, L. (2017). Vortices and antivortices in two-dimensional
ultracold Fermi gases. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep45702
chicago: Bighin, Giacomo, and Luca Salasnich. “Vortices and Antivortices in Two-Dimensional
Ultracold Fermi Gases.” Scientific Reports. Nature Publishing Group, 2017.
https://doi.org/10.1038/srep45702.
ieee: G. Bighin and L. Salasnich, “Vortices and antivortices in two-dimensional
ultracold Fermi gases,” Scientific Reports, vol. 7. Nature Publishing Group,
2017.
ista: Bighin G, Salasnich L. 2017. Vortices and antivortices in two-dimensional
ultracold Fermi gases. Scientific Reports. 7, 45702.
mla: Bighin, Giacomo, and Luca Salasnich. “Vortices and Antivortices in Two-Dimensional
Ultracold Fermi Gases.” Scientific Reports, vol. 7, 45702, Nature Publishing
Group, 2017, doi:10.1038/srep45702.
short: G. Bighin, L. Salasnich, Scientific Reports 7 (2017).
date_created: 2018-12-11T11:49:42Z
date_published: 2017-04-04T00:00:00Z
date_updated: 2023-09-22T09:43:10Z
day: '04'
ddc:
- '539'
department:
- _id: MiLe
doi: 10.1038/srep45702
external_id:
isi:
- '000398148100001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:32Z
date_updated: 2018-12-12T10:12:32Z
file_id: '4950'
file_name: IST-2017-809-v1+1_srep45702.pdf
file_size: 478289
relation: main_file
file_date_updated: 2018-12-12T10:12:32Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_identifier:
issn:
- '20452322'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6380'
pubrep_id: '809'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Vortices and antivortices in two-dimensional ultracold Fermi gases
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2017'
...
---
_id: '1016'
abstract:
- lang: eng
text: The integrity and dynamic properties of the microtubule cytoskeleton are indispensable
for the development of the mammalian brain. Consequently, mutations in the genes
that encode the structural component (the α/β-tubulin heterodimer) can give rise
to severe, sporadic neurodevelopmental disorders. These are commonly referred
to as the tubulinopathies. Here we report the addition of recessive quadrupedalism,
also known as Uner Tan syndrome (UTS), to the growing list of diseases caused
by tubulin variants. Analysis of a consanguineous UTS family identified a biallelic
TUBB2B mutation, resulting in a p.R390Q amino acid substitution. In addition to
the identifying quadrupedal locomotion, all three patients showed severe cerebellar
hypoplasia. None, however, displayed the basal ganglia malformations typically
associated with TUBB2B mutations. Functional analysis of the R390Q substitution
revealed that it did not affect the ability of β-tubulin to fold or become assembled
into the α/β-heterodimer, nor did it influence the incorporation of mutant-containing
heterodimers into microtubule polymers. The 390Q mutation in S. cerevisiae TUB2
did not affect growth under basal conditions, but did result in increased sensitivity
to microtubule-depolymerizing drugs, indicative of a mild impact of this mutation
on microtubule function. The TUBB2B mutation described here represents an unusual
recessive mode of inheritance for missense-mediated tubulinopathies and reinforces
the sensitivity of the developing cerebellum to microtubule defects.
article_processing_charge: No
author:
- first_name: Martin
full_name: Breuss, Martin
last_name: Breuss
- first_name: Thai
full_name: Nguyen, Thai
last_name: Nguyen
- first_name: Anjana
full_name: Srivatsan, Anjana
last_name: Srivatsan
- first_name: Ines
full_name: Leca, Ines
last_name: Leca
- first_name: Guoling
full_name: Tian, Guoling
last_name: Tian
- first_name: Tanja
full_name: Fritz, Tanja
last_name: Fritz
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Damir
full_name: Musaev, Damir
last_name: Musaev
- first_name: Jennifer
full_name: Mcevoy Venneri, Jennifer
last_name: Mcevoy Venneri
- first_name: James
full_name: Kiely, James
last_name: Kiely
- first_name: Rasim
full_name: Rosti, Rasim
last_name: Rosti
- first_name: Eric
full_name: Scott, Eric
last_name: Scott
- first_name: Uner
full_name: Tan, Uner
last_name: Tan
- first_name: Richard
full_name: Kolodner, Richard
last_name: Kolodner
- first_name: Nicholas
full_name: Cowan, Nicholas
last_name: Cowan
- first_name: David
full_name: Keays, David
last_name: Keays
- first_name: Joseph
full_name: Gleeson, Joseph
last_name: Gleeson
citation:
ama: Breuss M, Nguyen T, Srivatsan A, et al. Uner Tan syndrome caused by a homozygous
TUBB2B mutation affecting microtubule stability. Human Molecular Genetics.
2017;26(2):258-269. doi:10.1093/hmg/ddw383
apa: Breuss, M., Nguyen, T., Srivatsan, A., Leca, I., Tian, G., Fritz, T., … Gleeson,
J. (2017). Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting
microtubule stability. Human Molecular Genetics. Oxford University Press.
https://doi.org/10.1093/hmg/ddw383
chicago: Breuss, Martin, Thai Nguyen, Anjana Srivatsan, Ines Leca, Guoling Tian,
Tanja Fritz, Andi H Hansen, et al. “Uner Tan Syndrome Caused by a Homozygous TUBB2B
Mutation Affecting Microtubule Stability.” Human Molecular Genetics. Oxford
University Press, 2017. https://doi.org/10.1093/hmg/ddw383.
ieee: M. Breuss et al., “Uner Tan syndrome caused by a homozygous TUBB2B
mutation affecting microtubule stability,” Human Molecular Genetics, vol.
26, no. 2. Oxford University Press, pp. 258–269, 2017.
ista: Breuss M, Nguyen T, Srivatsan A, Leca I, Tian G, Fritz T, Hansen AH, Musaev
D, Mcevoy Venneri J, Kiely J, Rosti R, Scott E, Tan U, Kolodner R, Cowan N, Keays
D, Gleeson J. 2017. Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting
microtubule stability. Human Molecular Genetics. 26(2), 258–269.
mla: Breuss, Martin, et al. “Uner Tan Syndrome Caused by a Homozygous TUBB2B Mutation
Affecting Microtubule Stability.” Human Molecular Genetics, vol. 26, no.
2, Oxford University Press, 2017, pp. 258–69, doi:10.1093/hmg/ddw383.
short: M. Breuss, T. Nguyen, A. Srivatsan, I. Leca, G. Tian, T. Fritz, A.H. Hansen,
D. Musaev, J. Mcevoy Venneri, J. Kiely, R. Rosti, E. Scott, U. Tan, R. Kolodner,
N. Cowan, D. Keays, J. Gleeson, Human Molecular Genetics 26 (2017) 258–269.
date_created: 2018-12-11T11:49:42Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-22T09:42:42Z
day: '01'
department:
- _id: SiHi
doi: 10.1093/hmg/ddw383
external_id:
isi:
- '000397066400002'
intvolume: ' 26'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 258 - 269
publication: Human Molecular Genetics
publication_identifier:
issn:
- '09646906'
publication_status: published
publisher: Oxford University Press
publist_id: '6379'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule
stability
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 26
year: '2017'
...
---
_id: '1018'
abstract:
- lang: eng
text: In plants, the multistep phosphorelay (MSP) pathway mediates a range of regulatory
processes, including those activated by cytokinins. The crosstalk between cytokinin
response and light is known for a long time. However, the molecular mechanism
underlying the interactionbetween light and cytokinin signaling remains elusive.
In the screen for upstream regulators we identified a LONG PALE HYPOCOTYL (LPH)
gene whose activity is indispensable for spatiotemporally correct expression of
CYTOKININ INDEPENDENT-1 (CKI1), encoding the constitutively active sensor histidine
kinase that activates MSP signaling. lph is a new allele of HEME OXYGENASE 1 (HY1)
which encodes the key protein in the biosynthesis of phytochromobilin, a cofactor
of photoconvertiblephytochromes. Our analysis confirmed the light-dependent regulation
oftheCKI1 expression pattern. We show that CKI1 expression is under the control
of phytochrome A (phyA), functioning as a dual (both positive and negative) regulator
of CKI1 expression, presumably via the phyA-regulated transcription factors PHYTOCHROME
INTERACTING FACTOR 3 (PIF3) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1). Changes in
CKI1 expression observed in lph/hy1-7 and phy mutants correlatewithmisregulation
of MSP signaling, changedcytokinin sensitivity and developmental aberrations,previously
shown to be associated with cytokinin and/or CKI1 action. Besides that, we demonstrate
novel role of phyA-dependent CKI1 expression in the hypocotyl elongation and hook
development during skotomorphogenesis. Based on these results, we propose that
the light-dependent regulation of CKI1 provides a plausible mechanistic link underlying
the well-known interaction between light- and cytokinin-controlled plant development.
article_processing_charge: No
author:
- first_name: Tereza
full_name: Dobisova, Tereza
last_name: Dobisova
- first_name: Vendula
full_name: Hrdinova, Vendula
last_name: Hrdinova
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Sarka
full_name: Michlickova, Sarka
last_name: Michlickova
- first_name: Ivana
full_name: Urbankova, Ivana
last_name: Urbankova
- first_name: Romana
full_name: Hejatkova, Romana
last_name: Hejatkova
- first_name: Petra
full_name: Zadnikova, Petra
last_name: Zadnikova
- first_name: Markéta
full_name: Pernisová, Markéta
last_name: Pernisová
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jan
full_name: Hejátko, Jan
last_name: Hejátko
citation:
ama: Dobisova T, Hrdinova V, Cuesta C, et al. Light regulated expression of sensor
histidine kinase CKI1 controls cytokinin related development. Plant Physiology.
2017;174(1):387-404. doi:10.1104/pp.16.01964
apa: Dobisova, T., Hrdinova, V., Cuesta, C., Michlickova, S., Urbankova, I., Hejatkova,
R., … Hejátko, J. (2017). Light regulated expression of sensor histidine kinase
CKI1 controls cytokinin related development. Plant Physiology. American
Society of Plant Biologists. https://doi.org/10.1104/pp.16.01964
chicago: Dobisova, Tereza, Vendula Hrdinova, Candela Cuesta, Sarka Michlickova,
Ivana Urbankova, Romana Hejatkova, Petra Zadnikova, Markéta Pernisová, Eva Benková,
and Jan Hejátko. “Light Regulated Expression of Sensor Histidine Kinase CKI1 Controls
Cytokinin Related Development.” Plant Physiology. American Society of Plant
Biologists, 2017. https://doi.org/10.1104/pp.16.01964.
ieee: T. Dobisova et al., “Light regulated expression of sensor histidine
kinase CKI1 controls cytokinin related development,” Plant Physiology,
vol. 174, no. 1. American Society of Plant Biologists, pp. 387–404, 2017.
ista: Dobisova T, Hrdinova V, Cuesta C, Michlickova S, Urbankova I, Hejatkova R,
Zadnikova P, Pernisová M, Benková E, Hejátko J. 2017. Light regulated expression
of sensor histidine kinase CKI1 controls cytokinin related development. Plant
Physiology. 174(1), 387–404.
mla: Dobisova, Tereza, et al. “Light Regulated Expression of Sensor Histidine Kinase
CKI1 Controls Cytokinin Related Development.” Plant Physiology, vol. 174,
no. 1, American Society of Plant Biologists, 2017, pp. 387–404, doi:10.1104/pp.16.01964.
short: T. Dobisova, V. Hrdinova, C. Cuesta, S. Michlickova, I. Urbankova, R. Hejatkova,
P. Zadnikova, M. Pernisová, E. Benková, J. Hejátko, Plant Physiology 174 (2017)
387–404.
date_created: 2018-12-11T11:49:43Z
date_published: 2017-05-17T00:00:00Z
date_updated: 2023-09-22T09:41:48Z
day: '17'
department:
- _id: EvBe
doi: 10.1104/pp.16.01964
external_id:
isi:
- '000402057200028'
intvolume: ' 174'
isi: 1
issue: '1'
language:
- iso: eng
month: '05'
oa_version: None
page: 387 - 404
publication: Plant Physiology
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6375'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Light regulated expression of sensor histidine kinase CKI1 controls cytokinin
related development
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 174
year: '2017'
...
---
_id: '1019'
abstract:
- lang: eng
text: As a consequence of its difference in copy number between males and females,
the X chromosome is subject to unique evolutionary forces and gene regulatory
mechanisms. Previous studies of Drosophila melanogaster have shown that the expression
of X-linked, testis-specific reporter genes is suppressed in the male germline.
However, it is not known whether this phenomenon is restricted to testis-expressed
genes or if it is a more general property of genes with tissue-specific expression,
which are also underrepresented on the X chromosome. To test this, we compared
the expression of three tissue-specific reporter genes (ovary, accessory gland
and Malpighian tubule) inserted at various autosomal and X-chromosomal locations.
In contrast to testis-specific reporter genes, we found no reduction of X-linked
expression in any of the other tissues. In accessory gland and Malpighian tubule,
we detected higher expression of the X-linked reporter genes, which suggests that
they are at least partially dosage compensated. We found no difference in the
tissue-specificity of X-linked and autosomal reporter genes. These findings indicate
that, in general, the X chromosome is not a detrimental environment for tissue-specific
gene expression and that the suppression of X-linked expression is limited to
the male germline.
article_processing_charge: No
author:
- first_name: Eliza
full_name: Argyridou, Eliza
last_name: Argyridou
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Annabella
full_name: Königer, Annabella
last_name: Königer
- first_name: John
full_name: Parsch, John
last_name: Parsch
citation:
ama: Argyridou E, Huylmans AK, Königer A, Parsch J. X-linkage is not a general inhibitor
of tissue-specific gene expression in Drosophila melanogaster. Heredity.
2017;119(1):27-34. doi:10.1038/hdy.2017.12
apa: Argyridou, E., Huylmans, A. K., Königer, A., & Parsch, J. (2017). X-linkage
is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.
Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2017.12
chicago: Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch. “X-Linkage
Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.”
Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2017.12.
ieee: E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “X-linkage is not
a general inhibitor of tissue-specific gene expression in Drosophila melanogaster,”
Heredity, vol. 119, no. 1. Nature Publishing Group, pp. 27–34, 2017.
ista: Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. X-linkage is not a general
inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity.
119(1), 27–34.
mla: Argyridou, Eliza, et al. “X-Linkage Is Not a General Inhibitor of Tissue-Specific
Gene Expression in Drosophila Melanogaster.” Heredity, vol. 119, no. 1,
Nature Publishing Group, 2017, pp. 27–34, doi:10.1038/hdy.2017.12.
short: E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, Heredity 119 (2017) 27–34.
date_created: 2018-12-11T11:49:43Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2023-09-22T09:41:21Z
day: '01'
department:
- _id: BeVi
doi: 10.1038/hdy.2017.12
external_id:
isi:
- '000405397800004'
intvolume: ' 119'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 27 - 34
publication: Heredity
publication_identifier:
issn:
- 0018067X
publication_status: published
publisher: Nature Publishing Group
publist_id: '6374'
quality_controlled: '1'
related_material:
record:
- id: '9861'
relation: research_data
status: public
scopus_import: '1'
status: public
title: X-linkage is not a general inhibitor of tissue-specific gene expression in
Drosophila melanogaster
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 119
year: '2017'
...
---
_id: '9861'
abstract:
- lang: eng
text: As a consequence of its difference in copy number between males and females,
the X chromosome is subject to unique evolutionary forces and gene regulatory
mechanisms. Previous studies of Drosophila melanogaster have shown that the expression
of X-linked, testis-specific reporter genes is suppressed in the male germline.
However, it is not known whether this phenomenon is restricted to testis-expressed
genes or if it is a more general property of genes with tissue-specific expression,
which are also underrepresented on the X chromosome. To test this, we compared
the expression of three tissue-specific reporter genes (ovary, accessory gland
and Malpighian tubule) inserted at various autosomal and X-chromosomal locations.
In contrast to testis-specific reporter genes, we found no reduction of X-linked
expression in any of the other tissues. In accessory gland and Malpighian tubule,
we detected higher expression of the X-linked reporter genes, which suggests that
they are at least partially dosage compensated. We found no difference in the
tissue-specificity of X-linked and autosomal reporter genes. These findings indicate
that, in general, the X chromosome is not a detrimental environment for tissue-specific
gene expression and that the suppression of X-linked expression is limited to
the male germline.
article_processing_charge: No
author:
- first_name: Eliza
full_name: Argyridou, Eliza
last_name: Argyridou
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Annabella
full_name: Königer, Annabella
last_name: Königer
- first_name: John
full_name: Parsch, John
last_name: Parsch
citation:
ama: 'Argyridou E, Huylmans AK, Königer A, Parsch J. Data from: X-linkage is not
a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.
2017. doi:10.5061/dryad.02f6r'
apa: 'Argyridou, E., Huylmans, A. K., Königer, A., & Parsch, J. (2017). Data
from: X-linkage is not a general inhibitor of tissue-specific gene expression
in Drosophila melanogaster. Dryad. https://doi.org/10.5061/dryad.02f6r'
chicago: 'Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch.
“Data from: X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression
in Drosophila Melanogaster.” Dryad, 2017. https://doi.org/10.5061/dryad.02f6r.'
ieee: 'E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “Data from: X-linkage
is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.”
Dryad, 2017.'
ista: 'Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. Data from: X-linkage
is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster,
Dryad, 10.5061/dryad.02f6r.'
mla: 'Argyridou, Eliza, et al. Data from: X-Linkage Is Not a General Inhibitor
of Tissue-Specific Gene Expression in Drosophila Melanogaster. Dryad, 2017,
doi:10.5061/dryad.02f6r.'
short: E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, (2017).
date_created: 2021-08-10T08:12:52Z
date_published: 2017-02-14T00:00:00Z
date_updated: 2023-09-22T09:41:20Z
day: '14'
department:
- _id: BeVi
doi: 10.5061/dryad.02f6r
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.02f6r
month: '02'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1019'
relation: used_in_publication
status: public
status: public
title: 'Data from: X-linkage is not a general inhibitor of tissue-specific gene expression
in Drosophila melanogaster'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '1006'
abstract:
- lang: eng
text: 'Background: The phenomenon of immune priming, i.e. enhanced protection following
a secondary exposure to a pathogen, has now been demonstrated in a wide range
of invertebrate species. Despite accumulating phenotypic evidence, knowledge of
its mechanistic underpinnings is currently very limited. Here we used the system
of the red flour beetle, Tribolium castaneum and the insect pathogen Bacillus
thuringiensis (Bt) to further our molecular understanding of the oral immune priming
phenomenon. We addressed how ingestion of bacterial cues (derived from spore supernatants)
of an orally pathogenic and non-pathogenic Bt strain affects gene expression upon
later challenge exposure, using a whole-transcriptome sequencing approach. Results:
Whereas gene expression of individuals primed with the orally non-pathogenic strain
showed minor changes to controls, we found that priming with the pathogenic strain
induced regulation of a large set of distinct genes, many of which are known immune
candidates. Intriguingly, the immune repertoire activated upon priming and subsequent
challenge qualitatively differed from the one mounted upon infection with Bt without
previous priming. Moreover, a large subset of priming-specific genes showed an
inverse regulation compared to their regulation upon challenge only. Conclusions:
Our data demonstrate that gene expression upon infection is strongly affected
by previous immune priming. We hypothesise that this shift in gene expression
indicates activation of a more targeted and efficient response towards a previously
encountered pathogen, in anticipation of potential secondary encounter.'
article_processing_charge: No
author:
- first_name: Jenny
full_name: Greenwood, Jenny
last_name: Greenwood
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Robert
full_name: Peuß, Robert
last_name: Peuß
- first_name: Sarah
full_name: Behrens, Sarah
last_name: Behrens
- first_name: Daniela
full_name: Essar, Daniela
last_name: Essar
- first_name: Philip
full_name: Rosenstiel, Philip
last_name: Rosenstiel
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
citation:
ama: Greenwood J, Milutinovic B, Peuß R, et al. Oral immune priming with Bacillus
thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae.
BMC Genomics. 2017;18(1):329. doi:10.1186/s12864-017-3705-7
apa: Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel,
P., … Kurtz, J. (2017). Oral immune priming with Bacillus thuringiensis induces
a shift in the gene expression of Tribolium castaneum larvae. BMC Genomics.
BioMed Central. https://doi.org/10.1186/s12864-017-3705-7
chicago: Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela
Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Oral Immune
Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of
Tribolium Castaneum Larvae.” BMC Genomics. BioMed Central, 2017. https://doi.org/10.1186/s12864-017-3705-7.
ieee: J. Greenwood et al., “Oral immune priming with Bacillus thuringiensis
induces a shift in the gene expression of Tribolium castaneum larvae,” BMC
Genomics, vol. 18, no. 1. BioMed Central, p. 329, 2017.
ista: Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg
H, Kurtz J. 2017. Oral immune priming with Bacillus thuringiensis induces a shift
in the gene expression of Tribolium castaneum larvae. BMC Genomics. 18(1), 329.
mla: Greenwood, Jenny, et al. “Oral Immune Priming with Bacillus Thuringiensis Induces
a Shift in the Gene Expression of Tribolium Castaneum Larvae.” BMC Genomics,
vol. 18, no. 1, BioMed Central, 2017, p. 329, doi:10.1186/s12864-017-3705-7.
short: J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel,
H. Schulenburg, J. Kurtz, BMC Genomics 18 (2017) 329.
date_created: 2018-12-11T11:49:39Z
date_published: 2017-04-26T00:00:00Z
date_updated: 2023-09-22T09:47:44Z
day: '26'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1186/s12864-017-3705-7
external_id:
isi:
- '000400625200004'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:46Z
date_updated: 2018-12-12T10:16:46Z
file_id: '5236'
file_name: IST-2017-814-v1+1_s12864-017-3705-7.pdf
file_size: 2379672
relation: main_file
file_date_updated: 2018-12-12T10:16:46Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '1'
language:
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month: '04'
oa: 1
oa_version: Published Version
page: '329'
publication: BMC Genomics
publication_identifier:
issn:
- '14712164'
publication_status: published
publisher: BioMed Central
publist_id: '6392'
pubrep_id: '814'
quality_controlled: '1'
related_material:
record:
- id: '9859'
relation: research_data
status: public
- id: '9860'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Oral immune priming with Bacillus thuringiensis induces a shift in the gene
expression of Tribolium castaneum larvae
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 18
year: '2017'
...
---
_id: '1011'
abstract:
- lang: eng
text: Pushdown systems (PDSs) and recursive state machines (RSMs), which are linearly
equivalent, are standard models for interprocedural analysis. Yet RSMs are more
convenient as they (a) explicitly model function calls and returns, and (b) specify
many natural parameters for algorithmic analysis, e.g., the number of entries
and exits. We consider a general framework where RSM transitions are labeled from
a semiring and path properties are algebraic with semiring operations, which can
model, e.g., interprocedural reachability and dataflow analysis problems. Our
main contributions are new algorithms for several fundamental problems. As compared
to a direct translation of RSMs to PDSs and the best-known existing bounds of
PDSs, our analysis algorithm improves the complexity for finite-height semirings
(that subsumes reachability and standard dataflow properties). We further consider
the problem of extracting distance values from the representation structures computed
by our algorithm, and give efficient algorithms that distinguish the complexity
of a one-time preprocessing from the complexity of each individual query. Another
advantage of our algorithm is that our improvements carry over to the concurrent
setting, where we improve the bestknown complexity for the context-bounded analysis
of concurrent RSMs. Finally, we provide a prototype implementation that gives
a significant speed-up on several benchmarks from the SLAM/SDV project.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
- first_name: Samarth
full_name: Mishra, Samarth
last_name: Mishra
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Kragl B, Mishra S, Pavlogiannis A. Faster algorithms for weighted
recursive state machines. In: Yang H, ed. Vol 10201. Springer; 2017:287-313. doi:10.1007/978-3-662-54434-1_11'
apa: 'Chatterjee, K., Kragl, B., Mishra, S., & Pavlogiannis, A. (2017). Faster
algorithms for weighted recursive state machines. In H. Yang (Ed.) (Vol. 10201,
pp. 287–313). Presented at the ESOP: European Symposium on Programming, Uppsala,
Sweden: Springer. https://doi.org/10.1007/978-3-662-54434-1_11'
chicago: Chatterjee, Krishnendu, Bernhard Kragl, Samarth Mishra, and Andreas Pavlogiannis.
“Faster Algorithms for Weighted Recursive State Machines.” edited by Hongseok
Yang, 10201:287–313. Springer, 2017. https://doi.org/10.1007/978-3-662-54434-1_11.
ieee: 'K. Chatterjee, B. Kragl, S. Mishra, and A. Pavlogiannis, “Faster algorithms
for weighted recursive state machines,” presented at the ESOP: European Symposium
on Programming, Uppsala, Sweden, 2017, vol. 10201, pp. 287–313.'
ista: 'Chatterjee K, Kragl B, Mishra S, Pavlogiannis A. 2017. Faster algorithms
for weighted recursive state machines. ESOP: European Symposium on Programming,
LNCS, vol. 10201, 287–313.'
mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Weighted Recursive
State Machines. Edited by Hongseok Yang, vol. 10201, Springer, 2017, pp. 287–313,
doi:10.1007/978-3-662-54434-1_11.
short: K. Chatterjee, B. Kragl, S. Mishra, A. Pavlogiannis, in:, H. Yang (Ed.),
Springer, 2017, pp. 287–313.
conference:
end_date: 2017-04-29
location: Uppsala, Sweden
name: 'ESOP: European Symposium on Programming'
start_date: 2017-04-22
date_created: 2018-12-11T11:49:41Z
date_published: 2017-03-19T00:00:00Z
date_updated: 2023-09-22T09:44:50Z
day: '19'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-662-54434-1_11
ec_funded: 1
editor:
- first_name: Hongseok
full_name: Yang, Hongseok
last_name: Yang
external_id:
isi:
- '000681702400011'
intvolume: ' 10201'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1701.04914
month: '03'
oa: 1
oa_version: Submitted Version
page: 287 - 313
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '6384'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Faster algorithms for weighted recursive state machines
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10201
year: '2017'
...
---
_id: '1004'
abstract:
- lang: eng
text: The fundamental tasks of the root system are, besides anchoring, mediating
interactions between plant and soil and providing the plant with water and nutrients.
The architecture of the root system is controlled by endogenous mechanisms that
constantly integrate environmental signals, such as availability of nutrients
and water. Extremely important for efficient soil exploitation and survival under
less favorable conditions is the developmental flexibility of the root system
that is largely determined by its postembryonic branching capacity. Modulation
of initiation and outgrowth of lateral roots provides roots with an exceptional
plasticity, allows optimal adjustment to underground heterogeneity, and enables
effective soil exploitation and use of resources. Here we discuss recent advances
in understanding the molecular mechanisms that shape the plant root system and
integrate external cues to adapt to the changing environment.
article_processing_charge: No
author:
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Ötvös K, Benková E. Spatiotemporal mechanisms of root branching. Current
Opinion in Genetics & Development. 2017;45:82-89. doi:10.1016/j.gde.2017.03.010
apa: Ötvös, K., & Benková, E. (2017). Spatiotemporal mechanisms of root branching.
Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2017.03.010
chicago: Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.”
Current Opinion in Genetics & Development. Elsevier, 2017. https://doi.org/10.1016/j.gde.2017.03.010.
ieee: K. Ötvös and E. Benková, “Spatiotemporal mechanisms of root branching,” Current
Opinion in Genetics & Development, vol. 45. Elsevier, pp. 82–89, 2017.
ista: Ötvös K, Benková E. 2017. Spatiotemporal mechanisms of root branching. Current
Opinion in Genetics & Development. 45, 82–89.
mla: Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.”
Current Opinion in Genetics & Development, vol. 45, Elsevier, 2017,
pp. 82–89, doi:10.1016/j.gde.2017.03.010.
short: K. Ötvös, E. Benková, Current Opinion in Genetics & Development 45 (2017)
82–89.
date_created: 2018-12-11T11:49:38Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2023-09-22T09:48:15Z
day: '01'
ddc:
- '575'
department:
- _id: EvBe
doi: 10.1016/j.gde.2017.03.010
external_id:
isi:
- '000404880400013'
pmid:
- '28391060'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T08:00:36Z
date_updated: 2019-04-17T08:00:36Z
file_id: '6336'
file_name: Otvos_Benkova_CurOpDevBiol_2017.pdf
file_size: 364133
relation: main_file
success: 1
file_date_updated: 2019-04-17T08:00:36Z
has_accepted_license: '1'
intvolume: ' 45'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 82 - 89
pmid: 1
project:
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
publication: Current Opinion in Genetics & Development
publication_identifier:
issn:
- 0959437X
publication_status: published
publisher: Elsevier
publist_id: '6394'
pubrep_id: '1017'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spatiotemporal mechanisms of root branching
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 45
year: '2017'
...
---
_id: '1010'
abstract:
- lang: eng
text: 'We prove a local law in the bulk of the spectrum for random Gram matrices
XX∗, a generalization of sample covariance matrices, where X is a large matrix
with independent, centered entries with arbitrary variances. The limiting eigenvalue
density that generalizes the Marchenko-Pastur law is determined by solving a system
of nonlinear equations. Our entrywise and averaged local laws are on the optimal
scale with the optimal error bounds. They hold both in the square case (hard edge)
and in the properly rectangular case (soft edge). In the latter case we also establish
a macroscopic gap away from zero in the spectrum of XX∗. '
article_number: '25'
article_processing_charge: No
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: Alt J, Erdös L, Krüger TH. Local law for random Gram matrices. Electronic
Journal of Probability. 2017;22. doi:10.1214/17-EJP42
apa: Alt, J., Erdös, L., & Krüger, T. H. (2017). Local law for random Gram matrices.
Electronic Journal of Probability. Institute of Mathematical Statistics.
https://doi.org/10.1214/17-EJP42
chicago: Alt, Johannes, László Erdös, and Torben H Krüger. “Local Law for Random
Gram Matrices.” Electronic Journal of Probability. Institute of Mathematical
Statistics, 2017. https://doi.org/10.1214/17-EJP42.
ieee: J. Alt, L. Erdös, and T. H. Krüger, “Local law for random Gram matrices,”
Electronic Journal of Probability, vol. 22. Institute of Mathematical Statistics,
2017.
ista: Alt J, Erdös L, Krüger TH. 2017. Local law for random Gram matrices. Electronic
Journal of Probability. 22, 25.
mla: Alt, Johannes, et al. “Local Law for Random Gram Matrices.” Electronic Journal
of Probability, vol. 22, 25, Institute of Mathematical Statistics, 2017, doi:10.1214/17-EJP42.
short: J. Alt, L. Erdös, T.H. Krüger, Electronic Journal of Probability 22 (2017).
date_created: 2018-12-11T11:49:40Z
date_published: 2017-03-08T00:00:00Z
date_updated: 2023-09-22T09:45:23Z
day: '08'
ddc:
- '510'
- '539'
department:
- _id: LaEr
doi: 10.1214/17-EJP42
ec_funded: 1
external_id:
arxiv:
- '1606.07353'
isi:
- '000396611900025'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:39Z
date_updated: 2018-12-12T10:13:39Z
file_id: '5024'
file_name: IST-2017-807-v1+1_euclid.ejp.1488942016.pdf
file_size: 639384
relation: main_file
file_date_updated: 2018-12-12T10:13:39Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Electronic Journal of Probability
publication_identifier:
issn:
- '10836489'
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '6386'
pubrep_id: '807'
quality_controlled: '1'
related_material:
record:
- id: '149'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Local law for random Gram matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 22
year: '2017'
...
---
_id: '1009'
abstract:
- lang: eng
text: A standard objective in partially-observable Markov decision processes (POMDPs)
is to find a policy that maximizes the expected discounted-sum payoff. However,
such policies may still permit unlikely but highly undesirable outcomes, which
is problematic especially in safety-critical applications. Recently, there has
been a surge of interest in POMDPs where the goal is to maximize the probability
to ensure that the payoff is at least a given threshold, but these approaches
do not consider any optimization beyond satisfying this threshold constraint.
In this work we go beyond both the “expectation” and “threshold” approaches and
consider a “guaranteed payoff optimization (GPO)” problem for POMDPs, where we
are given a threshold t and the objective is to find a policy σ such that a) each
possible outcome of σ yields a discounted-sum payoff of at least t, and b) the
expected discounted-sum payoff of σ is optimal (or near-optimal) among all policies
satisfying a). We present a practical approach to tackle the GPO problem and evaluate
it on standard POMDP benchmarks.
acknowledgement: 'he research leading to these results was supported by the Austrian
Science Fund (FWF) NFN Grant no. S11407-N23 (RiSE/SHiNE); two ERC Starting grants
(279307: Graph Games, 279499: inVEST); the Vienna Science and Tech- nology Fund
(WWTF) through project ICT15-003; and the People Programme (Marie Curie Actions)
of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant
agreement no. [291734].'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
- first_name: Guillermo
full_name: Pérez, Guillermo
last_name: Pérez
- first_name: Jean
full_name: Raskin, Jean
last_name: Raskin
- first_name: Djordje
full_name: Zikelic, Djordje
last_name: Zikelic
citation:
ama: 'Chatterjee K, Novotný P, Pérez G, Raskin J, Zikelic D. Optimizing expectation
with guarantees in POMDPs. In: Proceedings of the 31st AAAI Conference on Artificial
Intelligence. Vol 5. AAAI Press; 2017:3725-3732.'
apa: 'Chatterjee, K., Novotný, P., Pérez, G., Raskin, J., & Zikelic, D. (2017).
Optimizing expectation with guarantees in POMDPs. In Proceedings of the 31st
AAAI Conference on Artificial Intelligence (Vol. 5, pp. 3725–3732). San Francisco,
CA, United States: AAAI Press.'
chicago: Chatterjee, Krishnendu, Petr Novotný, Guillermo Pérez, Jean Raskin, and
Djordje Zikelic. “Optimizing Expectation with Guarantees in POMDPs.” In Proceedings
of the 31st AAAI Conference on Artificial Intelligence, 5:3725–32. AAAI Press,
2017.
ieee: K. Chatterjee, P. Novotný, G. Pérez, J. Raskin, and D. Zikelic, “Optimizing
expectation with guarantees in POMDPs,” in Proceedings of the 31st AAAI Conference
on Artificial Intelligence, San Francisco, CA, United States, 2017, vol. 5,
pp. 3725–3732.
ista: 'Chatterjee K, Novotný P, Pérez G, Raskin J, Zikelic D. 2017. Optimizing expectation
with guarantees in POMDPs. Proceedings of the 31st AAAI Conference on Artificial
Intelligence. AAAI: Conference on Artificial Intelligence vol. 5, 3725–3732.'
mla: Chatterjee, Krishnendu, et al. “Optimizing Expectation with Guarantees in POMDPs.”
Proceedings of the 31st AAAI Conference on Artificial Intelligence, vol.
5, AAAI Press, 2017, pp. 3725–32.
short: K. Chatterjee, P. Novotný, G. Pérez, J. Raskin, D. Zikelic, in:, Proceedings
of the 31st AAAI Conference on Artificial Intelligence, AAAI Press, 2017, pp.
3725–3732.
conference:
end_date: 2017-02-10
location: San Francisco, CA, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2017-02-04
date_created: 2018-12-11T11:49:40Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-22T09:46:41Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
external_id:
isi:
- '000485630703107'
intvolume: ' 5'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.aaai.org/ocs/index.php/AAAI/AAAI17/paper/download/14354/14092
month: '01'
oa: 1
oa_version: Submitted Version
page: 3725 - 3732
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Proceedings of the 31st AAAI Conference on Artificial Intelligence
publication_status: published
publisher: AAAI Press
publist_id: '6387'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimizing expectation with guarantees in POMDPs
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 5
year: '2017'
...
---
_id: '9859'
abstract:
- lang: eng
text: 'Lists of all differentially expressed genes in the different priming-challenge
treatments (compared to the fully naïve control; xlsx file). Relevant columns
include the following: sample_1 and sample_2 – treatment groups being compared;
Normalised FPKM sample_1 and sample_2 – FPKM of samples being compared; log2(fold_change)
– log2(FPKM sample 2/FPKM sample 1), i.e. negative means sample 1 upregulated
compared with sample 2, positive means sample 2 upregulated compared with sample
1; cuffdiff test_statistic – test statistic of differential expression test; p_value
– p-value of differential expression test; q_value (FDR correction) – adjusted
P-value of differential expression test. (XLSX 598 kb)'
article_processing_charge: No
author:
- first_name: Jenny
full_name: Greenwood, Jenny
last_name: Greenwood
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Robert
full_name: Peuß, Robert
last_name: Peuß
- first_name: Sarah
full_name: Behrens, Sarah
last_name: Behrens
- first_name: Daniela
full_name: Essar, Daniela
last_name: Essar
- first_name: Philip
full_name: Rosenstiel, Philip
last_name: Rosenstiel
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
citation:
ama: 'Greenwood J, Milutinovic B, Peuß R, et al. Additional file 1: Table S1. of
Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression
of Tribolium castaneum larvae. 2017. doi:10.6084/m9.figshare.c.3756974_d1.v1'
apa: 'Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel,
P., … Kurtz, J. (2017). Additional file 1: Table S1. of Oral immune priming with
Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum
larvae. Springer Nature. https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1'
chicago: 'Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela
Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Additional
File 1: Table S1. of Oral Immune Priming with Bacillus Thuringiensis Induces a
Shift in the Gene Expression of Tribolium Castaneum Larvae.” Springer Nature,
2017. https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1.'
ieee: 'J. Greenwood et al., “Additional file 1: Table S1. of Oral immune
priming with Bacillus thuringiensis induces a shift in the gene expression of
Tribolium castaneum larvae.” Springer Nature, 2017.'
ista: 'Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg
H, Kurtz J. 2017. Additional file 1: Table S1. of Oral immune priming with Bacillus
thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae,
Springer Nature, 10.6084/m9.figshare.c.3756974_d1.v1.'
mla: 'Greenwood, Jenny, et al. Additional File 1: Table S1. of Oral Immune Priming
with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium
Castaneum Larvae. Springer Nature, 2017, doi:10.6084/m9.figshare.c.3756974_d1.v1.'
short: J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel,
H. Schulenburg, J. Kurtz, (2017).
date_created: 2021-08-10T07:59:02Z
date_published: 2017-04-26T00:00:00Z
date_updated: 2023-09-22T09:47:44Z
day: '26'
department:
- _id: SyCr
doi: 10.6084/m9.figshare.c.3756974_d1.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1
month: '04'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '1006'
relation: used_in_publication
status: public
status: public
title: 'Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis
induces a shift in the gene expression of Tribolium castaneum larvae'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9860'
article_processing_charge: No
author:
- first_name: Jenny
full_name: Greenwood, Jenny
last_name: Greenwood
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Robert
full_name: Peuß, Robert
last_name: Peuß
- first_name: Sarah
full_name: Behrens, Sarah
last_name: Behrens
- first_name: Daniela
full_name: Essar, Daniela
last_name: Essar
- first_name: Philip
full_name: Rosenstiel, Philip
last_name: Rosenstiel
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
citation:
ama: 'Greenwood J, Milutinovic B, Peuß R, et al. Additional file 5: Table S3. of
Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression
of Tribolium castaneum larvae. 2017. doi:10.6084/m9.figshare.c.3756974_d5.v1'
apa: 'Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel,
P., … Kurtz, J. (2017). Additional file 5: Table S3. of Oral immune priming with
Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum
larvae. Springer Nature. https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1'
chicago: 'Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela
Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Additional
File 5: Table S3. of Oral Immune Priming with Bacillus Thuringiensis Induces a
Shift in the Gene Expression of Tribolium Castaneum Larvae.” Springer Nature,
2017. https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1.'
ieee: 'J. Greenwood et al., “Additional file 5: Table S3. of Oral immune
priming with Bacillus thuringiensis induces a shift in the gene expression of
Tribolium castaneum larvae.” Springer Nature, 2017.'
ista: 'Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg
H, Kurtz J. 2017. Additional file 5: Table S3. of Oral immune priming with Bacillus
thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae,
Springer Nature, 10.6084/m9.figshare.c.3756974_d5.v1.'
mla: 'Greenwood, Jenny, et al. Additional File 5: Table S3. of Oral Immune Priming
with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium
Castaneum Larvae. Springer Nature, 2017, doi:10.6084/m9.figshare.c.3756974_d5.v1.'
short: J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel,
H. Schulenburg, J. Kurtz, (2017).
date_created: 2021-08-10T08:07:12Z
date_published: 2017-04-26T00:00:00Z
date_updated: 2023-09-22T09:47:44Z
day: '26'
department:
- _id: SyCr
doi: 10.6084/m9.figshare.c.3756974_d5.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1
month: '04'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '1006'
relation: used_in_publication
status: public
status: public
title: 'Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis
induces a shift in the gene expression of Tribolium castaneum larvae'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '1002'
abstract:
- lang: eng
text: " We present an interactive design system to create functional mechanical
\ objects. Our computational approach allows novice users to retarget an existing
mechanical template to a user-specified input shape. Our proposed representation
for a mechanical template encodes a parameterized mechanism, mechanical constraints
that ensure a physically valid configuration, spatial relationships of mechanical
parts to the user-provided shape, and functional constraints that specify an intended
functionality. We provide an intuitive interface and optimization-in-the-loop
approach for finding a valid configuration of the mechanism and the shape to
ensure that higher-level functional goals are met. Our algorithm interactively
optimizes the mechanism while the user manipulates the placement of mechanical
components and the shape. Our system allows users to efficiently explore various
design choices and to synthesize customized mechanical objects that can be fabricated
with rapid prototyping technologies. We demonstrate the efficacy of our approach
by retargeting various mechanical templates to different shapes and fabricating
the resulting functional mechanical objects.\r\n"
alternative_title:
- ACM Transactions on Graphics
article_number: '81'
article_processing_charge: No
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: Duygu
full_name: Ceylan, Duygu
last_name: Ceylan
- first_name: Wilmot
full_name: Li, Wilmot
last_name: Li
- 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, Ceylan D, Li W, Bickel B. Functionality-aware retargeting
of mechanisms to 3D shapes. In: Vol 36. ACM; 2017. doi:10.1145/3072959.3073710'
apa: 'Zhang, R., Auzinger, T., Ceylan, D., Li, W., & Bickel, B. (2017). Functionality-aware
retargeting of mechanisms to 3D shapes (Vol. 36). Presented at the SIGGRAPH: Computer
Graphics and Interactive Techniques, Los Angeles, CA, United States : ACM. https://doi.org/10.1145/3072959.3073710'
chicago: Zhang, Ran, Thomas Auzinger, Duygu Ceylan, Wilmot Li, and Bernd Bickel.
“Functionality-Aware Retargeting of Mechanisms to 3D Shapes,” Vol. 36. ACM, 2017.
https://doi.org/10.1145/3072959.3073710.
ieee: 'R. Zhang, T. Auzinger, D. Ceylan, W. Li, and B. Bickel, “Functionality-aware
retargeting of mechanisms to 3D shapes,” presented at the SIGGRAPH: Computer Graphics
and Interactive Techniques, Los Angeles, CA, United States , 2017, vol. 36, no.
4.'
ista: 'Zhang R, Auzinger T, Ceylan D, Li W, Bickel B. 2017. Functionality-aware
retargeting of mechanisms to 3D shapes. SIGGRAPH: Computer Graphics and Interactive
Techniques, ACM Transactions on Graphics, vol. 36, 81.'
mla: Zhang, Ran, et al. Functionality-Aware Retargeting of Mechanisms to 3D Shapes.
Vol. 36, no. 4, 81, ACM, 2017, doi:10.1145/3072959.3073710.
short: R. Zhang, T. Auzinger, D. Ceylan, W. Li, B. Bickel, in:, ACM, 2017.
conference:
end_date: 2017-08-03
location: 'Los Angeles, CA, United States '
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques'
start_date: 2017-07-30
date_created: 2018-12-11T11:49:38Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-22T09:49:31Z
day: '01'
ddc:
- '003'
- '004'
department:
- _id: BeBi
doi: 10.1145/3072959.3073710
ec_funded: 1
external_id:
isi:
- '000406432100049'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:05Z
date_updated: 2018-12-12T10:09:05Z
file_id: '4728'
file_name: IST-2018-1050-v1+1_MechRet.pdf
file_size: 25463895
relation: main_file
file_date_updated: 2018-12-12T10:09:05Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '4'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted 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_identifier:
issn:
- '07300301'
publication_status: published
publisher: ACM
publist_id: '6396'
pubrep_id: '1050'
quality_controlled: '1'
related_material:
record:
- id: '8386'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Functionality-aware retargeting of mechanisms to 3D shapes
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 36
year: '2017'
...
---
_id: '1001'
abstract:
- lang: eng
text: We present a computational approach for designing CurveUps, curvy shells that
form from an initially flat state. They consist of small rigid tiles that are
tightly held together by two pre-stretched elastic sheets attached to them. Our
method allows the realization of smooth, doubly curved surfaces that can be fabricated
as a flat piece. Once released, the restoring forces of the pre-stretched sheets
support the object to take shape in 3D. CurveUps are structurally stable in their
target configuration. The design process starts with a target surface. Our method
generates a tile layout in 2D and optimizes the distribution, shape, and attachment
areas of the tiles to obtain a configuration that is fabricable and in which the
curved up state closely matches the target. Our approach is based on an efficient
approximate model and a local optimization strategy for an otherwise intractable
nonlinear optimization problem. We demonstrate the effectiveness of our approach
for a wide range of shapes, all realized as physical prototypes.
alternative_title:
- ACM Transactions on Graphics
article_number: '64'
article_processing_charge: No
author:
- first_name: Ruslan
full_name: Guseinov, Ruslan
id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87
last_name: Guseinov
orcid: 0000-0001-9819-5077
- first_name: Eder
full_name: Miguel, Eder
last_name: Miguel
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: 'Guseinov R, Miguel E, Bickel B. CurveUps: Shaping objects from flat plates
with tension-actuated curvature. In: Vol 36. ACM; 2017. doi:10.1145/3072959.3073709'
apa: 'Guseinov, R., Miguel, E., & Bickel, B. (2017). CurveUps: Shaping objects
from flat plates with tension-actuated curvature (Vol. 36). Presented at the SIGGRAPH:
Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles,
CA, United States: ACM. https://doi.org/10.1145/3072959.3073709'
chicago: 'Guseinov, Ruslan, Eder Miguel, and Bernd Bickel. “CurveUps: Shaping Objects
from Flat Plates with Tension-Actuated Curvature,” Vol. 36. ACM, 2017. https://doi.org/10.1145/3072959.3073709.'
ieee: 'R. Guseinov, E. Miguel, and B. Bickel, “CurveUps: Shaping objects from flat
plates with tension-actuated curvature,” presented at the SIGGRAPH: Special Interest
Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United
States, 2017, vol. 36, no. 4.'
ista: 'Guseinov R, Miguel E, Bickel B. 2017. CurveUps: Shaping objects from flat
plates with tension-actuated curvature. SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 36, 64.'
mla: 'Guseinov, Ruslan, et al. CurveUps: Shaping Objects from Flat Plates with
Tension-Actuated Curvature. Vol. 36, no. 4, 64, ACM, 2017, doi:10.1145/3072959.3073709.'
short: R. Guseinov, E. Miguel, B. Bickel, in:, ACM, 2017.
conference:
end_date: 2017-08-25
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2017-08-19
date_created: 2018-12-11T11:49:38Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-22T09:49:58Z
day: '01'
ddc:
- '003'
- '004'
department:
- _id: BeBi
doi: 10.1145/3072959.3073709
ec_funded: 1
external_id:
isi:
- '000406432100032'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:24Z
date_updated: 2018-12-12T10:10:24Z
file_id: '4811'
file_name: IST-2018-1053-v1+1_CurveUp.pdf
file_size: 36159696
relation: main_file
file_date_updated: 2018-12-12T10:10:24Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '4'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
project:
- _id: 25082902-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '645599'
name: Soft-bodied intelligence for Manipulation
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication_status: published
publisher: ACM
publist_id: '6397'
pubrep_id: '1053'
quality_controlled: '1'
related_material:
record:
- id: '8366'
relation: dissertation_contains
status: public
status: public
title: 'CurveUps: Shaping objects from flat plates with tension-actuated curvature'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 36
year: '2017'
...
---
_id: '1003'
abstract:
- lang: eng
text: Network games (NGs) are played on directed graphs and are extensively used
in network design and analysis. Search problems for NGs include finding special
strategy profiles such as a Nash equilibrium and a globally optimal solution.
The networks modeled by NGs may be huge. In formal verification, abstraction has
proven to be an extremely effective technique for reasoning about systems with
big and even infinite state spaces. We describe an abstraction-refinement methodology
for reasoning about NGs. Our methodology is based on an abstraction function that
maps the state space of an NG to a much smaller state space. We search for a global
optimum and a Nash equilibrium by reasoning on an under- and an overapproximation
defined on top of this smaller state space. When the approximations are too coarse
to find such profiles, we refine the abstraction function. Our experimental results
demonstrate the efficiency of the methodology.
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shibashis
full_name: Guha, Shibashis
last_name: Guha
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: 'Avni G, Guha S, Kupferman O. An abstraction-refinement methodology for reasoning
about network games. In: AAAI Press; 2017:70-76. doi:10.24963/ijcai.2017/11'
apa: 'Avni, G., Guha, S., & Kupferman, O. (2017). An abstraction-refinement
methodology for reasoning about network games (pp. 70–76). Presented at the IJCAI:
International Joint Conference on Artificial Intelligence , Melbourne, Australia:
AAAI Press. https://doi.org/10.24963/ijcai.2017/11'
chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “An Abstraction-Refinement
Methodology for Reasoning about Network Games,” 70–76. AAAI Press, 2017. https://doi.org/10.24963/ijcai.2017/11.
ieee: 'G. Avni, S. Guha, and O. Kupferman, “An abstraction-refinement methodology
for reasoning about network games,” presented at the IJCAI: International Joint
Conference on Artificial Intelligence , Melbourne, Australia, 2017, pp. 70–76.'
ista: 'Avni G, Guha S, Kupferman O. 2017. An abstraction-refinement methodology
for reasoning about network games. IJCAI: International Joint Conference on Artificial
Intelligence , 70–76.'
mla: Avni, Guy, et al. An Abstraction-Refinement Methodology for Reasoning about
Network Games. AAAI Press, 2017, pp. 70–76, doi:10.24963/ijcai.2017/11.
short: G. Avni, S. Guha, O. Kupferman, in:, AAAI Press, 2017, pp. 70–76.
conference:
end_date: 2017-08-25
location: Melbourne, Australia
name: 'IJCAI: International Joint Conference on Artificial Intelligence '
start_date: 2017-08-19
date_created: 2018-12-11T11:49:38Z
date_published: 2017-05-30T00:00:00Z
date_updated: 2023-09-22T09:49:00Z
day: '30'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.24963/ijcai.2017/11
external_id:
isi:
- '000764137500011'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:58Z
date_updated: 2018-12-12T10:16:58Z
file_id: '5249'
file_name: IST-2017-818-v1+1_allIJCAI_CR.pdf
file_size: 365172
relation: main_file
file_date_updated: 2018-12-12T10:16:58Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 70 - 76
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
issn:
- '10450823'
publication_status: published
publisher: AAAI Press
publist_id: '6395'
pubrep_id: '818'
quality_controlled: '1'
related_material:
record:
- id: '6006'
relation: later_version
status: public
scopus_import: '1'
status: public
title: An abstraction-refinement methodology for reasoning about network games
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '1000'
abstract:
- lang: eng
text: 'We study probabilistic models of natural images and extend the autoregressive
family of PixelCNN models by incorporating latent variables. Subsequently, we
describe two new generative image models that exploit different image transformations
as latent variables: a quantized grayscale view of the image or a multi-resolution
image pyramid. The proposed models tackle two known shortcomings of existing PixelCNN
models: 1) their tendency to focus on low-level image details, while largely ignoring
high-level image information, such as object shapes, and 2) their computationally
costly procedure for image sampling. We experimentally demonstrate benefits of
our LatentPixelCNN models, in particular showing that they produce much more realistically
looking image samples than previous state-of-the-art probabilistic models. '
acknowledgement: We thank Tim Salimans for spotting a mistake in our preliminary arXiv
manuscript. This work was funded by the European Research Council under the European
Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 308036.
article_processing_charge: No
author:
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Kolesnikov A, Lampert C. PixelCNN models with auxiliary variables for natural
image modeling. In: 34th International Conference on Machine Learning.
Vol 70. JMLR; 2017:1905-1914.'
apa: 'Kolesnikov, A., & Lampert, C. (2017). PixelCNN models with auxiliary variables
for natural image modeling. In 34th International Conference on Machine Learning
(Vol. 70, pp. 1905–1914). Sydney, Australia: JMLR.'
chicago: Kolesnikov, Alexander, and Christoph Lampert. “PixelCNN Models with Auxiliary
Variables for Natural Image Modeling.” In 34th International Conference on
Machine Learning, 70:1905–14. JMLR, 2017.
ieee: A. Kolesnikov and C. Lampert, “PixelCNN models with auxiliary variables for
natural image modeling,” in 34th International Conference on Machine Learning,
Sydney, Australia, 2017, vol. 70, pp. 1905–1914.
ista: 'Kolesnikov A, Lampert C. 2017. PixelCNN models with auxiliary variables for
natural image modeling. 34th International Conference on Machine Learning. ICML:
International Conference on Machine Learning vol. 70, 1905–1914.'
mla: Kolesnikov, Alexander, and Christoph Lampert. “PixelCNN Models with Auxiliary
Variables for Natural Image Modeling.” 34th International Conference on Machine
Learning, vol. 70, JMLR, 2017, pp. 1905–14.
short: A. Kolesnikov, C. Lampert, in:, 34th International Conference on Machine
Learning, JMLR, 2017, pp. 1905–1914.
conference:
end_date: 2017-08-11
location: Sydney, Australia
name: 'ICML: International Conference on Machine Learning'
start_date: 2017-08-06
date_created: 2018-12-11T11:49:37Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2023-09-22T09:50:41Z
day: '01'
department:
- _id: ChLa
ec_funded: 1
external_id:
arxiv:
- '1612.08185'
isi:
- '000683309501102'
has_accepted_license: '1'
intvolume: ' 70'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1612.08185
month: '08'
oa: 1
oa_version: Submitted Version
page: 1905 - 1914
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication: 34th International Conference on Machine Learning
publication_identifier:
isbn:
- 978-151085514-4
publication_status: published
publisher: JMLR
publist_id: '6398'
quality_controlled: '1'
scopus_import: '1'
status: public
title: PixelCNN models with auxiliary variables for natural image modeling
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 70
year: '2017'
...
---
_id: '998'
abstract:
- lang: eng
text: 'A major open problem on the road to artificial intelligence is the development
of incrementally learning systems that learn about more and more concepts over
time from a stream of data. In this work, we introduce a new training strategy,
iCaRL, that allows learning in such a class-incremental way: only the training
data for a small number of classes has to be present at the same time and new
classes can be added progressively. iCaRL learns strong classifiers and a data
representation simultaneously. This distinguishes it from earlier works that were
fundamentally limited to fixed data representations and therefore incompatible
with deep learning architectures. We show by experiments on CIFAR-100 and ImageNet
ILSVRC 2012 data that iCaRL can learn many classes incrementally over a long period
of time where other strategies quickly fail. '
article_processing_charge: No
author:
- first_name: Sylvestre Alvise
full_name: Rebuffi, Sylvestre Alvise
last_name: Rebuffi
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Rebuffi SA, Kolesnikov A, Sperl G, Lampert C. iCaRL: Incremental classifier
and representation learning. In: Vol 2017. IEEE; 2017:5533-5542. doi:10.1109/CVPR.2017.587'
apa: 'Rebuffi, S. A., Kolesnikov, A., Sperl, G., & Lampert, C. (2017). iCaRL:
Incremental classifier and representation learning (Vol. 2017, pp. 5533–5542).
Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA,
United States: IEEE. https://doi.org/10.1109/CVPR.2017.587'
chicago: 'Rebuffi, Sylvestre Alvise, Alexander Kolesnikov, Georg Sperl, and Christoph
Lampert. “ICaRL: Incremental Classifier and Representation Learning,” 2017:5533–42.
IEEE, 2017. https://doi.org/10.1109/CVPR.2017.587.'
ieee: 'S. A. Rebuffi, A. Kolesnikov, G. Sperl, and C. Lampert, “iCaRL: Incremental
classifier and representation learning,” presented at the CVPR: Computer Vision
and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 5533–5542.'
ista: 'Rebuffi SA, Kolesnikov A, Sperl G, Lampert C. 2017. iCaRL: Incremental classifier
and representation learning. CVPR: Computer Vision and Pattern Recognition vol.
2017, 5533–5542.'
mla: 'Rebuffi, Sylvestre Alvise, et al. ICaRL: Incremental Classifier and Representation
Learning. Vol. 2017, IEEE, 2017, pp. 5533–42, doi:10.1109/CVPR.2017.587.'
short: S.A. Rebuffi, A. Kolesnikov, G. Sperl, C. Lampert, in:, IEEE, 2017, pp. 5533–5542.
conference:
end_date: 2017-07-26
location: Honolulu, HA, United States
name: 'CVPR: Computer Vision and Pattern Recognition'
start_date: 2017-07-21
date_created: 2018-12-11T11:49:37Z
date_published: 2017-04-14T00:00:00Z
date_updated: 2023-09-22T09:51:58Z
day: '14'
department:
- _id: ChLa
- _id: ChWo
doi: 10.1109/CVPR.2017.587
ec_funded: 1
external_id:
isi:
- '000418371405066'
intvolume: ' 2017'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1611.07725
month: '04'
oa: 1
oa_version: Submitted Version
page: 5533 - 5542
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
isbn:
- 978-153860457-1
publication_status: published
publisher: IEEE
publist_id: '6400'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'iCaRL: Incremental classifier and representation learning'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '990'
abstract:
- lang: eng
text: Assortative mating is an important driver of speciation in populations with
gene flow and is predicted to evolve under certain conditions in few-locus models.
However, the evolution of assortment is less understood for mating based on quantitative
traits, which are often characterized by high genetic variability and extensive
linkage disequilibrium between trait loci. We explore this scenario for a two-deme
model with migration, by considering a single polygenic trait subject to divergent
viability selection across demes, as well as assortative mating and sexual selection
within demes, and investigate how trait divergence is shaped by various evolutionary
forces. Our analysis reveals the existence of sharp thresholds of assortment strength,
at which divergence increases dramatically. We also study the evolution of assortment
via invasion of modifiers of mate discrimination and show that the ES assortment
strength has an intermediate value under a range of migration-selection parameters,
even in diverged populations, due to subtle effects which depend sensitively on
the extent of phenotypic variation within these populations. The evolutionary
dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal
models. We further investigate the sensitivity of our results to the assumptions
of the hypergeometric model, using individual-based simulations.
article_processing_charge: No
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Sachdeva H, Barton NH. Divergence and evolution of assortative mating in a
polygenic trait model of speciation with gene flow. Evolution; International
Journal of Organic Evolution. 2017;71(6):1478-1493. doi:10.1111/evo.13252
apa: Sachdeva, H., & Barton, N. H. (2017). Divergence and evolution of assortative
mating in a polygenic trait model of speciation with gene flow. Evolution;
International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13252
chicago: Sachdeva, Himani, and Nicholas H Barton. “Divergence and Evolution of Assortative
Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution;
International Journal of Organic Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13252.
ieee: H. Sachdeva and N. H. Barton, “Divergence and evolution of assortative mating
in a polygenic trait model of speciation with gene flow,” Evolution; International
Journal of Organic Evolution, vol. 71, no. 6. Wiley-Blackwell, pp. 1478–1493,
2017.
ista: Sachdeva H, Barton NH. 2017. Divergence and evolution of assortative mating
in a polygenic trait model of speciation with gene flow. Evolution; International
Journal of Organic Evolution. 71(6), 1478–1493.
mla: Sachdeva, Himani, and Nicholas H. Barton. “Divergence and Evolution of Assortative
Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution;
International Journal of Organic Evolution, vol. 71, no. 6, Wiley-Blackwell,
2017, pp. 1478–93, doi:10.1111/evo.13252.
short: H. Sachdeva, N.H. Barton, Evolution; International Journal of Organic Evolution
71 (2017) 1478–1493.
date_created: 2018-12-11T11:49:34Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-22T09:55:13Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/evo.13252
ec_funded: 1
external_id:
isi:
- '000403014800005'
pmid:
- '28419447'
file:
- access_level: open_access
checksum: 6d4c38cb1347fd43620d1736c6df5c79
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:37:04Z
date_updated: 2020-07-14T12:48:18Z
file_id: '6329'
file_name: 2017_Evolution_Sachdeva_supplement.pdf
file_size: 625260
relation: main_file
- access_level: open_access
checksum: f1d90dd8831b44baf49b4dd176f263af
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:37:04Z
date_updated: 2020-07-14T12:48:18Z
file_id: '6330'
file_name: 2017_Evolution_Sachdeva_article.pdf
file_size: 520110
relation: main_file
file_date_updated: 2020-07-14T12:48:18Z
has_accepted_license: '1'
intvolume: ' 71'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: '1478 - 1493 '
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution; International Journal of Organic Evolution
publication_identifier:
issn:
- '00143820'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6409'
pubrep_id: '977'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergence and evolution of assortative mating in a polygenic trait model of
speciation with gene flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 71
year: '2017'
...
---
_id: '988'
abstract:
- lang: eng
text: The current-phase relation (CPR) of a Josephson junction (JJ) determines how
the supercurrent evolves with the superconducting phase difference across the
junction. Knowledge of the CPR is essential in order to understand the response
of a JJ to various external parameters. Despite the rising interest in ultraclean
encapsulated graphene JJs, the CPR of such junctions remains unknown. Here, we
use a fully gate-tunable graphene superconducting quantum intereference device
(SQUID) to determine the CPR of ballistic graphene JJs. Each of the two JJs in
the SQUID is made with graphene encapsulated in hexagonal boron nitride. By independently
controlling the critical current of the JJs, we can operate the SQUID either in
a symmetric or asymmetric configuration. The highly asymmetric SQUID allows us
to phase-bias one of the JJs and thereby directly obtain its CPR. The CPR is found
to be skewed, deviating significantly from a sinusoidal form. The skewness can
be tuned with the gate voltage and oscillates in antiphase with Fabry-Pérot resistance
oscillations of the ballistic graphene cavity. We compare our experiments with
tight-binding calculations that include realistic graphene-superconductor interfaces
and find a good qualitative agreement.
article_processing_charge: No
author:
- first_name: Gaurav
full_name: Nanda, Gaurav
last_name: Nanda
- first_name: Juan L
full_name: Aguilera Servin, Juan L
id: 2A67C376-F248-11E8-B48F-1D18A9856A87
last_name: Aguilera Servin
orcid: 0000-0002-2862-8372
- first_name: Péter
full_name: Rakyta, Péter
last_name: Rakyta
- first_name: Andor
full_name: Kormányos, Andor
last_name: Kormányos
- first_name: Reinhold
full_name: Kleiner, Reinhold
last_name: Kleiner
- first_name: Dieter
full_name: Koelle, Dieter
last_name: Koelle
- first_name: Kazuo
full_name: Watanabe, Kazuo
last_name: Watanabe
- first_name: Takashi
full_name: Taniguchi, Takashi
last_name: Taniguchi
- first_name: Lieven
full_name: Vandersypen, Lieven
last_name: Vandersypen
- first_name: Srijit
full_name: Goswami, Srijit
last_name: Goswami
citation:
ama: Nanda G, Aguilera Servin JL, Rakyta P, et al. Current-phase relation of ballistic
graphene Josephson junctions. Nano Letters. 2017;17(6):3396-3401. doi:10.1021/acs.nanolett.7b00097
apa: Nanda, G., Aguilera Servin, J. L., Rakyta, P., Kormányos, A., Kleiner, R.,
Koelle, D., … Goswami, S. (2017). Current-phase relation of ballistic graphene
Josephson junctions. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b00097
chicago: Nanda, Gaurav, Juan L Aguilera Servin, Péter Rakyta, Andor Kormányos, Reinhold
Kleiner, Dieter Koelle, Kazuo Watanabe, Takashi Taniguchi, Lieven Vandersypen,
and Srijit Goswami. “Current-Phase Relation of Ballistic Graphene Josephson Junctions.”
Nano Letters. American Chemical Society, 2017. https://doi.org/10.1021/acs.nanolett.7b00097.
ieee: G. Nanda et al., “Current-phase relation of ballistic graphene Josephson
junctions,” Nano Letters, vol. 17, no. 6. American Chemical Society, pp.
3396–3401, 2017.
ista: Nanda G, Aguilera Servin JL, Rakyta P, Kormányos A, Kleiner R, Koelle D, Watanabe
K, Taniguchi T, Vandersypen L, Goswami S. 2017. Current-phase relation of ballistic
graphene Josephson junctions. Nano Letters. 17(6), 3396–3401.
mla: Nanda, Gaurav, et al. “Current-Phase Relation of Ballistic Graphene Josephson
Junctions.” Nano Letters, vol. 17, no. 6, American Chemical Society, 2017,
pp. 3396–401, doi:10.1021/acs.nanolett.7b00097.
short: G. Nanda, J.L. Aguilera Servin, P. Rakyta, A. Kormányos, R. Kleiner, D. Koelle,
K. Watanabe, T. Taniguchi, L. Vandersypen, S. Goswami, Nano Letters 17 (2017)
3396–3401.
date_created: 2018-12-11T11:49:33Z
date_published: 2017-05-05T00:00:00Z
date_updated: 2023-09-22T09:56:21Z
day: '05'
ddc:
- '621'
department:
- _id: NanoFab
doi: 10.1021/acs.nanolett.7b00097
external_id:
isi:
- '000403631600011'
file:
- access_level: open_access
checksum: 22021daa90cf13b01becd776838acb7b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:50Z
date_updated: 2020-07-14T12:48:18Z
file_id: '5037'
file_name: IST-2017-826-v1+1_2017_Aguilera-Servin_Current.pdf
file_size: 508638
relation: main_file
file_date_updated: 2020-07-14T12:48:18Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '6'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 3396 - 3401
publication: Nano Letters
publication_identifier:
issn:
- '15306984'
publication_status: published
publisher: American Chemical Society
publist_id: '6412'
pubrep_id: '826'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Current-phase relation of ballistic graphene Josephson junctions
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 17
year: '2017'
...
---
_id: '993'
abstract:
- lang: eng
text: In real-world applications, observations are often constrained to a small
fraction of a system. Such spatial subsampling can be caused by the inaccessibility
or the sheer size of the system, and cannot be overcome by longer sampling. Spatial
subsampling can strongly bias inferences about a system’s aggregated properties.
To overcome the bias, we derive analytically a subsampling scaling framework that
is applicable to different observables, including distributions of neuronal avalanches,
of number of people infected during an epidemic outbreak, and of node degrees.
We demonstrate how to infer the correct distributions of the underlying full system,
how to apply it to distinguish critical from subcritical systems, and how to disentangle
subsampling and finite size effects. Lastly, we apply subsampling scaling to neuronal
avalanche models and to recordings from developing neural networks. We show that
only mature, but not young networks follow power-law scaling, indicating self-organization
to criticality during development.
article_number: '15140'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Anna
full_name: Levina (Martius), Anna
id: 35AF8020-F248-11E8-B48F-1D18A9856A87
last_name: Levina (Martius)
- first_name: Viola
full_name: Priesemann, Viola
last_name: Priesemann
citation:
ama: Levina (Martius) A, Priesemann V. Subsampling scaling. Nature Communications.
2017;8. doi:10.1038/ncomms15140
apa: Levina (Martius), A., & Priesemann, V. (2017). Subsampling scaling. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15140
chicago: Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature
Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15140.
ieee: A. Levina (Martius) and V. Priesemann, “Subsampling scaling,” Nature Communications,
vol. 8. Nature Publishing Group, 2017.
ista: Levina (Martius) A, Priesemann V. 2017. Subsampling scaling. Nature Communications.
8, 15140.
mla: Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature
Communications, vol. 8, 15140, Nature Publishing Group, 2017, doi:10.1038/ncomms15140.
short: A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017).
date_created: 2018-12-11T11:49:35Z
date_published: 2017-05-04T00:00:00Z
date_updated: 2023-09-22T09:54:07Z
day: '04'
ddc:
- '005'
- '571'
department:
- _id: GaTk
- _id: JoCs
doi: 10.1038/ncomms15140
ec_funded: 1
external_id:
isi:
- '000400560700001'
file:
- access_level: open_access
checksum: 9880212f8c4c53404c7c6fbf9023c53a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:05Z
date_updated: 2020-07-14T12:48:19Z
file_id: '5122'
file_name: IST-2017-819-v1+1_2017_Levina_SubsamplingScaling.pdf
file_size: 746224
relation: main_file
file_date_updated: 2020-07-14T12:48:19Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6406'
pubrep_id: '819'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Subsampling scaling
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '995'
abstract:
- lang: eng
text: Recently it was shown that an impurity exchanging orbital angular momentum
with a surrounding bath can be described in terms of the angulon quasiparticle
[Phys. Rev. Lett. 118, 095301 (2017)]. The angulon consists of a quantum rotor
dressed by a many-particle field of boson excitations, and can be formed out of,
for example, a molecule or a nonspherical atom in superfluid helium, or out of
an electron coupled to lattice phonons or a Bose condensate. Here we develop an
approach to the angulon based on the path-integral formalism, which sets the ground
for a systematic, perturbative treatment of the angulon problem. The resulting
perturbation series can be interpreted in terms of Feynman diagrams, from which,
in turn, one can derive a set of diagrammatic rules. These rules extend the machinery
of the graphical theory of angular momentum - well known from theoretical atomic
spectroscopy - to the case where an environment with an infinite number of degrees
of freedom is present. In particular, we show that each diagram can be interpreted
as a 'skeleton', which enforces angular momentum conservation, dressed by an additional
many-body contribution. This connection between the angulon theory and the graphical
theory of angular momentum is particularly important as it allows to systematically
and substantially simplify the analytical representation of each diagram. In order
to exemplify the technique, we calculate the 1- and 2-loop contributions to the
angulon self-energy, the spectral function, and the quasiparticle weight. The
diagrammatic theory we develop paves the way to investigate next-to-leading order
quantities in a more compact way compared to the variational approaches.
article_number: '085410'
article_processing_charge: No
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Bighin G, Lemeshko M. Diagrammatic approach to orbital quantum impurities interacting
with a many-particle environment. Physical Review B - Condensed Matter and
Materials Physics. 2017;96(8). doi:10.1103/PhysRevB.96.085410
apa: Bighin, G., & Lemeshko, M. (2017). Diagrammatic approach to orbital quantum
impurities interacting with a many-particle environment. Physical Review B
- Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.085410
chicago: Bighin, Giacomo, and Mikhail Lemeshko. “Diagrammatic Approach to Orbital
Quantum Impurities Interacting with a Many-Particle Environment.” Physical
Review B - Condensed Matter and Materials Physics. American Physical Society,
2017. https://doi.org/10.1103/PhysRevB.96.085410.
ieee: G. Bighin and M. Lemeshko, “Diagrammatic approach to orbital quantum impurities
interacting with a many-particle environment,” Physical Review B - Condensed
Matter and Materials Physics, vol. 96, no. 8. American Physical Society, 2017.
ista: Bighin G, Lemeshko M. 2017. Diagrammatic approach to orbital quantum impurities
interacting with a many-particle environment. Physical Review B - Condensed Matter
and Materials Physics. 96(8), 085410.
mla: Bighin, Giacomo, and Mikhail Lemeshko. “Diagrammatic Approach to Orbital Quantum
Impurities Interacting with a Many-Particle Environment.” Physical Review B
- Condensed Matter and Materials Physics, vol. 96, no. 8, 085410, American
Physical Society, 2017, doi:10.1103/PhysRevB.96.085410.
short: G. Bighin, M. Lemeshko, Physical Review B - Condensed Matter and Materials
Physics 96 (2017).
date_created: 2018-12-11T11:49:36Z
date_published: 2017-08-07T00:00:00Z
date_updated: 2023-09-22T09:53:17Z
day: '07'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.96.085410
external_id:
isi:
- '000407017100009'
intvolume: ' 96'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.02616
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review B - Condensed Matter and Materials Physics
publication_identifier:
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
publist_id: '6404'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diagrammatic approach to orbital quantum impurities interacting with a many-particle
environment
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 96
year: '2017'
...
---
_id: '989'
abstract:
- lang: eng
text: We present a generalized optimal transport model in which the mass-preserving
constraint for the L2-Wasserstein distance is relaxed by introducing a source
term in the continuity equation. The source term is also incorporated in the path
energy by means of its squared L2-norm in time of a functional with linear growth
in space. This extension of the original transport model enables local density
modulations, which is a desirable feature in applications such as image warping
and blending. A key advantage of the use of a functional with linear growth in
space is that it allows for singular sources and sinks, which can be supported
on points or lines. On a technical level, the L2-norm in time ensures a disintegration
of the source in time, which we use to obtain the well-posedness of the model
and the existence of geodesic paths. The numerical discretization is based on
the proximal splitting approach [18] and selected numerical test cases show the
potential of the proposed approach. Furthermore, the approach is applied to the
warping and blending of textures.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Martin
full_name: Rumpf, Martin
last_name: Rumpf
- first_name: Stefan
full_name: Simon, Stefan
last_name: Simon
citation:
ama: 'Maas J, Rumpf M, Simon S. Transport based image morphing with intensity modulation.
In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:563-577.
doi:10.1007/978-3-319-58771-4_45'
apa: 'Maas, J., Rumpf, M., & Simon, S. (2017). Transport based image morphing
with intensity modulation. In F. Lauze, Y. Dong, & A. Bjorholm Dahl (Eds.)
(Vol. 10302, pp. 563–577). Presented at the SSVM: Scale Space and Variational
Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_45'
chicago: Maas, Jan, Martin Rumpf, and Stefan Simon. “Transport Based Image Morphing
with Intensity Modulation.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm
Dahl, 10302:563–77. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_45.
ieee: J. Maas, M. Rumpf, and S. Simon, “Transport based image morphing with intensity
modulation,” presented at the SSVM: Scale Space and Variational Methods in Computer
Vision, Kolding, Denmark, 2017, vol. 10302, pp. 563–577.
ista: Maas J, Rumpf M, Simon S. 2017. Transport based image morphing with intensity
modulation. SSVM: Scale Space and Variational Methods in Computer Vision, LNCS,
vol. 10302, 563–577.
mla: Maas, Jan, et al. Transport Based Image Morphing with Intensity Modulation.
Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 563–77, doi:10.1007/978-3-319-58771-4_45.
short: J. Maas, M. Rumpf, S. Simon, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.),
Springer, 2017, pp. 563–577.
conference:
end_date: 2017-06-08
location: Kolding, Denmark
name: 'SSVM: Scale Space and Variational Methods in Computer Vision'
start_date: 2017-06-04
date_created: 2018-12-11T11:49:34Z
date_published: 2017-05-18T00:00:00Z
date_updated: 2023-09-22T09:55:50Z
day: '18'
department:
- _id: JaMa
doi: 10.1007/978-3-319-58771-4_45
editor:
- first_name: François
full_name: Lauze, François
last_name: Lauze
- first_name: Yiqiu
full_name: Dong, Yiqiu
last_name: Dong
- first_name: Anders
full_name: Bjorholm Dahl, Anders
last_name: Bjorholm Dahl
external_id:
isi:
- '000432210900045'
intvolume: ' 10302'
isi: 1
language:
- iso: eng
month: '05'
oa_version: None
page: 563 - 577
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '6410'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transport based image morphing with intensity modulation
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10302
year: '2017'
...
---
_id: '994'
abstract:
- lang: eng
text: The formation of vortices is usually considered to be the main mechanism of
angular momentum disposal in superfluids. Recently, it was predicted that a superfluid
can acquire angular momentum via an alternative, microscopic route -- namely,
through interaction with rotating impurities, forming so-called `angulon quasiparticles'
[Phys. Rev. Lett. 114, 203001 (2015)]. The angulon instabilities correspond to
transfer of a small number of angular momentum quanta from the impurity to the
superfluid, as opposed to vortex instabilities, where angular momentum is quantized
in units of ℏ per atom. Furthermore, since conventional impurities (such as molecules)
represent three-dimensional (3D) rotors, the angular momentum transferred is intrinsically
3D as well, as opposed to a merely planar rotation which is inherent to vortices.
Herein we show that the angulon theory can explain the anomalous broadening of
the spectroscopic lines observed for CH 3 and NH 3 molecules in superfluid
helium nanodroplets, thereby providing a fingerprint of the emerging angulon instabilities
in experiment.
article_processing_charge: No
author:
- first_name: Igor
full_name: Cherepanov, Igor
id: 339C7E5A-F248-11E8-B48F-1D18A9856A87
last_name: Cherepanov
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Cherepanov I, Lemeshko M. Fingerprints of angulon instabilities in the spectra
of matrix-isolated molecules. Physical Review Materials. 2017;1(3). doi:10.1103/PhysRevMaterials.1.035602
apa: Cherepanov, I., & Lemeshko, M. (2017). Fingerprints of angulon instabilities
in the spectra of matrix-isolated molecules. Physical Review Materials.
American Physical Society. https://doi.org/10.1103/PhysRevMaterials.1.035602
chicago: Cherepanov, Igor, and Mikhail Lemeshko. “Fingerprints of Angulon Instabilities
in the Spectra of Matrix-Isolated Molecules.” Physical Review Materials.
American Physical Society, 2017. https://doi.org/10.1103/PhysRevMaterials.1.035602.
ieee: I. Cherepanov and M. Lemeshko, “Fingerprints of angulon instabilities in the
spectra of matrix-isolated molecules,” Physical Review Materials, vol.
1, no. 3. American Physical Society, 2017.
ista: Cherepanov I, Lemeshko M. 2017. Fingerprints of angulon instabilities in the
spectra of matrix-isolated molecules. Physical Review Materials. 1(3).
mla: Cherepanov, Igor, and Mikhail Lemeshko. “Fingerprints of Angulon Instabilities
in the Spectra of Matrix-Isolated Molecules.” Physical Review Materials,
vol. 1, no. 3, American Physical Society, 2017, doi:10.1103/PhysRevMaterials.1.035602.
short: I. Cherepanov, M. Lemeshko, Physical Review Materials 1 (2017).
date_created: 2018-12-11T11:49:35Z
date_published: 2017-08-08T00:00:00Z
date_updated: 2023-09-22T09:53:42Z
day: '08'
department:
- _id: MiLe
doi: 10.1103/PhysRevMaterials.1.035602
ec_funded: 1
external_id:
isi:
- '000416564000004'
intvolume: ' 1'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.09220
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Physical Review Materials
publication_status: published
publisher: American Physical Society
publist_id: '6405'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 1
year: '2017'
...
---
_id: '991'
abstract:
- lang: eng
text: Synaptotagmin 7 (Syt7) was originally identified as a slow Ca2+ sensor for
lysosome fusion, but its function at fast synapses is controversial. The paper
by Luo and Südhof (2017) in this issue of Neuron shows that at the calyx of Held
in the auditory brainstem Syt7 triggers asynchronous release during stimulus trains,
resulting in reliable and temporally precise high-frequency transmission. Thus,
a slow Ca2+ sensor contributes to the fast signaling properties of the calyx synapse.
article_processing_charge: No
author:
- first_name: Chong
full_name: Chen, Chong
id: 3DFD581A-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- 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: 'Chen C, Jonas PM. Synaptotagmins: That’s why so many. Neuron. 2017;94(4):694-696.
doi:10.1016/j.neuron.2017.05.011'
apa: 'Chen, C., & Jonas, P. M. (2017). Synaptotagmins: That’s why so many. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2017.05.011'
chicago: 'Chen, Chong, and Peter M Jonas. “Synaptotagmins: That’s Why so Many.”
Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2017.05.011.'
ieee: 'C. Chen and P. M. Jonas, “Synaptotagmins: That’s why so many,” Neuron,
vol. 94, no. 4. Elsevier, pp. 694–696, 2017.'
ista: 'Chen C, Jonas PM. 2017. Synaptotagmins: That’s why so many. Neuron. 94(4),
694–696.'
mla: 'Chen, Chong, and Peter M. Jonas. “Synaptotagmins: That’s Why so Many.” Neuron,
vol. 94, no. 4, Elsevier, 2017, pp. 694–96, doi:10.1016/j.neuron.2017.05.011.'
short: C. Chen, P.M. Jonas, Neuron 94 (2017) 694–696.
date_created: 2018-12-11T11:49:34Z
date_published: 2017-05-17T00:00:00Z
date_updated: 2023-09-22T09:54:37Z
day: '17'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2017.05.011
external_id:
isi:
- '000401415100002'
intvolume: ' 94'
isi: 1
issue: '4'
language:
- iso: eng
month: '05'
oa_version: None
page: 694 - 696
publication: Neuron
publication_identifier:
issn:
- '08966273'
publication_status: published
publisher: Elsevier
publist_id: '6408'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Synaptotagmins: That’s why so many'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 94
year: '2017'
...
---
_id: '954'
abstract:
- lang: eng
text: Understanding the relation between genotype and phenotype remains a major
challenge. The difficulty of predicting individual mutation effects, and particularly
the interactions between them, has prevented the development of a comprehensive
theory that links genotypic changes to their phenotypic effects. We show that
a general thermodynamic framework for gene regulation, based on a biophysical
understanding of protein-DNA binding, accurately predicts the sign of epistasis
in a canonical cis-regulatory element consisting of overlapping RNA polymerase
and repressor binding sites. Sign and magnitude of individual mutation effects
are sufficient to predict the sign of epistasis and its environmental dependence.
Thus, the thermodynamic model offers the correct null prediction for epistasis
between mutations across DNA-binding sites. Our results indicate that a predictive
theory for the effects of cis-regulatory mutations is possible from first principles,
as long as the essential molecular mechanisms and the constraints these impose
on a biological system are accounted for.
article_number: e25192
article_processing_charge: Yes
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- 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: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature
of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192
apa: Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C.
(2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element.
ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192
chicago: Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and
Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory
Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192.
ieee: M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the
mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife,
vol. 6. eLife Sciences Publications, 2017.
ista: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic
nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192.
mla: Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical
Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications,
2017, doi:10.7554/eLife.25192.
short: M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-05-18T00:00:00Z
date_updated: 2023-09-22T10:01:17Z
day: '18'
ddc:
- '576'
department:
- _id: CaGu
- _id: NiBa
- _id: JoBo
doi: 10.7554/eLife.25192
ec_funded: 1
external_id:
isi:
- '000404024800001'
file:
- access_level: open_access
checksum: 59cdd4400fb41280122d414fea971546
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:49Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5306'
file_name: IST-2017-841-v1+1_elife-25192-v2.pdf
file_size: 2441529
relation: main_file
- access_level: open_access
checksum: b69024880558b858eb8c5d47a92b6377
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:50Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5307'
file_name: IST-2017-841-v1+2_elife-25192-figures-v2.pdf
file_size: 3752660
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
issn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6460'
pubrep_id: '841'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the mechanistic nature of epistasis in a canonical cis-regulatory element
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 6
year: '2017'
...
---
_id: '955'
abstract:
- lang: eng
text: 'Gene expression is controlled by networks of regulatory proteins that interact
specifically with external signals and DNA regulatory sequences. These interactions
force the network components to co-evolve so as to continually maintain function.
Yet, existing models of evolution mostly focus on isolated genetic elements. In
contrast, we study the essential process by which regulatory networks grow: the
duplication and subsequent specialization of network components. We synthesize
a biophysical model of molecular interactions with the evolutionary framework
to find the conditions and pathways by which new regulatory functions emerge.
We show that specialization of new network components is usually slow, but can
be drastically accelerated in the presence of regulatory crosstalk and mutations
that promote promiscuous interactions between network components.'
article_number: '216'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- 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: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions
on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1).
doi:10.1038/s41467-017-00238-8
apa: Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution
of new regulatory functions on biophysically realistic fitness landscapes. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8
chicago: Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik.
“Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.”
Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8.
ieee: T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new
regulatory functions on biophysically realistic fitness landscapes,” Nature
Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
ista: Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory
functions on biophysically realistic fitness landscapes. Nature Communications.
8(1), 216.
mla: Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically
Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216,
Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.
short: T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications
8 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-08-09T00:00:00Z
date_updated: 2023-09-22T10:00:49Z
day: '09'
ddc:
- '539'
- '576'
department:
- _id: GaTk
- _id: NiBa
doi: 10.1038/s41467-017-00238-8
ec_funded: 1
external_id:
isi:
- '000407198800005'
file:
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checksum: 29a1b5db458048d3bd5c67e0e2a56818
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creator: system
date_created: 2018-12-12T10:14:14Z
date_updated: 2020-07-14T12:48:16Z
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date_updated: 2020-07-14T12:48:16Z
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file_size: 9715993
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has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6459'
pubrep_id: '864'
quality_controlled: '1'
related_material:
record:
- id: '6071'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Evolution of new regulatory functions on biophysically realistic fitness landscapes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '962'
abstract:
- lang: eng
text: 'We present a new algorithm for model counting of a class of string constraints.
In addition to the classic operation of concatenation, our class includes some
recursively defined operations such as Kleene closure, and replacement of substrings.
Additionally, our class also includes length constraints on the string expressions,
which means, by requiring reasoning about numbers, that we face a multi-sorted
logic. In the end, our string constraints are motivated by their use in programming
for web applications. Our algorithm comprises two novel features: the ability
to use a technique of (1) partial derivatives for constraints that are already
in a solved form, i.e. a form where its (string) satisfiability is clearly displayed,
and (2) non-progression, where cyclic reasoning in the reduction process may be
terminated (thus allowing for the algorithm to look elsewhere). Finally, we experimentally
compare our model counter with two recent works on model counting of similar constraints,
SMC [18] and ABC [5], to demonstrate its superior performance.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Minh
full_name: Trinh, Minh
last_name: Trinh
- first_name: Duc Hiep
full_name: Chu, Duc Hiep
id: 3598E630-F248-11E8-B48F-1D18A9856A87
last_name: Chu
- first_name: Joxan
full_name: Jaffar, Joxan
last_name: Jaffar
citation:
ama: 'Trinh M, Chu DH, Jaffar J. Model counting for recursively-defined strings.
In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:399-418. doi:10.1007/978-3-319-63390-9_21'
apa: 'Trinh, M., Chu, D. H., & Jaffar, J. (2017). Model counting for recursively-defined
strings. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10427, pp. 399–418). Presented
at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_21'
chicago: Trinh, Minh, Duc Hiep Chu, and Joxan Jaffar. “Model Counting for Recursively-Defined
Strings.” edited by Rupak Majumdar and Viktor Kunčak, 10427:399–418. Springer,
2017. https://doi.org/10.1007/978-3-319-63390-9_21.
ieee: 'M. Trinh, D. H. Chu, and J. Jaffar, “Model counting for recursively-defined
strings,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany,
2017, vol. 10427, pp. 399–418.'
ista: 'Trinh M, Chu DH, Jaffar J. 2017. Model counting for recursively-defined strings.
CAV: Computer Aided Verification, LNCS, vol. 10427, 399–418.'
mla: Trinh, Minh, et al. Model Counting for Recursively-Defined Strings.
Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 399–418,
doi:10.1007/978-3-319-63390-9_21.
short: M. Trinh, D.H. Chu, J. Jaffar, in:, R. Majumdar, V. Kunčak (Eds.), Springer,
2017, pp. 399–418.
conference:
end_date: 2017-07-28
location: Heidelberg, Germany
name: 'CAV: Computer Aided Verification'
start_date: 2017-07-24
date_created: 2018-12-11T11:49:26Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-22T09:58:02Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-319-63390-9_21
editor:
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
- first_name: Viktor
full_name: Kunčak, Viktor
last_name: Kunčak
external_id:
isi:
- '000431900900021'
intvolume: ' 10427'
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
page: 399 - 418
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '6443'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Model counting for recursively-defined strings
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10427
year: '2017'
...
---
_id: '953'
abstract:
- lang: eng
text: 'The role of natural selection in the evolution of adaptive phenotypes has
undergone constant probing by evolutionary biologists, employing both theoretical
and empirical approaches. As Darwin noted, natural selection can act together
with other processes, including random changes in the frequencies of phenotypic
differences that are not under strong selection, and changes in the environment,
which may reflect evolutionary changes in the organisms themselves. As understanding
of genetics developed after 1900, the new genetic discoveries were incorporated
into evolutionary biology. The resulting general principles were summarized by
Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine
how recent advances in genetics, developmental biology and molecular biology,
including epigenetics, relate to today''s understanding of the evolution of adaptations.
We illustrate how careful genetic studies have repeatedly shown that apparently
puzzling results in a wide diversity of organisms involve processes that are consistent
with neo-Darwinism. They do not support important roles in adaptation for processes
such as directed mutation or the inheritance of acquired characters, and therefore
no radical revision of our understanding of the mechanism of adaptive evolution
is needed.'
article_number: '20162864'
article_processing_charge: No
author:
- first_name: Deborah
full_name: Charlesworth, Deborah
last_name: Charlesworth
- 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: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
citation:
ama: Charlesworth D, Barton NH, Charlesworth B. The sources of adaptive evolution.
Proceedings of the Royal Society of London Series B Biological Sciences.
2017;284(1855). doi:10.1098/rspb.2016.2864
apa: Charlesworth, D., Barton, N. H., & Charlesworth, B. (2017). The sources
of adaptive evolution. Proceedings of the Royal Society of London Series B
Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.2864
chicago: Charlesworth, Deborah, Nicholas H Barton, and Brian Charlesworth. “The
Sources of Adaptive Evolution.” Proceedings of the Royal Society of London
Series B Biological Sciences. Royal Society, The, 2017. https://doi.org/10.1098/rspb.2016.2864.
ieee: D. Charlesworth, N. H. Barton, and B. Charlesworth, “The sources of adaptive
evolution,” Proceedings of the Royal Society of London Series B Biological
Sciences, vol. 284, no. 1855. Royal Society, The, 2017.
ista: Charlesworth D, Barton NH, Charlesworth B. 2017. The sources of adaptive evolution.
Proceedings of the Royal Society of London Series B Biological Sciences. 284(1855),
20162864.
mla: Charlesworth, Deborah, et al. “The Sources of Adaptive Evolution.” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 284, no.
1855, 20162864, Royal Society, The, 2017, doi:10.1098/rspb.2016.2864.
short: D. Charlesworth, N.H. Barton, B. Charlesworth, Proceedings of the Royal Society
of London Series B Biological Sciences 284 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-05-31T00:00:00Z
date_updated: 2023-09-22T10:01:48Z
day: '31'
department:
- _id: NiBa
doi: 10.1098/rspb.2016.2864
external_id:
isi:
- '000405148800021'
pmid:
- '28566483'
intvolume: ' 284'
isi: 1
issue: '1855'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454256/
month: '05'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '6462'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The sources of adaptive evolution
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 284
year: '2017'
...
---
_id: '959'
abstract:
- lang: eng
text: In this work it is shown that scale-free tails in metabolic flux distributions
inferred in stationary models are an artifact due to reactions involved in thermodynamically
unfeasible cycles, unbounded by physical constraints and in principle able to
perform work without expenditure of free energy. After implementing thermodynamic
constraints by removing such loops, metabolic flux distributions scale meaningfully
with the physical limiting factors, acquiring in turn a richer multimodal structure
potentially leading to symmetry breaking while optimizing for objective functions.
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: De Martino D. Scales and multimodal flux distributions in stationary metabolic
network models via thermodynamics. Physical Review E Statistical Nonlinear
and Soft Matter Physics . 2017;95(6):062419. doi:10.1103/PhysRevE.95.062419
apa: De Martino, D. (2017). Scales and multimodal flux distributions in stationary
metabolic network models via thermodynamics. Physical Review E Statistical
Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.95.062419
chicago: De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary
Metabolic Network Models via Thermodynamics.” Physical Review E Statistical
Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.95.062419.
ieee: D. De Martino, “Scales and multimodal flux distributions in stationary metabolic
network models via thermodynamics,” Physical Review E Statistical Nonlinear
and Soft Matter Physics , vol. 95, no. 6. American Institute of Physics, p.
062419, 2017.
ista: De Martino D. 2017. Scales and multimodal flux distributions in stationary
metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear
and Soft Matter Physics . 95(6), 062419.
mla: De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary
Metabolic Network Models via Thermodynamics.” Physical Review E Statistical
Nonlinear and Soft Matter Physics , vol. 95, no. 6, American Institute of
Physics, 2017, p. 062419, doi:10.1103/PhysRevE.95.062419.
short: D. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 95
(2017) 062419.
date_created: 2018-12-11T11:49:25Z
date_published: 2017-06-28T00:00:00Z
date_updated: 2023-09-22T09:59:01Z
day: '28'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.95.062419
ec_funded: 1
external_id:
isi:
- '000404546400004'
intvolume: ' 95'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/pdf/1703.00853.pdf
month: '06'
oa: 1
oa_version: Submitted Version
page: '062419'
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Physical Review E Statistical Nonlinear and Soft Matter Physics '
publication_identifier:
issn:
- '24700045'
publication_status: published
publisher: American Institute of Physics
publist_id: '6446'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scales and multimodal flux distributions in stationary metabolic network models
via thermodynamics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 95
year: '2017'
...
---
_id: '956'
abstract:
- lang: eng
text: We study a class of ergodic quantum Markov semigroups on finite-dimensional
unital C⁎-algebras. These semigroups have a unique stationary state σ, and we
are concerned with those that satisfy a quantum detailed balance condition with
respect to σ. We show that the evolution on the set of states that is given by
such a quantum Markov semigroup is gradient flow for the relative entropy with
respect to σ in a particular Riemannian metric on the set of states. This metric
is a non-commutative analog of the 2-Wasserstein metric, and in several interesting
cases we are able to show, in analogy with work of Otto on gradient flows with
respect to the classical 2-Wasserstein metric, that the relative entropy is strictly
and uniformly convex with respect to the Riemannian metric introduced here. As
a consequence, we obtain a number of new inequalities for the decay of relative
entropy for ergodic quantum Markov semigroups with detailed balance.
article_processing_charge: No
author:
- first_name: Eric
full_name: Carlen, Eric
last_name: Carlen
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
citation:
ama: Carlen E, Maas J. Gradient flow and entropy inequalities for quantum Markov
semigroups with detailed balance. Journal of Functional Analysis. 2017;273(5):1810-1869.
doi:10.1016/j.jfa.2017.05.003
apa: Carlen, E., & Maas, J. (2017). Gradient flow and entropy inequalities for
quantum Markov semigroups with detailed balance. Journal of Functional Analysis.
Academic Press. https://doi.org/10.1016/j.jfa.2017.05.003
chicago: Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for
Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis.
Academic Press, 2017. https://doi.org/10.1016/j.jfa.2017.05.003.
ieee: E. Carlen and J. Maas, “Gradient flow and entropy inequalities for quantum
Markov semigroups with detailed balance,” Journal of Functional Analysis,
vol. 273, no. 5. Academic Press, pp. 1810–1869, 2017.
ista: Carlen E, Maas J. 2017. Gradient flow and entropy inequalities for quantum
Markov semigroups with detailed balance. Journal of Functional Analysis. 273(5),
1810–1869.
mla: Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum
Markov Semigroups with Detailed Balance.” Journal of Functional Analysis,
vol. 273, no. 5, Academic Press, 2017, pp. 1810–69, doi:10.1016/j.jfa.2017.05.003.
short: E. Carlen, J. Maas, Journal of Functional Analysis 273 (2017) 1810–1869.
date_created: 2018-12-11T11:49:24Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-09-22T10:00:18Z
day: '01'
department:
- _id: JaMa
doi: 10.1016/j.jfa.2017.05.003
external_id:
isi:
- '000406082300005'
intvolume: ' 273'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.01254
month: '09'
oa: 1
oa_version: Submitted Version
page: 1810 - 1869
publication: Journal of Functional Analysis
publication_identifier:
issn:
- '00221236'
publication_status: published
publisher: Academic Press
publist_id: '6452'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gradient flow and entropy inequalities for quantum Markov semigroups with detailed
balance
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 273
year: '2017'
...
---
_id: '952'
abstract:
- lang: eng
text: A novel strategy for controlling the spread of arboviral diseases such as
dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing
Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness
costs through lower viability or fecundity. These maternally inherited bacteria
also produce a frequency-dependent advantage for infected females by inducing
cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected
females mated to infected males. These competing effects, a frequency-dependent
advantage and frequency-independent costs, produce bistable Wolbachia frequency
dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing
Wolbachia transinfections through local populations; but below pˆ, infection frequencies
tend to decline to zero. If pˆ is not too high, CI also drives spatial spread
once infections become established over sufficiently large areas. We illustrate
how simple models provide testable predictions concerning the spatial and temporal
dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape
of spreading waves, and the conditions for initiating spread from local introductions.
First, we consider the robustness of diffusion-based predictions to incorporating
two important features of wMel-Aedes aegypti biology that may be inconsistent
with the diffusion approximations, namely fast local dynamics induced by complete
CI (i.e., all embryos produced from incompatible crosses die) and long-tailed,
non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed
dispersal changes wave-width predictions only slightly; but it can significantly
reduce wave speed relative to the diffusion prediction; it also allows smaller
local introductions to initiate spatial spread. Second, we use approximations
for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected
Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti
populations near Cairns, Australia that demonstrate long-distance dispersal and
provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally,
we apply our analyses to produce operational guidelines for efficient transformation
of vector populations over large areas. We demonstrate that even very slow spatial
spread, on the order of 10-20 m/month (as predicted), can produce area-wide population
transformation within a few years following initial releases covering about 20-30%
of the target area.
article_processing_charge: No
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Turelli M, Barton NH. Deploying dengue-suppressing Wolbachia: Robust models
predict slow but effective spatial spread in Aedes aegypti. Theoretical Population
Biology. 2017;115:45-60. doi:10.1016/j.tpb.2017.03.003'
apa: 'Turelli, M., & Barton, N. H. (2017). Deploying dengue-suppressing Wolbachia:
Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical
Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2017.03.003'
chicago: 'Turelli, Michael, and Nicholas H Barton. “Deploying Dengue-Suppressing
Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.”
Theoretical Population Biology. Elsevier, 2017. https://doi.org/10.1016/j.tpb.2017.03.003.'
ieee: 'M. Turelli and N. H. Barton, “Deploying dengue-suppressing Wolbachia: Robust
models predict slow but effective spatial spread in Aedes aegypti,” Theoretical
Population Biology, vol. 115. Elsevier, pp. 45–60, 2017.'
ista: 'Turelli M, Barton NH. 2017. Deploying dengue-suppressing Wolbachia: Robust
models predict slow but effective spatial spread in Aedes aegypti. Theoretical
Population Biology. 115, 45–60.'
mla: 'Turelli, Michael, and Nicholas H. Barton. “Deploying Dengue-Suppressing Wolbachia:
Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical
Population Biology, vol. 115, Elsevier, 2017, pp. 45–60, doi:10.1016/j.tpb.2017.03.003.'
short: M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60.
date_created: 2018-12-11T11:49:22Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-22T10:02:21Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2017.03.003
external_id:
pmid:
- '28411063'
file:
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checksum: 9aeff86fa7de69f7a15cf4fc60d57d01
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T06:39:45Z
date_updated: 2020-07-14T12:48:16Z
file_id: '6327'
file_name: 2017_TheoreticalPopulationBio_Turelli.pdf
file_size: 2073856
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 115'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 45 - 60
pmid: 1
publication: Theoretical Population Biology
publication_identifier:
issn:
- '00405809'
publication_status: published
publisher: Elsevier
publist_id: '6463'
pubrep_id: '972'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective
spatial spread in Aedes aegypti'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2017'
...
---
_id: '951'
abstract:
- lang: eng
text: Dengue-suppressing Wolbachia strains are promising tools for arbovirus control,
particularly as they have the potential to self-spread following local introductions.
To test this, we followed the frequency of the transinfected Wolbachia strain
wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated
locations within the city in early 2013. Spatial spread was analysed graphically
using interpolation and by fitting a statistical model describing the position
and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and
0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per
year, roughly consistent with theoretical predictions. In contrast, the smallest
release (0.11 km2) produced erratic temporal and spatial dynamics, with little
evidence of spread after 2 years. This is consistent with the prediction concerning
fitness-decreasing Wolbachia transinfections that a minimum release area is needed
to achieve stable local establishment and spread in continuous habitats. Our graphical
and likelihood analyses produced broadly consistent estimates of wave speed and
wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental
heterogeneity will affect large-scale Wolbachia transformations of urban mosquito
populations. The persistence and spread of Wolbachia in release areas meeting
minimum area requirements indicates the promise of successful large-scale population
transfo
article_number: e2001894
article_processing_charge: No
author:
- first_name: Tom
full_name: Schmidt, Tom
last_name: Schmidt
- 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: Gordana
full_name: Rasic, Gordana
last_name: Rasic
- first_name: Andrew
full_name: Turley, Andrew
last_name: Turley
- first_name: Brian
full_name: Montgomery, Brian
last_name: Montgomery
- first_name: Inaki
full_name: Iturbe Ormaetxe, Inaki
last_name: Iturbe Ormaetxe
- first_name: Peter
full_name: Cook, Peter
last_name: Cook
- first_name: Peter
full_name: Ryan, Peter
last_name: Ryan
- first_name: Scott
full_name: Ritchie, Scott
last_name: Ritchie
- first_name: Ary
full_name: Hoffmann, Ary
last_name: Hoffmann
- first_name: Scott
full_name: O’Neill, Scott
last_name: O’Neill
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: Schmidt T, Barton NH, Rasic G, et al. Local introduction and heterogeneous
spatial spread of dengue-suppressing Wolbachia through an urban population of
Aedes Aegypti. PLoS Biology. 2017;15(5). doi:10.1371/journal.pbio.2001894
apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe,
I., … Turelli, M. (2017). Local introduction and heterogeneous spatial spread
of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894
chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery,
Inaki Iturbe Ormaetxe, Peter Cook, et al. “Local Introduction and Heterogeneous
Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of
Aedes Aegypti.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.
ieee: T. Schmidt et al., “Local introduction and heterogeneous spatial spread
of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti,”
PLoS Biology, vol. 15, no. 5. Public Library of Science, 2017.
ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I,
Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Local introduction
and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban
population of Aedes Aegypti. PLoS Biology. 15(5), e2001894.
mla: Schmidt, Tom, et al. “Local Introduction and Heterogeneous Spatial Spread of
Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS
Biology, vol. 15, no. 5, e2001894, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.
short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe,
P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, PLoS Biology
15 (2017).
date_created: 2018-12-11T11:49:22Z
date_published: 2017-05-30T00:00:00Z
date_updated: 2023-09-22T10:02:52Z
day: '30'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2001894
external_id:
isi:
- '000402520000012'
file:
- access_level: open_access
checksum: 107d290bd1159ec77b734eb2824b01c8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:30Z
date_updated: 2020-07-14T12:48:16Z
file_id: '4691'
file_name: IST-2017-843-v1+1_journal.pbio.2001894.pdf
file_size: 5541206
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_identifier:
issn:
- '15449173'
publication_status: published
publisher: Public Library of Science
publist_id: '6464'
pubrep_id: '843'
quality_controlled: '1'
related_material:
record:
- id: '9856'
relation: research_data
status: public
- id: '9857'
relation: research_data
status: public
- id: '9858'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia
through an urban population of Aedes Aegypti
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 15
year: '2017'
...
---
_id: '947'
abstract:
- lang: eng
text: Viewing the ways a living cell can organize its metabolism as the phase space
of a physical system, regulation can be seen as the ability to reduce the entropy
of that space by selecting specific cellular configurations that are, in some
sense, optimal. Here we quantify the amount of regulation required to control
a cell's growth rate by a maximum-entropy approach to the space of underlying
metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern
as described by genome-scale models. We link the mean growth rate achieved by
a population of cells to the minimal amount of metabolic regulation needed to
achieve it through a phase diagram that highlights how growth suppression can
be as costly (in regulatory terms) as growth enhancement. Moreover, we provide
an interpretation of the inverse temperature β controlling maximum-entropy distributions
based on the underlying growth dynamics. Specifically, we show that the asymptotic
value of β for a cell population can be expected to depend on (i) the carrying
capacity of the environment, (ii) the initial size of the colony, and (iii) the
probability distribution from which the inoculum was sampled. Results obtained
for E. coli and human cells are found to be remarkably consistent with empirical
evidence.
article_number: '010401'
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Fabrizio
full_name: Capuani, Fabrizio
last_name: Capuani
- first_name: Andrea
full_name: De Martino, Andrea
last_name: De Martino
citation:
ama: De Martino D, Capuani F, De Martino A. Quantifying the entropic cost of cellular
growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics
. 2017;96(1). doi:10.1103/PhysRevE.96.010401
apa: De Martino, D., Capuani, F., & De Martino, A. (2017). Quantifying the entropic
cost of cellular growth control. Physical Review E Statistical Nonlinear and
Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.010401
chicago: De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying
the Entropic Cost of Cellular Growth Control.” Physical Review E Statistical
Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.010401.
ieee: D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost
of cellular growth control,” Physical Review E Statistical Nonlinear and Soft
Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017.
ista: De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost
of cellular growth control. Physical Review E Statistical Nonlinear and Soft
Matter Physics . 96(1), 010401.
mla: De Martino, Daniele, et al. “Quantifying the Entropic Cost of Cellular Growth
Control.” Physical Review E Statistical Nonlinear and Soft Matter Physics
, vol. 96, no. 1, 010401, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.010401.
short: D. De Martino, F. Capuani, A. De Martino, Physical Review E Statistical
Nonlinear and Soft Matter Physics 96 (2017).
date_created: 2018-12-11T11:49:21Z
date_published: 2017-07-10T00:00:00Z
date_updated: 2023-09-22T10:03:50Z
day: '10'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.96.010401
ec_funded: 1
external_id:
isi:
- '000405194200002'
intvolume: ' 96'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.00219
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Physical Review E Statistical Nonlinear and Soft Matter Physics '
publication_identifier:
issn:
- '24700045'
publication_status: published
publisher: American Institute of Physics
publist_id: '6470'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantifying the entropic cost of cellular growth control
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 96
year: '2017'
...
---
_id: '9858'
article_processing_charge: No
author:
- first_name: Tom
full_name: Schmidt, Tom
last_name: Schmidt
- 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: Gordana
full_name: Rasic, Gordana
last_name: Rasic
- first_name: Andrew
full_name: Turley, Andrew
last_name: Turley
- first_name: Brian
full_name: Montgomery, Brian
last_name: Montgomery
- first_name: Inaki
full_name: Iturbe Ormaetxe, Inaki
last_name: Iturbe Ormaetxe
- first_name: Peter
full_name: Cook, Peter
last_name: Cook
- first_name: Peter
full_name: Ryan, Peter
last_name: Ryan
- first_name: Scott
full_name: Ritchie, Scott
last_name: Ritchie
- first_name: Ary
full_name: Hoffmann, Ary
last_name: Hoffmann
- first_name: Scott
full_name: O’Neill, Scott
last_name: O’Neill
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: Schmidt T, Barton NH, Rasic G, et al. Excel file with data on mosquito densities,
Wolbachia infection status and housing characteristics. 2017. doi:10.1371/journal.pbio.2001894.s016
apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe,
I., … Turelli, M. (2017). Excel file with data on mosquito densities, Wolbachia
infection status and housing characteristics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s016
chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery,
Inaki Iturbe Ormaetxe, Peter Cook, et al. “Excel File with Data on Mosquito Densities,
Wolbachia Infection Status and Housing Characteristics.” Public Library of Science,
2017. https://doi.org/10.1371/journal.pbio.2001894.s016.
ieee: T. Schmidt et al., “Excel file with data on mosquito densities, Wolbachia
infection status and housing characteristics.” Public Library of Science, 2017.
ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I,
Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Excel file
with data on mosquito densities, Wolbachia infection status and housing characteristics,
Public Library of Science, 10.1371/journal.pbio.2001894.s016.
mla: Schmidt, Tom, et al. Excel File with Data on Mosquito Densities, Wolbachia
Infection Status and Housing Characteristics. Public Library of Science, 2017,
doi:10.1371/journal.pbio.2001894.s016.
short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe,
P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).
date_created: 2021-08-10T07:47:07Z
date_published: 2017-05-30T00:00:00Z
date_updated: 2023-09-22T10:02:51Z
day: '30'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2001894.s016
month: '05'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '951'
relation: used_in_publication
status: public
status: public
title: Excel file with data on mosquito densities, Wolbachia infection status and
housing characteristics
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...