---
_id: '10381'
abstract:
- lang: eng
text: We study phase behaviour of lipid-bilayer vesicles functionalised by ligand–receptor
complexes made of synthetic DNA by introducing a modelling framework and a dedicated
experimental platform. In particular, we perform Monte Carlo simulations that
combine a coarse grained description of the lipid bilayer with state of art analytical
models for multivalent ligand–receptor interactions. Using density of state calculations,
we derive the partition function in pairs of vesicles and compute the number of
ligand–receptor bonds as a function of temperature. Numerical results are compared
to microscopy and fluorimetry experiments on large unilamellar vesicles decorated
by DNA linkers carrying complementary overhangs. We find that vesicle aggregation
is suppressed when the total number of linkers falls below a threshold value.
Within the model proposed here, this is due to the higher configurational costs
required to form inter-vesicle bridges as compared to intra-vesicle loops, which
are in turn related to membrane deformability. Our findings and our numerical/experimental
methodologies are applicable to the rational design of liposomes used as functional
materials and drug delivery applications, as well as to study inter-membrane interactions
in living systems, such as cell adhesion.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Stephan Jan
full_name: Bachmann, Stephan Jan
last_name: Bachmann
- first_name: Jurij
full_name: Kotar, Jurij
last_name: Kotar
- first_name: Lucia
full_name: Parolini, Lucia
last_name: Parolini
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Pietro
full_name: Cicuta, Pietro
last_name: Cicuta
- first_name: Lorenzo
full_name: Di Michele, Lorenzo
last_name: Di Michele
- first_name: Bortolo Matteo
full_name: Mognetti, Bortolo Matteo
last_name: Mognetti
citation:
ama: Bachmann SJ, Kotar J, Parolini L, et al. Melting transition in lipid vesicles
functionalised by mobile DNA linkers. Soft Matter. 2016;12(37):7804-7817.
doi:10.1039/c6sm01515h
apa: Bachmann, S. J., Kotar, J., Parolini, L., Šarić, A., Cicuta, P., Di Michele,
L., & Mognetti, B. M. (2016). Melting transition in lipid vesicles functionalised
by mobile DNA linkers. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c6sm01515h
chicago: Bachmann, Stephan Jan, Jurij Kotar, Lucia Parolini, Anđela Šarić, Pietro
Cicuta, Lorenzo Di Michele, and Bortolo Matteo Mognetti. “Melting Transition in
Lipid Vesicles Functionalised by Mobile DNA Linkers.” Soft Matter. Royal
Society of Chemistry, 2016. https://doi.org/10.1039/c6sm01515h.
ieee: S. J. Bachmann et al., “Melting transition in lipid vesicles functionalised
by mobile DNA linkers,” Soft Matter, vol. 12, no. 37. Royal Society of
Chemistry, pp. 7804–7817, 2016.
ista: Bachmann SJ, Kotar J, Parolini L, Šarić A, Cicuta P, Di Michele L, Mognetti
BM. 2016. Melting transition in lipid vesicles functionalised by mobile DNA linkers.
Soft Matter. 12(37), 7804–7817.
mla: Bachmann, Stephan Jan, et al. “Melting Transition in Lipid Vesicles Functionalised
by Mobile DNA Linkers.” Soft Matter, vol. 12, no. 37, Royal Society of
Chemistry, 2016, pp. 7804–17, doi:10.1039/c6sm01515h.
short: S.J. Bachmann, J. Kotar, L. Parolini, A. Šarić, P. Cicuta, L. Di Michele,
B.M. Mognetti, Soft Matter 12 (2016) 7804–7817.
date_created: 2021-11-29T11:09:55Z
date_published: 2016-08-19T00:00:00Z
date_updated: 2021-11-29T13:09:00Z
day: '19'
doi: 10.1039/c6sm01515h
extern: '1'
external_id:
arxiv:
- '1608.05788'
pmid:
- '27722701'
intvolume: ' 12'
issue: '37'
keyword:
- condensed matter physics
- general chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.05788
month: '08'
oa: 1
oa_version: Preprint
page: 7804-7817
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Melting transition in lipid vesicles functionalised by mobile DNA linkers
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 12
year: '2016'
...
---
_id: '1057'
abstract:
- lang: eng
text: Far-field super-resolution fluorescence microscopy discerns fluorophores residing
closer than the diffraction barrier by briefly transferring them in different
(typically ON and OFF) states before detection. In coordinate-targeted super-resolution
variants, such as stimulated emission depletion (STED) microscopy, this state
difference is created by the intensity minima and maxima of an optical pattern,
causing all fluorophores to assume the off state, for instance, except at the
minima. Although strong spatial confinement of the on state enables high resolution,
it also subjects the fluorophores to excess intensities and state cycles at the
maxima. Here, we address these issues by driving the fluorophores into a second
off state that is inert to the excess light. By using reversibly switchable fluorescent
proteins as labels, our approach reduces bleaching and enhances resolution and
contrast in live-cell STED microscopy. Using two or more transitions to off states
is a useful strategy for augmenting the power of coordinate-targeted super-resolution
microscopy.
acknowledgement: We thank T. Gilat and E. Rothermel (both MPI) for help with preparing
samples, and J. Keller for discussion. J.G.D. acknowledges support by the European
Union through a Marie Curie fellowship PIEF-GA-2011-299283. S.W.H. acknowledges
support by the Körber Foundation.
article_processing_charge: No
author:
- 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: Sven
full_name: Sidenstein, Sven
last_name: Sidenstein
- first_name: Carola
full_name: Gregor, Carola
last_name: Gregor
- first_name: Nicolai
full_name: Urban, Nicolai
last_name: Urban
- first_name: Peter
full_name: Ilgen, Peter
last_name: Ilgen
- first_name: Stefan
full_name: Jakobs, Stefan
last_name: Jakobs
- first_name: Stefan
full_name: Hell, Stefan
last_name: Hell
citation:
ama: Danzl JG, Sidenstein S, Gregor C, et al. Coordinate-targeted fluorescence nanoscopy
with multiple off states. Nature Photonics. 2016;10(2):122-128. doi:10.1038/nphoton.2015.266
apa: Danzl, J. G., Sidenstein, S., Gregor, C., Urban, N., Ilgen, P., Jakobs, S.,
& Hell, S. (2016). Coordinate-targeted fluorescence nanoscopy with multiple
off states. Nature Photonics. Nature Publishing Group. https://doi.org/10.1038/nphoton.2015.266
chicago: Danzl, Johann G, Sven Sidenstein, Carola Gregor, Nicolai Urban, Peter Ilgen,
Stefan Jakobs, and Stefan Hell. “Coordinate-Targeted Fluorescence Nanoscopy with
Multiple off States.” Nature Photonics. Nature Publishing Group, 2016.
https://doi.org/10.1038/nphoton.2015.266.
ieee: J. G. Danzl et al., “Coordinate-targeted fluorescence nanoscopy with
multiple off states,” Nature Photonics, vol. 10, no. 2. Nature Publishing
Group, pp. 122–128, 2016.
ista: Danzl JG, Sidenstein S, Gregor C, Urban N, Ilgen P, Jakobs S, Hell S. 2016.
Coordinate-targeted fluorescence nanoscopy with multiple off states. Nature Photonics.
10(2), 122–128.
mla: Danzl, Johann G., et al. “Coordinate-Targeted Fluorescence Nanoscopy with Multiple
off States.” Nature Photonics, vol. 10, no. 2, Nature Publishing Group,
2016, pp. 122–28, doi:10.1038/nphoton.2015.266.
short: J.G. Danzl, S. Sidenstein, C. Gregor, N. Urban, P. Ilgen, S. Jakobs, S. Hell,
Nature Photonics 10 (2016) 122–128.
date_created: 2018-12-11T11:49:55Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2021-01-12T06:47:58Z
day: '01'
doi: 10.1038/nphoton.2015.266
extern: '1'
intvolume: ' 10'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 122 - 128
publication: Nature Photonics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6331'
status: public
title: Coordinate-targeted fluorescence nanoscopy with multiple off states
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
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
license: https://creativecommons.org/licenses/by/4.0/
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 MH, 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. H., & Loitzenbauer, V. (2016).
Conditionally optimal algorithms for generalized Büchi Games (Vol. 58). Presented
at the MFCS: Mathematical Foundations of Computer Science (SG), Krakow, Poland:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2016.25'
chicago: Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H 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. H. Henzinger, and V. Loitzenbauer, “Conditionally
optimal algorithms for generalized Büchi Games,” presented at the MFCS: Mathematical
Foundations of Computer Science (SG), Krakow, Poland, 2016, vol. 58.'
ista: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2016. Conditionally
optimal algorithms for generalized Büchi Games. MFCS: Mathematical Foundations
of Computer Science (SG), 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.H. 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 (SG)'
start_date: 2016-08-22
date_created: 2018-12-11T11:49:58Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2025-06-02T08:53:50Z
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'
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 fur 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 fur
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
fur 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 fur Informatik,
2016, doi:10.4230/LIPIcs.ICALP.2016.100.
short: V.K. Chonev, J. Ouaknine, J. Worrell, in:, Schloss Dagstuhl- Leibniz-Zentrum
fur 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: 2021-01-12T06:48:03Z
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 fur 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: 3E5EF7F0-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'
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 fur 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 fur 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 fur 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 fur Informatik,
2016, doi:10.4230/LIPIcs.ICALP.2016.98.
short: K. Chatterjee, L. Doyen, in:, Schloss Dagstuhl- Leibniz-Zentrum fur 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: 2021-01-12T06:48:03Z
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 fur 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...
---
_id: '1071'
abstract:
- lang: eng
text: 'We consider data-structures for answering reachability and distance queries
on constant-treewidth graphs with n nodes, on the standard RAM computational model
with wordsize W=Theta(log n). Our first contribution is a data-structure that
after O(n) preprocessing time, allows (1) pair reachability queries in O(1) time;
and (2) single-source reachability queries in O(n/log n) time. This is (asymptotically)
optimal and is faster than DFS/BFS when answering more than a constant number
of single-source queries. The data-structure uses at all times O(n) space. Our
second contribution is a space-time tradeoff data-structure for distance queries.
For any epsilon in [1/2,1], we provide a data-structure with polynomial preprocessing
time that allows pair queries in O(n^{1-\epsilon} alpha(n)) time, where alpha
is the inverse of the Ackermann function, and at all times uses O(n^epsilon) space.
The input graph G is not considered in the space complexity. '
acknowledgement: 'The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE) and ERC Start grant
(279307: Graph Games).'
alternative_title:
- LIPIcs
article_number: '28'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Optimal reachability and a space
time tradeoff for distance queries in constant treewidth graphs. In: Vol 57. Schloss
Dagstuhl- Leibniz-Zentrum fur Informatik; 2016. doi:10.4230/LIPIcs.ESA.2016.28'
apa: 'Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2016). Optimal reachability
and a space time tradeoff for distance queries in constant treewidth graphs (Vol.
57). Presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark:
Schloss Dagstuhl- Leibniz-Zentrum fur Informatik. https://doi.org/10.4230/LIPIcs.ESA.2016.28'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
“Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant
Treewidth Graphs,” Vol. 57. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik,
2016. https://doi.org/10.4230/LIPIcs.ESA.2016.28.
ieee: 'K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal reachability
and a space time tradeoff for distance queries in constant treewidth graphs,”
presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark, 2016,
vol. 57.'
ista: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2016. Optimal reachability
and a space time tradeoff for distance queries in constant treewidth graphs. ESA:
European Symposium on Algorithms, LIPIcs, vol. 57, 28.'
mla: Chatterjee, Krishnendu, et al. Optimal Reachability and a Space Time Tradeoff
for Distance Queries in Constant Treewidth Graphs. Vol. 57, 28, Schloss Dagstuhl-
Leibniz-Zentrum fur Informatik, 2016, doi:10.4230/LIPIcs.ESA.2016.28.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Schloss Dagstuhl- Leibniz-Zentrum
fur Informatik, 2016.
conference:
end_date: 2016-08-24
location: Aarhus, Denmark
name: 'ESA: European Symposium on Algorithms'
start_date: 2016-08-22
date_created: 2018-12-11T11:49:59Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2023-09-07T12:01:58Z
day: '01'
ddc:
- '004'
- '006'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.ESA.2016.28
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:31Z
date_updated: 2018-12-12T10:14:31Z
file_id: '5084'
file_name: IST-2017-777-v1+1_LIPIcs-ESA-2016-28.pdf
file_size: 579225
relation: main_file
file_date_updated: 2018-12-12T10:14:31Z
has_accepted_license: '1'
intvolume: ' 57'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 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 fur Informatik
publist_id: '6312'
pubrep_id: '777'
quality_controlled: '1'
related_material:
record:
- id: '821'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Optimal reachability and a space time tradeoff for distance queries in constant
treewidth graphs
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: 57
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'
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: 2021-01-12T06:48:08Z
day: '19'
ddc:
- '580'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1038/celldisc.2016.18
ec_funded: 1
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'
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
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: '9456'
abstract:
- lang: eng
text: The discovery of introns four decades ago was one of the most unexpected findings
in molecular biology. Introns are sequences interrupting genes that must be removed
as part of messenger RNA production. Genome sequencing projects have shown that
most eukaryotic genes contain at least one intron, and frequently many. Comparison
of these genomes reveals a history of long evolutionary periods during which few
introns were gained, punctuated by episodes of rapid, extensive gain. However,
although several detailed mechanisms for such episodic intron generation have
been proposed, none has been empirically supported on a genomic scale. Here we
show how short, non-autonomous DNA transposons independently generated hundreds
to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte
Aureococcus anophagefferens. Each transposon carries one splice site. The other
splice site is co-opted from the gene sequence that is duplicated upon transposon
insertion, allowing perfect splicing out of the RNA. The distributions of sequences
that can be co-opted are biased with respect to codons, and phasing of transposon-generated
introns is similarly biased. These transposons insert between pre-existing nucleosomes,
so that multiple nearby insertions generate nucleosome-sized intervening segments.
Thus, transposon insertion and sequence co-option may explain the intron phase
biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall,
the two independent examples of proliferating elements illustrate a general DNA
transposon mechanism that can plausibly account for episodes of rapid, extensive
intron gain during eukaryotic evolution.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Jason T.
full_name: Huff, Jason T.
last_name: Huff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Scott W.
full_name: Roy, Scott W.
last_name: Roy
citation:
ama: Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns
on genomic scales. Nature. 2016;538(7626):533-536. doi:10.1038/nature20110
apa: Huff, J. T., Zilberman, D., & Roy, S. W. (2016). Mechanism for DNA transposons
to generate introns on genomic scales. Nature. Springer Nature . https://doi.org/10.1038/nature20110
chicago: Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA
Transposons to Generate Introns on Genomic Scales.” Nature. Springer Nature
, 2016. https://doi.org/10.1038/nature20110.
ieee: J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to
generate introns on genomic scales,” Nature, vol. 538, no. 7626. Springer
Nature , pp. 533–536, 2016.
ista: Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate
introns on genomic scales. Nature. 538(7626), 533–536.
mla: Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on
Genomic Scales.” Nature, vol. 538, no. 7626, Springer Nature , 2016, pp.
533–36, doi:10.1038/nature20110.
short: J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.
date_created: 2021-06-04T11:34:55Z
date_published: 2016-10-27T00:00:00Z
date_updated: 2021-12-14T07:55:30Z
day: '27'
department:
- _id: DaZi
doi: 10.1038/nature20110
extern: '1'
external_id:
pmid:
- '27760113'
intvolume: ' 538'
issue: '7626'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/
month: '10'
oa: 1
oa_version: Submitted Version
page: 533-536
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: 'Springer Nature '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanism for DNA transposons to generate introns on genomic scales
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 538
year: '2016'
...
---
_id: '9473'
abstract:
- lang: eng
text: Cytosine DNA methylation regulates the expression of eukaryotic genes and
transposons. Methylation is copied by methyltransferases after DNA replication,
which results in faithful transmission of methylation patterns during cell division
and, at least in flowering plants, across generations. Transgenerational inheritance
is mediated by a small group of cells that includes gametes and their progenitors.
However, methylation is usually analyzed in somatic tissues that do not contribute
to the next generation, and the mechanisms of transgenerational inheritance are
inferred from such studies. To gain a better understanding of how DNA methylation
is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the
cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases.
We find that DNA methylation dependency on these enzymes is similar in sperm,
vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin
in vegetative cells, likely reflecting transcription of heterochromatic transposons
in this cell type. We also show that lack of histone H1, which elevates heterochromatic
DNA methylation in somatic tissues, does not have this effect in pollen. Instead,
levels of CG methylation in wild-type sperm and vegetative cells, as well as in
wild-type microspores from which both pollen cell types originate, are substantially
higher than in wild-type somatic tissues and similar to those of H1-depleted roots.
Our results demonstrate that the mechanisms of methylation maintenance are similar
between pollen and somatic cells, but the efficiency of CG methylation is higher
in pollen, allowing methylation patterns to be accurately inherited across generations.
article_processing_charge: No
article_type: original
author:
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Toby
full_name: Buttress, Toby
last_name: Buttress
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Matthew
full_name: Couchman, Matthew
last_name: Couchman
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits
more robust maintenance of CG methylation than somatic tissues. Proceedings
of the National Academy of Sciences. 2016;113(52):15132-15137. doi:10.1073/pnas.1619074114
apa: Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L.,
… Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance
of CG methylation than somatic tissues. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1619074114
chicago: Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman,
Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual
Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2016. https://doi.org/10.1073/pnas.1619074114.
ieee: P.-H. Hsieh et al., “Arabidopsis male sexual lineage exhibits more
robust maintenance of CG methylation than somatic tissues,” Proceedings of
the National Academy of Sciences, vol. 113, no. 52. National Academy of Sciences,
pp. 15132–15137, 2016.
ista: Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng
X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG
methylation than somatic tissues. Proceedings of the National Academy of Sciences.
113(52), 15132–15137.
mla: Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust
Maintenance of CG Methylation than Somatic Tissues.” Proceedings of the National
Academy of Sciences, vol. 113, no. 52, National Academy of Sciences, 2016,
pp. 15132–37, doi:10.1073/pnas.1619074114.
short: P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman,
X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.
date_created: 2021-06-07T06:21:39Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:40Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619074114
extern: '1'
external_id:
pmid:
- '27956643'
intvolume: ' 113'
issue: '52'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619074114
month: '12'
oa: 1
oa_version: Published Version
page: 15132-15137
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation
than somatic tissues
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '9477'
abstract:
- lang: eng
text: Cytosine methylation is a DNA modification with important regulatory functions
in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive
DNA demethylation, which is required for proper gene expression in the endosperm,
a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm
cell carried in the pollen and a female central cell. Endosperm DNA demethylation
is observed specifically on the chromosomes inherited from the central cell in
Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase
in Arabidopsis. DEMETER is expressed in the central cell before fertilization,
suggesting that endosperm demethylation patterns are inherited from the central
cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed
to contribute to central cell demethylation. However, with the exception of three
maize genes, central cell DNA methylation has not been directly measured, leaving
the origin and mechanism of endosperm demethylation uncertain. Here, we report
genome-wide analysis of DNA methylation in the central cells of Arabidopsis and
rice—species that diverged 150 million years ago—as well as in rice egg cells.
We find that DNA demethylation in both species is initiated in central cells,
which requires DEMETER in Arabidopsis. However, we do not observe a global reduction
of CG methylation that would be indicative of lowered MET1 activity; on the contrary,
CG methylation efficiency is elevated in female gametes compared with nonsexual
tissues. Our results demonstrate that locus-specific, active DNA demethylation
in the central cell is the origin of maternal chromosome hypomethylation in the
endosperm.
article_processing_charge: No
article_type: original
author:
- first_name: Kyunghyuk
full_name: Park, Kyunghyuk
last_name: Park
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Jin-Sup
full_name: Park, Jin-Sup
last_name: Park
- first_name: Youbong
full_name: Hyun, Youbong
last_name: Hyun
- first_name: Takashi
full_name: Okamoto, Takashi
last_name: Okamoto
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Yeonhee
full_name: Choi, Yeonhee
last_name: Choi
- first_name: Stefan
full_name: Scholten, Stefan
last_name: Scholten
citation:
ama: Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
2016;113(52):15138-15143. doi:10.1073/pnas.1619047114
apa: Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten,
S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis
and rice. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1619047114
chicago: Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun,
Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the
Central Cells of Arabidopsis and Rice.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619047114.
ieee: K. Park et al., “DNA demethylation is initiated in the central cells
of Arabidopsis and rice,” Proceedings of the National Academy of Sciences,
vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.
ista: Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer
RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
113(52), 15138–15143.
mla: Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells
of Arabidopsis and Rice.” Proceedings of the National Academy of Sciences,
vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:10.1073/pnas.1619047114.
short: K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman,
R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy
of Sciences 113 (2016) 15138–15143.
date_created: 2021-06-07T07:10:59Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:07Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619047114
extern: '1'
external_id:
pmid:
- '27956642'
intvolume: ' 113'
issue: '52'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619047114
month: '12'
oa: 1
oa_version: Published Version
page: 15138-15143
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA demethylation is initiated in the central cells of Arabidopsis and rice
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '948'
abstract:
- lang: eng
text: Experience constantly shapes neural circuits through a variety of plasticity
mechanisms. While the functional roles of some plasticity mechanisms are well-understood,
it remains unclear how changes in neural excitability contribute to learning.
Here, we develop a normative interpretation of intrinsic plasticity (IP) as a
key component of unsupervised learning. We introduce a novel generative mixture
model that accounts for the class-specific statistics of stimulus intensities,
and we derive a neural circuit that learns the input classes and their intensities.
We will analytically show that inference and learning for our generative model
can be achieved by a neural circuit with intensity-sensitive neurons equipped
with a specific form of IP. Numerical experiments verify our analytical derivations
and show robust behavior for artificial and natural stimuli. Our results link
IP to non-trivial input statistics, in particular the statistics of stimulus intensities
for classes to which a neuron is sensitive. More generally, our work paves the
way toward new classification algorithms that are robust to intensity variations.
acknowledgement: DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and LU 1196/5-1
(JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement
no. 291734 (CS)
alternative_title:
- Advances in Neural Information Processing Systems
author:
- first_name: Travis
full_name: Monk, Travis
last_name: Monk
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
- first_name: Jörg
full_name: Lücke, Jörg
last_name: Lücke
citation:
ama: 'Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn
stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems;
2016:4285-4293.'
apa: 'Monk, T., Savin, C., & Lücke, J. (2016). Neurons equipped with intrinsic
plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented
at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural
Information Processing Systems.'
chicago: Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic
Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information
Processing Systems, 2016.
ieee: 'T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity
learn stimulus intensity statistics,” presented at the NIPS: Neural Information
Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.'
ista: 'Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity
learn stimulus intensity statistics. NIPS: Neural Information Processing Systems,
Advances in Neural Information Processing Systems, vol. 29, 4285–4293.'
mla: Monk, Travis, et al. Neurons Equipped with Intrinsic Plasticity Learn Stimulus
Intensity Statistics. Vol. 29, Neural Information Processing Systems, 2016,
pp. 4285–93.
short: T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems,
2016, pp. 4285–4293.
conference:
end_date: 2016-12-10
location: Barcelona, Spaine
name: 'NIPS: Neural Information Processing Systems'
start_date: 2016-12-05
date_created: 2018-12-11T11:49:21Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T08:22:08Z
day: '01'
department:
- _id: GaTk
ec_funded: 1
intvolume: ' 29'
language:
- iso: eng
main_file_link:
- url: https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics
month: '01'
oa_version: None
page: 4285 - 4293
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '6469'
quality_controlled: '1'
scopus_import: 1
status: public
title: Neurons equipped with intrinsic plasticity learn stimulus intensity statistics
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...
---
_id: '9591'
abstract:
- lang: eng
text: We give several results showing that different discrete structures typically
gain certain spanning substructures (in particular, Hamilton cycles) after a modest
random perturbation. First, we prove that adding linearly many random edges to
a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence
of a perfect matching or a loose Hamilton cycle. The proof involves an interesting
application of Szemerédi's Regularity Lemma, which might be independently useful.
We next prove that digraphs with certain strong expansion properties are pancyclic,
and use this to show that adding a linear number of random edges typically makes
a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent)
number of random edges in a tournament typically ensures the existence of multiple
edge-disjoint Hamilton cycles. All our results are tight.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Krivelevich, Michael
last_name: Krivelevich
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed
digraphs and hypergraphs. Combinatorics, Probability and Computing. 2016;25(6):909-927.
doi:10.1017/s0963548316000079
apa: Krivelevich, M., Kwan, M. A., & Sudakov, B. (2016). Cycles and matchings
in randomly perturbed digraphs and hypergraphs. Combinatorics, Probability
and Computing. Cambridge University Press. https://doi.org/10.1017/s0963548316000079
chicago: Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and
Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Combinatorics, Probability
and Computing. Cambridge University Press, 2016. https://doi.org/10.1017/s0963548316000079.
ieee: M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly
perturbed digraphs and hypergraphs,” Combinatorics, Probability and Computing,
vol. 25, no. 6. Cambridge University Press, pp. 909–927, 2016.
ista: Krivelevich M, Kwan MA, Sudakov B. 2016. Cycles and matchings in randomly
perturbed digraphs and hypergraphs. Combinatorics, Probability and Computing.
25(6), 909–927.
mla: Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs
and Hypergraphs.” Combinatorics, Probability and Computing, vol. 25, no.
6, Cambridge University Press, 2016, pp. 909–27, doi:10.1017/s0963548316000079.
short: M. Krivelevich, M.A. Kwan, B. Sudakov, Combinatorics, Probability and Computing
25 (2016) 909–927.
date_created: 2021-06-22T12:35:13Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2023-02-23T14:02:07Z
day: '01'
doi: 10.1017/s0963548316000079
extern: '1'
external_id:
arxiv:
- '1501.04816'
intvolume: ' 25'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1501.04816
month: '11'
oa: 1
oa_version: Preprint
page: 909-927
publication: Combinatorics, Probability and Computing
publication_identifier:
eissn:
- 1469-2163
issn:
- 0963-5483
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cycles and matchings in randomly perturbed digraphs and hypergraphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 25
year: '2016'
...
---
_id: '9654'
abstract:
- lang: eng
text: RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal
DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free
Pol I from the yeast Saccharomyces cerevisiae have revealed dimers of the enzyme
stabilized by a 'connector' element and an expanded cleft containing the active
centre in an inactive conformation. The central bridge helix was unfolded and
a Pol-I-specific 'expander' element occupied the DNA-template-binding site. The
structure of Pol I in its active transcribing conformation has yet to be determined,
whereas structures of Pol II and Pol III have been solved with bound DNA template
and RNA transcript. Here we report structures of active transcribing Pol I from
yeast solved by two different cryo-electron microscopy approaches. A single-particle
structure at 3.8 Å resolution reveals a contracted active centre cleft with bound
DNA and RNA, and a narrowed pore beneath the active site that no longer holds
the RNA-cleavage-stimulating domain of subunit A12.2. A structure at 29 Å resolution
that was determined from cryo-electron tomograms of Pol I enzymes transcribing
cellular rDNA confirms contraction of the cleft and reveals that incoming and
exiting rDNA enclose an angle of around 150°. The structures suggest a model for
the regulation of transcription elongation in which contracted and expanded polymerase
conformations are associated with active and inactive states, respectively.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Simon
full_name: Neyer, Simon
last_name: Neyer
- first_name: Michael
full_name: Kunz, Michael
last_name: Kunz
- first_name: Christian
full_name: Geiss, Christian
last_name: Geiss
- first_name: Merle
full_name: Hantsche, Merle
last_name: Hantsche
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Anja
full_name: Seybert, Anja
last_name: Seybert
- first_name: Christoph
full_name: Engel, Christoph
last_name: Engel
- first_name: Margot P.
full_name: Scheffer, Margot P.
last_name: Scheffer
- first_name: Patrick
full_name: Cramer, Patrick
last_name: Cramer
- first_name: Achilleas S.
full_name: Frangakis, Achilleas S.
last_name: Frangakis
citation:
ama: Neyer S, Kunz M, Geiss C, et al. Structure of RNA polymerase I transcribing
ribosomal DNA genes. Nature. 2016;540(7634):607-610. doi:10.1038/nature20561
apa: Neyer, S., Kunz, M., Geiss, C., Hantsche, M., Hodirnau, V.-V., Seybert, A.,
… Frangakis, A. S. (2016). Structure of RNA polymerase I transcribing ribosomal
DNA genes. Nature. Springer Nature. https://doi.org/10.1038/nature20561
chicago: Neyer, Simon, Michael Kunz, Christian Geiss, Merle Hantsche, Victor-Valentin
Hodirnau, Anja Seybert, Christoph Engel, Margot P. Scheffer, Patrick Cramer, and
Achilleas S. Frangakis. “Structure of RNA Polymerase I Transcribing Ribosomal
DNA Genes.” Nature. Springer Nature, 2016. https://doi.org/10.1038/nature20561.
ieee: S. Neyer et al., “Structure of RNA polymerase I transcribing ribosomal
DNA genes,” Nature, vol. 540, no. 7634. Springer Nature, pp. 607–610, 2016.
ista: Neyer S, Kunz M, Geiss C, Hantsche M, Hodirnau V-V, Seybert A, Engel C, Scheffer
MP, Cramer P, Frangakis AS. 2016. Structure of RNA polymerase I transcribing ribosomal
DNA genes. Nature. 540(7634), 607–610.
mla: Neyer, Simon, et al. “Structure of RNA Polymerase I Transcribing Ribosomal
DNA Genes.” Nature, vol. 540, no. 7634, Springer Nature, 2016, pp. 607–10,
doi:10.1038/nature20561.
short: S. Neyer, M. Kunz, C. Geiss, M. Hantsche, V.-V. Hodirnau, A. Seybert, C.
Engel, M.P. Scheffer, P. Cramer, A.S. Frangakis, Nature 540 (2016) 607–610.
date_created: 2021-07-14T09:04:24Z
date_published: 2016-12-22T00:00:00Z
date_updated: 2021-07-22T09:22:20Z
day: '22'
doi: 10.1038/nature20561
extern: '1'
external_id:
pmid:
- '27842382'
intvolume: ' 540'
issue: '7634'
language:
- iso: eng
month: '12'
oa_version: None
page: 607-610
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure of RNA polymerase I transcribing ribosomal DNA genes
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 540
year: '2016'
...
---
_id: '9681'
abstract:
- lang: eng
text: One of the most prominent consequences of the quantum nature of light atomic
nuclei is that their kinetic energy does not follow a Maxwell–Boltzmann distribution.
Deep inelastic neutron scattering (DINS) experiments can measure this effect.
Thus, the nuclear quantum kinetic energy can be probed directly in both ordered
and disordered samples. However, the relation between the quantum kinetic energy
and the atomic environment is a very indirect one, and cross-validation with theoretical
modeling is therefore urgently needed. Here, we use state of the art path integral
molecular dynamics techniques to compute the kinetic energy of hydrogen and oxygen
nuclei in liquid, solid, and gas-phase water close to the triple point, comparing
three different interatomic potentials and validating our results against equilibrium
isotope fractionation measurements. We will then show how accurate simulations
can draw a link between extremely precise fractionation experiments and DINS,
therefore establishing a reliable benchmark for future measurements and providing
key insights to increase further the accuracy of interatomic potentials for water.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Jörg
full_name: Behler, Jörg
last_name: Behler
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: 'Cheng B, Behler J, Ceriotti M. Nuclear quantum effects in water at the triple
point: Using theory as a link between experiments. The Journal of Physical
Chemistry Letters. 2016;7(12):2210-2215. doi:10.1021/acs.jpclett.6b00729'
apa: 'Cheng, B., Behler, J., & Ceriotti, M. (2016). Nuclear quantum effects
in water at the triple point: Using theory as a link between experiments. The
Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.6b00729'
chicago: 'Cheng, Bingqing, Jörg Behler, and Michele Ceriotti. “Nuclear Quantum Effects
in Water at the Triple Point: Using Theory as a Link between Experiments.” The
Journal of Physical Chemistry Letters. American Chemical Society, 2016. https://doi.org/10.1021/acs.jpclett.6b00729.'
ieee: 'B. Cheng, J. Behler, and M. Ceriotti, “Nuclear quantum effects in water at
the triple point: Using theory as a link between experiments,” The Journal
of Physical Chemistry Letters, vol. 7, no. 12. American Chemical Society,
pp. 2210–2215, 2016.'
ista: 'Cheng B, Behler J, Ceriotti M. 2016. Nuclear quantum effects in water at
the triple point: Using theory as a link between experiments. The Journal of Physical
Chemistry Letters. 7(12), 2210–2215.'
mla: 'Cheng, Bingqing, et al. “Nuclear Quantum Effects in Water at the Triple Point:
Using Theory as a Link between Experiments.” The Journal of Physical Chemistry
Letters, vol. 7, no. 12, American Chemical Society, 2016, pp. 2210–15, doi:10.1021/acs.jpclett.6b00729.'
short: B. Cheng, J. Behler, M. Ceriotti, The Journal of Physical Chemistry Letters
7 (2016) 2210–2215.
date_created: 2021-07-19T08:57:32Z
date_published: 2016-06-16T00:00:00Z
date_updated: 2023-02-23T14:04:49Z
day: '16'
doi: 10.1021/acs.jpclett.6b00729
extern: '1'
external_id:
pmid:
- '27203358'
intvolume: ' 7'
issue: '12'
language:
- iso: eng
month: '06'
oa_version: None
page: 2210-2215
pmid: 1
publication: The Journal of Physical Chemistry Letters
publication_identifier:
eissn:
- 1948-7185
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Nuclear quantum effects in water at the triple point: Using theory as a link
between experiments'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 7
year: '2016'
...
---
_id: '9704'
abstract:
- lang: eng
text: Emerging infectious diseases (EIDs) have contributed significantly to the
current biodiversity crisis, leading to widespread epidemics and population loss.
Owing to genetic variation in pathogen virulence, a complete understanding of
species decline requires the accurate identification and characterization of EIDs.
We explore this issue in the Western honeybee, where increasing mortality of populations
in the Northern Hemisphere has caused major concern. Specifically, we investigate
the importance of genetic identity of the main suspect in mortality, deformed
wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a
systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B)
is more virulent than the established DWV genotype (DWV-A) and is widespread in
the landscape. Furthermore, we show in a simple model that colonies infected with
DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential
for rapid DWV evolution by revealing extensive genome-wide recombination in vivo.
The emergence of DWV-B in naive honeybee populations, including via recombination
with DWV-A, could be of significant ecological and economic importance. Our findings
emphasize that knowledge of pathogen genetic identity and diversity is critical
to understanding drivers of species decline.
article_processing_charge: No
author:
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Myrsini
full_name: Natsopoulou, Myrsini
last_name: Natsopoulou
- first_name: Vincent
full_name: Doublet, Vincent
last_name: Doublet
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Silvio
full_name: Weging, Silvio
last_name: Weging
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Andreas
full_name: Gogol Döring, Andreas
last_name: Gogol Döring
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
citation:
ama: 'Mcmahon D, Natsopoulou M, Doublet V, et al. Data from: Elevated virulence
of an emerging viral genotype as a driver of honeybee loss. 2016. doi:10.5061/dryad.cq7t1'
apa: 'Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M.,
… Paxton, R. (2016). Data from: Elevated virulence of an emerging viral genotype
as a driver of honeybee loss. Dryad. https://doi.org/10.5061/dryad.cq7t1'
chicago: 'Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio
Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Data from: Elevated
Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Dryad,
2016. https://doi.org/10.5061/dryad.cq7t1.'
ieee: 'D. Mcmahon et al., “Data from: Elevated virulence of an emerging viral
genotype as a driver of honeybee loss.” Dryad, 2016.'
ista: 'Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring
A, Paxton R. 2016. Data from: Elevated virulence of an emerging viral genotype
as a driver of honeybee loss, Dryad, 10.5061/dryad.cq7t1.'
mla: 'Mcmahon, Dino, et al. Data from: Elevated Virulence of an Emerging Viral
Genotype as a Driver of Honeybee Loss. Dryad, 2016, doi:10.5061/dryad.cq7t1.'
short: D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A.
Gogol Döring, R. Paxton, (2016).
date_created: 2021-07-23T08:30:38Z
date_published: 2016-05-06T00:00:00Z
date_updated: 2023-02-21T16:54:31Z
day: '06'
department:
- _id: SyCr
doi: 10.5061/dryad.cq7t1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.cq7t1
month: '05'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1262'
relation: used_in_publication
status: public
status: public
title: 'Data from: Elevated virulence of an emerging viral genotype as a driver of
honeybee loss'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...