---
_id: '392'
abstract:
- lang: eng
text: We used femtosecond optical pump-probe spectroscopy to study the photoinduced
change in reflectivity of thin films of the electron-doped cuprate La2-xCexCuO4
(LCCO) with dopings of x=0.08 (underdoped) and x=0.11 (optimally doped). Above
Tc, we observe fluence-dependent relaxation rates that begin at a temperature
similar to the one where transport measurements first show signatures of antiferromagnetic
correlations. Upon suppressing superconductivity with a magnetic field, it is
found that the fluence and temperature dependence of relaxation rates are consistent
with bimolecular recombination of electrons and holes across a gap (2ΔAF) originating
from antiferromagnetic correlations which comprise the pseudogap in electron-doped
cuprates. This can be used to learn about coupling between electrons and high-energy
(ω>2ΔAF) excitations in these compounds and set limits on the time scales on
which antiferromagnetic correlations are static.
acknowledgement: Optical pump-probe work was supported by the Gordon and Betty Moore
Foundation's EPiQS initiative through Grant No. GBMF4540. Materials growth and characterization
was supported by AFOSR FA95501410332 and NSF DMR1410665.
author:
- first_name: Inna
full_name: Vishik, Inna
last_name: Vishik
- first_name: Fahad
full_name: Mahmood, Fahad
last_name: Mahmood
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
- first_name: Nuh
full_name: Gedik, Nuh
last_name: Gedik
- first_name: Joshu
full_name: Higgins, Joshu
last_name: Higgins
- first_name: Richard
full_name: Greene, Richard
last_name: Greene
citation:
ama: Vishik I, Mahmood F, Alpichshev Z, Gedik N, Higgins J, Greene R. Ultrafast
dynamics in the presence of antiferromagnetic correlations in electron doped cuprate
La2 xCexCuO4±δ. Physical Review B. 2017;95(11). doi:10.1103/PhysRevB.95.115125
apa: Vishik, I., Mahmood, F., Alpichshev, Z., Gedik, N., Higgins, J., & Greene,
R. (2017). Ultrafast dynamics in the presence of antiferromagnetic correlations
in electron doped cuprate La2 xCexCuO4±δ. Physical Review B. American Physical
Society. https://doi.org/10.1103/PhysRevB.95.115125
chicago: Vishik, Inna, Fahad Mahmood, Zhanybek Alpichshev, Nuh Gedik, Joshu Higgins,
and Richard Greene. “Ultrafast Dynamics in the Presence of Antiferromagnetic Correlations
in Electron Doped Cuprate La2 XCexCuO4±δ.” Physical Review B. American
Physical Society, 2017. https://doi.org/10.1103/PhysRevB.95.115125.
ieee: I. Vishik, F. Mahmood, Z. Alpichshev, N. Gedik, J. Higgins, and R. Greene,
“Ultrafast dynamics in the presence of antiferromagnetic correlations in electron
doped cuprate La2 xCexCuO4±δ,” Physical Review B, vol. 95, no. 11. American
Physical Society, 2017.
ista: Vishik I, Mahmood F, Alpichshev Z, Gedik N, Higgins J, Greene R. 2017. Ultrafast
dynamics in the presence of antiferromagnetic correlations in electron doped cuprate
La2 xCexCuO4±δ. Physical Review B. 95(11).
mla: Vishik, Inna, et al. “Ultrafast Dynamics in the Presence of Antiferromagnetic
Correlations in Electron Doped Cuprate La2 XCexCuO4±δ.” Physical Review B,
vol. 95, no. 11, American Physical Society, 2017, doi:10.1103/PhysRevB.95.115125.
short: I. Vishik, F. Mahmood, Z. Alpichshev, N. Gedik, J. Higgins, R. Greene, Physical
Review B 95 (2017).
date_created: 2018-12-11T11:46:13Z
date_published: 2017-03-13T00:00:00Z
date_updated: 2021-01-12T07:53:12Z
day: '13'
doi: 10.1103/PhysRevB.95.115125
extern: '1'
intvolume: ' 95'
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://dspace.mit.edu/handle/1721.1/109835
month: '03'
oa: 1
oa_version: None
publication: Physical Review B
publication_status: published
publisher: American Physical Society
publist_id: '7437'
status: public
title: Ultrafast dynamics in the presence of antiferromagnetic correlations in electron
doped cuprate La2 xCexCuO4±δ
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 95
year: '2017'
...
---
_id: '443'
abstract:
- lang: eng
text: Pancreatic cancer has a five-year survival rate of ~8%, with characteristic
molecular heterogeneity and restricted treatment options. Targeting metabolism
has emerged as a potentially effective therapeutic strategy for cancers such as
pancreatic cancer, which are driven by genetic alterations that are not tractable
drug targets. Although somatic mitochondrial genome (mtDNA) mutations have been
observed in various tumors types, understanding of metabolic genotype-phenotype
relationships is limited.
author:
- first_name: Rae
full_name: Hardie, Rae
last_name: Hardie
- first_name: Ellen
full_name: Van Dam, Ellen
last_name: Van Dam
- first_name: Mark
full_name: Cowley, Mark
last_name: Cowley
- first_name: Ting
full_name: Han, Ting
last_name: Han
- first_name: Seher
full_name: Balaban, Seher
last_name: Balaban
- first_name: Marina
full_name: Pajic, Marina
last_name: Pajic
- first_name: Mark
full_name: Pinese, Mark
last_name: Pinese
- first_name: Mary
full_name: Iconomou, Mary
last_name: Iconomou
- first_name: Robert
full_name: Shearer, Robert
last_name: Shearer
- first_name: Jessie
full_name: Mckenna, Jessie
last_name: Mckenna
- first_name: David
full_name: Miller, David
last_name: Miller
- first_name: Nicola
full_name: Waddell, Nicola
last_name: Waddell
- first_name: John
full_name: Pearson, John
last_name: Pearson
- first_name: Sean
full_name: Grimmond, Sean
last_name: Grimmond
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Andrew
full_name: Biankin, Andrew
last_name: Biankin
- first_name: Silas
full_name: Villas Boas, Silas
last_name: Villas Boas
- first_name: Andrew
full_name: Hoy, Andrew
last_name: Hoy
- first_name: Nigel
full_name: Turner, Nigel
last_name: Turner
- first_name: Darren
full_name: Saunders, Darren
last_name: Saunders
citation:
ama: Hardie R, Van Dam E, Cowley M, et al. Mitochondrial mutations and metabolic
adaptation in pancreatic cancer. Cancer & Metabolism. 2017;5(2). doi:10.1186/s40170-017-0164-1
apa: Hardie, R., Van Dam, E., Cowley, M., Han, T., Balaban, S., Pajic, M., … Saunders,
D. (2017). Mitochondrial mutations and metabolic adaptation in pancreatic cancer.
Cancer & Metabolism. BioMed Central. https://doi.org/10.1186/s40170-017-0164-1
chicago: Hardie, Rae, Ellen Van Dam, Mark Cowley, Ting Han, Seher Balaban, Marina
Pajic, Mark Pinese, et al. “Mitochondrial Mutations and Metabolic Adaptation in
Pancreatic Cancer.” Cancer & Metabolism. BioMed Central, 2017. https://doi.org/10.1186/s40170-017-0164-1.
ieee: R. Hardie et al., “Mitochondrial mutations and metabolic adaptation
in pancreatic cancer,” Cancer & Metabolism, vol. 5, no. 2. BioMed Central,
2017.
ista: Hardie R, Van Dam E, Cowley M, Han T, Balaban S, Pajic M, Pinese M, Iconomou
M, Shearer R, Mckenna J, Miller D, Waddell N, Pearson J, Grimmond S, Sazanov LA,
Biankin A, Villas Boas S, Hoy A, Turner N, Saunders D. 2017. Mitochondrial mutations
and metabolic adaptation in pancreatic cancer. Cancer & Metabolism. 5(2).
mla: Hardie, Rae, et al. “Mitochondrial Mutations and Metabolic Adaptation in Pancreatic
Cancer.” Cancer & Metabolism, vol. 5, no. 2, BioMed Central, 2017,
doi:10.1186/s40170-017-0164-1.
short: R. Hardie, E. Van Dam, M. Cowley, T. Han, S. Balaban, M. Pajic, M. Pinese,
M. Iconomou, R. Shearer, J. Mckenna, D. Miller, N. Waddell, J. Pearson, S. Grimmond,
L.A. Sazanov, A. Biankin, S. Villas Boas, A. Hoy, N. Turner, D. Saunders, Cancer
& Metabolism 5 (2017).
date_created: 2018-12-11T11:46:30Z
date_published: 2017-01-30T00:00:00Z
date_updated: 2021-01-12T07:56:55Z
day: '30'
ddc:
- '570'
doi: 10.1186/s40170-017-0164-1
extern: '1'
file:
- access_level: open_access
checksum: 337a65786875f64a1fe9fc0ac24767dc
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T08:17:56Z
date_updated: 2020-07-14T12:46:29Z
file_id: '5868'
file_name: 2017_Cancer_Hardie.pdf
file_size: 1609174
relation: main_file
file_date_updated: 2020-07-14T12:46:29Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Cancer & Metabolism
publication_status: published
publisher: BioMed Central
publist_id: '7380'
quality_controlled: '1'
status: public
title: Mitochondrial mutations and metabolic adaptation in pancreatic cancer
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: 5
year: '2017'
...
---
_id: '444'
abstract:
- lang: eng
text: Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular
energy generation, contributing to the proton motive force used to produce ATP.
It couples the transfer of two electrons between NADH and quinone to translocation
of four protons across the membrane. It is the largest protein assembly of bacterial
and mitochondrial respiratory chains, composed, in mammals, of up to 45 subunits
with a total molecular weight of ∼1 MDa. Bacterial enzyme is about half the size,
providing the important “minimal” model of complex I. The l-shaped complex consists
of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where
proton translocation takes place. Previously, we have solved the crystal structures
of the hydrophilic domain of complex I from Thermus thermophilus and of the membrane
domain from Escherichia coli, followed by the atomic structure of intact, entire
complex I from T. thermophilus. Recently, we have solved by cryo-EM a first complete
atomic structure of mammalian (ovine) mitochondrial complex I. Core subunits are
well conserved from the bacterial version, whilst supernumerary subunits form
an interlinked, stabilizing shell around the core. Subunits containing additional
cofactors, including Zn ion, NADPH and phosphopantetheine, probably have regulatory
roles. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative
diseases. The structure of mammalian enzyme provides many insights into complex
I mechanism, assembly, maturation and dysfunction, allowing detailed molecular
analysis of disease-causing mutations.
author:
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: 'Sazanov LA. Structure of respiratory complex I: “Minimal” bacterial and “de
luxe” mammalian versions. In: Wikström M, ed. Mechanisms of Primary Energy
Transduction in Biology . Mechanisms of Primary Energy Transduction in Biology
. Royal Society of Chemistry; 2017:25-59. doi:10.1039/9781788010405-00025'
apa: 'Sazanov, L. A. (2017). Structure of respiratory complex I: “Minimal” bacterial
and “de luxe” mammalian versions. In M. Wikström (Ed.), Mechanisms of primary
energy transduction in biology (pp. 25–59). Royal Society of Chemistry. https://doi.org/10.1039/9781788010405-00025'
chicago: 'Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial
and ‘de Luxe’ Mammalian Versions.” In Mechanisms of Primary Energy Transduction
in Biology , edited by Mårten Wikström, 25–59. Mechanisms of Primary Energy
Transduction in Biology . Royal Society of Chemistry, 2017. https://doi.org/10.1039/9781788010405-00025.'
ieee: 'L. A. Sazanov, “Structure of respiratory complex I: ‘Minimal’ bacterial and
‘de luxe’ mammalian versions,” in Mechanisms of primary energy transduction
in biology , M. Wikström, Ed. Royal Society of Chemistry, 2017, pp. 25–59.'
ista: 'Sazanov LA. 2017.Structure of respiratory complex I: “Minimal” bacterial
and “de luxe” mammalian versions. In: Mechanisms of primary energy transduction
in biology . , 25–59.'
mla: 'Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial
and ‘de Luxe’ Mammalian Versions.” Mechanisms of Primary Energy Transduction
in Biology , edited by Mårten Wikström, Royal Society of Chemistry, 2017,
pp. 25–59, doi:10.1039/9781788010405-00025.'
short: L.A. Sazanov, in:, M. Wikström (Ed.), Mechanisms of Primary Energy Transduction
in Biology , Royal Society of Chemistry, 2017, pp. 25–59.
date_created: 2018-12-11T11:46:30Z
date_published: 2017-11-29T00:00:00Z
date_updated: 2021-01-12T07:56:59Z
day: '29'
department:
- _id: LeSa
doi: 10.1039/9781788010405-00025
editor:
- first_name: Mårten
full_name: Wikström, Mårten
last_name: Wikström
language:
- iso: eng
month: '11'
oa_version: None
page: 25 - 59
publication: 'Mechanisms of primary energy transduction in biology '
publication_identifier:
isbn:
- 978-1-78262-865-1
publication_status: published
publisher: Royal Society of Chemistry
publist_id: '7379'
quality_controlled: '1'
series_title: 'Mechanisms of Primary Energy Transduction in Biology '
status: public
title: 'Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian
versions'
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '445'
abstract:
- lang: eng
text: The Loschmidt echo, defined as the overlap between quantum wave function evolved
with different Hamiltonians, quantifies the sensitivity of quantum dynamics to
perturbations and is often used as a probe of quantum chaos. In this work we consider
the behavior of the Loschmidt echo in the many-body localized phase, which is
characterized by emergent local integrals of motion and provides a generic example
of nonergodic dynamics. We demonstrate that the fluctuations of the Loschmidt
echo decay as a power law in time in the many-body localized phase, in contrast
to the exponential decay in few-body ergodic systems. We consider the spin-echo
generalization of the Loschmidt echo and argue that the corresponding correlation
function saturates to a finite value in localized systems. Slow, power-law decay
of fluctuations of such spin-echo-type overlap is related to the operator spreading
and is present only in the many-body localized phase, but not in a noninteracting
Anderson insulator. While most of the previously considered probes of dephasing
dynamics could be understood by approximating physical spin operators with local
integrals of motion, the Loschmidt echo and its generalizations crucially depend
on the full expansion of the physical operators via local integrals of motion
operators, as well as operators which flip local integrals of motion. Hence these
probes allow one to get insights into the relation between physical operators
and local integrals of motion and access the operator spreading in the many-body
localized phase.
acknowledgement: |-
This research was supported in part by the National
Science Foundation under Grant No. NSF PHY11-25915.
M.S. was supported by Gordon and Betty Moore Foundation’s
EPiQS Initiative through Grant No. GBMF4307. D.A. also
acknowledges support by Swiss National Science Foundation.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Dimitry
full_name: Abanin, Dimitry A
last_name: Abanin
citation:
ama: Serbyn M, Abanin D. Loschmidt echo in many body localized phases. Physical
Review B - Condensed Matter and Materials Physics. 2017;96(1). doi:10.1103/PhysRevB.96.014202
apa: Serbyn, M., & Abanin, D. (2017). Loschmidt echo in many body localized
phases. Physical Review B - Condensed Matter and Materials Physics. American
Physical Society. https://doi.org/10.1103/PhysRevB.96.014202
chicago: Serbyn, Maksym, and Dimitry Abanin. “Loschmidt Echo in Many Body Localized
Phases.” Physical Review B - Condensed Matter and Materials Physics. American
Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.014202.
ieee: M. Serbyn and D. Abanin, “Loschmidt echo in many body localized phases,” Physical
Review B - Condensed Matter and Materials Physics, vol. 96, no. 1. American
Physical Society, 2017.
ista: Serbyn M, Abanin D. 2017. Loschmidt echo in many body localized phases. Physical
Review B - Condensed Matter and Materials Physics. 96(1).
mla: Serbyn, Maksym, and Dimitry Abanin. “Loschmidt Echo in Many Body Localized
Phases.” Physical Review B - Condensed Matter and Materials Physics, vol.
96, no. 1, American Physical Society, 2017, doi:10.1103/PhysRevB.96.014202.
short: M. Serbyn, D. Abanin, Physical Review B - Condensed Matter and Materials
Physics 96 (2017).
date_created: 2018-12-11T11:46:31Z
date_published: 2017-07-12T00:00:00Z
date_updated: 2021-01-12T07:57:03Z
day: '12'
doi: 10.1103/PhysRevB.96.014202
extern: 1
intvolume: ' 96'
issue: '1'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1701.07772
month: '07'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '7378'
quality_controlled: 0
status: public
title: Loschmidt echo in many body localized phases
type: journal_article
volume: 96
year: '2017'
...
---
_id: '452'
abstract:
- lang: eng
text: 'Spinning tops and yo-yos have long fascinated cultures around the world with
their unexpected, graceful motions that seemingly elude gravity. Yet, due to the
exceeding difficulty of creating stably spinning objects of asymmetric shape in
a manual trial-and-error process, there has been little departure from rotationally
symmetric designs. With modern 3D printing technologies, however, we can manufacture
shapes of almost unbounded complexity at the press of a button, shifting this
design complexity toward computation. In this article, we describe an algorithm
to generate designs for spinning objects by optimizing their mass distribution:
as input, the user provides a solid 3D model and a desired axis of rotation. Our
approach then modifies the interior mass distribution such that the principal
directions of the moment of inertia align with the target rotation frame. To create
voids inside the model, we represent its volume with an adaptive multiresolution
voxelization and optimize the discrete voxel fill values using a continuous, nonlinear
formulation. We further optimize for rotational stability by maximizing the dominant
principal moment. Our method is well-suited for a variety of 3D printed models,
ranging from characters to abstract shapes. We demonstrate tops and yo-yos that
spin surprisingly stably despite their asymmetric appearance.'
acknowledgement: "This project was supported in part by the ERC Starting Grant iModel
(StG-2012-306877). Emily Whiting was supported by the ETH Zurich/Marie Curie COFUND
Postdoctoral Fellowship. \r\nFirst and foremost, we would like to thank our editor
Steve Marschner for his invaluable feedback. We were fortunate to get further help
from Maurizio Nitti for model design, Romain Prévost for Make-It-Stand comparisons,
Alexander Sorkine-Hornung, Kaan Yücer, and Changil Kim for video and photo assistance,
Ronnie Gänsli for metal casting, Alec Jacobson for the posed Elephant and Armadillo
models, and Romain Prévost and Amit Bermano for print preparation. Model sources
include: Woven Ring: generated by “Sculpture Generator 1” by Carlo H. Séquin, UC
Berkeley; Elephant: De Espona model library, courtesy of Robert Sumner; T-Rex: TurboSquid;
Armadillo: Stanford Computer Graphics Laboratory; and Utah Teapot: Martin Newell,
University of Utah. "
article_processing_charge: No
author:
- first_name: Moritz
full_name: Bächer, Moritz
last_name: Bächer
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Emily
full_name: Whiting, Emily
last_name: Whiting
- first_name: Olga
full_name: Sorkine Hornung, Olga
last_name: Sorkine Hornung
citation:
ama: 'Bächer M, Bickel B, Whiting E, Sorkine Hornung O. Spin it: Optimizing moment
of inertia for spinnable objects. Communications of the ACM. 2017;60(8):92-99.
doi:10.1145/3068766'
apa: 'Bächer, M., Bickel, B., Whiting, E., & Sorkine Hornung, O. (2017). Spin
it: Optimizing moment of inertia for spinnable objects. Communications of the
ACM. ACM. https://doi.org/10.1145/3068766'
chicago: 'Bächer, Moritz, Bernd Bickel, Emily Whiting, and Olga Sorkine Hornung.
“Spin It: Optimizing Moment of Inertia for Spinnable Objects.” Communications
of the ACM. ACM, 2017. https://doi.org/10.1145/3068766.'
ieee: 'M. Bächer, B. Bickel, E. Whiting, and O. Sorkine Hornung, “Spin it: Optimizing
moment of inertia for spinnable objects,” Communications of the ACM, vol.
60, no. 8. ACM, pp. 92–99, 2017.'
ista: 'Bächer M, Bickel B, Whiting E, Sorkine Hornung O. 2017. Spin it: Optimizing
moment of inertia for spinnable objects. Communications of the ACM. 60(8), 92–99.'
mla: 'Bächer, Moritz, et al. “Spin It: Optimizing Moment of Inertia for Spinnable
Objects.” Communications of the ACM, vol. 60, no. 8, ACM, 2017, pp. 92–99,
doi:10.1145/3068766.'
short: M. Bächer, B. Bickel, E. Whiting, O. Sorkine Hornung, Communications of the
ACM 60 (2017) 92–99.
date_created: 2018-12-11T11:46:33Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2022-03-18T12:55:28Z
day: '01'
doi: 10.1145/3068766
extern: '1'
intvolume: ' 60'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 92 - 99
publication: Communications of the ACM
publication_status: published
publisher: ACM
publist_id: '7370'
scopus_import: '1'
status: public
title: 'Spin it: Optimizing moment of inertia for spinnable objects'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2017'
...
---
_id: '453'
abstract:
- lang: eng
text: Most kinesin motors move in only one direction along microtubules. Members
of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed
motors and shown to produce piconewton forces. However, some fungal kinesin-5
motors are bidirectional. The force production of a bidirectional kinesin-5 has
not yet been measured. Therefore, it remains unknown whether the mechanism of
the unconventional minus-end-directed motility differs fundamentally from that
of plus-end-directed stepping. Using force spectroscopy, we have measured here
the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in
microtubule gliding assays in both plus- and minus-end direction. Correlation
analysis of pause forces demonstrated that individual Cin8 molecules produce additive
forces in both directions of movement. In ensembles, Cin8 motors were able to
produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties
appear to be conserved within the kinesin-5 subfamily. Force production was largely
independent of the directionality of movement, indicating similarities between
the motility mechanisms for both directions. These results provide constraints
for the development of models for the bidirectional motility mechanism of fission
yeast kinesin-5 and provide insight into the function of this mitotic motor.
acknowledgement: 'The plasmid for full-length kinesin-1 was a gift from G. Holzwarth
and J. Macosko with permission from J. Howard. We thank I. Lueke and N. I. Cade
for technical assistance. G.P. thanks the Francis Crick Institute, and in particular
the Surrey and Salbreux groups, for their hospitality during his sabbatical stay,
as well as Imperial College London for making it possible. This work was supported
by the Francis Crick Institute, which receives its core funding from Cancer Research
UK (FC001163), the United Kingdom Medical Research Council (FC001163), and the Wellcome
Trust (FC001163), and by Imperial College London. J.R. was also supported by a Sir
Henry Wellcome Postdoctoral Fellowship (100145/Z/12/Z) and T.S. by the European
Research Council (Advanced Grant, project 323042). '
article_processing_charge: No
article_type: original
author:
- first_name: Todd
full_name: Fallesen, Todd
last_name: Fallesen
- first_name: Johanna
full_name: Roostalu, Johanna
last_name: Roostalu
- first_name: Christian F
full_name: Düllberg, Christian F
id: 459064DC-F248-11E8-B48F-1D18A9856A87
last_name: Düllberg
orcid: 0000-0001-6335-9748
- first_name: Gunnar
full_name: Pruessner, Gunnar
last_name: Pruessner
- first_name: Thomas
full_name: Surrey, Thomas
last_name: Surrey
citation:
ama: Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. Ensembles of bidirectional
kinesin Cin8 produce additive forces in both directions of movement. Biophysical
Journal. 2017;113(9):2055-2067. doi:10.1016/j.bpj.2017.09.006
apa: Fallesen, T., Roostalu, J., Düllberg, C. F., Pruessner, G., & Surrey, T.
(2017). Ensembles of bidirectional kinesin Cin8 produce additive forces in both
directions of movement. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.09.006
chicago: Fallesen, Todd, Johanna Roostalu, Christian F Düllberg, Gunnar Pruessner,
and Thomas Surrey. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces
in Both Directions of Movement.” Biophysical Journal. Biophysical Society,
2017. https://doi.org/10.1016/j.bpj.2017.09.006.
ieee: T. Fallesen, J. Roostalu, C. F. Düllberg, G. Pruessner, and T. Surrey, “Ensembles
of bidirectional kinesin Cin8 produce additive forces in both directions of movement,”
Biophysical Journal, vol. 113, no. 9. Biophysical Society, pp. 2055–2067,
2017.
ista: Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. 2017. Ensembles
of bidirectional kinesin Cin8 produce additive forces in both directions of movement.
Biophysical Journal. 113(9), 2055–2067.
mla: Fallesen, Todd, et al. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive
Forces in Both Directions of Movement.” Biophysical Journal, vol. 113,
no. 9, Biophysical Society, 2017, pp. 2055–67, doi:10.1016/j.bpj.2017.09.006.
short: T. Fallesen, J. Roostalu, C.F. Düllberg, G. Pruessner, T. Surrey, Biophysical
Journal 113 (2017) 2055–2067.
date_created: 2018-12-11T11:46:33Z
date_published: 2017-11-07T00:00:00Z
date_updated: 2021-01-12T07:59:28Z
day: '07'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1016/j.bpj.2017.09.006
file:
- access_level: open_access
checksum: 99a2474088e20ac74b1882c4fbbb45b1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:03Z
date_updated: 2020-07-14T12:46:31Z
file_id: '5052'
file_name: IST-2018-965-v1+1_2017_Duellberg_Ensembles_of.pdf
file_size: 977192
relation: main_file
file_date_updated: 2020-07-14T12:46:31Z
has_accepted_license: '1'
intvolume: ' 113'
issue: '9'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 2055 - 2067
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '7369'
pubrep_id: '965'
quality_controlled: '1'
status: public
title: Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions
of movement
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: 113
year: '2017'
...
---
_id: '464'
abstract:
- lang: eng
text: The computation of the winning set for parity objectives and for Streett objectives
in graphs as well as in game graphs are central problems in computer-aided verification,
with application to the verification of closed systems with strong fairness conditions,
the verification of open systems, checking interface compatibility, well-formedness
of specifications, and the synthesis of reactive systems. We show how to compute
the winning set on n vertices for (1) parity-3 (aka one-pair Streett) objectives
in game graphs in time O(n5/2) and for (2) k-pair Streett objectives in graphs
in time O(n2+nklogn). For both problems this gives faster algorithms for dense
graphs and represents the first improvement in asymptotic running time in 15 years.
article_number: '26'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Veronika
full_name: Loitzenbauer, Veronika
last_name: Loitzenbauer
citation:
ama: Chatterjee K, Henzinger MH, Loitzenbauer V. Improved algorithms for parity
and Streett objectives. Logical Methods in Computer Science. 2017;13(3).
doi:10.23638/LMCS-13(3:26)2017
apa: Chatterjee, K., Henzinger, M. H., & Loitzenbauer, V. (2017). Improved algorithms
for parity and Streett objectives. Logical Methods in Computer Science.
International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:26)2017
chicago: Chatterjee, Krishnendu, Monika H Henzinger, and Veronika Loitzenbauer.
“Improved Algorithms for Parity and Streett Objectives.” Logical Methods in
Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:26)2017.
ieee: K. Chatterjee, M. H. Henzinger, and V. Loitzenbauer, “Improved algorithms
for parity and Streett objectives,” Logical Methods in Computer Science,
vol. 13, no. 3. International Federation of Computational Logic, 2017.
ista: Chatterjee K, Henzinger MH, Loitzenbauer V. 2017. Improved algorithms for
parity and Streett objectives. Logical Methods in Computer Science. 13(3), 26.
mla: Chatterjee, Krishnendu, et al. “Improved Algorithms for Parity and Streett
Objectives.” Logical Methods in Computer Science, vol. 13, no. 3, 26, International
Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:26)2017.
short: K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, Logical Methods in Computer
Science 13 (2017).
date_created: 2018-12-11T11:46:37Z
date_published: 2017-09-26T00:00:00Z
date_updated: 2023-02-23T10:08:55Z
day: '26'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.23638/LMCS-13(3:26)2017
ec_funded: 1
external_id:
arxiv:
- '1410.0833'
file:
- access_level: open_access
checksum: 12d469ae69b80361333d7dead965cf5d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:27Z
date_updated: 2020-07-14T12:46:32Z
file_id: '5010'
file_name: IST-2018-956-v1+1_2017_Chatterjee_Improved_algorithms.pdf
file_size: 582940
relation: main_file
file_date_updated: 2020-07-14T12:46:32Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _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'
publication: Logical Methods in Computer Science
publication_identifier:
issn:
- 1860-5974
publication_status: published
publisher: International Federation of Computational Logic
publist_id: '7357'
pubrep_id: '956'
quality_controlled: '1'
related_material:
record:
- id: '1661'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Improved algorithms for parity and Streett objectives
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '470'
abstract:
- lang: eng
text: This paper presents a method for simulating water surface waves as a displacement
field on a 2D domain. Our method relies on Lagrangian particles that carry packets
of water wave energy; each packet carries information about an entire group of
wave trains, as opposed to only a single wave crest. Our approach is unconditionally
stable and can simulate high resolution geometric details. This approach also
presents a straightforward interface for artistic control, because it is essentially
a particle system with intuitive parameters like wavelength and amplitude. Our
implementation parallelizes well and runs in real time for moderately challenging
scenarios.
acknowledged_ssus:
- _id: ScienComp
article_number: '103'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Jeschke S, Wojtan C. Water wave packets. ACM Transactions on Graphics.
2017;36(4). doi:10.1145/3072959.3073678
apa: Jeschke, S., & Wojtan, C. (2017). Water wave packets. ACM Transactions
on Graphics. ACM. https://doi.org/10.1145/3072959.3073678
chicago: Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions
on Graphics. ACM, 2017. https://doi.org/10.1145/3072959.3073678.
ieee: S. Jeschke and C. Wojtan, “Water wave packets,” ACM Transactions on Graphics,
vol. 36, no. 4. ACM, 2017.
ista: Jeschke S, Wojtan C. 2017. Water wave packets. ACM Transactions on Graphics.
36(4), 103.
mla: Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions
on Graphics, vol. 36, no. 4, 103, ACM, 2017, doi:10.1145/3072959.3073678.
short: S. Jeschke, C. Wojtan, ACM Transactions on Graphics 36 (2017).
date_created: 2018-12-11T11:46:39Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2023-02-23T12:20:26Z
day: '01'
ddc:
- '006'
department:
- _id: ChWo
doi: 10.1145/3072959.3073678
ec_funded: 1
file:
- access_level: open_access
checksum: 82a3b2bfeee4ddef16ecc21675d1a48a
content_type: application/pdf
creator: wojtan
date_created: 2020-01-24T09:32:35Z
date_updated: 2020-07-14T12:46:34Z
file_id: '7359'
file_name: wavepackets_final.pdf
file_size: 13131683
relation: main_file
file_date_updated: 2020-07-14T12:46:34Z
has_accepted_license: '1'
intvolume: ' 36'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: ACM Transactions on Graphics
publication_identifier:
issn:
- '07300301'
publication_status: published
publisher: ACM
publist_id: '7350'
quality_controlled: '1'
scopus_import: 1
status: public
title: Water wave packets
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2017'
...
---
_id: '471'
abstract:
- lang: eng
text: 'We present a new algorithm for the statistical model checking of Markov chains
with respect to unbounded temporal properties, including full linear temporal
logic. The main idea is that we monitor each simulation run on the fly, in order
to detect quickly if a bottom strongly connected component is entered with high
probability, in which case the simulation run can be terminated early. As a result,
our simulation runs are often much shorter than required by termination bounds
that are computed a priori for a desired level of confidence on a large state
space. In comparison to previous algorithms for statistical model checking our
method is not only faster in many cases but also requires less information about
the system, namely, only the minimum transition probability that occurs in the
Markov chain. In addition, our method can be generalised to unbounded quantitative
properties such as mean-payoff bounds. '
article_number: '12'
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking
for unbounded temporal properties. ACM Transactions on Computational Logic
(TOCL). 2017;18(2). doi:10.1145/3060139
apa: Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2017). Faster
statistical model checking for unbounded temporal properties. ACM Transactions
on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3060139
chicago: Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov.
“Faster Statistical Model Checking for Unbounded Temporal Properties.” ACM
Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3060139.
ieee: P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical
model checking for unbounded temporal properties,” ACM Transactions on Computational
Logic (TOCL), vol. 18, no. 2. ACM, 2017.
ista: Daca P, Henzinger TA, Kretinsky J, Petrov T. 2017. Faster statistical model
checking for unbounded temporal properties. ACM Transactions on Computational
Logic (TOCL). 18(2), 12.
mla: Daca, Przemyslaw, et al. “Faster Statistical Model Checking for Unbounded Temporal
Properties.” ACM Transactions on Computational Logic (TOCL), vol. 18, no.
2, 12, ACM, 2017, doi:10.1145/3060139.
short: P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, ACM Transactions on Computational
Logic (TOCL) 18 (2017).
date_created: 2018-12-11T11:46:39Z
date_published: 2017-05-01T00:00:00Z
date_updated: 2023-02-21T16:48:11Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/3060139
ec_funded: 1
intvolume: ' 18'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.05739
month: '05'
oa: 1
oa_version: Submitted Version
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ACM Transactions on Computational Logic (TOCL)
publication_identifier:
issn:
- '15293785'
publication_status: published
publisher: ACM
publist_id: '7349'
quality_controlled: '1'
related_material:
record:
- id: '1234'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Faster statistical model checking for unbounded temporal properties
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2017'
...
---
_id: '472'
abstract:
- lang: eng
text: α-Synuclein is a presynaptic protein the function of which has yet to be identified,
but its neuronal content increases in patients of synucleinopa-thies including
Parkinson’s disease. Chronic overexpression of α-synuclein reportedly expresses
various phenotypes of synaptic dysfunction, but the primary target of its toxicity
has not been determined. To investigate this, we acutely loaded human recombinant
α-synuclein or its pathological mutants in their monomeric forms into the calyces
of Held presynaptic terminals in slices from auditorily mature and immature rats
of either sex. Membrane capacitance measurements revealed significant and specific
inhibitory effects of WT monomeric α-synuclein on vesicle endocytosis throughout
development. However, the α-synuclein A53T mutant affected vesicle endocytosis
only at immature calyces, where as the A30P mutant had no effect throughout. The
endocytic impairment by WTα-synuclein was rescued by intraterminal coloading of
the microtubule (MT) polymerization blocker nocodazole. Furthermore, it was reversibly
rescued by presynaptically loaded photostatin-1, a pho-toswitcheable inhibitor
of MT polymerization, inalight-wavelength-dependent manner. Incontrast, endocyticinhibition
by the A53T mutant at immature calyces was not rescued by nocodazole. Functionally,
presynaptically loaded WT α-synuclein had no effect on basal synaptic transmission
evoked at a low frequency, but significantly attenuated exocytosis and impaired
the fidelity of neurotransmission during prolonged high-frequency stimulation.
We conclude that monomeric WTα-synuclein primarily inhibits vesicle endocytosis
via MT overassembly, thereby impairing high-frequency neurotransmission.
author:
- first_name: Kohgaku
full_name: Eguchi, Kohgaku
id: 2B7846DC-F248-11E8-B48F-1D18A9856A87
last_name: Eguchi
orcid: 0000-0002-6170-2546
- first_name: Zachari
full_name: Taoufiq, Zachari
last_name: Taoufiq
- first_name: Oliver
full_name: Thorn Seshold, Oliver
last_name: Thorn Seshold
- first_name: Dirk
full_name: Trauner, Dirk
last_name: Trauner
- first_name: Masato
full_name: Hasegawa, Masato
last_name: Hasegawa
- first_name: Tomoyuki
full_name: Takahashi, Tomoyuki
last_name: Takahashi
citation:
ama: Eguchi K, Taoufiq Z, Thorn Seshold O, Trauner D, Hasegawa M, Takahashi T. Wild-type
monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via
tubulin polymerization at the calyx of held. European Journal of Neuroscience.
2017;37(25):6043-6052. doi:10.1523/JNEUROSCI.0179-17.2017
apa: Eguchi, K., Taoufiq, Z., Thorn Seshold, O., Trauner, D., Hasegawa, M., &
Takahashi, T. (2017). Wild-type monomeric α-synuclein can impair vesicle endocytosis
and synaptic fidelity via tubulin polymerization at the calyx of held. European
Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1523/JNEUROSCI.0179-17.2017
chicago: Eguchi, Kohgaku, Zachari Taoufiq, Oliver Thorn Seshold, Dirk Trauner, Masato
Hasegawa, and Tomoyuki Takahashi. “Wild-Type Monomeric α-Synuclein Can Impair
Vesicle Endocytosis and Synaptic Fidelity via Tubulin Polymerization at the Calyx
of Held.” European Journal of Neuroscience. Wiley-Blackwell, 2017. https://doi.org/10.1523/JNEUROSCI.0179-17.2017.
ieee: K. Eguchi, Z. Taoufiq, O. Thorn Seshold, D. Trauner, M. Hasegawa, and T. Takahashi,
“Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity
via tubulin polymerization at the calyx of held,” European Journal of Neuroscience,
vol. 37, no. 25. Wiley-Blackwell, pp. 6043–6052, 2017.
ista: Eguchi K, Taoufiq Z, Thorn Seshold O, Trauner D, Hasegawa M, Takahashi T.
2017. Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic
fidelity via tubulin polymerization at the calyx of held. European Journal of
Neuroscience. 37(25), 6043–6052.
mla: Eguchi, Kohgaku, et al. “Wild-Type Monomeric α-Synuclein Can Impair Vesicle
Endocytosis and Synaptic Fidelity via Tubulin Polymerization at the Calyx of Held.”
European Journal of Neuroscience, vol. 37, no. 25, Wiley-Blackwell, 2017,
pp. 6043–52, doi:10.1523/JNEUROSCI.0179-17.2017.
short: K. Eguchi, Z. Taoufiq, O. Thorn Seshold, D. Trauner, M. Hasegawa, T. Takahashi,
European Journal of Neuroscience 37 (2017) 6043–6052.
date_created: 2018-12-11T11:46:40Z
date_published: 2017-06-21T00:00:00Z
date_updated: 2021-01-12T08:00:51Z
day: '21'
doi: 10.1523/JNEUROSCI.0179-17.2017
extern: '1'
intvolume: ' 37'
issue: '25'
language:
- iso: eng
month: '06'
oa_version: None
page: 6043 - 6052
publication: European Journal of Neuroscience
publication_identifier:
issn:
- '02706474'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7348'
quality_controlled: '1'
status: public
title: Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic
fidelity via tubulin polymerization at the calyx of held
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2017'
...
---
_id: '481'
abstract:
- lang: eng
text: We introduce planar matchings on directed pseudo-line arrangements, which
yield a planar set of pseudo-line segments such that only matching-partners are
adjacent. By translating the planar matching problem into a corresponding stable
roommates problem we show that such matchings always exist. Using our new framework,
we establish, for the first time, a complete, rigorous definition of weighted
straight skeletons, which are based on a so-called wavefront propagation process.
We present a generalized and unified approach to treat structural changes in the
wavefront that focuses on the restoration of weak planarity by finding planar
matchings.
acknowledgement: 'Supported by NSERC and the Ross and Muriel Cheriton Fellowship.
Research supported by Austrian Science Fund (FWF): P25816-N15.'
author:
- first_name: Therese
full_name: Biedl, Therese
last_name: Biedl
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Peter
full_name: Palfrader, Peter
last_name: Palfrader
citation:
ama: Biedl T, Huber S, Palfrader P. Planar matchings for weighted straight skeletons.
International Journal of Computational Geometry and Applications. 2017;26(3-4):211-229.
doi:10.1142/S0218195916600050
apa: Biedl, T., Huber, S., & Palfrader, P. (2017). Planar matchings for weighted
straight skeletons. International Journal of Computational Geometry and Applications.
World Scientific Publishing. https://doi.org/10.1142/S0218195916600050
chicago: Biedl, Therese, Stefan Huber, and Peter Palfrader. “Planar Matchings for
Weighted Straight Skeletons.” International Journal of Computational Geometry
and Applications. World Scientific Publishing, 2017. https://doi.org/10.1142/S0218195916600050.
ieee: T. Biedl, S. Huber, and P. Palfrader, “Planar matchings for weighted straight
skeletons,” International Journal of Computational Geometry and Applications,
vol. 26, no. 3–4. World Scientific Publishing, pp. 211–229, 2017.
ista: Biedl T, Huber S, Palfrader P. 2017. Planar matchings for weighted straight
skeletons. International Journal of Computational Geometry and Applications. 26(3–4),
211–229.
mla: Biedl, Therese, et al. “Planar Matchings for Weighted Straight Skeletons.”
International Journal of Computational Geometry and Applications, vol.
26, no. 3–4, World Scientific Publishing, 2017, pp. 211–29, doi:10.1142/S0218195916600050.
short: T. Biedl, S. Huber, P. Palfrader, International Journal of Computational
Geometry and Applications 26 (2017) 211–229.
date_created: 2018-12-11T11:46:43Z
date_published: 2017-04-13T00:00:00Z
date_updated: 2023-02-21T16:06:22Z
day: '13'
ddc:
- '004'
- '514'
- '516'
department:
- _id: HeEd
doi: 10.1142/S0218195916600050
file:
- access_level: open_access
checksum: f79e8558bfe4b368dfefeb8eec2e3a5e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:34Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4758'
file_name: IST-2018-949-v1+1_2016_huber_PLanar_matchings.pdf
file_size: 769296
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file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 26'
issue: 3-4
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 211 - 229
publication: International Journal of Computational Geometry and Applications
publication_status: published
publisher: World Scientific Publishing
publist_id: '7338'
pubrep_id: '949'
quality_controlled: '1'
related_material:
record:
- id: '10892'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Planar matchings for weighted straight skeletons
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: 26
year: '2017'
...
---
_id: '484'
abstract:
- lang: eng
text: We consider the dynamics of a large quantum system of N identical bosons in
3D interacting via a two-body potential of the form N3β-1w(Nβ(x - y)). For fixed
0 = β < 1/3 and large N, we obtain a norm approximation to the many-body evolution
in the Nparticle Hilbert space. The leading order behaviour of the dynamics is
determined by Hartree theory while the second order is given by Bogoliubov theory.
author:
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
- first_name: Marcin M
full_name: Napiórkowski, Marcin M
id: 4197AD04-F248-11E8-B48F-1D18A9856A87
last_name: Napiórkowski
citation:
ama: Nam P, Napiórkowski MM. Bogoliubov correction to the mean-field dynamics of
interacting bosons. Advances in Theoretical and Mathematical Physics. 2017;21(3):683-738.
doi:10.4310/ATMP.2017.v21.n3.a4
apa: Nam, P., & Napiórkowski, M. M. (2017). Bogoliubov correction to the mean-field
dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics.
International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a4
chicago: Nam, Phan, and Marcin M Napiórkowski. “Bogoliubov Correction to the Mean-Field
Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics.
International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a4.
ieee: P. Nam and M. M. Napiórkowski, “Bogoliubov correction to the mean-field dynamics
of interacting bosons,” Advances in Theoretical and Mathematical Physics,
vol. 21, no. 3. International Press, pp. 683–738, 2017.
ista: Nam P, Napiórkowski MM. 2017. Bogoliubov correction to the mean-field dynamics
of interacting bosons. Advances in Theoretical and Mathematical Physics. 21(3),
683–738.
mla: Nam, Phan, and Marcin M. Napiórkowski. “Bogoliubov Correction to the Mean-Field
Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics,
vol. 21, no. 3, International Press, 2017, pp. 683–738, doi:10.4310/ATMP.2017.v21.n3.a4.
short: P. Nam, M.M. Napiórkowski, Advances in Theoretical and Mathematical Physics
21 (2017) 683–738.
date_created: 2018-12-11T11:46:43Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:00:58Z
day: '01'
department:
- _id: RoSe
doi: 10.4310/ATMP.2017.v21.n3.a4
ec_funded: 1
intvolume: ' 21'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1509.04631
month: '01'
oa: 1
oa_version: Submitted Version
page: 683 - 738
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Advances in Theoretical and Mathematical Physics
publication_identifier:
issn:
- '10950761'
publication_status: published
publisher: International Press
publist_id: '7336'
quality_controlled: '1'
scopus_import: 1
status: public
title: Bogoliubov correction to the mean-field dynamics of interacting bosons
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2017'
...
---
_id: '483'
abstract:
- lang: eng
text: We prove the universality for the eigenvalue gap statistics in the bulk of
the spectrum for band matrices, in the regime where the band width is comparable
with the dimension of the matrix, W ~ N. All previous results concerning universality
of non-Gaussian random matrices are for mean-field models. By relying on a new
mean-field reduction technique, we deduce universality from quantum unique ergodicity
for band matrices.
author:
- first_name: Paul
full_name: Bourgade, Paul
last_name: Bourgade
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Horng
full_name: Yau, Horng
last_name: Yau
- first_name: Jun
full_name: Yin, Jun
last_name: Yin
citation:
ama: Bourgade P, Erdös L, Yau H, Yin J. Universality for a class of random band
matrices. Advances in Theoretical and Mathematical Physics. 2017;21(3):739-800.
doi:10.4310/ATMP.2017.v21.n3.a5
apa: Bourgade, P., Erdös, L., Yau, H., & Yin, J. (2017). Universality for a
class of random band matrices. Advances in Theoretical and Mathematical Physics.
International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a5
chicago: Bourgade, Paul, László Erdös, Horng Yau, and Jun Yin. “Universality for
a Class of Random Band Matrices.” Advances in Theoretical and Mathematical
Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a5.
ieee: P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Universality for a class of random
band matrices,” Advances in Theoretical and Mathematical Physics, vol.
21, no. 3. International Press, pp. 739–800, 2017.
ista: Bourgade P, Erdös L, Yau H, Yin J. 2017. Universality for a class of random
band matrices. Advances in Theoretical and Mathematical Physics. 21(3), 739–800.
mla: Bourgade, Paul, et al. “Universality for a Class of Random Band Matrices.”
Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International
Press, 2017, pp. 739–800, doi:10.4310/ATMP.2017.v21.n3.a5.
short: P. Bourgade, L. Erdös, H. Yau, J. Yin, Advances in Theoretical and Mathematical
Physics 21 (2017) 739–800.
date_created: 2018-12-11T11:46:43Z
date_published: 2017-08-25T00:00:00Z
date_updated: 2021-01-12T08:00:57Z
day: '25'
department:
- _id: LaEr
doi: 10.4310/ATMP.2017.v21.n3.a5
ec_funded: 1
intvolume: ' 21'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.02312
month: '08'
oa: 1
oa_version: Submitted Version
page: 739 - 800
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Advances in Theoretical and Mathematical Physics
publication_identifier:
issn:
- '10950761'
publication_status: published
publisher: International Press
publist_id: '7337'
quality_controlled: '1'
scopus_import: 1
status: public
title: Universality for a class of random band matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2017'
...
---
_id: '487'
abstract:
- lang: eng
text: In this paper we study network architecture for unlicensed cellular networking
for outdoor coverage in TV white spaces. The main technology proposed for TV white
spaces is 802.11af, a Wi-Fi variant adapted for TV frequencies. However, 802.11af
is originally designed for improved indoor propagation. We show that long links,
typical for outdoor use, exacerbate known Wi-Fi issues, such as hidden and exposed
terminal, and significantly reduce its efficiency. Instead, we propose CellFi,
an alternative architecture based on LTE. LTE is designed for long-range coverage
and throughput efficiency, but it is also designed to operate in tightly controlled
and centrally managed networks. CellFi overcomes these problems by designing an
LTE-compatible spectrum database component, mandatory for TV white space networking,
and introducing an interference management component for distributed coordination.
CellFi interference management is compatible with existing LTE mechanisms, requires
no explicit communication between base stations, and is more efficient than CSMA
for long links. We evaluate our design through extensive real world evaluation
on of-the-shelf LTE equipment and simulations. We show that, compared to 802.11af,
it increases coverage by 40% and reduces median flow completion times by 2.3x.
author:
- first_name: Ghufran
full_name: Baig, Ghufran
last_name: Baig
- first_name: Bozidar
full_name: Radunovic, Bozidar
last_name: Radunovic
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Matthew
full_name: Balkwill, Matthew
last_name: Balkwill
- first_name: Thomas
full_name: Karagiannis, Thomas
last_name: Karagiannis
- first_name: Lili
full_name: Qiu, Lili
last_name: Qiu
citation:
ama: 'Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. Towards
unlicensed cellular networks in TV white spaces. In: Proceedings of the 2017
13th International Conference on Emerging Networking EXperiments and Technologies.
ACM; 2017:2-14. doi:10.1145/3143361.3143367'
apa: 'Baig, G., Radunovic, B., Alistarh, D.-A., Balkwill, M., Karagiannis, T., &
Qiu, L. (2017). Towards unlicensed cellular networks in TV white spaces. In Proceedings
of the 2017 13th International Conference on emerging Networking EXperiments and
Technologies (pp. 2–14). Incheon, South Korea: ACM. https://doi.org/10.1145/3143361.3143367'
chicago: Baig, Ghufran, Bozidar Radunovic, Dan-Adrian Alistarh, Matthew Balkwill,
Thomas Karagiannis, and Lili Qiu. “Towards Unlicensed Cellular Networks in TV
White Spaces.” In Proceedings of the 2017 13th International Conference on
Emerging Networking EXperiments and Technologies, 2–14. ACM, 2017. https://doi.org/10.1145/3143361.3143367.
ieee: G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, and L.
Qiu, “Towards unlicensed cellular networks in TV white spaces,” in Proceedings
of the 2017 13th International Conference on emerging Networking EXperiments and
Technologies, Incheon, South Korea, 2017, pp. 2–14.
ista: 'Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. 2017.
Towards unlicensed cellular networks in TV white spaces. Proceedings of the 2017
13th International Conference on emerging Networking EXperiments and Technologies.
CoNEXT: Conference on emerging Networking EXperiments and Technologies, 2–14.'
mla: Baig, Ghufran, et al. “Towards Unlicensed Cellular Networks in TV White Spaces.”
Proceedings of the 2017 13th International Conference on Emerging Networking
EXperiments and Technologies, ACM, 2017, pp. 2–14, doi:10.1145/3143361.3143367.
short: G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, L. Qiu,
in:, Proceedings of the 2017 13th International Conference on Emerging Networking
EXperiments and Technologies, ACM, 2017, pp. 2–14.
conference:
end_date: 2017-12-15
location: Incheon, South Korea
name: 'CoNEXT: Conference on emerging Networking EXperiments and Technologies'
start_date: 2017-12-12
date_created: 2018-12-11T11:46:45Z
date_published: 2017-11-28T00:00:00Z
date_updated: 2023-02-23T12:21:11Z
day: '28'
department:
- _id: DaAl
doi: 10.1145/3143361.3143367
language:
- iso: eng
month: '11'
oa_version: None
page: 2 - 14
publication: Proceedings of the 2017 13th International Conference on emerging Networking
EXperiments and Technologies
publication_identifier:
isbn:
- 978-145035422-6
publication_status: published
publisher: ACM
publist_id: '7333'
quality_controlled: '1'
scopus_import: 1
status: public
title: Towards unlicensed cellular networks in TV white spaces
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '514'
abstract:
- lang: eng
text: 'Orientation in space is represented in specialized brain circuits. Persistent
head direction signals are transmitted from anterior thalamus to the presubiculum,
but the identity of the presubicular target neurons, their connectivity and function
in local microcircuits are unknown. Here, we examine how thalamic afferents recruit
presubicular principal neurons and Martinotti interneurons, and the ensuing synaptic
interactions between these cells. Pyramidal neuron activation of Martinotti cells
in superficial layers is strongly facilitating such that high-frequency head directional
stimulation efficiently unmutes synaptic excitation. Martinotti-cell feedback
plays a dual role: precisely timed spikes may not inhibit the firing of in-tune
head direction cells, while exerting lateral inhibition. Autonomous attractor
dynamics emerge from a modelled network implementing wiring motifs and timing
sensitive synaptic interactions in the pyramidal - Martinotti-cell feedback loop.
This inhibitory microcircuit is therefore tuned to refine and maintain head direction
information in the presubiculum.'
article_number: '16032'
author:
- first_name: Jean
full_name: Simonnet, Jean
last_name: Simonnet
- first_name: Mérie
full_name: Nassar, Mérie
last_name: Nassar
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Ivan
full_name: Cohen, Ivan
last_name: Cohen
- first_name: Bertrand
full_name: Mathon, Bertrand
last_name: Mathon
- first_name: Charlotte
full_name: Boccara, Charlotte
id: 3FC06552-F248-11E8-B48F-1D18A9856A87
last_name: Boccara
orcid: 0000-0001-7237-5109
- first_name: Richard
full_name: Miles, Richard
last_name: Miles
- first_name: Desdemona
full_name: Fricker, Desdemona
last_name: Fricker
citation:
ama: Simonnet J, Nassar M, Stella F, et al. Activity dependent feedback inhibition
may maintain head direction signals in mouse presubiculum. Nature Communications.
2017;8. doi:10.1038/ncomms16032
apa: Simonnet, J., Nassar, M., Stella, F., Cohen, I., Mathon, B., Boccara, C. N.,
… Fricker, D. (2017). Activity dependent feedback inhibition may maintain head
direction signals in mouse presubiculum. Nature Communications. Nature
Publishing Group. https://doi.org/10.1038/ncomms16032
chicago: Simonnet, Jean, Mérie Nassar, Federico Stella, Ivan Cohen, Bertrand Mathon,
Charlotte N. Boccara, Richard Miles, and Desdemona Fricker. “Activity Dependent
Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.”
Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms16032.
ieee: J. Simonnet et al., “Activity dependent feedback inhibition may maintain
head direction signals in mouse presubiculum,” Nature Communications, vol.
8. Nature Publishing Group, 2017.
ista: Simonnet J, Nassar M, Stella F, Cohen I, Mathon B, Boccara CN, Miles R, Fricker
D. 2017. Activity dependent feedback inhibition may maintain head direction signals
in mouse presubiculum. Nature Communications. 8, 16032.
mla: Simonnet, Jean, et al. “Activity Dependent Feedback Inhibition May Maintain
Head Direction Signals in Mouse Presubiculum.” Nature Communications, vol.
8, 16032, Nature Publishing Group, 2017, doi:10.1038/ncomms16032.
short: J. Simonnet, M. Nassar, F. Stella, I. Cohen, B. Mathon, C.N. Boccara, R.
Miles, D. Fricker, Nature Communications 8 (2017).
date_created: 2018-12-11T11:46:54Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2021-01-12T08:01:16Z
day: '01'
ddc:
- '571'
department:
- _id: JoCs
doi: 10.1038/ncomms16032
file:
- access_level: open_access
checksum: 76d8a2b72a58e56adb410ec37dfa7eee
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:31Z
date_updated: 2020-07-14T12:46:36Z
file_id: '5083'
file_name: IST-2018-937-v1+1_2017_Stella_Activity_dependent.pdf
file_size: 2948357
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7305'
pubrep_id: '937'
quality_controlled: '1'
scopus_import: 1
status: public
title: Activity dependent feedback inhibition may maintain head direction signals
in mouse presubiculum
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: 8
year: '2017'
...
---
_id: '515'
abstract:
- lang: eng
text: 'The oxidative phosphorylation electron transport chain (OXPHOS-ETC) of the
inner mitochondrial membrane is composed of five large protein complexes, named
CI-CV. These complexes convert energy from the food we eat into ATP, a small molecule
used to power a multitude of essential reactions throughout the cell. OXPHOS-ETC
complexes are organized into supercomplexes (SCs) of defined stoichiometry: CI
forms a supercomplex with CIII2 and CIV (SC I+III2+IV, known as the respirasome),
as well as with CIII2 alone (SC I+III2). CIII2 forms a supercomplex with CIV (SC
III2+IV) and CV forms dimers (CV2). Recent cryo-EM studies have revealed the structures
of SC I+III2+IV and SC I+III2. Furthermore, recent work has shed light on the
assembly and function of the SCs. Here we review and compare these recent studies
and discuss how they have advanced our understanding of mitochondrial electron
transport.'
article_type: original
author:
- first_name: James A
full_name: Letts, James A
id: 322DA418-F248-11E8-B48F-1D18A9856A87
last_name: Letts
orcid: 0000-0002-9864-3586
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: 'Letts JA, Sazanov LA. Clarifying the supercomplex: The higher-order organization
of the mitochondrial electron transport chain. Nature Structural and Molecular
Biology. 2017;24(10):800-808. doi:10.1038/nsmb.3460'
apa: 'Letts, J. A., & Sazanov, L. A. (2017). Clarifying the supercomplex: The
higher-order organization of the mitochondrial electron transport chain. Nature
Structural and Molecular Biology. Nature Publishing Group. https://doi.org/10.1038/nsmb.3460'
chicago: 'Letts, James A, and Leonid A Sazanov. “Clarifying the Supercomplex: The
Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature
Structural and Molecular Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/nsmb.3460.'
ieee: 'J. A. Letts and L. A. Sazanov, “Clarifying the supercomplex: The higher-order
organization of the mitochondrial electron transport chain,” Nature Structural
and Molecular Biology, vol. 24, no. 10. Nature Publishing Group, pp. 800–808,
2017.'
ista: 'Letts JA, Sazanov LA. 2017. Clarifying the supercomplex: The higher-order
organization of the mitochondrial electron transport chain. Nature Structural
and Molecular Biology. 24(10), 800–808.'
mla: 'Letts, James A., and Leonid A. Sazanov. “Clarifying the Supercomplex: The
Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature
Structural and Molecular Biology, vol. 24, no. 10, Nature Publishing Group,
2017, pp. 800–08, doi:10.1038/nsmb.3460.'
short: J.A. Letts, L.A. Sazanov, Nature Structural and Molecular Biology 24 (2017)
800–808.
date_created: 2018-12-11T11:46:54Z
date_published: 2017-10-05T00:00:00Z
date_updated: 2021-01-12T08:01:17Z
day: '05'
ddc:
- '572'
department:
- _id: LeSa
doi: 10.1038/nsmb.3460
ec_funded: 1
file:
- access_level: open_access
checksum: 9bc7e8c41b43636dd7566289e511f096
content_type: application/pdf
creator: lsazanov
date_created: 2019-11-07T12:51:07Z
date_updated: 2020-07-14T12:46:36Z
file_id: '6993'
file_name: 29893_2_merged_1501257589_red.pdf
file_size: 4118385
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 24'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 800 - 808
project:
- _id: 2590DB08-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '701309'
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
(H2020)
publication: Nature Structural and Molecular Biology
publication_identifier:
issn:
- '15459993'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7304'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Clarifying the supercomplex: The higher-order organization of the mitochondrial
electron transport chain'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2017'
...
---
_id: '513'
abstract:
- lang: eng
text: 'We present an experimental setup that creates a shear flow with zero mean
advection velocity achieved by counterbalancing the nonzero streamwise pressure
gradient by moving boundaries, which generates plane Couette-Poiseuille flow.
We obtain experimental results in the transitional regime for this flow. Using
flow visualization, we characterize the subcritical transition to turbulence in
Couette-Poiseuille flow and show the existence of turbulent spots generated by
a permanent perturbation. Due to the zero mean advection velocity of the base
profile, these turbulent structures are nearly stationary. We distinguish two
regions of the turbulent spot: the active turbulent core, which is characterized
by waviness of the streaks similar to traveling waves, and the surrounding region,
which includes in addition the weak undisturbed streaks and oblique waves at the
laminar-turbulent interface. We also study the dependence of the size of these
two regions on Reynolds number. Finally, we show that the traveling waves move
in the downstream (Poiseuille) direction.'
article_number: '043904'
author:
- first_name: Lukasz
full_name: Klotz, Lukasz
id: 2C9AF1C2-F248-11E8-B48F-1D18A9856A87
last_name: Klotz
orcid: 0000-0003-1740-7635
- first_name: Grégoire M
full_name: Lemoult, Grégoire M
id: 4787FE80-F248-11E8-B48F-1D18A9856A87
last_name: Lemoult
- first_name: Idalia
full_name: Frontczak, Idalia
last_name: Frontczak
- first_name: Laurette
full_name: Tuckerman, Laurette
last_name: Tuckerman
- first_name: José
full_name: Wesfreid, José
last_name: Wesfreid
citation:
ama: 'Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. Couette-Poiseuille
flow experiment with zero mean advection velocity: Subcritical transition to turbulence.
Physical Review Fluids. 2017;2(4). doi:10.1103/PhysRevFluids.2.043904'
apa: 'Klotz, L., Lemoult, G. M., Frontczak, I., Tuckerman, L., & Wesfreid, J.
(2017). Couette-Poiseuille flow experiment with zero mean advection velocity:
Subcritical transition to turbulence. Physical Review Fluids. American
Physical Society. https://doi.org/10.1103/PhysRevFluids.2.043904'
chicago: 'Klotz, Lukasz, Grégoire M Lemoult, Idalia Frontczak, Laurette Tuckerman,
and José Wesfreid. “Couette-Poiseuille Flow Experiment with Zero Mean Advection
Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids.
American Physical Society, 2017. https://doi.org/10.1103/PhysRevFluids.2.043904.'
ieee: 'L. Klotz, G. M. Lemoult, I. Frontczak, L. Tuckerman, and J. Wesfreid, “Couette-Poiseuille
flow experiment with zero mean advection velocity: Subcritical transition to turbulence,”
Physical Review Fluids, vol. 2, no. 4. American Physical Society, 2017.'
ista: 'Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. 2017. Couette-Poiseuille
flow experiment with zero mean advection velocity: Subcritical transition to turbulence.
Physical Review Fluids. 2(4), 043904.'
mla: 'Klotz, Lukasz, et al. “Couette-Poiseuille Flow Experiment with Zero Mean Advection
Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids,
vol. 2, no. 4, 043904, American Physical Society, 2017, doi:10.1103/PhysRevFluids.2.043904.'
short: L. Klotz, G.M. Lemoult, I. Frontczak, L. Tuckerman, J. Wesfreid, Physical
Review Fluids 2 (2017).
date_created: 2018-12-11T11:46:54Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2021-01-12T08:01:16Z
day: '01'
department:
- _id: BjHo
doi: 10.1103/PhysRevFluids.2.043904
intvolume: ' 2'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.02619
month: '04'
oa: 1
oa_version: Preprint
publication: Physical Review Fluids
publication_status: published
publisher: American Physical Society
publist_id: '7306'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical
transition to turbulence'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2017'
...
---
_id: '520'
abstract:
- lang: eng
text: Cyanobacteria are mostly engineered to be sustainable cell-factories by genetic
manipulations alone. Here, by modulating the concentration of allosteric effectors,
we focus on increasing product formation without further burdening the cells with
increased expression of enzymes. Resorting to a novel 96-well microplate cultivation
system for cyanobacteria, and using lactate-producing strains of Synechocystis
PCC6803 expressing different l-lactate dehydrogenases (LDH), we titrated the effect
of 2,5-anhydro-mannitol supplementation. The latter acts in cells as a nonmetabolizable
analogue of fructose 1,6-bisphosphate, a known allosteric regulator of one of
the tested LDHs. In this strain (SAA023), we achieved over 2-fold increase of
lactate productivity. Furthermore, we observed that as carbon is increasingly
deviated during growth toward product formation, there is an increased fixation
rate in the population of spontaneous mutants harboring an impaired production
pathway. This is a challenge in the development of green cell factories, which
may be countered by the incorporation in biotechnological processes of strategies
such as the one pioneered here.
article_type: letter_note
author:
- first_name: Wei
full_name: Du, Wei
last_name: Du
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Joeri
full_name: Jongbloets, Joeri
last_name: Jongbloets
- first_name: Douwe
full_name: Molenaar, Douwe
last_name: Molenaar
- first_name: Herwig
full_name: Bachmann, Herwig
last_name: Bachmann
- first_name: Klaas
full_name: Hellingwerf, Klaas
last_name: Hellingwerf
- first_name: Filipe
full_name: Branco Dos Santos, Filipe
last_name: Branco Dos Santos
citation:
ama: Du W, Angermayr A, Jongbloets J, et al. Nonhierarchical flux regulation exposes
the fitness burden associated with lactate production in Synechocystis sp. PCC6803.
ACS Synthetic Biology. 2017;6(3):395-401. doi:10.1021/acssynbio.6b00235
apa: Du, W., Angermayr, A., Jongbloets, J., Molenaar, D., Bachmann, H., Hellingwerf,
K., & Branco Dos Santos, F. (2017). Nonhierarchical flux regulation exposes
the fitness burden associated with lactate production in Synechocystis sp. PCC6803.
ACS Synthetic Biology. American Chemical Society. https://doi.org/10.1021/acssynbio.6b00235
chicago: Du, Wei, Andreas Angermayr, Joeri Jongbloets, Douwe Molenaar, Herwig Bachmann,
Klaas Hellingwerf, and Filipe Branco Dos Santos. “Nonhierarchical Flux Regulation
Exposes the Fitness Burden Associated with Lactate Production in Synechocystis
Sp. PCC6803.” ACS Synthetic Biology. American Chemical Society, 2017. https://doi.org/10.1021/acssynbio.6b00235.
ieee: W. Du et al., “Nonhierarchical flux regulation exposes the fitness
burden associated with lactate production in Synechocystis sp. PCC6803,” ACS
Synthetic Biology, vol. 6, no. 3. American Chemical Society, pp. 395–401,
2017.
ista: Du W, Angermayr A, Jongbloets J, Molenaar D, Bachmann H, Hellingwerf K, Branco
Dos Santos F. 2017. Nonhierarchical flux regulation exposes the fitness burden
associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic
Biology. 6(3), 395–401.
mla: Du, Wei, et al. “Nonhierarchical Flux Regulation Exposes the Fitness Burden
Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic
Biology, vol. 6, no. 3, American Chemical Society, 2017, pp. 395–401, doi:10.1021/acssynbio.6b00235.
short: W. Du, A. Angermayr, J. Jongbloets, D. Molenaar, H. Bachmann, K. Hellingwerf,
F. Branco Dos Santos, ACS Synthetic Biology 6 (2017) 395–401.
date_created: 2018-12-11T11:46:56Z
date_published: 2017-03-17T00:00:00Z
date_updated: 2021-01-12T08:01:21Z
day: '17'
department:
- _id: ToBo
doi: 10.1021/acssynbio.6b00235
external_id:
pmid:
- '27936615'
intvolume: ' 6'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 395 - 401
pmid: 1
publication: ACS Synthetic Biology
publication_identifier:
issn:
- '21615063'
publication_status: published
publisher: American Chemical Society
publist_id: '7298'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nonhierarchical flux regulation exposes the fitness burden associated with
lactate production in Synechocystis sp. PCC6803
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2017'
...
---
_id: '521'
abstract:
- lang: eng
text: Let X and Y be proper metric spaces. We show that a coarsely n-to-1 map f:X→Y
induces an n-to-1 map of Higson coronas. This viewpoint turns out to be successful
in showing that the classical dimension raising theorems hold in large scale;
that is, if f:X→Y is a coarsely n-to-1 map between proper metric spaces X and
Y then asdim(Y)≤asdim(X)+n−1. Furthermore we introduce coarsely open coarsely
n-to-1 maps, which include the natural quotient maps via a finite group action,
and prove that they preserve the asymptotic dimension.
author:
- first_name: Kyle
full_name: Austin, Kyle
last_name: Austin
- first_name: Ziga
full_name: Virk, Ziga
id: 2E36B656-F248-11E8-B48F-1D18A9856A87
last_name: Virk
citation:
ama: Austin K, Virk Z. Higson compactification and dimension raising. Topology
and its Applications. 2017;215:45-57. doi:10.1016/j.topol.2016.10.005
apa: Austin, K., & Virk, Z. (2017). Higson compactification and dimension raising.
Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2016.10.005
chicago: Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.”
Topology and Its Applications. Elsevier, 2017. https://doi.org/10.1016/j.topol.2016.10.005.
ieee: K. Austin and Z. Virk, “Higson compactification and dimension raising,” Topology
and its Applications, vol. 215. Elsevier, pp. 45–57, 2017.
ista: Austin K, Virk Z. 2017. Higson compactification and dimension raising. Topology
and its Applications. 215, 45–57.
mla: Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.”
Topology and Its Applications, vol. 215, Elsevier, 2017, pp. 45–57, doi:10.1016/j.topol.2016.10.005.
short: K. Austin, Z. Virk, Topology and Its Applications 215 (2017) 45–57.
date_created: 2018-12-11T11:46:56Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:01:21Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.topol.2016.10.005
intvolume: ' 215'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.03954v1
month: '01'
oa: 1
oa_version: Submitted Version
page: 45 - 57
publication: Topology and its Applications
publication_identifier:
issn:
- '01668641'
publication_status: published
publisher: Elsevier
publist_id: '7299'
quality_controlled: '1'
status: public
title: Higson compactification and dimension raising
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 215
year: '2017'
...
---
_id: '525'
abstract:
- lang: eng
text: 'The Casparian strip is an important barrier regulating water and nutrient
uptake into root tissues. New research reveals two peptide signals and their co-receptors
play critical roles patterning and maintaining barrier integrity. '
acknowledgement: "Biotechnology and Biological Sciences Research Council:\tBBSRC BB/M001806/1
and BB/H020314/1\t"
author:
- first_name: Daniel
full_name: Daniel von Wangenheim
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Tatsuaki
full_name: Goh, Tatsuaki
last_name: Goh
- first_name: Daniela
full_name: Dietrich, Daniela
last_name: Dietrich
- first_name: Malcolm
full_name: Bennett, Malcolm J
last_name: Bennett
citation:
ama: 'von Wangenheim D, Goh T, Dietrich D, Bennett M. Plant biology: Building barriers…
in roots. Current Biology. 2017;27(5):R172-R174. doi:10.1016/j.cub.2017.01.060'
apa: 'von Wangenheim, D., Goh, T., Dietrich, D., & Bennett, M. (2017). Plant
biology: Building barriers… in roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.01.060'
chicago: 'Wangenheim, Daniel von, Tatsuaki Goh, Daniela Dietrich, and Malcolm Bennett.
“Plant Biology: Building Barriers… in Roots.” Current Biology. Cell Press,
2017. https://doi.org/10.1016/j.cub.2017.01.060.'
ieee: 'D. von Wangenheim, T. Goh, D. Dietrich, and M. Bennett, “Plant biology: Building
barriers… in roots,” Current Biology, vol. 27, no. 5. Cell Press, pp. R172–R174,
2017.'
ista: 'von Wangenheim D, Goh T, Dietrich D, Bennett M. 2017. Plant biology: Building
barriers… in roots. Current Biology. 27(5), R172–R174.'
mla: 'von Wangenheim, Daniel, et al. “Plant Biology: Building Barriers… in Roots.”
Current Biology, vol. 27, no. 5, Cell Press, 2017, pp. R172–74, doi:10.1016/j.cub.2017.01.060.'
short: D. von Wangenheim, T. Goh, D. Dietrich, M. Bennett, Current Biology 27 (2017)
R172–R174.
date_created: 2018-12-11T11:46:58Z
date_published: 2017-03-06T00:00:00Z
date_updated: 2021-01-12T08:01:23Z
day: '06'
doi: 10.1016/j.cub.2017.01.060
extern: 1
file:
- access_level: open_access
checksum: 81fd4475c5a2a2c6f4313beeab215ed9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:11Z
date_updated: 2020-07-14T12:46:38Z
file_id: '5330'
file_name: IST-2018-983-v1+1_Plant_biology_Building_barriers__in_roots.pdf
file_size: 2840413
relation: main_file
file_date_updated: 2020-07-14T12:46:38Z
intvolume: ' 27'
issue: '5'
main_file_link:
- open_access: '1'
url: https://repository.ist.ac.at/id/eprint/983
month: '03'
oa: 1
page: R172 - R174
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '7294'
pubrep_id: '983'
quality_controlled: 0
status: public
title: 'Plant biology: Building barriers… in roots'
type: journal_article
volume: 27
year: '2017'
...
---
_id: '529'
abstract:
- lang: eng
text: The pituitary adenylyl cyclase-activating polypeptide (PACAP) and its G protein-coupled
receptors, PAC1, VPAC1 and VPAC2 form a system involved in a variety of biological
processes. Although some sympathetic stimulatory effects of this system have been
reported, its central cardiovascular regulatory properties are poorly characterized.
VPAC1 receptors are expressed in the nucleus ambiguus (nAmb), a key center controlling
cardiac parasympathetic tone. In this study, we report that selective VPAC1 activation
in rhodamine-labeled cardiac vagal preganglionic neurons of the rat nAmb produces
inositol 1,4,5-trisphosphate receptor-mediated Ca2+ mobilization, membrane depolarization
and activation of P/Q-type Ca2+ channels. In vivo, this pathway converges onto
transient reduction in heart rate of conscious rats. Therefore we demonstrate
a VPAC1-dependent mechanism in the central parasympathetic regulation of the heart
rate, adding to the complexity of PACAP-mediated cardiovascular modulation.
acknowledgement: This study was supported by startup funds from the Jefferson College
of Pharmacy, and by the National Institutes of Health DA023204 (to M.E.A) and P30
DA 013429 to Center for Substance Abuse Research, Temple University.
author:
- first_name: Florin
full_name: Gherghina, Florin L
last_name: Gherghina
- first_name: Andrei
full_name: Tica, Andrei A
last_name: Tica
- first_name: Elena
full_name: Elena Deliu
id: 37A40D7E-F248-11E8-B48F-1D18A9856A87
last_name: Deliu
orcid: 0000-0002-7370-5293
- first_name: Mary
full_name: Abood, Mary E
last_name: Abood
- first_name: G.
full_name: Brailoiu, G. Christina
last_name: Brailoiu
- first_name: Eugen
full_name: Brǎiloiu, Eugen
last_name: Brǎiloiu
citation:
ama: Gherghina F, Tica A, Deliu E, Abood M, Brailoiu G, Brǎiloiu E. Effects of VPAC1
activation in nucleus ambiguus neurons. Brain Research. 2017;1657:297-303.
doi:10.1016/j.brainres.2016.12.026
apa: Gherghina, F., Tica, A., Deliu, E., Abood, M., Brailoiu, G., & Brǎiloiu,
E. (2017). Effects of VPAC1 activation in nucleus ambiguus neurons. Brain Research.
Elsevier. https://doi.org/10.1016/j.brainres.2016.12.026
chicago: Gherghina, Florin, Andrei Tica, Elena Deliu, Mary Abood, G. Brailoiu, and
Eugen Brǎiloiu. “Effects of VPAC1 Activation in Nucleus Ambiguus Neurons.” Brain
Research. Elsevier, 2017. https://doi.org/10.1016/j.brainres.2016.12.026.
ieee: F. Gherghina, A. Tica, E. Deliu, M. Abood, G. Brailoiu, and E. Brǎiloiu, “Effects
of VPAC1 activation in nucleus ambiguus neurons,” Brain Research, vol.
1657. Elsevier, pp. 297–303, 2017.
ista: Gherghina F, Tica A, Deliu E, Abood M, Brailoiu G, Brǎiloiu E. 2017. Effects
of VPAC1 activation in nucleus ambiguus neurons. Brain Research. 1657, 297–303.
mla: Gherghina, Florin, et al. “Effects of VPAC1 Activation in Nucleus Ambiguus
Neurons.” Brain Research, vol. 1657, Elsevier, 2017, pp. 297–303, doi:10.1016/j.brainres.2016.12.026.
short: F. Gherghina, A. Tica, E. Deliu, M. Abood, G. Brailoiu, E. Brǎiloiu, Brain
Research 1657 (2017) 297–303.
date_created: 2018-12-11T11:46:59Z
date_published: 2017-02-15T00:00:00Z
date_updated: 2021-01-12T08:01:26Z
day: '15'
doi: 10.1016/j.brainres.2016.12.026
extern: 1
intvolume: ' 1657'
month: '02'
page: 297 - 303
publication: Brain Research
publication_status: published
publisher: Elsevier
publist_id: '7290'
quality_controlled: 0
status: public
title: Effects of VPAC1 activation in nucleus ambiguus neurons
type: journal_article
volume: 1657
year: '2017'
...
---
_id: '534'
abstract:
- lang: eng
text: We investigate the complexity of finding an embedded non-orientable surface
of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural
question in low-dimensional topology, and as a first non-trivial instance of embeddability
of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding
to the relatively few hardness results that are currently known in 3-manifold
topology. In addition, we show that the problem lies in NP when the Euler genus
g is odd, and we give an explicit algorithm in this case.
article_processing_charge: No
article_type: original
author:
- first_name: Benjamin
full_name: Burton, Benjamin
last_name: Burton
- first_name: Arnaud N
full_name: De Mesmay, Arnaud N
id: 3DB2F25C-F248-11E8-B48F-1D18A9856A87
last_name: De Mesmay
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-Manifolds.
Discrete & Computational Geometry. 2017;58(4):871-888. doi:10.1007/s00454-017-9900-0
apa: Burton, B., de Mesmay, A. N., & Wagner, U. (2017). Finding non-orientable
surfaces in 3-Manifolds. Discrete & Computational Geometry. Springer.
https://doi.org/10.1007/s00454-017-9900-0
chicago: Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable
Surfaces in 3-Manifolds.” Discrete & Computational Geometry. Springer,
2017. https://doi.org/10.1007/s00454-017-9900-0.
ieee: B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces
in 3-Manifolds,” Discrete & Computational Geometry, vol. 58, no. 4.
Springer, pp. 871–888, 2017.
ista: Burton B, de Mesmay AN, Wagner U. 2017. Finding non-orientable surfaces in
3-Manifolds. Discrete & Computational Geometry. 58(4), 871–888.
mla: Burton, Benjamin, et al. “Finding Non-Orientable Surfaces in 3-Manifolds.”
Discrete & Computational Geometry, vol. 58, no. 4, Springer, 2017,
pp. 871–88, doi:10.1007/s00454-017-9900-0.
short: B. Burton, A.N. de Mesmay, U. Wagner, Discrete & Computational Geometry
58 (2017) 871–888.
date_created: 2018-12-11T11:47:01Z
date_published: 2017-06-09T00:00:00Z
date_updated: 2023-02-21T17:01:34Z
day: '09'
department:
- _id: UlWa
doi: 10.1007/s00454-017-9900-0
external_id:
arxiv:
- '1602.07907'
intvolume: ' 58'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.07907
month: '06'
oa: 1
oa_version: Preprint
page: 871 - 888
publication: Discrete & Computational Geometry
publication_identifier:
issn:
- '01795376'
publication_status: published
publisher: Springer
publist_id: '7283'
quality_controlled: '1'
related_material:
record:
- id: '1379'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Finding non-orientable surfaces in 3-Manifolds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2017'
...
---
_id: '538'
abstract:
- lang: ger
text: 'Optogenetik und Photopharmakologie ermöglichen präzise räumliche und zeitliche
Kontrolle von Proteinwechselwirkung und -funktion in Zellen und Tieren. Optogenetische
Methoden, die auf grünes Licht ansprechen und zum Trennen von Proteinkomplexen
geeignet sind, sind nichtweitläufig verfügbar, würden jedoch mehrfarbige Experimente
zur Beantwortung von biologischen Fragestellungen ermöglichen. Hier demonstrieren
wir die Verwendung von Cobalamin(Vitamin B12)-bindenden Domänen von bakteriellen
CarH-Transkriptionsfaktoren zur Grünlicht-induzierten Dissoziation von Rezeptoren.
Fusioniert mit dem Fibroblasten-W achstumsfaktor-Rezeptor 1 führten diese im Dunkeln
in kultivierten Zellen zu Signalaktivität durch Oligomerisierung, welche durch
Beleuchten umgehend aufgehoben wurde. In Zebrafischembryonen, die einen derartigen
Rezeptor exprimieren, ermöglichte grünes Licht die Kontrolle über abnormale Signalaktivität
während der Embryonalentwicklung. '
author:
- first_name: Stephanie
full_name: Kainrath, Stephanie
id: 32CFBA64-F248-11E8-B48F-1D18A9856A87
last_name: Kainrath
- first_name: Manuela
full_name: Stadler, Manuela
last_name: Stadler
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
- first_name: Martin
full_name: Distel, Martin
last_name: Distel
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Grünlicht-induzierte
Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie.
2017;129(16):4679-4682. doi:10.1002/ange.201611998
apa: Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak,
H. L. (2017). Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende
Domänen. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201611998
chicago: Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel,
and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende
Domänen.” Angewandte Chemie. Wiley, 2017. https://doi.org/10.1002/ange.201611998.
ieee: S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak,
“Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen,”
Angewandte Chemie, vol. 129, no. 16. Wiley, pp. 4679–4682, 2017.
ista: Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017.
Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte
Chemie. 129(16), 4679–4682.
mla: Kainrath, Stephanie, et al. “Grünlicht-Induzierte Rezeptorinaktivierung Durch
Cobalamin-Bindende Domänen.” Angewandte Chemie, vol. 129, no. 16, Wiley,
2017, pp. 4679–82, doi:10.1002/ange.201611998.
short: S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak,
Angewandte Chemie 129 (2017) 4679–4682.
date_created: 2018-12-11T11:47:02Z
date_published: 2017-05-20T00:00:00Z
date_updated: 2021-01-12T08:01:33Z
day: '20'
ddc:
- '571'
department:
- _id: CaGu
- _id: HaJa
doi: 10.1002/ange.201611998
ec_funded: 1
file:
- access_level: open_access
checksum: d66fee867e7cdbfa3fe276c2fb0778bb
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call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
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call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Angewandte Chemie
publication_status: published
publisher: Wiley
publist_id: '7279'
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quality_controlled: '1'
status: public
title: Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen
tmp:
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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: 129
year: '2017'
...
---
_id: '540'
abstract:
- lang: eng
text: RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of
RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis
virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection.
A major genetic determinant for its ability to persist maps to a single amino
acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional
consequences remain elusive. To unravel the L protein interactions with the host
proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics.
A subsequent mass-spectrometric analysis of L protein pulldowns from infected
human cells revealed a comprehensive network of interacting host proteins. The
obtained LCMV L protein interactome was bioinformatically integrated with known
host protein interactors of RdRps from other RNA viruses, emphasizing interconnected
modules of human proteins. Functional characterization of selected interactors
highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors.
To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired
virus control in chronic infection. These results provide insights into the complex
interactions of the arenavirus LCMV and other viral RdRps with the host proteome
and contribute to a better molecular understanding of how chronic viruses interact
with their host.
article_number: e1006758
author:
- first_name: Kseniya
full_name: Khamina, Kseniya
last_name: Khamina
- first_name: Alexander
full_name: Lercher, Alexander
last_name: Lercher
- first_name: Michael
full_name: Caldera, Michael
last_name: Caldera
- first_name: Christopher
full_name: Schliehe, Christopher
last_name: Schliehe
- first_name: Bojan
full_name: Vilagos, Bojan
last_name: Vilagos
- first_name: Mehmet
full_name: Sahin, Mehmet
last_name: Sahin
- first_name: Lindsay
full_name: Kosack, Lindsay
last_name: Kosack
- first_name: Anannya
full_name: Bhattacharya, Anannya
last_name: Bhattacharya
- first_name: Peter
full_name: Májek, Peter
last_name: Májek
- first_name: Alexey
full_name: Stukalov, Alexey
last_name: Stukalov
- first_name: Roberto
full_name: Sacco, Roberto
id: 42C9F57E-F248-11E8-B48F-1D18A9856A87
last_name: Sacco
- first_name: Leo
full_name: James, Leo
last_name: James
- first_name: Daniel
full_name: Pinschewer, Daniel
last_name: Pinschewer
- first_name: Keiryn
full_name: Bennett, Keiryn
last_name: Bennett
- first_name: Jörg
full_name: Menche, Jörg
last_name: Menche
- first_name: Andreas
full_name: Bergthaler, Andreas
last_name: Bergthaler
citation:
ama: Khamina K, Lercher A, Caldera M, et al. Characterization of host proteins interacting
with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens.
2017;13(12). doi:10.1371/journal.ppat.1006758
apa: Khamina, K., Lercher, A., Caldera, M., Schliehe, C., Vilagos, B., Sahin, M.,
… Bergthaler, A. (2017). Characterization of host proteins interacting with the
lymphocytic choriomeningitis virus L protein. PLoS Pathogens. Public Library
of Science. https://doi.org/10.1371/journal.ppat.1006758
chicago: Khamina, Kseniya, Alexander Lercher, Michael Caldera, Christopher Schliehe,
Bojan Vilagos, Mehmet Sahin, Lindsay Kosack, et al. “Characterization of Host
Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS
Pathogens. Public Library of Science, 2017. https://doi.org/10.1371/journal.ppat.1006758.
ieee: K. Khamina et al., “Characterization of host proteins interacting with
the lymphocytic choriomeningitis virus L protein,” PLoS Pathogens, vol.
13, no. 12. Public Library of Science, 2017.
ista: Khamina K, Lercher A, Caldera M, Schliehe C, Vilagos B, Sahin M, Kosack L,
Bhattacharya A, Májek P, Stukalov A, Sacco R, James L, Pinschewer D, Bennett K,
Menche J, Bergthaler A. 2017. Characterization of host proteins interacting with
the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 13(12), e1006758.
mla: Khamina, Kseniya, et al. “Characterization of Host Proteins Interacting with
the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens, vol.
13, no. 12, e1006758, Public Library of Science, 2017, doi:10.1371/journal.ppat.1006758.
short: K. Khamina, A. Lercher, M. Caldera, C. Schliehe, B. Vilagos, M. Sahin, L.
Kosack, A. Bhattacharya, P. Májek, A. Stukalov, R. Sacco, L. James, D. Pinschewer,
K. Bennett, J. Menche, A. Bergthaler, PLoS Pathogens 13 (2017).
date_created: 2018-12-11T11:47:03Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:01:48Z
day: '01'
ddc:
- '576'
- '616'
department:
- _id: GaNo
doi: 10.1371/journal.ppat.1006758
file:
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checksum: 1aa20f19a1e90664fadce6e7d5284fdc
content_type: application/pdf
creator: system
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date_updated: 2020-07-14T12:46:44Z
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file_date_updated: 2020-07-14T12:46:44Z
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intvolume: ' 13'
issue: '12'
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- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: PLoS Pathogens
publication_identifier:
issn:
- '15537366'
publication_status: published
publisher: Public Library of Science
publist_id: '7276'
pubrep_id: '931'
quality_controlled: '1'
scopus_import: 1
status: public
title: Characterization of host proteins interacting with the lymphocytic choriomeningitis
virus L protein
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '466'
abstract:
- lang: eng
text: 'We consider Markov decision processes (MDPs) with multiple limit-average
(or mean-payoff) objectives. There exist two different views: (i) the expectation
semantics, where the goal is to optimize the expected mean-payoff objective, and
(ii) the satisfaction semantics, where the goal is to maximize the probability
of runs such that the mean-payoff value stays above a given vector. We consider
optimization with respect to both objectives at once, thus unifying the existing
semantics. Precisely, the goal is to optimize the expectation while ensuring the
satisfaction constraint. Our problem captures the notion of optimization with
respect to strategies that are risk-averse (i.e., ensure certain probabilistic
guarantee). Our main results are as follows: First, we present algorithms for
the decision problems which are always polynomial in the size of the MDP. We also
show that an approximation of the Pareto-curve can be computed in time polynomial
in the size of the MDP, and the approximation factor, but exponential in the number
of dimensions. Second, we present a complete characterization of the strategy
complexity (in terms of memory bounds and randomization) required to solve our
problem. '
article_number: '15'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Zuzana
full_name: Křetínská, Zuzana
last_name: Křetínská
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: Chatterjee K, Křetínská Z, Kretinsky J. Unifying two views on multiple mean-payoff
objectives in Markov decision processes. Logical Methods in Computer Science.
2017;13(2). doi:10.23638/LMCS-13(2:15)2017
apa: Chatterjee, K., Křetínská, Z., & Kretinsky, J. (2017). Unifying two views
on multiple mean-payoff objectives in Markov decision processes. Logical Methods
in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(2:15)2017
chicago: Chatterjee, Krishnendu, Zuzana Křetínská, and Jan Kretinsky. “Unifying
Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical
Methods in Computer Science. International Federation of Computational Logic,
2017. https://doi.org/10.23638/LMCS-13(2:15)2017.
ieee: K. Chatterjee, Z. Křetínská, and J. Kretinsky, “Unifying two views on multiple
mean-payoff objectives in Markov decision processes,” Logical Methods in Computer
Science, vol. 13, no. 2. International Federation of Computational Logic,
2017.
ista: Chatterjee K, Křetínská Z, Kretinsky J. 2017. Unifying two views on multiple
mean-payoff objectives in Markov decision processes. Logical Methods in Computer
Science. 13(2), 15.
mla: Chatterjee, Krishnendu, et al. “Unifying Two Views on Multiple Mean-Payoff
Objectives in Markov Decision Processes.” Logical Methods in Computer Science,
vol. 13, no. 2, 15, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(2:15)2017.
short: K. Chatterjee, Z. Křetínská, J. Kretinsky, Logical Methods in Computer Science
13 (2017).
date_created: 2018-12-11T11:46:38Z
date_published: 2017-07-03T00:00:00Z
date_updated: 2023-02-23T12:26:16Z
day: '03'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.23638/LMCS-13(2:15)2017
ec_funded: 1
file:
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checksum: bfa405385ec6229ad5ead89ab5751639
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:32Z
date_updated: 2020-07-14T12:46:33Z
file_id: '5354'
file_name: IST-2018-957-v1+1_2017_Chatterjee_Unifying_two.pdf
file_size: 511832
relation: main_file
file_date_updated: 2020-07-14T12:46:33Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '2'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
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call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
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call_identifier: H2020
grant_number: '701309'
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
(H2020)
publication: Logical Methods in Computer Science
publication_identifier:
issn:
- '18605974'
publication_status: published
publisher: International Federation of Computational Logic
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scopus_import: 1
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title: Unifying two views on multiple mean-payoff objectives in Markov decision processes
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type: journal_article
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volume: 13
year: '2017'
...
---
_id: '467'
abstract:
- lang: eng
text: Recently there has been a significant effort to handle quantitative properties
in formal verification and synthesis. While weighted automata over finite and
infinite words provide a natural and flexible framework to express quantitative
properties, perhaps surprisingly, some basic system properties such as average
response time cannot be expressed using weighted automata or in any other known
decidable formalism. In this work, we introduce nested weighted automata as a
natural extension of weighted automata, which makes it possible to express important
quantitative properties such as average response time. In nested weighted automata,
a master automaton spins off and collects results from weighted slave automata,
each of which computes a quantity along a finite portion of an infinite word.
Nested weighted automata can be viewed as the quantitative analogue of monitor
automata, which are used in runtime verification. We establish an almost-complete
decidability picture for the basic decision problems about nested weighted automata
and illustrate their applicability in several domains. In particular, nested weighted
automata can be used to decide average response time properties.
article_number: '31'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. ACM Transactions
on Computational Logic (TOCL). 2017;18(4). doi:10.1145/3152769
apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Nested weighted automata.
ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3152769
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted
Automata.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3152769.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” ACM
Transactions on Computational Logic (TOCL), vol. 18, no. 4. ACM, 2017.
ista: Chatterjee K, Henzinger TA, Otop J. 2017. Nested weighted automata. ACM Transactions
on Computational Logic (TOCL). 18(4), 31.
mla: Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” ACM Transactions
on Computational Logic (TOCL), vol. 18, no. 4, 31, ACM, 2017, doi:10.1145/3152769.
short: K. Chatterjee, T.A. Henzinger, J. Otop, ACM Transactions on Computational
Logic (TOCL) 18 (2017).
date_created: 2018-12-11T11:46:38Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-02-23T12:26:19Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1145/3152769
ec_funded: 1
external_id:
arxiv:
- '1606.03598'
intvolume: ' 18'
issue: '4'
language:
- iso: eng
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url: https://arxiv.org/abs/1606.03598
month: '12'
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oa_version: Preprint
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call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: ACM Transactions on Computational Logic (TOCL)
publication_identifier:
issn:
- '15293785'
publication_status: published
publisher: ACM
publist_id: '7354'
quality_controlled: '1'
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scopus_import: 1
status: public
title: Nested weighted automata
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2017'
...
---
_id: '465'
abstract:
- lang: eng
text: 'The edit distance between two words w 1 , w 2 is the minimal number of word
operations (letter insertions, deletions, and substitutions) necessary to transform
w 1 to w 2 . The edit distance generalizes to languages L 1 , L 2 , where the
edit distance from L 1 to L 2 is the minimal number k such that for every word
from L 1 there exists a word in L 2 with edit distance at most k . We study the
edit distance computation problem between pushdown automata and their subclasses.
The problem of computing edit distance to a pushdown automaton is undecidable,
and in practice, the interesting question is to compute the edit distance from
a pushdown automaton (the implementation, a standard model for programs with recursion)
to a regular language (the specification). In this work, we present a complete
picture of decidability and complexity for the following problems: (1) deciding
whether, for a given threshold k , the edit distance from a pushdown automaton
to a finite automaton is at most k , and (2) deciding whether the edit distance
from a pushdown automaton to a finite automaton is finite. '
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Jan
full_name: Otop, Jan
last_name: Otop
citation:
ama: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown
automata. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:23)2017
apa: Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2017).
Edit distance for pushdown automata. Logical Methods in Computer Science.
International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:23)2017
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan
Otop. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science.
International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:23)2017.
ieee: K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance
for pushdown automata,” Logical Methods in Computer Science, vol. 13, no.
3. International Federation of Computational Logic, 2017.
ista: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2017. Edit distance for
pushdown automata. Logical Methods in Computer Science. 13(3).
mla: Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” Logical
Methods in Computer Science, vol. 13, no. 3, International Federation of Computational
Logic, 2017, doi:10.23638/LMCS-13(3:23)2017.
short: K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Logical Methods
in Computer Science 13 (2017).
date_created: 2018-12-11T11:46:37Z
date_published: 2017-09-13T00:00:00Z
date_updated: 2023-02-23T12:26:25Z
day: '13'
ddc:
- '004'
department:
- _id: KrCh
- _id: ToHe
doi: 10.23638/LMCS-13(3:23)2017
ec_funded: 1
file:
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checksum: 08041379ba408d40664f449eb5907a8f
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creator: system
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month: '09'
oa: 1
oa_version: Published Version
project:
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call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
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call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
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call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
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name: 'Quantitative Graph Games: Theory and Applications'
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call_identifier: FWF
grant_number: S11407
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image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '512'
abstract:
- lang: eng
text: 'The fixation probability is the probability that a new mutant introduced
in a homogeneous population eventually takes over the entire population. The fixation
probability is a fundamental quantity of natural selection, and known to depend
on the population structure. Amplifiers of natural selection are population structures
which increase the fixation probability of advantageous mutants, as compared to
the baseline case of well-mixed populations. In this work we focus on symmetric
population structures represented as undirected graphs. In the regime of undirected
graphs, the strongest amplifier known has been the Star graph, and the existence
of undirected graphs with stronger amplification properties has remained open
for over a decade. In this work we present the Comet and Comet-swarm families
of undirected graphs. We show that for a range of fitness values of the mutants,
the Comet and Cometswarm graphs have fixation probability strictly larger than
the fixation probability of the Star graph, for fixed population size and at the
limit of large populations, respectively. '
article_number: '82'
article_processing_charge: No
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: 'Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Amplification on undirected
population structures: Comets beat stars. Scientific Reports. 2017;7(1).
doi:10.1038/s41598-017-00107-w'
apa: 'Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2017). Amplification
on undirected population structures: Comets beat stars. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/s41598-017-00107-w'
chicago: 'Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin
Nowak. “Amplification on Undirected Population Structures: Comets Beat Stars.”
Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/s41598-017-00107-w.'
ieee: 'A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, “Amplification
on undirected population structures: Comets beat stars,” Scientific Reports,
vol. 7, no. 1. Nature Publishing Group, 2017.'
ista: 'Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2017. Amplification on
undirected population structures: Comets beat stars. Scientific Reports. 7(1),
82.'
mla: 'Pavlogiannis, Andreas, et al. “Amplification on Undirected Population Structures:
Comets Beat Stars.” Scientific Reports, vol. 7, no. 1, 82, Nature Publishing
Group, 2017, doi:10.1038/s41598-017-00107-w.'
short: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Scientific Reports
7 (2017).
date_created: 2018-12-11T11:46:53Z
date_published: 2017-03-06T00:00:00Z
date_updated: 2023-02-23T12:26:57Z
day: '06'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1038/s41598-017-00107-w
ec_funded: 1
file:
- access_level: open_access
checksum: 7d05cbdd914e194a019c0f91fb64e9a8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:35Z
date_updated: 2020-07-14T12:46:36Z
file_id: '5357'
file_name: IST-2018-938-v1+1_2017_Pavlogiannis_Amplification_on.pdf
file_size: 1536783
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Scientific Reports
publication_identifier:
issn:
- '20452322'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7307'
pubrep_id: '938'
quality_controlled: '1'
related_material:
record:
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relation: earlier_version
status: public
scopus_import: 1
status: public
title: 'Amplification on undirected population structures: Comets beat stars'
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: 7
year: '2017'
...
---
_id: '10416'
abstract:
- lang: eng
text: 'A fundamental algorithmic problem at the heart of static analysis is Dyck
reachability. The input is a graph where the edges are labeled with different
types of opening and closing parentheses, and the reachability information is
computed via paths whose parentheses are properly matched. We present new results
for Dyck reachability problems with applications to alias analysis and data-dependence
analysis. Our main contributions, that include improved upper bounds as well as
lower bounds that establish optimality guarantees, are as follows: First, we consider
Dyck reachability on bidirected graphs, which is the standard way of performing
field-sensitive points-to analysis. Given a bidirected graph with n nodes and
m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)),
where α(n) is the inverse Ackermann function, improving the previously known O(n2)
time bound; (ii) a matching lower bound that shows that our algorithm is optimal
wrt to worst-case complexity; and (iii) an optimal average-case upper bound of
O(m) time, improving the previously known O(m · logn) bound. Second, we consider
the problem of context-sensitive data-dependence analysis, where the task is to
obtain analysis summaries of library code in the presence of callbacks. Our algorithm
preprocesses libraries in almost linear time, after which the contribution of
the library in the complexity of the client analysis is only linear, and only
wrt the number of call sites. Third, we prove that combinatorial algorithms for
Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained
without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication,
which is a long-standing open problem. Thus we establish that the existing combinatorial
algorithms for Dyck reachability are (conditionally) optimal for general graphs.
We also show that the same hardness holds for graphs of constant treewidth. Finally,
we provide a prototype implementation of our algorithms for both alias analysis
and data-dependence analysis. Our experimental evaluation demonstrates that the
new algorithms significantly outperform all existing methods on the two problems,
over real-world benchmarks.'
acknowledgement: "The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant
(279307: Graph Games).\r\n"
article_number: '30'
article_processing_charge: No
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Bhavya
full_name: Choudhary, Bhavya
last_name: Choudhary
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck reachability for data-dependence
and Alias analysis. Proceedings of the ACM on Programming Languages. 2017;2(POPL).
doi:10.1145/3158118
apa: 'Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck
reachability for data-dependence and Alias analysis. Proceedings of the ACM
on Programming Languages. Los Angeles, CA, United States: Association for
Computing Machinery. https://doi.org/10.1145/3158118'
chicago: Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. “Optimal
Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the
ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158118.
ieee: K. Chatterjee, B. Choudhary, and A. Pavlogiannis, “Optimal Dyck reachability
for data-dependence and Alias analysis,” Proceedings of the ACM on Programming
Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.
ista: Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability
for data-dependence and Alias analysis. Proceedings of the ACM on Programming
Languages. 2(POPL), 30.
mla: Chatterjee, Krishnendu, et al. “Optimal Dyck Reachability for Data-Dependence
and Alias Analysis.” Proceedings of the ACM on Programming Languages, vol.
2, no. POPL, 30, Association for Computing Machinery, 2017, doi:10.1145/3158118.
short: K. Chatterjee, B. Choudhary, A. Pavlogiannis, Proceedings of the ACM on Programming
Languages 2 (2017).
conference:
end_date: 2018-01-13
location: Los Angeles, CA, United States
name: 'POPL: Programming Languages'
start_date: 2018-01-07
date_created: 2021-12-05T23:01:48Z
date_published: 2017-12-27T00:00:00Z
date_updated: 2023-02-23T12:27:13Z
day: '27'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3158118
ec_funded: 1
external_id:
arxiv:
- '1910.00241'
file:
- access_level: open_access
checksum: faa3f7b3fe8aab84b50ed805c26a0ee5
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-07T08:06:28Z
date_updated: 2021-12-07T08:06:28Z
file_id: '10421'
file_name: 2017_ACMProgLang_Chatterjee.pdf
file_size: 460188
relation: main_file
success: 1
file_date_updated: 2021-12-07T08:06:28Z
has_accepted_license: '1'
intvolume: ' 2'
issue: POPL
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '5455'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Optimal Dyck reachability for data-dependence and Alias analysis
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: 2
year: '2017'
...
---
_id: '5455'
abstract:
- lang: eng
text: 'A fundamental algorithmic problem at the heart of static analysis is Dyck
reachability. The input is a graphwhere the edges are labeled with different types
of opening and closing parentheses, and the reachabilityinformation is computed
via paths whose parentheses are properly matched. We present new results for Dyckreachability
problems with applications to alias analysis and data-dependence analysis. Our
main contributions,that include improved upper bounds as well as lower bounds
that establish optimality guarantees, are asfollows:First, we consider Dyck reachability
on bidirected graphs, which is the standard way of performing field-sensitive
points-to analysis. Given a bidirected graph withnnodes andmedges, we present:
(i) an algorithmwith worst-case running timeO(m+n·α(n)), whereα(n)is the inverse
Ackermann function, improving thepreviously knownO(n2)time bound; (ii) a matching
lower bound that shows that our algorithm is optimalwrt to worst-case complexity;
and (iii) an optimal average-case upper bound ofO(m)time, improving thepreviously
knownO(m·logn)bound.Second, we consider the problem of context-sensitive data-dependence
analysis, where the task is to obtainanalysis summaries of library code in the
presence of callbacks. Our algorithm preprocesses libraries in almostlinear time,
after which the contribution of the library in the complexity of the client analysis
is only linear,and only wrt the number of call sites.Third, we prove that combinatorial
algorithms for Dyck reachability on general graphs with truly sub-cubic bounds
cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean
MatrixMultiplication, which is a long-standing open problem. Thus we establish
that the existing combinatorialalgorithms for Dyck reachability are (conditionally)
optimal for general graphs. We also show that the samehardness holds for graphs
of constant treewidth.Finally, we provide a prototype implementation of our algorithms
for both alias analysis and data-dependenceanalysis. Our experimental evaluation
demonstrates that the new algorithms significantly outperform allexisting methods
on the two problems, over real-world benchmarks.'
alternative_title:
- IST Austria Technical Report
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Bhavya
full_name: Choudhary, Bhavya
last_name: Choudhary
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck Reachability for
Data-Dependence and Alias Analysis. IST Austria; 2017. doi:10.15479/AT:IST-2017-870-v1-1
apa: Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck
reachability for data-dependence and alias analysis. IST Austria. https://doi.org/10.15479/AT:IST-2017-870-v1-1
chicago: Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. Optimal
Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017.
https://doi.org/10.15479/AT:IST-2017-870-v1-1.
ieee: K. Chatterjee, B. Choudhary, and A. Pavlogiannis, Optimal Dyck reachability
for data-dependence and alias analysis. IST Austria, 2017.
ista: Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability
for data-dependence and alias analysis, IST Austria, 37p.
mla: Chatterjee, Krishnendu, et al. Optimal Dyck Reachability for Data-Dependence
and Alias Analysis. IST Austria, 2017, doi:10.15479/AT:IST-2017-870-v1-1.
short: K. Chatterjee, B. Choudhary, A. Pavlogiannis, Optimal Dyck Reachability for
Data-Dependence and Alias Analysis, IST Austria, 2017.
date_created: 2018-12-12T11:39:26Z
date_published: 2017-10-23T00:00:00Z
date_updated: 2023-02-21T15:54:10Z
day: '23'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2017-870-v1-1
file:
- access_level: open_access
checksum: 177a84a46e3ac17e87b31534ad16a4c9
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:02Z
date_updated: 2020-07-14T12:46:59Z
file_id: '5524'
file_name: IST-2017-870-v1+1_main.pdf
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file_date_updated: 2020-07-14T12:46:59Z
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language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '37'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '870'
related_material:
record:
- id: '10416'
relation: later_version
status: public
status: public
title: Optimal Dyck reachability for data-dependence and alias analysis
type: technical_report
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2017'
...
---
_id: '5450'
abstract:
- lang: eng
text: 'In this report the implementation of the institutional data repository IST
DataRep at IST Austria will be covered: Starting with the research phase when
requirements for a repository were established, the procedure of choosing a repository-software
and its customization based on the results of user-testings will be discussed.
Followed by reflections on the marketing strategies in regard of impact, and at
the end sharing some experiences of one year operating IST DataRep.'
author:
- first_name: Barbara
full_name: Barbara Petritsch
id: 406048EC-F248-11E8-B48F-1D18A9856A87
last_name: Petritsch
orcid: 0000-0003-2724-4614
citation:
ama: Petritsch B. Implementing the Institutional Data Repository IST DataRep.
IST Austria; 2017.
apa: Petritsch, B. (2017). Implementing the institutional data repository IST
DataRep. IST Austria.
chicago: Petritsch, Barbara. Implementing the Institutional Data Repository IST
DataRep. IST Austria, 2017.
ieee: B. Petritsch, Implementing the institutional data repository IST DataRep.
IST Austria, 2017.
ista: Petritsch B. 2017. Implementing the institutional data repository IST DataRep,
IST Austria,p.
mla: Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep.
IST Austria, 2017.
short: B. Petritsch, Implementing the Institutional Data Repository IST DataRep,
IST Austria, 2017.
date_created: 2018-12-12T11:39:24Z
date_published: 2017-06-26T00:00:00Z
date_updated: 2020-07-14T23:05:03Z
day: '26'
department:
- _id: E-Lib
extern: 0
file:
- access_level: open_access
checksum: 6321792dcfa82bf490f17615a9b22355
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:22Z
date_updated: 2020-07-14T12:46:59Z
file_id: '5483'
file_name: IST-2017-724-v1+1_DataRep_Project_Report_2017.pdf
file_size: 3460985
relation: main_file
file_date_updated: 2020-07-14T12:46:59Z
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url: https://repository.ist.ac.at/id/eprint/724.
month: '06'
oa: 1
publication_date: 2017-06-26
publisher: IST Austria
pubrep_id: '724'
status: public
title: Implementing the institutional data repository IST DataRep
type: report
year: '2017'
...
---
_id: '10417'
abstract:
- lang: eng
text: "We present a new dynamic partial-order reduction method for stateless model
checking of concurrent programs. A common approach for exploring program behaviors
relies on enumerating the traces of the program, without storing the visited states
(aka stateless exploration). As the number of distinct traces grows exponentially,
dynamic partial-order reduction (DPOR) techniques have been successfully used
to partition the space of traces into equivalence classes (Mazurkiewicz partitioning),
with the goal of exploring only few representative traces from each class.\r\n\r\nWe
introduce a new equivalence on traces under sequential consistency semantics,
which we call the observation equivalence. Two traces are observationally equivalent
if every read event observes the same write event in both traces. While the traditional
Mazurkiewicz equivalence is control-centric, our new definition is data-centric.
We show that our observation equivalence is coarser than the Mazurkiewicz equivalence,
and in many cases even exponentially coarser. We devise a DPOR exploration of
the trace space, called data-centric DPOR, based on the observation equivalence."
acknowledgement: "The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant
(279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061."
article_number: '31'
article_processing_charge: No
article_type: original
author:
- first_name: Marek
full_name: Chalupa, Marek
last_name: Chalupa
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Nishant
full_name: Sinha, Nishant
last_name: Sinha
- first_name: Kapil
full_name: Vaidya, Kapil
last_name: Vaidya
citation:
ama: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic
partial order reduction. Proceedings of the ACM on Programming Languages.
2017;2(POPL). doi:10.1145/3158119
apa: 'Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K.
(2017). Data-centric dynamic partial order reduction. Proceedings of the ACM
on Programming Languages. Los Angeles, CA, United States: Association for
Computing Machinery. https://doi.org/10.1145/3158119'
chicago: Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha,
and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings
of the ACM on Programming Languages. Association for Computing Machinery,
2017. https://doi.org/10.1145/3158119.
ieee: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric
dynamic partial order reduction,” Proceedings of the ACM on Programming Languages,
vol. 2, no. POPL. Association for Computing Machinery, 2017.
ista: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric
dynamic partial order reduction. Proceedings of the ACM on Programming Languages.
2(POPL), 31.
mla: Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings
of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for
Computing Machinery, 2017, doi:10.1145/3158119.
short: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings
of the ACM on Programming Languages 2 (2017).
conference:
end_date: 2018-01-13
location: Los Angeles, CA, United States
name: 'POPL: Programming Languages'
start_date: 2018-01-07
date_created: 2021-12-05T23:01:49Z
date_published: 2017-12-27T00:00:00Z
date_updated: 2023-02-23T12:27:16Z
day: '27'
department:
- _id: KrCh
doi: 10.1145/3158119
ec_funded: 1
external_id:
arxiv:
- '1610.01188'
intvolume: ' 2'
issue: POPL
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://dl.acm.org/doi/10.1145/3158119
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '5448'
relation: earlier_version
status: public
- id: '5456'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Data-centric dynamic partial order reduction
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2
year: '2017'
...
---
_id: '5456'
abstract:
- lang: eng
text: "We present a new dynamic partial-order reduction method for stateless model
checking of concurrent programs. A common approach for exploring program behaviors
relies on enumerating the traces of the program, without storing the visited states
(aka stateless exploration). As the number of distinct traces grows exponentially,
dynamic partial-order reduction (DPOR) techniques have been successfully used
to partition the space of traces into equivalence classes (Mazurkiewicz partitioning),
with the goal of exploring only few representative traces from each class.\r\nWe
introduce a new equivalence on traces under sequential consistency semantics,
which we call the observation equivalence. Two traces are observationally equivalent
if every read event observes the same write event in both traces. While the traditional
Mazurkiewicz equivalence is control-centric, our new definition is data-centric.
We show that our observation equivalence is coarser than the Mazurkiewicz equivalence,
and in many cases even exponentially coarser. We devise a DPOR exploration of
the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1.
For acyclic architectures, our algorithm is guaranteed to explore exactly one
representative trace from each observation class, while spending polynomial time
per class. Hence, our algorithm is optimal wrt the observation equivalence, and
in several cases explores exponentially fewer traces than any enumerative method
based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider
an equivalence between traces which is finer than the observation equivalence;
but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially
coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence.
\r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based
DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show
a significant reduction in both running time and the number of explored equivalence
classes."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Marek
full_name: Chalupa, Marek
last_name: Chalupa
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Nishant
full_name: Sinha, Nishant
last_name: Sinha
- first_name: Kapil
full_name: Vaidya, Kapil
last_name: Vaidya
citation:
ama: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-Centric
Dynamic Partial Order Reduction. IST Austria; 2017. doi:10.15479/AT:IST-2017-872-v1-1
apa: Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K.
(2017). Data-centric dynamic partial order reduction. IST Austria. https://doi.org/10.15479/AT:IST-2017-872-v1-1
chicago: Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha,
and Kapil Vaidya. Data-Centric Dynamic Partial Order Reduction. IST Austria,
2017. https://doi.org/10.15479/AT:IST-2017-872-v1-1.
ieee: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, Data-centric
dynamic partial order reduction. IST Austria, 2017.
ista: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric
dynamic partial order reduction, IST Austria, 36p.
mla: Chalupa, Marek, et al. Data-Centric Dynamic Partial Order Reduction.
IST Austria, 2017, doi:10.15479/AT:IST-2017-872-v1-1.
short: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Data-Centric
Dynamic Partial Order Reduction, IST Austria, 2017.
date_created: 2018-12-12T11:39:26Z
date_published: 2017-10-23T00:00:00Z
date_updated: 2023-02-23T12:26:54Z
day: '23'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2017-872-v1-1
file:
- access_level: open_access
checksum: d2635c4cf013000f0a1b09e80f9e4ab7
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:26Z
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language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '36'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '872'
related_material:
record:
- id: '10417'
relation: later_version
status: public
- id: '5448'
relation: earlier_version
status: public
status: public
title: Data-centric dynamic partial order reduction
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '551'
abstract:
- lang: eng
text: 'Evolutionary graph theory studies the evolutionary dynamics in a population
structure given as a connected graph. Each node of the graph represents an individual
of the population, and edges determine how offspring are placed. We consider the
classical birth-death Moran process where there are two types of individuals,
namely, the residents with fitness 1 and mutants with fitness r. The fitness indicates
the reproductive strength. The evolutionary dynamics happens as follows: in the
initial step, in a population of all resident individuals a mutant is introduced,
and then at each step, an individual is chosen proportional to the fitness of
its type to reproduce, and the offspring replaces a neighbor uniformly at random.
The process stops when all individuals are either residents or mutants. The probability
that all individuals in the end are mutants is called the fixation probability,
which is a key factor in the rate of evolution. We consider the problem of approximating
the fixation probability. The class of algorithms that is extremely relevant for
approximation of the fixation probabilities is the Monte-Carlo simulation of the
process. Previous results present a polynomial-time Monte-Carlo algorithm for
undirected graphs when r is given in unary. First, we present a simple modification:
instead of simulating each step, we discard ineffective steps, where no node changes
type (i.e., either residents replace residents, or mutants replace mutants). Using
the above simple modification and our result that the number of effective steps
is concentrated around the expected number of effective steps, we present faster
polynomial-time Monte-Carlo algorithms for undirected graphs. Our algorithms are
always at least a factor O(n2/ log n) faster as compared to the previous algorithms,
where n is the number of nodes, and is polynomial even if r is given in binary.
We also present lower bounds showing that the upper bound on the expected number
of effective steps we present is asymptotically tight for undirected graphs. '
alternative_title:
- LIPIcs
article_number: '61'
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: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: 'Chatterjee K, Ibsen-Jensen R, Nowak M. Faster Monte Carlo algorithms for fixation
probability of the Moran process on undirected graphs. In: Leibniz International
Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.61'
apa: 'Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2017). Faster Monte Carlo
algorithms for fixation probability of the Moran process on undirected graphs.
In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg,
Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.61'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. “Faster
Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected
Graphs.” In Leibniz International Proceedings in Informatics, Vol. 83.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.61.
ieee: K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, “Faster Monte Carlo algorithms
for fixation probability of the Moran process on undirected graphs,” in Leibniz
International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.
ista: 'Chatterjee K, Ibsen-Jensen R, Nowak M. 2017. Faster Monte Carlo algorithms
for fixation probability of the Moran process on undirected graphs. Leibniz International
Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science
(SG), LIPIcs, vol. 83, 61.'
mla: Chatterjee, Krishnendu, et al. “Faster Monte Carlo Algorithms for Fixation
Probability of the Moran Process on Undirected Graphs.” Leibniz International
Proceedings in Informatics, vol. 83, 61, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.61.
short: K. Chatterjee, R. Ibsen-Jensen, M. Nowak, in:, Leibniz International Proceedings
in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.
conference:
end_date: 2017-08-25
location: Aalborg, Denmark
name: 'MFCS: Mathematical Foundations of Computer Science (SG)'
start_date: 2017-08-21
date_created: 2018-12-11T11:47:08Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2021-01-12T08:02:34Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.MFCS.2017.61
file:
- access_level: open_access
checksum: 2eed5224c0e4e259484a1d71acb8ba6a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:04Z
date_updated: 2020-07-14T12:47:00Z
file_id: '5322'
file_name: IST-2018-924-v1+1_LIPIcs-MFCS-2017-61.pdf
file_size: 535077
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
has_accepted_license: '1'
intvolume: ' 83'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Leibniz International Proceedings in Informatics
publication_identifier:
isbn:
- 978-395977046-0
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7263'
pubrep_id: '924'
quality_controlled: '1'
scopus_import: 1
status: public
title: Faster Monte Carlo algorithms for fixation probability of the Moran process
on undirected graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 83
year: '2017'
...
---
_id: '552'
abstract:
- lang: eng
text: 'Graph games provide the foundation for modeling and synthesis of reactive
processes. Such games are played over graphs where the vertices are controlled
by two adversarial players. We consider graph games where the objective of the
first player is the conjunction of a qualitative objective (specified as a parity
condition) and a quantitative objective (specified as a meanpayoff condition).
There are two variants of the problem, namely, the threshold problem where the
quantitative goal is to ensure that the mean-payoff value is above a threshold,
and the value problem where the quantitative goal is to ensure the optimal mean-payoff
value; in both cases ensuring the qualitative parity objective. The previous best-known
algorithms for game graphs with n vertices, m edges, parity objectives with d
priorities, and maximal absolute reward value W for mean-payoff objectives, are
as follows: O(nd+1 . m . w) for the threshold problem, and O(nd+2 · m · W) for
the value problem. Our main contributions are faster algorithms, and the running
times of our algorithms are as follows: O(nd-1 · m ·W) for the threshold problem,
and O(nd · m · W · log(n · W)) for the value problem. For mean-payoff parity objectives
with two priorities, our algorithms match the best-known bounds of the algorithms
for mean-payoff games (without conjunction with parity objectives). Our results
are relevant in synthesis of reactive systems with both functional requirement
(given as a qualitative objective) and performance requirement (given as a quantitative
objective).'
alternative_title:
- LIPIcs
article_number: '39'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Alexander
full_name: Svozil, Alexander
last_name: Svozil
citation:
ama: 'Chatterjee K, Henzinger MH, Svozil A. Faster algorithms for mean-payoff parity
games. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.39'
apa: 'Chatterjee, K., Henzinger, M. H., & Svozil, A. (2017). Faster algorithms
for mean-payoff parity games. In Leibniz International Proceedings in Informatics
(Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.MFCS.2017.39'
chicago: Chatterjee, Krishnendu, Monika H Henzinger, and Alexander Svozil. “Faster
Algorithms for Mean-Payoff Parity Games.” In Leibniz International Proceedings
in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.39.
ieee: K. Chatterjee, M. H. Henzinger, and A. Svozil, “Faster algorithms for mean-payoff
parity games,” in Leibniz International Proceedings in Informatics, Aalborg,
Denmark, 2017, vol. 83.
ista: 'Chatterjee K, Henzinger MH, Svozil A. 2017. Faster algorithms for mean-payoff
parity games. Leibniz International Proceedings in Informatics. MFCS: Mathematical
Foundations of Computer Science (SG), LIPIcs, vol. 83, 39.'
mla: Chatterjee, Krishnendu, et al. “Faster Algorithms for Mean-Payoff Parity Games.”
Leibniz International Proceedings in Informatics, vol. 83, 39, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.39.
short: K. Chatterjee, M.H. Henzinger, A. Svozil, in:, Leibniz International Proceedings
in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.
conference:
end_date: 2017-08-25
location: Aalborg, Denmark
name: 'MFCS: Mathematical Foundations of Computer Science (SG)'
start_date: 2017-08-21
date_created: 2018-12-11T11:47:08Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2023-02-14T10:06:46Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.MFCS.2017.39
ec_funded: 1
file:
- access_level: open_access
checksum: c67f4866ddbfd555afef1f63ae9a8fc7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:57Z
date_updated: 2020-07-14T12:47:00Z
file_id: '5248'
file_name: IST-2018-923-v1+1_LIPIcs-MFCS-2017-39.pdf
file_size: 610339
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
has_accepted_license: '1'
intvolume: ' 83'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Leibniz International Proceedings in Informatics
publication_identifier:
isbn:
- 978-395977046-0
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7262'
pubrep_id: '923'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Faster algorithms for mean-payoff parity games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 83
year: '2017'
...
---
_id: '553'
abstract:
- lang: eng
text: 'We consider two player, zero-sum, finite-state concurrent reachability games,
played for an infinite number of rounds, where in every round, each player simultaneously
and independently of the other players chooses an action, whereafter the successor
state is determined by a probability distribution given by the current state and
the chosen actions. Player 1 wins iff a designated goal state is eventually visited.
We are interested in the complexity of stationary strategies measured by their
patience, which is defined as the inverse of the smallest non-zero probability
employed. Our main results are as follows: We show that: (i) the optimal bound
on the patience of optimal and -optimal strategies, for both players is doubly
exponential; and (ii) even in games with a single non-absorbing state exponential
(in the number of actions) patience is necessary. '
alternative_title:
- LIPIcs
article_number: '55'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Kristofer
full_name: Hansen, Kristofer
last_name: Hansen
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Chatterjee K, Hansen K, Ibsen-Jensen R. Strategy complexity of concurrent
safety games. In: Leibniz International Proceedings in Informatics. Vol
83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.55'
apa: 'Chatterjee, K., Hansen, K., & Ibsen-Jensen, R. (2017). Strategy complexity
of concurrent safety games. In Leibniz International Proceedings in Informatics
(Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.MFCS.2017.55'
chicago: Chatterjee, Krishnendu, Kristofer Hansen, and Rasmus Ibsen-Jensen. “Strategy
Complexity of Concurrent Safety Games.” In Leibniz International Proceedings
in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.55.
ieee: K. Chatterjee, K. Hansen, and R. Ibsen-Jensen, “Strategy complexity of concurrent
safety games,” in Leibniz International Proceedings in Informatics, Aalborg,
Denmark, 2017, vol. 83.
ista: 'Chatterjee K, Hansen K, Ibsen-Jensen R. 2017. Strategy complexity of concurrent
safety games. Leibniz International Proceedings in Informatics. MFCS: Mathematical
Foundations of Computer Science (SG), LIPIcs, vol. 83, 55.'
mla: Chatterjee, Krishnendu, et al. “Strategy Complexity of Concurrent Safety Games.”
Leibniz International Proceedings in Informatics, vol. 83, 55, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.55.
short: K. Chatterjee, K. Hansen, R. Ibsen-Jensen, in:, Leibniz International Proceedings
in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.
conference:
end_date: 2017-08-25
location: Aalborg, Denmark
name: 'MFCS: Mathematical Foundations of Computer Science (SG)'
start_date: 2017-08-21
date_created: 2018-12-11T11:47:08Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2021-01-12T08:02:35Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.MFCS.2017.55
file:
- access_level: open_access
checksum: 7101facb56ade363205c695d72dbd173
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:29Z
date_updated: 2020-07-14T12:47:00Z
file_id: '4753'
file_name: IST-2018-922-v1+1_LIPIcs-MFCS-2017-55.pdf
file_size: 549967
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
has_accepted_license: '1'
intvolume: ' 83'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1506.02434
month: '11'
oa: 1
oa_version: Published Version
publication: Leibniz International Proceedings in Informatics
publication_identifier:
isbn:
- 978-395977046-0
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7261'
pubrep_id: '922'
quality_controlled: '1'
scopus_import: 1
status: public
title: Strategy complexity of concurrent safety games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 83
year: '2017'
...
---
_id: '560'
abstract:
- lang: eng
text: In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500
(doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily
slow convergence speed and every natural number d ? {4, 5, . . .}, there exist
d-dimensional stochastic differential equations with infinitely often differentiable
and globally bounded coefficients such that no approximation method based on finitely
many observations of the driving Brownian motion can converge in absolute mean
to the solution faster than the given speed of convergence. In this paper, we
strengthen the above result by proving that this slow convergence phenomenon also
arises in two (d = 2) and three (d = 3) space dimensions.
article_number: '0104'
author:
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
- first_name: Arnulf
full_name: Jentzen, Arnulf
last_name: Jentzen
- first_name: Diyora
full_name: Salimova, Diyora
last_name: Salimova
citation:
ama: 'Gerencser M, Jentzen A, Salimova D. On stochastic differential equations with
arbitrarily slow convergence rates for strong approximation in two space dimensions.
Proceedings of the Royal Society A: Mathematical, Physical and Engineering
Sciences. 2017;473(2207). doi:10.1098/rspa.2017.0104'
apa: 'Gerencser, M., Jentzen, A., & Salimova, D. (2017). On stochastic differential
equations with arbitrarily slow convergence rates for strong approximation in
two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical
and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rspa.2017.0104'
chicago: 'Gerencser, Mate, Arnulf Jentzen, and Diyora Salimova. “On Stochastic Differential
Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in
Two Space Dimensions.” Proceedings of the Royal Society A: Mathematical, Physical
and Engineering Sciences. Royal Society of London, 2017. https://doi.org/10.1098/rspa.2017.0104.'
ieee: 'M. Gerencser, A. Jentzen, and D. Salimova, “On stochastic differential equations
with arbitrarily slow convergence rates for strong approximation in two space
dimensions,” Proceedings of the Royal Society A: Mathematical, Physical and
Engineering Sciences, vol. 473, no. 2207. Royal Society of London, 2017.'
ista: 'Gerencser M, Jentzen A, Salimova D. 2017. On stochastic differential equations
with arbitrarily slow convergence rates for strong approximation in two space
dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering
Sciences. 473(2207), 0104.'
mla: 'Gerencser, Mate, et al. “On Stochastic Differential Equations with Arbitrarily
Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” Proceedings
of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol.
473, no. 2207, 0104, Royal Society of London, 2017, doi:10.1098/rspa.2017.0104.'
short: 'M. Gerencser, A. Jentzen, D. Salimova, Proceedings of the Royal Society
A: Mathematical, Physical and Engineering Sciences 473 (2017).'
date_created: 2018-12-11T11:47:11Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2021-01-12T08:03:04Z
day: '01'
department:
- _id: JaMa
doi: 10.1098/rspa.2017.0104
ec_funded: 1
intvolume: ' 473'
issue: '2207'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.03229
month: '11'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: 'Proceedings of the Royal Society A: Mathematical, Physical and Engineering
Sciences'
publication_identifier:
issn:
- '13645021'
publication_status: published
publisher: Royal Society of London
publist_id: '7256'
quality_controlled: '1'
scopus_import: 1
status: public
title: On stochastic differential equations with arbitrarily slow convergence rates
for strong approximation in two space dimensions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 473
year: '2017'
...
---
_id: '567'
abstract:
- lang: eng
text: "This book is a concise and self-contained introduction of recent techniques
to prove local spectral universality for large random matrices. Random matrix
theory is a fast expanding research area, and this book mainly focuses on the
methods that the authors participated in developing over the past few years. Many
other interesting topics are not included, and neither are several new developments
within the framework of these methods. The authors have chosen instead to present
key concepts that they believe are the core of these methods and should be relevant
for future applications. They keep technicalities to a minimum to make the book
accessible to graduate students. With this in mind, they include in this book
the basic notions and tools for high-dimensional analysis, such as large deviation,
entropy, Dirichlet form, and the logarithmic Sobolev inequality.\r\n"
alternative_title:
- Courant Lecture Notes
article_processing_charge: No
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Horng
full_name: Yau, Horng
last_name: Yau
citation:
ama: Erdös L, Yau H. A Dynamical Approach to Random Matrix Theory. Vol 28.
American Mathematical Society; 2017. doi:10.1090/cln/028
apa: Erdös, L., & Yau, H. (2017). A Dynamical Approach to Random Matrix Theory
(Vol. 28). American Mathematical Society. https://doi.org/10.1090/cln/028
chicago: Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix
Theory. Vol. 28. Courant Lecture Notes. American Mathematical Society, 2017.
https://doi.org/10.1090/cln/028.
ieee: L. Erdös and H. Yau, A Dynamical Approach to Random Matrix Theory,
vol. 28. American Mathematical Society, 2017.
ista: Erdös L, Yau H. 2017. A Dynamical Approach to Random Matrix Theory, American
Mathematical Society, 226p.
mla: Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory.
Vol. 28, American Mathematical Society, 2017, doi:10.1090/cln/028.
short: L. Erdös, H. Yau, A Dynamical Approach to Random Matrix Theory, American
Mathematical Society, 2017.
date_created: 2018-12-11T11:47:13Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2022-05-24T06:57:28Z
day: '01'
department:
- _id: LaEr
doi: 10.1090/cln/028
ec_funded: 1
intvolume: ' 28'
language:
- iso: eng
month: '01'
oa_version: None
page: '226'
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication_identifier:
eisbn:
- 978-1-4704-4194-4
isbn:
- 9-781-4704-3648-3
publication_status: published
publisher: American Mathematical Society
publist_id: '7247'
quality_controlled: '1'
series_title: Courant Lecture Notes
status: public
title: A Dynamical Approach to Random Matrix Theory
type: book
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2017'
...
---
_id: '568'
abstract:
- lang: eng
text: 'We study robust properties of zero sets of continuous maps f: X → ℝn. Formally,
we analyze the family Z< r(f) := (g-1(0): ||g - f|| < r) of all zero sets
of all continuous maps g closer to f than r in the max-norm. All of these sets
are outside A := (x: |f(x)| ≥ r) and we claim that Z< r(f) is fully determined
by A and an element of a certain cohomotopy group which (by a recent result) is
computable whenever the dimension of X is at most 2n - 3. By considering all r
> 0 simultaneously, the pointed cohomotopy groups form a persistence module-a
structure leading to persistence diagrams as in the case of persistent homology
or well groups. Eventually, we get a descriptor of persistent robust properties
of zero sets that has better descriptive power (Theorem A) and better computability
status (Theorem B) than the established well diagrams. Moreover, if we endow every
point of each zero set with gradients of the perturbation, the robust description
of the zero sets by elements of cohomotopy groups is in some sense the best possible
(Theorem C).'
author:
- first_name: Peter
full_name: Franek, Peter
id: 473294AE-F248-11E8-B48F-1D18A9856A87
last_name: Franek
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
citation:
ama: Franek P, Krcál M. Persistence of zero sets. Homology, Homotopy and Applications.
2017;19(2):313-342. doi:10.4310/HHA.2017.v19.n2.a16
apa: Franek, P., & Krcál, M. (2017). Persistence of zero sets. Homology,
Homotopy and Applications. International Press. https://doi.org/10.4310/HHA.2017.v19.n2.a16
chicago: Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology,
Homotopy and Applications. International Press, 2017. https://doi.org/10.4310/HHA.2017.v19.n2.a16.
ieee: P. Franek and M. Krcál, “Persistence of zero sets,” Homology, Homotopy
and Applications, vol. 19, no. 2. International Press, pp. 313–342, 2017.
ista: Franek P, Krcál M. 2017. Persistence of zero sets. Homology, Homotopy and
Applications. 19(2), 313–342.
mla: Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy
and Applications, vol. 19, no. 2, International Press, 2017, pp. 313–42, doi:10.4310/HHA.2017.v19.n2.a16.
short: P. Franek, M. Krcál, Homology, Homotopy and Applications 19 (2017) 313–342.
date_created: 2018-12-11T11:47:14Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:03:12Z
day: '01'
department:
- _id: UlWa
- _id: HeEd
doi: 10.4310/HHA.2017.v19.n2.a16
ec_funded: 1
intvolume: ' 19'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.04310
month: '01'
oa: 1
oa_version: Submitted Version
page: 313 - 342
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2590DB08-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '701309'
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
(H2020)
publication: Homology, Homotopy and Applications
publication_identifier:
issn:
- '15320073'
publication_status: published
publisher: International Press
publist_id: '7246'
quality_controlled: '1'
scopus_import: 1
status: public
title: Persistence of zero sets
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2017'
...
---
_id: '570'
abstract:
- lang: eng
text: 'Most phenotypes are determined by molecular systems composed of specifically
interacting molecules. However, unlike for individual components, little is known
about the distributions of mutational effects of molecular systems as a whole.
We ask how the distribution of mutational effects of a transcriptional regulatory
system differs from the distributions of its components, by first independently,
and then simultaneously, mutating a transcription factor and the associated promoter
it represses. We find that the system distribution exhibits increased phenotypic
variation compared to individual component distributions - an effect arising from
intermolecular epistasis between the transcription factor and its DNA-binding
site. In large part, this epistasis can be qualitatively attributed to the structure
of the transcriptional regulatory system and could therefore be a common feature
in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the
constraints of individual components, thereby increasing phenotypic variation
that selection could act on and facilitating adaptive evolution. '
article_number: e28921
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Srdjan
full_name: Sarikas, Srdjan
id: 35F0286E-F248-11E8-B48F-1D18A9856A87
last_name: Sarikas
- first_name: Hande
full_name: Acar, Hande
id: 2DDF136A-F248-11E8-B48F-1D18A9856A87
last_name: Acar
orcid: 0000-0003-1986-9753
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure
determines patterns of intermolecular epistasis. eLife. 2017;6. doi:10.7554/eLife.28921
apa: Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017).
Regulatory network structure determines patterns of intermolecular epistasis.
ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921
chicago: Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin
C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.”
ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.28921.
ieee: M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory
network structure determines patterns of intermolecular epistasis,” eLife,
vol. 6. eLife Sciences Publications, 2017.
ista: Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network
structure determines patterns of intermolecular epistasis. eLife. 6, e28921.
mla: Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of
Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications,
2017, doi:10.7554/eLife.28921.
short: M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).
date_created: 2018-12-11T11:47:14Z
date_published: 2017-11-13T00:00:00Z
date_updated: 2021-01-12T08:03:15Z
day: '13'
ddc:
- '576'
department:
- _id: CaGu
- _id: JoBo
- _id: NiBa
doi: 10.7554/eLife.28921
ec_funded: 1
file:
- access_level: open_access
checksum: 273ab17f33305e4eaafd911ff88e7c5b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:42Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5096'
file_name: IST-2017-918-v1+1_elife-28921-figures-v3.pdf
file_size: 8453470
relation: main_file
- access_level: open_access
checksum: b433f90576c7be597cd43367946f8e7f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:43Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5097'
file_name: IST-2017-918-v1+2_elife-28921-v3.pdf
file_size: 1953221
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
issn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7244'
pubrep_id: '918'
quality_controlled: '1'
scopus_import: 1
status: public
title: Regulatory network structure determines patterns of intermolecular epistasis
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: '2017'
...
---
_id: '569'
abstract:
- lang: eng
text: The actomyosin ring generates force to ingress the cytokinetic cleavage furrow
in animal cells, yet its filament organization and the mechanism of contractility
is not well understood. We quantified actin filament order in human cells using
fluorescence polarization microscopy and found that cleavage furrow ingression
initiates by contraction of an equatorial actin network with randomly oriented
filaments. The network subsequently gradually reoriented actin filaments along
the cell equator. This strictly depended on myosin II activity, suggesting local
network reorganization by mechanical forces. Cortical laser microsurgery revealed
that during cytokinesis progression, mechanical tension increased substantially
along the direction of the cell equator, while the network contracted laterally
along the pole-to-pole axis without a detectable increase in tension. Our data
suggest that an asymmetric increase in cortical tension promotes filament reorientation
along the cytokinetic cleavage furrow, which might have implications for diverse
other biological processes involving actomyosin rings.
article_number: e30867
author:
- first_name: Felix
full_name: Spira, Felix
last_name: Spira
- first_name: Sara
full_name: Cuylen Haering, Sara
last_name: Cuylen Haering
- first_name: Shalin
full_name: Mehta, Shalin
last_name: Mehta
- first_name: Matthias
full_name: Samwer, Matthias
last_name: Samwer
- first_name: Anne
full_name: Reversat, Anne
id: 35B76592-F248-11E8-B48F-1D18A9856A87
last_name: Reversat
orcid: 0000-0003-0666-8928
- first_name: Amitabh
full_name: Verma, Amitabh
last_name: Verma
- first_name: Rudolf
full_name: Oldenbourg, Rudolf
last_name: Oldenbourg
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Daniel
full_name: Gerlich, Daniel
last_name: Gerlich
citation:
ama: Spira F, Cuylen Haering S, Mehta S, et al. Cytokinesis in vertebrate cells
initiates by contraction of an equatorial actomyosin network composed of randomly
oriented filaments. eLife. 2017;6. doi:10.7554/eLife.30867
apa: Spira, F., Cuylen Haering, S., Mehta, S., Samwer, M., Reversat, A., Verma,
A., … Gerlich, D. (2017). Cytokinesis in vertebrate cells initiates by contraction
of an equatorial actomyosin network composed of randomly oriented filaments. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.30867
chicago: Spira, Felix, Sara Cuylen Haering, Shalin Mehta, Matthias Samwer, Anne
Reversat, Amitabh Verma, Rudolf Oldenbourg, Michael K Sixt, and Daniel Gerlich.
“Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin
Network Composed of Randomly Oriented Filaments.” ELife. eLife Sciences
Publications, 2017. https://doi.org/10.7554/eLife.30867.
ieee: F. Spira et al., “Cytokinesis in vertebrate cells initiates by contraction
of an equatorial actomyosin network composed of randomly oriented filaments,”
eLife, vol. 6. eLife Sciences Publications, 2017.
ista: Spira F, Cuylen Haering S, Mehta S, Samwer M, Reversat A, Verma A, Oldenbourg
R, Sixt MK, Gerlich D. 2017. Cytokinesis in vertebrate cells initiates by contraction
of an equatorial actomyosin network composed of randomly oriented filaments. eLife.
6, e30867.
mla: Spira, Felix, et al. “Cytokinesis in Vertebrate Cells Initiates by Contraction
of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.”
ELife, vol. 6, e30867, eLife Sciences Publications, 2017, doi:10.7554/eLife.30867.
short: F. Spira, S. Cuylen Haering, S. Mehta, M. Samwer, A. Reversat, A. Verma,
R. Oldenbourg, M.K. Sixt, D. Gerlich, ELife 6 (2017).
date_created: 2018-12-11T11:47:14Z
date_published: 2017-11-06T00:00:00Z
date_updated: 2023-02-23T12:30:29Z
day: '06'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.7554/eLife.30867
file:
- access_level: open_access
checksum: ba09c1451153d39e4f4b7cee013e314c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:40Z
date_updated: 2020-07-14T12:47:10Z
file_id: '4829'
file_name: IST-2017-919-v1+1_elife-30867-figures-v1.pdf
file_size: 9666973
relation: main_file
- access_level: open_access
checksum: 01eb51f1d6ad679947415a51c988e137
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:41Z
date_updated: 2020-07-14T12:47:10Z
file_id: '4830'
file_name: IST-2017-919-v1+2_elife-30867-v1.pdf
file_size: 5951246
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7245'
pubrep_id: '919'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin
network composed of randomly oriented filaments
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: '2017'
...
---
_id: '571'
abstract:
- lang: eng
text: Blood platelets are critical for hemostasis and thrombosis and play diverse
roles during immune responses. Despite these versatile tasks in mammalian biology,
their skills on a cellular level are deemed limited, mainly consisting in rolling,
adhesion, and aggregate formation. Here, we identify an unappreciated asset of
platelets and show that adherent platelets use adhesion receptors to mechanically
probe the adhesive substrate in their local microenvironment. When actomyosin-dependent
traction forces overcome substrate resistance, platelets migrate and pile up the
adhesive substrate together with any bound particulate material. They use this
ability to act as cellular scavengers, scanning the vascular surface for potential
invaders and collecting deposited bacteria. Microbe collection by migrating platelets
boosts the activity of professional phagocytes, exacerbating inflammatory tissue
injury in sepsis. This assigns platelets a central role in innate immune responses
and identifies them as potential targets to dampen inflammatory tissue damage
in clinical scenarios of severe systemic infection. In addition to their role
in thrombosis and hemostasis, platelets can also migrate to sites of infection
to help trap bacteria and clear the vascular surface.
author:
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
- first_name: Zerkah
full_name: Ahmad, Zerkah
last_name: Ahmad
- first_name: Gerhild
full_name: Rosenberger, Gerhild
last_name: Rosenberger
- first_name: Shuxia
full_name: Fan, Shuxia
last_name: Fan
- first_name: Leo
full_name: Nicolai, Leo
last_name: Nicolai
- first_name: Benjamin
full_name: Busch, Benjamin
last_name: Busch
- first_name: Gökce
full_name: Yavuz, Gökce
last_name: Yavuz
- first_name: Manja
full_name: Luckner, Manja
last_name: Luckner
- first_name: Hellen
full_name: Ishikawa Ankerhold, Hellen
last_name: Ishikawa Ankerhold
- first_name: Roman
full_name: Hennel, Roman
last_name: Hennel
- first_name: Alexandre
full_name: Benechet, Alexandre
last_name: Benechet
- first_name: Michael
full_name: Lorenz, Michael
last_name: Lorenz
- first_name: Sue
full_name: Chandraratne, Sue
last_name: Chandraratne
- first_name: Irene
full_name: Schubert, Irene
last_name: Schubert
- first_name: Sebastian
full_name: Helmer, Sebastian
last_name: Helmer
- first_name: Bianca
full_name: Striednig, Bianca
last_name: Striednig
- first_name: Konstantin
full_name: Stark, Konstantin
last_name: Stark
- first_name: Marek
full_name: Janko, Marek
last_name: Janko
- first_name: Ralph
full_name: Böttcher, Ralph
last_name: Böttcher
- first_name: Admar
full_name: Verschoor, Admar
last_name: Verschoor
- first_name: Catherine
full_name: Leon, Catherine
last_name: Leon
- first_name: Christian
full_name: Gachet, Christian
last_name: Gachet
- first_name: Thomas
full_name: Gudermann, Thomas
last_name: Gudermann
- first_name: Michael
full_name: Mederos Y Schnitzler, Michael
last_name: Mederos Y Schnitzler
- first_name: Zachary
full_name: Pincus, Zachary
last_name: Pincus
- first_name: Matteo
full_name: Iannacone, Matteo
last_name: Iannacone
- first_name: Rainer
full_name: Haas, Rainer
last_name: Haas
- first_name: Gerhard
full_name: Wanner, Gerhard
last_name: Wanner
- first_name: Kirsten
full_name: Lauber, Kirsten
last_name: Lauber
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Steffen
full_name: Massberg, Steffen
last_name: Massberg
citation:
ama: Gärtner FR, Ahmad Z, Rosenberger G, et al. Migrating platelets are mechano
scavengers that collect and bundle bacteria. Cell Press. 2017;171(6):1368-1382.
doi:10.1016/j.cell.2017.11.001
apa: Gärtner, F. R., Ahmad, Z., Rosenberger, G., Fan, S., Nicolai, L., Busch, B.,
… Massberg, S. (2017). Migrating platelets are mechano scavengers that collect
and bundle bacteria. Cell Press. Cell Press. https://doi.org/10.1016/j.cell.2017.11.001
chicago: Gärtner, Florian R, Zerkah Ahmad, Gerhild Rosenberger, Shuxia Fan, Leo
Nicolai, Benjamin Busch, Gökce Yavuz, et al. “Migrating Platelets Are Mechano
Scavengers That Collect and Bundle Bacteria.” Cell Press. Cell Press, 2017.
https://doi.org/10.1016/j.cell.2017.11.001.
ieee: F. R. Gärtner et al., “Migrating platelets are mechano scavengers that
collect and bundle bacteria,” Cell Press, vol. 171, no. 6. Cell Press,
pp. 1368–1382, 2017.
ista: Gärtner FR, Ahmad Z, Rosenberger G, Fan S, Nicolai L, Busch B, Yavuz G, Luckner
M, Ishikawa Ankerhold H, Hennel R, Benechet A, Lorenz M, Chandraratne S, Schubert
I, Helmer S, Striednig B, Stark K, Janko M, Böttcher R, Verschoor A, Leon C, Gachet
C, Gudermann T, Mederos Y Schnitzler M, Pincus Z, Iannacone M, Haas R, Wanner
G, Lauber K, Sixt MK, Massberg S. 2017. Migrating platelets are mechano scavengers
that collect and bundle bacteria. Cell Press. 171(6), 1368–1382.
mla: Gärtner, Florian R., et al. “Migrating Platelets Are Mechano Scavengers That
Collect and Bundle Bacteria.” Cell Press, vol. 171, no. 6, Cell Press,
2017, pp. 1368–82, doi:10.1016/j.cell.2017.11.001.
short: F.R. Gärtner, Z. Ahmad, G. Rosenberger, S. Fan, L. Nicolai, B. Busch, G.
Yavuz, M. Luckner, H. Ishikawa Ankerhold, R. Hennel, A. Benechet, M. Lorenz, S.
Chandraratne, I. Schubert, S. Helmer, B. Striednig, K. Stark, M. Janko, R. Böttcher,
A. Verschoor, C. Leon, C. Gachet, T. Gudermann, M. Mederos Y Schnitzler, Z. Pincus,
M. Iannacone, R. Haas, G. Wanner, K. Lauber, M.K. Sixt, S. Massberg, Cell Press
171 (2017) 1368–1382.
date_created: 2018-12-11T11:47:15Z
date_published: 2017-11-30T00:00:00Z
date_updated: 2021-01-12T08:03:15Z
day: '30'
department:
- _id: MiSi
doi: 10.1016/j.cell.2017.11.001
ec_funded: 1
intvolume: ' 171'
issue: '6'
language:
- iso: eng
month: '11'
oa_version: None
page: 1368 - 1382
project:
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '747687'
name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
publication: Cell Press
publication_identifier:
issn:
- '00928674'
publication_status: published
publisher: Cell Press
publist_id: '7243'
quality_controlled: '1'
scopus_import: 1
status: public
title: Migrating platelets are mechano scavengers that collect and bundle bacteria
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 171
year: '2017'
...
---
_id: '572'
abstract:
- lang: eng
text: In this review, we summarize the different biosynthesis-related pathways that
contribute to the regulation of endogenous auxin in plants. We demonstrate that
all known genes involved in auxin biosynthesis also have a role in root formation,
from the initiation of a root meristem during embryogenesis to the generation
of a functional root system with a primary root, secondary lateral root branches
and adventitious roots. Furthermore, the versatile adaptation of root development
in response to environmental challenges is mediated by both local and distant
control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial
and temporal regulation of auxin biosynthesis plays a central role in determining
root architecture.
article_number: '2587'
article_processing_charge: No
author:
- first_name: Damilola
full_name: Olatunji, Damilola
last_name: Olatunji
- first_name: Danny
full_name: Geelen, Danny
last_name: Geelen
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
citation:
ama: Olatunji D, Geelen D, Verstraeten I. Control of endogenous auxin levels in
plant root development. International Journal of Molecular Sciences. 2017;18(12).
doi:10.3390/ijms18122587
apa: Olatunji, D., Geelen, D., & Verstraeten, I. (2017). Control of endogenous
auxin levels in plant root development. International Journal of Molecular
Sciences. MDPI. https://doi.org/10.3390/ijms18122587
chicago: Olatunji, Damilola, Danny Geelen, and Inge Verstraeten. “Control of Endogenous
Auxin Levels in Plant Root Development.” International Journal of Molecular
Sciences. MDPI, 2017. https://doi.org/10.3390/ijms18122587.
ieee: D. Olatunji, D. Geelen, and I. Verstraeten, “Control of endogenous auxin levels
in plant root development,” International Journal of Molecular Sciences,
vol. 18, no. 12. MDPI, 2017.
ista: Olatunji D, Geelen D, Verstraeten I. 2017. Control of endogenous auxin levels
in plant root development. International Journal of Molecular Sciences. 18(12),
2587.
mla: Olatunji, Damilola, et al. “Control of Endogenous Auxin Levels in Plant Root
Development.” International Journal of Molecular Sciences, vol. 18, no.
12, 2587, MDPI, 2017, doi:10.3390/ijms18122587.
short: D. Olatunji, D. Geelen, I. Verstraeten, International Journal of Molecular
Sciences 18 (2017).
date_created: 2018-12-11T11:47:15Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:03:16Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3390/ijms18122587
file:
- access_level: open_access
checksum: 82d51f11e493f7eec02976d9a9a9805e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:55Z
date_updated: 2020-07-14T12:47:10Z
file_id: '4718'
file_name: IST-2017-917-v1+1_ijms-18-02587.pdf
file_size: 920962
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: International Journal of Molecular Sciences
publication_status: published
publisher: MDPI
publist_id: '7242'
pubrep_id: '917'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Control of endogenous auxin levels in plant root development
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2017'
...
---
_id: '5800'
abstract:
- lang: eng
text: This paper presents a novel study on the functional gradation of coordinate
planes in connection with the thinnest and tunnel-free (i.e., naive) discretization
of sphere in the integer space. For each of the 48-symmetric quadraginta octants
of naive sphere with integer radius and integer center, we show that the corresponding
voxel set forms a bijection with its projected pixel set on a unique coordinate
plane, which thereby serves as its functional plane. We use this fundamental property
to prove several other theoretical results for naive sphere. First, the quadraginta
octants form symmetry groups and subgroups with certain equivalent topological
properties. Second, a naive sphere is always unique and consists of fewest voxels.
Third, it is efficiently constructible from its functional-plane projection. And
finally, a special class of 4-symmetric discrete 3D circles can be constructed
on a naive sphere based on back projection from the functional plane.
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: Biswas R, Bhowmick P. On the functionality and usefulness of Quadraginta octants
of naive sphere. Journal of Mathematical Imaging and Vision. 2017;59(1):69-83.
doi:10.1007/s10851-017-0718-4
apa: Biswas, R., & Bhowmick, P. (2017). On the functionality and usefulness
of Quadraginta octants of naive sphere. Journal of Mathematical Imaging and
Vision. Springer Nature. https://doi.org/10.1007/s10851-017-0718-4
chicago: Biswas, Ranita, and Partha Bhowmick. “On the Functionality and Usefulness
of Quadraginta Octants of Naive Sphere.” Journal of Mathematical Imaging and
Vision. Springer Nature, 2017. https://doi.org/10.1007/s10851-017-0718-4.
ieee: R. Biswas and P. Bhowmick, “On the functionality and usefulness of Quadraginta
octants of naive sphere,” Journal of Mathematical Imaging and Vision, vol.
59, no. 1. Springer Nature, pp. 69–83, 2017.
ista: Biswas R, Bhowmick P. 2017. On the functionality and usefulness of Quadraginta
octants of naive sphere. Journal of Mathematical Imaging and Vision. 59(1), 69–83.
mla: Biswas, Ranita, and Partha Bhowmick. “On the Functionality and Usefulness of
Quadraginta Octants of Naive Sphere.” Journal of Mathematical Imaging and Vision,
vol. 59, no. 1, Springer Nature, 2017, pp. 69–83, doi:10.1007/s10851-017-0718-4.
short: R. Biswas, P. Bhowmick, Journal of Mathematical Imaging and Vision 59 (2017)
69–83.
date_created: 2019-01-08T20:42:08Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:03:34Z
day: '01'
doi: 10.1007/s10851-017-0718-4
extern: '1'
intvolume: ' 59'
issue: '1'
language:
- iso: eng
month: '09'
oa_version: None
page: 69-83
publication: Journal of Mathematical Imaging and Vision
publication_identifier:
issn:
- '09249907'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: On the functionality and usefulness of Quadraginta octants of naive sphere
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 59
year: '2017'
...
---
_id: '5799'
abstract:
- lang: eng
text: We construct a polyhedral surface called a graceful surface, which provides
best possible approximation to a given sphere regarding certain criteria. In digital
geometry terms, the graceful surface is uniquely characterized by its minimality
while guaranteeing the connectivity of certain discrete (polyhedral) curves defined
on it. The notion of “gracefulness” was first proposed in Brimkov and Barneva
(1999) and shown to be useful for triangular mesh discretization through graceful
planes and graceful lines. In this paper we extend the considerations to a nonlinear
object such as a sphere. In particular, we investigate the properties of a discrete
geodesic path between two voxels and show that discrete 3D circles, circular arcs,
and Mobius triangles are all constructible on a graceful sphere, with guaranteed
minimum thickness and the desired connectivity in the discrete topological space.
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
- first_name: Valentin E.
full_name: Brimkov, Valentin E.
last_name: Brimkov
citation:
ama: Biswas R, Bhowmick P, Brimkov VE. On the polyhedra of graceful spheres and
circular geodesics. Discrete Applied Mathematics. 2017;216:362-375. doi:10.1016/j.dam.2015.11.017
apa: Biswas, R., Bhowmick, P., & Brimkov, V. E. (2017). On the polyhedra of
graceful spheres and circular geodesics. Discrete Applied Mathematics.
Elsevier. https://doi.org/10.1016/j.dam.2015.11.017
chicago: Biswas, Ranita, Partha Bhowmick, and Valentin E. Brimkov. “On the Polyhedra
of Graceful Spheres and Circular Geodesics.” Discrete Applied Mathematics.
Elsevier, 2017. https://doi.org/10.1016/j.dam.2015.11.017.
ieee: R. Biswas, P. Bhowmick, and V. E. Brimkov, “On the polyhedra of graceful spheres
and circular geodesics,” Discrete Applied Mathematics, vol. 216. Elsevier,
pp. 362–375, 2017.
ista: Biswas R, Bhowmick P, Brimkov VE. 2017. On the polyhedra of graceful spheres
and circular geodesics. Discrete Applied Mathematics. 216, 362–375.
mla: Biswas, Ranita, et al. “On the Polyhedra of Graceful Spheres and Circular Geodesics.”
Discrete Applied Mathematics, vol. 216, Elsevier, 2017, pp. 362–75, doi:10.1016/j.dam.2015.11.017.
short: R. Biswas, P. Bhowmick, V.E. Brimkov, Discrete Applied Mathematics 216 (2017)
362–375.
date_created: 2019-01-08T20:41:12Z
date_published: 2017-01-10T00:00:00Z
date_updated: 2021-01-12T08:03:33Z
day: '10'
doi: 10.1016/j.dam.2015.11.017
extern: '1'
intvolume: ' 216'
language:
- iso: eng
month: '01'
oa_version: None
page: 362-375
publication: Discrete Applied Mathematics
publication_identifier:
issn:
- 0166-218X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: On the polyhedra of graceful spheres and circular geodesics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 216
year: '2017'
...
---
_id: '5801'
abstract:
- lang: eng
text: Space filling circles and spheres have various applications in mathematical
imaging and physical modeling. In this paper, we first show how the thinnest (i.e.,
2-minimal) model of digital sphere can be augmented to a space filling model by
fixing certain “simple voxels” and “filler voxels” associated with it. Based on
elementary number-theoretic properties of such voxels, we design an efficient
incremental algorithm for generation of these space filling spheres with successively
increasing radius. The novelty of the proposed technique is established further
through circular space filling on 3D digital plane. As evident from a preliminary
set of experimental result, this can particularly be useful for parallel computing
of 3D Voronoi diagrams in the digital space.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Shivam
full_name: Dwivedi, Shivam
last_name: Dwivedi
- first_name: Aniket
full_name: Gupta, Aniket
last_name: Gupta
- first_name: Siddhant
full_name: Roy, Siddhant
last_name: Roy
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: 'Dwivedi S, Gupta A, Roy S, Biswas R, Bhowmick P. Fast and Efficient Incremental
Algorithms for Circular and Spherical Propagation in Integer Space. In: 20th
IAPR International Conference. Vol 10502. Cham: Springer Nature; 2017:347-359.
doi:10.1007/978-3-319-66272-5_28'
apa: 'Dwivedi, S., Gupta, A., Roy, S., Biswas, R., & Bhowmick, P. (2017). Fast
and Efficient Incremental Algorithms for Circular and Spherical Propagation in
Integer Space. In 20th IAPR International Conference (Vol. 10502, pp. 347–359).
Cham: Springer Nature. https://doi.org/10.1007/978-3-319-66272-5_28'
chicago: 'Dwivedi, Shivam, Aniket Gupta, Siddhant Roy, Ranita Biswas, and Partha
Bhowmick. “Fast and Efficient Incremental Algorithms for Circular and Spherical
Propagation in Integer Space.” In 20th IAPR International Conference, 10502:347–59.
Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-66272-5_28.'
ieee: S. Dwivedi, A. Gupta, S. Roy, R. Biswas, and P. Bhowmick, “Fast and Efficient
Incremental Algorithms for Circular and Spherical Propagation in Integer Space,”
in 20th IAPR International Conference, Vienna, Austria, 2017, vol. 10502,
pp. 347–359.
ista: 'Dwivedi S, Gupta A, Roy S, Biswas R, Bhowmick P. 2017. Fast and Efficient
Incremental Algorithms for Circular and Spherical Propagation in Integer Space.
20th IAPR International Conference. DGCI: International Conference on Discrete
Geometry for Computer Imagery, LNCS, vol. 10502, 347–359.'
mla: Dwivedi, Shivam, et al. “Fast and Efficient Incremental Algorithms for Circular
and Spherical Propagation in Integer Space.” 20th IAPR International Conference,
vol. 10502, Springer Nature, 2017, pp. 347–59, doi:10.1007/978-3-319-66272-5_28.
short: S. Dwivedi, A. Gupta, S. Roy, R. Biswas, P. Bhowmick, in:, 20th IAPR International
Conference, Springer Nature, Cham, 2017, pp. 347–359.
conference:
end_date: 2017-09-21
location: Vienna, Austria
name: 'DGCI: International Conference on Discrete Geometry for Computer Imagery'
start_date: 2017-09-19
date_created: 2019-01-08T20:42:22Z
date_published: 2017-08-22T00:00:00Z
date_updated: 2022-01-27T15:34:25Z
day: '22'
doi: 10.1007/978-3-319-66272-5_28
extern: '1'
intvolume: ' 10502'
language:
- iso: eng
month: '08'
oa_version: None
page: 347-359
place: Cham
publication: 20th IAPR International Conference
publication_identifier:
eisbn:
- 978-3-319-66272-5
eissn:
- 1611-3349
isbn:
- 978-3-319-66271-8
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation
in Integer Space
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 10502
year: '2017'
...
---
_id: '5803'
abstract:
- lang: eng
text: Different distance metrics produce Voronoi diagrams with different properties.
It is a well-known that on the (real) 2D plane or even on any 3D plane, a Voronoi
diagram (VD) based on the Euclidean distance metric produces convex Voronoi regions.
In this paper, we first show that this metric produces a persistent VD on the
2D digital plane, as it comprises digitally convex Voronoi regions and hence correctly
approximates the corresponding VD on the 2D real plane. Next, we show that on
a 3D digital plane D, the Euclidean metric spanning over its voxel set does not
guarantee a digital VD which is persistent with the real-space VD. As a solution,
we introduce a novel concept of functional-plane-convexity, which is ensured by
the Euclidean metric spanning over the pedal set of D. Necessary proofs and some
visual result have been provided to adjudge the merit and usefulness of the proposed
concept.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: 'Biswas R, Bhowmick P. Construction of persistent Voronoi diagram on 3D digital
plane. In: Combinatorial Image Analysis. Vol 10256. Cham: Springer Nature;
2017:93-104. doi:10.1007/978-3-319-59108-7_8'
apa: 'Biswas, R., & Bhowmick, P. (2017). Construction of persistent Voronoi
diagram on 3D digital plane. In Combinatorial image analysis (Vol. 10256,
pp. 93–104). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-59108-7_8'
chicago: 'Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi
Diagram on 3D Digital Plane.” In Combinatorial Image Analysis, 10256:93–104.
Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-59108-7_8.'
ieee: 'R. Biswas and P. Bhowmick, “Construction of persistent Voronoi diagram on
3D digital plane,” in Combinatorial image analysis, vol. 10256, Cham: Springer
Nature, 2017, pp. 93–104.'
ista: 'Biswas R, Bhowmick P. 2017.Construction of persistent Voronoi diagram on
3D digital plane. In: Combinatorial image analysis. LNCS, vol. 10256, 93–104.'
mla: Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram
on 3D Digital Plane.” Combinatorial Image Analysis, vol. 10256, Springer
Nature, 2017, pp. 93–104, doi:10.1007/978-3-319-59108-7_8.
short: R. Biswas, P. Bhowmick, in:, Combinatorial Image Analysis, Springer Nature,
Cham, 2017, pp. 93–104.
conference:
end_date: 2017-06-21
location: Plovdiv, Bulgaria
name: 'IWCIA: International Workshop on Combinatorial Image Analysis'
start_date: 2017-06-19
date_created: 2019-01-08T20:42:56Z
date_published: 2017-05-17T00:00:00Z
date_updated: 2022-01-28T07:48:24Z
day: '17'
department:
- _id: HeEd
doi: 10.1007/978-3-319-59108-7_8
extern: '1'
intvolume: ' 10256'
language:
- iso: eng
month: '05'
oa_version: None
page: 93-104
place: Cham
publication: Combinatorial image analysis
publication_identifier:
isbn:
- 978-3-319-59107-0
- 978-3-319-59108-7
issn:
- 0302-9743
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Construction of persistent Voronoi diagram on 3D digital plane
type: book_chapter
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 10256
year: '2017'
...
---
_id: '5802'
abstract:
- lang: eng
text: This papers introduces a definition of digital primitives based on focal points
and weighted distances (with positive weights). The proposed definition is applicable
to general dimensions and covers in its gamut various regular curves and surfaces
like circles, ellipses, digital spheres and hyperspheres, ellipsoids and k-ellipsoids,
Cartesian k-ovals, etc. Several interesting properties are presented for this
class of digital primitives such as space partitioning, topological separation,
and connectivity properties. To demonstrate further the potential of this new
way of defining digital primitives, we propose, as extension, another class of
digital conics defined by focus-directrix combination.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Eric
full_name: Andres, Eric
last_name: Andres
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: 'Andres E, Biswas R, Bhowmick P. Digital primitives defined by weighted focal
set. In: 20th IAPR International Conference. Vol 10502. Cham: Springer
Nature; 2017:388-398. doi:10.1007/978-3-319-66272-5_31'
apa: 'Andres, E., Biswas, R., & Bhowmick, P. (2017). Digital primitives defined
by weighted focal set. In 20th IAPR International Conference (Vol. 10502,
pp. 388–398). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-66272-5_31'
chicago: 'Andres, Eric, Ranita Biswas, and Partha Bhowmick. “Digital Primitives
Defined by Weighted Focal Set.” In 20th IAPR International Conference,
10502:388–98. Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-66272-5_31.'
ieee: E. Andres, R. Biswas, and P. Bhowmick, “Digital primitives defined by weighted
focal set,” in 20th IAPR International Conference, Vienna, Austria, 2017,
vol. 10502, pp. 388–398.
ista: 'Andres E, Biswas R, Bhowmick P. 2017. Digital primitives defined by weighted
focal set. 20th IAPR International Conference. DGCI: International Conference
on Discrete Geometry for Computer Imagery, LNCS, vol. 10502, 388–398.'
mla: Andres, Eric, et al. “Digital Primitives Defined by Weighted Focal Set.” 20th
IAPR International Conference, vol. 10502, Springer Nature, 2017, pp. 388–98,
doi:10.1007/978-3-319-66272-5_31.
short: E. Andres, R. Biswas, P. Bhowmick, in:, 20th IAPR International Conference,
Springer Nature, Cham, 2017, pp. 388–398.
conference:
end_date: 2017-09-21
location: Vienna, Austria
name: 'DGCI: International Conference on Discrete Geometry for Computer Imagery'
start_date: 2017-09-19
date_created: 2019-01-08T20:42:39Z
date_published: 2017-08-22T00:00:00Z
date_updated: 2022-01-27T15:38:35Z
day: '22'
doi: 10.1007/978-3-319-66272-5_31
extern: '1'
intvolume: ' 10502'
language:
- iso: eng
month: '08'
oa_version: None
page: 388-398
place: Cham
publication: 20th IAPR International Conference
publication_identifier:
eisbn:
- 978-3-319-66272-5
eissn:
- 1611-3349
isbn:
- 978-3-319-66271-8
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Digital primitives defined by weighted focal set
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 10502
year: '2017'
...
---
_id: '593'
abstract:
- lang: eng
text: Bell correlations, indicating nonlocality in composite quantum systems, were
until recently only seen in small systems. Here, we demonstrate Bell correlations
in squeezed states of 5×105 Rb87 atoms. The correlations are inferred using collective
measurements as witnesses and are statistically significant to 124 standard deviations.
The states are both generated and characterized using optical-cavity aided measurements.
author:
- first_name: Nils
full_name: Engelsen, Nils
last_name: Engelsen
- first_name: Rajiv
full_name: Krishnakumar, Rajiv
last_name: Krishnakumar
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Mark
full_name: Kasevich, Mark
last_name: Kasevich
citation:
ama: Engelsen N, Krishnakumar R, Hosten O, Kasevich M. Bell correlations in spin-squeezed
states of 500 000 atoms. Physical Review Letters. 2017;118(14). doi:10.1103/PhysRevLett.118.140401
apa: Engelsen, N., Krishnakumar, R., Hosten, O., & Kasevich, M. (2017). Bell
correlations in spin-squeezed states of 500 000 atoms. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.118.140401
chicago: Engelsen, Nils, Rajiv Krishnakumar, Onur Hosten, and Mark Kasevich. “Bell
Correlations in Spin-Squeezed States of 500 000 Atoms.” Physical Review Letters.
American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.140401.
ieee: N. Engelsen, R. Krishnakumar, O. Hosten, and M. Kasevich, “Bell correlations
in spin-squeezed states of 500 000 atoms,” Physical Review Letters, vol.
118, no. 14. American Physical Society, 2017.
ista: Engelsen N, Krishnakumar R, Hosten O, Kasevich M. 2017. Bell correlations
in spin-squeezed states of 500 000 atoms. Physical Review Letters. 118(14).
mla: Engelsen, Nils, et al. “Bell Correlations in Spin-Squeezed States of 500 000
Atoms.” Physical Review Letters, vol. 118, no. 14, American Physical Society,
2017, doi:10.1103/PhysRevLett.118.140401.
short: N. Engelsen, R. Krishnakumar, O. Hosten, M. Kasevich, Physical Review Letters
118 (2017).
date_created: 2018-12-11T11:47:23Z
date_published: 2017-04-03T00:00:00Z
date_updated: 2021-01-12T08:05:16Z
day: '03'
doi: 10.1103/PhysRevLett.118.140401
extern: '1'
intvolume: ' 118'
issue: '14'
language:
- iso: eng
month: '04'
oa_version: None
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7212'
status: public
title: Bell correlations in spin-squeezed states of 500 000 atoms
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2017'
...
---
_id: '600'
abstract:
- lang: eng
text: Transcription initiation at the ribosomal RNA promoter requires RNA polymerase
(Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine
X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular
model for basal Pol I initiation. The three-subunit CF binds upstream promoter
DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center
cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp
domains enables cleft contraction, resulting in an active Pol I conformation and
RNA synthesis. Comparison with the Pol II system suggests that promoter specificity
relies on a distinct “bendability” and “meltability” of the promoter sequence
that enables contacts between initiation factors, DNA, and polymerase.
article_processing_charge: No
author:
- first_name: Christoph
full_name: Engel, Christoph
last_name: Engel
- first_name: Tobias
full_name: Gubbey, Tobias
last_name: Gubbey
- first_name: Simon
full_name: Neyer, Simon
last_name: Neyer
- first_name: Sarah
full_name: Sainsbury, Sarah
last_name: Sainsbury
- first_name: Christiane
full_name: Oberthuer, Christiane
last_name: Oberthuer
- first_name: Carlo
full_name: Baejen, Carlo
last_name: Baejen
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Patrick
full_name: Cramer, Patrick
last_name: Cramer
citation:
ama: Engel C, Gubbey T, Neyer S, et al. Structural basis of RNA polymerase I transcription
initiation. Cell. 2017;169(1):120-131.e22. doi:10.1016/j.cell.2017.03.003
apa: Engel, C., Gubbey, T., Neyer, S., Sainsbury, S., Oberthuer, C., Baejen, C.,
… Cramer, P. (2017). Structural basis of RNA polymerase I transcription initiation.
Cell. Cell Press. https://doi.org/10.1016/j.cell.2017.03.003
chicago: Engel, Christoph, Tobias Gubbey, Simon Neyer, Sarah Sainsbury, Christiane
Oberthuer, Carlo Baejen, Carrie Bernecky, and Patrick Cramer. “Structural Basis
of RNA Polymerase I Transcription Initiation.” Cell. Cell Press, 2017.
https://doi.org/10.1016/j.cell.2017.03.003.
ieee: C. Engel et al., “Structural basis of RNA polymerase I transcription
initiation,” Cell, vol. 169, no. 1. Cell Press, p. 120–131.e22, 2017.
ista: Engel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C, Baejen C, Bernecky C,
Cramer P. 2017. Structural basis of RNA polymerase I transcription initiation.
Cell. 169(1), 120–131.e22.
mla: Engel, Christoph, et al. “Structural Basis of RNA Polymerase I Transcription
Initiation.” Cell, vol. 169, no. 1, Cell Press, 2017, p. 120–131.e22, doi:10.1016/j.cell.2017.03.003.
short: C. Engel, T. Gubbey, S. Neyer, S. Sainsbury, C. Oberthuer, C. Baejen, C.
Bernecky, P. Cramer, Cell 169 (2017) 120–131.e22.
date_created: 2018-12-11T11:47:25Z
date_published: 2017-03-23T00:00:00Z
date_updated: 2021-01-12T08:05:36Z
day: '23'
doi: 10.1016/j.cell.2017.03.003
extern: '1'
intvolume: ' 169'
issue: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 120 - 131.e22
publication: Cell
publication_identifier:
issn:
- '00928674'
publication_status: published
publisher: Cell Press
publist_id: '7204'
quality_controlled: '1'
status: public
title: Structural basis of RNA polymerase I transcription initiation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 169
year: '2017'
...