---
_id: '15298'
abstract:
- lang: eng
text: Mountains are important suppliers of freshwater to downstream areas, affecting
large populations in particular in High Mountain Asia (HMA). Yet, the propagation
of water from HMA headwaters to downstream areas is not fully understood, as interactions
in the mountain water cycle between the cryo-, hydro- and biosphere remain elusive.
We review the definition of blue and green water fluxes as liquid water that contributes
to runoff at the outlet of the selected domain (blue) and water lost to the atmosphere
through vapor fluxes, that is evaporation from water, ground, and interception
plus transpiration (green) and propose to add the term white water to account
for the (often neglected) evaporation and sublimation from snow and ice. We provide
an assessment of models that can simulate the cryo-hydro-biosphere continuum and
the interactions between spheres in high mountain catchments, going beyond disciplinary
separations. Land surface models are uniquely able to account for such complexity,
since they solve the coupled fluxes of water, energy, and carbon between the land
surface and atmosphere. Due to the mechanistic nature of such models, specific
variables can be compared systematically to independent remote sensing observations
– providing vital insights into model accuracy and enabling the understanding
of the complex watersheds of HMA. We discuss recent developments in spaceborne
earth observation products that have the potential to support catchment modeling
in high mountain regions. We then present a pilot study application of the mechanistic
land surface model Tethys & Chloris to a glacierized watershed in the Nepalese
Himalayas and discuss the use of high-resolution earth observation data to constrain
the meteorological forcing uncertainty and validate model results. We use these
insights to highlight the remaining challenges and future opportunities that remote
sensing data presents for land surface modeling in HMA.
acknowledgement: 'This work was supported by the ESA and NRSCC Dragon 5 cooperation
project “Cryosphere-hydrosphere interactions of the Asian water towers: using remote
sensing to drive hyper-resolution ecohydrological modelling” [Grant no. 59199].
PB and FP acknowledge funding from the SNSF (High-elevation precipitation in High
Mountain Asia, HOPE)) [Grant no. 183633]. ESM, MK, SFu and FP acknowledge funding
from the ERC under the European Union’s Horizon 2020 research and innovation program
(Rapid mass losses of debris-covered glaciers in High Mountain Asia, RAVEN) [Grant
no. 772751]. LJ, CZ and MMe acknowledge the Second Tibetan Plateau Scientific Expedition
and Research Program (STEP) [grant no. 2019QZKK010308, no. 2019QZKK0206], the National
Natural Science Foundation of China projects (Grant no. 42171039, no. 91737205),
the Chinese Academy of Sciences President’s International Fellowship Initiative
[Grant no. 2020VTA0001], and the MOST High-Level Foreign Expert Program [Grant no.
G2022055010L].'
article_processing_charge: Yes
article_type: original
author:
- first_name: Pascal
full_name: Buri, Pascal
last_name: Buri
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: Thomas
full_name: Shaw, Thomas
id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e
last_name: Shaw
orcid: 0000-0001-7640-6152
- first_name: Catriona Louise
full_name: Fyffe, Catriona Louise
id: 001b0422-8d15-11ed-bc51-cab6c037a228
last_name: Fyffe
- first_name: Evan S.
full_name: Miles, Evan S.
last_name: Miles
- first_name: Michael
full_name: Mccarthy, Michael
id: 22a2674a-61ce-11ee-94b5-d18813baf16f
last_name: Mccarthy
- first_name: Marin
full_name: Kneib, Marin
last_name: Kneib
- first_name: Shaoting
full_name: Ren, Shaoting
last_name: Ren
- first_name: Achille
full_name: Jouberton, Achille
last_name: Jouberton
- first_name: Stefan
full_name: Fugger, Stefan
last_name: Fugger
- first_name: Li
full_name: Jia, Li
last_name: Jia
- first_name: Jing
full_name: Zhang, Jing
last_name: Zhang
- first_name: Cong
full_name: Shen, Cong
last_name: Shen
- first_name: Chaolei
full_name: Zheng, Chaolei
last_name: Zheng
- first_name: Massimo
full_name: Menenti, Massimo
last_name: Menenti
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
orcid: 0000-0002-5554-8087
citation:
ama: 'Buri P, Fatichi S, Shaw T, et al. Land surface modeling informed by earth
observation data: Toward understanding blue–green–white water fluxes in High Mountain
Asia. Geo-Spatial Information Science. 2024;27(3):703-727. doi:10.1080/10095020.2024.2330546'
apa: 'Buri, P., Fatichi, S., Shaw, T., Fyffe, C. L., Miles, E. S., McCarthy, M.,
… Pellicciotti, F. (2024). Land surface modeling informed by earth observation
data: Toward understanding blue–green–white water fluxes in High Mountain Asia.
Geo-Spatial Information Science. Taylor & Francis. https://doi.org/10.1080/10095020.2024.2330546'
chicago: 'Buri, Pascal, Simone Fatichi, Thomas Shaw, Catriona Louise Fyffe, Evan
S. Miles, Michael McCarthy, Marin Kneib, et al. “Land Surface Modeling Informed
by Earth Observation Data: Toward Understanding Blue–Green–White Water Fluxes
in High Mountain Asia.” Geo-Spatial Information Science. Taylor & Francis,
2024. https://doi.org/10.1080/10095020.2024.2330546.'
ieee: 'P. Buri et al., “Land surface modeling informed by earth observation
data: Toward understanding blue–green–white water fluxes in High Mountain Asia,”
Geo-Spatial Information Science, vol. 27, no. 3. Taylor & Francis,
pp. 703–727, 2024.'
ista: 'Buri P, Fatichi S, Shaw T, Fyffe CL, Miles ES, McCarthy M, Kneib M, Ren S,
Jouberton A, Fugger S, Jia L, Zhang J, Shen C, Zheng C, Menenti M, Pellicciotti
F. 2024. Land surface modeling informed by earth observation data: Toward understanding
blue–green–white water fluxes in High Mountain Asia. Geo-Spatial Information Science.
27(3), 703–727.'
mla: 'Buri, Pascal, et al. “Land Surface Modeling Informed by Earth Observation
Data: Toward Understanding Blue–Green–White Water Fluxes in High Mountain Asia.”
Geo-Spatial Information Science, vol. 27, no. 3, Taylor & Francis,
2024, pp. 703–27, doi:10.1080/10095020.2024.2330546.'
short: P. Buri, S. Fatichi, T. Shaw, C.L. Fyffe, E.S. Miles, M. McCarthy, M. Kneib,
S. Ren, A. Jouberton, S. Fugger, L. Jia, J. Zhang, C. Shen, C. Zheng, M. Menenti,
F. Pellicciotti, Geo-Spatial Information Science 27 (2024) 703–727.
das_tickbox: '0'
date_created: 2024-04-07T22:00:56Z
date_published: 2024-03-22T00:00:00Z
date_updated: 2026-10-02T09:12:24Z
day: '22'
ddc:
- '550'
department:
- _id: FrPe
doi: 10.1080/10095020.2024.2330546
external_id:
isi:
- '001189470100001'
file:
- access_level: open_access
checksum: afbfc4e9f1bf2a00711efc30ad667c40
content_type: application/pdf
creator: dernst
date_created: 2024-07-29T11:34:54Z
date_updated: 2024-07-29T11:34:54Z
file_id: '17342'
file_name: 2024_GeoSpatialInfo_Buri.pdf
file_size: 15678450
relation: main_file
success: 1
file_date_updated: 2024-07-29T11:34:54Z
fulldoi: https://doi.org/10.1080/10095020.2024.2330546
has_accepted_license: '1'
intvolume: ' 27'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 703-727
publication: Geo-Spatial Information Science
publication_identifier:
issn:
- 1009-5020
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: 'Land surface modeling informed by earth observation data: Toward understanding
blue–green–white water fluxes in High Mountain Asia'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 27
year: '2024'
...
---
_id: '14885'
abstract:
- lang: eng
text: The near-surface boundary layer can mediate the response of mountain glaciers
to external climate, cooling the overlying air and promoting a density-driven
glacier wind. The fundamental processes are conceptually well understood, though
the magnitudes of cooling and presence of glacier winds are poorly quantified
in space and time, increasing the forcing uncertainty for melt models. We utilize
a new data set of on-glacier meteorological measurements on three neighboring
glaciers in the Swiss Alps to explore their distinct response to regional climate
under the extreme 2022 summer. We find that synoptic wind origins and local terrain
modifications, not only glacier size, play an important role in the ability of
a glacier to cool the near-surface air. Warm air intrusions from valley or synoptically-driven
winds onto the glacier can occur between ∼19% and 64% of the time and contribute
between 3% and 81% of the total sensible heat flux to the surface during warm
afternoon hours, depending on the fetch of the glacier flowline and its susceptibility
to boundary layer erosion. In the context of extreme summer warmth, indicative
of future conditions, the boundary layer cooling (up to 6.5°C cooler than its
surroundings) and resultant katabatic wind flow are highly heterogeneous between
the study glaciers, highlighting the complex and likely non-linear response of
glaciers to an uncertain future.
acknowledgement: This project has received funding from the European Union's Horizon
2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement
No. 101026058. The authors acknowledge the invaluable field assistance of Marta
Corrà, Achille Jouberton, Marin Kneib, Stefan Fugger, Celine Ducret and Alexander
Groos. The authors would also like to thank Luca Carturan for advice regarding AWS
setup and maintenance and Simone Fatichi for provision and support in the use of
the Tethys-Chloris model. Open access funding provided by ETH-Bereich Forschungsanstalten.
article_number: e2023JD040214
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Thomas
full_name: Shaw, Thomas
id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e
last_name: Shaw
orcid: 0000-0001-7640-6152
- first_name: Pascal
full_name: Buri, Pascal
id: 317987aa-9421-11ee-ac5a-b941b041abba
last_name: Buri
- first_name: Michael
full_name: Mccarthy, Michael
id: 22a2674a-61ce-11ee-94b5-d18813baf16f
last_name: Mccarthy
- first_name: Evan S.
full_name: Miles, Evan S.
last_name: Miles
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
orcid: 0000-0002-5554-8087
citation:
ama: 'Shaw T, Buri P, McCarthy M, Miles ES, Pellicciotti F. Local controls on near-surface
glacier cooling under warm atmospheric conditions. Journal of Geophysical Research:
Atmospheres. 2024;129(2). doi:10.1029/2023JD040214'
apa: 'Shaw, T., Buri, P., McCarthy, M., Miles, E. S., & Pellicciotti, F. (2024).
Local controls on near-surface glacier cooling under warm atmospheric conditions.
Journal of Geophysical Research: Atmospheres. Wiley. https://doi.org/10.1029/2023JD040214'
chicago: 'Shaw, Thomas, Pascal Buri, Michael McCarthy, Evan S. Miles, and Francesca
Pellicciotti. “Local Controls on Near-Surface Glacier Cooling under Warm Atmospheric
Conditions.” Journal of Geophysical Research: Atmospheres. Wiley, 2024.
https://doi.org/10.1029/2023JD040214.'
ieee: 'T. Shaw, P. Buri, M. McCarthy, E. S. Miles, and F. Pellicciotti, “Local controls
on near-surface glacier cooling under warm atmospheric conditions,” Journal
of Geophysical Research: Atmospheres, vol. 129, no. 2. Wiley, 2024.'
ista: 'Shaw T, Buri P, McCarthy M, Miles ES, Pellicciotti F. 2024. Local controls
on near-surface glacier cooling under warm atmospheric conditions. Journal of
Geophysical Research: Atmospheres. 129(2), e2023JD040214.'
mla: 'Shaw, Thomas, et al. “Local Controls on Near-Surface Glacier Cooling under
Warm Atmospheric Conditions.” Journal of Geophysical Research: Atmospheres,
vol. 129, no. 2, e2023JD040214, Wiley, 2024, doi:10.1029/2023JD040214.'
short: 'T. Shaw, P. Buri, M. McCarthy, E.S. Miles, F. Pellicciotti, Journal of Geophysical
Research: Atmospheres 129 (2024).'
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: 'The meteorological data used in this analysis (Shaw, Buri,
McCarthy, Miles, & Pelliciotti, 2023) are made publicly available at the following
repository: https://zenodo.org/record/8277285. The source code of the T&C model
is available at https://doi.org/10.24433/CO.0905087.v2. Reanalysis data are openly
available from the ECMWF (https://cds.climate.copernicus.eu/). MeteoSwiss data can
be acquired through direct request to the company.'
date_created: 2024-01-28T23:01:42Z
date_published: 2024-01-28T00:00:00Z
date_updated: 2026-10-02T08:59:02Z
day: '28'
ddc:
- '550'
department:
- _id: FrPe
doi: 10.1029/2023JD040214
external_id:
isi:
- '001146838000001'
file:
- access_level: open_access
checksum: cad5b93caadb40c14e5faedc34f7bba7
content_type: application/pdf
creator: dernst
date_created: 2024-02-06T08:38:27Z
date_updated: 2024-02-06T08:38:27Z
file_id: '14943'
file_name: 2024_JGRAtmospheres_Shaw.pdf
file_size: 7481087
relation: main_file
success: 1
file_date_updated: 2024-02-06T08:38:27Z
fulldoi: https://doi.org/10.1029/2023JD040214
has_accepted_license: '1'
intvolume: ' 129'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: 'Journal of Geophysical Research: Atmospheres'
publication_identifier:
eissn:
- 2169-8996
issn:
- 2169-897X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '14919'
relation: research_data
status: public
- id: '23030'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Local controls on near-surface glacier cooling under warm atmospheric conditions
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 129
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18628'
abstract:
- lang: eng
text: 'Arctic tidewater glaciers are retreating, serving as key indicators of global
warming. This study aims to assess how subglacial hydrology affects glacier front
retreat by comparing two glacier–fjord models of the Hansbreen glacier: one incorporating
a detailed subglacial hydrology model and another simplifying the subglacial discharge
to a single channel centered in the flow line. We first validate the subglacial
hydrology model by comparing its discharge channels with observations of plume
activity. Simulations conducted from April to December 2010 revealed that the
glacier front position aligns more closely with the observations in the coupled
model than in the simplified version. Furthermore, the mass loss due to calving
and submarine melting is greater in the coupled model, with the calving mass loss
reaching 6 Mt by the end of the simulation compared to 4 Mt in the simplified
model. These findings highlight the critical role of subglacial hydrology in predicting
glacier dynamics and emphasize the importance of detailed modeling in understanding
the responses of Arctic tidewater glaciers to climate change.'
acknowledgement: "E. De Andrés is supported by Margarita-Salas Grant No. UP2021-035
under the Next Generation-EU program. This research was also funded by grant PID2020-113051RB-C31
from MCIN/AEI/10.13039/501100011033/FEDER, UE.\r\nWe gratefully acknowledge Michal
Cieply and Dariusz Ignatiuk from the Faculty of Natural Sciences, University of
Silesia in Katowice, Poland, for their essential contributions to the Hansbreen
data collection. We also extend our sincere thanks to Waldemar Walczowski from the
Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland, for providing
Hansbuka data. Additionally, we would like to thank two anonymous reviewers for
their constructive feedback, which helped to enhance the quality and clarity of
this work."
article_number: '193'
article_processing_charge: Yes
article_type: original
author:
- first_name: Eva
full_name: De Andrés, Eva
last_name: De Andrés
- first_name: José M
full_name: Muñoz Hermosilla, José M
id: e1037a6d-646e-11ef-b402-e0ed9ab0901e
last_name: Muñoz Hermosilla
orcid: 0000-0002-1990-8508
- first_name: Kaian
full_name: Shahateet, Kaian
last_name: Shahateet
- first_name: Jaime
full_name: Otero, Jaime
last_name: Otero
citation:
ama: 'De Andrés E, Muñoz Hermosilla JM, Shahateet K, Otero J. The importance of
solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen,
Svalbard. Hydrology. 2024;11(11). doi:10.3390/hydrology11110193'
apa: 'De Andrés, E., Muñoz Hermosilla, J. M., Shahateet, K., & Otero, J. (2024).
The importance of solving Subglaciar hydrology in modeling glacier retreat: A
case study of Hansbreen, Svalbard. Hydrology. MDPI. https://doi.org/10.3390/hydrology11110193'
chicago: 'De Andrés, Eva, José M Muñoz Hermosilla, Kaian Shahateet, and Jaime Otero.
“The Importance of Solving Subglaciar Hydrology in Modeling Glacier Retreat: A
Case Study of Hansbreen, Svalbard.” Hydrology. MDPI, 2024. https://doi.org/10.3390/hydrology11110193.'
ieee: 'E. De Andrés, J. M. Muñoz Hermosilla, K. Shahateet, and J. Otero, “The importance
of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen,
Svalbard,” Hydrology, vol. 11, no. 11. MDPI, 2024.'
ista: 'De Andrés E, Muñoz Hermosilla JM, Shahateet K, Otero J. 2024. The importance
of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen,
Svalbard. Hydrology. 11(11), 193.'
mla: 'De Andrés, Eva, et al. “The Importance of Solving Subglaciar Hydrology in
Modeling Glacier Retreat: A Case Study of Hansbreen, Svalbard.” Hydrology,
vol. 11, no. 11, 193, MDPI, 2024, doi:10.3390/hydrology11110193.'
short: E. De Andrés, J.M. Muñoz Hermosilla, K. Shahateet, J. Otero, Hydrology 11
(2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The data that support the results of this study and form
the basis for all the figures presented in this paper are openly available from
Zenodo at https://doi.org/10.5281/zenodo.8005258 (accessed on 6 November 2024).
date_created: 2024-12-08T23:01:55Z
date_published: 2024-11-12T00:00:00Z
date_updated: 2026-10-02T09:16:55Z
day: '12'
ddc:
- '550'
department:
- _id: FrPe
doi: 10.3390/hydrology11110193
file:
- access_level: open_access
checksum: 0665c5bfca97782bf0b041f23dd7e8d7
content_type: application/pdf
creator: dernst
date_created: 2024-12-09T09:43:33Z
date_updated: 2024-12-09T09:43:33Z
file_id: '18635'
file_name: 2024_Hydrology_deAndres.pdf
file_size: 5709093
relation: main_file
success: 1
file_date_updated: 2024-12-09T09:43:33Z
fulldoi: https://doi.org/10.3390/hydrology11110193
has_accepted_license: '1'
intvolume: ' 11'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Hydrology
publication_identifier:
eissn:
- 2306-5338
publication_status: published
publisher: MDPI
quality_controlled: '1'
related_material:
record:
- id: '18634'
relation: used_in_publication
status: public
- id: '23031'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'The importance of solving Subglaciar hydrology in modeling glacier retreat:
A case study of Hansbreen, Svalbard'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 11
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15362'
abstract:
- lang: eng
text: Constitutional heterozygous pathogenic variants in the exonuclease domain
of POLE and POLD1, which affect the proofreading activity of the corresponding
polymerases, cause a cancer predisposition syndrome characterized by increased
risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and
other tumor types. The generally accepted explanation for the connection between
the disruption of the proofreading activity of polymerases epsilon and delta and
cancer development is through an increase in the somatic mutation rate. Here we
studied an extended family with multiple members heterozygous for the pathogenic
POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and
cancer phenotypes. Through the analysis of mutational patterns of patient-derived
fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons,
we concluded that heterozygous POLD1 L474P just subtly increases the somatic and
germline mutation burden. In contrast, tumors developed in individuals with a
heterozygous mutation in the exonuclease domain of POLD1, including L474P, have
an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d.
We solved this contradiction through the observation that tumorigenesis involves
somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease
deficiency of polymerase delta has a recessive effect on mutation rate.
acknowledgement: 'This study was funded by the Spanish Ministry of Science and Innovation
(Agencia Estatal de Investigación), co-funded by FEDER funds a way to build Europe
[PID2020-112595RB-I00 (LV)], Instituto de Salud Carlos III [CIBERONC CB16/12/00234
(LV); ISCIII-AES-2017 PI17/01082 (JLS), PMP22/00064], Government of Catalonia [AGAUR
2021SGR01112, CERCA Program for institutional support (LV)], Scientific Foundation
Asociación Española Contra el Cáncer [AECC Investigador (MT)], Austrian Science
Fund FWF [Grant Agreement # I5127-B (FK)], German Research Foundation DFG [Grant
Agreement # 429960716 (FK)], and ERC Consolidator [Grant Agreement # 771209 ChrFL
(FK)].'
article_processing_charge: No
article_type: original
author:
- first_name: Maria A.
full_name: Andrianova, Maria A.
last_name: Andrianova
- first_name: Vladimir B.
full_name: Seplyarskiy, Vladimir B.
last_name: Seplyarskiy
- first_name: Mariona
full_name: Terradas, Mariona
last_name: Terradas
- first_name: Ana Beatriz
full_name: Sánchez-Heras, Ana Beatriz
last_name: Sánchez-Heras
- first_name: Pilar
full_name: Mur, Pilar
last_name: Mur
- first_name: José Luis
full_name: Soto, José Luis
last_name: Soto
- first_name: Gemma
full_name: Aiza, Gemma
last_name: Aiza
- first_name: Emma
full_name: Borràs, Emma
last_name: Borràs
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey S.
full_name: Kondrashov, Alexey S.
last_name: Kondrashov
- first_name: Georgii A.
full_name: Bazykin, Georgii A.
last_name: Bazykin
- first_name: Laura
full_name: Valle, Laura
last_name: Valle
citation:
ama: Andrianova MA, Seplyarskiy VB, Terradas M, et al. Discovery of recessive effect
of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated
normal and cancer cells. European Journal of Human Genetics. 2024;32:837-845.
doi:10.1038/s41431-024-01598-8
apa: Andrianova, M. A., Seplyarskiy, V. B., Terradas, M., Sánchez-Heras, A. B.,
Mur, P., Soto, J. L., … Valle, L. (2024). Discovery of recessive effect of human
polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated
normal and cancer cells. European Journal of Human Genetics. Springer Nature.
https://doi.org/10.1038/s41431-024-01598-8
chicago: Andrianova, Maria A., Vladimir B. Seplyarskiy, Mariona Terradas, Ana Beatriz
Sánchez-Heras, Pilar Mur, José Luis Soto, Gemma Aiza, et al. “Discovery of Recessive
Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis
of POLD1-Mutated Normal and Cancer Cells.” European Journal of Human Genetics.
Springer Nature, 2024. https://doi.org/10.1038/s41431-024-01598-8.
ieee: M. A. Andrianova et al., “Discovery of recessive effect of human polymerase
δ proofreading deficiency through mutational analysis of POLD1-mutated normal
and cancer cells,” European Journal of Human Genetics, vol. 32. Springer
Nature, pp. 837–845, 2024.
ista: Andrianova MA, Seplyarskiy VB, Terradas M, Sánchez-Heras AB, Mur P, Soto JL,
Aiza G, Borràs E, Kondrashov F, Kondrashov AS, Bazykin GA, Valle L. 2024. Discovery
of recessive effect of human polymerase δ proofreading deficiency through mutational
analysis of POLD1-mutated normal and cancer cells. European Journal of Human Genetics.
32, 837–845.
mla: Andrianova, Maria A., et al. “Discovery of Recessive Effect of Human Polymerase
δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal
and Cancer Cells.” European Journal of Human Genetics, vol. 32, Springer
Nature, 2024, pp. 837–45, doi:10.1038/s41431-024-01598-8.
short: M.A. Andrianova, V.B. Seplyarskiy, M. Terradas, A.B. Sánchez-Heras, P. Mur,
J.L. Soto, G. Aiza, E. Borràs, F. Kondrashov, A.S. Kondrashov, G.A. Bazykin, L.
Valle, European Journal of Human Genetics 32 (2024) 837–845.
das_tickbox: '1'
dataavailabilitystatement: DNA sequencing data are deposited in the European Genome-Phenome
Archive (EGA) with accession code EGAS00001006434. Called de novo and somatic mutations
are available online (https://figshare.com/account/home#/projects/156404).
date_created: 2024-05-05T22:01:04Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-10-02T09:48:07Z
day: '01'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41431-024-01598-8
ec_funded: 1
external_id:
isi:
- '001207703200001'
pmid:
- '38658779'
file:
- access_level: open_access
checksum: e45fc987f4e9ebafdd0ec4f0e9027de4
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T09:21:25Z
date_updated: 2025-01-09T09:21:25Z
file_id: '18799'
file_name: 2024_EJHG_Andrianova.pdf
file_size: 3060724
relation: main_file
success: 1
file_date_updated: 2025-01-09T09:21:25Z
fulldoi: https://doi.org/10.1038/s41431-024-01598-8
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 837-845
pmid: 1
project:
- _id: 9B767A34-BA93-11EA-9121-9846C619BF3A
grant_number: '429960716'
name: Evolution of Sensorimotor Transformation Across Diptera
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: 34e076d6-11ca-11ed-8bc3-aec76c41a181
grant_number: I05127
name: Evolutionary analysis of gene regulation
publication: European Journal of Human Genetics
publication_identifier:
eissn:
- 1476-5438
issn:
- 1018-4813
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Discovery of recessive effect of human polymerase δ proofreading deficiency
through mutational analysis of POLD1-mutated normal and cancer cells
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 32
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '15179'
abstract:
- lang: eng
text: The fungal bioluminescence pathway can be reconstituted in other organisms
allowing luminescence imaging without exogenously supplied substrate. The pathway
starts from hispidin biosynthesis—a step catalyzed by a large fungal polyketide
synthase that requires a posttranslational modification for activity. Here, we
report identification of alternative compact hispidin synthases encoded by a phylogenetically
diverse group of plants. A hybrid bioluminescence pathway that combines plant
and fungal genes is more compact, not dependent on availability of machinery for
posttranslational modifications, and confers autonomous bioluminescence in yeast,
mammalian, and plant hosts. The compact size of plant hispidin synthases enables
additional modes of delivery of autoluminescence, such as delivery with viral
vectors.
acknowledgement: "We thank Milaboratory (milaboratory.com) for the access to computing
and storage infrastructure. We thank J. Petrasek for providing the BY-2 cell culture
line. We thank Konstantin Lukyanov laboratory and Sergey Deyev laboratory for assistance
with experiments.\r\nThis study was partially funded by Light Bio and Planta. The
Synthetic biology Group is funded by the MRC London Institute of Medical Sciences
(UKRI MC-A658-5QEA0). Cloning and luminescent assays performed in BY-2 were partially
supported by RSF, project number 22-14-00400, https://rscf.ru/project/22-14-00400/.
Plant transformations were funded by RFBR and MOST, project number 21-54-52004.
Plant imaging experiments were funded by RSF, project number 22-74-00124, https://rscf.ru/project/22-74-00124/.
Viral delivery experiments were funded by the grant PID2019-108203RB-I00 Plan Nacional
I + D from the Ministerio de Ciencia e Innovación (Spain) through the Agencia Estatal
de Investigación (cofinanced by the European Regional Development Fund)."
article_number: adk1992
article_processing_charge: Yes
article_type: original
author:
- first_name: Kseniia A.
full_name: Palkina, Kseniia A.
last_name: Palkina
- first_name: Tatiana A.
full_name: Karataeva, Tatiana A.
last_name: Karataeva
- first_name: Maxim M.
full_name: Perfilov, Maxim M.
last_name: Perfilov
- first_name: Liliia I.
full_name: Fakhranurova, Liliia I.
last_name: Fakhranurova
- first_name: Nadezhda M.
full_name: Markina, Nadezhda M.
last_name: Markina
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Elena
full_name: Garcia-Perez, Elena
last_name: Garcia-Perez
- first_name: Marta
full_name: Vazquez-Vilar, Marta
last_name: Vazquez-Vilar
- first_name: Marta
full_name: Rodriguez-Rodriguez, Marta
last_name: Rodriguez-Rodriguez
- first_name: Victor
full_name: Vazquez-Vilriales, Victor
last_name: Vazquez-Vilriales
- first_name: Ekaterina S.
full_name: Shakhova, Ekaterina S.
last_name: Shakhova
- first_name: Tatiana
full_name: Mitiouchkina, Tatiana
last_name: Mitiouchkina
- first_name: Olga A.
full_name: Belozerova, Olga A.
last_name: Belozerova
- first_name: Sergey I.
full_name: Kovalchuk, Sergey I.
last_name: Kovalchuk
- first_name: Anna
full_name: Alekberova, Anna
last_name: Alekberova
- first_name: Alena K.
full_name: Malyshevskaia, Alena K.
last_name: Malyshevskaia
- first_name: Evgenia N.
full_name: Bugaeva, Evgenia N.
last_name: Bugaeva
- first_name: Elena B.
full_name: Guglya, Elena B.
last_name: Guglya
- first_name: Anastasia
full_name: Balakireva, Anastasia
last_name: Balakireva
- first_name: Nikita
full_name: Sytov, Nikita
last_name: Sytov
- first_name: Anastasia
full_name: Bezlikhotnova, Anastasia
last_name: Bezlikhotnova
- first_name: Daria I.
full_name: Boldyreva, Daria I.
last_name: Boldyreva
- first_name: Vladislav V.
full_name: Babenko, Vladislav V.
last_name: Babenko
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Vladimir V.
full_name: Choob, Vladimir V.
last_name: Choob
- first_name: Diego
full_name: Orzaez, Diego
last_name: Orzaez
- first_name: Ilia V.
full_name: Yampolsky, Ilia V.
last_name: Yampolsky
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Karen S.
full_name: Sarkisyan, Karen S.
last_name: Sarkisyan
citation:
ama: Palkina KA, Karataeva TA, Perfilov MM, et al. A hybrid pathway for self-sustained
luminescence. Science Advances. 2024;10(10). doi:10.1126/sciadv.adk1992
apa: Palkina, K. A., Karataeva, T. A., Perfilov, M. M., Fakhranurova, L. I., Markina,
N. M., Gonzalez Somermeyer, L., … Sarkisyan, K. S. (2024). A hybrid pathway for
self-sustained luminescence. Science Advances. American Association for
the Advancement of Science. https://doi.org/10.1126/sciadv.adk1992
chicago: Palkina, Kseniia A., Tatiana A. Karataeva, Maxim M. Perfilov, Liliia I.
Fakhranurova, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, Elena Garcia-Perez,
et al. “A Hybrid Pathway for Self-Sustained Luminescence.” Science Advances.
American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk1992.
ieee: K. A. Palkina et al., “A hybrid pathway for self-sustained luminescence,”
Science Advances, vol. 10, no. 10. American Association for the Advancement
of Science, 2024.
ista: Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Gonzalez
Somermeyer L, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales
V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia
AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI,
Babenko VV, Kondrashov F, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan
KS. 2024. A hybrid pathway for self-sustained luminescence. Science Advances.
10(10), adk1992.
mla: Palkina, Kseniia A., et al. “A Hybrid Pathway for Self-Sustained Luminescence.”
Science Advances, vol. 10, no. 10, adk1992, American Association for the
Advancement of Science, 2024, doi:10.1126/sciadv.adk1992.
short: K.A. Palkina, T.A. Karataeva, M.M. Perfilov, L.I. Fakhranurova, N.M. Markina,
L. Gonzalez Somermeyer, E. Garcia-Perez, M. Vazquez-Vilar, M. Rodriguez-Rodriguez,
V. Vazquez-Vilriales, E.S. Shakhova, T. Mitiouchkina, O.A. Belozerova, S.I. Kovalchuk,
A. Alekberova, A.K. Malyshevskaia, E.N. Bugaeva, E.B. Guglya, A. Balakireva, N.
Sytov, A. Bezlikhotnova, D.I. Boldyreva, V.V. Babenko, F. Kondrashov, V.V. Choob,
D. Orzaez, I.V. Yampolsky, A.S. Mishin, K.S. Sarkisyan, Science Advances 10 (2024).
das_tickbox: '1'
dataavailabilitystatement: All data needed to evaluate the conclusions in the paper
are present in the paper and/or the Supplementary Materials. The plasmids used in
this study will be made available for noncommercial use through Addgene under the
terms of UBMTA (www.addgene.org/agreement/1). The data are available at https://doi.org/10.6084/m9.figshare.24772872.
date_created: 2024-03-25T08:54:33Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2026-10-02T09:22:29Z
day: '01'
ddc:
- '580'
department:
- _id: FyKo
doi: 10.1126/sciadv.adk1992
external_id:
isi:
- '001187580500013'
pmid:
- '38457503'
file:
- access_level: open_access
checksum: a19c43b260ea0bbaf895a29712e3153c
content_type: application/pdf
creator: dernst
date_created: 2024-03-25T09:42:10Z
date_updated: 2024-03-25T09:42:10Z
file_id: '15185'
file_name: 2024_ScienceAdv_Palkina.pdf
file_size: 1499302
relation: main_file
success: 1
file_date_updated: 2024-03-25T09:42:10Z
fulldoi: https://doi.org/10.1126/sciadv.adk1992
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '10'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
record:
- id: '23032'
relation: research_data
status: public
researchdata_availability: yes (supplementary data)
scopus_import: '1'
status: public
supplementarymaterial: yes
title: A hybrid pathway for self-sustained luminescence
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 10
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18779'
abstract:
- lang: eng
text: Unsupervised segmentation in biological and non-biological images is only
partially resolved. Segmentation either requires arbitrary thresholds or large
teaching datasets. Here, we propose a spatial autocorrelation method based on
Local Moran’s I coefficient to differentiate signal,
background, and noise in any type of image. The method, originally described for
geoinformatics, does not require a predefined intensity threshold or teaching
algorithm for image segmentation and allows quantitative comparison of samples
obtained in different conditions. It utilizes relative intensity as well as spatial
information of neighboring elements to select spatially contiguous groups of pixels.
We demonstrate that Moran’s method outperforms threshold-based method in both
artificially generated as well as in natural images especially when background
noise is substantial. This superior performance can be attributed to the exclusion
of false positive pixels resulting from isolated, high intensity pixels in high
noise conditions. To test the method’s power in real situation, we used high power
confocal images of the somatosensory thalamus immunostained for Kv4.2 and Kv4.3
(A-type) voltage-gated potassium channels in mice. Moran’s method identified high-intensity
Kv4.2 and Kv4.3 ion channel clusters in the thalamic neuropil. Spatial distribution
of these clusters displayed strong correlation with large sensory axon terminals
of subcortical origin. The unique association of the special presynaptic terminals
and a postsynaptic voltage-gated ion channel cluster was confirmed with electron
microscopy. These data demonstrate that Moran’s method is a rapid, simple image
segmentation method optimal for variable and high noise conditions.
acknowledgement: "This research was supported by the Wellcome Trust (ZN, LA). In addition,
LA was supported by an ERC Advanced Grant (FRONTHAL, 742595) and the European Union
project RRF-2.3.1-\r\n21-2022-00004 within the framework of the Artificial Intelligence
National Laboratory and Lendület_2023_90. ZN is the recipient of a Hungarian Academy
of Sciences Momentum Grant (Lendület, LP2012-29) and an ERC Advanced Grant (293681).
We thank the Light Microscopy Center at Institute of Experimental Medicine for kindly
providing microscopy support. Authors would like to express their deepest gratitude
to Prof Luc Anselin (Center for Spatial Data Science, University of Chicago) and
Dr Szabolcs Káli (Instiute of Experimental Medicine, Budapest) for the valuable
discussion about analysis of spatial association, and to Krisztina Faddi for the
excellent technical assistance. "
article_number: '89361'
article_processing_charge: Yes
article_type: original
author:
- first_name: Csaba
full_name: Dávid, Csaba
last_name: Dávid
- first_name: Kristóf
full_name: Giber, Kristóf
last_name: Giber
- first_name: Margit Katalin
full_name: Szigeti, Margit Katalin
id: 44F4BDC0-F248-11E8-B48F-1D18A9856A87
last_name: Szigeti
orcid: 0000-0001-9500-8758
- first_name: Mihály
full_name: Köllő, Mihály
last_name: Köllő
- first_name: Zoltan
full_name: Nusser, Zoltan
last_name: Nusser
- first_name: Laszlo
full_name: Acsady, Laszlo
last_name: Acsady
citation:
ama: Dávid C, Giber K, Szigeti MK, Köllő M, Nusser Z, Acsady L. A novel image segmentation
method based on spatial autocorrelation identifies A-type potassium channel clusters
in the thalamus. eLife. 2024;12. doi:10.7554/elife.89361
apa: Dávid, C., Giber, K., Szigeti, M. K., Köllő, M., Nusser, Z., & Acsady,
L. (2024). A novel image segmentation method based on spatial autocorrelation
identifies A-type potassium channel clusters in the thalamus. ELife. eLife
Sciences Publications. https://doi.org/10.7554/elife.89361
chicago: Dávid, Csaba, Kristóf Giber, Margit Katalin Szigeti, Mihály Köllő, Zoltan
Nusser, and Laszlo Acsady. “A Novel Image Segmentation Method Based on Spatial
Autocorrelation Identifies A-Type Potassium Channel Clusters in the Thalamus.”
ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.89361.
ieee: C. Dávid, K. Giber, M. K. Szigeti, M. Köllő, Z. Nusser, and L. Acsady, “A
novel image segmentation method based on spatial autocorrelation identifies A-type
potassium channel clusters in the thalamus,” eLife, vol. 12. eLife Sciences
Publications, 2024.
ista: Dávid C, Giber K, Szigeti MK, Köllő M, Nusser Z, Acsady L. 2024. A novel image
segmentation method based on spatial autocorrelation identifies A-type potassium
channel clusters in the thalamus. eLife. 12, 89361.
mla: Dávid, Csaba, et al. “A Novel Image Segmentation Method Based on Spatial Autocorrelation
Identifies A-Type Potassium Channel Clusters in the Thalamus.” ELife, vol.
12, 89361, eLife Sciences Publications, 2024, doi:10.7554/elife.89361.
short: C. Dávid, K. Giber, M.K. Szigeti, M. Köllő, Z. Nusser, L. Acsady, ELife 12
(2024).
das_tickbox: '1'
dataavailabilitystatement: 'The code for the analysis is available online as a user-friendly
MATLAB script at: https://github.com/dcsabaCD225/Moran_Matlab/blob/main/moran_local.m
(copy archived at Csaba, 2024). All source data relevant to figures and charts are
included in source data files.'
date_created: 2025-01-08T13:25:45Z
date_published: 2024-12-10T00:00:00Z
date_updated: 2026-10-02T09:53:20Z
day: '10'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.7554/elife.89361
file:
- access_level: open_access
checksum: 1d64265f62a3bf14550b4f5c684f1782
content_type: application/pdf
creator: dernst
date_created: 2025-01-08T13:33:05Z
date_updated: 2025-01-08T13:33:05Z
file_id: '18780'
file_name: 2024_eLife_David.pdf
file_size: 9992462
relation: main_file
success: 1
file_date_updated: 2025-01-08T13:33:05Z
fulldoi: https://doi.org/10.7554/elife.89361
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: A novel image segmentation method based on spatial autocorrelation identifies
A-type potassium channel clusters in the thalamus
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 12
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17331'
abstract:
- lang: eng
text: Amyloidosis are a group of diseases in which soluble proteins aggregate and
deposit in fibrillar conformation extracellularly in tissues. The effectiveness
of therapeutic strategies depends on the specific protein involved, being crucial
to accurately determine its nature. Moreover, following the diagnosis, the search
for the mutation within relatives allows the clinical advice. Here we report the
precise diagnosis and explored the possible reasons of the structural pathogenicity
for a renal amyloidosis related to a fibrinogen Aα-chain variant. Whole-exome
sequencing and GATK calling pipeline were leveraged to characterize the protein
variant present in a patient with kidney failure. Bioinformatics strategies were
applied to suggest potential explanations of the variants aggregation. Our pipeline
allowed the identification of a single-point variant of fibrinogen Aα-chain, which
opened the possibility of curative transplantation. In silico structural analysis
suggested that the pathogenicity of the variant may be attributed to a heightened
susceptibility to yield a peptide prone to deposit as an oligomer with a β-sheet
structure. Exploiting the comprehensive coverage of whole-genome sequencing, we
managed to fill a vacant stage in the diagnosis of hereditary amyloidosis and
to stimulate the advancement in biomedicine.
acknowledgement: The authors acknowledge Rosana del Cid for her help with English
corrections, Mario Ramos for the figure editions, and Gabriela Finarelli for technical
assistance. S.A. Rosú, N.A. Ramella, and M.A. Tricerri acknowledge support from
Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) (Grant PIP
11220200102381), Agencia Nacional de Promoción Científica y Tecnológica (PICT 2019-03592),
Universidad Nacional de La Plata (UNLP) (Grants M234 and PPID M014), and Fundación
Florencio Fiorini. The authors warmly thank M.P. for her willingness to conduct
these studies.
article_processing_charge: No
article_type: original
author:
- first_name: Elizabeth R
full_name: Cattaneo, Elizabeth R
last_name: Cattaneo
- first_name: Romina A
full_name: Gisonno, Romina A
id: a9e08d76-6a98-11ec-8f7b-c777fe5ca519
last_name: Gisonno
- first_name: Martín C
full_name: Abba, Martín C
last_name: Abba
- first_name: Marianela
full_name: Santana, Marianela
last_name: Santana
- first_name: Silvana A
full_name: Rosú, Silvana A
last_name: Rosú
- first_name: Elsa
full_name: Nucifora, Elsa
last_name: Nucifora
- first_name: María A
full_name: Aguirre, María A
last_name: Aguirre
- first_name: María C
full_name: Giordani, María C
last_name: Giordani
- first_name: M. Alejandra
full_name: Tricerri, M. Alejandra
last_name: Tricerri
- first_name: Nahuel A
full_name: Ramella, Nahuel A
last_name: Ramella
citation:
ama: 'Cattaneo ER, Gisonno RA, Abba MC, et al. Hereditary amyloidosis: Insights
into a fibrinogen A variant protein. Proteins: Structure, Function and Bioinformatics.
2024;92(12):1366-1374. doi:10.1002/prot.26732'
apa: 'Cattaneo, E. R., Gisonno, R. A., Abba, M. C., Santana, M., Rosú, S. A., Nucifora,
E., … Ramella, N. A. (2024). Hereditary amyloidosis: Insights into a fibrinogen
A variant protein. Proteins: Structure, Function and Bioinformatics. Wiley.
https://doi.org/10.1002/prot.26732'
chicago: 'Cattaneo, Elizabeth R, Romina A Gisonno, Martín C Abba, Marianela Santana,
Silvana A Rosú, Elsa Nucifora, María A Aguirre, María C Giordani, M. Alejandra
Tricerri, and Nahuel A Ramella. “Hereditary Amyloidosis: Insights into a Fibrinogen
A Variant Protein.” Proteins: Structure, Function and Bioinformatics. Wiley,
2024. https://doi.org/10.1002/prot.26732.'
ieee: 'E. R. Cattaneo et al., “Hereditary amyloidosis: Insights into a fibrinogen
A variant protein,” Proteins: Structure, Function and Bioinformatics, vol.
92, no. 12. Wiley, pp. 1366–1374, 2024.'
ista: 'Cattaneo ER, Gisonno RA, Abba MC, Santana M, Rosú SA, Nucifora E, Aguirre
MA, Giordani MC, Tricerri MA, Ramella NA. 2024. Hereditary amyloidosis: Insights
into a fibrinogen A variant protein. Proteins: Structure, Function and Bioinformatics.
92(12), 1366–1374.'
mla: 'Cattaneo, Elizabeth R., et al. “Hereditary Amyloidosis: Insights into a Fibrinogen
A Variant Protein.” Proteins: Structure, Function and Bioinformatics, vol.
92, no. 12, Wiley, 2024, pp. 1366–74, doi:10.1002/prot.26732.'
short: 'E.R. Cattaneo, R.A. Gisonno, M.C. Abba, M. Santana, S.A. Rosú, E. Nucifora,
M.A. Aguirre, M.C. Giordani, M.A. Tricerri, N.A. Ramella, Proteins: Structure,
Function and Bioinformatics 92 (2024) 1366–1374.'
das_tickbox: '1'
dataavailabilitystatement: The data that support the findings of this study are available
on request from the corresponding author. The data are not publicly available due
to privacy or ethical restrictions.
date_created: 2024-07-28T22:01:10Z
date_published: 2024-12-01T00:00:00Z
date_updated: 2026-10-02T09:56:43Z
day: '01'
department:
- _id: GaNo
doi: 10.1002/prot.26732
external_id:
isi:
- '001272128100001'
pmid:
- '39031927'
fulldoi: https://doi.org/10.1002/prot.26732
intvolume: ' 92'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.22541/au.171804763.37967262/v1
month: '12'
oa: 1
oa_version: Preprint
page: 1366-1374
pmid: 1
publication: 'Proteins: Structure, Function and Bioinformatics'
publication_identifier:
eissn:
- 1097-0134
issn:
- 0887-3585
publication_status: published
publisher: Wiley
quality_controlled: '1'
researchdata_availability: upon request
scopus_import: '1'
status: public
supplementarymaterial: yes
title: 'Hereditary amyloidosis: Insights into a fibrinogen A variant protein'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 92
year: '2024'
...
---
_id: '17091'
abstract:
- lang: eng
text: DNA sequences are connected to genes and functions in the developing and adult
brain
article_processing_charge: No
article_type: letter_note
author:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
citation:
ama: Novarino G, Bock C. Mapping the brain’s gene-regulatory maze. Science.
2024;384(6698):860-861. doi:10.1126/science.adp4663
apa: Novarino, G., & Bock, C. (2024). Mapping the brain’s gene-regulatory maze.
Science. AAAS. https://doi.org/10.1126/science.adp4663
chicago: Novarino, Gaia, and Christoph Bock. “Mapping the Brain’s Gene-Regulatory
Maze.” Science. AAAS, 2024. https://doi.org/10.1126/science.adp4663.
ieee: G. Novarino and C. Bock, “Mapping the brain’s gene-regulatory maze,” Science,
vol. 384, no. 6698. AAAS, pp. 860–861, 2024.
ista: Novarino G, Bock C. 2024. Mapping the brain’s gene-regulatory maze. Science.
384(6698), 860–861.
mla: Novarino, Gaia, and Christoph Bock. “Mapping the Brain’s Gene-Regulatory Maze.”
Science, vol. 384, no. 6698, AAAS, 2024, pp. 860–61, doi:10.1126/science.adp4663.
short: G. Novarino, C. Bock, Science 384 (2024) 860–861.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-06-02T22:00:57Z
date_published: 2024-05-24T00:00:00Z
date_updated: 2026-10-02T09:50:30Z
day: '24'
department:
- _id: GaNo
doi: 10.1126/science.adp4663
external_id:
isi:
- '001230076500007'
pmid:
- '38781359'
fulldoi: https://doi.org/10.1126/science.adp4663
intvolume: ' 384'
isi: 1
issue: '6698'
language:
- iso: eng
month: '05'
oa_version: None
page: 860-861
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Mapping the brain’s gene-regulatory maze
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 384
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18307'
abstract:
- lang: eng
text: Vaccination is the most effective tool to control infectious diseases. However,
the evolution of vaccine resistance, exemplified by vaccine resistance in SARS-CoV-2,
remains a concern. Here, we model complex vaccination strategies against a pathogen
with multiple epitopes—molecules targeted by the vaccine. We found that a vaccine
targeting one epitope was ineffective in preventing vaccine escape. Vaccine resistance
in highly infectious pathogens was prevented by the full-epitope vaccine, that
is, one targeting all available epitopes, but only when the rate of pathogen evolution
was low. Strikingly, a bet-hedging strategy of random administration of vaccines
targeting different epitopes was the most effective in preventing vaccine resistance
in pathogens with the low rate of infection and high rate of evolution. Thus,
complex vaccination strategies, when biologically feasible, may be preferable
to the currently used single-vaccine approaches for long-term control of disease
outbreaks, especially when applied to livestock with near 100% vaccination rates.
acknowledgement: We thank Raimundo Julian Saona Urmeneta, Maike Morrison, Sergey Kryazhimskiy,
Hiroki Ishikawa, Simone Pigolotti, and Shingo Miyauchi for fruitful discussions.
We also thank the participants of the FRISBI seminar at ISTA for useful comments.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Simon
full_name: Rella, Simon
id: B4765ACA-AA38-11E9-AC9A-0930E6697425
last_name: Rella
- first_name: Yuliya A.
full_name: Kulikova, Yuliya A.
last_name: Kulikova
- first_name: Aygul
full_name: Minnegalieva, Aygul
id: 87DF77F0-1D9A-11EA-B6AE-CE443DDC885E
last_name: Minnegalieva
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: 'Rella S, Kulikova YA, Minnegalieva A, Kondrashov F. Complex vaccination strategies
prevent the emergence of vaccine resistance. Evolution: International journal
of organic evolution. 2024;78(10):1722-1738. doi:10.1093/evolut/qpae106'
apa: 'Rella, S., Kulikova, Y. A., Minnegalieva, A., & Kondrashov, F. (2024).
Complex vaccination strategies prevent the emergence of vaccine resistance. Evolution:
International Journal of Organic Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpae106'
chicago: 'Rella, Simon, Yuliya A. Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov.
“Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.”
Evolution: International Journal of Organic Evolution. Oxford University
Press, 2024. https://doi.org/10.1093/evolut/qpae106.'
ieee: 'S. Rella, Y. A. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination
strategies prevent the emergence of vaccine resistance,” Evolution: International
journal of organic evolution, vol. 78, no. 10. Oxford University Press, pp.
1722–1738, 2024.'
ista: 'Rella S, Kulikova YA, Minnegalieva A, Kondrashov F. 2024. Complex vaccination
strategies prevent the emergence of vaccine resistance. Evolution: International
journal of organic evolution. 78(10), 1722–1738.'
mla: 'Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence
of Vaccine Resistance.” Evolution: International Journal of Organic Evolution,
vol. 78, no. 10, Oxford University Press, 2024, pp. 1722–38, doi:10.1093/evolut/qpae106.'
short: 'S. Rella, Y.A. Kulikova, A. Minnegalieva, F. Kondrashov, Evolution: International
Journal of Organic Evolution 78 (2024) 1722–1738.'
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: Results and figures derive from the model, described in
detail in the main text. The code is available at github.com/Simon-Re/complex-vaccination.
date_created: 2024-10-13T22:01:50Z
date_published: 2024-10-01T00:00:00Z
date_updated: 2026-10-02T10:12:20Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1093/evolut/qpae106
external_id:
isi:
- '001286581900001'
pmid:
- '38990788'
file:
- access_level: open_access
checksum: 5c6e8475bb88b07d424a5130d5e91e74
content_type: application/pdf
creator: dernst
date_created: 2024-10-21T09:34:50Z
date_updated: 2024-10-21T09:34:50Z
file_id: '18453'
file_name: 2024_Evolution_Rella.pdf
file_size: 29360811
relation: main_file
success: 1
file_date_updated: 2024-10-21T09:34:50Z
fulldoi: https://doi.org/10.1093/evolut/qpae106
has_accepted_license: '1'
intvolume: ' 78'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1722-1738
pmid: 1
publication: 'Evolution: International journal of organic evolution'
publication_identifier:
eissn:
- 1558-5646
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/Simon-Re/complex-vaccination
record:
- id: '14862'
relation: research_data
status: public
- id: '20811'
relation: dissertation_contains
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Complex vaccination strategies prevent the emergence of vaccine resistance
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 78
year: '2024'
...
---
APC_amount: 6468 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '14793'
abstract:
- lang: eng
text: Superconductor/semiconductor hybrid devices have attracted increasing interest
in the past years. Superconducting electronics aims to complement semiconductor
technology, while hybrid architectures are at the forefront of new ideas such
as topological superconductivity and protected qubits. In this work, we engineer
the induced superconductivity in two-dimensional germanium hole gas by varying
the distance between the quantum well and the aluminum. We demonstrate a hard
superconducting gap and realize an electrically and flux tunable superconducting
diode using a superconducting quantum interference device (SQUID). This allows
to tune the current phase relation (CPR), to a regime where single Cooper pair
tunneling is suppressed, creating a sin(2y) CPR. Shapiro experiments complement
this interpretation and the microwave drive allows to create a diode with ≈ 100%
efficiency. The reported results open up the path towards integration of spin
qubit devices, microwave resonators and (protected) superconducting qubits on the
same silicon technology compatible platform.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: "We acknowledge Alexander Brinkmann, Alessandro Crippa, Francesco
Giazotto, Andrew Higginbotham, Andrea Iorio, Giordano Scappucci, Christian Schonenberger,
and Lukas Splitthoff for helpful discussions. We thank Marcel Verheijen for the
support in the TEM analysis. This research and related results were made possible
with the support of the NOMIS\r\nFoundation. It was supported by the Scientific
Service Units of ISTA through resources provided by the MIBA Machine Shop and the
nanofabrication facility, the European Union’s Horizon 2020 research andinnovation
programme under Grant Agreement No 862046, the HORIZONRIA\r\n101069515 project,
the European Innovation Council Pathfinder grant no. 101115315 (QuKiT), and the
FWF Projects #P-32235, #P-36507 and #F-8606. For the purpose of open access, the
authors have applied a CC BY public copyright licence to any Author Accepted Manuscript
version arising from this submission. R.S.S. acknowledges Spanish CM “Talento Program\"\r\nProject
No. 2022-T1/IND-24070. J.J. acknowledges European Research Council TOCINA 834290."
article_number: '169'
article_processing_charge: Yes
article_type: original
author:
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
- first_name: Oliver
full_name: Sagi, Oliver
id: 71616374-A8E9-11E9-A7CA-09ECE5697425
last_name: Sagi
- first_name: Levon
full_name: Baghumyan, Levon
id: 7aa1f788-b527-11ee-aa9e-e6111a79e0c7
last_name: Baghumyan
- first_name: Thijs
full_name: de Gijsel, Thijs
id: a0ece13c-b527-11ee-929d-bad130106eee
last_name: de Gijsel
- first_name: Jason
full_name: Jung, Jason
id: 4C9ACE7A-F248-11E8-B48F-1D18A9856A87
last_name: Jung
- first_name: Stefano
full_name: Calcaterra, Stefano
last_name: Calcaterra
- first_name: Andrea
full_name: Ballabio, Andrea
last_name: Ballabio
- first_name: Juan L
full_name: Aguilera Servin, Juan L
id: 2A67C376-F248-11E8-B48F-1D18A9856A87
last_name: Aguilera Servin
orcid: 0000-0002-2862-8372
- first_name: Kushagra
full_name: Aggarwal, Kushagra
id: b22ab905-3539-11eb-84c3-fc159dcd79cb
last_name: Aggarwal
orcid: 0000-0001-9985-9293
- first_name: Marian
full_name: Janik, Marian
id: 396A1950-F248-11E8-B48F-1D18A9856A87
last_name: Janik
orcid: 0009-0003-9037-8831
- first_name: Thomas
full_name: Adletzberger, Thomas
id: 38756BB2-F248-11E8-B48F-1D18A9856A87
last_name: Adletzberger
- first_name: Rubén
full_name: Seoane Souto, Rubén
last_name: Seoane Souto
- first_name: Martin
full_name: Leijnse, Martin
last_name: Leijnse
- first_name: Jeroen
full_name: Danon, Jeroen
last_name: Danon
- first_name: Constantin
full_name: Schrade, Constantin
last_name: Schrade
- first_name: Erik
full_name: Bakkers, Erik
last_name: Bakkers
- first_name: Daniel
full_name: Chrastina, Daniel
last_name: Chrastina
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Valentini M, Sagi O, Baghumyan L, et al. Parity-conserving Cooper-pair transport
and ideal superconducting diode in planar germanium. Nature Communications.
2024;15. doi:10.1038/s41467-023-44114-0
apa: Valentini, M., Sagi, O., Baghumyan, L., de Gijsel, T., Jung, J., Calcaterra,
S., … Katsaros, G. (2024). Parity-conserving Cooper-pair transport and ideal superconducting
diode in planar germanium. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-44114-0
chicago: Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason
Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Parity-Conserving Cooper-Pair
Transport and Ideal Superconducting Diode in Planar Germanium.” Nature Communications.
Springer Nature, 2024. https://doi.org/10.1038/s41467-023-44114-0.
ieee: M. Valentini et al., “Parity-conserving Cooper-pair transport and ideal
superconducting diode in planar germanium,” Nature Communications, vol.
15. Springer Nature, 2024.
ista: Valentini M, Sagi O, Baghumyan L, de Gijsel T, Jung J, Calcaterra S, Ballabio
A, Aguilera Servin JL, Aggarwal K, Janik M, Adletzberger T, Seoane Souto R, Leijnse
M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. 2024. Parity-conserving
Cooper-pair transport and ideal superconducting diode in planar germanium. Nature
Communications. 15, 169.
mla: Valentini, Marco, et al. “Parity-Conserving Cooper-Pair Transport and Ideal
Superconducting Diode in Planar Germanium.” Nature Communications, vol.
15, 169, Springer Nature, 2024, doi:10.1038/s41467-023-44114-0.
short: M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra,
A. Ballabio, J.L. Aguilera Servin, K. Aggarwal, M. Janik, T. Adletzberger, R.
Seoane Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella,
G. Katsaros, Nature Communications 15 (2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: All experimental data included in this work are available
at https://zenodo.org/records/10119346.
date_created: 2024-01-14T23:00:56Z
date_published: 2024-01-02T00:00:00Z
date_updated: 2026-10-02T10:23:53Z
day: '02'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1038/s41467-023-44114-0
ec_funded: 1
external_id:
isi:
- '001142794000839'
pmid:
- '38167818'
file:
- access_level: open_access
checksum: ef79173b45eeaf984ffa61ef2f8a52ab
content_type: application/pdf
creator: dernst
date_created: 2024-01-17T11:03:00Z
date_updated: 2024-01-17T11:03:00Z
file_id: '14825'
file_name: 2024_NatureComm_Valentini.pdf
file_size: 2336595
relation: main_file
success: 1
file_date_updated: 2024-01-17T11:03:00Z
fulldoi: https://doi.org/10.1038/s41467-023-44114-0
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 237E5020-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862046'
name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS
- _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452
grant_number: '101069515'
name: Integrated Germanium Quantum Technology
- _id: bdc2ca30-d553-11ed-ba76-cf164a5bb811
grant_number: '101115315'
name: Quantum bits with Kitaev Transmons
- _id: 237B3DA4-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: P32235
name: Towards scalable hut wire quantum devices
- _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a
grant_number: P36507
name: Merging spin and superconducting qubits in planar Ge
- _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e
grant_number: F8606
name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems:
Conventional and unconventional topological superconductors'
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13312'
relation: earlier_version
status: public
- id: '23036'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Parity-conserving Cooper-pair transport and ideal superconducting diode in
planar germanium
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18902'
acknowledgement: 'MZ is supported by National Science Center, Poland, 2021/42/E/NZ2/00188,
the Polish National Agency for Academic Exchange, and by a grant from the Priority
Research Area DigiWorld under the Strategic Programme Excellence Initiative at Jagiellonian
University. Work in JB’s lab is supported by the Francis Crick Institute, which
receives its core funding from Cancer Research UK, the UK Medical Research Council
and Wellcome Trust (all under CC001051). Work in the AK lab is supported by ISTA,
the European Research Council under Horizon Europe: grant 101044579, and Austrian
Science Fund (FWF): F78 (Neural Stem Cell Modulation).'
article_number: '929'
article_processing_charge: Yes
article_type: letter_note
author:
- first_name: Marcin
full_name: Zagorski, Marcin
last_name: Zagorski
- first_name: Nathalie
full_name: Brandenberg, Nathalie
last_name: Brandenberg
- first_name: Matthias
full_name: Lutolf, Matthias
last_name: Lutolf
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: Zagorski M, Brandenberg N, Lutolf M, et al. Assessing the precision of morphogen
gradients in neural tube development. Nature Communications. 2024;15. doi:10.1038/s41467-024-45148-8
apa: Zagorski, M., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, M. T., Briscoe,
J., & Kicheva, A. (2024). Assessing the precision of morphogen gradients in
neural tube development. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-45148-8
chicago: Zagorski, Marcin, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik,
Mark Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Assessing the Precision
of Morphogen Gradients in Neural Tube Development.” Nature Communications.
Springer Nature, 2024. https://doi.org/10.1038/s41467-024-45148-8.
ieee: M. Zagorski et al., “Assessing the precision of morphogen gradients
in neural tube development,” Nature Communications, vol. 15. Springer Nature,
2024.
ista: Zagorski M, Brandenberg N, Lutolf M, Tkačik G, Bollenbach MT, Briscoe J, Kicheva
A. 2024. Assessing the precision of morphogen gradients in neural tube development.
Nature Communications. 15, 929.
mla: Zagorski, Marcin, et al. “Assessing the Precision of Morphogen Gradients in
Neural Tube Development.” Nature Communications, vol. 15, 929, Springer
Nature, 2024, doi:10.1038/s41467-024-45148-8.
short: M. Zagorski, N. Brandenberg, M. Lutolf, G. Tkačik, M.T. Bollenbach, J. Briscoe,
A. Kicheva, Nature Communications 15 (2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: Source data for Figs. 1, 2 is provided in the Source data
file. All published data is available from us to interested researchers. Source
data are provided with this paper.
date_created: 2025-01-27T13:01:01Z
date_published: 2024-02-01T00:00:00Z
date_updated: 2026-10-02T10:12:59Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
- _id: AnKi
doi: 10.1038/s41467-024-45148-8
external_id:
isi:
- '001156218500022'
pmid:
- '38302459'
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isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa
grant_number: '101044579'
name: Mechanisms of tissue size regulation in spinal cord development
- _id: 059DF620-7A3F-11EA-A408-12923DDC885E
grant_number: F7802
name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen
control of growth and pattern in the spinal cord
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Assessing the precision of morphogen gradients in neural tube development
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2024'
...
---
DOAJ_listed: '1'
_id: '15320'
abstract:
- lang: eng
text: Josephson diodes are superconducting elements that show an asymmetry in the
critical current depending on the direction of the current. Here, we theoretically
explore how an alternating current bias can tune the response of such a diode.
We show that for slow driving there is always a regime where the system can only
carry zero-voltage dc current in one direction, thus effectively behaving as an
ideal Josephson diode. Under fast driving, the diode efficiency is also tunable,
although the ideal regime cannot be reached in this case. We also investigate
the residual dissipation due to the time-dependent current bias and show that
it remains small. All our conclusions are solely based on the critical current
asymmetry of the junction, and are thus compatible with any Josephson diode.
acknowledgement: "We acknowledge support from research grants Spanish CM Talento Program
(Project No. 2022-T1/IND-24070), Spanish Ministry of Science, innovation, and Universities
through Grant No. PID2022-140552NA-I00, Swedish Research Council under Grant Agreement
No. 2020-03412, the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation programme under Grant Agreement No. 856526, Nanolund,
FWF Project with [82],\r\nand Microsoft Corporation. "
article_number: L022002
article_processing_charge: Yes
article_type: letter_note
author:
- first_name: Rubén
full_name: Seoane Souto, Rubén
last_name: Seoane Souto
- first_name: Martin
full_name: Leijnse, Martin
last_name: Leijnse
- first_name: Constantin
full_name: Schrade, Constantin
last_name: Schrade
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: Jeroen
full_name: Danon, Jeroen
last_name: Danon
citation:
ama: Seoane Souto R, Leijnse M, Schrade C, Valentini M, Katsaros G, Danon J. Tuning
the Josephson diode response with an ac current. Physical Review Research.
2024;6(2). doi:10.1103/PhysRevResearch.6.L022002
apa: Seoane Souto, R., Leijnse, M., Schrade, C., Valentini, M., Katsaros, G., &
Danon, J. (2024). Tuning the Josephson diode response with an ac current. Physical
Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.L022002
chicago: Seoane Souto, Rubén, Martin Leijnse, Constantin Schrade, Marco Valentini,
Georgios Katsaros, and Jeroen Danon. “Tuning the Josephson Diode Response with
an Ac Current.” Physical Review Research. American Physical Society, 2024.
https://doi.org/10.1103/PhysRevResearch.6.L022002.
ieee: R. Seoane Souto, M. Leijnse, C. Schrade, M. Valentini, G. Katsaros, and J.
Danon, “Tuning the Josephson diode response with an ac current,” Physical Review
Research, vol. 6, no. 2. American Physical Society, 2024.
ista: Seoane Souto R, Leijnse M, Schrade C, Valentini M, Katsaros G, Danon J. 2024.
Tuning the Josephson diode response with an ac current. Physical Review Research.
6(2), L022002.
mla: Seoane Souto, Rubén, et al. “Tuning the Josephson Diode Response with an Ac
Current.” Physical Review Research, vol. 6, no. 2, L022002, American Physical
Society, 2024, doi:10.1103/PhysRevResearch.6.L022002.
short: R. Seoane Souto, M. Leijnse, C. Schrade, M. Valentini, G. Katsaros, J. Danon,
Physical Review Research 6 (2024).
das_tickbox: '0'
date_created: 2024-04-14T22:01:02Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2026-10-02T10:26:37Z
day: '01'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1103/PhysRevResearch.6.L022002
file:
- access_level: open_access
checksum: 7b9cb3b17d89f392bd582e30d7a72a29
content_type: application/pdf
creator: dernst
date_created: 2024-04-17T07:14:53Z
date_updated: 2024-04-17T07:14:53Z
file_id: '15327'
file_name: 2024_PhysReviewResearch_Souto.pdf
file_size: 1073544
relation: main_file
success: 1
file_date_updated: 2024-04-17T07:14:53Z
fulldoi: https://doi.org/10.1103/PhysRevResearch.6.L022002
has_accepted_license: '1'
intvolume: ' 6'
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Physical Review Research
publication_identifier:
eissn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Tuning the Josephson diode response with an ac current
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2024'
...
---
_id: '17389'
abstract:
- lang: eng
text: The potential of Si and SiGe-based devices for the scaling of quantum circuits
is tainted by device variability. Each device needs to be tuned to operation conditions
and each device realisation requires a different tuning protocol. We demonstrate
that it is possible to automate the tuning of a 4-gate Si FinFET, a 5-gate GeSi
nanowire and a 7-gate Ge/SiGe heterostructure double quantum dot device from scratch
with the same algorithm. We achieve tuning times of 30, 10, and 92 min, respectively.
The algorithm also provides insight into the parameter space landscape for each
of these devices, allowing for the characterization of the regions where double
quantum dot regimes are found. These results show that overarching solutions for
the tuning of quantum devices are enabled by machine learning.
acknowledged_ssus:
- _id: NanoFab
acknowledgement: We acknowledge Ang Li, Erik P. A. M. Bakkers (University of Eindhoven)
for the fabrication of the Ge/Si nanowire. This work was supported by the Royal
Society, the EPSRC National Quantum Technology Hub in Networked Quantum Information
Technology (EP/M013243/1), Quantum Technology Capital (EP/N014995/1), EPSRC Platform
Grant (EP/R029229/1), the European Research Council (Grant agreement 948932), the
Swiss Nanoscience Institute, the NCCR SPIN, the EU H2020 European Microkelvin Platform
EMP grant No. 824109, the Scientific Service Units of IST Austria through resources
provided by the nanofabrication facility, the FWF-I 05060 and the FWF-P 30207 project.
article_number: '17281'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: B.
full_name: Severin, B.
last_name: Severin
- first_name: D. T.
full_name: Lennon, D. T.
last_name: Lennon
- first_name: L. C.
full_name: Camenzind, L. C.
last_name: Camenzind
- first_name: F.
full_name: Vigneau, F.
last_name: Vigneau
- first_name: F.
full_name: Fedele, F.
last_name: Fedele
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
- first_name: A.
full_name: Ballabio, A.
last_name: Ballabio
- first_name: D.
full_name: Chrastina, D.
last_name: Chrastina
- first_name: G.
full_name: Isella, G.
last_name: Isella
- first_name: M.
full_name: de Kruijf, M.
last_name: de Kruijf
- first_name: M. J.
full_name: Carballido, M. J.
last_name: Carballido
- first_name: S.
full_name: Svab, S.
last_name: Svab
- first_name: A. V.
full_name: Kuhlmann, A. V.
last_name: Kuhlmann
- first_name: S.
full_name: Geyer, S.
last_name: Geyer
- first_name: F. N. M.
full_name: Froning, F. N. M.
last_name: Froning
- first_name: H.
full_name: Moon, H.
last_name: Moon
- first_name: M. A.
full_name: Osborne, M. A.
last_name: Osborne
- first_name: D.
full_name: Sejdinovic, D.
last_name: Sejdinovic
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: D. M.
full_name: Zumbühl, D. M.
last_name: Zumbühl
- first_name: G. A. D.
full_name: Briggs, G. A. D.
last_name: Briggs
- first_name: N.
full_name: Ares, N.
last_name: Ares
citation:
ama: Severin B, Lennon DT, Camenzind LC, et al. Cross-architecture tuning of silicon
and SiGe-based quantum devices using machine learning. Scientific Reports.
2024;14. doi:10.1038/s41598-024-67787-z
apa: Severin, B., Lennon, D. T., Camenzind, L. C., Vigneau, F., Fedele, F., Jirovec,
D., … Ares, N. (2024). Cross-architecture tuning of silicon and SiGe-based quantum
devices using machine learning. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-024-67787-z
chicago: Severin, B., D. T. Lennon, L. C. Camenzind, F. Vigneau, F. Fedele, Daniel
Jirovec, A. Ballabio, et al. “Cross-Architecture Tuning of Silicon and SiGe-Based
Quantum Devices Using Machine Learning.” Scientific Reports. Springer Nature,
2024. https://doi.org/10.1038/s41598-024-67787-z.
ieee: B. Severin et al., “Cross-architecture tuning of silicon and SiGe-based
quantum devices using machine learning,” Scientific Reports, vol. 14. Springer
Nature, 2024.
ista: Severin B, Lennon DT, Camenzind LC, Vigneau F, Fedele F, Jirovec D, Ballabio
A, Chrastina D, Isella G, de Kruijf M, Carballido MJ, Svab S, Kuhlmann AV, Geyer
S, Froning FNM, Moon H, Osborne MA, Sejdinovic D, Katsaros G, Zumbühl DM, Briggs
GAD, Ares N. 2024. Cross-architecture tuning of silicon and SiGe-based quantum
devices using machine learning. Scientific Reports. 14, 17281.
mla: Severin, B., et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum
Devices Using Machine Learning.” Scientific Reports, vol. 14, 17281, Springer
Nature, 2024, doi:10.1038/s41598-024-67787-z.
short: B. Severin, D.T. Lennon, L.C. Camenzind, F. Vigneau, F. Fedele, D. Jirovec,
A. Ballabio, D. Chrastina, G. Isella, M. de Kruijf, M.J. Carballido, S. Svab,
A.V. Kuhlmann, S. Geyer, F.N.M. Froning, H. Moon, M.A. Osborne, D. Sejdinovic,
G. Katsaros, D.M. Zumbühl, G.A.D. Briggs, N. Ares, Scientific Reports 14 (2024).
das_tickbox: '1'
dataavailabilitystatement: The data acquired by the algorithm during experiments is
available from the corresponding author upon reasonable request.
date_created: 2024-08-05T08:50:51Z
date_published: 2024-07-27T00:00:00Z
date_updated: 2026-10-02T11:04:33Z
day: '27'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1038/s41598-024-67787-z
external_id:
arxiv:
- '2107.12975'
isi:
- '001281273100062'
pmid:
- '39068242'
file:
- access_level: open_access
checksum: 0b34b89e5f4f3f7b32ffadf104394594
content_type: application/pdf
creator: dernst
date_created: 2024-08-05T08:52:14Z
date_updated: 2024-08-05T08:52:14Z
file_id: '17390'
file_name: 2024_ScientificReports_Severin.pdf
file_size: 2255741
relation: main_file
success: 1
file_date_updated: 2024-08-05T08:52:14Z
fulldoi: https://doi.org/10.1038/s41598-024-67787-z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1
grant_number: I05060
name: High impedance circuit quantum electrodynamics with hole spins
- _id: 2641CE5E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P30207
name: Hole spin orbit qubits in Ge quantum wells
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '10066'
relation: earlier_version
status: public
researchdata_availability: upon request
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Cross-architecture tuning of silicon and SiGe-based quantum devices using machine
learning
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 14
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18602'
abstract:
- lang: eng
text: Semiconductor quantum dots (QDs) in planar germanium (Ge) heterostructures
have emerged as front-runners for future hole-based quantum processors. Here,
we present strong coupling between a hole charge qubit, defined in a double quantum
dot (DQD) in planar Ge, and microwave photons in a high-impedance (Zr = 1.3 kΩ)
resonator based on an array of superconducting quantum interference devices (SQUIDs).
Our investigation reveals vacuum-Rabi splittings with coupling strengths up to
g0/2π = 260 MHz, and a cooperativity of C ~ 100, dependent on DQD tuning. Furthermore,
utilizing the frequency tunability of our resonator, we explore the quenched energy
splitting associated with strong Coulomb correlation effects in Ge QDs. The observed
enhanced coherence of the strongly correlated excited state signals the presence
of distinct symmetries within related spin functions, serving as a precursor to
the strong coupling between photons and spin-charge hybrid qubits in planar Ge.
This work paves the way towards coherent quantum connections between remote hole
qubits in planar Ge, required to scale up hole-based quantum processors.
acknowledgement: The authors thank Simone Frasca, Vincent Jouanny, Guillaume Beaulieu,
Camille Roy, Dominic Dahinden, Davide Lombardo, Daniel Chrastina, and Siddhart Gautam
for contributing to some cleanroom fabrication steps, the measurement setup, device
simulations, data analysis, and for the useful discussions. P.S. acknowledges support
from the Swiss National Science Foundation (SNSF) through the grants Ref. No. 200021
200418 and Ref. No. 206021_205335, and from the Swiss State Secretariat for Education,
Research and Innovation (SERI) under contract number 01042765 SEFRI MB22.00081.
W.J. acknowledges support from the EPFL QSE Postdoctoral Fellowship Grant. S.B.,
D.L., and P.S. acknowledge support from the NCCR Spin Qubit in Silicon (NCCR-SPIN)
Grant No. 51NF40-180604. M.J., G.K., G.I., and S.C. acknowledge support from the
Horizon Europe Project IGNITE ID 101070193. G.K. acknowledges support from the FWF
via the P32235 and I05060 projects.
article_number: '10177'
article_processing_charge: Yes
article_type: original
author:
- first_name: Franco
full_name: De Palma, Franco
last_name: De Palma
- first_name: Fabian
full_name: Oppliger, Fabian
last_name: Oppliger
- first_name: Wonjin
full_name: Jang, Wonjin
last_name: Jang
- first_name: Stefano
full_name: Bosco, Stefano
last_name: Bosco
- first_name: Marian
full_name: Janik, Marian
id: 396A1950-F248-11E8-B48F-1D18A9856A87
last_name: Janik
orcid: 0009-0003-9037-8831
- first_name: Stefano
full_name: Calcaterra, Stefano
last_name: Calcaterra
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Daniel
full_name: Loss, Daniel
last_name: Loss
- first_name: Pasquale
full_name: Scarlino, Pasquale
last_name: Scarlino
citation:
ama: De Palma F, Oppliger F, Jang W, et al. Strong hole-photon coupling in planar
Ge for probing charge degree and strongly correlated states. Nature Communications.
2024;15. doi:10.1038/s41467-024-54520-7
apa: De Palma, F., Oppliger, F., Jang, W., Bosco, S., Janik, M., Calcaterra, S.,
… Scarlino, P. (2024). Strong hole-photon coupling in planar Ge for probing charge
degree and strongly correlated states. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-024-54520-7
chicago: De Palma, Franco, Fabian Oppliger, Wonjin Jang, Stefano Bosco, Marian Janik,
Stefano Calcaterra, Georgios Katsaros, Giovanni Isella, Daniel Loss, and Pasquale
Scarlino. “Strong Hole-Photon Coupling in Planar Ge for Probing Charge Degree
and Strongly Correlated States.” Nature Communications. Springer Nature,
2024. https://doi.org/10.1038/s41467-024-54520-7.
ieee: F. De Palma et al., “Strong hole-photon coupling in planar Ge for probing
charge degree and strongly correlated states,” Nature Communications, vol.
15. Springer Nature, 2024.
ista: De Palma F, Oppliger F, Jang W, Bosco S, Janik M, Calcaterra S, Katsaros G,
Isella G, Loss D, Scarlino P. 2024. Strong hole-photon coupling in planar Ge for
probing charge degree and strongly correlated states. Nature Communications. 15,
10177.
mla: De Palma, Franco, et al. “Strong Hole-Photon Coupling in Planar Ge for Probing
Charge Degree and Strongly Correlated States.” Nature Communications, vol.
15, 10177, Springer Nature, 2024, doi:10.1038/s41467-024-54520-7.
short: F. De Palma, F. Oppliger, W. Jang, S. Bosco, M. Janik, S. Calcaterra, G.
Katsaros, G. Isella, D. Loss, P. Scarlino, Nature Communications 15 (2024).
das_tickbox: '1'
dataavailabilitystatement: The datasets generated during the current study are available
in Zenodo with the identifier https://doi.org/10.5281/zenodo.13935167.
date_created: 2024-12-01T23:01:53Z
date_published: 2024-12-01T00:00:00Z
date_updated: 2026-10-02T11:02:23Z
day: '01'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1038/s41467-024-54520-7
external_id:
isi:
- '001362684200001'
pmid:
- '39580488'
file:
- access_level: open_access
checksum: ef9f99a84089c388904cc8aa8d89c55a
content_type: application/pdf
creator: dernst
date_created: 2024-12-03T11:00:15Z
date_updated: 2024-12-03T11:00:15Z
file_id: '18611'
file_name: 2024_NatureComm_dePalma.pdf
file_size: 5288092
relation: main_file
success: 1
file_date_updated: 2024-12-03T11:00:15Z
fulldoi: https://doi.org/10.1038/s41467-024-54520-7
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 237B3DA4-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: P32235
name: Towards scalable hut wire quantum devices
- _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1
grant_number: I05060
name: High impedance circuit quantum electrodynamics with hole spins
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '23037'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Strong hole-photon coupling in planar Ge for probing charge degree and strongly
correlated states
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18653'
abstract:
- lang: eng
text: Charge sensing is a sensitive technique for probing quantum devices, of particular
importance for spin-qubit readout. To achieve good readout sensitivities, the
proximity of the charge sensor to the device to be measured is a necessity. However,
this proximity also means that the operation of the device affects, in turn, the
sensor tuning and ultimately the readout sensitivity. We present an approach for
compensating for this crosstalk effect allowing for the gate voltages of the measured
device to be swept in a 1-V × 1-V window while maintaining a sensor configuration
chosen by a Bayesian optimizer. Our algorithm will hopefully be a major contribution
to the suite of fully automated solutions required for the operation of large
quantum device architectures.
acknowledged_ssus:
- _id: NanoFab
acknowledgement: We thank Nicholas Sim for providing help with the experiment and
Sebastian Orbell for helpful discussions. This work was supported by the Royal Society,
the Engineering and Physical Sciences Research Council (EPSRC) National Quantum
Technology Hub in Networked Quantum Information Technology (Grant No. EP/M013243/1),
Quantum Technology Capital (Grant No. EP/N014995/1), the EPSRC Platform Grant (Grant
No. EP/R029229/1), the European Research Council (Grant Agreement No. 948932), the
Scientific Service Units of the Institute of Science and Technology Austria through
resources provided by the nanofabrication facility and, the FWF-I 05060 and HORIZON-RIA
101069515 projects.
article_number: '064026'
article_processing_charge: No
article_type: original
author:
- first_name: Joseph
full_name: Hickie, Joseph
last_name: Hickie
- first_name: Barnaby
full_name: Van Straaten, Barnaby
last_name: Van Straaten
- first_name: Federico
full_name: Fedele, Federico
last_name: Fedele
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
- first_name: Andrea
full_name: Ballabio, Andrea
last_name: Ballabio
- first_name: Daniel
full_name: Chrastina, Daniel
last_name: Chrastina
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: Natalia
full_name: Ares, Natalia
last_name: Ares
citation:
ama: Hickie J, Van Straaten B, Fedele F, et al. Automated long-range compensation
of an rf quantum dot sensor. Physical Review Applied. 2024;22(6). doi:10.1103/PhysRevApplied.22.064026
apa: Hickie, J., Van Straaten, B., Fedele, F., Jirovec, D., Ballabio, A., Chrastina,
D., … Ares, N. (2024). Automated long-range compensation of an rf quantum dot
sensor. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.22.064026
chicago: Hickie, Joseph, Barnaby Van Straaten, Federico Fedele, Daniel Jirovec,
Andrea Ballabio, Daniel Chrastina, Giovanni Isella, Georgios Katsaros, and Natalia
Ares. “Automated Long-Range Compensation of an Rf Quantum Dot Sensor.” Physical
Review Applied. American Physical Society, 2024. https://doi.org/10.1103/PhysRevApplied.22.064026.
ieee: J. Hickie et al., “Automated long-range compensation of an rf quantum
dot sensor,” Physical Review Applied, vol. 22, no. 6. American Physical
Society, 2024.
ista: Hickie J, Van Straaten B, Fedele F, Jirovec D, Ballabio A, Chrastina D, Isella
G, Katsaros G, Ares N. 2024. Automated long-range compensation of an rf quantum
dot sensor. Physical Review Applied. 22(6), 064026.
mla: Hickie, Joseph, et al. “Automated Long-Range Compensation of an Rf Quantum
Dot Sensor.” Physical Review Applied, vol. 22, no. 6, 064026, American
Physical Society, 2024, doi:10.1103/PhysRevApplied.22.064026.
short: J. Hickie, B. Van Straaten, F. Fedele, D. Jirovec, A. Ballabio, D. Chrastina,
G. Isella, G. Katsaros, N. Ares, Physical Review Applied 22 (2024).
das_tickbox: '0'
date_created: 2024-12-15T23:01:50Z
date_published: 2024-12-01T00:00:00Z
date_updated: 2026-10-02T11:04:04Z
day: '01'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1103/PhysRevApplied.22.064026
external_id:
isi:
- '001379155900003'
file:
- access_level: open_access
checksum: bc29a40819abc4969867b6cd6563f7ad
content_type: application/pdf
creator: dernst
date_created: 2024-12-16T11:13:48Z
date_updated: 2024-12-16T11:13:48Z
file_id: '18662'
file_name: 2024_PhysicalReviewApplied_Hickie.pdf
file_size: 3560132
relation: main_file
success: 1
file_date_updated: 2024-12-16T11:13:48Z
fulldoi: https://doi.org/10.1103/PhysRevApplied.22.064026
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1
grant_number: I05060
name: High impedance circuit quantum electrodynamics with hole spins
- _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452
grant_number: '101069515'
name: Integrated Germanium Quantum Technology
publication: Physical Review Applied
publication_identifier:
eissn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Automated long-range compensation of an rf quantum dot sensor
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 22
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '23037'
abstract:
- lang: eng
text: The data for all figures in the main text can be found in csv files in ASCII
format in the corresponing folders. For Figures 4-6, the panels are numbered from
top to bottom.
article_processing_charge: No
author:
- first_name: Franco
full_name: De Palma, Franco
last_name: De Palma
- first_name: Fabian
full_name: Oppliger, Fabian
last_name: Oppliger
- first_name: Wonjin
full_name: Jang, Wonjin
last_name: Jang
- first_name: Stefano
full_name: Bosco, Stefano
last_name: Bosco
- first_name: Marián
full_name: Janík, Marián
last_name: Janík
- first_name: Stefano
full_name: Calcaterra, Stefano
last_name: Calcaterra
- first_name: Georgios
full_name: Katsaros, Georgios
last_name: Katsaros
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Daniel
full_name: Loss, Daniel
last_name: Loss
- first_name: Pasquale
full_name: Scarlino, Pasquale
last_name: Scarlino
citation:
ama: De Palma F, Oppliger F, Jang W, et al. Online data of “Strong hole-photon coupling
in planar Ge for probing charge degree and strongly correlated states.” 2024.
doi:10.5281/zenodo.13935166
apa: De Palma, F., Oppliger, F., Jang, W., Bosco, S., Janík, M., Calcaterra, S.,
… Scarlino, P. (2024). Online data of “Strong hole-photon coupling in planar Ge
for probing charge degree and strongly correlated states.” Zenodo. https://doi.org/10.5281/zenodo.13935166
chicago: De Palma, Franco, Fabian Oppliger, Wonjin Jang, Stefano Bosco, Marián Janík,
Stefano Calcaterra, Georgios Katsaros, Giovanni Isella, Daniel Loss, and Pasquale
Scarlino. “Online Data of ‘Strong Hole-Photon Coupling in Planar Ge for Probing
Charge Degree and Strongly Correlated States.’” Zenodo, 2024. https://doi.org/10.5281/zenodo.13935166.
ieee: F. De Palma et al., “Online data of ‘Strong hole-photon coupling in
planar Ge for probing charge degree and strongly correlated states.’” Zenodo,
2024.
ista: De Palma F, Oppliger F, Jang W, Bosco S, Janík M, Calcaterra S, Katsaros G,
Isella G, Loss D, Scarlino P. 2024. Online data of ‘Strong hole-photon coupling
in planar Ge for probing charge degree and strongly correlated states’, Zenodo,
10.5281/zenodo.13935166.
mla: De Palma, Franco, et al. Online Data of “Strong Hole-Photon Coupling in
Planar Ge for Probing Charge Degree and Strongly Correlated States.” Zenodo,
2024, doi:10.5281/zenodo.13935166.
short: F. De Palma, F. Oppliger, W. Jang, S. Bosco, M. Janík, S. Calcaterra, G.
Katsaros, G. Isella, D. Loss, P. Scarlino, (2024).
contributor:
- contributor_type: project_member
first_name: Fabian
last_name: Oppliger
date_created: 2026-10-02T11:02:18Z
date_published: 2024-10-15T00:00:00Z
date_updated: 2026-10-02T11:02:23Z
day: '15'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.5281/zenodo.13935166
fulldoi: https://doi.org/10.5281/zenodo.13935166
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.13935166
month: '10'
oa: 1
oa_version: None
publisher: Zenodo
related_material:
record:
- id: '18602'
relation: used_in_publication
status: public
status: public
title: Online data of "Strong hole-photon coupling in planar Ge for probing charge
degree and strongly correlated states"
type: research_data_reference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15018'
abstract:
- lang: eng
text: The epitaxial growth of a strained Ge layer, which is a promising candidate
for the channel material of a hole spin qubit, has been demonstrated on 300 mm
Si wafers using commercially available Si0.3Ge0.7 strain relaxed buffer (SRB)
layers. The assessment of the layer and the interface qualities for a buried strained
Ge layer embedded in Si0.3Ge0.7 layers is reported. The XRD reciprocal space mapping
confirmed that the reduction of the growth temperature enables the 2-dimensional
growth of the Ge layer fully strained with respect to the Si0.3Ge0.7. Nevertheless,
dislocations at the top and/or bottom interface of the Ge layer were observed
by means of electron channeling contrast imaging, suggesting the importance of
the careful dislocation assessment. The interface abruptness does not depend on
the selection of the precursor gases, but it is strongly influenced by the growth
temperature which affects the coverage of the surface H-passivation. The mobility
of 2.7 × 105 cm2/Vs is promising, while the low percolation density of 3 × 1010
/cm2 measured with a Hall-bar device at 7 K illustrates the high quality of the
heterostructure thanks to the high Si0.3Ge0.7 SRB quality.
acknowledgement: The Ge project received funding from the European Union's Horizon
Europe programme under the Grant Agreement 101069515 – IGNITE. Siltronic AG is acknowledged
for providing the SRB wafers. This work was supported by Imec's Industrial Affiliation
Program on Quantum Computing.
article_number: '108231'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Yosuke
full_name: Shimura, Yosuke
last_name: Shimura
- first_name: Clement
full_name: Godfrin, Clement
last_name: Godfrin
- first_name: Andriy
full_name: Hikavyy, Andriy
last_name: Hikavyy
- first_name: Roy
full_name: Li, Roy
last_name: Li
- first_name: Juan L
full_name: Aguilera Servin, Juan L
id: 2A67C376-F248-11E8-B48F-1D18A9856A87
last_name: Aguilera Servin
orcid: 0000-0002-2862-8372
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: Paola
full_name: Favia, Paola
last_name: Favia
- first_name: Han
full_name: Han, Han
last_name: Han
- first_name: Danny
full_name: Wan, Danny
last_name: Wan
- first_name: Kristiaan
full_name: de Greve, Kristiaan
last_name: de Greve
- first_name: Roger
full_name: Loo, Roger
last_name: Loo
citation:
ama: Shimura Y, Godfrin C, Hikavyy A, et al. Compressively strained epitaxial Ge
layers for quantum computing applications. Materials Science in Semiconductor
Processing. 2024;174(5). doi:10.1016/j.mssp.2024.108231
apa: Shimura, Y., Godfrin, C., Hikavyy, A., Li, R., Aguilera Servin, J. L., Katsaros,
G., … Loo, R. (2024). Compressively strained epitaxial Ge layers for quantum computing
applications. Materials Science in Semiconductor Processing. Elsevier.
https://doi.org/10.1016/j.mssp.2024.108231
chicago: Shimura, Yosuke, Clement Godfrin, Andriy Hikavyy, Roy Li, Juan L Aguilera
Servin, Georgios Katsaros, Paola Favia, et al. “Compressively Strained Epitaxial
Ge Layers for Quantum Computing Applications.” Materials Science in Semiconductor
Processing. Elsevier, 2024. https://doi.org/10.1016/j.mssp.2024.108231.
ieee: Y. Shimura et al., “Compressively strained epitaxial Ge layers for
quantum computing applications,” Materials Science in Semiconductor Processing,
vol. 174, no. 5. Elsevier, 2024.
ista: Shimura Y, Godfrin C, Hikavyy A, Li R, Aguilera Servin JL, Katsaros G, Favia
P, Han H, Wan D, de Greve K, Loo R. 2024. Compressively strained epitaxial Ge
layers for quantum computing applications. Materials Science in Semiconductor
Processing. 174(5), 108231.
mla: Shimura, Yosuke, et al. “Compressively Strained Epitaxial Ge Layers for Quantum
Computing Applications.” Materials Science in Semiconductor Processing,
vol. 174, no. 5, 108231, Elsevier, 2024, doi:10.1016/j.mssp.2024.108231.
short: Y. Shimura, C. Godfrin, A. Hikavyy, R. Li, J.L. Aguilera Servin, G. Katsaros,
P. Favia, H. Han, D. Wan, K. de Greve, R. Loo, Materials Science in Semiconductor
Processing 174 (2024).
das_tickbox: '1'
dataavailabilitystatement: No data was used for the research described in the article.
date_created: 2024-02-22T14:10:40Z
date_published: 2024-05-20T00:00:00Z
date_updated: 2026-10-02T11:06:21Z
day: '20'
ddc:
- '530'
department:
- _id: GeKa
- _id: NanoFab
doi: 10.1016/j.mssp.2024.108231
external_id:
isi:
- '001188520000001'
file:
- access_level: open_access
checksum: 62e8e9ae960387a3dca32ec7f5e413ab
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T11:56:08Z
date_updated: 2024-07-22T11:56:08Z
file_id: '17312'
file_name: 2024_MaterialsScience_Shimura.pdf
file_size: 4220165
relation: main_file
success: 1
file_date_updated: 2024-07-22T11:56:08Z
fulldoi: https://doi.org/10.1016/j.mssp.2024.108231
has_accepted_license: '1'
intvolume: ' 174'
isi: 1
issue: '5'
keyword:
- Mechanical Engineering
- Mechanics of Materials
- Condensed Matter Physics
- General Materials Science
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452
grant_number: '101069515'
name: Integrated Germanium Quantum Technology
publication: Materials Science in Semiconductor Processing
publication_identifier:
issn:
- 1369-8001
publication_status: published
publisher: Elsevier
quality_controlled: '1'
researchdata_availability: not applicable
scopus_import: '1'
status: public
supplementarymaterial: no
title: Compressively strained epitaxial Ge layers for quantum computing applications
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 174
year: '2024'
...
---
_id: '17136'
abstract:
- lang: eng
text: "This paper focuses on Majority Dynamics in sparse graphs, in particular,
as a\r\ntool to study internal cuts. It is known that, in Majority Dynamics on
a finite\r\ngraph, each vertex eventually either comes to a fixed state, or oscillates
with\r\nperiod two. The empirical evidence acquired by simulations suggests that
for\r\nrandom odd-regular graphs, approximately half of the vertices end up\r\noscillating
with high probability. We notice a local symmetry between\r\noscillating and non-oscillating
vertices, that potentially can explain why the\r\nfraction of the oscillating
vertices is concentrated around $\\frac{1}{2}$. In\r\nour simulations, we observe
that the parts of random odd-regular graph under\r\nMajority Dynamics with high
probability do not contain $\\lceil \\frac{d}{2}\r\n\\rceil$-cores at any timestep,
and thus, one cannot use Majority Dynamics to\r\nprove that internal cuts exist
in odd-regular graphs almost surely. However, we\r\nsuggest a modification of
Majority Dynamics, that yields parts with desired\r\ncores with high probability."
acknowledgement: "I am grateful to Matthew Kwan for setting the problem, providing
useful literature,\r\nfruitful discussions, text review, mentorship, general encouragement
and support."
article_number: '2406.07026'
article_processing_charge: No
arxiv: 1
author:
- first_name: Pavel
full_name: Arkhipov, Pavel
id: b25f2ab2-1fed-11ee-8599-fe02d211784f
last_name: Arkhipov
citation:
ama: 'Arkhipov P. Majority dynamics and internal partitions of random regular graphs:
Experimental results. arXiv. doi:10.48550/arXiv.2406.07026'
apa: 'Arkhipov, P. (n.d.). Majority dynamics and internal partitions of random regular
graphs: Experimental results. arXiv. https://doi.org/10.48550/arXiv.2406.07026'
chicago: 'Arkhipov, Pavel. “Majority Dynamics and Internal Partitions of Random
Regular Graphs: Experimental Results.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2406.07026.'
ieee: 'P. Arkhipov, “Majority dynamics and internal partitions of random regular
graphs: Experimental results,” arXiv. .'
ista: 'Arkhipov P. Majority dynamics and internal partitions of random regular graphs:
Experimental results. arXiv, 2406.07026.'
mla: 'Arkhipov, Pavel. “Majority Dynamics and Internal Partitions of Random Regular
Graphs: Experimental Results.” ArXiv, 2406.07026, doi:10.48550/arXiv.2406.07026.'
short: P. Arkhipov, ArXiv (n.d.).
das_tickbox: '0'
date_created: 2024-06-12T07:01:52Z
date_published: 2024-06-11T00:00:00Z
date_updated: 2026-10-02T11:06:38Z
day: '11'
department:
- _id: GradSch
doi: 10.48550/arXiv.2406.07026
external_id:
arxiv:
- '2406.07026'
fulldoi: https://doi.org/10.48550/arXiv.2406.07026
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2406.07026
month: '06'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
researchdata_availability: yes
status: public
supplementarymaterial: no
title: 'Majority dynamics and internal partitions of random regular graphs: Experimental
results'
type: preprint
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '18174'
abstract:
- lang: eng
text: We investigate the phase ordering (pattern formation) of systems of two-dimensional
core–shell particles using Monte Carlo (MC) computer simulations and classical
density functional theory (DFT). The particles interact via a pair potential having
a hard core and a repulsive square shoulder. Our simulations show that on cooling,
the liquid state structure becomes increasingly characterized by long wavelength
density modulations and on further cooling forms a variety of other phases, including
clustered, striped, and other patterned phases. In DFT, the hard core part of
the potential is treated using either fundamental measure theory or a simple local
density approximation, whereas the soft shoulder is treated using the random phase
approximation. The different DFTs are benchmarked using large-scale grand-canonical-MC
and Gibbs-ensemble-MC simulations, demonstrating their predictive capabilities
and shortcomings. We find that having the liquid state static structure factor
S(k) for wavenumber k is sufficient to identify the Fourier modes governing both
the liquid and solid phases. This allows us to identify from easier-to-obtain
liquid state data the wavenumbers relevant to the periodic phases and to predict
roughly where in the phase diagram these patterned phases arise.
acknowledgement: The computational results presented here were enabled via a generous
share of CPU time, offered by the Vienna Scientific Cluster (VSC) under Project
No. 71263. The authors thank Ms. Katrin Muck for her guidance related to the use
of HPC. A.J.A. gratefully acknowledges support from the EPSRC under Grant No. EP/P015689/1.
article_number: '124503 '
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Wassermair, Michael
id: 23d132c4-4e98-11ef-b275-9e8d4cd8c917
last_name: Wassermair
orcid: 0009-0003-6339-4051
- first_name: Gerhard
full_name: Kahl, Gerhard
last_name: Kahl
- first_name: Roland
full_name: Roth, Roland
last_name: Roth
- first_name: Andrew J.
full_name: Archer, Andrew J.
last_name: Archer
citation:
ama: Wassermair M, Kahl G, Roth R, Archer AJ. Fingerprints of ordered self-assembled
structures in the liquid phase of a hard-core, square-shoulder system. The
Journal of chemical physics. 2024;161(12). doi:10.1063/5.0226954
apa: Wassermair, M., Kahl, G., Roth, R., & Archer, A. J. (2024). Fingerprints
of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder
system. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0226954
chicago: Wassermair, Michael, Gerhard Kahl, Roland Roth, and Andrew J. Archer. “Fingerprints
of Ordered Self-Assembled Structures in the Liquid Phase of a Hard-Core, Square-Shoulder
System.” The Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0226954.
ieee: M. Wassermair, G. Kahl, R. Roth, and A. J. Archer, “Fingerprints of ordered
self-assembled structures in the liquid phase of a hard-core, square-shoulder
system,” The Journal of chemical physics, vol. 161, no. 12. AIP Publishing,
2024.
ista: Wassermair M, Kahl G, Roth R, Archer AJ. 2024. Fingerprints of ordered self-assembled
structures in the liquid phase of a hard-core, square-shoulder system. The Journal
of chemical physics. 161(12), 124503.
mla: Wassermair, Michael, et al. “Fingerprints of Ordered Self-Assembled Structures
in the Liquid Phase of a Hard-Core, Square-Shoulder System.” The Journal of
Chemical Physics, vol. 161, no. 12, 124503, AIP Publishing, 2024, doi:10.1063/5.0226954.
short: M. Wassermair, G. Kahl, R. Roth, A.J. Archer, The Journal of Chemical Physics
161 (2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The data that support the findings of this study are available
from the corresponding author upon reasonable request.
date_created: 2024-10-06T22:01:12Z
date_published: 2024-09-28T00:00:00Z
date_updated: 2026-10-02T11:10:03Z
day: '28'
ddc:
- '530'
department:
- _id: GradSch
doi: 10.1063/5.0226954
external_id:
arxiv:
- '2409.06447'
isi:
- '001325268300004'
pmid:
- '39344889'
file:
- access_level: open_access
checksum: f3874e64ef94e94b2376f00a1fee24c3
content_type: application/pdf
creator: dernst
date_created: 2024-10-07T11:25:00Z
date_updated: 2024-10-07T11:25:00Z
file_id: '18185'
file_name: 2024_JourChemicalPhysics_Wassermair.pdf
file_size: 15009000
relation: main_file
success: 1
file_date_updated: 2024-10-07T11:25:00Z
fulldoi: https://doi.org/10.1063/5.0226954
has_accepted_license: '1'
intvolume: ' 161'
isi: 1
issue: '12'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: The Journal of chemical physics
publication_identifier:
eissn:
- 1089-7690
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
researchdata_availability: upon request
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Fingerprints of ordered self-assembled structures in the liquid phase of a
hard-core, square-shoulder system
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 161
year: '2024'
...
---
_id: '14653'
abstract:
- lang: eng
text: 'Mass spectrometry imaging (MSI) is a powerful analytical technique for the
two-dimensional (2D) localization of chemicals on surfaces. Conventional MSI experiments
require to predefine the surface of interest based on photographic or microscopic
images. Typically, these boundaries can no longer be changed or adjusted once
the experiment has been started. In terms of a more interactive approach we recently
developed a pen-like ionization interface which is directly connected to the mass
spectrometer. The device allows the user to ionize chemicals by desorption electrospray
ionization (DESI) and to freely move the interface over a surface of interest.
A mini camera, which is mounted on the tip of the pen, magnifies the desorption
area and enables a simple positioning of the pen. The combination of optical data
from the camera module and chemical data obtained by mass analysis facilitates
a novel type of imaging experiment: interactive mass spectrometry imaging (IMSI).
For this application, we present a novel approach for a robust, optical flow-based
motion detection. While the live video stream from the camera is used to track
the pen''s motion across the surface a post-acquisition algorithm correlates the
coordinates of the pen trajectory with respective mass spectra obtained from a
simultaneous mass spectrometric data acquisition. This algorithm is no longer
dependent on a single, manually applied optical marker on the sample surface,
which has to be visible on all video frames throughout the analysis. The advanced
DESI-IMSI method was successfully tested on inkjet-printed letters as well as
mouse brain tissue samples. Validation of the results was done by comparing DESI-IMSI
with standard DESI-MSI data.'
acknowledgement: We would like to thank Marco Sealey Cardona, PhD for help with the
mouse brain samples and acknowledge the financial support by 1669 Förderkreis of
the University of Innsbruck, Austria Wirtschaftsservice (AWS), D. Swarovski KG and
Tyrolean Science Fund (TWF).
article_number: '117168'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Florian
full_name: Kluibenschedl, Florian
id: 7499e70e-eb2c-11ec-b98b-f925648bc9d9
last_name: Kluibenschedl
orcid: 0000-0003-4695-5526
- first_name: Anna
full_name: Ploner, Anna
last_name: Ploner
- first_name: Christina
full_name: Meisenbichler, Christina
last_name: Meisenbichler
- first_name: Robert
full_name: Konrat, Robert
last_name: Konrat
- first_name: Thomas
full_name: Müller, Thomas
last_name: Müller
citation:
ama: Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. Advanced motion
tracking for interactive mass spectrometry imaging (IMSI). International Journal
of Mass Spectrometry. 2024;495. doi:10.1016/j.ijms.2023.117168
apa: Kluibenschedl, F., Ploner, A., Meisenbichler, C., Konrat, R., & Müller,
T. (2024). Advanced motion tracking for interactive mass spectrometry imaging
(IMSI). International Journal of Mass Spectrometry. Elsevier. https://doi.org/10.1016/j.ijms.2023.117168
chicago: Kluibenschedl, Florian, Anna Ploner, Christina Meisenbichler, Robert Konrat,
and Thomas Müller. “Advanced Motion Tracking for Interactive Mass Spectrometry
Imaging (IMSI).” International Journal of Mass Spectrometry. Elsevier,
2024. https://doi.org/10.1016/j.ijms.2023.117168.
ieee: F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, and T. Müller, “Advanced
motion tracking for interactive mass spectrometry imaging (IMSI),” International
Journal of Mass Spectrometry, vol. 495. Elsevier, 2024.
ista: Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. 2024. Advanced
motion tracking for interactive mass spectrometry imaging (IMSI). International
Journal of Mass Spectrometry. 495, 117168.
mla: Kluibenschedl, Florian, et al. “Advanced Motion Tracking for Interactive Mass
Spectrometry Imaging (IMSI).” International Journal of Mass Spectrometry,
vol. 495, 117168, Elsevier, 2024, doi:10.1016/j.ijms.2023.117168.
short: F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, T. Müller, International
Journal of Mass Spectrometry 495 (2024).
das_tickbox: '1'
dataavailabilitystatement: Data will be made available on request.
date_created: 2023-12-10T23:00:57Z
date_published: 2024-01-01T00:00:00Z
date_updated: 2026-10-02T11:07:09Z
day: '01'
ddc:
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department:
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doi: 10.1016/j.ijms.2023.117168
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title: Advanced motion tracking for interactive mass spectrometry imaging (IMSI)
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