---
_id: '6987'
abstract:
- lang: eng
text: Cells are arranged into species-specific patterns during early embryogenesis.
Such cell division patterns are important since they often reflect the distribution
of localized cortical factors from eggs/fertilized eggs to specific cells as well
as the emergence of organismal form. However, it has proven difficult to reveal
the mechanisms that underlie the emergence of cell positioning patterns that underlie
embryonic shape, likely because a systems-level approach is required that integrates
cell biological, genetic, developmental, and mechanical parameters. The choice
of organism to address such questions is also important. Because ascidians display
the most extreme form of invariant cleavage pattern among the metazoans, we have
been analyzing the cell biological mechanisms that underpin three aspects of cell
division (unequal cell division (UCD), oriented cell division (OCD), and asynchronous
cell cycles) which affect the overall shape of the blastula-stage ascidian embryo
composed of 64 cells. In ascidians, UCD creates two small cells at the 16-cell
stage that in turn undergo two further successive rounds of UCD. Starting at the
16-cell stage, the cell cycle becomes asynchronous, whereby the vegetal half divides
before the animal half, thus creating 24-, 32-, 44-, and then 64-cell stages.
Perturbing either UCD or the alternate cell division rhythm perturbs cell position.
We propose that dynamic cell shape changes propagate throughout the embryo via
cell-cell contacts to create the ascidian-specific invariant cleavage pattern.
alternative_title:
- RESULTS
article_processing_charge: No
author:
- first_name: Alex
full_name: McDougall, Alex
last_name: McDougall
- first_name: Janet
full_name: Chenevert, Janet
last_name: Chenevert
- first_name: Benoit G
full_name: Godard, Benoit G
id: 33280250-F248-11E8-B48F-1D18A9856A87
last_name: Godard
- first_name: Remi
full_name: Dumollard, Remi
last_name: Dumollard
citation:
ama: 'McDougall A, Chenevert J, Godard BG, Dumollard R. Emergence of embryo shape
during cleavage divisions. In: Tworzydlo W, Bilinski SM, eds. Evo-Devo: Non-Model
Species in Cell and Developmental Biology. Vol 68. Springer Nature; 2019:127-154.
doi:10.1007/978-3-030-23459-1_6'
apa: 'McDougall, A., Chenevert, J., Godard, B. G., & Dumollard, R. (2019). Emergence
of embryo shape during cleavage divisions. In W. Tworzydlo & S. M. Bilinski
(Eds.), Evo-Devo: Non-model species in cell and developmental biology (Vol.
68, pp. 127–154). Springer Nature. https://doi.org/10.1007/978-3-030-23459-1_6'
chicago: 'McDougall, Alex, Janet Chenevert, Benoit G Godard, and Remi Dumollard.
“Emergence of Embryo Shape during Cleavage Divisions.” In Evo-Devo: Non-Model
Species in Cell and Developmental Biology, edited by Waclaw Tworzydlo and
Szczepan M. Bilinski, 68:127–54. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23459-1_6.'
ieee: 'A. McDougall, J. Chenevert, B. G. Godard, and R. Dumollard, “Emergence of
embryo shape during cleavage divisions,” in Evo-Devo: Non-model species in
cell and developmental biology, vol. 68, W. Tworzydlo and S. M. Bilinski,
Eds. Springer Nature, 2019, pp. 127–154.'
ista: 'McDougall A, Chenevert J, Godard BG, Dumollard R. 2019.Emergence of embryo
shape during cleavage divisions. In: Evo-Devo: Non-model species in cell and developmental
biology. RESULTS, vol. 68, 127–154.'
mla: 'McDougall, Alex, et al. “Emergence of Embryo Shape during Cleavage Divisions.”
Evo-Devo: Non-Model Species in Cell and Developmental Biology, edited by
Waclaw Tworzydlo and Szczepan M. Bilinski, vol. 68, Springer Nature, 2019, pp.
127–54, doi:10.1007/978-3-030-23459-1_6.'
short: 'A. McDougall, J. Chenevert, B.G. Godard, R. Dumollard, in:, W. Tworzydlo,
S.M. Bilinski (Eds.), Evo-Devo: Non-Model Species in Cell and Developmental Biology,
Springer Nature, 2019, pp. 127–154.'
date_created: 2019-11-04T16:20:19Z
date_published: 2019-10-10T00:00:00Z
date_updated: 2023-09-05T15:01:12Z
day: '10'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1007/978-3-030-23459-1_6
editor:
- first_name: Waclaw
full_name: Tworzydlo, Waclaw
last_name: Tworzydlo
- first_name: Szczepan M.
full_name: Bilinski, Szczepan M.
last_name: Bilinski
external_id:
pmid:
- '31598855'
file:
- access_level: open_access
checksum: 7f43e1e3706d15061475c5c57efc2786
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T10:09:30Z
date_updated: 2020-07-14T12:47:46Z
file_id: '7829'
file_name: 2019_RESULTS_McDougall.pdf
file_size: 19317348
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 68'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 127-154
pmid: 1
publication: 'Evo-Devo: Non-model species in cell and developmental biology'
publication_identifier:
eissn:
- 1861-0412
isbn:
- '9783030234584'
- '9783030234591'
issn:
- 0080-1844
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Emergence of embryo shape during cleavage divisions
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 68
year: '2019'
...
---
_id: '6762'
abstract:
- lang: eng
text: "We present and study novel optimal control problems motivated by the search
for photovoltaic materials with high power-conversion efficiency. The material
must perform the first step: convert light (photons) into electronic excitations.
We formulate various desirable properties of the excitations as mathematical control
goals at the Kohn-Sham-DFT level\r\nof theory, with the control being given by
the nuclear charge distribution. We prove that nuclear distributions exist which
give rise to optimal HOMO-LUMO excitations, and present illustrative numerical
simulations for 1D finite nanocrystals. We observe pronounced goal-dependent features
such as large electron-hole separation, and a hierarchy of length scales: internal
HOMO and LUMO wavelengths < atomic spacings < (irregular) fluctuations of the
doping profiles < system size."
article_processing_charge: No
author:
- first_name: Gero
full_name: Friesecke, Gero
last_name: Friesecke
- first_name: Michael
full_name: Kniely, Michael
id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87
last_name: Kniely
orcid: 0000-0001-5645-4333
citation:
ama: Friesecke G, Kniely M. New optimal control problems in density functional theory
motivated by photovoltaics. Multiscale Modeling and Simulation. 2019;17(3):926-947.
doi:10.1137/18M1207272
apa: Friesecke, G., & Kniely, M. (2019). New optimal control problems in density
functional theory motivated by photovoltaics. Multiscale Modeling and Simulation.
SIAM. https://doi.org/10.1137/18M1207272
chicago: Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density
Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation.
SIAM, 2019. https://doi.org/10.1137/18M1207272.
ieee: G. Friesecke and M. Kniely, “New optimal control problems in density functional
theory motivated by photovoltaics,” Multiscale Modeling and Simulation,
vol. 17, no. 3. SIAM, pp. 926–947, 2019.
ista: Friesecke G, Kniely M. 2019. New optimal control problems in density functional
theory motivated by photovoltaics. Multiscale Modeling and Simulation. 17(3),
926–947.
mla: Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density
Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation,
vol. 17, no. 3, SIAM, 2019, pp. 926–47, doi:10.1137/18M1207272.
short: G. Friesecke, M. Kniely, Multiscale Modeling and Simulation 17 (2019) 926–947.
date_created: 2019-08-04T21:59:21Z
date_published: 2019-07-16T00:00:00Z
date_updated: 2023-09-05T15:05:45Z
day: '16'
department:
- _id: JuFi
doi: 10.1137/18M1207272
external_id:
arxiv:
- '1808.04200'
isi:
- '000487931800002'
intvolume: ' 17'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.04200
month: '07'
oa: 1
oa_version: Preprint
page: 926-947
publication: Multiscale Modeling and Simulation
publication_identifier:
eissn:
- '15403467'
issn:
- '15403459'
publication_status: published
publisher: SIAM
quality_controlled: '1'
scopus_import: '1'
status: public
title: New optimal control problems in density functional theory motivated by photovoltaics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 17
year: '2019'
...
---
_id: '10874'
abstract:
- lang: eng
text: In this article we prove an analogue of a theorem of Lachaud, Ritzenthaler,
and Zykin, which allows us to connect invariants of binary octics to Siegel modular
forms of genus 3. We use this connection to show that certain modular functions,
when restricted to the hyperelliptic locus, assume values whose denominators are
products of powers of primes of bad reduction for the associated hyperelliptic
curves. We illustrate our theorem with explicit computations. This work is motivated
by the study of the values of these modular functions at CM points of the Siegel
upper half-space, which, if their denominators are known, can be used to effectively
compute models of (hyperelliptic, in our case) curves with CM.
acknowledgement: "The authors would like to thank the Lorentz Center in Leiden for
hosting the Women in Numbers Europe 2 workshop and providing a productive and enjoyable
environment for our initial work on this project. We are grateful to the organizers
of WIN-E2, Irene Bouw, Rachel Newton and Ekin Ozman, for making this conference
and this collaboration possible. We\r\nthank Irene Bouw and Christophe Ritzenhaler
for helpful discussions. Ionica acknowledges support from the Thomas Jefferson Fund
of the Embassy of France in the United States and the FACE Foundation. Most of Kılıçer’s
work was carried out during her stay in Universiteit Leiden and Carl von Ossietzky
Universität Oldenburg. Massierer was supported by the Australian Research Council
(DP150101689). Vincent is supported by the National Science Foundation under Grant
No. DMS-1802323 and by the Thomas Jefferson Fund of the Embassy of France in the
United States and the FACE Foundation. "
article_number: '9'
article_processing_charge: No
article_type: original
author:
- first_name: Sorina
full_name: Ionica, Sorina
last_name: Ionica
- first_name: Pınar
full_name: Kılıçer, Pınar
last_name: Kılıçer
- first_name: Kristin
full_name: Lauter, Kristin
last_name: Lauter
- first_name: Elisa
full_name: Lorenzo García, Elisa
last_name: Lorenzo García
- first_name: Maria-Adelina
full_name: Manzateanu, Maria-Adelina
id: be8d652e-a908-11ec-82a4-e2867729459c
last_name: Manzateanu
- first_name: Maike
full_name: Massierer, Maike
last_name: Massierer
- first_name: Christelle
full_name: Vincent, Christelle
last_name: Vincent
citation:
ama: Ionica S, Kılıçer P, Lauter K, et al. Modular invariants for genus 3 hyperelliptic
curves. Research in Number Theory. 2019;5. doi:10.1007/s40993-018-0146-6
apa: Ionica, S., Kılıçer, P., Lauter, K., Lorenzo García, E., Manzateanu, M.-A.,
Massierer, M., & Vincent, C. (2019). Modular invariants for genus 3 hyperelliptic
curves. Research in Number Theory. Springer Nature. https://doi.org/10.1007/s40993-018-0146-6
chicago: Ionica, Sorina, Pınar Kılıçer, Kristin Lauter, Elisa Lorenzo García, Maria-Adelina
Manzateanu, Maike Massierer, and Christelle Vincent. “Modular Invariants for Genus
3 Hyperelliptic Curves.” Research in Number Theory. Springer Nature, 2019.
https://doi.org/10.1007/s40993-018-0146-6.
ieee: S. Ionica et al., “Modular invariants for genus 3 hyperelliptic curves,”
Research in Number Theory, vol. 5. Springer Nature, 2019.
ista: Ionica S, Kılıçer P, Lauter K, Lorenzo García E, Manzateanu M-A, Massierer
M, Vincent C. 2019. Modular invariants for genus 3 hyperelliptic curves. Research
in Number Theory. 5, 9.
mla: Ionica, Sorina, et al. “Modular Invariants for Genus 3 Hyperelliptic Curves.”
Research in Number Theory, vol. 5, 9, Springer Nature, 2019, doi:10.1007/s40993-018-0146-6.
short: S. Ionica, P. Kılıçer, K. Lauter, E. Lorenzo García, M.-A. Manzateanu, M.
Massierer, C. Vincent, Research in Number Theory 5 (2019).
date_created: 2022-03-18T12:09:48Z
date_published: 2019-01-02T00:00:00Z
date_updated: 2023-09-05T15:39:31Z
day: '02'
department:
- _id: TiBr
doi: 10.1007/s40993-018-0146-6
external_id:
arxiv:
- '1807.08986'
intvolume: ' 5'
keyword:
- Algebra and Number Theory
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.08986
month: '01'
oa: 1
oa_version: Preprint
publication: Research in Number Theory
publication_identifier:
eissn:
- 2363-9555
issn:
- 2522-0160
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modular invariants for genus 3 hyperelliptic curves
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 5
year: '2019'
...
---
_id: '7100'
abstract:
- lang: eng
text: We present microscopic derivations of the defocusing two-dimensional cubic
nonlinear Schrödinger equation and the Gross–Pitaevskii equation starting froman
interacting N-particle system of bosons. We consider the interaction potential
to be given either by Wβ(x)=N−1+2βW(Nβx), for any β>0, or to be given by VN(x)=e2NV(eNx),
for some spherical symmetric, nonnegative and compactly supported W,V∈L∞(R2,R).
In both cases we prove the convergence of the reduced density corresponding to
the exact time evolution to the projector onto the solution of the corresponding
nonlinear Schrödinger equation in trace norm. For the latter potential VN we show
that it is crucial to take the microscopic structure of the condensate into account
in order to obtain the correct dynamics.
acknowledgement: OA fund by IST Austria
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Maximilian
full_name: Jeblick, Maximilian
last_name: Jeblick
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: Peter
full_name: Pickl, Peter
last_name: Pickl
citation:
ama: Jeblick M, Leopold NK, Pickl P. Derivation of the time dependent Gross–Pitaevskii
equation in two dimensions. Communications in Mathematical Physics. 2019;372(1):1-69.
doi:10.1007/s00220-019-03599-x
apa: Jeblick, M., Leopold, N. K., & Pickl, P. (2019). Derivation of the time
dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical
Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03599-x
chicago: Jeblick, Maximilian, Nikolai K Leopold, and Peter Pickl. “Derivation of
the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” Communications
in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03599-x.
ieee: M. Jeblick, N. K. Leopold, and P. Pickl, “Derivation of the time dependent
Gross–Pitaevskii equation in two dimensions,” Communications in Mathematical
Physics, vol. 372, no. 1. Springer Nature, pp. 1–69, 2019.
ista: Jeblick M, Leopold NK, Pickl P. 2019. Derivation of the time dependent Gross–Pitaevskii
equation in two dimensions. Communications in Mathematical Physics. 372(1), 1–69.
mla: Jeblick, Maximilian, et al. “Derivation of the Time Dependent Gross–Pitaevskii
Equation in Two Dimensions.” Communications in Mathematical Physics, vol.
372, no. 1, Springer Nature, 2019, pp. 1–69, doi:10.1007/s00220-019-03599-x.
short: M. Jeblick, N.K. Leopold, P. Pickl, Communications in Mathematical Physics
372 (2019) 1–69.
date_created: 2019-11-25T08:08:02Z
date_published: 2019-11-08T00:00:00Z
date_updated: 2023-09-06T10:47:43Z
day: '08'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s00220-019-03599-x
ec_funded: 1
external_id:
isi:
- '000495193700002'
file:
- access_level: open_access
checksum: cd283b475dd739e04655315abd46f528
content_type: application/pdf
creator: dernst
date_created: 2019-11-25T08:11:11Z
date_updated: 2020-07-14T12:47:49Z
file_id: '7101'
file_name: 2019_CommMathPhys_Jeblick.pdf
file_size: 884469
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
intvolume: ' 372'
isi: 1
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 1-69
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- 1432-0916
issn:
- 0010-3616
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Derivation of the time dependent Gross–Pitaevskii equation in two dimensions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 372
year: '2019'
...
---
_id: '7106'
abstract:
- lang: eng
text: PIN-FORMED (PIN) transporters mediate directional, intercellular movement
of the phytohormone auxin in land plants. To elucidate the evolutionary origins
of this developmentally crucial mechanism, we analysed the single PIN homologue
of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized
auxin exporter in land plants and heterologous models. While its role in algae
remains unclear, PIN-driven auxin export is probably an ancient and conserved
trait within streptophytes.
article_processing_charge: No
article_type: original
author:
- first_name: Roman
full_name: Skokan, Roman
last_name: Skokan
- first_name: Eva
full_name: Medvecká, Eva
last_name: Medvecká
- first_name: Tom
full_name: Viaene, Tom
last_name: Viaene
- first_name: Stanislav
full_name: Vosolsobě, Stanislav
last_name: Vosolsobě
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Karel
full_name: Müller, Karel
last_name: Müller
- first_name: Petr
full_name: Skůpa, Petr
last_name: Skůpa
- first_name: Michal
full_name: Karady, Michal
last_name: Karady
- first_name: Yuzhou
full_name: Zhang, Yuzhou
last_name: Zhang
- first_name: Dorina P.
full_name: Janacek, Dorina P.
last_name: Janacek
- first_name: Ulrich Z.
full_name: Hammes, Ulrich Z.
last_name: Hammes
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Skokan R, Medvecká E, Viaene T, et al. PIN-driven auxin transport emerged early
in streptophyte evolution. Nature Plants. 2019;5(11):1114-1119. doi:10.1038/s41477-019-0542-5
apa: Skokan, R., Medvecká, E., Viaene, T., Vosolsobě, S., Zwiewka, M., Müller, K.,
… Friml, J. (2019). PIN-driven auxin transport emerged early in streptophyte evolution.
Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0542-5
chicago: Skokan, Roman, Eva Medvecká, Tom Viaene, Stanislav Vosolsobě, Marta Zwiewka,
Karel Müller, Petr Skůpa, et al. “PIN-Driven Auxin Transport Emerged Early in
Streptophyte Evolution.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0542-5.
ieee: R. Skokan et al., “PIN-driven auxin transport emerged early in streptophyte
evolution,” Nature Plants, vol. 5, no. 11. Springer Nature, pp. 1114–1119,
2019.
ista: Skokan R, Medvecká E, Viaene T, Vosolsobě S, Zwiewka M, Müller K, Skůpa P,
Karady M, Zhang Y, Janacek DP, Hammes UZ, Ljung K, Nodzyński T, Petrášek J, Friml
J. 2019. PIN-driven auxin transport emerged early in streptophyte evolution. Nature
Plants. 5(11), 1114–1119.
mla: Skokan, Roman, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte
Evolution.” Nature Plants, vol. 5, no. 11, Springer Nature, 2019, pp. 1114–19,
doi:10.1038/s41477-019-0542-5.
short: R. Skokan, E. Medvecká, T. Viaene, S. Vosolsobě, M. Zwiewka, K. Müller, P.
Skůpa, M. Karady, Y. Zhang, D.P. Janacek, U.Z. Hammes, K. Ljung, T. Nodzyński,
J. Petrášek, J. Friml, Nature Plants 5 (2019) 1114–1119.
date_created: 2019-11-25T09:08:04Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-09-06T11:09:49Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41477-019-0542-5
ec_funded: 1
external_id:
isi:
- '000496526100010'
pmid:
- '31712756'
file:
- access_level: open_access
checksum: 94e0426856aad9a9bd0135d5436efbf1
content_type: application/pdf
creator: dernst
date_created: 2020-10-14T08:54:49Z
date_updated: 2020-10-14T08:54:49Z
file_id: '8660'
file_name: 2019_NaturePlants_Skokan_accepted.pdf
file_size: 1980851
relation: main_file
success: 1
file_date_updated: 2020-10-14T08:54:49Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 1114-1119
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
publication: Nature Plants
publication_identifier:
issn:
- 2055-0278
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: PIN-driven auxin transport emerged early in streptophyte evolution
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 5
year: '2019'
...
---
_id: '7105'
abstract:
- lang: eng
text: Cell migration is hypothesized to involve a cycle of behaviours beginning
with leading edge extension. However, recent evidence suggests that the leading
edge may be dispensable for migration, raising the question of what actually controls
cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages
to bridge the different temporal scales of the behaviours controlling motility.
This approach reveals that edge fluctuations during random motility are not persistent
and are weakly correlated with motion. In contrast, flow of the actin network
behind the leading edge is highly persistent. Quantification of actin flow structure
during migration reveals a stable organization and asymmetry in the cell-wide
flowfield that strongly correlates with cell directionality. This organization
is regulated by a gradient of actin network compression and destruction, which
is controlled by myosin contraction and cofilin-mediated disassembly. It is this
stable actin-flow polarity, which integrates rapid fluctuations of the leading
edge, that controls inherent cellular persistence.
article_processing_charge: No
article_type: original
author:
- first_name: Lawrence
full_name: Yolland, Lawrence
last_name: Yolland
- first_name: Mubarik
full_name: Burki, Mubarik
last_name: Burki
- first_name: Stefania
full_name: Marcotti, Stefania
last_name: Marcotti
- first_name: Andrei
full_name: Luchici, Andrei
last_name: Luchici
- first_name: Fiona N.
full_name: Kenny, Fiona N.
last_name: Kenny
- first_name: John Robert
full_name: Davis, John Robert
last_name: Davis
- first_name: Eduardo
full_name: Serna-Morales, Eduardo
last_name: Serna-Morales
- first_name: Jan
full_name: Müller, Jan
id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D
last_name: Müller
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Andrew
full_name: Davidson, Andrew
last_name: Davidson
- first_name: Will
full_name: Wood, Will
last_name: Wood
- first_name: Linus J.
full_name: Schumacher, Linus J.
last_name: Schumacher
- first_name: Robert G.
full_name: Endres, Robert G.
last_name: Endres
- first_name: Mark
full_name: Miodownik, Mark
last_name: Miodownik
- first_name: Brian M.
full_name: Stramer, Brian M.
last_name: Stramer
citation:
ama: Yolland L, Burki M, Marcotti S, et al. Persistent and polarized global actin
flow is essential for directionality during cell migration. Nature Cell Biology.
2019;21(11):1370-1381. doi:10.1038/s41556-019-0411-5
apa: Yolland, L., Burki, M., Marcotti, S., Luchici, A., Kenny, F. N., Davis, J.
R., … Stramer, B. M. (2019). Persistent and polarized global actin flow is essential
for directionality during cell migration. Nature Cell Biology. Springer
Nature. https://doi.org/10.1038/s41556-019-0411-5
chicago: Yolland, Lawrence, Mubarik Burki, Stefania Marcotti, Andrei Luchici, Fiona
N. Kenny, John Robert Davis, Eduardo Serna-Morales, et al. “Persistent and Polarized
Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature
Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0411-5.
ieee: L. Yolland et al., “Persistent and polarized global actin flow is essential
for directionality during cell migration,” Nature Cell Biology, vol. 21,
no. 11. Springer Nature, pp. 1370–1381, 2019.
ista: Yolland L, Burki M, Marcotti S, Luchici A, Kenny FN, Davis JR, Serna-Morales
E, Müller J, Sixt MK, Davidson A, Wood W, Schumacher LJ, Endres RG, Miodownik
M, Stramer BM. 2019. Persistent and polarized global actin flow is essential for
directionality during cell migration. Nature Cell Biology. 21(11), 1370–1381.
mla: Yolland, Lawrence, et al. “Persistent and Polarized Global Actin Flow Is Essential
for Directionality during Cell Migration.” Nature Cell Biology, vol. 21,
no. 11, Springer Nature, 2019, pp. 1370–81, doi:10.1038/s41556-019-0411-5.
short: L. Yolland, M. Burki, S. Marcotti, A. Luchici, F.N. Kenny, J.R. Davis, E.
Serna-Morales, J. Müller, M.K. Sixt, A. Davidson, W. Wood, L.J. Schumacher, R.G.
Endres, M. Miodownik, B.M. Stramer, Nature Cell Biology 21 (2019) 1370–1381.
date_created: 2019-11-25T08:55:00Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-09-06T11:08:52Z
day: '01'
department:
- _id: MiSi
doi: 10.1038/s41556-019-0411-5
external_id:
isi:
- '000495888300009'
pmid:
- '31685997'
intvolume: ' 21'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891
month: '11'
oa: 1
oa_version: Submitted Version
page: 1370-1381
pmid: 1
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: Persistent and polarized global actin flow is essential for directionality
during cell migration
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 21
year: '2019'
...
---
_id: '7109'
abstract:
- lang: eng
text: We show how to construct temporal testers for the logic MITL, a prominent
linear-time logic for real-time systems. A temporal tester is a transducer that
inputs a signal holding the Boolean value of atomic propositions and outputs the
truth value of a formula along time. Here we consider testers over continuous-time
Boolean signals that use clock variables to enforce duration constraints, as in
timed automata. We first rewrite the MITL formula into a “simple” formula using
a limited set of temporal modalities. We then build testers for these specific
modalities and show how to compose testers for simple formulae into complex ones.
Temporal testers can be turned into acceptors, yielding a compositional translation
from MITL to timed automata. This construction is much simpler than previously
known and remains asymptotically optimal. It supports both past and future operators
and can easily be extended.
article_number: '19'
article_processing_charge: No
article_type: original
author:
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Ničković, Dejan
last_name: Ničković
- first_name: Amir
full_name: Pnueli, Amir
last_name: Pnueli
citation:
ama: Ferrere T, Maler O, Ničković D, Pnueli A. From real-time logic to timed automata.
Journal of the ACM. 2019;66(3). doi:10.1145/3286976
apa: Ferrere, T., Maler, O., Ničković, D., & Pnueli, A. (2019). From real-time
logic to timed automata. Journal of the ACM. ACM. https://doi.org/10.1145/3286976
chicago: Ferrere, Thomas, Oded Maler, Dejan Ničković, and Amir Pnueli. “From Real-Time
Logic to Timed Automata.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3286976.
ieee: T. Ferrere, O. Maler, D. Ničković, and A. Pnueli, “From real-time logic to
timed automata,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.
ista: Ferrere T, Maler O, Ničković D, Pnueli A. 2019. From real-time logic to timed
automata. Journal of the ACM. 66(3), 19.
mla: Ferrere, Thomas, et al. “From Real-Time Logic to Timed Automata.” Journal
of the ACM, vol. 66, no. 3, 19, ACM, 2019, doi:10.1145/3286976.
short: T. Ferrere, O. Maler, D. Ničković, A. Pnueli, Journal of the ACM 66 (2019).
date_created: 2019-11-26T10:22:32Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-09-06T11:11:56Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/3286976
external_id:
isi:
- '000495406300005'
intvolume: ' 66'
isi: 1
issue: '3'
language:
- iso: eng
month: '05'
oa_version: None
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Journal of the ACM
publication_identifier:
issn:
- 0004-5411
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: From real-time logic to timed automata
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 66
year: '2019'
...
---
_id: '7108'
abstract:
- lang: eng
text: We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial
complex is shellable is NP-hard, hence NP-complete. This resolves a question raised,
e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d
≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable
is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible
pure d-dimensional complexes. Another simple corollary of our result is that it
is NP-hard to decide whether a given poset is CL-shellable.
article_number: '21'
article_processing_charge: No
article_type: original
author:
- first_name: Xavier
full_name: Goaoc, Xavier
last_name: Goaoc
- first_name: Pavel
full_name: Patak, Pavel
id: B593B804-1035-11EA-B4F1-947645A5BB83
last_name: Patak
- first_name: Zuzana
full_name: Patakova, Zuzana
id: 48B57058-F248-11E8-B48F-1D18A9856A87
last_name: Patakova
orcid: 0000-0002-3975-1683
- first_name: Martin
full_name: Tancer, Martin
last_name: Tancer
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete.
Journal of the ACM. 2019;66(3). doi:10.1145/3314024
apa: Goaoc, X., Patak, P., Patakova, Z., Tancer, M., & Wagner, U. (2019). Shellability
is NP-complete. Journal of the ACM. ACM. https://doi.org/10.1145/3314024
chicago: Goaoc, Xavier, Pavel Patak, Zuzana Patakova, Martin Tancer, and Uli Wagner.
“Shellability Is NP-Complete.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3314024.
ieee: X. Goaoc, P. Patak, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is
NP-complete,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.
ista: Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. 2019. Shellability is NP-complete.
Journal of the ACM. 66(3), 21.
mla: Goaoc, Xavier, et al. “Shellability Is NP-Complete.” Journal of the ACM,
vol. 66, no. 3, 21, ACM, 2019, doi:10.1145/3314024.
short: X. Goaoc, P. Patak, Z. Patakova, M. Tancer, U. Wagner, Journal of the ACM
66 (2019).
date_created: 2019-11-26T10:13:59Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-06T11:10:58Z
day: '01'
department:
- _id: UlWa
doi: 10.1145/3314024
external_id:
arxiv:
- '1711.08436'
isi:
- '000495406300007'
intvolume: ' 66'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/pdf/1711.08436.pdf
month: '06'
oa: 1
oa_version: Preprint
publication: Journal of the ACM
publication_identifier:
issn:
- 0004-5411
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '184'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Shellability is NP-complete
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 66
year: '2019'
...
---
_id: '7147'
abstract:
- lang: eng
text: "The expression of a gene is characterised by its transcription factors and
the function processing them. If the transcription factors are not affected by
gene products, the regulating function is often represented as a combinational
logic circuit, where the outputs (product) are determined by current input values
(transcription factors) only, and are hence independent on their relative arrival
times. However, the simultaneous arrival of transcription factors (TFs) in genetic
circuits is a strong assumption, given that the processes of transcription and
translation of a gene into a protein introduce intrinsic time delays and that
there is no global synchronisation among the arrival times of different molecular
species at molecular targets.\r\n\r\nIn this paper, we construct an experimentally
implementable genetic circuit with two inputs and a single output, such that,
in presence of small delays in input arrival, the circuit exhibits qualitatively
distinct observable phenotypes. In particular, these phenotypes are long lived
transients: they all converge to a single value, but so slowly, that they seem
stable for an extended time period, longer than typical experiment duration. We
used rule-based language to prototype our circuit, and we implemented a search
for finding the parameter combinations raising the phenotypes of interest.\r\n\r\nThe
behaviour of our prototype circuit has wide implications. First, it suggests that
GRNs can exploit event timing to create phenotypes. Second, it opens the possibility
that GRNs are using event timing to react to stimuli and memorise events, without
explicit feedback in regulation. From the modelling perspective, our prototype
circuit demonstrates the critical importance of analysing the transient dynamics
at the promoter binding sites of the DNA, before applying rapid equilibrium assumptions."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- 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: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
citation:
ama: 'Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. Transient memory in gene
regulation. In: 17th International Conference on Computational Methods in Systems
Biology. Vol 11773. Springer Nature; 2019:155-187. doi:10.1007/978-3-030-31304-3_9'
apa: 'Guet, C. C., Henzinger, T. A., Igler, C., Petrov, T., & Sezgin, A. (2019).
Transient memory in gene regulation. In 17th International Conference on Computational
Methods in Systems Biology (Vol. 11773, pp. 155–187). Trieste, Italy: Springer
Nature. https://doi.org/10.1007/978-3-030-31304-3_9'
chicago: Guet, Calin C, Thomas A Henzinger, Claudia Igler, Tatjana Petrov, and Ali
Sezgin. “Transient Memory in Gene Regulation.” In 17th International Conference
on Computational Methods in Systems Biology, 11773:155–87. Springer Nature,
2019. https://doi.org/10.1007/978-3-030-31304-3_9.
ieee: C. C. Guet, T. A. Henzinger, C. Igler, T. Petrov, and A. Sezgin, “Transient
memory in gene regulation,” in 17th International Conference on Computational
Methods in Systems Biology, Trieste, Italy, 2019, vol. 11773, pp. 155–187.
ista: 'Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. 2019. Transient memory
in gene regulation. 17th International Conference on Computational Methods in
Systems Biology. CMSB: Computational Methods in Systems Biology, LNCS, vol. 11773,
155–187.'
mla: Guet, Calin C., et al. “Transient Memory in Gene Regulation.” 17th International
Conference on Computational Methods in Systems Biology, vol. 11773, Springer
Nature, 2019, pp. 155–87, doi:10.1007/978-3-030-31304-3_9.
short: C.C. Guet, T.A. Henzinger, C. Igler, T. Petrov, A. Sezgin, in:, 17th International
Conference on Computational Methods in Systems Biology, Springer Nature, 2019,
pp. 155–187.
conference:
end_date: 2019-09-20
location: Trieste, Italy
name: 'CMSB: Computational Methods in Systems Biology'
start_date: 2019-09-18
date_created: 2019-12-04T16:07:50Z
date_published: 2019-09-17T00:00:00Z
date_updated: 2023-09-06T11:18:08Z
day: '17'
department:
- _id: CaGu
- _id: ToHe
doi: 10.1007/978-3-030-31304-3_9
external_id:
isi:
- '000557875100009'
intvolume: ' 11773'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
page: 155-187
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 251EE76E-B435-11E9-9278-68D0E5697425
grant_number: '24573'
name: Design principles underlying genetic switch architecture
publication: 17th International Conference on Computational Methods in Systems Biology
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030313036'
- '9783030313043'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transient memory in gene regulation
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11773
year: '2019'
...
---
_id: '7136'
abstract:
- lang: eng
text: "It is well established that the notion of min-entropy fails to satisfy the
\\emph{chain rule} of the form H(X,Y)=H(X|Y)+H(Y), known for Shannon Entropy.
Such a property would help to analyze how min-entropy is split among smaller blocks.
Problems of this kind arise for example when constructing extractors and dispersers.\r\nWe
show that any sequence of variables exhibits a very strong strong block-source
structure (conditional distributions of blocks are nearly flat) when we \\emph{spoil
few correlated bits}. This implies, conditioned on the spoiled bits, that \\emph{splitting-recombination
properties} hold. In particular, we have many nice properties that min-entropy
doesn't obey in general, for example strong chain rules, \"information can't hurt\"
inequalities, equivalences of average and worst-case conditional entropy definitions
and others. Quantitatively, for any sequence X1,…,Xt of random variables over
an alphabet X we prove that, when conditioned on m=t⋅O(loglog|X|+loglog(1/ϵ)+logt)
bits of auxiliary information, all conditional distributions of the form Xi|X2019 IEEE International Symposium on Information Theory. IEEE; 2019. doi:10.1109/isit.2019.8849240'
apa: 'Skórski, M. (2019). Strong chain rules for min-entropy under few bits spoiled.
In 2019 IEEE International Symposium on Information Theory. Paris, France:
IEEE. https://doi.org/10.1109/isit.2019.8849240'
chicago: Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.”
In 2019 IEEE International Symposium on Information Theory. IEEE, 2019.
https://doi.org/10.1109/isit.2019.8849240.
ieee: M. Skórski, “Strong chain rules for min-entropy under few bits spoiled,” in
2019 IEEE International Symposium on Information Theory, Paris, France,
2019.
ista: 'Skórski M. 2019. Strong chain rules for min-entropy under few bits spoiled.
2019 IEEE International Symposium on Information Theory. ISIT: International Symposium
on Information Theory, 8849240.'
mla: Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.”
2019 IEEE International Symposium on Information Theory, 8849240, IEEE,
2019, doi:10.1109/isit.2019.8849240.
short: M. Skórski, in:, 2019 IEEE International Symposium on Information Theory,
IEEE, 2019.
conference:
end_date: 2019-07-12
location: Paris, France
name: 'ISIT: International Symposium on Information Theory'
start_date: 2019-07-07
date_created: 2019-11-28T10:19:21Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-09-06T11:15:41Z
day: '01'
department:
- _id: KrPi
doi: 10.1109/isit.2019.8849240
external_id:
arxiv:
- '1702.08476'
isi:
- '000489100301043'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.08476
month: '07'
oa: 1
oa_version: Preprint
publication: 2019 IEEE International Symposium on Information Theory
publication_identifier:
isbn:
- '9781538692912'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strong chain rules for min-entropy under few bits spoiled
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...