---
_id: '1022'
abstract:
- lang: eng
text: We introduce a multiscale topological description of the Megaparsec web-like
cosmic matter distribution. Betti numbers and topological persistence offer a
powerful means of describing the rich connectivity structure of the cosmic web
and of its multiscale arrangement of matter and galaxies. Emanating from algebraic
topology and Morse theory, Betti numbers and persistence diagrams represent an
extension and deepening of the cosmologically familiar topological genus measure
and the related geometric Minkowski functionals. In addition to a description
of the mathematical background, this study presents the computational procedure
for computing Betti numbers and persistence diagrams for density field filtrations.
The field may be computed starting from a discrete spatial distribution of galaxies
or simulation particles. The main emphasis of this study concerns an extensive
and systematic exploration of the imprint of different web-like morphologies and
different levels of multiscale clustering in the corresponding computed Betti
numbers and persistence diagrams. To this end, we use Voronoi clustering models
as templates for a rich variety of web-like configurations and the fractal-like
Soneira-Peebles models exemplify a range of multiscale configurations. We have
identified the clear imprint of cluster nodes, filaments, walls, and voids in
persistence diagrams, along with that of the nested hierarchy of structures in
multiscale point distributions. We conclude by outlining the potential of persistent
topology for understanding the connectivity structure of the cosmic web, in large
simulations of cosmic structure formation and in the challenging context of the
observed galaxy distribution in large galaxy surveys.
acknowledgement: Part of this work has been supported by the 7th Framework Programme
for Research of the European Commission, under FETOpen grant number 255827 (CGL
Computational Geometry Learning) and ERC advanced grant, URSAT (Understanding Random
Systems via Algebraic Topology) number 320422.
article_processing_charge: No
author:
- first_name: Pratyush
full_name: Pranav, Pratyush
last_name: Pranav
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Rien
full_name: Van De Weygaert, Rien
last_name: Van De Weygaert
- first_name: Gert
full_name: Vegter, Gert
last_name: Vegter
- first_name: Michael
full_name: Kerber, Michael
last_name: Kerber
- first_name: Bernard
full_name: Jones, Bernard
last_name: Jones
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: Pranav P, Edelsbrunner H, Van De Weygaert R, et al. The topology of the cosmic
web in terms of persistent Betti numbers. Monthly Notices of the Royal Astronomical
Society. 2017;465(4):4281-4310. doi:10.1093/mnras/stw2862
apa: Pranav, P., Edelsbrunner, H., Van De Weygaert, R., Vegter, G., Kerber, M.,
Jones, B., & Wintraecken, M. (2017). The topology of the cosmic web in terms
of persistent Betti numbers. Monthly Notices of the Royal Astronomical Society.
Oxford University Press. https://doi.org/10.1093/mnras/stw2862
chicago: Pranav, Pratyush, Herbert Edelsbrunner, Rien Van De Weygaert, Gert Vegter,
Michael Kerber, Bernard Jones, and Mathijs Wintraecken. “The Topology of the Cosmic
Web in Terms of Persistent Betti Numbers.” Monthly Notices of the Royal Astronomical
Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stw2862.
ieee: P. Pranav et al., “The topology of the cosmic web in terms of persistent
Betti numbers,” Monthly Notices of the Royal Astronomical Society, vol.
465, no. 4. Oxford University Press, pp. 4281–4310, 2017.
ista: Pranav P, Edelsbrunner H, Van De Weygaert R, Vegter G, Kerber M, Jones B,
Wintraecken M. 2017. The topology of the cosmic web in terms of persistent Betti
numbers. Monthly Notices of the Royal Astronomical Society. 465(4), 4281–4310.
mla: Pranav, Pratyush, et al. “The Topology of the Cosmic Web in Terms of Persistent
Betti Numbers.” Monthly Notices of the Royal Astronomical Society, vol.
465, no. 4, Oxford University Press, 2017, pp. 4281–310, doi:10.1093/mnras/stw2862.
short: P. Pranav, H. Edelsbrunner, R. Van De Weygaert, G. Vegter, M. Kerber, B.
Jones, M. Wintraecken, Monthly Notices of the Royal Astronomical Society 465 (2017)
4281–4310.
date_created: 2018-12-11T11:49:44Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-22T09:40:55Z
day: '01'
department:
- _id: HeEd
doi: 10.1093/mnras/stw2862
external_id:
isi:
- '000395170200039'
intvolume: ' 465'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.04519
month: '01'
oa: 1
oa_version: Submitted Version
page: 4281 - 4310
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
issn:
- '00358711'
publication_status: published
publisher: Oxford University Press
publist_id: '6373'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The topology of the cosmic web in terms of persistent Betti numbers
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 465
year: '2017'
...
---
_id: '1023'
abstract:
- lang: eng
text: We consider products of independent square non-Hermitian random matrices.
More precisely, let X1,…, Xn be independent N × N random matrices with independent
entries (real or complex with independent real and imaginary parts) with zero
mean and variance 1/N. Soshnikov-O’Rourke [19] and Götze-Tikhomirov [15] showed
that the empirical spectral distribution of the product of n random matrices with
iid entries converges to (equation found). We prove that if the entries of the
matrices X1,…, Xn are independent (but not necessarily identically distributed)
and satisfy uniform subexponential decay condition, then in the bulk the convergence
of the ESD of X1,…, Xn to (0.1) holds up to the scale N–1/2+ε.
article_number: '22'
article_processing_charge: No
author:
- first_name: Yuriy
full_name: Nemish, Yuriy
id: 4D902E6A-F248-11E8-B48F-1D18A9856A87
last_name: Nemish
orcid: 0000-0002-7327-856X
citation:
ama: Nemish Y. Local law for the product of independent non-Hermitian random matrices
with independent entries. Electronic Journal of Probability. 2017;22. doi:10.1214/17-EJP38
apa: Nemish, Y. (2017). Local law for the product of independent non-Hermitian random
matrices with independent entries. Electronic Journal of Probability. Institute
of Mathematical Statistics. https://doi.org/10.1214/17-EJP38
chicago: Nemish, Yuriy. “Local Law for the Product of Independent Non-Hermitian
Random Matrices with Independent Entries.” Electronic Journal of Probability.
Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/17-EJP38.
ieee: Y. Nemish, “Local law for the product of independent non-Hermitian random
matrices with independent entries,” Electronic Journal of Probability,
vol. 22. Institute of Mathematical Statistics, 2017.
ista: Nemish Y. 2017. Local law for the product of independent non-Hermitian random
matrices with independent entries. Electronic Journal of Probability. 22, 22.
mla: Nemish, Yuriy. “Local Law for the Product of Independent Non-Hermitian Random
Matrices with Independent Entries.” Electronic Journal of Probability,
vol. 22, 22, Institute of Mathematical Statistics, 2017, doi:10.1214/17-EJP38.
short: Y. Nemish, Electronic Journal of Probability 22 (2017).
date_created: 2018-12-11T11:49:44Z
date_published: 2017-02-06T00:00:00Z
date_updated: 2023-09-22T09:27:51Z
day: '06'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1214/17-EJP38
external_id:
isi:
- '000396611900022'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:29Z
date_updated: 2018-12-12T10:15:29Z
file_id: '5149'
file_name: IST-2017-802-v1+1_euclid.ejp.1487991681.pdf
file_size: 742275
relation: main_file
file_date_updated: 2018-12-12T10:15:29Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '02'
oa: 1
oa_version: Published Version
publication: Electronic Journal of Probability
publication_identifier:
issn:
- '10836489'
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '6370'
pubrep_id: '802'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local law for the product of independent non-Hermitian random matrices with
independent entries
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 22
year: '2017'
...
---
_id: '1024'
abstract:
- lang: eng
text: The history of auxin and cytokinin biology including the initial discoveries
by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt
(1919) is a beautiful demonstration of unceasing continuity of research. Novel
findings are integrated into existing hypotheses and models and deepen our understanding
of biological principles. At the same time new questions are triggered and hand
to hand with this new methodologies are developed to address these new challenges.
alternative_title:
- Methods in Molecular Biology
author:
- first_name: Andrej
full_name: Hurny, Andrej
id: 4DC4AF46-F248-11E8-B48F-1D18A9856A87
last_name: Hurny
orcid: 0000-0003-3638-1426
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Hurny A, Benková E. Methodological advances in auxin and cytokinin biology.
Auxins and Cytokinins in Plant Biology. 2017;1569:1-29. doi:10.1007/978-1-4939-6831-2_1
apa: Hurny, A., & Benková, E. (2017). Methodological advances in auxin and cytokinin
biology. Auxins and Cytokinins in Plant Biology. Springer. https://doi.org/10.1007/978-1-4939-6831-2_1
chicago: Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin
Biology.” Auxins and Cytokinins in Plant Biology. Springer, 2017. https://doi.org/10.1007/978-1-4939-6831-2_1.
ieee: A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,”
Auxins and Cytokinins in Plant Biology, vol. 1569. Springer, pp. 1–29,
2017.
ista: Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology.
Auxins and Cytokinins in Plant Biology. 1569, 1–29.
mla: Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin
Biology.” Auxins and Cytokinins in Plant Biology, vol. 1569, Springer,
2017, pp. 1–29, doi:10.1007/978-1-4939-6831-2_1.
short: A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017)
1–29.
date_created: 2018-12-11T11:49:45Z
date_published: 2017-03-17T00:00:00Z
date_updated: 2024-03-25T23:30:09Z
day: '17'
ddc:
- '575'
department:
- _id: EvBe
doi: 10.1007/978-1-4939-6831-2_1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:18Z
date_updated: 2019-10-15T07:47:05Z
file_id: '5068'
file_name: IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf
file_size: 840646
relation: main_file
file_date_updated: 2019-10-15T07:47:05Z
has_accepted_license: '1'
intvolume: ' 1569'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 1 - 29
project:
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
publication: Auxins and Cytokinins in Plant Biology
publication_identifier:
issn:
- '10643745'
publication_status: published
publisher: Springer
publist_id: '6369'
pubrep_id: '1019'
quality_controlled: '1'
related_material:
record:
- id: '539'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Methodological advances in auxin and cytokinin biology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1569
year: '2017'
...
---
_id: '1025'
abstract:
- lang: eng
text: Many organ surfaces are covered by a protective epithelial-cell layer. It
emerges that such layers are maintained by cell stretching that triggers cell
division mediated by the force-sensitive ion-channel protein Piezo1. See Letter
p.118
article_processing_charge: No
author:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: 'Heisenberg C-PJ. Cell biology: Stretched divisions. Nature. 2017;543(7643):43-44.
doi:10.1038/nature21502'
apa: 'Heisenberg, C.-P. J. (2017). Cell biology: Stretched divisions. Nature.
Nature Publishing Group. https://doi.org/10.1038/nature21502'
chicago: 'Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature.
Nature Publishing Group, 2017. https://doi.org/10.1038/nature21502.'
ieee: 'C.-P. J. Heisenberg, “Cell biology: Stretched divisions,” Nature,
vol. 543, no. 7643. Nature Publishing Group, pp. 43–44, 2017.'
ista: 'Heisenberg C-PJ. 2017. Cell biology: Stretched divisions. Nature. 543(7643),
43–44.'
mla: 'Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature,
vol. 543, no. 7643, Nature Publishing Group, 2017, pp. 43–44, doi:10.1038/nature21502.'
short: C.-P.J. Heisenberg, Nature 543 (2017) 43–44.
date_created: 2018-12-11T11:49:45Z
date_published: 2017-03-02T00:00:00Z
date_updated: 2023-09-22T09:26:59Z
day: '02'
department:
- _id: CaHe
doi: 10.1038/nature21502
external_id:
isi:
- '000395671500025'
intvolume: ' 543'
isi: 1
issue: '7643'
language:
- iso: eng
month: '03'
oa_version: None
page: 43 - 44
publication: Nature
publication_identifier:
issn:
- '00280836'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6367'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Cell biology: Stretched divisions'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 543
year: '2017'
...
---
_id: '1026'
abstract:
- lang: eng
text: The optogenetic revolution enabled spatially-precise and temporally-precise
control over protein function, signaling pathway activation, and animal behavior
with tremendous success in the dissection of signaling networks and neural circuits.
Very recently, optogenetic methods have been paired with optical reporters in
novel drug screening platforms. In these all-optical platforms, light remotely
activated ion channels and kinases thereby obviating the use of electrophysiology
or reagents. Consequences were remarkable operational simplicity, throughput,
and cost-effectiveness that culminated in the identification of new drug candidates.
These blueprints for all-optical assays also revealed potential pitfalls and inspire
all-optical variants of other screens, such as those that aim at better understanding
dynamic drug action or orphan protein function.
acknowledgement: This work was supported by grants of the European Union Seventh Framework
Programme (CIG-303564), the Human Frontier Science Program (RGY0084_2012), and the
Austrian Science Fund FWF (W1232 MolecularDrugTargets).
article_processing_charge: No
article_type: original
author:
- first_name: Viviana
full_name: Agus, Viviana
last_name: Agus
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: 'Agus V, Janovjak HL. Optogenetic methods in drug screening: Technologies and
applications. Current Opinion in Biotechnology. 2017;48:8-14. doi:10.1016/j.copbio.2017.02.006'
apa: 'Agus, V., & Janovjak, H. L. (2017). Optogenetic methods in drug screening:
Technologies and applications. Current Opinion in Biotechnology. Elsevier.
https://doi.org/10.1016/j.copbio.2017.02.006'
chicago: 'Agus, Viviana, and Harald L Janovjak. “Optogenetic Methods in Drug Screening:
Technologies and Applications.” Current Opinion in Biotechnology. Elsevier,
2017. https://doi.org/10.1016/j.copbio.2017.02.006.'
ieee: 'V. Agus and H. L. Janovjak, “Optogenetic methods in drug screening: Technologies
and applications,” Current Opinion in Biotechnology, vol. 48. Elsevier,
pp. 8–14, 2017.'
ista: 'Agus V, Janovjak HL. 2017. Optogenetic methods in drug screening: Technologies
and applications. Current Opinion in Biotechnology. 48, 8–14.'
mla: 'Agus, Viviana, and Harald L. Janovjak. “Optogenetic Methods in Drug Screening:
Technologies and Applications.” Current Opinion in Biotechnology, vol.
48, Elsevier, 2017, pp. 8–14, doi:10.1016/j.copbio.2017.02.006.'
short: V. Agus, H.L. Janovjak, Current Opinion in Biotechnology 48 (2017) 8–14.
date_created: 2018-12-11T11:49:45Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-09-22T09:26:06Z
day: '01'
department:
- _id: HaJa
doi: 10.1016/j.copbio.2017.02.006
ec_funded: 1
external_id:
isi:
- '000418313200003'
intvolume: ' 48'
isi: 1
language:
- iso: eng
month: '12'
oa_version: None
page: 8 - 14
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors (HFSP Young Investigator)
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
- _id: 255A6082-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Current Opinion in Biotechnology
publication_identifier:
issn:
- '09581669'
publication_status: published
publisher: Elsevier
publist_id: '6365'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Optogenetic methods in drug screening: Technologies and applications'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 48
year: '2017'
...
---
_id: '1027'
abstract:
- lang: eng
text: The rising prevalence of antibiotic resistant bacteria is an increasingly
serious public health challenge. To address this problem, recent work ranging
from clinical studies to theoretical modeling has provided valuable insights into
the mechanisms of resistance, its emergence and spread, and ways to counteract
it. A deeper understanding of the underlying dynamics of resistance evolution
will require a combination of experimental and theoretical expertise from different
disciplines and new technology for studying evolution in the laboratory. Here,
we review recent advances in the quantitative understanding of the mechanisms
and evolution of antibiotic resistance. We focus on key theoretical concepts and
new technology that enables well-controlled experiments. We further highlight
key challenges that can be met in the near future to ultimately develop effective
strategies for combating resistance.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Lukacisinova M, Bollenbach MT. Toward a quantitative understanding of antibiotic
resistance evolution. Current Opinion in Biotechnology. 2017;46:90-97.
doi:10.1016/j.copbio.2017.02.013
apa: Lukacisinova, M., & Bollenbach, M. T. (2017). Toward a quantitative understanding
of antibiotic resistance evolution. Current Opinion in Biotechnology. Elsevier.
https://doi.org/10.1016/j.copbio.2017.02.013
chicago: Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative
Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology.
Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.013.
ieee: M. Lukacisinova and M. T. Bollenbach, “Toward a quantitative understanding
of antibiotic resistance evolution,” Current Opinion in Biotechnology,
vol. 46. Elsevier, pp. 90–97, 2017.
ista: Lukacisinova M, Bollenbach MT. 2017. Toward a quantitative understanding of
antibiotic resistance evolution. Current Opinion in Biotechnology. 46, 90–97.
mla: Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding
of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology,
vol. 46, Elsevier, 2017, pp. 90–97, doi:10.1016/j.copbio.2017.02.013.
short: M. Lukacisinova, M.T. Bollenbach, Current Opinion in Biotechnology 46 (2017)
90–97.
date_created: 2018-12-11T11:49:45Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2024-03-25T23:30:15Z
day: '01'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1016/j.copbio.2017.02.013
ec_funded: 1
external_id:
isi:
- '000408077400015'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:57:57Z
date_updated: 2019-01-18T09:57:57Z
file_id: '5846'
file_name: 2017_CurrentOpinion_Lukaciinova.pdf
file_size: 858338
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:57:57Z
has_accepted_license: '1'
intvolume: ' 46'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: 90 - 97
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
publication: Current Opinion in Biotechnology
publication_status: published
publisher: Elsevier
publist_id: '6364'
pubrep_id: '801'
quality_controlled: '1'
related_material:
record:
- id: '6263'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Toward a quantitative understanding of antibiotic resistance evolution
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 46
year: '2017'
...
---
_id: '1028'
abstract:
- lang: eng
text: Optogenetics and photopharmacology provide spatiotemporally precise control
over protein interactions and protein function in cells and animals. Optogenetic
methods that are sensitive to green light and can be used to break protein complexes
are not broadly available but would enable multichromatic experiments with previously
inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12)
binding domains of bacterial CarH transcription factors for green-light-induced
receptor dissociation. In cultured cells, we observed oligomerization-induced
cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding
domains in the dark that was rapidly eliminated upon illumination. In zebrafish
embryos expressing fusion receptors, green light endowed control over aberrant
fibroblast growth factor signaling during development. Green-light-induced domain
dissociation and light-inactivated receptors will critically expand the optogenetic
toolbox for control of biological processes.
acknowledgement: "This work was supported by a grant from the European Union\U0010FC1Ds
Seventh Framework Programme (CIG-303564). E.R. was supported by the graduate program
MolecularDrugTargets (Austrian Science Fund (FWF), W1232) and a FemTech fellowship
(Austrian Research Promotion Agency, 3580812)"
article_processing_charge: No
author:
- first_name: Stephanie
full_name: Kainrath, Stephanie
id: 32CFBA64-F248-11E8-B48F-1D18A9856A87
last_name: Kainrath
- first_name: Manuela
full_name: Stadler, Manuela
last_name: Stadler
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
- first_name: Martin
full_name: Distel, Martin
last_name: Distel
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced
inactivation of receptor signaling using cobalamin-binding domains. Angewandte
Chemie - International Edition. 2017;56(16):4608-4611. doi:10.1002/anie.201611998
apa: Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak,
H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding
domains. Angewandte Chemie - International Edition. Wiley-Blackwell. https://doi.org/10.1002/anie.201611998
chicago: Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel,
and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling
Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition.
Wiley-Blackwell, 2017. https://doi.org/10.1002/anie.201611998.
ieee: S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak,
“Green-light-induced inactivation of receptor signaling using cobalamin-binding
domains,” Angewandte Chemie - International Edition, vol. 56, no. 16. Wiley-Blackwell,
pp. 4608–4611, 2017.
ista: Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017.
Green-light-induced inactivation of receptor signaling using cobalamin-binding
domains. Angewandte Chemie - International Edition. 56(16), 4608–4611.
mla: Kainrath, Stephanie, et al. “Green-Light-Induced Inactivation of Receptor Signaling
Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition,
vol. 56, no. 16, Wiley-Blackwell, 2017, pp. 4608–11, doi:10.1002/anie.201611998.
short: S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak,
Angewandte Chemie - International Edition 56 (2017) 4608–4611.
date_created: 2018-12-11T11:49:46Z
date_published: 2017-03-20T00:00:00Z
date_updated: 2024-03-25T23:30:08Z
day: '20'
ddc:
- '540'
department:
- _id: CaGu
- _id: HaJa
doi: 10.1002/anie.201611998
ec_funded: 1
external_id:
isi:
- '000398154000038'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:39:55Z
date_updated: 2019-01-18T09:39:55Z
file_id: '5845'
file_name: 2017_communications_Kainrath.pdf
file_size: 2614942
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:39:55Z
has_accepted_license: '1'
intvolume: ' 56'
isi: 1
issue: '16'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 4608-4611
project:
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets [do not use to be deleted]
publication: Angewandte Chemie - International Edition
publication_identifier:
issn:
- '14337851'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6362'
quality_controlled: '1'
related_material:
record:
- id: '418'
relation: dissertation_contains
status: public
- id: '7680'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Green-light-induced inactivation of receptor signaling using cobalamin-binding
domains
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 56
year: '2017'
...
---
_id: '1029'
abstract:
- lang: eng
text: RNA Polymerase II pauses and backtracks during transcription, with many consequences
for gene expression and cellular physiology. Here, we show that the energy required
to melt double-stranded nucleic acids in the transcription bubble predicts pausing
in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do.
In addition, the same energy difference also determines when the RNA polymerase
backtracks instead of continuing to move forward. This data-driven model corroborates—in
a genome wide and quantitative manner—previous evidence that sequence-dependent
thermodynamic features of nucleic acids influence both transcriptional pausing
and backtracking.
article_number: e0174066
article_processing_charge: Yes
author:
- first_name: Martin
full_name: Lukacisin, Martin
id: 298FFE8C-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisin
orcid: 0000-0001-6549-4177
- first_name: Matthieu
full_name: Landon, Matthieu
last_name: Landon
- first_name: Rishi
full_name: Jajoo, Rishi
last_name: Jajoo
citation:
ama: Lukacisin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties
of nucleic acids influence both transcriptional pausing and backtracking in yeast.
PLoS One. 2017;12(3). doi:10.1371/journal.pone.0174066
apa: Lukacisin, M., Landon, M., & Jajoo, R. (2017). Sequence-specific thermodynamic
properties of nucleic acids influence both transcriptional pausing and backtracking
in yeast. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0174066
chicago: Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “Sequence-Specific
Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing
and Backtracking in Yeast.” PLoS One. Public Library of Science, 2017.
https://doi.org/10.1371/journal.pone.0174066.
ieee: M. Lukacisin, M. Landon, and R. Jajoo, “Sequence-specific thermodynamic properties
of nucleic acids influence both transcriptional pausing and backtracking in yeast,”
PLoS One, vol. 12, no. 3. Public Library of Science, 2017.
ista: Lukacisin M, Landon M, Jajoo R. 2017. Sequence-specific thermodynamic properties
of nucleic acids influence both transcriptional pausing and backtracking in yeast.
PLoS One. 12(3), e0174066.
mla: Lukacisin, Martin, et al. “Sequence-Specific Thermodynamic Properties of Nucleic
Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS
One, vol. 12, no. 3, e0174066, Public Library of Science, 2017, doi:10.1371/journal.pone.0174066.
short: M. Lukacisin, M. Landon, R. Jajoo, PLoS One 12 (2017).
date_created: 2018-12-11T11:49:46Z
date_published: 2017-03-16T00:00:00Z
date_updated: 2024-03-25T23:30:03Z
day: '16'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1371/journal.pone.0174066
external_id:
isi:
- '000396318300121'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:47Z
date_updated: 2018-12-12T10:09:47Z
file_id: '4772'
file_name: IST-2017-800-v1+1_journal.pone.0174066.pdf
file_size: 3429381
relation: main_file
file_date_updated: 2018-12-12T10:09:47Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_identifier:
issn:
- '19326203'
publication_status: published
publisher: Public Library of Science
publist_id: '6361'
pubrep_id: '800'
quality_controlled: '1'
related_material:
record:
- id: '5556'
relation: popular_science
status: public
- id: '6392'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Sequence-specific thermodynamic properties of nucleic acids influence both
transcriptional pausing and backtracking in yeast
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 12
year: '2017'
...
---
_id: '103'
abstract:
- lang: eng
text: We investigate effects of quasiparticle poisoning in a Majorana island with
strong tunnel coupling to normal-metal leads. In addition to the main Coulomb
blockade diamonds, "shadow" diamonds appear, shifted by 1e in gate voltage,
consistent with transport through an excited (poisoned) state of the island. Comparison
to a simple model yields an estimate of parity lifetime for the strongly coupled
island (∼1 μs) and sets a bound for a weakly coupled island (>10 μs). Fluctuations
in the gate-voltage spacing of Coulomb peaks at high field, reflecting Majorana
hybridization, are enhanced by the reduced lever arm at strong coupling. When
converted from gate voltage to energy units, fluctuations are consistent with
previous measurements.
acknowledgement: Research supported by Microsoft, the Danish National Research Foundation,
the Lundbeck Foundation, Carlsberg Foundation, Villum Foundation, and the European
Commission.
article_number: '137701'
arxiv: 1
author:
- first_name: S M
full_name: Albrecht, S M
last_name: Albrecht
- first_name: Esben
full_name: Hansen, Esben
last_name: Hansen
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
- first_name: Thomas
full_name: Jespersen, Thomas
last_name: Jespersen
- first_name: Jesper
full_name: Nygård, Jesper
last_name: Nygård
- first_name: Peter
full_name: Krogstrup, Peter
last_name: Krogstrup
- first_name: Jeroen
full_name: Danon, Jeroen
last_name: Danon
- first_name: Karsten
full_name: Flensberg, Karsten
last_name: Flensberg
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
citation:
ama: Albrecht SM, Hansen E, Higginbotham AP, et al. Transport signatures of quasiparticle
poisoning in a majorana island. APS Physics, Physical Review Letters. 2017;118(13).
doi:10.1103/PhysRevLett.118.137701
apa: Albrecht, S. M., Hansen, E., Higginbotham, A. P., Kuemmeth, F., Jespersen,
T., Nygård, J., … Marcus, C. (2017). Transport signatures of quasiparticle poisoning
in a majorana island. APS Physics, Physical Review Letters. American Physical
Society. https://doi.org/10.1103/PhysRevLett.118.137701
chicago: Albrecht, S M, Esben Hansen, Andrew P Higginbotham, Ferdinand Kuemmeth,
Thomas Jespersen, Jesper Nygård, Peter Krogstrup, Jeroen Danon, Karsten Flensberg,
and Charles Marcus. “Transport Signatures of Quasiparticle Poisoning in a Majorana
Island.” APS Physics, Physical Review Letters. American Physical Society,
2017. https://doi.org/10.1103/PhysRevLett.118.137701.
ieee: S. M. Albrecht et al., “Transport signatures of quasiparticle poisoning
in a majorana island,” APS Physics, Physical Review Letters, vol. 118,
no. 13. American Physical Society, 2017.
ista: Albrecht SM, Hansen E, Higginbotham AP, Kuemmeth F, Jespersen T, Nygård J,
Krogstrup P, Danon J, Flensberg K, Marcus C. 2017. Transport signatures of quasiparticle
poisoning in a majorana island. APS Physics, Physical Review Letters. 118(13),
137701.
mla: Albrecht, S. M., et al. “Transport Signatures of Quasiparticle Poisoning in
a Majorana Island.” APS Physics, Physical Review Letters, vol. 118, no.
13, 137701, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.137701.
short: S.M. Albrecht, E. Hansen, A.P. Higginbotham, F. Kuemmeth, T. Jespersen, J.
Nygård, P. Krogstrup, J. Danon, K. Flensberg, C. Marcus, APS Physics, Physical
Review Letters 118 (2017).
date_created: 2018-12-11T11:44:39Z
date_published: 2017-03-31T00:00:00Z
date_updated: 2021-01-12T06:47:47Z
day: '31'
doi: 10.1103/PhysRevLett.118.137701
extern: '1'
external_id:
arxiv:
- '1612.05748'
intvolume: ' 118'
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1612.05748
month: '03'
oa: 1
oa_version: Preprint
publication: APS Physics, Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7951'
quality_controlled: '1'
status: public
title: Transport signatures of quasiparticle poisoning in a majorana island
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2017'
...
---
_id: '1030'
abstract:
- lang: ger
text: Auf der Suche nach einem Bibliothekssystem entschied sich die Forschungseinrichtung
IST Austria im Jahr 2014 für das Open-Source-Produkt Koha. In einem ersten Schritt
wurden zunächst Grundfunktionen aktiviert um im Anschluss diverse zusätzliche
Tools zum Einsatz zu bringen. Die große Flexibilität des Systems erlaubt maßgeschneiderte
Lösungen für unterschiedlichste Institutionen. Trotz Herausforderungen kann die
Bibliothek auf eine erfolgreiche Implementierung zurückblicken.
- lang: eng
text: "IST Austria was looking for a new library system until 2014 when the research
institute decided\r\nto implement Koha. The library first activated basic functions
of the open-source product and\r\nthen brought additional tools into operation.
The high flexibility of the system allows customized\r\nsolutions for different
institutions. Although the library faced some challenges, it can now look\r\nback
on a successful implementation."
article_processing_charge: No
article_type: original
author:
- first_name: Márton
full_name: Villányi, Márton
id: 3FFCCD3A-F248-11E8-B48F-1D18A9856A87
last_name: Villányi
orcid: 0000-0001-8126-0426
citation:
ama: Villányi M. Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken
– Werkstattbericht der IST Austria Library. Informationspraxis. 2017;3(1).
doi:10.11588/ip.2017.1.35227
apa: Villányi, M. (2017). Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken
– Werkstattbericht der IST Austria Library. Informationspraxis. Verein
Informationspraxis . https://doi.org/10.11588/ip.2017.1.35227
chicago: Villányi, Márton. “Ein Freies Bibliothekssystem Für Wissenschaftliche Bibliotheken
– Werkstattbericht Der IST Austria Library.” Informationspraxis. Verein
Informationspraxis , 2017. https://doi.org/10.11588/ip.2017.1.35227.
ieee: M. Villányi, “Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken
– Werkstattbericht der IST Austria Library,” Informationspraxis, vol. 3,
no. 1. Verein Informationspraxis , 2017.
ista: Villányi M. 2017. Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken
– Werkstattbericht der IST Austria Library. Informationspraxis. 3(1).
mla: Villányi, Márton. “Ein Freies Bibliothekssystem Für Wissenschaftliche Bibliotheken
– Werkstattbericht Der IST Austria Library.” Informationspraxis, vol. 3,
no. 1, Verein Informationspraxis , 2017, doi:10.11588/ip.2017.1.35227.
short: M. Villányi, Informationspraxis 3 (2017).
date_created: 2018-12-11T11:49:46Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-10-18T07:49:29Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.11588/ip.2017.1.35227
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:20Z
date_updated: 2018-12-12T10:08:20Z
file_id: '4680'
file_name: IST-2017-799-v1+1_35227-112025-1-PB.pdf
file_size: 201163
relation: main_file
file_date_updated: 2018-12-12T10:08:20Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
popular_science: '1'
publication: Informationspraxis
publication_identifier:
issn:
- 2297-3249
publication_status: published
publisher: 'Verein Informationspraxis '
publist_id: '6360'
pubrep_id: '799'
status: public
title: Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht
der IST Austria Library
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: 3
year: '2017'
...
---
_id: '10369'
abstract:
- lang: eng
text: Biological membranes have a central role in mediating the organization of
membrane-curving proteins, a dynamic process that has proven to be challenging
to probe experimentally. Using atomic force microscopy, we capture the hierarchically
organized assemblies of Bin/amphiphysin/Rvs (BAR) proteins on supported lipid
membranes. Their structure reveals distinct long linear aggregates of proteins,
regularly spaced by up to 300 nm. Employing accurate free-energy calculations
from large-scale coarse-grained computer simulations, we found that the membrane
mediates the interaction among protein filaments as a combination of short- and
long-ranged interactions. The long-ranged component acts at strikingly long distances,
giving rise to a variety of micron-sized ordered patterns. This mechanism may
contribute to the long-ranged spatiotemporal control of membrane remodeling by
proteins in the cell.
acknowledgement: M.S. and G.A.V. acknowledge their research reported in this publication
as being supported by the National Institute of General Medical Sciences of the
National Institutes of Health under Award Number R01-GM063796. Computational resources
were provided to M.S. and G.A.V. by the National Science Foundation through XSEDE
(Grant TG-MCA94P017, supercomputers Stampede and Gordon), and also by the Blue Waters
computing project at the National Center for Supercomputing Applications (University
of Illinois at Urbana–Champaign, NSF Awards OCI-0725070 and ACI-1238993). A.Š. acknowledges
support from the Human Frontier Science Program and Royal Society. J.M.H. and K.Y.C.L.
acknowledge the support from the National Science Foundation (Grant MCB-1413613)
and the NSF-supported MRSEC program at the University of Chicago (Grant DMR-1420709).
We are grateful to Carsten Mim and Vinzenz Unger of Northwestern University for
generously providing us with the protein. We thank all the members of the Voth group
for fruitful discussions, especially John M. A. Grime.
article_processing_charge: No
article_type: original
author:
- first_name: Mijo
full_name: Simunovic, Mijo
last_name: Simunovic
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: J. Michael
full_name: Henderson, J. Michael
last_name: Henderson
- first_name: Ka Yee C.
full_name: Lee, Ka Yee C.
last_name: Lee
- first_name: Gregory A.
full_name: Voth, Gregory A.
last_name: Voth
citation:
ama: Simunovic M, Šarić A, Henderson JM, Lee KYC, Voth GA. Long-range organization
of membrane-curving proteins. ACS Central Science. 2017;3(12):1246-1253.
doi:10.1021/acscentsci.7b00392
apa: Simunovic, M., Šarić, A., Henderson, J. M., Lee, K. Y. C., & Voth, G. A.
(2017). Long-range organization of membrane-curving proteins. ACS Central Science.
American Chemical Society. https://doi.org/10.1021/acscentsci.7b00392
chicago: Simunovic, Mijo, Anđela Šarić, J. Michael Henderson, Ka Yee C. Lee, and
Gregory A. Voth. “Long-Range Organization of Membrane-Curving Proteins.” ACS
Central Science. American Chemical Society, 2017. https://doi.org/10.1021/acscentsci.7b00392.
ieee: M. Simunovic, A. Šarić, J. M. Henderson, K. Y. C. Lee, and G. A. Voth, “Long-range
organization of membrane-curving proteins,” ACS Central Science, vol. 3,
no. 12. American Chemical Society, pp. 1246–1253, 2017.
ista: Simunovic M, Šarić A, Henderson JM, Lee KYC, Voth GA. 2017. Long-range organization
of membrane-curving proteins. ACS Central Science. 3(12), 1246–1253.
mla: Simunovic, Mijo, et al. “Long-Range Organization of Membrane-Curving Proteins.”
ACS Central Science, vol. 3, no. 12, American Chemical Society, 2017, pp.
1246–53, doi:10.1021/acscentsci.7b00392.
short: M. Simunovic, A. Šarić, J.M. Henderson, K.Y.C. Lee, G.A. Voth, ACS Central
Science 3 (2017) 1246–1253.
date_created: 2021-11-29T08:49:50Z
date_published: 2017-11-21T00:00:00Z
date_updated: 2021-11-29T09:28:06Z
day: '21'
ddc:
- '540'
doi: 10.1021/acscentsci.7b00392
extern: '1'
external_id:
pmid:
- '29296664'
file:
- access_level: open_access
checksum: 1cf3e5e5342f2d728f47560acc3ec560
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-29T09:00:40Z
date_updated: 2021-11-29T09:00:40Z
file_id: '10371'
file_name: 2017_ACSCentSci_Simunovic.pdf
file_size: 2635263
relation: main_file
success: 1
file_date_updated: 2021-11-29T09:00:40Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '12'
keyword:
- general chemical engineering
- general chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://pubs.acs.org/doi/10.1021/acscentsci.7b00392
month: '11'
oa: 1
oa_version: Published Version
page: 1246-1253
pmid: 1
publication: ACS Central Science
publication_identifier:
eissn:
- 2374-7951
issn:
- 2374-7943
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long-range organization of membrane-curving proteins
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 3
year: '2017'
...
---
_id: '10370'
abstract:
- lang: eng
text: Eukaryotic cells are densely packed with macromolecular complexes and intertwining
organelles, continually transported and reshaped. Intriguingly, organelles avoid
clashing and entangling with each other in such limited space. Mitochondria form
extensive networks constantly remodeled by fission and fusion. Here, we show that
mitochondrial fission is triggered by mechanical forces. Mechano-stimulation of
mitochondria – via encounter with motile intracellular pathogens, via external
pressure applied by an atomic force microscope, or via cell migration across uneven
microsurfaces – results in the recruitment of the mitochondrial fission machinery,
and subsequent division. We propose that MFF, owing to affinity for narrow mitochondria,
acts as a membrane-bound force sensor to recruit the fission machinery to mechanically
strained sites. Thus, mitochondria adapt to the environment by sensing and responding
to biomechanical cues. Our findings that mechanical triggers can be coupled to
biochemical responses in membrane dynamics may explain how organelles orderly
cohabit in the crowded cytoplasm.
article_number: e30292
article_processing_charge: No
article_type: original
author:
- first_name: Sebastian Carsten Johannes
full_name: Helle, Sebastian Carsten Johannes
last_name: Helle
- first_name: Qian
full_name: Feng, Qian
last_name: Feng
- first_name: Mathias J
full_name: Aebersold, Mathias J
last_name: Aebersold
- first_name: Luca
full_name: Hirt, Luca
last_name: Hirt
- first_name: Raphael R
full_name: Grüter, Raphael R
last_name: Grüter
- first_name: Afshin
full_name: Vahid, Afshin
last_name: Vahid
- first_name: Andrea
full_name: Sirianni, Andrea
last_name: Sirianni
- first_name: Serge
full_name: Mostowy, Serge
last_name: Mostowy
- first_name: Jess G
full_name: Snedeker, Jess G
last_name: Snedeker
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
- first_name: Tomaso
full_name: Zambelli, Tomaso
last_name: Zambelli
- first_name: Benoît
full_name: Kornmann, Benoît
last_name: Kornmann
citation:
ama: Helle SCJ, Feng Q, Aebersold MJ, et al. Mechanical force induces mitochondrial
fission. eLife. 2017;6. doi:10.7554/elife.30292
apa: Helle, S. C. J., Feng, Q., Aebersold, M. J., Hirt, L., Grüter, R. R., Vahid,
A., … Kornmann, B. (2017). Mechanical force induces mitochondrial fission. ELife.
eLife Sciences Publications. https://doi.org/10.7554/elife.30292
chicago: Helle, Sebastian Carsten Johannes, Qian Feng, Mathias J Aebersold, Luca
Hirt, Raphael R Grüter, Afshin Vahid, Andrea Sirianni, et al. “Mechanical Force
Induces Mitochondrial Fission.” ELife. eLife Sciences Publications, 2017.
https://doi.org/10.7554/elife.30292.
ieee: S. C. J. Helle et al., “Mechanical force induces mitochondrial fission,”
eLife, vol. 6. eLife Sciences Publications, 2017.
ista: Helle SCJ, Feng Q, Aebersold MJ, Hirt L, Grüter RR, Vahid A, Sirianni A, Mostowy
S, Snedeker JG, Šarić A, Idema T, Zambelli T, Kornmann B. 2017. Mechanical force
induces mitochondrial fission. eLife. 6, e30292.
mla: Helle, Sebastian Carsten Johannes, et al. “Mechanical Force Induces Mitochondrial
Fission.” ELife, vol. 6, e30292, eLife Sciences Publications, 2017, doi:10.7554/elife.30292.
short: S.C.J. Helle, Q. Feng, M.J. Aebersold, L. Hirt, R.R. Grüter, A. Vahid, A.
Sirianni, S. Mostowy, J.G. Snedeker, A. Šarić, T. Idema, T. Zambelli, B. Kornmann,
ELife 6 (2017).
date_created: 2021-11-29T08:51:38Z
date_published: 2017-11-09T00:00:00Z
date_updated: 2021-11-29T09:28:14Z
day: '09'
ddc:
- '572'
doi: 10.7554/elife.30292
extern: '1'
external_id:
pmid:
- '29119945'
file:
- access_level: open_access
checksum: c35f42dcfb007f6d6c761a27e24c26d3
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-29T09:07:41Z
date_updated: 2021-11-29T09:07:41Z
file_id: '10372'
file_name: 2017_eLife_Helle.pdf
file_size: 6120157
relation: main_file
success: 1
file_date_updated: 2021-11-29T09:07:41Z
has_accepted_license: '1'
intvolume: ' 6'
keyword:
- general immunology and microbiology
- general biochemistry
- genetics and molecular biology
- general medicine
- general neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://elifesciences.org/articles/30292
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanical force induces mitochondrial fission
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2017'
...
---
_id: '10373'
abstract:
- lang: eng
text: 'Electric charges are conserved. The same would be expected to hold for magnetic
charges, yet magnetic monopoles have never been observed. It is therefore surprising
that the laws of nonequilibrium thermodynamics, combined with Maxwell’s equations,
suggest that colloidal particles heated or cooled in certain polar or paramagnetic
solvents may behave as if they carry an electric/magnetic charge. Here, we present
numerical simulations that show that the field distribution around a pair of such
heated/cooled colloidal particles agrees quantitatively with the theoretical predictions
for a pair of oppositely charged electric or magnetic monopoles. However, in other
respects, the nonequilibrium colloidal particles do not behave as monopoles: They
cannot be moved by a homogeneous applied field. The numerical evidence for the
monopole-like fields around heated/cooled colloidal particles is crucial because
the experimental and numerical determination of forces between such colloidal
particles would be complicated by the presence of other effects, such as thermophoresis.'
acknowledgement: P.W. acknowledges many invaluable discussions with Martin Neumann,
Chao Zhang, Michiel Sprik, Aleks Reinhardt, Carl Pölking, and Tine Curk. We acknowledge
financial support from the Austrian Academy of Sciences through a doctoral (DOC)
fellowship (to P.W.), the Austrian Science Fund (FWF) within the Spezialforschungsbereich
Vienna Computational Materials Laboratory (Project F41) (C.D.), and the European
Union Early Training Network NANOTRANS (Grant 674979 to D. Frenkel). The results
presented here have been achieved in part using the Vienna Scientific Cluster.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Peter
full_name: Wirnsberger, Peter
last_name: Wirnsberger
- first_name: Domagoj
full_name: Fijan, Domagoj
last_name: Fijan
- first_name: Roger A.
full_name: Lightwood, Roger A.
last_name: Lightwood
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Christoph
full_name: Dellago, Christoph
last_name: Dellago
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. Numerical
evidence for thermally induced monopoles. Proceedings of the National Academy
of Sciences. 2017;114(19):4911-4914. doi:10.1073/pnas.1621494114
apa: Wirnsberger, P., Fijan, D., Lightwood, R. A., Šarić, A., Dellago, C., &
Frenkel, D. (2017). Numerical evidence for thermally induced monopoles. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1621494114
chicago: Wirnsberger, Peter, Domagoj Fijan, Roger A. Lightwood, Anđela Šarić, Christoph
Dellago, and Daan Frenkel. “Numerical Evidence for Thermally Induced Monopoles.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2017. https://doi.org/10.1073/pnas.1621494114.
ieee: P. Wirnsberger, D. Fijan, R. A. Lightwood, A. Šarić, C. Dellago, and D. Frenkel,
“Numerical evidence for thermally induced monopoles,” Proceedings of the National
Academy of Sciences, vol. 114, no. 19. National Academy of Sciences, pp. 4911–4914,
2017.
ista: Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. 2017.
Numerical evidence for thermally induced monopoles. Proceedings of the National
Academy of Sciences. 114(19), 4911–4914.
mla: Wirnsberger, Peter, et al. “Numerical Evidence for Thermally Induced Monopoles.”
Proceedings of the National Academy of Sciences, vol. 114, no. 19, National
Academy of Sciences, 2017, pp. 4911–14, doi:10.1073/pnas.1621494114.
short: P. Wirnsberger, D. Fijan, R.A. Lightwood, A. Šarić, C. Dellago, D. Frenkel,
Proceedings of the National Academy of Sciences 114 (2017) 4911–4914.
date_created: 2021-11-29T09:28:24Z
date_published: 2017-04-24T00:00:00Z
date_updated: 2021-11-29T09:59:12Z
day: '24'
doi: 10.1073/pnas.1621494114
extern: '1'
external_id:
arxiv:
- '1610.06840'
pmid:
- '28439003'
intvolume: ' 114'
issue: '19'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pnas.org/content/114/19/4911
month: '04'
oa: 1
oa_version: Published Version
page: 4911-4914
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Numerical evidence for thermally induced monopoles
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 114
year: '2017'
...
---
_id: '10374'
abstract:
- lang: eng
text: The formation of filaments from naturally occurring protein molecules is a
process at the core of a range of functional and aberrant biological phenomena,
such as the assembly of the cytoskeleton or the appearance of aggregates in Alzheimer's
disease. The macroscopic behaviour associated with such processes is remarkably
diverse, ranging from simple nucleated growth to highly cooperative processes
with a well-defined lagtime. Thus, conventionally, different molecular mechanisms
have been used to explain the self-assembly of different proteins. Here we show
that this range of behaviour can be quantitatively captured by a single unifying
Petri net that describes filamentous growth in terms of aggregate number and aggregate
mass concentrations. By considering general features associated with a particular
network connectivity, we are able to establish directly the rate-determining steps
of the overall aggregation reaction from the system's scaling behaviour. We illustrate
the power of this framework on a range of different experimental and simulated
aggregating systems. The approach is general and will be applicable to any future
extensions of the reaction network of filamentous self-assembly.
acknowledgement: The research leading to these results has received funding from the
European Research Council under the European Union's Seventh Framework Programme
(FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969) (SL, TPJK),
Sidney Sussex College Cambridge (GM), the Frances and Augusta Newman Foundation
(TPJK), the Biotechnology and Biological Science Research Council (TPJK), the Swedish
Research Council (SL), the Academy of Medical Sciences (AŠ), Wellcome Trust (AŠ),
and the Cambridge Centre for Misfolding Diseases (CMD, TPJK, MV).
article_processing_charge: No
article_type: original
author:
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Luke
full_name: Rajah, Luke
last_name: Rajah
- first_name: Samuel A. I.
full_name: Cohen, Samuel A. I.
last_name: Cohen
- first_name: Manuela
full_name: Pfammatter, Manuela
last_name: Pfammatter
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Erik
full_name: Hellstrand, Erik
last_name: Hellstrand
- first_name: Alexander K.
full_name: Buell, Alexander K.
last_name: Buell
- first_name: Adriano
full_name: Aguzzi, Adriano
last_name: Aguzzi
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
citation:
ama: Meisl G, Rajah L, Cohen SAI, et al. Scaling behaviour and rate-determining
steps in filamentous self-assembly. Chemical Science. 2017;8(10):7087-7097.
doi:10.1039/c7sc01965c
apa: Meisl, G., Rajah, L., Cohen, S. A. I., Pfammatter, M., Šarić, A., Hellstrand,
E., … Knowles, T. P. J. (2017). Scaling behaviour and rate-determining steps in
filamentous self-assembly. Chemical Science. Royal Society of Chemistry.
https://doi.org/10.1039/c7sc01965c
chicago: Meisl, Georg, Luke Rajah, Samuel A. I. Cohen, Manuela Pfammatter, Anđela
Šarić, Erik Hellstrand, Alexander K. Buell, et al. “Scaling Behaviour and Rate-Determining
Steps in Filamentous Self-Assembly.” Chemical Science. Royal Society of
Chemistry, 2017. https://doi.org/10.1039/c7sc01965c.
ieee: G. Meisl et al., “Scaling behaviour and rate-determining steps in filamentous
self-assembly,” Chemical Science, vol. 8, no. 10. Royal Society of Chemistry,
pp. 7087–7097, 2017.
ista: Meisl G, Rajah L, Cohen SAI, Pfammatter M, Šarić A, Hellstrand E, Buell AK,
Aguzzi A, Linse S, Vendruscolo M, Dobson CM, Knowles TPJ. 2017. Scaling behaviour
and rate-determining steps in filamentous self-assembly. Chemical Science. 8(10),
7087–7097.
mla: Meisl, Georg, et al. “Scaling Behaviour and Rate-Determining Steps in Filamentous
Self-Assembly.” Chemical Science, vol. 8, no. 10, Royal Society of Chemistry,
2017, pp. 7087–97, doi:10.1039/c7sc01965c.
short: G. Meisl, L. Rajah, S.A.I. Cohen, M. Pfammatter, A. Šarić, E. Hellstrand,
A.K. Buell, A. Aguzzi, S. Linse, M. Vendruscolo, C.M. Dobson, T.P.J. Knowles,
Chemical Science 8 (2017) 7087–7097.
date_created: 2021-11-29T09:29:31Z
date_published: 2017-08-31T00:00:00Z
date_updated: 2021-11-29T10:00:00Z
day: '31'
ddc:
- '540'
doi: 10.1039/c7sc01965c
extern: '1'
external_id:
pmid:
- '29147538'
intvolume: ' 8'
issue: '10'
keyword:
- general chemistry
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/3.0/
main_file_link:
- open_access: '1'
url: https://pubs.rsc.org/en/content/articlelanding/2017/SC/C7SC01965C
month: '08'
oa: 1
oa_version: Published Version
page: 7087-7097
pmid: 1
publication: Chemical Science
publication_identifier:
eissn:
- 2041-6539
issn:
- 2041-6520
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scaling behaviour and rate-determining steps in filamentous self-assembly
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode
name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)
short: CC BY-NC (3.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 8
year: '2017'
...
---
_id: '10375'
abstract:
- lang: eng
text: 'Cellular membranes exhibit a large variety of shapes, strongly coupled to
their function. Many biological processes involve dynamic reshaping of membranes,
usually mediated by proteins. This interaction works both ways: while proteins
influence the membrane shape, the membrane shape affects the interactions between
the proteins. To study these membrane-mediated interactions on closed and anisotropically
curved membranes, we use colloids adhered to ellipsoidal membrane vesicles as
a model system. We find that two particles on a closed system always attract each
other, and tend to align with the direction of largest curvature. Multiple particles
form arcs, or, at large enough numbers, a complete ring surrounding the vesicle
in its equatorial plane. The resulting vesicle shape resembles a snowman. Our
results indicate that these physical interactions on membranes with anisotropic
shapes can be exploited by cells to drive macromolecules to preferred regions
of cellular or intracellular membranes, and utilized to initiate dynamic processes
such as cell division. The same principle could be used to find the midplane of
an artificial vesicle, as a first step towards dividing it into two equal parts.'
acknowledgement: This work was supported by the Netherlands Organisation for Scientific
Research (NWO/OCW), as part of the Frontiers of Nanoscience program.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Afshin
full_name: Vahid, Afshin
last_name: Vahid
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
citation:
ama: Vahid A, Šarić A, Idema T. Curvature variation controls particle aggregation
on fluid vesicles. Soft Matter. 2017;13(28):4924-4930. doi:10.1039/c7sm00433h
apa: Vahid, A., Šarić, A., & Idema, T. (2017). Curvature variation controls
particle aggregation on fluid vesicles. Soft Matter. Royal Society of Chemistry.
https://doi.org/10.1039/c7sm00433h
chicago: Vahid, Afshin, Anđela Šarić, and Timon Idema. “Curvature Variation Controls
Particle Aggregation on Fluid Vesicles.” Soft Matter. Royal Society of
Chemistry, 2017. https://doi.org/10.1039/c7sm00433h.
ieee: A. Vahid, A. Šarić, and T. Idema, “Curvature variation controls particle aggregation
on fluid vesicles,” Soft Matter, vol. 13, no. 28. Royal Society of Chemistry,
pp. 4924–4930, 2017.
ista: Vahid A, Šarić A, Idema T. 2017. Curvature variation controls particle aggregation
on fluid vesicles. Soft Matter. 13(28), 4924–4930.
mla: Vahid, Afshin, et al. “Curvature Variation Controls Particle Aggregation on
Fluid Vesicles.” Soft Matter, vol. 13, no. 28, Royal Society of Chemistry,
2017, pp. 4924–30, doi:10.1039/c7sm00433h.
short: A. Vahid, A. Šarić, T. Idema, Soft Matter 13 (2017) 4924–4930.
date_created: 2021-11-29T10:00:39Z
date_published: 2017-06-15T00:00:00Z
date_updated: 2021-11-29T10:33:36Z
day: '15'
doi: 10.1039/c7sm00433h
extern: '1'
external_id:
arxiv:
- '1703.00776'
pmid:
- '28677712'
intvolume: ' 13'
issue: '28'
keyword:
- condensed matter physics
- general chemistry
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
main_file_link:
- open_access: '1'
url: https://pubs.rsc.org/en/content/articlelanding/2017/SM/C7SM00433H
month: '06'
oa: 1
oa_version: Published Version
page: 4924-4930
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Curvature variation controls particle aggregation on fluid vesicles
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 13
year: '2017'
...
---
_id: '10416'
abstract:
- lang: eng
text: 'A fundamental algorithmic problem at the heart of static analysis is Dyck
reachability. The input is a graph where the edges are labeled with different
types of opening and closing parentheses, and the reachability information is
computed via paths whose parentheses are properly matched. We present new results
for Dyck reachability problems with applications to alias analysis and data-dependence
analysis. Our main contributions, that include improved upper bounds as well as
lower bounds that establish optimality guarantees, are as follows: First, we consider
Dyck reachability on bidirected graphs, which is the standard way of performing
field-sensitive points-to analysis. Given a bidirected graph with n nodes and
m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)),
where α(n) is the inverse Ackermann function, improving the previously known O(n2)
time bound; (ii) a matching lower bound that shows that our algorithm is optimal
wrt to worst-case complexity; and (iii) an optimal average-case upper bound of
O(m) time, improving the previously known O(m · logn) bound. Second, we consider
the problem of context-sensitive data-dependence analysis, where the task is to
obtain analysis summaries of library code in the presence of callbacks. Our algorithm
preprocesses libraries in almost linear time, after which the contribution of
the library in the complexity of the client analysis is only linear, and only
wrt the number of call sites. Third, we prove that combinatorial algorithms for
Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained
without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication,
which is a long-standing open problem. Thus we establish that the existing combinatorial
algorithms for Dyck reachability are (conditionally) optimal for general graphs.
We also show that the same hardness holds for graphs of constant treewidth. Finally,
we provide a prototype implementation of our algorithms for both alias analysis
and data-dependence analysis. Our experimental evaluation demonstrates that the
new algorithms significantly outperform all existing methods on the two problems,
over real-world benchmarks.'
acknowledgement: "The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant
(279307: Graph Games).\r\n"
article_number: '30'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Bhavya
full_name: Choudhary, Bhavya
last_name: Choudhary
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck reachability for data-dependence
and Alias analysis. Proceedings of the ACM on Programming Languages. 2017;2(POPL).
doi:10.1145/3158118
apa: 'Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck
reachability for data-dependence and Alias analysis. Proceedings of the ACM
on Programming Languages. Los Angeles, CA, United States: Association for
Computing Machinery. https://doi.org/10.1145/3158118'
chicago: Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. “Optimal
Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the
ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158118.
ieee: K. Chatterjee, B. Choudhary, and A. Pavlogiannis, “Optimal Dyck reachability
for data-dependence and Alias analysis,” Proceedings of the ACM on Programming
Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.
ista: Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability
for data-dependence and Alias analysis. Proceedings of the ACM on Programming
Languages. 2(POPL), 30.
mla: Chatterjee, Krishnendu, et al. “Optimal Dyck Reachability for Data-Dependence
and Alias Analysis.” Proceedings of the ACM on Programming Languages, vol.
2, no. POPL, 30, Association for Computing Machinery, 2017, doi:10.1145/3158118.
short: K. Chatterjee, B. Choudhary, A. Pavlogiannis, Proceedings of the ACM on Programming
Languages 2 (2017).
conference:
end_date: 2018-01-13
location: Los Angeles, CA, United States
name: 'POPL: Programming Languages'
start_date: 2018-01-07
date_created: 2021-12-05T23:01:48Z
date_published: 2017-12-27T00:00:00Z
date_updated: 2023-02-23T12:27:13Z
day: '27'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3158118
ec_funded: 1
external_id:
arxiv:
- '1910.00241'
file:
- access_level: open_access
checksum: faa3f7b3fe8aab84b50ed805c26a0ee5
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-07T08:06:28Z
date_updated: 2021-12-07T08:06:28Z
file_id: '10421'
file_name: 2017_ACMProgLang_Chatterjee.pdf
file_size: 460188
relation: main_file
success: 1
file_date_updated: 2021-12-07T08:06:28Z
has_accepted_license: '1'
intvolume: ' 2'
issue: POPL
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '5455'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Optimal Dyck reachability for data-dependence and Alias analysis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2
year: '2017'
...
---
_id: '10417'
abstract:
- lang: eng
text: "We present a new dynamic partial-order reduction method for stateless model
checking of concurrent programs. A common approach for exploring program behaviors
relies on enumerating the traces of the program, without storing the visited states
(aka stateless exploration). As the number of distinct traces grows exponentially,
dynamic partial-order reduction (DPOR) techniques have been successfully used
to partition the space of traces into equivalence classes (Mazurkiewicz partitioning),
with the goal of exploring only few representative traces from each class.\r\n\r\nWe
introduce a new equivalence on traces under sequential consistency semantics,
which we call the observation equivalence. Two traces are observationally equivalent
if every read event observes the same write event in both traces. While the traditional
Mazurkiewicz equivalence is control-centric, our new definition is data-centric.
We show that our observation equivalence is coarser than the Mazurkiewicz equivalence,
and in many cases even exponentially coarser. We devise a DPOR exploration of
the trace space, called data-centric DPOR, based on the observation equivalence."
acknowledgement: "The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant
(279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061."
article_number: '31'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Marek
full_name: Chalupa, Marek
last_name: Chalupa
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Nishant
full_name: Sinha, Nishant
last_name: Sinha
- first_name: Kapil
full_name: Vaidya, Kapil
last_name: Vaidya
citation:
ama: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic
partial order reduction. Proceedings of the ACM on Programming Languages.
2017;2(POPL). doi:10.1145/3158119
apa: 'Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K.
(2017). Data-centric dynamic partial order reduction. Proceedings of the ACM
on Programming Languages. Los Angeles, CA, United States: Association for
Computing Machinery. https://doi.org/10.1145/3158119'
chicago: Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha,
and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings
of the ACM on Programming Languages. Association for Computing Machinery,
2017. https://doi.org/10.1145/3158119.
ieee: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric
dynamic partial order reduction,” Proceedings of the ACM on Programming Languages,
vol. 2, no. POPL. Association for Computing Machinery, 2017.
ista: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric
dynamic partial order reduction. Proceedings of the ACM on Programming Languages.
2(POPL), 31.
mla: Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings
of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for
Computing Machinery, 2017, doi:10.1145/3158119.
short: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings
of the ACM on Programming Languages 2 (2017).
conference:
end_date: 2018-01-13
location: Los Angeles, CA, United States
name: 'POPL: Programming Languages'
start_date: 2018-01-07
date_created: 2021-12-05T23:01:49Z
date_published: 2017-12-27T00:00:00Z
date_updated: 2023-02-23T12:27:16Z
day: '27'
department:
- _id: KrCh
doi: 10.1145/3158119
ec_funded: 1
external_id:
arxiv:
- '1610.01188'
intvolume: ' 2'
issue: POPL
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://dl.acm.org/doi/10.1145/3158119
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '5448'
relation: earlier_version
status: public
- id: '5456'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Data-centric dynamic partial order reduction
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2
year: '2017'
...
---
_id: '10418'
abstract:
- lang: eng
text: We present a new proof rule for proving almost-sure termination of probabilistic
programs, including those that contain demonic non-determinism. An important question
for a probabilistic program is whether the probability mass of all its diverging
runs is zero, that is that it terminates "almost surely". Proving that can be
hard, and this paper presents a new method for doing so. It applies directly to
the program's source code, even if the program contains demonic choice. Like others,
we use variant functions (a.k.a. "super-martingales") that are real-valued and
decrease randomly on each loop iteration; but our key innovation is that the amount
as well as the probability of the decrease are parametric. We prove the soundness
of the new rule, indicate where its applicability goes beyond existing rules,
and explain its connection to classical results on denumerable (non-demonic) Markov
chains.
acknowledgement: "McIver and Morgan are grateful to David Basin and the Information
Security Group at ETH Zürich for hosting a six-month stay in Switzerland, during
part of which this work began. And thanks particularly to Andreas Lochbihler, who
shared with us the probabilistic termination problem that led to it. They acknowledge
the support of ARC grant DP140101119. Part of this work was carried out during the
Workshop on Probabilistic Programming Semantics\r\nat McGill University’s Bellairs
Research Institute on Barbados organised by Alexandra Silva and\r\nPrakash Panangaden.
Kaminski and Katoen are grateful to Sebastian Junges for spotting a flaw in §5.4."
article_number: '33'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Annabelle
full_name: Mciver, Annabelle
last_name: Mciver
- first_name: Carroll
full_name: Morgan, Carroll
last_name: Morgan
- first_name: Benjamin Lucien
full_name: Kaminski, Benjamin Lucien
last_name: Kaminski
- first_name: Joost P
full_name: Katoen, Joost P
id: 4524F760-F248-11E8-B48F-1D18A9856A87
last_name: Katoen
citation:
ama: Mciver A, Morgan C, Kaminski BL, Katoen JP. A new proof rule for almost-sure
termination. Proceedings of the ACM on Programming Languages. 2017;2(POPL).
doi:10.1145/3158121
apa: 'Mciver, A., Morgan, C., Kaminski, B. L., & Katoen, J. P. (2017). A new
proof rule for almost-sure termination. Proceedings of the ACM on Programming
Languages. Los Angeles, CA, United States: Association for Computing Machinery.
https://doi.org/10.1145/3158121'
chicago: Mciver, Annabelle, Carroll Morgan, Benjamin Lucien Kaminski, and Joost
P Katoen. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the
ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158121.
ieee: A. Mciver, C. Morgan, B. L. Kaminski, and J. P. Katoen, “A new proof rule
for almost-sure termination,” Proceedings of the ACM on Programming Languages,
vol. 2, no. POPL. Association for Computing Machinery, 2017.
ista: Mciver A, Morgan C, Kaminski BL, Katoen JP. 2017. A new proof rule for almost-sure
termination. Proceedings of the ACM on Programming Languages. 2(POPL), 33.
mla: Mciver, Annabelle, et al. “A New Proof Rule for Almost-Sure Termination.” Proceedings
of the ACM on Programming Languages, vol. 2, no. POPL, 33, Association for
Computing Machinery, 2017, doi:10.1145/3158121.
short: A. Mciver, C. Morgan, B.L. Kaminski, J.P. Katoen, Proceedings of the ACM
on Programming Languages 2 (2017).
conference:
end_date: 2018-01-13
location: Los Angeles, CA, United States
name: 'POPL: Programming Languages'
start_date: 2018-01-07
date_created: 2021-12-05T23:01:49Z
date_published: 2017-12-07T00:00:00Z
date_updated: 2021-12-07T08:04:14Z
day: '07'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1145/3158121
external_id:
arxiv:
- '1711.03588'
intvolume: ' 2'
issue: POPL
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://dl.acm.org/doi/10.1145/3158121
month: '12'
oa: 1
oa_version: Published Version
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: A new proof rule for almost-sure termination
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2
year: '2017'
...
---
_id: '1061'
abstract:
- lang: eng
text: 'Background: Metabolic engineering and synthetic biology of cyanobacteria
offer a promising sustainable alternative approach for fossil-based ethylene production,
by using sunlight via oxygenic photosynthesis, to convert carbon dioxide directly
into ethylene. Towards this, both well-studied cyanobacteria, i.e., Synechocystis
sp PCC 6803 and Synechococcus elongatus PCC 7942, have been engineered to produce
ethylene by introducing the ethylene-forming enzyme (Efe) from Pseudomonas syringae
pv. phaseolicola PK2 (the Kudzu strain), which catalyzes the conversion of the
ubiquitous tricarboxylic acid cycle intermediate 2-oxoglutarate into ethylene.
Results: This study focuses on Synechocystis sp PCC 6803 and shows stable ethylene
production through the integration of a codon-optimized version of the efe gene
under control of the Ptrc promoter and the core Shine-Dalgarno sequence (5\''-AGGAGG-3\'')
as the ribosome-binding site (RBS), at the slr0168 neutral site. We have increased
ethylene production twofold by RBS screening and further investigated improving
ethylene production from a single gene copy of efe, using multiple tandem promoters
and by putting our best construct on an RSF1010-based broad-host-self-replicating
plasmid, which has a higher copy number than the genome. Moreover, to raise the
intracellular amounts of the key Efe substrate, 2-oxoglutarate, from which ethylene
is formed, we constructed a glycogen-synthesis knockout mutant (glgC) and introduced
the ethylene biosynthetic pathway in it. Under nitrogen limiting conditions, the
glycogen knockout strain has increased intracellular 2-oxoglutarate levels; however,
surprisingly, ethylene production was lower in this strain than in the wild-type
background. Conclusion: Making use of different RBS sequences, production of ethylene
ranging over a 20-fold difference has been achieved. However, a further increase
of production through multiple tandem promoters and a broad-host plasmid was not
achieved speculating that the transcription strength and the gene copy number
are not the limiting factors in our system.'
article_number: '34'
article_processing_charge: No
author:
- first_name: Vinod
full_name: Veetil, Vinod
last_name: Veetil
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Klaas
full_name: Hellingwerf, Klaas
last_name: Hellingwerf
citation:
ama: Veetil V, Angermayr A, Hellingwerf K. Ethylene production with engineered Synechocystis
sp PCC 6803 strains. Microbial Cell Factories. 2017;16(1). doi:10.1186/s12934-017-0645-5
apa: Veetil, V., Angermayr, A., & Hellingwerf, K. (2017). Ethylene production
with engineered Synechocystis sp PCC 6803 strains. Microbial Cell Factories.
BioMed Central. https://doi.org/10.1186/s12934-017-0645-5
chicago: Veetil, Vinod, Andreas Angermayr, and Klaas Hellingwerf. “Ethylene Production
with Engineered Synechocystis Sp PCC 6803 Strains.” Microbial Cell Factories.
BioMed Central, 2017. https://doi.org/10.1186/s12934-017-0645-5.
ieee: V. Veetil, A. Angermayr, and K. Hellingwerf, “Ethylene production with engineered
Synechocystis sp PCC 6803 strains,” Microbial Cell Factories, vol. 16,
no. 1. BioMed Central, 2017.
ista: Veetil V, Angermayr A, Hellingwerf K. 2017. Ethylene production with engineered
Synechocystis sp PCC 6803 strains. Microbial Cell Factories. 16(1), 34.
mla: Veetil, Vinod, et al. “Ethylene Production with Engineered Synechocystis Sp
PCC 6803 Strains.” Microbial Cell Factories, vol. 16, no. 1, 34, BioMed
Central, 2017, doi:10.1186/s12934-017-0645-5.
short: V. Veetil, A. Angermayr, K. Hellingwerf, Microbial Cell Factories 16 (2017).
date_created: 2018-12-11T11:49:56Z
date_published: 2017-02-23T00:00:00Z
date_updated: 2023-09-20T12:09:21Z
day: '23'
ddc:
- '579'
doi: 10.1186/s12934-017-0645-5
extern: '1'
external_id:
isi:
- '000397733000001'
pmid:
- '28231787'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:50Z
date_updated: 2018-12-12T10:16:50Z
file_id: '5240'
file_name: IST-2017-792-v1+1_s12934-017-0645-5.pdf
file_size: 1361313
relation: main_file
file_date_updated: 2018-12-12T10:16:50Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Microbial Cell Factories
publication_identifier:
issn:
- '14752859'
publication_status: published
publisher: BioMed Central
publist_id: '6325'
pubrep_id: '792'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ethylene production with engineered Synechocystis sp PCC 6803 strains
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 16
year: '2017'
...
---
_id: '1062'
abstract:
- lang: eng
text: Mouse chromaffin cells (MCCs) generate action potential (AP) firing that regulates
the Ca2+‐dependent release of catecholamines (CAs). Recent findings indicate that
MCCs possess a variety of spontaneous firing modes that span from the common ‘tonic‐irregular’
to the less frequent ‘burst’ firing. This latter is evident in a small fraction
of MCCs but occurs regularly when Nav1.3/1.7 channels are made less available
or when the Slo1β2‐subunit responsible for BK channel inactivation is deleted.
Burst firing causes large increases of Ca2+‐entry and potentiates CA release by
∼3.5‐fold and thus may be a key mechanism for regulating MCC function. With the
aim to uncover a physiological role for burst‐firing we investigated the effects
of acidosis on MCC activity. Lowering the extracellular pH (pHo) from 7.4 to 7.0
and 6.6 induces cell depolarizations of 10–15 mV that generate repeated bursts.
Bursts at pHo 6.6 lasted ∼330 ms, occurred at 1–2 Hz and caused an ∼7‐fold increase
of CA cumulative release. Burst firing originates from the inhibition of the pH‐sensitive
TASK‐1/TASK‐3 channels and from a 40% BK channel conductance reduction at pHo
7.0. The same pHo had little or no effect on Nav, Cav, Kv and SK channels that
support AP firing in MCCs. Burst firing of pHo 6.6 could be mimicked by mixtures
of the TASK‐1 blocker A1899 (300 nm) and BK blocker paxilline (300 nm) and could
be prevented by blocking L‐type channels by adding 3 μm nifedipine. Mixtures of
the two blockers raised cumulative CA‐secretion even more than low pHo (∼12‐fold),
showing that the action of protons on vesicle release is mainly a result of the
ionic conductance changes that increase Ca2+‐entry during bursts. Our data provide
direct evidence suggesting that MCCs respond to low pHo with sustained depolarization,
burst firing and enhanced CA‐secretion, thus mimicking the physiological response
of CCs to acute acidosis and hyperkalaemia generated during heavy exercise and
muscle fatigue.
article_processing_charge: No
author:
- first_name: Laura
full_name: Guarina, Laura
last_name: Guarina
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Valentina
full_name: Carabelli, Valentina
last_name: Carabelli
- first_name: Emilio
full_name: Carbone, Emilio
last_name: Carbone
citation:
ama: Guarina L, Vandael DH, Carabelli V, Carbone E. Low pH inf o boosts burst firing
and catecholamine release by blocking TASK-1 and BK channels while preserving
Cav1 channels in mouse chromaffin cells. Journal of Physiology. 2017;595(8):2587-2609.
doi:10.1113/JP273735
apa: Guarina, L., Vandael, D. H., Carabelli, V., & Carbone, E. (2017). Low pH
inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK
channels while preserving Cav1 channels in mouse chromaffin cells. Journal
of Physiology. Wiley-Blackwell. https://doi.org/10.1113/JP273735
chicago: Guarina, Laura, David H Vandael, Valentina Carabelli, and Emilio Carbone.
“Low PH Inf o Boosts Burst Firing and Catecholamine Release by Blocking TASK-1
and BK Channels While Preserving Cav1 Channels in Mouse Chromaffin Cells.” Journal
of Physiology. Wiley-Blackwell, 2017. https://doi.org/10.1113/JP273735.
ieee: L. Guarina, D. H. Vandael, V. Carabelli, and E. Carbone, “Low pH inf o boosts
burst firing and catecholamine release by blocking TASK-1 and BK channels while
preserving Cav1 channels in mouse chromaffin cells,” Journal of Physiology,
vol. 595, no. 8. Wiley-Blackwell, pp. 2587–2609, 2017.
ista: Guarina L, Vandael DH, Carabelli V, Carbone E. 2017. Low pH inf o boosts burst
firing and catecholamine release by blocking TASK-1 and BK channels while preserving
Cav1 channels in mouse chromaffin cells. Journal of Physiology. 595(8), 2587–2609.
mla: Guarina, Laura, et al. “Low PH Inf o Boosts Burst Firing and Catecholamine
Release by Blocking TASK-1 and BK Channels While Preserving Cav1 Channels in Mouse
Chromaffin Cells.” Journal of Physiology, vol. 595, no. 8, Wiley-Blackwell,
2017, pp. 2587–609, doi:10.1113/JP273735.
short: L. Guarina, D.H. Vandael, V. Carabelli, E. Carbone, Journal of Physiology
595 (2017) 2587–2609.
date_created: 2018-12-11T11:49:56Z
date_published: 2017-04-15T00:00:00Z
date_updated: 2023-09-20T12:09:47Z
day: '15'
doi: 10.1113/JP273735
extern: '1'
external_id:
isi:
- '000399430300022'
intvolume: ' 595'
isi: 1
issue: '8'
language:
- iso: eng
month: '04'
oa_version: None
page: '2587 - 2609 '
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6326'
quality_controlled: '1'
status: public
title: Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1
and BK channels while preserving Cav1 channels in mouse chromaffin cells
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 595
year: '2017'
...