---
_id: '1545'
abstract:
- lang: eng
text: We provide general conditions for which bosonic quadratic Hamiltonians on
Fock spaces can be diagonalized by Bogoliubov transformations. Our results cover
the case when quantum systems have infinite degrees of freedom and the associated
one-body kinetic and paring operators are unbounded. Our sufficient conditions
are optimal in the sense that they become necessary when the relevant one-body
operators commute.
acknowledgement: We thank Jan Dereziński for several inspiring discussions and useful
remarks. We thank the referee for helpful comments. J.P.S. thanks the Erwin Schrödinger
Institute for the hospitality during the thematic programme “Quantum many-body systems,
random matrices, and disorder”. We gratefully acknowledge the financial supports
by the European Union's Seventh Framework Programme under the ERC Advanced Grant
ERC-2012-AdG 321029 (J.P.S.) and the REA grant agreement No. 291734 (P.T.N.), as
well as the support of the National Science Center (NCN) grant No. 2012/07/N/ST1/03185
and the Austrian Science Fund (FWF) project No. P 27533-N27 (M.N.).
article_processing_charge: No
arxiv: 1
author:
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
- first_name: Marcin M
full_name: Napiórkowski, Marcin M
id: 4197AD04-F248-11E8-B48F-1D18A9856A87
last_name: Napiórkowski
- first_name: Jan
full_name: Solovej, Jan
last_name: Solovej
citation:
ama: Nam P, Napiórkowski MM, Solovej J. Diagonalization of bosonic quadratic Hamiltonians
by Bogoliubov transformations. Journal of Functional Analysis. 2016;270(11):4340-4368.
doi:10.1016/j.jfa.2015.12.007
apa: Nam, P., Napiórkowski, M. M., & Solovej, J. (2016). Diagonalization of
bosonic quadratic Hamiltonians by Bogoliubov transformations. Journal of Functional
Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2015.12.007
chicago: Nam, Phan, Marcin M Napiórkowski, and Jan Solovej. “Diagonalization of
Bosonic Quadratic Hamiltonians by Bogoliubov Transformations.” Journal of Functional
Analysis. Academic Press, 2016. https://doi.org/10.1016/j.jfa.2015.12.007.
ieee: P. Nam, M. M. Napiórkowski, and J. Solovej, “Diagonalization of bosonic quadratic
Hamiltonians by Bogoliubov transformations,” Journal of Functional Analysis,
vol. 270, no. 11. Academic Press, pp. 4340–4368, 2016.
ista: Nam P, Napiórkowski MM, Solovej J. 2016. Diagonalization of bosonic quadratic
Hamiltonians by Bogoliubov transformations. Journal of Functional Analysis. 270(11),
4340–4368.
mla: Nam, Phan, et al. “Diagonalization of Bosonic Quadratic Hamiltonians by Bogoliubov
Transformations.” Journal of Functional Analysis, vol. 270, no. 11, Academic
Press, 2016, pp. 4340–68, doi:10.1016/j.jfa.2015.12.007.
short: P. Nam, M.M. Napiórkowski, J. Solovej, Journal of Functional Analysis 270
(2016) 4340–4368.
corr_author: '1'
date_created: 2018-12-11T11:52:38Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2025-09-18T11:04:09Z
day: '01'
department:
- _id: RoSe
doi: 10.1016/j.jfa.2015.12.007
ec_funded: 1
external_id:
arxiv:
- '1508.07321'
isi:
- '000375241700011'
intvolume: ' 270'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1508.07321
month: '06'
oa: 1
oa_version: Submitted Version
page: 4340 - 4368
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _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: Journal of Functional Analysis
publication_status: published
publisher: Academic Press
publist_id: '5626'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 270
year: '2016'
...
---
_id: '1059'
abstract:
- lang: eng
text: A range of bright and photostable rhodamines and carbopyronines with absorption
maxima in the range of λ=500-630 nm were prepared, and enabled the specific labeling
of cytoskeletal filaments using HaloTag technology followed by staining with 1
μm solutions of the dye-ligand conjugates. The synthesis, photophysical parameters,
fluorogenic behavior, and structure-property relationships of the new dyes are
discussed. Light microscopy with stimulated emission depletion (STED) provided
one- and two-color images of living cells with an optical resolution of 40-60
nm.
acknowledgement: We thank Prof. Y. Okada (RIKEN Quantitative Biology Center, Osaka,
Japan) for the gift of β-tubulin-Halo plasmid, T. Gilat and Dr. E. Rothermel (MPIBPC,
Göttingen, Germany) for cell culture and transfection, M. Pulst, J. Bienert (MPIBPC),
Dr. M. John, Dr. H. Frauendorf, and co-workers (Institut für Organische und Biomolekulare
Chemie, Georg-August-Universität, Göttingen, Germany) for UV/Vis, NMR, and ESI-MS
spectra, Prof. M. L. Bossi (University of Buenos-Aires, Argentina) for measuring
fluorescence lifetimes, and Dr. S. Vos and Prof. P. Cramer (MPIBPC) for access to
a Tecan microplate reader. S.W.H. acknowledges a grant from the Bundesministerium
für Bildung und Forschung (BMBF 513) within the program “Optische Technologien für
Biowissenschaften und Gesundheit” (FKZ 13N11066). J.G.D. was supported by funds
from the People Programme (Marie Curie Actions) of the European Union's Seventh
Framework Programme (FP7/2007–2013; REA grant agreement PIEF-GA-2011-299283).
article_processing_charge: No
author:
- first_name: Alexey
full_name: Butkevich, Alexey
last_name: Butkevich
- first_name: Gyuzel
full_name: Mitronova, Gyuzel
last_name: Mitronova
- first_name: Sven
full_name: Sidenstein, Sven
last_name: Sidenstein
- first_name: Jessica
full_name: Klocke, Jessica
last_name: Klocke
- first_name: Dirk
full_name: Kamin, Dirk
last_name: Kamin
- first_name: Dirk
full_name: Meineke, Dirk
last_name: Meineke
- first_name: Elisa
full_name: D'Este, Elisa
last_name: D'Este
- first_name: Philip
full_name: Kraemer, Philip
last_name: Kraemer
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Vladimir
full_name: Belov, Vladimir
last_name: Belov
- first_name: Stefan
full_name: Hell, Stefan
last_name: Hell
citation:
ama: Butkevich A, Mitronova G, Sidenstein S, et al. Fluorescent rhodamines and fluorogenic
carbopyronines for super-resolution STED microscopy in living cells. Angewandte
Chemie - International Edition. 2016;55(10):3290-3294. doi:10.1002/anie.201511018
apa: Butkevich, A., Mitronova, G., Sidenstein, S., Klocke, J., Kamin, D., Meineke,
D., … Hell, S. (2016). Fluorescent rhodamines and fluorogenic carbopyronines for
super-resolution STED microscopy in living cells. Angewandte Chemie - International
Edition. Wiley-Blackwell. https://doi.org/10.1002/anie.201511018
chicago: Butkevich, Alexey, Gyuzel Mitronova, Sven Sidenstein, Jessica Klocke, Dirk
Kamin, Dirk Meineke, Elisa D’Este, et al. “Fluorescent Rhodamines and Fluorogenic
Carbopyronines for Super-Resolution STED Microscopy in Living Cells.” Angewandte
Chemie - International Edition. Wiley-Blackwell, 2016. https://doi.org/10.1002/anie.201511018.
ieee: A. Butkevich et al., “Fluorescent rhodamines and fluorogenic carbopyronines
for super-resolution STED microscopy in living cells,” Angewandte Chemie -
International Edition, vol. 55, no. 10. Wiley-Blackwell, pp. 3290–3294, 2016.
ista: Butkevich A, Mitronova G, Sidenstein S, Klocke J, Kamin D, Meineke D, D’Este
E, Kraemer P, Danzl JG, Belov V, Hell S. 2016. Fluorescent rhodamines and fluorogenic
carbopyronines for super-resolution STED microscopy in living cells. Angewandte
Chemie - International Edition. 55(10), 3290–3294.
mla: Butkevich, Alexey, et al. “Fluorescent Rhodamines and Fluorogenic Carbopyronines
for Super-Resolution STED Microscopy in Living Cells.” Angewandte Chemie -
International Edition, vol. 55, no. 10, Wiley-Blackwell, 2016, pp. 3290–94,
doi:10.1002/anie.201511018.
short: A. Butkevich, G. Mitronova, S. Sidenstein, J. Klocke, D. Kamin, D. Meineke,
E. D’Este, P. Kraemer, J.G. Danzl, V. Belov, S. Hell, Angewandte Chemie - International
Edition 55 (2016) 3290–3294.
date_created: 2018-12-11T11:49:55Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2021-01-12T06:47:59Z
day: '01'
doi: 10.1002/anie.201511018
extern: '1'
intvolume: ' 55'
issue: '10'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa_version: None
page: 3290 - 3294
publication: Angewandte Chemie - International Edition
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6330'
status: public
title: Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution
STED microscopy in living cells
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...
---
_id: '1060'
abstract:
- lang: eng
text: Superresolution fluorescence microscopy of multiple fluorophores still requires
development. Here we present simultaneous three-colour stimulated emission depletion
(STED) nanoscopy relying on a single STED beam at 620 nm. Toggling the STED beam
between two or more power levels ("multilevelSTEDv) optimizes resolution
and contrast in all colour channels, which are intrinsically co-aligned and well
separated. Three-colour recording is demonstrated by imaging the nanoscale cytoskeletal
organization in cultured hippocampal neurons. The down to ∼35 nm resolution identified
periodic actin/betaII spectrin lattices along dendrites and spines; however, at
presynaptic and postsynaptic sites, these patterns were found to be absent. Both
our multicolour scheme and the 620 nm STED line should be attractive for routine
STED microscopy applications.
acknowledgement: We acknowledge the assistance of I. Herfort with neuron preparation,
and of J. Bienert and K. Müller with analyses of the dye 540R derivatives. We thank
T. Gilat and E. Rothermel for sample preparation as well as J. Keller, F. Winter
(all MPI-BPC) and C.A. Wurm (Abberior Instruments) for helpful discussion, and S.J.
Sahl (MPI-BPC) for a critical reading of the manuscript.
article_processing_charge: No
author:
- first_name: Sven
full_name: Sidenstein, Sven
last_name: Sidenstein
- first_name: Elisa
full_name: D'Este, Elisa
last_name: D'Este
- first_name: Marvin
full_name: Böhm, Marvin
last_name: Böhm
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Vladimir
full_name: Belov, Vladimir
last_name: Belov
- first_name: Stefan
full_name: Hell, Stefan
last_name: Hell
citation:
ama: Sidenstein S, D’Este E, Böhm M, Danzl JG, Belov V, Hell S. Multicolour multilevel
STED nanoscopy of actin/spectrin organization at synapses. Scientific Reports.
2016;6:1-8. doi:10.1038/srep26725
apa: Sidenstein, S., D’Este, E., Böhm, M., Danzl, J. G., Belov, V., & Hell,
S. (2016). Multicolour multilevel STED nanoscopy of actin/spectrin organization
at synapses. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep26725
chicago: Sidenstein, Sven, Elisa D’Este, Marvin Böhm, Johann G Danzl, Vladimir Belov,
and Stefan Hell. “Multicolour Multilevel STED Nanoscopy of Actin/Spectrin Organization
at Synapses.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep26725.
ieee: S. Sidenstein, E. D’Este, M. Böhm, J. G. Danzl, V. Belov, and S. Hell, “Multicolour
multilevel STED nanoscopy of actin/spectrin organization at synapses,” Scientific
Reports, vol. 6. Nature Publishing Group, pp. 1–8, 2016.
ista: Sidenstein S, D’Este E, Böhm M, Danzl JG, Belov V, Hell S. 2016. Multicolour
multilevel STED nanoscopy of actin/spectrin organization at synapses. Scientific
Reports. 6, 1–8.
mla: Sidenstein, Sven, et al. “Multicolour Multilevel STED Nanoscopy of Actin/Spectrin
Organization at Synapses.” Scientific Reports, vol. 6, Nature Publishing
Group, 2016, pp. 1–8, doi:10.1038/srep26725.
short: S. Sidenstein, E. D’Este, M. Böhm, J.G. Danzl, V. Belov, S. Hell, Scientific
Reports 6 (2016) 1–8.
date_created: 2018-12-11T11:49:56Z
date_published: 2016-05-25T00:00:00Z
date_updated: 2021-01-12T06:47:59Z
day: '25'
doi: 10.1038/srep26725
extern: '1'
intvolume: ' 6'
language:
- iso: eng
month: '05'
oa_version: None
page: 1 - 8
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6329'
status: public
title: Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1068'
abstract:
- lang: eng
text: 'Games on graphs provide the appropriate framework to study several central
problems in computer science, such as verification and synthesis of reactive systems.
One of the most basic objectives for games on graphs is the liveness (or Büchi)
objective that given a target set of vertices requires that some vertex in the
target set is visited infinitely often. We study generalized Büchi objectives
(i.e., conjunction of liveness objectives), and implications between two generalized
Büchi objectives (known as GR(1) objectives), that arise in numerous applications
in computer-aided verification. We present improved algorithms and conditional
super-linear lower bounds based on widely believed assumptions about the complexity
of (A1) combinatorial Boolean matrix multiplication and (A2) CNF-SAT. We consider
graph games with n vertices, m edges, and generalized Büchi objectives with k
conjunctions. First, we present an algorithm with running time O(k*n^2), improving
the previously known O(k*n*m) and O(k^2*n^2) worst-case bounds. Our algorithm
is optimal for dense graphs under (A1). Second, we show that the basic algorithm
for the problem is optimal for sparse graphs when the target sets have constant
size under (A2). Finally, we consider GR(1) objectives, with k_1 conjunctions
in the antecedent and k_2 conjunctions in the consequent, and present an O(k_1
k_2 n^{2.5})-time algorithm, improving the previously known O(k_1*k_2*n*m)-time
algorithm for m > n^{1.5}. '
acknowledgement: K. C., M. H., and W. D. are partially supported by the Vienna Science
and Technology Fund (WWTF) through project ICT15-003. K. C. is partially supported
by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC
Start grant (279307
alternative_title:
- LIPIcs
article_number: '25'
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: Wolfgang
full_name: Dvorák, Wolfgang
last_name: Dvorák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Veronika
full_name: Loitzenbauer, Veronika
last_name: Loitzenbauer
citation:
ama: 'Chatterjee K, Dvorák W, Henzinger M, Loitzenbauer V. Conditionally optimal
algorithms for generalized Büchi Games. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2016. doi:10.4230/LIPIcs.MFCS.2016.25'
apa: 'Chatterjee, K., Dvorák, W., Henzinger, M., & Loitzenbauer, V. (2016).
Conditionally optimal algorithms for generalized Büchi Games (Vol. 58). Presented
at the MFCS: Mathematical Foundations of Computer Science, Krakow, Poland: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2016.25'
chicago: Chatterjee, Krishnendu, Wolfgang Dvorák, Monika Henzinger, and Veronika
Loitzenbauer. “Conditionally Optimal Algorithms for Generalized Büchi Games,”
Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.MFCS.2016.25.
ieee: 'K. Chatterjee, W. Dvorák, M. Henzinger, and V. Loitzenbauer, “Conditionally
optimal algorithms for generalized Büchi Games,” presented at the MFCS: Mathematical
Foundations of Computer Science, Krakow, Poland, 2016, vol. 58.'
ista: 'Chatterjee K, Dvorák W, Henzinger M, Loitzenbauer V. 2016. Conditionally
optimal algorithms for generalized Büchi Games. MFCS: Mathematical Foundations
of Computer Science, LIPIcs, vol. 58, 25.'
mla: Chatterjee, Krishnendu, et al. Conditionally Optimal Algorithms for Generalized
Büchi Games. Vol. 58, 25, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2016, doi:10.4230/LIPIcs.MFCS.2016.25.
short: K. Chatterjee, W. Dvorák, M. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2016.
conference:
end_date: 2016-08-26
location: Krakow, Poland
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2016-08-22
date_created: 2018-12-11T11:49:58Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2025-07-10T11:49:55Z
day: '01'
ddc:
- '000'
- '004'
- '006'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.MFCS.2016.25
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:02Z
date_updated: 2018-12-12T10:16:02Z
file_id: '5187'
file_name: IST-2017-779-v1+1_LIPIcs-MFCS-2016-25.pdf
file_size: 632786
relation: main_file
file_date_updated: 2018-12-12T10:16:02Z
has_accepted_license: '1'
intvolume: ' 58'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6317'
pubrep_id: '779'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Conditionally optimal algorithms for generalized Büchi Games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2016'
...
---
_id: '1069'
abstract:
- lang: eng
text: "The Continuous Skolem Problem asks whether a real-valued function satisfying
a linear differen-\r\ntial equation has a zero in a given interval of real numbers.
This is a fundamental reachability\r\nproblem for continuous linear dynamical
systems, such as linear hybrid automata and continuous-\r\ntime Markov chains.
Decidability of the problem is currently open – indeed decidability is open\r\neven
for the sub-problem in which a zero is sought in a bounded interval. In this paper
we show\r\ndecidability of the bounded problem subject to Schanuel’s Conjecture,
a unifying conjecture in\r\ntranscendental number theory. We furthermore analyse
the unbounded problem in terms of the\r\nfrequencies of the differential equation,
that is, the imaginary parts of the characteristic roots.\r\nWe show that the
unbounded problem can be reduced to the bounded problem if there is at most\r\none
rationally linearly independent frequency, or if there are two rationally linearly
independent\r\nfrequencies and all characteristic roots are simple. We complete
the picture by showing that de-\r\ncidability of the unbounded problem in the
case of two (or more) rationally linearly independent\r\nfrequencies would entail
a major new effectiveness result in Diophantine approximation, namely\r\ncomputability
of the Diophantine-approximation types of all real algebraic numbers."
acknowledgement: 'Ventsislav Chonev is supported by Austrian Science Fund (FWF) NFN
Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and ERC
Advanced Grant (267989: QUAREM).'
alternative_title:
- LIPIcs
article_number: '100'
article_processing_charge: No
author:
- first_name: Ventsislav K
full_name: Chonev, Ventsislav K
id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87
last_name: Chonev
- first_name: Joël
full_name: Ouaknine, Joël
last_name: Ouaknine
- first_name: James
full_name: Worrell, James
last_name: Worrell
citation:
ama: 'Chonev VK, Ouaknine J, Worrell J. On the skolem problem for continuous linear
dynamical systems. In: Vol 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2016. doi:10.4230/LIPIcs.ICALP.2016.100'
apa: 'Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On the skolem problem
for continuous linear dynamical systems (Vol. 55). Presented at the ICALP: Automata,
Languages and Programming, Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für
Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2016.100'
chicago: Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Skolem
Problem for Continuous Linear Dynamical Systems,” Vol. 55. Schloss Dagstuhl -
Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.ICALP.2016.100.
ieee: 'V. K. Chonev, J. Ouaknine, and J. Worrell, “On the skolem problem for continuous
linear dynamical systems,” presented at the ICALP: Automata, Languages and Programming,
Rome, Italy, 2016, vol. 55.'
ista: 'Chonev VK, Ouaknine J, Worrell J. 2016. On the skolem problem for continuous
linear dynamical systems. ICALP: Automata, Languages and Programming, LIPIcs,
vol. 55, 100.'
mla: Chonev, Ventsislav K., et al. On the Skolem Problem for Continuous Linear
Dynamical Systems. Vol. 55, 100, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2016, doi:10.4230/LIPIcs.ICALP.2016.100.
short: V.K. Chonev, J. Ouaknine, J. Worrell, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2016.
conference:
end_date: 2016-07-15
location: Rome, Italy
name: 'ICALP: Automata, Languages and Programming'
start_date: 2016-07-12
date_created: 2018-12-11T11:49:59Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2025-06-03T11:32:08Z
day: '01'
ddc:
- '004'
- '006'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.ICALP.2016.100
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:26Z
date_updated: 2018-12-12T10:16:26Z
file_id: '5213'
file_name: IST-2017-778-v1+1_LIPIcs-ICALP-2016-100.pdf
file_size: 521415
relation: main_file
file_date_updated: 2018-12-12T10:16:26Z
has_accepted_license: '1'
intvolume: ' 55'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _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
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6314'
pubrep_id: '778'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the skolem problem for continuous linear dynamical systems
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...
---
_id: '1070'
abstract:
- lang: eng
text: 'We present a logic that extends CTL (Computation Tree Logic) with operators
that express synchronization properties. A property is synchronized in a system
if it holds in all paths of a certain length. The new logic is obtained by using
the same path quantifiers and temporal operators as in CTL, but allowing a different
order of the quantifiers. This small syntactic variation induces a logic that
can express non-regular properties for which known extensions of MSO with equality
of path length are undecidable. We show that our variant of CTL is decidable and
that the model-checking problem is in Delta_3^P = P^{NP^NP}, and is DP-hard. We
analogously consider quantifier exchange in extensions of CTL, and we present
operators defined using basic operators of CTL* that express the occurrence of
infinitely many synchronization points. We show that the model-checking problem
remains in Delta_3^P. The distinguishing power of CTL and of our new logic coincide
if the Next operator is allowed in the logics, thus the classical bisimulation
quotient can be used for state-space reduction before model checking. '
acknowledgement: "This research was partially supported by Austrian Science Fund (FWF)
NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), Vienna
Science and Technology Fund (WWTF) through project ICT15-003, and European project
Cassting (FP7-601148).\r\n\r\nWe thank Stefan Göller and anonymous reviewers for
their insightful\r\ncomments and suggestions.\r\n"
alternative_title:
- LIPIcs
article_number: '98'
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: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: 'Chatterjee K, Doyen L. Computation tree logic for synchronization properties.
In: Vol 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.ICALP.2016.98'
apa: 'Chatterjee, K., & Doyen, L. (2016). Computation tree logic for synchronization
properties (Vol. 55). Presented at the ICALP: Automata, Languages and Programming,
Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2016.98'
chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Computation Tree Logic for
Synchronization Properties,” Vol. 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2016. https://doi.org/10.4230/LIPIcs.ICALP.2016.98.
ieee: 'K. Chatterjee and L. Doyen, “Computation tree logic for synchronization properties,”
presented at the ICALP: Automata, Languages and Programming, Rome, Italy, 2016,
vol. 55.'
ista: 'Chatterjee K, Doyen L. 2016. Computation tree logic for synchronization properties.
ICALP: Automata, Languages and Programming, LIPIcs, vol. 55, 98.'
mla: Chatterjee, Krishnendu, and Laurent Doyen. Computation Tree Logic for Synchronization
Properties. Vol. 55, 98, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2016, doi:10.4230/LIPIcs.ICALP.2016.98.
short: K. Chatterjee, L. Doyen, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2016.
conference:
end_date: 2016-07-15
location: Rome, Italy
name: 'ICALP: Automata, Languages and Programming'
start_date: 2016-07-12
date_created: 2018-12-11T11:49:59Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2025-06-03T11:18:54Z
day: '01'
ddc:
- '005'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.ICALP.2016.98
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:52Z
date_updated: 2018-12-12T10:08:52Z
file_id: '4714'
file_name: IST-2017-812-v1+1_LIPIcs-ICALP-2016-98.pdf
file_size: 546133
relation: main_file
file_date_updated: 2018-12-12T10:08:52Z
has_accepted_license: '1'
intvolume: ' 55'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6313'
pubrep_id: '812'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computation tree logic for synchronization properties
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...
---
_id: '10746'
abstract:
- lang: eng
text: Vortex states in superconducting (SC) structures, their dynamics and ways
to manipulate them are topics of great interest. We report a new method of magnetic
force microscopy (MFM) that allows the study of vortex states in mesoscopic SC
samples. For the case of a SC ring, which is biased to a half-integer flux quantum,
the flux modulation through the ring caused by the motion of the magnetic tip
drives the ring between two consecutive fluxoid states. The corresponding current
switching in the ring produces strong position-dependent forces on the cantilever.
In the regime where the frequency of the thermally activated jumps between fluxoid
states is close to the frequency of the cantilever, large changes in the cantilever
frequency and dissipation are observed. This effect may be understood as a stochastic
resonance (SR) process. These changes in the cantilever’s mechanical properties
are used to “image” the barrier energies between fluxoid states. Additionally,
SR imaging of the barrier energies are used to study the effect of the locally
applied magnetic field from the MFM tip on the barrier heights. We report the
results of measurements for Al rings. Further, the same imaging technique can
be applied to more sophisticated SC structures such as arrays of Josephson junctions.
alternative_title:
- Bulletin of the American Physical Society
article_number: E25.00007
article_processing_charge: No
author:
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: Tyler
full_name: Naibert, Tyler
last_name: Naibert
- first_name: Victor
full_name: Chua, Victor
last_name: Chua
- first_name: Raffi
full_name: Budakian, Raffi
last_name: Budakian
citation:
ama: 'Polshyn H, Naibert T, Chua V, Budakian R. Study of vortex states and dynamics
in mesoscopic superconducting samples with MFM. In: APS March Meeting 2016.
Vol 61. American Physical Society; 2016.'
apa: 'Polshyn, H., Naibert, T., Chua, V., & Budakian, R. (2016). Study of vortex
states and dynamics in mesoscopic superconducting samples with MFM. In APS
March Meeting 2016 (Vol. 61). Baltimore, MD, United States: American Physical
Society.'
chicago: Polshyn, Hryhoriy, Tyler Naibert, Victor Chua, and Raffi Budakian. “Study
of Vortex States and Dynamics in Mesoscopic Superconducting Samples with MFM.”
In APS March Meeting 2016, Vol. 61. American Physical Society, 2016.
ieee: H. Polshyn, T. Naibert, V. Chua, and R. Budakian, “Study of vortex states
and dynamics in mesoscopic superconducting samples with MFM,” in APS March
Meeting 2016, Baltimore, MD, United States, 2016, vol. 61, no. 2.
ista: 'Polshyn H, Naibert T, Chua V, Budakian R. 2016. Study of vortex states and
dynamics in mesoscopic superconducting samples with MFM. APS March Meeting 2016.
APS: American Physical Society, Bulletin of the American Physical Society, vol.
61, E25.00007.'
mla: Polshyn, Hryhoriy, et al. “Study of Vortex States and Dynamics in Mesoscopic
Superconducting Samples with MFM.” APS March Meeting 2016, vol. 61, no.
2, E25.00007, American Physical Society, 2016.
short: H. Polshyn, T. Naibert, V. Chua, R. Budakian, in:, APS March Meeting 2016,
American Physical Society, 2016.
conference:
end_date: 2016-03-18
location: Baltimore, MD, United States
name: 'APS: American Physical Society'
start_date: 2016-03-14
date_created: 2022-02-08T09:55:09Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2022-02-08T10:44:06Z
day: '01'
extern: '1'
intvolume: ' 61'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://meetings.aps.org/Meeting/MAR16/Session/E25.7
month: '03'
oa: 1
oa_version: Published Version
publication: APS March Meeting 2016
publication_identifier:
issn:
- 0003-0503
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Study of vortex states and dynamics in mesoscopic superconducting samples with
MFM
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 61
year: '2016'
...
---
_id: '10747'
abstract:
- lang: eng
text: Vortex interactions are key to explaining the behavior of many two dimensional
superconducting systems. We report on the development of a technique to locally
probe vortex interactions in a 2D array of Josephson junctions. Scanning a magnetic
tip attached to an ultra-soft cantilever over the array produces changes in the
frequency of the cantilever along certain lines, forming geometric patterns in
the scans. Different tip-surface separations and external magnetic fields produce
a number of different patterns. These patterns correspond to tip locations in
which two configurations of vortices in the lattice have degenerate energies.
By imaging the locations of these degeneracies, information on the local vortex
interactions may be obtained.
alternative_title:
- Bulletin of the American Physical Society
article_number: H25.00006
article_processing_charge: No
author:
- first_name: Tyler
full_name: Naibert, Tyler
last_name: Naibert
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: Brian
full_name: Wolin, Brian
last_name: Wolin
- first_name: Malcolm
full_name: Durkin, Malcolm
last_name: Durkin
- first_name: Rita
full_name: Garrido Menacho, Rita
last_name: Garrido Menacho
- first_name: Ian Mondragon
full_name: Shem, Ian Mondragon
last_name: Shem
- first_name: Victor
full_name: Chua, Victor
last_name: Chua
- first_name: Taylor
full_name: Hughes, Taylor
last_name: Hughes
- first_name: Nadya
full_name: Mason, Nadya
last_name: Mason
- first_name: Raffi
full_name: Budakian, Raffi
last_name: Budakian
citation:
ama: 'Naibert T, Polshyn H, Wolin B, et al. Stochastic resonance magnetic force
microscopy imaging of Josephson arrays. In: APS March Meeting 2016. Vol
61. American Physical Society; 2016.'
apa: 'Naibert, T., Polshyn, H., Wolin, B., Durkin, M., Garrido Menacho, R., Shem,
I. M., … Budakian, R. (2016). Stochastic resonance magnetic force microscopy imaging
of Josephson arrays. In APS March Meeting 2016 (Vol. 61). Baltimore, MD,
United States: American Physical Society.'
chicago: Naibert, Tyler, Hryhoriy Polshyn, Brian Wolin, Malcolm Durkin, Rita Garrido
Menacho, Ian Mondragon Shem, Victor Chua, Taylor Hughes, Nadya Mason, and Raffi
Budakian. “Stochastic Resonance Magnetic Force Microscopy Imaging of Josephson
Arrays.” In APS March Meeting 2016, Vol. 61. American Physical Society,
2016.
ieee: T. Naibert et al., “Stochastic resonance magnetic force microscopy
imaging of Josephson arrays,” in APS March Meeting 2016, Baltimore, MD,
United States, 2016, vol. 61, no. 2.
ista: 'Naibert T, Polshyn H, Wolin B, Durkin M, Garrido Menacho R, Shem IM, Chua
V, Hughes T, Mason N, Budakian R. 2016. Stochastic resonance magnetic force microscopy
imaging of Josephson arrays. APS March Meeting 2016. APS: American Physical Society,
Bulletin of the American Physical Society, vol. 61, H25.00006.'
mla: Naibert, Tyler, et al. “Stochastic Resonance Magnetic Force Microscopy Imaging
of Josephson Arrays.” APS March Meeting 2016, vol. 61, no. 2, H25.00006,
American Physical Society, 2016.
short: T. Naibert, H. Polshyn, B. Wolin, M. Durkin, R. Garrido Menacho, I.M. Shem,
V. Chua, T. Hughes, N. Mason, R. Budakian, in:, APS March Meeting 2016, American
Physical Society, 2016.
conference:
end_date: 2016-03-18
location: Baltimore, MD, United States
name: 'APS: American Physical Society'
start_date: 2016-03-14
date_created: 2022-02-08T10:10:39Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2022-02-08T10:43:33Z
day: '01'
extern: '1'
intvolume: ' 61'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://meetings.aps.org/Meeting/MAR16/Session/H25.6
month: '03'
oa: 1
oa_version: Published Version
publication: APS March Meeting 2016
publication_identifier:
issn:
- 0003-0503
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Stochastic resonance magnetic force microscopy imaging of Josephson arrays
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 61
year: '2016'
...
---
_id: '1081'
abstract:
- lang: eng
text: The asymmetric localization of proteins in the plasma membrane domains of
eukaryotic cells is a fundamental manifestation of cell polarity that is central
to multicellular organization and developmental patterning. In plants, the mechanisms
underlying the polar localization of cargo proteins are still largely unknown
and appear to be fundamentally distinct from those operating in mammals. Here,
we present a systematic, quantitative comparative analysis of the polar delivery
and subcellular localization of proteins that characterize distinct polar plasma
membrane domains in plant cells. The combination of microscopic analyses and computational
modeling revealed a mechanistic framework common to diverse polar cargos and underlying
the establishment and maintenance of apical, basal, and lateral polar domains
in plant cells. This mechanism depends on the polar secretion, constitutive endocytic
recycling, and restricted lateral diffusion of cargos within the plasma membrane.
Moreover, our observations suggest that polar cargo distribution involves the
individual protein potential to form clusters within the plasma membrane and interact
with the extracellular matrix. Our observations provide insights into the shared
cellular mechanisms of polar cargo delivery and polarity maintenance in plant
cells.
acknowledgement: "We thank Bonnie Bartel, Jenny Russinova and Niko Geldner\r\nfor
sharing published material, Martine de Cock and Annick\r\nBleys for help in preparing
the manuscript. This work was\r\nsupported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP);
Czech Science Foundation\r\nGAČR (GA13-40637S); project CEITEC—Central European\r\nInstitute
of Technology (CZ.1.05/1.1.00/02.0068). SV is a\r\npostdoctoral fellow of the Research
Foundation-Flanders.\r\nSN is a Project Assistant Professor supported by the Japanese\r\nSociety
for the Promotion of Science (JSPS; 30612022 to SN),\r\nthe NC-CARP project of the
Ministry of Education, Culture,\r\nSports, Science and Technology in Japan to SN."
article_number: '16018'
article_processing_charge: No
author:
- first_name: Łukasz
full_name: Łangowski, Łukasz
last_name: Łangowski
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Hongjiang
full_name: Li, Hongjiang
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Łangowski Ł, Wabnik KT, Li H, et al. Cellular mechanisms for cargo delivery
and polarity maintenance at different polar domains in plant cells. Cell Discovery.
2016;2. doi:10.1038/celldisc.2016.18
apa: Łangowski, Ł., Wabnik, K. T., Li, H., Vanneste, S., Naramoto, S., Tanaka, H.,
& Friml, J. (2016). Cellular mechanisms for cargo delivery and polarity maintenance
at different polar domains in plant cells. Cell Discovery. Nature Publishing
Group. https://doi.org/10.1038/celldisc.2016.18
chicago: Łangowski, Łukasz, Krzysztof T Wabnik, Hongjiang Li, Steffen Vanneste,
Satoshi Naramoto, Hirokazu Tanaka, and Jiří Friml. “Cellular Mechanisms for Cargo
Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.”
Cell Discovery. Nature Publishing Group, 2016. https://doi.org/10.1038/celldisc.2016.18.
ieee: Ł. Łangowski et al., “Cellular mechanisms for cargo delivery and polarity
maintenance at different polar domains in plant cells,” Cell Discovery,
vol. 2. Nature Publishing Group, 2016.
ista: Łangowski Ł, Wabnik KT, Li H, Vanneste S, Naramoto S, Tanaka H, Friml J. 2016.
Cellular mechanisms for cargo delivery and polarity maintenance at different polar
domains in plant cells. Cell Discovery. 2, 16018.
mla: Łangowski, Łukasz, et al. “Cellular Mechanisms for Cargo Delivery and Polarity
Maintenance at Different Polar Domains in Plant Cells.” Cell Discovery,
vol. 2, 16018, Nature Publishing Group, 2016, doi:10.1038/celldisc.2016.18.
short: Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J.
Friml, Cell Discovery 2 (2016).
date_created: 2018-12-11T11:50:02Z
date_published: 2016-07-19T00:00:00Z
date_updated: 2025-09-22T14:19:46Z
day: '19'
ddc:
- '580'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1038/celldisc.2016.18
ec_funded: 1
external_id:
isi:
- '000414797400001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:33Z
date_updated: 2018-12-12T10:13:33Z
file_id: '5017'
file_name: IST-2017-757-v1+1_celldisc201618.pdf
file_size: 5261671
relation: main_file
file_date_updated: 2018-12-12T10:13:33Z
has_accepted_license: '1'
intvolume: ' 2'
isi: 1
language:
- iso: eng
month: '07'
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: Cell Discovery
publication_status: published
publisher: Nature Publishing Group
publist_id: '6299'
pubrep_id: '757'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cellular mechanisms for cargo delivery and polarity maintenance at different
polar domains in plant cells
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 2
year: '2016'
...
---
_id: '10810'
abstract:
- lang: eng
text: "The main goal of the SCP-ECG standard is to address ECG data and related
metadata structuring, semantics and syntax, with the objective of facilitating
interoperability and thus supporting and promoting the exchange of the relevant
information for unary and serial ECG diagnosis. Starting with version V3.0, the
standard now also provides support for the storage of continuous, long-term ECG
recordings and affords a repository for selected ECG sequences and the related
metadata to accommodate stress tests, drug trials and protocol-based ECG recordings.
The global and per-lead measurements sections have been extended and three new
sections have been introduced for storing beat-by-beat and/or spike-by-spike measurements\r\nand
annotations. The used terminology and the provided measurements and annotations
have been harmonized with the ISO/IEEE 11073-10102 Annotated ECG standard. Emphasis
has also been put on harmonizing the Universal Statement Codes with the CDISC
and the categorized AHA statement codes and similarly the drug and implanted devices
codes with the ATC and NASPE/BPEG codes. "
acknowledgement: The authors are thankful to Drs. Roger Abaecherli, Nikus Kjell, Paul
Kligfield, Jay Mason, Patrice Nony, Vito Starc, Anders Thurin and the late Galen
Wagner for their in depth review and constructive comments.
article_processing_charge: No
author:
- first_name: Paul
full_name: Rubel, Paul
last_name: Rubel
- first_name: Danilo
full_name: Pani, Danilo
last_name: Pani
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Jocelyne
full_name: Fayn, Jocelyne
last_name: Fayn
- first_name: Fabio
full_name: Badilini, Fabio
last_name: Badilini
- first_name: Peter
full_name: Macfarlane, Peter
last_name: Macfarlane
- first_name: Alpo
full_name: Varri, Alpo
last_name: Varri
citation:
ama: 'Rubel P, Pani D, Schlögl A, et al. SCP-ECG V3.0: An enhanced standard communication
protocol for computer-assisted electrocardiography. In: 2016 Computing in Cardiology
Conference. Vol 43. Computing in Cardiology; 2016:309-312. doi:10.22489/cinc.2016.090-500'
apa: 'Rubel, P., Pani, D., Schlögl, A., Fayn, J., Badilini, F., Macfarlane, P.,
& Varri, A. (2016). SCP-ECG V3.0: An enhanced standard communication protocol
for computer-assisted electrocardiography. In 2016 Computing in Cardiology
Conference (Vol. 43, pp. 309–312). Vancouver, Canada: Computing in Cardiology.
https://doi.org/10.22489/cinc.2016.090-500'
chicago: 'Rubel, Paul, Danilo Pani, Alois Schlögl, Jocelyne Fayn, Fabio Badilini,
Peter Macfarlane, and Alpo Varri. “SCP-ECG V3.0: An Enhanced Standard Communication
Protocol for Computer-Assisted Electrocardiography.” In 2016 Computing in Cardiology
Conference, 43:309–12. Computing in Cardiology, 2016. https://doi.org/10.22489/cinc.2016.090-500.'
ieee: 'P. Rubel et al., “SCP-ECG V3.0: An enhanced standard communication
protocol for computer-assisted electrocardiography,” in 2016 Computing in Cardiology
Conference, Vancouver, Canada, 2016, vol. 43, pp. 309–312.'
ista: 'Rubel P, Pani D, Schlögl A, Fayn J, Badilini F, Macfarlane P, Varri A. 2016.
SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted
electrocardiography. 2016 Computing in Cardiology Conference. CinC: Computing
in Cardiology vol. 43, 309–312.'
mla: 'Rubel, Paul, et al. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol
for Computer-Assisted Electrocardiography.” 2016 Computing in Cardiology Conference,
vol. 43, Computing in Cardiology, 2016, pp. 309–12, doi:10.22489/cinc.2016.090-500.'
short: P. Rubel, D. Pani, A. Schlögl, J. Fayn, F. Badilini, P. Macfarlane, A. Varri,
in:, 2016 Computing in Cardiology Conference, Computing in Cardiology, 2016, pp.
309–312.
conference:
end_date: 2016-09-14
location: Vancouver, Canada
name: 'CinC: Computing in Cardiology'
start_date: 2016-09-11
date_created: 2022-03-03T10:43:10Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2022-03-04T07:34:45Z
day: '01'
department:
- _id: CampIT
doi: 10.22489/cinc.2016.090-500
intvolume: ' 43'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.22489/cinc.2016.090-500
month: '03'
oa: 1
oa_version: Published Version
page: 309-312
publication: 2016 Computing in Cardiology Conference
publication_identifier:
issn:
- 2325-887X
publication_status: published
publisher: Computing in Cardiology
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted
electrocardiography'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2016'
...
---
_id: '1082'
abstract:
- lang: eng
text: In many applications, it is desirable to extract only the relevant aspects
of data. A principled way to do this is the information bottleneck (IB) method,
where one seeks a code that maximises information about a relevance variable,
Y, while constraining the information encoded about the original data, X. Unfortunately
however, the IB method is computationally demanding when data are high-dimensional
and/or non-gaussian. Here we propose an approximate variational scheme for maximising
a lower bound on the IB objective, analogous to variational EM. Using this method,
we derive an IB algorithm to recover features that are both relevant and sparse.
Finally, we demonstrate how kernelised versions of the algorithm can be used to
address a broad range of problems with non-linear relation between X and Y.
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
arxiv: 1
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Chalk MJ, Marre O, Tkačik G. Relevant sparse codes with variational information
bottleneck. In: Vol 29. Neural Information Processing Systems Foundation; 2016:1965-1973.'
apa: 'Chalk, M. J., Marre, O., & Tkačik, G. (2016). Relevant sparse codes with
variational information bottleneck (Vol. 29, pp. 1965–1973). Presented at the
NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information
Processing Systems Foundation.'
chicago: Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Relevant Sparse Codes
with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing
Systems Foundation, 2016.
ieee: 'M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational
information bottleneck,” presented at the NIPS: Neural Information Processing
Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.'
ista: 'Chalk MJ, Marre O, Tkačik G. 2016. Relevant sparse codes with variational
information bottleneck. NIPS: Neural Information Processing Systems, Advances
in Neural Information Processing Systems, vol. 29, 1965–1973.'
mla: Chalk, Matthew J., et al. Relevant Sparse Codes with Variational Information
Bottleneck. Vol. 29, Neural Information Processing Systems Foundation, 2016,
pp. 1965–73.
short: M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems
Foundation, 2016, pp. 1965–1973.
conference:
end_date: 2016-12-10
location: Barcelona, Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2016-12-05
date_created: 2018-12-11T11:50:03Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2025-06-03T11:33:51Z
day: '01'
department:
- _id: GaTk
external_id:
arxiv:
- '1605.07332'
intvolume: ' 29'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1605.07332
month: '12'
oa: 1
oa_version: Preprint
page: 1965-1973
publication_status: published
publisher: Neural Information Processing Systems Foundation
publist_id: '6298'
quality_controlled: '1'
related_material:
link:
- relation: other
url: https://papers.nips.cc/paper/6101-relevant-sparse-codes-with-variational-information-bottleneck
scopus_import: '1'
status: public
title: Relevant sparse codes with variational information bottleneck
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...
---
_id: '1083'
abstract:
- lang: eng
text: ' Cholecystokinin-expressing interneurons (CCK-INs) mediate behavior state-dependent
inhibition in cortical circuits and themselves receive strong GABAergic input.
However, it remains unclear to what extent GABABreceptors (GABABRs) contribute
to their inhibitory control. Using immunoelectron microscopy, we found that CCK-INs
in the rat hippocampus possessed high levels of dendritic GABABRs and KCTD12 auxiliary
proteins, whereas postsynaptic effector Kir3 channels were present at lower levels.
Consistently, whole-cell recordings revealed slow GABABR-mediated inhibitory postsynaptic
currents (IPSCs) in most CCK-INs. In spite of the higher surface density of GABABRs
in CCK-INs than in CA1 principal cells, the amplitudes of IPSCs were comparable,
suggesting that the expression of Kir3 channels is the limiting factor for the
GABABR currents in these INs. Morphological analysis showed that CCK-INs were
diverse, comprising perisomatic-targeting basket cells (BCs), as well as dendrite-targeting
(DT) interneurons, including a previously undescribed DT type. GABABR-mediated
IPSCs in CCK-INs were large in BCs, but small in DT subtypes. In response to prolonged
activation, GABABR-mediated currents displayed strong desensitization, which was
absent in KCTD12-deficient mice. This study highlights that GABABRs differentially
control CCK-IN subtypes, and the kinetics and desensitization of GABABR-mediated
currents are modulated by KCTD12 proteins. '
acknowledgement: "This work was supported by the Deutsche Forschungsgemeinschaft (DFG
SFB 780 A2, A.K.; SFB TR3 I.V. and EXC 257, I.V.; FOR 2143, A.K. and I.V.), Spemann
Graduate School (D.A.), BIOSS-2 (A6, A.K.), the Swiss National Science Foundation
(3100A0-117816, B.B.), The McNaught Bequest (S.A.B. and I.V.), and Tenovus Scotland
(I.V.).\r\n\r\n\r\nWe thank Cheryl Hutton and Chinmaya Sadangi for their contributions
to neuronal reconstruction as well as Natalie Wernet, Sigrun Nestel, Anikó Schneider,
Ina Wolter, and Ulrich Noeller for their excellent technical support. VGAT-Venus
transgenic rats were generated by Drs Y. Yanagawa, M. Hirabayashi, and Y. Kawaguchi
in National Institute for Physiological Sciences, Okazaki, Japan, using pCS2-Venus
provided by Dr A. Miyawaki. The monoclonal mouse CCK antibody was generously provided
by Dr G.V. Ohning, CURE Center, UCLA, CA. "
article_processing_charge: No
author:
- first_name: Sam
full_name: Booker, Sam
last_name: Booker
- first_name: Daniel
full_name: Althof, Daniel
last_name: Althof
- first_name: Anna
full_name: Gross, Anna
last_name: Gross
- first_name: Desiree
full_name: Loreth, Desiree
last_name: Loreth
- first_name: Johanna
full_name: Müller, Johanna
last_name: Müller
- first_name: Andreas
full_name: Unger, Andreas
last_name: Unger
- first_name: Bernd
full_name: Fakler, Bernd
last_name: Fakler
- first_name: Andrea
full_name: Varro, Andrea
last_name: Varro
- first_name: Masahiko
full_name: Watanabe, Masahiko
last_name: Watanabe
- first_name: Martin
full_name: Gassmann, Martin
last_name: Gassmann
- first_name: Bernhard
full_name: Bettler, Bernhard
last_name: Bettler
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Imre
full_name: Vida, Imre
last_name: Vida
- first_name: Ákos
full_name: Kulik, Ákos
last_name: Kulik
citation:
ama: Booker S, Althof D, Gross A, et al. KCTD12 auxiliary proteins modulate kinetics
of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons.
Cerebral Cortex. 2016;27(3):2318-2334. doi:10.1093/cercor/bhw090
apa: Booker, S., Althof, D., Gross, A., Loreth, D., Müller, J., Unger, A., … Kulik,
Á. (2016). KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated
inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex.
Oxford University Press. https://doi.org/10.1093/cercor/bhw090
chicago: Booker, Sam, Daniel Althof, Anna Gross, Desiree Loreth, Johanna Müller,
Andreas Unger, Bernd Fakler, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics
of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.”
Cerebral Cortex. Oxford University Press, 2016. https://doi.org/10.1093/cercor/bhw090.
ieee: S. Booker et al., “KCTD12 auxiliary proteins modulate kinetics of GABAB
receptor-mediated inhibition in Cholecystokinin-containing interneurons,” Cerebral
Cortex, vol. 27, no. 3. Oxford University Press, pp. 2318–2334, 2016.
ista: Booker S, Althof D, Gross A, Loreth D, Müller J, Unger A, Fakler B, Varro
A, Watanabe M, Gassmann M, Bettler B, Shigemoto R, Vida I, Kulik Á. 2016. KCTD12
auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in
Cholecystokinin-containing interneurons. Cerebral Cortex. 27(3), 2318–2334.
mla: Booker, Sam, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated
Inhibition in Cholecystokinin-Containing Interneurons.” Cerebral Cortex,
vol. 27, no. 3, Oxford University Press, 2016, pp. 2318–34, doi:10.1093/cercor/bhw090.
short: S. Booker, D. Althof, A. Gross, D. Loreth, J. Müller, A. Unger, B. Fakler,
A. Varro, M. Watanabe, M. Gassmann, B. Bettler, R. Shigemoto, I. Vida, Á. Kulik,
Cerebral Cortex 27 (2016) 2318–2334.
date_created: 2018-12-11T11:50:03Z
date_published: 2016-04-12T00:00:00Z
date_updated: 2025-09-22T14:19:11Z
day: '12'
department:
- _id: RySh
doi: 10.1093/cercor/bhw090
external_id:
isi:
- '000397636600048'
intvolume: ' 27'
isi: 1
issue: '3'
language:
- iso: eng
month: '04'
oa_version: None
page: 2318 - 2334
publication: Cerebral Cortex
publication_status: published
publisher: Oxford University Press
publist_id: '6297'
quality_controlled: '1'
scopus_import: '1'
status: public
title: KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition
in Cholecystokinin-containing interneurons
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 27
year: '2016'
...
---
_id: '1088'
abstract:
- lang: eng
text: Cell geometry is tightly coupled to gene expression patterns within the tissue
microenvironment. This perspective synthesizes evidence that the 3D organization
of chromosomes is a critical intermediate for geometric control of genomic programs.
Using a combination of experiments and modeling we outline approaches to decipher
the mechano-genomic code that governs cellular homeostasis and reprogramming.
author:
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: G V
full_name: Shivashankar, G V
last_name: Shivashankar
citation:
ama: Uhler C, Shivashankar GV. Geometric control and modeling of genome reprogramming.
BioArchitecture. 2016;6(4):76-84. doi:10.1080/19490992.2016.1201620
apa: Uhler, C., & Shivashankar, G. V. (2016). Geometric control and modeling
of genome reprogramming. BioArchitecture. Taylor & Francis. https://doi.org/10.1080/19490992.2016.1201620
chicago: Uhler, Caroline, and G V Shivashankar. “Geometric Control and Modeling
of Genome Reprogramming.” BioArchitecture. Taylor & Francis, 2016.
https://doi.org/10.1080/19490992.2016.1201620.
ieee: C. Uhler and G. V. Shivashankar, “Geometric control and modeling of genome
reprogramming,” BioArchitecture, vol. 6, no. 4. Taylor & Francis, pp.
76–84, 2016.
ista: Uhler C, Shivashankar GV. 2016. Geometric control and modeling of genome reprogramming.
BioArchitecture. 6(4), 76–84.
mla: Uhler, Caroline, and G. V. Shivashankar. “Geometric Control and Modeling of
Genome Reprogramming.” BioArchitecture, vol. 6, no. 4, Taylor & Francis,
2016, pp. 76–84, doi:10.1080/19490992.2016.1201620.
short: C. Uhler, G.V. Shivashankar, BioArchitecture 6 (2016) 76–84.
date_created: 2018-12-11T11:50:05Z
date_published: 2016-07-27T00:00:00Z
date_updated: 2021-01-12T06:48:11Z
day: '27'
doi: 10.1080/19490992.2016.1201620
extern: '1'
intvolume: ' 6'
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
page: 76 - 84
publication: BioArchitecture
publication_status: published
publisher: Taylor & Francis
publist_id: '6289'
quality_controlled: '1'
status: public
title: Geometric control and modeling of genome reprogramming
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1090'
abstract:
- lang: eng
text: ' While weighted automata provide a natural framework to express quantitative
properties, many basic properties like average response time cannot be expressed
with weighted automata. Nested weighted automata extend weighted automata and
consist of a master automaton and a set of slave automata that are invoked by
the master automaton. Nested weighted automata are strictly more expressive than
weighted automata (e.g., average response time can be expressed with nested weighted
automata), but the basic decision questions have higher complexity (e.g., for
deterministic automata, the emptiness question for nested weighted automata is
PSPACE-hard, whereas the corresponding complexity for weighted automata is PTIME).
We consider a natural subclass of nested weighted automata where at any point
at most a bounded number k of slave automata can be active. We focus on automata
whose master value function is the limit average. We show that these nested weighted
automata with bounded width are strictly more expressive than weighted automata
(e.g., average response time with no overlapping requests can be expressed with
bound k=1, but not with non-nested weighted automata). We show that the complexity
of the basic decision problems (i.e., emptiness and universality) for the subclass
with k constant matches the complexity for weighted automata. Moreover, when k
is part of the input given in unary we establish PSPACE-completeness.'
acknowledgement: "This research was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23\r\n(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award),
ERC Start grant (279307: Graph Games), Vienna\r\nScience and Technology Fund (WWTF)
through project ICT15-003 and by the National Science Centre\r\n(NCN), Poland under
grant 2014/15/D/ST6/04543."
alternative_title:
- LIPIcs
article_number: '24'
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
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J. Nested weighted limit-average automata
of bounded width. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2016. doi:10.4230/LIPIcs.MFCS.2016.24'
apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2016). Nested weighted limit-average
automata of bounded width (Vol. 58). Presented at the MFCS: Mathematical Foundations
of Computer Science, Krakow; Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.MFCS.2016.24'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted
Limit-Average Automata of Bounded Width,” Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2016. https://doi.org/10.4230/LIPIcs.MFCS.2016.24.
ieee: 'K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted limit-average
automata of bounded width,” presented at the MFCS: Mathematical Foundations of
Computer Science, Krakow; Poland, 2016, vol. 58.'
ista: 'Chatterjee K, Henzinger TA, Otop J. 2016. Nested weighted limit-average automata
of bounded width. MFCS: Mathematical Foundations of Computer Science, LIPIcs,
vol. 58, 24.'
mla: Chatterjee, Krishnendu, et al. Nested Weighted Limit-Average Automata of
Bounded Width. Vol. 58, 24, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2016, doi:10.4230/LIPIcs.MFCS.2016.24.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2016.
conference:
end_date: 2016-08-26
location: Krakow; Poland
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2016-08-22
date_created: 2018-12-11T11:50:05Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2025-07-10T11:50:02Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
- _id: ToHe
doi: 10.4230/LIPIcs.MFCS.2016.24
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:31Z
date_updated: 2018-12-12T10:17:31Z
file_id: '5286'
file_name: IST-2017-795-v1+1_LIPIcs-MFCS-2016-24.pdf
file_size: 564560
relation: main_file
file_date_updated: 2018-12-12T10:17:31Z
has_accepted_license: '1'
intvolume: ' 58'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6286'
pubrep_id: '795'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nested weighted limit-average automata of bounded width
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2016'
...
---
_id: '1094'
abstract:
- lang: eng
text: Immunogold labeling of freeze-fracture replicas has recently been used for
high-resolution visualization of protein localization in electron microscopy.
This method has higher labeling efficiency than conventional immunogold methods
for membrane molecules allowing precise quantitative measurements. However, one
of the limitations of freeze-fracture replica immunolabeling is difficulty in
keeping structural orientation and identifying labeled profiles in complex tissues
like brain. The difficulty is partly due to fragmentation of freeze-fracture replica
preparations during labeling procedures and limited morphological clues on the
replica surface. To overcome these issues, we introduce here a grid-glued replica
method combined with SEM observation. This method allows histological staining
before dissolving the tissue and easy handling of replicas during immunogold labeling,
and keeps the whole replica surface intact without fragmentation. The procedure
described here is also useful for matched double-replica analysis allowing further
identification of labeled profiles in corresponding P-face and E-face.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: 'We thank Prof. Elek Molnár for providing us a pan-AMPAR anti-body
used in Fig.2 and Dr. Ludek Lovicar for technical assistance in scanning electron
microscope imaging. This work was supported by the European Union (HBP—Project Ref.
604102). '
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: 'Harada H, Shigemoto R. Immunogold protein localization on grid-glued freeze-fracture
replicas. In: High-Resolution Imaging of Cellular Proteins. Vol 1474. Springer;
2016:203-216. doi:10.1007/978-1-4939-6352-2_12'
apa: Harada, H., & Shigemoto, R. (2016). Immunogold protein localization on
grid-glued freeze-fracture replicas. In High-Resolution Imaging of Cellular
Proteins (Vol. 1474, pp. 203–216). Springer. https://doi.org/10.1007/978-1-4939-6352-2_12
chicago: Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization
on Grid-Glued Freeze-Fracture Replicas.” In High-Resolution Imaging of Cellular
Proteins, 1474:203–16. Springer, 2016. https://doi.org/10.1007/978-1-4939-6352-2_12.
ieee: H. Harada and R. Shigemoto, “Immunogold protein localization on grid-glued
freeze-fracture replicas,” in High-Resolution Imaging of Cellular Proteins,
vol. 1474, Springer, 2016, pp. 203–216.
ista: 'Harada H, Shigemoto R. 2016.Immunogold protein localization on grid-glued
freeze-fracture replicas. In: High-Resolution Imaging of Cellular Proteins. Methods
in Molecular Biology, vol. 1474, 203–216.'
mla: Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on
Grid-Glued Freeze-Fracture Replicas.” High-Resolution Imaging of Cellular Proteins,
vol. 1474, Springer, 2016, pp. 203–16, doi:10.1007/978-1-4939-6352-2_12.
short: H. Harada, R. Shigemoto, in:, High-Resolution Imaging of Cellular Proteins,
Springer, 2016, pp. 203–216.
date_created: 2018-12-11T11:50:06Z
date_published: 2016-08-12T00:00:00Z
date_updated: 2025-04-15T07:12:21Z
day: '12'
department:
- _id: RySh
doi: 10.1007/978-1-4939-6352-2_12
ec_funded: 1
intvolume: ' 1474'
language:
- iso: eng
month: '08'
oa_version: None
page: 203 - 216
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
publication: High-Resolution Imaging of Cellular Proteins
publication_identifier:
eissn:
- 1611-3349
issn:
- 0302-9743
publication_status: published
publisher: Springer
publist_id: '6281'
quality_controlled: '1'
status: public
title: Immunogold protein localization on grid-glued freeze-fracture replicas
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 1474
year: '2016'
...
---
_id: '1095'
abstract:
- lang: eng
text: ' The semantics of concurrent data structures is usually given by a sequential
specification and a consistency condition. Linearizability is the most popular
consistency condition due to its simplicity and general applicability. Nevertheless,
for applications that do not require all guarantees offered by linearizability,
recent research has focused on improving performance and scalability of concurrent
data structures by relaxing their semantics. In this paper, we present local linearizability,
a relaxed consistency condition that is applicable to container-type concurrent
data structures like pools, queues, and stacks. While linearizability requires
that the effect of each operation is observed by all threads at the same time,
local linearizability only requires that for each thread T, the effects of its
local insertion operations and the effects of those removal operations that remove
values inserted by T are observed by all threads at the same time. We investigate
theoretical and practical properties of local linearizability and its relationship
to many existing consistency conditions. We present a generic implementation method
for locally linearizable data structures that uses existing linearizable data
structures as building blocks. Our implementations show performance and scalability
improvements over the original building blocks and outperform the fastest existing
container-type implementations. '
acknowledgement: "This work has been supported by the National Research Network RiSE
on Rigorous Systems Engineering\r\n(Austrian Science Fund (FWF): S11402-N23, S11403-N23,
S11404-N23, S11411-N23), a Google\r\nPhD Fellowship, an Erwin Schrödinger Fellowship
(Austrian Science Fund (FWF): J3696-N26), EPSRC\r\ngrants EP/H005633/1 and EP/K008528/1,
the Vienna Science and Technology Fund (WWTF) trough\r\ngrant PROSEED, the European
Research Council (ERC) under grant 267989 (QUAREM) and by the\r\nAustrian Science
Fund (FWF) under grant Z211-N23 (Wittgenstein Award)."
alternative_title:
- LIPIcs
article_number: '6'
author:
- first_name: Andreas
full_name: Haas, Andreas
last_name: Haas
- 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: Andreas
full_name: Holzer, Andreas
last_name: Holzer
- first_name: Christoph
full_name: Kirsch, Christoph
last_name: Kirsch
- first_name: Michael
full_name: Lippautz, Michael
last_name: Lippautz
- first_name: Hannes
full_name: Payer, Hannes
last_name: Payer
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
- first_name: Ana
full_name: Sokolova, Ana
last_name: Sokolova
- first_name: Helmut
full_name: Veith, Helmut
last_name: Veith
citation:
ama: 'Haas A, Henzinger TA, Holzer A, et al. Local linearizability for concurrent
container-type data structures. In: Leibniz International Proceedings in Informatics.
Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.6'
apa: 'Haas, A., Henzinger, T. A., Holzer, A., Kirsch, C., Lippautz, M., Payer, H.,
… Veith, H. (2016). Local linearizability for concurrent container-type data structures.
In Leibniz International Proceedings in Informatics (Vol. 59). Quebec City;
Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2016.6'
chicago: Haas, Andreas, Thomas A Henzinger, Andreas Holzer, Christoph Kirsch, Michael
Lippautz, Hannes Payer, Ali Sezgin, Ana Sokolova, and Helmut Veith. “Local Linearizability
for Concurrent Container-Type Data Structures.” In Leibniz International Proceedings
in Informatics, Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.6.
ieee: A. Haas et al., “Local linearizability for concurrent container-type
data structures,” in Leibniz International Proceedings in Informatics,
Quebec City; Canada, 2016, vol. 59.
ista: 'Haas A, Henzinger TA, Holzer A, Kirsch C, Lippautz M, Payer H, Sezgin A,
Sokolova A, Veith H. 2016. Local linearizability for concurrent container-type
data structures. Leibniz International Proceedings in Informatics. CONCUR: Concurrency
Theory, LIPIcs, vol. 59, 6.'
mla: Haas, Andreas, et al. “Local Linearizability for Concurrent Container-Type
Data Structures.” Leibniz International Proceedings in Informatics, vol.
59, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.6.
short: A. Haas, T.A. Henzinger, A. Holzer, C. Kirsch, M. Lippautz, H. Payer, A.
Sezgin, A. Sokolova, H. Veith, in:, Leibniz International Proceedings in Informatics,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.
conference:
end_date: 2016-08-26
location: Quebec City; Canada
name: 'CONCUR: Concurrency Theory'
start_date: 2016-08-23
date_created: 2018-12-11T11:50:07Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2025-04-15T06:25:58Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.CONCUR.2016.6
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:10Z
date_updated: 2018-12-12T10:10:10Z
file_id: '4795'
file_name: IST-2017-793-v1+1_LIPIcs-CONCUR-2016-6.pdf
file_size: 589747
relation: main_file
file_date_updated: 2018-12-12T10:10:10Z
has_accepted_license: '1'
intvolume: ' 59'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: Leibniz International Proceedings in Informatics
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6280'
pubrep_id: '793'
quality_controlled: '1'
scopus_import: 1
status: public
title: Local linearizability for concurrent container-type data structures
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 59
year: '2016'
...
---
_id: '1097'
abstract:
- lang: eng
text: We present an interactive system for computational design, optimization, and
fabrication of multicopters. Our computational approach allows non-experts to
design, explore, and evaluate a wide range of different multicopters. We provide
users with an intuitive interface for assembling a multicopter from a collection
of components (e.g., propellers, motors, and carbon fiber rods). Our algorithm
interactively optimizes shape and controller parameters of the current design
to ensure its proper operation. In addition, we allow incorporating a variety
of other metrics (such as payload, battery usage, size, and cost) into the design
process and exploring tradeoffs between them. We show the efficacy of our method
and system by designing, optimizing, fabricating, and operating multicopters with
complex geometries and propeller configurations. We also demonstrate the ability
of our optimization algorithm to improve the multicopter performance under different
metrics.
acknowledgement: "We thank Nobuyuki Umetani for his insightful suggestions in our
discussions. We thank Alan Schultz and his colleagues at NRL for building the hexacopter
and for the valuable discussions. We thank Randall Davis, Boris Katz, and Howard
Shrobe at MIT for their advice. We are grateful to Nick Bandiera for preprocessing
mechanical parts and providing 3D printing technical support; Charles Blouin from
RCBenchmark for dynamometer hardware support; Brian Saavedra for the composition
UI; Yingzhe Yuan for data acquisition and video recording in the experiments; Michael
Foshey and David Kim for their comments on the draft of the paper. \r\n\r\n\r\nThis
work was partially supported by Air Force Research Laboratory’s sponsorship of Julia:
A Fresh Approach to Technical Computing and Data Processing (Sponsor Award ID FA8750-15-2-
0272, MIT Award ID 024831-00003), and NSF Expedition project (Sponsor Award ID CCF-1138967,
MIT Award ID 020610-00002). The views expressed herein are not endorsed by the sponsors.
This project has also received funding from the European Union’s Horizon 2020 research
and innovation program under grant agreement No 645599. "
alternative_title:
- ACM Transactions on Graphics
article_number: '227'
article_processing_charge: No
author:
- first_name: Tao
full_name: Du, Tao
last_name: Du
- first_name: Adriana
full_name: Schulz, Adriana
last_name: Schulz
- first_name: Bo
full_name: Zhu, Bo
last_name: Zhu
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
citation:
ama: 'Du T, Schulz A, Zhu B, Bickel B, Matusik W. Computational multicopter design.
In: Vol 35. ACM; 2016. doi:10.1145/2980179.2982427'
apa: 'Du, T., Schulz, A., Zhu, B., Bickel, B., & Matusik, W. (2016). Computational
multicopter design (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition
on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. https://doi.org/10.1145/2980179.2982427'
chicago: Du, Tao, Adriana Schulz, Bo Zhu, Bernd Bickel, and Wojciech Matusik. “Computational
Multicopter Design,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2980179.2982427.
ieee: 'T. Du, A. Schulz, B. Zhu, B. Bickel, and W. Matusik, “Computational multicopter
design,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer
Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no.
6.'
ista: 'Du T, Schulz A, Zhu B, Bickel B, Matusik W. 2016. Computational multicopter
design. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive
Techniques in Asia, ACM Transactions on Graphics, vol. 35, 227.'
mla: Du, Tao, et al. Computational Multicopter Design. Vol. 35, no. 6, 227,
ACM, 2016, doi:10.1145/2980179.2982427.
short: T. Du, A. Schulz, B. Zhu, B. Bickel, W. Matusik, in:, ACM, 2016.
conference:
end_date: 2016-12-08
location: Macao, China
name: 'SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive
Techniques in Asia'
start_date: 2016-12-05
date_created: 2018-12-11T11:50:07Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2025-09-22T14:17:29Z
day: '01'
ddc:
- '006'
department:
- _id: BeBi
doi: 10.1145/2980179.2982427
ec_funded: 1
external_id:
isi:
- '000388446200069'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:42Z
date_updated: 2018-12-12T10:17:42Z
file_id: '5298'
file_name: IST-2017-759-v1+1_copter.pdf
file_size: 33114420
relation: main_file
file_date_updated: 2018-12-12T10:17:42Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
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
publication_status: published
publisher: ACM
publist_id: '6278'
pubrep_id: '759'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computational multicopter design
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 35
year: '2016'
...
---
_id: '1098'
abstract:
- lang: eng
text: Better understanding of the potential benefits of information transfer and
representation learning is an important step towards the goal of building intelligent
systems that are able to persist in the world and learn over time. In this work,
we consider a setting where the learner encounters a stream of tasks but is able
to retain only limited information from each encountered task, such as a learned
predictor. In contrast to most previous works analyzing this scenario, we do not
make any distributional assumptions on the task generating process. Instead, we
formulate a complexity measure that captures the diversity of the observed tasks.
We provide a lifelong learning algorithm with error guarantees for every observed
task (rather than on average). We show sample complexity reductions in comparison
to solving every task in isolation in terms of our task complexity measure. Further,
our algorithmic framework can naturally be viewed as learning a representation
from encountered tasks with a neural network.
acknowledgement: "This work was in parts funded by the European Research Council under
the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement
no 308036.\r\n\r\n"
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
author:
- first_name: Anastasia
full_name: Pentina, Anastasia
id: 42E87FC6-F248-11E8-B48F-1D18A9856A87
last_name: Pentina
- first_name: Ruth
full_name: Urner, Ruth
last_name: Urner
citation:
ama: 'Pentina A, Urner R. Lifelong learning with weighted majority votes. In: Vol
29. Neural Information Processing Systems Foundation; 2016:3619-3627.'
apa: 'Pentina, A., & Urner, R. (2016). Lifelong learning with weighted majority
votes (Vol. 29, pp. 3619–3627). Presented at the NIPS: Neural Information Processing
Systems, Barcelona, Spain: Neural Information Processing Systems Foundation.'
chicago: Pentina, Anastasia, and Ruth Urner. “Lifelong Learning with Weighted Majority
Votes,” 29:3619–27. Neural Information Processing Systems Foundation, 2016.
ieee: 'A. Pentina and R. Urner, “Lifelong learning with weighted majority votes,”
presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain,
2016, vol. 29, pp. 3619–3627.'
ista: 'Pentina A, Urner R. 2016. Lifelong learning with weighted majority votes.
NIPS: Neural Information Processing Systems, Advances in Neural Information Processing
Systems, vol. 29, 3619–3627.'
mla: Pentina, Anastasia, and Ruth Urner. Lifelong Learning with Weighted Majority
Votes. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp.
3619–27.
short: A. Pentina, R. Urner, in:, Neural Information Processing Systems Foundation,
2016, pp. 3619–3627.
conference:
end_date: 2016-12-10
location: Barcelona, Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2016-12-05
date_created: 2018-12-11T11:50:08Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2025-06-03T11:35:58Z
day: '01'
ddc:
- '006'
department:
- _id: ChLa
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:42Z
date_updated: 2018-12-12T10:12:42Z
file_id: '4961'
file_name: IST-2017-775-v1+1_main.pdf
file_size: 237111
relation: main_file
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:43Z
date_updated: 2018-12-12T10:12:43Z
file_id: '4962'
file_name: IST-2017-775-v1+2_supplementary.pdf
file_size: 185818
relation: main_file
file_date_updated: 2018-12-12T10:12:43Z
has_accepted_license: '1'
intvolume: ' 29'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 3619-3627
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_status: published
publisher: Neural Information Processing Systems Foundation
publist_id: '6277'
pubrep_id: '775'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lifelong learning with weighted majority votes
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...
---
_id: '1099'
abstract:
- lang: eng
text: We present FlexMolds, a novel computational approach to automatically design
flexible, reusable molds that, once 3D printed, allow us to physically fabricate,
by means of liquid casting, multiple copies of complex shapes with rich surface
details and complex topology. The approach to design such flexible molds is based
on a greedy bottom-up search of possible cuts over an object, evaluating for each
possible cut the feasibility of the resulting mold. We use a dynamic simulation
approach to evaluate candidate molds, providing a heuristic to generate forces
that are able to open, detach, and remove a complex mold from the object it surrounds.
We have tested the approach with a number of objects with nontrivial shapes and
topologies.
acknowledgement: "The armadillo, bunny and dragon models are courtesy of the Stanford
\ 3D Scanning Repository. The bimba, fertility and elephant models are courtesy
of the AIM@SHAPE Shape Repository. \r\nThis project has received funding from the
European Union’s Horizon 2020 research and innovation programme under grant
\ agreement\r\nNo. 645599."
alternative_title:
- ACM Transactions on Graphics
article_number: '223'
article_processing_charge: No
author:
- first_name: Luigi
full_name: Malomo, Luigi
last_name: Malomo
- first_name: Nico
full_name: Pietroni, Nico
last_name: Pietroni
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Paolo
full_name: Cignoni, Paolo
last_name: Cignoni
citation:
ama: 'Malomo L, Pietroni N, Bickel B, Cignoni P. FlexMolds: Automatic design of
flexible shells for molding. In: Vol 35. ACM; 2016. doi:10.1145/2980179.2982397'
apa: 'Malomo, L., Pietroni, N., Bickel, B., & Cignoni, P. (2016). FlexMolds:
Automatic design of flexible shells for molding (Vol. 35). Presented at the SIGGRAPH
Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques
in Asia, Macao, China: ACM. https://doi.org/10.1145/2980179.2982397'
chicago: 'Malomo, Luigi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “FlexMolds:
Automatic Design of Flexible Shells for Molding,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2980179.2982397.'
ieee: 'L. Malomo, N. Pietroni, B. Bickel, and P. Cignoni, “FlexMolds: Automatic
design of flexible shells for molding,” presented at the SIGGRAPH Asia: Conference
and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao,
China, 2016, vol. 35, no. 6.'
ista: 'Malomo L, Pietroni N, Bickel B, Cignoni P. 2016. FlexMolds: Automatic design
of flexible shells for molding. SIGGRAPH Asia: Conference and Exhibition on Computer
Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol.
35, 223.'
mla: 'Malomo, Luigi, et al. FlexMolds: Automatic Design of Flexible Shells for
Molding. Vol. 35, no. 6, 223, ACM, 2016, doi:10.1145/2980179.2982397.'
short: L. Malomo, N. Pietroni, B. Bickel, P. Cignoni, in:, ACM, 2016.
conference:
end_date: 2016-12-08
location: Macao, China
name: 'SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive
Techniques in Asia'
start_date: 2016-12-05
date_created: 2018-12-11T11:50:08Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2025-09-22T14:16:02Z
day: '01'
ddc:
- '000'
- '005'
department:
- _id: BeBi
doi: 10.1145/2980179.2982397
ec_funded: 1
external_id:
isi:
- '000388446200065'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:01Z
date_updated: 2018-12-12T10:12:01Z
file_id: '4918'
file_name: IST-2017-760-v1+1_flexmolds.pdf
file_size: 11122029
relation: main_file
file_date_updated: 2018-12-12T10:12:01Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
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
publication_status: published
publisher: ACM
publist_id: '6276'
pubrep_id: '760'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'FlexMolds: Automatic design of flexible shells for molding'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 35
year: '2016'
...
---
_id: '1101'
abstract:
- lang: eng
text: Optical sensors based on the phenomenon of Förster resonance energy transfer
(FRET) are powerful tools that have advanced the study of small molecules in biological
systems. However, sensor construction is not trivial and often requires multiple
rounds of engineering or an ability to screen large numbers of variants. A method
that would allow the accurate rational design of FRET sensors would expedite the
production of biologically useful sensors. Here, we present Rangefinder, a computational
algorithm that allows rapid in silico screening of dye attachment sites in a ligand-binding
protein for the conjugation of a dye molecule to act as a Förster acceptor for
a fused fluorescent protein. We present three ratiometric fluorescent sensors
designed with Rangefinder, including a maltose sensor with a dynamic range of
>300% and the first sensors for the most abundant sialic acid in human cells,
N-acetylneuraminic acid. Provided a ligand-binding protein exists, it is our expectation
that this model will facilitate the design of an optical sensor for any small
molecule of interest.
acknowledgement: "J.A.M., J.H.W., and W.H.Z. were supported by Australian\r\nPostgraduate
Awards (APA), AS Sargeson Supplementary\r\nscholarships, and RSC supplementary scholarships.
C.J.J.\r\nacknowledges support from a Human Frontiers in Science\r\nYoung Investigator
Award and a Discovery Project and Future\r\nFellowship from the Australian Research
Council. M.L.O. is\r\nsupported by an Australian Research Council Discovery Project\r\n(DP130102153)
and the Merit Allocation Scheme of the\r\nNational Computational Infrastructure."
article_processing_charge: No
author:
- first_name: Joshua
full_name: Mitchell, Joshua
last_name: Mitchell
- first_name: Jason
full_name: Whitfield, Jason
last_name: Whitfield
- first_name: William
full_name: Zhang, William
last_name: Zhang
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Megan
full_name: O'Mara, Megan
last_name: O'Mara
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: 'Mitchell J, Whitfield J, Zhang W, et al. Rangefinder: A semisynthetic FRET
sensor design algorithm. ACS SENSORS. 2016;1(11):1286-1290. doi:10.1021/acssensors.6b00576'
apa: 'Mitchell, J., Whitfield, J., Zhang, W., Henneberger, C., Janovjak, H. L.,
O’Mara, M., & Jackson, C. (2016). Rangefinder: A semisynthetic FRET sensor
design algorithm. ACS SENSORS. American Chemical Society. https://doi.org/10.1021/acssensors.6b00576'
chicago: 'Mitchell, Joshua, Jason Whitfield, William Zhang, Christian Henneberger,
Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Rangefinder: A Semisynthetic
FRET Sensor Design Algorithm.” ACS SENSORS. American Chemical Society,
2016. https://doi.org/10.1021/acssensors.6b00576.'
ieee: 'J. Mitchell et al., “Rangefinder: A semisynthetic FRET sensor design
algorithm,” ACS SENSORS, vol. 1, no. 11. American Chemical Society, pp.
1286–1290, 2016.'
ista: 'Mitchell J, Whitfield J, Zhang W, Henneberger C, Janovjak HL, O’Mara M, Jackson
C. 2016. Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS.
1(11), 1286–1290.'
mla: 'Mitchell, Joshua, et al. “Rangefinder: A Semisynthetic FRET Sensor Design
Algorithm.” ACS SENSORS, vol. 1, no. 11, American Chemical Society, 2016,
pp. 1286–90, doi:10.1021/acssensors.6b00576.'
short: J. Mitchell, J. Whitfield, W. Zhang, C. Henneberger, H.L. Janovjak, M. O’Mara,
C. Jackson, ACS SENSORS 1 (2016) 1286–1290.
date_created: 2018-12-11T11:50:09Z
date_published: 2016-11-10T00:00:00Z
date_updated: 2025-09-22T14:14:58Z
day: '10'
department:
- _id: HaJa
doi: 10.1021/acssensors.6b00576
external_id:
isi:
- '000388914800003'
intvolume: ' 1'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 1286 - 1290
publication: ACS SENSORS
publication_status: published
publisher: American Chemical Society
publist_id: '6274'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Rangefinder: A semisynthetic FRET sensor design algorithm'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 1
year: '2016'
...