---
_id: '9603'
abstract:
- lang: eng
text: Mosaic analysis with double markers (MADM) offers one approach to visualize
and concomitantly manipulate genetically defined cells in mice with single-cell
resolution. MADM applications include the analysis of lineage, single-cell morphology
and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous
gene functions in vivo in health and disease. Yet, MADM can only be applied to
<25% of all mouse genes on select chromosomes to date. To overcome this limitation,
we generate transgenic mice with knocked-in MADM cassettes near the centromeres
of all 19 autosomes and validate their use across organs. With this resource,
>96% of the entire mouse genome can now be subjected to single-cell genetic mosaic
analysis. Beyond a proof of principle, we apply our MADM library to systematically
trace sister chromatid segregation in distinct mitotic cell lineages. We find
striking chromosome-specific biases in segregation patterns, reflecting a putative
mechanism for the asymmetric segregation of genetic determinants in somatic stem
cell division.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
acknowledgement: We thank the Bioimaging, Life Science, and Pre-Clinical Facilities
at IST Austria; M.P. Postiglione, C. Simbriger, K. Valoskova, C. Schwayer, T. Hussain,
M. Pieber, and V. Wimmer for initial experiments, technical support, and/or assistance;
R. Shigemoto for sharing iv (Dnah11 mutant) mice; and M. Sixt and all members of
the Hippenmeyer lab for discussion. This work was supported by National Institutes
of Health grants ( R01-NS050580 to L.L. and F32MH096361 to L.A.S.). L.L. is an investigator
of HHMI. N.A. received support from FWF Firnberg-Programm ( T 1031 ). A.H.H. is
a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences . This
work also received support from IST Austria institutional funds , FWF SFB F78 to
S.H., the People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme ( FP7/2007-2013 ) under REA grant agreement no 618444 to S.H.,
and the European Research Council (ERC) under the European Union’s Horizon 2020
Research and Innovation Programme (grant agreement no. 725780 LinPro ) to S.H.
article_number: '109274'
article_processing_charge: No
article_type: original
author:
- first_name: Ximena
full_name: Contreras, Ximena
id: 475990FE-F248-11E8-B48F-1D18A9856A87
last_name: Contreras
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Amarbayasgalan
full_name: Davaatseren, Amarbayasgalan
id: 70ADC922-B424-11E9-99E3-BA18E6697425
last_name: Davaatseren
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Johanna
full_name: Sonntag, Johanna
id: 32FE7D7C-F248-11E8-B48F-1D18A9856A87
last_name: Sonntag
- first_name: Lill
full_name: Andersen, Lill
last_name: Andersen
- first_name: Tina
full_name: Bernthaler, Tina
last_name: Bernthaler
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Anna-Magdalena
full_name: Heger, Anna-Magdalena
id: 4B76FFD2-F248-11E8-B48F-1D18A9856A87
last_name: Heger
- first_name: Randy L.
full_name: Johnson, Randy L.
last_name: Johnson
- first_name: Lindsay A.
full_name: Schwarz, Lindsay A.
last_name: Schwarz
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Contreras X, Amberg N, Davaatseren A, et al. A genome-wide library of MADM
mice for single-cell genetic mosaic analysis. Cell Reports. 2021;35(12).
doi:10.1016/j.celrep.2021.109274
apa: Contreras, X., Amberg, N., Davaatseren, A., Hansen, A. H., Sonntag, J., Andersen,
L., … Hippenmeyer, S. (2021). A genome-wide library of MADM mice for single-cell
genetic mosaic analysis. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2021.109274
chicago: Contreras, Ximena, Nicole Amberg, Amarbayasgalan Davaatseren, Andi H Hansen,
Johanna Sonntag, Lill Andersen, Tina Bernthaler, et al. “A Genome-Wide Library
of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports. Cell
Press, 2021. https://doi.org/10.1016/j.celrep.2021.109274.
ieee: X. Contreras et al., “A genome-wide library of MADM mice for single-cell
genetic mosaic analysis,” Cell Reports, vol. 35, no. 12. Cell Press, 2021.
ista: Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler
T, Streicher C, Heger A-M, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer
S. 2021. A genome-wide library of MADM mice for single-cell genetic mosaic analysis.
Cell Reports. 35(12), 109274.
mla: Contreras, Ximena, et al. “A Genome-Wide Library of MADM Mice for Single-Cell
Genetic Mosaic Analysis.” Cell Reports, vol. 35, no. 12, 109274, Cell Press,
2021, doi:10.1016/j.celrep.2021.109274.
short: X. Contreras, N. Amberg, A. Davaatseren, A.H. Hansen, J. Sonntag, L. Andersen,
T. Bernthaler, C. Streicher, A.-M. Heger, R.L. Johnson, L.A. Schwarz, L. Luo,
T. Rülicke, S. Hippenmeyer, Cell Reports 35 (2021).
date_created: 2021-06-27T22:01:48Z
date_published: 2021-06-22T00:00:00Z
date_updated: 2023-08-10T13:55:00Z
day: '22'
ddc:
- '570'
department:
- _id: SiHi
- _id: LoSw
- _id: PreCl
doi: 10.1016/j.celrep.2021.109274
ec_funded: 1
external_id:
isi:
- '000664463600016'
file:
- access_level: open_access
checksum: d49520fdcbbb5c2f883bddb67cee5d77
content_type: application/pdf
creator: asandaue
date_created: 2021-06-28T14:06:24Z
date_updated: 2021-06-28T14:06:24Z
file_id: '9613'
file_name: 2021_CellReports_Contreras.pdf
file_size: 7653149
relation: main_file
success: 1
file_date_updated: 2021-06-28T14:06:24Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '12'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular Mechanisms of Radial Neuronal Migration
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Cell Reports
publication_identifier:
eissn:
- '22111247'
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/
scopus_import: '1'
status: public
title: A genome-wide library of MADM mice for single-cell genetic mosaic analysis
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 35
year: '2021'
...
---
_id: '9604'
abstract:
- lang: eng
text: Generalizing Lee’s inductive argument for counting the cells of higher order
Voronoi tessellations in ℝ² to ℝ³, we get precise relations in terms of Morse
theoretic quantities for piecewise constant functions on planar arrangements.
Specifically, we prove that for a generic set of n ≥ 5 points in ℝ³, the number
of regions in the order-k Voronoi tessellation is N_{k-1} - binom(k,2)n + n, for
1 ≤ k ≤ n-1, in which N_{k-1} is the sum of Euler characteristics of these function’s
first k-1 sublevel sets. We get similar expressions for the vertices, edges, and
polygons of the order-k Voronoi tessellation.
alternative_title:
- LIPIcs
article_number: '16'
article_processing_charge: No
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Sebastiano
full_name: Cultrera di Montesano, Sebastiano
id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
last_name: Cultrera di Montesano
orcid: 0000-0001-6249-0832
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Morteza
full_name: Saghafian, Morteza
last_name: Saghafian
citation:
ama: 'Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Counting cells
of order-k voronoi tessellations in ℝ3 with morse theory. In: Leibniz
International Proceedings in Informatics. Vol 189. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2021. doi:10.4230/LIPIcs.SoCG.2021.16'
apa: 'Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., & Saghafian,
M. (2021). Counting cells of order-k voronoi tessellations in ℝ3 with
morse theory. In Leibniz International Proceedings in Informatics (Vol.
189). Online: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2021.16'
chicago: Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner,
and Morteza Saghafian. “Counting Cells of Order-k Voronoi Tessellations in ℝ3
with Morse Theory.” In Leibniz International Proceedings in Informatics,
Vol. 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.SoCG.2021.16.
ieee: R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Counting
cells of order-k voronoi tessellations in ℝ3 with morse theory,” in
Leibniz International Proceedings in Informatics, Online, 2021, vol. 189.
ista: 'Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. 2021. Counting
cells of order-k voronoi tessellations in ℝ3 with morse theory. Leibniz
International Proceedings in Informatics. SoCG: International Symposium on Computational
Geometry, LIPIcs, vol. 189, 16.'
mla: Biswas, Ranita, et al. “Counting Cells of Order-k Voronoi Tessellations in
ℝ3 with Morse Theory.” Leibniz International Proceedings in Informatics,
vol. 189, 16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:10.4230/LIPIcs.SoCG.2021.16.
short: R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, in:,
Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2021.
conference:
end_date: 2021-06-11
location: Online
name: 'SoCG: International Symposium on Computational Geometry'
start_date: 2021-06-07
date_created: 2021-06-27T22:01:48Z
date_published: 2021-06-02T00:00:00Z
date_updated: 2023-02-23T14:02:28Z
day: '02'
ddc:
- '516'
department:
- _id: HeEd
doi: 10.4230/LIPIcs.SoCG.2021.16
ec_funded: 1
file:
- access_level: open_access
checksum: 22b11a719018b22ecba2471b51f2eb40
content_type: application/pdf
creator: asandaue
date_created: 2021-06-28T13:11:39Z
date_updated: 2021-06-28T13:11:39Z
file_id: '9611'
file_name: 2021_LIPIcs_Biswas.pdf
file_size: 727817
relation: main_file
success: 1
file_date_updated: 2021-06-28T13:11:39Z
has_accepted_license: '1'
intvolume: ' 189'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
- _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316
grant_number: I4887
name: Discretization in Geometry and Dynamics
publication: Leibniz International Proceedings in Informatics
publication_identifier:
isbn:
- '9783959771849'
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Counting cells of order-k voronoi tessellations in ℝ3 with morse
theory
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 189
year: '2021'
...
---
_id: '9605'
abstract:
- lang: eng
text: 'Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within
distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter
family of spaces that grow larger when r increases or k decreases, called the
multicover bifiltration. Motivated by the problem of computing the homology of
this bifiltration, we introduce two closely related combinatorial bifiltrations,
one polyhedral and the other simplicial, which are both topologically equivalent
to the multicover bifiltration and far smaller than a Čech-based model considered
in prior work of Sheehy. Our polyhedral construction is a bifiltration of the
rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using
a variant of an algorithm given by these authors as well. Using an implementation
for dimension 2 and 3, we provide experimental results. Our simplicial construction
is useful for understanding the polyhedral construction and proving its correctness. '
acknowledgement: The authors want to thank the reviewers for many helpful comments
and suggestions.
alternative_title:
- LIPIcs
article_number: '27'
article_processing_charge: No
arxiv: 1
author:
- first_name: René
full_name: Corbet, René
last_name: Corbet
- first_name: Michael
full_name: Kerber, Michael
last_name: Kerber
- first_name: Michael
full_name: Lesnick, Michael
last_name: Lesnick
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
citation:
ama: 'Corbet R, Kerber M, Lesnick M, Osang GF. Computing the multicover bifiltration.
In: Leibniz International Proceedings in Informatics. Vol 189. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:10.4230/LIPIcs.SoCG.2021.27'
apa: 'Corbet, R., Kerber, M., Lesnick, M., & Osang, G. F. (2021). Computing
the multicover bifiltration. In Leibniz International Proceedings in Informatics
(Vol. 189). Online: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2021.27'
chicago: Corbet, René, Michael Kerber, Michael Lesnick, and Georg F Osang. “Computing
the Multicover Bifiltration.” In Leibniz International Proceedings in Informatics,
Vol. 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.SoCG.2021.27.
ieee: R. Corbet, M. Kerber, M. Lesnick, and G. F. Osang, “Computing the multicover
bifiltration,” in Leibniz International Proceedings in Informatics, Online,
2021, vol. 189.
ista: 'Corbet R, Kerber M, Lesnick M, Osang GF. 2021. Computing the multicover bifiltration.
Leibniz International Proceedings in Informatics. SoCG: International Symposium
on Computational Geometry, LIPIcs, vol. 189, 27.'
mla: Corbet, René, et al. “Computing the Multicover Bifiltration.” Leibniz International
Proceedings in Informatics, vol. 189, 27, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2021, doi:10.4230/LIPIcs.SoCG.2021.27.
short: R. Corbet, M. Kerber, M. Lesnick, G.F. Osang, in:, Leibniz International
Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2021.
conference:
end_date: 2021-06-11
location: Online
name: 'SoCG: International Symposium on Computational Geometry'
start_date: 2021-06-07
date_created: 2021-06-27T22:01:49Z
date_published: 2021-06-02T00:00:00Z
date_updated: 2023-10-04T12:03:39Z
day: '02'
ddc:
- '516'
department:
- _id: HeEd
doi: 10.4230/LIPIcs.SoCG.2021.27
external_id:
arxiv:
- '2103.07823'
file:
- access_level: open_access
checksum: 0de217501e7ba8b267d58deed0d51761
content_type: application/pdf
creator: cziletti
date_created: 2021-06-28T12:40:47Z
date_updated: 2021-06-28T12:40:47Z
file_id: '9610'
file_name: 2021_LIPIcs_Corbet.pdf
file_size: '1367983'
relation: main_file
success: 1
file_date_updated: 2021-06-28T12:40:47Z
has_accepted_license: '1'
intvolume: ' 189'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Leibniz International Proceedings in Informatics
publication_identifier:
isbn:
- '9783959771849'
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
link:
- relation: extended_version
url: https://arxiv.org/abs/2103.07823
record:
- id: '12709'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Computing the multicover bifiltration
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 189
year: '2021'
...
---
_id: '9606'
abstract:
- lang: eng
text: Sound propagation is a macroscopic manifestation of the interplay between
the equilibrium thermodynamics and the dynamical transport properties of fluids.
Here, for a two-dimensional system of ultracold fermions, we calculate the first
and second sound velocities across the whole BCS-BEC crossover, and we analyze
the system response to an external perturbation. In the low-temperature regime
we reproduce the recent measurements [Phys. Rev. Lett. 124, 240403 (2020)] of
the first sound velocity, which, due to the decoupling of density and entropy
fluctuations, is the sole mode excited by a density probe. Conversely, a heat
perturbation excites only the second sound, which, being sensitive to the superfluid
depletion, vanishes in the deep BCS regime and jumps discontinuously to zero at
the Berezinskii-Kosterlitz-Thouless superfluid transition. A mixing between the
modes occurs only in the finite-temperature BEC regime, where our theory converges
to the purely bosonic results.
acknowledgement: "G.B. acknowledges support from the Austrian Science Fund (FWF),
under Project No. M2641-N27. This work was\r\npartially supported by the University
of Padua, BIRD project “Superfluid properties of Fermi gases in optical potentials.”\r\nThe
authors thank Miki Ota, Tomoki Ozawa, Sandro Stringari, Tilman Enss, Hauke Biss,
Henning Moritz, and Nicolò Defenu for fruitful discussions. The authors thank Henning
Moritz and Markus Bohlen for providing their experimental\r\ndata."
article_number: L061303
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: A.
full_name: Tononi, A.
last_name: Tononi
- first_name: Alberto
full_name: Cappellaro, Alberto
id: 9d13b3cb-30a2-11eb-80dc-f772505e8660
last_name: Cappellaro
orcid: 0000-0001-6110-2359
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: L.
full_name: Salasnich, L.
last_name: Salasnich
citation:
ama: Tononi A, Cappellaro A, Bighin G, Salasnich L. Propagation of first and second
sound in a two-dimensional Fermi superfluid. Physical Review A. 2021;103(6).
doi:10.1103/PhysRevA.103.L061303
apa: Tononi, A., Cappellaro, A., Bighin, G., & Salasnich, L. (2021). Propagation
of first and second sound in a two-dimensional Fermi superfluid. Physical Review
A. American Physical Society. https://doi.org/10.1103/PhysRevA.103.L061303
chicago: Tononi, A., Alberto Cappellaro, Giacomo Bighin, and L. Salasnich. “Propagation
of First and Second Sound in a Two-Dimensional Fermi Superfluid.” Physical
Review A. American Physical Society, 2021. https://doi.org/10.1103/PhysRevA.103.L061303.
ieee: A. Tononi, A. Cappellaro, G. Bighin, and L. Salasnich, “Propagation of first
and second sound in a two-dimensional Fermi superfluid,” Physical Review A,
vol. 103, no. 6. American Physical Society, 2021.
ista: Tononi A, Cappellaro A, Bighin G, Salasnich L. 2021. Propagation of first
and second sound in a two-dimensional Fermi superfluid. Physical Review A. 103(6),
L061303.
mla: Tononi, A., et al. “Propagation of First and Second Sound in a Two-Dimensional
Fermi Superfluid.” Physical Review A, vol. 103, no. 6, L061303, American
Physical Society, 2021, doi:10.1103/PhysRevA.103.L061303.
short: A. Tononi, A. Cappellaro, G. Bighin, L. Salasnich, Physical Review A 103
(2021).
date_created: 2021-06-27T22:01:49Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-10T13:37:25Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.103.L061303
external_id:
arxiv:
- '2009.06491'
isi:
- '000662296700014'
intvolume: ' 103'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2009.06491
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- '24699934'
issn:
- '24699926'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Propagation of first and second sound in a two-dimensional Fermi superfluid
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 103
year: '2021'
...
---
_id: '9607'
abstract:
- lang: eng
text: While high risk of failure is an inherent part of developing innovative therapies,
it can be reduced by adherence to evidence-based rigorous research practices.
Numerous analyses conducted to date have clearly identified measures that need
to be taken to improve research rigor. Supported through the European Union's
Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical
research quality system that can be applied in both public and private sectors
and is free for anyone to use. The EQIPD Quality System was designed to be suited
to boost innovation by ensuring the generation of robust and reliable preclinical
data while being lean, effective and not becoming a burden that could negatively
impact the freedom to explore scientific questions. EQIPD defines research quality
as the extent to which research data are fit for their intended use. Fitness,
in this context, is defined by the stakeholders, who are the scientists directly
involved in the research, but also their funders, sponsors, publishers, research
tool manufacturers and collaboration partners such as peers in a multi-site research
project. The essence of the EQIPD Quality System is the set of 18 core requirements
that can be addressed flexibly, according to user-specific needs and following
a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations
for quality-related measures, defines criteria for adequate processes (i.e., performance
standards) and provides examples of how such measures can be developed and implemented.
However, it does not prescribe any pre-determined solutions. EQIPD has also developed
tools (for optional use) to support users in implementing the system and assessment
services for those research units that successfully implement the quality system
and seek formal accreditation. Building upon the feedback from users and continuous
improvement, a sustainable EQIPD Quality System will ultimately serve the entire
community of scientists conducting non-regulated preclinical research, by helping
them generate reliable data that are fit for their intended use.
acknowledgement: This project has received funding from the Innovative Medicines Initiative
2 Joint Undertaking under grant agreement No 777364. This Joint Undertaking receives
support from the European Union’s Horizon 2020 research and innovation programme
and EFPIA. The authors are very grateful to Martin Heinrich (Abbvie, Ludwigshafen,
Germany) for the exceptional IT support and programming the EQIPD Planning Tool
and the Creator Tool and to Dr Shai Silberberg (NINDS, USA), Dr. Renza Roncarati
(PAASP Italy) and Dr Judith Homberg (Radboud University, Nijmegen) for highly stimulating
contributions to the discussions and comments on earlier versions of this manuscript.
We also wish to express our thanks to Dr. Sara Stöber (concentris research management
GmbH, Fürstenfeldbruck, Germany) for excellent and continuous support of this project.
Creation of the EQIPD Stakeholder group was supported by Noldus Information Technology
bv (Wageningen, the Netherlands).
article_processing_charge: No
article_type: original
author:
- first_name: Anton
full_name: Bespalov, Anton
last_name: Bespalov
- first_name: René
full_name: Bernard, René
last_name: Bernard
- first_name: Anja
full_name: Gilis, Anja
last_name: Gilis
- first_name: Björn
full_name: Gerlach, Björn
last_name: Gerlach
- first_name: Javier
full_name: Guillén, Javier
last_name: Guillén
- first_name: Vincent
full_name: Castagné, Vincent
last_name: Castagné
- first_name: Isabel A.
full_name: Lefevre, Isabel A.
last_name: Lefevre
- first_name: Fiona
full_name: Ducrey, Fiona
last_name: Ducrey
- first_name: Lee
full_name: Monk, Lee
last_name: Monk
- first_name: Sandrine
full_name: Bongiovanni, Sandrine
last_name: Bongiovanni
- first_name: Bruce
full_name: Altevogt, Bruce
last_name: Altevogt
- first_name: María
full_name: Arroyo-Araujo, María
last_name: Arroyo-Araujo
- first_name: Lior
full_name: Bikovski, Lior
last_name: Bikovski
- first_name: Natasja
full_name: De Bruin, Natasja
last_name: De Bruin
- first_name: Esmeralda
full_name: Castaños-Vélez, Esmeralda
last_name: Castaños-Vélez
- first_name: Alexander
full_name: Dityatev, Alexander
last_name: Dityatev
- first_name: Christoph H.
full_name: Emmerich, Christoph H.
last_name: Emmerich
- first_name: Raafat
full_name: Fares, Raafat
last_name: Fares
- first_name: Chantelle
full_name: Ferland-Beckham, Chantelle
last_name: Ferland-Beckham
- first_name: Christelle
full_name: Froger-Colléaux, Christelle
last_name: Froger-Colléaux
- first_name: Valerie
full_name: Gailus-Durner, Valerie
last_name: Gailus-Durner
- first_name: Sabine M.
full_name: Hölter, Sabine M.
last_name: Hölter
- first_name: Martine Cj
full_name: Hofmann, Martine Cj
last_name: Hofmann
- first_name: Patricia
full_name: Kabitzke, Patricia
last_name: Kabitzke
- first_name: Martien Jh
full_name: Kas, Martien Jh
last_name: Kas
- first_name: Claudia
full_name: Kurreck, Claudia
last_name: Kurreck
- first_name: Paul
full_name: Moser, Paul
last_name: Moser
- first_name: Malgorzata
full_name: Pietraszek, Malgorzata
last_name: Pietraszek
- first_name: Piotr
full_name: Popik, Piotr
last_name: Popik
- first_name: Heidrun
full_name: Potschka, Heidrun
last_name: Potschka
- first_name: Ernesto
full_name: Prado Montes De Oca, Ernesto
last_name: Prado Montes De Oca
- first_name: Leonardo
full_name: Restivo, Leonardo
last_name: Restivo
- first_name: Gernot
full_name: Riedel, Gernot
last_name: Riedel
- first_name: Merel
full_name: Ritskes-Hoitinga, Merel
last_name: Ritskes-Hoitinga
- first_name: Janko
full_name: Samardzic, Janko
last_name: Samardzic
- first_name: Michael
full_name: Schunn, Michael
id: 4272DB4A-F248-11E8-B48F-1D18A9856A87
last_name: Schunn
orcid: 0000-0003-4326-5300
- first_name: Claudia
full_name: Stöger, Claudia
last_name: Stöger
- first_name: Vootele
full_name: Voikar, Vootele
last_name: Voikar
- first_name: Jan
full_name: Vollert, Jan
last_name: Vollert
- first_name: Kimberley E.
full_name: Wever, Kimberley E.
last_name: Wever
- first_name: Kathleen
full_name: Wuyts, Kathleen
last_name: Wuyts
- first_name: Malcolm R.
full_name: Macleod, Malcolm R.
last_name: Macleod
- first_name: Ulrich
full_name: Dirnagl, Ulrich
last_name: Dirnagl
- first_name: Thomas
full_name: Steckler, Thomas
last_name: Steckler
citation:
ama: Bespalov A, Bernard R, Gilis A, et al. Introduction to the EQIPD quality system.
eLife. 2021;10. doi:10.7554/eLife.63294
apa: Bespalov, A., Bernard, R., Gilis, A., Gerlach, B., Guillén, J., Castagné, V.,
… Steckler, T. (2021). Introduction to the EQIPD quality system. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.63294
chicago: Bespalov, Anton, René Bernard, Anja Gilis, Björn Gerlach, Javier Guillén,
Vincent Castagné, Isabel A. Lefevre, et al. “Introduction to the EQIPD Quality
System.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.63294.
ieee: A. Bespalov et al., “Introduction to the EQIPD quality system,” eLife,
vol. 10. eLife Sciences Publications, 2021.
ista: Bespalov A, Bernard R, Gilis A, Gerlach B, Guillén J, Castagné V, Lefevre
IA, Ducrey F, Monk L, Bongiovanni S, Altevogt B, Arroyo-Araujo M, Bikovski L,
De Bruin N, Castaños-Vélez E, Dityatev A, Emmerich CH, Fares R, Ferland-Beckham
C, Froger-Colléaux C, Gailus-Durner V, Hölter SM, Hofmann MC, Kabitzke P, Kas
MJ, Kurreck C, Moser P, Pietraszek M, Popik P, Potschka H, Prado Montes De Oca
E, Restivo L, Riedel G, Ritskes-Hoitinga M, Samardzic J, Schunn M, Stöger C, Voikar
V, Vollert J, Wever KE, Wuyts K, Macleod MR, Dirnagl U, Steckler T. 2021. Introduction
to the EQIPD quality system. eLife. 10.
mla: Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” ELife,
vol. 10, eLife Sciences Publications, 2021, doi:10.7554/eLife.63294.
short: A. Bespalov, R. Bernard, A. Gilis, B. Gerlach, J. Guillén, V. Castagné, I.A.
Lefevre, F. Ducrey, L. Monk, S. Bongiovanni, B. Altevogt, M. Arroyo-Araujo, L.
Bikovski, N. De Bruin, E. Castaños-Vélez, A. Dityatev, C.H. Emmerich, R. Fares,
C. Ferland-Beckham, C. Froger-Colléaux, V. Gailus-Durner, S.M. Hölter, M.C. Hofmann,
P. Kabitzke, M.J. Kas, C. Kurreck, P. Moser, M. Pietraszek, P. Popik, H. Potschka,
E. Prado Montes De Oca, L. Restivo, G. Riedel, M. Ritskes-Hoitinga, J. Samardzic,
M. Schunn, C. Stöger, V. Voikar, J. Vollert, K.E. Wever, K. Wuyts, M.R. Macleod,
U. Dirnagl, T. Steckler, ELife 10 (2021).
date_created: 2021-06-27T22:01:49Z
date_published: 2021-05-24T00:00:00Z
date_updated: 2023-08-10T13:36:50Z
day: '24'
ddc:
- '570'
department:
- _id: PreCl
doi: 10.7554/eLife.63294
external_id:
isi:
- '000661272000001'
pmid:
- '34028353'
file:
- access_level: open_access
checksum: 885b746051a7a6b6e24e3d2781a48fde
content_type: application/pdf
creator: asandaue
date_created: 2021-06-28T11:35:30Z
date_updated: 2021-06-28T11:35:30Z
file_id: '9609'
file_name: 2021_ELife_Bespalov.pdf
file_size: 2500720
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success: 1
file_date_updated: 2021-06-28T11:35:30Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Introduction to the EQIPD quality system
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: 10
year: '2021'
...
---
_id: '9618'
abstract:
- lang: eng
text: The control of nonequilibrium quantum dynamics in many-body systems is challenging
because interactions typically lead to thermalization and a chaotic spreading
throughout Hilbert space. We investigate nonequilibrium dynamics after rapid quenches
in a many-body system composed of 3 to 200 strongly interacting qubits in one
and two spatial dimensions. Using a programmable quantum simulator based on Rydberg
atom arrays, we show that coherent revivals associated with so-called quantum
many-body scars can be stabilized by periodic driving, which generates a robust
subharmonic response akin to discrete time-crystalline order. We map Hilbert space
dynamics, geometry dependence, phase diagrams, and system-size dependence of this
emergent phenomenon, demonstrating new ways to steer complex dynamics in many-body
systems and enabling potential applications in quantum information science.
acknowledgement: 'We thank many members of the Harvard AMO community, particularly
E. Urbach, S. Dakoulas, and J. Doyle for their efforts enabling safe and productive
operation of our laboratories during 2020. We thank D. Abanin, I. Cong, F. Machado,
H. Pichler, N. Yao, B. Ye, and H. Zhou for stimulating discussions. Funding: We
acknowledge financial support from the Center for Ultracold Atoms, the National
Science Foundation, the Vannevar Bush Faculty Fellowship, the U.S. Department of
Energy (LBNL QSA Center and grant no. DE-SC0021013), the Office of Naval Research,
the Army Research Office MURI, the DARPA DRINQS program (grant no. D18AC00033),
and the DARPA ONISQ program (grant no. W911NF2010021). The authors acknowledge support
from the NSF Graduate Research Fellowship Program (grant DGE1745303) and The Fannie
and John Hertz Foundation (D.B.); a National Defense Science and Engineering Graduate
(NDSEG) fellowship (H.L.); a fellowship from the Max Planck/Harvard Research Center
for Quantum Optics (G.S.); Gordon College (T.T.W.); the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
agreement no. 850899) (A.A.M. and M.S.); a Department of Energy Computational Science
Graduate Fellowship under award number DE-SC0021110 (N.M.); the Moore Foundation’s
EPiQS Initiative grant no. GBMF4306, the NUS Development grant AY2019/2020, and
the Stanford Institute of Theoretical Physics (W.W.H.); and the Miller Institute
for Basic Research in Science (S.C.). Author contributions: D.B., A.O., H.L., A.K.,
G.S., S.E., and T.T.W. contributed to the building of the experimental setup, performed
the measurements, and analyzed the data. A.A.M., N.M., W.W.H., S.C., and M.S. performed
theoretical analysis. All work was supervised by M.G., V.V., and M.D.L. All authors
discussed the results and contributed to the manuscript. Competing interests: M.G.,
V.V., and M.D.L. are co-founders and shareholders of QuEra Computing. A.O. is a
shareholder of QuEra Computing. Data and materials availability: All data needed
to evaluate the conclusions in the paper are present in the paper and the supplementary
materials.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: D.
full_name: Bluvstein, D.
last_name: Bluvstein
- first_name: A.
full_name: Omran, A.
last_name: Omran
- first_name: H.
full_name: Levine, H.
last_name: Levine
- first_name: A.
full_name: Keesling, A.
last_name: Keesling
- first_name: G.
full_name: Semeghini, G.
last_name: Semeghini
- first_name: S.
full_name: Ebadi, S.
last_name: Ebadi
- first_name: T. T.
full_name: Wang, T. T.
last_name: Wang
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: N.
full_name: Maskara, N.
last_name: Maskara
- first_name: W. W.
full_name: Ho, W. W.
last_name: Ho
- first_name: S.
full_name: Choi, S.
last_name: Choi
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: M.
full_name: Greiner, M.
last_name: Greiner
- first_name: V.
full_name: Vuletić, V.
last_name: Vuletić
- first_name: M. D.
full_name: Lukin, M. D.
last_name: Lukin
citation:
ama: Bluvstein D, Omran A, Levine H, et al. Controlling quantum many-body dynamics
in driven Rydberg atom arrays. Science. 2021;371(6536):1355-1359. doi:10.1126/science.abg2530
apa: Bluvstein, D., Omran, A., Levine, H., Keesling, A., Semeghini, G., Ebadi, S.,
… Lukin, M. D. (2021). Controlling quantum many-body dynamics in driven Rydberg
atom arrays. Science. AAAS. https://doi.org/10.1126/science.abg2530
chicago: Bluvstein, D., A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi,
T. T. Wang, et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom
Arrays.” Science. AAAS, 2021. https://doi.org/10.1126/science.abg2530.
ieee: D. Bluvstein et al., “Controlling quantum many-body dynamics in driven
Rydberg atom arrays,” Science, vol. 371, no. 6536. AAAS, pp. 1355–1359,
2021.
ista: Bluvstein D, Omran A, Levine H, Keesling A, Semeghini G, Ebadi S, Wang TT,
Michailidis A, Maskara N, Ho WW, Choi S, Serbyn M, Greiner M, Vuletić V, Lukin
MD. 2021. Controlling quantum many-body dynamics in driven Rydberg atom arrays.
Science. 371(6536), 1355–1359.
mla: Bluvstein, D., et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg
Atom Arrays.” Science, vol. 371, no. 6536, AAAS, 2021, pp. 1355–59, doi:10.1126/science.abg2530.
short: D. Bluvstein, A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T.T.
Wang, A. Michailidis, N. Maskara, W.W. Ho, S. Choi, M. Serbyn, M. Greiner, V.
Vuletić, M.D. Lukin, Science 371 (2021) 1355–1359.
date_created: 2021-06-29T12:04:05Z
date_published: 2021-03-26T00:00:00Z
date_updated: 2023-08-10T13:57:07Z
day: '26'
ddc:
- '539'
department:
- _id: MaSe
doi: 10.1126/science.abg2530
ec_funded: 1
external_id:
arxiv:
- '2012.12276'
isi:
- '000636043400048'
pmid:
- '33632894'
file:
- access_level: open_access
checksum: 0b356fd10ab9bb95177d4c047d4e9c1a
content_type: application/pdf
creator: patrickd
date_created: 2021-09-23T14:00:05Z
date_updated: 2021-09-23T14:00:05Z
file_id: '10040'
file_name: scars_subharmonic_combined_manuscript_2_11_2021 (2)-1.pdf
file_size: 3671159
relation: main_file
success: 1
file_date_updated: 2021-09-23T14:00:05Z
has_accepted_license: '1'
intvolume: ' 371'
isi: 1
issue: '6536'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '03'
oa: 1
oa_version: Preprint
page: 1355-1359
pmid: 1
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Controlling quantum many-body dynamics in driven Rydberg atom arrays
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 371
year: '2021'
...
---
_id: '9620'
abstract:
- lang: eng
text: "In this note, we introduce a distributed twist on the classic coupon collector
problem: a set of m collectors wish to each obtain a set of n coupons; for this,
they can each sample coupons uniformly at random, but can also meet in pairwise
interactions, during which they can exchange coupons. By doing so, they hope to
reduce the number of coupons that must be sampled by each collector in order to
obtain a full set. This extension is natural when considering real-world manifestations
of the coupon collector phenomenon, and has been remarked upon and studied empirically
(Hayes and Hannigan 2006, Ahmad et al. 2014, Delmarcelle 2019).\r\n\r\nWe provide
the first theoretical analysis for such a scenario. We find that “coupon collecting
with friends” can indeed significantly reduce the number of coupons each collector
must sample, and raises interesting connections to the more traditional variants
of the problem. While our analysis is in most cases asymptotically tight, there
are several open questions raised, regarding finer-grained analysis of both “coupon
collecting with friends,” and of a long-studied variant of the original problem
in which a collector requires multiple full sets of coupons."
acknowledgement: Peter Davies is supported by the European Union’s Horizon2020 research
and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Peter
full_name: Davies, Peter
id: 11396234-BB50-11E9-B24C-90FCE5697425
last_name: Davies
orcid: 0000-0002-5646-9524
citation:
ama: 'Alistarh D-A, Davies P. Collecting coupons is faster with friends. In: Structural
Information and Communication Complexity. Vol 12810. Springer Nature; 2021:3-12.
doi:10.1007/978-3-030-79527-6_1'
apa: 'Alistarh, D.-A., & Davies, P. (2021). Collecting coupons is faster with
friends. In Structural Information and Communication Complexity (Vol. 12810,
pp. 3–12). Wrocław, Poland: Springer Nature. https://doi.org/10.1007/978-3-030-79527-6_1'
chicago: Alistarh, Dan-Adrian, and Peter Davies. “Collecting Coupons Is Faster with
Friends.” In Structural Information and Communication Complexity, 12810:3–12.
Springer Nature, 2021. https://doi.org/10.1007/978-3-030-79527-6_1.
ieee: D.-A. Alistarh and P. Davies, “Collecting coupons is faster with friends,”
in Structural Information and Communication Complexity, Wrocław, Poland,
2021, vol. 12810, pp. 3–12.
ista: 'Alistarh D-A, Davies P. 2021. Collecting coupons is faster with friends.
Structural Information and Communication Complexity. SIROCCO: International Colloquium
on Structural Information and Communication Complexity, LNCS, vol. 12810, 3–12.'
mla: Alistarh, Dan-Adrian, and Peter Davies. “Collecting Coupons Is Faster with
Friends.” Structural Information and Communication Complexity, vol. 12810,
Springer Nature, 2021, pp. 3–12, doi:10.1007/978-3-030-79527-6_1.
short: D.-A. Alistarh, P. Davies, in:, Structural Information and Communication
Complexity, Springer Nature, 2021, pp. 3–12.
conference:
end_date: 2021-07-01
location: Wrocław, Poland
name: ' SIROCCO: International Colloquium on Structural Information and Communication
Complexity'
start_date: 2021-06-28
date_created: 2021-07-01T11:04:43Z
date_published: 2021-06-20T00:00:00Z
date_updated: 2023-02-23T14:02:46Z
day: '20'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1007/978-3-030-79527-6_1
ec_funded: 1
file:
- access_level: open_access
checksum: fe37fb9af3f5016c1084af9d6e7109bd
content_type: application/pdf
creator: pdavies
date_created: 2021-07-01T11:21:40Z
date_updated: 2021-07-01T11:21:40Z
file_id: '9621'
file_name: Population_Coupon_Collector.pdf
file_size: 319728
relation: main_file
file_date_updated: 2021-07-01T11:21:40Z
has_accepted_license: '1'
intvolume: ' 12810'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Preprint
page: 3-12
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Structural Information and Communication Complexity
publication_identifier:
eisbn:
- '9783030795276'
eissn:
- 1611-3349
isbn:
- '9783030795269'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Collecting coupons is faster with friends
type: conference
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 12810
year: '2021'
...
---
_id: '9623'
abstract:
- lang: eng
text: "Cytoplasmic reorganizations are essential for morphogenesis. In large cells
like oocytes, these reorganizations become crucial in patterning the oocyte for
later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm
(ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization
with the contraction of the actomyosin cortex along the animal-vegetal axis of
the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER),
maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the
myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here
we have used the species Phallusia mammillata to investigate the changes in cell
shape that accompany these reorganizations and the mechanochemical mechanisms
underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV)
axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening
followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show
that the fast oscillation corresponds to a dynamic polarization of the actin cortex
as a result of a fertilization-induced increase in cortical tension in the oocyte
that triggers a rupture of the cortex at the animal pole and the establishment
of vegetal-directed cortical flows. These flows are responsible for the vegetal
accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion
of the VP, leading to CP formation, correlates with a relaxation of the vegetal
cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm
is a solid-like layer that buckles under compression forces arising from the contracting
actin cortex at the VP. Straightening of the myoplasm when actin flows stops,
facilitates the expansion of the VP and the CP. Altogether, our results present
a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation.
\r\n"
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Silvia
full_name: Caballero Mancebo, Silvia
id: 2F1E1758-F248-11E8-B48F-1D18A9856A87
last_name: Caballero Mancebo
orcid: 0000-0002-5223-3346
citation:
ama: Caballero Mancebo S. Fertilization-induced deformations are controlled by the
actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021.
doi:10.15479/at:ista:9623
apa: Caballero Mancebo, S. (2021). Fertilization-induced deformations are controlled
by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9623
chicago: Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled
by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9623.
ieee: S. Caballero Mancebo, “Fertilization-induced deformations are controlled by
the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,”
Institute of Science and Technology Austria, 2021.
ista: Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled
by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes.
Institute of Science and Technology Austria.
mla: Caballero Mancebo, Silvia. Fertilization-Induced Deformations Are Controlled
by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9623.
short: S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by
the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes,
Institute of Science and Technology Austria, 2021.
date_created: 2021-07-01T14:50:17Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-09-07T13:33:27Z
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaHe
doi: 10.15479/at:ista:9623
file:
- access_level: closed
checksum: e039225a47ef32666d59bf35ddd30ecf
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: scaballe
date_created: 2021-07-01T14:48:54Z
date_updated: 2022-07-02T22:30:06Z
embargo_to: open_access
file_id: '9624'
file_name: PhDThesis_SCM.docx
file_size: 131946790
relation: source_file
- access_level: open_access
checksum: dd4d78962ea94ad95e97ca7d9af08f4b
content_type: application/pdf
creator: scaballe
date_created: 2021-07-01T14:46:25Z
date_updated: 2022-07-02T22:30:06Z
embargo: 2022-07-01
file_id: '9625'
file_name: PhDThesis_SCM.pdf
file_size: 17094958
relation: main_file
file_date_updated: 2022-07-02T22:30:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '111'
publication_identifier:
isbn:
- 978-3-99078-012-1
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9750'
relation: part_of_dissertation
status: public
- id: '9006'
relation: part_of_dissertation
status: public
status: public
supervisor:
- 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
title: Fertilization-induced deformations are controlled by the actin cortex and a
mitochondria-rich subcortical layer in ascidian oocytes
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9626'
abstract:
- lang: eng
text: SnSe, a wide-bandgap semiconductor, has attracted significant attention from
the thermoelectric (TE) community due to its outstanding TE performance deriving
from the ultralow thermal conductivity and advantageous electronic structures.
Here, we promoted the TE performance of n-type SnSe polycrystals through bandgap
engineering and vacancy compensation. We found that PbTe can significantly reduce
the wide bandgap of SnSe to reduce the impurity transition energy, largely enhancing
the carrier concentration. Also, PbTe-induced crystal symmetry promotion increases
the carrier mobility, preserving large Seebeck coefficient. Consequently, a maximum
ZT of ∼1.4 at 793 K is obtained in Br doped SnSe–13%PbTe. Furthermore, we found
that extra Sn in n-type SnSe can compensate for the intrinsic Sn vacancies and
form electron donor-like metallic Sn nanophases. The Sn nanophases near the grain
boundary could also reduce the intergrain energy barrier which largely enhances
the carrier mobility. As a result, a maximum ZT value of ∼1.7 at 793 K and an
average ZT (ZTave) of ∼0.58 in 300–793 K are achieved in Br doped Sn1.08Se–13%PbTe.
Our findings provide a novel strategy to promote the TE performance in wide-bandgap
semiconductors.
acknowledgement: This work was supported by National Natural Science Foundation of
China (51772012), National Key Research and Development Program of China (2018YFA0702100
and 2018YFB0703600), the Beijing Natural Science Foundation (JQ18004). This work
was also supported by Lise Meitner Project (M2889-N) and the National Postdoctoral
Program for Innovative Talents (BX20200028). L.D.Z. appreciates the support of the
High Performance Computing (HPC) resources at Beihang University, the National Science
Fund for Distinguished Young Scholars (51925101), and center for High Pressure Science
and Technology Advanced Research (HPSTAR) for SEM measurements.
article_number: '100452'
article_processing_charge: No
article_type: original
author:
- first_name: Lizhong
full_name: Su, Lizhong
last_name: Su
- first_name: Tao
full_name: Hong, Tao
last_name: Hong
- first_name: Dongyang
full_name: Wang, Dongyang
last_name: Wang
- first_name: Sining
full_name: Wang, Sining
last_name: Wang
- first_name: Bingchao
full_name: Qin, Bingchao
last_name: Qin
- first_name: Mengmeng
full_name: Zhang, Mengmeng
last_name: Zhang
- first_name: Xiang
full_name: Gao, Xiang
last_name: Gao
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Li Dong
full_name: Zhao, Li Dong
last_name: Zhao
citation:
ama: Su L, Hong T, Wang D, et al. Realizing high doping efficiency and thermoelectric
performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation.
Materials Today Physics. 2021;20. doi:10.1016/j.mtphys.2021.100452
apa: Su, L., Hong, T., Wang, D., Wang, S., Qin, B., Zhang, M., … Zhao, L. D. (2021).
Realizing high doping efficiency and thermoelectric performance in n-type SnSe
polycrystals via bandgap engineering and vacancy compensation. Materials Today
Physics. Elsevier. https://doi.org/10.1016/j.mtphys.2021.100452
chicago: Su, Lizhong, Tao Hong, Dongyang Wang, Sining Wang, Bingchao Qin, Mengmeng
Zhang, Xiang Gao, Cheng Chang, and Li Dong Zhao. “Realizing High Doping Efficiency
and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering
and Vacancy Compensation.” Materials Today Physics. Elsevier, 2021. https://doi.org/10.1016/j.mtphys.2021.100452.
ieee: L. Su et al., “Realizing high doping efficiency and thermoelectric
performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation,”
Materials Today Physics, vol. 20. Elsevier, 2021.
ista: Su L, Hong T, Wang D, Wang S, Qin B, Zhang M, Gao X, Chang C, Zhao LD. 2021.
Realizing high doping efficiency and thermoelectric performance in n-type SnSe
polycrystals via bandgap engineering and vacancy compensation. Materials Today
Physics. 20, 100452.
mla: Su, Lizhong, et al. “Realizing High Doping Efficiency and Thermoelectric Performance
in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.”
Materials Today Physics, vol. 20, 100452, Elsevier, 2021, doi:10.1016/j.mtphys.2021.100452.
short: L. Su, T. Hong, D. Wang, S. Wang, B. Qin, M. Zhang, X. Gao, C. Chang, L.D.
Zhao, Materials Today Physics 20 (2021).
date_created: 2021-07-04T22:01:24Z
date_published: 2021-06-03T00:00:00Z
date_updated: 2023-08-10T13:56:31Z
day: '03'
department:
- _id: MaIb
doi: 10.1016/j.mtphys.2021.100452
external_id:
isi:
- '000703159600010'
intvolume: ' 20'
isi: 1
language:
- iso: eng
month: '06'
oa_version: None
publication: Materials Today Physics
publication_identifier:
eissn:
- 2542-5293
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Realizing high doping efficiency and thermoelectric performance in n-type SnSe
polycrystals via bandgap engineering and vacancy compensation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 20
year: '2021'
...
---
_id: '9627'
abstract:
- lang: eng
text: "We compute the deficiency spaces of operators of the form \U0001D43B\U0001D434⊗̂
\U0001D43C+\U0001D43C⊗̂ \U0001D43B\U0001D435, for symmetric \U0001D43B\U0001D434
and self-adjoint \U0001D43B\U0001D435. This enables us to construct self-adjoint
extensions (if they exist) by means of von Neumann's theory. The structure of
the deficiency spaces for this case was asserted already in Ibort et al. [Boundary
dynamics driven entanglement, J. Phys. A: Math. Theor. 47(38) (2014) 385301],
but only proven under the restriction of \U0001D43B\U0001D435 having discrete,
non-degenerate spectrum."
acknowledgement: M. W. gratefully acknowledges financial support by the German Academic
Scholarship Foundation (Studienstiftung des deutschen Volkes). T.W. thanks PAO Gazprom
Neft, the Euler International Mathematical Institute in Saint Petersburg and ORISA
GmbH for their financial support in the form of scholarships during his Master's
and Bachelor's studies respectively. The authors want to thank Mark Malamud for
pointing out the reference [1] to them. This work was supported by the Ministry
of Science and Higher Education of the Russian Federation, agreement No 075-15-2019-1619.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Daniel
full_name: Lenz, Daniel
last_name: Lenz
- first_name: Timon
full_name: Weinmann, Timon
last_name: Weinmann
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
citation:
ama: Lenz D, Weinmann T, Wirth M. Self-adjoint extensions of bipartite Hamiltonians.
Proceedings of the Edinburgh Mathematical Society. 2021;64(3):443-447.
doi:10.1017/S0013091521000080
apa: Lenz, D., Weinmann, T., & Wirth, M. (2021). Self-adjoint extensions of
bipartite Hamiltonians. Proceedings of the Edinburgh Mathematical Society.
Cambridge University Press. https://doi.org/10.1017/S0013091521000080
chicago: Lenz, Daniel, Timon Weinmann, and Melchior Wirth. “Self-Adjoint Extensions
of Bipartite Hamiltonians.” Proceedings of the Edinburgh Mathematical Society.
Cambridge University Press, 2021. https://doi.org/10.1017/S0013091521000080.
ieee: D. Lenz, T. Weinmann, and M. Wirth, “Self-adjoint extensions of bipartite
Hamiltonians,” Proceedings of the Edinburgh Mathematical Society, vol.
64, no. 3. Cambridge University Press, pp. 443–447, 2021.
ista: Lenz D, Weinmann T, Wirth M. 2021. Self-adjoint extensions of bipartite Hamiltonians.
Proceedings of the Edinburgh Mathematical Society. 64(3), 443–447.
mla: Lenz, Daniel, et al. “Self-Adjoint Extensions of Bipartite Hamiltonians.” Proceedings
of the Edinburgh Mathematical Society, vol. 64, no. 3, Cambridge University
Press, 2021, pp. 443–47, doi:10.1017/S0013091521000080.
short: D. Lenz, T. Weinmann, M. Wirth, Proceedings of the Edinburgh Mathematical
Society 64 (2021) 443–447.
date_created: 2021-07-04T22:01:24Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-17T07:12:05Z
day: '01'
department:
- _id: JaMa
doi: 10.1017/S0013091521000080
external_id:
arxiv:
- '1912.03670'
isi:
- '000721363700003'
intvolume: ' 64'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1017/S0013091521000080
month: '08'
oa: 1
oa_version: Published Version
page: 443-447
publication: Proceedings of the Edinburgh Mathematical Society
publication_identifier:
eissn:
- 1464-3839
issn:
- 0013-0915
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-adjoint extensions of bipartite Hamiltonians
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 64
year: '2021'
...
---
_id: '9629'
abstract:
- lang: eng
text: Intestinal organoids derived from single cells undergo complex crypt–villus
patterning and morphogenesis. However, the nature and coordination of the underlying
forces remains poorly characterized. Here, using light-sheet microscopy and large-scale
imaging quantification, we demonstrate that crypt formation coincides with a stark
reduction in lumen volume. We develop a 3D biophysical model to computationally
screen different mechanical scenarios of crypt morphogenesis. Combining this with
live-imaging data and multiple mechanical perturbations, we show that actomyosin-driven
crypt apical contraction and villus basal tension work synergistically with lumen
volume reduction to drive crypt morphogenesis, and demonstrate the existence of
a critical point in differential tensions above which crypt morphology becomes
robust to volume changes. Finally, we identified a sodium/glucose cotransporter
that is specific to differentiated enterocytes that modulates lumen volume reduction
through cell swelling in the villus region. Together, our study uncovers the cellular
basis of how cell fate modulates osmotic and actomyosin forces to coordinate robust
morphogenesis.
acknowledgement: 'We acknowledge the members of the Lennon-Duménil laboratory for
sharing the mouse line of Myh9-GFP. We are grateful to the members of the Liberali
laboratory and the FMI facilities for their support. We thank E. Tagliavini for
IT support; L. Gelman for assistance and training; S. Bichet and A. Bogucki for
helping with histology of mouse tissues; H. Kohler for fluorescence-activated cell
sorting; G. Q. G. de Medeiros for maintenance of light-sheet microscopy; M. G. Stadler
for scRNA-seq analysis; G. Gay for discussions on the 3D vertex model; the members
of the Liberali laboratory, C. P. Heisenberg and C. Tsiairis for reading and providing
feedback on the manuscript. Funding: Q.Y. is supported by a Postdoc fellowship from
Peter und Taul Engelhorn Stiftung (PTES). This work received funding from the European
Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme
Grant Agreement no. 758617 (to P.L.), the Swiss National Foundation (SNF) (POOP3_157531,
to P.L.) and from the ERC under the EU Horizon 2020 Research and Innovation Program
Grant Agreements 851288 (to E.H.) and the Austrian Science Fund (FWF) (P31639, to
E.H.).'
article_processing_charge: No
article_type: original
author:
- first_name: Qiutan
full_name: Yang, Qiutan
last_name: Yang
- first_name: Shi-lei
full_name: Xue, Shi-lei
id: 31D2C804-F248-11E8-B48F-1D18A9856A87
last_name: Xue
- first_name: Chii Jou
full_name: Chan, Chii Jou
last_name: Chan
- first_name: Markus
full_name: Rempfler, Markus
last_name: Rempfler
- first_name: Dario
full_name: Vischi, Dario
last_name: Vischi
- first_name: Francisca
full_name: Maurer-Gutierrez, Francisca
last_name: Maurer-Gutierrez
- first_name: Takashi
full_name: Hiiragi, Takashi
last_name: Hiiragi
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Prisca
full_name: Liberali, Prisca
last_name: Liberali
citation:
ama: Yang Q, Xue S, Chan CJ, et al. Cell fate coordinates mechano-osmotic forces
in intestinal crypt formation. Nature Cell Biology. 2021;23:733–744. doi:10.1038/s41556-021-00700-2
apa: Yang, Q., Xue, S., Chan, C. J., Rempfler, M., Vischi, D., Maurer-Gutierrez,
F., … Liberali, P. (2021). Cell fate coordinates mechano-osmotic forces in intestinal
crypt formation. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-021-00700-2
chicago: Yang, Qiutan, Shi-lei Xue, Chii Jou Chan, Markus Rempfler, Dario Vischi,
Francisca Maurer-Gutierrez, Takashi Hiiragi, Edouard B Hannezo, and Prisca Liberali.
“Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.”
Nature Cell Biology. Springer Nature, 2021. https://doi.org/10.1038/s41556-021-00700-2.
ieee: Q. Yang et al., “Cell fate coordinates mechano-osmotic forces in intestinal
crypt formation,” Nature Cell Biology, vol. 23. Springer Nature, pp. 733–744,
2021.
ista: Yang Q, Xue S, Chan CJ, Rempfler M, Vischi D, Maurer-Gutierrez F, Hiiragi
T, Hannezo EB, Liberali P. 2021. Cell fate coordinates mechano-osmotic forces
in intestinal crypt formation. Nature Cell Biology. 23, 733–744.
mla: Yang, Qiutan, et al. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal
Crypt Formation.” Nature Cell Biology, vol. 23, Springer Nature, 2021,
pp. 733–744, doi:10.1038/s41556-021-00700-2.
short: Q. Yang, S. Xue, C.J. Chan, M. Rempfler, D. Vischi, F. Maurer-Gutierrez,
T. Hiiragi, E.B. Hannezo, P. Liberali, Nature Cell Biology 23 (2021) 733–744.
date_created: 2021-07-04T22:01:25Z
date_published: 2021-06-21T00:00:00Z
date_updated: 2023-08-10T13:57:36Z
day: '21'
department:
- _id: EdHa
doi: 10.1038/s41556-021-00700-2
ec_funded: 1
external_id:
isi:
- '000664016300003'
pmid:
- '34155381'
intvolume: ' 23'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2020.05.13.094359
month: '06'
oa: 1
oa_version: Preprint
page: 733–744
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 268294B6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31639
name: Active mechano-chemical description of the cell cytoskeleton
publication: Nature Cell Biology
publication_identifier:
eissn:
- 1476-4679
issn:
- 1465-7392
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell fate coordinates mechano-osmotic forces in intestinal crypt formation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 23
year: '2021'
...
---
_id: '9636'
article_processing_charge: No
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Higginbotham AP. Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor
hybrid.” 2021.
apa: Higginbotham, A. P. (2021). Data for “Breakdown of induced p ± ip pairing in
a superconductor-semiconductor hybrid.” Institute of Science and Technology Austria.
chicago: Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing
in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology
Austria, 2021.
ieee: A. P. Higginbotham, “Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor
hybrid.’” Institute of Science and Technology Austria, 2021.
ista: Higginbotham AP. 2021. Data for ‘Breakdown of induced p ± ip pairing in a
superconductor-semiconductor hybrid’, Institute of Science and Technology Austria.
mla: Higginbotham, Andrew P. Data for “Breakdown of Induced p ± Ip Pairing in
a Superconductor-Semiconductor Hybrid.” Institute of Science and Technology
Austria, 2021.
short: A.P. Higginbotham, (2021).
date_created: 2021-07-07T20:43:10Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2024-02-21T12:36:52Z
department:
- _id: AnHi
file:
- access_level: open_access
checksum: 18e90687ec7bbd75f8bfea4d8293fb30
content_type: application/zip
creator: ahigginb
date_created: 2021-07-07T20:37:28Z
date_updated: 2021-07-07T20:37:28Z
file_id: '9637'
file_name: figures_data.zip
file_size: 3345244
relation: main_file
success: 1
file_date_updated: 2021-07-07T20:37:28Z
has_accepted_license: '1'
oa: 1
oa_version: Submitted Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10029'
relation: used_in_publication
status: public
status: public
title: Data for "Breakdown of induced p ± ip pairing in a superconductor-semiconductor
hybrid"
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: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9640'
abstract:
- lang: eng
text: 'Selection and random drift determine the probability that novel mutations
fixate in a population. Population structure is known to affect the dynamics of
the evolutionary process. Amplifiers of selection are population structures that
increase the fixation probability of beneficial mutants compared to well-mixed
populations. Over the past 15 years, extensive research has produced remarkable
structures called strong amplifiers which guarantee that every beneficial mutation
fixates with high probability. But strong amplification has come at the cost of
considerably delaying the fixation event, which can slow down the overall rate
of evolution. However, the precise relationship between fixation probability and
time has remained elusive. Here we characterize the slowdown effect of strong
amplification. First, we prove that all strong amplifiers must delay the fixation
event at least to some extent. Second, we construct strong amplifiers that delay
the fixation event only marginally as compared to the well-mixed populations.
Our results thus establish a tight relationship between fixation probability and
time: Strong amplification always comes at a cost of a slowdown, but more than
a marginal slowdown is not needed.'
acknowledgement: 'K.C. acknowledges support from ERC Start grant no. (279307: Graph
Games), ERC Consolidator grant no. (863818: ForM-SMart), Austrian Science Fund (FWF)
grant no. P23499-N23 and S11407-N23 (RiSE). M.A.N. acknowledges support from Office
of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.'
article_number: '4009'
article_processing_charge: No
article_type: original
author:
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin A.
full_name: Nowak, Martin A.
last_name: Nowak
citation:
ama: Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Fast and strong amplifiers
of natural selection. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-24271-w
apa: Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2021). Fast
and strong amplifiers of natural selection. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-021-24271-w
chicago: Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin
A. Nowak. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-24271-w.
ieee: J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Fast and strong
amplifiers of natural selection,” Nature Communications, vol. 12, no. 1.
Springer Nature, 2021.
ista: Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2021. Fast and strong amplifiers
of natural selection. Nature Communications. 12(1), 4009.
mla: Tkadlec, Josef, et al. “Fast and Strong Amplifiers of Natural Selection.” Nature
Communications, vol. 12, no. 1, 4009, Springer Nature, 2021, doi:10.1038/s41467-021-24271-w.
short: J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Nature Communications
12 (2021).
date_created: 2021-07-11T22:01:15Z
date_published: 2021-06-29T00:00:00Z
date_updated: 2025-07-14T09:10:05Z
day: '29'
ddc:
- '510'
department:
- _id: KrCh
doi: 10.1038/s41467-021-24271-w
ec_funded: 1
external_id:
isi:
- '000671752100003'
pmid:
- '34188036'
file:
- access_level: open_access
checksum: 5767418926a7f7fb76151de29473dae0
content_type: application/pdf
creator: cziletti
date_created: 2021-07-19T13:02:20Z
date_updated: 2021-07-19T13:02:20Z
file_id: '9692'
file_name: 2021_NatCoom_Tkadlec.pdf
file_size: 628992
relation: main_file
success: 1
file_date_updated: 2021-07-19T13:02:20Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms 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: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast and strong amplifiers of natural selection
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: 12
year: '2021'
...
---
_id: '9641'
abstract:
- lang: eng
text: At the encounter with a novel environment, contextual memory formation is
greatly enhanced, accompanied with increased arousal and active exploration. Although
this phenomenon has been widely observed in animal and human daily life, how the
novelty in the environment is detected and contributes to contextual memory formation
has lately started to be unveiled. The hippocampus has been studied for many decades
for its largely known roles in encoding spatial memory, and a growing body of
evidence indicates a differential involvement of dorsal and ventral hippocampal
divisions in novelty detection. In this brief review article, we discuss the recent
findings of the role of mossy cells in the ventral hippocampal moiety in novelty
detection and put them in perspective with other novelty-related pathways in the
hippocampus. We propose a mechanism for novelty-driven memory acquisition in the
dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate
granule cells. By this projection, the ventral hippocampus sends novelty signals
to the dorsal hippocampus, opening a gate for memory encoding in dentate granule
cells based on information coming from the entorhinal cortex. We conclude that,
contrary to the presently accepted functional independence, the dorsal and ventral
hippocampi cooperate to link the novelty and contextual information, and this
dorso-ventral interaction is crucial for the novelty-dependent memory formation.
acknowledgement: This work was supported by a European Research Council Advanced Grant
694539 to Ryuichi Shigemoto.
article_number: '107486'
article_processing_charge: No
article_type: original
author:
- first_name: Felipe
full_name: Fredes, Felipe
last_name: Fredes
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection.
Neurobiology of Learning and Memory. 2021;183. doi:10.1016/j.nlm.2021.107486
apa: Fredes, F., & Shigemoto, R. (2021). The role of hippocampal mossy cells
in novelty detection. Neurobiology of Learning and Memory. Elsevier. https://doi.org/10.1016/j.nlm.2021.107486
chicago: Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells
in Novelty Detection.” Neurobiology of Learning and Memory. Elsevier, 2021.
https://doi.org/10.1016/j.nlm.2021.107486.
ieee: F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty
detection,” Neurobiology of Learning and Memory, vol. 183. Elsevier, 2021.
ista: Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty
detection. Neurobiology of Learning and Memory. 183, 107486.
mla: Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells
in Novelty Detection.” Neurobiology of Learning and Memory, vol. 183, 107486,
Elsevier, 2021, doi:10.1016/j.nlm.2021.107486.
short: F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021).
date_created: 2021-07-11T22:01:16Z
date_published: 2021-06-30T00:00:00Z
date_updated: 2023-08-10T14:10:37Z
day: '30'
ddc:
- '610'
department:
- _id: RySh
doi: 10.1016/j.nlm.2021.107486
ec_funded: 1
external_id:
isi:
- '000677694900004'
pmid:
- '34214666'
file:
- access_level: open_access
checksum: 8e8298a9e8c7df146ad23f32c2a63929
content_type: application/pdf
creator: cziletti
date_created: 2021-07-19T13:46:06Z
date_updated: 2021-07-19T13:46:06Z
file_id: '9694'
file_name: 2021_NeurobLearnMemory_Fredes.pdf
file_size: 1994793
relation: main_file
success: 1
file_date_updated: 2021-07-19T13:46:06Z
has_accepted_license: '1'
intvolume: ' 183'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
publication: Neurobiology of Learning and Memory
publication_identifier:
eissn:
- '10959564'
issn:
- '10747427'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The role of hippocampal mossy cells in novelty detection
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 183
year: '2021'
...
---
_id: '9642'
abstract:
- lang: eng
text: Perineuronal nets (PNNs), components of the extracellular matrix, preferentially
coat parvalbumin-positive interneurons and constrain critical-period plasticity
in the adult cerebral cortex. Current strategies to remove PNN are long-lasting,
invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic
ketamine as a method with minimal behavioral effect. We find that this paradigm
strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like
plasticity. Microglia are critically involved in PNN loss because they engage
with parvalbumin-positive neurons in their defined cortical layer. We identify
external 60-Hz light-flickering entrainment to recapitulate microglia-mediated
PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques,
does not induce PNN loss, suggesting microglia might functionally tune to distinct
brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative
form of PNN intervention in the healthy adult brain.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: We thank the scientific service units at IST Austria, especially
the IST bioimaging facility, the preclinical facility, and, specifically, Michael
Schunn and Sonja Haslinger for excellent support; Plexxikon for the PLX food; the
Csicsvari group for advice and equipment for in vivo recording; Jürgen Siegert for
the light-entrainment design; Marco Benevento, Soledad Gonzalo Cogno, Pat King,
and all Siegert group members for constant feedback on the project and manuscript;
Lorena Pantano (PILM Bioinformatics Core) for assisting with sample-size determination
for OD plasticity experiments; and Ana Morello from MIT for technical assistance
with VEPs recordings. This research was supported by a DOC Fellowship from the Austrian
Academy of Sciences at the Institute of Science and Technology Austria to R.S.,
from the European Union Horizon 2020 research and innovation program under the Marie
Skłodowska-Curie Actions program (grants 665385 to G.C.; 754411 to R.J.A.C.), the
European Research Council (grant 715571 to S.S.), and the National Eye Institute
of the National Institutes of Health under award numbers R01EY029245 (to M.F.B.)
and R01EY023037 (diversity supplement to H.D.J-C.).
article_number: '109313'
article_processing_charge: No
article_type: original
author:
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Rouven
full_name: Schulz, Rouven
id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87
last_name: Schulz
orcid: 0000-0001-5297-733X
- first_name: Héctor
full_name: De Jesús-Cortés, Héctor
last_name: De Jesús-Cortés
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Balint
full_name: Nagy, Balint
id: 93C65ECC-A6F2-11E9-8DF9-9712E6697425
last_name: Nagy
- first_name: Francis
full_name: Reilly-Andújar, Francis
last_name: Reilly-Andújar
- first_name: Gloria
full_name: Colombo, Gloria
id: 3483CF6C-F248-11E8-B48F-1D18A9856A87
last_name: Colombo
orcid: 0000-0001-9434-8902
- first_name: Ryan J
full_name: Cubero, Ryan J
id: 850B2E12-9CD4-11E9-837F-E719E6697425
last_name: Cubero
orcid: 0000-0003-0002-1867
- first_name: Florianne E
full_name: Schoot Uiterkamp, Florianne E
id: 3526230C-F248-11E8-B48F-1D18A9856A87
last_name: Schoot Uiterkamp
- first_name: Mark F.
full_name: Bear, Mark F.
last_name: Bear
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Venturino A, Schulz R, De Jesús-Cortés H, et al. Microglia enable mature perineuronal
nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment
in the healthy brain. Cell Reports. 2021;36(1). doi:10.1016/j.celrep.2021.109313
apa: Venturino, A., Schulz, R., De Jesús-Cortés, H., Maes, M. E., Nagy, B., Reilly-Andújar,
F., … Siegert, S. (2021). Microglia enable mature perineuronal nets disassembly
upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain.
Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2021.109313
chicago: Venturino, Alessandro, Rouven Schulz, Héctor De Jesús-Cortés, Margaret
E Maes, Balint Nagy, Francis Reilly-Andújar, Gloria Colombo, et al. “Microglia
Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure
or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports. Elsevier,
2021. https://doi.org/10.1016/j.celrep.2021.109313.
ieee: A. Venturino et al., “Microglia enable mature perineuronal nets disassembly
upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain,”
Cell Reports, vol. 36, no. 1. Elsevier, 2021.
ista: Venturino A, Schulz R, De Jesús-Cortés H, Maes ME, Nagy B, Reilly-Andújar
F, Colombo G, Cubero RJ, Schoot Uiterkamp FE, Bear MF, Siegert S. 2021. Microglia
enable mature perineuronal nets disassembly upon anesthetic ketamine exposure
or 60-Hz light entrainment in the healthy brain. Cell Reports. 36(1), 109313.
mla: Venturino, Alessandro, et al. “Microglia Enable Mature Perineuronal Nets Disassembly
upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.”
Cell Reports, vol. 36, no. 1, 109313, Elsevier, 2021, doi:10.1016/j.celrep.2021.109313.
short: A. Venturino, R. Schulz, H. De Jesús-Cortés, M.E. Maes, B. Nagy, F. Reilly-Andújar,
G. Colombo, R.J. Cubero, F.E. Schoot Uiterkamp, M.F. Bear, S. Siegert, Cell Reports
36 (2021).
date_created: 2021-07-11T22:01:16Z
date_published: 2021-07-06T00:00:00Z
date_updated: 2023-08-10T14:09:39Z
day: '06'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1016/j.celrep.2021.109313
ec_funded: 1
external_id:
isi:
- '000670188500004'
pmid:
- '34233180'
file:
- access_level: open_access
checksum: f056255f6d01fd9a86b5387635928173
content_type: application/pdf
creator: cziletti
date_created: 2021-07-19T13:32:17Z
date_updated: 2021-07-19T13:32:17Z
file_id: '9693'
file_name: 2021_CellReports_Venturino.pdf
file_size: 56388540
relation: main_file
success: 1
file_date_updated: 2021-07-19T13:32:17Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25D4A630-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715571'
name: Microglia action towards neuronal circuit formation and function in health
and disease
publication: Cell Reports
publication_identifier:
eissn:
- '22111247'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/the-twinkle-and-the-brain/
scopus_import: '1'
status: public
title: Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine
exposure or 60-Hz light entrainment in the healthy brain
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: 36
year: '2021'
...
---
_id: '9644'
abstract:
- lang: eng
text: 'We present a new approach to proving non-termination of non-deterministic
integer programs. Our technique is rather simple but efficient. It relies on a
purely syntactic reversal of the program''s transition system followed by a constraint-based
invariant synthesis with constraints coming from both the original and the reversed
transition system. The latter task is performed by a simple call to an off-the-shelf
SMT-solver, which allows us to leverage the latest advances in SMT-solving. Moreover,
our method offers a combination of features not present (as a whole) in previous
approaches: it handles programs with non-determinism, provides relative completeness
guarantees and supports programs with polynomial arithmetic. The experiments performed
with our prototype tool RevTerm show that our approach, despite its simplicity
and stronger theoretical guarantees, is at least on par with the state-of-the-art
tools, often achieving a non-trivial improvement under a proper configuration
of its parameters.'
acknowledgement: We thank the anonymous reviewers for their helpful comments. This
research was partially supported by the ERCCoG 863818 (ForM-SMArt) and the Czech
Science Foundation grant No. GJ19-15134Y.
article_processing_charge: No
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: Ehsan Kafshdar
full_name: Goharshady, Ehsan Kafshdar
last_name: Goharshady
- first_name: Petr
full_name: Novotný, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotný
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Chatterjee K, Goharshady EK, Novotný P, Zikelic D. Proving non-termination
by program reversal. In: Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation. Association
for Computing Machinery; 2021:1033-1048. doi:10.1145/3453483.3454093'
apa: 'Chatterjee, K., Goharshady, E. K., Novotný, P., & Zikelic, D. (2021).
Proving non-termination by program reversal. In Proceedings of the 42nd ACM
SIGPLAN International Conference on Programming Language Design and Implementation
(pp. 1033–1048). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454093'
chicago: Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, and Dorde
Zikelic. “Proving Non-Termination by Program Reversal.” In Proceedings of the
42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation,
1033–48. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454093.
ieee: K. Chatterjee, E. K. Goharshady, P. Novotný, and D. Zikelic, “Proving non-termination
by program reversal,” in Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation, Online, 2021,
pp. 1033–1048.
ista: 'Chatterjee K, Goharshady EK, Novotný P, Zikelic D. 2021. Proving non-termination
by program reversal. Proceedings of the 42nd ACM SIGPLAN International Conference
on Programming Language Design and Implementation. PLDI: Programming Language
Design and Implementation, 1033–1048.'
mla: Chatterjee, Krishnendu, et al. “Proving Non-Termination by Program Reversal.”
Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, Association for Computing Machinery, 2021,
pp. 1033–48, doi:10.1145/3453483.3454093.
short: K. Chatterjee, E.K. Goharshady, P. Novotný, D. Zikelic, in:, Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 1033–1048.
conference:
end_date: 2021-06-26
location: Online
name: 'PLDI: Programming Language Design and Implementation'
start_date: 2021-06-20
date_created: 2021-07-11T22:01:17Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2025-07-14T09:10:06Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3453483.3454093
ec_funded: 1
external_id:
arxiv:
- '2104.01189'
isi:
- '000723661700067'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2104.01189
month: '06'
oa: 1
oa_version: Preprint
page: 1033-1048
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450383912'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '14539'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Proving non-termination by program reversal
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9645'
abstract:
- lang: eng
text: "We consider the fundamental problem of reachability analysis over imperative
programs with real variables. Previous works that tackle reachability are either
unable to handle programs consisting of general loops (e.g. symbolic execution),
or lack completeness guarantees (e.g. abstract interpretation), or are not automated
(e.g. incorrectness logic). In contrast, we propose a novel approach for reachability
analysis that can handle general and complex loops, is complete, and can be entirely
automated for a wide family of programs. Through the notion of Inductive Reachability
Witnesses (IRWs), our approach extends ideas from both invariant generation and
termination to reachability analysis.\r\n\r\nWe first show that our IRW-based
approach is sound and complete for reachability analysis of imperative programs.
Then, we focus on linear and polynomial programs and develop automated methods
for synthesizing linear and polynomial IRWs. In the linear case, we follow the
well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial
case, where we present a push-button semi-complete algorithm. We achieve this
using a novel combination of classical theorems in real algebraic geometry, such
as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally,
our experimental results show we can prove complex reachability objectives over
various benchmarks that were beyond the reach of previous methods."
acknowledgement: This research was partially supported by the ERC CoG 863818 (ForM-SMArt),
the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the
Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC
Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW).
article_processing_charge: No
author:
- first_name: Ali
full_name: Asadi, Ali
last_name: Asadi
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- 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: Mohammad
full_name: Mahdavi, Mohammad
last_name: Mahdavi
citation:
ama: 'Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability
witnesses via Stellensätze. In: Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation. Association
for Computing Machinery; 2021:772-787. doi:10.1145/3453483.3454076'
apa: 'Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., & Mahdavi, M. (2021).
Polynomial reachability witnesses via Stellensätze. In Proceedings of the 42nd
ACM SIGPLAN International Conference on Programming Language Design and Implementation
(pp. 772–787). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454076'
chicago: Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady,
and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In
Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, 772–87. Association for Computing Machinery,
2021. https://doi.org/10.1145/3453483.3454076.
ieee: A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial
reachability witnesses via Stellensätze,” in Proceedings of the 42nd ACM SIGPLAN
International Conference on Programming Language Design and Implementation,
Online, 2021, pp. 772–787.
ista: 'Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability
witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation. PLDI: Programming
Language Design and Implementation, 772–787.'
mla: Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 772–87,
doi:10.1145/3453483.3454076.
short: A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 772–787.
conference:
end_date: 2021-06-26
location: Online
name: ' PLDI: Programming Language Design and Implementation'
start_date: 2021-06-20
date_created: 2021-07-11T22:01:17Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2025-07-14T09:10:06Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3453483.3454076
ec_funded: 1
external_id:
isi:
- '000723661700050'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-03183862/
month: '06'
oa: 1
oa_version: Submitted Version
page: 772-787
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450383912'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Polynomial reachability witnesses via Stellensätze
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9646'
abstract:
- lang: eng
text: We consider the fundamental problem of deriving quantitative bounds on the
probability that a given assertion is violated in a probabilistic program. We
provide automated algorithms that obtain both lower and upper bounds on the assertion
violation probability. The main novelty of our approach is that we prove new and
dedicated fixed-point theorems which serve as the theoretical basis of our algorithms
and enable us to reason about assertion violation bounds in terms of pre and post
fixed-point functions. To synthesize such fixed-points, we devise algorithms that
utilize a wide range of mathematical tools, including repulsing ranking supermartingales,
Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization.
On the theoretical side, we provide (i) the first automated algorithm for lower-bounds
on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds
of exponential form in affine programs, and (iii) provably and significantly tighter
upper-bounds than the previous approaches. On the practical side, we show our
algorithms can handle a wide variety of programs from the literature and synthesize
bounds that are remarkably tighter than previous results, in some cases by thousands
of orders of magnitude.
acknowledgement: 'We are very thankful to the anonymous reviewers for the helpful
and valuable comments. The work was partially supported by the National Natural
Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research
Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and
DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).'
article_processing_charge: No
arxiv: 1
author:
- first_name: Jinyi
full_name: Wang, Jinyi
last_name: Wang
- first_name: Yican
full_name: Sun, Yican
last_name: Sun
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of
assertion violations in probabilistic programs. In: Proceedings of the 42nd
ACM SIGPLAN International Conference on Programming Language Design and Implementation.
Association for Computing Machinery; 2021:1171-1186. doi:10.1145/3453483.3454102'
apa: 'Wang, J., Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2021).
Quantitative analysis of assertion violations in probabilistic programs. In Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation (pp. 1171–1186). Online: Association for Computing Machinery.
https://doi.org/10.1145/3453483.3454102'
chicago: Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar
Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.”
In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, 1171–86. Association for Computing Machinery,
2021. https://doi.org/10.1145/3453483.3454102.
ieee: J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative
analysis of assertion violations in probabilistic programs,” in Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Online, 2021, pp. 1171–1186.
ista: 'Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis
of assertion violations in probabilistic programs. Proceedings of the 42nd ACM
SIGPLAN International Conference on Programming Language Design and Implementation.
PLDI: Programming Language Design and Implementation, 1171–1186.'
mla: Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic
Programs.” Proceedings of the 42nd ACM SIGPLAN International Conference on
Programming Language Design and Implementation, Association for Computing
Machinery, 2021, pp. 1171–86, doi:10.1145/3453483.3454102.
short: J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186.
conference:
end_date: 2021-06-26
location: Online
name: 'PLDI: Programming Language Design and Implementation'
start_date: 2021-06-20
date_created: 2021-07-11T22:01:18Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2025-07-14T09:10:06Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3453483.3454102
ec_funded: 1
external_id:
arxiv:
- '2011.14617'
isi:
- '000723661700076'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2011.14617
month: '06'
oa: 1
oa_version: Preprint
page: 1171-1186
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450383912'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantitative analysis of assertion violations in probabilistic programs
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9647'
abstract:
- lang: eng
text: 'Gene expression is regulated by the set of transcription factors (TFs) that
bind to the promoter. The ensuing regulating function is often represented as
a combinational logic circuit, where output (gene expression) is determined by
current input values (promoter bound TFs) only. However, the simultaneous arrival
of TFs is a strong assumption, since transcription and translation of genes introduce
intrinsic time delays and there is no global synchronisation among the arrival
times of different molecular species at their targets. We present an experimentally
implementable genetic circuit with two inputs and one output, which in the presence
of small delays in input arrival, exhibits qualitatively distinct population-level
phenotypes, over timescales that are longer than typical cell doubling times.
From a dynamical systems point of view, these phenotypes represent long-lived
transients: although they converge to the same value eventually, they do so after
a very long time span. The key feature of this toy model genetic circuit is that,
despite having only two inputs and one output, it is regulated by twenty-three
distinct DNA-TF configurations, two of which are more stable than others (DNA
looped states), one promoting and another blocking the expression of the output
gene. Small delays in input arrival time result in a majority of cells in the
population quickly reaching the stable state associated with the first input,
while exiting of this stable state occurs at a slow timescale. In order to mechanistically
model the behaviour of this genetic circuit, we used a rule-based modelling language,
and implemented a grid-search to find parameter combinations giving rise to long-lived
transients. Our analysis shows that in the absence of feedback, there exist path-dependent
gene regulatory mechanisms based on the long timescale of transients. The behaviour
of this toy model circuit suggests that gene regulatory networks can exploit event
timing to create phenotypes, and it opens the possibility that they could use
event timing to memorise events, without regulatory feedback. The model reveals
the importance of (i) mechanistically modelling the transitions between the different
DNA-TF states, and (ii) employing transient analysis thereof.'
acknowledgement: 'Tatjana Petrov’s research was supported in part by SNSF Advanced
Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science,
Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence
2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia
Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences.
Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund
(FWF) under grant Z211-N23 (Wittgenstein Award).'
article_processing_charge: No
article_type: original
author:
- first_name: Tatjana
full_name: Petrov, Tatjana
last_name: Petrov
- first_name: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in
gene regulation. Theoretical Computer Science. 2021;893:1-16. doi:10.1016/j.tcs.2021.05.023
apa: Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., & Guet, C. C. (2021).
Long lived transients in gene regulation. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2021.05.023
chicago: Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin
C Guet. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science.
Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.05.023.
ieee: T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived
transients in gene regulation,” Theoretical Computer Science, vol. 893.
Elsevier, pp. 1–16, 2021.
ista: Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients
in gene regulation. Theoretical Computer Science. 893, 1–16.
mla: Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” Theoretical
Computer Science, vol. 893, Elsevier, 2021, pp. 1–16, doi:10.1016/j.tcs.2021.05.023.
short: T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer
Science 893 (2021) 1–16.
date_created: 2021-07-11T22:01:18Z
date_published: 2021-06-04T00:00:00Z
date_updated: 2023-08-10T14:11:19Z
day: '04'
ddc:
- '004'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1016/j.tcs.2021.05.023
external_id:
isi:
- '000710180500002'
file:
- access_level: open_access
checksum: d3aef34cfb13e53bba4cf44d01680793
content_type: application/pdf
creator: dernst
date_created: 2022-05-12T12:13:27Z
date_updated: 2022-05-12T12:13:27Z
file_id: '11364'
file_name: 2021_TheoreticalComputerScience_Petrov.pdf
file_size: 2566504
relation: main_file
success: 1
file_date_updated: 2022-05-12T12:13:27Z
has_accepted_license: '1'
intvolume: ' 893'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1-16
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long lived transients in gene regulation
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 893
year: '2021'
...
---
_id: '9656'
abstract:
- lang: eng
text: Tropisms, growth responses to environmental stimuli such as light or gravity,
are spectacular examples of adaptive plant development. The plant hormone auxin
serves as a major coordinative signal. The PIN auxin exporters, through their
dynamic polar subcellular localizations, redirect auxin fluxes in response to
environmental stimuli and the resulting auxin gradients across organs underly
differential cell elongation and bending. In this review, we discuss recent advances
concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation
and trafficking. We also cover how environmental cues regulate PIN actions during
tropisms, and a crucial role of auxin feedback on PIN polarity during bending
termination. Finally, the interactions between different tropisms are reviewed
to understand plant adaptive growth in the natural environment.
acknowledgement: We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and
Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript.
We apologize to those researchers whose great work was not cited. This work is supported
by the European Research Council under the European Union’s Horizon 2020 research
and innovation Programme (ERC grant agreement number 742985), and the Austrian Science
Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship
Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture
University (9232308314).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Linlin
full_name: Qi, Linlin
id: 44B04502-A9ED-11E9-B6FC-583AE6697425
last_name: Qi
orcid: 0000-0001-5187-8401
- first_name: SS
full_name: Alotaibi, SS
last_name: Alotaibi
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport
regulations in plant tropic responses. New Phytologist. 2021;232(2):510-522.
doi:10.1111/nph.17617
apa: Han, H., Adamowski, M., Qi, L., Alotaibi, S., & Friml, J. (2021). PIN-mediated
polar auxin transport regulations in plant tropic responses. New Phytologist.
Wiley. https://doi.org/10.1111/nph.17617
chicago: Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml.
“PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New
Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17617.
ieee: H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar
auxin transport regulations in plant tropic responses,” New Phytologist,
vol. 232, no. 2. Wiley, pp. 510–522, 2021.
ista: Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin
transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522.
mla: Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant
Tropic Responses.” New Phytologist, vol. 232, no. 2, Wiley, 2021, pp. 510–22,
doi:10.1111/nph.17617.
short: H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021)
510–522.
date_created: 2021-07-14T15:29:14Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2023-08-10T14:02:41Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/nph.17617
ec_funded: 1
external_id:
isi:
- '000680587100001'
pmid:
- '34254313'
file:
- access_level: open_access
checksum: 6422a6eb329b52d96279daaee0fcf189
content_type: application/pdf
creator: kschuh
date_created: 2021-10-07T13:42:47Z
date_updated: 2021-10-07T13:42:47Z
file_id: '10105'
file_name: 2021_NewPhytologist_Han.pdf
file_size: 1939800
relation: main_file
success: 1
file_date_updated: 2021-10-07T13:42:47Z
has_accepted_license: '1'
intvolume: ' 232'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 510-522
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646x
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: PIN-mediated polar auxin transport regulations in plant tropic responses
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: 232
year: '2021'
...