---
_id: '7569'
abstract:
- lang: eng
text: 'Genes differ in the frequency at which they are expressed and in the form
of regulation used to control their activity. In particular, positive or negative
regulation can lead to activation of a gene in response to an external signal.
Previous works proposed that the form of regulation of a gene correlates with
its frequency of usage: positive regulation when the gene is frequently expressed
and negative regulation when infrequently expressed. Such network design means
that, in the absence of their regulators, the genes are found in their least required
activity state, hence regulatory intervention is often necessary. Due to the multitude
of genes and regulators, spurious binding and unbinding events, called “crosstalk”,
could occur. To determine how the form of regulation affects the global crosstalk
in the network, we used a mathematical model that includes multiple regulators
and multiple target genes. We found that crosstalk depends non-monotonically on
the availability of regulators. Our analysis showed that excess use of regulation
entailed by the formerly suggested network design caused high crosstalk levels
in a large part of the parameter space. We therefore considered the opposite ‘idle’
design, where the default unregulated state of genes is their frequently required
activity state. We found, that ‘idle’ design minimized the use of regulation and
thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae
using transcription factors binding data. We demonstrated that even partial network
data could suffice to estimate its global crosstalk, suggesting its applicability
to additional organisms. We found that S. cerevisiae estimated crosstalk is lower
than that of a random network, suggesting that natural selection reduces crosstalk.
In summary, our study highlights a new type of protein production cost which is
typically overlooked: that of regulatory interference caused by the presence of
excess regulators in the cell. It demonstrates the importance of whole-network
descriptions, which could show effects missed by single-gene models.'
article_number: e1007642
article_processing_charge: No
article_type: original
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Tamar
full_name: Friedlander, Tamar
last_name: Friedlander
citation:
ama: Grah R, Friedlander T. The relation between crosstalk and gene regulation form
revisited. PLOS Computational Biology. 2020;16(2). doi:10.1371/journal.pcbi.1007642
apa: Grah, R., & Friedlander, T. (2020). The relation between crosstalk and
gene regulation form revisited. PLOS Computational Biology. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1007642
chicago: Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene
Regulation Form Revisited.” PLOS Computational Biology. Public Library
of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.
ieee: R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation
form revisited,” PLOS Computational Biology, vol. 16, no. 2. Public Library
of Science, 2020.
ista: Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation
form revisited. PLOS Computational Biology. 16(2), e1007642.
mla: Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene
Regulation Form Revisited.” PLOS Computational Biology, vol. 16, no. 2,
e1007642, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.
short: R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).
date_created: 2020-03-06T07:39:38Z
date_published: 2020-02-25T00:00:00Z
date_updated: 2023-09-12T11:02:24Z
day: '25'
ddc:
- '000'
- '570'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pcbi.1007642
external_id:
isi:
- '000526725200019'
file:
- access_level: open_access
checksum: 5239dd134dc6e1c71fe7b3ce2953da37
content_type: application/pdf
creator: dernst
date_created: 2020-03-09T15:12:21Z
date_updated: 2020-07-14T12:48:00Z
file_id: '7579'
file_name: 2020_PlosCompBio_Grah.pdf
file_size: 2209325
relation: main_file
file_date_updated: 2020-07-14T12:48:00Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '9716'
relation: research_data
status: deleted
- id: '9776'
relation: research_data
status: public
- id: '9779'
relation: used_in_publication
status: public
- id: '8155'
relation: dissertation_contains
status: public
- id: '9777'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The relation between crosstalk and gene regulation form revisited
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 16
year: '2020'
...
---
_id: '8813'
abstract:
- lang: eng
text: 'In mammals, chromatin marks at imprinted genes are asymmetrically inherited
to control parentally-biased gene expression. This control is thought predominantly
to involve parent-specific differentially methylated regions (DMR) in genomic
DNA. However, neither parent-of-origin-specific transcription nor DMRs have been
comprehensively mapped. We here address this by integrating transcriptomic and
epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis
identified 71 genes expressed with previously unknown parent-of-origin-specific
expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental
expression of nBiX genes disappeared soon after implantation. Micro-whole-genome
bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859
DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated
with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated
imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted
gene, and five novel clusters contained exclusively nBiX-genes. These data suggest
a complex program of stage-specific imprinting involving different tiers of regulation.'
article_processing_charge: No
author:
- first_name: Laura
full_name: Santini, Laura
last_name: Santini
- first_name: Florian
full_name: Halbritter, Florian
last_name: Halbritter
- first_name: Fabian
full_name: Titz-Teixeira, Fabian
last_name: Titz-Teixeira
- first_name: Toru
full_name: Suzuki, Toru
last_name: Suzuki
- first_name: Maki
full_name: Asami, Maki
last_name: Asami
- first_name: Julia
full_name: Ramesmayer, Julia
last_name: Ramesmayer
- first_name: Xiaoyan
full_name: Ma, Xiaoyan
last_name: Ma
- first_name: Andreas
full_name: Lackner, Andreas
last_name: Lackner
- first_name: Nick
full_name: Warr, Nick
last_name: Warr
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Ernest
full_name: Laue, Ernest
last_name: Laue
- first_name: Matthias
full_name: Farlik, Matthias
last_name: Farlik
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Andreas
full_name: Beyer, Andreas
last_name: Beyer
- first_name: Anthony C. F.
full_name: Perry, Anthony C. F.
last_name: Perry
- first_name: Martin
full_name: Leeb, Martin
last_name: Leeb
citation:
ama: Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts
are predominantly DNA methylation independent. bioRxiv. doi:10.1101/2020.11.03.366948
apa: Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer,
J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA
methylation independent. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.03.366948
chicago: Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki,
Maki Asami, Julia Ramesmayer, Xiaoyan Ma, et al. “Novel Imprints in Mouse Blastocysts
Are Predominantly DNA Methylation Independent.” BioRxiv. Cold Spring Harbor
Laboratory, n.d. https://doi.org/10.1101/2020.11.03.366948.
ieee: L. Santini et al., “Novel imprints in mouse blastocysts are predominantly
DNA methylation independent,” bioRxiv. Cold Spring Harbor Laboratory.
ista: Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J,
Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer
A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA
methylation independent. bioRxiv, 10.1101/2020.11.03.366948.
mla: Santini, Laura, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly
DNA Methylation Independent.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.11.03.366948.
short: L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, J. Ramesmayer,
X. Ma, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C.
Bock, A. Beyer, A.C.F. Perry, M. Leeb, BioRxiv (n.d.).
date_created: 2020-11-26T07:17:19Z
date_published: 2020-11-05T00:00:00Z
date_updated: 2023-09-12T11:05:28Z
day: '05'
department:
- _id: SiHi
doi: 10.1101/2020.11.03.366948
external_id:
pmid:
- 'PPR234457 '
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.11.03.366948
month: '11'
oa: 1
oa_version: Preprint
pmid: 1
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
status: public
title: Novel imprints in mouse blastocysts are predominantly DNA methylation independent
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '9777'
article_processing_charge: No
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Tamar
full_name: Friedlander, Tamar
last_name: Friedlander
citation:
ama: Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002
apa: Grah, R., & Friedlander, T. (2020). Maximizing crosstalk. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1007642.s002
chicago: Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library
of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s002.
ieee: R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science,
2020.
ista: Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science,
10.1371/journal.pcbi.1007642.s002.
mla: Grah, Rok, and Tamar Friedlander. Maximizing Crosstalk. Public Library
of Science, 2020, doi:10.1371/journal.pcbi.1007642.s002.
short: R. Grah, T. Friedlander, (2020).
date_created: 2021-08-06T07:21:51Z
date_published: 2020-02-25T00:00:00Z
date_updated: 2023-09-12T11:02:25Z
day: '25'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1007642.s002
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pcbi.1007642.s002
month: '02'
oa: 1
oa_version: None
publisher: Public Library of Science
related_material:
record:
- id: '7569'
relation: used_in_publication
status: public
status: public
title: Maximizing crosstalk
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8332'
abstract:
- lang: eng
text: "Designing and verifying concurrent programs is a notoriously challenging,
time consuming, and error prone task, even for experts. This is due to the sheer
number of possible interleavings of a concurrent program, all of which have to
be tracked and accounted for in a formal proof. Inventing an inductive invariant
that captures all interleavings of a low-level implementation is theoretically
possible, but practically intractable. We develop a refinement-based verification
framework that provides mechanisms to simplify proof construction by decomposing
the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we
present a foundation for refinement reasoning over structured concurrent programs.
We introduce layered concurrent programs as a compact notation to represent multi-layer
refinement proofs. A layered concurrent program specifies a sequence of connected
concurrent programs, from most concrete to most abstract, such that common parts
of different programs are written exactly once. Each program in this sequence
is expressed as structured concurrent program, i.e., a program over (potentially
recursive) procedures, imperative control flow, gated atomic actions, structured
parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based
verifiers, which represent concurrent systems as flat transition relations. We
present a powerful refinement proof rule that decomposes refinement checking over
structured programs into modular verification conditions. Refinement checking
is supported by a new form of modular, parameterized invariants, called yield
invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn
a second line of work, we present two new reduction-based program transformations
that target asynchronous programs. These transformations reduce the number of
interleavings that need to be considered, thus reducing the complexity of invariants.
Synchronization simplifies the verification of asynchronous programs by introducing
the fiction, for proof purposes, that asynchronous operations complete synchronously.
Synchronization summarizes an asynchronous computation as immediate atomic effect.
Inductive sequentialization establishes sequential reductions that captures every
behavior of the original program up to reordering of coarse-grained commutative
actions. A sequential reduction of a concurrent program is easy to reason about
since it corresponds to a simple execution of the program in an idealized synchronous
environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur
approach is implemented the CIVL verifier, which has been successfully used for
the verification of several complex concurrent programs. In our methodology, the
overall correctness of a program is established piecemeal by focusing on the invariant
required for each refinement step separately. While the programmer does the creative
work of specifying the chain of programs and the inductive invariant justifying
each link in the chain, the tool automatically constructs the verification conditions
underlying each refinement step."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
citation:
ama: 'Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization.
2020. doi:10.15479/AT:ISTA:8332'
apa: 'Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization,
sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332'
chicago: 'Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization,
Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332.'
ieee: 'B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,”
Institute of Science and Technology Austria, 2020.'
ista: 'Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization,
sequentialization. Institute of Science and Technology Austria.'
mla: 'Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization,
Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332.'
short: 'B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization,
Institute of Science and Technology Austria, 2020.'
date_created: 2020-09-04T12:24:12Z
date_published: 2020-09-03T00:00:00Z
date_updated: 2023-09-13T08:45:08Z
day: '03'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ToHe
doi: 10.15479/AT:ISTA:8332
file:
- access_level: open_access
checksum: 26fe261550f691280bda4c454bf015c7
content_type: application/pdf
creator: bkragl
date_created: 2020-09-04T12:17:47Z
date_updated: 2020-09-04T12:17:47Z
file_id: '8333'
file_name: kragl-thesis.pdf
file_size: 1348815
relation: main_file
- access_level: closed
checksum: b9694ce092b7c55557122adba8337ebc
content_type: application/zip
creator: bkragl
date_created: 2020-09-04T13:00:17Z
date_updated: 2020-09-04T13:00:17Z
file_id: '8335'
file_name: kragl-thesis.zip
file_size: 372312
relation: source_file
file_date_updated: 2020-09-04T13:00:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '120'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '133'
relation: part_of_dissertation
status: public
- id: '8012'
relation: part_of_dissertation
status: public
- id: '8195'
relation: part_of_dissertation
status: public
- id: '160'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
title: 'Verifying concurrent programs: Refinement, synchronization, sequentialization'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '14326'
abstract:
- lang: eng
text: "Learning object-centric representations of complex scenes is a promising
step towards enabling efficient abstract reasoning from low-level perceptual features.
Yet, most deep learning approaches learn distributed representations that do not
capture the compositional properties of natural scenes. In this paper, we present
the Slot Attention module, an architectural component that interfaces with perceptual
representations such as the output of a convolutional neural network and produces
a set of task-dependent abstract representations which we call slots. These slots
are exchangeable and can bind to any object in the input by specializing through
a competitive procedure over multiple rounds of attention. We empirically demonstrate
that Slot Attention can extract object-centric representations that enable generalization
to unseen compositions when trained on unsupervised object discovery and supervised
property prediction tasks.\r\n\r\n"
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Dirk
full_name: Weissenborn, Dirk
last_name: Weissenborn
- first_name: Thomas
full_name: Unterthiner, Thomas
last_name: Unterthiner
- first_name: Aravindh
full_name: Mahendran, Aravindh
last_name: Mahendran
- first_name: Georg
full_name: Heigold, Georg
last_name: Heigold
- first_name: Jakob
full_name: Uszkoreit, Jakob
last_name: Uszkoreit
- first_name: Alexey
full_name: Dosovitskiy, Alexey
last_name: Dosovitskiy
- first_name: Thomas
full_name: Kipf, Thomas
last_name: Kipf
citation:
ama: 'Locatello F, Weissenborn D, Unterthiner T, et al. Object-centric learning
with slot attention. In: Advances in Neural Information Processing Systems.
Vol 33. Curran Associates; 2020:11525-11538.'
apa: 'Locatello, F., Weissenborn, D., Unterthiner, T., Mahendran, A., Heigold, G.,
Uszkoreit, J., … Kipf, T. (2020). Object-centric learning with slot attention.
In Advances in Neural Information Processing Systems (Vol. 33, pp. 11525–11538).
Virtual: Curran Associates.'
chicago: Locatello, Francesco, Dirk Weissenborn, Thomas Unterthiner, Aravindh Mahendran,
Georg Heigold, Jakob Uszkoreit, Alexey Dosovitskiy, and Thomas Kipf. “Object-Centric
Learning with Slot Attention.” In Advances in Neural Information Processing
Systems, 33:11525–38. Curran Associates, 2020.
ieee: F. Locatello et al., “Object-centric learning with slot attention,”
in Advances in Neural Information Processing Systems, Virtual, 2020, vol.
33, pp. 11525–11538.
ista: 'Locatello F, Weissenborn D, Unterthiner T, Mahendran A, Heigold G, Uszkoreit
J, Dosovitskiy A, Kipf T. 2020. Object-centric learning with slot attention. Advances
in Neural Information Processing Systems. NeurIPS: Neural Information Processing
Systems vol. 33, 11525–11538.'
mla: Locatello, Francesco, et al. “Object-Centric Learning with Slot Attention.”
Advances in Neural Information Processing Systems, vol. 33, Curran Associates,
2020, pp. 11525–38.
short: F. Locatello, D. Weissenborn, T. Unterthiner, A. Mahendran, G. Heigold, J.
Uszkoreit, A. Dosovitskiy, T. Kipf, in:, Advances in Neural Information Processing
Systems, Curran Associates, 2020, pp. 11525–11538.
conference:
end_date: 2020-12-12
location: Virtual
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2020-12-06
date_created: 2023-09-13T12:03:46Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2023-09-13T12:19:19Z
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2006.15055'
intvolume: ' 33'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2006.15055
oa: 1
oa_version: Preprint
page: 11525-11538
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713829546'
publication_status: published
publisher: Curran Associates
quality_controlled: '1'
status: public
title: Object-centric learning with slot attention
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2020'
...
---
_id: '71'
abstract:
- lang: eng
text: "We consider dynamical transport metrics for probability measures on discretisations
of a bounded convex domain in ℝd. These metrics are natural discrete counterparts
to the Kantorovich metric \U0001D54E2, defined using a Benamou-Brenier type formula.
Under mild assumptions we prove an asymptotic upper bound for the discrete transport
metric Wt in terms of \U0001D54E2, as the size of the mesh T tends to 0. However,
we show that the corresponding lower bound may fail in general, even on certain
one-dimensional and symmetric two-dimensional meshes. In addition, we show that
the asymptotic lower bound holds under an isotropy assumption on the mesh, which
turns out to be essentially necessary. This assumption is satisfied, e.g., for
tilings by convex regular polygons, and it implies Gromov-Hausdorff convergence
of the transport metric."
article_processing_charge: No
article_type: original
author:
- first_name: Peter
full_name: Gladbach, Peter
last_name: Gladbach
- first_name: Eva
full_name: Kopfer, Eva
last_name: Kopfer
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
citation:
ama: Gladbach P, Kopfer E, Maas J. Scaling limits of discrete optimal transport.
SIAM Journal on Mathematical Analysis. 2020;52(3):2759-2802. doi:10.1137/19M1243440
apa: Gladbach, P., Kopfer, E., & Maas, J. (2020). Scaling limits of discrete
optimal transport. SIAM Journal on Mathematical Analysis. Society for Industrial
and Applied Mathematics. https://doi.org/10.1137/19M1243440
chicago: Gladbach, Peter, Eva Kopfer, and Jan Maas. “Scaling Limits of Discrete
Optimal Transport.” SIAM Journal on Mathematical Analysis. Society for
Industrial and Applied Mathematics, 2020. https://doi.org/10.1137/19M1243440.
ieee: P. Gladbach, E. Kopfer, and J. Maas, “Scaling limits of discrete optimal transport,”
SIAM Journal on Mathematical Analysis, vol. 52, no. 3. Society for Industrial
and Applied Mathematics, pp. 2759–2802, 2020.
ista: Gladbach P, Kopfer E, Maas J. 2020. Scaling limits of discrete optimal transport.
SIAM Journal on Mathematical Analysis. 52(3), 2759–2802.
mla: Gladbach, Peter, et al. “Scaling Limits of Discrete Optimal Transport.” SIAM
Journal on Mathematical Analysis, vol. 52, no. 3, Society for Industrial and
Applied Mathematics, 2020, pp. 2759–802, doi:10.1137/19M1243440.
short: P. Gladbach, E. Kopfer, J. Maas, SIAM Journal on Mathematical Analysis 52
(2020) 2759–2802.
date_created: 2018-12-11T11:44:28Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2023-09-18T08:13:15Z
day: '01'
department:
- _id: JaMa
doi: 10.1137/19M1243440
external_id:
arxiv:
- '1809.01092'
isi:
- '000546975100017'
intvolume: ' 52'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.01092
month: '10'
oa: 1
oa_version: Preprint
page: 2759-2802
publication: SIAM Journal on Mathematical Analysis
publication_identifier:
eissn:
- '10957154'
issn:
- '00361410'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
publist_id: '7983'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scaling limits of discrete optimal transport
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 52
year: '2020'
...
---
_id: '5681'
abstract:
- lang: eng
text: 'We introduce dynamically warping grids for adaptive liquid simulation. Our
primary contributions are a strategy for dynamically deforming regular grids over
the course of a simulation and a method for efficiently utilizing these deforming
grids for liquid simulation. Prior work has shown that unstructured grids are
very effective for adaptive fluid simulations. However, unstructured grids often
lead to complicated implementations and a poor cache hit rate due to inconsistent
memory access. Regular grids, on the other hand, provide a fast, fixed memory
access pattern and straightforward implementation. Our method combines the advantages
of both: we leverage the simplicity of regular grids while still achieving practical
and controllable spatial adaptivity. We demonstrate that our method enables adaptive
simulations that are fast, flexible, and robust to null-space issues. At the same
time, our method is simple to implement and takes advantage of existing highly-tuned
algorithms.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: This work was partially supported by JSPS Grant-in-Aid forYoung Scientists
(Start-up) 16H07410, the ERC StartingGrantsrealFlow(StG-2015-637014) andBigSplash(StG-2014-638176).
This research was supported by the Scientific Ser-vice Units (SSU) of IST Austria
through resources providedby Scientific Computing. We would like to express my grati-tude
to Nobuyuki Umetani and Tomas Skrivan for insight-ful discussion.
article_processing_charge: No
article_type: original
author:
- first_name: Ibayashi
full_name: Hikaru, Ibayashi
last_name: Hikaru
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Nils
full_name: Thuerey, Nils
last_name: Thuerey
- first_name: Takeo
full_name: Igarashi, Takeo
last_name: Igarashi
- first_name: Ryoichi
full_name: Ando, Ryoichi
last_name: Ando
citation:
ama: Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. Simulating liquids on dynamically
warping grids. IEEE Transactions on Visualization and Computer Graphics.
2020;26(6):2288-2302. doi:10.1109/TVCG.2018.2883628
apa: Hikaru, I., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2020). Simulating
liquids on dynamically warping grids. IEEE Transactions on Visualization and
Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2018.2883628
chicago: Hikaru, Ibayashi, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi
Ando. “Simulating Liquids on Dynamically Warping Grids.” IEEE Transactions
on Visualization and Computer Graphics. IEEE, 2020. https://doi.org/10.1109/TVCG.2018.2883628.
ieee: I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Simulating liquids
on dynamically warping grids,” IEEE Transactions on Visualization and Computer
Graphics, vol. 26, no. 6. IEEE, pp. 2288–2302, 2020.
ista: Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. 2020. Simulating liquids
on dynamically warping grids. IEEE Transactions on Visualization and Computer
Graphics. 26(6), 2288–2302.
mla: Hikaru, Ibayashi, et al. “Simulating Liquids on Dynamically Warping Grids.”
IEEE Transactions on Visualization and Computer Graphics, vol. 26, no.
6, IEEE, 2020, pp. 2288–302, doi:10.1109/TVCG.2018.2883628.
short: I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, IEEE Transactions
on Visualization and Computer Graphics 26 (2020) 2288–2302.
date_created: 2018-12-16T22:59:21Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2023-09-18T09:30:01Z
day: '01'
ddc:
- '006'
department:
- _id: ChWo
doi: 10.1109/TVCG.2018.2883628
external_id:
isi:
- '000532295600014'
pmid:
- '30507534'
file:
- access_level: open_access
checksum: 8d4c55443a0ee335bb5bb652de503042
content_type: application/pdf
creator: wojtan
date_created: 2020-10-08T08:34:53Z
date_updated: 2020-10-08T08:34:53Z
file_id: '8626'
file_name: preprint.pdf
file_size: 21910098
relation: main_file
success: 1
file_date_updated: 2020-10-08T08:34:53Z
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 2288-2302
pmid: 1
publication: IEEE Transactions on Visualization and Computer Graphics
publication_identifier:
eissn:
- '19410506'
issn:
- '10772626'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Simulating liquids on dynamically warping grids
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 26
year: '2020'
...
---
_id: '8958'
abstract:
- lang: eng
text: "The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom
too many'' has been disavowed. Inspired by the possibility to experimentally manipulate
and enhance chemical reactivity in helium nanodroplets, we investigate the rotation
of coupled cold molecules in the presence of a many-body environment.\r\nIn this
thesis, we introduce new variational approaches to quantum impurities and apply
them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other
point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed
out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox,
we reveal the self-localization transition for the angulon quasiparticle. We show
that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath
coupling already at the mean-field level. The transition is accompanied by the
spherical-symmetry breaking of the angulon ground state and a discontinuity in
the first derivative of the ground-state energy. Moreover, the type of symmetry
breaking is dictated by the symmetry of the microscopic impurity-bath interaction,
which leads to a number of distinct self-localized states. \r\nFor the system
containing multiple impurities, by analogy with the bipolaron, we introduce the
biangulon quasiparticle describing two rotating molecules that align with respect
to each other due to the effective attractive interaction mediated by the excitations
of the bath. We study this system from the strong-coupling regime to the weak
molecule-bath interaction regime. We show that the molecules tend to have a strong
alignment in the ground state, the biangulon shows shifted angulon instabilities
and an additional spectral instability, where resonant angular momentum transfer
between the molecules and the bath takes place. Finally, we introduce a diagonalization
scheme that allows us to describe the transition from two separated angulons to
a biangulon as a function of the distance between the two molecules."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Xiang
full_name: Li, Xiang
id: 4B7E523C-F248-11E8-B48F-1D18A9856A87
last_name: Li
citation:
ama: Li X. Rotation of coupled cold molecules in the presence of a many-body environment.
2020. doi:10.15479/AT:ISTA:8958
apa: Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body
environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958
chicago: Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body
Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958.
ieee: X. Li, “Rotation of coupled cold molecules in the presence of a many-body
environment,” Institute of Science and Technology Austria, 2020.
ista: Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body
environment. Institute of Science and Technology Austria.
mla: Li, Xiang. Rotation of Coupled Cold Molecules in the Presence of a Many-Body
Environment. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8958.
short: X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body
Environment, Institute of Science and Technology Austria, 2020.
date_created: 2020-12-21T09:44:30Z
date_published: 2020-12-21T00:00:00Z
date_updated: 2023-09-20T11:30:58Z
day: '21'
ddc:
- '539'
degree_awarded: PhD
department:
- _id: MiLe
doi: 10.15479/AT:ISTA:8958
ec_funded: 1
file:
- access_level: open_access
checksum: 3994c54a1241451d561db1d4f43bad30
content_type: application/pdf
creator: xli
date_created: 2020-12-22T10:55:56Z
date_updated: 2020-12-22T10:55:56Z
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file_name: THESIS_Xiang_Li.pdf
file_size: 3622305
relation: main_file
success: 1
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checksum: 0954ecfc5554c05615c14de803341f00
content_type: application/x-zip-compressed
creator: xli
date_created: 2020-12-22T10:56:03Z
date_updated: 2020-12-30T07:18:03Z
file_id: '8968'
file_name: THESIS_Xiang_Li.zip
file_size: 4018859
relation: source_file
file_date_updated: 2020-12-30T07:18:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '125'
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '5886'
relation: part_of_dissertation
status: public
- id: '8587'
relation: part_of_dissertation
status: public
- id: '1120'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
title: Rotation of coupled cold molecules in the presence of a many-body environment
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8386'
abstract:
- lang: eng
text: "Form versus function is a long-standing debate in various design-related
fields, such as architecture as well as graphic and industrial design. A good
design that balances form and function often requires considerable human effort
and collaboration among experts from different professional fields. Computational
design tools provide a new paradigm for designing functional objects. In computational
design, form and function are represented as mathematical\r\nquantities, with
the help of numerical and combinatorial algorithms, they can assist even novice
users in designing versatile models that exhibit their desired functionality.
This thesis presents three disparate research studies on the computational design
of functional objects: The appearance of 3d print—we optimize the volumetric material
distribution for faithfully replicating colored surface texture in 3d printing;
the dynamic motion of mechanical structures—\r\nour design system helps the novice
user to retarget various mechanical templates with different functionality to
complex 3d shapes; and a more abstract functionality, multistability—our algorithm
automatically generates models that exhibit multiple stable target poses. For
each of these cases, our computational design tools not only ensure the functionality
of the results but also permit the user aesthetic freedom over the form. Moreover,
fabrication constraints\r\nwere taken into account, which allow for the immediate
creation of physical realization via 3D printing or laser cutting."
acknowledged_ssus:
- _id: SSU
acknowledgement: The research in this thesis has received funding from the European
Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie
grant agreement No 642841 (DISTRO) and the European Research Council grant agreement
No 715767 (MATERIALIZABLE). All the research projects in this thesis were also supported
by Scientific Service Units (SSUs) at IST Austria.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Ran
full_name: Zhang, Ran
id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0002-3808-281X
citation:
ama: Zhang R. Structure-aware computational design and its application to 3D printable
volume scattering, mechanism, and multistability. 2020. doi:10.15479/AT:ISTA:8386
apa: Zhang, R. (2020). Structure-aware computational design and its application
to 3D printable volume scattering, mechanism, and multistability. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8386
chicago: Zhang, Ran. “Structure-Aware Computational Design and Its Application to
3D Printable Volume Scattering, Mechanism, and Multistability.” Institute of Science
and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8386.
ieee: R. Zhang, “Structure-aware computational design and its application to 3D
printable volume scattering, mechanism, and multistability,” Institute of Science
and Technology Austria, 2020.
ista: Zhang R. 2020. Structure-aware computational design and its application to
3D printable volume scattering, mechanism, and multistability. Institute of Science
and Technology Austria.
mla: Zhang, Ran. Structure-Aware Computational Design and Its Application to
3D Printable Volume Scattering, Mechanism, and Multistability. Institute of
Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8386.
short: R. Zhang, Structure-Aware Computational Design and Its Application to 3D
Printable Volume Scattering, Mechanism, and Multistability, Institute of Science
and Technology Austria, 2020.
date_created: 2020-09-14T01:04:53Z
date_published: 2020-09-14T00:00:00Z
date_updated: 2023-09-22T09:49:31Z
day: '14'
ddc:
- '003'
degree_awarded: PhD
department:
- _id: BeBi
doi: 10.15479/AT:ISTA:8386
ec_funded: 1
file:
- access_level: closed
checksum: edcf578b6e1c9b0dd81ff72d319b66ba
content_type: application/x-zip-compressed
creator: rzhang
date_created: 2020-09-14T01:02:59Z
date_updated: 2020-09-14T12:18:43Z
file_id: '8388'
file_name: Thesis_Ran.zip
file_size: 1245800191
relation: source_file
- access_level: open_access
checksum: 817e20c33be9247f906925517c56a40d
content_type: application/pdf
creator: rzhang
date_created: 2020-09-15T12:51:53Z
date_updated: 2020-09-15T12:51:53Z
file_id: '8396'
file_name: PhD_thesis_Ran Zhang_20200915.pdf
file_size: 161385316
relation: main_file
success: 1
file_date_updated: 2020-09-15T12:51:53Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '148'
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '486'
relation: part_of_dissertation
status: public
- id: '1002'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
title: Structure-aware computational design and its application to 3D printable volume
scattering, mechanism, and multistability
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7996'
abstract:
- lang: eng
text: "Quantum computation enables the execution of algorithms that have exponential
complexity. This might open the path towards the synthesis of new materials or
medical drugs, optimization of transport or financial strategies etc., intractable
on even the fastest classical computers. A quantum computer consists of interconnected
two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide,
there are ongoing efforts to find the qubit architecture which will unite quantum
error correction compatible single and two qubit fidelities, long distance qubit
to qubit coupling and \r\n calability. Superconducting qubits have gone the furthest
in this race, demonstrating an algorithm running on 53 coupled qubits, but still
the fidelities are not even close to those required for realizing a single logical
qubit. emiconductor qubits offer extremely good characteristics, but they are
currently investigated across different platforms. Uniting those good characteristics
into a single platform might be a big step towards the quantum computer realization.\r\nHere
we describe the implementation of a hole spin qubit hosted in a Ge hut wire double
quantum dot. The high and tunable spin-orbit coupling together with a heavy hole
state character is expected to allow fast spin manipulation and long coherence
times. Furthermore large lever arms, for hut wire devices, should allow good coupling
to superconducting resonators enabling efficient long distance spin to spin coupling
and a sensitive gate reflectometry spin readout. The developed cryogenic setup
(printed circuit board sample holders, filtering, high-frequency wiring) enabled
us to perform low temperature spin dynamics experiments. Indeed, we measured the
fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz,
while the dephasing times of 130 ns oppose the long decoherence predictions. In
order to further investigate this, a double quantum dot gate was connected directly
to a lumped element\r\nresonator which enabled gate reflectometry readout. The
vanishing inter-dot transition signal, for increasing external magnetic field,
revealed the spin nature of the measured quantity."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
citation:
ama: Kukucka J. Implementation of a hole spin qubit in Ge hut wires and dispersive
spin sensing. 2020. doi:10.15479/AT:ISTA:7996
apa: Kukucka, J. (2020). Implementation of a hole spin qubit in Ge hut wires
and dispersive spin sensing. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:7996
chicago: Kukucka, Josip. “Implementation of a Hole Spin Qubit in Ge Hut Wires and
Dispersive Spin Sensing.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7996.
ieee: J. Kukucka, “Implementation of a hole spin qubit in Ge hut wires and dispersive
spin sensing,” Institute of Science and Technology Austria, 2020.
ista: Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive
spin sensing. Institute of Science and Technology Austria.
mla: Kukucka, Josip. Implementation of a Hole Spin Qubit in Ge Hut Wires and
Dispersive Spin Sensing. Institute of Science and Technology Austria, 2020,
doi:10.15479/AT:ISTA:7996.
short: J. Kukucka, Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive
Spin Sensing, Institute of Science and Technology Austria, 2020.
date_created: 2020-06-22T09:22:23Z
date_published: 2020-06-22T00:00:00Z
date_updated: 2023-09-26T15:50:22Z
day: '22'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GeKa
doi: 10.15479/AT:ISTA:7996
file:
- access_level: closed
checksum: 467e52feb3e361ce8cf5fe8d5c254ece
content_type: application/x-zip-compressed
creator: dernst
date_created: 2020-06-22T09:22:04Z
date_updated: 2020-07-14T12:48:07Z
file_id: '7997'
file_name: JK_thesis_latex_source_files.zip
file_size: 392794743
relation: main_file
- access_level: open_access
checksum: 1de716bf110dbd77d383e479232bf496
content_type: application/pdf
creator: dernst
date_created: 2020-06-22T09:21:29Z
date_updated: 2020-07-14T12:48:07Z
file_id: '7998'
file_name: PhD_thesis_JK_pdfa.pdf
file_size: 28453247
relation: main_file
file_date_updated: 2020-07-14T12:48:07Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '178'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1328'
relation: part_of_dissertation
status: public
- id: '7541'
relation: part_of_dissertation
status: public
- id: '77'
relation: part_of_dissertation
status: public
- id: '23'
relation: part_of_dissertation
status: public
- id: '840'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
title: Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8272'
abstract:
- lang: eng
text: We study turn-based stochastic zero-sum games with lexicographic preferences
over reachability and safety objectives. Stochastic games are standard models
in control, verification, and synthesis of stochastic reactive systems that exhibit
both randomness as well as angelic and demonic non-determinism. Lexicographic
order allows to consider multiple objectives with a strict preference order over
the satisfaction of the objectives. To the best of our knowledge, stochastic games
with lexicographic objectives have not been studied before. We establish determinacy
of such games and present strategy and computational complexity results. For strategy
complexity, we show that lexicographically optimal strategies exist that are deterministic
and memory is only required to remember the already satisfied and violated objectives.
For a constant number of objectives, we show that the relevant decision problem
is in NP∩coNP , matching the current known bound for single objectives; and
in general the decision problem is PSPACE -hard and can be solved in NEXPTIME∩coNEXPTIME
. We present an algorithm that computes the lexicographically optimal strategies
via a reduction to computation of optimal strategies in a sequence of single-objectives
games. We have implemented our algorithm and report experimental results on various
case studies.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Joost P
full_name: Katoen, Joost P
id: 4524F760-F248-11E8-B48F-1D18A9856A87
last_name: Katoen
- first_name: Maximilian
full_name: Weininger, Maximilian
last_name: Weininger
- first_name: Tobias
full_name: Winkler, Tobias
last_name: Winkler
citation:
ama: 'Chatterjee K, Katoen JP, Weininger M, Winkler T. Stochastic games with lexicographic
reachability-safety objectives. In: International Conference on Computer Aided
Verification. Vol 12225. Springer Nature; 2020:398-420. doi:10.1007/978-3-030-53291-8_21'
apa: Chatterjee, K., Katoen, J. P., Weininger, M., & Winkler, T. (2020). Stochastic
games with lexicographic reachability-safety objectives. In International Conference
on Computer Aided Verification (Vol. 12225, pp. 398–420). Springer Nature.
https://doi.org/10.1007/978-3-030-53291-8_21
chicago: Chatterjee, Krishnendu, Joost P Katoen, Maximilian Weininger, and Tobias
Winkler. “Stochastic Games with Lexicographic Reachability-Safety Objectives.”
In International Conference on Computer Aided Verification, 12225:398–420.
Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53291-8_21.
ieee: K. Chatterjee, J. P. Katoen, M. Weininger, and T. Winkler, “Stochastic games
with lexicographic reachability-safety objectives,” in International Conference
on Computer Aided Verification, 2020, vol. 12225, pp. 398–420.
ista: 'Chatterjee K, Katoen JP, Weininger M, Winkler T. 2020. Stochastic games with
lexicographic reachability-safety objectives. International Conference on Computer
Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 12225, 398–420.'
mla: Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Reachability-Safety
Objectives.” International Conference on Computer Aided Verification, vol.
12225, Springer Nature, 2020, pp. 398–420, doi:10.1007/978-3-030-53291-8_21.
short: K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International
Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420.
conference:
name: 'CAV: Computer Aided Verification'
date_created: 2020-08-16T22:00:58Z
date_published: 2020-07-14T00:00:00Z
date_updated: 2023-10-03T11:36:13Z
day: '14'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-030-53291-8_21
ec_funded: 1
external_id:
arxiv:
- '2005.04018'
isi:
- '000695272500021'
file:
- access_level: open_access
checksum: 093d4788d7d5b2ce0ffe64fbe7820043
content_type: application/pdf
creator: dernst
date_created: 2020-08-17T11:32:44Z
date_updated: 2020-08-17T11:32:44Z
file_id: '8276'
file_name: 2020_LNCS_CAV_Chatterjee.pdf
file_size: 625056
relation: main_file
success: 1
file_date_updated: 2020-08-17T11:32:44Z
has_accepted_license: '1'
intvolume: ' 12225'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 398-420
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: International Conference on Computer Aided Verification
publication_identifier:
eissn:
- '16113349'
isbn:
- '9783030532901'
issn:
- '03029743'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '12738'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Stochastic games with lexicographic reachability-safety objectives
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12225
year: '2020'
...
---
_id: '7572'
abstract:
- lang: eng
text: The polymerization–depolymerization dynamics of cytoskeletal proteins play
essential roles in the self-organization of cytoskeletal structures, in eukaryotic
as well as prokaryotic cells. While advances in fluorescence microscopy and in
vitro reconstitution experiments have helped to study the dynamic properties of
these complex systems, methods that allow to collect and analyze large quantitative
datasets of the underlying polymer dynamics are still missing. Here, we present
a novel image analysis workflow to study polymerization dynamics of active filaments
in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial
tubulin FtsZ as an example, we demonstrate that our method is able to specifically
detect, track and analyze growth and shrinkage of polymers, even in dense networks
of filaments. We believe that this automated method can facilitate the analysis
of a large variety of dynamic cytoskeletal systems, using standard time-lapse
movies obtained from experiments in vitro as well as in the living cell. Moreover,
we provide scripts implementing this method as supplementary material.
alternative_title:
- Methods in Cell Biology
article_processing_charge: No
author:
- first_name: Paulo R
full_name: Dos Santos Caldas, Paulo R
id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87
last_name: Dos Santos Caldas
orcid: 0000-0001-6730-4461
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: 'Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. Computational analysis
of filament polymerization dynamics in cytoskeletal networks. In: Tran P, ed.
Methods in Cell Biology. Vol 158. Elsevier; 2020:145-161. doi:10.1016/bs.mcb.2020.01.006'
apa: Dos Santos Caldas, P. R., Radler, P., Sommer, C. M., & Loose, M. (2020).
Computational analysis of filament polymerization dynamics in cytoskeletal networks.
In P. Tran (Ed.), Methods in Cell Biology (Vol. 158, pp. 145–161). Elsevier.
https://doi.org/10.1016/bs.mcb.2020.01.006
chicago: Dos Santos Caldas, Paulo R, Philipp Radler, Christoph M Sommer, and Martin
Loose. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal
Networks.” In Methods in Cell Biology, edited by Phong Tran, 158:145–61.
Elsevier, 2020. https://doi.org/10.1016/bs.mcb.2020.01.006.
ieee: P. R. Dos Santos Caldas, P. Radler, C. M. Sommer, and M. Loose, “Computational
analysis of filament polymerization dynamics in cytoskeletal networks,” in Methods
in Cell Biology, vol. 158, P. Tran, Ed. Elsevier, 2020, pp. 145–161.
ista: 'Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. 2020.Computational analysis
of filament polymerization dynamics in cytoskeletal networks. In: Methods in Cell
Biology. Methods in Cell Biology, vol. 158, 145–161.'
mla: Dos Santos Caldas, Paulo R., et al. “Computational Analysis of Filament Polymerization
Dynamics in Cytoskeletal Networks.” Methods in Cell Biology, edited by
Phong Tran, vol. 158, Elsevier, 2020, pp. 145–61, doi:10.1016/bs.mcb.2020.01.006.
short: P.R. Dos Santos Caldas, P. Radler, C.M. Sommer, M. Loose, in:, P. Tran (Ed.),
Methods in Cell Biology, Elsevier, 2020, pp. 145–161.
date_created: 2020-03-08T23:00:47Z
date_published: 2020-02-27T00:00:00Z
date_updated: 2023-10-04T09:50:24Z
day: '27'
department:
- _id: MaLo
doi: 10.1016/bs.mcb.2020.01.006
ec_funded: 1
editor:
- first_name: 'Phong '
full_name: 'Tran, Phong '
last_name: Tran
external_id:
isi:
- '000611826500008'
intvolume: ' 158'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/839571
month: '02'
oa: 1
oa_version: Preprint
page: 145-161
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: 260D98C8-B435-11E9-9278-68D0E5697425
name: Reconstitution of Bacterial Cell Division Using Purified Components
publication: Methods in Cell Biology
publication_identifier:
issn:
- 0091679X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '8358'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Computational analysis of filament polymerization dynamics in cytoskeletal
networks
type: book_chapter
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 158
year: '2020'
...
---
_id: '7387'
abstract:
- lang: eng
text: Most bacteria accomplish cell division with the help of a dynamic protein
complex called the divisome, which spans the cell envelope in the plane of division.
Assembly and activation of this machinery are coordinated by the tubulin-related
GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers
in vitro1, as well as in live cells, in which filaments circle around the cell
division site2,3. Treadmilling of FtsZ is thought to actively move proteins around
the division septum, thereby distributing peptidoglycan synthesis and coordinating
the inward growth of the septum to form the new poles of the daughter cells4.
However, the molecular mechanisms underlying this function are largely unknown.
Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins,
we reconstituted part of the bacterial cell division machinery using its purified
components FtsZ, FtsA and truncated transmembrane proteins essential for cell
division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ
co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed
collective behaviour, individual peptides showed random motion and transient confinement.
Our work suggests that divisome proteins follow treadmilling FtsZ filaments by
a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling
activity at the division site.
acknowledgement: We acknowledge members of the Loose laboratory at IST Austria for
helpful discussions—in particular, P. Caldas for help with the treadmilling analysis,
M. Jimenez, A. Raso and N. Ropero for providing Alexa Fluor 488- and Alexa Fluor
647-labelled FtsA for the MST and analytical ultracentrifugation experiments. We
thank C. You for providing the DODA-tris-NTA phospholipids, as well as J. Piehler
and C. Richter (Department of Biology, University of Osnabruck, Germany) for the
SLIMfast single-molecule tracking software and help with the confinement analysis.
We thank J. Errington and H. Murray (both at Newcastle University, UK) for critical
reading of the manuscript, and J. Brugués (MPI-CBG and MPI-PKS, Dresden, Germany)
for help with the MATLAB programming and reading of the manuscript. This work was
supported by the European Research Council through grant ERC-2015-StG-679239 to
M.L. and grants HFSP LT 000824/2016-L4 and EMBO ALTF 1163-2015 to N.B., a grant
from the Ministry of Economy and Competitiveness of the Spanish Government (BFU2016-75471-C2-1-P)
to C.A. and G.R., and a Wellcome Trust Senior Investigator award (101824/Z/13/Z)
and a grant from the BBSRC (BB/R017409/1) to W.V.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Víctor M.
full_name: Hernández-Rocamora, Víctor M.
last_name: Hernández-Rocamora
- first_name: Carlos
full_name: Alfonso, Carlos
last_name: Alfonso
- first_name: Maria D
full_name: Lopez Pelegrin, Maria D
id: 319AA9CE-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Pelegrin
- first_name: Germán
full_name: Rivas, Germán
last_name: Rivas
- first_name: Waldemar
full_name: Vollmer, Waldemar
last_name: Vollmer
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Baranova NS, Radler P, Hernández-Rocamora VM, et al. Diffusion and capture
permits dynamic coupling between treadmilling FtsZ filaments and cell division
proteins. Nature Microbiology. 2020;5:407-417. doi:10.1038/s41564-019-0657-5
apa: Baranova, N. S., Radler, P., Hernández-Rocamora, V. M., Alfonso, C., Lopez
Pelegrin, M. D., Rivas, G., … Loose, M. (2020). Diffusion and capture permits
dynamic coupling between treadmilling FtsZ filaments and cell division proteins.
Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0657-5
chicago: Baranova, Natalia S., Philipp Radler, Víctor M. Hernández-Rocamora, Carlos
Alfonso, Maria D Lopez Pelegrin, Germán Rivas, Waldemar Vollmer, and Martin Loose.
“Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments
and Cell Division Proteins.” Nature Microbiology. Springer Nature, 2020.
https://doi.org/10.1038/s41564-019-0657-5.
ieee: N. S. Baranova et al., “Diffusion and capture permits dynamic coupling
between treadmilling FtsZ filaments and cell division proteins,” Nature Microbiology,
vol. 5. Springer Nature, pp. 407–417, 2020.
ista: Baranova NS, Radler P, Hernández-Rocamora VM, Alfonso C, Lopez Pelegrin MD,
Rivas G, Vollmer W, Loose M. 2020. Diffusion and capture permits dynamic coupling
between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology.
5, 407–417.
mla: Baranova, Natalia S., et al. “Diffusion and Capture Permits Dynamic Coupling
between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology,
vol. 5, Springer Nature, 2020, pp. 407–17, doi:10.1038/s41564-019-0657-5.
short: N.S. Baranova, P. Radler, V.M. Hernández-Rocamora, C. Alfonso, M.D. Lopez
Pelegrin, G. Rivas, W. Vollmer, M. Loose, Nature Microbiology 5 (2020) 407–417.
date_created: 2020-01-28T16:14:41Z
date_published: 2020-01-20T00:00:00Z
date_updated: 2023-10-06T12:22:38Z
day: '20'
department:
- _id: MaLo
doi: 10.1038/s41564-019-0657-5
ec_funded: 1
external_id:
isi:
- '000508584700007'
pmid:
- '31959972'
intvolume: ' 5'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://europepmc.org/article/PMC/7048620
month: '01'
oa: 1
oa_version: Submitted Version
page: 407-417
pmid: 1
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: 259B655A-B435-11E9-9278-68D0E5697425
grant_number: LT000824/2016
name: Reconstitution of bacterial cell wall sythesis
- _id: 2596EAB6-B435-11E9-9278-68D0E5697425
grant_number: ALTF 2015-1163
name: Synthesis of bacterial cell wall
publication: Nature Microbiology
publication_identifier:
issn:
- 2058-5276
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/little-cell-big-cover-story/
record:
- id: '14280'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments
and cell division proteins
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2020'
...
---
_id: '8163'
abstract:
- lang: eng
text: Fejes Tóth [3] studied approximations of smooth surfaces in three-space by
piecewise flat triangular meshes with a given number of vertices on the surface
that are optimal with respect to Hausdorff distance. He proves that this Hausdorff
distance decreases inversely proportional with the number of vertices of the approximating
mesh if the surface is convex. He also claims that this Hausdorff distance is
inversely proportional to the square of the number of vertices for a specific
non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by
two congruent circles. We refute this claim, and show that the asymptotic behavior
of the Hausdorff distance is linear, that is the same as for convex surfaces.
acknowledgement: "The authors are greatly indebted to Dror Atariah, Günther Rote and
John Sullivan for discussion and suggestions. The authors also thank Jean-Daniel
Boissonnat, Ramsay Dyer, David de Laat and Rien van de Weijgaert for discussion.
This work has been supported in part by the European Union’s Seventh Framework Programme
for Research of the\r\nEuropean Commission, under FET-Open grant number 255827 (CGL
Computational Geometry Learning) and ERC Grant Agreement number 339025 GUDHI (Algorithmic
Foundations of Geometry Understanding in Higher Dimensions), the European Union’s
Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie
grant agreement number 754411,and the Austrian Science Fund (FWF): Z00342 N31."
article_processing_charge: No
article_type: original
author:
- first_name: Gert
full_name: Vegter, Gert
last_name: Vegter
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: Vegter G, Wintraecken M. Refutation of a claim made by Fejes Tóth on the accuracy
of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 2020;57(2):193-199.
doi:10.1556/012.2020.57.2.1454
apa: Vegter, G., & Wintraecken, M. (2020). Refutation of a claim made by Fejes
Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica.
Akadémiai Kiadó. https://doi.org/10.1556/012.2020.57.2.1454
chicago: Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes
Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum
Hungarica. Akadémiai Kiadó, 2020. https://doi.org/10.1556/012.2020.57.2.1454.
ieee: G. Vegter and M. Wintraecken, “Refutation of a claim made by Fejes Tóth on
the accuracy of surface meshes,” Studia Scientiarum Mathematicarum Hungarica,
vol. 57, no. 2. Akadémiai Kiadó, pp. 193–199, 2020.
ista: Vegter G, Wintraecken M. 2020. Refutation of a claim made by Fejes Tóth on
the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 57(2),
193–199.
mla: Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes
Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum
Hungarica, vol. 57, no. 2, Akadémiai Kiadó, 2020, pp. 193–99, doi:10.1556/012.2020.57.2.1454.
short: G. Vegter, M. Wintraecken, Studia Scientiarum Mathematicarum Hungarica 57
(2020) 193–199.
date_created: 2020-07-24T07:09:18Z
date_published: 2020-07-24T00:00:00Z
date_updated: 2023-10-10T13:05:27Z
day: '24'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1556/012.2020.57.2.1454
ec_funded: 1
external_id:
isi:
- '000570978400005'
file:
- access_level: open_access
content_type: application/pdf
creator: mwintrae
date_created: 2020-07-24T07:09:06Z
date_updated: 2020-07-24T07:09:06Z
file_id: '8164'
file_name: 57-2-05_4214-1454Vegter-Wintraecken_OpenAccess_CC-BY-NC.pdf
file_size: 1476072
relation: main_file
file_date_updated: 2020-07-24T07:09:06Z
has_accepted_license: '1'
intvolume: ' 57'
isi: 1
issue: '2'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 193-199
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
publication: Studia Scientiarum Mathematicarum Hungarica
publication_identifier:
eissn:
- 1588-2896
issn:
- 0081-6906
publication_status: published
publisher: Akadémiai Kiadó
quality_controlled: '1'
scopus_import: '1'
status: public
title: Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2020'
...
---
_id: '8671'
abstract:
- lang: eng
text: 'We study relations between evidence theory and S-approximation spaces. Both
theories have their roots in the analysis of Dempsterchr(''39'')s multivalued
mappings and lower and upper probabilities, and have close relations to rough
sets. We show that an S-approximation space, satisfying a monotonicity condition,
can induce a natural belief structure which is a fundamental block in evidence
theory. We also demonstrate that one can induce a natural belief structure on
one set, given a belief structure on another set, if the two sets are related
by a partial monotone S-approximation space. '
acknowledgement: We are very grateful to the anonymous reviewer for detailed comments
and suggestions that significantly improved the presentation of this paper. The
research was partially supported by a DOC fellowship of the Austrian Academy of
Sciences.
article_processing_charge: No
article_type: original
author:
- first_name: A.
full_name: Shakiba, A.
last_name: Shakiba
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: M.R.
full_name: Hooshmandasl, M.R.
last_name: Hooshmandasl
- first_name: M.
full_name: Alambardar Meybodi, M.
last_name: Alambardar Meybodi
citation:
ama: Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. A note on
belief structures and s-approximation spaces. Iranian Journal of Mathematical
Sciences and Informatics. 2020;15(2):117-128. doi:10.29252/ijmsi.15.2.117
apa: Shakiba, A., Goharshady, A. K., Hooshmandasl, M. R., & Alambardar Meybodi,
M. (2020). A note on belief structures and s-approximation spaces. Iranian
Journal of Mathematical Sciences and Informatics. Iranian Academic Center
for Education, Culture and Research. https://doi.org/10.29252/ijmsi.15.2.117
chicago: Shakiba, A., Amir Kafshdar Goharshady, M.R. Hooshmandasl, and M. Alambardar
Meybodi. “A Note on Belief Structures and S-Approximation Spaces.” Iranian
Journal of Mathematical Sciences and Informatics. Iranian Academic Center
for Education, Culture and Research, 2020. https://doi.org/10.29252/ijmsi.15.2.117.
ieee: A. Shakiba, A. K. Goharshady, M. R. Hooshmandasl, and M. Alambardar Meybodi,
“A note on belief structures and s-approximation spaces,” Iranian Journal of
Mathematical Sciences and Informatics, vol. 15, no. 2. Iranian Academic Center
for Education, Culture and Research, pp. 117–128, 2020.
ista: Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. 2020. A note
on belief structures and s-approximation spaces. Iranian Journal of Mathematical
Sciences and Informatics. 15(2), 117–128.
mla: Shakiba, A., et al. “A Note on Belief Structures and S-Approximation Spaces.”
Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no.
2, Iranian Academic Center for Education, Culture and Research, 2020, pp. 117–28,
doi:10.29252/ijmsi.15.2.117.
short: A. Shakiba, A.K. Goharshady, M.R. Hooshmandasl, M. Alambardar Meybodi, Iranian
Journal of Mathematical Sciences and Informatics 15 (2020) 117–128.
date_created: 2020-10-18T22:01:36Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2023-10-16T09:25:00Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.29252/ijmsi.15.2.117
external_id:
arxiv:
- '1805.10672'
file:
- access_level: open_access
checksum: f299661a6d51cda6d255a76be696f48d
content_type: application/pdf
creator: dernst
date_created: 2020-10-19T11:14:20Z
date_updated: 2020-10-19T11:14:20Z
file_id: '8676'
file_name: 2020_ijmsi_Shakiba_accepted.pdf
file_size: 261688
relation: main_file
success: 1
file_date_updated: 2020-10-19T11:14:20Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 117-128
project:
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: Iranian Journal of Mathematical Sciences and Informatics
publication_identifier:
eissn:
- 2008-9473
issn:
- 1735-4463
publication_status: published
publisher: Iranian Academic Center for Education, Culture and Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: A note on belief structures and s-approximation spaces
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2020'
...
---
_id: '6359'
abstract:
- lang: eng
text: The strong rate of convergence of the Euler-Maruyama scheme for nondegenerate
SDEs with irregular drift coefficients is considered. In the case of α-Hölder
drift in the recent literature the rate α/2 was proved in many related situations.
By exploiting the regularising effect of the noise more efficiently, we show that
the rate is in fact arbitrarily close to 1/2 for all α>0. The result extends to
Dini continuous coefficients, while in d=1 also to all bounded measurable coefficients.
article_number: '82'
article_processing_charge: No
article_type: original
author:
- first_name: Konstantinos
full_name: Dareiotis, Konstantinos
last_name: Dareiotis
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
citation:
ama: Dareiotis K, Gerencser M. On the regularisation of the noise for the Euler-Maruyama
scheme with irregular drift. Electronic Journal of Probability. 2020;25.
doi:10.1214/20-EJP479
apa: Dareiotis, K., & Gerencser, M. (2020). On the regularisation of the noise
for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP479
chicago: Dareiotis, Konstantinos, and Mate Gerencser. “On the Regularisation of
the Noise for the Euler-Maruyama Scheme with Irregular Drift.” Electronic Journal
of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP479.
ieee: K. Dareiotis and M. Gerencser, “On the regularisation of the noise for the
Euler-Maruyama scheme with irregular drift,” Electronic Journal of Probability,
vol. 25. Institute of Mathematical Statistics, 2020.
ista: Dareiotis K, Gerencser M. 2020. On the regularisation of the noise for the
Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability.
25, 82.
mla: Dareiotis, Konstantinos, and Mate Gerencser. “On the Regularisation of the
Noise for the Euler-Maruyama Scheme with Irregular Drift.” Electronic Journal
of Probability, vol. 25, 82, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP479.
short: K. Dareiotis, M. Gerencser, Electronic Journal of Probability 25 (2020).
date_created: 2019-04-30T07:40:17Z
date_published: 2020-07-16T00:00:00Z
date_updated: 2023-10-16T09:22:50Z
day: '16'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1214/20-EJP479
external_id:
arxiv:
- '1812.04583'
isi:
- '000550150700001'
file:
- access_level: open_access
checksum: 8e7c42e72596f6889d786e8e8b89994f
content_type: application/pdf
creator: dernst
date_created: 2020-09-21T13:15:02Z
date_updated: 2020-09-21T13:15:02Z
file_id: '8549'
file_name: 2020_EJournProbab_Dareiotis.pdf
file_size: 273042
relation: main_file
success: 1
file_date_updated: 2020-09-21T13:15:02Z
has_accepted_license: '1'
intvolume: ' 25'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Electronic Journal of Probability
publication_identifier:
eissn:
- 1083-6489
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the regularisation of the noise for the Euler-Maruyama scheme with irregular
drift
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: 25
year: '2020'
...
---
_id: '8390'
abstract:
- lang: eng
text: "Deep neural networks have established a new standard for data-dependent feature
extraction pipelines in the Computer Vision literature. Despite their remarkable
performance in the standard supervised learning scenario, i.e. when models are
trained with labeled data and tested on samples that follow a similar distribution,
neural networks have been shown to struggle with more advanced generalization
abilities, such as transferring knowledge across visually different domains, or
generalizing to new unseen combinations of known concepts. In this thesis we argue
that, in contrast to the usual black-box behavior of neural networks, leveraging
more structured internal representations is a promising direction\r\nfor tackling
such problems. In particular, we focus on two forms of structure. First, we tackle
modularity: We show that (i) compositional architectures are a natural tool for
modeling reasoning tasks, in that they efficiently capture their combinatorial
nature, which is key for generalizing beyond the compositions seen during training.
We investigate how to to learn such models, both formally and experimentally,
for the task of abstract visual reasoning. Then, we show that (ii) in some settings,
modularity allows us to efficiently break down complex tasks into smaller, easier,
modules, thereby improving computational efficiency; We study this behavior in
the context of generative models for colorization, as well as for small objects
detection. Secondly, we investigate the inherently layered structure of representations
learned by neural networks, and analyze its role in the context of transfer learning
and domain adaptation across visually\r\ndissimilar domains. "
acknowledged_ssus:
- _id: CampIT
- _id: ScienComp
acknowledgement: Last but not least, I would like to acknowledge the support of the
IST IT and scientific computing team for helping provide a great work environment.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Amélie
full_name: Royer, Amélie
id: 3811D890-F248-11E8-B48F-1D18A9856A87
last_name: Royer
orcid: 0000-0002-8407-0705
citation:
ama: Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning
models. 2020. doi:10.15479/AT:ISTA:8390
apa: Royer, A. (2020). Leveraging structure in Computer Vision tasks for flexible
Deep Learning models. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8390
chicago: Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible
Deep Learning Models.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8390.
ieee: A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep
Learning models,” Institute of Science and Technology Austria, 2020.
ista: Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible
Deep Learning models. Institute of Science and Technology Austria.
mla: Royer, Amélie. Leveraging Structure in Computer Vision Tasks for Flexible
Deep Learning Models. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8390.
short: A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep
Learning Models, Institute of Science and Technology Austria, 2020.
date_created: 2020-09-14T13:42:09Z
date_published: 2020-09-14T00:00:00Z
date_updated: 2023-10-16T10:04:02Z
day: '14'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ChLa
doi: 10.15479/AT:ISTA:8390
file:
- access_level: open_access
checksum: c914d2f88846032f3d8507734861b6ee
content_type: application/pdf
creator: dernst
date_created: 2020-09-14T13:39:14Z
date_updated: 2020-09-14T13:39:14Z
file_id: '8391'
file_name: 2020_Thesis_Royer.pdf
file_size: 30224591
relation: main_file
success: 1
- access_level: closed
checksum: ae98fb35d912cff84a89035ae5794d3c
content_type: application/x-zip-compressed
creator: dernst
date_created: 2020-09-14T13:39:17Z
date_updated: 2020-09-14T13:39:17Z
file_id: '8392'
file_name: thesis_sources.zip
file_size: 74227627
relation: main_file
file_date_updated: 2020-09-14T13:39:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '197'
publication_identifier:
isbn:
- 978-3-99078-007-7
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7936'
relation: part_of_dissertation
status: public
- id: '7937'
relation: part_of_dissertation
status: public
- id: '8193'
relation: part_of_dissertation
status: public
- id: '8092'
relation: part_of_dissertation
status: public
- id: '911'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
title: Leveraging structure in Computer Vision tasks for flexible Deep Learning models
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8186'
abstract:
- lang: eng
text: "Numerous methods have been proposed for probabilistic generative modelling
of\r\n3D objects. However, none of these is able to produce textured objects,
which\r\nrenders them of limited use for practical tasks. In this work, we present
the\r\nfirst generative model of textured 3D meshes. Training such a model would\r\ntraditionally
require a large dataset of textured meshes, but unfortunately,\r\nexisting datasets
of meshes lack detailed textures. We instead propose a new\r\ntraining methodology
that allows learning from collections of 2D images without\r\nany 3D information.
To do so, we train our model to explain a distribution of\r\nimages by modelling
each image as a 3D foreground object placed in front of a\r\n2D background. Thus,
it learns to generate meshes that when rendered, produce\r\nimages similar to
those in its training set.\r\n A well-known problem when generating meshes with
deep networks is the\r\nemergence of self-intersections, which are problematic
for many use-cases. As a\r\nsecond contribution we therefore introduce a new generation
process for 3D\r\nmeshes that guarantees no self-intersections arise, based on
the physical\r\nintuition that faces should push one another out of the way as
they move.\r\n We conduct extensive experiments on our approach, reporting quantitative
and\r\nqualitative results on both synthetic data and natural images. These show
our\r\nmethod successfully learns to generate plausible and diverse textured 3D\r\nsamples
for five challenging object classes."
article_processing_charge: No
author:
- first_name: Paul M
full_name: Henderson, Paul M
id: 13C09E74-18D9-11E9-8878-32CFE5697425
last_name: Henderson
orcid: 0000-0002-5198-7445
- first_name: Vagia
full_name: Tsiminaki, Vagia
last_name: Tsiminaki
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Henderson PM, Tsiminaki V, Lampert C. Leveraging 2D data to learn textured
3D mesh generation. In: Proceedings of the IEEE/CVF Conference on Computer
Vision and Pattern Recognition. IEEE; 2020:7498-7507. doi:10.1109/CVPR42600.2020.00752'
apa: 'Henderson, P. M., Tsiminaki, V., & Lampert, C. (2020). Leveraging 2D data
to learn textured 3D mesh generation. In Proceedings of the IEEE/CVF Conference
on Computer Vision and Pattern Recognition (pp. 7498–7507). Virtual: IEEE.
https://doi.org/10.1109/CVPR42600.2020.00752'
chicago: Henderson, Paul M, Vagia Tsiminaki, and Christoph Lampert. “Leveraging
2D Data to Learn Textured 3D Mesh Generation.” In Proceedings of the IEEE/CVF
Conference on Computer Vision and Pattern Recognition, 7498–7507. IEEE, 2020.
https://doi.org/10.1109/CVPR42600.2020.00752.
ieee: P. M. Henderson, V. Tsiminaki, and C. Lampert, “Leveraging 2D data to learn
textured 3D mesh generation,” in Proceedings of the IEEE/CVF Conference on
Computer Vision and Pattern Recognition, Virtual, 2020, pp. 7498–7507.
ista: 'Henderson PM, Tsiminaki V, Lampert C. 2020. Leveraging 2D data to learn textured
3D mesh generation. Proceedings of the IEEE/CVF Conference on Computer Vision
and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition,
7498–7507.'
mla: Henderson, Paul M., et al. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.”
Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition,
IEEE, 2020, pp. 7498–507, doi:10.1109/CVPR42600.2020.00752.
short: P.M. Henderson, V. Tsiminaki, C. Lampert, in:, Proceedings of the IEEE/CVF
Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–7507.
conference:
end_date: 2020-06-19
location: Virtual
name: 'CVPR: Conference on Computer Vision and Pattern Recognition'
start_date: 2020-06-14
date_created: 2020-07-31T16:53:49Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2023-10-17T07:37:11Z
day: '01'
ddc:
- '004'
department:
- _id: ChLa
doi: 10.1109/CVPR42600.2020.00752
external_id:
arxiv:
- '2004.04180'
file:
- access_level: open_access
content_type: application/pdf
creator: phenders
date_created: 2020-07-31T16:57:12Z
date_updated: 2020-07-31T16:57:12Z
file_id: '8187'
file_name: paper.pdf
file_size: 10262773
relation: main_file
success: 1
file_date_updated: 2020-07-31T16:57:12Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://openaccess.thecvf.com/content_CVPR_2020/papers/Henderson_Leveraging_2D_Data_to_Learn_Textured_3D_Mesh_Generation_CVPR_2020_paper.pdf
month: '07'
oa: 1
oa_version: Submitted Version
page: 7498-7507
publication: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern
Recognition
publication_identifier:
eisbn:
- '9781728171685'
eissn:
- 2575-7075
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Leveraging 2D data to learn textured 3D mesh generation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7416'
abstract:
- lang: eng
text: Earlier, we demonstrated that transcript levels of METAL TOLERANCE PROTEIN2
(MTP2) and of HEAVY METAL ATPase2 (HMA2) increase strongly in roots of Arabidopsis
upon prolonged zinc (Zn) deficiency and respond to shoot physiological Zn status,
and not to the local Zn status in roots. This provided evidence for shoot-to-root
communication in the acclimation of plants to Zn deficiency. Zn-deficient soils
limit both the yield and quality of agricultural crops and can result in clinically
relevant nutritional Zn deficiency in human populations. Implementing Zn deficiency
during cultivation of the model plant Arabidopsis thaliana on agar-solidified
media is difficult because trace element contaminations are present in almost
all commercially available agars. Here, we demonstrate root morphological acclimations
to Zn deficiency on agar-solidified medium following the effective removal of
contaminants. These advancements allow reproducible phenotyping toward understanding
fundamental plant responses to deficiencies of Zn and other essential trace elements.
article_number: '1687175'
article_processing_charge: No
article_type: original
author:
- first_name: Scott A
full_name: Sinclair, Scott A
id: 2D99FE6A-F248-11E8-B48F-1D18A9856A87
last_name: Sinclair
orcid: 0000-0002-4566-0593
- first_name: U.
full_name: Krämer, U.
last_name: Krämer
citation:
ama: Sinclair SA, Krämer U. Generation of effective zinc-deficient agar-solidified
media allows identification of root morphology changes in response to zinc limitation.
Plant Signaling & Behavior. 2020;15(1). doi:10.1080/15592324.2019.1687175
apa: Sinclair, S. A., & Krämer, U. (2020). Generation of effective zinc-deficient
agar-solidified media allows identification of root morphology changes in response
to zinc limitation. Plant Signaling & Behavior. Taylor & Francis.
https://doi.org/10.1080/15592324.2019.1687175
chicago: Sinclair, Scott A, and U. Krämer. “Generation of Effective Zinc-Deficient
Agar-Solidified Media Allows Identification of Root Morphology Changes in Response
to Zinc Limitation.” Plant Signaling & Behavior. Taylor & Francis,
2020. https://doi.org/10.1080/15592324.2019.1687175.
ieee: S. A. Sinclair and U. Krämer, “Generation of effective zinc-deficient agar-solidified
media allows identification of root morphology changes in response to zinc limitation,”
Plant Signaling & Behavior, vol. 15, no. 1. Taylor & Francis, 2020.
ista: Sinclair SA, Krämer U. 2020. Generation of effective zinc-deficient agar-solidified
media allows identification of root morphology changes in response to zinc limitation.
Plant Signaling & Behavior. 15(1), 1687175.
mla: Sinclair, Scott A., and U. Krämer. “Generation of Effective Zinc-Deficient
Agar-Solidified Media Allows Identification of Root Morphology Changes in Response
to Zinc Limitation.” Plant Signaling & Behavior, vol. 15, no. 1, 1687175,
Taylor & Francis, 2020, doi:10.1080/15592324.2019.1687175.
short: S.A. Sinclair, U. Krämer, Plant Signaling & Behavior 15 (2020).
date_created: 2020-01-30T10:12:04Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2023-10-17T09:01:48Z
day: '01'
department:
- _id: JiFr
doi: 10.1080/15592324.2019.1687175
external_id:
isi:
- '000494909300001'
pmid:
- '31696764'
intvolume: ' 15'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012054
month: '01'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Plant Signaling & Behavior
publication_identifier:
issn:
- 1559-2324
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Generation of effective zinc-deficient agar-solidified media allows identification
of root morphology changes in response to zinc limitation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2020'
...
---
_id: '7464'
abstract:
- lang: eng
text: 'Retrovirus assembly is driven by the multidomain structural protein Gag.
Interactions between the capsid domains (CA) of Gag result in Gag multimerization,
leading to an immature virus particle that is formed by a protein lattice based
on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter-
and intra-hexamer contacts differ, especially in the N-terminal sub-domain of
CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts
with and stabilizes the immature hexamer, and is required for production of infectious
virus particles. We have used in vitro assembly, cryo-electron tomography and
subtomogram averaging, atomistic molecular dynamics simulations and mutational
analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV).
In particular, we sought to understand the structural conservation of the immature
lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6
strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles
(VLPs), which took three morphologically highly distinct forms: narrow tubes,
wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution
unexpectedly showed that all three morphologies are based on an immature lattice
with preserved key structural components, highlighting the structural versatility
of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed
that both lentiviruses maintain similar immature interfaces, which are established
by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates
immature assembly via conserved lysine residues within the CACTD and SP. Lastly,
we demonstrate that IP6 stimulates in vitro assembly of immature particles of
several other retroviruses in the lentivirus genus, suggesting a conserved role
for IP6 in lentiviral assembly.'
acknowledged_ssus:
- _id: ScienComp
article_number: e1008277
article_processing_charge: No
article_type: original
author:
- first_name: Robert A.
full_name: Dick, Robert A.
last_name: Dick
- first_name: Chaoyi
full_name: Xu, Chaoyi
last_name: Xu
- first_name: Dustin R.
full_name: Morado, Dustin R.
last_name: Morado
- first_name: Vladyslav
full_name: Kravchuk, Vladyslav
id: 4D62F2A6-F248-11E8-B48F-1D18A9856A87
last_name: Kravchuk
orcid: 0000-0001-9523-9089
- first_name: Clifton L.
full_name: Ricana, Clifton L.
last_name: Ricana
- first_name: Terri D.
full_name: Lyddon, Terri D.
last_name: Lyddon
- first_name: Arianna M.
full_name: Broad, Arianna M.
last_name: Broad
- first_name: J. Ryan
full_name: Feathers, J. Ryan
last_name: Feathers
- first_name: Marc C.
full_name: Johnson, Marc C.
last_name: Johnson
- first_name: Volker M.
full_name: Vogt, Volker M.
last_name: Vogt
- first_name: Juan R.
full_name: Perilla, Juan R.
last_name: Perilla
- first_name: John A. G.
full_name: Briggs, John A. G.
last_name: Briggs
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal
a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 2020;16(1).
doi:10.1371/journal.ppat.1008277
apa: Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T.
D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved
role for IP6 in lentivirus assembly. PLOS Pathogens. Public Library of
Science. https://doi.org/10.1371/journal.ppat.1008277
chicago: Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton
L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV
Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS
Pathogens. Public Library of Science, 2020. https://doi.org/10.1371/journal.ppat.1008277.
ieee: R. A. Dick et al., “Structures of immature EIAV Gag lattices reveal
a conserved role for IP6 in lentivirus assembly,” PLOS Pathogens, vol.
16, no. 1. Public Library of Science, 2020.
ista: Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers
JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of
immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly.
PLOS Pathogens. 16(1), e1008277.
mla: Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a
Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens, vol. 16,
no. 1, e1008277, Public Library of Science, 2020, doi:10.1371/journal.ppat.1008277.
short: R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M.
Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K.
Schur, PLOS Pathogens 16 (2020).
date_created: 2020-02-06T18:47:17Z
date_published: 2020-01-27T00:00:00Z
date_updated: 2023-10-17T12:29:34Z
day: '27'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1371/journal.ppat.1008277
external_id:
isi:
- '000510746400010'
pmid:
- '31986188'
file:
- access_level: open_access
checksum: a297f54d1fef0efe4789ca00f37f241e
content_type: application/pdf
creator: dernst
date_created: 2020-02-11T10:07:28Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7484'
file_name: 2020_PLOSPatho_Dick.pdf
file_size: 4551246
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
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name: Structural conservation and diversity in retroviral capsid
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title: Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in
lentivirus assembly
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...