---
_id: '11447'
abstract:
- lang: eng
text: Empirical essays of fitness landscapes suggest that they may be rugged, that
is having multiple fitness peaks. Such fitness landscapes, those that have multiple
peaks, necessarily have special local structures, called reciprocal sign epistasis
(Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the
quantitative relationship between the number of fitness peaks and the number of
reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk
et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis
is a necessary but not sufficient condition for the existence of multiple peaks.
Applying discrete Morse theory, which to our knowledge has never been used in
this context, we extend this result by giving the minimal number of reciprocal
sign epistatic interactions required to create a given number of peaks.
acknowledgement: We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful
discussions. Open access funding provided by Austrian Science Fund (FWF). Partially
supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund
(I5127-B) grants to FAK.
article_number: '74'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Raimundo J
full_name: Saona Urmeneta, Raimundo J
id: BD1DF4C4-D767-11E9-B658-BC13E6697425
last_name: Saona Urmeneta
orcid: 0000-0001-5103-038X
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
citation:
ama: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number
of peaks and the number of reciprocal sign epistatic interactions. Bulletin
of Mathematical Biology. 2022;84(8). doi:10.1007/s11538-022-01029-z
apa: Saona Urmeneta, R. J., Kondrashov, F., & Khudiakova, K. (2022). Relation
between the number of peaks and the number of reciprocal sign epistatic interactions.
Bulletin of Mathematical Biology. Springer Nature. https://doi.org/10.1007/s11538-022-01029-z
chicago: Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova.
“Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic
Interactions.” Bulletin of Mathematical Biology. Springer Nature, 2022.
https://doi.org/10.1007/s11538-022-01029-z.
ieee: R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between
the number of peaks and the number of reciprocal sign epistatic interactions,”
Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022.
ista: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the
number of peaks and the number of reciprocal sign epistatic interactions. Bulletin
of Mathematical Biology. 84(8), 74.
mla: Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and
the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical
Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z.
short: R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical
Biology 84 (2022).
date_created: 2022-06-17T16:16:15Z
date_published: 2022-06-17T00:00:00Z
date_updated: 2023-08-03T07:20:53Z
day: '17'
ddc:
- '510'
- '570'
department:
- _id: GradSch
- _id: NiBa
- _id: JaMa
doi: 10.1007/s11538-022-01029-z
ec_funded: 1
external_id:
isi:
- '000812509800001'
file:
- access_level: open_access
checksum: 05a1fe7d10914a00c2bca9b447993a65
content_type: application/pdf
creator: dernst
date_created: 2022-06-20T07:51:32Z
date_updated: 2022-06-20T07:51:32Z
file_id: '11455'
file_name: 2022_BulletinMathBiology_Saona.pdf
file_size: 463025
relation: main_file
success: 1
file_date_updated: 2022-06-20T07:51:32Z
has_accepted_license: '1'
intvolume: ' 84'
isi: 1
issue: '8'
keyword:
- Computational Theory and Mathematics
- General Agricultural and Biological Sciences
- Pharmacology
- General Environmental Science
- General Biochemistry
- Genetics and Molecular Biology
- General Mathematics
- Immunology
- General Neuroscience
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: c098eddd-5a5b-11eb-8a69-abe27170a68f
grant_number: I05127
name: Evolutionary analysis of gene regulation
publication: Bulletin of Mathematical Biology
publication_identifier:
eissn:
- 1522-9602
issn:
- 0092-8240
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s11538-022-01118-z
scopus_import: '1'
status: public
title: Relation between the number of peaks and the number of reciprocal sign epistatic
interactions
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: 84
year: '2022'
...
---
_id: '11448'
abstract:
- lang: eng
text: Studies of protein fitness landscapes reveal biophysical constraints guiding
protein evolution and empower prediction of functional proteins. However, generalisation
of these findings is limited due to scarceness of systematic data on fitness landscapes
of proteins with a defined evolutionary relationship. We characterized the fitness
peaks of four orthologous fluorescent proteins with a broad range of sequence
divergence. While two of the four studied fitness peaks were sharp, the other
two were considerably flatter, being almost entirely free of epistatic interactions.
Mutationally robust proteins, characterized by a flat fitness peak, were not optimal
templates for machine-learning-driven protein design – instead, predictions were
more accurate for fragile proteins with epistatic landscapes. Our work paves insights
for practical application of fitness landscape heterogeneity in protein engineering.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: "We thank Ondřej Draganov, Rodrigo Redondo, Bor Kavčič, Mia Juračić
and Andrea Pauli for discussion and technical advice. We thank Anita Testa Salmazo
for advice on resin protein purification, Dmitry Bolotin and the Milaboratory (milaboratory.com)
for access to computing and storage infrastructure, and Josef Houser and Eva Fujdiarova
for technical assistance and data interpretation. Core facility Biomolecular Interactions
and Crystallization of CEITEC Masaryk University is gratefully acknowledged for
the obtaining of the scientific data presented in this paper. This research was
supported by the Scientific Service Units (SSU) of IST-Austria\r\nthrough resources
provided by the Bioimaging Facility (BIF), and the Life Science Facility (LSF).
MiSeq and HiSeq NGS sequencing was performed by the Next Generation Sequencing Facility
at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC),
Austria. FACS was performed at the BioOptics Facility of the Institute of Molecular
Pathology (IMP), Austria. We also thank the Biomolecular Crystallography Facility
in the Vanderbilt University Center for Structural Biology. We are grateful to Joel
M Harp for help with X-ray data collection. This work was supported by the ERC Consolidator
grant to FAK (771209—CharFL). KSS acknowledges support by President’s Grant МК–5405.2021.1.4,
the Imperial College Research Fellowship and the MRC London Institute of Medical
Sciences (UKRI MC-A658-5QEA0).\r\nAF is supported by the Marie Skłodowska-Curie
Fellowship (H2020-MSCA-IF-2019, Grant Agreement No. 898203, Project acronym \"FLINDIP\").
Experiments were partially carried out using equipment provided by the Institute
of Bioorganic Chemistry of the Russian Academy of Sciences Сore Facility (CKP IBCH).
This work was supported by a Russian Science Foundation grant 19-74-10102.This project
has received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665,385."
article_number: '75842'
article_processing_charge: No
article_type: original
author:
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Aubin
full_name: Fleiss, Aubin
last_name: Fleiss
- first_name: Alexander S
full_name: Mishin, Alexander S
last_name: Mishin
- first_name: Nina G
full_name: Bozhanova, Nina G
last_name: Bozhanova
- first_name: Anna A
full_name: Igolkina, Anna A
last_name: Igolkina
- first_name: Jens
full_name: Meiler, Jens
last_name: Meiler
- first_name: Maria-Elisenda
full_name: Alaball Pujol, Maria-Elisenda
last_name: Alaball Pujol
- first_name: Ekaterina V
full_name: Putintseva, Ekaterina V
last_name: Putintseva
- first_name: Karen S
full_name: Sarkisyan, Karen S
last_name: Sarkisyan
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP
fitness landscape and data-driven protein design. eLife. 2022;11. doi:10.7554/elife.75842
apa: Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina,
A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape
and data-driven protein design. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.75842
chicago: Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova,
Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva,
Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape
and Data-Driven Protein Design.” ELife. eLife Sciences Publications, 2022.
https://doi.org/10.7554/elife.75842.
ieee: L. Gonzalez Somermeyer et al., “Heterogeneity of the GFP fitness landscape
and data-driven protein design,” eLife, vol. 11. eLife Sciences Publications,
2022.
ista: Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler
J, Alaball Pujol M-E, Putintseva EV, Sarkisyan KS, Kondrashov F. 2022. Heterogeneity
of the GFP fitness landscape and data-driven protein design. eLife. 11, 75842.
mla: Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape
and Data-Driven Protein Design.” ELife, vol. 11, 75842, eLife Sciences
Publications, 2022, doi:10.7554/elife.75842.
short: L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina,
J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov,
ELife 11 (2022).
date_created: 2022-06-18T09:06:59Z
date_published: 2022-05-05T00:00:00Z
date_updated: 2023-08-03T07:20:15Z
day: '05'
ddc:
- '570'
department:
- _id: GradSch
- _id: FyKo
doi: 10.7554/elife.75842
ec_funded: 1
external_id:
isi:
- '000799197200001'
file:
- access_level: open_access
checksum: 7573c28f44028ab0cc81faef30039e44
content_type: application/pdf
creator: dernst
date_created: 2022-06-20T07:44:19Z
date_updated: 2022-06-20T07:44:19Z
file_id: '11454'
file_name: 2022_eLife_Somermeyer.pdf
file_size: 5297213
relation: main_file
success: 1
file_date_updated: 2022-06-20T07:44:19Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Heterogeneity of the GFP fitness landscape and data-driven protein design
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: '2022'
...
---
_id: '11459'
abstract:
- lang: eng
text: 'We present a novel approach to differential cost analysis that, given a program
revision, attempts to statically bound the difference in resource usage, or cost,
between the two program versions. Differential cost analysis is particularly interesting
because of the many compelling applications for it, such as detecting resource-use
regressions at code-review time or proving the absence of certain side-channel
vulnerabilities. One prior approach to differential cost analysis is to apply
relational reasoning that conceptually constructs a product program on which one
can over-approximate the difference in costs between the two program versions.
However, a significant challenge in any relational approach is effectively aligning
the program versions to get precise results. In this paper, our key insight is
that we can avoid the need for and the limitations of program alignment if, instead,
we bound the difference of two cost-bound summaries rather than directly bounding
the concrete cost difference. In particular, our method computes a threshold value
for the maximal difference in cost between two program versions simultaneously
using two kinds of cost-bound summaries---a potential function that evaluates
to an upper bound for the cost incurred in the first program and an anti-potential
function that evaluates to a lower bound for the cost incurred in the second.
Our method has a number of desirable properties: it can be fully automated, it
allows optimizing the threshold value on relative cost, it is suitable for programs
that are not syntactically similar, and it supports non-determinism. We have evaluated
an implementation of our approach on a number of program pairs collected from
the literature, and we find that our method computes tight threshold values on
relative cost in most examples.'
acknowledgement: "We thank Shaun Willows, Thomas Lugnet, and the Living Room Application
Vending team for suggesting threshold\r\nbounds as a developer-friendly way to interact
with a differential cost analyzer, and we thank Jim Christy, Daniel\r\nSchoepe,
and the Prime Video Automated Reasoning team for their support and helpful suggestions
throughout the\r\nproject. We also thank Michael Emmi for feedback on an earlier
version of this paper. And finally, we thank the anonymous reviewers for their useful
feedback and Aws Albarghouthi for shepherding the final version of the paper. Ðorđe
Žikelić was also partially supported by ERC CoG 863818 (FoRM-SMArt)."
article_processing_charge: No
arxiv: 1
author:
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
- first_name: Bor-Yuh Evan
full_name: Chang, Bor-Yuh Evan
last_name: Chang
- first_name: Pauline
full_name: Bolignano, Pauline
last_name: Bolignano
- first_name: Franco
full_name: Raimondi, Franco
last_name: Raimondi
citation:
ama: 'Zikelic D, Chang B-YE, Bolignano P, Raimondi F. Differential cost analysis
with simultaneous potentials and anti-potentials. In: Proceedings of the 43rd
ACM SIGPLAN International Conference on Programming Language Design and Implementation.
Association for Computing Machinery; 2022:442-457. doi:10.1145/3519939.3523435'
apa: 'Zikelic, D., Chang, B.-Y. E., Bolignano, P., & Raimondi, F. (2022). Differential
cost analysis with simultaneous potentials and anti-potentials. In Proceedings
of the 43rd ACM SIGPLAN International Conference on Programming Language Design
and Implementation (pp. 442–457). San Diego, CA, United States: Association
for Computing Machinery. https://doi.org/10.1145/3519939.3523435'
chicago: Zikelic, Dorde, Bor-Yuh Evan Chang, Pauline Bolignano, and Franco Raimondi.
“Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.”
In Proceedings of the 43rd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, 442–57. Association for Computing Machinery,
2022. https://doi.org/10.1145/3519939.3523435.
ieee: D. Zikelic, B.-Y. E. Chang, P. Bolignano, and F. Raimondi, “Differential cost
analysis with simultaneous potentials and anti-potentials,” in Proceedings
of the 43rd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, San Diego, CA, United States, 2022, pp. 442–457.
ista: 'Zikelic D, Chang B-YE, Bolignano P, Raimondi F. 2022. Differential cost analysis
with simultaneous potentials and anti-potentials. Proceedings of the 43rd ACM
SIGPLAN International Conference on Programming Language Design and Implementation.
PLDI: Programming Language Design and Implementation, 442–457.'
mla: Zikelic, Dorde, et al. “Differential Cost Analysis with Simultaneous Potentials
and Anti-Potentials.” Proceedings of the 43rd ACM SIGPLAN International Conference
on Programming Language Design and Implementation, Association for Computing
Machinery, 2022, pp. 442–57, doi:10.1145/3519939.3523435.
short: D. Zikelic, B.-Y.E. Chang, P. Bolignano, F. Raimondi, in:, Proceedings of
the 43rd ACM SIGPLAN International Conference on Programming Language Design and
Implementation, Association for Computing Machinery, 2022, pp. 442–457.
conference:
end_date: 2022-06-17
location: San Diego, CA, United States
name: 'PLDI: Programming Language Design and Implementation'
start_date: 2022-06-13
date_created: 2022-06-21T09:26:15Z
date_published: 2022-06-09T00:00:00Z
date_updated: 2025-07-14T09:09:54Z
day: '09'
ddc:
- '000'
department:
- _id: GradSch
- _id: KrCh
doi: 10.1145/3519939.3523435
ec_funded: 1
external_id:
arxiv:
- '2204.00870'
isi:
- '000850435600030'
file:
- access_level: open_access
checksum: 7eb915a2ca5b5ce4729321f33b2e16e1
content_type: application/pdf
creator: dernst
date_created: 2022-06-27T07:38:21Z
date_updated: 2022-06-27T07:38:21Z
file_id: '11466'
file_name: 2022_PLDI_Zikelic.pdf
file_size: 318697
relation: main_file
success: 1
file_date_updated: 2022-06-27T07:38:21Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: 442-457
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the 43rd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450392655'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Differential cost analysis with simultaneous potentials and anti-potentials
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: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2022'
...
---
_id: '11462'
abstract:
- lang: eng
text: Nanobodies (VHH) from camelid antibody libraries hold great promise as therapeutic
agents and components of immunoassay systems. Synthetic antibody libraries that
could be designed and generated once and for various applications could yield
binders to virtually any targets, even for non-immunogenic or toxic ones, in a
short term. One of the most difficult tasks is to obtain antibodies with a high
affinity and specificity to polyglycosylated proteins. It requires antibody libraries
with extremely high functional diversity and the use of sophisticated selection
techniques. Here we report a development of a novel sandwich immunoassay involving
a combination of the synthetic library-derived VHH-Fc fusion protein as a capture
antibody and the immune single-chain fragment variable (scFv) as a tracer for
the detection of pregnancy-associated glycoprotein (PAG) of cattle (Bos taurus).
We succeeded in the generation of a number of specific scFv antibodies against
PAG from the mouse immune library. Subsequent selection using the immobilized
scFv-Fc capture antibody allowed to isolate 1.9 nM VHH binder from the diverse
synthetic library without any overlapping with the capture antibody binding site.
The prototype sandwich ELISA based on the synthetic VHH and the immune scFv was
established. This is the first successful example of the combination of synthetic
and immune antibody libraries in a single sandwich immunoassay. Thus, our approach
could be used for the express isolation of antibody pairs and the development
of sandwich immunoassays for challenging antigens.
acknowledgement: This study was financially supported by the State Committee on Science
and Technology. We would like to thank Elena Tumar and Elena Kisileva at the Institute
of Bioorganic Chemistry of NASB for their kind assistance with mouse immunizations.
article_processing_charge: No
article_type: original
author:
- first_name: Dmitri
full_name: Dormeshkin, Dmitri
last_name: Dormeshkin
- first_name: Michail
full_name: Shapira, Michail
last_name: Shapira
- first_name: Alena
full_name: Karputs, Alena
last_name: Karputs
- first_name: Anton
full_name: Kavaleuski, Anton
id: 62304f89-eb97-11eb-a6c2-8903dd183976
last_name: Kavaleuski
orcid: 0000-0003-2091-526X
- first_name: Ivan
full_name: Kuzminski, Ivan
last_name: Kuzminski
- first_name: Elena
full_name: Stepanova, Elena
last_name: Stepanova
- first_name: Andrei
full_name: Gilep, Andrei
last_name: Gilep
citation:
ama: Dormeshkin D, Shapira M, Karputs A, et al. Combining of synthetic VHH and immune
scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied
Microbiology and Biotechnology. 2022;106:5093-5103. doi:10.1007/s00253-022-12022-w
apa: Dormeshkin, D., Shapira, M., Karputs, A., Kavaleuski, A., Kuzminski, I., Stepanova,
E., & Gilep, A. (2022). Combining of synthetic VHH and immune scFv libraries
for pregnancy-associated glycoproteins ELISA development. Applied Microbiology
and Biotechnology. Springer Nature. https://doi.org/10.1007/s00253-022-12022-w
chicago: Dormeshkin, Dmitri, Michail Shapira, Alena Karputs, Anton Kavaleuski, Ivan
Kuzminski, Elena Stepanova, and Andrei Gilep. “Combining of Synthetic VHH and
Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.”
Applied Microbiology and Biotechnology. Springer Nature, 2022. https://doi.org/10.1007/s00253-022-12022-w.
ieee: D. Dormeshkin et al., “Combining of synthetic VHH and immune scFv libraries
for pregnancy-associated glycoproteins ELISA development,” Applied Microbiology
and Biotechnology, vol. 106. Springer Nature, pp. 5093–5103, 2022.
ista: Dormeshkin D, Shapira M, Karputs A, Kavaleuski A, Kuzminski I, Stepanova E,
Gilep A. 2022. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated
glycoproteins ELISA development. Applied Microbiology and Biotechnology. 106,
5093–5103.
mla: Dormeshkin, Dmitri, et al. “Combining of Synthetic VHH and Immune ScFv Libraries
for Pregnancy-Associated Glycoproteins ELISA Development.” Applied Microbiology
and Biotechnology, vol. 106, Springer Nature, 2022, pp. 5093–103, doi:10.1007/s00253-022-12022-w.
short: D. Dormeshkin, M. Shapira, A. Karputs, A. Kavaleuski, I. Kuzminski, E. Stepanova,
A. Gilep, Applied Microbiology and Biotechnology 106 (2022) 5093–5103.
date_created: 2022-06-26T22:01:34Z
date_published: 2022-08-01T00:00:00Z
date_updated: 2023-10-10T07:15:02Z
day: '01'
department:
- _id: GradSch
- _id: LeSa
doi: 10.1007/s00253-022-12022-w
external_id:
isi:
- '000813677500001'
pmid:
- '35723693'
intvolume: ' 106'
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 5093-5103
pmid: 1
publication: Applied Microbiology and Biotechnology
publication_identifier:
eissn:
- 1432-0614
issn:
- 0175-7598
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Combining of synthetic VHH and immune scFv libraries for pregnancy-associated
glycoproteins ELISA development
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 106
year: '2022'
...
---
_id: '11473'
abstract:
- lang: eng
text: "The polaron model is a basic model of quantum field theory describing a single
particle\r\ninteracting with a bosonic field. It arises in many physical contexts.
We are mostly concerned\r\nwith models applicable in the context of an impurity
atom in a Bose-Einstein condensate as\r\nwell as the problem of electrons moving
in polar crystals.\r\nThe model has a simple structure in which the interaction
of the particle with the field is given\r\nby a term linear in the field’s creation
and annihilation operators. In this work, we investigate\r\nthe properties of
this model by providing rigorous estimates on various energies relevant to the\r\nproblem.
The estimates are obtained, for the most part, by suitable operator techniques
which\r\nconstitute the principal mathematical substance of the thesis.\r\nThe
first application of these techniques is to derive the polaron model rigorously
from first\r\nprinciples, i.e., from a full microscopic quantum-mechanical many-body
problem involving an\r\nimpurity in an otherwise homogeneous system. We accomplish
this for the N + 1 Bose gas\r\nin the mean-field regime by showing that a suitable
polaron-type Hamiltonian arises at weak\r\ninteractions as a low-energy effective
theory for this problem.\r\nIn the second part, we investigate rigorously the
ground state of the model at fixed momentum\r\nand for large values of the coupling
constant. Qualitatively, the system is expected to display\r\na transition from
the quasi-particle behavior at small momenta, where the dispersion relation\r\nis
parabolic and the particle moves through the medium dragging along a cloud of
phonons, to\r\nthe radiative behavior at larger momenta where the polaron decelerates
and emits free phonons.\r\nAt the same time, in the strong coupling regime, the
bosonic field is expected to behave purely\r\nclassically. Accordingly, the effective
mass of the polaron at strong coupling is conjectured to\r\nbe asymptotically
equal to the one obtained from the semiclassical counterpart of the problem,\r\nfirst
studied by Landau and Pekar in the 1940s. For polaron models with regularized
form\r\nfactors and phonon dispersion relations of superfluid type, i.e., bounded
below by a linear\r\nfunction of the wavenumbers for all phonon momenta as in
the interacting Bose gas, we prove\r\nthat for a large window of momenta below
the radiation threshold, the energy-momentum\r\nrelation at strong coupling is
indeed essentially a parabola with semi-latus rectum equal to the\r\nLandau–Pekar
effective mass, as expected.\r\nFor the Fröhlich polaron describing electrons
in polar crystals where the dispersion relation is\r\nof the optical type and
the form factor is formally UV–singular due to the nature of the point\r\ncharge-dipole
interaction, we are able to give the corresponding upper bound. In contrast to\r\nthe
regular case, this requires the inclusion of the quantum fluctuations of the phonon
field,\r\nwhich makes the problem considerably more difficult.\r\nThe results
are supplemented by studies on the absolute ground-state energy at strong coupling,\r\na
proof of the divergence of the effective mass with the coupling constant for a
wide class of\r\npolaron models, as well as the discussion of the apparent UV
singularity of the Fröhlich model\r\nand the application of the techniques used
for its removal for the energy estimates.\r\n"
acknowledged_ssus:
- _id: SSU
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Krzysztof
full_name: Mysliwy, Krzysztof
id: 316457FC-F248-11E8-B48F-1D18A9856A87
last_name: Mysliwy
citation:
ama: 'Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy
estimates. 2022. doi:10.15479/at:ista:11473'
apa: 'Mysliwy, K. (2022). Polarons in Bose gases and polar crystals: Some rigorous
energy estimates. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11473'
chicago: 'Mysliwy, Krzysztof. “Polarons in Bose Gases and Polar Crystals: Some Rigorous
Energy Estimates.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11473.'
ieee: 'K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy
estimates,” Institute of Science and Technology Austria, 2022.'
ista: 'Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous
energy estimates. Institute of Science and Technology Austria.'
mla: 'Mysliwy, Krzysztof. Polarons in Bose Gases and Polar Crystals: Some Rigorous
Energy Estimates. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11473.'
short: 'K. Mysliwy, Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy
Estimates, Institute of Science and Technology Austria, 2022.'
date_created: 2022-06-30T12:15:03Z
date_published: 2022-07-01T00:00:00Z
date_updated: 2023-09-07T13:43:52Z
day: '01'
ddc:
- '515'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RoSe
doi: 10.15479/at:ista:11473
ec_funded: 1
file:
- access_level: open_access
checksum: 7970714a20a6052f75fb27a6c3e9976e
content_type: application/pdf
creator: kmysliwy
date_created: 2022-07-05T08:12:56Z
date_updated: 2022-07-05T08:12:56Z
file_id: '11486'
file_name: thes1_no_isbn_2_1b.pdf
file_size: 1830973
relation: main_file
success: 1
- access_level: closed
checksum: 647a2011fdf56277096c9350fefe1097
content_type: application/zip
creator: kmysliwy
date_created: 2022-07-05T08:15:52Z
date_updated: 2022-07-05T08:17:12Z
file_id: '11487'
file_name: thes_source.zip
file_size: 5831060
relation: source_file
file_date_updated: 2022-07-05T08:17:12Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '138'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10564'
relation: part_of_dissertation
status: public
- id: '8705'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
title: 'Polarons in Bose gases and polar crystals: Some rigorous energy estimates'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2022'
...
---
_id: '11476'
abstract:
- lang: eng
text: "Messaging platforms like Signal are widely deployed and provide strong security
in an asynchronous setting. It is a challenging problem to construct a protocol
with similar security guarantees that can efficiently scale to large groups. A
major bottleneck are the frequent key rotations users need to perform to achieve
post compromise forward security.\r\n\r\nIn current proposals – most notably in
TreeKEM (which is part of the IETF’s Messaging Layer Security (MLS) protocol draft)
– for users in a group of size n to rotate their keys, they must each craft a
message of size log(n) to be broadcast to the group using an (untrusted) delivery
server.\r\n\r\nIn larger groups, having users sequentially rotate their keys requires
too much bandwidth (or takes too long), so variants allowing any T≤n users to
simultaneously rotate their keys in just 2 communication rounds have been suggested
(e.g. “Propose and Commit” by MLS). Unfortunately, 2-round concurrent updates
are either damaging or expensive (or both); i.e. they either result in future
operations being more costly (e.g. via “blanking” or “tainting”) or are costly
themselves requiring Ω(T) communication for each user [Bienstock et al., TCC’20].\r\n\r\nIn
this paper we propose CoCoA; a new scheme that allows for T concurrent updates
that are neither damaging nor costly. That is, they add no cost to future operations
yet they only require Ω(log2(n)) communication per user. To circumvent the [Bienstock
et al.] lower bound, CoCoA increases the number of rounds needed to complete all
updates from 2 up to (at most) log(n); though typically fewer rounds are needed.\r\n\r\nThe
key insight of our protocol is the following: in the (non-concurrent version of)
TreeKEM, a delivery server which gets T concurrent update requests will approve
one and reject the remaining T−1. In contrast, our server attempts to apply all
of them. If more than one user requests to rotate the same key during a round,
the server arbitrarily picks a winner. Surprisingly, we prove that regardless
of how the server chooses the winners, all previously compromised users will recover
after at most log(n) such update rounds.\r\n\r\nTo keep the communication complexity
low, CoCoA is a server-aided CGKA. That is, the delivery server no longer blindly
forwards packets, but instead actively computes individualized packets tailored
to each user. As the server is untrusted, this change requires us to develop new
mechanisms ensuring robustness of the protocol."
acknowledgement: We thank Marta Mularczyk and Yiannis Tselekounis for their very helpful
feedback on an earlier draft of this paper.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Joël
full_name: Alwen, Joël
last_name: Alwen
- first_name: Benedikt
full_name: Auerbach, Benedikt
id: D33D2B18-E445-11E9-ABB7-15F4E5697425
last_name: Auerbach
orcid: 0000-0002-7553-6606
- first_name: Miguel
full_name: Cueto Noval, Miguel
id: ffc563a3-f6e0-11ea-865d-e3cce03d17cc
last_name: Cueto Noval
- first_name: Karen
full_name: Klein, Karen
id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87
last_name: Klein
- first_name: Guillermo
full_name: Pascual Perez, Guillermo
id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87
last_name: Pascual Perez
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Michael
full_name: Walter, Michael
last_name: Walter
citation:
ama: 'Alwen J, Auerbach B, Cueto Noval M, et al. CoCoA: Concurrent continuous group
key agreement. In: Advances in Cryptology – EUROCRYPT 2022. Vol 13276.
Cham: Springer Nature; 2022:815–844. doi:10.1007/978-3-031-07085-3_28'
apa: 'Alwen, J., Auerbach, B., Cueto Noval, M., Klein, K., Pascual Perez, G., Pietrzak,
K. Z., & Walter, M. (2022). CoCoA: Concurrent continuous group key agreement.
In Advances in Cryptology – EUROCRYPT 2022 (Vol. 13276, pp. 815–844). Cham:
Springer Nature. https://doi.org/10.1007/978-3-031-07085-3_28'
chicago: 'Alwen, Joël, Benedikt Auerbach, Miguel Cueto Noval, Karen Klein, Guillermo
Pascual Perez, Krzysztof Z Pietrzak, and Michael Walter. “CoCoA: Concurrent Continuous
Group Key Agreement.” In Advances in Cryptology – EUROCRYPT 2022, 13276:815–844.
Cham: Springer Nature, 2022. https://doi.org/10.1007/978-3-031-07085-3_28.'
ieee: 'J. Alwen et al., “CoCoA: Concurrent continuous group key agreement,”
in Advances in Cryptology – EUROCRYPT 2022, Trondheim, Norway, 2022, vol.
13276, pp. 815–844.'
ista: 'Alwen J, Auerbach B, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ,
Walter M. 2022. CoCoA: Concurrent continuous group key agreement. Advances in
Cryptology – EUROCRYPT 2022. EUROCRYPT: Annual International Conference on the
Theory and Applications of Cryptology and Information Security, LNCS, vol. 13276,
815–844.'
mla: 'Alwen, Joël, et al. “CoCoA: Concurrent Continuous Group Key Agreement.” Advances
in Cryptology – EUROCRYPT 2022, vol. 13276, Springer Nature, 2022, pp. 815–844,
doi:10.1007/978-3-031-07085-3_28.'
short: J. Alwen, B. Auerbach, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak,
M. Walter, in:, Advances in Cryptology – EUROCRYPT 2022, Springer Nature, Cham,
2022, pp. 815–844.
conference:
end_date: 2022-06-03
location: Trondheim, Norway
name: 'EUROCRYPT: Annual International Conference on the Theory and Applications
of Cryptology and Information Security'
start_date: 2022-05-30
date_created: 2022-06-30T16:48:00Z
date_published: 2022-05-25T00:00:00Z
date_updated: 2023-08-03T07:25:02Z
day: '25'
department:
- _id: GradSch
- _id: KrPi
doi: 10.1007/978-3-031-07085-3_28
ec_funded: 1
external_id:
isi:
- '000832305300028'
intvolume: ' 13276'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2022/251
month: '05'
oa: 1
oa_version: Preprint
page: 815–844
place: Cham
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Advances in Cryptology – EUROCRYPT 2022
publication_identifier:
eisbn:
- '9783031070853'
eissn:
- 1611-3349
isbn:
- '9783031070846'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'CoCoA: Concurrent continuous group key agreement'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13276
year: '2022'
...
---
_id: '11542'
article_processing_charge: No
author:
- first_name: Rouven
full_name: Schulz, Rouven
id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87
last_name: Schulz
orcid: 0000-0001-5297-733X
citation:
ama: Schulz R. Source Data (Chimeric GPCRs mimic distinct signaling pathways and
modulate microglia responses). 2022. doi:10.15479/AT:ISTA:11542
apa: Schulz, R. (2022). Source Data (Chimeric GPCRs mimic distinct signaling pathways
and modulate microglia responses). Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:11542
chicago: Schulz, Rouven. “Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways
and Modulate Microglia Responses).” Institute of Science and Technology Austria,
2022. https://doi.org/10.15479/AT:ISTA:11542.
ieee: R. Schulz, “Source Data (Chimeric GPCRs mimic distinct signaling pathways
and modulate microglia responses).” Institute of Science and Technology Austria,
2022.
ista: Schulz R. 2022. Source Data (Chimeric GPCRs mimic distinct signaling pathways
and modulate microglia responses), Institute of Science and Technology Austria,
10.15479/AT:ISTA:11542.
mla: Schulz, Rouven. Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways
and Modulate Microglia Responses). Institute of Science and Technology Austria,
2022, doi:10.15479/AT:ISTA:11542.
short: R. Schulz, (2022).
contributor:
- contributor_type: contact_person
first_name: Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
date_created: 2022-07-08T11:03:02Z
date_published: 2022-01-01T00:00:00Z
date_updated: 2024-02-21T12:34:51Z
department:
- _id: GradSch
- _id: SaSi
doi: 10.15479/AT:ISTA:11542
file:
- access_level: open_access
checksum: 71e8186583f3adbb6c69a88ac9e6e49b
content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
creator: rschulz
date_created: 2022-07-08T10:56:52Z
date_updated: 2022-07-08T10:56:52Z
file_id: '11543'
file_name: Source Data.xlsx
file_size: 135784571
relation: main_file
success: 1
file_date_updated: 2022-07-08T10:56:52Z
has_accepted_license: '1'
oa: 1
oa_version: None
publisher: Institute of Science and Technology Austria
related_material:
link:
- relation: contains
url: https://www.biorxiv.org/content/10.1101/2021.06.21.449162v1
record:
- id: '11995'
relation: used_in_publication
status: public
status: public
title: Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate
microglia responses)
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11556'
abstract:
- lang: eng
text: "We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation
kinetics and extend them for aggregation processes with collisional fragmentation
(shattering). We test the performance and accuracy of the extended methods and
compare their performance with efficient deterministic finite-difference method
applied to the same model. We validate the stochastic methods on the test problems
and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation
kinetics recently detected in deterministic simulations. We confirm the emergence
of steady oscillations of densities in such systems and prove the stability of
the\r\noscillations with respect to fluctuations and noise."
acknowledgement: Zhores supercomputer of Skolkovo Institute of Science and Technology
[68] has been used in the present research. S.A.M. was supported by Moscow Center
for Fundamental and Applied Mathematics (the agreement with the Ministry of Education
and Science of the Russian Federation No. 075-15-2019-1624). A.I.O. acknowledges
RFBR project No. 20-31-90022. N.V.B. acknowledges the support of the Analytical
Center (subsidy agreement 000000D730321P5Q0002, Grant No. 70-2021-00145 02.11.2021).
article_number: '111439'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Aleksei
full_name: Kalinov, Aleksei
id: 44b7120e-eb97-11eb-a6c2-e1557aa81d02
last_name: Kalinov
orcid: 0000-0003-2189-3904
- first_name: A.I.
full_name: Osinskiy, A.I.
last_name: Osinskiy
- first_name: S.A.
full_name: Matveev, S.A.
last_name: Matveev
- first_name: W.
full_name: Otieno, W.
last_name: Otieno
- first_name: N.V.
full_name: Brilliantov, N.V.
last_name: Brilliantov
citation:
ama: Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation
Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal
of Computational Physics. 2022;467. doi:10.1016/j.jcp.2022.111439
apa: Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., & Brilliantov,
N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation
kinetics. Journal of Computational Physics. Elsevier. https://doi.org/10.1016/j.jcp.2022.111439
chicago: Kalinov, Aleksei, A.I. Osinskiy, S.A. Matveev, W. Otieno, and N.V. Brilliantov.
“Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.”
Journal of Computational Physics. Elsevier, 2022. https://doi.org/10.1016/j.jcp.2022.111439.
ieee: A. Kalinov, A. I. Osinskiy, S. A. Matveev, W. Otieno, and N. V. Brilliantov,
“Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics,”
Journal of Computational Physics, vol. 467. Elsevier, 2022.
ista: Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. 2022. Direct
simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics.
Journal of Computational Physics. 467, 111439.
mla: Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in
Aggregation-Fragmentation Kinetics.” Journal of Computational Physics,
vol. 467, 111439, Elsevier, 2022, doi:10.1016/j.jcp.2022.111439.
short: A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal
of Computational Physics 467 (2022).
date_created: 2022-07-11T12:19:59Z
date_published: 2022-10-15T00:00:00Z
date_updated: 2023-08-03T11:55:06Z
day: '15'
ddc:
- '518'
department:
- _id: GradSch
- _id: ChWo
doi: 10.1016/j.jcp.2022.111439
external_id:
arxiv:
- '2103.09481'
isi:
- '000917225500013'
intvolume: ' 467'
isi: 1
keyword:
- Computer Science Applications
- Physics and Astronomy (miscellaneous)
- Applied Mathematics
- Computational Mathematics
- Modeling and Simulation
- Numerical Analysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2103.09481
month: '10'
oa: 1
oa_version: Preprint
publication: Journal of Computational Physics
publication_identifier:
issn:
- 0021-9991
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Direct simulation Monte Carlo for new regimes in aggregation-fragmentation
kinetics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 467
year: '2022'
...
---
_id: '11626'
abstract:
- lang: eng
text: Plant growth and development is well known to be both, flexible and dynamic.
The high capacity for post-embryonic organ formation and tissue regeneration requires
tightly regulated intercellular communication and coordinated tissue polarization.
One of the most important drivers for patterning and polarity in plant development
is the phytohormone auxin. Auxin has the unique characteristic to establish polarized
channels for its own active directional cell to cell transport. This fascinating
phenomenon is called auxin canalization. Those auxin transport channels are characterized
by the expression and polar, subcellular localization of PIN auxin efflux carriers.
PIN proteins have the ability to dynamically change their localization and auxin
itself can affect this by interfering with trafficking. Most of the underlying
molecular mechanisms of canalization still remain enigmatic. What is known so
far is that canonical auxin signaling is indispensable but also other non-canonical
signaling components are thought to play a role. In order to shed light into the
mysteries auf auxin canalization this study revisits the branches of auxin signaling
in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like
responses but does not directly activate canonical transcriptional auxin signaling.
We revisit the direct auxin effect on PIN trafficking where we found that, contradictory
to previous observations, auxin is very specifically promoting endocytosis of
PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular
processes related to PIN subcellular dynamics are involved in the establishment
of auxin conducting channels and the formation of vascular tissue. We are re-evaluating
the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture
about its developmental phneotypes and involvement in auxin signaling and canalization.
Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL)
and auxin and found that SL is interfering with essentially all processes involved
in auxin canalization in a non-transcriptional manner. Lastly we identify a new
way of SL perception and signaling which is emanating from mitochondria, is independent
of canonical SL signaling and is modulating primary root growth.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
citation:
ama: Gallei MC. Auxin and strigolactone non-canonical signaling regulating development
in Arabidopsis thaliana. 2022. doi:10.15479/at:ista:11626
apa: Gallei, M. C. (2022). Auxin and strigolactone non-canonical signaling regulating
development in Arabidopsis thaliana. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:11626
chicago: Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating
Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria,
2022. https://doi.org/10.15479/at:ista:11626.
ieee: M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating
development in Arabidopsis thaliana,” Institute of Science and Technology Austria,
2022.
ista: Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating
development in Arabidopsis thaliana. Institute of Science and Technology Austria.
mla: Gallei, Michelle C. Auxin and Strigolactone Non-Canonical Signaling Regulating
Development in Arabidopsis Thaliana. Institute of Science and Technology Austria,
2022, doi:10.15479/at:ista:11626.
short: M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development
in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.
date_created: 2022-07-20T11:21:53Z
date_published: 2022-07-20T00:00:00Z
date_updated: 2024-10-29T10:22:45Z
day: '20'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/at:ista:11626
ec_funded: 1
file:
- access_level: open_access
checksum: bd7ac35403cf5b4b2607287d2a104b3a
content_type: application/pdf
creator: mgallei
date_created: 2022-07-25T09:08:47Z
date_updated: 2022-07-25T09:08:47Z
file_id: '11645'
file_name: Thesis_Gallei.pdf
file_size: 9730864
relation: main_file
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creator: mgallei
date_created: 2022-07-25T09:09:09Z
date_updated: 2022-07-25T09:39:58Z
file_id: '11646'
file_name: Thesis_Gallei_source.docx
file_size: 19560720
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content_type: application/pdf
creator: mgallei
date_created: 2022-07-25T09:09:32Z
date_updated: 2022-07-25T09:39:58Z
description: This is the print version of the thesis including the full appendix
file_id: '11647'
file_name: Thesis_Gallei_to_print.pdf
file_size: 24542837
relation: source_file
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content_type: application/pdf
creator: mgallei
date_created: 2022-07-25T11:48:45Z
date_updated: 2022-07-25T11:48:45Z
file_id: '11650'
file_name: Thesis_Gallei_Appendix.pdf
file_size: 15435966
relation: main_file
file_date_updated: 2022-07-25T11:48:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '248'
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication_identifier:
isbn:
- 978-3-99078-019-0
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9287'
relation: part_of_dissertation
status: public
- id: '7142'
relation: part_of_dissertation
status: public
- id: '7465'
relation: part_of_dissertation
status: public
- id: '8138'
relation: part_of_dissertation
status: public
- id: '6260'
relation: part_of_dissertation
status: public
- id: '8931'
relation: part_of_dissertation
status: public
- id: '10411'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Eilon
full_name: Shani, Eilon
last_name: Shani
title: Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis
thaliana
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '11653'
abstract:
- lang: eng
text: Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual
lineages of parthenogenetic females, which produce rare males at low frequencies.
Although they are known to have ZW chromosomes, these are not well characterized,
and it is unclear whether they are shared across the clade. Furthermore, the underlying
genetic architecture of the transmission of asexuality, which can occur when rare
males mate with closely related sexual females, is not well understood. We produced
a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized
in detail the pair of sex chromosomes of this species. We combined this new assembly
with short-read genomic data for the sexual species A. sp. Kazakhstan and several
asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization
of sex-chromosome evolution across the genus. We identified a small differentiated
region of the ZW pair that is shared by all sexual and asexual lineages, supporting
the shared ancestry of the sex chromosomes. We also inferred that recombination
suppression has spread to larger sections of the chromosome independently in the
American and Eurasian lineages. Finally, we took advantage of a rare male, which
we backcrossed to sexual females, to explore the genetic basis of asexuality.
Our results suggest that parthenogenesis is likely partly controlled by a locus
on the Z chromosome, highlighting the interplay between sex determination and
asexuality.
article_processing_charge: No
author:
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
citation:
ama: Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome
evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:10.15479/AT:ISTA:11653
apa: Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022,
“ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:11653
chicago: Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022,
‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’”
Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:11653.
ieee: M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome
evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute
of Science and Technology Austria, 2022.
ista: Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW
sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:11653.
mla: Elkrewi, Marwan N. Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW
Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.”
Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:11653.
short: M.N. Elkrewi, (2022).
contributor:
- first_name: Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Uladzislava
last_name: Khauratovich
- first_name: Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
- first_name: Vincent K
id: 57854184-AAE0-11E9-8D04-98D6E5697425
last_name: Bett
- first_name: Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
- first_name: Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Luca
last_name: Sax
- first_name: Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
- first_name: Francisco
last_name: 'Hontoria '
- first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
date_created: 2022-07-26T11:01:47Z
date_published: 2022-08-05T00:00:00Z
date_updated: 2024-02-21T12:35:53Z
day: '05'
ddc:
- '570'
department:
- _id: GradSch
- _id: BeVi
doi: 10.15479/AT:ISTA:11653
file:
- access_level: open_access
checksum: 5f1d7c6d7ab5375ed2564521432bed0c
content_type: application/x-zip-compressed
creator: melkrewi
date_created: 2022-07-26T12:37:52Z
date_updated: 2022-08-08T22:30:04Z
description: |
The folder contains the following datasets (fasta files, and text files):
Sup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan
male draft assembly
Sup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana
Sup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and
A. parthenogenetica females and rare male.
Sup. Dataset 4: Artemia sinica Male:female FST per 1Kb window
Sup. Dataset 5: FASTA file with candidate W scaffolds
Sup. Dataset 6: Candidate W-derived transcripts and alignments
Sup. Dataset 7: Gene expression with genomic location
Sup. Dataset 8: VCF for asexual female and rare male
Sup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)
Sup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using
A. sp. Kazakhstan as the reference), and inferred ancestry
Sup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their
locations in the Artemia sinica male genome.
embargo: 2022-08-07
file_id: '11655'
file_name: Data.zip
file_size: 2209382998
relation: main_file
title: Supplementary Datasets
file_date_updated: 2022-08-08T22:30:04Z
has_accepted_license: '1'
month: '08'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12248'
relation: used_in_publication
status: public
status: public
title: Data from Elkrewi, Khauratovich, Toups et al. 2022, "ZW sex-chromosome evolution
and contagious parthenogenesis in Artemia brine shrimp"
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11658'
abstract:
- lang: eng
text: The depth of a cell in an arrangement of n (non-vertical) great-spheres in
Sd is the number of great-spheres that pass above the cell. We prove Euler-type
relations, which imply extensions of the classic Dehn–Sommerville relations for
convex polytopes to sublevel sets of the depth function, and we use the relations
to extend the expressions for the number of faces of neighborly polytopes to the
number of cells of levels in neighborly arrangements.
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme,
grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant
no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization
in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.
article_processing_charge: No
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Sebastiano
full_name: Cultrera di Montesano, Sebastiano
id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
last_name: Cultrera di Montesano
orcid: 0000-0001-6249-0832
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Morteza
full_name: Saghafian, Morteza
id: f86f7148-b140-11ec-9577-95435b8df824
last_name: Saghafian
citation:
ama: 'Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements:
Dehn–Sommerville–Euler relations with applications. Leibniz International Proceedings
on Mathematics.'
apa: 'Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., & Saghafian,
M. (n.d.). Depth in arrangements: Dehn–Sommerville–Euler relations with applications.
Leibniz International Proceedings on Mathematics. Schloss Dagstuhl - Leibniz
Zentrum für Informatik.'
chicago: 'Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner,
and Morteza Saghafian. “Depth in Arrangements: Dehn–Sommerville–Euler Relations
with Applications.” Leibniz International Proceedings on Mathematics. Schloss
Dagstuhl - Leibniz Zentrum für Informatik, n.d.'
ieee: 'R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Depth
in arrangements: Dehn–Sommerville–Euler relations with applications,” Leibniz
International Proceedings on Mathematics. Schloss Dagstuhl - Leibniz Zentrum
für Informatik.'
ista: 'Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in
arrangements: Dehn–Sommerville–Euler relations with applications. Leibniz International
Proceedings on Mathematics.'
mla: 'Biswas, Ranita, et al. “Depth in Arrangements: Dehn–Sommerville–Euler Relations
with Applications.” Leibniz International Proceedings on Mathematics, Schloss
Dagstuhl - Leibniz Zentrum für Informatik.'
short: R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Leibniz
International Proceedings on Mathematics (n.d.).
date_created: 2022-07-27T09:27:34Z
date_published: 2022-07-27T00:00:00Z
date_updated: 2022-07-28T07:57:48Z
day: '27'
ddc:
- '510'
department:
- _id: GradSch
- _id: HeEd
ec_funded: 1
file:
- access_level: open_access
checksum: b2f511e8b1cae5f1892b0cdec341acac
content_type: application/pdf
creator: scultrer
date_created: 2022-07-27T09:25:53Z
date_updated: 2022-07-27T09:25:53Z
file_id: '11659'
file_name: D-S-E.pdf
file_size: 639266
relation: main_file
file_date_updated: 2022-07-27T09:25:53Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Leibniz International Proceedings on Mathematics
publication_status: submitted
publisher: Schloss Dagstuhl - Leibniz Zentrum für Informatik
quality_controlled: '1'
status: public
title: 'Depth in arrangements: Dehn–Sommerville–Euler relations with applications'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11660'
abstract:
- lang: eng
text: 'We characterize critical points of 1-dimensional maps paired in persistent
homology geometrically and this way get elementary proofs of theorems about the
symmetry of persistence diagrams and the variation of such maps. In particular,
we identify branching points and endpoints of networks as the sole source of asymmetry
and relate the cycle basis in persistent homology with a version of the stable
marriage problem. Our analysis provides the foundations of fast algorithms for
maintaining collections of interrelated sorted lists together with their persistence
diagrams. '
acknowledgement: 'This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme,
grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant
no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization
in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35. '
alternative_title:
- LIPIcs
article_processing_charge: No
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Sebastiano
full_name: Cultrera di Montesano, Sebastiano
id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
last_name: Cultrera di Montesano
orcid: 0000-0001-6249-0832
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Morteza
full_name: Saghafian, Morteza
last_name: Saghafian
citation:
ama: 'Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to
the persistence of 1D maps. I: Geometric characterization of critical point pairs.
LIPIcs.'
apa: 'Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., & Saghafian,
M. (n.d.). A window to the persistence of 1D maps. I: Geometric characterization
of critical point pairs. LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik.'
chicago: 'Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner,
and Morteza Saghafian. “A Window to the Persistence of 1D Maps. I: Geometric Characterization
of Critical Point Pairs.” LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, n.d.'
ieee: 'R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “A
window to the persistence of 1D maps. I: Geometric characterization of critical
point pairs,” LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.'
ista: 'Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window
to the persistence of 1D maps. I: Geometric characterization of critical point
pairs. LIPIcs.'
mla: 'Biswas, Ranita, et al. “A Window to the Persistence of 1D Maps. I: Geometric
Characterization of Critical Point Pairs.” LIPIcs, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik.'
short: R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, LIPIcs
(n.d.).
date_created: 2022-07-27T09:31:15Z
date_published: 2022-07-25T00:00:00Z
date_updated: 2022-07-28T08:05:34Z
day: '25'
ddc:
- '510'
department:
- _id: GradSch
- _id: HeEd
ec_funded: 1
file:
- access_level: open_access
checksum: 95903f9d1649e8e437a967b6f2f64730
content_type: application/pdf
creator: scultrer
date_created: 2022-07-27T09:30:30Z
date_updated: 2022-07-27T09:30:30Z
file_id: '11661'
file_name: window 1.pdf
file_size: 564836
relation: main_file
file_date_updated: 2022-07-27T09:30:30Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: LIPIcs
publication_status: submitted
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
status: public
title: 'A window to the persistence of 1D maps. I: Geometric characterization of critical
point pairs'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11723'
abstract:
- lang: eng
text: Plant cell growth responds rapidly to various stimuli, adapting architecture
to environmental changes. Two major endogenous signals regulating growth are the
phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs).
Both trigger very rapid cellular responses and also exert long-term effects [Du
et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol.
182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways
converge to regulate growth, remains unknown. Here, using vertical confocal microscopy
combined with a microfluidic chip, we addressed the mechanism of RALF action on
growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana
root growth inhibition and apoplast alkalinization during the initial phase of
the response, and revealed that RALF1 reversibly inhibits primary root growth
through apoplast alkalinization faster than within 1 min. This rapid apoplast
alkalinization was the result of RALF1-induced net H+ influx and was mediated
by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between
RALF1 and the auxin signaling pathways during root growth regulation. The results
showed that RALF-FER signaling triggered auxin signaling with a delay of approximately
1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced
growth inhibition. This biphasic RALF1 action on growth allows plants to respond
rapidly to environmental stimuli and also reprogram growth and development in
the long term.
acknowledgement: We thank Sarah M. Assmann, Kris Vissenberg, and Nadine Paris for
kindly sharing seeds; Matyáš Fendrych for initiating this project and providing
constant support; Lukas Fiedler for revising the manuscript; and Huibin Han and
Arseny Savin for contributing to genotyping. This work was supported by the Austrian
Science Fund (FWF) I 3630-B25 (to J.F.) and the Doctoral Fellowship Progrmme of
the Austrian Academy of Sciences (to L.L.) We also acknowledge Taif University Researchers
Supporting Project TURSP-HC2021/02 and funding “Plants as a tool for sustainable
global development (no. CZ.02.1.01/0.0/0.0/16_019/0000827).”
article_number: e2121058119
article_processing_charge: No
article_type: original
author:
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Huihuang
full_name: Chen, Huihuang
id: 83c96512-15b2-11ec-abd3-b7eede36184f
last_name: Chen
- first_name: Saqer S.
full_name: Alotaibi, Saqer S.
last_name: Alotaibi
- first_name: Aleš
full_name: Pěnčík, Aleš
last_name: Pěnčík
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth
inhibition upstream of auxin biosynthesis. Proceedings of the National Academy
of Sciences. 2022;119(31). doi:10.1073/pnas.2121058119
apa: Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., &
Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream
of auxin biosynthesis. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2121058119
chicago: Li, Lanxin, Huihuang Chen, Saqer S. Alotaibi, Aleš Pěnčík, Maciek Adamowski,
Ondřej Novák, and Jiří Friml. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition
Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2121058119.
ieee: L. Li et al., “RALF1 peptide triggers biphasic root growth inhibition
upstream of auxin biosynthesis,” Proceedings of the National Academy of Sciences,
vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.
ista: Li L, Chen H, Alotaibi SS, Pěnčík A, Adamowski M, Novák O, Friml J. 2022.
RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis.
Proceedings of the National Academy of Sciences. 119(31), e2121058119.
mla: Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition
Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences,
vol. 119, no. 31, e2121058119, Proceedings of the National Academy of Sciences,
2022, doi:10.1073/pnas.2121058119.
short: L. Li, H. Chen, S.S. Alotaibi, A. Pěnčík, M. Adamowski, O. Novák, J. Friml,
Proceedings of the National Academy of Sciences 119 (2022).
date_created: 2022-08-04T20:06:49Z
date_published: 2022-07-25T00:00:00Z
date_updated: 2024-10-29T10:12:30Z
day: '25'
ddc:
- '580'
department:
- _id: GradSch
- _id: JiFr
doi: 10.1073/pnas.2121058119
external_id:
isi:
- '000881496900002'
pmid:
- '35878023'
file:
- access_level: open_access
checksum: ae6f19b0d9efba6687f9e4dc1bab1d6e
content_type: application/pdf
creator: dernst
date_created: 2022-08-08T07:42:09Z
date_updated: 2022-08-08T07:42:09Z
file_id: '11747'
file_name: 2022_PNAS_Li.pdf
file_size: 2506262
relation: main_file
success: 1
file_date_updated: 2022-08-08T07:42:09Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '31'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
- _id: 26B4D67E-B435-11E9-9278-68D0E5697425
grant_number: '25351'
name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated
Rapid Growth Inhibition in Arabidopsis Root'
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 119
year: '2022'
...
---
_id: '11732'
abstract:
- lang: eng
text: We study the BCS energy gap Ξ in the high–density limit and derive an asymptotic
formula, which strongly depends on the strength of the interaction potential V
on the Fermi surface. In combination with the recent result by one of us (Math.
Phys. Anal. Geom. 25, 3, 2022) on the critical temperature Tc at high densities,
we prove the universality of the ratio of the energy gap and the critical temperature.
acknowledgement: "We are grateful to Robert Seiringer for helpful discussions and
many valuable comments\r\non an earlier version of the manuscript. J.H. acknowledges
partial financial support by the ERC Advanced Grant “RMTBeyond’ No. 101020331. Open
access funding provided by Institute of Science and Technology (IST Austria)"
article_number: '5'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Sven Joscha
full_name: Henheik, Sven Joscha
id: 31d731d7-d235-11ea-ad11-b50331c8d7fb
last_name: Henheik
orcid: 0000-0003-1106-327X
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
citation:
ama: Henheik SJ, Lauritsen AB. The BCS energy gap at high density. Journal of
Statistical Physics. 2022;189. doi:10.1007/s10955-022-02965-9
apa: Henheik, S. J., & Lauritsen, A. B. (2022). The BCS energy gap at high density.
Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-022-02965-9
chicago: Henheik, Sven Joscha, and Asbjørn Bækgaard Lauritsen. “The BCS Energy Gap
at High Density.” Journal of Statistical Physics. Springer Nature, 2022.
https://doi.org/10.1007/s10955-022-02965-9.
ieee: S. J. Henheik and A. B. Lauritsen, “The BCS energy gap at high density,” Journal
of Statistical Physics, vol. 189. Springer Nature, 2022.
ista: Henheik SJ, Lauritsen AB. 2022. The BCS energy gap at high density. Journal
of Statistical Physics. 189, 5.
mla: Henheik, Sven Joscha, and Asbjørn Bækgaard Lauritsen. “The BCS Energy Gap at
High Density.” Journal of Statistical Physics, vol. 189, 5, Springer Nature,
2022, doi:10.1007/s10955-022-02965-9.
short: S.J. Henheik, A.B. Lauritsen, Journal of Statistical Physics 189 (2022).
date_created: 2022-08-05T11:36:56Z
date_published: 2022-07-29T00:00:00Z
date_updated: 2023-09-05T14:57:49Z
day: '29'
ddc:
- '530'
department:
- _id: GradSch
- _id: LaEr
- _id: RoSe
doi: 10.1007/s10955-022-02965-9
ec_funded: 1
external_id:
isi:
- '000833007200002'
file:
- access_level: open_access
checksum: b398c4dbf65f71d417981d6e366427e9
content_type: application/pdf
creator: dernst
date_created: 2022-08-08T07:36:34Z
date_updated: 2022-08-08T07:36:34Z
file_id: '11746'
file_name: 2022_JourStatisticalPhysics_Henheik.pdf
file_size: 419563
relation: main_file
success: 1
file_date_updated: 2022-08-08T07:36:34Z
has_accepted_license: '1'
intvolume: ' 189'
isi: 1
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Journal of Statistical Physics
publication_identifier:
eissn:
- 1572-9613
issn:
- 0022-4715
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The BCS energy gap at high density
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 189
year: '2022'
...
---
_id: '11775'
abstract:
- lang: eng
text: 'Quantitative monitoring can be universal and approximate: For every finite
sequence of observations, the specification provides a value and the monitor outputs
a best-effort approximation of it. The quality of the approximation may depend
on the resources that are available to the monitor. By taking to the limit the
sequences of specification values and monitor outputs, we obtain precision-resource
trade-offs also for limit monitoring. This paper provides a formal framework for
studying such trade-offs using an abstract interpretation for monitors: For each
natural number n, the aggregate semantics of a monitor at time n is an equivalence
relation over all sequences of at most n observations so that two equivalent sequences
are indistinguishable to the monitor and thus mapped to the same output. This
abstract interpretation of quantitative monitors allows us to measure the number
of equivalence classes (or “resource use”) that is necessary for a certain precision
up to a certain time, or at any time. Our framework offers several insights. For
example, we identify a family of specifications for which any resource-optimal
exact limit monitor is independent of any error permitted over finite traces.
Moreover, we present a specification for which any resource-optimal approximate
limit monitor does not minimize its resource use at any time. '
acknowledgement: We thank the anonymous reviewers for their helpful comments. This
work was supported in part by the ERC-2020-AdG 101020093.
alternative_title:
- LNCS
article_processing_charge: Yes
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Nicolas Adrien
full_name: Mazzocchi, Nicolas Adrien
id: b26baa86-3308-11ec-87b0-8990f34baa85
last_name: Mazzocchi
- first_name: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
citation:
ama: 'Henzinger TA, Mazzocchi NA, Sarac NE. Abstract monitors for quantitative specifications.
In: 22nd International Conference on Runtime Verification. Vol 13498. Springer
Nature; 2022:200-220. doi:10.1007/978-3-031-17196-3_11'
apa: 'Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2022). Abstract monitors
for quantitative specifications. In 22nd International Conference on Runtime
Verification (Vol. 13498, pp. 200–220). Tbilisi, Georgia: Springer Nature.
https://doi.org/10.1007/978-3-031-17196-3_11'
chicago: Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Abstract
Monitors for Quantitative Specifications.” In 22nd International Conference
on Runtime Verification, 13498:200–220. Springer Nature, 2022. https://doi.org/10.1007/978-3-031-17196-3_11.
ieee: T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Abstract monitors for
quantitative specifications,” in 22nd International Conference on Runtime Verification,
Tbilisi, Georgia, 2022, vol. 13498, pp. 200–220.
ista: 'Henzinger TA, Mazzocchi NA, Sarac NE. 2022. Abstract monitors for quantitative
specifications. 22nd International Conference on Runtime Verification. RV: Runtime
Verification, LNCS, vol. 13498, 200–220.'
mla: Henzinger, Thomas A., et al. “Abstract Monitors for Quantitative Specifications.”
22nd International Conference on Runtime Verification, vol. 13498, Springer
Nature, 2022, pp. 200–20, doi:10.1007/978-3-031-17196-3_11.
short: T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 22nd International Conference
on Runtime Verification, Springer Nature, 2022, pp. 200–220.
conference:
end_date: 2022-09-30
location: Tbilisi, Georgia
name: 'RV: Runtime Verification'
start_date: 2022-09-28
date_created: 2022-08-08T17:09:09Z
date_published: 2022-09-23T00:00:00Z
date_updated: 2023-08-03T13:38:46Z
day: '23'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.1007/978-3-031-17196-3_11
ec_funded: 1
external_id:
isi:
- '000866539700011'
file:
- access_level: open_access
checksum: 05c7dcfbb9053a98f46441fb2eccb213
content_type: application/pdf
creator: dernst
date_created: 2023-01-20T07:34:50Z
date_updated: 2023-01-20T07:34:50Z
file_id: '12317'
file_name: 2022_LNCS_RV_Henzinger.pdf
file_size: 477110
relation: main_file
success: 1
file_date_updated: 2023-01-20T07:34:50Z
has_accepted_license: '1'
intvolume: ' 13498'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 200-220
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 22nd International Conference on Runtime Verification
publication_identifier:
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Abstract monitors for quantitative specifications
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13498
year: '2022'
...
---
_id: '11777'
abstract:
- lang: eng
text: "In this dissertation we study coboundary expansion of simplicial complex
with a view of giving geometric applications.\r\nOur main novel tool is an equivariant
version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological
overlap theorem leads to various geometric applications including a quantitative
non-embeddability result for sufficiently thick buildings (which partially resolves
a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing
number of (bounded degree) expander graphs. Additionally, we will give new proofs
for several known lower bounds for geometric problems such as the number of Tverberg
partitions or the crossing number of complete bipartite graphs.\r\nFor the aforementioned
applications one is naturally lead to study expansion properties of joins of simplicial
complexes. In the presence of a special certificate for expansion (as it is the
case, e.g., for spherical buildings), the join of two expanders is an expander.
On the flip-side, we report quite some evidence that coboundary expansion exhibits
very non-product-like behaviour under taking joins. For instance, we exhibit infinite
families of graphs $(G_n)_{n\\in \\mathbb{N}}$ and $(H_n)_{n\\in\\mathbb{N}}$
whose join $G_n*H_n$ has expansion of lower order than the product of the expansion
constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the
normalized coboundary expansion constants for the complete multipartite complex
$[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).\r\nVia the probabilistic
method the latter result extends to an upper bound of $(d+1)/2^d+\\varepsilon$
on the coboundary expansion constant of the spherical building associated with
$\\mathrm{PGL}_{d+2}(\\mathbb{F}_q)$ for any $\\varepsilon>0$ and sufficiently
large $q=q(\\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and
Mozes -- in a rather strong sense.\r\nBy improving on existing lower bounds we
make further progress towards closing the gap between the known lower and upper
bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements
we achieve using computer-aided proofs and flag algebras. The exact value even
for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown
but we are happy to conjecture a precise value for every $n$. %Moreover, we show
that a previously shown lower bound on the expansion constant of the spherical
building associated with $\\mathrm{PGL}_{2}(\\mathbb{F}_q)$ is not tight.\r\nIn
a loosely structured, last chapter of this thesis we collect further smaller observations
related to expansion. We point out a link between discrete Morse theory and a
technique for showing coboundary expansion, elaborate a bit on the hardness of
computing coboundary expansion constants, propose a new criterion for coboundary
expansion (in a very dense setting) and give one way of making the folklore result
that expansion of links is a necessary condition for a simplicial complex to be
an expander precise."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Pascal
full_name: Wild, Pascal
id: 4C20D868-F248-11E8-B48F-1D18A9856A87
last_name: Wild
citation:
ama: Wild P. High-dimensional expansion and crossing numbers of simplicial complexes.
2022. doi:10.15479/at:ista:11777
apa: Wild, P. (2022). High-dimensional expansion and crossing numbers of simplicial
complexes. Institute of Science and Technology. https://doi.org/10.15479/at:ista:11777
chicago: Wild, Pascal. “High-Dimensional Expansion and Crossing Numbers of Simplicial
Complexes.” Institute of Science and Technology, 2022. https://doi.org/10.15479/at:ista:11777.
ieee: P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,”
Institute of Science and Technology, 2022.
ista: Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial
complexes. Institute of Science and Technology.
mla: Wild, Pascal. High-Dimensional Expansion and Crossing Numbers of Simplicial
Complexes. Institute of Science and Technology, 2022, doi:10.15479/at:ista:11777.
short: P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes,
Institute of Science and Technology, 2022.
date_created: 2022-08-10T15:51:19Z
date_published: 2022-08-11T00:00:00Z
date_updated: 2023-06-22T09:56:36Z
day: '11'
ddc:
- '500'
- '516'
- '514'
degree_awarded: PhD
department:
- _id: GradSch
- _id: UlWa
doi: 10.15479/at:ista:11777
ec_funded: 1
file:
- access_level: open_access
checksum: f5f3af1fb7c8a24b71ddc88ad7f7c5b4
content_type: text/x-python
creator: pwild
date_created: 2022-08-10T15:34:04Z
date_updated: 2022-08-10T15:34:04Z
description: Code for computer-assisted proofs in Section 8.4.7 in Thesis
file_id: '11780'
file_name: flags.py
file_size: 16828
relation: supplementary_material
- access_level: open_access
checksum: 1f7c12dfe3bdaa9b147e4fbc3d34e3d5
content_type: text/x-c++src
creator: pwild
date_created: 2022-08-10T15:34:10Z
date_updated: 2022-08-10T15:34:10Z
description: Code for proof of Lemma 8.20 in Thesis
file_id: '11781'
file_name: lowerbound.cpp
file_size: 12226
relation: supplementary_material
- access_level: open_access
checksum: 4cf81455c49e5dec3b9b2e3980137eeb
content_type: text/x-python
creator: pwild
date_created: 2022-08-10T15:34:17Z
date_updated: 2022-08-10T15:34:17Z
description: Code for proof of Proposition 7.9 in Thesis
file_id: '11782'
file_name: upperbound.py
file_size: 3240
relation: supplementary_material
- access_level: open_access
checksum: 4e96575b10cbe4e0d0db2045b2847774
content_type: application/pdf
creator: pwild
date_created: 2022-08-11T16:08:33Z
date_updated: 2022-08-11T16:08:33Z
file_id: '11809'
file_name: finalthesisPascalWildPDFA.pdf
file_size: 5086282
relation: main_file
title: High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes
- access_level: closed
checksum: 92d94842a1fb6dca5808448137573b2e
content_type: application/zip
creator: pwild
date_created: 2022-08-11T16:09:19Z
date_updated: 2022-08-11T16:09:19Z
file_id: '11810'
file_name: ThesisSubmission.zip
file_size: 18150068
relation: source_file
file_date_updated: 2022-08-11T16:09:19Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '170'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-021-3
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology
status: public
supervisor:
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
title: High-dimensional expansion and crossing numbers of simplicial complexes
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '11839'
abstract:
- lang: eng
text: "It is a highly desirable property for deep networks to be robust against\r\nsmall
input changes. One popular way to achieve this property is by designing\r\nnetworks
with a small Lipschitz constant. In this work, we propose a new\r\ntechnique for
constructing such Lipschitz networks that has a number of\r\ndesirable properties:
it can be applied to any linear network layer\r\n(fully-connected or convolutional),
it provides formal guarantees on the\r\nLipschitz constant, it is easy to implement
and efficient to run, and it can be\r\ncombined with any training objective and
optimization method. In fact, our\r\ntechnique is the first one in the literature
that achieves all of these\r\nproperties simultaneously. Our main contribution
is a rescaling-based weight\r\nmatrix parametrization that guarantees each network
layer to have a Lipschitz\r\nconstant of at most 1 and results in the learned
weight matrices to be close to\r\northogonal. Hence we call such layers almost-orthogonal
Lipschitz (AOL).\r\nExperiments and ablation studies in the context of image classification
with\r\ncertified robust accuracy confirm that AOL layers achieve results that
are on\r\npar with most existing methods. Yet, they are simpler to implement and
more\r\nbroadly applicable, because they do not require computationally expensive\r\nmatrix
orthogonalization or inversion steps as part of the network\r\narchitecture. We
provide code at https://github.com/berndprach/AOL."
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Bernd
full_name: Prach, Bernd
id: 2D561D42-C427-11E9-89B4-9C1AE6697425
last_name: Prach
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Prach B, Lampert C. Almost-orthogonal layers for efficient general-purpose
Lipschitz networks. In: Computer Vision – ECCV 2022. Vol 13681. Springer
Nature; 2022:350-365. doi:10.1007/978-3-031-19803-8_21'
apa: 'Prach, B., & Lampert, C. (2022). Almost-orthogonal layers for efficient
general-purpose Lipschitz networks. In Computer Vision – ECCV 2022 (Vol.
13681, pp. 350–365). Tel Aviv, Israel: Springer Nature. https://doi.org/10.1007/978-3-031-19803-8_21'
chicago: Prach, Bernd, and Christoph Lampert. “Almost-Orthogonal Layers for Efficient
General-Purpose Lipschitz Networks.” In Computer Vision – ECCV 2022, 13681:350–65.
Springer Nature, 2022. https://doi.org/10.1007/978-3-031-19803-8_21.
ieee: B. Prach and C. Lampert, “Almost-orthogonal layers for efficient general-purpose
Lipschitz networks,” in Computer Vision – ECCV 2022, Tel Aviv, Israel,
2022, vol. 13681, pp. 350–365.
ista: 'Prach B, Lampert C. 2022. Almost-orthogonal layers for efficient general-purpose
Lipschitz networks. Computer Vision – ECCV 2022. ECCV: European Conference on
Computer Vision, LNCS, vol. 13681, 350–365.'
mla: Prach, Bernd, and Christoph Lampert. “Almost-Orthogonal Layers for Efficient
General-Purpose Lipschitz Networks.” Computer Vision – ECCV 2022, vol.
13681, Springer Nature, 2022, pp. 350–65, doi:10.1007/978-3-031-19803-8_21.
short: B. Prach, C. Lampert, in:, Computer Vision – ECCV 2022, Springer Nature,
2022, pp. 350–365.
conference:
end_date: 2022-10-27
location: Tel Aviv, Israel
name: 'ECCV: European Conference on Computer Vision'
start_date: 2022-10-23
date_created: 2022-08-12T15:09:47Z
date_published: 2022-10-23T00:00:00Z
date_updated: 2023-05-03T08:00:46Z
day: '23'
department:
- _id: GradSch
- _id: ChLa
doi: 10.1007/978-3-031-19803-8_21
external_id:
arxiv:
- '2208.03160'
intvolume: ' 13681'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2208.03160'
month: '10'
oa: 1
oa_version: Preprint
page: 350-365
publication: Computer Vision – ECCV 2022
publication_identifier:
eisbn:
- '9783031198038'
isbn:
- '9783031198021'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Almost-orthogonal layers for efficient general-purpose Lipschitz networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13681
year: '2022'
...
---
_id: '11879'
abstract:
- lang: eng
text: "As the overall global mean surface temperature is increasing due to climate
change, plant\r\nadaptation to those stressful conditions is of utmost importance
for their survival. Plants are\r\nsessile organisms, thus to compensate for their
lack of mobility, they evolved a variety of\r\nmechanisms enabling them to flexibly
adjust their physiological, growth and developmental\r\nprocesses to fluctuating
temperatures and to survive in harsh environments. While these unique\r\nadaptation
abilities provide an important evolutionary advantage, overall modulation of plant\r\ngrowth
and developmental program due to non-optimal temperature negatively affects biomass\r\nproduction,
crop productivity or sensitivity to pathogens. Thus, understanding molecular\r\nprocesses
underlying plant adaptation to increased temperature can provide important\r\nresources
for breeding strategies to ensure sufficient agricultural food production.\r\nAn
increase in ambient temperature by a few degrees leads to profound changes in
organ growth\r\nincluding enhanced hypocotyl elongation, expansion of petioles,
hyponastic growth of leaves and\r\ncotyledons, collectively named thermomorphogenesis
(Casal & Balasubramanian, 2019). Auxin,\r\none of the best-studied growth hormones,
plays an essential role in this process by direct\r\nactivation of transcriptional
and non-transcriptional processes resulting in elongation growth\r\n(Majda & Robert,
2018).To modulate hypocotyl growth in response to high ambient temperature\r\n(hAT),
auxin needs to be redistributed accordingly. PINs, auxin efflux transporters,
are key\r\ncomponents of the polar auxin transport (PAT) machinery, which controls
the amount and\r\ndirection of auxin translocated in the plant tissues and organs(Adamowski
& Friml, 2015). Hence,\r\nPIN-mediated transport is tightly linked with thermo-morphogenesis,
and interference with PAT\r\nthrough either chemical or genetic means dramatically
affecting the adaptive responses to hAT.\r\nIntriguingly, despite the key role
of PIN mediated transport in growth response to hAT, whether\r\nand how PINs at
the level of expression adapt to fluctuation in temperature is scarcely\r\nunderstood.\r\nWith
genetic, molecular and advanced bio-imaging approaches, we demonstrate the role
of PIN\r\nauxin transporters in the regulation of hypocotyl growth in response
to hAT. We show that via\r\nadjustment of PIN3, PIN4 and PIN7 expression in cotyledons
and hypocotyls, auxin distribution is modulated thereby determining elongation
pattern of epidermal cells at hAT. Furthermore, we\r\nidentified three Zinc-Finger
(ZF) transcription factors as novel molecular components of the\r\nthermo-regulatory
network, which through negative regulation of PIN transcription adjust the\r\ntransport
of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of
the\r\nnegative feedback loop attenuating the activity of the thermo-sensing pathway
to restrain\r\nexaggerated growth and developmental responses to hAT."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: SSU
acknowledgement: I would like to acknowledge ISTA and all the people from the Scientific
Service Units and at ISTA, in particular Dorota Jaworska for excellent technical
and scientific support as well as ÖAW for funding my research for over 3 years (DOC
ÖAW Fellowship PR1022OEAW02).
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Christina
full_name: Artner, Christina
id: 45DF286A-F248-11E8-B48F-1D18A9856A87
last_name: Artner
citation:
ama: Artner C. Modulation of auxin transport via ZF proteins adjust plant response
to high ambient temperature. 2022. doi:10.15479/at:ista:11879
apa: Artner, C. (2022). Modulation of auxin transport via ZF proteins adjust
plant response to high ambient temperature. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:11879
chicago: Artner, Christina. “Modulation of Auxin Transport via ZF Proteins Adjust
Plant Response to High Ambient Temperature.” Institute of Science and Technology
Austria, 2022. https://doi.org/10.15479/at:ista:11879.
ieee: C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response
to high ambient temperature,” Institute of Science and Technology Austria, 2022.
ista: Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant
response to high ambient temperature. Institute of Science and Technology Austria.
mla: Artner, Christina. Modulation of Auxin Transport via ZF Proteins Adjust
Plant Response to High Ambient Temperature. Institute of Science and Technology
Austria, 2022, doi:10.15479/at:ista:11879.
short: C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response
to High Ambient Temperature, Institute of Science and Technology Austria, 2022.
date_created: 2022-08-17T07:58:53Z
date_published: 2022-08-17T00:00:00Z
date_updated: 2023-09-09T22:30:04Z
day: '17'
ddc:
- '580'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EvBe
doi: 10.15479/at:ista:11879
file:
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checksum: a2c2fdc28002538840490bfa6a08b2cb
content_type: application/pdf
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date_created: 2022-08-17T12:08:49Z
date_updated: 2023-09-09T22:30:03Z
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content_type: application/octet-stream
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date_created: 2022-08-17T12:08:59Z
date_updated: 2023-09-09T22:30:03Z
embargo_to: open_access
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file_size: 19097730
relation: source_file
file_date_updated: 2023-09-09T22:30:03Z
has_accepted_license: '1'
keyword:
- high ambient temperature
- auxin
- PINs
- Zinc-Finger proteins
- thermomorphogenesis
- stress
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '128'
project:
- _id: 2685A872-B435-11E9-9278-68D0E5697425
name: Hormonal regulation of plant adaptive responses to environmental signals
publication_identifier:
isbn:
- 978-3-99078-022-0
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: Modulation of auxin transport via ZF proteins adjust plant response to high
ambient temperature
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11932'
abstract:
- lang: eng
text: "The ability to form and retrieve memories is central to survival. In mammals,
the hippocampus\r\nis a brain region essential to the acquisition and consolidation
of new memories. It is also\r\ninvolved in keeping track of one’s position in
space and aids navigation. Although this\r\nspace-memory has been a source of
contradiction, evidence supports the view that the role of\r\nthe hippocampus
in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced
by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory;
however, the detailed mechanisms by which these maps are formed and stored are
not\r\nyet agreed upon. Some influential theories describe this process as involving
three fundamental\r\nsteps: initial encoding by the hippocampus, interactions
between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal
consolidation. In this thesis, I will show how\r\nthe investigation of cognitive
maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe
first study included in this thesis deals with the initial encoding of spatial
memories in\r\nthe hippocampus. Much is known about encoding at the level of single
cells, but less about\r\ntheir co-activity or joint contribution to the encoding
of novel spatial information. I will\r\ndescribe the structure of an interaction
network that allows for efficient encoding of noisy\r\nspatial information during
the first exploration of a novel environment.\r\nThe second study describes the
interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas
directly and indirectly connected. It is known that the PFC, in concert\r\nwith
the hippocampus, is involved in various processes, including memory storage and
spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives
information from the\r\nhippocampus are not clear. I will show how a transient
improvement in theta phase locking of\r\nPFC cells enables interactions of cell
pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant
spatial locations in the hippocampus and the medial entorhinal cortex. I will
show how the accumulation of firing around\r\ngoal locations, a correlate of learning,
can shed light on the transition from short- to long-term\r\nspatial memories
and the speed of consolidation in different brain areas.\r\nThe studies included
in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve
statistical analyses and models of neural responses of cells in different brain
areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing
the impact of the findings\r\non principles of memory formation and retention,
including the mechanisms, the speed, and\r\nthe duration of these processes."
acknowledgement: I acknowledge the support from the European Union’s Horizon 2020
research and innovation program under the Marie Skłodowska-Curie Grant Agreement
No. 665385.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
citation:
ama: Nardin M. On the encoding, transfer, and consolidation of spatial memories.
2022. doi:10.15479/at:ista:11932
apa: Nardin, M. (2022). On the encoding, transfer, and consolidation of spatial
memories. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11932
chicago: Nardin, Michele. “On the Encoding, Transfer, and Consolidation of Spatial
Memories.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11932.
ieee: M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,”
Institute of Science and Technology Austria, 2022.
ista: Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories.
Institute of Science and Technology Austria.
mla: Nardin, Michele. On the Encoding, Transfer, and Consolidation of Spatial
Memories. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11932.
short: M. Nardin, On the Encoding, Transfer, and Consolidation of Spatial Memories,
Institute of Science and Technology Austria, 2022.
date_created: 2022-08-19T08:52:30Z
date_published: 2022-08-19T00:00:00Z
date_updated: 2023-09-05T12:02:14Z
day: '19'
ddc:
- '573'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoCs
doi: 10.15479/at:ista:11932
ec_funded: 1
file:
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checksum: 2dbb70c74aaa3b64c1f463e943baf09c
content_type: application/zip
creator: mnardin
date_created: 2022-08-19T16:31:34Z
date_updated: 2023-06-20T22:30:04Z
embargo_to: open_access
file_id: '11935'
file_name: Michele Nardin, Ph.D. Thesis - ISTA (1).zip
file_size: 13515457
relation: source_file
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checksum: 0ec94035ea35a47a9f589ed168e60b48
content_type: application/pdf
creator: mnardin
date_created: 2022-08-22T09:43:50Z
date_updated: 2023-06-20T22:30:04Z
embargo: 2023-06-19
file_id: '11941'
file_name: Michele_Nardin_Phd_Thesis_PDFA.pdf
file_size: 9906458
relation: main_file
file_date_updated: 2023-06-20T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '136'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10077'
relation: part_of_dissertation
status: public
- id: '6194'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
title: On the encoding, transfer, and consolidation of spatial memories
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '11945'
abstract:
- lang: eng
text: "G protein-coupled receptors (GPCRs) respond to specific ligands and regulate
multiple processes ranging from cell growth and immune responses to neuronal signal
transmission. However, ligands for many GPCRs remain unknown, suffer from off-target
effects or have poor bioavailability. Additional challenges exist to dissect cell-type
specific responses when the same GPCR is expressed on several cell types within
the body. Here, we overcome these limitations by engineering DREADD-based GPCR
chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic
a GPCR-of-interest in a desired cell type.\r\nWe validated our approach with β2-adrenergic
receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable
responses on second messenger and kinase activity, post-translational modifications,
and protein-protein interactions. Since β2AR is also enriched in microglia, which
can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR
in primary microglia and successfully recapitulate β2AR-mediated filopodia formation
through CNO stimulation. To dissect the role of selected GPCRs during microglial
inflammation, we additionally generated DREADD-based chimeras for microglia-enriched
GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65
both modulated the inflammatory response with a similar profile as endogenously
expressed β2AR, while DREADD-GPR109A showed no impact.\r\nOur DREADD-based approach
provides the means to obtain mechanistic and functional insights into GPCR signaling
on a cell-type specific level."
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rouven
full_name: Schulz, Rouven
id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87
last_name: Schulz
orcid: 0000-0001-5297-733X
citation:
ama: Schulz R. Chimeric G protein-coupled receptors mimic distinct signaling pathways
and modulate microglia function. 2022. doi:10.15479/at:ista:11945
apa: Schulz, R. (2022). Chimeric G protein-coupled receptors mimic distinct signaling
pathways and modulate microglia function. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:11945
chicago: Schulz, Rouven. “Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling
Pathways and Modulate Microglia Function.” Institute of Science and Technology
Austria, 2022. https://doi.org/10.15479/at:ista:11945.
ieee: R. Schulz, “Chimeric G protein-coupled receptors mimic distinct signaling
pathways and modulate microglia function,” Institute of Science and Technology
Austria, 2022.
ista: Schulz R. 2022. Chimeric G protein-coupled receptors mimic distinct signaling
pathways and modulate microglia function. Institute of Science and Technology
Austria.
mla: Schulz, Rouven. Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling
Pathways and Modulate Microglia Function. Institute of Science and Technology
Austria, 2022, doi:10.15479/at:ista:11945.
short: R. Schulz, Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling
Pathways and Modulate Microglia Function, Institute of Science and Technology
Austria, 2022.
date_created: 2022-08-23T11:33:11Z
date_published: 2022-08-23T00:00:00Z
date_updated: 2023-08-03T13:02:26Z
day: '23'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SaSi
doi: 10.15479/at:ista:11945
file:
- access_level: open_access
checksum: 61b1b666a210ff7cdd0e95ea75207a13
content_type: application/pdf
creator: rschulz
date_created: 2022-08-25T08:59:57Z
date_updated: 2022-08-25T08:59:57Z
file_id: '11970'
file_name: Thesis_Rouven_Schulz_2022_final.pdf
file_size: 28079331
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checksum: 2b8f95ea1c134dbdb927b41b1dbeeeb5
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: rschulz
date_created: 2022-08-25T09:00:11Z
date_updated: 2022-08-25T09:33:31Z
file_id: '11971'
file_name: Thesis_Rouven_Schulz_2022_final.docx
file_size: 27226963
relation: source_file
file_date_updated: 2022-08-25T09:33:31Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '133'
project:
- _id: 267F75D8-B435-11E9-9278-68D0E5697425
name: Modulating microglia through G protein-coupled receptor (GPCR) signaling
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11995'
relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
title: Chimeric G protein-coupled receptors mimic distinct signaling pathways and
modulate microglia function
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...