---
_id: '15186'
abstract:
- lang: eng
text: The elimination of rain evaporation in the planetary boundary layer (PBL)
has been found to lead to convective self‐aggregation (CSA) even without radiative
feedback, but the precise mechanisms underlying this phenomenon remain unclear.
We conducted cloud‐resolving simulations with two domain sizes and progressively
reduced rain evaporation in the PBL. Surprisingly, CSA only occurred when rain
evaporation was almost completely removed. The additional convective heating resulting
from the reduction of evaporative cooling in the moist patch was found to be the
trigger, thereafter a dry subsidence intrusion into the PBL in the dry patch takes
over and sets CSA in motion. Temperature and moisture anomalies oppose each other
in their buoyancy effects, hence explaining the need for almost total rain evaporation
removal. We also found radiative cooling and not cold pools to be the leading
cause for the comparative ease of CSA to take place in the larger domain.
acknowledgement: "YLH is supported by funding from the European Union's Horizon 2020
research and innovation programme under the Marie Skłodowska-Curie Grant 101034413.
CM gratefully acknowledges funding from the European Research Council (ERC) under
the European Union's Horizon 2020 research and innovation program (Project CLUSTER,
Grant 805041). The authors warmly thank Steven Sherwood, Jiawei Bao, Bidyut Goswami,
and Martin Janssens for stimulating and helpful discussions. They also thank Christopher
Holloway and an anonymous reviewer for providing helpful feedback that greatly improved
this manuscript.\r\n"
article_number: ' e2023GL106523'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Yi-Ling
full_name: Hwong, Yi-Ling
id: 1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22
last_name: Hwong
orcid: 0000-0001-9281-3479
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
citation:
ama: Hwong Y-L, Muller CJ. The unreasonable efficiency of total rain evaporation
removal in triggering convective self‐aggregation. Geophysical Research Letters.
2024;51(6). doi:10.1029/2023gl106523
apa: Hwong, Y.-L., & Muller, C. J. (2024). The unreasonable efficiency of total
rain evaporation removal in triggering convective self‐aggregation. Geophysical
Research Letters. American Geophysical Union. https://doi.org/10.1029/2023gl106523
chicago: Hwong, Yi-Ling, and Caroline J Muller. “The Unreasonable Efficiency of
Total Rain Evaporation Removal in Triggering Convective Self‐aggregation.” Geophysical
Research Letters. American Geophysical Union, 2024. https://doi.org/10.1029/2023gl106523.
ieee: Y.-L. Hwong and C. J. Muller, “The unreasonable efficiency of total rain evaporation
removal in triggering convective self‐aggregation,” Geophysical Research Letters,
vol. 51, no. 6. American Geophysical Union, 2024.
ista: Hwong Y-L, Muller CJ. 2024. The unreasonable efficiency of total rain evaporation
removal in triggering convective self‐aggregation. Geophysical Research Letters.
51(6), e2023GL106523.
mla: Hwong, Yi-Ling, and Caroline J. Muller. “The Unreasonable Efficiency of Total
Rain Evaporation Removal in Triggering Convective Self‐aggregation.” Geophysical
Research Letters, vol. 51, no. 6, e2023GL106523, American Geophysical Union,
2024, doi:10.1029/2023gl106523.
short: Y.-L. Hwong, C.J. Muller, Geophysical Research Letters 51 (2024).
date_created: 2024-03-25T10:27:30Z
date_published: 2024-03-19T00:00:00Z
date_updated: 2024-03-25T11:32:06Z
day: '19'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1029/2023gl106523
ec_funded: 1
file:
- access_level: open_access
checksum: eacb011091a503b9e7b748fef639ba4c
content_type: application/pdf
creator: dernst
date_created: 2024-03-25T11:28:25Z
date_updated: 2024-03-25T11:28:25Z
file_id: '15187'
file_name: 2024_GeophysResLetters_Hwong.pdf
file_size: 1280108
relation: main_file
success: 1
file_date_updated: 2024-03-25T11:28:25Z
has_accepted_license: '1'
intvolume: ' 51'
issue: '6'
keyword:
- General Earth and Planetary Sciences
- Geophysics
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: 629205d8-2b32-11ec-9570-e1356ff73576
call_identifier: H2020
grant_number: '805041'
name: organization of CLoUdS, and implications of Tropical cyclones and for the
Energetics of the tropics, in current and waRming climate
publication: Geophysical Research Letters
publication_identifier:
eissn:
- 1944-8007
issn:
- 0094-8276
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
status: public
title: The unreasonable efficiency of total rain evaporation removal in triggering
convective self‐aggregation
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2024'
...
---
_id: '15181'
abstract:
- lang: eng
text: We demonstrate the failure of the adiabatic Born-Oppenheimer approximation
to describe the ground state of a quantum impurity within an ultracold Fermi gas
despite substantial mass differences between the bath and impurity species. Increasing
repulsion leads to the appearance of nonadiabatic couplings between the fast bath
and slow impurity degrees of freedom, which reduce the parity symmetry of the
latter according to the pseudo Jahn-Teller effect. The presence of this mechanism
is associated to a conical intersection involving the impurity position and the
inverse of the interaction strength, which acts as a synthetic dimension. We elucidate
the presence of these effects via a detailed ground-state analysis involving the
comparison of ab initio fully correlated simulations with effective models. Our
study suggests ultracold atomic ensembles as potent emulators of complex molecular
phenomena.
acknowledgement: "This work has been funded by the Cluster of Excellence “Advanced
Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG) - EXC 2056 - Project
ID 390715994.\r\nG.M.K. gratefully acknowledges funding from the European Union’s
Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 101034413."
article_number: '013257'
article_processing_charge: Yes
article_type: original
author:
- first_name: A.
full_name: Becker, A.
last_name: Becker
- first_name: Georgios
full_name: Koutentakis, Georgios
id: d7b23d3a-9e21-11ec-b482-f76739596b95
last_name: Koutentakis
- first_name: P.
full_name: Schmelcher, P.
last_name: Schmelcher
citation:
ama: Becker A, Koutentakis G, Schmelcher P. Synthetic dimension-induced pseudo Jahn-Teller
effect in one-dimensional confined fermions. Physical Review Research.
2024;6(1). doi:10.1103/physrevresearch.6.013257
apa: Becker, A., Koutentakis, G., & Schmelcher, P. (2024). Synthetic dimension-induced
pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review
Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013257
chicago: Becker, A., Georgios Koutentakis, and P. Schmelcher. “Synthetic Dimension-Induced
Pseudo Jahn-Teller Effect in One-Dimensional Confined Fermions.” Physical Review
Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013257.
ieee: A. Becker, G. Koutentakis, and P. Schmelcher, “Synthetic dimension-induced
pseudo Jahn-Teller effect in one-dimensional confined fermions,” Physical Review
Research, vol. 6, no. 1. American Physical Society, 2024.
ista: Becker A, Koutentakis G, Schmelcher P. 2024. Synthetic dimension-induced pseudo
Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research.
6(1), 013257.
mla: Becker, A., et al. “Synthetic Dimension-Induced Pseudo Jahn-Teller Effect in
One-Dimensional Confined Fermions.” Physical Review Research, vol. 6, no.
1, 013257, American Physical Society, 2024, doi:10.1103/physrevresearch.6.013257.
short: A. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 6 (2024).
date_created: 2024-03-25T08:57:07Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2024-03-25T09:27:37Z
day: '01'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/physrevresearch.6.013257
ec_funded: 1
external_id:
arxiv:
- '2310.17995'
file:
- access_level: open_access
checksum: 4e0e58d1f58386fb016284c84db2a300
content_type: application/pdf
creator: dernst
date_created: 2024-03-25T09:24:55Z
date_updated: 2024-03-25T09:24:55Z
file_id: '15183'
file_name: 2024_PhysicalReviewResearch_Becker.pdf
file_size: 2207067
relation: main_file
success: 1
file_date_updated: 2024-03-25T09:24:55Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined
fermions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2024'
...
---
_id: '15182'
abstract:
- lang: eng
text: Thermoelectric materials convert heat into electricity, with a broad range
of applications near room temperature (RT). However, the library of RT high-performance
materials is limited. Traditional high-temperature synthetic methods constrain
the range of materials achievable, hindering the ability to surpass crystal structure
limitations and engineer defects. Here, a solution-based synthetic approach is
introduced, enabling RT synthesis of powders and exploration of densification
at lower temperatures to influence the material's microstructure. The approach
is exemplified by Ag2Se, an n-type alternative to bismuth telluride. It is demonstrated
that the concentration of Ag interstitials, grain boundaries, and dislocations
are directly correlated to the sintering temperature, and achieve a figure of
merit of 1.1 from RT to 100 °C after optimization. Moreover, insights into and
resolve Ag2Se's challenges are provided, including stoichiometry issues leading
to irreproducible performances. This work highlights the potential of RT solution
synthesis in expanding the repertoire of high-performance thermoelectric materials
for practical applications.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: NanoFab
acknowledgement: This work was supported by the Scientific Service Units (SSU) of
ISTA through resources provided by the Electron Microscopy Facility (EMF), the Lab
Support Facility (LSF), and the Nanofabrication Facility (NNF). This work was financially
supported by ISTA and the Werner Siemens Foundation. The USTEM Service Unit of the
Technical University of Vienna is acknowledged for EBSD sample preparation and analysis.
R.L.B. acknowledges the National Science Foundation for funding the mass spectrometry
analysis under award DMR 1904719. J.L. is a Serra Húnter Fellow and is grateful
to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and
GC 2021 SGR 01061.
article_number: '2400408'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Tobias
full_name: Kleinhanns, Tobias
id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425
last_name: Kleinhanns
- first_name: Francesco
full_name: Milillo, Francesco
id: 38b830db-ea88-11ee-bf9b-929beaf79054
last_name: Milillo
- first_name: Mariano
full_name: Calcabrini, Mariano
id: 45D7531A-F248-11E8-B48F-1D18A9856A87
last_name: Calcabrini
orcid: 0000-0003-4566-5877
- first_name: Christine
full_name: Fiedler, Christine
id: bd3fceba-dc74-11ea-a0a7-c17f71817366
last_name: Fiedler
- first_name: Sharona
full_name: Horta, Sharona
id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc
last_name: Horta
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Marissa J.
full_name: Strumolo, Marissa J.
last_name: Strumolo
- first_name: Roger
full_name: Hasler, Roger
last_name: Hasler
- first_name: Jordi
full_name: Llorca, Jordi
last_name: Llorca
- first_name: Michael
full_name: Tkadletz, Michael
last_name: Tkadletz
- first_name: Richard L.
full_name: Brutchey, Richard L.
last_name: Brutchey
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: 'Kleinhanns T, Milillo F, Calcabrini M, et al. A route to high thermoelectric
performance: Solution‐based control of microstructure and composition in Ag2Se.
Advanced Energy Materials. 2024. doi:10.1002/aenm.202400408'
apa: 'Kleinhanns, T., Milillo, F., Calcabrini, M., Fiedler, C., Horta, S., Balazs,
D., … Ibáñez, M. (2024). A route to high thermoelectric performance: Solution‐based
control of microstructure and composition in Ag2Se. Advanced Energy Materials.
Wiley. https://doi.org/10.1002/aenm.202400408'
chicago: 'Kleinhanns, Tobias, Francesco Milillo, Mariano Calcabrini, Christine Fiedler,
Sharona Horta, Daniel Balazs, Marissa J. Strumolo, et al. “A Route to High Thermoelectric
Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.”
Advanced Energy Materials. Wiley, 2024. https://doi.org/10.1002/aenm.202400408.'
ieee: 'T. Kleinhanns et al., “A route to high thermoelectric performance:
Solution‐based control of microstructure and composition in Ag2Se,” Advanced
Energy Materials. Wiley, 2024.'
ista: 'Kleinhanns T, Milillo F, Calcabrini M, Fiedler C, Horta S, Balazs D, Strumolo
MJ, Hasler R, Llorca J, Tkadletz M, Brutchey RL, Ibáñez M. 2024. A route to high
thermoelectric performance: Solution‐based control of microstructure and composition
in Ag2Se. Advanced Energy Materials., 2400408.'
mla: 'Kleinhanns, Tobias, et al. “A Route to High Thermoelectric Performance: Solution‐based
Control of Microstructure and Composition in Ag2Se.” Advanced Energy Materials,
2400408, Wiley, 2024, doi:10.1002/aenm.202400408.'
short: T. Kleinhanns, F. Milillo, M. Calcabrini, C. Fiedler, S. Horta, D. Balazs,
M.J. Strumolo, R. Hasler, J. Llorca, M. Tkadletz, R.L. Brutchey, M. Ibáñez, Advanced
Energy Materials (2024).
date_created: 2024-03-25T08:57:40Z
date_published: 2024-03-13T00:00:00Z
date_updated: 2024-03-25T09:21:05Z
day: '13'
department:
- _id: MaIb
- _id: LifeSc
doi: 10.1002/aenm.202400408
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/aenm.202400408
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: Advanced Energy Materials
publication_identifier:
eissn:
- 1614-6840
issn:
- 1614-6832
publication_status: epub_ahead
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A route to high thermoelectric performance: Solution‐based control of microstructure
and composition in Ag2Se'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '15165'
abstract:
- lang: eng
text: Current knowledge suggests a drought Indian monsoon (perhaps a severe one)
when the El Nino Southern Oscillation and Pacific Decadal Oscillation each exhibit
positive phases (a joint positive phase). For the monsoons, which are exceptions
in this regard, we found northeast India often gets excess pre-monsoon rainfall.
Further investigation reveals that this excess pre-monsoon rainfall is produced
by the interaction of the large-scale circulation associated with the joint phase
with the mountains in northeast India. We posit that a warmer troposphere, a consequence
of excess rainfall over northeast India, drives a stronger monsoon circulation
and enhances monsoon rainfall over central India. Hence, we argue that pre-monsoon
rainfall over northeast India can be used for seasonal monsoon rainfall prediction
over central India. Most importantly, its predictive value is at its peak when
the Pacific Ocean exhibits a joint positive phase and the threat of extreme drought
monsoon looms over India.
acknowledgement: The author gratefully acknowledges ISTA for supporting this research
through funding from the European Research Council (ERC) under the European Union’s
Horizon 2020 research and innovation programme (Project CLUSTER, grant agreement
No. 805041).
article_number: e2023GL106569
article_processing_charge: Yes
article_type: original
author:
- first_name: Bidyut B
full_name: Goswami, Bidyut B
id: 3a4ac09c-6d61-11ec-bf66-884cde66b64b
last_name: Goswami
orcid: 0000-0001-8602-3083
citation:
ama: GOSWAMI BB. A pre-monsoon signal of false alarms of Indian monsoon droughts.
Geophysical Research Letters. 2024;51(5). doi:10.1029/2023GL106569
apa: GOSWAMI, B. B. (2024). A pre-monsoon signal of false alarms of Indian monsoon
droughts. Geophysical Research Letters. Wiley. https://doi.org/10.1029/2023GL106569
chicago: GOSWAMI, BIDYUT B. “A Pre-Monsoon Signal of False Alarms of Indian Monsoon
Droughts.” Geophysical Research Letters. Wiley, 2024. https://doi.org/10.1029/2023GL106569.
ieee: B. B. GOSWAMI, “A pre-monsoon signal of false alarms of Indian monsoon droughts,”
Geophysical Research Letters, vol. 51, no. 5. Wiley, 2024.
ista: GOSWAMI BB. 2024. A pre-monsoon signal of false alarms of Indian monsoon droughts.
Geophysical Research Letters. 51(5), e2023GL106569.
mla: GOSWAMI, BIDYUT B. “A Pre-Monsoon Signal of False Alarms of Indian Monsoon
Droughts.” Geophysical Research Letters, vol. 51, no. 5, e2023GL106569,
Wiley, 2024, doi:10.1029/2023GL106569.
short: B.B. GOSWAMI, Geophysical Research Letters 51 (2024).
date_created: 2024-03-24T23:00:58Z
date_published: 2024-03-16T00:00:00Z
date_updated: 2024-03-25T10:00:57Z
day: '16'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1029/2023GL106569
ec_funded: 1
file:
- access_level: open_access
checksum: 243bd966aca968ec7d9e474af8639f8d
content_type: application/pdf
creator: dernst
date_created: 2024-03-25T08:36:00Z
date_updated: 2024-03-25T08:36:00Z
file_id: '15178'
file_name: 2024_GeophysResLetters_Goswami.pdf
file_size: 2887134
relation: main_file
success: 1
file_date_updated: 2024-03-25T08:36:00Z
has_accepted_license: '1'
intvolume: ' 51'
issue: '5'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 629205d8-2b32-11ec-9570-e1356ff73576
call_identifier: H2020
grant_number: '805041'
name: organization of CLoUdS, and implications of Tropical cyclones and for the
Energetics of the tropics, in current and waRming climate
publication: Geophysical Research Letters
publication_identifier:
eissn:
- 1944-8007
issn:
- 0094-8276
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: A pre-monsoon signal of false alarms of Indian monsoon droughts
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2024'
...
---
_id: '15146'
abstract:
- lang: eng
text: The extracellular matrix (ECM) serves as a scaffold for cells and plays an
essential role in regulating numerous cellular processes, including cell migration
and proliferation. Due to limitations in specimen preparation for conventional
room-temperature electron microscopy, we lack structural knowledge on how ECM
components are secreted, remodeled, and interact with surrounding cells. We have
developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion
beam milling, the lift-out extraction procedure, and cryo-electron tomography.
Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting
in a versatile tool closely mimicking ECM environments. This allows us to visualize
ECM for the first time in its hydrated, native context. Our data reveal an intricate
network of extracellular fibers, their positioning relative to matrix-secreting
cells, and previously unresolved structural entities. Our workflow and results
add to the structural atlas of the ECM, providing novel insights into its secretion
and assembly.
acknowledged_ssus:
- _id: LifeSc
- _id: ScienComp
- _id: EM-Fac
- _id: M-Shop
acknowledgement: "Open Access funding provided by IST Austria. We thank Armel Nicolas
and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante,
and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and
Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the
Miba Machine shop for their support. We also thank Wanda Kukulski (University of
Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group
for helpful discussions. Matt Swulius and Jessica Heebner provided great support
in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure
illustration.\r\n\r\nThis research was supported by the Scientific Service Units
of ISTA through resources provided by Scientific Computing, the Lab Support Facility,
and the Electron Microscopy Facility. We acknowledge funding support from the following
sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation
of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds
(to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the
European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt),
and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been
made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg
from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community
Foundation (to F.K.M. Schur)."
article_number: e202309125
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Jesse
full_name: Hansen, Jesse
id: 1063c618-6f9b-11ec-9123-f912fccded63
last_name: Hansen
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Vanessa
full_name: Zheden, Vanessa
id: 39C5A68A-F248-11E8-B48F-1D18A9856A87
last_name: Zheden
orcid: 0000-0002-9438-4783
- first_name: Jonna H
full_name: Alanko, Jonna H
id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87
last_name: Alanko
orcid: 0000-0002-7698-3061
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal
the ultrastructural landscape of extracellular matrix. Journal of Cell Biology.
2024;223(6). doi:10.1083/jcb.202309125
apa: Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V.,
… Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural
landscape of extracellular matrix. Journal of Cell Biology. Rockefeller
University Press. https://doi.org/10.1083/jcb.202309125
chicago: Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler,
Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and
Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural
Landscape of Extracellular Matrix.” Journal of Cell Biology. Rockefeller
University Press, 2024. https://doi.org/10.1083/jcb.202309125.
ieee: B. Zens et al., “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural
landscape of extracellular matrix,” Journal of Cell Biology, vol. 223,
no. 6. Rockefeller University Press, 2024.
ista: Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V,
Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the
ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6),
e202309125.
mla: Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural
Landscape of Extracellular Matrix.” Journal of Cell Biology, vol. 223,
no. 6, e202309125, Rockefeller University Press, 2024, doi:10.1083/jcb.202309125.
short: B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V.
Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024).
date_created: 2024-03-21T06:45:51Z
date_published: 2024-03-20T00:00:00Z
date_updated: 2024-03-25T13:03:57Z
day: '20'
ddc:
- '570'
department:
- _id: FlSc
- _id: MiSi
- _id: Bio
- _id: EM-Fac
doi: 10.1083/jcb.202309125
ec_funded: 1
external_id:
pmid:
- '38506714'
file:
- access_level: open_access
checksum: 90d1984a93660735e506c2a304bc3f73
content_type: application/pdf
creator: dernst
date_created: 2024-03-25T12:52:04Z
date_updated: 2024-03-25T12:52:04Z
file_id: '15188'
file_name: 2024_JCB_Zens.pdf
file_size: 11907016
relation: main_file
success: 1
file_date_updated: 2024-03-25T12:52:04Z
has_accepted_license: '1'
intvolume: ' 223'
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
- _id: 7bd318a1-9f16-11ee-852c-cc9217763180
grant_number: E435
name: In Situ Actin Structures via Hybrid Cryo-electron Microscopy
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
- _id: 059B463C-7A3F-11EA-A408-12923DDC885E
name: NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria
- _id: 2615199A-B435-11E9-9278-68D0E5697425
grant_number: '21317'
name: Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis
- _id: 62909c6f-2b32-11ec-9570-e1476aab5308
grant_number: CZI01
name: CryoMinflux-guided in-situ visual proteomics and structure determination
publication: Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular
matrix
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 223
year: '2024'
...
---
_id: '14931'
abstract:
- lang: eng
text: We prove an upper bound on the ground state energy of the dilute spin-polarized
Fermi gas capturing the leading correction to the kinetic energy resulting from
repulsive interactions. One of the main ingredients in the proof is a rigorous
implementation of the fermionic cluster expansion of Gaudin et al. (1971) [15].
acknowledgement: A.B.L. would like to thank Johannes Agerskov and Jan Philip Solovej
for valuable discussions. We thank Alessandro Giuliani for helpful discussions and
for pointing out the reference [18]. Funding from the European Union's Horizon 2020
research and innovation programme under the ERC grant agreement No 694227 is acknowledged.
Financial support by the Austrian Science Fund (FWF) through project number I 6427-N
(as part of the SFB/TRR 352) is gratefully acknowledged.
article_number: '110320'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Lauritsen AB, Seiringer R. Ground state energy of the dilute spin-polarized
Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis.
2024;286(7). doi:10.1016/j.jfa.2024.110320'
apa: 'Lauritsen, A. B., & Seiringer, R. (2024). Ground state energy of the dilute
spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional
Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2024.110320'
chicago: 'Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy
of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal
of Functional Analysis. Elsevier, 2024. https://doi.org/10.1016/j.jfa.2024.110320.'
ieee: 'A. B. Lauritsen and R. Seiringer, “Ground state energy of the dilute spin-polarized
Fermi gas: Upper bound via cluster expansion,” Journal of Functional Analysis,
vol. 286, no. 7. Elsevier, 2024.'
ista: 'Lauritsen AB, Seiringer R. 2024. Ground state energy of the dilute spin-polarized
Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis.
286(7), 110320.'
mla: 'Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of
the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal
of Functional Analysis, vol. 286, no. 7, 110320, Elsevier, 2024, doi:10.1016/j.jfa.2024.110320.'
short: A.B. Lauritsen, R. Seiringer, Journal of Functional Analysis 286 (2024).
date_created: 2024-02-04T23:00:53Z
date_published: 2024-01-24T00:00:00Z
date_updated: 2024-03-28T10:54:02Z
day: '24'
department:
- _id: RoSe
doi: 10.1016/j.jfa.2024.110320
ec_funded: 1
external_id:
arxiv:
- '2301.04894'
intvolume: ' 286'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.jfa.2024.110320
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b
grant_number: I06427
name: Mathematical Challenges in BCS Theory of Superconductivity
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096--0783
issn:
- 0022-1236
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via
cluster expansion'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 286
year: '2024'
...
---
_id: '12428'
abstract:
- lang: eng
text: The mammary gland consists of a bilayered epithelial structure with an extensively
branched morphology. The majority of this epithelial tree is laid down during
puberty, during which actively proliferating terminal end buds repeatedly elongate
and bifurcate to form the basic structure of the ductal tree. Mammary ducts consist
of a basal and luminal cell layer with a multitude of identified sub-lineages
within both layers. The understanding of how these different cell lineages are
cooperatively driving branching morphogenesis is a problem of crossing multiple
scales, as this requires information on the macroscopic branched structure of
the gland, as well as data on single-cell dynamics driving the morphogenic program.
Here we describe a method to combine genetic lineage tracing with whole-gland
branching analysis. Quantitative data on the global organ structure can be used
to derive a model for mammary gland branching morphogenesis and provide a backbone
on which the dynamics of individual cell lineages can be simulated and compared
to lineage-tracing approaches. Eventually, these quantitative models and experiments
allow to understand the couplings between the macroscopic shape of the mammary
gland and the underlying single-cell dynamics driving branching morphogenesis.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Colinda L.G.J.
full_name: Scheele, Colinda L.G.J.
last_name: Scheele
citation:
ama: 'Hannezo EB, Scheele CLGJ. A Guide Toward Multi-scale and Quantitative Branching
Analysis in the Mammary Gland. In: Margadant C, ed. Cell Migration in Three
Dimensions. Vol 2608. MIMB. Springer Nature; 2023:183-205. doi:10.1007/978-1-0716-2887-4_12'
apa: Hannezo, E. B., & Scheele, C. L. G. J. (2023). A Guide Toward Multi-scale
and Quantitative Branching Analysis in the Mammary Gland. In C. Margadant (Ed.),
Cell Migration in Three Dimensions (Vol. 2608, pp. 183–205). Springer Nature.
https://doi.org/10.1007/978-1-0716-2887-4_12
chicago: Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale
and Quantitative Branching Analysis in the Mammary Gland.” In Cell Migration
in Three Dimensions, edited by Coert Margadant, 2608:183–205. MIMB. Springer
Nature, 2023. https://doi.org/10.1007/978-1-0716-2887-4_12.
ieee: E. B. Hannezo and C. L. G. J. Scheele, “A Guide Toward Multi-scale and Quantitative
Branching Analysis in the Mammary Gland,” in Cell Migration in Three Dimensions,
vol. 2608, C. Margadant, Ed. Springer Nature, 2023, pp. 183–205.
ista: 'Hannezo EB, Scheele CLGJ. 2023.A Guide Toward Multi-scale and Quantitative
Branching Analysis in the Mammary Gland. In: Cell Migration in Three Dimensions.
Methods in Molecular Biology, vol. 2608, 183–205.'
mla: Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale
and Quantitative Branching Analysis in the Mammary Gland.” Cell Migration in
Three Dimensions, edited by Coert Margadant, vol. 2608, Springer Nature, 2023,
pp. 183–205, doi:10.1007/978-1-0716-2887-4_12.
short: E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in
Three Dimensions, Springer Nature, 2023, pp. 183–205.
date_created: 2023-01-29T23:00:58Z
date_published: 2023-01-19T00:00:00Z
date_updated: 2023-02-03T10:58:56Z
day: '19'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1007/978-1-0716-2887-4_12
editor:
- first_name: Coert
full_name: Margadant, Coert
last_name: Margadant
external_id:
pmid:
- '36653709'
file:
- access_level: open_access
checksum: aec1b8d3ba938ddf9d8fcb777f3c38ee
content_type: application/pdf
creator: dernst
date_created: 2023-02-03T10:56:39Z
date_updated: 2023-02-03T10:56:39Z
file_id: '12500'
file_name: 2023_MIMB_Hannezo.pdf
file_size: 826598
relation: main_file
success: 1
file_date_updated: 2023-02-03T10:56:39Z
has_accepted_license: '1'
intvolume: ' 2608'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 183-205
pmid: 1
publication: Cell Migration in Three Dimensions
publication_identifier:
eisbn:
- '9781071628874'
eissn:
- 1940-6029
isbn:
- '9781071628867'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary
Gland
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: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2608
year: '2023'
...
---
_id: '12534'
abstract:
- lang: eng
text: Brownian motion of a mobile impurity in a bath is affected by spin-orbit coupling
(SOC). Here, we discuss a Caldeira-Leggett-type model that can be used to propose
and interpret quantum simulators of this problem in cold Bose gases. First, we
derive a master equation that describes the model and explore it in a one-dimensional
(1D) setting. To validate the standard assumptions needed for our derivation,
we analyze available experimental data without SOC; as a byproduct, this analysis
suggests that the quench dynamics of the impurity is beyond the 1D Bose-polaron
approach at temperatures currently accessible in a cold-atom laboratory—motion
of the impurity is mainly driven by dissipation. For systems with SOC, we demonstrate
that 1D spin-orbit coupling can be gauged out even in the presence of dissipation—the
information about SOC is incorporated in the initial conditions. Observables sensitive
to this information (such as spin densities) can be used to study formation of
steady spin polarization domains during quench dynamics.
acknowledgement: "We thank Rafael Barfknecht for help at the initial stages of this
project; Fabian Brauneis for useful discussions; Miguel A. Garcia-March, Georgios
Koutentakis, and Simeon Mistakidis\r\nfor comments on the paper. M.L. acknowledges
support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON)."
article_number: '013029'
article_processing_charge: No
article_type: original
author:
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Alberto
full_name: Cappellaro, Alberto
id: 9d13b3cb-30a2-11eb-80dc-f772505e8660
last_name: Cappellaro
orcid: 0000-0001-6110-2359
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. Dissipative dynamics of
an impurity with spin-orbit coupling. Physical Review Research. 2023;5(1).
doi:10.1103/physrevresearch.5.013029
apa: Ghazaryan, A., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Dissipative
dynamics of an impurity with spin-orbit coupling. Physical Review Research.
American Physical Society. https://doi.org/10.1103/physrevresearch.5.013029
chicago: Ghazaryan, Areg, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev.
“Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review
Research. American Physical Society, 2023. https://doi.org/10.1103/physrevresearch.5.013029.
ieee: A. Ghazaryan, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Dissipative dynamics
of an impurity with spin-orbit coupling,” Physical Review Research, vol.
5, no. 1. American Physical Society, 2023.
ista: Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. 2023. Dissipative dynamics
of an impurity with spin-orbit coupling. Physical Review Research. 5(1), 013029.
mla: Ghazaryan, Areg, et al. “Dissipative Dynamics of an Impurity with Spin-Orbit
Coupling.” Physical Review Research, vol. 5, no. 1, 013029, American Physical
Society, 2023, doi:10.1103/physrevresearch.5.013029.
short: A. Ghazaryan, A. Cappellaro, M. Lemeshko, A. Volosniev, Physical Review Research
5 (2023).
date_created: 2023-02-10T09:02:26Z
date_published: 2023-01-20T00:00:00Z
date_updated: 2023-02-20T07:02:00Z
day: '20'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/physrevresearch.5.013029
ec_funded: 1
file:
- access_level: open_access
checksum: 6068b62874c0099628a108bb9c5c6bd2
content_type: application/pdf
creator: dernst
date_created: 2023-02-13T10:38:10Z
date_updated: 2023-02-13T10:38:10Z
file_id: '12546'
file_name: 2023_PhysicalReviewResearch_Ghazaryan.pdf
file_size: 865150
relation: main_file
success: 1
file_date_updated: 2023-02-13T10:38:10Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dissipative dynamics of an impurity with spin-orbit coupling
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2023'
...
---
_id: '12158'
abstract:
- lang: eng
text: 'Post-translational histone modifications modulate chromatin activity to affect
gene expression. How chromatin states underlie lineage choice in single cells
is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage
(sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3)
histone modifications in the mouse bone marrow. During differentiation, hematopoietic
stem and progenitor cells (HSPCs) acquire active chromatin states mediated by
cell-type-specifying transcription factors, which are unique for each lineage.
By contrast, most alterations in repressive marks during differentiation occur
independent of the final cell type. Chromatin trajectory analysis shows that lineage
choice at the chromatin level occurs at the progenitor stage. Joint profiling
of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage
have distinct active chromatin but share similar myeloid-specific heterochromatin
states. This implies a hierarchical regulation of chromatin during hematopoiesis:
heterochromatin dynamics distinguish differentiation trajectories and lineages,
while euchromatin dynamics reflect cell types within lineages.'
acknowledgement: We thank A. Giladi for sharing mRNA abundance tables of cell types
together with J. van den Berg for critical reading of the manuscript. We thank M.
Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich
Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973).
Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström
under CC-BY-SA 3.0 license. This work was supported by European Research Council
Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor
Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991),
HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z.
The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF
(ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which
is partly financed by the Dutch Cancer Society. The funders had no role in study
design, data collection and analysis, decision to publish or preparation of the
manuscript.
article_processing_charge: No
article_type: review
author:
- first_name: Peter
full_name: Zeller, Peter
last_name: Zeller
- first_name: Jake
full_name: Yeung, Jake
id: 123012b2-db30-11eb-b4d8-a35840c0551b
last_name: Yeung
orcid: 0000-0003-1732-1559
- first_name: Helena
full_name: Viñas Gaza, Helena
last_name: Viñas Gaza
- first_name: Buys Anton
full_name: de Barbanson, Buys Anton
last_name: de Barbanson
- first_name: Vivek
full_name: Bhardwaj, Vivek
last_name: Bhardwaj
- first_name: Maria
full_name: Florescu, Maria
last_name: Florescu
- first_name: Reinier
full_name: van der Linden, Reinier
last_name: van der Linden
- first_name: Alexander
full_name: van Oudenaarden, Alexander
last_name: van Oudenaarden
citation:
ama: Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical
chromatin dynamics during hematopoiesis. Nature Genetics. 2023;55:333-345.
doi:10.1038/s41588-022-01260-3
apa: Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu,
M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical
chromatin dynamics during hematopoiesis. Nature Genetics. Springer Nature.
https://doi.org/10.1038/s41588-022-01260-3
chicago: Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson,
Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden.
“Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.”
Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-022-01260-3.
ieee: P. Zeller et al., “Single-cell sortChIC identifies hierarchical chromatin
dynamics during hematopoiesis,” Nature Genetics, vol. 55. Springer Nature,
pp. 333–345, 2023.
ista: Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M,
van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical
chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.
mla: Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin
Dynamics during Hematopoiesis.” Nature Genetics, vol. 55, Springer Nature,
2023, pp. 333–45, doi:10.1038/s41588-022-01260-3.
short: P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu,
R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.
date_created: 2023-01-12T12:09:09Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2023-02-27T07:48:24Z
day: '01'
ddc:
- '570'
- '000'
department:
- _id: ScienComp
doi: 10.1038/s41588-022-01260-3
file:
- access_level: open_access
checksum: 6fdb8e34fbeea63edd0f2c6c2cc5823e
content_type: application/pdf
creator: dernst
date_created: 2023-02-27T07:46:45Z
date_updated: 2023-02-27T07:46:45Z
file_id: '12688'
file_name: 2023_NatureGenetics_Zeller.pdf
file_size: 21484855
relation: main_file
success: 1
file_date_updated: 2023-02-27T07:46:45Z
has_accepted_license: '1'
intvolume: ' 55'
keyword:
- Genetics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 333-345
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2023'
...
---
_id: '12676'
abstract:
- lang: eng
text: Turn-based stochastic games (aka simple stochastic games) are two-player zero-sum
games played on directed graphs with probabilistic transitions. The goal of player-max
is to maximize the probability to reach a target state against the adversarial
player-min. These games lie in NP ∩ coNP and are among the rare combinatorial
problems that belong to this complexity class for which the existence of polynomial-time
algorithm is a major open question. While randomized sub-exponential time algorithm
exists, all known deterministic algorithms require exponential time in the worst-case.
An important open question has been whether faster algorithms can be obtained
parametrized by the treewidth of the game graph. Even deterministic sub-exponential
time algorithm for constant treewidth turn-based stochastic games has remain elusive.
In this work our main result is a deterministic algorithm to solve turn-based
stochastic games that, given a game with n states, treewidth at most t, and the
bit-complexity of the probabilistic transition function log D, has running time
O ((tn2 log D)t log n). In particular, our algorithm is quasi-polynomial time
for games with constant or poly-logarithmic treewidth.
acknowledgement: This research was partially supported by the ERC CoG 863818 (ForM-SMArt)
grant.
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Raimundo J
full_name: Saona Urmeneta, Raimundo J
id: BD1DF4C4-D767-11E9-B658-BC13E6697425
last_name: Saona Urmeneta
orcid: 0000-0001-5103-038X
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
citation:
ama: 'Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. Faster algorithm
for turn-based stochastic games with bounded treewidth. In: Proceedings of
the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial
and Applied Mathematics; 2023:4590-4605. doi:10.1137/1.9781611977554.ch173'
apa: 'Chatterjee, K., Meggendorfer, T., Saona Urmeneta, R. J., & Svoboda, J.
(2023). Faster algorithm for turn-based stochastic games with bounded treewidth.
In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms
(pp. 4590–4605). Florence, Italy: Society for Industrial and Applied Mathematics.
https://doi.org/10.1137/1.9781611977554.ch173'
chicago: Chatterjee, Krishnendu, Tobias Meggendorfer, Raimundo J Saona Urmeneta,
and Jakub Svoboda. “Faster Algorithm for Turn-Based Stochastic Games with Bounded
Treewidth.” In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete
Algorithms, 4590–4605. Society for Industrial and Applied Mathematics, 2023.
https://doi.org/10.1137/1.9781611977554.ch173.
ieee: K. Chatterjee, T. Meggendorfer, R. J. Saona Urmeneta, and J. Svoboda, “Faster
algorithm for turn-based stochastic games with bounded treewidth,” in Proceedings
of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Florence, Italy,
2023, pp. 4590–4605.
ista: 'Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. 2023. Faster
algorithm for turn-based stochastic games with bounded treewidth. Proceedings
of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium
on Discrete Algorithms, 4590–4605.'
mla: Chatterjee, Krishnendu, et al. “Faster Algorithm for Turn-Based Stochastic
Games with Bounded Treewidth.” Proceedings of the 2023 Annual ACM-SIAM Symposium
on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023,
pp. 4590–605, doi:10.1137/1.9781611977554.ch173.
short: K. Chatterjee, T. Meggendorfer, R.J. Saona Urmeneta, J. Svoboda, in:, Proceedings
of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial
and Applied Mathematics, 2023, pp. 4590–4605.
conference:
end_date: 2023-01-25
location: Florence, Italy
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2023-01-22
date_created: 2023-02-24T12:20:47Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2023-02-27T09:01:16Z
day: '01'
department:
- _id: GradSch
- _id: KrCh
doi: 10.1137/1.9781611977554.ch173
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1137/1.9781611977554.ch173
month: '02'
oa: 1
oa_version: Published Version
page: 4590-4605
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
isbn:
- '9781611977554'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
status: public
title: Faster algorithm for turn-based stochastic games with bounded treewidth
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12735'
abstract:
- lang: eng
text: "Asynchronous programming has gained significant popularity over the last
decade: support for this programming pattern is available in many popular languages
via libraries and native language implementations, typically in the form of coroutines
or the async/await construct. Instead of programming via shared memory, this concept
assumes implicit synchronization through message passing. The key data structure
enabling such communication is the rendezvous channel. Roughly, a rendezvous channel
is a blocking queue of size zero, so both send(e) and receive() operations wait
for each other, performing a rendezvous when they meet. To optimize the message
passing pattern, channels are usually equipped with a fixed-size buffer, so sends
do not suspend and put elements into the buffer until its capacity is exceeded.
This primitive is known as a buffered channel.\r\n\r\nThis paper presents a fast
and scalable algorithm for both rendezvous and buffered channels. Similarly to
modern queues, our solution is based on an infinite array with two positional
counters for send(e) and receive() operations, leveraging the unconditional Fetch-And-Add
instruction to update them. Yet, the algorithm requires non-trivial modifications
of this classic pattern, in order to support the full channel semantics, such
as buffering and cancellation of waiting requests. We compare the performance
of our solution to that of the Kotlin implementation, as well as against other
academic proposals, showing up to 9.8× speedup. To showcase its expressiveness
and performance, we also integrated the proposed algorithm into the standard Kotlin
Coroutines library, replacing the previous channel implementations."
article_processing_charge: No
author:
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Roman
full_name: Elizarov, Roman
last_name: Elizarov
citation:
ama: 'Koval N, Alistarh D-A, Elizarov R. Fast and scalable channels in Kotlin Coroutines.
In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of
Parallel Programming. Association for Computing Machinery; 2023:107-118. doi:10.1145/3572848.3577481'
apa: 'Koval, N., Alistarh, D.-A., & Elizarov, R. (2023). Fast and scalable channels
in Kotlin Coroutines. In Proceedings of the ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming (pp. 107–118). Montreal, QC, Canada:
Association for Computing Machinery. https://doi.org/10.1145/3572848.3577481'
chicago: Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Fast and Scalable
Channels in Kotlin Coroutines.” In Proceedings of the ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming, 107–18. Association for
Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577481.
ieee: N. Koval, D.-A. Alistarh, and R. Elizarov, “Fast and scalable channels in
Kotlin Coroutines,” in Proceedings of the ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming, Montreal, QC, Canada, 2023, pp. 107–118.
ista: 'Koval N, Alistarh D-A, Elizarov R. 2023. Fast and scalable channels in Kotlin
Coroutines. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice
of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel
Programming, 107–118.'
mla: Koval, Nikita, et al. “Fast and Scalable Channels in Kotlin Coroutines.” Proceedings
of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
Association for Computing Machinery, 2023, pp. 107–18, doi:10.1145/3572848.3577481.
short: N. Koval, D.-A. Alistarh, R. Elizarov, in:, Proceedings of the ACM SIGPLAN
Symposium on Principles and Practice of Parallel Programming, Association for
Computing Machinery, 2023, pp. 107–118.
conference:
end_date: 2023-03-01
location: Montreal, QC, Canada
name: 'PPoPP: Sympopsium on Principles and Practice of Parallel Programming'
start_date: 2023-02-25
date_created: 2023-03-19T23:00:58Z
date_published: 2023-02-25T00:00:00Z
date_updated: 2023-03-20T07:29:28Z
day: '25'
department:
- _id: DaAl
doi: 10.1145/3572848.3577481
external_id:
arxiv:
- '2211.04986'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2211.04986
month: '02'
oa: 1
oa_version: Preprint
page: 107-118
publication: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of
Parallel Programming
publication_identifier:
isbn:
- '9798400700156'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast and scalable channels in Kotlin Coroutines
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12736'
abstract:
- lang: eng
text: Although a wide variety of handcrafted concurrent data structures have been
proposed, there is considerable interest in universal approaches (Universal Constructions
or UCs) for building concurrent data structures. UCs (semi-)automatically convert
a sequential data structure into a concurrent one. The simplest approach uses
locks [3, 6] that protect a sequential data structure and allow only one process
to access it at a time. However, the resulting data structure is blocking. Most
work on UCs instead focuses on obtaining non-blocking progress guarantees such
as obstruction-freedom, lock-freedom or wait-freedom. Many non-blocking UCs have
appeared. Key examples include the seminal wait-free UC [2] by Herlihy, a NUMA-aware
UC [10] by Yi et al., and an efficient UC for large objects [1] by Fatourou et
al.
acknowledgement: 'This work was supported by: the Natural Sciences and Engineering
Research Council of Canada (NSERC) Discovery Program grant: RGPIN-2019-04227, and
the Canada Foundation for Innovation John R. Evans Leaders Fund (CFI-JELF) with
equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512.'
article_processing_charge: No
author:
- first_name: Vitaly
full_name: Aksenov, Vitaly
last_name: Aksenov
- first_name: Trevor A
full_name: Brown, Trevor A
id: 3569F0A0-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Alexander
full_name: Fedorov, Alexander
id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6
last_name: Fedorov
- first_name: Ilya
full_name: Kokorin, Ilya
last_name: Kokorin
citation:
ama: Aksenov V, Brown TA, Fedorov A, Kokorin I. Unexpected Scaling in Path Copying
Trees. Association for Computing Machinery; 2023:438-440. doi:10.1145/3572848.3577512
apa: 'Aksenov, V., Brown, T. A., Fedorov, A., & Kokorin, I. (2023). Unexpected
scaling in path copying trees. Proceedings of the ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming (pp. 438–440). Montreal,
QB, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577512'
chicago: Aksenov, Vitaly, Trevor A Brown, Alexander Fedorov, and Ilya Kokorin. Unexpected
Scaling in Path Copying Trees. Proceedings of the ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming. Association for Computing
Machinery, 2023. https://doi.org/10.1145/3572848.3577512.
ieee: V. Aksenov, T. A. Brown, A. Fedorov, and I. Kokorin, Unexpected scaling
in path copying trees. Association for Computing Machinery, 2023, pp. 438–440.
ista: Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path
copying trees, Association for Computing Machinery,p.
mla: Aksenov, Vitaly, et al. “Unexpected Scaling in Path Copying Trees.” Proceedings
of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
Association for Computing Machinery, 2023, pp. 438–40, doi:10.1145/3572848.3577512.
short: V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path
Copying Trees, Association for Computing Machinery, 2023.
conference:
end_date: 2023-03-01
location: Montreal, QB, Canada
name: 'PPoPP: Sympopsium on Principles and Practice of Parallel Programming'
start_date: 2023-02-25
date_created: 2023-03-19T23:00:58Z
date_published: 2023-02-25T00:00:00Z
date_updated: 2023-03-20T07:57:27Z
day: '25'
department:
- _id: DaAl
- _id: GradSch
doi: 10.1145/3572848.3577512
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/3572848.3577512
month: '02'
oa: 1
oa_version: Published Version
page: 438-440
publication: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of
Parallel Programming
publication_identifier:
isbn:
- '9798400700156'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: Unexpected scaling in path copying trees
type: conference_poster
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12760'
abstract:
- lang: eng
text: "Dynamic programming (DP) is one of the fundamental paradigms in algorithm
design. However,\r\nmany DP algorithms have to fill in large DP tables, represented
by two-dimensional arrays, which causes at least quadratic running times and space
usages. This has led to the development of improved algorithms for special cases
when the DPs satisfy additional properties like, e.g., the Monge property or total
monotonicity.\r\nIn this paper, we consider a new condition which assumes (among
some other technical assumptions) that the rows of the DP table are monotone.
Under this assumption, we introduce\r\na novel data structure for computing (1
+ ϵ)-approximate DP solutions in near-linear time and\r\nspace in the static setting,
and with polylogarithmic update times when the DP entries change\r\ndynamically.
To the best of our knowledge, our new condition is incomparable to previous conditions
and is the first which allows to derive dynamic algorithms based on existing DPs.
Instead of using two-dimensional arrays to store the DP tables, we store the rows
of the DP tables using monotone piecewise constant functions. This allows us to
store length-n DP table rows with entries in [0, W] using only polylog(n, W) bits,
and to perform operations, such as (min, +)-convolution or rounding, on these
functions in polylogarithmic time.\r\nWe further present several applications
of our data structure. For bicriteria versions of k-balanced graph partitioning
and simultaneous source location, we obtain the first dynamic algorithms with
subpolynomial update times, as well as the first static algorithms using only
near-linear time and space. Additionally, we obtain the currently fastest algorithm
for fully dynamic knapsack."
acknowledgement: "Monika Henzinger: This project has received funding from the European
Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation
programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic
Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project
“Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional
funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nStefan Neumann: This research
is supported by the the ERC Advanced Grant REBOUND (834862) and the EC H2020 RIA
project SoBigData++ (871042).\r\nStefan Schmid: Research supported by Austrian Science
Fund (FWF) project I 5025-N (DELTA), 2020-2024."
alternative_title:
- LIPIcs
article_number: '36'
article_processing_charge: No
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Stefan
full_name: Neumann, Stefan
last_name: Neumann
- first_name: Harald
full_name: Räcke, Harald
last_name: Räcke
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
citation:
ama: 'Henzinger MH, Neumann S, Räcke H, Schmid S. Dynamic maintenance of monotone
dynamic programs and applications. In: 40th International Symposium on Theoretical
Aspects of Computer Science. Vol 254. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2023. doi:10.4230/LIPIcs.STACS.2023.36'
apa: 'Henzinger, M. H., Neumann, S., Räcke, H., & Schmid, S. (2023). Dynamic
maintenance of monotone dynamic programs and applications. In 40th International
Symposium on Theoretical Aspects of Computer Science (Vol. 254). Hamburg,
Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2023.36'
chicago: Henzinger, Monika H, Stefan Neumann, Harald Räcke, and Stefan Schmid. “Dynamic
Maintenance of Monotone Dynamic Programs and Applications.” In 40th International
Symposium on Theoretical Aspects of Computer Science, Vol. 254. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.STACS.2023.36.
ieee: M. H. Henzinger, S. Neumann, H. Räcke, and S. Schmid, “Dynamic maintenance
of monotone dynamic programs and applications,” in 40th International Symposium
on Theoretical Aspects of Computer Science, Hamburg, Germany, 2023, vol. 254.
ista: 'Henzinger MH, Neumann S, Räcke H, Schmid S. 2023. Dynamic maintenance of
monotone dynamic programs and applications. 40th International Symposium on Theoretical
Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer
Science, LIPIcs, vol. 254, 36.'
mla: Henzinger, Monika H., et al. “Dynamic Maintenance of Monotone Dynamic Programs
and Applications.” 40th International Symposium on Theoretical Aspects of Computer
Science, vol. 254, 36, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023, doi:10.4230/LIPIcs.STACS.2023.36.
short: M.H. Henzinger, S. Neumann, H. Räcke, S. Schmid, in:, 40th International
Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023.
conference:
end_date: 2023-03-09
location: Hamburg, Germany
name: 'STACS: Symposium on Theoretical Aspects of Computer Science'
start_date: 2023-03-07
date_created: 2023-03-26T22:01:07Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-03-27T06:46:27Z
day: '01'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.STACS.2023.36
external_id:
arxiv:
- '2301.01744'
file:
- access_level: open_access
checksum: 22141ab8bc55188e2dfff665e5daecbd
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T06:37:22Z
date_updated: 2023-03-27T06:37:22Z
file_id: '12769'
file_name: 2023_LIPICS_HenzingerM.pdf
file_size: 872706
relation: main_file
success: 1
file_date_updated: 2023-03-27T06:37:22Z
has_accepted_license: '1'
intvolume: ' 254'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: 40th International Symposium on Theoretical Aspects of Computer Science
publication_identifier:
isbn:
- '9783959772662'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic maintenance of monotone dynamic programs and 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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 254
year: '2023'
...
---
_id: '12716'
abstract:
- lang: eng
text: "The process of detecting and evaluating sensory information to guide behaviour
is termed perceptual decision-making (PDM), and is critical for the ability of
an organism to interact with its external world. Individuals with autism, a neurodevelopmental
condition primarily characterised by social and communication difficulties, frequently
exhibit altered sensory processing and PDM difficulties are widely reported. Recent
technological advancements have pushed forward our understanding of the genetic
changes accompanying this condition, however our understanding of how these mutations
affect the function of specific neuronal circuits and bring about the corresponding
behavioural changes remains limited. Here, we use an innate PDM task, the looming
avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality
across three molecularly distinct genetic mouse models of autism (Cul3, Setd5
and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli,
their responses are consistently delayed, requiring longer to initiate an appropriate
response than their wild-type siblings. Mutant animals show abnormal adaptation
in both their stimulus- evoked escape responses and exploratory dynamics following
repeated stimulus presentations. Similarly delayed behavioural responses are observed
in wild-type animals when faced with more ambiguous threats, suggesting the mutant
phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur
knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed
dissection of the neuronal mechanisms underlying the behavioural impairment. In
vivo extracellular recording revealed that visual responses were unaffected within
a key brain region for the rapid processing of visual threats, the superior colliculus
(SC), indicating that the behavioural delay was unlikely to originate from sensory
impairments. Delayed behavioural responses were recapitulated in the Setd5 model
following optogenetic stimulation of the excitatory output neurons of the SC,
which are known to mediate escape initiation through the activation of cells in
the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings
of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three
genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by
the misregulation of voltage-gated potassium channels. Overall, our results show
that the ability to use visual information to drive efficient escape responses
is impaired in three diverse genetic mouse models of autism and that, in one of
the models studied, this behavioural delay likely originates from differences
in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore,
this work showcases the use of an innate behavioural paradigm to mechanistically
dissect PDM processes in autism."
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: LifeSc
- _id: M-Shop
- _id: CampIT
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Laura
full_name: Burnett, Laura
id: 3B717F68-F248-11E8-B48F-1D18A9856A87
last_name: Burnett
orcid: 0000-0002-8937-410X
citation:
ama: Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate
rapid perceptual decision-making through subcortical circuits in mouse models
of autism. 2023. doi:10.15479/at:ista:12716
apa: Burnett, L. (2023). To flee, or not to flee? Using innate defensive behaviours
to investigate rapid perceptual decision-making through subcortical circuits in
mouse models of autism. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12716
chicago: Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours
to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in
Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12716.
ieee: L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to
investigate rapid perceptual decision-making through subcortical circuits in mouse
models of autism,” Institute of Science and Technology Austria, 2023.
ista: Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours
to investigate rapid perceptual decision-making through subcortical circuits in
mouse models of autism. Institute of Science and Technology Austria.
mla: Burnett, Laura. To Flee, or Not to Flee? Using Innate Defensive Behaviours
to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in
Mouse Models of Autism. Institute of Science and Technology Austria, 2023,
doi:10.15479/at:ista:12716.
short: L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to
Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse
Models of Autism, Institute of Science and Technology Austria, 2023.
date_created: 2023-03-08T15:19:45Z
date_published: 2023-03-10T00:00:00Z
date_updated: 2023-04-05T10:59:04Z
day: '10'
ddc:
- '599'
- '573'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaJö
doi: 10.15479/at:ista:12716
ec_funded: 1
file:
- access_level: closed
checksum: 6c6d9cc2c4cdacb74e6b1047a34d7332
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: lburnett
date_created: 2023-03-08T15:08:46Z
date_updated: 2023-03-08T15:08:46Z
file_id: '12717'
file_name: Burnett_Thesis_2023.docx
file_size: 23029260
relation: source_file
- access_level: open_access
checksum: cebc77705288bf4382db9b3541483cd0
content_type: application/pdf
creator: lburnett
date_created: 2023-03-08T15:08:46Z
date_updated: 2023-03-08T15:08:46Z
file_id: '12718'
file_name: Burnett_Thesis_2023_pdfA.pdf
file_size: 11959869
relation: main_file
success: 1
file_date_updated: 2023-03-08T15:08:46Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '178'
project:
- _id: 2634E9D2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '756502'
name: Circuits of Visual Attention
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
title: To flee, or not to flee? Using innate defensive behaviours to investigate rapid
perceptual decision-making through subcortical circuits in mouse models of autism
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '12854'
abstract:
- lang: eng
text: "The main idea behind BUBAAK is to run multiple program analyses in parallel
and use runtime monitoring and enforcement to observe and control their progress
in real time. The analyses send information about (un)explored states of the program
and discovered invariants to a monitor. The monitor processes the received data
and can force an analysis to stop the search of certain program parts (which have
already been analyzed by other analyses), or to make it utilize a program invariant
found by another analysis.\r\nAt SV-COMP 2023, the implementation of data exchange
between the monitor and the analyses was not yet completed, which is why BUBAAK
only ran several analyses in parallel, without any coordination. Still, BUBAAK
won the meta-category FalsificationOverall and placed very well in several other
(sub)-categories of the competition."
acknowledgement: This work was supported by the ERC-2020-AdG 10102009 grant.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Chalupa M, Henzinger TA. Bubaak: Runtime monitoring of program verifiers.
In: Tools and Algorithms for the Construction and Analysis of Systems.
Vol 13994. Springer Nature; 2023:535-540. doi:10.1007/978-3-031-30820-8_32'
apa: 'Chalupa, M., & Henzinger, T. A. (2023). Bubaak: Runtime monitoring of
program verifiers. In Tools and Algorithms for the Construction and Analysis
of Systems (Vol. 13994, pp. 535–540). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_32'
chicago: 'Chalupa, Marek, and Thomas A Henzinger. “Bubaak: Runtime Monitoring of
Program Verifiers.” In Tools and Algorithms for the Construction and Analysis
of Systems, 13994:535–40. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_32.'
ieee: 'M. Chalupa and T. A. Henzinger, “Bubaak: Runtime monitoring of program verifiers,”
in Tools and Algorithms for the Construction and Analysis of Systems, Paris,
France, 2023, vol. 13994, pp. 535–540.'
ista: 'Chalupa M, Henzinger TA. 2023. Bubaak: Runtime monitoring of program verifiers.
Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools
and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994,
535–540.'
mla: 'Chalupa, Marek, and Thomas A. Henzinger. “Bubaak: Runtime Monitoring of Program
Verifiers.” Tools and Algorithms for the Construction and Analysis of Systems,
vol. 13994, Springer Nature, 2023, pp. 535–40, doi:10.1007/978-3-031-30820-8_32.'
short: M. Chalupa, T.A. Henzinger, in:, Tools and Algorithms for the Construction
and Analysis of Systems, Springer Nature, 2023, pp. 535–540.
conference:
end_date: 2023-04-27
location: Paris, France
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2023-04-22
date_created: 2023-04-20T08:22:53Z
date_published: 2023-04-20T00:00:00Z
date_updated: 2023-04-25T07:02:43Z
day: '20'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-30820-8_32
ec_funded: 1
file:
- access_level: open_access
checksum: 120d2c2a38384058ad0630fdf8288312
content_type: application/pdf
creator: dernst
date_created: 2023-04-25T06:58:36Z
date_updated: 2023-04-25T06:58:36Z
file_id: '12864'
file_name: 2023_LNCS_Chalupa.pdf
file_size: 16096413
relation: main_file
success: 1
file_date_updated: 2023-04-25T06:58:36Z
has_accepted_license: '1'
intvolume: ' 13994'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 535-540
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Tools and Algorithms for the Construction and Analysis of Systems
publication_identifier:
eisbn:
- '9783031308208'
eissn:
- 1611-3349
isbn:
- '9783031308192'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Bubaak: Runtime monitoring of program verifiers'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13994
year: '2023'
...
---
_id: '12846'
abstract:
- lang: eng
text: We present a formula for the signed area of a spherical polygon via prequantization.
In contrast to the traditional formula based on the Gauss-Bonnet theorem that
requires measuring angles, the new formula mimics Green's theorem and is applicable
to a wider range of degenerate spherical curves and polygons.
acknowledgement: The authors acknowledge Chris Wojtan for his continuous support to
the present work through discussions and advice. The second author thanks Anna Sisak
for a fruitful discussion on prequantum bundles. This project was funded in part
by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).
article_number: '2303.14555'
article_processing_charge: No
author:
- first_name: Albert
full_name: Chern, Albert
last_name: Chern
- first_name: Sadashige
full_name: Ishida, Sadashige
id: 6F7C4B96-A8E9-11E9-A7CA-09ECE5697425
last_name: Ishida
citation:
ama: Chern A, Ishida S. Area formula for spherical polygons via prequantization.
arXiv. doi:10.48550/arXiv.2303.14555
apa: Chern, A., & Ishida, S. (n.d.). Area formula for spherical polygons via
prequantization. arXiv. https://doi.org/10.48550/arXiv.2303.14555
chicago: Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons
via Prequantization.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2303.14555.
ieee: A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,”
arXiv. .
ista: Chern A, Ishida S. Area formula for spherical polygons via prequantization.
arXiv, 2303.14555.
mla: Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via
Prequantization.” ArXiv, 2303.14555, doi:10.48550/arXiv.2303.14555.
short: A. Chern, S. Ishida, ArXiv (n.d.).
date_created: 2023-04-18T19:16:06Z
date_published: 2023-03-25T00:00:00Z
date_updated: 2023-04-25T06:51:21Z
day: '25'
department:
- _id: GradSch
- _id: ChWo
doi: 10.48550/arXiv.2303.14555
external_id:
arxiv:
- '2303.14555'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2303.14555
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
publication: arXiv
publication_status: submitted
status: public
title: Area formula for spherical polygons via prequantization
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12856'
abstract:
- lang: eng
text: "As the complexity and criticality of software increase every year, so does
the importance of run-time monitoring. Third-party monitoring, with limited knowledge
of the monitored software, and best-effort monitoring, which keeps pace with the
monitored software, are especially valuable, yet underexplored areas of run-time
monitoring. Most existing monitoring frameworks do not support their combination
because they either require access to the monitored code for instrumentation purposes
or the processing of all observed events, or both.\r\n\r\nWe present a middleware
framework, VAMOS, for the run-time monitoring of software which is explicitly
designed to support third-party and best-effort scenarios. The design goals of
VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the
ability to monitor black-box code through a variety of different event channels,
and the connectability to monitors written in different specification languages),
and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker
and event recognition systems with aspects of stream processing systems.\r\nWe
implemented a prototype toolchain for VAMOS and conducted experiments including
a case study of monitoring for data races. The results indicate that VAMOS enables
writing useful yet efficient monitors, is compatible with a variety of event sources
and monitor specifications, and simplifies key aspects of setting up a monitoring
system from scratch."
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093. The
authors would like to thank the anonymous FASE reviewers for their valuable feedback
and suggestions.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- first_name: Fabian
full_name: Mühlböck, Fabian
id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425
last_name: Mühlböck
orcid: 0000-0003-1548-0177
- first_name: Stefanie
full_name: Muroya Lei, Stefanie
id: a376de31-8972-11ed-ae7b-d0251c13c8ff
last_name: Muroya Lei
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. Vamos: Middleware for best-effort
third-party monitoring. In: Fundamental Approaches to Software Engineering.
Vol 13991. Springer Nature; 2023:260-281. doi:10.1007/978-3-031-30826-0_15'
apa: 'Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023).
Vamos: Middleware for best-effort third-party monitoring. In Fundamental Approaches
to Software Engineering (Vol. 13991, pp. 260–281). Paris, France: Springer
Nature. https://doi.org/10.1007/978-3-031-30826-0_15'
chicago: 'Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger.
“Vamos: Middleware for Best-Effort Third-Party Monitoring.” In Fundamental
Approaches to Software Engineering, 13991:260–81. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30826-0_15.'
ieee: 'M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “Vamos: Middleware
for best-effort third-party monitoring,” in Fundamental Approaches to Software
Engineering, Paris, France, 2023, vol. 13991, pp. 260–281.'
ista: 'Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. Vamos: Middleware
for best-effort third-party monitoring. Fundamental Approaches to Software Engineering.
FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13991, 260–281.'
mla: 'Chalupa, Marek, et al. “Vamos: Middleware for Best-Effort Third-Party Monitoring.”
Fundamental Approaches to Software Engineering, vol. 13991, Springer Nature,
2023, pp. 260–81, doi:10.1007/978-3-031-30826-0_15.'
short: M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, in:, Fundamental
Approaches to Software Engineering, Springer Nature, 2023, pp. 260–281.
conference:
end_date: 2023-04-27
location: Paris, France
name: 'FASE: Fundamental Approaches to Software Engineering'
start_date: 2023-04-22
date_created: 2023-04-20T08:29:42Z
date_published: 2023-04-20T00:00:00Z
date_updated: 2023-04-25T07:19:07Z
day: '20'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-30826-0_15
ec_funded: 1
file:
- access_level: open_access
checksum: 17a7c8e08be609cf2408d37ea55e322c
content_type: application/pdf
creator: dernst
date_created: 2023-04-25T07:16:36Z
date_updated: 2023-04-25T07:16:36Z
file_id: '12865'
file_name: 2023_LNCS_ChalupaM.pdf
file_size: 580828
relation: main_file
success: 1
file_date_updated: 2023-04-25T07:16:36Z
has_accepted_license: '1'
intvolume: ' 13991'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 260-281
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Fundamental Approaches to Software Engineering
publication_identifier:
eisbn:
- '9783031308260'
eissn:
- 1611-3349
isbn:
- '9783031308253'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '12407'
relation: earlier_version
status: public
status: public
title: 'Vamos: Middleware for best-effort third-party monitoring'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13991
year: '2023'
...
---
_id: '12407'
abstract:
- lang: eng
text: "As the complexity and criticality of software increase every year, so does
the importance of run-time monitoring. Third-party monitoring, with limited knowledge
of the monitored software, and best-effort monitoring, which keeps pace with the
monitored software, are especially valuable, yet underexplored areas of run-time
monitoring. Most existing monitoring frameworks do not support their combination
because they either require access to the monitored code for instrumentation purposes
or the processing of all observed events, or both.\r\n\r\nWe present a middleware
framework, VAMOS, for the run-time monitoring of software which is explicitly
designed to support third-party and best-effort scenarios. The design goals of
VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the
ability to monitor black-box code through a variety of different event channels,
and the connectability to monitors written in different specification languages),
and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker
and event recognition systems with aspects of stream processing systems.\r\n\r\nWe
implemented a prototype toolchain for VAMOS and conducted experiments including
a case study of monitoring for data races. The results indicate that VAMOS enables
writing useful yet efficient monitors, is compatible with a variety of event sources
and monitor specifications, and simplifies key aspects of setting up a monitoring
system from scratch."
acknowledgement: "This work was supported in part by the ERC-2020-AdG 101020093. \r\nThe
authors would like to thank the anonymous FASE reviewers for their valuable feedback
and suggestions."
alternative_title:
- IST Austria Technical Report
article_processing_charge: No
author:
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- first_name: Fabian
full_name: Mühlböck, Fabian
id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425
last_name: Mühlböck
orcid: 0000-0003-1548-0177
- first_name: Stefanie
full_name: Muroya Lei, Stefanie
id: a376de31-8972-11ed-ae7b-d0251c13c8ff
last_name: Muroya Lei
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. VAMOS: Middleware for
Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria;
2023. doi:10.15479/AT:ISTA:12407'
apa: 'Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023).
VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12407'
chicago: 'Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger.
VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of
Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12407.'
ieee: 'M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, VAMOS: Middleware
for Best-Effort Third-Party Monitoring. Institute of Science and Technology
Austria, 2023.'
ista: 'Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. VAMOS: Middleware
for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria,
38p.'
mla: 'Chalupa, Marek, et al. VAMOS: Middleware for Best-Effort Third-Party Monitoring.
Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12407.'
short: 'M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, VAMOS: Middleware
for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria,
2023.'
date_created: 2023-01-27T03:18:08Z
date_published: 2023-01-27T00:00:00Z
date_updated: 2023-04-25T07:19:06Z
day: '27'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.15479/AT:ISTA:12407
ec_funded: 1
file:
- access_level: open_access
checksum: 55426e463fdeafe9777fc3ff635154c7
content_type: application/pdf
creator: fmuehlbo
date_created: 2023-01-27T03:18:34Z
date_updated: 2023-01-27T03:18:34Z
file_id: '12408'
file_name: main.pdf
file_size: 662409
relation: main_file
success: 1
file_date_updated: 2023-01-27T03:18:34Z
has_accepted_license: '1'
keyword:
- runtime monitoring
- best effort
- third party
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '38'
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication_identifier:
eissn:
- 2664-1690
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12856'
relation: later_version
status: public
status: public
title: 'VAMOS: Middleware for Best-Effort Third-Party Monitoring'
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: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12668'
abstract:
- lang: eng
text: "Background: Plant and animal embryogenesis have conserved and distinct features.
Cell fate transitions occur during embryogenesis in both plants and animals. The
epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults:
Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis
of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific
and proximal–distal distinct chromatin accessibility and dynamics concordant with
transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3,
H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific
epigenomic dynamics during zygotic genome activation. Polycomb repressive complex
2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later
H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to
establish a permissive chromatin environment facilitating the access of transcription
factors to cis-elements for fate patterning. Embryonic maturation is characterized
by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates
in restricting totipotency while preventing extensive organogenesis. Finally,
epigenomic signatures are correlated with biased expression among homeolog triads
and divergent expression after polyploidization, revealing an epigenomic contributor
to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively,
we present an invaluable resource for comparative and mechanistic analysis of
the epigenomic regulation of crop embryogenesis."
article_number: '7'
article_processing_charge: No
article_type: original
author:
- first_name: Long
full_name: Zhao, Long
last_name: Zhao
- first_name: Yiman
full_name: Yang, Yiman
last_name: Yang
- first_name: Jinchao
full_name: Chen, Jinchao
last_name: Chen
- first_name: Xuelei
full_name: Lin, Xuelei
last_name: Lin
- first_name: Hao
full_name: Zhang, Hao
last_name: Zhang
- first_name: Hao
full_name: Wang, Hao
last_name: Wang
- first_name: Hongzhe
full_name: Wang, Hongzhe
last_name: Wang
- first_name: Xiaomin
full_name: Bie, Xiaomin
last_name: Bie
- first_name: Jiafu
full_name: Jiang, Jiafu
last_name: Jiang
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Xiangdong
full_name: Fu, Xiangdong
last_name: Fu
- first_name: Xiansheng
full_name: Zhang, Xiansheng
last_name: Zhang
- first_name: Zhuo
full_name: Du, Zhuo
last_name: Du
- first_name: Jun
full_name: Xiao, Jun
last_name: Xiao
citation:
ama: Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during
embryogenesis of hexaploid wheat. Genome Biology. 2023;24. doi:10.1186/s13059-022-02844-2
apa: Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023).
Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat.
Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-022-02844-2
chicago: Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang,
Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis
of Hexaploid Wheat.” Genome Biology. Springer Nature, 2023. https://doi.org/10.1186/s13059-022-02844-2.
ieee: L. Zhao et al., “Dynamic chromatin regulatory programs during embryogenesis
of hexaploid wheat,” Genome Biology, vol. 24. Springer Nature, 2023.
ista: Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng
X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during
embryogenesis of hexaploid wheat. Genome Biology. 24, 7.
mla: Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis
of Hexaploid Wheat.” Genome Biology, vol. 24, 7, Springer Nature, 2023,
doi:10.1186/s13059-022-02844-2.
short: L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J.
Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023).
date_created: 2023-02-23T09:13:49Z
date_published: 2023-01-13T00:00:00Z
date_updated: 2023-05-08T10:52:49Z
day: '13'
department:
- _id: XiFe
doi: 10.1186/s13059-022-02844-2
extern: '1'
external_id:
pmid:
- '36639687'
intvolume: ' 24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/s13059-022-02844-2
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
issn:
- 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2023'
...
---
_id: '12920'
abstract:
- lang: eng
text: The multicomponent approach allows to incorporate several functionalities
into a single covalent organic framework (COF) and consequently allows the construction
of bifunctional materials for cooperative catalysis. The well-defined structure
of such multicomponent COFs is furthermore ideally suited for structure-activity
relationship studies. We report a series of multicomponent COFs that contain acridine-
and 2,2’-bipyridine linkers connected through 1,3,5-benzenetrialdehyde derivatives.
The acridine motif is responsible for broad light absorption, while the bipyridine
unit enables complexation of nickel catalysts. These features enable the usage
of the framework materials as catalysts for light-mediated carbon−heteroatom cross-couplings.
Variation of the node units shows that the catalytic activity correlates to the
keto-enamine tautomer isomerism. This allows switching between high charge-carrier
mobility and persistent, localized charge-separated species depending on the nodes,
a tool to tailor the materials for specific reactions. Moreover, nickel-loaded
COFs are recyclable and catalyze cross-couplings even using red light irradiation.
article_number: e202202967
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Traxler, Michael
last_name: Traxler
- first_name: Susanne
full_name: Reischauer, Susanne
last_name: Reischauer
- first_name: Sarah
full_name: Vogl, Sarah
last_name: Vogl
- first_name: Jérôme
full_name: Roeser, Jérôme
last_name: Roeser
- first_name: Jabor
full_name: Rabeah, Jabor
last_name: Rabeah
- first_name: Christopher
full_name: Penschke, Christopher
last_name: Penschke
- first_name: Peter
full_name: Saalfrank, Peter
last_name: Saalfrank
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: Arne
full_name: Thomas, Arne
last_name: Thomas
citation:
ama: Traxler M, Reischauer S, Vogl S, et al. Programmable photocatalytic activity
of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry
– A European Journal. 2023;29(4). doi:10.1002/chem.202202967
apa: Traxler, M., Reischauer, S., Vogl, S., Roeser, J., Rabeah, J., Penschke, C.,
… Thomas, A. (2023). Programmable photocatalytic activity of multicomponent covalent
organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal.
Wiley. https://doi.org/10.1002/chem.202202967
chicago: Traxler, Michael, Susanne Reischauer, Sarah Vogl, Jérôme Roeser, Jabor
Rabeah, Christopher Penschke, Peter Saalfrank, Bartholomäus Pieber, and Arne Thomas.
“Programmable Photocatalytic Activity of Multicomponent Covalent Organic Frameworks
Used as Metallaphotocatalysts.” Chemistry – A European Journal. Wiley,
2023. https://doi.org/10.1002/chem.202202967.
ieee: M. Traxler et al., “Programmable photocatalytic activity of multicomponent
covalent organic frameworks used as metallaphotocatalysts,” Chemistry – A European
Journal, vol. 29, no. 4. Wiley, 2023.
ista: Traxler M, Reischauer S, Vogl S, Roeser J, Rabeah J, Penschke C, Saalfrank
P, Pieber B, Thomas A. 2023. Programmable photocatalytic activity of multicomponent
covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European
Journal. 29(4), e202202967.
mla: Traxler, Michael, et al. “Programmable Photocatalytic Activity of Multicomponent
Covalent Organic Frameworks Used as Metallaphotocatalysts.” Chemistry – A European
Journal, vol. 29, no. 4, e202202967, Wiley, 2023, doi:10.1002/chem.202202967.
short: M. Traxler, S. Reischauer, S. Vogl, J. Roeser, J. Rabeah, C. Penschke, P.
Saalfrank, B. Pieber, A. Thomas, Chemistry – A European Journal 29 (2023).
date_created: 2023-05-08T08:25:34Z
date_published: 2023-01-18T00:00:00Z
date_updated: 2023-05-15T08:39:24Z
day: '18'
doi: 10.1002/chem.202202967
extern: '1'
intvolume: ' 29'
issue: '4'
keyword:
- General Chemistry
- Catalysis
- Organic Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/chem.202202967
month: '01'
oa: 1
oa_version: Published Version
publication: Chemistry – A European Journal
publication_identifier:
eissn:
- 1521-3765
issn:
- 0947-6539
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Programmable photocatalytic activity of multicomponent covalent organic frameworks
used as metallaphotocatalysts
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2023'
...