---
_id: '8203'
abstract:
- lang: eng
text: Using inelastic cotunneling spectroscopy we observe a zero field splitting
within the spin triplet manifold of Ge hut wire quantum dots. The states with
spin ±1 in the confinement direction are energetically favored by up to 55 μeV
compared to the spin 0 triplet state because of the strong spin–orbit coupling.
The reported effect should be observable in a broad class of strongly confined
hole quantum-dot systems and might need to be considered when operating hole spin
qubits.
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: "We acknowledge G. Burkard, V. N. Golovach, C. Kloeffel, D.Loss,
P. Rabl, and M. Rancič ́ for helpful discussions. We\r\nfurther acknowledge T.
Adletzberger, J. Aguilera, T. Asenov, S. Bagiante, T. Menner, L. Shafeek, P. Taus,
P. Traunmüller, and D. Waldhausl for their invaluable assistance. This research
was supported by the Scientific Service Units of IST Austria through resources provided
by the MIBA Machine Shop and the nanofabrication facility, by the FWF-P 32235 project,
by the National Key R&D Program of China (2016YFA0301701, 2016YFA0300600), and by
the European Union’s Horizon 2020 research and innovation program under grant agreement
no. 862046. All data of this publication are available at 10.15479/AT:ISTA:7689."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
- first_name: Lada
full_name: Vukušić, Lada
id: 31E9F056-F248-11E8-B48F-1D18A9856A87
last_name: Vukušić
orcid: 0000-0003-2424-8636
- first_name: Hannes
full_name: Watzinger, Hannes
id: 35DF8E50-F248-11E8-B48F-1D18A9856A87
last_name: Watzinger
- first_name: Fei
full_name: Gao, Fei
last_name: Gao
- first_name: Ting
full_name: Wang, Ting
last_name: Wang
orcid: 0000-0002-4619-9575
- first_name: Jian-Jun
full_name: Zhang, Jian-Jun
last_name: Zhang
- first_name: Karsten
full_name: Held, Karsten
last_name: Held
citation:
ama: Katsaros G, Kukucka J, Vukušić L, et al. Zero field splitting of heavy-hole
states in quantum dots. Nano Letters. 2020;20(7):5201-5206. doi:10.1021/acs.nanolett.0c01466
apa: Katsaros, G., Kukucka, J., Vukušić, L., Watzinger, H., Gao, F., Wang, T., …
Held, K. (2020). Zero field splitting of heavy-hole states in quantum dots. Nano
Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.0c01466
chicago: Katsaros, Georgios, Josip Kukucka, Lada Vukušić, Hannes Watzinger, Fei
Gao, Ting Wang, Jian-Jun Zhang, and Karsten Held. “Zero Field Splitting of Heavy-Hole
States in Quantum Dots.” Nano Letters. American Chemical Society, 2020.
https://doi.org/10.1021/acs.nanolett.0c01466.
ieee: G. Katsaros et al., “Zero field splitting of heavy-hole states in quantum
dots,” Nano Letters, vol. 20, no. 7. American Chemical Society, pp. 5201–5206,
2020.
ista: Katsaros G, Kukucka J, Vukušić L, Watzinger H, Gao F, Wang T, Zhang J-J, Held
K. 2020. Zero field splitting of heavy-hole states in quantum dots. Nano Letters.
20(7), 5201–5206.
mla: Katsaros, Georgios, et al. “Zero Field Splitting of Heavy-Hole States in Quantum
Dots.” Nano Letters, vol. 20, no. 7, American Chemical Society, 2020, pp.
5201–06, doi:10.1021/acs.nanolett.0c01466.
short: G. Katsaros, J. Kukucka, L. Vukušić, H. Watzinger, F. Gao, T. Wang, J.-J.
Zhang, K. Held, Nano Letters 20 (2020) 5201–5206.
corr_author: '1'
date_created: 2020-08-06T09:25:04Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2025-04-15T08:39:16Z
day: '01'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1021/acs.nanolett.0c01466
ec_funded: 1
external_id:
isi:
- '000548893200066'
pmid:
- '32479090'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-08-06T09:35:37Z
date_updated: 2020-08-06T09:35:37Z
file_id: '8204'
file_name: 2020_NanoLetters_Katsaros.pdf
file_size: 3308906
relation: main_file
success: 1
file_date_updated: 2020-08-06T09:35:37Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 5201-5206
pmid: 1
project:
- _id: 237B3DA4-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: P32235
name: Towards scalable hut wire quantum devices
- _id: 237E5020-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862046'
name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS
publication: Nano Letters
publication_identifier:
eissn:
- 1530-6992
issn:
- 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
record:
- id: '7689'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Zero field splitting of heavy-hole states in quantum dots
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 20
year: '2020'
...
---
_id: '8220'
abstract:
- lang: eng
text: Understanding to what extent stem cell potential is a cell-intrinsic property
or an emergent behavior coming from global tissue dynamics and geometry is a key
outstanding question of systems and stem cell biology. Here, we propose a theory
of stem cell dynamics as a stochastic competition for access to a spatially localized
niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce
a steady cellular stream which advects cells away from the niche, while random
rearrangements enable cells away from the niche to be favorably repositioned.
Importantly, even when assuming that all cells in a tissue are molecularly equivalent,
we predict a common (“universal”) functional dependence of the long-term clonal
survival probability on distance from the niche, as well as the emergence of a
well-defined number of functional stem cells, dependent only on the rate of random
movements vs. mitosis-driven advection. We test the predictions of this theory
on datasets of pubertal mammary gland tips and embryonic kidney tips, as well
as homeostatic intestinal crypts. Importantly, we find good agreement for the
predicted functional dependency of the competition as a function of position,
and thus functional stem cell number in each organ. This argues for a key role
of positional fluctuations in dictating stem cell number and dynamics, and we
discuss the applicability of this theory to other settings.
acknowledgement: "We thank all members of the E.H., B.D.S., and J.v.R. groups for
stimulating discussions. This project was supported by\r\nthe European Research
Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from
the CancerGenomics.nl (Netherlands Organization for Scientific Research) program
(J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by
Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust
Grant 098357/Z/12/Z."
article_processing_charge: No
article_type: original
author:
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Colinda L.G.J.
full_name: Scheele, Colinda L.G.J.
last_name: Scheele
- first_name: Kasumi
full_name: Kishi, Kasumi
id: 3065DFC4-F248-11E8-B48F-1D18A9856A87
last_name: Kishi
orcid: 0000-0001-6060-4795
- first_name: Saskia I.J.
full_name: Ellenbroek, Saskia I.J.
last_name: Ellenbroek
- first_name: Benjamin D.
full_name: Simons, Benjamin D.
last_name: Simons
- first_name: Jacco
full_name: Van Rheenen, Jacco
last_name: Van Rheenen
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival
as a noisy competition for niche access. Proceedings of the National Academy
of Sciences of the United States of America. 2020;117(29):16969-16975. doi:10.1073/pnas.1921205117
apa: Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J.,
Simons, B. D., Van Rheenen, J., & Hannezo, E. B. (2020). Stem cell lineage
survival as a noisy competition for niche access. Proceedings of the National
Academy of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.1921205117
chicago: Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia
I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo.
“Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921205117.
ieee: B. Corominas-Murtra et al., “Stem cell lineage survival as a noisy
competition for niche access,” Proceedings of the National Academy of Sciences
of the United States of America, vol. 117, no. 29. National Academy of Sciences,
pp. 16969–16975, 2020.
ista: Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van
Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition
for niche access. Proceedings of the National Academy of Sciences of the United
States of America. 117(29), 16969–16975.
mla: Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition
for Niche Access.” Proceedings of the National Academy of Sciences of the United
States of America, vol. 117, no. 29, National Academy of Sciences, 2020, pp.
16969–75, doi:10.1073/pnas.1921205117.
short: B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D.
Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences
of the United States of America 117 (2020) 16969–16975.
corr_author: '1'
date_created: 2020-08-09T22:00:52Z
date_published: 2020-07-21T00:00:00Z
date_updated: 2026-04-03T09:29:04Z
day: '21'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1073/pnas.1921205117
ec_funded: 1
external_id:
isi:
- '000553292900014'
pmid:
- '32611816'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-08-10T06:50:28Z
date_updated: 2020-08-10T06:50:28Z
file_id: '8223'
file_name: 2020_PNAS_Corominas.pdf
file_size: 1111604
relation: main_file
success: 1
file_date_updated: 2020-08-10T06:50:28Z
has_accepted_license: '1'
intvolume: ' 117'
isi: 1
issue: '29'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 16969-16975
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: press_release
url: https://ist.ac.at/en/news/order-from-noise/
scopus_import: '1'
status: public
title: Stem cell lineage survival as a noisy competition for niche access
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 117
year: '2020'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '8225'
abstract:
- lang: eng
text: Birch pollen allergy is among the most prevalent pollen allergies in Northern
and Central Europe. This IgE-mediated disease can be treated with allergen immunotherapy
(AIT), which typically gives rise to IgG antibodies inducing tolerance. Although
the main mechanisms of allergen immunotherapy (AIT) are known, questions regarding
possible Fc-mediated effects of IgG antibodies remain unanswered. This can mainly
be attributed to the unavailability of appropriate tools, i.e., well-characterised
recombinant antibodies (rAbs). We hereby aimed at providing human rAbs of several
classes for mechanistic studies and as possible candidates for passive immunotherapy.
We engineered IgE, IgG1, and IgG4 sharing the same variable region against the
major birch pollen allergen Bet v 1 using Polymerase Incomplete Primer Extension
(PIPE) cloning. We tested IgE functionality and IgG blocking capabilities using
appropriate model cell lines. In vitro studies showed IgE engagement with FcεRI
and CD23 and Bet v 1-dependent degranulation. Overall, we hereby present fully
functional, human IgE, IgG1, and IgG4 sharing the same variable region against
Bet v 1 and showcase possible applications in first mechanistic studies. Furthermore,
our IgG antibodies might be useful candidates for passive immunotherapy of birch
pollen allergy.
article_number: '5693'
article_processing_charge: No
article_type: original
author:
- first_name: Verena K.
full_name: Köhler, Verena K.
last_name: Köhler
orcid: 0000-0001-5581-398X
- first_name: Silvia
full_name: Crescioli, Silvia
last_name: Crescioli
orcid: 0000-0002-1909-5957
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Heather J.
full_name: Bax, Heather J.
last_name: Bax
orcid: 0000-0003-0432-4160
- first_name: Gerhard
full_name: Hofer, Gerhard
last_name: Hofer
- first_name: Christina L.
full_name: Pranger, Christina L.
last_name: Pranger
- first_name: Karin
full_name: Hufnagl, Karin
last_name: Hufnagl
- first_name: Rodolfo
full_name: Bianchini, Rodolfo
last_name: Bianchini
orcid: 0000-0003-0351-6937
- first_name: Sabine
full_name: Flicker, Sabine
last_name: Flicker
orcid: 0000-0003-4768-8693
- first_name: Walter
full_name: Keller, Walter
last_name: Keller
orcid: 0000-0002-2261-958X
- first_name: Sophia N.
full_name: Karagiannis, Sophia N.
last_name: Karagiannis
orcid: 0000-0002-4100-7810
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
orcid: 0000-0003-4019-5765
citation:
ama: 'Köhler VK, Crescioli S, Singer J, et al. Filling the antibody pipeline in
allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen
Bet v 1. International Journal of Molecular Sciences. 2020;21(16). doi:10.3390/ijms21165693'
apa: 'Köhler, V. K., Crescioli, S., Singer, J., Bax, H. J., Hofer, G., Pranger,
C. L., … Jensen-Jarolim, E. (2020). Filling the antibody pipeline in allergy:
PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet
v 1. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21165693'
chicago: 'Köhler, Verena K., Silvia Crescioli, Judit Singer, Heather J. Bax, Gerhard
Hofer, Christina L. Pranger, Karin Hufnagl, et al. “Filling the Antibody Pipeline
in Allergy: PIPE Cloning of IgE, IgG1 and IgG4 against the Major Birch Pollen
Allergen Bet v 1.” International Journal of Molecular Sciences. MDPI, 2020.
https://doi.org/10.3390/ijms21165693.'
ieee: 'V. K. Köhler et al., “Filling the antibody pipeline in allergy: PIPE
cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1,”
International Journal of Molecular Sciences, vol. 21, no. 16. MDPI, 2020.'
ista: 'Köhler VK, Crescioli S, Singer J, Bax HJ, Hofer G, Pranger CL, Hufnagl K,
Bianchini R, Flicker S, Keller W, Karagiannis SN, Jensen-Jarolim E. 2020. Filling
the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the
major birch pollen allergen Bet v 1. International Journal of Molecular Sciences.
21(16), 5693.'
mla: 'Köhler, Verena K., et al. “Filling the Antibody Pipeline in Allergy: PIPE
Cloning of IgE, IgG1 and IgG4 against the Major Birch Pollen Allergen Bet v 1.”
International Journal of Molecular Sciences, vol. 21, no. 16, 5693, MDPI,
2020, doi:10.3390/ijms21165693.'
short: V.K. Köhler, S. Crescioli, J. Singer, H.J. Bax, G. Hofer, C.L. Pranger, K.
Hufnagl, R. Bianchini, S. Flicker, W. Keller, S.N. Karagiannis, E. Jensen-Jarolim,
International Journal of Molecular Sciences 21 (2020).
date_created: 2020-08-10T11:47:29Z
date_published: 2020-08-08T00:00:00Z
date_updated: 2024-10-15T13:11:23Z
day: '08'
ddc:
- '570'
doi: 10.3390/ijms21165693
extern: '1'
external_id:
pmid:
- '32784509'
file:
- access_level: open_access
checksum: dac7ccef7cdcea9be292664d8c488425
content_type: application/pdf
creator: dernst
date_created: 2020-09-10T07:06:22Z
date_updated: 2020-09-10T07:06:22Z
file_id: '8356'
file_name: 2020_IntMolecSciences_Koehler.pdf
file_size: 2680908
relation: main_file
success: 1
file_date_updated: 2020-09-10T07:06:22Z
has_accepted_license: '1'
intvolume: ' 21'
issue: '16'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: International Journal of Molecular Sciences
publication_identifier:
issn:
- 1422-0067
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: 'Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4
against the major birch pollen allergen Bet v 1'
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: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
volume: 21
year: '2020'
...
---
OA_place: publisher
OA_type: hybrid
_id: '8226'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Jelena
full_name: Gotovina, Jelena
last_name: Gotovina
orcid: 0000-0003-1503-5276
- first_name: Rodolfo
full_name: Bianchini, Rodolfo
last_name: Bianchini
orcid: 0000-0003-0351-6937
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Ina
full_name: Herrmann, Ina
last_name: Herrmann
orcid: 0000-0003-2772-9144
- first_name: Giulia
full_name: Pellizzari, Giulia
last_name: Pellizzari
orcid: 0000-0003-0387-1912
- first_name: Ian D.
full_name: Haidl, Ian D.
last_name: Haidl
orcid: 0000-0002-5301-0822
- first_name: Karin
full_name: Hufnagl, Karin
last_name: Hufnagl
orcid: 0000-0002-2288-2468
- first_name: Sophia N.
full_name: Karagiannis, Sophia N.
last_name: Karagiannis
orcid: 0000-0002-4100-7810
- first_name: Jean S.
full_name: Marshall, Jean S.
last_name: Marshall
orcid: 0000-0002-5642-1379
- first_name: Erika
full_name: Jensen‐Jarolim, Erika
last_name: Jensen‐Jarolim
orcid: 0000-0003-4019-5765
citation:
ama: Gotovina J, Bianchini R, Singer J, et al. Epinephrine drives human M2a allergic
macrophages to a regulatory phenotype reducing mast cell degranulation in vitro.
Allergy. 2020. doi:10.1111/all.14299
apa: Gotovina, J., Bianchini, R., Singer, J., Herrmann, I., Pellizzari, G., Haidl,
I. D., … Jensen‐Jarolim, E. (2020). Epinephrine drives human M2a allergic macrophages
to a regulatory phenotype reducing mast cell degranulation in vitro. Allergy.
Wiley. https://doi.org/10.1111/all.14299
chicago: Gotovina, Jelena, Rodolfo Bianchini, Judit Singer, Ina Herrmann, Giulia
Pellizzari, Ian D. Haidl, Karin Hufnagl, Sophia N. Karagiannis, Jean S. Marshall,
and Erika Jensen‐Jarolim. “Epinephrine Drives Human M2a Allergic Macrophages to
a Regulatory Phenotype Reducing Mast Cell Degranulation in Vitro.” Allergy.
Wiley, 2020. https://doi.org/10.1111/all.14299.
ieee: J. Gotovina et al., “Epinephrine drives human M2a allergic macrophages
to a regulatory phenotype reducing mast cell degranulation in vitro,” Allergy.
Wiley, 2020.
ista: Gotovina J, Bianchini R, Singer J, Herrmann I, Pellizzari G, Haidl ID, Hufnagl
K, Karagiannis SN, Marshall JS, Jensen‐Jarolim E. 2020. Epinephrine drives human
M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation
in vitro. Allergy.
mla: Gotovina, Jelena, et al. “Epinephrine Drives Human M2a Allergic Macrophages
to a Regulatory Phenotype Reducing Mast Cell Degranulation in Vitro.” Allergy,
Wiley, 2020, doi:10.1111/all.14299.
short: J. Gotovina, R. Bianchini, J. Singer, I. Herrmann, G. Pellizzari, I.D. Haidl,
K. Hufnagl, S.N. Karagiannis, J.S. Marshall, E. Jensen‐Jarolim, Allergy (2020).
date_created: 2020-08-10T11:50:30Z
date_published: 2020-04-04T00:00:00Z
date_updated: 2024-10-15T13:13:56Z
day: '04'
doi: 10.1111/all.14299
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/all.14299
month: '04'
oa: 1
oa_version: Published Version
publication: Allergy
publication_identifier:
issn:
- 0105-4538
- 1398-9995
publication_status: epub_ahead
publisher: Wiley
quality_controlled: '1'
status: public
title: Epinephrine drives human M2a allergic macrophages to a regulatory phenotype
reducing mast cell degranulation in vitro
type: journal_article
user_id: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
year: '2020'
...
---
_id: '8254'
abstract:
- lang: eng
text: "Here are the research data underlying the publication \"Estimating inbreeding
and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further
information are summed up in the README document.\r\nThe files for this record
have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192."
article_processing_charge: No
author:
- first_name: Louise S
full_name: Arathoon, Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
orcid: 0000-0003-1771-714X
citation:
ama: Arathoon LS. Estimating inbreeding and its effects in a long-term study of
snapdragons (Antirrhinum majus). 2020. doi:10.15479/AT:ISTA:8254
apa: Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term
study of snapdragons (Antirrhinum majus). Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:8254
chicago: Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term
Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology
Austria, 2020. https://doi.org/10.15479/AT:ISTA:8254.
ieee: L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study
of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria,
2020.
ista: Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study
of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria,
10.15479/AT:ISTA:8254.
mla: Arathoon, Louise S. Estimating Inbreeding and Its Effects in a Long-Term
Study of Snapdragons (Antirrhinum Majus). Institute of Science and Technology
Austria, 2020, doi:10.15479/AT:ISTA:8254.
short: L.S. Arathoon, (2020).
contributor:
- contributor_type: data_collector
first_name: Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
- contributor_type: project_member
first_name: Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- contributor_type: project_member
first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- contributor_type: project_member
first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- contributor_type: project_member
first_name: Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- contributor_type: project_member
first_name: Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
corr_author: '1'
date_created: 2020-08-12T12:49:23Z
date_published: 2020-08-18T00:00:00Z
date_updated: 2024-10-09T21:02:14Z
day: '18'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:8254
file:
- access_level: open_access
checksum: 4f1382ed4384751b6013398c11557bf6
content_type: application/x-zip-compressed
creator: dernst
date_created: 2020-08-18T08:03:23Z
date_updated: 2020-08-18T08:03:23Z
file_id: '8280'
file_name: Data_Rcode_MathematicaNB.zip
file_size: 5778420
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success: 1
file_date_updated: 2020-08-18T08:03:23Z
has_accepted_license: '1'
month: '08'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9192'
relation: later_version
status: public
- id: '11321'
relation: later_version
status: public
status: public
title: Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum
majus)
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8261'
abstract:
- lang: eng
text: Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal
CA3 region, but how they process spatial information remains enigmatic. To examine
the role of GCs in spatial coding, we measured excitatory postsynaptic potentials
(EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt.
Intracellular recording from morphologically identified GCs revealed that most
cells were active, but activity level varied over a wide range. Whereas only ∼5%
of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus,
the GC population broadly encodes spatial information, but only a subset relays
this information to the CA3 network. Fourier analysis indicated that GCs received
conjunctive place-grid-like synaptic input, suggesting code conversion in single
neurons. GC firing was correlated with dendritic complexity and intrinsic excitability,
but not extrinsic excitatory input or dendritic cable properties. Thus, functional
maturation may control input-output transformation and spatial code conversion.
acknowledged_ssus:
- _id: M-Shop
- _id: ScienComp
- _id: PreCl
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung
(Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari,
Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of
this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery
Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp
recording. We are grateful to Florian Marr for cell labeling, cell reconstruction,
and technical assistance; Ben Suter for helpful discussions; Christina Altmutter
for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor
Asenov (Machine Shop) for device construction. We also thank the Scientific Service
Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical
Facility) for efficient support.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- 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: Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow
from input to output in hippocampal granule cells. Neuron. 2020;107(6):1212-1225.
doi:10.1016/j.neuron.2020.07.006
apa: Zhang, X., Schlögl, A., & Jonas, P. M. (2020). Selective routing of spatial
information flow from input to output in hippocampal granule cells. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2020.07.006
chicago: Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of
Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron.
Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.07.006.
ieee: X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information
flow from input to output in hippocampal granule cells,” Neuron, vol. 107,
no. 6. Elsevier, pp. 1212–1225, 2020.
ista: Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information
flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225.
mla: Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from
Input to Output in Hippocampal Granule Cells.” Neuron, vol. 107, no. 6,
Elsevier, 2020, pp. 1212–25, doi:10.1016/j.neuron.2020.07.006.
short: X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.
corr_author: '1'
date_created: 2020-08-14T09:36:05Z
date_published: 2020-09-23T00:00:00Z
date_updated: 2025-04-15T08:29:03Z
day: '23'
ddc:
- '570'
department:
- _id: PeJo
- _id: ScienComp
doi: 10.1016/j.neuron.2020.07.006
ec_funded: 1
external_id:
isi:
- '000579698700009'
pmid:
- '32763145'
file:
- access_level: open_access
checksum: 44a5960fc083a4cb3488d22224859fdc
content_type: application/pdf
creator: dernst
date_created: 2020-12-04T09:29:21Z
date_updated: 2020-12-04T09:29:21Z
file_id: '8920'
file_name: 2020_Neuron_Zhang.pdf
file_size: 3011120
relation: main_file
success: 1
file_date_updated: 2020-12-04T09:29:21Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1212-1225
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/the-bouncer-in-the-brain/
scopus_import: '1'
status: public
title: Selective routing of spatial information flow from input to output in hippocampal
granule cells
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2020'
...
---
_id: '8268'
abstract:
- lang: eng
text: 'Modern scientific instruments produce vast amounts of data, which can overwhelm
the processing ability of computer systems. Lossy compression of data is an intriguing
solution, but comes with its own drawbacks, such as potential signal loss, and
the need for careful optimization of the compression ratio. In this work, we focus
on a setting where this problem is especially acute: compressive sensing frameworks
for interferometry and medical imaging. We ask the following question: can the
precision of the data representation be lowered for all inputs, with recovery
guarantees and practical performance Our first contribution is a theoretical analysis
of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data,
meaning both the measurement matrix and the observation vector are quantized aggressively.
We present a variant of low precision normalized IHT that, under mild conditions,
can still provide recovery guarantees. The second contribution is the application
of our quantization framework to radio astronomy and magnetic resonance imaging.
We show that lowering the precision of the data can significantly accelerate image
recovery. We evaluate our approach on telescope data and samples of brain images
using CPU and FPGA implementations achieving up to a 9x speedup with negligible
loss of recovery quality.'
acknowledgement: The authors would like to thank Dr. Michiel Brentjens at the Netherlands
Institute for Radio Astronomy (ASTRON) for providing radio interferometer data and
Dr. Josip Marjanovic and Dr. Franciszek Hennel at the Magnetic Resonance Technology
of ETH Zurich for providing their insights on the experiments. CZ and the DS3Lab
gratefully acknowledge the support from the Swiss Data Science Center, Alibaba,
Google Focused Research Awards, Huawei, MeteoSwiss, Oracle Labs, Swisscom, Zurich
Insurance, Chinese Scholarship Council, and the Department of Computer Science at
ETH Zurich.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nezihe Merve
full_name: Gurel, Nezihe Merve
last_name: Gurel
- first_name: Kaan
full_name: Kara, Kaan
last_name: Kara
- first_name: Alen
full_name: Stojanov, Alen
last_name: Stojanov
- first_name: Tyler
full_name: Smith, Tyler
last_name: Smith
- first_name: Thomas
full_name: Lemmin, Thomas
last_name: Lemmin
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Markus
full_name: Puschel, Markus
last_name: Puschel
- first_name: Ce
full_name: Zhang, Ce
last_name: Zhang
citation:
ama: 'Gurel NM, Kara K, Stojanov A, et al. Compressive sensing using iterative hard
thresholding with low precision data representation: Theory and applications.
IEEE Transactions on Signal Processing. 2020;68:4268-4282. doi:10.1109/TSP.2020.3010355'
apa: 'Gurel, N. M., Kara, K., Stojanov, A., Smith, T., Lemmin, T., Alistarh, D.-A.,
… Zhang, C. (2020). Compressive sensing using iterative hard thresholding with
low precision data representation: Theory and applications. IEEE Transactions
on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2020.3010355'
chicago: 'Gurel, Nezihe Merve, Kaan Kara, Alen Stojanov, Tyler Smith, Thomas Lemmin,
Dan-Adrian Alistarh, Markus Puschel, and Ce Zhang. “Compressive Sensing Using
Iterative Hard Thresholding with Low Precision Data Representation: Theory and
Applications.” IEEE Transactions on Signal Processing. IEEE, 2020. https://doi.org/10.1109/TSP.2020.3010355.'
ieee: 'N. M. Gurel et al., “Compressive sensing using iterative hard thresholding
with low precision data representation: Theory and applications,” IEEE Transactions
on Signal Processing, vol. 68. IEEE, pp. 4268–4282, 2020.'
ista: 'Gurel NM, Kara K, Stojanov A, Smith T, Lemmin T, Alistarh D-A, Puschel M,
Zhang C. 2020. Compressive sensing using iterative hard thresholding with low
precision data representation: Theory and applications. IEEE Transactions on Signal
Processing. 68, 4268–4282.'
mla: 'Gurel, Nezihe Merve, et al. “Compressive Sensing Using Iterative Hard Thresholding
with Low Precision Data Representation: Theory and Applications.” IEEE Transactions
on Signal Processing, vol. 68, IEEE, 2020, pp. 4268–82, doi:10.1109/TSP.2020.3010355.'
short: N.M. Gurel, K. Kara, A. Stojanov, T. Smith, T. Lemmin, D.-A. Alistarh, M.
Puschel, C. Zhang, IEEE Transactions on Signal Processing 68 (2020) 4268–4282.
date_created: 2020-08-16T22:00:56Z
date_published: 2020-07-20T00:00:00Z
date_updated: 2025-07-10T11:55:10Z
day: '20'
department:
- _id: DaAl
doi: 10.1109/TSP.2020.3010355
external_id:
arxiv:
- '1802.04907'
isi:
- '000562044500001'
intvolume: ' 68'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.04907
month: '07'
oa: 1
oa_version: Preprint
page: 4268-4282
publication: IEEE Transactions on Signal Processing
publication_identifier:
eissn:
- 1941-0476
issn:
- 1053-587X
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Compressive sensing using iterative hard thresholding with low precision data
representation: Theory and applications'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68
year: '2020'
...
---
OA_place: publisher
OA_type: free access
_id: '8271'
acknowledgement: We thank Dr. Gai Huang for his comments and help. We apologize to
authors whose work could not be cited due to space limitation. No conflict of interest
declared.
article_processing_charge: No
article_type: original
author:
- first_name: Peng
full_name: He, Peng
last_name: He
- first_name: Yuzhou
full_name: Zhang, Yuzhou
id: 3B6137F2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-2627-6956
- first_name: Guanghui
full_name: Xiao, Guanghui
last_name: Xiao
citation:
ama: He P, Zhang Y, Xiao G. Origin of a subgenome and genome evolution of allotetraploid
cotton species. Molecular Plant. 2020;13(9):1238-1240. doi:10.1016/j.molp.2020.07.006
apa: He, P., Zhang, Y., & Xiao, G. (2020). Origin of a subgenome and genome
evolution of allotetraploid cotton species. Molecular Plant. Elsevier.
https://doi.org/10.1016/j.molp.2020.07.006
chicago: He, Peng, Yuzhou Zhang, and Guanghui Xiao. “Origin of a Subgenome and Genome
Evolution of Allotetraploid Cotton Species.” Molecular Plant. Elsevier,
2020. https://doi.org/10.1016/j.molp.2020.07.006.
ieee: P. He, Y. Zhang, and G. Xiao, “Origin of a subgenome and genome evolution
of allotetraploid cotton species,” Molecular Plant, vol. 13, no. 9. Elsevier,
pp. 1238–1240, 2020.
ista: He P, Zhang Y, Xiao G. 2020. Origin of a subgenome and genome evolution of
allotetraploid cotton species. Molecular Plant. 13(9), 1238–1240.
mla: He, Peng, et al. “Origin of a Subgenome and Genome Evolution of Allotetraploid
Cotton Species.” Molecular Plant, vol. 13, no. 9, Elsevier, 2020, pp. 1238–40,
doi:10.1016/j.molp.2020.07.006.
short: P. He, Y. Zhang, G. Xiao, Molecular Plant 13 (2020) 1238–1240.
date_created: 2020-08-16T22:00:57Z
date_published: 2020-09-07T00:00:00Z
date_updated: 2026-06-18T19:32:01Z
day: '07'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.molp.2020.07.006
external_id:
isi:
- '000566895400007'
pmid:
- '32688032'
intvolume: ' 13'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.molp.2020.07.006
month: '09'
oa: 1
oa_version: Published Version
page: 1238-1240
pmid: 1
publication: Molecular Plant
publication_identifier:
eissn:
- 1752-9867
issn:
- 1674-2052
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Origin of a subgenome and genome evolution of allotetraploid cotton species
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2020'
...
---
_id: '8272'
abstract:
- lang: eng
text: We study turn-based stochastic zero-sum games with lexicographic preferences
over reachability and safety objectives. Stochastic games are standard models
in control, verification, and synthesis of stochastic reactive systems that exhibit
both randomness as well as angelic and demonic non-determinism. Lexicographic
order allows to consider multiple objectives with a strict preference order over
the satisfaction of the objectives. To the best of our knowledge, stochastic games
with lexicographic objectives have not been studied before. We establish determinacy
of such games and present strategy and computational complexity results. For strategy
complexity, we show that lexicographically optimal strategies exist that are deterministic
and memory is only required to remember the already satisfied and violated objectives.
For a constant number of objectives, we show that the relevant decision problem
is in NP∩coNP , matching the current known bound for single objectives; and
in general the decision problem is PSPACE -hard and can be solved in NEXPTIME∩coNEXPTIME
. We present an algorithm that computes the lexicographically optimal strategies
via a reduction to computation of optimal strategies in a sequence of single-objectives
games. We have implemented our algorithm and report experimental results on various
case studies.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Joost P
full_name: Katoen, Joost P
id: 4524F760-F248-11E8-B48F-1D18A9856A87
last_name: Katoen
orcid: 0000-0002-6143-1926
- first_name: Maximilian
full_name: Weininger, Maximilian
last_name: Weininger
- first_name: Tobias
full_name: Winkler, Tobias
last_name: Winkler
citation:
ama: 'Chatterjee K, Katoen JP, Weininger M, Winkler T. Stochastic games with lexicographic
reachability-safety objectives. In: International Conference on Computer Aided
Verification. Vol 12225. Springer Nature; 2020:398-420. doi:10.1007/978-3-030-53291-8_21'
apa: Chatterjee, K., Katoen, J. P., Weininger, M., & Winkler, T. (2020). Stochastic
games with lexicographic reachability-safety objectives. In International Conference
on Computer Aided Verification (Vol. 12225, pp. 398–420). Springer Nature.
https://doi.org/10.1007/978-3-030-53291-8_21
chicago: Chatterjee, Krishnendu, Joost P Katoen, Maximilian Weininger, and Tobias
Winkler. “Stochastic Games with Lexicographic Reachability-Safety Objectives.”
In International Conference on Computer Aided Verification, 12225:398–420.
Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53291-8_21.
ieee: K. Chatterjee, J. P. Katoen, M. Weininger, and T. Winkler, “Stochastic games
with lexicographic reachability-safety objectives,” in International Conference
on Computer Aided Verification, 2020, vol. 12225, pp. 398–420.
ista: 'Chatterjee K, Katoen JP, Weininger M, Winkler T. 2020. Stochastic games with
lexicographic reachability-safety objectives. International Conference on Computer
Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 12225, 398–420.'
mla: Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Reachability-Safety
Objectives.” International Conference on Computer Aided Verification, vol.
12225, Springer Nature, 2020, pp. 398–420, doi:10.1007/978-3-030-53291-8_21.
short: K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International
Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420.
conference:
name: 'CAV: Computer Aided Verification'
date_created: 2020-08-16T22:00:58Z
date_published: 2020-07-14T00:00:00Z
date_updated: 2026-04-16T09:31:14Z
day: '14'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-030-53291-8_21
ec_funded: 1
external_id:
arxiv:
- '2005.04018'
isi:
- '000695272500021'
file:
- access_level: open_access
checksum: 093d4788d7d5b2ce0ffe64fbe7820043
content_type: application/pdf
creator: dernst
date_created: 2020-08-17T11:32:44Z
date_updated: 2020-08-17T11:32:44Z
file_id: '8276'
file_name: 2020_LNCS_CAV_Chatterjee.pdf
file_size: 625056
relation: main_file
success: 1
file_date_updated: 2020-08-17T11:32:44Z
has_accepted_license: '1'
intvolume: ' 12225'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 398-420
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: International Conference on Computer Aided Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030532901'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '12738'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Stochastic games with lexicographic reachability-safety objectives
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 12225
year: '2020'
...
---
_id: '8284'
abstract:
- lang: eng
text: Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit
Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven
proton pumps, such as respiratory complex I. The mechanism of coupling between
ion or electron transfer and proton translocation in this large protein family
is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus
flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit
protomers with 50 trans-membrane helices each. Surface charge distribution within
each monomer is remarkably asymmetric, revealing probable proton and sodium translocation
pathways. On the basis of the structure we propose a mechanism where the coupling
between sodium and proton translocation is facilitated by a series of electrostatic
interactions between a cation and key charged residues. This mechanism is likely
to be applicable to the entire family of redox proton pumps, where electron transfer
to substrates replaces cation movements.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
acknowledgement: This research was supported by the Scientific Service Units (SSU)
of IST Austria through resources provided by the Electron Microscopy Facility (EMF),
the Life Science Facility (LSF) and the IST high-performance computing cluster.
We thank Dr Victor-Valentin Hodirnau and Daniel Johann Gütl from IST Austria for
assistance with collecting cryo-EM data. We thank Prof. Masahiro Ito (Graduate School
of Life Sciences, Toyo University, Japan) for a kind provision of plasmid DNA encoding
Mrp from A. flavithermus WK1. JS is a recipient of a DOC Fellowship of the Austrian
Academy of Sciences at the Institute of Science and Technology, Austria.
article_number: e59407
article_processing_charge: No
article_type: original
author:
- first_name: Julia
full_name: Steiner, Julia
id: 3BB67EB0-F248-11E8-B48F-1D18A9856A87
last_name: Steiner
orcid: 0000-0003-0493-3775
- 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: Steiner J, Sazanov LA. Structure and mechanism of the Mrp complex, an ancient
cation/proton antiporter. eLife. 2020;9. doi:10.7554/eLife.59407
apa: Steiner, J., & Sazanov, L. A. (2020). Structure and mechanism of the Mrp
complex, an ancient cation/proton antiporter. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.59407
chicago: Steiner, Julia, and Leonid A Sazanov. “Structure and Mechanism of the Mrp
Complex, an Ancient Cation/Proton Antiporter.” ELife. eLife Sciences Publications,
2020. https://doi.org/10.7554/eLife.59407.
ieee: J. Steiner and L. A. Sazanov, “Structure and mechanism of the Mrp complex,
an ancient cation/proton antiporter,” eLife, vol. 9. eLife Sciences Publications,
2020.
ista: Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an
ancient cation/proton antiporter. eLife. 9, e59407.
mla: Steiner, Julia, and Leonid A. Sazanov. “Structure and Mechanism of the Mrp
Complex, an Ancient Cation/Proton Antiporter.” ELife, vol. 9, e59407, eLife
Sciences Publications, 2020, doi:10.7554/eLife.59407.
short: J. Steiner, L.A. Sazanov, ELife 9 (2020).
date_created: 2020-08-24T06:24:04Z
date_published: 2020-07-31T00:00:00Z
date_updated: 2026-04-08T07:23:36Z
day: '31'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.7554/eLife.59407
external_id:
isi:
- '000562123600001'
pmid:
- '32735215'
file:
- access_level: open_access
checksum: b3656d14d5ddbb9d26e3074eea2d0c15
content_type: application/pdf
creator: cziletti
date_created: 2020-08-24T13:31:53Z
date_updated: 2020-08-24T13:31:53Z
file_id: '8289'
file_name: 2020_eLife_Steiner.pdf
file_size: 7320493
relation: main_file
success: 1
file_date_updated: 2020-08-24T13:31:53Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26169496-B435-11E9-9278-68D0E5697425
grant_number: '24741'
name: Revealing the functional mechanism of Mrp antiporter, an ancestor of complex
I
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/
record:
- id: '8353'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 9
year: '2020'
...
---
_id: '8287'
abstract:
- lang: eng
text: Reachability analysis aims at identifying states reachable by a system within
a given time horizon. This task is known to be computationally expensive for linear
hybrid systems. Reachability analysis works by iteratively applying continuous
and discrete post operators to compute states reachable according to continuous
and discrete dynamics, respectively. In this paper, we enhance both of these operators
and make sure that most of the involved computations are performed in low-dimensional
state space. In particular, we improve the continuous-post operator by performing
computations in high-dimensional state space only for time intervals relevant
for the subsequent application of the discrete-post operator. Furthermore, the
new discrete-post operator performs low-dimensional computations by leveraging
the structure of the guard and assignment of a considered transition. We illustrate
the potential of our approach on a number of challenging benchmarks.
article_processing_charge: No
arxiv: 1
author:
- first_name: Sergiy
full_name: Bogomolov, Sergiy
last_name: Bogomolov
- first_name: Marcelo
full_name: Forets, Marcelo
last_name: Forets
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Kostiantyn
full_name: Potomkin, Kostiantyn
last_name: Potomkin
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
citation:
ama: 'Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis
of linear hybrid systems via block decomposition. In: Proceedings of the International
Conference on Embedded Software. ; 2020.'
apa: Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2020).
Reachability analysis of linear hybrid systems via block decomposition. In Proceedings
of the International Conference on Embedded Software. Virtual .
chicago: Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and
Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block
Decomposition.” In Proceedings of the International Conference on Embedded
Software, 2020.
ieee: S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability
analysis of linear hybrid systems via block decomposition,” in Proceedings
of the International Conference on Embedded Software, Virtual , 2020.
ista: 'Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability
analysis of linear hybrid systems via block decomposition. Proceedings of the
International Conference on Embedded Software. EMSOFT: Embedded Software.'
mla: Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via
Block Decomposition.” Proceedings of the International Conference on Embedded
Software, 2020.
short: S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings
of the International Conference on Embedded Software, 2020.
conference:
end_date: 2020-09-25
location: 'Virtual '
name: 'EMSOFT: Embedded Software'
start_date: 2020-09-20
date_created: 2020-08-24T12:56:20Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2026-04-03T09:32:00Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
ec_funded: 1
external_id:
arxiv:
- '1905.02458'
isi:
- '000587712700072'
file:
- access_level: open_access
checksum: d19e97d0f8a3a441dc078ec812297d75
content_type: application/pdf
creator: cschilli
date_created: 2020-08-24T12:53:15Z
date_updated: 2020-08-24T12:53:15Z
file_id: '8288'
file_name: 2020EMSOFT.pdf
file_size: 696384
relation: main_file
success: 1
file_date_updated: 2020-08-24T12:53:15Z
has_accepted_license: '1'
isi: 1
keyword:
- reachability
- hybrid systems
- decomposition
language:
- iso: eng
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Proceedings of the International Conference on Embedded Software
publication_status: published
quality_controlled: '1'
related_material:
record:
- id: '8790'
relation: later_version
status: public
status: public
title: Reachability analysis of linear hybrid systems via block decomposition
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2020'
...
---
_id: '8294'
abstract:
- lang: eng
text: 'Automated root growth analysis and tracking of root tips. '
author:
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
citation:
ama: Hauschild R. RGtracker. 2020. doi:10.15479/AT:ISTA:8294
apa: Hauschild, R. (2020). RGtracker. IST Austria. https://doi.org/10.15479/AT:ISTA:8294
chicago: Hauschild, Robert. “RGtracker.” IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:8294.
ieee: R. Hauschild, “RGtracker.” IST Austria, 2020.
ista: Hauschild R. 2020. RGtracker, IST Austria, 10.15479/AT:ISTA:8294.
mla: Hauschild, Robert. RGtracker. IST Austria, 2020, doi:10.15479/AT:ISTA:8294.
short: R. Hauschild, (2020).
corr_author: '1'
date_created: 2020-08-25T12:52:48Z
date_published: 2020-09-10T00:00:00Z
date_updated: 2024-10-09T21:05:14Z
day: '10'
ddc:
- '570'
department:
- _id: Bio
doi: 10.15479/AT:ISTA:8294
file:
- access_level: open_access
checksum: 108352149987ac6f066e4925bd56e35e
content_type: text/plain
creator: rhauschild
date_created: 2020-09-08T14:26:31Z
date_updated: 2020-09-08T14:26:31Z
file_id: '8346'
file_name: readme.txt
file_size: 882
relation: main_file
success: 1
- access_level: open_access
checksum: ffd6c643b28e0cc7c6d0060a18a7e8ea
content_type: application/octet-stream
creator: rhauschild
date_created: 2020-09-08T14:26:33Z
date_updated: 2020-09-08T14:26:33Z
file_id: '8347'
file_name: RGtracker.mlappinstall
file_size: 246121
relation: main_file
success: 1
file_date_updated: 2020-09-08T14:26:33Z
has_accepted_license: '1'
license: https://opensource.org/licenses/BSD-3-Clause
month: '09'
oa: 1
publisher: IST Austria
status: public
title: RGtracker
tmp:
legal_code_url: https://opensource.org/licenses/BSD-3-Clause
name: The 3-Clause BSD License
short: 3-Clause BSD
type: software
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8307'
abstract:
- lang: eng
text: "Classic Byzantine fault-tolerant consensus protocols forfeit liveness in
the face of asynchrony in order to preserve safety, whereas most deployed blockchain
protocols forfeit safety in order to remain live. In this work, we achieve the
best of both worlds by proposing a novel abstractions called the finality gadget.
A finality gadget allows for transactions to always optimistically commit but
informs the clients that these transactions might be unsafe. As a result, a blockchain
can execute transactions optimistically and only commit them after they have been
sufficiently and provably audited. In\r\nthis work, we formally model the finality
gadget abstraction, prove that it is impossible to solve it deterministically
in full asynchrony (even though it is stronger than consensus) and provide a partially
synchronous protocol which is currently securing a major blockchain. This way
we show that the protocol designer can decouple safety and liveness in order to
speed up recovery from failures. We believe that there can be other types of finality
gadgets that provide weaker safety (e.g., probabilistic) in order to gain more
efficiency and this can depend on the probability that the network is not in synchrony."
article_number: '2007.01560'
article_processing_charge: No
arxiv: 1
author:
- first_name: Alistair
full_name: Stewart, Alistair
last_name: Stewart
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
citation:
ama: 'Stewart A, Kokoris Kogias E. GRANDPA: A Byzantine finality gadget. arXiv.
doi:10.48550/arXiv.2007.01560'
apa: 'Stewart, A., & Kokoris Kogias, E. (n.d.). GRANDPA: A Byzantine finality
gadget. arXiv. https://doi.org/10.48550/arXiv.2007.01560'
chicago: 'Stewart, Alistair, and Eleftherios Kokoris Kogias. “GRANDPA: A Byzantine
Finality Gadget.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2007.01560.'
ieee: 'A. Stewart and E. Kokoris Kogias, “GRANDPA: A Byzantine finality gadget,”
arXiv. .'
ista: 'Stewart A, Kokoris Kogias E. GRANDPA: A Byzantine finality gadget. arXiv,
2007.01560.'
mla: 'Stewart, Alistair, and Eleftherios Kokoris Kogias. “GRANDPA: A Byzantine Finality
Gadget.” ArXiv, 2007.01560, doi:10.48550/arXiv.2007.01560.'
short: A. Stewart, E. Kokoris Kogias, ArXiv (n.d.).
date_created: 2020-08-26T12:32:10Z
date_published: 2020-07-03T00:00:00Z
date_updated: 2025-06-26T11:27:41Z
day: '03'
doi: 10.48550/arXiv.2007.01560
extern: '1'
external_id:
arxiv:
- '2007.01560'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2007.01560
month: '07'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: 'GRANDPA: A Byzantine finality gadget'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
OA_place: repository
OA_type: green
_id: '8308'
abstract:
- lang: eng
text: 'Many-body localization provides a mechanism to avoid thermalization in isolated
interacting quantum systems. The breakdown of thermalization may be complete,
when all eigenstates in the many-body spectrum become localized, or partial, when
the so-called many-body mobility edge separates localized and delocalized parts
of the spectrum. Previously, De Roeck et al. [Phys. Rev. B 93, 014203 (2016)]
suggested a possible instability of the many-body mobility edge in energy density.
The local ergodic regions—so-called “bubbles”—resonantly spread throughout the
system, leading to delocalization. In order to study such instability mechanism,
in this work we design a model featuring many-body mobility edge in particle density:
the states at small particle density are localized, while increasing the density
of particles leads to delocalization. Using numerical simulations with matrix
product states, we demonstrate the stability of many-body localization with respect
to small bubbles in large dilute systems for experimentally relevant timescales.
In addition, we demonstrate that processes where the bubble spreads are favored
over processes that lead to resonant tunneling, suggesting a possible mechanism
behind the observed stability of many-body mobility edge. We conclude by proposing
experiments to probe particle density mobility edge in the Bose-Hubbard model.'
acknowledgement: 'Acknowledgments. We acknowledge useful discussions with W. De Roeck
and A. Michailidis. P.B. was supported by the European Union''s Horizon 2020 research
and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 665385.
D.A. was supported by the Swiss National Science Foundation. M.S. was supported
by European Research Council (ERC) under the European Union''s Horizon 2020 research
and innovation program (Grant Agreement No. 850899). This work benefited from visits
to KITP, supported by the National Science Foundation under Grant No. NSF PHY-1748958
and from the program “Thermalization, Many Body Localization and Hydrodynamics”
at International Centre for Theoretical Sciences (Code: ICTS/hydrodynamics2019/11).'
article_number: 060202(R)
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Pietro
full_name: Brighi, Pietro
id: 4115AF5C-F248-11E8-B48F-1D18A9856A87
last_name: Brighi
orcid: 0000-0002-7969-2729
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Brighi P, Abanin DA, Serbyn M. Stability of mobility edges in disordered interacting
systems. Physical Review B. 2020;102(6). doi:10.1103/physrevb.102.060202
apa: Brighi, P., Abanin, D. A., & Serbyn, M. (2020). Stability of mobility edges
in disordered interacting systems. Physical Review B. American Physical
Society. https://doi.org/10.1103/physrevb.102.060202
chicago: Brighi, Pietro, Dmitry A. Abanin, and Maksym Serbyn. “Stability of Mobility
Edges in Disordered Interacting Systems.” Physical Review B. American Physical
Society, 2020. https://doi.org/10.1103/physrevb.102.060202.
ieee: P. Brighi, D. A. Abanin, and M. Serbyn, “Stability of mobility edges in disordered
interacting systems,” Physical Review B, vol. 102, no. 6. American Physical
Society, 2020.
ista: Brighi P, Abanin DA, Serbyn M. 2020. Stability of mobility edges in disordered
interacting systems. Physical Review B. 102(6), 060202(R).
mla: Brighi, Pietro, et al. “Stability of Mobility Edges in Disordered Interacting
Systems.” Physical Review B, vol. 102, no. 6, 060202(R), American Physical
Society, 2020, doi:10.1103/physrevb.102.060202.
short: P. Brighi, D.A. Abanin, M. Serbyn, Physical Review B 102 (2020).
corr_author: '1'
date_created: 2020-08-26T19:27:42Z
date_published: 2020-08-26T00:00:00Z
date_updated: 2026-04-07T13:26:31Z
day: '26'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/physrevb.102.060202
ec_funded: 1
external_id:
arxiv:
- '2005.02999'
isi:
- '000562628300001'
file:
- access_level: open_access
checksum: 716442fa7861323fcc80b93718ca009c
content_type: application/pdf
creator: mserbyn
date_created: 2020-08-26T19:28:55Z
date_updated: 2020-08-26T19:28:55Z
file_id: '8309'
file_name: PhysRevB.102.060202.pdf
file_size: 488825
relation: main_file
success: 1
- access_level: open_access
checksum: be0abdc8f60fe065ea6dc92e08487122
content_type: application/pdf
creator: mserbyn
date_created: 2020-08-26T19:29:00Z
date_updated: 2020-08-26T19:29:00Z
file_id: '8310'
file_name: Supplementary-mbme.pdf
file_size: 711405
relation: main_file
success: 1
file_date_updated: 2020-08-26T19:29:00Z
has_accepted_license: '1'
intvolume: ' 102'
isi: 1
issue: '6'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '12732'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Stability of mobility edges in disordered interacting systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 102
year: '2020'
...
---
_id: '8318'
abstract:
- lang: eng
text: Complex I is the first and the largest enzyme of respiratory chains in bacteria
and mitochondria. The mechanism which couples spatially separated transfer of
electrons to proton translocation in complex I is not known. Here we report five
crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like
compounds. We also determined cryo-EM structures of major and minor native states
of the complex, differing in the position of the peripheral arm. Crystal structures
show that binding of quinone-like compounds (but not of NADH) leads to a related
global conformational change, accompanied by local re-arrangements propagating
from the quinone site to the nearest proton channel. Normal mode and molecular
dynamics analyses indicate that these are likely to represent the first steps
in the proton translocation mechanism. Our results suggest that quinone binding
and chemistry play a key role in the coupling mechanism of complex I.
acknowledgement: This work was funded by the Medical Research Council, UK and IST
Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light
Source for provision of synchrotron radiation facilities. We are grateful to the
staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light
Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance
computing cluster.
article_number: '4135'
article_processing_charge: No
article_type: original
author:
- first_name: Javier
full_name: Gutierrez-Fernandez, Javier
id: 3D9511BA-F248-11E8-B48F-1D18A9856A87
last_name: Gutierrez-Fernandez
- first_name: Karol
full_name: Kaszuba, Karol
id: 3FDF9472-F248-11E8-B48F-1D18A9856A87
last_name: Kaszuba
- first_name: Gurdeep S.
full_name: Minhas, Gurdeep S.
last_name: Minhas
- first_name: Rozbeh
full_name: Baradaran, Rozbeh
last_name: Baradaran
- first_name: Margherita
full_name: Tambalo, Margherita
id: 4187dfe4-ec23-11ea-ae46-f08ab378313a
last_name: Tambalo
- first_name: David T.
full_name: Gallagher, David T.
last_name: Gallagher
- 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: Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in
the mechanism of respiratory complex I. Nature Communications. 2020;11(1).
doi:10.1038/s41467-020-17957-0
apa: Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo,
M., Gallagher, D. T., & Sazanov, L. A. (2020). Key role of quinone in the
mechanism of respiratory complex I. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-020-17957-0
chicago: Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran,
Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone
in the Mechanism of Respiratory Complex I.” Nature Communications. Springer
Nature, 2020. https://doi.org/10.1038/s41467-020-17957-0.
ieee: J. Gutierrez-Fernandez et al., “Key role of quinone in the mechanism
of respiratory complex I,” Nature Communications, vol. 11, no. 1. Springer
Nature, 2020.
ista: Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher
DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex
I. Nature Communications. 11(1), 4135.
mla: Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of
Respiratory Complex I.” Nature Communications, vol. 11, no. 1, 4135, Springer
Nature, 2020, doi:10.1038/s41467-020-17957-0.
short: J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo,
D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).
date_created: 2020-08-30T22:01:10Z
date_published: 2020-08-18T00:00:00Z
date_updated: 2026-04-02T14:36:31Z
day: '18'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1038/s41467-020-17957-0
external_id:
isi:
- '000607072900001'
pmid:
- '32811817'
file:
- access_level: open_access
checksum: 52b96f41d7d0db9728064c08da00d030
content_type: application/pdf
creator: cziletti
date_created: 2020-08-31T13:40:00Z
date_updated: 2020-08-31T13:40:00Z
file_id: '8326'
file_name: 2020_NatComm_Gutierrez-Fernandez.pdf
file_size: 7527373
relation: main_file
success: 1
file_date_updated: 2020-08-31T13:40:00Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/
scopus_import: '1'
status: public
title: Key role of quinone in the mechanism of respiratory complex I
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 11
year: '2020'
...
---
_id: '8320'
abstract:
- lang: eng
text: The genetic code is considered to use five nucleic bases (adenine, guanine,
cytosine, thymine and uracil), which form two pairs for encoding information in
DNA and two pairs for encoding information in RNA. Nevertheless, in recent years
several artificial base pairs have been developed in attempts to expand the genetic
code. Employment of these additional base pairs increases the information capacity
and variety of DNA sequences, and provides a platform for the site-specific, enzymatic
incorporation of extra functional components into DNA and RNA. As a result, of
the development of such expanded systems, many artificial base pairs have been
synthesized and tested under various conditions. Following many stages of enhancement,
unnatural base pairs have been modified to eliminate their weak points, qualifying
them for specific research needs. Moreover, the first attempts to create a semi-synthetic
organism containing DNA with unnatural base pairs seem to have been successful.
This further extends the possible applications of these kinds of pairs. Herein,
we describe the most significant qualities of unnatural base pairs and their actual
applications.
acknowledgement: We would like to thank our co-workers and members of the Alkalaeva
lab for participating in discussions about the topics covered in this essay.
article_processing_charge: No
article_type: original
author:
- first_name: S. A.
full_name: Mukba, S. A.
last_name: Mukba
- first_name: Petr
full_name: Vlasov, Petr
id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
last_name: Vlasov
- first_name: P. M.
full_name: Kolosov, P. M.
last_name: Kolosov
- first_name: E. Y.
full_name: Shuvalova, E. Y.
last_name: Shuvalova
- first_name: T. V.
full_name: Egorova, T. V.
last_name: Egorova
- first_name: E. Z.
full_name: Alkalaeva, E. Z.
last_name: Alkalaeva
citation:
ama: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding
the genetic code: Unnatural base pairs in biological systems. Molecular Biology.
2020;54(4):475-484. doi:10.1134/S0026893320040111'
apa: 'Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V.,
& Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs
in biological systems. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320040111'
chicago: 'Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova,
and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological
Systems.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320040111.'
ieee: 'S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and
E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological
systems,” Molecular Biology, vol. 54, no. 4. Springer Nature, pp. 475–484,
2020.'
ista: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020.
Expanding the genetic code: Unnatural base pairs in biological systems. Molecular
Biology. 54(4), 475–484.'
mla: 'Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in
Biological Systems.” Molecular Biology, vol. 54, no. 4, Springer Nature,
2020, pp. 475–84, doi:10.1134/S0026893320040111.'
short: S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva,
Molecular Biology 54 (2020) 475–484.
date_created: 2020-08-30T22:01:11Z
date_published: 2020-08-19T00:00:00Z
date_updated: 2025-07-10T11:57:02Z
day: '19'
department:
- _id: FyKo
doi: 10.1134/S0026893320040111
external_id:
isi:
- '000562110300001'
intvolume: ' 54'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa_version: None
page: 475-484
publication: Molecular Biology
publication_identifier:
eissn:
- 1608-3245
issn:
- 0026-8933
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8321'
relation: original
status: public
scopus_import: '1'
status: public
title: 'Expanding the genetic code: Unnatural base pairs in biological systems'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2020'
...
---
_id: '8321'
abstract:
- lang: eng
text: The genetic code is considered to use five nucleic bases (adenine, guanine,
cytosine, thymine and uracil), which form two pairs for encoding information in
DNA and two pairs for encoding information in RNA. Nevertheless, in recent years
several artificial base pairs have been developed in attempts to expand the genetic
code. Employment of these additional base pairs increases the information capacity
and variety of DNA sequences, and provides a platform for the site-specific, enzymatic
incorporation of extra functional components into DNA and RNA. As a result, of
the development of such expanded systems, many artificial base pairs have been
synthesized and tested under various conditions. Following many stages of enhancement,
unnatural base pairs have been modified to eliminate their weak points, qualifying
them for specific research needs. Moreover, the first attempts to create a semi-synthetic
organism containing DNA with unnatural base pairs seem to have been successful.
This further extends the possible applications of these kinds of pairs. Herein,
we describe the most significant qualities of unnatural base pairs and their actual
applications.
article_processing_charge: No
article_type: original
author:
- first_name: S. A.
full_name: Mukba, S. A.
last_name: Mukba
- first_name: Petr
full_name: Vlasov, Petr
id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
last_name: Vlasov
- first_name: P. M.
full_name: Kolosov, P. M.
last_name: Kolosov
- first_name: E. Y.
full_name: Shuvalova, E. Y.
last_name: Shuvalova
- first_name: T. V.
full_name: Egorova, T. V.
last_name: Egorova
- first_name: E. Z.
full_name: Alkalaeva, E. Z.
last_name: Alkalaeva
citation:
ama: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding
the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia
biologiia. 2020;54(4):531-541. doi:10.31857/S0026898420040126'
apa: 'Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V.,
& Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs
in biological systems. Molekuliarnaia biologiia. Russian Academy of Sciences.
https://doi.org/10.31857/S0026898420040126'
chicago: 'Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova,
and E. Z. Alkalaeva. “Expanding the genetic code: Unnatural base pairs in biological
systems.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020.
https://doi.org/10.31857/S0026898420040126.'
ieee: 'S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and
E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological
systems,” Molekuliarnaia biologiia, vol. 54, no. 4. Russian Academy of
Sciences, pp. 531–541, 2020.'
ista: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020.
Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia
biologiia. 54(4), 531–541.'
mla: 'Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in
biological systems.” Molekuliarnaia biologiia, vol. 54, no. 4, Russian
Academy of Sciences, 2020, pp. 531–41, doi:10.31857/S0026898420040126.'
short: S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva,
Molekuliarnaia biologiia 54 (2020) 531–541.
date_created: 2020-08-30T22:01:11Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2025-07-10T11:57:03Z
day: '01'
department:
- _id: FyKo
doi: 10.31857/S0026898420040126
external_id:
pmid:
- '32799218'
intvolume: ' 54'
issue: '4'
language:
- iso: rus
month: '07'
oa_version: None
page: 531-541
pmid: 1
publication: Molekuliarnaia biologiia
publication_identifier:
issn:
- 0026-8984
publication_status: published
publisher: Russian Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '8320'
relation: translation
status: public
scopus_import: '1'
status: public
title: 'Expanding the genetic code: Unnatural base pairs in biological systems'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2020'
...
---
_id: '8323'
article_processing_charge: No
article_type: letter_note
author:
- first_name: János
full_name: Pach, János
id: E62E3130-B088-11EA-B919-BF823C25FEA4
last_name: Pach
citation:
ama: Pach J. A farewell to Ricky Pollack. Discrete and Computational Geometry.
2020;64:571-574. doi:10.1007/s00454-020-00237-5
apa: Pach, J. (2020). A farewell to Ricky Pollack. Discrete and Computational
Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00237-5
chicago: Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational
Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00237-5.
ieee: J. Pach, “A farewell to Ricky Pollack,” Discrete and Computational Geometry,
vol. 64. Springer Nature, pp. 571–574, 2020.
ista: Pach J. 2020. A farewell to Ricky Pollack. Discrete and Computational Geometry.
64, 571–574.
mla: Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry,
vol. 64, Springer Nature, 2020, pp. 571–74, doi:10.1007/s00454-020-00237-5.
short: J. Pach, Discrete and Computational Geometry 64 (2020) 571–574.
corr_author: '1'
date_created: 2020-08-30T22:01:12Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2024-10-09T20:59:55Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00454-020-00237-5
external_id:
isi:
- '000561483500001'
intvolume: ' 64'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s00454-020-00237-5
month: '10'
oa: 1
oa_version: None
page: 571-574
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- '14320444'
issn:
- '01795376'
publication_status: published
publisher: Springer Nature
scopus_import: '1'
status: public
title: A farewell to Ricky Pollack
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 64
year: '2020'
...
---
_id: '8324'
abstract:
- lang: eng
text: The notion of program sensitivity (aka Lipschitz continuity) specifies that
changes in the program input result in proportional changes to the program output.
For probabilistic programs the notion is naturally extended to expected sensitivity.
A previous approach develops a relational program logic framework for proving
expected sensitivity of probabilistic while loops, where the number of iterations
is fixed and bounded. In this work, we consider probabilistic while loops where
the number of iterations is not fixed, but randomized and depends on the initial
input values. We present a sound approach for proving expected sensitivity of
such programs. Our sound approach is martingale-based and can be automated through
existing martingale-synthesis algorithms. Furthermore, our approach is compositional
for sequential composition of while loops under a mild side condition. We demonstrate
the effectiveness of our approach on several classical examples from Gambler's
Ruin, stochastic hybrid systems and stochastic gradient descent. We also present
experimental results showing that our automated approach can handle various probabilistic
programs in the literature.
acknowledgement: We thank anonymous reviewers for helpful comments, especially for
pointing to us a scenario of piecewise-linear approximation (Remark5). The research
was partially supported by the National Natural Science Foundation of China (NSFC)
under Grant No. 61802254, 61672229, 61832015,61772336,11871221 and Austrian Science
Fund (FWF) NFN under Grant No. S11407-N23 (RiSE/SHiNE). We thank Prof. Yuxi Fu,
director of the BASICS Lab at Shanghai Jiao Tong University, for his support.
article_number: '25'
article_processing_charge: No
arxiv: 1
author:
- first_name: Peixin
full_name: Wang, Peixin
last_name: Wang
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Yuxin
full_name: Deng, Yuxin
last_name: Deng
- first_name: Ming
full_name: Xu, Ming
last_name: Xu
citation:
ama: 'Wang P, Fu H, Chatterjee K, Deng Y, Xu M. Proving expected sensitivity of
probabilistic programs with randomized variable-dependent termination time. In:
Proceedings of the ACM on Programming Languages. Vol 4. ACM; 2020. doi:10.1145/3371093'
apa: Wang, P., Fu, H., Chatterjee, K., Deng, Y., & Xu, M. (2020). Proving expected
sensitivity of probabilistic programs with randomized variable-dependent termination
time. In Proceedings of the ACM on Programming Languages (Vol. 4). ACM.
https://doi.org/10.1145/3371093
chicago: Wang, Peixin, Hongfei Fu, Krishnendu Chatterjee, Yuxin Deng, and Ming Xu.
“Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent
Termination Time.” In Proceedings of the ACM on Programming Languages,
Vol. 4. ACM, 2020. https://doi.org/10.1145/3371093.
ieee: P. Wang, H. Fu, K. Chatterjee, Y. Deng, and M. Xu, “Proving expected sensitivity
of probabilistic programs with randomized variable-dependent termination time,”
in Proceedings of the ACM on Programming Languages, 2020, vol. 4, no. POPL.
ista: Wang P, Fu H, Chatterjee K, Deng Y, Xu M. 2020. Proving expected sensitivity
of probabilistic programs with randomized variable-dependent termination time.
Proceedings of the ACM on Programming Languages. vol. 4, 25.
mla: Wang, Peixin, et al. “Proving Expected Sensitivity of Probabilistic Programs
with Randomized Variable-Dependent Termination Time.” Proceedings of the ACM
on Programming Languages, vol. 4, no. POPL, 25, ACM, 2020, doi:10.1145/3371093.
short: P. Wang, H. Fu, K. Chatterjee, Y. Deng, M. Xu, in:, Proceedings of the ACM
on Programming Languages, ACM, 2020.
date_created: 2020-08-30T22:01:12Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2025-04-15T06:30:10Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1145/3371093
external_id:
arxiv:
- '1902.04744'
file:
- access_level: open_access
checksum: c6193d109ff4ecb17e7a6513d8eb34c0
content_type: application/pdf
creator: cziletti
date_created: 2020-09-01T11:12:58Z
date_updated: 2020-09-01T11:12:58Z
file_id: '8328'
file_name: 2019_ACM_POPL_Wang.pdf
file_size: 564151
relation: main_file
success: 1
file_date_updated: 2020-09-01T11:12:58Z
has_accepted_license: '1'
intvolume: ' 4'
issue: POPL
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://doi.org/10.5281/zenodo.3533633
scopus_import: '1'
status: public
title: Proving expected sensitivity of probabilistic programs with randomized variable-dependent
termination time
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2020'
...
---
_id: '8325'
abstract:
- lang: eng
text: "Let \U0001D439:ℤ2→ℤ be the pointwise minimum of several linear functions.
The theory of smoothing allows us to prove that under certain conditions there
exists the pointwise minimal function among all integer-valued superharmonic functions
coinciding with F “at infinity”. We develop such a theory to prove existence of
so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo,
G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the
phenomena of the identity in the sandpile group for planar domains where solitons
appear according to experiments. We prove that sandpile states, defined using
our smoothing procedure, move changeless when we apply the wave operator (that
is why we call them solitons), and can interact, forming triads and nodes. "
acknowledgement: We thank Andrea Sportiello for sharing his insights on perturbative
regimes of the Abelian sandpile model which was the starting point of our work.
We also thank Grigory Mikhalkin, who encouraged us to approach this problem. We
thank an anonymous referee. Also we thank Misha Khristoforov and Sergey Lanzat who
participated on the initial state of this project, when we had nothing except the
computer simulation and pictures. We thank Mikhail Raskin for providing us the code
on Golly for faster simulations. Ilia Zharkov, Ilia Itenberg, Kristin Shaw, Max
Karev, Lionel Levine, Ernesto Lupercio, Pavol Ševera, Yulieth Prieto, Michael Polyak,
Danila Cherkashin asked us a lot of questions and listened to us; not all of their
questions found answers here, but we are going to treat them in subsequent papers.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nikita
full_name: Kalinin, Nikita
last_name: Kalinin
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
citation:
ama: Kalinin N, Shkolnikov M. Sandpile solitons via smoothing of superharmonic functions.
Communications in Mathematical Physics. 2020;378(9):1649-1675. doi:10.1007/s00220-020-03828-8
apa: Kalinin, N., & Shkolnikov, M. (2020). Sandpile solitons via smoothing of
superharmonic functions. Communications in Mathematical Physics. Springer
Nature. https://doi.org/10.1007/s00220-020-03828-8
chicago: Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing
of Superharmonic Functions.” Communications in Mathematical Physics. Springer
Nature, 2020. https://doi.org/10.1007/s00220-020-03828-8.
ieee: N. Kalinin and M. Shkolnikov, “Sandpile solitons via smoothing of superharmonic
functions,” Communications in Mathematical Physics, vol. 378, no. 9. Springer
Nature, pp. 1649–1675, 2020.
ista: Kalinin N, Shkolnikov M. 2020. Sandpile solitons via smoothing of superharmonic
functions. Communications in Mathematical Physics. 378(9), 1649–1675.
mla: Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of
Superharmonic Functions.” Communications in Mathematical Physics, vol.
378, no. 9, Springer Nature, 2020, pp. 1649–75, doi:10.1007/s00220-020-03828-8.
short: N. Kalinin, M. Shkolnikov, Communications in Mathematical Physics 378 (2020)
1649–1675.
date_created: 2020-08-30T22:01:13Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2025-07-10T11:57:03Z
day: '01'
department:
- _id: TaHa
doi: 10.1007/s00220-020-03828-8
ec_funded: 1
external_id:
arxiv:
- '1711.04285'
isi:
- '000560620600001'
intvolume: ' 378'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.04285
month: '09'
oa: 1
oa_version: Preprint
page: 1649-1675
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- 1432-0916
issn:
- 0010-3616
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sandpile solitons via smoothing of superharmonic functions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 378
year: '2020'
...