---
_id: '14834'
abstract:
- lang: eng
text: Bacteria divide by binary fission. The protein machine responsible for this
process is the divisome, a transient assembly of more than 30 proteins in and
on the surface of the cytoplasmic membrane. Together, they constrict the cell
envelope and remodel the peptidoglycan layer to eventually split the cell into
two. For Escherichia coli, most molecular players involved in this process have
probably been identified, but obtaining the quantitative information needed for
a mechanistic understanding can often not be achieved from experiments in vivo
alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution
experiments have been crucial to shed light on molecular processes normally hidden
in the complex environment of the living cell. In this review, we summarize how
rebuilding the divisome from purified components – or at least parts of it - have
been instrumental to obtain the detailed mechanistic understanding of the bacterial
cell division machinery that we have today.
acknowledgement: We acknowledge members of the Loose laboratory at ISTA for helpful
discussions—in particular M. Kojic for his insightful comments. This work was supported
by the Austrian Science Fund (FWF P34607) to M.L.
article_number: '151380'
article_processing_charge: Yes
article_type: review
author:
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: 'Radler P, Loose M. A dynamic duo: Understanding the roles of FtsZ and FtsA
for Escherichia coli cell division through in vitro approaches. European Journal
of Cell Biology. 2024;103(1). doi:10.1016/j.ejcb.2023.151380'
apa: 'Radler, P., & Loose, M. (2024). A dynamic duo: Understanding the roles
of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches.
European Journal of Cell Biology. Elsevier. https://doi.org/10.1016/j.ejcb.2023.151380'
chicago: 'Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles
of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.”
European Journal of Cell Biology. Elsevier, 2024. https://doi.org/10.1016/j.ejcb.2023.151380.'
ieee: 'P. Radler and M. Loose, “A dynamic duo: Understanding the roles of FtsZ and
FtsA for Escherichia coli cell division through in vitro approaches,” European
Journal of Cell Biology, vol. 103, no. 1. Elsevier, 2024.'
ista: 'Radler P, Loose M. 2024. A dynamic duo: Understanding the roles of FtsZ and
FtsA for Escherichia coli cell division through in vitro approaches. European
Journal of Cell Biology. 103(1), 151380.'
mla: 'Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles
of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.”
European Journal of Cell Biology, vol. 103, no. 1, 151380, Elsevier, 2024,
doi:10.1016/j.ejcb.2023.151380.'
short: P. Radler, M. Loose, European Journal of Cell Biology 103 (2024).
date_created: 2024-01-18T08:16:43Z
date_published: 2024-01-12T00:00:00Z
date_updated: 2024-01-23T08:37:13Z
day: '12'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1016/j.ejcb.2023.151380
external_id:
pmid:
- '38218128'
has_accepted_license: '1'
intvolume: ' 103'
issue: '1'
keyword:
- Cell Biology
- General Medicine
- Histology
- Pathology and Forensic Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.ejcb.2023.151380
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: "Understanding bacterial cell division by in vitro\r\nreconstitution"
publication: European Journal of Cell Biology
publication_identifier:
issn:
- 0171-9335
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli
cell division through in vitro approaches'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 103
year: '2024'
...
---
_id: '15033'
abstract:
- lang: eng
text: The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF)
is among the best studied trafficking regulators in plants, playing crucial and
unique developmental roles in patterning and polarity. The current models place
GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at
the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis
(CME). The mechanistic basis of the developmental function of GN, distinct from
the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains
elusive. Insights from this study largely extend the current notions of GN function.
We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures
distinct from clathrin-coated pits, while CME and secretion proceed normally in
gn knockouts. The functional GN mutant variant GNfewerroots,
absent from the GA, suggests that the cell periphery is the major site of GN action
responsible for its developmental function. Following inhibition by Brefeldin
A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting
selective molecular associations en route to the cell periphery. A study of GN-GNL1
chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN
function in a partially redundant manner. Together, this study offers significant
steps toward the elucidation of the mechanism underlying unique cellular and development
functions of GNOM.
acknowledgement: "The authors would like to gratefully acknowledge Dr Xixi Zhang for
cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research\r\nCouncil
Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří
Friml"
article_processing_charge: Yes
article_type: original
author:
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Ivana
full_name: Matijevic, Ivana
id: 83c17ce3-15b2-11ec-abd3-f486545870bd
last_name: Matijevic
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM
ARF-GEF mediated from the cell periphery. eLife. 2024;13. doi:10.7554/elife.68993
apa: Adamowski, M., Matijevic, I., & Friml, J. (2024). Developmental patterning
function of GNOM ARF-GEF mediated from the cell periphery. ELife. eLife
Sciences Publications. https://doi.org/10.7554/elife.68993
chicago: Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning
Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife. eLife
Sciences Publications, 2024. https://doi.org/10.7554/elife.68993.
ieee: M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function
of GNOM ARF-GEF mediated from the cell periphery,” eLife, vol. 13. eLife
Sciences Publications, 2024.
ista: Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function
of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.
mla: Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF
Mediated from the Cell Periphery.” ELife, vol. 13, eLife Sciences Publications,
2024, doi:10.7554/elife.68993.
short: M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).
date_created: 2024-02-27T07:10:11Z
date_published: 2024-02-21T00:00:00Z
date_updated: 2024-02-28T12:29:43Z
day: '21'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.7554/elife.68993
ec_funded: 1
has_accepted_license: '1'
intvolume: ' 13'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.7554/eLife.68993
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: epub_ahead
publisher: eLife Sciences Publications
quality_controlled: '1'
status: public
title: Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2024'
...
---
_id: '14776'
abstract:
- lang: eng
text: Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally
important roles in folding and quality control of newly synthesized proteins that
transiently pass through the ER en route to their final destinations. These soluble
residents of the ER are themselves endowed with an ER retrieval signal that enables
the cell to bring the escaped residents back from the Golgi. Here, by using purified
proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific
protease, introduces two breaks at the C-terminus of the N. tabacum ER resident
calreticulin-3. These cleavages resulted in removal of either a dipeptide or a
hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of
the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative
mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated
loss of the ER accumulation of the protein. Notably, upon its escape from the
ER, calreticulin-3 was further processed by an unknown protease(s) to generate
the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted
into the apoplast. Our study thus identified a specific proteolytic enzyme capable
of precise detachment of the ER retrieval signal from a plant ER resident protein,
with implications for the further fate of the escaped resident.
acknowledgement: "We thank C.U.T. Hellen for critically reading the manuscript. The
MALDI MS facility and CLSM became available to us in the framework of Moscow State
University Development Programs PNG 5.13 and PNR 5.13.\r\nThis work was funded by
the Russian Science Foundation, grant numbers 19-14-00010 and 22-14-00071."
article_number: '16527'
article_processing_charge: Yes
article_type: original
author:
- first_name: Anastasiia
full_name: Teplova, Anastasiia
id: e3736151-106c-11ec-b916-c2558e2762c6
last_name: Teplova
- first_name: Artemii A.
full_name: Pigidanov, Artemii A.
last_name: Pigidanov
- first_name: Marina V.
full_name: Serebryakova, Marina V.
last_name: Serebryakova
- first_name: Sergei A.
full_name: Golyshev, Sergei A.
last_name: Golyshev
- first_name: Raisa A.
full_name: Galiullina, Raisa A.
last_name: Galiullina
- first_name: Nina V.
full_name: Chichkova, Nina V.
last_name: Chichkova
- first_name: Andrey B.
full_name: Vartapetian, Andrey B.
last_name: Vartapetian
citation:
ama: Teplova A, Pigidanov AA, Serebryakova MV, et al. Phytaspase Is capable of detaching
the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International
Journal of Molecular Sciences. 2023;24(22). doi:10.3390/ijms242216527
apa: Teplova, A., Pigidanov, A. A., Serebryakova, M. V., Golyshev, S. A., Galiullina,
R. A., Chichkova, N. V., & Vartapetian, A. B. (2023). Phytaspase Is capable
of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3.
International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms242216527
chicago: Teplova, Anastasiia, Artemii A. Pigidanov, Marina V. Serebryakova, Sergei
A. Golyshev, Raisa A. Galiullina, Nina V. Chichkova, and Andrey B. Vartapetian.
“Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal
from Tobacco Calreticulin-3.” International Journal of Molecular Sciences.
MDPI, 2023. https://doi.org/10.3390/ijms242216527.
ieee: A. Teplova et al., “Phytaspase Is capable of detaching the endoplasmic
reticulum retrieval signal from tobacco calreticulin-3,” International Journal
of Molecular Sciences, vol. 24, no. 22. MDPI, 2023.
ista: Teplova A, Pigidanov AA, Serebryakova MV, Golyshev SA, Galiullina RA, Chichkova
NV, Vartapetian AB. 2023. Phytaspase Is capable of detaching the endoplasmic reticulum
retrieval signal from tobacco calreticulin-3. International Journal of Molecular
Sciences. 24(22), 16527.
mla: Teplova, Anastasiia, et al. “Phytaspase Is Capable of Detaching the Endoplasmic
Reticulum Retrieval Signal from Tobacco Calreticulin-3.” International Journal
of Molecular Sciences, vol. 24, no. 22, 16527, MDPI, 2023, doi:10.3390/ijms242216527.
short: A. Teplova, A.A. Pigidanov, M.V. Serebryakova, S.A. Golyshev, R.A. Galiullina,
N.V. Chichkova, A.B. Vartapetian, International Journal of Molecular Sciences
24 (2023).
date_created: 2024-01-10T09:24:35Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2024-01-10T13:41:10Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3390/ijms242216527
external_id:
isi:
- '001113792600001'
pmid:
- '38003717'
file:
- access_level: open_access
checksum: 4df7d206ba022b7f54eff1f0aec1659a
content_type: application/pdf
creator: dernst
date_created: 2024-01-10T13:39:42Z
date_updated: 2024-01-10T13:39:42Z
file_id: '14791'
file_name: 2023_IJMS_Teplova.pdf
file_size: 2637784
relation: main_file
success: 1
file_date_updated: 2024-01-10T13:39:42Z
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
issue: '22'
keyword:
- Inorganic Chemistry
- Organic Chemistry
- Physical and Theoretical Chemistry
- Computer Science Applications
- Spectroscopy
- Molecular Biology
- General Medicine
- Catalysis
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: International Journal of Molecular Sciences
publication_identifier:
issn:
- 1422-0067
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal
from tobacco calreticulin-3
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2023'
...
---
_id: '14783'
abstract:
- lang: eng
text: Connexin 43, an astroglial gap junction protein, is enriched in perisynaptic
astroglial processes and plays major roles in synaptic transmission. We have previously
found that astroglial Cx43 controls synaptic glutamate levels and allows for activity-dependent
glutamine release to sustain physiological synaptic transmissions and cognitiogns.
However, whether Cx43 is important for the release of synaptic vesicles, which
is a critical component of synaptic efficacy, remains unanswered. Here, using
transgenic mice with a glial conditional knockout of Cx43 (Cx43−/−), we investigate
whether and how astrocytes regulate the release of synaptic vesicles from hippocampal
synapses. We report that CA1 pyramidal neurons and their synapses develop normally
in the absence of astroglial Cx43. However, a significant impairment in synaptic
vesicle distribution and release dynamics were observed. In particular, the FM1-43
assays performed using two-photon live imaging and combined with multi-electrode
array stimulation in acute hippocampal slices, revealed a slower rate of synaptic
vesicle release in Cx43−/− mice. Furthermore, paired-pulse recordings showed that
synaptic vesicle release probability was also reduced and is dependent on glutamine
supply via Cx43 hemichannel (HC). Taken together, we have uncovered a role for
Cx43 in regulating presynaptic functions by controlling the rate and probability
of synaptic vesicle release. Our findings further highlight the significance of
astroglial Cx43 in synaptic transmission and efficacy.
acknowledgement: 'This research was funded by grants from the European Research Council
(Consolidator grant #683154) and European Union’s Horizon 2020 research and innovation
program (Marie Sklodowska-Curie Innovative Training Networks, grant #722053, EU-GliaPhD)
to N.R., as well as from FP7-PEOPLE Marie Curie Intra-European Fellowship for career
development (grant #622289) to G.C. We thank Elena Dossi, Grégory Ghézali, and Jérémie
Teillon for support with setting up the MEA system for the two-photon microscope.
We would also like to thank Tayfun Palaz for their technical assistance with the
EM preparations.'
article_number: '1133'
article_processing_charge: Yes
article_type: original
author:
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Oana
full_name: Chever, Oana
last_name: Chever
- first_name: Astrid
full_name: Rollenhagen, Astrid
last_name: Rollenhagen
- first_name: Nicole
full_name: Quenech’du, Nicole
last_name: Quenech’du
- first_name: Pascal
full_name: Ezan, Pascal
last_name: Ezan
- first_name: Joachim H. R.
full_name: Lübke, Joachim H. R.
last_name: Lübke
- first_name: Nathalie
full_name: Rouach, Nathalie
last_name: Rouach
citation:
ama: Cheung GT, Chever O, Rollenhagen A, et al. Astroglial connexin 43 regulates
synaptic vesicle release at hippocampal synapses. Cells. 2023;12(8). doi:10.3390/cells12081133
apa: Cheung, G. T., Chever, O., Rollenhagen, A., Quenech’du, N., Ezan, P., Lübke,
J. H. R., & Rouach, N. (2023). Astroglial connexin 43 regulates synaptic vesicle
release at hippocampal synapses. Cells. MDPI. https://doi.org/10.3390/cells12081133
chicago: Cheung, Giselle T, Oana Chever, Astrid Rollenhagen, Nicole Quenech’du,
Pascal Ezan, Joachim H. R. Lübke, and Nathalie Rouach. “Astroglial Connexin 43
Regulates Synaptic Vesicle Release at Hippocampal Synapses.” Cells. MDPI,
2023. https://doi.org/10.3390/cells12081133.
ieee: G. T. Cheung et al., “Astroglial connexin 43 regulates synaptic vesicle
release at hippocampal synapses,” Cells, vol. 12, no. 8. MDPI, 2023.
ista: Cheung GT, Chever O, Rollenhagen A, Quenech’du N, Ezan P, Lübke JHR, Rouach
N. 2023. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal
synapses. Cells. 12(8), 1133.
mla: Cheung, Giselle T., et al. “Astroglial Connexin 43 Regulates Synaptic Vesicle
Release at Hippocampal Synapses.” Cells, vol. 12, no. 8, 1133, MDPI, 2023,
doi:10.3390/cells12081133.
short: G.T. Cheung, O. Chever, A. Rollenhagen, N. Quenech’du, P. Ezan, J.H.R. Lübke,
N. Rouach, Cells 12 (2023).
date_created: 2024-01-10T09:46:35Z
date_published: 2023-04-11T00:00:00Z
date_updated: 2024-01-16T09:29:35Z
day: '11'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.3390/cells12081133
external_id:
isi:
- '000977445700001'
pmid:
- '37190042'
file:
- access_level: open_access
checksum: 6798cd75d8857976fbc58a43fd173d68
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T09:26:52Z
date_updated: 2024-01-16T09:26:52Z
file_id: '14808'
file_name: 2023_Cells_Cheung.pdf
file_size: 7931643
relation: main_file
success: 1
file_date_updated: 2024-01-16T09:26:52Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '8'
keyword:
- General Medicine
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cells
publication_identifier:
issn:
- 2073-4409
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2023'
...
---
_id: '14830'
abstract:
- lang: eng
text: We study the problem of learning controllers for discrete-time non-linear
stochastic dynamical systems with formal reach-avoid guarantees. This work presents
the first method for providing formal reach-avoid guarantees, which combine and
generalize stability and safety guarantees, with a tolerable probability threshold
p in [0,1] over the infinite time horizon. Our method leverages advances in machine
learning literature and it represents formal certificates as neural networks.
In particular, we learn a certificate in the form of a reach-avoid supermartingale
(RASM), a novel notion that we introduce in this work. Our RASMs provide reachability
and avoidance guarantees by imposing constraints on what can be viewed as a stochastic
extension of level sets of Lyapunov functions for deterministic systems. Our approach
solves several important problems -- it can be used to learn a control policy
from scratch, to verify a reach-avoid specification for a fixed control policy,
or to fine-tune a pre-trained policy if it does not satisfy the reach-avoid specification.
We validate our approach on 3 stochastic non-linear reinforcement learning tasks.
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093, ERC
CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.
article_processing_charge: No
arxiv: 1
author:
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- 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: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Zikelic D, Lechner M, Henzinger TA, Chatterjee K. Learning control policies
for stochastic systems with reach-avoid guarantees. In: Proceedings of the
37th AAAI Conference on Artificial Intelligence. Vol 37. Association for the
Advancement of Artificial Intelligence; 2023:11926-11935. doi:10.1609/aaai.v37i10.26407'
apa: 'Zikelic, D., Lechner, M., Henzinger, T. A., & Chatterjee, K. (2023). Learning
control policies for stochastic systems with reach-avoid guarantees. In Proceedings
of the 37th AAAI Conference on Artificial Intelligence (Vol. 37, pp. 11926–11935).
Washington, DC, United States: Association for the Advancement of Artificial Intelligence.
https://doi.org/10.1609/aaai.v37i10.26407'
chicago: Zikelic, Dorde, Mathias Lechner, Thomas A Henzinger, and Krishnendu Chatterjee.
“Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.”
In Proceedings of the 37th AAAI Conference on Artificial Intelligence,
37:11926–35. Association for the Advancement of Artificial Intelligence, 2023.
https://doi.org/10.1609/aaai.v37i10.26407.
ieee: D. Zikelic, M. Lechner, T. A. Henzinger, and K. Chatterjee, “Learning control
policies for stochastic systems with reach-avoid guarantees,” in Proceedings
of the 37th AAAI Conference on Artificial Intelligence, Washington, DC, United
States, 2023, vol. 37, no. 10, pp. 11926–11935.
ista: 'Zikelic D, Lechner M, Henzinger TA, Chatterjee K. 2023. Learning control
policies for stochastic systems with reach-avoid guarantees. Proceedings of the
37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial
Intelligence vol. 37, 11926–11935.'
mla: Zikelic, Dorde, et al. “Learning Control Policies for Stochastic Systems with
Reach-Avoid Guarantees.” Proceedings of the 37th AAAI Conference on Artificial
Intelligence, vol. 37, no. 10, Association for the Advancement of Artificial
Intelligence, 2023, pp. 11926–35, doi:10.1609/aaai.v37i10.26407.
short: D. Zikelic, M. Lechner, T.A. Henzinger, K. Chatterjee, in:, Proceedings of
the 37th AAAI Conference on Artificial Intelligence, Association for the Advancement
of Artificial Intelligence, 2023, pp. 11926–11935.
conference:
end_date: 2023-02-14
location: Washington, DC, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2023-02-07
date_created: 2024-01-18T07:44:31Z
date_published: 2023-06-26T00:00:00Z
date_updated: 2025-07-14T09:10:02Z
day: '26'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1609/aaai.v37i10.26407
ec_funded: 1
external_id:
arxiv:
- '2210.05308'
intvolume: ' 37'
issue: '10'
keyword:
- General Medicine
language:
- iso: eng
month: '06'
oa_version: Preprint
page: 11926-11935
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Proceedings of the 37th AAAI Conference on Artificial Intelligence
publication_identifier:
eissn:
- 2374-3468
issn:
- 2159-5399
publication_status: published
publisher: Association for the Advancement of Artificial Intelligence
quality_controlled: '1'
related_material:
record:
- id: '14600'
relation: earlier_version
status: public
status: public
title: Learning control policies for stochastic systems with reach-avoid guarantees
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2023'
...
---
_id: '14835'
abstract:
- lang: ger
text: Aromatische Seitenketten sind wichtige Indikatoren für die Plastizität von
Proteinen und bilden oft entscheidende Kontakte bei Protein‐Protein‐Wechselwirkungen.
Wir untersuchten aromatische Reste in den beiden strukturell homologen cross‐β
Amyloidfibrillen HET‐s und HELLF mit Hilfe eines spezifischen Ansatzes zur Isotopenmarkierung
und Festkörper NMR mit Drehung am magischen Winkel. Das dynamische Verhalten der
aromatischen Reste Phe und Tyr deutet darauf hin, dass der hydrophobe Amyloidkern
starr ist und keine Anzeichen von “atmenden Bewegungen” auf einer Zeitskala von
Hunderten von Millisekunden zeigt. Aromatische Reste, die exponiert an der Fibrillenoberfläche
sitzen, haben zwar eine starre Ringachse, weisen aber Ringflips auf verschiedenen
Zeitskalen von Nanosekunden bis Mikrosekunden auf. Unser Ansatz bietet einen direkten
Einblick in die Bewegungen des hydrophoben Kerns und ermöglicht eine bessere Bewertung
der Konformationsheterogenität, die aus einem NMR‐Strukturensemble einer solchen
Cross‐β‐Amyloidstruktur hervorgeht.
acknowledgement: Wir danken Albert A. Smith (Leipzig) für aufschlussreiche Diskussionen.
Diese Arbeit wurde mit Mitteln des Europäischen Forschungsrats (StG-2012-311318
an P.S.) unterstützt und nutzte die Plattformen des Grenoble Instruct-ERIC Center
(ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) im Rahmen der Grenoble Partnership for Structural
Biology (PSB) sowie die Einrichtungen und das Fachwissen der Biophysical and Structural
Chemistry Platform (BPCS) am IECB, CNRS UAR3033, INSERM US001 und der Universität
Bordeaux.
article_number: e202219314
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Mélanie
full_name: Berbon, Mélanie
last_name: Berbon
- first_name: Alicia
full_name: Vallet, Alicia
last_name: Vallet
- first_name: Axelle
full_name: Grelard, Axelle
last_name: Grelard
- first_name: Estelle
full_name: Morvan, Estelle
last_name: Morvan
- first_name: Benjamin
full_name: Bardiaux, Benjamin
last_name: Bardiaux
- first_name: Roman
full_name: Lichtenecker, Roman
last_name: Lichtenecker
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
- first_name: Antoine
full_name: Loquet, Antoine
last_name: Loquet
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Becker LM, Berbon M, Vallet A, et al. Der starre Kern und die flexible Oberfläche
von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen
Resten. Angewandte Chemie. 2023;135(19). doi:10.1002/ange.202219314
apa: Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B.,
… Schanda, P. (2023). Der starre Kern und die flexible Oberfläche von Amyloidfibrillen
– Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. Angewandte
Chemie. Wiley. https://doi.org/10.1002/ange.202219314
chicago: Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle
Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet,
and Paul Schanda. “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen
– Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.” Angewandte
Chemie. Wiley, 2023. https://doi.org/10.1002/ange.202219314.
ieee: L. M. Becker et al., “Der starre Kern und die flexible Oberfläche von
Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten,”
Angewandte Chemie, vol. 135, no. 19. Wiley, 2023.
ista: Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker
R, Ernst M, Loquet A, Schanda P. 2023. Der starre Kern und die flexible Oberfläche
von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen
Resten. Angewandte Chemie. 135(19), e202219314.
mla: Becker, Lea Marie, et al. “Der starre Kern und die flexible Oberfläche von
Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.”
Angewandte Chemie, vol. 135, no. 19, e202219314, Wiley, 2023, doi:10.1002/ange.202219314.
short: L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R.
Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie 135 (2023).
date_created: 2024-01-18T10:01:01Z
date_published: 2023-05-02T00:00:00Z
date_updated: 2024-01-23T12:23:35Z
day: '02'
ddc:
- '540'
department:
- _id: PaSc
doi: 10.1002/ange.202219314
file:
- access_level: open_access
checksum: 98e68d370159f7be52a3d7c8a8ee1198
content_type: application/pdf
creator: dernst
date_created: 2024-01-23T08:57:01Z
date_updated: 2024-01-23T08:57:01Z
file_id: '14876'
file_name: 2023_AngewChem_Becker.pdf
file_size: 1004676
relation: main_file
success: 1
file_date_updated: 2024-01-23T08:57:01Z
has_accepted_license: '1'
intvolume: ' 135'
issue: '19'
keyword:
- General Medicine
language:
- iso: ger
month: '05'
oa: 1
oa_version: Published Version
publication: Angewandte Chemie
publication_identifier:
eissn:
- 1521-3757
issn:
- 0044-8249
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning
NMR Spektroskopie von aromatischen Resten
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2023'
...
---
_id: '14854'
abstract:
- lang: eng
text: "\r\nAbstract\r\nWe study the spectrum of the Fröhlich Hamiltonian for the
polaron at fixed total momentum. We prove the existence of excited eigenvalues
between the ground state energy and the essential spectrum at strong coupling.
In fact, our main result shows that the number of excited energy bands diverges
in the strong coupling limit. To prove this we derive upper bounds for the min-max
values of the corresponding fiber Hamiltonians and compare them with the bottom
of the essential spectrum, a lower bound on which was recently obtained by Brooks
and Seiringer (Comm. Math. Phys. 404:1 (2023), 287–337). The upper bounds are
given in terms of the ground state energy band shifted by momentum-independent
excitation energies determined by an effective Hamiltonian of Bogoliubov type."
article_processing_charge: No
article_type: original
author:
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Mitrouskas DJ, Seiringer R. Ubiquity of bound states for the strongly coupled
polaron. Pure and Applied Analysis. 2023;5(4):973-1008. doi:10.2140/paa.2023.5.973
apa: Mitrouskas, D. J., & Seiringer, R. (2023). Ubiquity of bound states for
the strongly coupled polaron. Pure and Applied Analysis. Mathematical Sciences
Publishers. https://doi.org/10.2140/paa.2023.5.973
chicago: Mitrouskas, David Johannes, and Robert Seiringer. “Ubiquity of Bound States
for the Strongly Coupled Polaron.” Pure and Applied Analysis. Mathematical
Sciences Publishers, 2023. https://doi.org/10.2140/paa.2023.5.973.
ieee: D. J. Mitrouskas and R. Seiringer, “Ubiquity of bound states for the strongly
coupled polaron,” Pure and Applied Analysis, vol. 5, no. 4. Mathematical
Sciences Publishers, pp. 973–1008, 2023.
ista: Mitrouskas DJ, Seiringer R. 2023. Ubiquity of bound states for the strongly
coupled polaron. Pure and Applied Analysis. 5(4), 973–1008.
mla: Mitrouskas, David Johannes, and Robert Seiringer. “Ubiquity of Bound States
for the Strongly Coupled Polaron.” Pure and Applied Analysis, vol. 5, no.
4, Mathematical Sciences Publishers, 2023, pp. 973–1008, doi:10.2140/paa.2023.5.973.
short: D.J. Mitrouskas, R. Seiringer, Pure and Applied Analysis 5 (2023) 973–1008.
date_created: 2024-01-22T08:24:23Z
date_published: 2023-12-15T00:00:00Z
date_updated: 2024-01-23T12:55:12Z
day: '15'
department:
- _id: RoSe
doi: 10.2140/paa.2023.5.973
intvolume: ' 5'
issue: '4'
keyword:
- General Medicine
language:
- iso: eng
month: '12'
oa_version: None
page: 973-1008
publication: Pure and Applied Analysis
publication_identifier:
issn:
- 2578-5885
- 2578-5893
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
status: public
title: Ubiquity of bound states for the strongly coupled polaron
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2023'
...
---
_id: '14274'
abstract:
- lang: eng
text: Immune responses rely on the rapid and coordinated migration of leukocytes.
Whereas it is well established that single-cell migration is often guided by gradients
of chemokines and other chemoattractants, it remains poorly understood how these
gradients are generated, maintained, and modulated. By combining experimental
data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor
(GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor
that steers migration, CCR7 also acts as a generator and a modulator of chemotactic
gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively
internalize the receptor and ligand as part of the canonical GPCR desensitization
response. We show that CCR7 internalization also acts as an effective sink for
the chemoattractant, dynamically shaping the spatiotemporal distribution of the
chemokine. This mechanism drives complex collective migration patterns, enabling
DCs to create or sharpen chemotactic gradients. We further show that these self-generated
gradients can sustain the long-range guidance of DCs, adapt collective migration
patterns to the size and geometry of the environment, and provide a guidance cue
for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses
and consumes its ligand can thus provide a novel mode of cellular self-organization.
acknowledgement: "We thank I. de Vries and the Scientific Service Units (Life Sciences,
Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute
of Science and Technology Austria for excellent support, as well as all the rotation
students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis
work was supported by grants from the European Research Council under the European
Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant
agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20)
to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research
Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U.
was supported by the European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie grant agreement no. 754411."
article_number: adc9584
article_processing_charge: No
article_type: original
author:
- first_name: Jonna H
full_name: Alanko, Jonna H
id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87
last_name: Alanko
orcid: 0000-0002-7698-3061
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
- first_name: Nikola
full_name: Canigova, Nikola
id: 3795523E-F248-11E8-B48F-1D18A9856A87
last_name: Canigova
orcid: 0000-0002-8518-5926
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink
for CCL19 to coordinate collective leukocyte migration. Science Immunology.
2023;8(87). doi:10.1126/sciimmunol.adc9584
apa: Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin,
J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate
collective leukocyte migration. Science Immunology. American Association
for the Advancement of Science. https://doi.org/10.1126/sciimmunol.adc9584
chicago: Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz,
Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor
and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science
Immunology. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciimmunol.adc9584.
ieee: J. H. Alanko et al., “CCR7 acts as both a sensor and a sink for CCL19
to coordinate collective leukocyte migration,” Science Immunology, vol.
8, no. 87. American Association for the Advancement of Science, 2023.
ista: Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB,
Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective
leukocyte migration. Science Immunology. 8(87), adc9584.
mla: Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to
Coordinate Collective Leukocyte Migration.” Science Immunology, vol. 8,
no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:10.1126/sciimmunol.adc9584.
short: J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B.
Hannezo, M.K. Sixt, Science Immunology 8 (2023).
date_created: 2023-09-06T08:07:51Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-12-21T14:30:01Z
day: '01'
department:
- _id: MiSi
- _id: EdHa
- _id: NanoFab
doi: 10.1126/sciimmunol.adc9584
ec_funded: 1
external_id:
isi:
- '001062110600003'
pmid:
- '37656776'
intvolume: ' 8'
isi: 1
issue: '87'
keyword:
- General Medicine
- Immunology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1126/sciimmunol.adc9584
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 265E2996-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01250-B20
name: Nano-Analytics of Cellular Systems
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Science Immunology
publication_identifier:
issn:
- 2470-9468
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
record:
- id: '14279'
relation: research_data
status: public
- id: '14697'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte
migration
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2023'
...
---
_id: '12172'
abstract:
- lang: eng
text: In industrial reactors and equipment, non-ideality is quite a common phenomenon
rather than an exception. These deviations from ideality impact the process's
overall efficiency and the effectiveness of the equipment. To recognize the associated
non-ideality, one needs to have enough understanding of the formulation of the
equations and in-depth knowledge of the residence time distribution (RTD) data
of real reactors. In the current work, step input and pulse input were used to
create RTD data for Cascade continuous stirred tank reactors (CSTRs). For the
aforementioned configuration, experiments were run at various flow rates to validate
the developed characteristic equations. To produce RTD data, distilled water was
utilized as the flowing fluid, and NaOH was the tracer substance. The ideal behavior
of tracer concentration exits age distribution, and cumulative fraction for each
setup and each input was plotted and experimental results were compared with perfect
behavior. Deviation of concentration exit age distribution and cumulative fractional
distribution from ideal behavior is more in pulse input as compared to a step
input. For ideal cases, the exit age distribution curve and cumulative fraction
curves are independent of the type of input. But a significant difference was
observed for the two cases, which may be due to non-measurable fluctuations in
volumetric flow rate, non-achievement of instant injection of tracer in case of
pulse input, and slight variations in the sampling period. Further, with increasing
flow rate, concentration, exit age, and cumulative fractional curves shifted upward,
and this behavior matches with the actual case.
article_processing_charge: No
article_type: original
author:
- first_name: Bushra
full_name: Khatoon, Bushra
last_name: Khatoon
- first_name: Shoaib
full_name: Kamil, Shoaib
id: 185a19af-dc7d-11ea-9b2f-8eb2201959e9
last_name: Kamil
- first_name: Hitesh
full_name: Babu, Hitesh
last_name: Babu
- first_name: M.
full_name: Siraj Alam, M.
last_name: Siraj Alam
citation:
ama: 'Khatoon B, Kamil S, Babu H, Siraj Alam M. Experimental analysis of Cascade
CSTRs with step and pulse inputs. Materials Today: Proceedings. 2023;78(Part
1):40-47. doi:10.1016/j.matpr.2022.11.037'
apa: 'Khatoon, B., Kamil, S., Babu, H., & Siraj Alam, M. (2023). Experimental
analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings.
Elsevier. https://doi.org/10.1016/j.matpr.2022.11.037'
chicago: 'Khatoon, Bushra, Shoaib Kamil, Hitesh Babu, and M. Siraj Alam. “Experimental
Analysis of Cascade CSTRs with Step and Pulse Inputs.” Materials Today: Proceedings.
Elsevier, 2023. https://doi.org/10.1016/j.matpr.2022.11.037.'
ieee: 'B. Khatoon, S. Kamil, H. Babu, and M. Siraj Alam, “Experimental analysis
of Cascade CSTRs with step and pulse inputs,” Materials Today: Proceedings,
vol. 78, no. Part 1. Elsevier, pp. 40–47, 2023.'
ista: 'Khatoon B, Kamil S, Babu H, Siraj Alam M. 2023. Experimental analysis of
Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. 78(Part
1), 40–47.'
mla: 'Khatoon, Bushra, et al. “Experimental Analysis of Cascade CSTRs with Step
and Pulse Inputs.” Materials Today: Proceedings, vol. 78, no. Part 1, Elsevier,
2023, pp. 40–47, doi:10.1016/j.matpr.2022.11.037.'
short: 'B. Khatoon, S. Kamil, H. Babu, M. Siraj Alam, Materials Today: Proceedings
78 (2023) 40–47.'
date_created: 2023-01-12T12:11:26Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-08-16T09:08:11Z
day: '20'
department:
- _id: BjHo
doi: 10.1016/j.matpr.2022.11.037
intvolume: ' 78'
issue: Part 1
keyword:
- General Medicine
language:
- iso: eng
month: '03'
oa_version: None
page: 40-47
publication: 'Materials Today: Proceedings'
publication_identifier:
issn:
- 2214-7853
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Experimental analysis of Cascade CSTRs with step and pulse inputs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
year: '2023'
...
---
_id: '11448'
abstract:
- lang: eng
text: Studies of protein fitness landscapes reveal biophysical constraints guiding
protein evolution and empower prediction of functional proteins. However, generalisation
of these findings is limited due to scarceness of systematic data on fitness landscapes
of proteins with a defined evolutionary relationship. We characterized the fitness
peaks of four orthologous fluorescent proteins with a broad range of sequence
divergence. While two of the four studied fitness peaks were sharp, the other
two were considerably flatter, being almost entirely free of epistatic interactions.
Mutationally robust proteins, characterized by a flat fitness peak, were not optimal
templates for machine-learning-driven protein design – instead, predictions were
more accurate for fragile proteins with epistatic landscapes. Our work paves insights
for practical application of fitness landscape heterogeneity in protein engineering.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: "We thank Ondřej Draganov, Rodrigo Redondo, Bor Kavčič, Mia Juračić
and Andrea Pauli for discussion and technical advice. We thank Anita Testa Salmazo
for advice on resin protein purification, Dmitry Bolotin and the Milaboratory (milaboratory.com)
for access to computing and storage infrastructure, and Josef Houser and Eva Fujdiarova
for technical assistance and data interpretation. Core facility Biomolecular Interactions
and Crystallization of CEITEC Masaryk University is gratefully acknowledged for
the obtaining of the scientific data presented in this paper. This research was
supported by the Scientific Service Units (SSU) of IST-Austria\r\nthrough resources
provided by the Bioimaging Facility (BIF), and the Life Science Facility (LSF).
MiSeq and HiSeq NGS sequencing was performed by the Next Generation Sequencing Facility
at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC),
Austria. FACS was performed at the BioOptics Facility of the Institute of Molecular
Pathology (IMP), Austria. We also thank the Biomolecular Crystallography Facility
in the Vanderbilt University Center for Structural Biology. We are grateful to Joel
M Harp for help with X-ray data collection. This work was supported by the ERC Consolidator
grant to FAK (771209—CharFL). KSS acknowledges support by President’s Grant МК–5405.2021.1.4,
the Imperial College Research Fellowship and the MRC London Institute of Medical
Sciences (UKRI MC-A658-5QEA0).\r\nAF is supported by the Marie Skłodowska-Curie
Fellowship (H2020-MSCA-IF-2019, Grant Agreement No. 898203, Project acronym \"FLINDIP\").
Experiments were partially carried out using equipment provided by the Institute
of Bioorganic Chemistry of the Russian Academy of Sciences Сore Facility (CKP IBCH).
This work was supported by a Russian Science Foundation grant 19-74-10102.This project
has received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665,385."
article_number: '75842'
article_processing_charge: No
article_type: original
author:
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Aubin
full_name: Fleiss, Aubin
last_name: Fleiss
- first_name: Alexander S
full_name: Mishin, Alexander S
last_name: Mishin
- first_name: Nina G
full_name: Bozhanova, Nina G
last_name: Bozhanova
- first_name: Anna A
full_name: Igolkina, Anna A
last_name: Igolkina
- first_name: Jens
full_name: Meiler, Jens
last_name: Meiler
- first_name: Maria-Elisenda
full_name: Alaball Pujol, Maria-Elisenda
last_name: Alaball Pujol
- first_name: Ekaterina V
full_name: Putintseva, Ekaterina V
last_name: Putintseva
- first_name: Karen S
full_name: Sarkisyan, Karen S
last_name: Sarkisyan
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP
fitness landscape and data-driven protein design. eLife. 2022;11. doi:10.7554/elife.75842
apa: Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina,
A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape
and data-driven protein design. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.75842
chicago: Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova,
Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva,
Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape
and Data-Driven Protein Design.” ELife. eLife Sciences Publications, 2022.
https://doi.org/10.7554/elife.75842.
ieee: L. Gonzalez Somermeyer et al., “Heterogeneity of the GFP fitness landscape
and data-driven protein design,” eLife, vol. 11. eLife Sciences Publications,
2022.
ista: Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler
J, Alaball Pujol M-E, Putintseva EV, Sarkisyan KS, Kondrashov F. 2022. Heterogeneity
of the GFP fitness landscape and data-driven protein design. eLife. 11, 75842.
mla: Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape
and Data-Driven Protein Design.” ELife, vol. 11, 75842, eLife Sciences
Publications, 2022, doi:10.7554/elife.75842.
short: L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina,
J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov,
ELife 11 (2022).
date_created: 2022-06-18T09:06:59Z
date_published: 2022-05-05T00:00:00Z
date_updated: 2023-08-03T07:20:15Z
day: '05'
ddc:
- '570'
department:
- _id: GradSch
- _id: FyKo
doi: 10.7554/elife.75842
ec_funded: 1
external_id:
isi:
- '000799197200001'
file:
- access_level: open_access
checksum: 7573c28f44028ab0cc81faef30039e44
content_type: application/pdf
creator: dernst
date_created: 2022-06-20T07:44:19Z
date_updated: 2022-06-20T07:44:19Z
file_id: '11454'
file_name: 2022_eLife_Somermeyer.pdf
file_size: 5297213
relation: main_file
success: 1
file_date_updated: 2022-06-20T07:44:19Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Heterogeneity of the GFP fitness landscape and data-driven protein design
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: '2022'
...
---
_id: '11471'
abstract:
- lang: eng
text: 'Variational quantum algorithms are promising algorithms for achieving quantum
advantage on nearterm devices. The quantum hardware is used to implement a variational
wave function and measure observables, whereas the classical computer is used
to store and update the variational parameters. The optimization landscape of
expressive variational ansätze is however dominated by large regions in parameter
space, known as barren plateaus, with vanishing gradients, which prevents efficient
optimization. In this work we propose a general algorithm to avoid barren plateaus
in the initialization and throughout the optimization. To this end we define a
notion of weak barren plateaus (WBPs) based on the entropies of local reduced
density matrices. The presence of WBPs can be efficiently quantified using recently
introduced shadow tomography of the quantum state with a classical computer. We
demonstrate that avoidance of WBPs suffices to ensure sizable gradients in the
initialization. In addition, we demonstrate that decreasing the gradient step
size, guided by the entropies allows WBPs to be avoided during the optimization
process. This paves the way for efficient barren plateau-free optimization on
near-term devices. '
acknowledgement: "We thank Marco Cerezo, Zoe Holmes, and Nicholas Hunter-Jones for
fruitful discussion and valuable feedback. We also acknowledge Adam Smith, Johannes
Jakob Meyer, and Victor V. Albert for comments on the paper. The simulations were
performed in the Julia programming\r\nlanguage [65] using the Yao module [66]. S.H.S.,
R.A.M., A.A.M. and M.S. acknowledge support by the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation program (Grant Agreement
No. 850899)."
article_number: '020365'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Stefan
full_name: Sack, Stefan
id: dd622248-f6e0-11ea-865d-ce382a1c81a5
last_name: Sack
orcid: 0000-0001-5400-8508
- first_name: Raimel A
full_name: Medina Ramos, Raimel A
id: CE680B90-D85A-11E9-B684-C920E6697425
last_name: Medina Ramos
orcid: 0000-0002-5383-2869
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: Richard
full_name: Kueng, Richard
last_name: Kueng
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. Avoiding barren
plateaus using classical shadows. PRX Quantum. 2022;3(2). doi:10.1103/prxquantum.3.020365
apa: Sack, S., Medina Ramos, R. A., Michailidis, A., Kueng, R., & Serbyn, M.
(2022). Avoiding barren plateaus using classical shadows. PRX Quantum.
American Physical Society. https://doi.org/10.1103/prxquantum.3.020365
chicago: Sack, Stefan, Raimel A Medina Ramos, Alexios Michailidis, Richard Kueng,
and Maksym Serbyn. “Avoiding Barren Plateaus Using Classical Shadows.” PRX
Quantum. American Physical Society, 2022. https://doi.org/10.1103/prxquantum.3.020365.
ieee: S. Sack, R. A. Medina Ramos, A. Michailidis, R. Kueng, and M. Serbyn, “Avoiding
barren plateaus using classical shadows,” PRX Quantum, vol. 3, no. 2. American
Physical Society, 2022.
ista: Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. 2022. Avoiding
barren plateaus using classical shadows. PRX Quantum. 3(2), 020365.
mla: Sack, Stefan, et al. “Avoiding Barren Plateaus Using Classical Shadows.” PRX
Quantum, vol. 3, no. 2, 020365, American Physical Society, 2022, doi:10.1103/prxquantum.3.020365.
short: S. Sack, R.A. Medina Ramos, A. Michailidis, R. Kueng, M. Serbyn, PRX Quantum
3 (2022).
date_created: 2022-06-29T20:21:32Z
date_published: 2022-06-29T00:00:00Z
date_updated: 2023-12-13T14:47:24Z
day: '29'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/prxquantum.3.020365
ec_funded: 1
external_id:
arxiv:
- '2201.08194'
isi:
- '000822564300001'
file:
- access_level: open_access
checksum: a7706b28d24a0e32a55ea04b82a2df43
content_type: application/pdf
creator: dernst
date_created: 2022-06-30T07:14:48Z
date_updated: 2022-06-30T07:14:48Z
file_id: '11472'
file_name: 2022_PRXQuantum_Sack.pdf
file_size: 4231591
relation: main_file
success: 1
file_date_updated: 2022-06-30T07:14:48Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
issue: '2'
keyword:
- General Medicine
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: PRX Quantum
publication_identifier:
issn:
- 2691-3399
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '14622'
relation: dissertation_contains
status: public
status: public
title: Avoiding barren plateaus using classical shadows
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: '2022'
...
---
_id: '11713'
abstract:
- lang: eng
text: "Objective: MazF is a sequence-specific endoribonuclease-toxin of the MazEF
toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions
at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli.
The MazEF system has been used in various biotechnology and synthetic biology
applications. In this study, we infer how ectopic mazF overexpression affects
production of heterologous proteins. To this end, we quantified the levels of
fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing
or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the
5′-untranslated region of these reporter mRNAs under the same conditions by comparing
expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless
mRNA).\r\nResults: Flow cytometry analysis indicates that during mazF overexpression,
fluorescent proteins are translated from the canonical as well as leaderless mRNAs.
Our analysis further indicates that longer mazF overexpression generally increases
the concentration of fluorescent proteins translated from ACA-less mRNAs, however
it also substantially increases bacterial population heterogeneity. Finally, our
results suggest that the strength and duration of mazF overexpression should be
optimized for each experimental setup, to maximize the heterologous protein production
and minimize the amount of phenotypic heterogeneity in bacterial populations,
which is unfavorable in biotechnological processes."
acknowledgement: "We acknowledge the Max Perutz Labs FACS Facility together with Thomas
Sauer. NN is grateful to Călin C. Guet for his support.\r\nThis work was funded
by the Elise Richter grant V738 of the Austrian Science Fund (FWF), and the FWF
Lise Meitner grant M1697, to NN; and by the FWF grant P22249, FWF Special Research
Program RNA-REG F43 (subproject F4316), and FWF doctoral program RNA Biology (W1207),
to IM. Open access funding provided by the Austrian Science Fund."
article_number: '173'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Martina
full_name: Sauert, Martina
last_name: Sauert
- first_name: Tanino G.
full_name: Albanese, Tanino G.
last_name: Albanese
- first_name: Isabella
full_name: Moll, Isabella
last_name: Moll
citation:
ama: Nikolic N, Sauert M, Albanese TG, Moll I. Quantifying heterologous gene expression
during ectopic MazF production in Escherichia coli. BMC Research Notes.
2022;15. doi:10.1186/s13104-022-06061-9
apa: Nikolic, N., Sauert, M., Albanese, T. G., & Moll, I. (2022). Quantifying
heterologous gene expression during ectopic MazF production in Escherichia coli.
BMC Research Notes. Springer Nature. https://doi.org/10.1186/s13104-022-06061-9
chicago: Nikolic, Nela, Martina Sauert, Tanino G. Albanese, and Isabella Moll. “Quantifying
Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.”
BMC Research Notes. Springer Nature, 2022. https://doi.org/10.1186/s13104-022-06061-9.
ieee: N. Nikolic, M. Sauert, T. G. Albanese, and I. Moll, “Quantifying heterologous
gene expression during ectopic MazF production in Escherichia coli,” BMC Research
Notes, vol. 15. Springer Nature, 2022.
ista: Nikolic N, Sauert M, Albanese TG, Moll I. 2022. Quantifying heterologous gene
expression during ectopic MazF production in Escherichia coli. BMC Research Notes.
15, 173.
mla: Nikolic, Nela, et al. “Quantifying Heterologous Gene Expression during Ectopic
MazF Production in Escherichia Coli.” BMC Research Notes, vol. 15, 173,
Springer Nature, 2022, doi:10.1186/s13104-022-06061-9.
short: N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022).
date_created: 2022-08-01T09:04:27Z
date_published: 2022-05-13T00:00:00Z
date_updated: 2022-08-01T09:27:40Z
day: '13'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1186/s13104-022-06061-9
external_id:
pmid:
- '35562780'
file:
- access_level: open_access
checksum: 008156e5340e9789f0f6d82bde4d347a
content_type: application/pdf
creator: dernst
date_created: 2022-08-01T09:24:42Z
date_updated: 2022-08-01T09:24:42Z
file_id: '11714'
file_name: 2022_BMCResearchNotes_Nikolic.pdf
file_size: 1545310
relation: main_file
success: 1
file_date_updated: 2022-08-01T09:24:42Z
has_accepted_license: '1'
intvolume: ' 15'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26956E74-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: V00738
name: Bacterial toxin-antitoxin systems as antiphage defense mechanisms
publication: BMC Research Notes
publication_identifier:
issn:
- 1756-0500
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1186/s13104-022-06152-7
scopus_import: '1'
status: public
title: Quantifying heterologous gene expression during ectopic MazF production in
Escherichia coli
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2022'
...
---
_id: '13993'
abstract:
- lang: eng
text: Photoionization is a process taking place on attosecond time scales. How its
properties evolve from isolated particles to the condensed phase is an open question
of both fundamental and practical relevance. Here, we review recent work that
has advanced the study of photoionization dynamics from atoms to molecules, clusters
and the liquid phase. The first measurements of molecular photoionization delays
have revealed the attosecond dynamics of electron emission from a molecular shape
resonance and their sensitivity to the molecular potential. Using electron-ion
coincidence spectroscopy these measurements have been extended from isolated molecules
to clusters. A continuous increase of the delays with the water-cluster size has
been observed up to a size of 4-5 molecules, followed by a saturation towards
larger clusters. Comparison with calculations has revealed a correlation of the
time delay with the spatial extension of the created electron hole. Using cylindrical
liquid-microjet techniques, these measurements have also been extended to liquid
water, revealing a delay relative to isolated water molecules that was very similar
to the largest water clusters studied. Detailed modeling based on Monte-Carlo
simulations confirmed that these delays are dominated by the contributions of
the first two solvation shells, which agrees with the results of the cluster measurements.
These combined results open the perspective of experimentally characterizing the
delocalization of electronic wave functions in complex systems and studying their
evolution on attosecond time scales.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaochun
full_name: Gong, Xiaochun
last_name: Gong
- first_name: Inga
full_name: Jordan, Inga
last_name: Jordan
- first_name: Martin
full_name: Huppert, Martin
last_name: Huppert
- first_name: Saijoscha
full_name: Heck, Saijoscha
last_name: Heck
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Denis
full_name: Jelovina, Denis
last_name: Jelovina
- first_name: Axel
full_name: Schild, Axel
last_name: Schild
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: 'Gong X, Jordan I, Huppert M, et al. Attosecond photoionization dynamics: from
molecules over clusters to the liquid phase. Chimia. 2022;76(6):520-528.
doi:10.2533/chimia.2022.520'
apa: 'Gong, X., Jordan, I., Huppert, M., Heck, S., Baykusheva, D. R., Jelovina,
D., … Wörner, H. J. (2022). Attosecond photoionization dynamics: from molecules
over clusters to the liquid phase. Chimia. Swiss Chemical Society. https://doi.org/10.2533/chimia.2022.520'
chicago: 'Gong, Xiaochun, Inga Jordan, Martin Huppert, Saijoscha Heck, Denitsa Rangelova
Baykusheva, Denis Jelovina, Axel Schild, and Hans Jakob Wörner. “Attosecond Photoionization
Dynamics: From Molecules over Clusters to the Liquid Phase.” Chimia. Swiss
Chemical Society, 2022. https://doi.org/10.2533/chimia.2022.520.'
ieee: 'X. Gong et al., “Attosecond photoionization dynamics: from molecules
over clusters to the liquid phase,” Chimia, vol. 76, no. 6. Swiss Chemical
Society, pp. 520–528, 2022.'
ista: 'Gong X, Jordan I, Huppert M, Heck S, Baykusheva DR, Jelovina D, Schild A,
Wörner HJ. 2022. Attosecond photoionization dynamics: from molecules over clusters
to the liquid phase. Chimia. 76(6), 520–528.'
mla: 'Gong, Xiaochun, et al. “Attosecond Photoionization Dynamics: From Molecules
over Clusters to the Liquid Phase.” Chimia, vol. 76, no. 6, Swiss Chemical
Society, 2022, pp. 520–28, doi:10.2533/chimia.2022.520.'
short: X. Gong, I. Jordan, M. Huppert, S. Heck, D.R. Baykusheva, D. Jelovina, A.
Schild, H.J. Wörner, Chimia 76 (2022) 520–528.
date_created: 2023-08-09T13:08:15Z
date_published: 2022-06-29T00:00:00Z
date_updated: 2023-08-22T07:26:39Z
day: '29'
doi: 10.2533/chimia.2022.520
extern: '1'
intvolume: ' 76'
issue: '6'
keyword:
- General Medicine
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.2533/chimia.2022.520
month: '06'
oa: 1
oa_version: Published Version
page: 520-528
publication: Chimia
publication_identifier:
eissn:
- 2673-2424
issn:
- 0009-4293
publication_status: published
publisher: Swiss Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Attosecond photoionization dynamics: from molecules over clusters to the liquid
phase'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 76
year: '2022'
...
---
_id: '12157'
abstract:
- lang: eng
text: 'Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood.
Here, we model this process analytically, in the plausible setting of a highly
polygenic, quantitative trait that experiences a sudden shift in the fitness optimum.
We show how the mean phenotype changes over time, depending on the effect sizes
of loci that contribute to variance in the trait, and characterize the allele
dynamics at these loci. Notably, we describe the two phases of the allele dynamics:
The first is a rapid phase, in which directional selection introduces small frequency
differences between alleles whose effects are aligned with or opposed to the shift,
ultimately leading to small differences in their probability of fixation during
a second, longer phase, governed by stabilizing selection. As we discuss, key
results should hold in more general settings and have important implications for
efforts to identify the genetic basis of adaptation in humans and other species.'
acknowledgement: "We thank Guy Amster, Jeremy Berg, Nick Barton, Yuval Simons and
Molly Przeworski for many helpful discussions, and Jeremy Berg, Graham Coop, Joachim
Hermisson, Guillaume Martin, Will Milligan, Peter Ralph, Yuval Simons, Leo Speidel
and Molly Przeworski for comments on the manuscript.\r\nNational Institutes of Health
GM115889 Laura Katharine Hayward Guy Sella \r\nNational Institutes of Health GM121372
Laura Katharine Hayward"
article_number: '66697'
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Hayward, Laura
id: fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b
last_name: Hayward
- first_name: Guy
full_name: Sella, Guy
last_name: Sella
citation:
ama: Hayward L, Sella G. Polygenic adaptation after a sudden change in environment.
eLife. 2022;11. doi:10.7554/elife.66697
apa: Hayward, L., & Sella, G. (2022). Polygenic adaptation after a sudden change
in environment. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.66697
chicago: Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change
in Environment.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/elife.66697.
ieee: L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,”
eLife, vol. 11. eLife Sciences Publications, 2022.
ista: Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment.
eLife. 11, 66697.
mla: Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change
in Environment.” ELife, vol. 11, 66697, eLife Sciences Publications, 2022,
doi:10.7554/elife.66697.
short: L. Hayward, G. Sella, ELife 11 (2022).
date_created: 2023-01-12T12:09:00Z
date_published: 2022-09-26T00:00:00Z
date_updated: 2023-08-04T09:04:58Z
day: '26'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.7554/elife.66697
external_id:
isi:
- '000890735600001'
file:
- access_level: open_access
checksum: 28de155b231ac1c8d4501c98b2fb359a
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T12:21:32Z
date_updated: 2023-01-24T12:21:32Z
file_id: '12363'
file_name: 2022_eLife_Hayward.pdf
file_size: 18935612
relation: main_file
success: 1
file_date_updated: 2023-01-24T12:21:32Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Polygenic adaptation after a sudden change in environment
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: '2022'
...
---
_id: '12235'
abstract:
- lang: eng
text: "Background: About 800 women die every day worldwide from pregnancy-related
complications, including excessive blood loss, infections and high-blood pressure
(World Health Organization, 2019). To improve screening for high-risk pregnancies,
we set out to identify patterns of maternal hematological changes associated with
future pregnancy complications.\r\n\r\nMethods: Using mixed effects models, we
established changes in 14 complete blood count (CBC) parameters for 1710 healthy
pregnancies and compared them to measurements from 98 pregnancy-induced hypertension,
106 gestational diabetes and 339 postpartum hemorrhage cases.\r\n\r\nResults:
Results show interindividual variations, but good individual repeatability in
CBC values during physiological pregnancies, allowing the identification of specific
alterations in women with obstetric complications. For example, in women with
uncomplicated pregnancies, haemoglobin count decreases of 0.12 g/L (95% CI −0.16,
−0.09) significantly per gestation week (p value <.001). Interestingly, this decrease
is three times more pronounced in women who will develop pregnancy-induced hypertension,
with an additional decrease of 0.39 g/L (95% CI −0.51, −0.26). We also confirm
that obstetric complications and white CBC predict the likelihood of giving birth
earlier during pregnancy.\r\n\r\nConclusion: We provide a comprehensive description
of the associations between haematological changes through pregnancy and three
major obstetric complications to support strategies for prevention, early-diagnosis
and maternal care."
acknowledgement: This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181),
and by core funding from the Institute of Science and Technology Austria. We would
like to thank the participants of the study and all the midwives and doctors involved
for the computerized obstetrical data from the CHUV Maternity Hospital. Open access
funding provided by Universite de Lausanne.
article_processing_charge: No
article_type: original
author:
- first_name: Marion
full_name: Patxot, Marion
last_name: Patxot
- first_name: Miloš
full_name: Stojanov, Miloš
last_name: Stojanov
- first_name: Sven Erik
full_name: Ojavee, Sven Erik
last_name: Ojavee
- first_name: Rosanna Pescini
full_name: Gobert, Rosanna Pescini
last_name: Gobert
- first_name: Zoltán
full_name: Kutalik, Zoltán
last_name: Kutalik
- first_name: Mathilde
full_name: Gavillet, Mathilde
last_name: Gavillet
- first_name: David
full_name: Baud, David
last_name: Baud
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: 'Patxot M, Stojanov M, Ojavee SE, et al. Haematological changes from conception
to childbirth: An indicator of major pregnancy complications. European Journal
of Haematology. 2022;109(5):566-575. doi:10.1111/ejh.13844'
apa: 'Patxot, M., Stojanov, M., Ojavee, S. E., Gobert, R. P., Kutalik, Z., Gavillet,
M., … Robinson, M. R. (2022). Haematological changes from conception to childbirth:
An indicator of major pregnancy complications. European Journal of Haematology.
Wiley. https://doi.org/10.1111/ejh.13844'
chicago: 'Patxot, Marion, Miloš Stojanov, Sven Erik Ojavee, Rosanna Pescini Gobert,
Zoltán Kutalik, Mathilde Gavillet, David Baud, and Matthew Richard Robinson. “Haematological
Changes from Conception to Childbirth: An Indicator of Major Pregnancy Complications.”
European Journal of Haematology. Wiley, 2022. https://doi.org/10.1111/ejh.13844.'
ieee: 'M. Patxot et al., “Haematological changes from conception to childbirth:
An indicator of major pregnancy complications,” European Journal of Haematology,
vol. 109, no. 5. Wiley, pp. 566–575, 2022.'
ista: 'Patxot M, Stojanov M, Ojavee SE, Gobert RP, Kutalik Z, Gavillet M, Baud D,
Robinson MR. 2022. Haematological changes from conception to childbirth: An indicator
of major pregnancy complications. European Journal of Haematology. 109(5), 566–575.'
mla: 'Patxot, Marion, et al. “Haematological Changes from Conception to Childbirth:
An Indicator of Major Pregnancy Complications.” European Journal of Haematology,
vol. 109, no. 5, Wiley, 2022, pp. 566–75, doi:10.1111/ejh.13844.'
short: M. Patxot, M. Stojanov, S.E. Ojavee, R.P. Gobert, Z. Kutalik, M. Gavillet,
D. Baud, M.R. Robinson, European Journal of Haematology 109 (2022) 566–575.
date_created: 2023-01-16T09:50:58Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2023-08-04T09:36:21Z
day: '01'
ddc:
- '570'
- '610'
department:
- _id: MaRo
doi: 10.1111/ejh.13844
external_id:
isi:
- '000849690500001'
pmid:
- '36059200'
file:
- access_level: open_access
checksum: a676d732f67c2990197e34f96b219370
content_type: application/pdf
creator: dernst
date_created: 2023-01-27T11:42:43Z
date_updated: 2023-01-27T11:42:43Z
file_id: '12426'
file_name: 2022_EuropJourHaematology_Patxot.pdf
file_size: 1225073
relation: main_file
success: 1
file_date_updated: 2023-01-27T11:42:43Z
has_accepted_license: '1'
intvolume: ' 109'
isi: 1
issue: '5'
keyword:
- Hematology
- General Medicine
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 566-575
pmid: 1
publication: European Journal of Haematology
publication_identifier:
eissn:
- 1600-0609
issn:
- 0902-4441
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Haematological changes from conception to childbirth: An indicator of major
pregnancy complications'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 109
year: '2022'
...
---
_id: '12276'
abstract:
- lang: eng
text: Ongoing development of quantum simulators allows for a progressively finer
degree of control of quantum many-body systems. This motivates the development
of efficient approaches to facilitate the control of such systems and enable the
preparation of nontrivial quantum states. Here we formulate an approach to control
quantum systems based on matrix product states (MPSs). We compare counterdiabatic
and leakage minimization approaches to the so-called local steering problem that
consists in finding the best value of the control parameters for generating a
unitary evolution of the specific MPS in a given direction. In order to benchmark
the different approaches, we apply them to the generalization of the PXP model
known to exhibit coherent quantum dynamics due to quantum many-body scars. We
find that the leakage-based approach generally outperforms the counterdiabatic
framework and use it to construct a Floquet model with quantum scars. We perform
the first steps towards global trajectory optimization and demonstrate entanglement
steering capabilities in the generalized PXP model. Finally, we apply our leakage
minimization approach to construct quantum scars in the periodically driven nonintegrable
Ising model.
acknowledgement: We thank A. A. Michailidis for insightful discussions. M.L. and M.S.
acknowledge support from the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 850899).
D.A. is supported by the European Research Council (ERC) under the European Union’s
Horizon 2020 research and innovation programme (Grant Agreement No. 864597) and
by the Swiss National Science Foundation. The infinite TEBD simulations were performed
using the ITensor library [67].
article_number: '030343'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
- first_name: Barbara
full_name: Roos, Barbara
id: 5DA90512-D80F-11E9-8994-2E2EE6697425
last_name: Roos
orcid: 0000-0002-9071-5880
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Ljubotina M, Roos B, Abanin DA, Serbyn M. Optimal steering of matrix product
states and quantum many-body scars. PRX Quantum. 2022;3(3). doi:10.1103/prxquantum.3.030343
apa: Ljubotina, M., Roos, B., Abanin, D. A., & Serbyn, M. (2022). Optimal steering
of matrix product states and quantum many-body scars. PRX Quantum. American
Physical Society. https://doi.org/10.1103/prxquantum.3.030343
chicago: Ljubotina, Marko, Barbara Roos, Dmitry A. Abanin, and Maksym Serbyn. “Optimal
Steering of Matrix Product States and Quantum Many-Body Scars.” PRX Quantum.
American Physical Society, 2022. https://doi.org/10.1103/prxquantum.3.030343.
ieee: M. Ljubotina, B. Roos, D. A. Abanin, and M. Serbyn, “Optimal steering of matrix
product states and quantum many-body scars,” PRX Quantum, vol. 3, no. 3.
American Physical Society, 2022.
ista: Ljubotina M, Roos B, Abanin DA, Serbyn M. 2022. Optimal steering of matrix
product states and quantum many-body scars. PRX Quantum. 3(3), 030343.
mla: Ljubotina, Marko, et al. “Optimal Steering of Matrix Product States and Quantum
Many-Body Scars.” PRX Quantum, vol. 3, no. 3, 030343, American Physical
Society, 2022, doi:10.1103/prxquantum.3.030343.
short: M. Ljubotina, B. Roos, D.A. Abanin, M. Serbyn, PRX Quantum 3 (2022).
date_created: 2023-01-16T10:01:56Z
date_published: 2022-09-23T00:00:00Z
date_updated: 2023-01-30T11:05:23Z
day: '23'
ddc:
- '530'
department:
- _id: MaSe
- _id: RoSe
doi: 10.1103/prxquantum.3.030343
ec_funded: 1
external_id:
arxiv:
- '2204.02899'
file:
- access_level: open_access
checksum: ef8f0a1b5a019b3958009162de0fa4c3
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T11:02:50Z
date_updated: 2023-01-30T11:02:50Z
file_id: '12457'
file_name: 2022_PRXQuantum_Ljubotina.pdf
file_size: 7661905
relation: main_file
success: 1
file_date_updated: 2023-01-30T11:02:50Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '3'
keyword:
- General Medicine
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: PRX Quantum
publication_identifier:
eissn:
- 2691-3399
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal steering of matrix product states and quantum many-body scars
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2022'
...
---
_id: '12288'
abstract:
- lang: eng
text: To understand the function of neuronal circuits, it is crucial to disentangle
the connectivity patterns within the network. However, most tools currently used
to explore connectivity have low throughput, low selectivity, or limited accessibility.
Here, we report the development of an improved packaging system for the production
of the highly neurotropic RVdGenvA-CVS-N2c rabies viral vectors, yielding titers
orders of magnitude higher with no background contamination, at a fraction of
the production time, while preserving the efficiency of transsynaptic labeling.
Along with the production pipeline, we developed suites of ‘starter’ AAV and bicistronic
RVdG-CVS-N2c vectors, enabling retrograde labeling from a wide range of neuronal
populations, tailored for diverse experimental requirements. We demonstrate the
power and flexibility of the new system by uncovering hidden local and distal
inhibitory connections in the mouse hippocampal formation and by imaging the functional
properties of a cortical microcircuit across weeks. Our novel production pipeline
provides a convenient approach to generate new rabies vectors, while our toolkit
flexibly and efficiently expands the current capacity to label, manipulate and
image the neuronal activity of interconnected neuronal circuits in vitro and in
vivo.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: We thank F Marr for technical assistance, A Murray for RVdG-CVS-N2c
viruses and Neuro2A packaging cell-lines and J Watson for reading the manuscript.
This research was supported by the Scientific Service Units (SSU) of IST-Austria
through resources provided by the Imaging and Optics Facility (IOF) and the Preclinical
Facility (PCF). This project was funded by the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (ERC advanced
grant No 692692, PJ, ERC starting grant No 756502, MJ), the Fond zur Förderung der
Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, PJ), the Human Frontier
Science Program (LT000256/2018-L, AS) and EMBO (ALTF 1098-2017, AS).
article_number: '79848'
article_processing_charge: No
article_type: original
author:
- first_name: Anton L
full_name: Sumser, Anton L
id: 3320A096-F248-11E8-B48F-1D18A9856A87
last_name: Sumser
orcid: 0000-0002-4792-1881
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Yoav
full_name: Ben Simon, Yoav
id: 43DF3136-F248-11E8-B48F-1D18A9856A87
last_name: Ben Simon
citation:
ama: Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. Fast, high-throughput production
of improved rabies viral vectors for specific, efficient and versatile transsynaptic
retrograde labeling. eLife. 2022;11. doi:10.7554/elife.79848
apa: Sumser, A. L., Jösch, M. A., Jonas, P. M., & Ben Simon, Y. (2022). Fast,
high-throughput production of improved rabies viral vectors for specific, efficient
and versatile transsynaptic retrograde labeling. ELife. eLife Sciences
Publications. https://doi.org/10.7554/elife.79848
chicago: Sumser, Anton L, Maximilian A Jösch, Peter M Jonas, and Yoav Ben Simon.
“Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific,
Efficient and Versatile Transsynaptic Retrograde Labeling.” ELife. eLife
Sciences Publications, 2022. https://doi.org/10.7554/elife.79848.
ieee: A. L. Sumser, M. A. Jösch, P. M. Jonas, and Y. Ben Simon, “Fast, high-throughput
production of improved rabies viral vectors for specific, efficient and versatile
transsynaptic retrograde labeling,” eLife, vol. 11. eLife Sciences Publications,
2022.
ista: Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. 2022. Fast, high-throughput production
of improved rabies viral vectors for specific, efficient and versatile transsynaptic
retrograde labeling. eLife. 11, 79848.
mla: Sumser, Anton L., et al. “Fast, High-Throughput Production of Improved Rabies
Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.”
ELife, vol. 11, 79848, eLife Sciences Publications, 2022, doi:10.7554/elife.79848.
short: A.L. Sumser, M.A. Jösch, P.M. Jonas, Y. Ben Simon, ELife 11 (2022).
date_created: 2023-01-16T10:04:15Z
date_published: 2022-09-15T00:00:00Z
date_updated: 2023-08-04T10:29:48Z
day: '15'
ddc:
- '570'
department:
- _id: MaJö
- _id: PeJo
doi: 10.7554/elife.79848
ec_funded: 1
external_id:
isi:
- '000892204300001'
pmid:
- '36040301'
file:
- access_level: open_access
checksum: 5a2a65e3e7225090c3d8199f3bbd7b7b
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T11:50:53Z
date_updated: 2023-01-30T11:50:53Z
file_id: '12463'
file_name: 2022_eLife_Sumser.pdf
file_size: 8506811
relation: main_file
success: 1
file_date_updated: 2023-01-30T11:50:53Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 2634E9D2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '756502'
name: Circuits of Visual Attention
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: 266D407A-B435-11E9-9278-68D0E5697425
grant_number: LT000256
name: Neuronal networks of salience and spatial detection in the murine superior
colliculus
- _id: 264FEA02-B435-11E9-9278-68D0E5697425
grant_number: ALTF 1098-2017
name: Connecting sensory with motor processing in the superior colliculus
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast, high-throughput production of improved rabies viral vectors for specific,
efficient and versatile transsynaptic retrograde labeling
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: '2022'
...
---
_id: '12510'
abstract:
- lang: eng
text: "We introduce a new statistical verification algorithm that formally quantifies
the behavioral robustness of any time-continuous process formulated as a continuous-depth
model. Our algorithm solves a set of global optimization (Go) problems over a
given time horizon to construct a tight enclosure (Tube) of the set of all process
executions starting from a ball of initial states. We call our algorithm GoTube.
Through its construction, GoTube ensures that the bounding tube is conservative
up to a desired probability and up to a desired tightness.\r\n GoTube is implemented
in JAX and optimized to scale to complex continuous-depth neural network models.
Compared to advanced reachability analysis tools for time-continuous neural networks,
GoTube does not accumulate overapproximation errors between time steps and avoids
the infamous wrapping effect inherent in symbolic techniques. We show that GoTube
substantially outperforms state-of-the-art verification tools in terms of the
size of the initial ball, speed, time-horizon, task completion, and scalability
on a large set of experiments.\r\n GoTube is stable and sets the state-of-the-art
in terms of its ability to scale to time horizons well beyond what has been previously
possible."
acknowledgement: SG is funded by the Austrian Science Fund (FWF) project number W1255-N23.
ML and TH are supported in part by FWF under grant Z211-N23 (Wittgenstein Award)
and the ERC-2020-AdG 101020093. SS is supported by NSF awards DCL-2040599, CCF-1918225,
and CPS-1446832. RH and DR are partially supported by Boeing. RG is partially supported
by Horizon-2020 ECSEL Project grant No. 783163 (iDev40).
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Sophie A.
full_name: Gruenbacher, Sophie A.
last_name: Gruenbacher
- 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: Daniela
full_name: Rus, Daniela
last_name: Rus
- 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: Scott A.
full_name: Smolka, Scott A.
last_name: Smolka
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: 'Gruenbacher SA, Lechner M, Hasani R, et al. GoTube: Scalable statistical verification
of continuous-depth models. Proceedings of the AAAI Conference on Artificial
Intelligence. 2022;36(6):6755-6764. doi:10.1609/aaai.v36i6.20631'
apa: 'Gruenbacher, S. A., Lechner, M., Hasani, R., Rus, D., Henzinger, T. A., Smolka,
S. A., & Grosu, R. (2022). GoTube: Scalable statistical verification of continuous-depth
models. Proceedings of the AAAI Conference on Artificial Intelligence.
Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v36i6.20631'
chicago: 'Gruenbacher, Sophie A., Mathias Lechner, Ramin Hasani, Daniela Rus, Thomas
A Henzinger, Scott A. Smolka, and Radu Grosu. “GoTube: Scalable Statistical Verification
of Continuous-Depth Models.” Proceedings of the AAAI Conference on Artificial
Intelligence. Association for the Advancement of Artificial Intelligence,
2022. https://doi.org/10.1609/aaai.v36i6.20631.'
ieee: 'S. A. Gruenbacher et al., “GoTube: Scalable statistical verification
of continuous-depth models,” Proceedings of the AAAI Conference on Artificial
Intelligence, vol. 36, no. 6. Association for the Advancement of Artificial
Intelligence, pp. 6755–6764, 2022.'
ista: 'Gruenbacher SA, Lechner M, Hasani R, Rus D, Henzinger TA, Smolka SA, Grosu
R. 2022. GoTube: Scalable statistical verification of continuous-depth models.
Proceedings of the AAAI Conference on Artificial Intelligence. 36(6), 6755–6764.'
mla: 'Gruenbacher, Sophie A., et al. “GoTube: Scalable Statistical Verification
of Continuous-Depth Models.” Proceedings of the AAAI Conference on Artificial
Intelligence, vol. 36, no. 6, Association for the Advancement of Artificial
Intelligence, 2022, pp. 6755–64, doi:10.1609/aaai.v36i6.20631.'
short: S.A. Gruenbacher, M. Lechner, R. Hasani, D. Rus, T.A. Henzinger, S.A. Smolka,
R. Grosu, Proceedings of the AAAI Conference on Artificial Intelligence 36 (2022)
6755–6764.
date_created: 2023-02-05T17:27:42Z
date_published: 2022-06-28T00:00:00Z
date_updated: 2023-09-26T10:46:59Z
day: '28'
department:
- _id: ToHe
doi: 10.1609/aaai.v36i6.20631
ec_funded: 1
external_id:
arxiv:
- '2107.08467'
intvolume: ' 36'
issue: '6'
keyword:
- General Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2107.08467
month: '06'
oa: 1
oa_version: Preprint
page: 6755-6764
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Proceedings of the AAAI Conference on Artificial Intelligence
publication_identifier:
eissn:
- 2374-3468
isbn:
- '978577358350'
issn:
- 2159-5399
publication_status: published
publisher: Association for the Advancement of Artificial Intelligence
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'GoTube: Scalable statistical verification of continuous-depth models'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2022'
...
---
_id: '12511'
abstract:
- lang: eng
text: "We consider the problem of formally verifying almost-sure (a.s.) asymptotic
stability in discrete-time nonlinear stochastic control systems. While verifying
stability in deterministic control systems is extensively studied in the literature,
verifying stability in stochastic control systems is an open problem. The few
existing works on this topic either consider only specialized forms of stochasticity
or make restrictive assumptions on the system, rendering them inapplicable to
learning algorithms with neural network policies. \r\n In this work, we present
an approach for general nonlinear stochastic control problems with two novel aspects:
(a) instead of classical stochastic extensions of Lyapunov functions, we use ranking
supermartingales (RSMs) to certify a.s. asymptotic stability, and (b) we present
a method for learning neural network RSMs. \r\n We prove that our approach guarantees
a.s. asymptotic stability of the system and\r\n provides the first method to obtain
bounds on the stabilization time, which stochastic Lyapunov functions do not.\r\n
Finally, we validate our approach experimentally on a set of nonlinear stochastic
reinforcement learning environments with neural network policies."
acknowledgement: "This work was supported in part by the ERC-2020-AdG 101020093, ERC
CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation
programme\r\nunder the Marie Skłodowska-Curie Grant Agreement No. 665385."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
- 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
citation:
ama: Lechner M, Zikelic D, Chatterjee K, Henzinger TA. Stability verification in
stochastic control systems via neural network supermartingales. Proceedings
of the AAAI Conference on Artificial Intelligence. 2022;36(7):7326-7336. doi:10.1609/aaai.v36i7.20695
apa: Lechner, M., Zikelic, D., Chatterjee, K., & Henzinger, T. A. (2022). Stability
verification in stochastic control systems via neural network supermartingales.
Proceedings of the AAAI Conference on Artificial Intelligence. Association
for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v36i7.20695
chicago: Lechner, Mathias, Dorde Zikelic, Krishnendu Chatterjee, and Thomas A Henzinger.
“Stability Verification in Stochastic Control Systems via Neural Network Supermartingales.”
Proceedings of the AAAI Conference on Artificial Intelligence. Association
for the Advancement of Artificial Intelligence, 2022. https://doi.org/10.1609/aaai.v36i7.20695.
ieee: M. Lechner, D. Zikelic, K. Chatterjee, and T. A. Henzinger, “Stability verification
in stochastic control systems via neural network supermartingales,” Proceedings
of the AAAI Conference on Artificial Intelligence, vol. 36, no. 7. Association
for the Advancement of Artificial Intelligence, pp. 7326–7336, 2022.
ista: Lechner M, Zikelic D, Chatterjee K, Henzinger TA. 2022. Stability verification
in stochastic control systems via neural network supermartingales. Proceedings
of the AAAI Conference on Artificial Intelligence. 36(7), 7326–7336.
mla: Lechner, Mathias, et al. “Stability Verification in Stochastic Control Systems
via Neural Network Supermartingales.” Proceedings of the AAAI Conference on
Artificial Intelligence, vol. 36, no. 7, Association for the Advancement of
Artificial Intelligence, 2022, pp. 7326–36, doi:10.1609/aaai.v36i7.20695.
short: M. Lechner, D. Zikelic, K. Chatterjee, T.A. Henzinger, Proceedings of the
AAAI Conference on Artificial Intelligence 36 (2022) 7326–7336.
date_created: 2023-02-05T17:29:50Z
date_published: 2022-06-28T00:00:00Z
date_updated: 2025-07-14T09:09:58Z
day: '28'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1609/aaai.v36i7.20695
ec_funded: 1
external_id:
arxiv:
- '2112.09495'
intvolume: ' 36'
issue: '7'
keyword:
- General Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2112.09495
month: '06'
oa: 1
oa_version: Preprint
page: 7326-7336
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Proceedings of the AAAI Conference on Artificial Intelligence
publication_identifier:
eissn:
- 2374-3468
isbn:
- '9781577358350'
issn:
- 2159-5399
publication_status: published
publisher: Association for the Advancement of Artificial Intelligence
quality_controlled: '1'
related_material:
record:
- id: '14539'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Stability verification in stochastic control systems via neural network supermartingales
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2022'
...
---
_id: '10806'
abstract:
- lang: eng
text: Ligands are a fundamental part of nanocrystals. They control and direct nanocrystal
syntheses and provide colloidal stability. Bound ligands also affect the nanocrystals’
chemical reactivity and electronic structure. Surface chemistry is thus crucial
to understand nanocrystal properties and functionality. Here, we investigate the
synthesis of metal oxide nanocrystals (CeO2-x, ZnO, and NiO) from metal nitrate
precursors, in the presence of oleylamine ligands. Surprisingly, the nanocrystals
are capped exclusively with a fatty acid instead of oleylamine. Analysis of the
reaction mixtures with nuclear magnetic resonance spectroscopy revealed several
reaction byproducts and intermediates that are common to the decomposition of
Ce, Zn, Ni, and Zr nitrate precursors. Our evidence supports the oxidation of
alkylamine and formation of a carboxylic acid, thus unraveling this counterintuitive
surface chemistry.
acknowledgement: 'This work was financially supported by IST Austria and the Werner
Siemens Foundation. M.C. has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
No. 665385. The work was also financially supported by University of Basel, SNSF
NCCR Molecular Systems Engineering (project number: 182895) and SNSF R’equip (project
number: 189622). J.L. is a Serra Húnter Fellow and is grateful to ICREA Academia
program and MICINN/FEDER RTI2018-093996-B-C31 and GC 2017 SGR 128 projects.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Mariano
full_name: Calcabrini, Mariano
id: 45D7531A-F248-11E8-B48F-1D18A9856A87
last_name: Calcabrini
- first_name: Dietger
full_name: Van den Eynden, Dietger
last_name: Van den Eynden
- first_name: Sergi
full_name: Sanchez Ribot, Sergi
id: ddae5a59-f6e0-11ea-865d-d9dc61e77a2a
last_name: Sanchez Ribot
- first_name: Rohan
full_name: Pokratath, Rohan
last_name: Pokratath
- first_name: Jordi
full_name: Llorca, Jordi
last_name: Llorca
- first_name: Jonathan
full_name: De Roo, Jonathan
last_name: De Roo
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: 'Calcabrini M, Van den Eynden D, Sanchez Ribot S, et al. Ligand conversion
in nanocrystal synthesis: The oxidation of alkylamines to fatty acids by nitrate.
JACS Au. 2021;1(11):1898-1903. doi:10.1021/jacsau.1c00349'
apa: 'Calcabrini, M., Van den Eynden, D., Sanchez Ribot, S., Pokratath, R., Llorca,
J., De Roo, J., & Ibáñez, M. (2021). Ligand conversion in nanocrystal synthesis:
The oxidation of alkylamines to fatty acids by nitrate. JACS Au. American
Chemical Society. https://doi.org/10.1021/jacsau.1c00349'
chicago: 'Calcabrini, Mariano, Dietger Van den Eynden, Sergi Sanchez Ribot, Rohan
Pokratath, Jordi Llorca, Jonathan De Roo, and Maria Ibáñez. “Ligand Conversion
in Nanocrystal Synthesis: The Oxidation of Alkylamines to Fatty Acids by Nitrate.”
JACS Au. American Chemical Society, 2021. https://doi.org/10.1021/jacsau.1c00349.'
ieee: 'M. Calcabrini et al., “Ligand conversion in nanocrystal synthesis:
The oxidation of alkylamines to fatty acids by nitrate,” JACS Au, vol.
1, no. 11. American Chemical Society, pp. 1898–1903, 2021.'
ista: 'Calcabrini M, Van den Eynden D, Sanchez Ribot S, Pokratath R, Llorca J, De
Roo J, Ibáñez M. 2021. Ligand conversion in nanocrystal synthesis: The oxidation
of alkylamines to fatty acids by nitrate. JACS Au. 1(11), 1898–1903.'
mla: 'Calcabrini, Mariano, et al. “Ligand Conversion in Nanocrystal Synthesis: The
Oxidation of Alkylamines to Fatty Acids by Nitrate.” JACS Au, vol. 1, no.
11, American Chemical Society, 2021, pp. 1898–903, doi:10.1021/jacsau.1c00349.'
short: M. Calcabrini, D. Van den Eynden, S. Sanchez Ribot, R. Pokratath, J. Llorca,
J. De Roo, M. Ibáñez, JACS Au 1 (2021) 1898–1903.
date_created: 2022-03-02T15:24:16Z
date_published: 2021-11-22T00:00:00Z
date_updated: 2023-05-05T08:45:36Z
day: '22'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1021/jacsau.1c00349
ec_funded: 1
file:
- access_level: open_access
checksum: 1c66a35369e911312a359111420318a9
content_type: application/pdf
creator: cchlebak
date_created: 2022-03-02T15:33:18Z
date_updated: 2022-03-02T15:33:18Z
file_id: '10807'
file_name: 2021_JACSAu_Calcabrini.pdf
file_size: 1257973
relation: main_file
success: 1
file_date_updated: 2022-03-02T15:33:18Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '11'
keyword:
- general medicine
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1898-1903
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: JACS Au
publication_identifier:
eissn:
- 2691-3704
issn:
- 2691-3704
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: https://doi.org/10.26434/chemrxiv-2021-cn2fr
record:
- id: '12885'
relation: dissertation_contains
status: public
status: public
title: 'Ligand conversion in nanocrystal synthesis: The oxidation of alkylamines to
fatty acids by nitrate'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 1
year: '2021'
...