---
OA_place: publisher
_id: '7460'
abstract:
- lang: eng
text: "Many methods for the reconstruction of shapes from sets of points produce
ordered simplicial complexes, which are collections of vertices, edges, triangles,
and their higher-dimensional analogues, called simplices, in which every simplex
gets assigned a real value measuring its size. This thesis studies ordered simplicial
complexes, with a focus on their topology, which reflects the connectedness of
the represented shapes and the presence of holes. We are interested both in understanding
better the structure of these complexes, as well as in developing algorithms for
applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure
for a simplex is the radius of the smallest empty circumsphere. Based on it, we
revisit Alpha and Wrap complexes and experimentally determine their probabilistic
properties for random data. Also, we prove the existence of tri-partitions, propose
algorithms to open and close holes, and extend the concepts from Euclidean to
Bregman geometries."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Katharina
full_name: Ölsböck, Katharina
id: 4D4AA390-F248-11E8-B48F-1D18A9856A87
last_name: Ölsböck
orcid: 0000-0002-4672-8297
citation:
ama: Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460
apa: Ölsböck, K. (2020). The hole system of triangulated shapes. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460
chicago: Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute
of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460.
ieee: K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science
and Technology Austria, 2020.
ista: Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science
and Technology Austria.
mla: Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute
of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460.
short: K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science
and Technology Austria, 2020.
corr_author: '1'
date_created: 2020-02-06T14:56:53Z
date_published: 2020-02-10T00:00:00Z
date_updated: 2026-04-08T07:23:21Z
day: '10'
ddc:
- '514'
degree_awarded: PhD
department:
- _id: HeEd
- _id: GradSch
doi: 10.15479/AT:ISTA:7460
file:
- access_level: open_access
checksum: 1df9f8c530b443c0e63a3f2e4fde412e
content_type: application/pdf
creator: koelsboe
date_created: 2020-02-06T14:43:54Z
date_updated: 2020-07-14T12:47:58Z
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file_name: thesis_ist-final_noack.pdf
file_size: 76195184
relation: main_file
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checksum: 7a52383c812b0be64d3826546509e5a4
content_type: application/x-zip-compressed
creator: koelsboe
date_created: 2020-02-06T14:52:45Z
date_updated: 2020-07-14T12:47:58Z
description: latex source files, figures
file_id: '7462'
file_name: latex-files.zip
file_size: 122103715
relation: source_file
file_date_updated: 2020-07-14T12:47:58Z
fulldoi: https://doi.org/10.15479/AT:ISTA:7460
has_accepted_license: '1'
keyword:
- shape reconstruction
- hole manipulation
- ordered complexes
- Alpha complex
- Wrap complex
- computational topology
- Bregman geometry
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '155'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6608'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: The hole system of triangulated shapes
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2020'
...
---
_id: '7464'
abstract:
- lang: eng
text: 'Retrovirus assembly is driven by the multidomain structural protein Gag.
Interactions between the capsid domains (CA) of Gag result in Gag multimerization,
leading to an immature virus particle that is formed by a protein lattice based
on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter-
and intra-hexamer contacts differ, especially in the N-terminal sub-domain of
CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts
with and stabilizes the immature hexamer, and is required for production of infectious
virus particles. We have used in vitro assembly, cryo-electron tomography and
subtomogram averaging, atomistic molecular dynamics simulations and mutational
analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV).
In particular, we sought to understand the structural conservation of the immature
lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6
strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles
(VLPs), which took three morphologically highly distinct forms: narrow tubes,
wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution
unexpectedly showed that all three morphologies are based on an immature lattice
with preserved key structural components, highlighting the structural versatility
of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed
that both lentiviruses maintain similar immature interfaces, which are established
by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates
immature assembly via conserved lysine residues within the CACTD and SP. Lastly,
we demonstrate that IP6 stimulates in vitro assembly of immature particles of
several other retroviruses in the lentivirus genus, suggesting a conserved role
for IP6 in lentiviral assembly.'
acknowledged_ssus:
- _id: ScienComp
article_number: e1008277
article_processing_charge: No
article_type: original
author:
- first_name: Robert A.
full_name: Dick, Robert A.
last_name: Dick
- first_name: Chaoyi
full_name: Xu, Chaoyi
last_name: Xu
- first_name: Dustin R.
full_name: Morado, Dustin R.
last_name: Morado
- first_name: Vladyslav
full_name: Kravchuk, Vladyslav
id: 4D62F2A6-F248-11E8-B48F-1D18A9856A87
last_name: Kravchuk
orcid: 0000-0001-9523-9089
- first_name: Clifton L.
full_name: Ricana, Clifton L.
last_name: Ricana
- first_name: Terri D.
full_name: Lyddon, Terri D.
last_name: Lyddon
- first_name: Arianna M.
full_name: Broad, Arianna M.
last_name: Broad
- first_name: J. Ryan
full_name: Feathers, J. Ryan
last_name: Feathers
- first_name: Marc C.
full_name: Johnson, Marc C.
last_name: Johnson
- first_name: Volker M.
full_name: Vogt, Volker M.
last_name: Vogt
- first_name: Juan R.
full_name: Perilla, Juan R.
last_name: Perilla
- first_name: John A. G.
full_name: Briggs, John A. G.
last_name: Briggs
- 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: Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal
a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 2020;16(1).
doi:10.1371/journal.ppat.1008277
apa: Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T.
D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved
role for IP6 in lentivirus assembly. PLOS Pathogens. Public Library of
Science. https://doi.org/10.1371/journal.ppat.1008277
chicago: Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton
L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV
Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS
Pathogens. Public Library of Science, 2020. https://doi.org/10.1371/journal.ppat.1008277.
ieee: R. A. Dick et al., “Structures of immature EIAV Gag lattices reveal
a conserved role for IP6 in lentivirus assembly,” PLOS Pathogens, vol.
16, no. 1. Public Library of Science, 2020.
ista: Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers
JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of
immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly.
PLOS Pathogens. 16(1), e1008277.
mla: Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a
Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens, vol. 16,
no. 1, e1008277, Public Library of Science, 2020, doi:10.1371/journal.ppat.1008277.
short: R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M.
Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K.
Schur, PLOS Pathogens 16 (2020).
corr_author: '1'
date_created: 2020-02-06T18:47:17Z
date_published: 2020-01-27T00:00:00Z
date_updated: 2025-04-15T08:24:51Z
day: '27'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1371/journal.ppat.1008277
external_id:
isi:
- '000510746400010'
pmid:
- '31986188'
file:
- access_level: open_access
checksum: a297f54d1fef0efe4789ca00f37f241e
content_type: application/pdf
creator: dernst
date_created: 2020-02-11T10:07:28Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7484'
file_name: 2020_PLOSPatho_Dick.pdf
file_size: 4551246
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
fulldoi: https://doi.org/10.1371/journal.ppat.1008277
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: PLOS Pathogens
publication_identifier:
issn:
- 1553-7374
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '9723'
relation: research_data
status: deleted
scopus_import: '1'
status: public
title: Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in
lentivirus assembly
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2020'
...
---
_id: '7465'
abstract:
- lang: eng
text: The flexible development of plants is characterized by a high capacity for
post-embryonic organ formation and tissue regeneration, processes, which require
tightly regulated intercellular communication and coordinated tissue (re-)polarization.
The phytohormone auxin, the main driver for these processes, is able to establish
polarized auxin transport channels, which are characterized by the expression
and polar, subcellular localization of the PIN1 auxin transport proteins. These
channels are demarcating the position of future vascular strands necessary for
organ formation and tissue regeneration. Major progress has been made in the last
years to understand how PINs can change their polarity in different contexts and
thus guide auxin flow through the plant. However, it still remains elusive how
auxin mediates the establishment of auxin conducting channels and the formation
of vascular tissue and which cellular processes are involved. By the means of
sophisticated regeneration experiments combined with local auxin applications
in Arabidopsis thaliana inflorescence stems we show that (i) PIN subcellular dynamics,
(ii) PIN internalization by clathrin-mediated trafficking and (iii) an intact
actin cytoskeleton required for post-endocytic trafficking are indispensable for
auxin channel formation, de novo vascular formation and vascular regeneration
after wounding. These observations provide novel insights into cellular mechanism
of coordinated tissue polarization during auxin canalization.
article_number: '110414'
article_processing_charge: No
article_type: original
author:
- first_name: Ewa
full_name: Mazur, Ewa
last_name: Mazur
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Hélène S.
full_name: Robert, Hélène S.
last_name: Robert
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. Clathrin-mediated
trafficking and PIN trafficking are required for auxin canalization and vascular
tissue formation in Arabidopsis. Plant Science. 2020;293(4). doi:10.1016/j.plantsci.2020.110414
apa: Mazur, E., Gallei, M. C., Adamowski, M., Han, H., Robert, H. S., & Friml,
J. (2020). Clathrin-mediated trafficking and PIN trafficking are required for
auxin canalization and vascular tissue formation in Arabidopsis. Plant Science.
Elsevier. https://doi.org/10.1016/j.plantsci.2020.110414
chicago: Mazur, Ewa, Michelle C Gallei, Maciek Adamowski, Huibin Han, Hélène S.
Robert, and Jiří Friml. “Clathrin-Mediated Trafficking and PIN Trafficking Are
Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.”
Plant Science. Elsevier, 2020. https://doi.org/10.1016/j.plantsci.2020.110414.
ieee: E. Mazur, M. C. Gallei, M. Adamowski, H. Han, H. S. Robert, and J. Friml,
“Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization
and vascular tissue formation in Arabidopsis,” Plant Science, vol. 293,
no. 4. Elsevier, 2020.
ista: Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. 2020. Clathrin-mediated
trafficking and PIN trafficking are required for auxin canalization and vascular
tissue formation in Arabidopsis. Plant Science. 293(4), 110414.
mla: Mazur, Ewa, et al. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required
for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” Plant
Science, vol. 293, no. 4, 110414, Elsevier, 2020, doi:10.1016/j.plantsci.2020.110414.
short: E. Mazur, M.C. Gallei, M. Adamowski, H. Han, H.S. Robert, J. Friml, Plant
Science 293 (2020).
corr_author: '1'
date_created: 2020-02-09T23:00:50Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2026-04-07T14:18:57Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.plantsci.2020.110414
ec_funded: 1
external_id:
isi:
- '000520609800009'
pmid:
- '32081263'
file:
- access_level: open_access
checksum: f7f27c6a8fea985ceb9279be2204461c
content_type: application/pdf
creator: dernst
date_created: 2020-02-10T08:59:36Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7471'
file_name: 2020_PlantScience_Mazur.pdf
file_size: 3499069
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
fulldoi: https://doi.org/10.1016/j.plantsci.2020.110414
has_accepted_license: '1'
intvolume: ' 293'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Plant Science
publication_identifier:
eissn:
- 1873-2259
issn:
- 0168-9452
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '11626'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization
and vascular tissue formation in Arabidopsis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 293
year: '2020'
...
---
_id: '7466'
abstract:
- lang: eng
text: Unpaired ligands are secreted signals that act via a GP130-like receptor,
domeless, to activate JAK/STAT signalling in Drosophila. Like many mammalian cytokines,
unpaireds can be activated by infection and other stresses and can promote insulin
resistance in target tissues. However, the importance of this effect in non-inflammatory
physiology is unknown. Here, we identify a requirement for unpaired-JAK signalling
as a metabolic regulator in healthy adult Drosophila muscle. Adult muscles show
basal JAK-STAT signalling activity in the absence of any immune challenge. Plasmatocytes
(Drosophila macrophages) are an important source of this tonic signal. Loss of
the dome receptor on adult muscles significantly reduces lifespan and causes local
and systemic metabolic pathology. These pathologies result from hyperactivation
of AKT and consequent deregulation of metabolism. Thus, we identify a cytokine
signal that must be received in muscle to control AKT activity and metabolic homeostasis.
article_number: e51595
article_processing_charge: No
article_type: original
author:
- first_name: Katrin
full_name: Kierdorf, Katrin
last_name: Kierdorf
- first_name: Fabian
full_name: Hersperger, Fabian
last_name: Hersperger
- first_name: Jessica
full_name: Sharrock, Jessica
last_name: Sharrock
- first_name: Crystal M.
full_name: Vincent, Crystal M.
last_name: Vincent
- first_name: Pinar
full_name: Ustaoglu, Pinar
last_name: Ustaoglu
- first_name: Jiawen
full_name: Dou, Jiawen
last_name: Dou
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Olaf
full_name: Groß, Olaf
last_name: Groß
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Marc S.
full_name: Dionne, Marc S.
last_name: Dionne
citation:
ama: Kierdorf K, Hersperger F, Sharrock J, et al. Muscle function and homeostasis
require cytokine inhibition of AKT activity in Drosophila. eLife. 2020;9.
doi:10.7554/eLife.51595
apa: Kierdorf, K., Hersperger, F., Sharrock, J., Vincent, C. M., Ustaoglu, P., Dou,
J., … Dionne, M. S. (2020). Muscle function and homeostasis require cytokine inhibition
of AKT activity in Drosophila. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.51595
chicago: Kierdorf, Katrin, Fabian Hersperger, Jessica Sharrock, Crystal M. Vincent,
Pinar Ustaoglu, Jiawen Dou, Attila György, Olaf Groß, Daria E Siekhaus, and Marc
S. Dionne. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT
Activity in Drosophila.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.51595.
ieee: K. Kierdorf et al., “Muscle function and homeostasis require cytokine
inhibition of AKT activity in Drosophila,” eLife, vol. 9. eLife Sciences
Publications, 2020.
ista: Kierdorf K, Hersperger F, Sharrock J, Vincent CM, Ustaoglu P, Dou J, György
A, Groß O, Siekhaus DE, Dionne MS. 2020. Muscle function and homeostasis require
cytokine inhibition of AKT activity in Drosophila. eLife. 9, e51595.
mla: Kierdorf, Katrin, et al. “Muscle Function and Homeostasis Require Cytokine
Inhibition of AKT Activity in Drosophila.” ELife, vol. 9, e51595, eLife
Sciences Publications, 2020, doi:10.7554/eLife.51595.
short: K. Kierdorf, F. Hersperger, J. Sharrock, C.M. Vincent, P. Ustaoglu, J. Dou,
A. György, O. Groß, D.E. Siekhaus, M.S. Dionne, ELife 9 (2020).
date_created: 2020-02-09T23:00:51Z
date_published: 2020-01-20T00:00:00Z
date_updated: 2026-04-03T09:24:34Z
day: '20'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.7554/eLife.51595
external_id:
isi:
- '000512304800001'
file:
- access_level: open_access
checksum: 3a072be843f416c7a7d532a51dc0addb
content_type: application/pdf
creator: dernst
date_created: 2020-02-10T08:53:16Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7470'
file_name: 2020_eLife_Kierdorf.pdf
file_size: 4959933
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
fulldoi: https://doi.org/10.7554/eLife.51595
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 253B6E48-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29638
name: The role of Drosophila TNF alpha in immune cell invasion
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Muscle function and homeostasis require cytokine inhibition of AKT activity
in Drosophila
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 9
year: '2020'
...
---
_id: '7474'
abstract:
- lang: eng
text: This booklet is a collection of abstracts presented at the AHPC conference.
article_processing_charge: No
citation:
ama: 'Schlögl A, Kiss J, Elefante S, eds. Austrian High-Performance-Computing
Meeting (AHPC2020). Klosterneuburg, Austria: IST Austria; 2020. doi:10.15479/AT:ISTA:7474'
apa: 'Schlögl, A., Kiss, J., & Elefante, S. (Eds.). (2020). Austrian High-Performance-Computing
meeting (AHPC2020). Presented at the AHPC: Austrian High-Performance-Computing
Meeting, Klosterneuburg, Austria: IST Austria. https://doi.org/10.15479/AT:ISTA:7474'
chicago: 'Schlögl, Alois, Janos Kiss, and Stefano Elefante, eds. Austrian High-Performance-Computing
Meeting (AHPC2020). Klosterneuburg, Austria: IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:7474.'
ieee: 'A. Schlögl, J. Kiss, and S. Elefante, Eds., Austrian High-Performance-Computing
meeting (AHPC2020). Klosterneuburg, Austria: IST Austria, 2020.'
ista: 'Schlögl A, Kiss J, Elefante S eds. 2020. Austrian High-Performance-Computing
meeting (AHPC2020), Klosterneuburg, Austria: IST Austria, 72p.'
mla: Schlögl, Alois, et al., editors. Austrian High-Performance-Computing Meeting
(AHPC2020). IST Austria, 2020, doi:10.15479/AT:ISTA:7474.
short: A. Schlögl, J. Kiss, S. Elefante, eds., Austrian High-Performance-Computing
Meeting (AHPC2020), IST Austria, Klosterneuburg, Austria, 2020.
conference:
end_date: 2020-02-21
location: Klosterneuburg, Austria
name: 'AHPC: Austrian High-Performance-Computing Meeting'
start_date: 2020-02-19
date_created: 2020-02-11T07:59:04Z
date_published: 2020-02-19T00:00:00Z
date_updated: 2023-05-16T07:48:28Z
day: '19'
ddc:
- '000'
department:
- _id: ScienComp
doi: 10.15479/AT:ISTA:7474
editor:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Janos
full_name: Kiss, Janos
id: 3D3A06F8-F248-11E8-B48F-1D18A9856A87
last_name: Kiss
- first_name: Stefano
full_name: Elefante, Stefano
id: 490F40CE-F248-11E8-B48F-1D18A9856A87
last_name: Elefante
file:
- access_level: open_access
checksum: 49798edb9e57bbd6be18362d1d7b18a9
content_type: application/pdf
creator: schloegl
date_created: 2020-02-19T06:53:38Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7504'
file_name: BOOKLET_AHPC2020.final.pdf
file_size: 90899507
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
fulldoi: https://doi.org/10.15479/AT:ISTA:7474
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '72'
place: Klosterneuburg, Austria
publication_identifier:
isbn:
- 978-3-99078-004-6
publication_status: published
publisher: IST Austria
quality_controlled: '1'
status: public
title: Austrian High-Performance-Computing meeting (AHPC2020)
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_editor
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7487'
abstract:
- lang: eng
text: 'Glutaminase (GA) catalyzes the first step in mitochondrial glutaminolysis
playing a key role in cancer metabolic reprogramming. Humans express two types
of GA isoforms: GLS and GLS2. GLS isozymes have been consistently related to cell
proliferation, but the role of GLS2 in cancer remains poorly understood. GLS2
is repressed in many tumor cells and a better understanding of its function in
tumorigenesis may further the development of new therapeutic approaches. We analyzed
GLS2 expression in HCC, GBM and neuroblastoma cells, as well as in monkey COS-7
cells. We studied GLS2 expression after induction of differentiation with phorbol
ester (PMA) and transduction with the full-length cDNA of GLS2. In parallel, we
investigated cell cycle progression and levels of p53, p21 and c-Myc proteins.
Using the baculovirus system, human GLS2 protein was overexpressed, purified and
analyzed for posttranslational modifications employing a proteomics LC-MS/MS platform.
We have demonstrated a dual targeting of GLS2 in human cancer cells. Immunocytochemistry
and subcellular fractionation gave consistent results demonstrating nuclear and
mitochondrial locations, with the latter being predominant. Nuclear targeting
was confirmed in cancer cells overexpressing c-Myc- and GFP-tagged GLS2 proteins.
We assessed the subnuclear location finding a widespread distribution of GLS2
in the nucleoplasm without clear overlapping with specific nuclear substructures.
GLS2 expression and nuclear accrual notably increased by treatment of SH-SY5Y
cells with PMA and it correlated with cell cycle arrest at G2/M, upregulation
of tumor suppressor p53 and p21 protein. A similar response was obtained by overexpression
of GLS2 in T98G glioma cells, including downregulation of oncogene c-Myc. Furthermore,
human GLS2 was identified as being hypusinated by MS analysis, a posttranslational
modification which may be relevant for its nuclear targeting and/or function.
Our studies provide evidence for a tumor suppressor role of GLS2 in certain types
of cancer. The data imply that GLS2 can be regarded as a highly mobile and multilocalizing
protein translocated to both mitochondria and nuclei. Upregulation of GLS2 in
cancer cells induced an antiproliferative response with cell cycle arrest at the
G2/M phase.'
article_number: '2259'
article_processing_charge: No
article_type: original
author:
- first_name: Amada R.
full_name: López De La Oliva, Amada R.
last_name: López De La Oliva
- first_name: José A.
full_name: Campos-Sandoval, José A.
last_name: Campos-Sandoval
- first_name: María C.
full_name: Gómez-García, María C.
last_name: Gómez-García
- first_name: Carolina
full_name: Cardona, Carolina
last_name: Cardona
- first_name: Mercedes
full_name: Martín-Rufián, Mercedes
last_name: Martín-Rufián
- first_name: Fernando J.
full_name: Sialana, Fernando J.
last_name: Sialana
- first_name: Laura
full_name: Castilla, Laura
last_name: Castilla
- first_name: Narkhyun
full_name: Bae, Narkhyun
id: 3A5F7CD8-F248-11E8-B48F-1D18A9856A87
last_name: Bae
- first_name: Carolina
full_name: Lobo, Carolina
last_name: Lobo
- first_name: Ana
full_name: Peñalver, Ana
last_name: Peñalver
- first_name: Marina
full_name: García-Frutos, Marina
last_name: García-Frutos
- first_name: David
full_name: Carro, David
last_name: Carro
- first_name: Victoria
full_name: Enrique, Victoria
last_name: Enrique
- first_name: José C.
full_name: Paz, José C.
last_name: Paz
- first_name: Raghavendra G.
full_name: Mirmira, Raghavendra G.
last_name: Mirmira
- first_name: Antonia
full_name: Gutiérrez, Antonia
last_name: Gutiérrez
- first_name: Francisco J.
full_name: Alonso, Francisco J.
last_name: Alonso
- first_name: Juan A.
full_name: Segura, Juan A.
last_name: Segura
- first_name: José M.
full_name: Matés, José M.
last_name: Matés
- first_name: Gert
full_name: Lubec, Gert
last_name: Lubec
- first_name: Javier
full_name: Márquez, Javier
last_name: Márquez
citation:
ama: López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, et al. Nuclear translocation
of glutaminase GLS2 in human cancer cells associates with proliferation arrest
and differentiation. Scientific reports. 2020;10(1). doi:10.1038/s41598-020-58264-4
apa: López De La Oliva, A. R., Campos-Sandoval, J. A., Gómez-García, M. C., Cardona,
C., Martín-Rufián, M., Sialana, F. J., … Márquez, J. (2020). Nuclear translocation
of glutaminase GLS2 in human cancer cells associates with proliferation arrest
and differentiation. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-58264-4
chicago: López De La Oliva, Amada R., José A. Campos-Sandoval, María C. Gómez-García,
Carolina Cardona, Mercedes Martín-Rufián, Fernando J. Sialana, Laura Castilla,
et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates
with Proliferation Arrest and Differentiation.” Scientific Reports. Springer
Nature, 2020. https://doi.org/10.1038/s41598-020-58264-4.
ieee: A. R. López De La Oliva et al., “Nuclear translocation of glutaminase
GLS2 in human cancer cells associates with proliferation arrest and differentiation,”
Scientific reports, vol. 10, no. 1. Springer Nature, 2020.
ista: López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, Cardona C, Martín-Rufián
M, Sialana FJ, Castilla L, Bae N, Lobo C, Peñalver A, García-Frutos M, Carro D,
Enrique V, Paz JC, Mirmira RG, Gutiérrez A, Alonso FJ, Segura JA, Matés JM, Lubec
G, Márquez J. 2020. Nuclear translocation of glutaminase GLS2 in human cancer
cells associates with proliferation arrest and differentiation. Scientific reports.
10(1), 2259.
mla: López De La Oliva, Amada R., et al. “Nuclear Translocation of Glutaminase GLS2
in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.”
Scientific Reports, vol. 10, no. 1, 2259, Springer Nature, 2020, doi:10.1038/s41598-020-58264-4.
short: A.R. López De La Oliva, J.A. Campos-Sandoval, M.C. Gómez-García, C. Cardona,
M. Martín-Rufián, F.J. Sialana, L. Castilla, N. Bae, C. Lobo, A. Peñalver, M.
García-Frutos, D. Carro, V. Enrique, J.C. Paz, R.G. Mirmira, A. Gutiérrez, F.J.
Alonso, J.A. Segura, J.M. Matés, G. Lubec, J. Márquez, Scientific Reports 10 (2020).
date_created: 2020-02-16T23:00:49Z
date_published: 2020-02-10T00:00:00Z
date_updated: 2026-04-02T11:51:06Z
day: '10'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.1038/s41598-020-58264-4
external_id:
isi:
- '000560694800012'
pmid:
- '32042057'
file:
- access_level: open_access
checksum: c780bd87476a9c9e12668ff66de3dc96
content_type: application/pdf
creator: dernst
date_created: 2020-02-18T07:43:21Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7495'
file_name: 2020_ScientificReport_Lopez.pdf
file_size: 4703751
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
fulldoi: https://doi.org/10.1038/s41598-020-58264-4
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41598-020-80651-0
scopus_import: '1'
status: public
title: Nuclear translocation of glutaminase GLS2 in human cancer cells associates
with proliferation arrest and differentiation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 10
year: '2020'
...
---
_id: '7488'
abstract:
- lang: eng
text: Characteristic or classic phenotype of Cornelia de Lange syndrome (CdLS) is
associated with a recognisable facial pattern. However, the heterogeneity in causal
genes and the presence of overlapping syndromes have made it increasingly difficult
to diagnose only by clinical features. DeepGestalt technology, and its app Face2Gene,
is having a growing impact on the diagnosis and management of genetic diseases
by analysing the features of affected individuals. Here, we performed a phenotypic
study on a cohort of 49 individuals harbouring causative variants in known CdLS
genes in order to evaluate Face2Gene utility and sensitivity in the clinical diagnosis
of CdLS. Based on the profile images of patients, a diagnosis of CdLS was within
the top five predicted syndromes for 97.9% of our cases and even listed as first
prediction for 83.7%. The age of patients did not seem to affect the prediction
accuracy, whereas our results indicate a correlation between the clinical score
and affected genes. Furthermore, each gene presents a different pattern recognition
that may be used to develop new neural networks with the goal of separating different
genetic subtypes in CdLS. Overall, we conclude that computer-assisted image analysis
based on deep learning could support the clinical diagnosis of CdLS.
article_number: '1042'
article_processing_charge: No
article_type: original
author:
- first_name: Ana
full_name: Latorre-Pellicer, Ana
last_name: Latorre-Pellicer
- first_name: Ángela
full_name: Ascaso, Ángela
last_name: Ascaso
- first_name: Laura
full_name: Trujillano, Laura
last_name: Trujillano
- first_name: Marta
full_name: Gil-Salvador, Marta
last_name: Gil-Salvador
- first_name: Maria
full_name: Arnedo, Maria
last_name: Arnedo
- first_name: Cristina
full_name: Lucia-Campos, Cristina
last_name: Lucia-Campos
- first_name: Rebeca
full_name: Antoñanzas-Pérez, Rebeca
last_name: Antoñanzas-Pérez
- first_name: Iñigo
full_name: Marcos-Alcalde, Iñigo
last_name: Marcos-Alcalde
- first_name: Ilaria
full_name: Parenti, Ilaria
id: D93538B0-5B71-11E9-AC62-02EBE5697425
last_name: Parenti
- first_name: Gloria
full_name: Bueno-Lozano, Gloria
last_name: Bueno-Lozano
- first_name: Antonio
full_name: Musio, Antonio
last_name: Musio
- first_name: Beatriz
full_name: Puisac, Beatriz
last_name: Puisac
- first_name: Frank J.
full_name: Kaiser, Frank J.
last_name: Kaiser
- first_name: Feliciano J.
full_name: Ramos, Feliciano J.
last_name: Ramos
- first_name: Paulino
full_name: Gómez-Puertas, Paulino
last_name: Gómez-Puertas
- first_name: Juan
full_name: Pié, Juan
last_name: Pié
citation:
ama: Latorre-Pellicer A, Ascaso Á, Trujillano L, et al. Evaluating Face2Gene as
a tool to identify Cornelia de Lange syndrome by facial phenotypes. International
Journal of Molecular Sciences. 2020;21(3). doi:10.3390/ijms21031042
apa: Latorre-Pellicer, A., Ascaso, Á., Trujillano, L., Gil-Salvador, M., Arnedo,
M., Lucia-Campos, C., … Pié, J. (2020). Evaluating Face2Gene as a tool to identify
Cornelia de Lange syndrome by facial phenotypes. International Journal of Molecular
Sciences. MDPI. https://doi.org/10.3390/ijms21031042
chicago: Latorre-Pellicer, Ana, Ángela Ascaso, Laura Trujillano, Marta Gil-Salvador,
Maria Arnedo, Cristina Lucia-Campos, Rebeca Antoñanzas-Pérez, et al. “Evaluating
Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes.”
International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21031042.
ieee: A. Latorre-Pellicer et al., “Evaluating Face2Gene as a tool to identify
Cornelia de Lange syndrome by facial phenotypes,” International Journal of
Molecular Sciences, vol. 21, no. 3. MDPI, 2020.
ista: Latorre-Pellicer A, Ascaso Á, Trujillano L, Gil-Salvador M, Arnedo M, Lucia-Campos
C, Antoñanzas-Pérez R, Marcos-Alcalde I, Parenti I, Bueno-Lozano G, Musio A, Puisac
B, Kaiser FJ, Ramos FJ, Gómez-Puertas P, Pié J. 2020. Evaluating Face2Gene as
a tool to identify Cornelia de Lange syndrome by facial phenotypes. International
Journal of Molecular Sciences. 21(3), 1042.
mla: Latorre-Pellicer, Ana, et al. “Evaluating Face2Gene as a Tool to Identify Cornelia
de Lange Syndrome by Facial Phenotypes.” International Journal of Molecular
Sciences, vol. 21, no. 3, 1042, MDPI, 2020, doi:10.3390/ijms21031042.
short: A. Latorre-Pellicer, Á. Ascaso, L. Trujillano, M. Gil-Salvador, M. Arnedo,
C. Lucia-Campos, R. Antoñanzas-Pérez, I. Marcos-Alcalde, I. Parenti, G. Bueno-Lozano,
A. Musio, B. Puisac, F.J. Kaiser, F.J. Ramos, P. Gómez-Puertas, J. Pié, International
Journal of Molecular Sciences 21 (2020).
corr_author: '1'
date_created: 2020-02-16T23:00:49Z
date_published: 2020-02-04T00:00:00Z
date_updated: 2025-07-10T11:54:41Z
day: '04'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.3390/ijms21031042
external_id:
isi:
- '000522551606028'
file:
- access_level: open_access
checksum: 0e6658c4fe329d55d4d9bef01c5b15d0
content_type: application/pdf
creator: dernst
date_created: 2020-02-18T07:49:22Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7496'
file_name: 2020_IntMolecSciences_Latorre.pdf
file_size: 4271234
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
fulldoi: https://doi.org/10.3390/ijms21031042
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '3'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- 1422-0067
issn:
- 1661-6596
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial
phenotypes
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: 21
year: '2020'
...
---
_id: '7489'
abstract:
- lang: eng
text: 'In the present work, we consider the evolution of two fluids separated by
a sharp interface in the presence of surface tension—like, for example, the evolution
of oil bubbles in water. Our main result is a weak–strong uniqueness principle
for the corresponding free boundary problem for the incompressible Navier–Stokes
equation: as long as a strong solution exists, any varifold solution must coincide
with it. In particular, in the absence of physical singularities, the concept
of varifold solutions—whose global in time existence has been shown by Abels (Interfaces
Free Bound 9(1):31–65, 2007) for general initial data—does not introduce a mechanism
for non-uniqueness. The key ingredient of our approach is the construction of
a relative entropy functional capable of controlling the interface error. If the
viscosities of the two fluids do not coincide, even for classical (strong) solutions
the gradient of the velocity field becomes discontinuous at the interface, introducing
the need for a careful additional adaption of the relative entropy.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Sebastian
full_name: Hensel, Sebastian
id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87
last_name: Hensel
orcid: 0000-0001-7252-8072
citation:
ama: Fischer JL, Hensel S. Weak–strong uniqueness for the Navier–Stokes equation
for two fluids with surface tension. Archive for Rational Mechanics and Analysis.
2020;236:967-1087. doi:10.1007/s00205-019-01486-2
apa: Fischer, J. L., & Hensel, S. (2020). Weak–strong uniqueness for the Navier–Stokes
equation for two fluids with surface tension. Archive for Rational Mechanics
and Analysis. Springer Nature. https://doi.org/10.1007/s00205-019-01486-2
chicago: Fischer, Julian L, and Sebastian Hensel. “Weak–Strong Uniqueness for the
Navier–Stokes Equation for Two Fluids with Surface Tension.” Archive for Rational
Mechanics and Analysis. Springer Nature, 2020. https://doi.org/10.1007/s00205-019-01486-2.
ieee: J. L. Fischer and S. Hensel, “Weak–strong uniqueness for the Navier–Stokes
equation for two fluids with surface tension,” Archive for Rational Mechanics
and Analysis, vol. 236. Springer Nature, pp. 967–1087, 2020.
ista: Fischer JL, Hensel S. 2020. Weak–strong uniqueness for the Navier–Stokes equation
for two fluids with surface tension. Archive for Rational Mechanics and Analysis.
236, 967–1087.
mla: Fischer, Julian L., and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes
Equation for Two Fluids with Surface Tension.” Archive for Rational Mechanics
and Analysis, vol. 236, Springer Nature, 2020, pp. 967–1087, doi:10.1007/s00205-019-01486-2.
short: J.L. Fischer, S. Hensel, Archive for Rational Mechanics and Analysis 236
(2020) 967–1087.
corr_author: '1'
date_created: 2020-02-16T23:00:50Z
date_published: 2020-05-01T00:00:00Z
date_updated: 2026-04-08T07:01:01Z
day: '01'
ddc:
- '530'
- '532'
department:
- _id: JuFi
doi: 10.1007/s00205-019-01486-2
ec_funded: 1
external_id:
isi:
- '000511060200001'
file:
- access_level: open_access
checksum: f107e21b58f5930876f47144be37cf6c
content_type: application/pdf
creator: dernst
date_created: 2020-11-20T09:14:22Z
date_updated: 2020-11-20T09:14:22Z
file_id: '8779'
file_name: 2020_ArchRatMechAn_Fischer.pdf
file_size: 1897571
relation: main_file
success: 1
file_date_updated: 2020-11-20T09:14:22Z
fulldoi: https://doi.org/10.1007/s00205-019-01486-2
has_accepted_license: '1'
intvolume: ' 236'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 967-1087
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
eissn:
- 1432-0673
issn:
- 0003-9527
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '10007'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface
tension
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: 236
year: '2020'
...
---
_id: '7490'
abstract:
- lang: eng
text: In plants, clathrin mediated endocytosis (CME) represents the major route
for cargo internalisation from the cell surface. It has been assumed to operate
in an evolutionary conserved manner as in yeast and animals. Here we report characterisation
of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement
in electron microscopy and quantitative live imaging techniques. Arabidopsis CME
appears to follow the constant curvature model and the bona fide CME population
generates vesicles of a predominantly hexagonal-basket type; larger and with faster
kinetics than in other models. Contrary to the existing paradigm, actin is dispensable
for CME events at the plasma membrane but plays a unique role in collecting endocytic
vesicles, sorting of internalised cargos and directional endosome movement that
itself actively promote CME events. Internalized vesicles display a strongly delayed
and sequential uncoating. These unique features highlight the independent evolution
of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
article_number: e52067
article_processing_charge: No
article_type: original
author:
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Narasimhan M, Johnson AJ, Prizak R, et al. Evolutionarily unique mechanistic
framework of clathrin-mediated endocytosis in plants. eLife. 2020;9. doi:10.7554/eLife.52067
apa: Narasimhan, M., Johnson, A. J., Prizak, R., Kaufmann, W., Tan, S., Casillas
Perez, B. E., & Friml, J. (2020). Evolutionarily unique mechanistic framework
of clathrin-mediated endocytosis in plants. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.52067
chicago: Narasimhan, Madhumitha, Alexander J Johnson, Roshan Prizak, Walter Kaufmann,
Shutang Tan, Barbara E Casillas Perez, and Jiří Friml. “Evolutionarily Unique
Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” ELife.
eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.52067.
ieee: M. Narasimhan et al., “Evolutionarily unique mechanistic framework
of clathrin-mediated endocytosis in plants,” eLife, vol. 9. eLife Sciences
Publications, 2020.
ista: Narasimhan M, Johnson AJ, Prizak R, Kaufmann W, Tan S, Casillas Perez BE,
Friml J. 2020. Evolutionarily unique mechanistic framework of clathrin-mediated
endocytosis in plants. eLife. 9, e52067.
mla: Narasimhan, Madhumitha, et al. “Evolutionarily Unique Mechanistic Framework
of Clathrin-Mediated Endocytosis in Plants.” ELife, vol. 9, e52067, eLife
Sciences Publications, 2020, doi:10.7554/eLife.52067.
short: M. Narasimhan, A.J. Johnson, R. Prizak, W. Kaufmann, S. Tan, B.E. Casillas
Perez, J. Friml, ELife 9 (2020).
date_created: 2020-02-16T23:00:50Z
date_published: 2020-01-23T00:00:00Z
date_updated: 2025-04-14T07:45:03Z
day: '23'
ddc:
- '570'
- '580'
department:
- _id: JiFr
- _id: GaTk
- _id: EM-Fac
- _id: SyCr
doi: 10.7554/eLife.52067
ec_funded: 1
external_id:
isi:
- '000514104100001'
pmid:
- '31971511'
file:
- access_level: open_access
checksum: 2052daa4be5019534f3a42f200a09f32
content_type: application/pdf
creator: dernst
date_created: 2020-02-18T07:21:16Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7494'
file_name: 2020_eLife_Narasimhan.pdf
file_size: 7247468
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
fulldoi: https://doi.org/10.7554/eLife.52067
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis
in plants
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2020'
...
---
_id: '7497'
abstract:
- lang: eng
text: Endophytic fungi can be beneficial to plant growth. However, the molecular
mechanisms underlying colonization of Acremonium spp. remain unclear. In this
study, a novel endophytic Acremonium strain was isolated from the buds of Panax
notoginseng and named Acremonium sp. D212. The Acremonium sp. D212 could colonize
the roots of P. notoginseng, enhance the resistance of P. notoginseng to root
rot disease, and promote root growth and saponin biosynthesis in P. notoginseng.
Acremonium sp. D212 could secrete indole‐3‐acetic acid (IAA) and jasmonic acid
(JA), and inoculation with the fungus increased the endogenous levels of IAA and
JA in P. notoginseng. Colonization of the Acremonium sp. D212 in the roots of
the rice line Nipponbare was dependent on the concentration of methyl jasmonate
(MeJA) (2 to 15 μM) and 1‐naphthalenacetic acid (NAA) (10 to 20 μM). Moreover,
the roots of the JA signalling‐defective coi1‐18 mutant were colonized by Acremonium
sp. D212 to a lesser degree than those of the wild‐type Nipponbare and miR393b‐overexpressing
lines, and the colonization was rescued by MeJA but not by NAA. It suggests that
the cross‐talk between JA signalling and the auxin biosynthetic pathway plays
a crucial role in the colonization of Acremonium sp. D212 in host plants.
acknowledgement: We thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese
Academy of Sciences) for providing generous support with the IAA and JA measurements.
We thank Professor Guohua Xu (Nanjing Agricultural University) for generously providing
the Nipponbare rice expressing DR5::GUS. We thank Professor Muyuan Zhu (Zhejiang
University) for generously providing a rice line expressing 35S::miR393b. We thank
Professor Yinong Yang (Pennsylvania State University) for generously providing the
rice line coi1-18. This work was supported by grants from the National Natural Science
Foundation of China (31660501, 31460453, 31860064 and 31470382), the Major Special
Program for Scientific Research, Education Department of Yunnan Province (ZD2015005),
the Project sponsored by SRF for ROCS, SEM ([2013] 1792), the Major Science and
Technique Programs in Yunnan Province (2016ZF001), the Key Projects of the Applied
Basic Research Plan of Yunnan Province (2017FA018), the National Key R&D Program
of China (2018YFD0201100) and the China Agriculture Research System (CARS-21).
article_processing_charge: No
article_type: original
author:
- first_name: L
full_name: Han, L
last_name: Han
- first_name: X
full_name: Zhou, X
last_name: Zhou
- first_name: Y
full_name: Zhao, Y
last_name: Zhao
- first_name: S
full_name: Zhu, S
last_name: Zhu
- first_name: L
full_name: Wu, L
last_name: Wu
- first_name: Y
full_name: He, Y
last_name: He
- first_name: X
full_name: Ping, X
last_name: Ping
- first_name: X
full_name: Lu, X
last_name: Lu
- first_name: W
full_name: Huang, W
last_name: Huang
- first_name: J
full_name: Qian, J
last_name: Qian
- first_name: L
full_name: Zhang, L
last_name: Zhang
- first_name: X
full_name: Jiang, X
last_name: Jiang
- first_name: D
full_name: Zhu, D
last_name: Zhu
- first_name: C
full_name: Luo, C
last_name: Luo
- first_name: S
full_name: Li, S
last_name: Li
- first_name: Q
full_name: Dong, Q
last_name: Dong
- first_name: Q
full_name: Fu, Q
last_name: Fu
- first_name: K
full_name: Deng, K
last_name: Deng
- first_name: X
full_name: Wang, X
last_name: Wang
- first_name: L
full_name: Wang, L
last_name: Wang
- first_name: S
full_name: Peng, S
last_name: Peng
- first_name: J
full_name: Wu, J
last_name: Wu
- first_name: W
full_name: Li, W
last_name: Li
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Y
full_name: Zhu, Y
last_name: Zhu
- first_name: X
full_name: He, X
last_name: He
- first_name: Y
full_name: Du, Y
last_name: Du
citation:
ama: Han L, Zhou X, Zhao Y, et al. Colonization of endophyte Acremonium sp. D212
in Panax notoginseng and rice mediated by auxin and jasmonic acid. Journal
of Integrative Plant Biology. 2020;62(9):1433-1451. doi:10.1111/jipb.12905
apa: Han, L., Zhou, X., Zhao, Y., Zhu, S., Wu, L., He, Y., … Du, Y. (2020). Colonization
of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin
and jasmonic acid. Journal of Integrative Plant Biology. Wiley. https://doi.org/10.1111/jipb.12905
chicago: Han, L, X Zhou, Y Zhao, S Zhu, L Wu, Y He, X Ping, et al. “Colonization
of Endophyte Acremonium Sp. D212 in Panax Notoginseng and Rice Mediated by Auxin
and Jasmonic Acid.” Journal of Integrative Plant Biology. Wiley, 2020.
https://doi.org/10.1111/jipb.12905.
ieee: L. Han et al., “Colonization of endophyte Acremonium sp. D212 in Panax
notoginseng and rice mediated by auxin and jasmonic acid,” Journal of Integrative
Plant Biology, vol. 62, no. 9. Wiley, pp. 1433–1451, 2020.
ista: Han L, Zhou X, Zhao Y, Zhu S, Wu L, He Y, Ping X, Lu X, Huang W, Qian J, Zhang
L, Jiang X, Zhu D, Luo C, Li S, Dong Q, Fu Q, Deng K, Wang X, Wang L, Peng S,
Wu J, Li W, Friml J, Zhu Y, He X, Du Y. 2020. Colonization of endophyte Acremonium
sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. Journal
of Integrative Plant Biology. 62(9), 1433–1451.
mla: Han, L., et al. “Colonization of Endophyte Acremonium Sp. D212 in Panax Notoginseng
and Rice Mediated by Auxin and Jasmonic Acid.” Journal of Integrative Plant
Biology, vol. 62, no. 9, Wiley, 2020, pp. 1433–51, doi:10.1111/jipb.12905.
short: L. Han, X. Zhou, Y. Zhao, S. Zhu, L. Wu, Y. He, X. Ping, X. Lu, W. Huang,
J. Qian, L. Zhang, X. Jiang, D. Zhu, C. Luo, S. Li, Q. Dong, Q. Fu, K. Deng, X.
Wang, L. Wang, S. Peng, J. Wu, W. Li, J. Friml, Y. Zhu, X. He, Y. Du, Journal
of Integrative Plant Biology 62 (2020) 1433–1451.
date_created: 2020-02-18T10:02:25Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2026-06-18T19:22:29Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/jipb.12905
external_id:
isi:
- '000515803000001'
pmid:
- '31912615'
fulldoi: https://doi.org/10.1111/jipb.12905
intvolume: ' 62'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jipb.12905
month: '09'
oa: 1
oa_version: Published Version
page: 1433-1451
pmid: 1
publication: Journal of Integrative Plant Biology
publication_identifier:
eissn:
- 1744-7909
issn:
- 1672-9072
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice
mediated by auxin and jasmonic acid
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 62
year: '2020'
...
---
_id: '7505'
abstract:
- lang: eng
text: Neural networks have demonstrated unmatched performance in a range of classification
tasks. Despite numerous efforts of the research community, novelty detection remains
one of the significant limitations of neural networks. The ability to identify
previously unseen inputs as novel is crucial for our understanding of the decisions
made by neural networks. At runtime, inputs not falling into any of the categories
learned during training cannot be classified correctly by the neural network.
Existing approaches treat the neural network as a black box and try to detect
novel inputs based on the confidence of the output predictions. However, neural
networks are not trained to reduce their confidence for novel inputs, which limits
the effectiveness of these approaches. We propose a framework to monitor a neural
network by observing the hidden layers. We employ a common abstraction from program
analysis - boxes - to identify novel behaviors in the monitored layers, i.e.,
inputs that cause behaviors outside the box. For each neuron, the boxes range
over the values seen in training. The framework is efficient and flexible to achieve
a desired trade-off between raising false warnings and detecting novel inputs.
We illustrate the performance and the robustness to variability in the unknown
classes on popular image-classification benchmarks.
acknowledgement: We thank Christoph Lampert and Nikolaus Mayer for fruitful discussions.
This research was supported in part by the Austrian Science Fund (FWF) under grants
S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award) and the European Union’s
Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie grant
agreement No. 754411.
alternative_title:
- Frontiers in Artificial Intelligence and Applications
article_processing_charge: No
arxiv: 1
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Anna
full_name: Lukina, Anna
id: CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425
last_name: Lukina
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
citation:
ama: 'Henzinger TA, Lukina A, Schilling C. Outside the box: Abstraction-based monitoring
of neural networks. In: 24th European Conference on Artificial Intelligence.
Vol 325. IOS Press; 2020:2433-2440. doi:10.3233/FAIA200375'
apa: 'Henzinger, T. A., Lukina, A., & Schilling, C. (2020). Outside the box:
Abstraction-based monitoring of neural networks. In 24th European Conference
on Artificial Intelligence (Vol. 325, pp. 2433–2440). Santiago de Compostela,
Spain: IOS Press. https://doi.org/10.3233/FAIA200375'
chicago: 'Henzinger, Thomas A, Anna Lukina, and Christian Schilling. “Outside the
Box: Abstraction-Based Monitoring of Neural Networks.” In 24th European Conference
on Artificial Intelligence, 325:2433–40. IOS Press, 2020. https://doi.org/10.3233/FAIA200375.'
ieee: 'T. A. Henzinger, A. Lukina, and C. Schilling, “Outside the box: Abstraction-based
monitoring of neural networks,” in 24th European Conference on Artificial Intelligence,
Santiago de Compostela, Spain, 2020, vol. 325, pp. 2433–2440.'
ista: 'Henzinger TA, Lukina A, Schilling C. 2020. Outside the box: Abstraction-based
monitoring of neural networks. 24th European Conference on Artificial Intelligence.
ECAI: European Conference on Artificial Intelligence, Frontiers in Artificial
Intelligence and Applications, vol. 325, 2433–2440.'
mla: 'Henzinger, Thomas A., et al. “Outside the Box: Abstraction-Based Monitoring
of Neural Networks.” 24th European Conference on Artificial Intelligence,
vol. 325, IOS Press, 2020, pp. 2433–40, doi:10.3233/FAIA200375.'
short: T.A. Henzinger, A. Lukina, C. Schilling, in:, 24th European Conference on
Artificial Intelligence, IOS Press, 2020, pp. 2433–2440.
conference:
end_date: 2020-09-08
location: Santiago de Compostela, Spain
name: 'ECAI: European Conference on Artificial Intelligence'
start_date: 2020-08-29
corr_author: '1'
date_created: 2020-02-21T16:44:03Z
date_published: 2020-02-24T00:00:00Z
date_updated: 2025-04-15T06:26:13Z
day: '24'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.3233/FAIA200375
ec_funded: 1
external_id:
arxiv:
- '1911.09032'
isi:
- '000650971303002'
file:
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checksum: 80642fa0b6cd7da95dcd87d63789ad5e
content_type: application/pdf
creator: dernst
date_created: 2020-09-21T07:12:32Z
date_updated: 2020-09-21T07:12:32Z
file_id: '8540'
file_name: 2020_ECAI_Henzinger.pdf
file_size: 1692214
relation: main_file
success: 1
file_date_updated: 2020-09-21T07:12:32Z
fulldoi: https://doi.org/10.3233/FAIA200375
has_accepted_license: '1'
intvolume: ' 325'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '02'
oa: 1
oa_version: Published Version
page: 2433-2440
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: 24th European Conference on Artificial Intelligence
publication_status: published
publisher: IOS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Outside the box: Abstraction-based monitoring of neural networks'
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 325
year: '2020'
...
---
_id: '7508'
abstract:
- lang: eng
text: In this paper, we introduce a novel method for deriving higher order corrections
to the mean-field description of the dynamics of interacting bosons. More precisely,
we consider the dynamics of N d-dimensional bosons for large N. The bosons initially
form a Bose–Einstein condensate and interact with each other via a pair potential
of the form (N−1)−1Ndβv(Nβ·)forβ∈[0,14d). We derive a sequence of N-body functions
which approximate the true many-body dynamics in L2(RdN)-norm to arbitrary precision
in powers of N−1. The approximating functions are constructed as Duhamel expansions
of finite order in terms of the first quantised analogue of a Bogoliubov time
evolution.
acknowledgement: "Open access funding provided by Institute of Science and Technology
(IST Austria).\r\nL.B. gratefully acknowledges the support by the German Research
Foundation (DFG) within the Research Training Group 1838 “Spectral Theory and Dynamics
of Quantum Systems”, and wishes to thank Stefan Teufel, Sören Petrat and Marcello
Porta for helpful discussions. This project has received funding from the European
Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 754411. N.P. gratefully acknowledges support from NSF grant
DMS-1516228 and DMS-1840314. P.P.’s research was funded by DFG Grant no. PI 1114/3-1.
Part of this work was done when N.P. and P.P. were visiting CCNU, Wuhan. N.P. and
P.P. thank A.S. for his hospitality at CCNU."
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Lea
full_name: Bossmann, Lea
id: A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425
last_name: Bossmann
orcid: 0000-0002-6854-1343
- first_name: Nataša
full_name: Pavlović, Nataša
last_name: Pavlović
- first_name: Peter
full_name: Pickl, Peter
last_name: Pickl
- first_name: Avy
full_name: Soffer, Avy
last_name: Soffer
citation:
ama: Bossmann L, Pavlović N, Pickl P, Soffer A. Higher order corrections to the
mean-field description of the dynamics of interacting bosons. Journal of Statistical
Physics. 2020;178:1362-1396. doi:10.1007/s10955-020-02500-8
apa: Bossmann, L., Pavlović, N., Pickl, P., & Soffer, A. (2020). Higher order
corrections to the mean-field description of the dynamics of interacting bosons.
Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-020-02500-8
chicago: Bossmann, Lea, Nataša Pavlović, Peter Pickl, and Avy Soffer. “Higher Order
Corrections to the Mean-Field Description of the Dynamics of Interacting Bosons.”
Journal of Statistical Physics. Springer Nature, 2020. https://doi.org/10.1007/s10955-020-02500-8.
ieee: L. Bossmann, N. Pavlović, P. Pickl, and A. Soffer, “Higher order corrections
to the mean-field description of the dynamics of interacting bosons,” Journal
of Statistical Physics, vol. 178. Springer Nature, pp. 1362–1396, 2020.
ista: Bossmann L, Pavlović N, Pickl P, Soffer A. 2020. Higher order corrections
to the mean-field description of the dynamics of interacting bosons. Journal of
Statistical Physics. 178, 1362–1396.
mla: Bossmann, Lea, et al. “Higher Order Corrections to the Mean-Field Description
of the Dynamics of Interacting Bosons.” Journal of Statistical Physics,
vol. 178, Springer Nature, 2020, pp. 1362–96, doi:10.1007/s10955-020-02500-8.
short: L. Bossmann, N. Pavlović, P. Pickl, A. Soffer, Journal of Statistical Physics
178 (2020) 1362–1396.
corr_author: '1'
date_created: 2020-02-23T09:45:51Z
date_published: 2020-02-21T00:00:00Z
date_updated: 2025-04-14T07:44:03Z
day: '21'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s10955-020-02500-8
ec_funded: 1
external_id:
arxiv:
- '1905.06164'
isi:
- '000516342200001'
file:
- access_level: open_access
checksum: 643e230bf147e64d9cdb3f6cc573679d
content_type: application/pdf
creator: dernst
date_created: 2020-11-20T09:26:46Z
date_updated: 2020-11-20T09:26:46Z
file_id: '8780'
file_name: 2020_JournStatPhysics_Bossmann.pdf
file_size: 576726
relation: main_file
success: 1
file_date_updated: 2020-11-20T09:26:46Z
fulldoi: https://doi.org/10.1007/s10955-020-02500-8
has_accepted_license: '1'
intvolume: ' 178'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1362-1396
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Statistical Physics
publication_identifier:
eissn:
- 1572-9613
issn:
- 0022-4715
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Higher order corrections to the mean-field description of the dynamics of interacting
bosons
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 178
year: '2020'
...
---
_id: '7509'
abstract:
- lang: eng
text: "In this paper we study the joint convexity/concavity of the trace functions
Ψp,q,s(A,B)=Tr(Bq2K∗ApKBq2)s, p,q,s∈R,\r\nwhere A and B are positive definite
matrices and K is any fixed invertible matrix. We will give full range of (p,q,s)∈R3
for Ψp,q,s to be jointly convex/concave for all K. As a consequence, we confirm
a conjecture of Carlen, Frank and Lieb. In particular, we confirm a weaker conjecture
of Audenaert and Datta and obtain the full range of (α,z) for α-z Rényi relative
entropies to be monotone under completely positive trace preserving maps. We also
give simpler proofs of many known results, including the concavity of Ψp,0,1/p
for 0Advances in Mathematics. 2020;365. doi:10.1016/j.aim.2020.107053
apa: Zhang, H. (2020). From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb
conjecture. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2020.107053
chicago: Zhang, Haonan. “From Wigner-Yanase-Dyson Conjecture to Carlen-Frank-Lieb
Conjecture.” Advances in Mathematics. Elsevier, 2020. https://doi.org/10.1016/j.aim.2020.107053.
ieee: H. Zhang, “From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture,”
Advances in Mathematics, vol. 365. Elsevier, 2020.
ista: Zhang H. 2020. From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture.
Advances in Mathematics. 365, 107053.
mla: Zhang, Haonan. “From Wigner-Yanase-Dyson Conjecture to Carlen-Frank-Lieb Conjecture.”
Advances in Mathematics, vol. 365, 107053, Elsevier, 2020, doi:10.1016/j.aim.2020.107053.
short: H. Zhang, Advances in Mathematics 365 (2020).
date_created: 2020-02-23T21:43:50Z
date_published: 2020-05-13T00:00:00Z
date_updated: 2025-04-14T07:44:03Z
day: '13'
ddc:
- '515'
department:
- _id: JaMa
doi: 10.1016/j.aim.2020.107053
ec_funded: 1
external_id:
arxiv:
- '1811.01205'
isi:
- '000522798000001'
fulldoi: https://doi.org/10.1016/j.aim.2020.107053
intvolume: ' 365'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1811.01205
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Advances in Mathematics
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 365
year: '2020'
...
---
_id: '7511'
abstract:
- lang: eng
text: Cryo electron tomography with subsequent subtomogram averaging is a powerful
technique to structurally analyze macromolecular complexes in their native context.
Although close to atomic resolution in principle can be obtained, it is not clear
how individual experimental parameters contribute to the attainable resolution.
Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize
the attainable resolution for subtomogram averaging. We systematically tested
various experimental parameters such as the order of projections, different angular
increments and the use of the Volta phase plate. We find that although any of
the prominently used acquisition schemes is sufficient to obtain subnanometer
resolution, dose-symmetric acquisition provides considerably better outcome. We
discuss our findings in order to provide guidance for data acquisition. Our data
is publicly available and might be used to further develop processing routines.
article_number: '876'
article_processing_charge: No
article_type: original
author:
- first_name: Beata
full_name: Turoňová, Beata
last_name: Turoňová
- first_name: Wim J.H.
full_name: Hagen, Wim J.H.
last_name: Hagen
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Shyamal
full_name: Mosalaganti, Shyamal
last_name: Mosalaganti
- first_name: J. Wouter
full_name: Beugelink, J. Wouter
last_name: Beugelink
- first_name: Christian E.
full_name: Zimmerli, Christian E.
last_name: Zimmerli
- first_name: Hans Georg
full_name: Kräusslich, Hans Georg
last_name: Kräusslich
- first_name: Martin
full_name: Beck, Martin
last_name: Beck
citation:
ama: Turoňová B, Hagen WJH, Obr M, et al. Benchmarking tomographic acquisition schemes
for high-resolution structural biology. Nature Communications. 2020;11.
doi:10.1038/s41467-020-14535-2
apa: Turoňová, B., Hagen, W. J. H., Obr, M., Mosalaganti, S., Beugelink, J. W.,
Zimmerli, C. E., … Beck, M. (2020). Benchmarking tomographic acquisition schemes
for high-resolution structural biology. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-020-14535-2
chicago: Turoňová, Beata, Wim J.H. Hagen, Martin Obr, Shyamal Mosalaganti, J. Wouter
Beugelink, Christian E. Zimmerli, Hans Georg Kräusslich, and Martin Beck. “Benchmarking
Tomographic Acquisition Schemes for High-Resolution Structural Biology.” Nature
Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-14535-2.
ieee: B. Turoňová et al., “Benchmarking tomographic acquisition schemes for
high-resolution structural biology,” Nature Communications, vol. 11. Springer
Nature, 2020.
ista: Turoňová B, Hagen WJH, Obr M, Mosalaganti S, Beugelink JW, Zimmerli CE, Kräusslich
HG, Beck M. 2020. Benchmarking tomographic acquisition schemes for high-resolution
structural biology. Nature Communications. 11, 876.
mla: Turoňová, Beata, et al. “Benchmarking Tomographic Acquisition Schemes for High-Resolution
Structural Biology.” Nature Communications, vol. 11, 876, Springer Nature,
2020, doi:10.1038/s41467-020-14535-2.
short: B. Turoňová, W.J.H. Hagen, M. Obr, S. Mosalaganti, J.W. Beugelink, C.E. Zimmerli,
H.G. Kräusslich, M. Beck, Nature Communications 11 (2020).
date_created: 2020-02-23T23:00:35Z
date_published: 2020-02-13T00:00:00Z
date_updated: 2026-04-03T09:27:26Z
day: '13'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1038/s41467-020-14535-2
external_id:
isi:
- '000514928000017'
pmid:
- '32054835'
file:
- access_level: open_access
checksum: 2c8d10475e1b0d397500760e28bdf561
content_type: application/pdf
creator: dernst
date_created: 2020-02-24T14:00:54Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7517'
file_name: 2020_NatureComm_Turonova.pdf
file_size: 2027529
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
fulldoi: https://doi.org/10.1038/s41467-020-14535-2
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Benchmarking tomographic acquisition schemes for high-resolution structural
biology
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 11
year: '2020'
...
---
_id: '7512'
abstract:
- lang: eng
text: We consider general self-adjoint polynomials in several independent random
matrices whose entries are centered and have the same variance. We show that under
certain conditions the local law holds up to the optimal scale, i.e., the eigenvalue
density on scales just above the eigenvalue spacing follows the global density
of states which is determined by free probability theory. We prove that these
conditions hold for general homogeneous polynomials of degree two and for symmetrized
products of independent matrices with i.i.d. entries, thus establishing the optimal
bulk local law for these classes of ensembles. In particular, we generalize a
similar result of Anderson for anticommutator. For more general polynomials our
conditions are effectively checkable numerically.
acknowledgement: "The authors are grateful to Oskari Ajanki for his invaluable help
at the initial stage of this project, to Serban Belinschi for useful discussions,
to Alexander Tikhomirov for calling our attention to the model example in Section
6.2 and to the anonymous referee for suggesting to simplify certain proofs. Erdös:
Partially funded by ERC Advanced Grant RANMAT No. 338804\r\n"
article_number: '108507'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
- first_name: Yuriy
full_name: Nemish, Yuriy
id: 4D902E6A-F248-11E8-B48F-1D18A9856A87
last_name: Nemish
orcid: 0000-0002-7327-856X
citation:
ama: Erdös L, Krüger TH, Nemish Y. Local laws for polynomials of Wigner matrices.
Journal of Functional Analysis. 2020;278(12). doi:10.1016/j.jfa.2020.108507
apa: Erdös, L., Krüger, T. H., & Nemish, Y. (2020). Local laws for polynomials
of Wigner matrices. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2020.108507
chicago: Erdös, László, Torben H Krüger, and Yuriy Nemish. “Local Laws for Polynomials
of Wigner Matrices.” Journal of Functional Analysis. Elsevier, 2020. https://doi.org/10.1016/j.jfa.2020.108507.
ieee: L. Erdös, T. H. Krüger, and Y. Nemish, “Local laws for polynomials of Wigner
matrices,” Journal of Functional Analysis, vol. 278, no. 12. Elsevier,
2020.
ista: Erdös L, Krüger TH, Nemish Y. 2020. Local laws for polynomials of Wigner matrices.
Journal of Functional Analysis. 278(12), 108507.
mla: Erdös, László, et al. “Local Laws for Polynomials of Wigner Matrices.” Journal
of Functional Analysis, vol. 278, no. 12, 108507, Elsevier, 2020, doi:10.1016/j.jfa.2020.108507.
short: L. Erdös, T.H. Krüger, Y. Nemish, Journal of Functional Analysis 278 (2020).
date_created: 2020-02-23T23:00:36Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2025-07-10T11:54:43Z
day: '01'
department:
- _id: LaEr
doi: 10.1016/j.jfa.2020.108507
ec_funded: 1
external_id:
arxiv:
- '1804.11340'
isi:
- '000522798900001'
fulldoi: https://doi.org/10.1016/j.jfa.2020.108507
intvolume: ' 278'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.11340
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local laws for polynomials of Wigner matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 278
year: '2020'
...
---
OA_place: publisher
_id: '7514'
abstract:
- lang: eng
text: "We study the interacting homogeneous Bose gas in two spatial dimensions in
the thermodynamic limit at fixed density. We shall be concerned with some mathematical
aspects of this complicated problem in many-body quantum mechanics. More specifically,
we consider the dilute limit where the scattering length of the interaction potential,
which is a measure for the effective range of the potential, is small compared
to the average distance between the particles. We are interested in a setting
with positive (i.e., non-zero) temperature. After giving a survey of the relevant
literature in the field, we provide some facts and examples to set expectations
for the two-dimensional system. The crucial difference to the three-dimensional
system is that there is no Bose–Einstein condensate at positive temperature due
to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic
formula for the free energy holds similarly to the three-dimensional case.\r\nWe
motivate this formula by considering a toy model with δ interaction potential.
By restricting this model Hamiltonian to certain trial states with a quasi-condensate
we obtain an upper bound for the free energy that still has the quasi-condensate
fraction as a free parameter. When minimizing over the quasi-condensate fraction,
we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity,
which plays an important role in our rigorous contribution. The mathematically
rigorous result that we prove concerns the specific free energy in the dilute
limit. We give upper and lower bounds on the free energy in terms of the free
energy of the non-interacting system and a correction term coming from the interaction.
Both bounds match and thus we obtain the leading term of an asymptotic approximation
in the dilute limit, provided the thermal wavelength of the particles is of the
same order (or larger) than the average distance between the particles. The remarkable
feature of this result is its generality: the correction term depends on the interaction
potential only through its scattering length and it holds for all nonnegative
interaction potentials with finite scattering length that are measurable. In particular,
this allows to model an interaction of hard disks."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Simon
full_name: Mayer, Simon
id: 30C4630A-F248-11E8-B48F-1D18A9856A87
last_name: Mayer
citation:
ama: Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:10.15479/AT:ISTA:7514
apa: Mayer, S. (2020). The free energy of a dilute two-dimensional Bose gas.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7514
chicago: Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute
of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7514.
ieee: S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute
of Science and Technology Austria, 2020.
ista: Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute
of Science and Technology Austria.
mla: Mayer, Simon. The Free Energy of a Dilute Two-Dimensional Bose Gas.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7514.
short: S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute
of Science and Technology Austria, 2020.
corr_author: '1'
date_created: 2020-02-24T09:17:27Z
date_published: 2020-02-24T00:00:00Z
date_updated: 2026-04-08T07:25:40Z
day: '24'
ddc:
- '510'
degree_awarded: PhD
department:
- _id: RoSe
- _id: GradSch
doi: 10.15479/AT:ISTA:7514
ec_funded: 1
file:
- access_level: open_access
checksum: b4de7579ddc1dbdd44ff3f17c48395f6
content_type: application/pdf
creator: dernst
date_created: 2020-02-24T09:15:06Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7515'
file_name: thesis.pdf
file_size: 1563429
relation: main_file
- access_level: closed
checksum: ad7425867b52d7d9e72296e87bc9cb67
content_type: application/x-zip-compressed
creator: dernst
date_created: 2020-02-24T09:15:16Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7516'
file_name: thesis_source.zip
file_size: 2028038
relation: source_file
file_date_updated: 2020-07-14T12:47:59Z
fulldoi: https://doi.org/10.15479/AT:ISTA:7514
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '148'
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7524'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
title: The free energy of a dilute two-dimensional Bose gas
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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2020'
...
---
_id: '7534'
abstract:
- lang: eng
text: 'In the past two decades, our understanding of the transition to turbulence
in shear flows with linearly stable laminar solutions has greatly improved. Regarding
the susceptibility of the laminar flow, two concepts have been particularly useful:
the edge states and the minimal seeds. In this nonlinear picture of the transition,
the basin boundary of turbulence is set by the edge state''s stable manifold and
this manifold comes closest in energy to the laminar equilibrium at the minimal
seed. We begin this paper by presenting numerical experiments in which three-dimensional
perturbations are too energetic to trigger turbulence in pipe flow but they do
lead to turbulence when their amplitude is reduced. We show that this seemingly
counterintuitive observation is in fact consistent with the fully nonlinear description
of the transition mediated by the edge state. In order to understand the physical
mechanisms behind this process, we measure the turbulent kinetic energy production
and dissipation rates as a function of the radial coordinate. Our main observation
is that the transition to turbulence relies on the energy amplification away from
the wall, as opposed to the turbulence itself, whose energy is predominantly produced
near the wall. This observation is further supported by the similar analyses on
the minimal seeds and the edge states. Furthermore, we show that the time evolution
of production-over-dissipation curves provides a clear distinction between the
different initial amplification stages of the transition to turbulence from the
minimal seed.'
article_number: '023903'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Elena
full_name: Marensi, Elena
last_name: Marensi
- first_name: Ashley P.
full_name: Willis, Ashley P.
last_name: Willis
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Budanur NB, Marensi E, Willis AP, Hof B. Upper edge of chaos and the energetics
of transition in pipe flow. Physical Review Fluids. 2020;5(2). doi:10.1103/physrevfluids.5.023903
apa: Budanur, N. B., Marensi, E., Willis, A. P., & Hof, B. (2020). Upper edge
of chaos and the energetics of transition in pipe flow. Physical Review Fluids.
American Physical Society. https://doi.org/10.1103/physrevfluids.5.023903
chicago: Budanur, Nazmi B, Elena Marensi, Ashley P. Willis, and Björn Hof. “Upper
Edge of Chaos and the Energetics of Transition in Pipe Flow.” Physical Review
Fluids. American Physical Society, 2020. https://doi.org/10.1103/physrevfluids.5.023903.
ieee: N. B. Budanur, E. Marensi, A. P. Willis, and B. Hof, “Upper edge of chaos
and the energetics of transition in pipe flow,” Physical Review Fluids,
vol. 5, no. 2. American Physical Society, 2020.
ista: Budanur NB, Marensi E, Willis AP, Hof B. 2020. Upper edge of chaos and the
energetics of transition in pipe flow. Physical Review Fluids. 5(2), 023903.
mla: Budanur, Nazmi B., et al. “Upper Edge of Chaos and the Energetics of Transition
in Pipe Flow.” Physical Review Fluids, vol. 5, no. 2, 023903, American
Physical Society, 2020, doi:10.1103/physrevfluids.5.023903.
short: N.B. Budanur, E. Marensi, A.P. Willis, B. Hof, Physical Review Fluids 5 (2020).
date_created: 2020-02-27T10:26:57Z
date_published: 2020-02-21T00:00:00Z
date_updated: 2023-08-18T06:44:46Z
day: '21'
department:
- _id: BjHo
doi: 10.1103/physrevfluids.5.023903
external_id:
arxiv:
- '1912.09270'
isi:
- '000515065100001'
fulldoi: https://doi.org/10.1103/physrevfluids.5.023903
intvolume: ' 5'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.09270
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review Fluids
publication_identifier:
issn:
- 2469-990X
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Upper edge of chaos and the energetics of transition in pipe flow
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2020'
...
---
_id: '7540'
abstract:
- lang: eng
text: ' In vitro propagation of the ornamentally interesting species Wikstroemia
gemmata is limited by the recalcitrance to form adventitious roots. In this article,
two strategies to improve the rooting capacity of in vitro microcuttings are presented.
Firstly, the effect of exogenous auxin was evaluated in both light and dark cultivated
stem segments and also the sucrose-content of the medium was varied in order to
determine better rooting conditions. Secondly, different spectral lights were
evaluated and the effect on shoot growth and root induction demonstrated that
the exact spectral composition of light is important for successful in vitro growth
and development of Wikstroemia gemmata. We show that exogenous auxin cannot compensate
for the poor rooting under unfavorable light conditions. Adapting the culture
conditions is therefore paramount for successful industrial propagation of Wikstroemia
gemmata. '
article_processing_charge: No
article_type: original
author:
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: H.
full_name: Buyle, H.
last_name: Buyle
- first_name: S.
full_name: Werbrouck, S.
last_name: Werbrouck
- first_name: M.C.
full_name: Van Labeke, M.C.
last_name: Van Labeke
- first_name: D.
full_name: Geelen, D.
last_name: Geelen
citation:
ama: Verstraeten I, Buyle H, Werbrouck S, Van Labeke MC, Geelen D. In vitro shoot
growth and adventitious rooting of Wikstroemia gemmata depends on light quality.
Israel Journal of Plant Sciences. 2020;67(1-2):16-26. doi:10.1163/22238980-20191110
apa: Verstraeten, I., Buyle, H., Werbrouck, S., Van Labeke, M. C., & Geelen,
D. (2020). In vitro shoot growth and adventitious rooting of Wikstroemia gemmata
depends on light quality. Israel Journal of Plant Sciences. Brill. https://doi.org/10.1163/22238980-20191110
chicago: Verstraeten, Inge, H. Buyle, S. Werbrouck, M.C. Van Labeke, and D. Geelen.
“In Vitro Shoot Growth and Adventitious Rooting of Wikstroemia Gemmata Depends
on Light Quality.” Israel Journal of Plant Sciences. Brill, 2020. https://doi.org/10.1163/22238980-20191110.
ieee: I. Verstraeten, H. Buyle, S. Werbrouck, M. C. Van Labeke, and D. Geelen, “In
vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on
light quality,” Israel Journal of Plant Sciences, vol. 67, no. 1–2. Brill,
pp. 16–26, 2020.
ista: Verstraeten I, Buyle H, Werbrouck S, Van Labeke MC, Geelen D. 2020. In vitro
shoot growth and adventitious rooting of Wikstroemia gemmata depends on light
quality. Israel Journal of Plant Sciences. 67(1–2), 16–26.
mla: Verstraeten, Inge, et al. “In Vitro Shoot Growth and Adventitious Rooting of
Wikstroemia Gemmata Depends on Light Quality.” Israel Journal of Plant Sciences,
vol. 67, no. 1–2, Brill, 2020, pp. 16–26, doi:10.1163/22238980-20191110.
short: I. Verstraeten, H. Buyle, S. Werbrouck, M.C. Van Labeke, D. Geelen, Israel
Journal of Plant Sciences 67 (2020) 16–26.
date_created: 2020-02-28T09:18:01Z
date_published: 2020-02-01T00:00:00Z
date_updated: 2023-08-18T06:45:15Z
day: '01'
department:
- _id: JiFr
doi: 10.1163/22238980-20191110
external_id:
isi:
- '000525343300004'
fulldoi: https://doi.org/10.1163/22238980-20191110
intvolume: ' 67'
isi: 1
issue: 1-2
language:
- iso: eng
month: '02'
oa_version: None
page: 16-26
publication: Israel Journal of Plant Sciences
publication_identifier:
eissn:
- 2223-8980
issn:
- 0792-9978
publication_status: published
publisher: Brill
quality_controlled: '1'
scopus_import: '1'
status: public
title: In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends
on light quality
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 67
year: '2020'
...
---
_id: '7541'
abstract:
- lang: eng
text: Semiconductor nanowires have been playing a crucial role in the development
of nanoscale devices for the realization of spin qubits, Majorana fermions, single
photon emitters, nanoprocessors, etc. The monolithic growth of site‐controlled
nanowires is a prerequisite toward the next generation of devices that will require
addressability and scalability. Here, combining top‐down nanofabrication and bottom‐up
self‐assembly, the growth of Ge wires on prepatterned Si (001) substrates with
controllable position, distance, length, and structure is reported. This is achieved
by a novel growth process that uses a SiGe strain‐relaxation template and can
be potentially generalized to other material combinations. Transport measurements
show an electrically tunable spin–orbit coupling, with a spin–orbit length similar
to that of III–V materials. Also, charge sensing between quantum dots in closely
spaced wires is observed, which underlines their potential for the realization
of advanced quantum devices. The reported results open a path toward scalable
qubit devices using nanowires on silicon.
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: 'This work was supported by the National Key R&D Program of China
(Grant Nos. 2016YFA0301701 and 2016YFA0300600), the NSFC (Grant Nos. 11574356, 11434010,
and 11404252), the Strategic Priority Research Program of CAS (Grant No. XDB30000000),
the ERC Starting Grant No. 335497, the FWF P32235 project, and the European Union''s
Horizon 2020 research and innovation program under Grant Agreement #862046. This
research was supported by the Scientific Service Units of IST Austria through resources
provided by the MIBA Machine Shop and the nanofabrication facility. F.L. thanks
support from DOE (Grant No. DE‐FG02‐04ER46148). H.H. thanks the Startup Funding
from Xi''an Jiaotong University.'
article_number: '1906523'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Fei
full_name: Gao, Fei
last_name: Gao
- first_name: Jian-Huan
full_name: Wang, Jian-Huan
last_name: Wang
- first_name: Hannes
full_name: Watzinger, Hannes
id: 35DF8E50-F248-11E8-B48F-1D18A9856A87
last_name: Watzinger
- first_name: Hao
full_name: Hu, Hao
last_name: Hu
- first_name: Marko J.
full_name: Rančić, Marko J.
last_name: Rančić
- first_name: Jie-Yin
full_name: Zhang, Jie-Yin
last_name: Zhang
- first_name: Ting
full_name: Wang, Ting
last_name: Wang
- first_name: Yuan
full_name: Yao, Yuan
last_name: Yao
- first_name: Gui-Lei
full_name: Wang, Gui-Lei
last_name: Wang
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
- first_name: Lada
full_name: Vukušić, Lada
id: 31E9F056-F248-11E8-B48F-1D18A9856A87
last_name: Vukušić
orcid: 0000-0003-2424-8636
- first_name: Christoph
full_name: Kloeffel, Christoph
last_name: Kloeffel
- first_name: Daniel
full_name: Loss, Daniel
last_name: Loss
- first_name: Feng
full_name: Liu, Feng
last_name: Liu
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: Jian-Jun
full_name: Zhang, Jian-Jun
last_name: Zhang
citation:
ama: Gao F, Wang J-H, Watzinger H, et al. Site-controlled uniform Ge/Si hut wires
with electrically tunable spin-orbit coupling. Advanced Materials. 2020;32(16).
doi:10.1002/adma.201906523
apa: Gao, F., Wang, J.-H., Watzinger, H., Hu, H., Rančić, M. J., Zhang, J.-Y., …
Zhang, J.-J. (2020). Site-controlled uniform Ge/Si hut wires with electrically
tunable spin-orbit coupling. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201906523
chicago: Gao, Fei, Jian-Huan Wang, Hannes Watzinger, Hao Hu, Marko J. Rančić, Jie-Yin
Zhang, Ting Wang, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically
Tunable Spin-Orbit Coupling.” Advanced Materials. Wiley, 2020. https://doi.org/10.1002/adma.201906523.
ieee: F. Gao et al., “Site-controlled uniform Ge/Si hut wires with electrically
tunable spin-orbit coupling,” Advanced Materials, vol. 32, no. 16. Wiley,
2020.
ista: Gao F, Wang J-H, Watzinger H, Hu H, Rančić MJ, Zhang J-Y, Wang T, Yao Y, Wang
G-L, Kukucka J, Vukušić L, Kloeffel C, Loss D, Liu F, Katsaros G, Zhang J-J. 2020.
Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling.
Advanced Materials. 32(16), 1906523.
mla: Gao, Fei, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically
Tunable Spin-Orbit Coupling.” Advanced Materials, vol. 32, no. 16, 1906523,
Wiley, 2020, doi:10.1002/adma.201906523.
short: F. Gao, J.-H. Wang, H. Watzinger, H. Hu, M.J. Rančić, J.-Y. Zhang, T. Wang,
Y. Yao, G.-L. Wang, J. Kukucka, L. Vukušić, C. Kloeffel, D. Loss, F. Liu, G. Katsaros,
J.-J. Zhang, Advanced Materials 32 (2020).
corr_author: '1'
date_created: 2020-02-28T09:47:00Z
date_published: 2020-04-23T00:00:00Z
date_updated: 2026-06-18T17:54:46Z
day: '23'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1002/adma.201906523
ec_funded: 1
external_id:
isi:
- '000516660900001'
pmid:
- '32105375'
file:
- access_level: open_access
checksum: c622737dc295972065782558337124a2
content_type: application/pdf
creator: dernst
date_created: 2020-11-20T10:11:35Z
date_updated: 2020-11-20T10:11:35Z
file_id: '8782'
file_name: 2020_AdvancedMaterials_Gao.pdf
file_size: 5242880
relation: main_file
success: 1
file_date_updated: 2020-11-20T10:11:35Z
fulldoi: https://doi.org/10.1002/adma.201906523
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '16'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25517E86-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335497'
name: Towards Spin qubits and Majorana fermions in Germanium self assembled hut-wires
- _id: 237B3DA4-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: P32235
name: Towards scalable hut wire quantum devices
- _id: 237E5020-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862046'
name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS
publication: Advanced Materials
publication_identifier:
issn:
- 0935-9648
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '9222'
relation: research_data
status: public
- id: '7996'
relation: dissertation_contains
status: public
- id: '17444'
relation: other
status: public
scopus_import: '1'
status: public
title: Site-controlled uniform Ge/Si hut wires with electrically tunable 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: 32
year: '2020'
...
---
_id: '7546'
abstract:
- lang: eng
text: The extent to which behavior is shaped by experience varies between individuals.
Genetic differences contribute to this variation, but the neural mechanisms are
not understood. Here, we dissect natural variation in the behavioral flexibility
of two Caenorhabditis elegans wild strains. In one strain, a memory of exposure
to 21% O2 suppresses CO2-evoked locomotory arousal; in the other, CO2 evokes arousal
regardless of previous O2 experience. We map that variation to a polymorphic dendritic
scaffold protein, ARCP-1, expressed in sensory neurons. ARCP-1 binds the Ca2+-dependent
phosphodiesterase PDE-1 and co-localizes PDE-1 with molecular sensors for CO2
at dendritic ends. Reducing ARCP-1 or PDE-1 activity promotes CO2 escape by altering
neuropeptide expression in the BAG CO2 sensors. Variation in ARCP-1 alters behavioral
plasticity in multiple paradigms. Our findings are reminiscent of genetic accommodation,
an evolutionary process by which phenotypic flexibility in response to environmental
variation is reset by genetic change.
article_processing_charge: No
article_type: original
author:
- first_name: Isabel
full_name: Beets, Isabel
last_name: Beets
- first_name: Gaotian
full_name: Zhang, Gaotian
last_name: Zhang
- first_name: Lorenz A.
full_name: Fenk, Lorenz A.
last_name: Fenk
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
- first_name: Geoffrey M.
full_name: Nelson, Geoffrey M.
last_name: Nelson
- first_name: Marie-Anne
full_name: Félix, Marie-Anne
last_name: Félix
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Beets I, Zhang G, Fenk LA, et al. Natural variation in a dendritic scaffold
protein remodels experience-dependent plasticity by altering neuropeptide expression.
Neuron. 2020;105(1):106-121.e10. doi:10.1016/j.neuron.2019.10.001
apa: Beets, I., Zhang, G., Fenk, L. A., Chen, C., Nelson, G. M., Félix, M.-A., &
de Bono, M. (2020). Natural variation in a dendritic scaffold protein remodels
experience-dependent plasticity by altering neuropeptide expression. Neuron.
Cell Press. https://doi.org/10.1016/j.neuron.2019.10.001
chicago: Beets, Isabel, Gaotian Zhang, Lorenz A. Fenk, Changchun Chen, Geoffrey
M. Nelson, Marie-Anne Félix, and Mario de Bono. “Natural Variation in a Dendritic
Scaffold Protein Remodels Experience-Dependent Plasticity by Altering Neuropeptide
Expression.” Neuron. Cell Press, 2020. https://doi.org/10.1016/j.neuron.2019.10.001.
ieee: I. Beets et al., “Natural variation in a dendritic scaffold protein
remodels experience-dependent plasticity by altering neuropeptide expression,”
Neuron, vol. 105, no. 1. Cell Press, p. 106–121.e10, 2020.
ista: Beets I, Zhang G, Fenk LA, Chen C, Nelson GM, Félix M-A, de Bono M. 2020.
Natural variation in a dendritic scaffold protein remodels experience-dependent
plasticity by altering neuropeptide expression. Neuron. 105(1), 106–121.e10.
mla: Beets, Isabel, et al. “Natural Variation in a Dendritic Scaffold Protein Remodels
Experience-Dependent Plasticity by Altering Neuropeptide Expression.” Neuron,
vol. 105, no. 1, Cell Press, 2020, p. 106–121.e10, doi:10.1016/j.neuron.2019.10.001.
short: I. Beets, G. Zhang, L.A. Fenk, C. Chen, G.M. Nelson, M.-A. Félix, M. de Bono,
Neuron 105 (2020) 106–121.e10.
corr_author: '1'
date_created: 2020-02-28T10:43:39Z
date_published: 2020-01-08T00:00:00Z
date_updated: 2024-10-09T20:59:20Z
day: '08'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.1016/j.neuron.2019.10.001
external_id:
isi:
- '000507341300012'
pmid:
- '31757604'
file:
- access_level: open_access
checksum: 799bfd297a008753a688b30d3958fa48
content_type: application/pdf
creator: dernst
date_created: 2020-03-02T15:43:57Z
date_updated: 2020-07-14T12:48:00Z
file_id: '7558'
file_name: 2020_Neuron_Beets.pdf
file_size: 3294066
relation: main_file
file_date_updated: 2020-07-14T12:48:00Z
fulldoi: https://doi.org/10.1016/j.neuron.2019.10.001
has_accepted_license: '1'
intvolume: ' 105'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 106-121.e10
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Cell Press
quality_controlled: '1'
status: public
title: Natural variation in a dendritic scaffold protein remodels experience-dependent
plasticity by altering neuropeptide expression
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2020'
...