---
_id: '10376'
abstract:
- lang: eng
text: Nucleation processes are at the heart of a large number of phenomena, from
cloud formation to protein crystallization. A recently emerging area where nucleation
is highly relevant is the initiation of filamentous protein self-assembly, a process
that has broad implications in many research areas ranging from medicine to nanotechnology.
As such, spontaneous nucleation of protein fibrils has received much attention
in recent years with many theoretical and experimental studies focusing on the
underlying physical principles. In this paper we make a step forward in this direction
and explore the early time behaviour of filamentous protein growth in the context
of nucleation theory. We first provide an overview of the thermodynamics and kinetics
of spontaneous nucleation of protein filaments in the presence of one relevant
degree of freedom, namely the cluster size. In this case, we review how key kinetic
observables, such as the reaction order of spontaneous nucleation, are directly
related to the physical size of the critical nucleus. We then focus on the increasingly
prominent case of filament nucleation that includes a conformational conversion
of the nucleating building-block as an additional slow step in the nucleation
process. Using computer simulations, we study the concentration dependence of
the nucleation rate. We find that, under these circumstances, the reaction order
of spontaneous nucleation with respect to the free monomer does no longer relate
to the overall physical size of the nucleating aggregate but rather to the portion
of the aggregate that actively participates in the conformational conversion.
Our results thus provide a novel interpretation of the common kinetic descriptors
of protein filament formation, including the reaction order of the nucleation
step or the scaling exponent of lag times, and put into perspective current theoretical
descriptions of protein aggregation.
acknowledgement: We acknowledge support from the Human Frontier Science Program and
Emmanuel College (A.Š.), St John’s and Peterhouse Colleges (T.C.T.M.), the Swiss
National Science Foundation (T.C.T.M.), the Biotechnology and Biological Sciences
Research Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.),
the European Research Council (T.C.T.M., T.P.J.K., and D.F.), and the Engineering
and Physical Sciences Research Council (D.F.).
article_number: '211926'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Thomas C. T.
full_name: Michaels, Thomas C. T.
last_name: Michaels
- first_name: Alessio
full_name: Zaccone, Alessio
last_name: Zaccone
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: 'Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. Kinetics of spontaneous
filament nucleation via oligomers: Insights from theory and simulation. The
Journal of Chemical Physics. 2016;145(21). doi:10.1063/1.4965040'
apa: 'Šarić, A., Michaels, T. C. T., Zaccone, A., Knowles, T. P. J., & Frenkel,
D. (2016). Kinetics of spontaneous filament nucleation via oligomers: Insights
from theory and simulation. The Journal of Chemical Physics. American Institute
of Physics. https://doi.org/10.1063/1.4965040'
chicago: 'Šarić, Anđela, Thomas C. T. Michaels, Alessio Zaccone, Tuomas P. J. Knowles,
and Daan Frenkel. “Kinetics of Spontaneous Filament Nucleation via Oligomers:
Insights from Theory and Simulation.” The Journal of Chemical Physics.
American Institute of Physics, 2016. https://doi.org/10.1063/1.4965040.'
ieee: 'A. Šarić, T. C. T. Michaels, A. Zaccone, T. P. J. Knowles, and D. Frenkel,
“Kinetics of spontaneous filament nucleation via oligomers: Insights from theory
and simulation,” The Journal of Chemical Physics, vol. 145, no. 21. American
Institute of Physics, 2016.'
ista: 'Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. 2016. Kinetics
of spontaneous filament nucleation via oligomers: Insights from theory and simulation.
The Journal of Chemical Physics. 145(21), 211926.'
mla: 'Šarić, Anđela, et al. “Kinetics of Spontaneous Filament Nucleation via Oligomers:
Insights from Theory and Simulation.” The Journal of Chemical Physics,
vol. 145, no. 21, 211926, American Institute of Physics, 2016, doi:10.1063/1.4965040.'
short: A. Šarić, T.C.T. Michaels, A. Zaccone, T.P.J. Knowles, D. Frenkel, The Journal
of Chemical Physics 145 (2016).
date_created: 2021-11-29T10:01:57Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-11-29T10:33:11Z
day: '01'
doi: 10.1063/1.4965040
extern: '1'
external_id:
arxiv:
- '1610.02320'
pmid:
- '28799382'
intvolume: ' 145'
issue: '21'
keyword:
- physical and theoretical chemistry
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.02320
month: '12'
oa: 1
oa_version: Preprint
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Kinetics of spontaneous filament nucleation via oligomers: Insights from theory
and simulation'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 145
year: '2016'
...
---
_id: '10377'
abstract:
- lang: eng
text: The interplay of membrane proteins is vital for many biological processes,
such as cellular transport, cell division, and signal transduction between nerve
cells. Theoretical considerations have led to the idea that the membrane itself
mediates protein self-organization in these processes through minimization of
membrane curvature energy. Here, we present a combined experimental and numerical
study in which we quantify these interactions directly for the first time. In
our experimental model system we control the deformation of a lipid membrane by
adhering colloidal particles. Using confocal microscopy, we establish that these
membrane deformations cause an attractive interaction force leading to reversible
binding. The attraction extends over 2.5 times the particle diameter and has a
strength of three times the thermal energy (−3.3 kBT). Coarse-grained Monte-Carlo
simulations of the system are in excellent agreement with the experimental results
and prove that the measured interaction is independent of length scale. Our combined
experimental and numerical results reveal membrane curvature as a common physical
origin for interactions between any membrane-deforming objects, from nanometre-sized
proteins to micrometre-sized particles.
acknowledgement: This work was supported by the Netherlands Organisation for Scientific
Research (NWO/OCW), as part of the Frontiers of Nanoscience program and VENI grant
680-47-431. We thank Jeroen Appel and Wim Pomp for advice on the protocol design
and Marcel Winter and Ruben Verweij for experimental support.
article_number: '32825'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Casper
full_name: van der Wel, Casper
last_name: van der Wel
- first_name: Afshin
full_name: Vahid, Afshin
last_name: Vahid
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
- first_name: Doris
full_name: Heinrich, Doris
last_name: Heinrich
- first_name: Daniela J.
full_name: Kraft, Daniela J.
last_name: Kraft
citation:
ama: van der Wel C, Vahid A, Šarić A, Idema T, Heinrich D, Kraft DJ. Lipid membrane-mediated
attraction between curvature inducing objects. Scientific Reports. 2016;6(1).
doi:10.1038/srep32825
apa: van der Wel, C., Vahid, A., Šarić, A., Idema, T., Heinrich, D., & Kraft,
D. J. (2016). Lipid membrane-mediated attraction between curvature inducing objects.
Scientific Reports. Springer Nature. https://doi.org/10.1038/srep32825
chicago: Wel, Casper van der, Afshin Vahid, Anđela Šarić, Timon Idema, Doris Heinrich,
and Daniela J. Kraft. “Lipid Membrane-Mediated Attraction between Curvature Inducing
Objects.” Scientific Reports. Springer Nature, 2016. https://doi.org/10.1038/srep32825.
ieee: C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, and D. J. Kraft,
“Lipid membrane-mediated attraction between curvature inducing objects,” Scientific
Reports, vol. 6, no. 1. Springer Nature, 2016.
ista: van der Wel C, Vahid A, Šarić A, Idema T, Heinrich D, Kraft DJ. 2016. Lipid
membrane-mediated attraction between curvature inducing objects. Scientific Reports.
6(1), 32825.
mla: van der Wel, Casper, et al. “Lipid Membrane-Mediated Attraction between Curvature
Inducing Objects.” Scientific Reports, vol. 6, no. 1, 32825, Springer Nature,
2016, doi:10.1038/srep32825.
short: C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, D.J. Kraft, Scientific
Reports 6 (2016).
date_created: 2021-11-29T10:34:08Z
date_published: 2016-09-13T00:00:00Z
date_updated: 2021-11-29T11:08:15Z
day: '13'
ddc:
- '540'
doi: 10.1038/srep32825
extern: '1'
external_id:
arxiv:
- '1603.04644'
pmid:
- '27618764'
file:
- access_level: open_access
checksum: d6cf16dd511e15726b001e7cc287cf1d
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-29T10:50:00Z
date_updated: 2021-11-29T10:50:00Z
file_id: '10379'
file_name: 2016_SciRep_vanderWel.pdf
file_size: 1598289
relation: main_file
success: 1
file_date_updated: 2021-11-29T10:50:00Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '1'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.nature.com/articles/srep32825
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/srep37382
scopus_import: '1'
status: public
title: Lipid membrane-mediated attraction between curvature inducing objects
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2016'
...
---
_id: '10378'
abstract:
- lang: eng
text: The ability of biological molecules to replicate themselves is the foundation
of life, requiring a complex cellular machinery. However, a range of aberrant
processes involve the self-replication of pathological protein structures without
any additional assistance. One example is the autocatalytic generation of pathological
protein aggregates, including amyloid fibrils, involved in neurodegenerative disorders.
Here, we use computer simulations to identify the necessary requirements for the
self-replication of fibrillar assemblies of proteins. We establish that a key
physical determinant for this process is the affinity of proteins for the surfaces
of fibrils. We find that self-replication can take place only in a very narrow
regime of inter-protein interactions, implying a high level of sensitivity to
system parameters and experimental conditions. We then compare our theoretical
predictions with kinetic and biosensor measurements of fibrils formed from the
Aβ peptide associated with Alzheimer’s disease. Our results show a quantitative
connection between the kinetics of self-replication and the surface coverage of
fibrils by monomeric proteins. These findings reveal the fundamental physical
requirements for the formation of supra-molecular structures able to replicate
themselves, and shed light on mechanisms in play in the proliferation of protein
aggregates in nature.
acknowledgement: We acknowledge support from the Human Frontier Science Program and
Emmanuel College (A.Š.), the Leverhulme Trust and Magdalene College (A.K.B.), St
John’s College (T.C.T.M.), the Biotechnology and Biological Sciences Research Council
(T.P.J.K. and C.M.D.), the Frances and Augustus Newman Foundation (T.P.J.K.), the
European Research Council (T.P.J.K., T.C.T.M., S.L. and D.F.), and the Engineering
and Physical Sciences Research Council (D.F.).
article_processing_charge: No
article_type: original
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Alexander K.
full_name: Buell, Alexander K.
last_name: Buell
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Thomas C. T.
full_name: Michaels, Thomas C. T.
last_name: Michaels
- first_name: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: Šarić A, Buell AK, Meisl G, et al. Physical determinants of the self-replication
of protein fibrils. Nature Physics. 2016;12(9):874-880. doi:10.1038/nphys3828
apa: Šarić, A., Buell, A. K., Meisl, G., Michaels, T. C. T., Dobson, C. M., Linse,
S., … Frenkel, D. (2016). Physical determinants of the self-replication of protein
fibrils. Nature Physics. Springer Nature. https://doi.org/10.1038/nphys3828
chicago: Šarić, Anđela, Alexander K. Buell, Georg Meisl, Thomas C. T. Michaels,
Christopher M. Dobson, Sara Linse, Tuomas P. J. Knowles, and Daan Frenkel. “Physical
Determinants of the Self-Replication of Protein Fibrils.” Nature Physics.
Springer Nature, 2016. https://doi.org/10.1038/nphys3828.
ieee: A. Šarić et al., “Physical determinants of the self-replication of
protein fibrils,” Nature Physics, vol. 12, no. 9. Springer Nature, pp.
874–880, 2016.
ista: Šarić A, Buell AK, Meisl G, Michaels TCT, Dobson CM, Linse S, Knowles TPJ,
Frenkel D. 2016. Physical determinants of the self-replication of protein fibrils.
Nature Physics. 12(9), 874–880.
mla: Šarić, Anđela, et al. “Physical Determinants of the Self-Replication of Protein
Fibrils.” Nature Physics, vol. 12, no. 9, Springer Nature, 2016, pp. 874–80,
doi:10.1038/nphys3828.
short: A. Šarić, A.K. Buell, G. Meisl, T.C.T. Michaels, C.M. Dobson, S. Linse, T.P.J.
Knowles, D. Frenkel, Nature Physics 12 (2016) 874–880.
date_created: 2021-11-29T10:36:11Z
date_published: 2016-07-18T00:00:00Z
date_updated: 2021-11-29T11:07:25Z
day: '18'
doi: 10.1038/nphys3828
extern: '1'
external_id:
pmid:
- '31031819'
intvolume: ' 12'
issue: '9'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://discovery.ucl.ac.uk/id/eprint/1517406/
month: '07'
oa: 1
oa_version: Preprint
page: 874-880
pmid: 1
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Physical determinants of the self-replication of protein fibrils
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 12
year: '2016'
...
---
_id: '10380'
abstract:
- lang: eng
text: Using non-equilibrium molecular dynamics simulations, it has been recently
demonstrated that water molecules align in response to an imposed temperature
gradient, resulting in an effective electric field. Here, we investigate how thermally
induced fields depend on the underlying treatment of long-ranged interactions.
For the short-ranged Wolf method and Ewald summation, we find the peak strength
of the field to range between 2 × 107 and 5 × 107 V/m for a temperature gradient
of 5.2 K/Å. Our value for the Wolf method is therefore an order of magnitude lower
than the literature value [J. A. Armstrong and F. Bresme, J. Chem. Phys. 139,
014504 (2013); J. Armstrong et al., J. Chem. Phys. 143, 036101 (2015)]. We show
that this discrepancy can be traced back to the use of an incorrect kernel in
the calculation of the electrostatic field. More seriously, we find that the Wolf
method fails to predict correct molecular orientations, resulting in dipole densities
with opposite sign to those computed using Ewald summation. By considering two
different multipole expansions, we show that, for inhomogeneous polarisations,
the quadrupole contribution can be significant and even outweigh the dipole contribution
to the field. Finally, we propose a more accurate way of calculating the electrostatic
potential and the field. In particular, we show that averaging the microscopic
field analytically to obtain the macroscopic Maxwell field reduces the error bars
by up to an order of magnitude. As a consequence, the simulation times required
to reach a given statistical accuracy decrease by up to two orders of magnitude.
acknowledgement: The authors should like to dedicate this paper to the memory of Simon
de Leeuw, who was a pioneer in the calculation of Coulomb effects in simulations.
P.W. would like to thank the Austrian Academy of Sciences for financial support
through a DOC Fellowship, and for covering the travel expenses for the CECAM workshop
in Zaragoza in May 2015, where these results were first presented. P.W. would also
like to thank Chao Zhang for pointing out the equivalence of the two expressions
for the electric field discussed in Sec. VI D, Michiel Sprik for emphasising the
importance of the quadrupole contribution in experimental studies of interfacial
systems, as well as Aleks Reinhardt and other members of the Frenkel and Dellago
groups for their advice. We further acknowledge support from the Federation of Austrian
Industry (IV) Carinthia (P.W.), the University of Zagreb and Erasmus SMP (D. Fijan),
the Human Frontier Science Program and Emmanuel College (A.Š.), the Austrian Science
Fund FWF within the SFB Vicom project F41 (C.D.), and the Engineering and Physical
Sciences Research Council Programme Grant No. EP/I001352/1 (D.F.). Additional data
related to this publication are available at the University of Cambridge data repository
(http://dx.doi.org/10.17863/CAM.118).
article_number: '224102'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: P.
full_name: Wirnsberger, P.
last_name: Wirnsberger
- first_name: D.
full_name: Fijan, D.
last_name: Fijan
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: M.
full_name: Neumann, M.
last_name: Neumann
- first_name: C.
full_name: Dellago, C.
last_name: Dellago
- first_name: D.
full_name: Frenkel, D.
last_name: Frenkel
citation:
ama: Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. Non-equilibrium
simulations of thermally induced electric fields in water. The Journal of Chemical
Physics. 2016;144(22). doi:10.1063/1.4953036
apa: Wirnsberger, P., Fijan, D., Šarić, A., Neumann, M., Dellago, C., & Frenkel,
D. (2016). Non-equilibrium simulations of thermally induced electric fields in
water. The Journal of Chemical Physics. American Institute of Physics.
https://doi.org/10.1063/1.4953036
chicago: Wirnsberger, P., D. Fijan, Anđela Šarić, M. Neumann, C. Dellago, and D.
Frenkel. “Non-Equilibrium Simulations of Thermally Induced Electric Fields in
Water.” The Journal of Chemical Physics. American Institute of Physics,
2016. https://doi.org/10.1063/1.4953036.
ieee: P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, and D. Frenkel,
“Non-equilibrium simulations of thermally induced electric fields in water,” The
Journal of Chemical Physics, vol. 144, no. 22. American Institute of Physics,
2016.
ista: Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. 2016. Non-equilibrium
simulations of thermally induced electric fields in water. The Journal of Chemical
Physics. 144(22), 224102.
mla: Wirnsberger, P., et al. “Non-Equilibrium Simulations of Thermally Induced Electric
Fields in Water.” The Journal of Chemical Physics, vol. 144, no. 22, 224102,
American Institute of Physics, 2016, doi:10.1063/1.4953036.
short: P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, D. Frenkel, The
Journal of Chemical Physics 144 (2016).
date_created: 2021-11-29T11:08:52Z
date_published: 2016-06-10T00:00:00Z
date_updated: 2021-11-29T13:09:08Z
day: '10'
doi: 10.1063/1.4953036
extern: '1'
external_id:
arxiv:
- '1602.02734'
pmid:
- '27305991'
intvolume: ' 144'
issue: '22'
keyword:
- physical and theoretical chemistry
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.02734
month: '06'
oa: 1
oa_version: Preprint
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-equilibrium simulations of thermally induced electric fields in water
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 144
year: '2016'
...
---
_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
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: '1181'
abstract:
- lang: eng
text: 'This review accompanies a 2016 SFN mini-symposium presenting examples of
current studies that address a central question: How do neural stem cells (NSCs)
divide in different ways to produce heterogeneous daughter types at the right
time and in proper numbers to build a cerebral cortex with the appropriate size
and structure? We will focus on four aspects of corticogenesis: cytokinesis events
that follow apical mitoses of NSCs; coordinating abscission with delamination
from the apical membrane; timing of neurogenesis and its indirect regulation through
emergence of intermediate progenitors; and capacity of single NSCs to generate
the correct number and laminar fate of cortical neurons. Defects in these mechanisms
can cause microcephaly and other brain malformations, and understanding them is
critical to designing diagnostic tools and preventive and corrective therapies.'
acknowledgement: This work was supported by National Institutes of Health Grants R01NS089795
and R01NS098370 to H.T.G., R01NS076640 to N.D.D., and R01MH094589 and R01NS089777
to B.C., Academia Sinica AS-104-TPB09-2 to S.-J.C, European Union FP7-CIG618444
and Human Frontiers Science Program RGP0053 to S.H., and Fonds Léon Fredericq, from
the Fondation Médicale Reine Elisabeth, and from the Fonation Simone et Pierre Clerdent
to L.N. The authors apologize to colleagues whose work could not be cited due to
space limitations.
author:
- first_name: Noelle
full_name: Dwyer, Noelle
last_name: Dwyer
- first_name: Bin
full_name: Chen, Bin
last_name: Chen
- first_name: Shen
full_name: Chou, Shen
last_name: Chou
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Laurent
full_name: Nguyen, Laurent
last_name: Nguyen
- first_name: Troy
full_name: Ghashghaei, Troy
last_name: Ghashghaei
citation:
ama: 'Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. Neural stem
cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and
productivity. Journal of Neuroscience. 2016;36(45):11394-11401. doi:10.1523/JNEUROSCI.2359-16.2016'
apa: 'Dwyer, N., Chen, B., Chou, S., Hippenmeyer, S., Nguyen, L., & Ghashghaei,
T. (2016). Neural stem cells to cerebral cortex: Emerging mechanisms regulating
progenitor behavior and productivity. Journal of Neuroscience. Society
for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2359-16.2016'
chicago: 'Dwyer, Noelle, Bin Chen, Shen Chou, Simon Hippenmeyer, Laurent Nguyen,
and Troy Ghashghaei. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms
Regulating Progenitor Behavior and Productivity.” Journal of Neuroscience.
Society for Neuroscience, 2016. https://doi.org/10.1523/JNEUROSCI.2359-16.2016.'
ieee: 'N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, and T. Ghashghaei,
“Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor
behavior and productivity,” Journal of Neuroscience, vol. 36, no. 45. Society
for Neuroscience, pp. 11394–11401, 2016.'
ista: 'Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. 2016. Neural
stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior
and productivity. Journal of Neuroscience. 36(45), 11394–11401.'
mla: 'Dwyer, Noelle, et al. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms
Regulating Progenitor Behavior and Productivity.” Journal of Neuroscience,
vol. 36, no. 45, Society for Neuroscience, 2016, pp. 11394–401, doi:10.1523/JNEUROSCI.2359-16.2016.'
short: N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, T. Ghashghaei, Journal
of Neuroscience 36 (2016) 11394–11401.
date_created: 2018-12-11T11:50:35Z
date_published: 2016-11-09T00:00:00Z
date_updated: 2021-01-12T06:48:54Z
day: '09'
department:
- _id: SiHi
doi: 10.1523/JNEUROSCI.2359-16.2016
intvolume: ' 36'
issue: '45'
language:
- iso: eng
month: '11'
oa_version: None
page: 11394 - 11401
project:
- _id: 25D7962E-B435-11E9-9278-68D0E5697425
grant_number: RGP0053/2014
name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal
Level
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '6172'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor
behavior and productivity'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2016'
...
---
_id: '1182'
abstract:
- lang: eng
text: 'Balanced knockout tournaments are ubiquitous in sports competitions and are
also used in decisionmaking and elections. The traditional computational question,
that asks to compute a draw (optimal draw) that maximizes the winning probability
for a distinguished player, has received a lot of attention. Previous works consider
the problem where the pairwise winning probabilities are known precisely, while
we study how robust is the winning probability with respect to small errors in
the pairwise winning probabilities. First, we present several illuminating examples
to establish: (a) there exist deterministic tournaments (where the pairwise winning
probabilities are 0 or 1) where one optimal draw is much more robust than the
other; and (b) in general, there exist tournaments with slightly suboptimal draws
that are more robust than all the optimal draws. The above examples motivate the
study of the computational problem of robust draws that guarantee a specified
winning probability. Second, we present a polynomial-time algorithm for approximating
the robustness of a draw for sufficiently small errors in pairwise winning probabilities,
and obtain that the stated computational problem is NP-complete. We also show
that two natural cases of deterministic tournaments where the optimal draw could
be computed in polynomial time also admit polynomial-time algorithms to compute
robust optimal draws.'
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: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
citation:
ama: 'Chatterjee K, Ibsen-Jensen R, Tkadlec J. Robust draws in balanced knockout
tournaments. In: Vol 2016-January. AAAI Press; 2016:172-179.'
apa: 'Chatterjee, K., Ibsen-Jensen, R., & Tkadlec, J. (2016). Robust draws in
balanced knockout tournaments (Vol. 2016–January, pp. 172–179). Presented at the
IJCAI: International Joint Conference on Artificial Intelligence, New York, NY,
USA: AAAI Press.'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Josef Tkadlec. “Robust
Draws in Balanced Knockout Tournaments,” 2016–January:172–79. AAAI Press, 2016.
ieee: 'K. Chatterjee, R. Ibsen-Jensen, and J. Tkadlec, “Robust draws in balanced
knockout tournaments,” presented at the IJCAI: International Joint Conference
on Artificial Intelligence, New York, NY, USA, 2016, vol. 2016–January, pp. 172–179.'
ista: 'Chatterjee K, Ibsen-Jensen R, Tkadlec J. 2016. Robust draws in balanced knockout
tournaments. IJCAI: International Joint Conference on Artificial Intelligence
vol. 2016–January, 172–179.'
mla: Chatterjee, Krishnendu, et al. Robust Draws in Balanced Knockout Tournaments.
Vol. 2016–January, AAAI Press, 2016, pp. 172–79.
short: K. Chatterjee, R. Ibsen-Jensen, J. Tkadlec, in:, AAAI Press, 2016, pp. 172–179.
conference:
end_date: 2016-07-15
location: New York, NY, USA
name: 'IJCAI: International Joint Conference on Artificial Intelligence'
start_date: 2016-07-09
date_created: 2018-12-11T11:50:35Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2023-02-21T10:04:26Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.05090v1
month: '01'
oa: 1
oa_version: Preprint
page: 172 - 179
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _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: AAAI Press
publist_id: '6171'
quality_controlled: '1'
related_material:
link:
- relation: table_of_contents
url: https://www.ijcai.org/proceedings/2016
scopus_import: 1
status: public
title: Robust draws in balanced knockout tournaments
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2016-January
year: '2016'
...
---
_id: '1183'
abstract:
- lang: eng
text: Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping
with other neurological conditions. We previously described abnormalities in the
branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we
show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid
transporter localized at the blood brain barrier (BBB), has an essential role
in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from
the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal
mRNA translation, and severe neurological abnormalities. Furthermore, we identified
several patients with autistic traits and motor delay carrying deleterious homozygous
mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular
administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate
a neurological syndrome defined by SLC7A5 mutations and support an essential role
for the BCAA in human brain function.
acknowledgement: "This work was supported by NICHD (P01HD070494) and SFARI (grant
275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\nWe thank A.C. Manzano, Mike Liu,
and F. Marr for technical assistance, and R. Shigemoto and the IST Austria Electron
Microscopy (EM) Facility for assistance. We acknowledge support from CIDR for genome-wide
SNP analysis (X01HG008823) and Broad Institute Center for Mendelian Disorders (UM1HG008900
to D. MacArthur), the Yale Center for Mendelian Disorders (U54HG006504 to M.G.),
the Gregory M. Kiez and Mehmet Kutman Foundation (M.G.), Italian Ministry of Instruction
University and Research (PON01_00937 to C.I.), and NIH (R01-GM108911 to A.S.). This
work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and
FWF (SFB35_3523) to G.N.\r\n\r\n#EMFacility"
article_processing_charge: No
article_type: original
author:
- first_name: Dora-Clara
full_name: Tarlungeanu, Dora-Clara
id: 2ABCE612-F248-11E8-B48F-1D18A9856A87
last_name: Tarlungeanu
- first_name: Elena
full_name: Deliu, Elena
id: 37A40D7E-F248-11E8-B48F-1D18A9856A87
last_name: Deliu
orcid: 0000-0002-7370-5293
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Majdi
full_name: Kara, Majdi
last_name: Kara
- first_name: Philipp
full_name: Janiesch, Philipp
last_name: Janiesch
- first_name: Mariafrancesca
full_name: Scalise, Mariafrancesca
last_name: Scalise
- first_name: Michele
full_name: Galluccio, Michele
last_name: Galluccio
- first_name: Mateja
full_name: Tesulov, Mateja
last_name: Tesulov
- first_name: Emanuela
full_name: Morelli, Emanuela
id: 3F4D1282-F248-11E8-B48F-1D18A9856A87
last_name: Morelli
- first_name: Fatma
full_name: Sönmez, Fatma
last_name: Sönmez
- first_name: Kaya
full_name: Bilgüvar, Kaya
last_name: Bilgüvar
- first_name: Ryuichi
full_name: Ohgaki, Ryuichi
last_name: Ohgaki
- first_name: Yoshikatsu
full_name: Kanai, Yoshikatsu
last_name: Kanai
- first_name: Anide
full_name: Johansen, Anide
last_name: Johansen
- first_name: Seham
full_name: Esharif, Seham
last_name: Esharif
- first_name: Tawfeg
full_name: Ben Omran, Tawfeg
last_name: Ben Omran
- first_name: Meral
full_name: Topcu, Meral
last_name: Topcu
- first_name: Avner
full_name: Schlessinger, Avner
last_name: Schlessinger
- first_name: Cesare
full_name: Indiveri, Cesare
last_name: Indiveri
- first_name: Kent
full_name: Duncan, Kent
last_name: Duncan
- first_name: Ahmet
full_name: Caglayan, Ahmet
last_name: Caglayan
- first_name: Murat
full_name: Günel, Murat
last_name: Günel
- first_name: Joseph
full_name: Gleeson, Joseph
last_name: Gleeson
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Tarlungeanu D-C, Deliu E, Dotter C, et al. Impaired amino acid transport at
the blood brain barrier is a cause of autism spectrum disorder. Cell. 2016;167(6):1481-1494.
doi:10.1016/j.cell.2016.11.013
apa: Tarlungeanu, D.-C., Deliu, E., Dotter, C., Kara, M., Janiesch, P., Scalise,
M., … Novarino, G. (2016). Impaired amino acid transport at the blood brain barrier
is a cause of autism spectrum disorder. Cell. Cell Press. https://doi.org/10.1016/j.cell.2016.11.013
chicago: Tarlungeanu, Dora-Clara, Elena Deliu, Christoph Dotter, Majdi Kara, Philipp
Janiesch, Mariafrancesca Scalise, Michele Galluccio, et al. “Impaired Amino Acid
Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.”
Cell. Cell Press, 2016. https://doi.org/10.1016/j.cell.2016.11.013.
ieee: D.-C. Tarlungeanu et al., “Impaired amino acid transport at the blood
brain barrier is a cause of autism spectrum disorder,” Cell, vol. 167,
no. 6. Cell Press, pp. 1481–1494, 2016.
ista: Tarlungeanu D-C, Deliu E, Dotter C, Kara M, Janiesch P, Scalise M, Galluccio
M, Tesulov M, Morelli E, Sönmez F, Bilgüvar K, Ohgaki R, Kanai Y, Johansen A,
Esharif S, Ben Omran T, Topcu M, Schlessinger A, Indiveri C, Duncan K, Caglayan
A, Günel M, Gleeson J, Novarino G. 2016. Impaired amino acid transport at the
blood brain barrier is a cause of autism spectrum disorder. Cell. 167(6), 1481–1494.
mla: Tarlungeanu, Dora-Clara, et al. “Impaired Amino Acid Transport at the Blood
Brain Barrier Is a Cause of Autism Spectrum Disorder.” Cell, vol. 167,
no. 6, Cell Press, 2016, pp. 1481–94, doi:10.1016/j.cell.2016.11.013.
short: D.-C. Tarlungeanu, E. Deliu, C. Dotter, M. Kara, P. Janiesch, M. Scalise,
M. Galluccio, M. Tesulov, E. Morelli, F. Sönmez, K. Bilgüvar, R. Ohgaki, Y. Kanai,
A. Johansen, S. Esharif, T. Ben Omran, M. Topcu, A. Schlessinger, C. Indiveri,
K. Duncan, A. Caglayan, M. Günel, J. Gleeson, G. Novarino, Cell 167 (2016) 1481–1494.
date_created: 2018-12-11T11:50:35Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2024-03-25T23:30:07Z
day: '01'
ddc:
- '576'
- '616'
department:
- _id: GaNo
doi: 10.1016/j.cell.2016.11.013
file:
- access_level: open_access
checksum: 7fe01ab12a6610d3db421e0136db2f77
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:44Z
date_updated: 2020-07-14T12:44:37Z
file_id: '5030'
file_name: IST-2017-771-v1+1_Tarlungeanu_et_al._Final_edited.pdf
file_size: 73907957
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 167'
issue: '6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 1481 - 1494
project:
- _id: 25473368-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: F03523
name: Transmembrane Transporters in Health and Disease
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '6170'
pubrep_id: '771'
quality_controlled: '1'
related_material:
record:
- id: '395'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Impaired amino acid transport at the blood brain barrier is a cause of autism
spectrum disorder
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 167
year: '2016'
...
---
_id: '11834'
abstract:
- lang: eng
text: "We present a deterministic incremental algorithm for exactly maintaining
the size of a minimum cut with ~O(1) amortized time per edge insertion and O(1)
query time. This result partially answers an open question posed by Thorup [Combinatorica
2007]. It also stays in sharp contrast to a polynomial conditional lower-bound
for the fully-dynamic weighted minimum cut problem. Our algorithm is obtained
by combining a recent sparsification technique of Kawarabayashi and Thorup [STOC
2015] and an exact incremental algorithm of Henzinger [J. of Algorithm 1997].\r\n\r\nWe
also study space-efficient incremental algorithms for the minimum cut problem.
Concretely, we show that there exists an O(n log n/epsilon^2) space Monte-Carlo
algorithm that can process a stream of edge insertions starting from an empty
graph, and with high probability, the algorithm maintains a (1+epsilon)-approximation
to the minimum cut. The algorithm has ~O(1) amortized update-time and constant
query-time."
alternative_title:
- LIPIcs
article_number: '46'
article_processing_charge: No
arxiv: 1
author:
- first_name: Gramoz
full_name: Goranci, Gramoz
last_name: Goranci
- 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: Mikkel
full_name: Thorup, Mikkel
last_name: Thorup
citation:
ama: 'Goranci G, Henzinger MH, Thorup M. Incremental exact min-cut in poly-logarithmic
amortized update time. In: 24th Annual European Symposium on Algorithms.
Vol 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPICS.ESA.2016.46'
apa: 'Goranci, G., Henzinger, M. H., & Thorup, M. (2016). Incremental exact
min-cut in poly-logarithmic amortized update time. In 24th Annual European
Symposium on Algorithms (Vol. 57). Aarhus, Denmark: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPICS.ESA.2016.46'
chicago: Goranci, Gramoz, Monika H Henzinger, and Mikkel Thorup. “Incremental Exact
Min-Cut in Poly-Logarithmic Amortized Update Time.” In 24th Annual European
Symposium on Algorithms, Vol. 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2016. https://doi.org/10.4230/LIPICS.ESA.2016.46.
ieee: G. Goranci, M. H. Henzinger, and M. Thorup, “Incremental exact min-cut in
poly-logarithmic amortized update time,” in 24th Annual European Symposium
on Algorithms, Aarhus, Denmark, 2016, vol. 57.
ista: 'Goranci G, Henzinger MH, Thorup M. 2016. Incremental exact min-cut in poly-logarithmic
amortized update time. 24th Annual European Symposium on Algorithms. ESA: Annual
European Symposium on Algorithms, LIPIcs, vol. 57, 46.'
mla: Goranci, Gramoz, et al. “Incremental Exact Min-Cut in Poly-Logarithmic Amortized
Update Time.” 24th Annual European Symposium on Algorithms, vol. 57, 46,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPICS.ESA.2016.46.
short: G. Goranci, M.H. Henzinger, M. Thorup, in:, 24th Annual European Symposium
on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.
conference:
end_date: 2016-08-24
location: Aarhus, Denmark
name: 'ESA: Annual European Symposium on Algorithms'
start_date: 2016-08-22
date_created: 2022-08-12T10:58:32Z
date_published: 2016-08-18T00:00:00Z
date_updated: 2023-02-16T12:05:59Z
day: '18'
doi: 10.4230/LIPICS.ESA.2016.46
extern: '1'
external_id:
arxiv:
- '1611.06500'
intvolume: ' 57'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPIcs.ESA.2016.46
month: '08'
oa: 1
oa_version: Published Version
publication: 24th Annual European Symposium on Algorithms
publication_identifier:
isbn:
- 978-3-95977-015-6
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Incremental exact min-cut in poly-logarithmic amortized update time
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2016'
...
---
_id: '11835'
abstract:
- lang: eng
text: "During the last 10 years it has become popular to study dynamic graph problems
in a emergency planning or sensitivity setting: Instead of considering the general
fully dynamic problem, we only have to process a single batch update of size d;
after the update we have to answer queries.\r\n\r\nIn this paper, we consider
the dynamic subgraph connectivity problem with sensitivity d: We are given a graph
of which some vertices are activated and some are deactivated. After that we get
a single update in which the states of up to $d$ vertices are changed. Then we
get a sequence of connectivity queries in the subgraph of activated vertices.\r\n\r\nWe
present the first fully dynamic algorithm for this problem which has an update
and query time only slightly worse than the best decremental algorithm. In addition,
we present the first incremental algorithm which is tight with respect to the
best known conditional lower bound; moreover, the algorithm is simple and we believe
it is implementable and efficient in practice."
alternative_title:
- LIPIcs
article_number: '48'
article_processing_charge: No
arxiv: 1
author:
- 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: Stefan
full_name: Neumann, Stefan
last_name: Neumann
citation:
ama: 'Henzinger MH, Neumann S. Incremental and fully dynamic subgraph connectivity
for emergency planning. In: 24th Annual European Symposium on Algorithms.
Vol 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPICS.ESA.2016.48'
apa: 'Henzinger, M. H., & Neumann, S. (2016). Incremental and fully dynamic
subgraph connectivity for emergency planning. In 24th Annual European Symposium
on Algorithms (Vol. 57). Aarhus, Denmark: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPICS.ESA.2016.48'
chicago: Henzinger, Monika H, and Stefan Neumann. “Incremental and Fully Dynamic
Subgraph Connectivity for Emergency Planning.” In 24th Annual European Symposium
on Algorithms, Vol. 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2016. https://doi.org/10.4230/LIPICS.ESA.2016.48.
ieee: M. H. Henzinger and S. Neumann, “Incremental and fully dynamic subgraph connectivity
for emergency planning,” in 24th Annual European Symposium on Algorithms,
Aarhus, Denmark, 2016, vol. 57.
ista: 'Henzinger MH, Neumann S. 2016. Incremental and fully dynamic subgraph connectivity
for emergency planning. 24th Annual European Symposium on Algorithms. ESA: Annual
European Symposium on Algorithms, LIPIcs, vol. 57, 48.'
mla: Henzinger, Monika H., and Stefan Neumann. “Incremental and Fully Dynamic Subgraph
Connectivity for Emergency Planning.” 24th Annual European Symposium on Algorithms,
vol. 57, 48, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPICS.ESA.2016.48.
short: M.H. Henzinger, S. Neumann, in:, 24th Annual European Symposium on Algorithms,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.
conference:
end_date: 2016-08-24
location: Aarhus, Denmark
name: 'ESA: Annual European Symposium on Algorithms'
start_date: 2016-08-22
date_created: 2022-08-12T11:05:41Z
date_published: 2016-08-18T00:00:00Z
date_updated: 2023-02-16T12:07:46Z
day: '18'
doi: 10.4230/LIPICS.ESA.2016.48
extern: '1'
external_id:
arxiv:
- '1611.05248'
intvolume: ' 57'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPIcs.ESA.2016.48
month: '08'
oa: 1
oa_version: Published Version
publication: 24th Annual European Symposium on Algorithms
publication_identifier:
isbn:
- 978-3-95977-015-6
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Incremental and fully dynamic subgraph connectivity for emergency planning
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2016'
...
---
_id: '11836'
abstract:
- lang: eng
text: "Given a graph where vertices are partitioned into k terminals and non-terminals,
the goal is to compress the graph (i.e., reduce the number of non-terminals) using
minor operations while preserving terminal distances approximately. The distortion
of a compressed graph is the maximum multiplicative blow-up of distances between
all pairs of terminals. We study the trade-off between the number of non-terminals
and the distortion. This problem generalizes the Steiner Point Removal (SPR) problem,
in which all non-terminals must be removed.\r\n\r\nWe introduce a novel black-box
reduction to convert any lower bound on distortion for the SPR problem into a
super-linear lower bound on the number of non-terminals, with the same distortion,
for our problem. This allows us to show that there exist graphs such that every
minor with distortion less than 2 / 2.5 / 3 must have Omega(k^2) / Omega(k^{5/4})
/ Omega(k^{6/5}) non-terminals, plus more trade-offs in between. The black-box
reduction has an interesting consequence: if the tight lower bound on distortion
for the SPR problem is super-constant, then allowing any O(k) non-terminals will
not help improving the lower bound to a constant.\r\n\r\nWe also build on the
existing results on spanners, distance oracles and connected 0-extensions to show
a number of upper bounds for general graphs, planar graphs, graphs that exclude
a fixed minor and bounded treewidth graphs. Among others, we show that any graph
admits a minor with O(log k) distortion and O(k^2) non-terminals, and any planar
graph admits a minor with\r\n1 + epsilon distortion and ~O((k/epsilon)^2) non-terminals."
alternative_title:
- LIPIcs
article_number: '131'
article_processing_charge: No
arxiv: 1
author:
- first_name: Yun Kuen
full_name: Cheung, Yun Kuen
last_name: Cheung
- first_name: Gramoz
full_name: Goranci, Gramoz
last_name: Goranci
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: 'Cheung YK, Goranci G, Henzinger MH. Graph minors for preserving terminal distances
approximately - lower and upper bounds. In: 43rd International Colloquium on
Automata, Languages, and Programming. Vol 55. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2016. doi:10.4230/LIPICS.ICALP.2016.131'
apa: 'Cheung, Y. K., Goranci, G., & Henzinger, M. H. (2016). Graph minors for
preserving terminal distances approximately - lower and upper bounds. In 43rd
International Colloquium on Automata, Languages, and Programming (Vol. 55).
Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ICALP.2016.131'
chicago: Cheung, Yun Kuen, Gramoz Goranci, and Monika H Henzinger. “Graph Minors
for Preserving Terminal Distances Approximately - Lower and Upper Bounds.” In
43rd International Colloquium on Automata, Languages, and Programming,
Vol. 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPICS.ICALP.2016.131.
ieee: Y. K. Cheung, G. Goranci, and M. H. Henzinger, “Graph minors for preserving
terminal distances approximately - lower and upper bounds,” in 43rd International
Colloquium on Automata, Languages, and Programming, Rome, Italy, 2016, vol.
55.
ista: 'Cheung YK, Goranci G, Henzinger MH. 2016. Graph minors for preserving terminal
distances approximately - lower and upper bounds. 43rd International Colloquium
on Automata, Languages, and Programming. ICALP: International Colloquium on Automata,
Languages, and Programming, LIPIcs, vol. 55, 131.'
mla: Cheung, Yun Kuen, et al. “Graph Minors for Preserving Terminal Distances Approximately
- Lower and Upper Bounds.” 43rd International Colloquium on Automata, Languages,
and Programming, vol. 55, 131, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2016, doi:10.4230/LIPICS.ICALP.2016.131.
short: Y.K. Cheung, G. Goranci, M.H. Henzinger, in:, 43rd International Colloquium
on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2016.
conference:
end_date: 2016-07-15
location: Rome, Italy
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2016-07-12
date_created: 2022-08-12T11:16:01Z
date_published: 2016-08-23T00:00:00Z
date_updated: 2023-02-16T12:09:54Z
day: '23'
doi: 10.4230/LIPICS.ICALP.2016.131
extern: '1'
external_id:
arxiv:
- '1604.08342'
intvolume: ' 55'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPICS.ICALP.2016.131
month: '08'
oa: 1
oa_version: Published Version
publication: 43rd International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- 978-3-95977-013-2
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Graph minors for preserving terminal distances approximately - lower and upper
bounds
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...
---
_id: '1184'
abstract:
- lang: eng
text: Across multicellular organisms, the costs of reproduction and self-maintenance
result in a life history trade-off between fecundity and longevity. Queens of
perennial social Hymenoptera are both highly fertile and long-lived, and thus,
this fundamental trade-off is lacking. Whether social insect males similarly evade
the fecundity/longevity trade-off remains largely unstudied. Wingless males of
the ant genus Cardiocondyla stay in their natal colonies throughout their relatively
long lives and mate with multiple female sexuals. Here, we show that Cardiocondyla
obscurior males that were allowed to mate with large numbers of female sexuals
had a shortened life span compared to males that mated at a low frequency or virgin
males. Although frequent mating negatively affects longevity, males clearly benefit
from a “live fast, die young strategy” by inseminating as many female sexuals
as possible at a cost to their own survival.
acknowledgement: 'German Science Foundation. Grant Number: SCHR 1135/2-1. We thank
M. Adam for handling part of the setups and J. Zoellner for behavioral observations.'
author:
- first_name: Sina
full_name: Metzler, Sina
id: 48204546-F248-11E8-B48F-1D18A9856A87
last_name: Metzler
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
citation:
ama: Metzler S, Heinze J, Schrempf A. Mating and longevity in ant males. Ecology
and Evolution. 2016;6(24):8903-8906. doi:10.1002/ece3.2474
apa: Metzler, S., Heinze, J., & Schrempf, A. (2016). Mating and longevity in
ant males. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.2474
chicago: Metzler, Sina, Jürgen Heinze, and Alexandra Schrempf. “Mating and Longevity
in Ant Males.” Ecology and Evolution. Wiley-Blackwell, 2016. https://doi.org/10.1002/ece3.2474.
ieee: S. Metzler, J. Heinze, and A. Schrempf, “Mating and longevity in ant males,”
Ecology and Evolution, vol. 6, no. 24. Wiley-Blackwell, pp. 8903–8906,
2016.
ista: Metzler S, Heinze J, Schrempf A. 2016. Mating and longevity in ant males.
Ecology and Evolution. 6(24), 8903–8906.
mla: Metzler, Sina, et al. “Mating and Longevity in Ant Males.” Ecology and Evolution,
vol. 6, no. 24, Wiley-Blackwell, 2016, pp. 8903–06, doi:10.1002/ece3.2474.
short: S. Metzler, J. Heinze, A. Schrempf, Ecology and Evolution 6 (2016) 8903–8906.
date_created: 2018-12-11T11:50:36Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:48:55Z
day: '01'
ddc:
- '576'
- '592'
department:
- _id: SyCr
doi: 10.1002/ece3.2474
file:
- access_level: open_access
checksum: 789026eb9e1be2a0da08376f29f569cf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:12Z
date_updated: 2020-07-14T12:44:37Z
file_id: '5062'
file_name: IST-2017-736-v1+1_Metzler_et_al-2016-Ecology_and_Evolution.pdf
file_size: 328414
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '24'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 8903 - 8906
publication: Ecology and Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6169'
pubrep_id: '736'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mating and longevity in ant males
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: 6
year: '2016'
...
---
_id: '1185'
abstract:
- lang: eng
text: The developmental programme of the pistil is under the control of both auxin
and cytokinin. Crosstalk between these factors converges on regulation of the
auxin carrier PIN-FORMED 1 (PIN1). Here, we show that in the triple transcription
factor mutant cytokinin response factor 2 (crf2) crf3 crf6 both pistil length
and ovule number were reduced. PIN1 expression was also lower in the triple mutant
and the phenotypes could not be rescued by exogenous cytokinin application. pin1
complementation studies using genomic PIN1 constructs showed that the pistil phenotypes
were only rescued when the PCRE1 domain, to which CRFs bind, was present. Without
this domain, pin mutants resemble the crf2 crf3 crf6 triple mutant, indicating
the pivotal role of CRFs in auxin-cytokinin crosstalk.
acknowledgement: M.C. was funded by a PhD fellowship from the Università degli Studi
di Milano-Bicocca and from Ministero dell'Istruzione, dell'Università e della Ricerca
(MIUR) [MIUR-PRIN 2012]. L.C. is also supported by MIUR [MIUR-PRIN 2012]. We would
like to thank Andrew MacCabe and Edward Kiegle for editing the paper.
author:
- first_name: Mara
full_name: Cucinotta, Mara
last_name: Cucinotta
- first_name: Silvia
full_name: Manrique, Silvia
last_name: Manrique
- first_name: Andrea
full_name: Guazzotti, Andrea
last_name: Guazzotti
- first_name: Nadia
full_name: Quadrelli, Nadia
last_name: Quadrelli
- first_name: Marta
full_name: Mendes, Marta
last_name: Mendes
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Lucia
full_name: Colombo, Lucia
last_name: Colombo
citation:
ama: Cucinotta M, Manrique S, Guazzotti A, et al. Cytokinin response factors integrate
auxin and cytokinin pathways for female reproductive organ development. Development.
2016;143(23):4419-4424. doi:10.1242/dev.143545
apa: Cucinotta, M., Manrique, S., Guazzotti, A., Quadrelli, N., Mendes, M., Benková,
E., & Colombo, L. (2016). Cytokinin response factors integrate auxin and cytokinin
pathways for female reproductive organ development. Development. Company
of Biologists. https://doi.org/10.1242/dev.143545
chicago: Cucinotta, Mara, Silvia Manrique, Andrea Guazzotti, Nadia Quadrelli, Marta
Mendes, Eva Benková, and Lucia Colombo. “Cytokinin Response Factors Integrate
Auxin and Cytokinin Pathways for Female Reproductive Organ Development.” Development.
Company of Biologists, 2016. https://doi.org/10.1242/dev.143545.
ieee: M. Cucinotta et al., “Cytokinin response factors integrate auxin and
cytokinin pathways for female reproductive organ development,” Development,
vol. 143, no. 23. Company of Biologists, pp. 4419–4424, 2016.
ista: Cucinotta M, Manrique S, Guazzotti A, Quadrelli N, Mendes M, Benková E, Colombo
L. 2016. Cytokinin response factors integrate auxin and cytokinin pathways for
female reproductive organ development. Development. 143(23), 4419–4424.
mla: Cucinotta, Mara, et al. “Cytokinin Response Factors Integrate Auxin and Cytokinin
Pathways for Female Reproductive Organ Development.” Development, vol.
143, no. 23, Company of Biologists, 2016, pp. 4419–24, doi:10.1242/dev.143545.
short: M. Cucinotta, S. Manrique, A. Guazzotti, N. Quadrelli, M. Mendes, E. Benková,
L. Colombo, Development 143 (2016) 4419–4424.
date_created: 2018-12-11T11:50:36Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:48:56Z
day: '01'
department:
- _id: EvBe
doi: 10.1242/dev.143545
intvolume: ' 143'
issue: '23'
language:
- iso: eng
month: '12'
oa_version: None
page: 4419 - 4424
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '6168'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cytokinin response factors integrate auxin and cytokinin pathways for female
reproductive organ development
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 143
year: '2016'
...
---
_id: '1186'
abstract:
- lang: eng
text: The human pathogen Streptococcus pneumoniae is decorated with a special class
of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine
(PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography,
NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies,
we provide structural information of choline-binding protein L (CbpL) and demonstrate
its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated
three-module protein composed of (i) an Excalibur Ca 2+ -binding domain -reported
in this work for the very first time-, (ii) an unprecedented anchorage module
showing alternate disposition of canonical and non-canonical choline-binding sites
that allows vine-like binding of fully-PCho-substituted teichoic acids (with two
choline moieties per unit), and (iii) a Ltp-Lipoprotein domain. Our structural
and infection assays indicate an important role of the whole multimodular protein
allowing both to locate CbpL at specific places on the cell wall and to interact
with host components in order to facilitate pneumococcal lung infection and transmigration
from nasopharynx to the lungs and blood. CbpL implication in both resistance against
killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein
as relevant among the pathogenic arsenal of the pneumococcus.
acknowledgement: We gratefully acknowledge Karsta Barnekow and Kristine Sievert-Giermann,
for technical assistance and Lothar Petruschka for in silico analysis (all Dept.
of Genetics, University of Greifswald). We are further grateful to the staff from
SLS synchrotron beamline for help in data collection. This work was supported by
grants from the Deutsche Forschungsgemeinschaft DFG GRK 1870 (to SH) and the Spanish
Ministry of Economy and Competitiveness (BFU2014-59389-P to JAH, CTQ2014-52633-P
to MB and SAF2012-39760-C02-02 to FG) and S2010/BMD-2457 (Community of Madrid to
JAH and FG).
article_number: '38094'
author:
- first_name: Javier
full_name: Gutierrez-Fernandez, Javier
id: 3D9511BA-F248-11E8-B48F-1D18A9856A87
last_name: Gutierrez-Fernandez
- first_name: Malek
full_name: Saleh, Malek
last_name: Saleh
- first_name: Martín
full_name: Alcorlo, Martín
last_name: Alcorlo
- first_name: Alejandro
full_name: Gómez Mejóa, Alejandro
last_name: Gómez Mejóa
- first_name: David
full_name: Pantoja Uceda, David
last_name: Pantoja Uceda
- first_name: Miguel
full_name: Treviño, Miguel
last_name: Treviño
- first_name: Franziska
full_name: Vob, Franziska
last_name: Vob
- first_name: Mohammed
full_name: Abdullah, Mohammed
last_name: Abdullah
- first_name: Sergio
full_name: Galán Bartual, Sergio
last_name: Galán Bartual
- first_name: Jolien
full_name: Seinen, Jolien
last_name: Seinen
- first_name: Pedro
full_name: Sánchez Murcia, Pedro
last_name: Sánchez Murcia
- first_name: Federico
full_name: Gago, Federico
last_name: Gago
- first_name: Marta
full_name: Bruix, Marta
last_name: Bruix
- first_name: Sven
full_name: Hammerschmidt, Sven
last_name: Hammerschmidt
- first_name: Juan
full_name: Hermoso, Juan
last_name: Hermoso
citation:
ama: Gutierrez-Fernandez J, Saleh M, Alcorlo M, et al. Modular architecture and
unique teichoic acid recognition features of choline-binding protein L CbpL contributing
to pneumococcal pathogenesis. Scientific Reports. 2016;6. doi:10.1038/srep38094
apa: Gutierrez-Fernandez, J., Saleh, M., Alcorlo, M., Gómez Mejóa, A., Pantoja Uceda,
D., Treviño, M., … Hermoso, J. (2016). Modular architecture and unique teichoic
acid recognition features of choline-binding protein L CbpL contributing to pneumococcal
pathogenesis. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep38094
chicago: Gutierrez-Fernandez, Javier, Malek Saleh, Martín Alcorlo, Alejandro Gómez
Mejóa, David Pantoja Uceda, Miguel Treviño, Franziska Vob, et al. “Modular Architecture
and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL
Contributing to Pneumococcal Pathogenesis.” Scientific Reports. Nature
Publishing Group, 2016. https://doi.org/10.1038/srep38094.
ieee: J. Gutierrez-Fernandez et al., “Modular architecture and unique teichoic
acid recognition features of choline-binding protein L CbpL contributing to pneumococcal
pathogenesis,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.
ista: Gutierrez-Fernandez J, Saleh M, Alcorlo M, Gómez Mejóa A, Pantoja Uceda D,
Treviño M, Vob F, Abdullah M, Galán Bartual S, Seinen J, Sánchez Murcia P, Gago
F, Bruix M, Hammerschmidt S, Hermoso J. 2016. Modular architecture and unique
teichoic acid recognition features of choline-binding protein L CbpL contributing
to pneumococcal pathogenesis. Scientific Reports. 6, 38094.
mla: Gutierrez-Fernandez, Javier, et al. “Modular Architecture and Unique Teichoic
Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal
Pathogenesis.” Scientific Reports, vol. 6, 38094, Nature Publishing Group,
2016, doi:10.1038/srep38094.
short: J. Gutierrez-Fernandez, M. Saleh, M. Alcorlo, A. Gómez Mejóa, D. Pantoja
Uceda, M. Treviño, F. Vob, M. Abdullah, S. Galán Bartual, J. Seinen, P. Sánchez
Murcia, F. Gago, M. Bruix, S. Hammerschmidt, J. Hermoso, Scientific Reports 6
(2016).
date_created: 2018-12-11T11:50:36Z
date_published: 2016-12-05T00:00:00Z
date_updated: 2021-01-12T06:48:56Z
day: '05'
ddc:
- '576'
- '610'
department:
- _id: LeSa
doi: 10.1038/srep38094
file:
- access_level: open_access
checksum: e007d78b483bc59bf5ab98e9d42a6ec1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:18Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4804'
file_name: IST-2017-735-v1+1_srep38094.pdf
file_size: 2716045
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6167'
pubrep_id: '735'
quality_controlled: '1'
scopus_import: 1
status: public
title: Modular architecture and unique teichoic acid recognition features of choline-binding
protein L CbpL contributing to pneumococcal pathogenesis
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: 6
year: '2016'
...
---
_id: '11866'
abstract:
- lang: eng
text: "We present a deterministic (1+o(1))-approximation O(n1/2+o(1)+D1+o(1))-time
algorithm for solving the single-source shortest paths problem on distributed
weighted networks (the CONGEST model); here n is the number of nodes in the network
and D is its (hop) diameter. This is the first non-trivial deterministic algorithm
for this problem. It also improves (i) the running time of the randomized (1+o(1))-approximation
Õ(n1/2D1/4+D)-time algorithm of Nanongkai [STOC 2014] by a factor of as large
as n1/8, and (ii) the O(є−1logє−1)-approximation factor of Lenzen and Patt-Shamir’s
Õ(n1/2+є+D)-time algorithm [STOC 2013] within the same running time. Our running
time matches the known time lower bound of Ω(n1/2/logn + D) [Das Sarma et al.
STOC 2011] modulo some lower-order terms, thus essentially settling the status
of this problem which was raised at least a decade ago [Elkin SIGACT News 2004].
It also implies a (2+o(1))-approximation O(n1/2+o(1)+D1+o(1))-time algorithm for
approximating a network’s weighted diameter which almost matches the lower bound
by Holzer et al. [PODC 2012].\r\n\r\nIn achieving this result, we develop two
techniques which might be of independent interest and useful in other settings:
(i) a deterministic process that replaces the “hitting set argument” commonly
used for shortest paths computation in various settings, and (ii) a simple, deterministic,
construction of an (no(1), o(1))-hop set of size O(n1+o(1)). We combine these
techniques with many distributed algorithmic techniques, some of which from problems
that are not directly related to shortest paths, e.g. ruling sets [Goldberg et
al. STOC 1987], source detection [Lenzen, Peleg PODC 2013], and partial distance
estimation [Lenzen, Patt-Shamir PODC 2015]. Our hop set construction also leads
to single-source shortest paths algorithms in two other settings: (i) a (1+o(1))-approximation
O(no(1))-time algorithm on congested cliques, and (ii) a (1+o(1))-approximation
O(no(1)logW)-pass O(n1+o(1)logW)-space streaming algorithm, when edge weights
are in {1, 2, …, W}. The first result answers an open problem in [Nanongkai, STOC
2014]. The second result partially answers an open problem raised by McGregor
in 2006 [sublinear.info
, Problem 14]."
article_processing_charge: No
arxiv: 1
author:
- 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: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Henzinger MH, Krinninger S, Nanongkai D. A deterministic almost-tight distributed
algorithm for approximating single-source shortest paths. In: 48th Annual ACM
SIGACT Symposium on Theory of Computing. Association for Computing Machinery;
2016:489-498. doi:10.1145/2897518.2897638'
apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2016). A deterministic
almost-tight distributed algorithm for approximating single-source shortest paths.
In 48th Annual ACM SIGACT Symposium on Theory of Computing (pp. 489–498).
Cambridge, MA, United States: Association for Computing Machinery. https://doi.org/10.1145/2897518.2897638'
chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “A Deterministic
Almost-Tight Distributed Algorithm for Approximating Single-Source Shortest Paths.”
In 48th Annual ACM SIGACT Symposium on Theory of Computing, 489–98. Association
for Computing Machinery, 2016. https://doi.org/10.1145/2897518.2897638.
ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “A deterministic almost-tight
distributed algorithm for approximating single-source shortest paths,” in 48th
Annual ACM SIGACT Symposium on Theory of Computing, Cambridge, MA, United
States, 2016, pp. 489–498.
ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2016. A deterministic almost-tight
distributed algorithm for approximating single-source shortest paths. 48th Annual
ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing,
489–498.'
mla: Henzinger, Monika H., et al. “A Deterministic Almost-Tight Distributed Algorithm
for Approximating Single-Source Shortest Paths.” 48th Annual ACM SIGACT Symposium
on Theory of Computing, Association for Computing Machinery, 2016, pp. 489–98,
doi:10.1145/2897518.2897638.
short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 48th Annual ACM SIGACT
Symposium on Theory of Computing, Association for Computing Machinery, 2016, pp.
489–498.
conference:
end_date: 2016-06-21
location: Cambridge, MA, United States
name: 'STOC: Symposium on Theory of Computing'
start_date: 2016-06-19
date_created: 2022-08-16T09:19:31Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2023-02-17T10:32:23Z
day: '01'
doi: 10.1145/2897518.2897638
extern: '1'
external_id:
arxiv:
- '1504.07056'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.07056
month: '06'
oa: 1
oa_version: Preprint
page: 489 - 498
publication: 48th Annual ACM SIGACT Symposium on Theory of Computing
publication_identifier:
isbn:
- 978-145034132-5
issn:
- 0737-8017
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: A deterministic almost-tight distributed algorithm for approximating single-source
shortest paths
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '11867'
abstract:
- lang: eng
text: We present two deterministic dynamic algorithms for the maximum matching problem.
(1) An algorithm that maintains a (2+є)-approximate maximum matching in general
graphs with O(poly(logn, 1/є)) update time. (2) An algorithm that maintains an
αK approximation of the value of the maximum matching with O(n2/K) update time
in bipartite graphs, for every sufficiently large constant positive integer K.
Here, 1≤ αK < 2 is a constant determined by the value of K. Result (1) is the
first deterministic algorithm that can maintain an o(logn)-approximate maximum
matching with polylogarithmic update time, improving the seminal result of Onak
et al. [STOC 2010]. Its approximation guarantee almost matches the guarantee of
the best randomized polylogarithmic update time algorithm [Baswana et al. FOCS
2011]. Result (2) achieves a better-than-two approximation with arbitrarily small
polynomial update time on bipartite graphs. Previously the best update time for
this problem was O(m1/4) [Bernstein et al. ICALP 2015], where m is the current
number of edges in the graph.
article_processing_charge: No
arxiv: 1
author:
- first_name: Sayan
full_name: Bhattacharya, Sayan
last_name: Bhattacharya
- 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: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Bhattacharya S, Henzinger MH, Nanongkai D. New deterministic approximation
algorithms for fully dynamic matching. In: 48th Annual ACM SIGACT Symposium
on Theory of Computing. Association for Computing Machinery; 2016:398-411.
doi:10.1145/2897518.2897568'
apa: 'Bhattacharya, S., Henzinger, M. H., & Nanongkai, D. (2016). New deterministic
approximation algorithms for fully dynamic matching. In 48th Annual ACM SIGACT
Symposium on Theory of Computing (pp. 398–411). Cambridge, MA, United States:
Association for Computing Machinery. https://doi.org/10.1145/2897518.2897568'
chicago: Bhattacharya, Sayan, Monika H Henzinger, and Danupon Nanongkai. “New Deterministic
Approximation Algorithms for Fully Dynamic Matching.” In 48th Annual ACM SIGACT
Symposium on Theory of Computing, 398–411. Association for Computing Machinery,
2016. https://doi.org/10.1145/2897518.2897568.
ieee: S. Bhattacharya, M. H. Henzinger, and D. Nanongkai, “New deterministic approximation
algorithms for fully dynamic matching,” in 48th Annual ACM SIGACT Symposium
on Theory of Computing, Cambridge, MA, United States, 2016, pp. 398–411.
ista: 'Bhattacharya S, Henzinger MH, Nanongkai D. 2016. New deterministic approximation
algorithms for fully dynamic matching. 48th Annual ACM SIGACT Symposium on Theory
of Computing. STOC: Symposium on Theory of Computing, 398–411.'
mla: Bhattacharya, Sayan, et al. “New Deterministic Approximation Algorithms for
Fully Dynamic Matching.” 48th Annual ACM SIGACT Symposium on Theory of Computing,
Association for Computing Machinery, 2016, pp. 398–411, doi:10.1145/2897518.2897568.
short: S. Bhattacharya, M.H. Henzinger, D. Nanongkai, in:, 48th Annual ACM SIGACT
Symposium on Theory of Computing, Association for Computing Machinery, 2016, pp.
398–411.
conference:
end_date: 2016-06-21
location: Cambridge, MA, United States
name: 'STOC: Symposium on Theory of Computing'
start_date: 2016-06-19
date_created: 2022-08-16T09:27:35Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2023-02-17T11:08:19Z
day: '01'
doi: 10.1145/2897518.2897568
extern: '1'
external_id:
arxiv:
- '1604.05765'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.05765
month: '06'
oa: 1
oa_version: Preprint
page: 398 - 411
publication: 48th Annual ACM SIGACT Symposium on Theory of Computing
publication_identifier:
isbn:
- 978-145034132-5
issn:
- 0737-8017
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: New deterministic approximation algorithms for fully dynamic matching
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1188'
abstract:
- lang: eng
text: "We consider a population dynamics model coupling cell growth to a diffusion
in the space of metabolic phenotypes as it can be obtained from realistic constraints-based
modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with
the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation
is solved for the steady state in the WKB\r\napproximation that maps it into the
ground state of a quantum particle in an\r\nAiry potential plus a centrifugal
term. We retrieve scaling laws for growth rate\r\nfluctuations and time response
with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal
populations can have a faster response\r\nto perturbations."
acknowledgement: D De Martino is supported by the People Programme (Marie Curie Actions)
of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant
agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011.
D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa
for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano
and Vera Luz Masoero for useful discussions, also late at night.
article_number: '123502'
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Davide
full_name: Masoero, Davide
last_name: Masoero
citation:
ama: 'De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth. Journal of Statistical Mechanics:
Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f'
apa: 'De Martino, D., & Masoero, D. (2016). Asymptotic analysis of noisy fitness
maximization, applied to metabolism & growth. Journal of Statistical
Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa4e8f'
chicago: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy
Fitness Maximization, Applied to Metabolism & Growth.” Journal of
Statistical Mechanics: Theory and Experiment. IOPscience, 2016. https://doi.org/10.1088/1742-5468/aa4e8f.'
ieee: 'D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth,” Journal of Statistical Mechanics:
Theory and Experiment, vol. 2016, no. 12. IOPscience, 2016.'
ista: 'De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth. Journal of Statistical Mechanics: Theory
and Experiment. 2016(12), 123502.'
mla: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness
Maximization, Applied to Metabolism & Growth.” Journal of Statistical
Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOPscience, 2016,
doi:10.1088/1742-5468/aa4e8f.'
short: 'D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and
Experiment 2016 (2016).'
date_created: 2018-12-11T11:50:37Z
date_published: 2016-12-30T00:00:00Z
date_updated: 2021-01-12T06:48:57Z
day: '30'
department:
- _id: GaTk
doi: 10.1088/1742-5468/aa4e8f
ec_funded: 1
intvolume: ' 2016'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.09048
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Journal of Statistical Mechanics: Theory and Experiment'
publication_status: published
publisher: IOPscience
publist_id: '6165'
quality_controlled: '1'
scopus_import: 1
status: public
title: Asymptotic analysis of noisy fitness maximization, applied to metabolism &
growth
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016
year: '2016'
...