---
_id: '10073'
abstract:
- lang: eng
text: Thermoelectric materials enable the direct conversion between heat and electricity.
SnTe is a promising candidate due to its high charge transport performance. Here,
we prepared SnTe nanocomposites by employing an aqueous method to synthetize SnTe
nanoparticles (NP), followed by a unique surface treatment prior NP consolidation.
This synthetic approach allowed optimizing the charge and phonon transport synergistically.
The novelty of this strategy was the use of a soluble PbS molecular complex prepared
using a thiol-amine solvent mixture that upon blending is adsorbed on the SnTe
NP surface. Upon consolidation with spark plasma sintering, SnTe-PbS nanocomposite
is formed. The presence of PbS complexes significantly compensates for the Sn
vacancy and increases the average grain size of the nanocomposite, thus improving
the carrier mobility. Moreover, lattice thermal conductivity is also reduced by
the Pb and S-induced mass and strain fluctuation. As a result, an enhanced ZT
of ca. 0.8 is reached at 873 K. Our finding provides a novel strategy to conduct
rational surface treatment on NP-based thermoelectrics.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "The authors thank the EMF facility in IST Austria for providing
SEM and EDX measurements.\r\n"
article_number: '5416'
article_processing_charge: Yes
article_type: original
author:
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: Chang C, Ibáñez M. Enhanced thermoelectric performance by surface engineering
in SnTe-PbS nanocomposites. Materials. 2021;14(18). doi:10.3390/ma14185416
apa: Chang, C., & Ibáñez, M. (2021). Enhanced thermoelectric performance by
surface engineering in SnTe-PbS nanocomposites. Materials. MDPI. https://doi.org/10.3390/ma14185416
chicago: Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by
Surface Engineering in SnTe-PbS Nanocomposites.” Materials. MDPI, 2021.
https://doi.org/10.3390/ma14185416.
ieee: C. Chang and M. Ibáñez, “Enhanced thermoelectric performance by surface engineering
in SnTe-PbS nanocomposites,” Materials, vol. 14, no. 18. MDPI, 2021.
ista: Chang C, Ibáñez M. 2021. Enhanced thermoelectric performance by surface engineering
in SnTe-PbS nanocomposites. Materials. 14(18), 5416.
mla: Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface
Engineering in SnTe-PbS Nanocomposites.” Materials, vol. 14, no. 18, 5416,
MDPI, 2021, doi:10.3390/ma14185416.
short: C. Chang, M. Ibáñez, Materials 14 (2021).
date_created: 2021-10-03T22:01:23Z
date_published: 2021-09-19T00:00:00Z
date_updated: 2023-08-14T08:00:01Z
day: '19'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.3390/ma14185416
external_id:
isi:
- '000700689400001'
pmid:
- '34576640'
file:
- access_level: open_access
checksum: 4929dfc673a3ae77c010b6174279cc1d
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-14T11:56:39Z
date_updated: 2021-10-14T11:56:39Z
file_id: '10140'
file_name: 2021_Materials_Chang.pdf
file_size: 4404141
relation: main_file
success: 1
file_date_updated: 2021-10-14T11:56:39Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '18'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
publication: Materials
publication_identifier:
eissn:
- 1996-1944
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites
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: 14
year: '2021'
...
---
_id: '10075'
abstract:
- lang: eng
text: We study the expressiveness and succinctness of good-for-games pushdown automata
(GFG-PDA) over finite words, that is, pushdown automata whose nondeterminism can
be resolved based on the run constructed so far, but independently of the remainder
of the input word. We prove that GFG-PDA recognise more languages than deterministic
PDA (DPDA) but not all context-free languages (CFL). This class is orthogonal
to unambiguous CFL. We further show that GFG-PDA can be exponentially more succinct
than DPDA, while PDA can be double-exponentially more succinct than GFG-PDA. We
also study GFGness in visibly pushdown automata (VPA), which enjoy better closure
properties than PDA, and for which we show GFGness to be ExpTime-complete. GFG-VPA
can be exponentially more succinct than deterministic VPA, while VPA can be exponentially
more succinct than GFG-VPA. Both of these lower bounds are tight. Finally, we
study the complexity of resolving nondeterminism in GFG-PDA. Every GFG-PDA has
a positional resolver, a function that resolves nondeterminism and that is only
dependant on the current configuration. Pushdown transducers are sufficient to
implement the resolvers of GFG-VPA, but not those of GFG-PDA. GFG-PDA with finite-state
resolvers are determinisable.
acknowledgement: 'Ismaël Jecker: Funded by the European Union’s Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie grant agreement No 754411.
Karoliina Lehtinen: Funded by the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement No 892704.'
alternative_title:
- LIPIcs
article_number: '53'
article_processing_charge: No
arxiv: 1
author:
- first_name: Shibashis
full_name: Guha, Shibashis
last_name: Guha
- first_name: Ismael R
full_name: Jecker, Ismael R
id: 85D7C63E-7D5D-11E9-9C0F-98C4E5697425
last_name: Jecker
- first_name: Karoliina
full_name: Lehtinen, Karoliina
last_name: Lehtinen
- first_name: Martin
full_name: Zimmermann, Martin
last_name: Zimmermann
citation:
ama: 'Guha S, Jecker IR, Lehtinen K, Zimmermann M. A bit of nondeterminism makes
pushdown automata expressive and succinct. In: 46th International Symposium
on Mathematical Foundations of Computer Science. Vol 202. Schloss Dagstuhl
- Leibniz Zentrum für Informatik; 2021. doi:10.4230/LIPIcs.MFCS.2021.53'
apa: 'Guha, S., Jecker, I. R., Lehtinen, K., & Zimmermann, M. (2021). A bit
of nondeterminism makes pushdown automata expressive and succinct. In 46th
International Symposium on Mathematical Foundations of Computer Science (Vol.
202). Tallinn, Estonia: Schloss Dagstuhl - Leibniz Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2021.53'
chicago: Guha, Shibashis, Ismael R Jecker, Karoliina Lehtinen, and Martin Zimmermann.
“A Bit of Nondeterminism Makes Pushdown Automata Expressive and Succinct.” In
46th International Symposium on Mathematical Foundations of Computer Science,
Vol. 202. Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.MFCS.2021.53.
ieee: S. Guha, I. R. Jecker, K. Lehtinen, and M. Zimmermann, “A bit of nondeterminism
makes pushdown automata expressive and succinct,” in 46th International Symposium
on Mathematical Foundations of Computer Science, Tallinn, Estonia, 2021, vol.
202.
ista: 'Guha S, Jecker IR, Lehtinen K, Zimmermann M. 2021. A bit of nondeterminism
makes pushdown automata expressive and succinct. 46th International Symposium
on Mathematical Foundations of Computer Science. MFCS: Mathematical Foundations
of Computer Science, LIPIcs, vol. 202, 53.'
mla: Guha, Shibashis, et al. “A Bit of Nondeterminism Makes Pushdown Automata Expressive
and Succinct.” 46th International Symposium on Mathematical Foundations of
Computer Science, vol. 202, 53, Schloss Dagstuhl - Leibniz Zentrum für Informatik,
2021, doi:10.4230/LIPIcs.MFCS.2021.53.
short: S. Guha, I.R. Jecker, K. Lehtinen, M. Zimmermann, in:, 46th International
Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl -
Leibniz Zentrum für Informatik, 2021.
conference:
end_date: 2021-08-27
location: Tallinn, Estonia
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2021-08-23
date_created: 2021-10-03T22:01:23Z
date_published: 2021-08-18T00:00:00Z
date_updated: 2022-05-13T08:21:56Z
day: '18'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.MFCS.2021.53
ec_funded: 1
external_id:
arxiv:
- '2105.02611'
file:
- access_level: open_access
checksum: f4d407d43a97330c3fb11e6a7a6fbfb2
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-06T12:44:05Z
date_updated: 2021-10-06T12:44:05Z
file_id: '10097'
file_name: 2021_LIPIcs_Guha.pdf
file_size: 825567
relation: main_file
success: 1
file_date_updated: 2021-10-06T12:44:05Z
has_accepted_license: '1'
intvolume: ' 202'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 46th International Symposium on Mathematical Foundations of Computer
Science
publication_identifier:
isbn:
- 978-3-9597-7201-3
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: A bit of nondeterminism makes pushdown automata expressive and succinct
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2021'
...
---
_id: '10076'
abstract:
- lang: eng
text: We present a novel approach for blockchain asset owners to reclaim their funds
in case of accidental private-key loss or transfer to a mistyped address. Our
solution can be deployed upon failure or absence of proactively implemented backup
mechanisms, such as secret sharing and cold storage. The main advantages against
previous proposals is it does not require any prior action from users and works
with both single-key and multi-sig accounts. We achieve this by a 3-phase Commit()→Reveal()→Claim()−or−Challenge() smart
contract that enables accessing funds of addresses for which the spending key
is not available. We provide an analysis of the threat and incentive models and
formalize the concept of reactive KEy-Loss Protection (KELP).
acknowledgement: The authors would like to thank all anonymous reviewers of FC21 WTSC
workshop for comments and suggestions that greatly improved the quality of this
paper.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sam
full_name: Blackshear, Sam
last_name: Blackshear
- first_name: Konstantinos
full_name: Chalkias, Konstantinos
last_name: Chalkias
- first_name: Panagiotis
full_name: Chatzigiannis, Panagiotis
last_name: Chatzigiannis
- first_name: Riyaz
full_name: Faizullabhoy, Riyaz
last_name: Faizullabhoy
- first_name: Irakliy
full_name: Khaburzaniya, Irakliy
last_name: Khaburzaniya
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Joshua
full_name: Lind, Joshua
last_name: Lind
- first_name: David
full_name: Wong, David
last_name: Wong
- first_name: Tim
full_name: Zakian, Tim
last_name: Zakian
citation:
ama: 'Blackshear S, Chalkias K, Chatzigiannis P, et al. Reactive key-loss protection
in blockchains. In: FC 2021 Workshops. Vol 12676. Springer Nature; 2021:431-450.
doi:10.1007/978-3-662-63958-0_34'
apa: 'Blackshear, S., Chalkias, K., Chatzigiannis, P., Faizullabhoy, R., Khaburzaniya,
I., Kokoris Kogias, E., … Zakian, T. (2021). Reactive key-loss protection in blockchains.
In FC 2021 Workshops (Vol. 12676, pp. 431–450). Virtual: Springer Nature.
https://doi.org/10.1007/978-3-662-63958-0_34'
chicago: Blackshear, Sam, Konstantinos Chalkias, Panagiotis Chatzigiannis, Riyaz
Faizullabhoy, Irakliy Khaburzaniya, Eleftherios Kokoris Kogias, Joshua Lind, David
Wong, and Tim Zakian. “Reactive Key-Loss Protection in Blockchains.” In FC
2021 Workshops, 12676:431–50. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-63958-0_34.
ieee: S. Blackshear et al., “Reactive key-loss protection in blockchains,”
in FC 2021 Workshops, Virtual, 2021, vol. 12676, pp. 431–450.
ista: 'Blackshear S, Chalkias K, Chatzigiannis P, Faizullabhoy R, Khaburzaniya I,
Kokoris Kogias E, Lind J, Wong D, Zakian T. 2021. Reactive key-loss protection
in blockchains. FC 2021 Workshops. FC: International Conference on Financial Cryptography
and Data Security, LNCS, vol. 12676, 431–450.'
mla: Blackshear, Sam, et al. “Reactive Key-Loss Protection in Blockchains.” FC
2021 Workshops, vol. 12676, Springer Nature, 2021, pp. 431–50, doi:10.1007/978-3-662-63958-0_34.
short: S. Blackshear, K. Chalkias, P. Chatzigiannis, R. Faizullabhoy, I. Khaburzaniya,
E. Kokoris Kogias, J. Lind, D. Wong, T. Zakian, in:, FC 2021 Workshops, Springer
Nature, 2021, pp. 431–450.
conference:
end_date: 2021-03-05
location: Virtual
name: 'FC: International Conference on Financial Cryptography and Data Security'
start_date: 2021-03-01
date_created: 2021-10-03T22:01:24Z
date_published: 2021-09-17T00:00:00Z
date_updated: 2023-08-14T07:06:16Z
day: '17'
department:
- _id: ElKo
doi: 10.1007/978-3-662-63958-0_34
external_id:
isi:
- '000713005000034'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://research.fb.com/publications/reactive-key-loss-protection-in-blockchains/
month: '09'
oa: 1
oa_version: Preprint
page: 431-450
publication: FC 2021 Workshops
publication_identifier:
eisbn:
- 978-3-662-63958-0
eissn:
- 1611-3349
isbn:
- 978-3-6626-3957-3
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reactive key-loss protection in blockchains
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: '12676 '
year: '2021'
...
---
_id: '10077'
abstract:
- lang: eng
text: Although much is known about how single neurons in the hippocampus represent
an animal’s position, how cell-cell interactions contribute to spatial coding
remains poorly understood. Using a novel statistical estimator and theoretical
modeling, both developed in the framework of maximum entropy models, we reveal
highly structured cell-to-cell interactions whose statistics depend on familiar
vs. novel environment. In both conditions the circuit interactions optimize the
encoding of spatial information, but for regimes that differ in the signal-to-noise
ratio of their spatial inputs. Moreover, the topology of the interactions facilitates
linear decodability, making the information easy to read out by downstream circuits.
These findings suggest that the efficient coding hypothesis is not applicable
only to individual neuron properties in the sensory periphery, but also to neural
interactions in the central brain.
acknowledgement: We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for
the acquisition of the data. We thank Federico Stella for comments on an earlier
version of the manuscript. MN was supported by European Union Horizon 2020 grant
665385, JC was supported by European Research Council consolidator grant 281511,
GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported
by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01,
by the National Science Foundation under NSF Award No. 1922658 and a Google faculty
award.
article_processing_charge: No
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
citation:
ama: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1
interactions optimizes spatial coding across experience. bioRxiv. doi:10.1101/2021.09.28.460602
apa: Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (n.d.). The structure
of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv.
Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.09.28.460602
chicago: Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin.
“The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across
Experience.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.09.28.460602.
ieee: M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal
CA1 interactions optimizes spatial coding across experience,” bioRxiv.
Cold Spring Harbor Laboratory.
ista: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1
interactions optimizes spatial coding across experience. bioRxiv, 10.1101/2021.09.28.460602.
mla: Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes
Spatial Coding across Experience.” BioRxiv, Cold Spring Harbor Laboratory,
doi:10.1101/2021.09.28.460602.
short: M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).
date_created: 2021-10-04T06:23:34Z
date_published: 2021-09-29T00:00:00Z
date_updated: 2024-03-25T23:30:09Z
day: '29'
department:
- _id: GradSch
- _id: JoCs
- _id: GaTk
doi: 10.1101/2021.09.28.460602
ec_funded: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2021.09.28.460602
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
related_material:
record:
- id: '11932'
relation: dissertation_contains
status: public
status: public
title: The structure of hippocampal CA1 interactions optimizes spatial coding across
experience
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: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '10080'
abstract:
- lang: eng
text: Hippocampal and neocortical neural activity is modulated by the position of
the individual in space. While hippocampal neurons provide the basis for a spatial
map, prefrontal cortical neurons generalize over environmental features. Whether
these generalized representations result from a bidirectional interaction with,
or are mainly derived from hippocampal spatial representations is not known. By
examining simultaneously recorded hippocampal and medial prefrontal neurons, we
observed that prefrontal spatial representations show a delayed coherence with
hippocampal ones. We also identified subpopulations of cells in the hippocampus
and medial prefrontal cortex that formed functional cross-area couplings; these
resembled the optimal connections predicted by a probabilistic model of spatial
information transfer and generalization. Moreover, cross-area couplings were strongest
and had the shortest delay preceding spatial decision-making. Our results suggest
that generalized spatial coding in the medial prefrontal cortex is inherited from
spatial representations in the hippocampus, and that the routing of information
can change dynamically with behavioral demands.
acknowledgement: We thank Federico Stella for invaluable suggestions and discussions.
We thank Yosman BapatDhar and Andrea Cumpelik for comments, help and suggestions
on the exposure of the text. We thank Predrag Živadinović and Juliana Couras for
comments on the text and the figures. This work was supported by the EU-FP7 MC-ITN
IN-SENS (grant 607616).
article_processing_charge: No
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Karola
full_name: Käfer, Karola
id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87
last_name: Käfer
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Nardin M, Käfer K, Csicsvari JL. The generalized spatial representation in
the prefrontal cortex is inherited from the hippocampus. bioRxiv. doi:10.1101/2021.09.30.462269
apa: Nardin, M., Käfer, K., & Csicsvari, J. L. (n.d.). The generalized spatial
representation in the prefrontal cortex is inherited from the hippocampus. bioRxiv.
Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.09.30.462269
chicago: Nardin, Michele, Karola Käfer, and Jozsef L Csicsvari. “The Generalized
Spatial Representation in the Prefrontal Cortex Is Inherited from the Hippocampus.”
BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.09.30.462269.
ieee: M. Nardin, K. Käfer, and J. L. Csicsvari, “The generalized spatial representation
in the prefrontal cortex is inherited from the hippocampus,” bioRxiv. Cold
Spring Harbor Laboratory.
ista: Nardin M, Käfer K, Csicsvari JL. The generalized spatial representation in
the prefrontal cortex is inherited from the hippocampus. bioRxiv, 10.1101/2021.09.30.462269.
mla: Nardin, Michele, et al. “The Generalized Spatial Representation in the Prefrontal
Cortex Is Inherited from the Hippocampus.” BioRxiv, Cold Spring Harbor
Laboratory, doi:10.1101/2021.09.30.462269.
short: M. Nardin, K. Käfer, J.L. Csicsvari, BioRxiv (n.d.).
date_created: 2021-10-04T06:28:32Z
date_published: 2021-10-02T00:00:00Z
date_updated: 2021-10-05T12:34:26Z
day: '02'
department:
- _id: GradSch
- _id: JoCs
doi: 10.1101/2021.09.30.462269
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2021.09.30.462269
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 257BBB4C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '607616'
name: Inter-and intracellular signalling in schizophrenia
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
status: public
title: The generalized spatial representation in the prefrontal cortex is inherited
from the hippocampus
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '10083'
abstract:
- lang: eng
text: "Plant motions occur across a wide spectrum of timescales, ranging from seed
dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term
adaptation of gross architecture. Relatively fast motions include water-driven
growth as exemplified by root cell expansion under abiotic/biotic stresses or
during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered
by the phytohormone auxin. However, the cellular and molecular mechanisms are
still largely unknown. This thesis covers the studies about this topic as follows.
By taking advantage of microfluidics combined with live imaging, pharmaceutical
tools, and transgenic lines, we examined the kinetics of and causal relationship
among various auxininduced rapid cellular changes in root growth, apoplastic pH,
cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology.
We revealed that CMT reorientation and vacuolar constriction are the consequence
of growth itself instead of responding directly to auxin. In contrast, auxin induces
apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered
apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+
inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling.
To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined
microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct
a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway
is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we
uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface
signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during
auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly
activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract
instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and
TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and
TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore
the relation of two signaling pathways. Assisted with biochemistry and fluorescent
imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with
each other. The ability of TIR1/AFB binding to membrane lipid provides a basis
for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides,
transgenic analysis combined with genetic engineering and biochemistry showed
that vi\r\nthey do function in the same pathway. Particularly, auxin-induced
TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely,
TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling.
To follow the study of rapid growth regulation, we analyzed another rapid growth
regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid
and reversible growth inhibition caused by H + influx, highly resembling but not
dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression
of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1
hour, contributing to the sustained RALF1-triggered growth inhibition. These studies
collectively contribute to understanding rapid regulation on plant cell\r\ngrowth,
novel auxin signaling pathway as well as auxin-peptide crosstalk. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lanxin
full_name: Li, Lanxin
last_name: Li
citation:
ama: Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:10.15479/at:ista:10083
apa: Li, L. (2021). Rapid cell growth regulation in Arabidopsis. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:10083
chicago: Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of
Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10083.
ieee: L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science
and Technology Austria, 2021.
ista: Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science
and Technology Austria.
mla: Li, Lanxin. Rapid Cell Growth Regulation in Arabidopsis. Institute of
Science and Technology Austria, 2021, doi:10.15479/at:ista:10083.
short: L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science
and Technology Austria, 2021.
date_created: 2021-10-04T13:33:10Z
date_published: 2021-10-06T00:00:00Z
date_updated: 2025-05-07T11:12:33Z
day: '06'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/at:ista:10083
ec_funded: 1
file:
- access_level: open_access
checksum: 3b2f55b3b8ae05337a0dcc1cd8595b10
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-14T08:00:07Z
date_updated: 2022-12-20T23:30:03Z
embargo: 2022-10-14
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creator: cchlebak
date_created: 2021-10-14T08:00:13Z
date_updated: 2022-12-20T23:30:03Z
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file_id: '10139'
file_name: 0._IST_Austria_Thesis_Lanxin_Li_1014.docx
file_size: 15058499
relation: source_file
file_date_updated: 2022-12-20T23:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 26B4D67E-B435-11E9-9278-68D0E5697425
grant_number: '25351'
name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated
Rapid Growth Inhibition in Arabidopsis Root'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '442'
relation: part_of_dissertation
status: public
- id: '8931'
relation: part_of_dissertation
status: public
- id: '9287'
relation: part_of_dissertation
status: public
- id: '8283'
relation: part_of_dissertation
status: public
- id: '8986'
relation: part_of_dissertation
status: public
- id: '10015'
relation: part_of_dissertation
status: public
- id: '10095'
relation: part_of_dissertation
status: public
- id: '6627'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Rapid cell growth regulation in Arabidopsis
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10095'
abstract:
- lang: eng
text: Growth regulation tailors plant development to its environment. A showcase
is response to gravity, where shoots bend up and roots down1. This paradox is
based on opposite effects of the phytohormone auxin, which promotes cell expansion
in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2.
Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics
in Arabidopsis thaliana, we advance our understanding how auxin inhibits root
growth. We show that auxin activates two distinct, antagonistically acting signalling
pathways that converge on the rapid regulation of the apoplastic pH, a causative
growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts
with and mediates phosphorylation and activation of plasma membrane H+-ATPases
for apoplast acidification, while intracellular canonical auxin signalling promotes
net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation
of these two counteracting mechanisms poises the root for a rapid, fine-tuned
growth modulation while navigating complex soil environment.
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
- _id: Bio
acknowledgement: We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance
and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science,
Machine Shop and Bioimaging Facilities of IST Austria. This project has received
funding from the European Research Council Advanced Grant (ETAP-742985) and the
Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health
(GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO;
VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N)
and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R.,
the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research
to M.R and D.W., the Australian Research Council and China National Distinguished
Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685)
and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and
innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385
and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship
Council to J.C.
article_number: '266395'
article_processing_charge: No
author:
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Mark
full_name: Roosjen, Mark
last_name: Roosjen
- first_name: Koji
full_name: Takahashi, Koji
last_name: Takahashi
- first_name: Lesia
full_name: Rodriguez Solovey, Lesia
id: 3922B506-F248-11E8-B48F-1D18A9856A87
last_name: Rodriguez Solovey
orcid: 0000-0002-7244-7237
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Jian
full_name: Chen, Jian
last_name: Chen
- first_name: Lana
full_name: Shabala, Lana
last_name: Shabala
- first_name: Wouter
full_name: Smet, Wouter
last_name: Smet
- first_name: Hong
full_name: Ren, Hong
last_name: Ren
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Sergey
full_name: Shabala, Sergey
last_name: Shabala
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Toshinori
full_name: Kinoshita, Toshinori
last_name: Kinoshita
- first_name: William M.
full_name: Gray, William M.
last_name: Gray
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin
signalling for H+-fluxes in root growth. Research Square. doi:10.21203/rs.3.rs-266395/v3
apa: Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L.,
Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling
for H+-fluxes in root growth. Research Square. https://doi.org/10.21203/rs.3.rs-266395/v3
chicago: Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez
Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin
Signalling for H+-Fluxes in Root Growth.” Research Square, n.d. https://doi.org/10.21203/rs.3.rs-266395/v3.
ieee: L. Li et al., “Cell surface and intracellular auxin signalling for
H+-fluxes in root growth,” Research Square. .
ista: Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J,
Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D,
Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling
for H+-fluxes in root growth. Research Square, 266395.
mla: Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes
in Root Growth.” Research Square, 266395, doi:10.21203/rs.3.rs-266395/v3.
short: L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J.
Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel,
D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.).
date_created: 2021-10-06T08:56:22Z
date_published: 2021-09-09T00:00:00Z
date_updated: 2024-10-29T10:22:44Z
day: '09'
department:
- _id: JiFr
- _id: NanoFab
doi: 10.21203/rs.3.rs-266395/v3
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.doi.org/10.21203/rs.3.rs-266395/v3
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _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
- _id: 26B4D67E-B435-11E9-9278-68D0E5697425
grant_number: '25351'
name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated
Rapid Growth Inhibition in Arabidopsis Root'
publication: Research Square
publication_identifier:
issn:
- 2693-5015
publication_status: accepted
related_material:
record:
- id: '10083'
relation: dissertation_contains
status: public
- id: '10223'
relation: later_version
status: public
status: public
title: Cell surface and intracellular auxin signalling for H+-fluxes in root growth
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10103'
abstract:
- lang: eng
text: The small cellular molecule inositol hexakisphosphate (IP6) has been known
for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like
particles. However, the molecular details underlying this effect have been determined
only recently, with the identification of the IP6 binding site in the immature
Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice
via a second IP6 binding site, and enhances core stability, creating a favorable
environment for reverse transcription. IP6 also enhances assembly of other retroviruses,
from both the Lentivirus and the Alpharetrovirus genera. These findings suggest
that IP6 may have a conserved function throughout the family Retroviridae. Here,
we discuss the different steps in the viral life cycle that are influenced by
IP6, and describe in detail how IP6 interacts with the immature and mature lattices
of different retroviruses.
acknowledgement: We thank Volker M. Vogt for his critical comments in preparation
of the review.
article_number: '1853'
article_processing_charge: Yes
article_type: original
author:
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Robert A.
full_name: Dick, Robert A.
last_name: Dick
citation:
ama: Obr M, Schur FK, Dick RA. A structural perspective of the role of IP6 in immature
and mature retroviral assembly. Viruses. 2021;13(9). doi:10.3390/v13091853
apa: Obr, M., Schur, F. K., & Dick, R. A. (2021). A structural perspective of
the role of IP6 in immature and mature retroviral assembly. Viruses. MDPI.
https://doi.org/10.3390/v13091853
chicago: Obr, Martin, Florian KM Schur, and Robert A. Dick. “A Structural Perspective
of the Role of IP6 in Immature and Mature Retroviral Assembly.” Viruses.
MDPI, 2021. https://doi.org/10.3390/v13091853.
ieee: M. Obr, F. K. Schur, and R. A. Dick, “A structural perspective of the role
of IP6 in immature and mature retroviral assembly,” Viruses, vol. 13, no.
9. MDPI, 2021.
ista: Obr M, Schur FK, Dick RA. 2021. A structural perspective of the role of IP6
in immature and mature retroviral assembly. Viruses. 13(9), 1853.
mla: Obr, Martin, et al. “A Structural Perspective of the Role of IP6 in Immature
and Mature Retroviral Assembly.” Viruses, vol. 13, no. 9, 1853, MDPI, 2021,
doi:10.3390/v13091853.
short: M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021).
date_created: 2021-10-07T09:13:29Z
date_published: 2021-09-17T00:00:00Z
date_updated: 2023-08-14T07:21:51Z
day: '17'
ddc:
- '616'
department:
- _id: FlSc
doi: 10.3390/v13091853
external_id:
isi:
- '000699841100001'
pmid:
- '34578434'
file:
- access_level: open_access
checksum: bcfd72a12977d48e22df3d0cc55aacf1
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-08T10:38:15Z
date_updated: 2021-10-08T10:38:15Z
file_id: '10115'
file_name: 2021_Viruses_Obr.pdf
file_size: 4146796
relation: main_file
success: 1
file_date_updated: 2021-10-08T10:38:15Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '9'
keyword:
- virology
- infectious diseases
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Viruses
publication_identifier:
issn:
- 1999-4915
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: A structural perspective of the role of IP6 in immature and mature retroviral
assembly
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: 13
year: '2021'
...
---
_id: '10108'
abstract:
- lang: eng
text: We argue that the time is ripe to investigate differential monitoring, in
which the specification of a program's behavior is implicitly given by a second
program implementing the same informal specification. Similar ideas have been
proposed before, and are currently implemented in restricted form for testing
and specialized run-time analyses, aspects of which we combine. We discuss the
challenges of implementing differential monitoring as a general-purpose, black-box
run-time monitoring framework, and present promising results of a preliminary
implementation, showing low monitoring overheads for diverse programs.
acknowledgement: The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer,
Adrian Francalanza, Owolabi Legunsen, Mae Milano, Manuel Rigger, Cesar Sanchez,
and the members of the IST Verification Seminar for their helpful comments and insights
on various stages of this work, as well as the reviewers of RV’21 for their helpful
suggestions on the actual paper.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Fabian
full_name: Mühlböck, Fabian
id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425
last_name: Mühlböck
orcid: 0000-0003-1548-0177
- 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: 'Mühlböck F, Henzinger TA. Differential monitoring. In: International Conference
on Runtime Verification. Vol 12974. Cham: Springer Nature; 2021:231-243. doi:10.1007/978-3-030-88494-9_12'
apa: 'Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. In International
Conference on Runtime Verification (Vol. 12974, pp. 231–243). Cham: Springer
Nature. https://doi.org/10.1007/978-3-030-88494-9_12'
chicago: 'Mühlböck, Fabian, and Thomas A Henzinger. “Differential Monitoring.” In
International Conference on Runtime Verification, 12974:231–43. Cham: Springer
Nature, 2021. https://doi.org/10.1007/978-3-030-88494-9_12.'
ieee: F. Mühlböck and T. A. Henzinger, “Differential monitoring,” in International
Conference on Runtime Verification, Virtual, 2021, vol. 12974, pp. 231–243.
ista: 'Mühlböck F, Henzinger TA. 2021. Differential monitoring. International Conference
on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 231–243.'
mla: Mühlböck, Fabian, and Thomas A. Henzinger. “Differential Monitoring.” International
Conference on Runtime Verification, vol. 12974, Springer Nature, 2021, pp.
231–43, doi:10.1007/978-3-030-88494-9_12.
short: F. Mühlböck, T.A. Henzinger, in:, International Conference on Runtime Verification,
Springer Nature, Cham, 2021, pp. 231–243.
conference:
end_date: 2021-10-14
location: Virtual
name: 'RV: Runtime Verification'
start_date: 2021-10-11
date_created: 2021-10-07T23:30:10Z
date_published: 2021-10-06T00:00:00Z
date_updated: 2023-08-14T07:20:30Z
day: '06'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-030-88494-9_12
external_id:
isi:
- '000719383800012'
file:
- access_level: open_access
checksum: 554c7fdb259eda703a8b6328a6dad55a
content_type: application/pdf
creator: fmuehlbo
date_created: 2021-10-07T23:32:18Z
date_updated: 2021-10-07T23:32:18Z
file_id: '10109'
file_name: differentialmonitoring-cameraready-openaccess.pdf
file_size: 350632
relation: main_file
success: 1
file_date_updated: 2021-10-07T23:32:18Z
has_accepted_license: '1'
intvolume: ' 12974'
isi: 1
keyword:
- run-time verification
- software engineering
- implicit specification
language:
- iso: eng
month: '10'
oa: 1
oa_version: Preprint
page: 231-243
place: Cham
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: International Conference on Runtime Verification
publication_identifier:
eisbn:
- 978-3-030-88494-9
eissn:
- 1611-3349
isbn:
- 978-3-030-88493-2
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '9946'
relation: extended_version
status: public
scopus_import: '1'
status: public
title: Differential monitoring
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12974
year: '2021'
...
---
_id: '10110'
abstract:
- lang: eng
text: Pattern separation is a fundamental brain computation that converts small
differences in input patterns into large differences in output patterns. Several
synaptic mechanisms of pattern separation have been proposed, including code expansion,
inhibition and plasticity; however, which of these mechanisms play a role in the
entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation
circuit, remains unclear. Here we show that a biologically realistic, full-scale
EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive
inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator.
Both external gamma-modulated inhibition and internal lateral inhibition mediated
by PV+-INs substantially contributed to pattern separation. Both local connectivity
and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness.
Similarly, mossy fiber synapses with conditional detonator properties contributed
to pattern separation. By contrast, perforant path synapses with Hebbian synaptic
plasticity and direct EC–CA3 connection shifted the network towards pattern completion.
Our results demonstrate that the specific properties of cells and synapses optimize
higher-order computations in biological networks and might be useful to improve
the deep learning capabilities of technical networks.
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: 'Claudia '
full_name: 'Espinoza Martinez, Claudia '
id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87
last_name: Espinoza Martinez
orcid: 0000-0003-4710-2082
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
- first_name: Benjamin
full_name: Suter, Benjamin
id: 4952F31E-F248-11E8-B48F-1D18A9856A87
last_name: Suter
orcid: 0000-0002-9885-6936
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity
rules and synaptic properties shape the efficacy of pattern separation in the
entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:10.15479/AT:ISTA:10110
apa: Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &
Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the
efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.
IST Austria. https://doi.org/10.15479/AT:ISTA:10110
chicago: Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang,
Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties
Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3
Network.” IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:10110.
ieee: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M.
Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern
separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.
ista: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021.
How connectivity rules and synaptic properties shape the efficacy of pattern separation
in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, 10.15479/AT:ISTA:10110.
mla: Guzmán, José, et al. How Connectivity Rules and Synaptic Properties Shape
the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3
Network. IST Austria, 2021, doi:10.15479/AT:ISTA:10110.
short: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas,
(2021).
date_created: 2021-10-08T06:44:22Z
date_published: 2021-12-16T00:00:00Z
date_updated: 2024-03-25T23:30:07Z
day: '16'
ddc:
- '005'
department:
- _id: PeJo
- _id: ScienComp
doi: 10.15479/AT:ISTA:10110
file:
- access_level: open_access
checksum: f92f8931cad0aa7e411c1715337bf408
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2021-10-08T08:46:04Z
date_updated: 2021-10-08T08:46:04Z
file_id: '10114'
file_name: patternseparation-main (1).zip
file_size: 332990101
relation: main_file
success: 1
file_date_updated: 2021-10-08T08:46:04Z
has_accepted_license: '1'
license: https://opensource.org/licenses/GPL-3.0
month: '12'
oa: 1
publisher: IST Austria
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/spot-the-difference/
record:
- id: '10816'
relation: used_for_analysis_in
status: public
status: public
title: How connectivity rules and synaptic properties shape the efficacy of pattern
separation in the entorhinal cortex–dentate gyrus–CA3 network
tmp:
legal_code_url: https://www.gnu.org/licenses/gpl-3.0.en.html
name: GNU General Public License 3.0
short: GPL 3.0
type: software
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '10116'
abstract:
- lang: eng
text: The ubiquitous Ca2+ sensor calmodulin (CaM) binds and regulates many proteins,
including ion channels, CaM kinases, and calcineurin, according to Ca2+-CaM levels.
What regulates neuronal CaM levels, is, however, unclear. CaM-binding transcription
activators (CAMTAs) are ancient proteins expressed broadly in nervous systems
and whose loss confers pleiotropic behavioral defects in flies, mice, and humans.
Using Caenorhabditis elegans and Drosophila, we show that CAMTAs control neuronal
CaM levels. The behavioral and neuronal Ca2+ signaling defects in mutants lacking
camt-1, the sole C. elegans CAMTA, can be rescued by supplementing neuronal CaM.
CAMT-1 binds multiple sites in the CaM promoter and deleting these sites phenocopies
camt-1. Our data suggest CAMTAs mediate a conserved and general mechanism that
controls neuronal CaM levels, thereby regulating Ca2+ signaling, physiology, and
behavior.
acknowledgement: The authors thank the MRC-LMB Flow Cytometry facility and Imaging
Service for support, the Cancer Research UK Cambridge Institute Genomics Core for
Next Generation Sequencing, Julie Ahringer and Alex Appert for advice and technical
help for ChIP-seq experiments, Paula Freire-Pritchett, Tim Stevens, and Gurpreet
Ghattaoraya for RNA-seq and ChIP-seq analyses, Nikos Chronis for the TN-XL plasmid,
Hong-Sheng Li and Daisuke Yamamoto for generously sending the tes2 and cro mutants,
Daria Siekhaus for hosting the fly work, Michaela Misova for technical assistance.
The authors are very grateful to Salihah Ece Sönmez for teaching us how to dissect,
mount and stain Drosophila retinae. This work was supported by an Advanced ERC grant
(269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB, and an IST
Plus Fellowship to TV-B (Marie Sklodowska-Curie Agreement no 754411).
article_number: e68238
article_processing_charge: No
article_type: original
author:
- first_name: Thanh
full_name: Vuong-Brender, Thanh
id: D389312E-10C4-11EA-ABF4-A4B43DDC885E
last_name: Vuong-Brender
- first_name: Sean
full_name: Flynn, Sean
last_name: Flynn
- first_name: Yvonne
full_name: Vallis, Yvonne
id: 05A2795C-31B5-11EA-83A7-7DA23DDC885E
last_name: Vallis
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
citation:
ama: Vuong-Brender T, Flynn S, Vallis Y, de Bono M. Neuronal calmodulin levels are
controlled by CAMTA transcription factors. eLife. 2021;10. doi:10.7554/eLife.68238
apa: Vuong-Brender, T., Flynn, S., Vallis, Y., & de Bono, M. (2021). Neuronal
calmodulin levels are controlled by CAMTA transcription factors. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.68238
chicago: Vuong-Brender, Thanh, Sean Flynn, Yvonne Vallis, and Mario de Bono. “Neuronal
Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” ELife.
eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.68238.
ieee: T. Vuong-Brender, S. Flynn, Y. Vallis, and M. de Bono, “Neuronal calmodulin
levels are controlled by CAMTA transcription factors,” eLife, vol. 10.
eLife Sciences Publications, 2021.
ista: Vuong-Brender T, Flynn S, Vallis Y, de Bono M. 2021. Neuronal calmodulin levels
are controlled by CAMTA transcription factors. eLife. 10, e68238.
mla: Vuong-Brender, Thanh, et al. “Neuronal Calmodulin Levels Are Controlled by
CAMTA Transcription Factors.” ELife, vol. 10, e68238, eLife Sciences Publications,
2021, doi:10.7554/eLife.68238.
short: T. Vuong-Brender, S. Flynn, Y. Vallis, M. de Bono, ELife 10 (2021).
date_created: 2021-10-10T22:01:22Z
date_published: 2021-09-17T00:00:00Z
date_updated: 2023-08-14T07:23:39Z
day: '17'
ddc:
- '610'
department:
- _id: MaDe
doi: 10.7554/eLife.68238
ec_funded: 1
external_id:
isi:
- '000695716100001'
pmid:
- '34499028'
file:
- access_level: open_access
checksum: b465e172d2b1f57aa26a2571a085d052
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-11T14:15:07Z
date_updated: 2021-10-11T14:15:07Z
file_id: '10122'
file_name: 2021_eLife_VuongBrender.pdf
file_size: 1774624
relation: main_file
success: 1
file_date_updated: 2021-10-11T14:15:07Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neuronal calmodulin levels are controlled by CAMTA transcription factors
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '10117'
abstract:
- lang: eng
text: Proximity labeling provides a powerful in vivo tool to characterize the proteome
of subcellular structures and the interactome of specific proteins. The nematode
Caenorhabditis elegans is one of the most intensely studied organisms in biology,
offering many advantages for biochemistry. Using the highly active biotin ligase
TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage
of TurboID is that biotin's high affinity for streptavidin means biotin-labeled
proteins can be affinity-purified under harsh denaturing conditions. By combining
extensive sonication with aggressive denaturation using SDS and urea, we achieved
near-complete solubilization of worm proteins. We then used this protocol to characterize
the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among
the smallest C. elegans cells. To probe the method's sensitivity, we expressed
TurboID exclusively in the two AFD neurons and showed that the protocol could
identify known and previously unknown proteins expressed selectively in AFD. The
active zones of synapses are composed of a protein matrix that is difficult to
solubilize and purify. To test if our protocol could solubilize active zone proteins,
we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic
active zone protein. We identified many known ELKS-1-interacting active zone proteins,
as well as previously uncharacterized synaptic proteins. Versatile vectors and
the inherent advantages of using C. elegans, including fast growth and the ability
to rapidly make and functionally test knock-ins, make proximity labeling a valuable
addition to the armory of this model organism.
acknowledgement: We thank de Bono lab members for helpful comments on the manuscript,
IST Austria and University of Vienna Mass Spec Facilities for invaluable discussions
and comments for the optimization of mass spec analyses of worm samples. The biotin
auxotropic E. coli strain MG1655bioB:kan was gift from John Cronan (University of
Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford
University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54
3′UTR entry vector were kindly shared by Dr Dominique Glauser (University of Fribourg).
Codon-optimized mScarlet vector was a generous gift from Dr Manuel Zimmer (University
of Vienna).
article_number: '101094'
article_processing_charge: Yes
article_type: original
author:
- first_name: Murat
full_name: Artan, Murat
id: C407B586-6052-11E9-B3AE-7006E6697425
last_name: Artan
orcid: 0000-0001-8945-6992
- first_name: Stephen
full_name: Barratt, Stephen
id: 57740d2b-2a88-11ec-97cf-d9e6d1b39677
last_name: Barratt
- first_name: Sean M.
full_name: Flynn, Sean M.
last_name: Flynn
- first_name: Farida
full_name: Begum, Farida
last_name: Begum
- first_name: Mark
full_name: Skehel, Mark
last_name: Skehel
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
citation:
ama: Artan M, Barratt S, Flynn SM, et al. Interactome analysis of Caenorhabditis
elegans synapses by TurboID-based proximity labeling. Journal of Biological
Chemistry. 2021;297(3). doi:10.1016/J.JBC.2021.101094
apa: Artan, M., Barratt, S., Flynn, S. M., Begum, F., Skehel, M., Nicolas, A., &
de Bono, M. (2021). Interactome analysis of Caenorhabditis elegans synapses by
TurboID-based proximity labeling. Journal of Biological Chemistry. Elsevier.
https://doi.org/10.1016/J.JBC.2021.101094
chicago: Artan, Murat, Stephen Barratt, Sean M. Flynn, Farida Begum, Mark Skehel,
Armel Nicolas, and Mario de Bono. “Interactome Analysis of Caenorhabditis Elegans
Synapses by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry.
Elsevier, 2021. https://doi.org/10.1016/J.JBC.2021.101094.
ieee: M. Artan et al., “Interactome analysis of Caenorhabditis elegans synapses
by TurboID-based proximity labeling,” Journal of Biological Chemistry,
vol. 297, no. 3. Elsevier, 2021.
ista: Artan M, Barratt S, Flynn SM, Begum F, Skehel M, Nicolas A, de Bono M. 2021.
Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity
labeling. Journal of Biological Chemistry. 297(3), 101094.
mla: Artan, Murat, et al. “Interactome Analysis of Caenorhabditis Elegans Synapses
by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry,
vol. 297, no. 3, 101094, Elsevier, 2021, doi:10.1016/J.JBC.2021.101094.
short: M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de
Bono, Journal of Biological Chemistry 297 (2021).
date_created: 2021-10-10T22:01:23Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2023-08-14T07:24:09Z
day: '01'
ddc:
- '612'
department:
- _id: MaDe
- _id: LifeSc
doi: 10.1016/J.JBC.2021.101094
ec_funded: 1
external_id:
isi:
- '000706409200006'
file:
- access_level: open_access
checksum: 19e39d36c5b9387c6dc0e89c9ae856ab
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-11T12:20:58Z
date_updated: 2021-10-11T12:20:58Z
file_id: '10121'
file_name: 2021_JBC_Artan.pdf
file_size: 1680010
relation: main_file
success: 1
file_date_updated: 2021-10-11T12:20:58Z
has_accepted_license: '1'
intvolume: ' 297'
isi: 1
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Biological Chemistry
publication_identifier:
eissn:
- 1083-351X
issn:
- 0021-9258
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity
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: 297
year: '2021'
...
---
_id: '10123'
abstract:
- lang: eng
text: Solution synthesis of particles emerged as an alternative to prepare thermoelectric
materials with less demanding processing conditions than conventional solid-state
synthetic methods. However, solution synthesis generally involves the presence
of additional molecules or ions belonging to the precursors or added to enable
solubility and/or regulate nucleation and growth. These molecules or ions can
end up in the particles as surface adsorbates and interfere in the material properties.
This work demonstrates that ionic adsorbates, in particular Na⁺ ions, are electrostatically
adsorbed in SnSe particles synthesized in water and play a crucial role not only
in directing the material nano/microstructure but also in determining the transport
properties of the consolidated material. In dense pellets prepared by sintering
SnSe particles, Na remains within the crystal lattice as dopant, in dislocations,
precipitates, and forming grain boundary complexions. These results highlight
the importance of considering all the possible unintentional impurities to establish
proper structure-property relationships and control material properties in solution-processed
thermoelectric materials.
acknowledged_ssus:
- _id: EM-Fac
- _id: NanoFab
acknowledgement: 'Y.L. and M.C. contributed equally to this work. This research was
supported by the Scientific Service Units (SSU) of IST Austria through resources
provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility
(NNF). This work was financially supported by IST Austria and the Werner Siemens
Foundation. Y.L. acknowledges funding from the European Union''s Horizon 2020 research
and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411.
M.C. has received funding from the European Union''s Horizon 2020 research and innovation
program under the Marie Skłodowska-Curie Grant Agreement No. 665385. Y.Y. and O.C.-M.
acknowledge the financial support from DFG within the project SFB 917: Nanoswitches.
J.L. is a Serra Húnter Fellow and is grateful to ICREA Academia program. C.C. acknowledges
funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N.'
article_number: '2106858'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Mariano
full_name: Calcabrini, Mariano
id: 45D7531A-F248-11E8-B48F-1D18A9856A87
last_name: Calcabrini
orcid: 0000-0003-4566-5877
- first_name: Yuan
full_name: Yu, Yuan
last_name: Yu
- first_name: Aziz
full_name: Genç, Aziz
last_name: Genç
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Tobias
full_name: Kleinhanns, Tobias
id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425
last_name: Kleinhanns
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Jordi
full_name: Llorca, Jordi
last_name: Llorca
- first_name: Oana
full_name: Cojocaru‐Mirédin, Oana
last_name: Cojocaru‐Mirédin
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: 'Liu Y, Calcabrini M, Yu Y, et al. The importance of surface adsorbates in
solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials.
2021;33(52). doi:10.1002/adma.202106858'
apa: 'Liu, Y., Calcabrini, M., Yu, Y., Genç, A., Chang, C., Costanzo, T., … Ibáñez,
M. (2021). The importance of surface adsorbates in solution‐processed thermoelectric
materials: The case of SnSe. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202106858'
chicago: 'Liu, Yu, Mariano Calcabrini, Yuan Yu, Aziz Genç, Cheng Chang, Tommaso
Costanzo, Tobias Kleinhanns, et al. “The Importance of Surface Adsorbates in Solution‐processed
Thermoelectric Materials: The Case of SnSe.” Advanced Materials. Wiley,
2021. https://doi.org/10.1002/adma.202106858.'
ieee: 'Y. Liu et al., “The importance of surface adsorbates in solution‐processed
thermoelectric materials: The case of SnSe,” Advanced Materials, vol. 33,
no. 52. Wiley, 2021.'
ista: 'Liu Y, Calcabrini M, Yu Y, Genç A, Chang C, Costanzo T, Kleinhanns T, Lee
S, Llorca J, Cojocaru‐Mirédin O, Ibáñez M. 2021. The importance of surface adsorbates
in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials.
33(52), 2106858.'
mla: 'Liu, Yu, et al. “The Importance of Surface Adsorbates in Solution‐processed
Thermoelectric Materials: The Case of SnSe.” Advanced Materials, vol. 33,
no. 52, 2106858, Wiley, 2021, doi:10.1002/adma.202106858.'
short: Y. Liu, M. Calcabrini, Y. Yu, A. Genç, C. Chang, T. Costanzo, T. Kleinhanns,
S. Lee, J. Llorca, O. Cojocaru‐Mirédin, M. Ibáñez, Advanced Materials 33 (2021).
date_created: 2021-10-11T20:07:24Z
date_published: 2021-12-29T00:00:00Z
date_updated: 2023-08-14T07:25:27Z
day: '29'
ddc:
- '620'
department:
- _id: EM-Fac
- _id: MaIb
doi: 10.1002/adma.202106858
ec_funded: 1
external_id:
isi:
- '000709899300001'
pmid:
- '34626034'
file:
- access_level: open_access
checksum: 990bccc527c64d85cf1c97885110b5f4
content_type: application/pdf
creator: cchlebak
date_created: 2022-02-03T13:16:14Z
date_updated: 2022-02-03T13:16:14Z
file_id: '10720'
file_name: 2021_AdvancedMaterials_Liu.pdf
file_size: 5595666
relation: main_file
success: 1
file_date_updated: 2022-02-03T13:16:14Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '52'
keyword:
- mechanical engineering
- mechanics of materials
- general materials science
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: Advanced Materials
publication_identifier:
eissn:
- 1521-4095
issn:
- 0935-9648
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '12885'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'The importance of surface adsorbates in solution‐processed thermoelectric
materials: The case of SnSe'
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: 33
year: '2021'
...
---
_id: '10134'
abstract:
- lang: eng
text: We investigate the effect of coupling between translational and internal degrees
of freedom of composite quantum particles on their localization in a random potential.
We show that entanglement between the two degrees of freedom weakens localization
due to the upper bound imposed on the inverse participation ratio by purity of
a quantum state. We perform numerical calculations for a two-particle system bound
by a harmonic force in a 1D disordered lattice and a rigid rotor in a 2D disordered
lattice. We illustrate that the coupling has a dramatic effect on localization
properties, even with a small number of internal states participating in quantum
dynamics.
acknowledgement: "We acknowledge helpful discussions with W. G. Unruh and A. Rodriguez.
F. S. is supported by European Union’s\r\nHorizon 2020 research and innovation programme
under the Marie Skłodowska-Curie Grant No. 754411. M. L. acknowledges support by
the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). W. H. Z.
is\r\nsupported by Department of Energy under the Los\r\nAlamos National Laboratory
LDRD Program as well as by the U.S. Department of Energy, Office of Science, Basic\r\nEnergy
Sciences, Materials Sciences and Engineering Division, Condensed Matter Theory Program.
R. V. K. is supported by NSERC of Canada.\r\n"
article_number: '160602'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Fumika
full_name: Suzuki, Fumika
id: 650C99FC-1079-11EA-A3C0-73AE3DDC885E
last_name: Suzuki
orcid: 0000-0003-4982-5970
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Wojciech H.
full_name: Zurek, Wojciech H.
last_name: Zurek
- first_name: Roman V.
full_name: Krems, Roman V.
last_name: Krems
citation:
ama: Suzuki F, Lemeshko M, Zurek WH, Krems RV. Anderson localization of composite
particles. Physical Review Letters. 2021;127(16). doi:10.1103/physrevlett.127.160602
apa: Suzuki, F., Lemeshko, M., Zurek, W. H., & Krems, R. V. (2021). Anderson
localization of composite particles. Physical Review Letters. American
Physical Society . https://doi.org/10.1103/physrevlett.127.160602
chicago: Suzuki, Fumika, Mikhail Lemeshko, Wojciech H. Zurek, and Roman V. Krems.
“Anderson Localization of Composite Particles.” Physical Review Letters.
American Physical Society , 2021. https://doi.org/10.1103/physrevlett.127.160602.
ieee: F. Suzuki, M. Lemeshko, W. H. Zurek, and R. V. Krems, “Anderson localization
of composite particles,” Physical Review Letters, vol. 127, no. 16. American
Physical Society , 2021.
ista: Suzuki F, Lemeshko M, Zurek WH, Krems RV. 2021. Anderson localization of composite
particles. Physical Review Letters. 127(16), 160602.
mla: Suzuki, Fumika, et al. “Anderson Localization of Composite Particles.” Physical
Review Letters, vol. 127, no. 16, 160602, American Physical Society , 2021,
doi:10.1103/physrevlett.127.160602.
short: F. Suzuki, M. Lemeshko, W.H. Zurek, R.V. Krems, Physical Review Letters 127
(2021).
date_created: 2021-10-13T09:21:33Z
date_published: 2021-10-12T00:00:00Z
date_updated: 2024-02-29T12:34:10Z
day: '12'
department:
- _id: MiLe
doi: 10.1103/physrevlett.127.160602
ec_funded: 1
external_id:
arxiv:
- '2011.06279'
isi:
- '000707495700001'
intvolume: ' 127'
isi: 1
issue: '16'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2011.06279
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: 'American Physical Society '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anderson localization of composite particles
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 127
year: '2021'
...
---
_id: '10135'
abstract:
- lang: eng
text: "Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically
throughout their whole life and thereby flexibly adapt to ever-changing environmental
conditions. Plant hormones auxin and cytokinin are the main regulators of the
lateral root organogenesis. Additionally to their solo activities, the interaction
between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root
development and growth. In particular, cytokinin modulates auxin distribution
within the developing lateral root by affecting the endomembrane trafficking of
auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al.,
2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore,
it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational
level. Impact of cytokinin and other plant hormones on auxin transporters (including
PIN1) on the posttranslational level is described in detail in the introduction
part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights
into the molecular machinery underlying cytokinin effect on the endomembrane trafficking
in the plant cell, in particular on the PIN1 degradation, we conducted two large
proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical
proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin
treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A).
We found that DRP2A plays a role in cytokinin regulated processes during the plant
growth and that cytokinin treatment promotes destabilization of DRP2A protein.
However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In
the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial
role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation.
Altogether, we identified proteins, which bind to cytokinin and proteins that
in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation
pattern. By combining information from these two screens, we can pave our way
towards understanding of noncanonical cytokinin effects."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Hana
full_name: Semerádová, Hana
id: 42FE702E-F248-11E8-B48F-1D18A9856A87
last_name: Semerádová
citation:
ama: Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis. 2021. doi:10.15479/at:ista:10135
apa: Semerádová, H. (2021). Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:10135
chicago: Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane
Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology
Austria, 2021. https://doi.org/10.15479/at:ista:10135.
ieee: H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis,” Institute of Science and Technology
Austria, 2021.
ista: Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis. Institute of Science and Technology
Austria.
mla: Semerádová, Hana. Molecular Mechanisms of the Cytokinin-Regulated Endomembrane
Trafficking to Coordinate Plant Organogenesis. Institute of Science and Technology
Austria, 2021, doi:10.15479/at:ista:10135.
short: H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane
Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology
Austria, 2021.
date_created: 2021-10-13T13:42:48Z
date_published: 2021-10-13T00:00:00Z
date_updated: 2024-01-25T10:53:29Z
day: '13'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EvBe
doi: 10.15479/at:ista:10135
file:
- access_level: closed
checksum: ce7108853e6cec6224f17cd6429b51fe
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cziletti
date_created: 2021-10-27T07:45:37Z
date_updated: 2022-12-20T23:30:05Z
embargo_to: open_access
file_id: '10186'
file_name: Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx
file_size: 28508629
relation: source_file
- access_level: open_access
checksum: 0d7afb846e8e31ec794de47bf44e12ef
content_type: application/pdf
creator: cziletti
date_created: 2021-10-27T07:45:57Z
date_updated: 2022-12-20T23:30:05Z
embargo: 2022-10-28
file_id: '10187'
file_name: Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf
file_size: 10623525
relation: main_file
file_date_updated: 2022-12-20T23:30:05Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 261821BC-B435-11E9-9278-68D0E5697425
grant_number: '24746'
name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to
coordinate plant organogenesis.
publication_identifier:
isbn:
- 978-3-99078-014-5
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9160'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to
coordinate plant organogenesis
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '10146'
abstract:
- lang: eng
text: The enzymes of the mitochondrial electron transport chain are key players
of cell metabolism. Despite being active when isolated, in vivo they associate
into supercomplexes1, whose precise role is debated. Supercomplexes CIII2CIV1-2
(refs. 2,3), CICIII2 (ref. 4) and CICIII2CIV (respirasome)5,6,7,8,9,10 exist in
mammals, but in contrast to CICIII2 and the respirasome, to date the only known
eukaryotic structures of CIII2CIV1-2 come from Saccharomyces cerevisiae11,12 and
plants13, which have different organization. Here we present the first, to our
knowledge, structures of mammalian (mouse and ovine) CIII2CIV and its assembly
intermediates, in different conformations. We describe the assembly of CIII2CIV
from the CIII2 precursor to the final CIII2CIV conformation, driven by the insertion
of the N terminus of the assembly factor SCAF1 (ref. 14) deep into CIII2, while
its C terminus is integrated into CIV. Our structures (which include CICIII2 and
the respirasome) also confirm that SCAF1 is exclusively required for the assembly
of CIII2CIV and has no role in the assembly of the respirasome. We show that CIII2
is asymmetric due to the presence of only one copy of subunit 9, which straddles
both monomers and prevents the attachment of a second copy of SCAF1 to CIII2,
explaining the presence of one copy of CIV in CIII2CIV in mammals. Finally, we
show that CIII2 and CIV gain catalytic advantage when assembled into the supercomplex
and propose a role for CIII2CIV in fine tuning the efficiency of electron transfer
in the electron transport chain.
acknowledged_ssus:
- _id: PreCl
- _id: EM-Fac
- _id: ScienComp
acknowledgement: We thank the pre-clinical facility of the IST Austria and A. Venturino
for assistance with the animals; and V.-V. Hodirnau for assistance during the Titan
Krios data collection, performed at the IST Austria. The data processing was performed
at the IST high-performance computing cluster. This project has received funding
from the European Union’s Horizon 2020 research and innovation program under the
Marie Skłodowska-Curie grant agreement no. 754411.
article_processing_charge: No
article_type: original
author:
- first_name: Irene
full_name: Vercellino, Irene
id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87
last_name: Vercellino
orcid: 0000-0001-5618-3449
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Vercellino I, Sazanov LA. Structure and assembly of the mammalian mitochondrial
supercomplex CIII2CIV. Nature. 2021;598(7880):364-367. doi:10.1038/s41586-021-03927-z
apa: Vercellino, I., & Sazanov, L. A. (2021). Structure and assembly of the
mammalian mitochondrial supercomplex CIII2CIV. Nature. Springer
Nature. https://doi.org/10.1038/s41586-021-03927-z
chicago: Vercellino, Irene, and Leonid A Sazanov. “Structure and Assembly of the
Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature. Springer
Nature, 2021. https://doi.org/10.1038/s41586-021-03927-z.
ieee: I. Vercellino and L. A. Sazanov, “Structure and assembly of the mammalian
mitochondrial supercomplex CIII2CIV,” Nature, vol. 598, no.
7880. Springer Nature, pp. 364–367, 2021.
ista: Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial
supercomplex CIII2CIV. Nature. 598(7880), 364–367.
mla: Vercellino, Irene, and Leonid A. Sazanov. “Structure and Assembly of the Mammalian
Mitochondrial Supercomplex CIII2CIV.” Nature, vol. 598, no.
7880, Springer Nature, 2021, pp. 364–67, doi:10.1038/s41586-021-03927-z.
short: I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367.
date_created: 2021-10-17T22:01:17Z
date_published: 2021-10-14T00:00:00Z
date_updated: 2023-08-14T08:01:21Z
day: '14'
department:
- _id: LeSa
doi: 10.1038/s41586-021-03927-z
ec_funded: 1
external_id:
isi:
- '000704581600001'
pmid:
- '34616041'
intvolume: ' 598'
isi: 1
issue: '7880'
language:
- iso: eng
month: '10'
oa_version: None
page: 364-367
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/boosting-the-cells-power-house/
scopus_import: '1'
status: public
title: Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 598
year: '2021'
...
---
_id: '10148'
abstract:
- lang: eng
text: Tactile feedback of an object’s surface enables us to discern its material
properties and affordances. This understanding is used in digital fabrication
processes by creating objects with high-resolution surface variations to influence
a user’s tactile perception. As the design of such surface haptics commonly relies
on knowledge from real-life experiences, it is unclear how to adapt this information
for digital design methods. In this work, we investigate replicating the haptics
of real materials. Using an existing process for capturing an object’s microgeometry,
we digitize and reproduce the stable surface information of a set of 15 fabric
samples. In a psychophysical experiment, we evaluate the tactile qualities of
our set of original samples and their replicas. From our results, we see that
direct reproduction of surface variations is able to influence different psychophysical
dimensions of the tactile perception of surface textures. While the fabrication
process did not preserve all properties, our approach underlines that replication
of surface microgeometries benefits fabrication methods in terms of haptic perception
by covering a large range of tactile variations. Moreover, by changing the surface
structure of a single fabricated material, its material perception can be influenced.
We conclude by proposing strategies for capturing and reproducing digitized textures
to better resemble the perceived haptics of the originals.
acknowledgement: Our gratitude goes out to Kamila Mushkina, Akhmajon Makhsadov, Jordan
Espenshade, Bruno Fruchard, Roland Bennewitz, and Robert Drumm. This project has
received funding from the EU’s Horizon 2020 research and innovation programme, under
the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO).
article_processing_charge: No
author:
- first_name: Donald
full_name: Degraen, Donald
last_name: Degraen
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Antonio
full_name: Kruger, Antonio
last_name: Kruger
citation:
ama: 'Degraen D, Piovarci M, Bickel B, Kruger A. Capturing tactile properties of
real surfaces for haptic reproduction. In: 34th Annual ACM Symposium. Association
for Computing Machinery; 2021:954-971. doi:10.1145/3472749.3474798'
apa: 'Degraen, D., Piovarci, M., Bickel, B., & Kruger, A. (2021). Capturing
tactile properties of real surfaces for haptic reproduction. In 34th Annual
ACM Symposium (pp. 954–971). Virtual: Association for Computing Machinery.
https://doi.org/10.1145/3472749.3474798'
chicago: Degraen, Donald, Michael Piovarci, Bernd Bickel, and Antonio Kruger. “Capturing
Tactile Properties of Real Surfaces for Haptic Reproduction.” In 34th Annual
ACM Symposium, 954–71. Association for Computing Machinery, 2021. https://doi.org/10.1145/3472749.3474798.
ieee: D. Degraen, M. Piovarci, B. Bickel, and A. Kruger, “Capturing tactile properties
of real surfaces for haptic reproduction,” in 34th Annual ACM Symposium,
Virtual, 2021, pp. 954–971.
ista: 'Degraen D, Piovarci M, Bickel B, Kruger A. 2021. Capturing tactile properties
of real surfaces for haptic reproduction. 34th Annual ACM Symposium. UIST: User
Interface Software and Technology, 954–971.'
mla: Degraen, Donald, et al. “Capturing Tactile Properties of Real Surfaces for
Haptic Reproduction.” 34th Annual ACM Symposium, Association for Computing
Machinery, 2021, pp. 954–71, doi:10.1145/3472749.3474798.
short: D. Degraen, M. Piovarci, B. Bickel, A. Kruger, in:, 34th Annual ACM Symposium,
Association for Computing Machinery, 2021, pp. 954–971.
conference:
end_date: 2021-10-14
location: Virtual
name: 'UIST: User Interface Software and Technology'
start_date: 2021-10-10
date_created: 2021-10-18T07:36:11Z
date_published: 2021-10-10T00:00:00Z
date_updated: 2021-10-19T19:29:06Z
day: '10'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3472749.3474798
ec_funded: 1
file:
- access_level: open_access
checksum: b0b26464df79b3a59e8ed82e4e19ab15
content_type: application/pdf
creator: bbickel
date_created: 2021-10-18T07:36:03Z
date_updated: 2021-10-18T07:36:03Z
file_id: '10149'
file_name: degraen-UIST2021_Texture_Appropriation_CR_preprint.pdf
file_size: 29796364
relation: main_file
file_date_updated: 2021-10-18T07:36:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Preprint
page: 954-971
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
publication: 34th Annual ACM Symposium
publication_identifier:
isbn:
- 978-1-4503-8635-7
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: Capturing tactile properties of real surfaces for haptic reproduction
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '10153'
abstract:
- lang: eng
text: "Gradual typing is a principled means for mixing typed and untyped code. But
typed and untyped code often exhibit different programming patterns. There is
already substantial research investigating gradually giving types to code exhibiting
typical untyped patterns, and some research investigating gradually removing types
from code exhibiting typical typed patterns. This paper investigates how to extend
these established gradual-typing concepts to give formal guarantees not only about
how to change types as code evolves but also about how to change such programming
patterns as well.\r\n\r\nIn particular, we explore mixing untyped \"structural\"
code with typed \"nominal\" code in an object-oriented language. But whereas previous
work only allowed \"nominal\" objects to be treated as \"structural\" objects,
we also allow \"structural\" objects to dynamically acquire certain nominal types,
namely interfaces. We present a calculus that supports such \"cross-paradigm\"
code migration and interoperation in a manner satisfying both the static and dynamic
gradual guarantees, and demonstrate that the calculus can be implemented efficiently."
acknowledgement: "We thank the reviewers for their valuable suggestions towards improving
the paper. We also \r\nthank Mae Milano and Adrian Sampson, as well as the members
of the Programming Languages Discussion Group at Cornell University and of the Programming
Research Laboratory at Northeastern University, for their helpful feedback on preliminary
findings of this work.\r\n\r\nThis material is based upon work supported in part
by the National Science Foundation (NSF) through grant CCF-1350182 and the Austrian
Science Fund (FWF) through grant Z211-N23 (Wittgenstein~Award).\r\nAny opinions,
findings, and conclusions or recommendations expressed in this material are those
of the authors and do not necessarily reflect the views of the NSF or the FWF."
article_number: '127'
article_processing_charge: No
article_type: original
author:
- first_name: Fabian
full_name: Mühlböck, Fabian
id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425
last_name: Mühlböck
orcid: 0000-0003-1548-0177
- first_name: Ross
full_name: Tate, Ross
last_name: Tate
citation:
ama: Mühlböck F, Tate R. Transitioning from structural to nominal code with efficient
gradual typing. Proceedings of the ACM on Programming Languages. 2021;5.
doi:10.1145/3485504
apa: 'Mühlböck, F., & Tate, R. (2021). Transitioning from structural to nominal
code with efficient gradual typing. Proceedings of the ACM on Programming Languages.
Chicago, IL, United States: Association for Computing Machinery. https://doi.org/10.1145/3485504'
chicago: Mühlböck, Fabian, and Ross Tate. “Transitioning from Structural to Nominal
Code with Efficient Gradual Typing.” Proceedings of the ACM on Programming
Languages. Association for Computing Machinery, 2021. https://doi.org/10.1145/3485504.
ieee: F. Mühlböck and R. Tate, “Transitioning from structural to nominal code with
efficient gradual typing,” Proceedings of the ACM on Programming Languages,
vol. 5. Association for Computing Machinery, 2021.
ista: Mühlböck F, Tate R. 2021. Transitioning from structural to nominal code with
efficient gradual typing. Proceedings of the ACM on Programming Languages. 5,
127.
mla: Mühlböck, Fabian, and Ross Tate. “Transitioning from Structural to Nominal
Code with Efficient Gradual Typing.” Proceedings of the ACM on Programming
Languages, vol. 5, 127, Association for Computing Machinery, 2021, doi:10.1145/3485504.
short: F. Mühlböck, R. Tate, Proceedings of the ACM on Programming Languages 5 (2021).
conference:
end_date: 2021-10-23
location: Chicago, IL, United States
name: 'OOPSLA: Object-Oriented Programming, Systems, Languages, and Applications'
start_date: 2021-10-17
date_created: 2021-10-19T12:48:44Z
date_published: 2021-10-15T00:00:00Z
date_updated: 2021-11-12T11:30:07Z
day: '15'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1145/3485504
file:
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checksum: 71011efd2da771cafdec7f0d9693f8c1
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creator: fmuehlbo
date_created: 2021-10-19T12:52:23Z
date_updated: 2021-10-19T12:52:23Z
file_id: '10154'
file_name: monnom-oopsla21.pdf
file_size: 770269
relation: main_file
success: 1
file_date_updated: 2021-10-19T12:52:23Z
has_accepted_license: '1'
intvolume: ' 5'
keyword:
- gradual typing
- gradual guarantee
- nominal
- structural
- call tags
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: Transitioning from structural to nominal code with efficient gradual typing
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 5
year: '2021'
...
---
_id: '10163'
abstract:
- lang: eng
text: The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol
II) is a regulatory hub for transcription and RNA processing. Here, we identify
PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability
that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a
CTD reader domain that preferentially binds two phosphorylated Serine-2 marks
in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated
Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length
of genes. PHF3 knock-out or SPOC deletion in human cells results in increased
Pol II stalling, reduced elongation rate and an increase in mRNA stability, with
marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed
in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation.
Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation
by bridging transcription with mRNA decay.
acknowledgement: 'D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz
Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help
with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase;
Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for
design of the arrest assay sequences; Petra van der Lelij for help with generating
mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan
Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing
reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski
for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility
for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing;
Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich
Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for
sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne
Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis;
staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support;
Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for
critical comments on the manuscript; Life Science Editors for editing assistance.
M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K.
is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S.
is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian
Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology
Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S
and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic
(CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (Grant agreement
no. 649030); this publication reflects only the author’s view and the Research Executive
Agency is not responsible for any use that may be made of the information it contains.
M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research
is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276,
P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative
‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural
Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action
BM1405 Non-globular proteins - from sequence to structure, function and application
in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF
LS17-008), and by the University of Vienna. This project was funded by the MFPL
start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the
Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”)
to D.S.'
article_number: '6078'
article_processing_charge: No
article_type: original
author:
- first_name: Lisa-Marie
full_name: Appel, Lisa-Marie
last_name: Appel
- first_name: Vedran
full_name: Franke, Vedran
last_name: Franke
- first_name: Melania
full_name: Bruno, Melania
last_name: Bruno
- first_name: Irina
full_name: Grishkovskaya, Irina
last_name: Grishkovskaya
- first_name: Aiste
full_name: Kasiliauskaite, Aiste
last_name: Kasiliauskaite
- first_name: Tanja
full_name: Kaufmann, Tanja
last_name: Kaufmann
- first_name: Ursula E.
full_name: Schoeberl, Ursula E.
last_name: Schoeberl
- first_name: Martin G.
full_name: Puchinger, Martin G.
last_name: Puchinger
- first_name: Sebastian
full_name: Kostrhon, Sebastian
last_name: Kostrhon
- first_name: Carmen
full_name: Ebenwaldner, Carmen
last_name: Ebenwaldner
- first_name: Marek
full_name: Sebesta, Marek
last_name: Sebesta
- first_name: Etienne
full_name: Beltzung, Etienne
last_name: Beltzung
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Gen
full_name: Lin, Gen
last_name: Lin
- first_name: Anna
full_name: Vlasova, Anna
last_name: Vlasova
- first_name: Martin
full_name: Leeb, Martin
last_name: Leeb
- first_name: Rushad
full_name: Pavri, Rushad
last_name: Pavri
- first_name: Alexander
full_name: Stark, Alexander
last_name: Stark
- first_name: Altuna
full_name: Akalin, Altuna
last_name: Akalin
- first_name: Richard
full_name: Stefl, Richard
last_name: Stefl
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Kristina
full_name: Djinovic-Carugo, Kristina
last_name: Djinovic-Carugo
- first_name: Dea
full_name: Slade, Dea
last_name: Slade
citation:
ama: Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression
through the Pol II CTD reader domain SPOC. Nature Communications. 2021;12(1).
doi:10.1038/s41467-021-26360-2
apa: Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A.,
Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through
the Pol II CTD reader domain SPOC. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-021-26360-2
chicago: Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste
Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal
Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26360-2.
ieee: L.-M. Appel et al., “PHF3 regulates neuronal gene expression through
the Pol II CTD reader domain SPOC,” Nature Communications, vol. 12, no.
1. Springer Nature, 2021.
ista: Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann
T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung
E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R,
Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression
through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.
mla: Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through
the Pol II CTD Reader Domain SPOC.” Nature Communications, vol. 12, no.
1, 6078, Springer Nature, 2021, doi:10.1038/s41467-021-26360-2.
short: L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T.
Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta,
E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A.
Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications
12 (2021).
date_created: 2021-10-20T14:40:32Z
date_published: 2021-10-19T00:00:00Z
date_updated: 2023-08-14T08:02:31Z
day: '19'
ddc:
- '610'
department:
- _id: CaBe
doi: 10.1038/s41467-021-26360-2
external_id:
isi:
- '000709050300001'
file:
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checksum: d99fcd51aebde19c21314e3de0148007
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creator: cchlebak
date_created: 2021-10-21T13:51:49Z
date_updated: 2021-10-21T13:51:49Z
file_id: '10169'
file_name: 2021_NatComm_Appel.pdf
file_size: 5111706
relation: main_file
success: 1
file_date_updated: 2021-10-21T13:51:49Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- general physics and astronomy
- general biochemistry
- genetics and molecular biology
- general chemistry
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: 'Preprint '
relation: earlier_version
url: https://www.biorxiv.org/content/10.1101/2020.02.11.943159
status: public
title: PHF3 regulates neuronal gene expression through the Pol II CTD reader domain
SPOC
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '10166'
abstract:
- lang: eng
text: While sexual reproduction is widespread among many taxa, asexual lineages
have repeatedly evolved from sexual ancestors. Despite extensive research on the
evolution of sex, it is still unclear whether this switch represents a major transition
requiring major molecular reorganization, and how convergent the changes involved
are. In this study, we investigated the phylogenetic relationship and patterns
of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp,
to assess how gene expression patterns are affected by the transition to asexuality.
We find only a few genes that are consistently associated with the evolution of
asexuality, suggesting that this shift may not require an extensive overhauling
of the meiotic machinery. While genes with sex-biased expression have high rates
of expression divergence within Eurasian Artemia, neither female- nor male-biased
genes appear to show unusual evolutionary patterns after sexuality is lost, contrary
to theoretical expectations.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We thank the Vicoso laboratory, Thomas Lenormand and Tanja Schwander
for helpful discussions, the group of Gonzalo Gajardo, especially Cristian Gallardo-Escárate
and Margarita Parraguez Donoso, for sequencing data and advice, and the IST Scientific
Computing Group for their support. This work was supported by the European Research
Council under the European Union's Horizon 2020 research and innovation program
(grant agreement no. 715257).
article_number: '20211720'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Francisco
full_name: Hontoria, Francisco
last_name: Hontoria
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and
evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal
Society B: Biological Sciences. 2021;288(1959). doi:10.1098/rspb.2021.1720'
apa: 'Huylmans, A. K., Macon, A., Hontoria, F., & Vicoso, B. (2021). Transitions
to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings
of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2021.1720'
chicago: 'Huylmans, Ann K, Ariana Macon, Francisco Hontoria, and Beatriz Vicoso.
“Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.”
Proceedings of the Royal Society B: Biological Sciences. The Royal Society,
2021. https://doi.org/10.1098/rspb.2021.1720.'
ieee: 'A. K. Huylmans, A. Macon, F. Hontoria, and B. Vicoso, “Transitions to asexuality
and evolution of gene expression in Artemia brine shrimp,” Proceedings of the
Royal Society B: Biological Sciences, vol. 288, no. 1959. The Royal Society,
2021.'
ista: 'Huylmans AK, Macon A, Hontoria F, Vicoso B. 2021. Transitions to asexuality
and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal
Society B: Biological Sciences. 288(1959), 20211720.'
mla: 'Huylmans, Ann K., et al. “Transitions to Asexuality and Evolution of Gene
Expression in Artemia Brine Shrimp.” Proceedings of the Royal Society B: Biological
Sciences, vol. 288, no. 1959, 20211720, The Royal Society, 2021, doi:10.1098/rspb.2021.1720.'
short: 'A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal
Society B: Biological Sciences 288 (2021).'
date_created: 2021-10-21T07:46:06Z
date_published: 2021-09-22T00:00:00Z
date_updated: 2024-02-21T12:40:29Z
day: '22'
ddc:
- '595'
department:
- _id: BeVi
doi: 10.1098/rspb.2021.1720
ec_funded: 1
external_id:
isi:
- '000697643700001'
pmid:
- '34547909'
file:
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checksum: 76e7f253b7040bca2ad76f82bd7c45c0
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-22T11:48:02Z
date_updated: 2021-10-22T11:48:02Z
file_id: '10172'
file_name: 2021_ProRoSocBBioSci_Huylmans.pdf
file_size: 995806
relation: main_file
success: 1
file_date_updated: 2021-10-22T11:48:02Z
has_accepted_license: '1'
intvolume: ' 288'
isi: 1
issue: '1959'
keyword:
- asexual reproduction
- parthenogenesis
- sex-biased genes
- sexual conflict
- automixis
- crustaceans
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: 'Proceedings of the Royal Society B: Biological Sciences'
publication_identifier:
eissn:
- 1471-2954
issn:
- 0962-8452
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
related_material:
link:
- relation: supplementary_material
url: https://doi.org/10.6084/m9.figshare.c.5615488.v1
record:
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relation: research_data
status: public
scopus_import: '1'
status: public
title: Transitions to asexuality and evolution of gene expression in Artemia brine
shrimp
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: 288
year: '2021'
...