---
_id: '8599'
abstract:
- lang: eng
text: A graph game is a two-player zero-sum game in which the players move a token
throughout a graph to produce an infinite path, which determines the winner or
payoff of the game. In bidding games, both players have budgets, and in each turn,
we hold an "auction" (bidding) to determine which player moves the token. In this
survey, we consider several bidding mechanisms and study their effect on the properties
of the game. Specifically, bidding games, and in particular bidding games of infinite
duration, have an intriguing equivalence with random-turn games in which in each
turn, the player who moves is chosen randomly. We show how minor changes in the
bidding mechanism lead to unexpected differences in the equivalence with random-turn
games.
acknowledgement: We would like to thank all our collaborators Milad Aghajohari, Ventsislav
Chonev, Rasmus Ibsen-Jensen, Ismäel Jecker, Petr Novotný, Josef Tkadlec, and Ðorđe
Žikelić; we hope the collaboration was as fun and meaningful for you as it was for
us.
alternative_title:
- LIPIcs
article_number: '2'
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Avni G, Henzinger TA. A survey of bidding games on graphs. In: 31st International
Conference on Concurrency Theory. Vol 171. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2020. doi:10.4230/LIPIcs.CONCUR.2020.2'
apa: 'Avni, G., & Henzinger, T. A. (2020). A survey of bidding games on graphs.
In 31st International Conference on Concurrency Theory (Vol. 171). Virtual:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2020.2'
chicago: Avni, Guy, and Thomas A Henzinger. “A Survey of Bidding Games on Graphs.”
In 31st International Conference on Concurrency Theory, Vol. 171. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.CONCUR.2020.2.
ieee: G. Avni and T. A. Henzinger, “A survey of bidding games on graphs,” in 31st
International Conference on Concurrency Theory, Virtual, 2020, vol. 171.
ista: 'Avni G, Henzinger TA. 2020. A survey of bidding games on graphs. 31st International
Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs,
vol. 171, 2.'
mla: Avni, Guy, and Thomas A. Henzinger. “A Survey of Bidding Games on Graphs.”
31st International Conference on Concurrency Theory, vol. 171, 2, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.CONCUR.2020.2.
short: G. Avni, T.A. Henzinger, in:, 31st International Conference on Concurrency
Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.
conference:
end_date: 2020-09-04
location: Virtual
name: 'CONCUR: Conference on Concurrency Theory'
start_date: 2020-09-01
date_created: 2020-10-04T22:01:36Z
date_published: 2020-08-06T00:00:00Z
date_updated: 2021-01-12T08:20:13Z
day: '06'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.CONCUR.2020.2
file:
- access_level: open_access
checksum: 8f33b098e73724e0ac817f764d8e1a2d
content_type: application/pdf
creator: dernst
date_created: 2020-10-05T14:13:19Z
date_updated: 2020-10-05T14:13:19Z
file_id: '8611'
file_name: 2020_LIPIcsCONCUR_Avni.pdf
file_size: 868510
relation: main_file
success: 1
file_date_updated: 2020-10-05T14:13:19Z
has_accepted_license: '1'
intvolume: ' 171'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 31st International Conference on Concurrency Theory
publication_identifier:
isbn:
- '9783959771603'
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: A survey of bidding games on graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 171
year: '2020'
...
---
_id: '8600'
abstract:
- lang: eng
text: 'A vector addition system with states (VASS) consists of a finite set of states
and counters. A transition changes the current state to the next state, and every
counter is either incremented, or decremented, or left unchanged. A state and
value for each counter is a configuration; and a computation is an infinite sequence
of configurations with transitions between successive configurations. A probabilistic
VASS consists of a VASS along with a probability distribution over the transitions
for each state. Qualitative properties such as state and configuration reachability
have been widely studied for VASS. In this work we consider multi-dimensional
long-run average objectives for VASS and probabilistic VASS. For a counter, the
cost of a configuration is the value of the counter; and the long-run average
value of a computation for the counter is the long-run average of the costs of
the configurations in the computation. The multi-dimensional long-run average
problem given a VASS and a threshold value for each counter, asks whether there
is a computation such that for each counter the long-run average value for the
counter does not exceed the respective threshold. For probabilistic VASS, instead
of the existence of a computation, we consider whether the expected long-run average
value for each counter does not exceed the respective threshold. Our main results
are as follows: we show that the multi-dimensional long-run average problem (a)
is NP-complete for integer-valued VASS; (b) is undecidable for natural-valued
VASS (i.e., nonnegative counters); and (c) can be solved in polynomial time for
probabilistic integer-valued VASS, and probabilistic natural-valued VASS when
all computations are non-terminating.'
alternative_title:
- LIPIcs
article_number: '23'
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J. Multi-dimensional long-run average problems
for vector addition systems with states. In: 31st International Conference
on Concurrency Theory. Vol 171. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2020. doi:10.4230/LIPIcs.CONCUR.2020.23'
apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2020). Multi-dimensional
long-run average problems for vector addition systems with states. In 31st
International Conference on Concurrency Theory (Vol. 171). Virtual: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2020.23'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Multi-Dimensional
Long-Run Average Problems for Vector Addition Systems with States.” In 31st
International Conference on Concurrency Theory, Vol. 171. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.CONCUR.2020.23.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Multi-dimensional long-run average
problems for vector addition systems with states,” in 31st International Conference
on Concurrency Theory, Virtual, 2020, vol. 171.
ista: 'Chatterjee K, Henzinger TA, Otop J. 2020. Multi-dimensional long-run average
problems for vector addition systems with states. 31st International Conference
on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol.
171, 23.'
mla: Chatterjee, Krishnendu, et al. “Multi-Dimensional Long-Run Average Problems
for Vector Addition Systems with States.” 31st International Conference on
Concurrency Theory, vol. 171, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2020, doi:10.4230/LIPIcs.CONCUR.2020.23.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, 31st International Conference
on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.
conference:
end_date: 2020-09-04
location: Virtual
name: 'CONCUR: Conference on Concurrency Theory'
start_date: 2020-09-01
date_created: 2020-10-04T22:01:36Z
date_published: 2020-08-06T00:00:00Z
date_updated: 2021-01-12T08:20:15Z
day: '06'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.4230/LIPIcs.CONCUR.2020.23
external_id:
arxiv:
- '2007.08917'
file:
- access_level: open_access
checksum: 5039752f644c4b72b9361d21a5e31baf
content_type: application/pdf
creator: dernst
date_created: 2020-10-05T14:04:25Z
date_updated: 2020-10-05T14:04:25Z
file_id: '8610'
file_name: 2020_LIPIcsCONCUR_Chatterjee.pdf
file_size: 601231
relation: main_file
success: 1
file_date_updated: 2020-10-05T14:04:25Z
has_accepted_license: '1'
intvolume: ' 171'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 31st International Conference on Concurrency Theory
publication_identifier:
isbn:
- '9783959771603'
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multi-dimensional long-run average problems for vector addition systems with
states
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 171
year: '2020'
...
---
_id: '8607'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis (CME) and its core endocytic machinery are evolutionarily
conserved across all eukaryotes. In mammals, the heterotetrameric adaptor protein
complex-2 (AP-2) sorts plasma membrane (PM) cargoes into vesicles through the
recognition of motifs based on tyrosine or di-leucine in their cytoplasmic tails.
However, in plants, very little is known on how PM proteins are sorted for CME
and whether similar motifs are required. In Arabidopsis thaliana, the brassinosteroid
(BR) receptor, BR INSENSITIVE1 (BRI1), undergoes endocytosis that depends on clathrin
and AP-2. Here we demonstrate that BRI1 binds directly to the medium AP-2 subunit,
AP2M. The cytoplasmic domain of BRI1 contains five putative canonical surface-exposed
tyrosine-based endocytic motifs. The tyrosine-to-phenylalanine substitution in
Y898KAI reduced BRI1 internalization without affecting its kinase activity. Consistently,
plants carrying the BRI1Y898F mutation were hypersensitive to BRs. Our study demonstrates
that AP-2-dependent internalization of PM proteins via the recognition of functional
tyrosine motifs also operates in plants.
article_processing_charge: No
article_type: original
author:
- first_name: D
full_name: Liu, D
last_name: Liu
- first_name: R
full_name: Kumar, R
last_name: Kumar
- first_name: Claus
full_name: LAN, Claus
last_name: LAN
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: W
full_name: Siao, W
last_name: Siao
- first_name: I
full_name: Vanhoutte, I
last_name: Vanhoutte
- first_name: P
full_name: Wang, P
last_name: Wang
- first_name: KW
full_name: Bender, KW
last_name: Bender
- first_name: K
full_name: Yperman, K
last_name: Yperman
- first_name: S
full_name: Martins, S
last_name: Martins
- first_name: X
full_name: Zhao, X
last_name: Zhao
- first_name: G
full_name: Vert, G
last_name: Vert
- first_name: D
full_name: Van Damme, D
last_name: Van Damme
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: E
full_name: Russinova, E
last_name: Russinova
citation:
ama: Liu D, Kumar R, LAN C, et al. Endocytosis of BRASSINOSTEROID INSENSITIVE1 is
partly driven by a canonical tyrosine-based Motif. Plant Cell. 2020;32(11):3598-3612.
doi:10.1105/tpc.20.00384
apa: Liu, D., Kumar, R., LAN, C., Johnson, A. J., Siao, W., Vanhoutte, I., … Russinova,
E. (2020). Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical
tyrosine-based Motif. Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.20.00384
chicago: Liu, D, R Kumar, Claus LAN, Alexander J Johnson, W Siao, I Vanhoutte, P
Wang, et al. “Endocytosis of BRASSINOSTEROID INSENSITIVE1 Is Partly Driven by
a Canonical Tyrosine-Based Motif.” Plant Cell. American Society of Plant
Biologists, 2020. https://doi.org/10.1105/tpc.20.00384.
ieee: D. Liu et al., “Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly
driven by a canonical tyrosine-based Motif,” Plant Cell, vol. 32, no. 11.
American Society of Plant Biologists, pp. 3598–3612, 2020.
ista: Liu D, Kumar R, LAN C, Johnson AJ, Siao W, Vanhoutte I, Wang P, Bender K,
Yperman K, Martins S, Zhao X, Vert G, Van Damme D, Friml J, Russinova E. 2020.
Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based
Motif. Plant Cell. 32(11), 3598–3612.
mla: Liu, D., et al. “Endocytosis of BRASSINOSTEROID INSENSITIVE1 Is Partly Driven
by a Canonical Tyrosine-Based Motif.” Plant Cell, vol. 32, no. 11, American
Society of Plant Biologists, 2020, pp. 3598–612, doi:10.1105/tpc.20.00384.
short: D. Liu, R. Kumar, C. LAN, A.J. Johnson, W. Siao, I. Vanhoutte, P. Wang, K.
Bender, K. Yperman, S. Martins, X. Zhao, G. Vert, D. Van Damme, J. Friml, E. Russinova,
Plant Cell 32 (2020) 3598–3612.
date_created: 2020-10-05T12:45:16Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2023-09-05T12:21:32Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.20.00384
ec_funded: 1
external_id:
isi:
- '000600226800021'
pmid:
- '32958564'
intvolume: ' 32'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://europepmc.org/article/MED/32958564
month: '11'
oa: 1
oa_version: Published Version
page: 3598-3612
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Plant Cell
publication_identifier:
eissn:
- 1532-298x
issn:
- 1040-4651
publication_status: published
publisher: American Society of Plant Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical
tyrosine-based Motif
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 32
year: '2020'
...
---
_id: '8616'
abstract:
- lang: eng
text: The brain vasculature supplies neurons with glucose and oxygen, but little
is known about how vascular plasticity contributes to brain function. Using longitudinal
in vivo imaging, we reported that a substantial proportion
of blood vessels in the adult brain sporadically occluded and regressed. Their
regression proceeded through sequential stages of blood-flow occlusion, endothelial
cell collapse, relocation or loss of pericytes, and retraction of glial endfeet.
Regressing vessels were found to be widespread in mouse, monkey and human brains.
Both brief occlusions of the middle cerebral artery and lipopolysaccharide-mediated
inflammation induced an increase of vessel regression. Blockage of leukocyte adhesion
to endothelial cells alleviated LPS-induced vessel regression. We further revealed
that blood vessel regression caused a reduction of neuronal activity due to a
dysfunction in mitochondrial metabolism and glutamate production. Our results
elucidate the mechanism of vessel regression and its role in neuronal function
in the adult brain.
acknowledgement: 'The project was initiated in the Jan lab at UCSF. We thank Lily
Jan and Yuh-Nung Jan’s generous support. We thank Liqun Luo’s lab for providing
MADM-7 mice and Rolf A Brekken for VEGF-antibodies. Drs. Yuanquan Song (UPenn),
Zhaozhu Hu (JHU), Ji Hu (ShanghaiTech), Yang Xiang (U. Mass), Hao Wang (Zhejiang
U.) and Ruikang Wang (U. Washington) for critical input, colleagues at Children’s
Research Institute, Departments of Neuroscience, Neurology and Neurotherapeutics,
Pediatrics from UT Southwestern, and colleagues from the Jan lab for discussion.
Dr. Bridget Samuels, Sean Morrison (UT Southwestern), and Nannan Lu (Zhejiang U.)
for critical reading. We acknowledge the assistance of the CIBR Imaging core. We
also thank UT Southwestern Live Cell Imaging Facility, a Shared Resource of the
Harold C. Simmons Cancer Center, supported in part by an NCI Cancer Center Support
Grant, P30 CA142543K. This work is supported by CIBR funds and the American Heart
Association AWRP Summer 2016 Innovative Research Grant (17IRG33410377) to W-P.G.;
National Natural Science Foundation of China (No.81370031) to Z.Z.;National Key
Research and Development Program of China (2016YFE0125400)to F.H.;National Natural
Science Foundations of China (No. 81473202) to Y.L.; National Natural Science Foundation
of China (No.31600839) and Shenzhen Science and Technology Research Program (JCYJ20170818163320865)
to B.P.; National Natural Science Foundation of China (No. 31800864) and Westlake
University start-up funds to J-M. J. NIH R01NS088627 to W.L.J.; NIH: R01 AG020670
and RF1AG054111 to H.Z.; R01 NS088555 to A.M.S., and European Research Council No.725780
to S.H.;W-P.G. was a recipient of Bugher-American Heart Association Dan Adams Thinking
Outside the Box Award.'
article_processing_charge: No
author:
- first_name: Xiaofei
full_name: Gao, Xiaofei
last_name: Gao
- first_name: Jun-Liszt
full_name: Li, Jun-Liszt
last_name: Li
- first_name: Xingjun
full_name: Chen, Xingjun
last_name: Chen
- first_name: Bo
full_name: Ci, Bo
last_name: Ci
- first_name: Fei
full_name: Chen, Fei
last_name: Chen
- first_name: Nannan
full_name: Lu, Nannan
last_name: Lu
- first_name: Bo
full_name: Shen, Bo
last_name: Shen
- first_name: Lijun
full_name: Zheng, Lijun
last_name: Zheng
- first_name: Jie-Min
full_name: Jia, Jie-Min
last_name: Jia
- first_name: Yating
full_name: Yi, Yating
last_name: Yi
- first_name: Shiwen
full_name: Zhang, Shiwen
last_name: Zhang
- first_name: Ying-Chao
full_name: Shi, Ying-Chao
last_name: Shi
- first_name: Kaibin
full_name: Shi, Kaibin
last_name: Shi
- first_name: Nicholas E
full_name: Propson, Nicholas E
last_name: Propson
- first_name: Yubin
full_name: Huang, Yubin
last_name: Huang
- first_name: Katherine
full_name: Poinsatte, Katherine
last_name: Poinsatte
- first_name: Zhaohuan
full_name: Zhang, Zhaohuan
last_name: Zhang
- first_name: Yuanlei
full_name: Yue, Yuanlei
last_name: Yue
- first_name: Dale B
full_name: Bosco, Dale B
last_name: Bosco
- first_name: Ying-mei
full_name: Lu, Ying-mei
last_name: Lu
- first_name: Shi-bing
full_name: Yang, Shi-bing
last_name: Yang
- first_name: Ralf H.
full_name: Adams, Ralf H.
last_name: Adams
- first_name: Volkhard
full_name: Lindner, Volkhard
last_name: Lindner
- first_name: Fen
full_name: Huang, Fen
last_name: Huang
- first_name: Long-Jun
full_name: Wu, Long-Jun
last_name: Wu
- first_name: Hui
full_name: Zheng, Hui
last_name: Zheng
- first_name: Feng
full_name: Han, Feng
last_name: Han
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Ann M.
full_name: Stowe, Ann M.
last_name: Stowe
- first_name: Bo
full_name: Peng, Bo
last_name: Peng
- first_name: Marta
full_name: Margeta, Marta
last_name: Margeta
- first_name: Xiaoqun
full_name: Wang, Xiaoqun
last_name: Wang
- first_name: Qiang
full_name: Liu, Qiang
last_name: Liu
- first_name: Jakob
full_name: Körbelin, Jakob
last_name: Körbelin
- first_name: Martin
full_name: Trepel, Martin
last_name: Trepel
- first_name: Hui
full_name: Lu, Hui
last_name: Lu
- first_name: Bo O.
full_name: Zhou, Bo O.
last_name: Zhou
- first_name: Hu
full_name: Zhao, Hu
last_name: Zhao
- first_name: Wenzhi
full_name: Su, Wenzhi
last_name: Su
- first_name: Robert M.
full_name: Bachoo, Robert M.
last_name: Bachoo
- first_name: Woo-ping
full_name: Ge, Woo-ping
last_name: Ge
citation:
ama: Gao X, Li J-L, Chen X, et al. Reduction of neuronal activity mediated by blood-vessel
regression in the brain. bioRxiv. doi:10.1101/2020.09.15.262782
apa: Gao, X., Li, J.-L., Chen, X., Ci, B., Chen, F., Lu, N., … Ge, W. (n.d.). Reduction
of neuronal activity mediated by blood-vessel regression in the brain. bioRxiv.
Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.09.15.262782
chicago: Gao, Xiaofei, Jun-Liszt Li, Xingjun Chen, Bo Ci, Fei Chen, Nannan Lu, Bo
Shen, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression
in the Brain.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.09.15.262782.
ieee: X. Gao et al., “Reduction of neuronal activity mediated by blood-vessel
regression in the brain,” bioRxiv. Cold Spring Harbor Laboratory.
ista: Gao X, Li J-L, Chen X, Ci B, Chen F, Lu N, Shen B, Zheng L, Jia J-M, Yi Y,
Zhang S, Shi Y-C, Shi K, Propson NE, Huang Y, Poinsatte K, Zhang Z, Yue Y, Bosco
DB, Lu Y, Yang S, Adams RH, Lindner V, Huang F, Wu L-J, Zheng H, Han F, Hippenmeyer
S, Stowe AM, Peng B, Margeta M, Wang X, Liu Q, Körbelin J, Trepel M, Lu H, Zhou
BO, Zhao H, Su W, Bachoo RM, Ge W. Reduction of neuronal activity mediated by
blood-vessel regression in the brain. bioRxiv, 10.1101/2020.09.15.262782.
mla: Gao, Xiaofei, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel
Regression in the Brain.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.09.15.262782.
short: X. Gao, J.-L. Li, X. Chen, B. Ci, F. Chen, N. Lu, B. Shen, L. Zheng, J.-M.
Jia, Y. Yi, S. Zhang, Y.-C. Shi, K. Shi, N.E. Propson, Y. Huang, K. Poinsatte,
Z. Zhang, Y. Yue, D.B. Bosco, Y. Lu, S. Yang, R.H. Adams, V. Lindner, F. Huang,
L.-J. Wu, H. Zheng, F. Han, S. Hippenmeyer, A.M. Stowe, B. Peng, M. Margeta, X.
Wang, Q. Liu, J. Körbelin, M. Trepel, H. Lu, B.O. Zhou, H. Zhao, W. Su, R.M. Bachoo,
W. Ge, BioRxiv (n.d.).
date_created: 2020-10-06T08:58:59Z
date_published: 2020-09-15T00:00:00Z
date_updated: 2021-01-12T08:20:19Z
day: '15'
department:
- _id: SiHi
doi: 10.1101/2020.09.15.262782
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.09.15.262782
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
status: public
title: Reduction of neuronal activity mediated by blood-vessel regression in the brain
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8620'
abstract:
- lang: eng
text: "The development of the human brain occurs through a tightly regulated series
of dynamic and adaptive processes during prenatal and postnatal life. A disruption
of this strictly orchestrated series of events can lead to a number of neurodevelopmental
conditions, including Autism Spectrum Disorders (ASDs). ASDs are a very common,
etiologically and phenotypically heterogeneous group of disorders sharing the
core symptoms of social interaction and communication deficits and restrictive
and repetitive interests and behaviors. They are estimated to affect one in 59
individuals in the U.S. and, over the last three decades, mutations in more than
a hundred genetic loci have been convincingly linked to ASD pathogenesis. Yet,
for the vast majority of these ASD-risk genes their role during brain development
and precise molecular function still remain elusive.\r\nDe novo loss of function
mutations in the ubiquitin ligase-encoding gene Cullin 3 (CUL3) lead to ASD. In
the study described here, we used Cul3 mouse models to evaluate the consequences
of Cul3 mutations in vivo. Our results show that Cul3 heterozygous knockout mice
exhibit deficits in motor coordination as well as ASD-relevant social and cognitive
impairments. Cul3+/-, Cul3+/fl Emx1-Cre and Cul3fl/fl Emx1-Cre mutant brains display
cortical lamination abnormalities due to defective migration of post-mitotic excitatory
neurons, as well as reduced numbers of excitatory and inhibitory neurons. In line
with the observed abnormal cortical organization, Cul3 heterozygous deletion is
associated with decreased spontaneous excitatory and inhibitory activity in the
cortex. At the molecular level we show that Cul3 regulates cytoskeletal and adhesion
protein abundance in the mouse embryonic cortex. Abnormal regulation of cytoskeletal
proteins in Cul3 mutant neural cells results in atypical organization of the actin
mesh at the cell leading edge. Of note, heterozygous deletion of Cul3 in adult
mice does not induce the majority of the behavioral defects observed in constitutive
Cul3 haploinsufficient animals, pointing to a critical time-window for Cul3 deficiency.\r\nIn
conclusion, our data indicate that Cul3 plays a critical role in the regulation
of cytoskeletal proteins and neuronal migration. ASD-associated defects and behavioral
abnormalities are primarily due to dosage sensitive Cul3 functions at early brain
developmental stages."
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: I would like to especially thank Armel Nicolas from the Proteomics
and Christoph Sommer from the Bioimaging Facilities for the data analysis, and to
thank the team of the Preclinical Facility, especially Sabina Deixler, Angela Schlerka,
Anita Lepold, Mihalea Mihai and Michael Schun for taking care of the mouse line
maintenance and their great support.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
citation:
ama: Morandell J. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis.
2020. doi:10.15479/AT:ISTA:8620
apa: Morandell, J. (2020). Illuminating the role of Cul3 in autism spectrum disorder
pathogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8620
chicago: Morandell, Jasmin. “Illuminating the Role of Cul3 in Autism Spectrum Disorder
Pathogenesis.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8620.
ieee: J. Morandell, “Illuminating the role of Cul3 in autism spectrum disorder pathogenesis,”
Institute of Science and Technology Austria, 2020.
ista: Morandell J. 2020. Illuminating the role of Cul3 in autism spectrum disorder
pathogenesis. Institute of Science and Technology Austria.
mla: Morandell, Jasmin. Illuminating the Role of Cul3 in Autism Spectrum Disorder
Pathogenesis. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8620.
short: J. Morandell, Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis,
Institute of Science and Technology Austria, 2020.
date_created: 2020-10-07T14:53:13Z
date_published: 2020-10-12T00:00:00Z
date_updated: 2024-09-10T12:04:25Z
day: '12'
ddc:
- '610'
degree_awarded: PhD
department:
- _id: GaNo
doi: 10.15479/AT:ISTA:8620
file:
- access_level: open_access
checksum: 7ee83e42de3e5ce2fedb44dff472f75f
content_type: application/pdf
creator: jmorande
date_created: 2020-10-07T14:41:49Z
date_updated: 2021-10-16T22:30:04Z
embargo: 2021-10-15
file_id: '8621'
file_name: Jasmin_Morandell_Thesis-2020_final.pdf
file_size: 16155786
relation: main_file
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checksum: 5e0464af453734210ce7aab7b4a92e3a
content_type: application/x-zip-compressed
creator: jmorande
date_created: 2020-10-07T14:45:07Z
date_updated: 2021-10-16T22:30:04Z
embargo_to: open_access
file_id: '8622'
file_name: Jasmin_Morandell_Thesis-2020_final.zip
file_size: 24344152
relation: source_file
file_date_updated: 2021-10-16T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '138'
project:
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 05A0D778-7A3F-11EA-A408-12923DDC885E
grant_number: F07807
name: Neural stem cells in autism and epilepsy
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7800'
relation: part_of_dissertation
status: public
- id: '8131'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
title: Illuminating the role of Cul3 in autism spectrum disorder pathogenesis
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8623'
abstract:
- lang: eng
text: We introduce the monitoring of trace properties under assumptions. An assumption
limits the space of possible traces that the monitor may encounter. An assumption
may result from knowledge about the system that is being monitored, about the
environment, or about another, connected monitor. We define monitorability under
assumptions and study its theoretical properties. In particular, we show that
for every assumption A, the boolean combinations of properties that are safe or
co-safe relative to A are monitorable under A. We give several examples and constructions
on how an assumption can make a non-monitorable property monitorable, and how
an assumption can make a monitorable property monitorable with fewer resources,
such as integer registers.
acknowledgement: This research was supported in part by the Austrian Science Fund
(FWF) under grant Z211-N23 (Wittgenstein Award).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
citation:
ama: 'Henzinger TA, Sarac NE. Monitorability under assumptions. In: Runtime Verification.
Vol 12399. Springer Nature; 2020:3-18. doi:10.1007/978-3-030-60508-7_1'
apa: 'Henzinger, T. A., & Sarac, N. E. (2020). Monitorability under assumptions.
In Runtime Verification (Vol. 12399, pp. 3–18). Los Angeles, CA, United
States: Springer Nature. https://doi.org/10.1007/978-3-030-60508-7_1'
chicago: Henzinger, Thomas A, and Naci E Sarac. “Monitorability under Assumptions.”
In Runtime Verification, 12399:3–18. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-60508-7_1.
ieee: T. A. Henzinger and N. E. Sarac, “Monitorability under assumptions,” in Runtime
Verification, Los Angeles, CA, United States, 2020, vol. 12399, pp. 3–18.
ista: 'Henzinger TA, Sarac NE. 2020. Monitorability under assumptions. Runtime Verification.
RV: Runtime Verification, LNCS, vol. 12399, 3–18.'
mla: Henzinger, Thomas A., and Naci E. Sarac. “Monitorability under Assumptions.”
Runtime Verification, vol. 12399, Springer Nature, 2020, pp. 3–18, doi:10.1007/978-3-030-60508-7_1.
short: T.A. Henzinger, N.E. Sarac, in:, Runtime Verification, Springer Nature, 2020,
pp. 3–18.
conference:
end_date: 2020-10-09
location: Los Angeles, CA, United States
name: 'RV: Runtime Verification'
start_date: 2020-10-06
date_created: 2020-10-07T15:05:37Z
date_published: 2020-10-02T00:00:00Z
date_updated: 2023-09-05T15:08:26Z
day: '02'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-60508-7_1
external_id:
isi:
- '000728160600001'
file:
- access_level: open_access
checksum: 00661f9b7034f52e18bf24fa552b8194
content_type: application/pdf
creator: esarac
date_created: 2020-10-15T14:28:06Z
date_updated: 2020-10-15T14:28:06Z
file_id: '8665'
file_name: monitorability.pdf
file_size: 478148
relation: main_file
success: 1
file_date_updated: 2020-10-15T14:28:06Z
has_accepted_license: '1'
intvolume: ' 12399'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 3-18
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Runtime Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030605070'
- '9783030605087'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monitorability under assumptions
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 12399
year: '2020'
...
---
_id: '8634'
abstract:
- lang: eng
text: In laboratory studies and numerical simulations, we observe clear signatures
of unstable time-periodic solutions in a moderately turbulent quasi-two-dimensional
flow. We validate the dynamical relevance of such solutions by demonstrating that
turbulent flows in both experiment and numerics transiently display time-periodic
dynamics when they shadow unstable periodic orbits (UPOs). We show that UPOs we
computed are also statistically significant, with turbulent flows spending a sizable
fraction of the total time near these solutions. As a result, the average rates
of energy input and dissipation for the turbulent flow and frequently visited
UPOs differ only by a few percent.
acknowledgement: M. F. S. and R. O. G. acknowledge funding from the National Science
Foundation (CMMI-1234436, DMS1125302, CMMI-1725587) and Defense Advanced Research
Projects Agency (HR0011-16-2-0033). B. S.has received funding from the People Programme
(Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007–2013/
under REA Grant Agreement No. 291734.
article_number: '064501'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Balachandra
full_name: Suri, Balachandra
id: 47A5E706-F248-11E8-B48F-1D18A9856A87
last_name: Suri
- first_name: Logan
full_name: Kageorge, Logan
last_name: Kageorge
- first_name: Roman O.
full_name: Grigoriev, Roman O.
last_name: Grigoriev
- first_name: Michael F.
full_name: Schatz, Michael F.
last_name: Schatz
citation:
ama: Suri B, Kageorge L, Grigoriev RO, Schatz MF. Capturing turbulent dynamics and
statistics in experiments with unstable periodic orbits. Physical Review Letters.
2020;125(6). doi:10.1103/physrevlett.125.064501
apa: Suri, B., Kageorge, L., Grigoriev, R. O., & Schatz, M. F. (2020). Capturing
turbulent dynamics and statistics in experiments with unstable periodic orbits.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.125.064501
chicago: Suri, Balachandra, Logan Kageorge, Roman O. Grigoriev, and Michael F. Schatz.
“Capturing Turbulent Dynamics and Statistics in Experiments with Unstable Periodic
Orbits.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/physrevlett.125.064501.
ieee: B. Suri, L. Kageorge, R. O. Grigoriev, and M. F. Schatz, “Capturing turbulent
dynamics and statistics in experiments with unstable periodic orbits,” Physical
Review Letters, vol. 125, no. 6. American Physical Society, 2020.
ista: Suri B, Kageorge L, Grigoriev RO, Schatz MF. 2020. Capturing turbulent dynamics
and statistics in experiments with unstable periodic orbits. Physical Review Letters.
125(6), 064501.
mla: Suri, Balachandra, et al. “Capturing Turbulent Dynamics and Statistics in Experiments
with Unstable Periodic Orbits.” Physical Review Letters, vol. 125, no.
6, 064501, American Physical Society, 2020, doi:10.1103/physrevlett.125.064501.
short: B. Suri, L. Kageorge, R.O. Grigoriev, M.F. Schatz, Physical Review Letters
125 (2020).
date_created: 2020-10-08T17:27:32Z
date_published: 2020-08-05T00:00:00Z
date_updated: 2023-09-05T12:08:29Z
day: '05'
department:
- _id: BjHo
doi: 10.1103/physrevlett.125.064501
ec_funded: 1
external_id:
arxiv:
- '2008.02367'
isi:
- '000555785600005'
intvolume: ' 125'
isi: 1
issue: '6'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2008.02367
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Capturing turbulent dynamics and statistics in experiments with unstable periodic
orbits
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 125
year: '2020'
...
---
_id: '8643'
abstract:
- lang: eng
text: The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic
complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing
and escape in mice, a result thought to be caused by a PBG projection to the central
nucleus of the amygdala. However, the isthmic complex, including the PBG, has
been classically considered satellite nuclei of the Superior Colliculus (SC),
which upon stimulation of its medial part also triggers fear and avoidance reactions.
As the PBG-SC connectivity is not well characterized, we investigated whether
the topology of the PBG projection to the SC could be related to the behavioral
consequences of PBG stimulation. To that end, we performed immunohistochemistry,
in situ hybridization and neural tracer injections in the SC and PBG in a diurnal
rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic
and cholinergic markers and were distributed in clearly defined anterior (aPBG)
and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically
to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral
SC and projected exclusively to the contralateral SC. This contralateral projection
forms a dense field of terminals that is restricted to the medial SC, in correspondence
with the SC representation of the aerial binocular field which, we also found,
in O. degus prompted escape reactions upon looming stimulation. Therefore, this
specialized topography allows binocular interactions in the SC region controlling
responses to aerial predators, suggesting a link between the mechanisms by which
the SC and PBG produce defensive behaviors.
acknowledgement: 'We thank Elisa Sentis and Solano Henriquez for their expert technical
assistance. Dr. David Sterratt for his helpful advice in using the Retistruct package.
Dr. Joao Botelho for his valuable assistance in scanning the retinas. To Mrs. Diane
Greenstein for kindly reading and correcting our manuscript. Macarena Ruiz for her
helpful comments during figures elaboration. Dr. Alexia Nunez-Parra for kindly providing
us with the transgenic mouse line. Dr. Harald Luksch for granting us access to the
confocal microscope at his lab. This study was supported by: FONDECYT 1151432 (to
G.M.), FONDECYT 1170027 (to J.M.) and Doctoral fellowship CONICYT 21161599 (to A.D.).'
article_number: '16220'
article_processing_charge: No
article_type: original
author:
- first_name: Alfonso
full_name: Deichler, Alfonso
last_name: Deichler
- first_name: Denisse
full_name: Carrasco, Denisse
last_name: Carrasco
- first_name: Luciana
full_name: Lopez-Jury, Luciana
last_name: Lopez-Jury
- first_name: Tomas A
full_name: Vega Zuniga, Tomas A
id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87
last_name: Vega Zuniga
- first_name: Natalia
full_name: Marquez, Natalia
last_name: Marquez
- first_name: Jorge
full_name: Mpodozis, Jorge
last_name: Mpodozis
- first_name: Gonzalo
full_name: Marin, Gonzalo
last_name: Marin
citation:
ama: Deichler A, Carrasco D, Lopez-Jury L, et al. A specialized reciprocal connectivity
suggests a link between the mechanisms by which the superior colliculus and parabigeminal
nucleus produce defensive behaviors in rodents. Scientific Reports. 2020;10.
doi:10.1038/s41598-020-72848-0
apa: Deichler, A., Carrasco, D., Lopez-Jury, L., Vega Zuniga, T. A., Marquez, N.,
Mpodozis, J., & Marin, G. (2020). A specialized reciprocal connectivity suggests
a link between the mechanisms by which the superior colliculus and parabigeminal
nucleus produce defensive behaviors in rodents. Scientific Reports. Springer
Nature. https://doi.org/10.1038/s41598-020-72848-0
chicago: Deichler, Alfonso, Denisse Carrasco, Luciana Lopez-Jury, Tomas A Vega Zuniga,
Natalia Marquez, Jorge Mpodozis, and Gonzalo Marin. “A Specialized Reciprocal
Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus
and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific
Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-72848-0.
ieee: A. Deichler et al., “A specialized reciprocal connectivity suggests
a link between the mechanisms by which the superior colliculus and parabigeminal
nucleus produce defensive behaviors in rodents,” Scientific Reports, vol.
10. Springer Nature, 2020.
ista: Deichler A, Carrasco D, Lopez-Jury L, Vega Zuniga TA, Marquez N, Mpodozis
J, Marin G. 2020. A specialized reciprocal connectivity suggests a link between
the mechanisms by which the superior colliculus and parabigeminal nucleus produce
defensive behaviors in rodents. Scientific Reports. 10, 16220.
mla: Deichler, Alfonso, et al. “A Specialized Reciprocal Connectivity Suggests a
Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal
Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports, vol.
10, 16220, Springer Nature, 2020, doi:10.1038/s41598-020-72848-0.
short: A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J.
Mpodozis, G. Marin, Scientific Reports 10 (2020).
date_created: 2020-10-11T22:01:14Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2023-08-22T09:58:21Z
day: '01'
ddc:
- '570'
department:
- _id: MaJö
doi: 10.1038/s41598-020-72848-0
external_id:
isi:
- '000577142600032'
file:
- access_level: open_access
checksum: f6dd99954f1c0ffb4da5a1d2d739bf31
content_type: application/pdf
creator: dernst
date_created: 2020-10-12T12:39:10Z
date_updated: 2020-10-12T12:39:10Z
file_id: '8651'
file_name: 2020_ScientificReport_Deichler.pdf
file_size: 3906744
relation: main_file
success: 1
file_date_updated: 2020-10-12T12:39:10Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_identifier:
eissn:
- '20452322'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A specialized reciprocal connectivity suggests a link between the mechanisms
by which the superior colliculus and parabigeminal nucleus produce defensive behaviors
in rodents
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2020'
...
---
_id: '8644'
abstract:
- lang: eng
text: Determining the phase diagram of systems consisting of smaller subsystems
'connected' via a tunable coupling is a challenging task relevant for a variety
of physical settings. A general question is whether new phases, not present in
the uncoupled limit, may arise. We use machine learning and a suitable quasidistance
between different points of the phase diagram to study layered spin models, in
which the spin variables constituting each of the uncoupled systems (to which
we refer as layers) are coupled to each other via an interlayer coupling. In such
systems, in general, composite order parameters involving spins of different layers
may emerge as a consequence of the interlayer coupling. We focus on the layered
Ising and Ashkin–Teller models as a paradigmatic case study, determining their
phase diagram via the application of a machine learning algorithm to the Monte
Carlo data. Remarkably our technique is able to correctly characterize all the
system phases also in the case of hidden order parameters, i.e. order parameters
whose expression in terms of the microscopic configurations would require additional
preprocessing of the data fed to the algorithm. We correctly retrieve the three
known phases of the Ashkin–Teller model with ferromagnetic couplings, including
the phase described by a composite order parameter. For the bilayer and trilayer
Ising models the phases we find are only the ferromagnetic and the paramagnetic
ones. Within the approach we introduce, owing to the construction of convolutional
neural networks, naturally suitable for layered image-like data with arbitrary
number of layers, no preprocessing of the Monte Carlo data is needed, also with
regard to its spatial structure. The physical meaning of our results is discussed
and compared with analytical data, where available. Yet, the method can be used
without any a priori knowledge of the phases one seeks to find and can be applied
to other models and structures.
acknowledgement: We thank Gesualdo Delfino, Michele Fabrizio, Piero Ferrarese, Robert
Konik, Christoph Lampert and Mikhail Lemeshko for stimulating discussions at various
stages of this work. WR has received funding from the EU Horizon 2020 program under
the Marie Skłodowska-Curie Grant Agreement No. 665385 and is a recipient of a DOC
Fellowship of the Austrian Academy of Sciences. GB acknowledges support from the
Austrian Science Fund (FWF), under project No. M2641-N27. ND acknowledges support
by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via Collaborative
Research Center SFB 1225 (ISOQUANT)--project-id 273811115--and under Germany's Excellence
Strategy 'EXC-2181/1-390900948' (the Heidelberg STRUCTURES Excellence Cluster).
article_number: '093026'
article_processing_charge: No
article_type: original
author:
- first_name: Wojciech
full_name: Rzadkowski, Wojciech
id: 48C55298-F248-11E8-B48F-1D18A9856A87
last_name: Rzadkowski
orcid: 0000-0002-1106-4419
- first_name: N
full_name: Defenu, N
last_name: Defenu
- first_name: S
full_name: Chiacchiera, S
last_name: Chiacchiera
- first_name: A
full_name: Trombettoni, A
last_name: Trombettoni
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
citation:
ama: Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. Detecting composite
orders in layered models via machine learning. New Journal of Physics.
2020;22(9). doi:10.1088/1367-2630/abae44
apa: Rzadkowski, W., Defenu, N., Chiacchiera, S., Trombettoni, A., & Bighin,
G. (2020). Detecting composite orders in layered models via machine learning.
New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/abae44
chicago: Rzadkowski, Wojciech, N Defenu, S Chiacchiera, A Trombettoni, and Giacomo
Bighin. “Detecting Composite Orders in Layered Models via Machine Learning.” New
Journal of Physics. IOP Publishing, 2020. https://doi.org/10.1088/1367-2630/abae44.
ieee: W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, and G. Bighin, “Detecting
composite orders in layered models via machine learning,” New Journal of Physics,
vol. 22, no. 9. IOP Publishing, 2020.
ista: Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. 2020. Detecting
composite orders in layered models via machine learning. New Journal of Physics.
22(9), 093026.
mla: Rzadkowski, Wojciech, et al. “Detecting Composite Orders in Layered Models
via Machine Learning.” New Journal of Physics, vol. 22, no. 9, 093026,
IOP Publishing, 2020, doi:10.1088/1367-2630/abae44.
short: W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, G. Bighin, New
Journal of Physics 22 (2020).
date_created: 2020-10-11T22:01:14Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2024-08-07T07:16:53Z
day: '01'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1088/1367-2630/abae44
ec_funded: 1
external_id:
isi:
- '000573298000001'
file:
- access_level: open_access
checksum: c9238fff422e7a957c3a0d559f756b3a
content_type: application/pdf
creator: dernst
date_created: 2020-10-12T12:18:47Z
date_updated: 2020-10-12T12:18:47Z
file_id: '8650'
file_name: 2020_NewJournalPhysics_Rzdkowski.pdf
file_size: 2725143
relation: main_file
success: 1
file_date_updated: 2020-10-12T12:18:47Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 05A235A0-7A3F-11EA-A408-12923DDC885E
grant_number: '25681'
name: Analytic and machine learning approaches to composite quantum impurities
- _id: 26986C82-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02641
name: A path-integral approach to composite impurities
publication: New Journal of Physics
publication_identifier:
issn:
- '13672630'
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
related_material:
record:
- id: '10759'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Detecting composite orders in layered models via machine 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: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 22
year: '2020'
...
---
_id: '8645'
abstract:
- lang: eng
text: 'Epistasis, the context-dependence of the contribution of an amino acid substitution
to fitness, is common in evolution. To detect epistasis, fitness must be measured
for at least four genotypes: the reference genotype, two different single mutants
and a double mutant with both of the single mutations. For higher-order epistasis
of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional
hypercube in genotype space forming a ‘combinatorially complete dataset’. So far,
only a handful of such datasets have been produced by manual curation. Concurrently,
random mutagenesis experiments have produced measurements of fitness and other
phenotypes in a high-throughput manner, potentially containing a number of combinatorially
complete datasets. We present an effective recursive algorithm for finding all
hypercube structures in random mutagenesis experimental data. To test the algorithm,
we applied it to the data from a recent HIS3 protein dataset and found all 199
847 053 unique combinatorially complete genotype combinations of dimensionality
ranging from 2 to 12. The algorithm may be useful for researchers looking for
higher-order epistasis in their high-throughput experimental data.'
acknowledgement: 'This work was supported by the European Research Council under the
European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement
335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute
of Science and Technology. The work was started at the School of Molecular and Theoretical
Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman
Scientists Support Grant in Centre for Genomic Regulation (CRG). '
article_processing_charge: No
article_type: original
author:
- first_name: Laura A
full_name: Esteban, Laura A
last_name: Esteban
- first_name: Lyubov R
full_name: Lonishin, Lyubov R
last_name: Lonishin
- first_name: Daniil M
full_name: Bobrovskiy, Daniil M
last_name: Bobrovskiy
- first_name: Gregory
full_name: Leleytner, Gregory
last_name: Leleytner
- first_name: Natalya S
full_name: Bogatyreva, Natalya S
last_name: Bogatyreva
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: 'Dmitry N '
full_name: 'Ivankov, Dmitry N '
last_name: Ivankov
citation:
ama: 'Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million
combinatorially complete datasets from a single experiment. Bioinformatics.
2020;36(6):1960-1962. doi:10.1093/bioinformatics/btz841'
apa: 'Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva,
N. S., Kondrashov, F., & Ivankov, D. N. (2020). HypercubeME: Two hundred million
combinatorially complete datasets from a single experiment. Bioinformatics.
Oxford Academic. https://doi.org/10.1093/bioinformatics/btz841'
chicago: 'Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner,
Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N Ivankov. “HypercubeME:
Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.”
Bioinformatics. Oxford Academic, 2020. https://doi.org/10.1093/bioinformatics/btz841.'
ieee: 'L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially
complete datasets from a single experiment,” Bioinformatics, vol. 36, no.
6. Oxford Academic, pp. 1960–1962, 2020.'
ista: 'Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov
F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete
datasets from a single experiment. Bioinformatics. 36(6), 1960–1962.'
mla: 'Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially
Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no.
6, Oxford Academic, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841.'
short: L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva,
F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.
date_created: 2020-10-11T22:01:14Z
date_published: 2020-03-15T00:00:00Z
date_updated: 2023-08-22T09:57:29Z
day: '15'
ddc:
- '000'
- '570'
department:
- _id: FyKo
doi: 10.1093/bioinformatics/btz841
ec_funded: 1
external_id:
isi:
- '000538696800054'
pmid:
- '31742320'
file:
- access_level: open_access
checksum: 21d6f71839deb3b83e4a356193f72767
content_type: application/pdf
creator: dernst
date_created: 2020-10-12T12:02:09Z
date_updated: 2020-10-12T12:02:09Z
file_id: '8649'
file_name: 2020_Bioinformatics_Esteban.pdf
file_size: 308341
relation: main_file
success: 1
file_date_updated: 2020-10-12T12:02:09Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '6'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 1960-1962
pmid: 1
project:
- _id: 26120F5C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335980'
name: Systematic investigation of epistasis in molecular evolution
publication: Bioinformatics
publication_identifier:
eissn:
- 1460-2059
issn:
- 1367-4803
publication_status: published
publisher: Oxford Academic
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'HypercubeME: Two hundred million combinatorially complete datasets from a
single experiment'
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 36
year: '2020'
...
---
_id: '8652'
abstract:
- lang: eng
text: Nature creates electrons with two values of the spin projection quantum number.
In certain applications, it is important to filter electrons with one spin projection
from the rest. Such filtering is not trivial, since spin-dependent interactions
are often weak, and cannot lead to any substantial effect. Here we propose an
efficient spin filter based upon scattering from a two-dimensional crystal, which
is made of aligned point magnets. The polarization of the outgoing electron flux
is controlled by the crystal, and reaches maximum at specific values of the parameters.
In our scheme, polarization increase is accompanied by higher reflectivity of
the crystal. High transmission is feasible in scattering from a quantum cavity
made of two crystals. Our findings can be used for studies of low-energy spin-dependent
scattering from two-dimensional ordered structures made of magnetic atoms or aligned
chiral molecules.
acknowledgement: "This work has received funding from the European Union’s Horizon
2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement
No. 754411 (A.G.V. and A.G.). M.L. acknowledges support by the Austrian Science
Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC)
Starting\r\nGrant No. 801770 (ANGULON)."
article_number: '178'
article_processing_charge: Yes
article_type: original
author:
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- 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: Ghazaryan A, Lemeshko M, Volosniev A. Filtering spins by scattering from a
lattice of point magnets. Communications Physics. 2020;3. doi:10.1038/s42005-020-00445-8
apa: Ghazaryan, A., Lemeshko, M., & Volosniev, A. (2020). Filtering spins by
scattering from a lattice of point magnets. Communications Physics. Springer
Nature. https://doi.org/10.1038/s42005-020-00445-8
chicago: Ghazaryan, Areg, Mikhail Lemeshko, and Artem Volosniev. “Filtering Spins
by Scattering from a Lattice of Point Magnets.” Communications Physics.
Springer Nature, 2020. https://doi.org/10.1038/s42005-020-00445-8.
ieee: A. Ghazaryan, M. Lemeshko, and A. Volosniev, “Filtering spins by scattering
from a lattice of point magnets,” Communications Physics, vol. 3. Springer
Nature, 2020.
ista: Ghazaryan A, Lemeshko M, Volosniev A. 2020. Filtering spins by scattering
from a lattice of point magnets. Communications Physics. 3, 178.
mla: Ghazaryan, Areg, et al. “Filtering Spins by Scattering from a Lattice of Point
Magnets.” Communications Physics, vol. 3, 178, Springer Nature, 2020, doi:10.1038/s42005-020-00445-8.
short: A. Ghazaryan, M. Lemeshko, A. Volosniev, Communications Physics 3 (2020).
date_created: 2020-10-13T09:48:59Z
date_published: 2020-10-09T00:00:00Z
date_updated: 2023-08-22T09:58:46Z
day: '09'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1038/s42005-020-00445-8
ec_funded: 1
external_id:
isi:
- '000581681000001'
file:
- access_level: open_access
checksum: 60cd35b99f0780acffc7b6060e49ec8b
content_type: application/pdf
creator: dernst
date_created: 2020-10-14T15:16:28Z
date_updated: 2020-10-14T15:16:28Z
file_id: '8662'
file_name: 2020_CommPhysics_Ghazaryan.pdf
file_size: 1462934
relation: main_file
success: 1
file_date_updated: 2020-10-14T15:16:28Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Communications Physics
publication_identifier:
issn:
- 2399-3650
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Filtering spins by scattering from a lattice of point magnets
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 3
year: '2020'
...
---
_id: '8653'
abstract:
- lang: eng
text: "Mutations are the raw material of evolution and come in many different flavors.
Point mutations change a single letter in the DNA sequence, while copy number
mutations like duplications or deletions add or remove many letters of the DNA
sequence simultaneously. Each type of mutation exhibits specific properties like
its rate of formation and reversal. \r\nGene expression is a fundamental phenotype
that can be altered by both, point and copy number mutations. The following thesis
is concerned with the dynamics of gene expression evolution and how it is affected
by the properties exhibited by point and copy number mutations. Specifically,
we are considering i) copy number mutations during adaptation to fluctuating environments
and ii) the interaction of copy number and point mutations during adaptation to
constant environments. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
citation:
ama: Tomanek I. The evolution of gene expression by copy number and point mutations.
2020. doi:10.15479/AT:ISTA:8653
apa: Tomanek, I. (2020). The evolution of gene expression by copy number and
point mutations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8653
chicago: Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and
Point Mutations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8653.
ieee: I. Tomanek, “The evolution of gene expression by copy number and point mutations,”
Institute of Science and Technology Austria, 2020.
ista: Tomanek I. 2020. The evolution of gene expression by copy number and point
mutations. Institute of Science and Technology Austria.
mla: Tomanek, Isabella. The Evolution of Gene Expression by Copy Number and Point
Mutations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8653.
short: I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations,
Institute of Science and Technology Austria, 2020.
date_created: 2020-10-13T13:02:33Z
date_published: 2020-10-13T00:00:00Z
date_updated: 2023-09-07T13:22:42Z
day: '13'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:8653
file:
- access_level: closed
checksum: c01d9f59794b4b70528f37637c17ad02
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: itomanek
date_created: 2020-10-16T12:14:21Z
date_updated: 2021-10-20T22:30:03Z
embargo_to: open_access
file_id: '8666'
file_name: Thesis_ITomanek_final_201016.docx
file_size: 25131884
relation: source_file
- access_level: open_access
checksum: f8edbc3b0f81a780e13ca1e561d42d8b
content_type: application/pdf
creator: itomanek
date_created: 2020-10-16T12:14:21Z
date_updated: 2021-10-20T22:30:03Z
embargo: 2021-10-19
file_id: '8667'
file_name: Thesis_ITomanek_final_201016.pdf
file_size: 15405675
relation: main_file
file_date_updated: 2021-10-20T22:30:03Z
has_accepted_license: '1'
keyword:
- duplication
- amplification
- promoter
- CNV
- AMGET
- experimental evolution
- Escherichia coli
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '117'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7652'
relation: research_data
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: The evolution of gene expression by copy number and point mutations
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8657'
abstract:
- lang: eng
text: "Synthesis of proteins – translation – is a fundamental process of life. Quantitative
studies anchor translation into the context of bacterial physiology and reveal
several mathematical relationships, called “growth laws,” which capture physiological
feedbacks between protein synthesis and cell growth. Growth laws describe the
dependency of the ribosome abundance as a function of growth rate, which can change
depending on the growth conditions. Perturbations of translation reveal that bacteria
employ a compensatory strategy in which the reduced translation capability results
in increased expression of the translation machinery.\r\nPerturbations of translation
are achieved in various ways; clinically interesting is the application of translation-targeting
antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology
are often poorly understood. Bacterial responses to two or more simultaneously
applied antibiotics are even more puzzling. The combined antibiotic effect determines
the type of drug interaction, which ranges from synergy (the effect is stronger
than expected) to antagonism (the effect is weaker) and suppression (one of the
drugs loses its potency).\r\nIn the first part of this work, we systematically
measure the pairwise interaction network for translation inhibitors that interfere
with different steps in translation. We find that the interactions are surprisingly
diverse and tend to be more antagonistic. To explore the underlying mechanisms,
we begin with a minimal biophysical model of combined antibiotic action. We base
this model on the kinetics of antibiotic uptake and binding together with the
physiological response described by the growth laws. The biophysical model explains
some drug interactions, but not all; it specifically fails to predict suppression.\r\nIn
the second part of this work, we hypothesize that elusive suppressive drug interactions
result from the interplay between ribosomes halted in different stages of translation.
To elucidate this putative mechanism of drug interactions between translation
inhibitors, we generate translation bottlenecks genetically using in- ducible
control of translation factors that regulate well-defined translation cycle steps.
These perturbations accurately mimic antibiotic action and drug interactions,
supporting that the interplay of different translation bottlenecks partially causes
these interactions.\r\nWe extend this approach by varying two translation bottlenecks
simultaneously. This approach reveals the suppression of translocation inhibition
by inhibited translation. We rationalize this effect by modeling dense traffic
of ribosomes that move on transcripts in a translation factor-mediated manner.
This model predicts a dissolution of traffic jams caused by inhibited translocation
when the density of ribosome traffic is reduced by lowered initiation. We base
this model on the growth laws and quantitative relationships between different
translation and growth parameters.\r\nIn the final part of this work, we describe
a set of tools aimed at quantification of physiological and translation parameters.
We further develop a simple model that directly connects the abundance of a translation
factor with the growth rate, which allows us to extract physiological parameters
describing initiation. We demonstrate the development of tools for measuring translation
rate.\r\nThis thesis showcases how a combination of high-throughput growth rate
mea- surements, genetics, and modeling can reveal mechanisms of drug interactions.
Furthermore, by a gradual transition from combinations of antibiotics to precise
genetic interventions, we demonstrated the equivalency between genetic and chemi-
cal perturbations of translation. These findings tile the path for quantitative
studies of antibiotic combinations and illustrate future approaches towards the
quantitative description of translation."
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
acknowledgement: I thank Life Science Facilities for their continuous support with
providing top-notch laboratory materials, keeping the devices humming, and coordinating
the repairs and building of custom-designed laboratory equipment with the MIBA Machine
shop.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
citation:
ama: 'Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics
and physiology. 2020. doi:10.15479/AT:ISTA:8657'
apa: 'Kavcic, B. (2020). Perturbations of protein synthesis: from antibiotics
to genetics and physiology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8657'
chicago: 'Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to
Genetics and Physiology.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8657.'
ieee: 'B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics
and physiology,” Institute of Science and Technology Austria, 2020.'
ista: 'Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics
and physiology. Institute of Science and Technology Austria.'
mla: 'Kavcic, Bor. Perturbations of Protein Synthesis: From Antibiotics to Genetics
and Physiology. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8657.'
short: 'B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics
and Physiology, Institute of Science and Technology Austria, 2020.'
date_created: 2020-10-13T16:46:14Z
date_published: 2020-10-14T00:00:00Z
date_updated: 2023-09-07T13:20:48Z
day: '14'
ddc:
- '571'
- '530'
- '570'
degree_awarded: PhD
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:8657
file:
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content_type: application/pdf
creator: bkavcic
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date_updated: 2021-10-07T22:30:03Z
embargo: 2021-10-06
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file_size: 52636162
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creator: bkavcic
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date_updated: 2021-10-07T22:30:03Z
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file_name: 2020b.zip
file_size: 321681247
relation: source_file
file_date_updated: 2021-10-07T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '271'
publication_identifier:
isbn:
- 978-3-99078-011-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7673'
relation: part_of_dissertation
status: public
- id: '8250'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
title: 'Perturbations of protein synthesis: from antibiotics to genetics and physiology'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8669'
abstract:
- lang: eng
text: Pancreatic islets play an essential role in regulating blood glucose level.
Although the molecular pathways underlying islet cell differentiation are beginning
to be resolved, the cellular basis of islet morphogenesis and fate allocation
remain unclear. By combining unbiased and targeted lineage tracing, we address
the events leading to islet formation in the mouse. From the statistical analysis
of clones induced at multiple embryonic timepoints, here we show that, during
the secondary transition, islet formation involves the aggregation of multiple
equipotent endocrine progenitors that transition from a phase of stochastic amplification
by cell division into a phase of sublineage restriction and limited islet fission.
Together, these results explain quantitatively the heterogeneous size distribution
and degree of polyclonality of maturing islets, as well as dispersion of progenitors
within and between islets. Further, our results show that, during the secondary
transition, α- and β-cells are generated in a contemporary manner. Together, these
findings provide insight into the cellular basis of islet development.
article_number: '5037'
article_processing_charge: No
article_type: original
author:
- first_name: Magdalena K.
full_name: Sznurkowska, Magdalena K.
last_name: Sznurkowska
- 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: Roberta
full_name: Azzarelli, Roberta
last_name: Azzarelli
- first_name: Lemonia
full_name: Chatzeli, Lemonia
last_name: Chatzeli
- first_name: Tatsuro
full_name: Ikeda, Tatsuro
last_name: Ikeda
- first_name: Shosei
full_name: Yoshida, Shosei
last_name: Yoshida
- first_name: Anna
full_name: Philpott, Anna
last_name: Philpott
- first_name: Benjamin D
full_name: Simons, Benjamin D
last_name: Simons
citation:
ama: Sznurkowska MK, Hannezo EB, Azzarelli R, et al. Tracing the cellular basis
of islet specification in mouse pancreas. Nature Communications. 2020;11.
doi:10.1038/s41467-020-18837-3
apa: Sznurkowska, M. K., Hannezo, E. B., Azzarelli, R., Chatzeli, L., Ikeda, T.,
Yoshida, S., … Simons, B. D. (2020). Tracing the cellular basis of islet specification
in mouse pancreas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18837-3
chicago: Sznurkowska, Magdalena K., Edouard B Hannezo, Roberta Azzarelli, Lemonia
Chatzeli, Tatsuro Ikeda, Shosei Yoshida, Anna Philpott, and Benjamin D Simons.
“Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature
Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18837-3.
ieee: M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification
in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 2020.
ista: Sznurkowska MK, Hannezo EB, Azzarelli R, Chatzeli L, Ikeda T, Yoshida S, Philpott
A, Simons BD. 2020. Tracing the cellular basis of islet specification in mouse
pancreas. Nature Communications. 11, 5037.
mla: Sznurkowska, Magdalena K., et al. “Tracing the Cellular Basis of Islet Specification
in Mouse Pancreas.” Nature Communications, vol. 11, 5037, Springer Nature,
2020, doi:10.1038/s41467-020-18837-3.
short: M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida,
A. Philpott, B.D. Simons, Nature Communications 11 (2020).
date_created: 2020-10-18T22:01:35Z
date_published: 2020-10-07T00:00:00Z
date_updated: 2023-08-22T10:18:17Z
day: '07'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1038/s41467-020-18837-3
external_id:
isi:
- '000577244600003'
pmid:
- '33028844'
file:
- access_level: open_access
checksum: 0ecc0eab72d2d50694852579611a6624
content_type: application/pdf
creator: dernst
date_created: 2020-10-19T11:27:46Z
date_updated: 2020-10-19T11:27:46Z
file_id: '8677'
file_name: 2020_NatureComm_Sznurkowska.pdf
file_size: 5540540
relation: main_file
success: 1
file_date_updated: 2020-10-19T11:27:46Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tracing the cellular basis of islet specification in mouse pancreas
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '8670'
abstract:
- lang: eng
text: The α–z Rényi relative entropies are a two-parameter family of Rényi relative
entropies that are quantum generalizations of the classical α-Rényi relative entropies.
In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α,
z) for which the data processing inequality (DPI) is valid. In this paper, we
give algebraic conditions for the equality in DPI. For the full range of parameters
(α, z), we give necessary conditions and sufficient conditions. For most parameters,
we give equivalent conditions. This generalizes and strengthens the results of
Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)].
acknowledgement: This research was supported by the European Union’s Horizon 2020
research and innovation program under the Marie Skłodowska-Curie Grant Agreement
No. 754411. The author would like to thank Anna Vershynina and Sarah Chehade for
their helpful comments.
article_number: '102201'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Haonan
full_name: Zhang, Haonan
id: D8F41E38-9E66-11E9-A9E2-65C2E5697425
last_name: Zhang
citation:
ama: Zhang H. Equality conditions of data processing inequality for α-z Rényi relative
entropies. Journal of Mathematical Physics. 2020;61(10). doi:10.1063/5.0022787
apa: Zhang, H. (2020). Equality conditions of data processing inequality for α-z
Rényi relative entropies. Journal of Mathematical Physics. AIP Publishing.
https://doi.org/10.1063/5.0022787
chicago: Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z
Rényi Relative Entropies.” Journal of Mathematical Physics. AIP Publishing,
2020. https://doi.org/10.1063/5.0022787.
ieee: H. Zhang, “Equality conditions of data processing inequality for α-z Rényi
relative entropies,” Journal of Mathematical Physics, vol. 61, no. 10.
AIP Publishing, 2020.
ista: Zhang H. 2020. Equality conditions of data processing inequality for α-z Rényi
relative entropies. Journal of Mathematical Physics. 61(10), 102201.
mla: Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi
Relative Entropies.” Journal of Mathematical Physics, vol. 61, no. 10,
102201, AIP Publishing, 2020, doi:10.1063/5.0022787.
short: H. Zhang, Journal of Mathematical Physics 61 (2020).
date_created: 2020-10-18T22:01:36Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2023-08-22T10:32:29Z
day: '01'
department:
- _id: JaMa
doi: 10.1063/5.0022787
ec_funded: 1
external_id:
arxiv:
- '2007.06644'
isi:
- '000578529200001'
intvolume: ' 61'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2007.06644
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Mathematical Physics
publication_identifier:
issn:
- '00222488'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Equality conditions of data processing inequality for α-z Rényi relative entropies
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 61
year: '2020'
...
---
_id: '8671'
abstract:
- lang: eng
text: 'We study relations between evidence theory and S-approximation spaces. Both
theories have their roots in the analysis of Dempsterchr(''39'')s multivalued
mappings and lower and upper probabilities, and have close relations to rough
sets. We show that an S-approximation space, satisfying a monotonicity condition,
can induce a natural belief structure which is a fundamental block in evidence
theory. We also demonstrate that one can induce a natural belief structure on
one set, given a belief structure on another set, if the two sets are related
by a partial monotone S-approximation space. '
acknowledgement: We are very grateful to the anonymous reviewer for detailed comments
and suggestions that significantly improved the presentation of this paper. The
research was partially supported by a DOC fellowship of the Austrian Academy of
Sciences.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: A.
full_name: Shakiba, A.
last_name: Shakiba
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: M.R.
full_name: Hooshmandasl, M.R.
last_name: Hooshmandasl
- first_name: M.
full_name: Alambardar Meybodi, M.
last_name: Alambardar Meybodi
citation:
ama: Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. A note on
belief structures and s-approximation spaces. Iranian Journal of Mathematical
Sciences and Informatics. 2020;15(2):117-128. doi:10.29252/ijmsi.15.2.117
apa: Shakiba, A., Goharshady, A. K., Hooshmandasl, M. R., & Alambardar Meybodi,
M. (2020). A note on belief structures and s-approximation spaces. Iranian
Journal of Mathematical Sciences and Informatics. Iranian Academic Center
for Education, Culture and Research. https://doi.org/10.29252/ijmsi.15.2.117
chicago: Shakiba, A., Amir Kafshdar Goharshady, M.R. Hooshmandasl, and M. Alambardar
Meybodi. “A Note on Belief Structures and S-Approximation Spaces.” Iranian
Journal of Mathematical Sciences and Informatics. Iranian Academic Center
for Education, Culture and Research, 2020. https://doi.org/10.29252/ijmsi.15.2.117.
ieee: A. Shakiba, A. K. Goharshady, M. R. Hooshmandasl, and M. Alambardar Meybodi,
“A note on belief structures and s-approximation spaces,” Iranian Journal of
Mathematical Sciences and Informatics, vol. 15, no. 2. Iranian Academic Center
for Education, Culture and Research, pp. 117–128, 2020.
ista: Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. 2020. A note
on belief structures and s-approximation spaces. Iranian Journal of Mathematical
Sciences and Informatics. 15(2), 117–128.
mla: Shakiba, A., et al. “A Note on Belief Structures and S-Approximation Spaces.”
Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no.
2, Iranian Academic Center for Education, Culture and Research, 2020, pp. 117–28,
doi:10.29252/ijmsi.15.2.117.
short: A. Shakiba, A.K. Goharshady, M.R. Hooshmandasl, M. Alambardar Meybodi, Iranian
Journal of Mathematical Sciences and Informatics 15 (2020) 117–128.
date_created: 2020-10-18T22:01:36Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2023-10-16T09:25:00Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.29252/ijmsi.15.2.117
external_id:
arxiv:
- '1805.10672'
file:
- access_level: open_access
checksum: f299661a6d51cda6d255a76be696f48d
content_type: application/pdf
creator: dernst
date_created: 2020-10-19T11:14:20Z
date_updated: 2020-10-19T11:14:20Z
file_id: '8676'
file_name: 2020_ijmsi_Shakiba_accepted.pdf
file_size: 261688
relation: main_file
success: 1
file_date_updated: 2020-10-19T11:14:20Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 117-128
project:
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: Iranian Journal of Mathematical Sciences and Informatics
publication_identifier:
eissn:
- 2008-9473
issn:
- 1735-4463
publication_status: published
publisher: Iranian Academic Center for Education, Culture and Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: A note on belief structures and s-approximation spaces
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2020'
...
---
_id: '8672'
abstract:
- lang: eng
text: Cell fate transitions are key to development and homeostasis. It is thus essential
to understand the cellular mechanisms controlling fate transitions. Cell division
has been implicated in fate decisions in many stem cell types, including neuronal
and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells,
the role of division remains unclear. Here, we show that exit from naive pluripotency
in mouse ES cells generally occurs after a division. We further show that exit
timing is strongly correlated between sister cells, which remain connected by
cytoplasmic bridges long after division, and that bridge abscission progressively
accelerates as cells exit naive pluripotency. Finally, interfering with abscission
impairs naive pluripotency exit, and artificially inducing abscission accelerates
it. Altogether, our data indicate that a switch in the division machinery leading
to faster abscission regulates pluripotency exit. Our study identifies abscission
as a key cellular process coupling cell division to fate transitions.
acknowledgement: This work was supported by the Medical Research Council UK (MRC Program
award MC_UU_12018/5 ), the European Research Council (starting grant 311637 -MorphoCorDiv
and consolidator grant 820188 -NanoMechShape to E.K.P.), and the Leverhulme Trust
(Leverhulme Prize in Biological Sciences to E.K.P.). K.J.C. acknowledges support
from the Royal Society (Royal Society Research Fellowship). A.C. acknowledges support
from EMBO ( ALTF 2015-563 ), the Wellcome Trust ( 201334/Z/16/Z ), and the Fondation
Bettencourt-Schueller (Prix Jeune Chercheur, 2015).
article_processing_charge: No
article_type: original
author:
- first_name: Agathe
full_name: Chaigne, Agathe
last_name: Chaigne
- first_name: Céline
full_name: Labouesse, Céline
last_name: Labouesse
- first_name: Ian J.
full_name: White, Ian J.
last_name: White
- first_name: Meghan
full_name: Agnew, Meghan
last_name: Agnew
- 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: Kevin J.
full_name: Chalut, Kevin J.
last_name: Chalut
- first_name: Ewa K.
full_name: Paluch, Ewa K.
last_name: Paluch
citation:
ama: Chaigne A, Labouesse C, White IJ, et al. Abscission couples cell division to
embryonic stem cell fate. Developmental Cell. 2020;55(2):195-208. doi:10.1016/j.devcel.2020.09.001
apa: Chaigne, A., Labouesse, C., White, I. J., Agnew, M., Hannezo, E. B., Chalut,
K. J., & Paluch, E. K. (2020). Abscission couples cell division to embryonic
stem cell fate. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.09.001
chicago: Chaigne, Agathe, Céline Labouesse, Ian J. White, Meghan Agnew, Edouard
B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Abscission Couples Cell Division
to Embryonic Stem Cell Fate.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.09.001.
ieee: A. Chaigne et al., “Abscission couples cell division to embryonic stem
cell fate,” Developmental Cell, vol. 55, no. 2. Elsevier, pp. 195–208,
2020.
ista: Chaigne A, Labouesse C, White IJ, Agnew M, Hannezo EB, Chalut KJ, Paluch EK.
2020. Abscission couples cell division to embryonic stem cell fate. Developmental
Cell. 55(2), 195–208.
mla: Chaigne, Agathe, et al. “Abscission Couples Cell Division to Embryonic Stem
Cell Fate.” Developmental Cell, vol. 55, no. 2, Elsevier, 2020, pp. 195–208,
doi:10.1016/j.devcel.2020.09.001.
short: A. Chaigne, C. Labouesse, I.J. White, M. Agnew, E.B. Hannezo, K.J. Chalut,
E.K. Paluch, Developmental Cell 55 (2020) 195–208.
date_created: 2020-10-18T22:01:37Z
date_published: 2020-10-26T00:00:00Z
date_updated: 2023-08-22T10:16:58Z
day: '26'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1016/j.devcel.2020.09.001
external_id:
isi:
- '000582501100012'
pmid:
- '32979313'
file:
- access_level: open_access
checksum: 88e1a031a61689165d19a19c2f16d795
content_type: application/pdf
creator: dernst
date_created: 2021-02-04T10:20:02Z
date_updated: 2021-02-04T10:20:02Z
file_id: '9086'
file_name: 2020_DevelopmCell_Chaigne.pdf
file_size: 6929686
relation: main_file
success: 1
file_date_updated: 2021-02-04T10:20:02Z
has_accepted_license: '1'
intvolume: ' 55'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 195-208
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- '18781551'
issn:
- '15345807'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Abscission couples cell division to embryonic stem cell fate
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 55
year: '2020'
...
---
_id: '8674'
abstract:
- lang: eng
text: 'Extrasynaptic actions of glutamate are limited by high-affinity transporters
expressed by perisynaptic astroglial processes (PAPs): this helps maintain point-to-point
transmission in excitatory circuits. Memory formation in the brain is associated
with synaptic remodeling, but how this affects PAPs and therefore extrasynaptic
glutamate actions is poorly understood. Here, we used advanced imaging methods,
in situ and in vivo, to find that a classical synaptic memory mechanism, long-term
potentiation (LTP), triggers withdrawal of PAPs from potentiated synapses. Optical
glutamate sensors combined with patch-clamp and 3D molecular localization reveal
that LTP induction thus prompts spatial retreat of astroglial glutamate transporters,
boosting glutamate spillover and NMDA-receptor-mediated inter-synaptic cross-talk.
The LTP-triggered PAP withdrawal involves NKCC1 transporters and the actin-controlling
protein cofilin but does not depend on major Ca2+-dependent cascades in astrocytes.
We have therefore uncovered a mechanism by which a memory trace at one synapse
could alter signal handling by multiple neighboring connections.'
acknowledgement: We thank J. Angibaud for organotypic cultures and R. Chereau and
J. Tonnesen for help with the STED microscope; also D. Gonzales and the Neurocentre
Magendie INSERM U1215 Genotyping Platform, for breeding management and genotyping.
This work was supported by the Wellcome Trust Principal Fellowships 101896 and 212251,
ERC Advanced Grant 323113, ERC Proof-of-Concept Grant 767372, EC FP7 ITN 606950,
and EU CSA 811011 (D.A.R.); NRW-Rückkehrerpogramm, UCL Excellence Fellowship, German
Research Foundation (DFG) SPP1757 and SFB1089 (C.H.); Human Frontiers Science Program
(C.H., C.J.J., and H.J.); EMBO Long-Term Fellowship (L.B.); Marie Curie FP7 PIRG08-GA-2010-276995
(A.P.), ASTROMODULATION (S.R.); Equipe FRM DEQ 201 303 26519, Conseil Régional d’Aquitaine
R12056GG, INSERM (S.H.R.O.); ANR SUPERTri, ANR Castro (ANR-17-CE16-0002), R-13-BSV4-0007-01,
Université de Bordeaux, labex BRAIN (S.H.R.O. and U.V.N.); CNRS (A.P., S.H.R.O.,
and U.V.N.); HFSP, ANR CEXC, and France-BioImaging ANR-10-INSB-04 (U.V.N.); and
FP7 MemStick Project No. 201600 (M.G.S.).
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Lucie
full_name: Bard, Lucie
last_name: Bard
- first_name: Aude
full_name: Panatier, Aude
last_name: Panatier
- first_name: James P.
full_name: Reynolds, James P.
last_name: Reynolds
- first_name: Olga
full_name: Kopach, Olga
last_name: Kopach
- first_name: Nikolay I.
full_name: Medvedev, Nikolay I.
last_name: Medvedev
- first_name: Daniel
full_name: Minge, Daniel
last_name: Minge
- first_name: Michel K.
full_name: Herde, Michel K.
last_name: Herde
- first_name: Stefanie
full_name: Anders, Stefanie
last_name: Anders
- first_name: Igor
full_name: Kraev, Igor
last_name: Kraev
- first_name: Janosch P.
full_name: Heller, Janosch P.
last_name: Heller
- first_name: Sylvain
full_name: Rama, Sylvain
last_name: Rama
- first_name: Kaiyu
full_name: Zheng, Kaiyu
last_name: Zheng
- first_name: Thomas P.
full_name: Jensen, Thomas P.
last_name: Jensen
- first_name: Inmaculada
full_name: Sanchez-Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez-Romero
- first_name: Colin J.
full_name: Jackson, Colin J.
last_name: Jackson
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Ole Petter
full_name: Ottersen, Ole Petter
last_name: Ottersen
- first_name: Erlend Arnulf
full_name: Nagelhus, Erlend Arnulf
last_name: Nagelhus
- first_name: Stephane H.R.
full_name: Oliet, Stephane H.R.
last_name: Oliet
- first_name: Michael G.
full_name: Stewart, Michael G.
last_name: Stewart
- first_name: U. VAlentin
full_name: Nägerl, U. VAlentin
last_name: Nägerl
- first_name: 'Dmitri A. '
full_name: 'Rusakov, Dmitri A. '
last_name: Rusakov
citation:
ama: Henneberger C, Bard L, Panatier A, et al. LTP induction boosts glutamate spillover
by driving withdrawal of perisynaptic astroglia. Neuron. 2020;108(5):P919-936.E11.
doi:10.1016/j.neuron.2020.08.030
apa: Henneberger, C., Bard, L., Panatier, A., Reynolds, J. P., Kopach, O., Medvedev,
N. I., … Rusakov, D. A. (2020). LTP induction boosts glutamate spillover by driving
withdrawal of perisynaptic astroglia. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.08.030
chicago: Henneberger, Christian, Lucie Bard, Aude Panatier, James P. Reynolds, Olga
Kopach, Nikolay I. Medvedev, Daniel Minge, et al. “LTP Induction Boosts Glutamate
Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron. Elsevier,
2020. https://doi.org/10.1016/j.neuron.2020.08.030.
ieee: C. Henneberger et al., “LTP induction boosts glutamate spillover by
driving withdrawal of perisynaptic astroglia,” Neuron, vol. 108, no. 5.
Elsevier, p. P919–936.E11, 2020.
ista: Henneberger C, Bard L, Panatier A, Reynolds JP, Kopach O, Medvedev NI, Minge
D, Herde MK, Anders S, Kraev I, Heller JP, Rama S, Zheng K, Jensen TP, Sanchez-Romero
I, Jackson CJ, Janovjak HL, Ottersen OP, Nagelhus EA, Oliet SHR, Stewart MG, Nägerl
UVa, Rusakov DA. 2020. LTP induction boosts glutamate spillover by driving withdrawal
of perisynaptic astroglia. Neuron. 108(5), P919–936.E11.
mla: Henneberger, Christian, et al. “LTP Induction Boosts Glutamate Spillover by
Driving Withdrawal of Perisynaptic Astroglia.” Neuron, vol. 108, no. 5,
Elsevier, 2020, p. P919–936.E11, doi:10.1016/j.neuron.2020.08.030.
short: C. Henneberger, L. Bard, A. Panatier, J.P. Reynolds, O. Kopach, N.I. Medvedev,
D. Minge, M.K. Herde, S. Anders, I. Kraev, J.P. Heller, S. Rama, K. Zheng, T.P.
Jensen, I. Sanchez-Romero, C.J. Jackson, H.L. Janovjak, O.P. Ottersen, E.A. Nagelhus,
S.H.R. Oliet, M.G. Stewart, U.Va. Nägerl, D.A. Rusakov, Neuron 108 (2020) P919–936.E11.
date_created: 2020-10-18T22:01:38Z
date_published: 2020-12-09T00:00:00Z
date_updated: 2023-08-22T09:59:29Z
day: '09'
ddc:
- '570'
department:
- _id: HaJa
doi: 10.1016/j.neuron.2020.08.030
external_id:
isi:
- '000603428000010'
pmid:
- '32976770'
file:
- access_level: open_access
checksum: 054562bb50165ef9a1f46631c1c5e36b
content_type: application/pdf
creator: dernst
date_created: 2020-12-10T14:42:09Z
date_updated: 2020-12-10T14:42:09Z
file_id: '8939'
file_name: 2020_Neuron_Henneberger.pdf
file_size: 7518960
relation: main_file
success: 1
file_date_updated: 2020-12-10T14:42:09Z
has_accepted_license: '1'
intvolume: ' 108'
isi: 1
issue: '5'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: P919-936.E11
pmid: 1
publication: Neuron
publication_identifier:
eissn:
- '10974199'
issn:
- '08966273'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic
astroglia
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 108
year: '2020'
...
---
_id: '8679'
abstract:
- lang: eng
text: A central goal of artificial intelligence in high-stakes decision-making applications
is to design a single algorithm that simultaneously expresses generalizability
by learning coherent representations of their world and interpretable explanations
of its dynamics. Here, we combine brain-inspired neural computation principles
and scalable deep learning architectures to design compact neural controllers
for task-specific compartments of a full-stack autonomous vehicle control system.
We discover that a single algorithm with 19 control neurons, connecting 32 encapsulated
input features to outputs by 253 synapses, learns to map high-dimensional inputs
into steering commands. This system shows superior generalizability, interpretability
and robustness compared with orders-of-magnitude larger black-box learning systems.
The obtained neural agents enable high-fidelity autonomy for task-specific parts
of a complex autonomous system.
article_processing_charge: No
article_type: original
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Alexander
full_name: Amini, Alexander
last_name: Amini
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. Neural circuit
policies enabling auditable autonomy. Nature Machine Intelligence. 2020;2:642-652.
doi:10.1038/s42256-020-00237-3
apa: Lechner, M., Hasani, R., Amini, A., Henzinger, T. A., Rus, D., & Grosu,
R. (2020). Neural circuit policies enabling auditable autonomy. Nature Machine
Intelligence. Springer Nature. https://doi.org/10.1038/s42256-020-00237-3
chicago: Lechner, Mathias, Ramin Hasani, Alexander Amini, Thomas A Henzinger, Daniela
Rus, and Radu Grosu. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature
Machine Intelligence. Springer Nature, 2020. https://doi.org/10.1038/s42256-020-00237-3.
ieee: M. Lechner, R. Hasani, A. Amini, T. A. Henzinger, D. Rus, and R. Grosu, “Neural
circuit policies enabling auditable autonomy,” Nature Machine Intelligence,
vol. 2. Springer Nature, pp. 642–652, 2020.
ista: Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. 2020. Neural circuit
policies enabling auditable autonomy. Nature Machine Intelligence. 2, 642–652.
mla: Lechner, Mathias, et al. “Neural Circuit Policies Enabling Auditable Autonomy.”
Nature Machine Intelligence, vol. 2, Springer Nature, 2020, pp. 642–52,
doi:10.1038/s42256-020-00237-3.
short: M. Lechner, R. Hasani, A. Amini, T.A. Henzinger, D. Rus, R. Grosu, Nature
Machine Intelligence 2 (2020) 642–652.
date_created: 2020-10-19T13:46:06Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2023-08-22T10:36:06Z
day: '01'
department:
- _id: ToHe
doi: 10.1038/s42256-020-00237-3
external_id:
isi:
- '000583337200011'
intvolume: ' 2'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 642-652
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Nature Machine Intelligence
publication_identifier:
eissn:
- 2522-5839
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-deep-learning-models/
scopus_import: '1'
status: public
title: Neural circuit policies enabling auditable autonomy
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 2
year: '2020'
...
---
_id: '8680'
abstract:
- lang: eng
text: Animal development entails the organization of specific cell types in space
and time, and spatial patterns must form in a robust manner. In the zebrafish
spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen
signaling and large-scale cellular rearrangements during morphogenesis and growth.
By directly measuring adhesion forces and preferences for three types of endogenous
neural progenitors, we provide evidence for the differential adhesion model in
which differences in intercellular adhesion mediate cell sorting. Cell type–specific
combinatorial expression of different classes of cadherins (N-cadherin, cadherin
11, and protocadherin 19) results in homotypic preference ex vivo and patterning
robustness in vivo. Furthermore, the differential adhesion code is regulated by
the sonic hedgehog morphogen gradient. We propose that robust patterning during
tissue morphogenesis results from interplay between adhesion-based self-organization
and morphogen-directed patterning.
acknowledgement: "We thank the members of the Megason and Heisenberg labs for critical
discussions of and technical assistance during the work and B. Appel, S. Holley,
J. Jontes, and D. Gilmour for transgenic fish. This work is supported by the Damon
Runyon Cancer Foundation, a NICHD K99 fellowship (1K99HD092623), a Travelling Fellowship
of the Company of Biologists, a Collaborative Research grant from the Burroughs
Wellcome Foundation (T.Y.-C.T.), NIH grant 01GM107733 (T.Y.-C.T. and S.G.M.), NIH
grant R01NS102322 (T.C.-C. and H.K.), and an ERC advanced grant\r\n(MECSPEC) (C.-P.H.)."
article_processing_charge: No
article_type: original
author:
- first_name: Tony Y.-C.
full_name: Tsai, Tony Y.-C.
last_name: Tsai
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Peng
full_name: Xia, Peng
id: 4AB6C7D0-F248-11E8-B48F-1D18A9856A87
last_name: Xia
orcid: 0000-0002-5419-7756
- first_name: Tugba
full_name: Colak-Champollion, Tugba
last_name: Colak-Champollion
- first_name: Holger
full_name: Knaut, Holger
last_name: Knaut
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Sean G.
full_name: Megason, Sean G.
last_name: Megason
citation:
ama: Tsai TY-C, Sikora MK, Xia P, et al. An adhesion code ensures robust pattern
formation during tissue morphogenesis. Science. 2020;370(6512):113-116.
doi:10.1126/science.aba6637
apa: Tsai, T. Y.-C., Sikora, M. K., Xia, P., Colak-Champollion, T., Knaut, H., Heisenberg,
C.-P. J., & Megason, S. G. (2020). An adhesion code ensures robust pattern
formation during tissue morphogenesis. Science. American Association for
the Advancement of Science. https://doi.org/10.1126/science.aba6637
chicago: Tsai, Tony Y.-C., Mateusz K Sikora, Peng Xia, Tugba Colak-Champollion,
Holger Knaut, Carl-Philipp J Heisenberg, and Sean G. Megason. “An Adhesion Code
Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science.
American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba6637.
ieee: T. Y.-C. Tsai et al., “An adhesion code ensures robust pattern formation
during tissue morphogenesis,” Science, vol. 370, no. 6512. American Association
for the Advancement of Science, pp. 113–116, 2020.
ista: Tsai TY-C, Sikora MK, Xia P, Colak-Champollion T, Knaut H, Heisenberg C-PJ,
Megason SG. 2020. An adhesion code ensures robust pattern formation during tissue
morphogenesis. Science. 370(6512), 113–116.
mla: Tsai, Tony Y. C., et al. “An Adhesion Code Ensures Robust Pattern Formation
during Tissue Morphogenesis.” Science, vol. 370, no. 6512, American Association
for the Advancement of Science, 2020, pp. 113–16, doi:10.1126/science.aba6637.
short: T.Y.-C. Tsai, M.K. Sikora, P. Xia, T. Colak-Champollion, H. Knaut, C.-P.J.
Heisenberg, S.G. Megason, Science 370 (2020) 113–116.
date_created: 2020-10-19T14:09:38Z
date_published: 2020-10-02T00:00:00Z
date_updated: 2023-08-22T10:36:35Z
day: '02'
department:
- _id: CaHe
doi: 10.1126/science.aba6637
ec_funded: 1
external_id:
isi:
- '000579169000053'
intvolume: ' 370'
isi: 1
issue: '6512'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/803635v1
month: '10'
oa: 1
oa_version: Preprint
page: 113-116
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/sticking-together/
scopus_import: '1'
status: public
title: An adhesion code ensures robust pattern formation during tissue morphogenesis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 370
year: '2020'
...