---
_id: '8535'
abstract:
- lang: eng
text: We propose a method to enhance the visual detail of a water surface simulation.
Our method works as a post-processing step which takes a simulation as input and
increases its apparent resolution by simulating many detailed Lagrangian water
waves on top of it. We extend linear water wave theory to work in non-planar domains
which deform over time, and we discretize the theory using Lagrangian wave packets
attached to spline curves. The method is numerically stable and trivially parallelizable,
and it produces high frequency ripples with dispersive wave-like behaviors customized
to the underlying fluid simulation.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We wish to thank the anonymous reviewers and the members of the Visual
Computing Group at IST Austria for their valuable feedback. This research was supported
by the Scientific Service Units (SSU) of IST Austria through resources provided
by Scientific Computing. This project has received funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
under grant agreement No. 638176 and Marie SkłodowskaCurie Grant Agreement No. 665385.
article_number: '65'
article_processing_charge: No
article_type: original
author:
- first_name: Tomas
full_name: Skrivan, Tomas
id: 486A5A46-F248-11E8-B48F-1D18A9856A87
last_name: Skrivan
- first_name: Andreas
full_name: Soderstrom, Andreas
last_name: Soderstrom
- first_name: John
full_name: Johansson, John
last_name: Johansson
- first_name: Christoph
full_name: Sprenger, Christoph
last_name: Sprenger
- first_name: Ken
full_name: Museth, Ken
last_name: Museth
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. Wave
curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM
Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392466'
apa: 'Skrivan, T., Soderstrom, A., Johansson, J., Sprenger, C., Museth, K., &
Wojtan, C. (2020). Wave curves: Simulating Lagrangian water waves on dynamically
deforming surfaces. ACM Transactions on Graphics. Association for Computing
Machinery. https://doi.org/10.1145/3386569.3392466'
chicago: 'Skrivan, Tomas, Andreas Soderstrom, John Johansson, Christoph Sprenger,
Ken Museth, and Chris Wojtan. “Wave Curves: Simulating Lagrangian Water Waves
on Dynamically Deforming Surfaces.” ACM Transactions on Graphics. Association
for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392466.'
ieee: 'T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, and C. Wojtan,
“Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces,”
ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing
Machinery, 2020.'
ista: 'Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. 2020.
Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces.
ACM Transactions on Graphics. 39(4), 65.'
mla: 'Skrivan, Tomas, et al. “Wave Curves: Simulating Lagrangian Water Waves on
Dynamically Deforming Surfaces.” ACM Transactions on Graphics, vol. 39,
no. 4, 65, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392466.'
short: T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, C. Wojtan,
ACM Transactions on Graphics 39 (2020).
date_created: 2020-09-20T22:01:37Z
date_published: 2020-07-08T00:00:00Z
date_updated: 2023-08-22T09:28:27Z
day: '08'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/3386569.3392466
ec_funded: 1
external_id:
isi:
- '000583700300038'
file:
- access_level: open_access
checksum: c3a680893f01cc4a9e961ff0a4cfa12f
content_type: application/pdf
creator: dernst
date_created: 2020-09-21T07:51:44Z
date_updated: 2020-09-21T07:51:44Z
file_id: '8541'
file_name: 2020_ACM_Skrivan.pdf
file_size: 20223953
relation: main_file
success: 1
file_date_updated: 2020-09-21T07:51:44Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 39
year: '2020'
...
---
_id: '8536'
abstract:
- lang: eng
text: This work analyzes the latency of the simplified successive cancellation (SSC)
decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It
is shown that, unlike conventional successive cancellation decoding, where latency
is linear in the block length, the latency of SSC decoding is sublinear. More
specifically, the latency of SSC decoding is O(N 1−1/µ ), where N is the block
length and µ is the scaling exponent of the channel, which captures the speed
of convergence of the rate to capacity. Numerical results demonstrate the tightness
of the bound and show that most of the latency reduction arises from the parallel
decoding of subcodes of rate 0 and 1.
acknowledgement: M. Mondelli was partially supported by grants NSF DMS-1613091, CCF-1714305,
IIS-1741162 and ONR N00014-18-1-2729. S. A. Hashemi is supported by a Postdoctoral
Fellowship from the Natural Sciences and Engineering Research Council of Canada
(NSERC) and by Huawei.
article_number: 401-406
article_processing_charge: No
arxiv: 1
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Seyyed Ali
full_name: Hashemi, Seyyed Ali
last_name: Hashemi
- first_name: John
full_name: Cioffi, John
last_name: Cioffi
- first_name: Andrea
full_name: Goldsmith, Andrea
last_name: Goldsmith
citation:
ama: 'Mondelli M, Hashemi SA, Cioffi J, Goldsmith A. Simplified successive cancellation
decoding of polar codes has sublinear latency. In: IEEE International Symposium
on Information Theory - Proceedings. Vol 2020-June. IEEE; 2020. doi:10.1109/ISIT44484.2020.9174141'
apa: 'Mondelli, M., Hashemi, S. A., Cioffi, J., & Goldsmith, A. (2020). Simplified
successive cancellation decoding of polar codes has sublinear latency. In IEEE
International Symposium on Information Theory - Proceedings (Vol. 2020–June).
Los Angeles, CA, United States: IEEE. https://doi.org/10.1109/ISIT44484.2020.9174141'
chicago: Mondelli, Marco, Seyyed Ali Hashemi, John Cioffi, and Andrea Goldsmith.
“Simplified Successive Cancellation Decoding of Polar Codes Has Sublinear Latency.”
In IEEE International Symposium on Information Theory - Proceedings, Vol.
2020–June. IEEE, 2020. https://doi.org/10.1109/ISIT44484.2020.9174141.
ieee: M. Mondelli, S. A. Hashemi, J. Cioffi, and A. Goldsmith, “Simplified successive
cancellation decoding of polar codes has sublinear latency,” in IEEE International
Symposium on Information Theory - Proceedings, Los Angeles, CA, United States,
2020, vol. 2020–June.
ista: 'Mondelli M, Hashemi SA, Cioffi J, Goldsmith A. 2020. Simplified successive
cancellation decoding of polar codes has sublinear latency. IEEE International
Symposium on Information Theory - Proceedings. ISIT: Internation Symposium on
Information Theory vol. 2020–June, 401–406.'
mla: Mondelli, Marco, et al. “Simplified Successive Cancellation Decoding of Polar
Codes Has Sublinear Latency.” IEEE International Symposium on Information Theory
- Proceedings, vol. 2020–June, 401–406, IEEE, 2020, doi:10.1109/ISIT44484.2020.9174141.
short: M. Mondelli, S.A. Hashemi, J. Cioffi, A. Goldsmith, in:, IEEE International
Symposium on Information Theory - Proceedings, IEEE, 2020.
conference:
end_date: 2020-06-26
location: Los Angeles, CA, United States
name: 'ISIT: Internation Symposium on Information Theory'
start_date: 2020-06-21
date_created: 2020-09-20T22:01:37Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2023-08-07T13:36:24Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/ISIT44484.2020.9174141
external_id:
arxiv:
- '1909.04892'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1909.04892
month: '06'
oa: 1
oa_version: Preprint
publication: IEEE International Symposium on Information Theory - Proceedings
publication_identifier:
isbn:
- '9781728164328'
issn:
- '21578095'
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '9047'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Simplified successive cancellation decoding of polar codes has sublinear latency
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2020-June
year: '2020'
...
---
_id: '8538'
abstract:
- lang: eng
text: We prove some recent experimental observations of Dan Reznik concerning periodic
billiard orbits in ellipses. For example, the sum of cosines of the angles of
a periodic billiard polygon remains constant in the 1-parameter family of such
polygons (that exist due to the Poncelet porism). In our proofs, we use geometric
and complex analytic methods.
acknowledgement: " This paper would not be written if not for Dan Reznik’s curiosity
and persistence; we are very grateful to him. We also thank R. Garcia and J. Koiller
for interesting discussions. It is a pleasure to thank the Mathematical Institute
of the University of Heidelberg for its stimulating atmosphere. ST thanks M. Bialy
for interesting discussions and the Tel Aviv\r\nUniversity for its invariable hospitality.
AA was supported by European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation programme (grant agreement No 78818 Alpha). RS is supported
by NSF Grant DMS-1807320. ST was supported by NSF grant DMS-1510055 and SFB/TRR
191."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Richard
full_name: Schwartz, Richard
last_name: Schwartz
- first_name: Serge
full_name: Tabachnikov, Serge
last_name: Tabachnikov
citation:
ama: Akopyan A, Schwartz R, Tabachnikov S. Billiards in ellipses revisited. European
Journal of Mathematics. 2020. doi:10.1007/s40879-020-00426-9
apa: Akopyan, A., Schwartz, R., & Tabachnikov, S. (2020). Billiards in ellipses
revisited. European Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s40879-020-00426-9
chicago: Akopyan, Arseniy, Richard Schwartz, and Serge Tabachnikov. “Billiards in
Ellipses Revisited.” European Journal of Mathematics. Springer Nature,
2020. https://doi.org/10.1007/s40879-020-00426-9.
ieee: A. Akopyan, R. Schwartz, and S. Tabachnikov, “Billiards in ellipses revisited,”
European Journal of Mathematics. Springer Nature, 2020.
ista: Akopyan A, Schwartz R, Tabachnikov S. 2020. Billiards in ellipses revisited.
European Journal of Mathematics.
mla: Akopyan, Arseniy, et al. “Billiards in Ellipses Revisited.” European Journal
of Mathematics, Springer Nature, 2020, doi:10.1007/s40879-020-00426-9.
short: A. Akopyan, R. Schwartz, S. Tabachnikov, European Journal of Mathematics
(2020).
date_created: 2020-09-20T22:01:38Z
date_published: 2020-09-09T00:00:00Z
date_updated: 2021-12-02T15:10:17Z
day: '09'
department:
- _id: HeEd
doi: 10.1007/s40879-020-00426-9
ec_funded: 1
external_id:
arxiv:
- '2001.02934'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2001.02934
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
publication: European Journal of Mathematics
publication_identifier:
eissn:
- 2199-6768
issn:
- 2199-675X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Billiards in ellipses revisited
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2020'
...
---
_id: '8539'
abstract:
- lang: eng
text: Cohomological and K-theoretic stable bases originated from the study of quantum
cohomology and quantum K-theory. Restriction formula for cohomological stable
bases played an important role in computing the quantum connection of cotangent
bundle of partial flag varieties. In this paper we study the K-theoretic stable
bases of cotangent bundles of flag varieties. We describe these bases in terms
of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar.
Using this algebraic description and the method of root polynomials, we give a
restriction formula of the stable bases. We apply it to obtain the restriction
formula for partial flag varieties. We also build a relation between the stable
basis and the Casselman basis in the principal series representations of the Langlands
dual group. As an application, we give a closed formula for the transition matrix
between Casselman basis and the characteristic functions.
- lang: fre
text: "Les bases stables cohomologiques et K-théoriques proviennent de l’étude de
la cohomologie quantique et de la K-théorie quantique. La formule de restriction
pour les bases stables cohomologiques a joué un rôle important dans le calcul
de la connexion quantique du fibré cotangent de variétés de drapeaux partielles.
Dans cet article, nous étudions les bases stables K-théoriques de fibré cotangents
des variétés de drapeaux. Nous décrivons ces bases en fonction de l’action de
l’algèbre de Hecke affine et de l’algèbre de Kostant-Kumar. En utilisant cette
description algébrique et la méthode des polynômes de racine, nous donnons une
formule de restriction des bases stables. Nous l’appliquons\r\npour obtenir la
formule de restriction pour les variétés de drapeaux partielles. Nous construisons
également une relation entre la base stable et la base de Casselman dans les représentations
de la série principale du groupe dual de Langlands p-adique. Comme une application,
nous donnons une formule close pour la matrice de transition entre la base de
Casselman et les fonctions caractéristiques. "
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: C.
full_name: Su, C.
last_name: Su
- first_name: Gufang
full_name: Zhao, Gufang
id: 2BC2AC5E-F248-11E8-B48F-1D18A9856A87
last_name: Zhao
- first_name: C.
full_name: Zhong, C.
last_name: Zhong
citation:
ama: Su C, Zhao G, Zhong C. On the K-theory stable bases of the springer resolution.
Annales Scientifiques de l’Ecole Normale Superieure. 2020;53(3):663-671.
doi:10.24033/asens.2431
apa: Su, C., Zhao, G., & Zhong, C. (2020). On the K-theory stable bases of the
springer resolution. Annales Scientifiques de l’Ecole Normale Superieure.
Société Mathématique de France. https://doi.org/10.24033/asens.2431
chicago: Su, C., Gufang Zhao, and C. Zhong. “On the K-Theory Stable Bases of the
Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure.
Société Mathématique de France, 2020. https://doi.org/10.24033/asens.2431.
ieee: C. Su, G. Zhao, and C. Zhong, “On the K-theory stable bases of the springer
resolution,” Annales Scientifiques de l’Ecole Normale Superieure, vol.
53, no. 3. Société Mathématique de France, pp. 663–671, 2020.
ista: Su C, Zhao G, Zhong C. 2020. On the K-theory stable bases of the springer
resolution. Annales Scientifiques de l’Ecole Normale Superieure. 53(3), 663–671.
mla: Su, C., et al. “On the K-Theory Stable Bases of the Springer Resolution.” Annales
Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3, Société Mathématique
de France, 2020, pp. 663–71, doi:10.24033/asens.2431.
short: C. Su, G. Zhao, C. Zhong, Annales Scientifiques de l’Ecole Normale Superieure
53 (2020) 663–671.
date_created: 2020-09-20T22:01:38Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2023-08-22T09:27:57Z
day: '01'
department:
- _id: TaHa
doi: 10.24033/asens.2431
external_id:
arxiv:
- '1708.08013'
isi:
- '000592182600004'
intvolume: ' 53'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.08013
month: '06'
oa: 1
oa_version: Preprint
page: 663-671
publication: Annales Scientifiques de l'Ecole Normale Superieure
publication_identifier:
issn:
- 0012-9593
publication_status: published
publisher: Société Mathématique de France
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the K-theory stable bases of the springer resolution
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 53
year: '2020'
...
---
_id: '8557'
abstract:
- lang: eng
text: The infiltration of immune cells into tissues underlies the establishment
of tissue resident macrophages, and responses to infections and tumors. Yet the
mechanisms immune cells utilize to negotiate tissue barriers in living organisms
are not well understood, and a role for cortical actin has not been examined.
Here we find that the tissue invasion of Drosophila macrophages, also known as
plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated
by the Drosophila member of the fos proto oncogene transcription factor family
(Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances
F-actin levels around the entire macrophage surface by increasing mRNA levels
of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking
filamin Cheerio which are themselves required for invasion. Cortical F-actin levels
are critical as expressing a dominant active form of Diaphanous, a actin polymerizing
Formin, can rescue the Dfos Dominant Negative macrophage invasion defect. In vivo
imaging shows that Dfos is required to enhance the efficiency of the initial phases
of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program
in macrophages counteracts the constraint produced by the tension of surrounding
tissues and buffers the mechanical properties of the macrophage nucleus from affecting
tissue entry. We thus identify tuning the cortical actin cytoskeleton through
Dfos as a key process allowing efficient forward movement of an immune cell into
surrounding tissues.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: 'We thank the following for their contributions: The Drosophila Genomics
Resource Center supported by NIH grant 2P40OD010949-10A1 for plasmids, K. Brueckner.
B. Stramer, M. Uhlirova, O. Schuldiner, the Bloomington Drosophila Stock Center
supported by NIH grant P40OD018537 and the Vienna Drosophila Resource Center for
fly stocks, FlyBase (Thurmond et al., 2019) for essential genomic information, and
the BDGP in situ database for data (Tomancak et al., 2002, 2007). For antibodies,
we thank the Developmental Studies Hybridoma Bank, which was created by the Eunice
Kennedy Shriver National Institute of Child Health and Human Development of the
NIH, and is maintained at the University of Iowa, as well as J. Zeitlinger for her
generous gift of Dfos antibody. We thank the Vienna BioCenter Core Facilities for
RNA sequencing and analysis and the Life Scientific Service Units at IST Austria
for technical support and assistance with microscopy and FACS analysis. We thank
C.P. Heisenberg, P. Martin, M. Sixt and Siekhaus group members for discussions and
T.Hurd, A. Ratheesh and P. Rangan for comments on the manuscript. A.G. was supported
by the Austrian Science Fund (FWF) grant DASI_FWF01_P29638S, D.E.S. by Marie Curie
CIG 334077/IRTIM. M.S. is supported by the FWF, PhD program W1212 915 and the European
Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883). S.W. is
supported by an OEAW, DOC fellowship.'
article_processing_charge: No
author:
- first_name: Vera
full_name: Belyaeva, Vera
id: 47F080FE-F248-11E8-B48F-1D18A9856A87
last_name: Belyaeva
- first_name: Stephanie
full_name: Wachner, Stephanie
id: 2A95E7B0-F248-11E8-B48F-1D18A9856A87
last_name: Wachner
- first_name: Igor
full_name: Gridchyn, Igor
id: 4B60654C-F248-11E8-B48F-1D18A9856A87
last_name: Gridchyn
orcid: 0000-0002-1807-1929
- first_name: Markus
full_name: Linder, Markus
last_name: Linder
- first_name: Shamsi
full_name: Emtenani, Shamsi
id: 49D32318-F248-11E8-B48F-1D18A9856A87
last_name: Emtenani
orcid: 0000-0001-6981-6938
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Maria
full_name: Sibilia, Maria
last_name: Sibilia
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
citation:
ama: Belyaeva V, Wachner S, Gridchyn I, et al. Cortical actin properties controlled
by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance.
bioRxiv. doi:10.1101/2020.09.18.301481
apa: Belyaeva, V., Wachner, S., Gridchyn, I., Linder, M., Emtenani, S., György,
A., … Siekhaus, D. E. (n.d.). Cortical actin properties controlled by Drosophila
Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv.
https://doi.org/10.1101/2020.09.18.301481
chicago: Belyaeva, Vera, Stephanie Wachner, Igor Gridchyn, Markus Linder, Shamsi
Emtenani, Attila György, Maria Sibilia, and Daria E Siekhaus. “Cortical Actin
Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding
Tissue Resistance.” BioRxiv, n.d. https://doi.org/10.1101/2020.09.18.301481.
ieee: V. Belyaeva et al., “Cortical actin properties controlled by Drosophila
Fos aid macrophage infiltration against surrounding tissue resistance,” bioRxiv.
.
ista: Belyaeva V, Wachner S, Gridchyn I, Linder M, Emtenani S, György A, Sibilia
M, Siekhaus DE. Cortical actin properties controlled by Drosophila Fos aid macrophage
infiltration against surrounding tissue resistance. bioRxiv, 10.1101/2020.09.18.301481.
mla: Belyaeva, Vera, et al. “Cortical Actin Properties Controlled by Drosophila
Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” BioRxiv,
doi:10.1101/2020.09.18.301481.
short: V. Belyaeva, S. Wachner, I. Gridchyn, M. Linder, S. Emtenani, A. György,
M. Sibilia, D.E. Siekhaus, BioRxiv (n.d.).
date_created: 2020-09-23T09:36:47Z
date_published: 2020-09-18T00:00:00Z
date_updated: 2024-03-25T23:30:12Z
day: '18'
department:
- _id: DaSi
- _id: JoCs
doi: 10.1101/2020.09.18.301481
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.09.18.301481
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 253B6E48-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29638
name: Drosophila TNFa´s Funktion in Immunzellen
- _id: 2536F660-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
- _id: 26199CA4-B435-11E9-9278-68D0E5697425
grant_number: '24800'
name: Tissue barrier penetration is crucial for immunity and metastasis
publication: bioRxiv
publication_status: submitted
related_material:
record:
- id: '10614'
relation: later_version
status: public
- id: '8983'
relation: dissertation_contains
status: public
status: public
title: Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration
against surrounding tissue resistance
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8562'
abstract:
- lang: eng
text: "Cold bent glass is a promising and cost-efficient method for realizing doubly
curved glass facades. They are produced by attaching planar glass sheets to curved
frames and require keeping the occurring stress within safe limits.\r\nHowever,
it is very challenging to navigate the design space of cold bent glass panels
due to the fragility of the material, which impedes the form-finding for practically
feasible and aesthetically pleasing cold bent glass facades. We propose an interactive,
data-driven approach for designing cold bent glass facades that can be seamlessly
integrated into a typical architectural design pipeline. Our method allows non-expert
users to interactively edit a parametric surface while providing real-time feedback
on the deformed shape and maximum stress of cold bent glass panels. Designs are
automatically refined to minimize several fairness criteria while maximal stresses
are kept within glass limits. We achieve interactive frame rates by using a differentiable
Mixture Density Network trained from more than a million simulations. Given a
curved boundary, our regression model is capable of handling multistable\r\nconfigurations
and accurately predicting the equilibrium shape of the panel and its corresponding
maximal stress. We show predictions are highly accurate and validate our results
with a physical realization of a cold bent glass surface."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank IST Austria’s Scientific Computing team for their support,
Corinna Datsiou and Sophie Pennetier for their expert input on the practical applications
of cold bent glass, and Zaha Hadid Architects and Waagner Biro for providing the
architectural datasets. Photo of Fondation Louis Vuitton by Francisco Anzola / CC
BY 2.0 / cropped.\r\nPhoto of Opus by Danica O. Kus. This project has received funding
from the European Union’s\r\nHorizon 2020 research and innovation program under
grant agreement No 675789 - Algebraic Representations in Computer-Aided Design for
complEx Shapes (ARCADES), from the European Research Council (ERC) under grant agreement
No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design
and Modeling, and SFB-Transregio “Discretization in Geometry and Dynamics” through
grant I 2978 of the Austrian Science Fund (FWF). F. Rist and K. Gavriil have been
partially supported by KAUST baseline funding."
article_number: '208'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Konstantinos
full_name: Gavriil, Konstantinos
last_name: Gavriil
- first_name: Ruslan
full_name: Guseinov, Ruslan
id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87
last_name: Guseinov
orcid: 0000-0001-9819-5077
- first_name: Jesus
full_name: Perez Rodriguez, Jesus
id: 2DC83906-F248-11E8-B48F-1D18A9856A87
last_name: Perez Rodriguez
- first_name: Davide
full_name: Pellis, Davide
last_name: Pellis
- first_name: Paul M
full_name: Henderson, Paul M
id: 13C09E74-18D9-11E9-8878-32CFE5697425
last_name: Henderson
orcid: 0000-0002-5198-7445
- first_name: Florian
full_name: Rist, Florian
last_name: Rist
- first_name: Helmut
full_name: Pottmann, Helmut
last_name: Pottmann
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Gavriil K, Guseinov R, Perez Rodriguez J, et al. Computational design of cold
bent glass façades. ACM Transactions on Graphics. 2020;39(6). doi:10.1145/3414685.3417843
apa: Gavriil, K., Guseinov, R., Perez Rodriguez, J., Pellis, D., Henderson, P. M.,
Rist, F., … Bickel, B. (2020). Computational design of cold bent glass façades.
ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3414685.3417843
chicago: Gavriil, Konstantinos, Ruslan Guseinov, Jesus Perez Rodriguez, Davide Pellis,
Paul M Henderson, Florian Rist, Helmut Pottmann, and Bernd Bickel. “Computational
Design of Cold Bent Glass Façades.” ACM Transactions on Graphics. Association
for Computing Machinery, 2020. https://doi.org/10.1145/3414685.3417843.
ieee: K. Gavriil et al., “Computational design of cold bent glass façades,”
ACM Transactions on Graphics, vol. 39, no. 6. Association for Computing
Machinery, 2020.
ista: Gavriil K, Guseinov R, Perez Rodriguez J, Pellis D, Henderson PM, Rist F,
Pottmann H, Bickel B. 2020. Computational design of cold bent glass façades. ACM
Transactions on Graphics. 39(6), 208.
mla: Gavriil, Konstantinos, et al. “Computational Design of Cold Bent Glass Façades.”
ACM Transactions on Graphics, vol. 39, no. 6, 208, Association for Computing
Machinery, 2020, doi:10.1145/3414685.3417843.
short: K. Gavriil, R. Guseinov, J. Perez Rodriguez, D. Pellis, P.M. Henderson, F.
Rist, H. Pottmann, B. Bickel, ACM Transactions on Graphics 39 (2020).
date_created: 2020-09-23T11:30:02Z
date_published: 2020-11-26T00:00:00Z
date_updated: 2024-02-21T12:43:21Z
day: '26'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3414685.3417843
ec_funded: 1
external_id:
arxiv:
- '2009.03667'
isi:
- '000595589100048'
file:
- access_level: open_access
checksum: c7f67717ad74e670b7daeae732abe151
content_type: application/pdf
creator: bbickel
date_created: 2023-05-23T20:54:43Z
date_updated: 2023-05-23T20:54:43Z
file_id: '13084'
file_name: coldglass.pdf
file_size: 28964641
relation: main_file
success: 1
file_date_updated: 2023-05-23T20:54:43Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/bend-dont-break/
record:
- id: '8366'
relation: dissertation_contains
status: public
- id: '8761'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Computational design of cold bent glass façades
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 39
year: '2020'
...
---
_id: '8563'
abstract:
- lang: eng
text: "Supplementary data provided for the provided for the publication:\r\nIgor
Gridchyn , Philipp Schoenenberger , Joseph O'Neill , Jozsef Csicsvari (2020) Optogenetic
inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron
connections during behavior. Elife."
article_processing_charge: No
author:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Igor
full_name: Gridchyn, Igor
id: 4B60654C-F248-11E8-B48F-1D18A9856A87
last_name: Gridchyn
orcid: 0000-0002-1807-1929
- first_name: Philipp
full_name: Schönenberger, Philipp
id: 3B9D816C-F248-11E8-B48F-1D18A9856A87
last_name: Schönenberger
citation:
ama: Csicsvari JL, Gridchyn I, Schönenberger P. Optogenetic alteration of hippocampal
network activity. 2020. doi:10.15479/AT:ISTA:8563
apa: Csicsvari, J. L., Gridchyn, I., & Schönenberger, P. (2020). Optogenetic
alteration of hippocampal network activity. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:8563
chicago: Csicsvari, Jozsef L, Igor Gridchyn, and Philipp Schönenberger. “Optogenetic
Alteration of Hippocampal Network Activity.” Institute of Science and Technology
Austria, 2020. https://doi.org/10.15479/AT:ISTA:8563.
ieee: J. L. Csicsvari, I. Gridchyn, and P. Schönenberger, “Optogenetic alteration
of hippocampal network activity.” Institute of Science and Technology Austria,
2020.
ista: Csicsvari JL, Gridchyn I, Schönenberger P. 2020. Optogenetic alteration of
hippocampal network activity, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8563.
mla: Csicsvari, Jozsef L., et al. Optogenetic Alteration of Hippocampal Network
Activity. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8563.
short: J.L. Csicsvari, I. Gridchyn, P. Schönenberger, (2020).
contributor:
- contributor_type: project_leader
first_name: Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
date_created: 2020-09-23T14:39:54Z
date_published: 2020-10-19T00:00:00Z
date_updated: 2024-02-21T12:43:41Z
day: '19'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:8563
file:
- access_level: open_access
checksum: a16098a6d172f9c42ab5af5f6991668c
content_type: application/x-compressed
creator: jozsef
date_created: 2020-09-23T14:36:17Z
date_updated: 2020-09-23T14:36:17Z
file_id: '8564'
file_name: upload.tgz
file_size: 145243906
relation: main_file
success: 1
- access_level: open_access
checksum: 0bfc54b7e14c0694cd081617318ba606
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: jozsef
date_created: 2020-10-19T10:12:29Z
date_updated: 2020-10-19T10:12:29Z
file_id: '8675'
file_name: redme.docx
file_size: 11648
relation: main_file
success: 1
file_date_updated: 2020-10-19T10:12:29Z
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8740'
relation: used_in_publication
status: public
status: public
title: Optogenetic alteration of hippocampal network activity
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8568'
abstract:
- lang: eng
text: Aqueous iodine based electrochemical energy storage is considered a potential
candidate to improve sustainability and performance of current battery and supercapacitor
technology. It harnesses the redox activity of iodide, iodine, and polyiodide
species in the confined geometry of nanoporous carbon electrodes. However, current
descriptions of the electrochemical reaction mechanism to interconvert these species
are elusive. Here we show that electrochemical oxidation of iodide in nanoporous
carbons forms persistent solid iodine deposits. Confinement slows down dissolution
into triiodide and pentaiodide, responsible for otherwise significant self-discharge
via shuttling. The main tools for these insights are in situ Raman spectroscopy
and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ
Raman confirms the reversible formation of triiodide and pentaiodide. In situ
SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon
nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying
the solid iodine volume fraction and visualizing the iodine structure on 3D lattice
models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate
strategies for improved iodine pore filling capacity and prevention of self-discharge,
applicable to hybrid supercapacitors and batteries.
article_number: '4838'
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
- first_name: Harald
full_name: Fitzek, Harald
last_name: Fitzek
- first_name: Gerald
full_name: Kothleitner, Gerald
last_name: Kothleitner
- first_name: Volker
full_name: Presser, Volker
last_name: Presser
- first_name: Bernhard
full_name: Gollas, Bernhard
last_name: Gollas
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Qamar
full_name: Abbas, Qamar
last_name: Abbas
citation:
ama: Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine
electrodeposition in nanoporous carbons. Nature Communications. 2020;11.
doi:10.1038/s41467-020-18610-6
apa: Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger,
S. A., & Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition
in nanoporous carbons. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18610-6
chicago: Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard
Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible
Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications.
Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18610-6.
ieee: C. Prehal et al., “Persistent and reversible solid iodine electrodeposition
in nanoporous carbons,” Nature Communications, vol. 11. Springer Nature,
2020.
ista: Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas
Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous
carbons. Nature Communications. 11, 4838.
mla: Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition
in Nanoporous Carbons.” Nature Communications, vol. 11, 4838, Springer
Nature, 2020, doi:10.1038/s41467-020-18610-6.
short: C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger,
Q. Abbas, Nature Communications 11 (2020).
date_created: 2020-09-25T07:23:13Z
date_published: 2020-09-24T00:00:00Z
date_updated: 2023-08-22T09:37:24Z
day: '24'
ddc:
- '530'
department:
- _id: StFr
doi: 10.1038/s41467-020-18610-6
external_id:
isi:
- '000573756600004'
file:
- access_level: open_access
checksum: eada7bc8dd16a49390137cff882ef328
content_type: application/pdf
creator: dernst
date_created: 2020-09-28T13:16:15Z
date_updated: 2020-09-28T13:16:15Z
file_id: '8585'
file_name: 2020_NatureComm_Prehal.pdf
file_size: 1822469
relation: main_file
success: 1
file_date_updated: 2020-09-28T13:16:15Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '09'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-020-19720-x
status: public
title: Persistent and reversible solid iodine electrodeposition in nanoporous carbons
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: 11
year: '2020'
...
---
_id: '8569'
abstract:
- lang: eng
text: Concerted radial migration of newly born cortical projection neurons, from
their birthplace to their final target lamina, is a key step in the assembly of
the cerebral cortex. The cellular and molecular mechanisms regulating the specific
sequential steps of radial neuronal migration in vivo are however still unclear,
let alone the effects and interactions with the extracellular environment. In
any in vivo context, cells will always be exposed to a complex extracellular environment
consisting of (1) secreted factors acting as potential signaling cues, (2) the
extracellular matrix, and (3) other cells providing cell–cell interaction through
receptors and/or direct physical stimuli. Most studies so far have described and
focused mainly on intrinsic cell-autonomous gene functions in neuronal migration
but there is accumulating evidence that non-cell-autonomous-, local-, systemic-,
and/or whole tissue-wide effects substantially contribute to the regulation of
radial neuronal migration. These non-cell-autonomous effects may differentially
affect cortical neuron migration in distinct cellular environments. However, the
cellular and molecular natures of such non-cell-autonomous mechanisms are mostly
unknown. Furthermore, physical forces due to collective migration and/or community
effects (i.e., interactions with surrounding cells) may play important roles in
neocortical projection neuron migration. In this concise review, we first outline
distinct models of non-cell-autonomous interactions of cortical projection neurons
along their radial migration trajectory during development. We then summarize
experimental assays and platforms that can be utilized to visualize and potentially
probe non-cell-autonomous mechanisms. Lastly, we define key questions to address
in the future.
acknowledgement: AH was a recipient of a DOC Fellowship (24812) of the Austrian Academy
of Sciences. This work also received support from IST Austria institutional funds;
the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework
Programme (FP7/2007–2013) under REA Grant Agreement No. 618444 to SH.
article_number: '574382'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Hansen AH, Hippenmeyer S. Non-cell-autonomous mechanisms in radial projection
neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental
Biology. 2020;8(9). doi:10.3389/fcell.2020.574382
apa: Hansen, A. H., & Hippenmeyer, S. (2020). Non-cell-autonomous mechanisms
in radial projection neuron migration in the developing cerebral cortex. Frontiers
in Cell and Developmental Biology. Frontiers. https://doi.org/10.3389/fcell.2020.574382
chicago: Hansen, Andi H, and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms
in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” Frontiers
in Cell and Developmental Biology. Frontiers, 2020. https://doi.org/10.3389/fcell.2020.574382.
ieee: A. H. Hansen and S. Hippenmeyer, “Non-cell-autonomous mechanisms in radial
projection neuron migration in the developing cerebral cortex,” Frontiers in
Cell and Developmental Biology, vol. 8, no. 9. Frontiers, 2020.
ista: Hansen AH, Hippenmeyer S. 2020. Non-cell-autonomous mechanisms in radial projection
neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental
Biology. 8(9), 574382.
mla: Hansen, Andi H., and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in
Radial Projection Neuron Migration in the Developing Cerebral Cortex.” Frontiers
in Cell and Developmental Biology, vol. 8, no. 9, 574382, Frontiers, 2020,
doi:10.3389/fcell.2020.574382.
short: A.H. Hansen, S. Hippenmeyer, Frontiers in Cell and Developmental Biology
8 (2020).
date_created: 2020-09-26T06:11:07Z
date_published: 2020-09-25T00:00:00Z
date_updated: 2024-03-25T23:30:23Z
day: '25'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.3389/fcell.2020.574382
ec_funded: 1
external_id:
isi:
- '000577915900001'
pmid:
- '33102480'
file:
- access_level: open_access
checksum: 01f731824194c94c81a5da360d997073
content_type: application/pdf
creator: dernst
date_created: 2020-09-28T13:11:17Z
date_updated: 2020-09-28T13:11:17Z
file_id: '8584'
file_name: 2020_Frontiers_Hansen.pdf
file_size: 5527139
relation: main_file
success: 1
file_date_updated: 2020-09-28T13:11:17Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular Mechanisms of Radial Neuronal Migration
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
publication: Frontiers in Cell and Developmental Biology
publication_identifier:
issn:
- 2296-634X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
related_material:
record:
- id: '9962'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Non-cell-autonomous mechanisms in radial projection neuron migration in the
developing cerebral cortex
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: 8
year: '2020'
...
---
_id: '8571'
abstract:
- lang: eng
text: We present the results of a friendly competition for formal verification of
continuous and hybrid systems with nonlinear continuous dynamics. The friendly
competition took place as part of the workshop Applied Verification for Continuous
and Hybrid Systems (ARCH) in 2020. This year, 6 tools Ariadne, CORA, DynIbex,
Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. These
tools are applied to solve reachability analysis problems on six benchmark problems,
two of them featuring hybrid dynamics. We do not rank the tools based on the results,
but show the current status and discover the potential advantages of different
tools.
acknowledgement: Christian Schilling acknowledges support in part by the Austrian
Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award) and the European Union’s
Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie
grant agreement No. 754411.
article_processing_charge: No
author:
- first_name: Luca
full_name: Geretti, Luca
last_name: Geretti
- first_name: Julien
full_name: Alexandre Dit Sandretto, Julien
last_name: Alexandre Dit Sandretto
- first_name: Matthias
full_name: Althoff, Matthias
last_name: Althoff
- first_name: Luis
full_name: Benet, Luis
last_name: Benet
- first_name: Alexandre
full_name: Chapoutot, Alexandre
last_name: Chapoutot
- first_name: Xin
full_name: Chen, Xin
last_name: Chen
- first_name: Pieter
full_name: Collins, Pieter
last_name: Collins
- first_name: Marcelo
full_name: Forets, Marcelo
last_name: Forets
- first_name: Daniel
full_name: Freire, Daniel
last_name: Freire
- first_name: Fabian
full_name: Immler, Fabian
last_name: Immler
- first_name: Niklas
full_name: Kochdumper, Niklas
last_name: Kochdumper
- first_name: David
full_name: Sanders, David
last_name: Sanders
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
citation:
ama: 'Geretti L, Alexandre Dit Sandretto J, Althoff M, et al. ARCH-COMP20 Category
Report: Continuous and hybrid systems with nonlinear dynamics. In: EPiC Series
in Computing. Vol 74. EasyChair; 2020:49-75. doi:10.29007/zkf6'
apa: 'Geretti, L., Alexandre Dit Sandretto, J., Althoff, M., Benet, L., Chapoutot,
A., Chen, X., … Schilling, C. (2020). ARCH-COMP20 Category Report: Continuous
and hybrid systems with nonlinear dynamics. In EPiC Series in Computing
(Vol. 74, pp. 49–75). EasyChair. https://doi.org/10.29007/zkf6'
chicago: 'Geretti, Luca, Julien Alexandre Dit Sandretto, Matthias Althoff, Luis
Benet, Alexandre Chapoutot, Xin Chen, Pieter Collins, et al. “ARCH-COMP20 Category
Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” In EPiC Series
in Computing, 74:49–75. EasyChair, 2020. https://doi.org/10.29007/zkf6.'
ieee: 'L. Geretti et al., “ARCH-COMP20 Category Report: Continuous and hybrid
systems with nonlinear dynamics,” in EPiC Series in Computing, 2020, vol.
74, pp. 49–75.'
ista: 'Geretti L, Alexandre Dit Sandretto J, Althoff M, Benet L, Chapoutot A, Chen
X, Collins P, Forets M, Freire D, Immler F, Kochdumper N, Sanders D, Schilling
C. 2020. ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear
dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification
on Continuous and Hybrid Systems vol. 74, 49–75.'
mla: 'Geretti, Luca, et al. “ARCH-COMP20 Category Report: Continuous and Hybrid
Systems with Nonlinear Dynamics.” EPiC Series in Computing, vol. 74, EasyChair,
2020, pp. 49–75, doi:10.29007/zkf6.'
short: L. Geretti, J. Alexandre Dit Sandretto, M. Althoff, L. Benet, A. Chapoutot,
X. Chen, P. Collins, M. Forets, D. Freire, F. Immler, N. Kochdumper, D. Sanders,
C. Schilling, in:, EPiC Series in Computing, EasyChair, 2020, pp. 49–75.
conference:
end_date: 2020-07-12
name: 'ARCH: International Workshop on Applied Verification on Continuous and Hybrid
Systems'
start_date: 2020-07-12
date_created: 2020-09-26T14:41:29Z
date_published: 2020-09-25T00:00:00Z
date_updated: 2021-01-12T08:20:06Z
day: '25'
department:
- _id: ToHe
doi: 10.29007/zkf6
ec_funded: 1
intvolume: ' 74'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://easychair.org/publications/download/nrdD
month: '09'
oa: 1
oa_version: Published Version
page: 49-75
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: EPiC Series in Computing
publication_status: published
publisher: EasyChair
quality_controlled: '1'
status: public
title: 'ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear
dynamics'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2020'
...
---
_id: '8572'
abstract:
- lang: eng
text: 'We present the results of the ARCH 2020 friendly competition for formal verification
of continuous and hybrid systems with linear continuous dynamics. In its fourth
edition, eight tools have been applied to solve eight different benchmark problems
in the category for linear continuous dynamics (in alphabetical order): CORA,
C2E2, HyDRA, Hylaa, Hylaa-Continuous, JuliaReach, SpaceEx, and XSpeed. This report
is a snapshot of the current landscape of tools and the types of benchmarks they
are particularly suited for. Due to the diversity of problems, we are not ranking
tools, yet the presented results provide one of the most complete assessments
of tools for the safety verification of continuous and hybrid systems with linear
continuous dynamics up to this date.'
acknowledgement: "The authors gratefully acknowledge financial support by the European
Commission project\r\njustITSELF under grant number 817629, by the Austrian Science
Fund (FWF) under grant\r\nZ211-N23 (Wittgenstein Award), by the European Union’s
Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie
grant agreement No. 754411, and by the\r\nScience and Engineering Research Board
(SERB) project with file number IMP/2018/000523.\r\nThis material is based upon
work supported by the Air Force Office of Scientific Research under\r\naward number
FA9550-19-1-0288. Any opinions, finding, and conclusions or recommendations\r\nexpressed
in this material are those of the author(s) and do not necessarily reflect the views
of\r\nthe United States Air Force."
article_processing_charge: No
author:
- first_name: Matthias
full_name: Althoff, Matthias
last_name: Althoff
- first_name: Stanley
full_name: Bak, Stanley
last_name: Bak
- first_name: Zongnan
full_name: Bao, Zongnan
last_name: Bao
- first_name: Marcelo
full_name: Forets, Marcelo
last_name: Forets
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Daniel
full_name: Freire, Daniel
last_name: Freire
- first_name: Niklas
full_name: Kochdumper, Niklas
last_name: Kochdumper
- first_name: Yangge
full_name: Li, Yangge
last_name: Li
- first_name: Sayan
full_name: Mitra, Sayan
last_name: Mitra
- first_name: Rajarshi
full_name: Ray, Rajarshi
last_name: Ray
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Stefan
full_name: Schupp, Stefan
last_name: Schupp
- first_name: Mark
full_name: Wetzlinger, Mark
last_name: Wetzlinger
citation:
ama: 'Althoff M, Bak S, Bao Z, et al. ARCH-COMP20 Category Report: Continuous and
hybrid systems with linear dynamics. In: EPiC Series in Computing. Vol
74. EasyChair; 2020:16-48. doi:10.29007/7dt2'
apa: 'Althoff, M., Bak, S., Bao, Z., Forets, M., Frehse, G., Freire, D., … Wetzlinger,
M. (2020). ARCH-COMP20 Category Report: Continuous and hybrid systems with linear
dynamics. In EPiC Series in Computing (Vol. 74, pp. 16–48). EasyChair.
https://doi.org/10.29007/7dt2'
chicago: 'Althoff, Matthias, Stanley Bak, Zongnan Bao, Marcelo Forets, Goran Frehse,
Daniel Freire, Niklas Kochdumper, et al. “ARCH-COMP20 Category Report: Continuous
and Hybrid Systems with Linear Dynamics.” In EPiC Series in Computing,
74:16–48. EasyChair, 2020. https://doi.org/10.29007/7dt2.'
ieee: 'M. Althoff et al., “ARCH-COMP20 Category Report: Continuous and hybrid
systems with linear dynamics,” in EPiC Series in Computing, 2020, vol.
74, pp. 16–48.'
ista: 'Althoff M, Bak S, Bao Z, Forets M, Frehse G, Freire D, Kochdumper N, Li Y,
Mitra S, Ray R, Schilling C, Schupp S, Wetzlinger M. 2020. ARCH-COMP20 Category
Report: Continuous and hybrid systems with linear dynamics. EPiC Series in Computing.
ARCH: International Workshop on Applied Verification on Continuous and Hybrid
Systems vol. 74, 16–48.'
mla: 'Althoff, Matthias, et al. “ARCH-COMP20 Category Report: Continuous and Hybrid
Systems with Linear Dynamics.” EPiC Series in Computing, vol. 74, EasyChair,
2020, pp. 16–48, doi:10.29007/7dt2.'
short: M. Althoff, S. Bak, Z. Bao, M. Forets, G. Frehse, D. Freire, N. Kochdumper,
Y. Li, S. Mitra, R. Ray, C. Schilling, S. Schupp, M. Wetzlinger, in:, EPiC Series
in Computing, EasyChair, 2020, pp. 16–48.
conference:
end_date: 2020-07-12
name: 'ARCH: International Workshop on Applied Verification on Continuous and Hybrid
Systems'
start_date: 2020-07-12
date_created: 2020-09-26T14:49:43Z
date_published: 2020-09-25T00:00:00Z
date_updated: 2021-01-12T08:20:06Z
day: '25'
department:
- _id: ToHe
doi: 10.29007/7dt2
ec_funded: 1
intvolume: ' 74'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://easychair.org/publications/download/DRpS
month: '09'
oa: 1
oa_version: Published Version
page: 16-48
project:
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: EPiC Series in Computing
publication_status: published
publisher: EasyChair
quality_controlled: '1'
status: public
title: 'ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2020'
...
---
_id: '8574'
abstract:
- lang: eng
text: "This thesis concerns itself with the interactions of evolutionary and ecological
forces and the consequences on genetic diversity and the ultimate survival of
populations. It is important to understand what signals processes \r\nleave on
the genome and what we can infer from such data, which is usually abundant but
noisy. Furthermore, understanding how and when populations adapt or go extinct
is important for practical purposes, such as the genetic management of populations,
as well as for theoretical questions, since local adaptation can be the first
step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy
to approximate the demographic changes of a population in a simple setting, namely
the logistic growth model with immigration. We show that this method is not only
a powerful \r\ntool in physics but can be gainfully applied in an ecological framework.
We investigate how well it approximates the real \r\nbehavior of the system, and
find that is does so, even in unexpected situations. Finally, we illustrate how
it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution
of allele frequencies and population sizes in an infinite island model.\r\nWe
give conditions under which polygenic adaptation to a rare habitat is possible.
The model we use is based on the diffusion approximation, considers eco-evolutionary
feedback mechanisms (hard selection), and treats both \r\ndrift and environmental
fluctuations explicitly. We also look at limiting scenarios, for which we derive
analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation
tool to obtain patterns of diversity in a spatially explicit subdivided population,
in which the demographic history of each subpopulation can be specified. We compare
\r\nthe results to existing predictions, and explore the relative importance of
time and space under a variety of spatial arrangements and demographic histories,
such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook
to further research. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Eniko
full_name: Szep, Eniko
id: 485BB5A4-F248-11E8-B48F-1D18A9856A87
last_name: Szep
citation:
ama: Szep E. Local adaptation in metapopulations. 2020. doi:10.15479/AT:ISTA:8574
apa: Szep, E. (2020). Local adaptation in metapopulations. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:8574
chicago: Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science
and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8574.
ieee: E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology
Austria, 2020.
ista: Szep E. 2020. Local adaptation in metapopulations. Institute of Science and
Technology Austria.
mla: Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science
and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574.
short: E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology
Austria, 2020.
date_created: 2020-09-28T07:33:38Z
date_published: 2020-09-20T00:00:00Z
date_updated: 2023-09-07T13:11:39Z
day: '20'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:8574
file:
- access_level: open_access
checksum: 20e71f015fbbd78fea708893ad634ed0
content_type: application/pdf
creator: dernst
date_created: 2020-09-28T07:25:35Z
date_updated: 2020-09-28T07:25:35Z
file_id: '8575'
file_name: thesis_EnikoSzep_final.pdf
file_size: 6354833
relation: main_file
success: 1
- access_level: closed
checksum: a8de2c14a1bb4e53c857787efbb289e1
content_type: application/x-zip-compressed
creator: dernst
date_created: 2020-09-28T07:25:37Z
date_updated: 2020-09-28T07:25:37Z
file_id: '8576'
file_name: thesisFiles_EnikoSzep.zip
file_size: 23020401
relation: source_file
file_date_updated: 2020-09-28T07:25:37Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '158'
publication_identifier:
eissn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Local adaptation in metapopulations
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8579'
abstract:
- lang: eng
text: Copper (Cu) is an essential trace element for all living organisms and used
as cofactor in key enzymes of important biological processes, such as aerobic
respiration or superoxide dismutation. However, due to its toxicity, cells have
developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for
cuproprotein biogenesis with the need to remove excess Cu. This review summarizes
our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative
bacteria and describes the multiple strategies that bacteria use for uptake, storage
and export of Cu. We furthermore describe general mechanistic principles that
aid the bacterial response to toxic Cu concentrations and illustrate dedicated
Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress
in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu
quota for cell proliferation is of particular importance for microbial pathogens
because Cu is utilized by the host immune system for attenuating pathogen survival
in host cells.
article_number: '242'
article_processing_charge: No
article_type: original
author:
- first_name: Andreea
full_name: Andrei, Andreea
last_name: Andrei
- first_name: Yavuz
full_name: Öztürk, Yavuz
last_name: Öztürk
- first_name: Bahia
full_name: Khalfaoui-Hassani, Bahia
last_name: Khalfaoui-Hassani
- first_name: Juna
full_name: Rauch, Juna
last_name: Rauch
- first_name: Dorian
full_name: Marckmann, Dorian
last_name: Marckmann
- first_name: Petru Iulian
full_name: Trasnea, Petru Iulian
id: D560034C-10C4-11EA-ABF4-A4B43DDC885E
last_name: Trasnea
- first_name: Fevzi
full_name: Daldal, Fevzi
last_name: Daldal
- first_name: Hans-Georg
full_name: Koch, Hans-Georg
last_name: Koch
citation:
ama: 'Andrei A, Öztürk Y, Khalfaoui-Hassani B, et al. Cu homeostasis in bacteria:
The ins and outs. Membranes. 2020;10(9). doi:10.3390/membranes10090242'
apa: 'Andrei, A., Öztürk, Y., Khalfaoui-Hassani, B., Rauch, J., Marckmann, D., Trasnea,
P. I., … Koch, H.-G. (2020). Cu homeostasis in bacteria: The ins and outs. Membranes.
MDPI. https://doi.org/10.3390/membranes10090242'
chicago: 'Andrei, Andreea, Yavuz Öztürk, Bahia Khalfaoui-Hassani, Juna Rauch, Dorian
Marckmann, Petru Iulian Trasnea, Fevzi Daldal, and Hans-Georg Koch. “Cu Homeostasis
in Bacteria: The Ins and Outs.” Membranes. MDPI, 2020. https://doi.org/10.3390/membranes10090242.'
ieee: 'A. Andrei et al., “Cu homeostasis in bacteria: The ins and outs,”
Membranes, vol. 10, no. 9. MDPI, 2020.'
ista: 'Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI,
Daldal F, Koch H-G. 2020. Cu homeostasis in bacteria: The ins and outs. Membranes.
10(9), 242.'
mla: 'Andrei, Andreea, et al. “Cu Homeostasis in Bacteria: The Ins and Outs.” Membranes,
vol. 10, no. 9, 242, MDPI, 2020, doi:10.3390/membranes10090242.'
short: A. Andrei, Y. Öztürk, B. Khalfaoui-Hassani, J. Rauch, D. Marckmann, P.I.
Trasnea, F. Daldal, H.-G. Koch, Membranes 10 (2020).
date_created: 2020-09-28T08:59:26Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2023-08-22T09:34:06Z
day: '01'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.3390/membranes10090242
external_id:
isi:
- '000581446000001'
file:
- access_level: open_access
checksum: ceb43d7554e712dea6f36f9287271737
content_type: application/pdf
creator: dernst
date_created: 2020-09-28T11:36:50Z
date_updated: 2020-09-28T11:36:50Z
file_id: '8583'
file_name: 2020_Membranes_Andrei.pdf
file_size: 4612258
relation: main_file
success: 1
file_date_updated: 2020-09-28T11:36:50Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Membranes
publication_identifier:
eissn:
- '20770375'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Cu homeostasis in bacteria: The ins and outs'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2020'
...
---
_id: '8580'
abstract:
- lang: eng
text: We evaluate the usefulness of persistent homology in the analysis of heart
rate variability. In our approach we extract several topological descriptors characterising
datasets of RR-intervals, which are later used in classical machine learning algorithms.
By this method we are able to differentiate the group of patients with the history
of transient ischemic attack and the group of hypertensive patients.
article_number: '9158054'
article_processing_charge: No
author:
- first_name: Grzegorz
full_name: Graff, Grzegorz
last_name: Graff
- first_name: Beata
full_name: Graff, Beata
last_name: Graff
- first_name: Grzegorz
full_name: Jablonski, Grzegorz
id: 4483EF78-F248-11E8-B48F-1D18A9856A87
last_name: Jablonski
orcid: 0000-0002-3536-9866
- first_name: Krzysztof
full_name: Narkiewicz, Krzysztof
last_name: Narkiewicz
citation:
ama: 'Graff G, Graff B, Jablonski G, Narkiewicz K. The application of persistent
homology in the analysis of heart rate variability. In: 11th Conference of
the European Study Group on Cardiovascular Oscillations: Computation and Modelling
in Physiology: New Challenges and Opportunities, . IEEE; 2020. doi:10.1109/ESGCO49734.2020.9158054'
apa: 'Graff, G., Graff, B., Jablonski, G., & Narkiewicz, K. (2020). The application
of persistent homology in the analysis of heart rate variability. In 11th Conference
of the European Study Group on Cardiovascular Oscillations: Computation and Modelling
in Physiology: New Challenges and Opportunities, . Pisa, Italy: IEEE. https://doi.org/10.1109/ESGCO49734.2020.9158054'
chicago: 'Graff, Grzegorz, Beata Graff, Grzegorz Jablonski, and Krzysztof Narkiewicz.
“The Application of Persistent Homology in the Analysis of Heart Rate Variability.”
In 11th Conference of the European Study Group on Cardiovascular Oscillations:
Computation and Modelling in Physiology: New Challenges and Opportunities, .
IEEE, 2020. https://doi.org/10.1109/ESGCO49734.2020.9158054.'
ieee: 'G. Graff, B. Graff, G. Jablonski, and K. Narkiewicz, “The application of
persistent homology in the analysis of heart rate variability,” in 11th Conference
of the European Study Group on Cardiovascular Oscillations: Computation and Modelling
in Physiology: New Challenges and Opportunities, , Pisa, Italy, 2020.'
ista: 'Graff G, Graff B, Jablonski G, Narkiewicz K. 2020. The application of persistent
homology in the analysis of heart rate variability. 11th Conference of the European
Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology:
New Challenges and Opportunities, . ESGCO: European Study Group on Cardiovascular
Oscillations, 9158054.'
mla: 'Graff, Grzegorz, et al. “The Application of Persistent Homology in the Analysis
of Heart Rate Variability.” 11th Conference of the European Study Group on
Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges
and Opportunities, , 9158054, IEEE, 2020, doi:10.1109/ESGCO49734.2020.9158054.'
short: 'G. Graff, B. Graff, G. Jablonski, K. Narkiewicz, in:, 11th Conference of
the European Study Group on Cardiovascular Oscillations: Computation and Modelling
in Physiology: New Challenges and Opportunities, , IEEE, 2020.'
conference:
end_date: 2020-07-15
location: Pisa, Italy
name: 'ESGCO: European Study Group on Cardiovascular Oscillations'
start_date: 2020-07-15
date_created: 2020-09-28T08:59:27Z
date_published: 2020-08-01T00:00:00Z
date_updated: 2023-08-22T09:33:34Z
day: '01'
department:
- _id: HeEd
doi: 10.1109/ESGCO49734.2020.9158054
external_id:
isi:
- '000621172600045'
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
publication: '11th Conference of the European Study Group on Cardiovascular Oscillations:
Computation and Modelling in Physiology: New Challenges and Opportunities, '
publication_identifier:
isbn:
- '9781728157511'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: The application of persistent homology in the analysis of heart rate variability
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2020'
...
---
_id: '8581'
abstract:
- lang: eng
text: The majority of adenosine triphosphate (ATP) powering cellular processes in
eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present
the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo,
determined by cryo-electron microscopy. Subunits in the membrane domain are arranged
in the ‘proton translocation cluster’ attached to the c-ring and a more distant
‘hook apparatus’ holding subunit e. Unexpectedly, this subunit is anchored to
a lipid ‘plug’ capping the c-ring. We present a detailed proton translocation
pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM
maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled
c-ring, suggesting permeability transition pore opening. We propose a model for
the permeability transition pore opening, whereby subunit e pulls the lipid plug
out of the c-ring. Our structure will allow the design of drugs for many emerging
applications in medicine.
acknowledged_ssus:
- _id: EM-Fac
- _id: ScienComp
acknowledgement: We thank J. Novacek from CEITEC (Brno, Czech Republic) for assistance
with collecting the FEI Krios dataset and iNEXT for providing access to CEITEC.
We thank the IST Austria EM facility for access and assistance with collecting the
FEI Glacios dataset. Data processing was performed at the IST high-performance computing
cluster. This work has been supported by iNEXT EM HEDC (proposal 4506), funded by
the Horizon 2020 Programme of the European Commission.
article_processing_charge: No
article_type: original
author:
- first_name: Gergely
full_name: Pinke, Gergely
id: 4D5303E6-F248-11E8-B48F-1D18A9856A87
last_name: Pinke
- first_name: Long
full_name: Zhou, Long
id: 3E751364-F248-11E8-B48F-1D18A9856A87
last_name: Zhou
orcid: 0000-0002-1864-8951
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Pinke G, Zhou L, Sazanov LA. Cryo-EM structure of the entire mammalian F-type
ATP synthase. Nature Structural and Molecular Biology. 2020;27(11):1077-1085.
doi:10.1038/s41594-020-0503-8
apa: Pinke, G., Zhou, L., & Sazanov, L. A. (2020). Cryo-EM structure of the
entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology.
Springer Nature. https://doi.org/10.1038/s41594-020-0503-8
chicago: Pinke, Gergely, Long Zhou, and Leonid A Sazanov. “Cryo-EM Structure of
the Entire Mammalian F-Type ATP Synthase.” Nature Structural and Molecular
Biology. Springer Nature, 2020. https://doi.org/10.1038/s41594-020-0503-8.
ieee: G. Pinke, L. Zhou, and L. A. Sazanov, “Cryo-EM structure of the entire mammalian
F-type ATP synthase,” Nature Structural and Molecular Biology, vol. 27,
no. 11. Springer Nature, pp. 1077–1085, 2020.
ista: Pinke G, Zhou L, Sazanov LA. 2020. Cryo-EM structure of the entire mammalian
F-type ATP synthase. Nature Structural and Molecular Biology. 27(11), 1077–1085.
mla: Pinke, Gergely, et al. “Cryo-EM Structure of the Entire Mammalian F-Type ATP
Synthase.” Nature Structural and Molecular Biology, vol. 27, no. 11, Springer
Nature, 2020, pp. 1077–85, doi:10.1038/s41594-020-0503-8.
short: G. Pinke, L. Zhou, L.A. Sazanov, Nature Structural and Molecular Biology
27 (2020) 1077–1085.
date_created: 2020-09-28T08:59:27Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2023-08-22T09:33:09Z
day: '01'
department:
- _id: LeSa
doi: 10.1038/s41594-020-0503-8
external_id:
isi:
- '000569299400004'
pmid:
- '32929284'
intvolume: ' 27'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 1077-1085
pmid: 1
publication: Nature Structural and Molecular Biology
publication_identifier:
eissn:
- '15459985'
issn:
- '15459993'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/structure-of-atpase-solved/
scopus_import: '1'
status: public
title: Cryo-EM structure of the entire mammalian F-type ATP synthase
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 27
year: '2020'
...
---
_id: '8586'
abstract:
- lang: eng
text: Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights
into biological processes and structures within a native context. However, a major
challenge still lies in the efficient and reproducible preparation of adherent
cells for subsequent cryo-EM analysis. This is due to the sensitivity of many
cellular specimens to the varying seeding and culturing conditions required for
EM experiments, the often limited amount of cellular material and also the fragility
of EM grids and their substrate. Here, we present low-cost and reusable 3D printed
grid holders, designed to improve specimen preparation when culturing challenging
cellular samples directly on grids. The described grid holders increase cell culture
reproducibility and throughput, and reduce the resources required for cell culturing.
We show that grid holders can be integrated into various cryo-EM workflows, including
micro-patterning approaches to control cell seeding on grids, and for generating
samples for cryo-focused ion beam milling and cryo-electron tomography experiments.
Their adaptable design allows for the generation of specialized grid holders customized
to a large variety of applications.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: This work was supported by the Austrian Science Fund (FWF, P33367)
to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was
also supported by the Scientific Service Units (SSU) of IST Austria through resources
provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the
BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi
Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing
our grid holders in different experimental setups and Daniel Gütl and the Kondrashov
group (IST Austria) for granting us repeated access to their 3D printers. We also
thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary
BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised
foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William
Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science)
for illustrating the graphical abstract.
article_number: '107633'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- 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: Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders
for improved cellular specimen preparation in cryo-electron microscopy. Journal
of Structural Biology. 2020;212(3). doi:10.1016/j.jsb.2020.107633
apa: Fäßler, F., Zens, B., Hauschild, R., & Schur, F. K. (2020). 3D printed
cell culture grid holders for improved cellular specimen preparation in cryo-electron
microscopy. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2020.107633
chicago: Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur.
“3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation
in Cryo-Electron Microscopy.” Journal of Structural Biology. Elsevier,
2020. https://doi.org/10.1016/j.jsb.2020.107633.
ieee: F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture
grid holders for improved cellular specimen preparation in cryo-electron microscopy,”
Journal of Structural Biology, vol. 212, no. 3. Elsevier, 2020.
ista: Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid
holders for improved cellular specimen preparation in cryo-electron microscopy.
Journal of Structural Biology. 212(3), 107633.
mla: Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved
Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural
Biology, vol. 212, no. 3, 107633, Elsevier, 2020, doi:10.1016/j.jsb.2020.107633.
short: F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology
212 (2020).
date_created: 2020-09-29T13:24:06Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2024-03-25T23:30:04Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1016/j.jsb.2020.107633
external_id:
isi:
- '000600997800008'
file:
- access_level: open_access
checksum: c48cbf594e84fc2f91966ffaafc0918c
content_type: application/pdf
creator: dernst
date_created: 2020-12-10T14:01:10Z
date_updated: 2020-12-10T14:01:10Z
file_id: '8937'
file_name: 2020_JourStrucBiology_Faessler.pdf
file_size: 7076870
relation: main_file
success: 1
file_date_updated: 2020-12-10T14:01:10Z
has_accepted_license: '1'
intvolume: ' 212'
isi: 1
issue: '3'
keyword:
- electron microscopy
- cryo-EM
- EM sample preparation
- 3D printing
- cell culture
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
- _id: 059B463C-7A3F-11EA-A408-12923DDC885E
name: NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '14592'
relation: used_in_publication
status: public
- id: '12491'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 3D printed cell culture grid holders for improved cellular specimen preparation
in cryo-electron microscopy
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: 212
year: '2020'
...
---
_id: '8587'
abstract:
- lang: eng
text: Inspired by the possibility to experimentally manipulate and enhance chemical
reactivity in helium nanodroplets, we investigate the effective interaction and
the resulting correlations between two diatomic molecules immersed in a bath of
bosons. By analogy with the bipolaron, we introduce the biangulon quasiparticle
describing two rotating molecules that align with respect to each other due to
the effective attractive interaction mediated by the excitations of the bath.
We study this system in different parameter regimes and apply several theoretical
approaches to describe its properties. Using a Born–Oppenheimer approximation,
we investigate the dependence of the effective intermolecular interaction on the
rotational state of the two molecules. In the strong-coupling regime, a product-state
ansatz shows that the molecules tend to have a strong alignment in the ground
state. To investigate the system in the weak-coupling regime, we apply a one-phonon
excitation variational ansatz, which allows us to access the energy spectrum.
In comparison to the angulon quasiparticle, the biangulon shows shifted angulon
instabilities and an additional spectral instability, where resonant angular momentum
transfer between the molecules and the bath takes place. These features are proposed
as an experimentally observable signature for the formation of the biangulon quasiparticle.
Finally, by using products of single angulon and bare impurity wave functions
as basis states, we introduce a diagonalization scheme that allows us to describe
the transition from two separated angulons to a biangulon as a function of the
distance between the two molecules.
acknowledgement: We are grateful to Areg Ghazaryan for valuable discussions. M.L.
acknowledges support from the Austrian Science Fund (FWF) under Project No. P29902-N27
and from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).
G.B. acknowledges support from the Austrian Science Fund (FWF) under Project No.
M2461-N27. A.D. acknowledges funding from the European Union’s Horizon 2020 research
and innovation programme under the European Research Council (ERC) Grant Agreement
No. 694227 and under the Marie Sklodowska-Curie Grant Agreement No. 836146. R.S.
was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)
under Germany’s Excellence Strategy – EXC-2111 – 390814868.
article_number: '164302'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Xiang
full_name: Li, Xiang
id: 4B7E523C-F248-11E8-B48F-1D18A9856A87
last_name: Li
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Richard
full_name: Schmidt, Richard
last_name: Schmidt
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Andreas
full_name: Deuchert, Andreas
id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87
last_name: Deuchert
orcid: 0000-0003-3146-6746
citation:
ama: Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. Intermolecular
forces and correlations mediated by a phonon bath. The Journal of Chemical
Physics. 2020;152(16). doi:10.1063/1.5144759
apa: Li, X., Yakaboylu, E., Bighin, G., Schmidt, R., Lemeshko, M., & Deuchert,
A. (2020). Intermolecular forces and correlations mediated by a phonon bath. The
Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5144759
chicago: Li, Xiang, Enderalp Yakaboylu, Giacomo Bighin, Richard Schmidt, Mikhail
Lemeshko, and Andreas Deuchert. “Intermolecular Forces and Correlations Mediated
by a Phonon Bath.” The Journal of Chemical Physics. AIP Publishing, 2020.
https://doi.org/10.1063/1.5144759.
ieee: X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, and A. Deuchert,
“Intermolecular forces and correlations mediated by a phonon bath,” The Journal
of Chemical Physics, vol. 152, no. 16. AIP Publishing, 2020.
ista: Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. 2020. Intermolecular
forces and correlations mediated by a phonon bath. The Journal of Chemical Physics.
152(16), 164302.
mla: Li, Xiang, et al. “Intermolecular Forces and Correlations Mediated by a Phonon
Bath.” The Journal of Chemical Physics, vol. 152, no. 16, 164302, AIP Publishing,
2020, doi:10.1063/1.5144759.
short: X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, A. Deuchert, The
Journal of Chemical Physics 152 (2020).
date_created: 2020-09-30T10:33:17Z
date_published: 2020-04-27T00:00:00Z
date_updated: 2024-08-07T07:16:53Z
day: '27'
department:
- _id: MiLe
- _id: RoSe
doi: 10.1063/1.5144759
ec_funded: 1
external_id:
arxiv:
- '1912.02658'
isi:
- '000530448300001'
intvolume: ' 152'
isi: 1
issue: '16'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.02658
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
- _id: 26986C82-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02641
name: A path-integral approach to composite impurities
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
record:
- id: '8958'
relation: dissertation_contains
status: public
status: public
title: Intermolecular forces and correlations mediated by a phonon bath
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 152
year: '2020'
...
---
_id: '8588'
abstract:
- lang: eng
text: Dipolar (or spatially indirect) excitons (IXs) in semiconductor double quantum
well (DQW) subjected to an electric field are neutral species with a dipole moment
oriented perpendicular to the DQW plane. Here, we theoretically study interactions
between IXs in stacked DQW bilayers, where the dipolar coupling can be either
attractive or repulsive depending on the relative positions of the particles.
By using microscopic band structure calculations to determine the electronic states
forming the excitons, we show that the attractive dipolar interaction between
stacked IXs deforms their electronic wave function, thereby increasing the inter-DQW
interaction energy and making the IX even more electrically polarizable. Many-particle
interaction effects are addressed by considering the coupling between a single
IX in one of the DQWs to a cloud of IXs in the other DQW, which is modeled either
as a closed-packed lattice or as a continuum IX fluid. We find that the lattice
model yields IX interlayer binding energies decreasing with increasing lattice
density. This behavior is due to the dominating role of the intra-DQW dipolar
repulsion, which prevents more than one exciton from entering the attractive region
of the inter-DQW coupling. Finally, both models shows that the single IX distorts
the distribution of IXs in the adjacent DQW, thus inducing the formation of an
IX dipolar polaron (dipolaron). While the interlayer binding energy reduces with
IX density for lattice dipolarons, the continuous polaron model predicts a nonmonotonous
dependence on density in semiquantitative agreement with a recent experimental
study [cf. Hubert et al., Phys. Rev. X 9, 021026 (2019)].
acknowledgement: "We thank W. Kaganer for discussions and for comment on the manuscript.
We acknowledge the financial support from the German-Israeli Foundation (GIF), grant
agreement I-1277-303.10/2014. M.L. acknowledges support by the Austrian Science
Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC)
Starting Grant No. 801770 (ANGULON). A.G. acknowledges support by the European Unions
Horizon 2020 research and innovation\r\nprogram under the Marie Skodowska-Curie
grant agreement No 754411. P.V.S acknowledges financial support\r\nfrom the Deutsche
Forschungsgemeinschaft (DFG) under\r\nProject No. SA 598/12-1."
article_number: '045307'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: C.
full_name: Hubert, C.
last_name: Hubert
- first_name: K.
full_name: Cohen, K.
last_name: Cohen
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: R.
full_name: Rapaport, R.
last_name: Rapaport
- first_name: P. V.
full_name: Santos, P. V.
last_name: Santos
citation:
ama: Hubert C, Cohen K, Ghazaryan A, Lemeshko M, Rapaport R, Santos PV. Attractive
interactions, molecular complexes, and polarons in coupled dipolar exciton fluids.
Physical Review B. 2020;102(4). doi:10.1103/physrevb.102.045307
apa: Hubert, C., Cohen, K., Ghazaryan, A., Lemeshko, M., Rapaport, R., & Santos,
P. V. (2020). Attractive interactions, molecular complexes, and polarons in coupled
dipolar exciton fluids. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.102.045307
chicago: Hubert, C., K. Cohen, Areg Ghazaryan, Mikhail Lemeshko, R. Rapaport, and
P. V. Santos. “Attractive Interactions, Molecular Complexes, and Polarons in Coupled
Dipolar Exciton Fluids.” Physical Review B. American Physical Society,
2020. https://doi.org/10.1103/physrevb.102.045307.
ieee: C. Hubert, K. Cohen, A. Ghazaryan, M. Lemeshko, R. Rapaport, and P. V. Santos,
“Attractive interactions, molecular complexes, and polarons in coupled dipolar
exciton fluids,” Physical Review B, vol. 102, no. 4. American Physical
Society, 2020.
ista: Hubert C, Cohen K, Ghazaryan A, Lemeshko M, Rapaport R, Santos PV. 2020. Attractive
interactions, molecular complexes, and polarons in coupled dipolar exciton fluids.
Physical Review B. 102(4), 045307.
mla: Hubert, C., et al. “Attractive Interactions, Molecular Complexes, and Polarons
in Coupled Dipolar Exciton Fluids.” Physical Review B, vol. 102, no. 4,
045307, American Physical Society, 2020, doi:10.1103/physrevb.102.045307.
short: C. Hubert, K. Cohen, A. Ghazaryan, M. Lemeshko, R. Rapaport, P.V. Santos,
Physical Review B 102 (2020).
date_created: 2020-09-30T10:33:43Z
date_published: 2020-07-21T00:00:00Z
date_updated: 2023-09-05T12:12:10Z
day: '21'
department:
- _id: MiLe
doi: 10.1103/physrevb.102.045307
ec_funded: 1
external_id:
arxiv:
- '1910.06015'
isi:
- '000550579100004'
intvolume: ' 102'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1910.06015
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Attractive interactions, molecular complexes, and polarons in coupled dipolar
exciton fluids
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 102
year: '2020'
...
---
_id: '8589'
abstract:
- lang: eng
text: The plant hormone auxin plays indispensable roles in plant growth and development.
An essential level of regulation in auxin action is the directional auxin transport
within cells. The establishment of auxin gradient in plant tissue has been attributed
to local auxin biosynthesis and directional intercellular auxin transport, which
both are controlled by various environmental and developmental signals. It is
well established that asymmetric auxin distribution in cells is achieved by polarly
localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights
into cellular mechanisms of PIN polarization obtained from the last decades, the
molecular mechanism and specific regulators mediating PIN polarization remains
elusive. In this thesis, we aim to find novel players in PIN subcellular polarity
regulation during Arabidopsis development. We first characterize the physiological
effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and
PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling
pathway in shoot gravitropism bending termination. In addition, we also explore
the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation
on PIN polarity. In Chapter 1, we give an overview of the current knowledge about
PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we
study the physiological effect of PA on shoot gravitropic bending. Our results
show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering
with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending
hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear
auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization
and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics
approach and identify the motor protein Myosin XI and its binding protein, the
MadB2 family, as an essential regulator of PIN polarity for auxin-canalization
related developmental processes. In Chapter 5, we demonstrate the vital role of
actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular
trafficking. Overall, the data presented in this PhD thesis brings novel insights
into the PIN polar localization regulation that resulted in the (re)establishment
of the polar auxin flow and gradient in response to environmental stimuli during
plant development.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: I also want to thank the China Scholarship Council for supporting
my study during the year from 2015 to 2019. I also want to thank IST facilities
– the Bioimaging facility, the media kitchen, the plant facility and all of the
campus services, for their support.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
citation:
ama: Han H. Novel insights into PIN polarity regulation during Arabidopsis development.
2020. doi:10.15479/AT:ISTA:8589
apa: Han, H. (2020). Novel insights into PIN polarity regulation during Arabidopsis
development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8589
chicago: Han, Huibin. “Novel Insights into PIN Polarity Regulation during Arabidopsis
Development.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8589.
ieee: H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,”
Institute of Science and Technology Austria, 2020.
ista: Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis
development. Institute of Science and Technology Austria.
mla: Han, Huibin. Novel Insights into PIN Polarity Regulation during Arabidopsis
Development. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8589.
short: H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development,
Institute of Science and Technology Austria, 2020.
date_created: 2020-09-30T14:50:51Z
date_published: 2020-09-30T00:00:00Z
date_updated: 2023-09-07T13:13:05Z
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status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Novel insights into PIN polarity regulation during Arabidopsis development
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8592'
abstract:
- lang: eng
text: Glioblastoma is the most malignant cancer in the brain and currently incurable.
It is urgent to identify effective targets for this lethal disease. Inhibition
of such targets should suppress the growth of cancer cells and, ideally also precancerous
cells for early prevention, but minimally affect their normal counterparts. Using
genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor
cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility
of cells within the development hierarchy of glioma to the knockout of insulin‐like
growth factor I receptor (IGF1R) is determined not only by their oncogenic states,
but also by their cell identities/states. Knockout of IGF1R selectively disrupts
the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable
outcome of IGF1R knockout on cell growth requires the mutant cells to commit to
the OPC identity regardless of its development hierarchical status. At the molecular
level, oncogenic mutations reprogram the cellular network of OPCs and force them
to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally
available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed.
The findings reveal the cellular window of IGF1R targeting and establish IGF1R
as an effective target for the prevention and treatment of glioblastoma.
acknowledgement: The authors thank Drs. J. Eisen, QR. Lu, S. Duan, Z‐H. Li, W. Mo,
and Q. Wu for their critical comments on the manuscript. They also thank Dr. H.
Zong for providing the CKO_NG2‐CreER model. This work is supported by the National
Key Research and Development Program of China, Stem Cell and Translational Research
(2016YFA0101201 to C.L., 2016YFA0100303 to Y.J.W.), the National Natural Science
Foundation of China (81673035 and 81972915 to C.L., 81472722 to Y.J.W.), the Science
Foundation for Distinguished Young Scientists of Zhejiang Province (LR17H160001
to C.L.), Fundamental Research Funds for the Central Universities (2016QNA7023 and
2017QNA7028 to C.L.) and the Thousand Talent Program for Young Outstanding Scientists,
China (to C.L.), IST Austria institutional funds (to S.H.), European Research Council
(ERC) under the European Union's Horizon 2020 research and innovation programme
(725780 LinPro to S.H.). C.L. is a scholar of K. C. Wong Education Foundation.
article_number: '2001724'
article_processing_charge: No
article_type: original
author:
- first_name: Anhao
full_name: Tian, Anhao
last_name: Tian
- first_name: Bo
full_name: Kang, Bo
last_name: Kang
- first_name: Baizhou
full_name: Li, Baizhou
last_name: Li
- first_name: Biying
full_name: Qiu, Biying
last_name: Qiu
- first_name: Wenhong
full_name: Jiang, Wenhong
last_name: Jiang
- first_name: Fangjie
full_name: Shao, Fangjie
last_name: Shao
- first_name: Qingqing
full_name: Gao, Qingqing
last_name: Gao
- first_name: Rui
full_name: Liu, Rui
last_name: Liu
- first_name: Chengwei
full_name: Cai, Chengwei
last_name: Cai
- first_name: Rui
full_name: Jing, Rui
last_name: Jing
- first_name: Wei
full_name: Wang, Wei
last_name: Wang
- first_name: Pengxiang
full_name: Chen, Pengxiang
last_name: Chen
- first_name: Qinghui
full_name: Liang, Qinghui
last_name: Liang
- first_name: Lili
full_name: Bao, Lili
last_name: Bao
- first_name: Jianghong
full_name: Man, Jianghong
last_name: Man
- first_name: Yan
full_name: Wang, Yan
last_name: Wang
- first_name: Yu
full_name: Shi, Yu
last_name: Shi
- first_name: Jin
full_name: Li, Jin
last_name: Li
- first_name: Minmin
full_name: Yang, Minmin
last_name: Yang
- first_name: Lisha
full_name: Wang, Lisha
last_name: Wang
- first_name: Jianmin
full_name: Zhang, Jianmin
last_name: Zhang
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Junming
full_name: Zhu, Junming
last_name: Zhu
- first_name: Xiuwu
full_name: Bian, Xiuwu
last_name: Bian
- first_name: Ying‐Jie
full_name: Wang, Ying‐Jie
last_name: Wang
- first_name: Chong
full_name: Liu, Chong
last_name: Liu
citation:
ama: Tian A, Kang B, Li B, et al. Oncogenic state and cell identity combinatorially
dictate the susceptibility of cells within glioma development hierarchy to IGF1R
targeting. Advanced Science. 2020;7(21). doi:10.1002/advs.202001724
apa: Tian, A., Kang, B., Li, B., Qiu, B., Jiang, W., Shao, F., … Liu, C. (2020).
Oncogenic state and cell identity combinatorially dictate the susceptibility of
cells within glioma development hierarchy to IGF1R targeting. Advanced Science.
Wiley. https://doi.org/10.1002/advs.202001724
chicago: Tian, Anhao, Bo Kang, Baizhou Li, Biying Qiu, Wenhong Jiang, Fangjie Shao,
Qingqing Gao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate
the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.”
Advanced Science. Wiley, 2020. https://doi.org/10.1002/advs.202001724.
ieee: A. Tian et al., “Oncogenic state and cell identity combinatorially
dictate the susceptibility of cells within glioma development hierarchy to IGF1R
targeting,” Advanced Science, vol. 7, no. 21. Wiley, 2020.
ista: Tian A, Kang B, Li B, Qiu B, Jiang W, Shao F, Gao Q, Liu R, Cai C, Jing R,
Wang W, Chen P, Liang Q, Bao L, Man J, Wang Y, Shi Y, Li J, Yang M, Wang L, Zhang
J, Hippenmeyer S, Zhu J, Bian X, Wang Y, Liu C. 2020. Oncogenic state and cell
identity combinatorially dictate the susceptibility of cells within glioma development
hierarchy to IGF1R targeting. Advanced Science. 7(21), 2001724.
mla: Tian, Anhao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate
the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.”
Advanced Science, vol. 7, no. 21, 2001724, Wiley, 2020, doi:10.1002/advs.202001724.
short: A. Tian, B. Kang, B. Li, B. Qiu, W. Jiang, F. Shao, Q. Gao, R. Liu, C. Cai,
R. Jing, W. Wang, P. Chen, Q. Liang, L. Bao, J. Man, Y. Wang, Y. Shi, J. Li, M.
Yang, L. Wang, J. Zhang, S. Hippenmeyer, J. Zhu, X. Bian, Y. Wang, C. Liu, Advanced
Science 7 (2020).
date_created: 2020-10-01T09:44:13Z
date_published: 2020-11-04T00:00:00Z
date_updated: 2023-08-22T09:53:01Z
day: '04'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1002/advs.202001724
ec_funded: 1
external_id:
isi:
- '000573860700001'
file:
- access_level: open_access
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creator: dernst
date_created: 2020-12-10T14:07:24Z
date_updated: 2020-12-10T14:07:24Z
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file_name: 2020_AdvScience_Tian.pdf
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success: 1
file_date_updated: 2020-12-10T14:07:24Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '21'
keyword:
- General Engineering
- General Physics and Astronomy
- General Materials Science
- Medicine (miscellaneous)
- General Chemical Engineering
- Biochemistry
- Genetics and Molecular Biology (miscellaneous)
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Advanced Science
publication_identifier:
issn:
- 2198-3844
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Oncogenic state and cell identity combinatorially dictate the susceptibility
of cells within glioma development hierarchy to IGF1R targeting
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: 7
year: '2020'
...