---
_id: '14259'
abstract:
- lang: eng
text: "We provide a learning-based technique for guessing a winning strategy in
a parity game originating from an LTL synthesis problem. A cheaply obtained guess
can be useful in several applications. Not only can the guessed strategy be applied
as best-effort in cases where the game’s huge size prohibits rigorous approaches,
but it can also increase the scalability of rigorous LTL synthesis in several
ways. Firstly, checking whether a guessed strategy is winning is easier than constructing
one. Secondly, even if the guess is wrong in some places, it can be fixed by strategy
iteration faster than constructing one from scratch. Thirdly, the guess can be
used in on-the-fly approaches to prioritize exploration in the most fruitful directions.\r\nIn
contrast to previous works, we (i) reflect the highly structured logical information
in game’s states, the so-called semantic labelling, coming from the recent LTL-to-automata
translations, and (ii) learn to reflect it properly by learning from previously
solved games, bringing the solving process closer to human-like reasoning."
acknowledgement: This research was funded in part by the German Research Foundation
(DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro).
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Maximilian
full_name: Prokop, Maximilian
last_name: Prokop
- first_name: Sabine
full_name: Rieder, Sabine
last_name: Rieder
citation:
ama: 'Kretinsky J, Meggendorfer T, Prokop M, Rieder S. Guessing winning policies
in LTL synthesis by semantic learning. In: 35th International Conference on
Computer Aided Verification . Vol 13964. Springer Nature; 2023:390-414. doi:10.1007/978-3-031-37706-8_20'
apa: 'Kretinsky, J., Meggendorfer, T., Prokop, M., & Rieder, S. (2023). Guessing
winning policies in LTL synthesis by semantic learning. In 35th International
Conference on Computer Aided Verification (Vol. 13964, pp. 390–414). Paris,
France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_20'
chicago: Kretinsky, Jan, Tobias Meggendorfer, Maximilian Prokop, and Sabine Rieder.
“Guessing Winning Policies in LTL Synthesis by Semantic Learning.” In 35th
International Conference on Computer Aided Verification , 13964:390–414. Springer
Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_20.
ieee: J. Kretinsky, T. Meggendorfer, M. Prokop, and S. Rieder, “Guessing winning
policies in LTL synthesis by semantic learning,” in 35th International Conference
on Computer Aided Verification , Paris, France, 2023, vol. 13964, pp. 390–414.
ista: 'Kretinsky J, Meggendorfer T, Prokop M, Rieder S. 2023. Guessing winning policies
in LTL synthesis by semantic learning. 35th International Conference on Computer
Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 390–414.'
mla: Kretinsky, Jan, et al. “Guessing Winning Policies in LTL Synthesis by Semantic
Learning.” 35th International Conference on Computer Aided Verification ,
vol. 13964, Springer Nature, 2023, pp. 390–414, doi:10.1007/978-3-031-37706-8_20.
short: J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International
Conference on Computer Aided Verification , Springer Nature, 2023, pp. 390–414.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-03T22:01:16Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2023-09-06T08:27:33Z
day: '17'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-031-37706-8_20
file:
- access_level: open_access
checksum: ed66278b61bb869e1baba3d9b9081271
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T08:25:50Z
date_updated: 2023-09-06T08:25:50Z
file_id: '14276'
file_name: 2023_LNCS_CAV_Kretinsky.pdf
file_size: 428354
relation: main_file
success: 1
file_date_updated: 2023-09-06T08:25:50Z
has_accepted_license: '1'
intvolume: ' 13964'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 390-414
publication: '35th International Conference on Computer Aided Verification '
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377051'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Guessing winning policies in LTL synthesis by semantic learning
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13964
year: '2023'
...
---
_id: '14260'
abstract:
- lang: eng
text: "This paper presents Lincheck, a new practical and user-friendly framework
for testing concurrent algorithms on the Java Virtual Machine (JVM). Lincheck
provides a simple and declarative way to write concurrent tests: instead of describing
how to perform the test, users specify what to test by declaring all the operations
to examine; the framework automatically handles the rest. As a result, tests written
with Lincheck are concise and easy to understand. The framework automatically
generates a set of concurrent scenarios, examines them using stress-testing or
bounded model checking, and verifies that the results of each invocation are correct.
Notably, if an error is detected via model checking, Lincheck provides an easy-to-follow
trace to reproduce it, significantly simplifying the bug investigation.\r\n\r\nTo
the best of our knowledge, Lincheck is the first production-ready tool on the
JVM that offers such a simple way of writing concurrent tests, without requiring
special skills or expertise. We successfully integrated Lincheck in the development
process of several large projects, such as Kotlin Coroutines, and identified new
bugs in popular concurrency libraries, such as a race in Java’s standard ConcurrentLinkedDeque
and a liveliness bug in Java’s AbstractQueuedSynchronizer framework, which is
used in most of the synchronization primitives. We believe that Lincheck can significantly
improve the quality and productivity of concurrent algorithms research and development
and become the state-of-the-art tool for checking their correctness."
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Alexander
full_name: Fedorov, Alexander
id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6
last_name: Fedorov
- first_name: Maria
full_name: Sokolova, Maria
last_name: Sokolova
- first_name: Dmitry
full_name: Tsitelov, Dmitry
last_name: Tsitelov
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical
framework for testing concurrent data structures on JVM. In: 35th International
Conference on Computer Aided Verification . Vol 13964. Springer Nature; 2023:156-169.
doi:10.1007/978-3-031-37706-8_8'
apa: 'Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., & Alistarh, D.-A.
(2023). Lincheck: A practical framework for testing concurrent data structures
on JVM. In 35th International Conference on Computer Aided Verification
(Vol. 13964, pp. 156–169). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_8'
chicago: 'Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and
Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data
Structures on JVM.” In 35th International Conference on Computer Aided Verification
, 13964:156–69. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_8.'
ieee: 'N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck:
A practical framework for testing concurrent data structures on JVM,” in 35th
International Conference on Computer Aided Verification , Paris, France, 2023,
vol. 13964, pp. 156–169.'
ista: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck:
A practical framework for testing concurrent data structures on JVM. 35th International
Conference on Computer Aided Verification . CAV: Computer Aided Verification,
LNCS, vol. 13964, 156–169.'
mla: 'Koval, Nikita, et al. “Lincheck: A Practical Framework for Testing Concurrent
Data Structures on JVM.” 35th International Conference on Computer Aided Verification
, vol. 13964, Springer Nature, 2023, pp. 156–69, doi:10.1007/978-3-031-37706-8_8.'
short: N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, in:, 35th
International Conference on Computer Aided Verification , Springer Nature, 2023,
pp. 156–169.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-03T22:01:16Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2024-02-27T07:46:52Z
day: '17'
ddc:
- '000'
department:
- _id: DaAl
- _id: GradSch
doi: 10.1007/978-3-031-37706-8_8
file:
- access_level: open_access
checksum: c346016393123a0a2338ad4d976f61bc
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T08:16:25Z
date_updated: 2023-09-06T08:16:25Z
file_id: '14275'
file_name: 2023_LNCS_Koval.pdf
file_size: 421408
relation: main_file
success: 1
file_date_updated: 2023-09-06T08:16:25Z
has_accepted_license: '1'
intvolume: ' 13964'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 156-169
publication: '35th International Conference on Computer Aided Verification '
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377051'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14995'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Lincheck: A practical framework for testing concurrent data structures on JVM'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13964
year: '2023'
...
---
_id: '14261'
abstract:
- lang: eng
text: In this work, a generalized, adapted Numerov implementation capable of determining
band structures of periodic quantum systems is outlined. Based on the input potential,
the presented approach numerically solves the Schrödinger equation in position
space at each momentum space point. Thus, in addition to the band structure, the
method inherently provides information about the state functions and probability
densities in position space at each momentum space point considered. The generalized,
adapted Numerov framework provided reliable estimates for a variety of increasingly
complex test suites in one, two, and three dimensions. The accuracy of the proposed
methodology was benchmarked against results obtained for the analytically solvable
Kronig-Penney model. Furthermore, the presented numerical solver was applied to
a model potential representing a 2D optical lattice being a challenging application
relevant, for example, in the field of quantum computing.
acknowledgement: Financial supports for this work via a PhD scholarship for J. Gamper
issued by the Leopold-Franzens-University of Innsbruck (Vicerector Prof. Dr Ulrike
Tanzer) are gratefully acknowledged. The computational results presented have been
achieved (in part) using the HPC infrastructure of the University of Innsbruck.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jakob
full_name: Gamper, Jakob
last_name: Gamper
- first_name: Florian
full_name: Kluibenschedl, Florian
id: 7499e70e-eb2c-11ec-b98b-f925648bc9d9
last_name: Kluibenschedl
- first_name: Alexander K.H.
full_name: Weiss, Alexander K.H.
last_name: Weiss
- first_name: Thomas S.
full_name: Hofer, Thomas S.
last_name: Hofer
citation:
ama: Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. Accessing position space wave
functions in band structure calculations of periodic systems - a generalized,
adapted numerov implementation for one-, two-, and three-dimensional quantum problems.
Journal of Physical Chemistry Letters. 2023;14(33):7395-7403. doi:10.1021/acs.jpclett.3c01707
apa: Gamper, J., Kluibenschedl, F., Weiss, A. K. H., & Hofer, T. S. (2023).
Accessing position space wave functions in band structure calculations of periodic
systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional
quantum problems. Journal of Physical Chemistry Letters. American Chemical
Society. https://doi.org/10.1021/acs.jpclett.3c01707
chicago: Gamper, Jakob, Florian Kluibenschedl, Alexander K.H. Weiss, and Thomas
S. Hofer. “Accessing Position Space Wave Functions in Band Structure Calculations
of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-,
Two-, and Three-Dimensional Quantum Problems.” Journal of Physical Chemistry
Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01707.
ieee: J. Gamper, F. Kluibenschedl, A. K. H. Weiss, and T. S. Hofer, “Accessing position
space wave functions in band structure calculations of periodic systems - a generalized,
adapted numerov implementation for one-, two-, and three-dimensional quantum problems,”
Journal of Physical Chemistry Letters, vol. 14, no. 33. American Chemical
Society, pp. 7395–7403, 2023.
ista: Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. 2023. Accessing position space
wave functions in band structure calculations of periodic systems - a generalized,
adapted numerov implementation for one-, two-, and three-dimensional quantum problems.
Journal of Physical Chemistry Letters. 14(33), 7395–7403.
mla: Gamper, Jakob, et al. “Accessing Position Space Wave Functions in Band Structure
Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation
for One-, Two-, and Three-Dimensional Quantum Problems.” Journal of Physical
Chemistry Letters, vol. 14, no. 33, American Chemical Society, 2023, pp. 7395–403,
doi:10.1021/acs.jpclett.3c01707.
short: J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical
Chemistry Letters 14 (2023) 7395–7403.
date_created: 2023-09-03T22:01:16Z
date_published: 2023-08-11T00:00:00Z
date_updated: 2023-09-06T11:04:31Z
day: '11'
ddc:
- '530'
- '540'
department:
- _id: GradSch
doi: 10.1021/acs.jpclett.3c01707
external_id:
isi:
- '001048165800001'
pmid:
- '37566743'
file:
- access_level: open_access
checksum: 637454e2b3a357498d8d622d241c4bf6
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T07:32:39Z
date_updated: 2023-09-06T07:32:39Z
file_id: '14272'
file_name: 2023_JourPhysChemistry_Gamper.pdf
file_size: 4986859
relation: main_file
success: 1
file_date_updated: 2023-09-06T07:32:39Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '33'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 7395-7403
pmid: 1
publication: Journal of Physical Chemistry Letters
publication_identifier:
eissn:
- 1948-7185
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Accessing position space wave functions in band structure calculations of periodic
systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional
quantum problems
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: 14
year: '2023'
...
---
_id: '14274'
abstract:
- lang: eng
text: Immune responses rely on the rapid and coordinated migration of leukocytes.
Whereas it is well established that single-cell migration is often guided by gradients
of chemokines and other chemoattractants, it remains poorly understood how these
gradients are generated, maintained, and modulated. By combining experimental
data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor
(GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor
that steers migration, CCR7 also acts as a generator and a modulator of chemotactic
gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively
internalize the receptor and ligand as part of the canonical GPCR desensitization
response. We show that CCR7 internalization also acts as an effective sink for
the chemoattractant, dynamically shaping the spatiotemporal distribution of the
chemokine. This mechanism drives complex collective migration patterns, enabling
DCs to create or sharpen chemotactic gradients. We further show that these self-generated
gradients can sustain the long-range guidance of DCs, adapt collective migration
patterns to the size and geometry of the environment, and provide a guidance cue
for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses
and consumes its ligand can thus provide a novel mode of cellular self-organization.
acknowledgement: "We thank I. de Vries and the Scientific Service Units (Life Sciences,
Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute
of Science and Technology Austria for excellent support, as well as all the rotation
students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis
work was supported by grants from the European Research Council under the European
Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant
agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20)
to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research
Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U.
was supported by the European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie grant agreement no. 754411."
article_number: adc9584
article_processing_charge: No
article_type: original
author:
- first_name: Jonna H
full_name: Alanko, Jonna H
id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87
last_name: Alanko
orcid: 0000-0002-7698-3061
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
- first_name: Nikola
full_name: Canigova, Nikola
id: 3795523E-F248-11E8-B48F-1D18A9856A87
last_name: Canigova
orcid: 0000-0002-8518-5926
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- 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: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink
for CCL19 to coordinate collective leukocyte migration. Science Immunology.
2023;8(87). doi:10.1126/sciimmunol.adc9584
apa: Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin,
J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate
collective leukocyte migration. Science Immunology. American Association
for the Advancement of Science. https://doi.org/10.1126/sciimmunol.adc9584
chicago: Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz,
Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor
and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science
Immunology. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciimmunol.adc9584.
ieee: J. H. Alanko et al., “CCR7 acts as both a sensor and a sink for CCL19
to coordinate collective leukocyte migration,” Science Immunology, vol.
8, no. 87. American Association for the Advancement of Science, 2023.
ista: Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB,
Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective
leukocyte migration. Science Immunology. 8(87), adc9584.
mla: Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to
Coordinate Collective Leukocyte Migration.” Science Immunology, vol. 8,
no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:10.1126/sciimmunol.adc9584.
short: J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B.
Hannezo, M.K. Sixt, Science Immunology 8 (2023).
date_created: 2023-09-06T08:07:51Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-12-21T14:30:01Z
day: '01'
department:
- _id: MiSi
- _id: EdHa
- _id: NanoFab
doi: 10.1126/sciimmunol.adc9584
ec_funded: 1
external_id:
isi:
- '001062110600003'
pmid:
- '37656776'
intvolume: ' 8'
isi: 1
issue: '87'
keyword:
- General Medicine
- Immunology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1126/sciimmunol.adc9584
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 265E2996-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01250-B20
name: Nano-Analytics of Cellular Systems
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Science Immunology
publication_identifier:
issn:
- 2470-9468
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
record:
- id: '14279'
relation: research_data
status: public
- id: '14697'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte
migration
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2023'
...
---
_id: '14277'
abstract:
- lang: eng
text: Living tissues are characterized by an intrinsically mechanochemical interplay
of active physical forces and complex biochemical signaling pathways. Either feature
alone can give rise to complex emergent phenomena, for example, mechanically driven
glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion
instabilities. An important question is how to quantitatively assess the contribution
of these different cues to the large-scale dynamics of biological materials. We
address this in Madin-Darby canine kidney (MDCK) monolayers, considering both
mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling
activity and cellular density as well as a mechanically active tissue rheology
via a self-propelled vertex model. We show that the relative strength of active
migration forces to mechanochemical couplings controls a transition from a uniform
active glass to periodic spatiotemporal waves. We parametrize the model from published
experimental data sets on MDCK monolayers and use it to make new predictions on
the correlation functions of cellular dynamics and the dynamics of topological
defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers
are best described by an intermediary parameter region in which both mechanochemical
couplings and noisy active propulsion have a strong influence on the dynamics.
Finally, we study how tissue rheology and ERK waves produce feedback on one another
and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical
waves at both the local and global levels.
acknowledgement: We thank all members of the Hannezo group for discussions and suggestions,
as well as Sound Wai Phow for technical assistance. This work received funding from
the European Research Council under the EU Horizon 2020 research and innovation
program Grant Agreement No. 851288 (E.H.), JSPS KAKENHI Grant No. 21H05290, and
the Ministry of Education under the Research Centres of Excellence program through
the MBI at NUS.
article_number: '013001'
article_processing_charge: Yes
article_type: original
author:
- first_name: Daniel R
full_name: Boocock, Daniel R
id: 453AF628-F248-11E8-B48F-1D18A9856A87
last_name: Boocock
orcid: 0000-0002-1585-2631
- first_name: Tsuyoshi
full_name: Hirashima, Tsuyoshi
last_name: Hirashima
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning
and glassy dynamics in cellular monolayers. PRX Life. 2023;1(1). doi:10.1103/prxlife.1.013001
apa: Boocock, D. R., Hirashima, T., & Hannezo, E. B. (2023). Interplay between
mechanochemical patterning and glassy dynamics in cellular monolayers. PRX
Life. American Physical Society. https://doi.org/10.1103/prxlife.1.013001
chicago: Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay
between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.”
PRX Life. American Physical Society, 2023. https://doi.org/10.1103/prxlife.1.013001.
ieee: D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical
patterning and glassy dynamics in cellular monolayers,” PRX Life, vol.
1, no. 1. American Physical Society, 2023.
ista: Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical
patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001.
mla: Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and
Glassy Dynamics in Cellular Monolayers.” PRX Life, vol. 1, no. 1, 013001,
American Physical Society, 2023, doi:10.1103/prxlife.1.013001.
short: D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).
date_created: 2023-09-06T08:30:59Z
date_published: 2023-07-20T00:00:00Z
date_updated: 2023-09-15T06:39:17Z
day: '20'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1103/prxlife.1.013001
ec_funded: 1
file:
- access_level: open_access
checksum: f881d98c89eb9f1aa136d7b781511553
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T06:30:50Z
date_updated: 2023-09-15T06:30:50Z
file_id: '14335'
file_name: 2023_PRXLife_Boocock.pdf
file_size: 2559520
relation: main_file
success: 1
file_date_updated: 2023-09-15T06:30:50Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: PRX Life
publication_identifier:
issn:
- 2835-8279
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Interplay between mechanochemical patterning and glassy dynamics in cellular
monolayers
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2023'
...
---
_id: '14279'
abstract:
- lang: eng
text: "The zip file includes source data used in the manuscript \"CCR7 acts as both
a sensor and a sink for CCL19 to coordinate collective leukocyte migration\",
as well as a representative Jupyter notebook to reproduce the main figures. Please
see the preprint on bioRxiv and the DOI link there to access the final published
version. Note the title change between the preprint and the published manuscript.\r\nA
sample script for particle-based simulations of collective chemotaxis by self-generated
gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb)
to generate exemplary cell trajectories. A detailed description of the simulation
setup is provided in the supplementary information of the manuscipt."
article_processing_charge: No
author:
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
citation:
ama: Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink
for CCL19 to coordinate collective leukocyte migration.” 2023. doi:10.5281/ZENODO.8133960
apa: Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor
and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. https://doi.org/10.5281/ZENODO.8133960
chicago: Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor
and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023.
https://doi.org/10.5281/ZENODO.8133960.
ieee: M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and
a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023.
ista: Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor
and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, 10.5281/ZENODO.8133960.
mla: Ucar, Mehmet C. Source Data for the Manuscript “CCR7 Acts as Both a Sensor
and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Zenodo,
2023, doi:10.5281/ZENODO.8133960.
short: M.C. Ucar, (2023).
date_created: 2023-09-06T08:39:25Z
date_published: 2023-07-11T00:00:00Z
date_updated: 2023-10-03T11:42:58Z
day: '11'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.5281/ZENODO.8133960
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8133960
month: '07'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14274'
relation: used_in_publication
status: public
status: public
title: Source data for the manuscript "CCR7 acts as both a sensor and a sink for CCL19
to coordinate collective leukocyte migration"
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: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14280'
abstract:
- lang: eng
text: "Cell division in Escherichia coli is performed by the divisome, a multi-protein
complex composed of more than 30 proteins. The divisome spans from the cytoplasm
through the inner membrane to the cell wall and the outer membrane. Divisome assembly
is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes
at the center of the E. coli cell and determines the position of the future cell
septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue
FtsZ, which forms treadmilling filaments. These filaments are recruited to the
inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts
with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic
components of the divisome. \r\nA previous model postulated that FtsA regulates
maturation of the divisome by switching from an oligomeric, inactive state to
a monomeric and active state. This model was based mostly on in vivo studies,
as a biochemical characterization of FtsA has been hampered by difficulties in
purifying the protein. Here, we studied FtsA using an in vitro reconstitution
approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic,
treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space
and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that
the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact
directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments.
When we investigated the underlying mechanism by imaging single molecules of FtsNcyto,
we found the peptide to interact transiently with FtsA. An in depth analysis of
the single molecule trajectories helped to postulate a model where PG synthases
follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing
up on these findings we were interested in how the self-interaction of FtsA changes
when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer
switch. For this, we compared the behavior of the previously identified, hyperactive
mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and
transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly
however, we found that this was not due to a difference in the self-interaction
strength of the two variants, but a difference in their membrane residence time.
Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured
self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces
a rearrangement of the oligomeric architecture of FtsA. In further consequence
this change leads to more persistent FtsZ filaments which results in a defined
signalling zone, allowing formation of the mature divisome. The observed difference
between FtsA WT and R286W is due to the vastly different membrane turnover of
the proteins. R286W cycles 5-10x faster compared to WT which allows to sample
FtsZ filaments at faster frequencies. These findings can explain the observed
differences in toxicity for overexpression of FtsA WT and R286W and help to understand
how FtsA regulates divisome maturation."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
citation:
ama: Radler P. Spatiotemporal signaling during assembly of the bacterial divisome.
2023. doi:10.15479/at:ista:14280
apa: Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial
divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280
chicago: Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial
Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.
ieee: P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,”
Institute of Science and Technology Austria, 2023.
ista: Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial
divisome. Institute of Science and Technology Austria.
mla: Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial
Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280.
short: P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome,
Institute of Science and Technology Austria, 2023.
date_created: 2023-09-06T10:58:25Z
date_published: 2023-09-25T00:00:00Z
date_updated: 2024-02-21T12:35:18Z
day: '25'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaLo
doi: 10.15479/at:ista:14280
ec_funded: 1
file:
- access_level: closed
checksum: 87eef11fbc5c7df0826f12a3a629b444
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: pradler
date_created: 2023-10-04T10:11:53Z
date_updated: 2023-10-04T10:28:35Z
file_id: '14390'
file_name: PhD Thesis_Philipp Radler_20231004.docx
file_size: 114932847
relation: source_file
- access_level: closed
checksum: 3253e099b7126469d941fd9419d68b4f
content_type: application/pdf
creator: pradler
date_created: 2023-10-04T10:11:21Z
date_updated: 2023-10-04T10:28:35Z
embargo: 2024-10-04
embargo_to: open_access
file_id: '14391'
file_name: PhD Thesis_Philipp Radler_20231004.pdf
file_size: 37838778
relation: main_file
file_date_updated: 2023-10-04T10:28:35Z
has_accepted_license: '1'
keyword:
- Cell Division
- Reconstitution
- FtsZ
- FtsA
- Divisome
- E.coli
language:
- iso: eng
month: '09'
oa_version: Published Version
page: '156'
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: "Understanding bacterial cell division by in vitro\r\nreconstitution"
- _id: 2596EAB6-B435-11E9-9278-68D0E5697425
grant_number: ALTF 2015-1163
name: Synthesis of bacterial cell wall
- _id: 259B655A-B435-11E9-9278-68D0E5697425
grant_number: LT000824/2016
name: Reconstitution of bacterial cell wall sythesis
publication_identifier:
isbn:
- 978-3-99078-033-6
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11373'
relation: part_of_dissertation
status: public
- id: '7387'
relation: part_of_dissertation
status: public
- id: '10934'
relation: research_data
status: public
status: public
supervisor:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
title: Spatiotemporal signaling during assembly of the bacterial divisome
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: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14281'
abstract:
- lang: eng
text: In nature, proteins that switch between two conformations in response to environmental
stimuli structurally transduce biochemical information in a manner analogous to
how transistors control information flow in computing devices. Designing proteins
with two distinct but fully structured conformations is a challenge for protein
design as it requires sculpting an energy landscape with two distinct minima.
Here we describe the design of “hinge” proteins that populate one designed state
in the absence of ligand and a second designed state in the presence of ligand.
X-ray crystallography, electron microscopy, double electron-electron resonance
spectroscopy, and binding measurements demonstrate that despite the significant
structural differences the two states are designed with atomic level accuracy
and that the conformational and binding equilibria are closely coupled.
article_processing_charge: No
article_type: original
author:
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Philip J. Y.
full_name: Leung, Philip J. Y.
last_name: Leung
- first_name: Maxx H.
full_name: Tessmer, Maxx H.
last_name: Tessmer
- first_name: Adam
full_name: Broerman, Adam
last_name: Broerman
- first_name: Cullen
full_name: Demakis, Cullen
last_name: Demakis
- first_name: Acacia F.
full_name: Dishman, Acacia F.
last_name: Dishman
- first_name: Arvind
full_name: Pillai, Arvind
last_name: Pillai
- first_name: Abbas
full_name: Idris, Abbas
last_name: Idris
- first_name: David
full_name: Juergens, David
last_name: Juergens
- first_name: Justas
full_name: Dauparas, Justas
last_name: Dauparas
- first_name: Xinting
full_name: Li, Xinting
last_name: Li
- first_name: Paul M.
full_name: Levine, Paul M.
last_name: Levine
- first_name: Mila
full_name: Lamb, Mila
last_name: Lamb
- first_name: Ryanne K.
full_name: Ballard, Ryanne K.
last_name: Ballard
- first_name: Stacey R.
full_name: Gerben, Stacey R.
last_name: Gerben
- first_name: Hannah
full_name: Nguyen, Hannah
last_name: Nguyen
- first_name: Alex
full_name: Kang, Alex
last_name: Kang
- first_name: Banumathi
full_name: Sankaran, Banumathi
last_name: Sankaran
- first_name: Asim K.
full_name: Bera, Asim K.
last_name: Bera
- first_name: Brian F.
full_name: Volkman, Brian F.
last_name: Volkman
- first_name: Jeff
full_name: Nivala, Jeff
last_name: Nivala
- first_name: Stefan
full_name: Stoll, Stefan
last_name: Stoll
- first_name: David
full_name: Baker, David
last_name: Baker
citation:
ama: Praetorius FM, Leung PJY, Tessmer MH, et al. Design of stimulus-responsive
two-state hinge proteins. Science. 2023;381(6659):754-760. doi:10.1126/science.adg7731
apa: Praetorius, F. M., Leung, P. J. Y., Tessmer, M. H., Broerman, A., Demakis,
C., Dishman, A. F., … Baker, D. (2023). Design of stimulus-responsive two-state
hinge proteins. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.adg7731
chicago: Praetorius, Florian M, Philip J. Y. Leung, Maxx H. Tessmer, Adam Broerman,
Cullen Demakis, Acacia F. Dishman, Arvind Pillai, et al. “Design of Stimulus-Responsive
Two-State Hinge Proteins.” Science. American Association for the Advancement
of Science, 2023. https://doi.org/10.1126/science.adg7731.
ieee: F. M. Praetorius et al., “Design of stimulus-responsive two-state hinge
proteins,” Science, vol. 381, no. 6659. American Association for the Advancement
of Science, pp. 754–760, 2023.
ista: Praetorius FM, Leung PJY, Tessmer MH, Broerman A, Demakis C, Dishman AF, Pillai
A, Idris A, Juergens D, Dauparas J, Li X, Levine PM, Lamb M, Ballard RK, Gerben
SR, Nguyen H, Kang A, Sankaran B, Bera AK, Volkman BF, Nivala J, Stoll S, Baker
D. 2023. Design of stimulus-responsive two-state hinge proteins. Science. 381(6659),
754–760.
mla: Praetorius, Florian M., et al. “Design of Stimulus-Responsive Two-State Hinge
Proteins.” Science, vol. 381, no. 6659, American Association for the Advancement
of Science, 2023, pp. 754–60, doi:10.1126/science.adg7731.
short: F.M. Praetorius, P.J.Y. Leung, M.H. Tessmer, A. Broerman, C. Demakis, A.F.
Dishman, A. Pillai, A. Idris, D. Juergens, J. Dauparas, X. Li, P.M. Levine, M.
Lamb, R.K. Ballard, S.R. Gerben, H. Nguyen, A. Kang, B. Sankaran, A.K. Bera, B.F.
Volkman, J. Nivala, S. Stoll, D. Baker, Science 381 (2023) 754–760.
date_created: 2023-09-06T12:04:23Z
date_published: 2023-08-17T00:00:00Z
date_updated: 2023-11-07T12:42:09Z
day: '17'
doi: 10.1126/science.adg7731
extern: '1'
external_id:
pmid:
- '37590357'
intvolume: ' 381'
issue: '6659'
language:
- iso: eng
month: '08'
oa_version: None
page: 754-760
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Design of stimulus-responsive two-state hinge proteins
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 381
year: '2023'
...
---
_id: '14294'
abstract:
- lang: eng
text: Growth factors and cytokines signal by binding to the extracellular domains
of their receptors and drive association and transphosphorylation of the receptor
intracellular tyrosine kinase domains, initiating downstream signaling cascades.
To enable systematic exploration of how receptor valency and geometry affects
signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using
repeat protein building blocks that can be modularly extended. By incorporating
a de novo designed fibroblast growth-factor receptor (FGFR) binding module into
these scaffolds, we generated a series of synthetic signaling ligands that exhibit
potent valency- and geometry-dependent Ca2+ release and MAPK pathway activation.
The high specificity of the designed agonists reveal distinct roles for two FGFR
splice variants in driving endothelial and mesenchymal cell fates during early
vascular development. The ability to incorporate receptor binding domains and
repeat extensions in a modular fashion makes our designed scaffolds broadly useful
for probing and manipulating cellular signaling pathways.
article_processing_charge: No
author:
- first_name: Natasha I
full_name: Edman, Natasha I
last_name: Edman
- first_name: Rachel L
full_name: Redler, Rachel L
last_name: Redler
- first_name: Ashish
full_name: Phal, Ashish
last_name: Phal
- first_name: Thomas
full_name: Schlichthaerle, Thomas
last_name: Schlichthaerle
- first_name: Sanjay R
full_name: Srivatsan, Sanjay R
last_name: Srivatsan
- first_name: Ali
full_name: Etemadi, Ali
last_name: Etemadi
- first_name: Seong
full_name: An, Seong
last_name: An
- first_name: Andrew
full_name: Favor, Andrew
last_name: Favor
- first_name: Devon
full_name: Ehnes, Devon
last_name: Ehnes
- first_name: Zhe
full_name: Li, Zhe
last_name: Li
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Max
full_name: Gordon, Max
last_name: Gordon
- first_name: Wei
full_name: Yang, Wei
last_name: Yang
- first_name: Brian
full_name: Coventry, Brian
last_name: Coventry
- first_name: Derrick R
full_name: Hicks, Derrick R
last_name: Hicks
- first_name: Longxing
full_name: Cao, Longxing
last_name: Cao
- first_name: Neville
full_name: Bethel, Neville
last_name: Bethel
- first_name: Piper
full_name: Heine, Piper
last_name: Heine
- first_name: Analisa N
full_name: Murray, Analisa N
last_name: Murray
- first_name: Stacey
full_name: Gerben, Stacey
last_name: Gerben
- first_name: Lauren
full_name: Carter, Lauren
last_name: Carter
- first_name: Marcos
full_name: Miranda, Marcos
last_name: Miranda
- first_name: Babak
full_name: Negahdari, Babak
last_name: Negahdari
- first_name: Sangwon
full_name: Lee, Sangwon
last_name: Lee
- first_name: Cole
full_name: Trapnell, Cole
last_name: Trapnell
- first_name: Lance
full_name: Stewart, Lance
last_name: Stewart
- first_name: Damian C
full_name: Ekiert, Damian C
last_name: Ekiert
- first_name: Joseph
full_name: Schlessinger, Joseph
last_name: Schlessinger
- first_name: Jay
full_name: Shendure, Jay
last_name: Shendure
- first_name: Gira
full_name: Bhabha, Gira
last_name: Bhabha
- first_name: Hannele
full_name: Ruohola-Baker, Hannele
last_name: Ruohola-Baker
- first_name: David
full_name: Baker, David
last_name: Baker
citation:
ama: Edman NI, Redler RL, Phal A, et al. Modulation of FGF pathway signaling and
vascular differentiation using designed oligomeric assemblies. bioRxiv.
doi:10.1101/2023.03.14.532666
apa: Edman, N. I., Redler, R. L., Phal, A., Schlichthaerle, T., Srivatsan, S. R.,
Etemadi, A., … Baker, D. (n.d.). Modulation of FGF pathway signaling and vascular
differentiation using designed oligomeric assemblies. bioRxiv. https://doi.org/10.1101/2023.03.14.532666
chicago: Edman, Natasha I, Rachel L Redler, Ashish Phal, Thomas Schlichthaerle,
Sanjay R Srivatsan, Ali Etemadi, Seong An, et al. “Modulation of FGF Pathway Signaling
and Vascular Differentiation Using Designed Oligomeric Assemblies.” BioRxiv,
n.d. https://doi.org/10.1101/2023.03.14.532666.
ieee: N. I. Edman et al., “Modulation of FGF pathway signaling and vascular
differentiation using designed oligomeric assemblies,” bioRxiv. .
ista: Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An
S, Favor A, Ehnes D, Li Z, Praetorius FM, Gordon M, Yang W, Coventry B, Hicks
DR, Cao L, Bethel N, Heine P, Murray AN, Gerben S, Carter L, Miranda M, Negahdari
B, Lee S, Trapnell C, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha
G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular
differentiation using designed oligomeric assemblies. bioRxiv, 10.1101/2023.03.14.532666.
mla: Edman, Natasha I., et al. “Modulation of FGF Pathway Signaling and Vascular
Differentiation Using Designed Oligomeric Assemblies.” BioRxiv, doi:10.1101/2023.03.14.532666.
short: N.I. Edman, R.L. Redler, A. Phal, T. Schlichthaerle, S.R. Srivatsan, A. Etemadi,
S. An, A. Favor, D. Ehnes, Z. Li, F.M. Praetorius, M. Gordon, W. Yang, B. Coventry,
D.R. Hicks, L. Cao, N. Bethel, P. Heine, A.N. Murray, S. Gerben, L. Carter, M.
Miranda, B. Negahdari, S. Lee, C. Trapnell, L. Stewart, D.C. Ekiert, J. Schlessinger,
J. Shendure, G. Bhabha, H. Ruohola-Baker, D. Baker, BioRxiv (n.d.).
date_created: 2023-09-06T12:31:49Z
date_published: 2023-03-15T00:00:00Z
date_updated: 2023-11-07T12:21:58Z
day: '15'
doi: 10.1101/2023.03.14.532666
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.03.14.532666
month: '03'
oa: 1
oa_version: Preprint
publication: bioRxiv
publication_status: submitted
status: public
title: Modulation of FGF pathway signaling and vascular differentiation using designed
oligomeric assemblies
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14313'
abstract:
- lang: eng
text: To respond to auxin, the chief orchestrator of their multicellularity, plants
evolved multiple receptor systems and signal transduction cascades. Despite decades
of research, however, we are still lacking a satisfactory synthesis of various
auxin signaling mechanisms. The chief discrepancy and historical controversy of
the field is that of rapid and slow auxin effects on plant physiology and development.
How is it possible that ions begin to trickle across the plasma membrane as soon
as auxin enters the cell, even though the best-characterized transcriptional auxin
pathway can take effect only after tens of minutes? Recently, unexpected progress
has been made in understanding this and other unknowns of auxin signaling. We
provide a perspective on these exciting developments and concepts whose general
applicability might have ramifications beyond auxin signaling.
acknowledgement: The opening quote is not intended to reflect any political views
of the authors. The authors by no means endorse the rhetoric of Donald Rumsfeld
or the 2003 invasion of Iraq by the United States. Nevertheless, Rumsfeld's quote
led to both public and academic debates on the concept of known and unknown unknowns,
which can be applied to the recent unexpected developments in the auxin signaling
field. We thank Linlin Qi and Huihuang Chen for their suggestions on figure presentation
and inspiring discussions of TIR1/AFB signaling. Finally, we thank Aroosa Hussain
for discussion of Greek mythology.
article_number: '102443'
article_processing_charge: No
article_type: review
author:
- first_name: Lukas
full_name: Fiedler, Lukas
id: 7c417475-8972-11ed-ae7b-8b674ca26986
last_name: Fiedler
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Fiedler L, Friml J. Rapid auxin signaling: Unknowns old and new. Current
Opinion in Plant Biology. 2023;75(10). doi:10.1016/j.pbi.2023.102443'
apa: 'Fiedler, L., & Friml, J. (2023). Rapid auxin signaling: Unknowns old and
new. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2023.102443'
chicago: 'Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and
New.” Current Opinion in Plant Biology. Elsevier, 2023. https://doi.org/10.1016/j.pbi.2023.102443.'
ieee: 'L. Fiedler and J. Friml, “Rapid auxin signaling: Unknowns old and new,” Current
Opinion in Plant Biology, vol. 75, no. 10. Elsevier, 2023.'
ista: 'Fiedler L, Friml J. 2023. Rapid auxin signaling: Unknowns old and new. Current
Opinion in Plant Biology. 75(10), 102443.'
mla: 'Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.”
Current Opinion in Plant Biology, vol. 75, no. 10, 102443, Elsevier, 2023,
doi:10.1016/j.pbi.2023.102443.'
short: L. Fiedler, J. Friml, Current Opinion in Plant Biology 75 (2023).
date_created: 2023-09-10T22:01:11Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-11-07T08:17:13Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.pbi.2023.102443
external_id:
pmid:
- '37666097'
file:
- access_level: open_access
checksum: 1c476c3414d2dfb0c85db0cb6cfd8a28
content_type: application/pdf
creator: amally
date_created: 2023-11-02T17:03:20Z
date_updated: 2023-11-02T17:03:20Z
file_id: '14482'
file_name: Fiedler CurrOpinOlantBiol 2023_revised.pdf
file_size: 737872
relation: main_file
success: 1
file_date_updated: 2023-11-02T17:03:20Z
has_accepted_license: '1'
intvolume: ' 75'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Current Opinion in Plant Biology
publication_identifier:
issn:
- 1369-5266
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Rapid auxin signaling: Unknowns old and new'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 75
year: '2023'
...
---
_id: '14314'
abstract:
- lang: eng
text: The execution of cognitive functions requires coordinated circuit activity
across different brain areas that involves the associated firing of neuronal assemblies.
Here, we tested the circuit mechanism behind assembly interactions between the
hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording
neuronal populations during a rule-switching task. We identified functionally
coupled CA1-mPFC cells that synchronized their activity beyond that expected from
common spatial coding or oscillatory firing. When such cell pairs fired together,
the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent
theta firing phases, independent of the theta timing of their CA1 counterpart.
These functionally connected CA1-mPFC cells formed interconnected assemblies.
While firing together with their CA1 assembly partners, mPFC cells fired along
specific theta sequences. Our results suggest that upregulated theta oscillatory
firing of mPFC cells can signal transient interactions with specific CA1 assemblies,
thus enabling distributed computations.
acknowledgement: We thank A. Cumpelik, H. Chiossi, and L. Bollman for comments on
an earlier version of this manuscript. This work was funded by EU-FP7 MC-ITN IN-SENS
(grant 607616).
article_number: '113015'
article_processing_charge: Yes
article_type: original
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Karola
full_name: Käfer, Karola
id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87
last_name: Käfer
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Nardin M, Käfer K, Stella F, Csicsvari JL. Theta oscillations as a substrate
for medial prefrontal-hippocampal assembly interactions. Cell Reports.
2023;42(9). doi:10.1016/j.celrep.2023.113015
apa: Nardin, M., Käfer, K., Stella, F., & Csicsvari, J. L. (2023). Theta oscillations
as a substrate for medial prefrontal-hippocampal assembly interactions. Cell
Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.113015
chicago: Nardin, Michele, Karola Käfer, Federico Stella, and Jozsef L Csicsvari.
“Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly
Interactions.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.113015.
ieee: M. Nardin, K. Käfer, F. Stella, and J. L. Csicsvari, “Theta oscillations as
a substrate for medial prefrontal-hippocampal assembly interactions,” Cell
Reports, vol. 42, no. 9. Elsevier, 2023.
ista: Nardin M, Käfer K, Stella F, Csicsvari JL. 2023. Theta oscillations as a substrate
for medial prefrontal-hippocampal assembly interactions. Cell Reports. 42(9),
113015.
mla: Nardin, Michele, et al. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal
Assembly Interactions.” Cell Reports, vol. 42, no. 9, 113015, Elsevier,
2023, doi:10.1016/j.celrep.2023.113015.
short: M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023).
date_created: 2023-09-10T22:01:11Z
date_published: 2023-09-26T00:00:00Z
date_updated: 2023-09-15T07:14:12Z
day: '26'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1016/j.celrep.2023.113015
ec_funded: 1
external_id:
pmid:
- '37632747'
file:
- access_level: open_access
checksum: ca77a304fb813c292550b8604b0fb41d
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T07:12:46Z
date_updated: 2023-09-15T07:12:46Z
file_id: '14337'
file_name: 2023_CellPress_Nardin.pdf
file_size: 4879455
relation: main_file
success: 1
file_date_updated: 2023-09-15T07:12:46Z
has_accepted_license: '1'
intvolume: ' 42'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 257BBB4C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '607616'
name: Inter-and intracellular signalling in schizophrenia
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Theta oscillations as a substrate for medial prefrontal-hippocampal assembly
interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '14315'
abstract:
- lang: eng
text: During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly
demolish the nuclear pore complex. However, for poorly understood reasons, caspases
are also activated during cell differentiation. Here, we show that sublethal activation
of caspases during myogenesis results in the transient proteolysis of four peripheral
Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective,
and we identified in an unbiased manner several classes of cytoplasmic, plasma
membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC
trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic
reticulum stress. Our results suggest that caspases can reversibly modulate nuclear
transport activity, which allows them to function as agents of cell differentiation
and adaptation at sublethal levels.
acknowledgement: 'We thank the members of the Hetzer laboratory, Tony Hunter (Salk),
Lorenzo Puri (Sanford Burnham Prebys), and Jongmin Kim (Massachusetts General Hospital)
for the critical reading of the manuscript; Kenneth Diffenderfer and Aimee Pankonin
(Stem Cell Core at the Salk Institute) for help with neurogenesis; Carol Marchetto
and Fred Gage (Salk) for providing H9 embryonic stem cells; Lorenzo Puri, Alexandra
Sacco, and Luca Caputo (Sanford Burnham Prebys) for helpful discussions and sharing
mouse primary myoblasts. This work was supported by a Glenn Foundation for Medical
Research Postdoctoral Fellowship in Aging Research (UHC), the NOMIS foundation (MWH),
and the National Institutes of Health (R01 NS096786 to MWH and K01 AR080828 to UHC).
This work was also supported by the Mass Spectrometry Core of the Salk Institute
with funding from NIH-NCI CCSG: P30 014195 and the Helmsley Center for Genomic Medicine.
We thank Jolene Diedrich and Antonio Pinto for technical support.'
article_number: RP89066
article_processing_charge: Yes
article_type: original
author:
- first_name: Ukrae H.
full_name: Cho, Ukrae H.
last_name: Cho
- first_name: Martin W
full_name: Hetzer, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: Hetzer
orcid: 0000-0002-2111-992X
citation:
ama: Cho UH, Hetzer M. Caspase-mediated nuclear pore complex trimming in cell differentiation
and endoplasmic reticulum stress. eLife. 2023;12. doi:10.7554/eLife.89066
apa: Cho, U. H., & Hetzer, M. (2023). Caspase-mediated nuclear pore complex
trimming in cell differentiation and endoplasmic reticulum stress. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.89066
chicago: Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex
Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife.
eLife Sciences Publications, 2023. https://doi.org/10.7554/eLife.89066.
ieee: U. H. Cho and M. Hetzer, “Caspase-mediated nuclear pore complex trimming in
cell differentiation and endoplasmic reticulum stress,” eLife, vol. 12.
eLife Sciences Publications, 2023.
ista: Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in
cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066.
mla: Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming
in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife, vol.
12, RP89066, eLife Sciences Publications, 2023, doi:10.7554/eLife.89066.
short: U.H. Cho, M. Hetzer, ELife 12 (2023).
date_created: 2023-09-10T22:01:11Z
date_published: 2023-09-04T00:00:00Z
date_updated: 2023-09-15T07:07:10Z
day: '04'
ddc:
- '570'
department:
- _id: MaHe
doi: 10.7554/eLife.89066
external_id:
pmid:
- '37665327'
file:
- access_level: open_access
checksum: db24bf3d595507387b48d3799c33e289
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T06:59:10Z
date_updated: 2023-09-15T06:59:10Z
file_id: '14336'
file_name: 2023_eLife_Cho.pdf
file_size: 3703097
relation: main_file
success: 1
file_date_updated: 2023-09-15T06:59:10Z
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Caspase-mediated nuclear pore complex trimming in cell differentiation and
endoplasmic reticulum stress
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2023'
...
---
_id: '14316'
abstract:
- lang: eng
text: Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport.
In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted
to generate distinct transport vesicles at the trans-Golgi network (TGN), and
the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories
for these adaptors. Recently, we showed that vesicle transport from the TGN is
crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p
are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However,
these observations were incompatible with previous studies showing that these
adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall
mechanism responsible for regulation of Vps21p activity remains ambiguous. Here,
we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated
Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired
transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to
the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA
adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and
Ypt32p were found to have partially overlapping functions for recruitment of AP-1
and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors
for Vps21p activation in the TGN–endosome trafficking pathway.
article_number: jcs261448
article_processing_charge: No
article_type: original
author:
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Kaito
full_name: Aoshima, Kaito
last_name: Aoshima
- first_name: Hiroki
full_name: Shimamura, Hiroki
last_name: Shimamura
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Junko Y.
full_name: Toshima, Junko Y.
last_name: Toshima
- first_name: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. Distinct
role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome
trafficking pathway. Journal of Cell Science. 2023;136(17). doi:10.1242/jcs.261448
apa: Nagano, M., Aoshima, K., Shimamura, H., Siekhaus, D. E., Toshima, J. Y., &
Toshima, J. (2023). Distinct role of TGN-resident clathrin adaptors for Vps21p
activation in the TGN-endosome trafficking pathway. Journal of Cell Science.
The Company of Biologists. https://doi.org/10.1242/jcs.261448
chicago: Nagano, Makoto, Kaito Aoshima, Hiroki Shimamura, Daria E Siekhaus, Junko
Y. Toshima, and Jiro Toshima. “Distinct Role of TGN-Resident Clathrin Adaptors
for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of
Cell Science. The Company of Biologists, 2023. https://doi.org/10.1242/jcs.261448.
ieee: M. Nagano, K. Aoshima, H. Shimamura, D. E. Siekhaus, J. Y. Toshima, and J.
Toshima, “Distinct role of TGN-resident clathrin adaptors for Vps21p activation
in the TGN-endosome trafficking pathway,” Journal of Cell Science, vol.
136, no. 17. The Company of Biologists, 2023.
ista: Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. 2023.
Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome
trafficking pathway. Journal of Cell Science. 136(17), jcs261448.
mla: Nagano, Makoto, et al. “Distinct Role of TGN-Resident Clathrin Adaptors for
Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of Cell
Science, vol. 136, no. 17, jcs261448, The Company of Biologists, 2023, doi:10.1242/jcs.261448.
short: M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima,
Journal of Cell Science 136 (2023).
date_created: 2023-09-10T22:01:12Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-09-20T09:14:15Z
day: '01'
department:
- _id: DaSi
doi: 10.1242/jcs.261448
external_id:
pmid:
- '37539494'
intvolume: ' 136'
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.03.27.534325
month: '09'
oa: 1
oa_version: Preprint
pmid: 1
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the
TGN-endosome trafficking pathway
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2023'
...
---
_id: '14317'
abstract:
- lang: eng
text: "Markov decision processes can be viewed as transformers of probability distributions.
While this view is useful from a practical standpoint to reason about trajectories
of distributions, basic reachability and safety problems are known to be computationally
intractable (i.e., Skolem-hard) to solve in such models. Further, we show that
even for simple examples of MDPs, strategies for safety objectives over distributions
can require infinite memory and randomization.\r\nIn light of this, we present
a novel overapproximation approach to synthesize strategies in an MDP, such that
a safety objective over the distributions is met. More precisely, we develop a
new framework for template-based synthesis of certificates as affine distributional
and inductive invariants for safety objectives in MDPs. We provide two algorithms
within this framework. One can only synthesize memoryless strategies, but has
relative completeness guarantees, while the other can synthesize general strategies.
The runtime complexity of both algorithms is in PSPACE. We implement these algorithms
and show that they can solve several non-trivial examples."
acknowledgement: This work was supported in part by the ERC CoG 863818 (FoRM-SMArt)
and the European Union’s Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 665385 as well as DST/CEFIPRA/INRIA project
EQuaVE and SERB Matrices grant MTR/2018/00074.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: S.
full_name: Akshay, S.
last_name: Akshay
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers:
Affine invariant synthesis for safety objectives. In: International Conference
on Computer Aided Verification. Vol 13966. Springer Nature; 2023:86-112. doi:10.1007/978-3-031-37709-9_5'
apa: 'Akshay, S., Chatterjee, K., Meggendorfer, T., & Zikelic, D. (2023). MDPs
as distribution transformers: Affine invariant synthesis for safety objectives.
In International Conference on Computer Aided Verification (Vol. 13966,
pp. 86–112). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_5'
chicago: 'Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic.
“MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.”
In International Conference on Computer Aided Verification, 13966:86–112.
Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_5.'
ieee: 'S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution
transformers: Affine invariant synthesis for safety objectives,” in International
Conference on Computer Aided Verification, Paris, France, 2023, vol. 13966,
pp. 86–112.'
ista: 'Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution
transformers: Affine invariant synthesis for safety objectives. International
Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS,
vol. 13966, 86–112.'
mla: 'Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis
for Safety Objectives.” International Conference on Computer Aided Verification,
vol. 13966, Springer Nature, 2023, pp. 86–112, doi:10.1007/978-3-031-37709-9_5.'
short: S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International
Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-10T22:01:12Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2025-07-14T09:09:56Z
day: '17'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-031-37709-9_5
ec_funded: 1
file:
- access_level: open_access
checksum: f143c8eedf609f20f2aad2eeb496d53f
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T08:46:43Z
date_updated: 2023-09-20T08:46:43Z
file_id: '14349'
file_name: 2023_LNCS_Akshay.pdf
file_size: 531745
relation: main_file
success: 1
file_date_updated: 2023-09-20T08:46:43Z
has_accepted_license: '1'
intvolume: ' 13966'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 86-112
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: International Conference on Computer Aided Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377082'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'MDPs as distribution transformers: Affine invariant synthesis for safety objectives'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13966
year: '2023'
...
---
_id: '14318'
abstract:
- lang: eng
text: "Probabilistic recurrence relations (PRRs) are a standard formalism for describing
the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider
the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime
T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims
at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem,
the classical and most well-known approach is the cookbook method by Karp (JACM
1994), while other approaches are mostly limited to deriving tail bounds of specific
PRRs via involved custom analysis.\r\nIn this work, we propose a novel approach
for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing
time and random passed sizes observe discrete or (piecewise) uniform distribution
and whose recursive call is either a single procedure call or a divide-and-conquer.
We first establish a theoretical approach via Markov’s inequality, and then instantiate
the theoretical approach with a template-based algorithmic approach via a refined
treatment of exponentiation. Experimental evaluation shows that our algorithmic
approach is capable of deriving tail bounds that are (i) asymptotically tighter
than Karp’s method, (ii) match the best-known manually-derived asymptotic tail
bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor)
than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover,
our algorithmic approach handles all examples (including realistic PRRs such as
QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing
that our approach is efficient in practice."
acknowledgement: We thank Prof. Bican Xia for valuable information on the exponential
theory of reals. The work is partially supported by the National Natural Science
Foundation of China (NSFC) with Grant No. 62172271, ERC CoG 863818 (ForM-SMArt),
the Hong Kong Research Grants Council ECS Project Number 26208122, the HKUST-Kaisa
Joint Research Institute Project Grant HKJRI3A-055 and the HKUST Startup Grant R9272.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Yican
full_name: Sun, Yican
last_name: Sun
- first_name: Hongfei
full_name: Fu, Hongfei
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: 'Sun Y, Fu H, Chatterjee K, Goharshady AK. Automated tail bound analysis for probabilistic
recurrence relations. In: Computer Aided Verification. Vol 13966. Springer
Nature; 2023:16-39. doi:10.1007/978-3-031-37709-9_2'
apa: 'Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2023). Automated
tail bound analysis for probabilistic recurrence relations. In Computer Aided
Verification (Vol. 13966, pp. 16–39). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_2'
chicago: Sun, Yican, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady.
“Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” In Computer
Aided Verification, 13966:16–39. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_2.
ieee: Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Automated tail bound
analysis for probabilistic recurrence relations,” in Computer Aided Verification,
Paris, France, 2023, vol. 13966, pp. 16–39.
ista: 'Sun Y, Fu H, Chatterjee K, Goharshady AK. 2023. Automated tail bound analysis
for probabilistic recurrence relations. Computer Aided Verification. CAV: Computer
Aided Verification, LNCS, vol. 13966, 16–39.'
mla: Sun, Yican, et al. “Automated Tail Bound Analysis for Probabilistic Recurrence
Relations.” Computer Aided Verification, vol. 13966, Springer Nature, 2023,
pp. 16–39, doi:10.1007/978-3-031-37709-9_2.
short: Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification,
Springer Nature, 2023, pp. 16–39.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-10T22:01:12Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2025-07-14T09:09:57Z
day: '17'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-031-37709-9_2
ec_funded: 1
file:
- access_level: open_access
checksum: 42917e086f8c7699f3bccf84f74fe000
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T08:24:47Z
date_updated: 2023-09-20T08:24:47Z
file_id: '14348'
file_name: 2023_LNCS_Sun.pdf
file_size: 624647
relation: main_file
success: 1
file_date_updated: 2023-09-20T08:24:47Z
has_accepted_license: '1'
intvolume: ' 13966'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 16-39
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Computer Aided Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377082'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/boyvolcano/PRR
scopus_import: '1'
status: public
title: Automated tail bound analysis for probabilistic recurrence relations
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13966
year: '2023'
...
---
_id: '14319'
abstract:
- lang: eng
text: "We study multigraphs whose edge-sets are the union of three perfect matchings,
M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6
n - 2, we show there exists a matching M of G with jM \\ Mij = ai for each i 2
f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture
however that if G is bipartite, the same result holds with n - 2 replaced by n
- 1. We give a construction that shows such a result would be tight. We\r\nalso
make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour\r\nmultiplicities."
acknowledgement: Anastos has received funding from the European Union’s Horizon 2020
research and in-novation programme under the Marie Sk lodowska-Curie grant agreement
No 101034413.Fabian’s research is supported by the Deutsche Forschungsgemeinschaft
(DFG, GermanResearch Foundation) Graduiertenkolleg “Facets of Complexity” (GRK 2434).
article_number: P3.10
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
- first_name: David
full_name: Fabian, David
last_name: Fabian
- first_name: Alp
full_name: Müyesser, Alp
last_name: Müyesser
- first_name: Tibor
full_name: Szabó, Tibor
last_name: Szabó
citation:
ama: Anastos M, Fabian D, Müyesser A, Szabó T. Splitting matchings and the Ryser-Brualdi-Stein
conjecture for multisets. Electronic Journal of Combinatorics. 2023;30(3).
doi:10.37236/11714
apa: Anastos, M., Fabian, D., Müyesser, A., & Szabó, T. (2023). Splitting matchings
and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of
Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/11714
chicago: Anastos, Michael, David Fabian, Alp Müyesser, and Tibor Szabó. “Splitting
Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” Electronic
Journal of Combinatorics. Electronic Journal of Combinatorics, 2023. https://doi.org/10.37236/11714.
ieee: M. Anastos, D. Fabian, A. Müyesser, and T. Szabó, “Splitting matchings and
the Ryser-Brualdi-Stein conjecture for multisets,” Electronic Journal of Combinatorics,
vol. 30, no. 3. Electronic Journal of Combinatorics, 2023.
ista: Anastos M, Fabian D, Müyesser A, Szabó T. 2023. Splitting matchings and the
Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics.
30(3), P3.10.
mla: Anastos, Michael, et al. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture
for Multisets.” Electronic Journal of Combinatorics, vol. 30, no. 3, P3.10,
Electronic Journal of Combinatorics, 2023, doi:10.37236/11714.
short: M. Anastos, D. Fabian, A. Müyesser, T. Szabó, Electronic Journal of Combinatorics
30 (2023).
date_created: 2023-09-10T22:01:12Z
date_published: 2023-07-28T00:00:00Z
date_updated: 2023-09-15T08:12:30Z
day: '28'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.37236/11714
ec_funded: 1
external_id:
arxiv:
- '2212.03100'
file:
- access_level: open_access
checksum: 52c46c8cb329f9aaee9ade01525f317b
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T08:02:09Z
date_updated: 2023-09-15T08:02:09Z
file_id: '14338'
file_name: 2023_elecJournCombinatorics_Anastos.pdf
file_size: 247917
relation: main_file
success: 1
file_date_updated: 2023-09-15T08:02:09Z
has_accepted_license: '1'
intvolume: ' 30'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Electronic Journal of Combinatorics
publication_identifier:
eissn:
- 1077-8926
publication_status: published
publisher: Electronic Journal of Combinatorics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2023'
...
---
_id: '14320'
abstract:
- lang: eng
text: The development of two-dimensional materials has resulted in a diverse range
of novel, high-quality compounds with increasing complexity. A key requirement
for a comprehensive quantitative theory is the accurate determination of these
materials' band structure parameters. However, this task is challenging due to
the intricate band structures and the indirect nature of experimental probes.
In this work, we introduce a general framework to derive band structure parameters
from experimental data using deep neural networks. We applied our method to the
penetration field capacitance measurement of trilayer graphene, an effective probe
of its density of states. First, we demonstrate that a trained deep network gives
accurate predictions for the penetration field capacitance as a function of tight-binding
parameters. Next, we use the fast and accurate predictions from the trained network
to automatically determine tight-binding parameters directly from experimental
data, with extracted parameters being in a good agreement with values in the literature.
We conclude by discussing potential applications of our method to other materials
and experimental techniques beyond penetration field capacitance.
acknowledgement: A.F.Y. acknowledges primary support from the Department of Energy
under award DE-SC0020043, and additional support from the Gordon and Betty Moore
Foundation under award GBMF9471 for group operations.
article_number: '125411'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Paul M
full_name: Henderson, Paul M
id: 13C09E74-18D9-11E9-8878-32CFE5697425
last_name: Henderson
orcid: 0000-0002-5198-7445
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Alexander A.
full_name: Zibrov, Alexander A.
last_name: Zibrov
- first_name: Andrea F.
full_name: Young, Andrea F.
last_name: Young
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: 'Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. Deep learning extraction
of band structure parameters from density of states: A case study on trilayer
graphene. Physical Review B. 2023;108(12). doi:10.1103/physrevb.108.125411'
apa: 'Henderson, P. M., Ghazaryan, A., Zibrov, A. A., Young, A. F., & Serbyn,
M. (2023). Deep learning extraction of band structure parameters from density
of states: A case study on trilayer graphene. Physical Review B. American
Physical Society. https://doi.org/10.1103/physrevb.108.125411'
chicago: 'Henderson, Paul M, Areg Ghazaryan, Alexander A. Zibrov, Andrea F. Young,
and Maksym Serbyn. “Deep Learning Extraction of Band Structure Parameters from
Density of States: A Case Study on Trilayer Graphene.” Physical Review B.
American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.125411.'
ieee: 'P. M. Henderson, A. Ghazaryan, A. A. Zibrov, A. F. Young, and M. Serbyn,
“Deep learning extraction of band structure parameters from density of states:
A case study on trilayer graphene,” Physical Review B, vol. 108, no. 12.
American Physical Society, 2023.'
ista: 'Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. 2023. Deep learning
extraction of band structure parameters from density of states: A case study on
trilayer graphene. Physical Review B. 108(12), 125411.'
mla: 'Henderson, Paul M., et al. “Deep Learning Extraction of Band Structure Parameters
from Density of States: A Case Study on Trilayer Graphene.” Physical Review
B, vol. 108, no. 12, 125411, American Physical Society, 2023, doi:10.1103/physrevb.108.125411.'
short: P.M. Henderson, A. Ghazaryan, A.A. Zibrov, A.F. Young, M. Serbyn, Physical
Review B 108 (2023).
date_created: 2023-09-12T07:12:12Z
date_published: 2023-09-15T00:00:00Z
date_updated: 2023-09-20T09:38:24Z
day: '15'
department:
- _id: MaSe
- _id: ChLa
- _id: MiLe
doi: 10.1103/physrevb.108.125411
external_id:
arxiv:
- '2210.06310'
intvolume: ' 108'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2210.06310
month: '09'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Deep learning extraction of band structure parameters from density of states:
A case study on trilayer graphene'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '14321'
abstract:
- lang: eng
text: We demonstrate the possibility of a coupling between the magnetization direction
of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate
the mechanism of the coupling, we analyze a minimal Stoner model that includes
Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet.
The proposed mechanism allows us to study magnetic anisotropy of the system with
an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can
change magnetocrystalline anisotropy of the substrate. Our research aims to motivate
further experimental studies of the current-free chirality induced spin selectivity
effect involving both enantiomers.
acknowledgement: "We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan,
and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from
the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received
funding from the European Union’s Horizon Europe research and innovation program
under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot."
article_number: '104103'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Ragheed
full_name: Al Hyder, Ragheed
id: d1c405be-ae15-11ed-8510-ccf53278162e
last_name: Al Hyder
- first_name: Alberto
full_name: Cappellaro, Alberto
id: 9d13b3cb-30a2-11eb-80dc-f772505e8660
last_name: Cappellaro
orcid: 0000-0001-6110-2359
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet
can affect its magnetization direction. The Journal of Chemical Physics.
2023;159(10). doi:10.1063/5.0165806
apa: Al Hyder, R., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Achiral
dipoles on a ferromagnet can affect its magnetization direction. The Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0165806
chicago: Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev.
“Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” The
Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0165806.
ieee: R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles
on a ferromagnet can affect its magnetization direction,” The Journal of Chemical
Physics, vol. 159, no. 10. AIP Publishing, 2023.
ista: Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on
a ferromagnet can affect its magnetization direction. The Journal of Chemical
Physics. 159(10), 104103.
mla: Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its
Magnetization Direction.” The Journal of Chemical Physics, vol. 159, no.
10, 104103, AIP Publishing, 2023, doi:10.1063/5.0165806.
short: R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical
Physics 159 (2023).
date_created: 2023-09-13T09:25:09Z
date_published: 2023-09-11T00:00:00Z
date_updated: 2023-09-20T09:48:12Z
day: '11'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1063/5.0165806
ec_funded: 1
external_id:
arxiv:
- '2306.17592'
pmid:
- '37694742'
file:
- access_level: open_access
checksum: 507ab65ab29e2c987c94cabad7c5370b
content_type: application/pdf
creator: acappell
date_created: 2023-09-13T09:34:20Z
date_updated: 2023-09-13T09:34:20Z
file_id: '14322'
file_name: 104103_1_5.0165806.pdf
file_size: 5749653
relation: main_file
success: 1
file_date_updated: 2023-09-13T09:34:20Z
has_accepted_license: '1'
intvolume: ' 159'
issue: '10'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: bd7b5202-d553-11ed-ba76-9b1c1b258338
grant_number: '101062862'
name: Non-equilibrium Field Theory of Molecular Rotations
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Achiral dipoles on a ferromagnet can affect its magnetization direction
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 159
year: '2023'
...
---
_id: '14323'
abstract:
- lang: eng
text: Morphogens are signaling molecules that are known for their prominent role
in pattern formation within developing tissues. In addition to patterning, morphogens
also control tissue growth. However, the underlying mechanisms are poorly understood.
We studied the role of morphogens in regulating tissue growth in the developing
vertebrate neural tube. In this system, opposing morphogen gradients of Shh and
BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations
in these morphogen pathways result in alterations in tissue growth and cell cycle
progression, however, it has been unclear what cellular process is affected. To
address this, we analysed the rates of cell proliferation and cell death in mouse
mutants in which signaling is perturbed, as well as in chick neural plate explants
exposed to defined concentrations of signaling activators or inhibitors. Our results
indicated that the rate of cell proliferation was not altered in these assays.
By contrast, both the Shh and BMP signaling pathways had profound effects on neural
progenitor survival. Our results indicate that these pathways synergise to promote
cell survival within neural progenitors. Consistent with this, we found that progenitors
within the intermediate region of the neural tube, where the combined levels of
Shh and BMP are the lowest, are most prone to cell death when signaling activity
is inhibited. In addition, we found that downregulation of Shh results in increased
apoptosis within the roof plate, which is the dorsal source of BMP ligand production.
This revealed a cross-interaction between the Shh and BMP morphogen signaling
pathways that may be relevant for understanding how gradients scale in neural
tubes with different overall sizes. We further studied the mechanism acting downstream
of Shh in cell survival regulation using genetic and genomic approaches. We propose
that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether,
our study points to a novel role of opposing morphogen gradients in tissue size
regulation and provides new insights into complex interactions between Shh and
BMP signaling gradients in the neural tube.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Katarzyna
full_name: Kuzmicz-Kowalska, Katarzyna
id: 4CED352A-F248-11E8-B48F-1D18A9856A87
last_name: Kuzmicz-Kowalska
citation:
ama: Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP
in the developing spinal cord. 2023. doi:10.15479/at:ista:14323
apa: Kuzmicz-Kowalska, K. (2023). Regulation of neural progenitor survival by
Shh and BMP in the developing spinal cord. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:14323
chicago: Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival
by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:14323.
ieee: K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and
BMP in the developing spinal cord,” Institute of Science and Technology Austria,
2023.
ista: Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh
and BMP in the developing spinal cord. Institute of Science and Technology Austria.
mla: Kuzmicz-Kowalska, Katarzyna. Regulation of Neural Progenitor Survival by
Shh and BMP in the Developing Spinal Cord. Institute of Science and Technology
Austria, 2023, doi:10.15479/at:ista:14323.
short: K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and
BMP in the Developing Spinal Cord, Institute of Science and Technology Austria,
2023.
date_created: 2023-09-13T10:07:18Z
date_published: 2023-09-13T00:00:00Z
date_updated: 2024-03-07T15:02:59Z
day: '13'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: AnKi
doi: 10.15479/at:ista:14323
file:
- access_level: closed
checksum: bd83596869c814b24aeff7077d031c0e
content_type: application/pdf
creator: kkuzmicz
date_created: 2023-09-13T09:52:52Z
date_updated: 2023-09-13T10:08:25Z
embargo: 2025-03-13
embargo_to: open_access
file_id: '14324'
file_name: PhDThesis_KK_final_pdfA.pdf
file_size: 10147911
relation: main_file
- access_level: closed
checksum: aa2757ae4c3478041fd7e62c587d3e4d
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: kkuzmicz
date_created: 2023-09-13T09:53:29Z
date_updated: 2023-09-13T09:53:29Z
file_id: '14325'
file_name: thesis_KK_final_corrections_092023.docx
file_size: 103980668
relation: source_file
file_date_updated: 2023-09-13T10:08:25Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '09'
oa_version: Published Version
page: '151'
project:
- _id: 267AF0E4-B435-11E9-9278-68D0E5697425
name: The role of morphogens in the regulation of neural tube growth
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7883'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
title: Regulation of neural progenitor survival by Shh and BMP in the developing spinal
cord
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14333'
abstract:
- lang: eng
text: "As causal ground truth is incredibly rare, causal discovery algorithms are\r\ncommonly
only evaluated on simulated data. This is concerning, given that\r\nsimulations
reflect common preconceptions about generating processes regarding\r\nnoise distributions,
model classes, and more. In this work, we propose a novel\r\nmethod for falsifying
the output of a causal discovery algorithm in the absence\r\nof ground truth.
Our key insight is that while statistical learning seeks\r\nstability across subsets
of data points, causal learning should seek stability\r\nacross subsets of variables.
Motivated by this insight, our method relies on a\r\nnotion of compatibility between
causal graphs learned on different subsets of\r\nvariables. We prove that detecting
incompatibilities can falsify wrongly\r\ninferred causal relations due to violation
of assumptions or errors from finite\r\nsample effects. Although passing such
compatibility tests is only a necessary\r\ncriterion for good performance, we
argue that it provides strong evidence for\r\nthe causal models whenever compatibility
entails strong implications for the\r\njoint distribution. We also demonstrate
experimentally that detection of\r\nincompatibilities can aid in causal model
selection."
article_number: '2307.09552'
article_processing_charge: No
arxiv: 1
author:
- first_name: Philipp M.
full_name: Faller, Philipp M.
last_name: Faller
- first_name: Leena Chennuru
full_name: Vankadara, Leena Chennuru
last_name: Vankadara
- first_name: Atalanti A.
full_name: Mastakouri, Atalanti A.
last_name: Mastakouri
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Dominik
full_name: Janzing, Dominik
last_name: Janzing
citation:
ama: 'Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility:
Evaluating causal discovery without ground truth. arXiv. doi:10.48550/arXiv.2307.09552'
apa: 'Faller, P. M., Vankadara, L. C., Mastakouri, A. A., Locatello, F., & Janzing,
D. (n.d.). Self-compatibility: Evaluating causal discovery without ground truth.
arXiv. https://doi.org/10.48550/arXiv.2307.09552'
chicago: 'Faller, Philipp M., Leena Chennuru Vankadara, Atalanti A. Mastakouri,
Francesco Locatello, and Dominik Janzing. “Self-Compatibility: Evaluating Causal
Discovery without Ground Truth.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.09552.'
ieee: 'P. M. Faller, L. C. Vankadara, A. A. Mastakouri, F. Locatello, and D. Janzing,
“Self-compatibility: Evaluating causal discovery without ground truth,” arXiv.
.'
ista: 'Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility:
Evaluating causal discovery without ground truth. arXiv, 2307.09552.'
mla: 'Faller, Philipp M., et al. “Self-Compatibility: Evaluating Causal Discovery
without Ground Truth.” ArXiv, 2307.09552, doi:10.48550/arXiv.2307.09552.'
short: P.M. Faller, L.C. Vankadara, A.A. Mastakouri, F. Locatello, D. Janzing, ArXiv
(n.d.).
date_created: 2023-09-13T12:44:59Z
date_published: 2023-07-18T00:00:00Z
date_updated: 2023-09-13T12:47:53Z
day: '18'
department:
- _id: FrLo
doi: 10.48550/arXiv.2307.09552
extern: '1'
external_id:
arxiv:
- '2307.09552'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2307.09552
month: '07'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: 'Self-compatibility: Evaluating causal discovery without ground truth'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...