---
_id: '820'
abstract:
- lang: eng
text: "The lac operon is a classic model system for bacterial gene regulation, and
has been studied extensively in E. coli, a classic model organism. However, not
much is known about E. coli’s ecology and life outside the laboratory, in particular
in soil and water environments. The natural diversity of the lac operon outside
the laboratory, its role in the ecology of E. coli and the selection pressures
it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore
the genetic diversity, phylogenetic history and signatures of selection of the
lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia.
I found that complete lac operons were present in all isolates examined, which
in all but one case were functional. The lac operon phylogeny conformed to the
whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal
gene transfer as an explanation for the presence of functional lac operons in
these clades. All lac operon genes showed a signature of purifying selection;
this signature was strongest for the lacY gene. Lac operon genes of human and
environmental isolates showed similar signatures of selection, except the lacZ
gene, which showed a stronger signature of selection in environmental isolates.\r\nIn
Chapter Three, I try to identify the natural genetic variation relevant for phenotype
and fitness in the lac operon, comparing growth rate on lactose and LacZ activity
of the lac operons of these wild isolates in a common genetic background. Sequence
variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase
binding motif, predicted variation in LacZ activity at full induction, using a
thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation
in LacZ activity, nor RNA polymerase binding predicted by the model correlated
with variation in growth rate. Lac operons of human and environmental isolates
did not differ systematically in either growth rate on lactose or LacZ protein
activity, suggesting that these lac operons have been exposed to similar selection
pressures. We thus have no evidence that the phenotypic variation we measured
is relevant for fitness.\r\nTo start assessing the effect of genomic background
on the growth phenotype conferred by the lac operon, I compared growth on minimal
medium with lactose between lac operon constructs and the corresponding original
isolates, I found that maximal growth rate was determined by genomic background,
with almost all backgrounds conferring higher growth rates than lab strain K12
MG1655. However, I found no evidence that the lactose concentration at which growth
was half maximal depended on genomic background."
acknowledgement: "ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon
Bollback for giving me the chance to do this work, for sharing the ideas that lay
at the basis of this work, for his honesty and openness, showing himself to me as
a person and not just as a boss. Thanks to Nick Barton for his guidance at the last
stage, reading and commenting extensively on several versions of this manuscript,
and for his encouragement; thanks to both Jon and Nick for their kindness and patience.
Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be
in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter
my thesis committee at the last moment, and for his very sharp, helpful and relevant
comments during and after the defense. Thanks to my collaborators and discussion
partners: Anne Kupczok, for her guidance, ideas and discussions during the construction
of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh
for making me aware of the issue of parameter identifiability, suggesting how to
solve it, and for his unfortunate idea to start the plasmid enterprise in the first
place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments
on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting,
fast forwarding the analysis to turbo speed and making beautiful figures, and making
the discussion fun on top of it all; Vanessa Barone for her last minute comments,
especially on Chapter Three, providing a sharp and very helpful experimentalist
perspective at the last moment; Maros Pleska and Marjon de Vos for their comments
on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation
between growth rate and lactose concentration; Bor Kavcic for his input on growth
rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton,
Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific
environment to work in, as well as a lot of warmth and colour to everyday life.
And thanks to the friends I found here, to the people who were there for me and
to the people who changed my life, making it stranger and more beautiful than I
could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof,
Karin, Irene, Misha, Mato, Guillaume and Zanin. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Fabienne
full_name: Jesse, Fabienne
id: 4C8C26A4-F248-11E8-B48F-1D18A9856A87
last_name: Jesse
citation:
ama: Jesse F. The lac operon in the wild. 2017. doi:10.15479/AT:ISTA:th_857
apa: Jesse, F. (2017). The lac operon in the wild. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:th_857
chicago: Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and
Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_857.
ieee: F. Jesse, “The lac operon in the wild,” Institute of Science and Technology
Austria, 2017.
ista: Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology
Austria.
mla: Jesse, Fabienne. The Lac Operon in the Wild. Institute of Science and
Technology Austria, 2017, doi:10.15479/AT:ISTA:th_857.
short: F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology
Austria, 2017.
date_created: 2018-12-11T11:48:41Z
date_published: 2017-08-25T00:00:00Z
date_updated: 2023-09-07T12:01:21Z
day: '25'
ddc:
- '576'
- '577'
- '579'
degree_awarded: PhD
department:
- _id: JoBo
doi: 10.15479/AT:ISTA:th_857
ec_funded: 1
file:
- access_level: open_access
checksum: c62257a7bff0c5f39e1abffc6bfcca5c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:00Z
date_updated: 2020-07-14T12:48:10Z
file_id: '5252'
file_name: IST-2017-857-v1+1_thesis_fabienne.pdf
file_size: 3417773
relation: main_file
- access_level: closed
checksum: fc87d7d72fce52824a3ae7dcad0413a8
content_type: application/x-tex
creator: dernst
date_created: 2019-04-05T08:51:59Z
date_updated: 2020-07-14T12:48:10Z
file_id: '6212'
file_name: 2017_thesis_Jesse_source.tex
file_size: 215899
relation: source_file
file_date_updated: 2020-07-14T12:48:10Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '87'
project:
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6829'
pubrep_id: '857'
status: public
supervisor:
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
title: The lac operon in the wild
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '838'
abstract:
- lang: eng
text: 'In this thesis we discuss the exact security of message authentications codes
HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length
keyed hash function f into a variable input-length function. A practical single-key
variant of NMAC called HMAC is a very popular and widely deployed message authentication
code (MAC). PMAC is a block-cipher based mode of operation, which also happens
to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti
and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF),
and thus also a MAC, under two assumptions. Unfortunately, for many instantiations
of HMAC one of them has been found to be wrong. To restore the provable guarantees
for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC
was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a
pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure
variable input-length PRF. For adversaries making q queries, each of length at
most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves
an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently
best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by
giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one
initially XORs a mask to every message block, where the mask for the i th block
is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is
the i -th codeword of the Gray code. Our attack applies more generally to any
sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As
for NMAC , our first contribution is a simpler and uniform proof: If f is an ε
-secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q
queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length
at most ` blocks each. We also show that this ε + `qδ bound is basically tight
by constructing an f for which an attack with advantage `qδ exists. Moreover,
we analyze the PRF-security of a modification of NMAC called NI by An and Bellare
that avoids the constant rekeying on multi-block messages in NMAC and allows for
an information-theoretic analysis. We carry out such an analysis, obtaining a
tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2
q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved
by using τ i ’s that are k -wise independent, for k > 1 (the original has k
= 1). We observe that the security of PMAC will not increase in general if k =
2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4.
Due to simple extension attacks, this is the best bound one can hope for, using
any distribution on the masks. Whether k = 3 is already sufficient to get this
level of security is left as an open problem. Keywords: Message authentication
codes, Pseudorandom functions, HMAC, PMAC. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michal
full_name: Rybar, Michal
id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87
last_name: Rybar
citation:
ama: Rybar M. (The exact security of) Message authentication codes. 2017. doi:10.15479/AT:ISTA:th_828
apa: Rybar, M. (2017). (The exact security of) Message authentication codes.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_828
chicago: Rybar, Michal. “(The Exact Security of) Message Authentication Codes.”
Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_828.
ieee: M. Rybar, “(The exact security of) Message authentication codes,” Institute
of Science and Technology Austria, 2017.
ista: Rybar M. 2017. (The exact security of) Message authentication codes. Institute
of Science and Technology Austria.
mla: Rybar, Michal. (The Exact Security of) Message Authentication Codes.
Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_828.
short: M. Rybar, (The Exact Security of) Message Authentication Codes, Institute
of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:46Z
date_published: 2017-06-26T00:00:00Z
date_updated: 2023-09-07T12:02:28Z
day: '26'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: KrPi
doi: 10.15479/AT:ISTA:th_828
file:
- access_level: open_access
checksum: ff8639ec4bded6186f44c7bd3ee26804
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:13Z
date_updated: 2020-07-14T12:48:12Z
file_id: '4799'
file_name: IST-2017-828-v1+3_2017_Rybar_thesis.pdf
file_size: 847400
relation: main_file
- access_level: closed
checksum: 3462101745ce8ad199c2d0f75dae4a7e
content_type: application/zip
creator: dernst
date_created: 2019-04-05T08:24:11Z
date_updated: 2020-07-14T12:48:12Z
file_id: '6202'
file_name: 2017_Thesis_Rybar_source.zip
file_size: 26054879
relation: source_file
file_date_updated: 2020-07-14T12:48:12Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '86'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6810'
pubrep_id: '828'
related_material:
record:
- id: '2082'
relation: part_of_dissertation
status: public
- id: '6196'
relation: part_of_dissertation
status: public
status: public
title: (The exact security of) Message authentication codes
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '6196'
abstract:
- lang: eng
text: PMAC is a simple and parallel block-cipher mode of operation, which was introduced
by Black and Rogaway at Eurocrypt 2002. If instantiated with a (pseudo)random
permutation over n-bit strings, PMAC constitutes a provably secure variable input-length
(pseudo)random function. For adversaries making q queries, each of length at most
l (in n-bit blocks), and of total length σ ≤ ql, the original paper proves an
upper bound on the distinguishing advantage of Ο(σ2/2n), while the currently
best bound is Ο (qσ/2n).In this work we show that this bound is tight by giving
an attack with advantage Ω (q2l/2n). In the PMAC construction one initially XORs
a mask to every message block, where the mask for the ith block is computed as
τi := γi·L, where L is a (secret) random value, and γi is the i-th codeword of
the Gray code. Our attack applies more generally to any sequence of γi’s which
contains a large coset of a subgroup of GF(2n). We then investigate if the security
of PMAC can be further improved by using τi’s that are k-wise independent, for
k > 1 (the original distribution is only 1-wise independent). We observe that
the security of PMAC will not increase in general, even if the masks are chosen
from a 2-wise independent distribution, and then prove that the security increases
to O(q<2/2n), if the τi are 4-wise independent. Due to simple extension attacks,
this is the best bound one can hope for, using any distribution on the masks.
Whether 3-wise independence is already sufficient to get this level of security
is left as an open problem.
author:
- first_name: Peter
full_name: Gazi, Peter
id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
last_name: Gazi
- 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: Michal
full_name: Rybar, Michal
id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87
last_name: Rybar
citation:
ama: Gazi P, Pietrzak KZ, Rybar M. The exact security of PMAC. IACR Transactions
on Symmetric Cryptology. 2017;2016(2):145-161. doi:10.13154/TOSC.V2016.I2.145-161
apa: Gazi, P., Pietrzak, K. Z., & Rybar, M. (2017). The exact security of PMAC.
IACR Transactions on Symmetric Cryptology. Ruhr University Bochum. https://doi.org/10.13154/TOSC.V2016.I2.145-161
chicago: Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact Security
of PMAC.” IACR Transactions on Symmetric Cryptology. Ruhr University Bochum,
2017. https://doi.org/10.13154/TOSC.V2016.I2.145-161.
ieee: P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact security of PMAC,” IACR
Transactions on Symmetric Cryptology, vol. 2016, no. 2. Ruhr University Bochum,
pp. 145–161, 2017.
ista: Gazi P, Pietrzak KZ, Rybar M. 2017. The exact security of PMAC. IACR Transactions
on Symmetric Cryptology. 2016(2), 145–161.
mla: Gazi, Peter, et al. “The Exact Security of PMAC.” IACR Transactions on Symmetric
Cryptology, vol. 2016, no. 2, Ruhr University Bochum, 2017, pp. 145–61, doi:10.13154/TOSC.V2016.I2.145-161.
short: P. Gazi, K.Z. Pietrzak, M. Rybar, IACR Transactions on Symmetric Cryptology
2016 (2017) 145–161.
date_created: 2019-04-04T13:48:23Z
date_published: 2017-02-03T00:00:00Z
date_updated: 2023-09-07T12:02:27Z
day: '03'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.13154/TOSC.V2016.I2.145-161
ec_funded: 1
file:
- access_level: open_access
checksum: f23161d685dd957ae8d7274132999684
content_type: application/pdf
creator: dernst
date_created: 2019-04-04T13:53:58Z
date_updated: 2020-07-14T12:47:24Z
file_id: '6197'
file_name: 2017_IACR_Gazi.pdf
file_size: 597335
relation: main_file
file_date_updated: 2020-07-14T12:47:24Z
has_accepted_license: '1'
intvolume: ' 2016'
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 145-161
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: IACR Transactions on Symmetric Cryptology
publication_identifier:
eissn:
- 2519-173X
publication_status: published
publisher: Ruhr University Bochum
quality_controlled: '1'
related_material:
record:
- id: '838'
relation: dissertation_contains
status: public
status: public
title: The exact security of PMAC
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016
year: '2017'
...
---
_id: '837'
abstract:
- lang: eng
text: 'The hippocampus is a key brain region for memory and notably for spatial
memory, and is needed for both spatial working and reference memories. Hippocampal
place cells selectively discharge in specific locations of the environment to
form mnemonic represen tations of space. Several behavioral protocols have been
designed to test spatial memory which requires the experimental subject to utilize
working memory and reference memory. However, less is known about how these memory
traces are presented in the hippo campus, especially considering tasks that require
both spatial working and long -term reference memory demand. The aim of my thesis
was to elucidate how spatial working memory, reference memory, and the combination
of both are represented in the hippocampus. In this thesis, using a radial eight
-arm maze, I examined how the combined demand on these memories influenced place
cell assemblies while reference memories were partially updated by changing some
of the reward- arms. This was contrasted with task varian ts requiring working
or reference memories only. Reference memory update led to gradual place field
shifts towards the rewards on the switched arms. Cells developed enhanced firing
in passes between newly -rewarded arms as compared to those containing an unchanged
reward. The working memory task did not show such gradual changes. Place assemblies
on occasions replayed trajectories of the maze; at decision points the next arm
choice was preferentially replayed in tasks needing reference memory while in
the pure working memory task the previously visited arm was replayed. Hence trajectory
replay only reflected the decision of the animal in tasks needing reference memory
update. At the reward locations, in all three tasks outbound trajectories of the
current arm were preferentially replayed, showing the animals’ next path to the
center. At reward locations trajectories were replayed preferentially in reverse
temporal order. Moreover, in the center reverse replay was seen in the working
memory task but in the other tasks forward replay was seen. Hence, the direction
of reactivation was determined by the goal locations so that part of the trajectory
which was closer to the goal was reactivated later in an HSE while places further
away from the goal were reactivated earlier. Altogether my work demonstrated that
reference memory update triggers several levels of reorganization of the hippocampal
cognitive map which are not seen in simpler working memory demand s. Moreover,
hippocampus is likely to be involved in spatial decisions through reactivating
planned trajectories when reference memory recall is required for such a decision. '
acknowledgement: 'I am very grateful for the opportunity I have had as a graduate
student to explore and incredibly interesting branch of neuroscience, and for the
people who made it possible. Firstly, I would like to offer my thanks to my supervisor
Professor Jozsef Csicsvari for his great support, guidance and patience offered
over the years. The door to his office was always open whenever I had questions.
I have learned a lot from him about carefully designing experiments, asking interesting
questions and how to integrate results into a broader picture. I also express my
gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific
role model who is always willing to teach , and advice and talk through problems
with his full attention. Many thanks to my wonderful “office mates” over the years
and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree
Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián
Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in
the lab for the many useful discussions about science and for making the laboratory
such a nice and friendly place to work in. A special thank goes to Michael LoBianco
and Jago Wallenschus for wonderful technical support. I would also like to thank
Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam
and thesi s committee members despite their busy schedule. I am also very thankful
to IST Austria for their support all throughout my PhD. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Haibing
full_name: Xu, Haibing
id: 310349D0-F248-11E8-B48F-1D18A9856A87
last_name: Xu
citation:
ama: Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial
tasks. 2017. doi:10.15479/AT:ISTA:th_858
apa: Xu, H. (2017). Reactivation of the hippocampal cognitive map in goal-directed
spatial tasks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_858
chicago: Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed
Spatial Tasks.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_858.
ieee: H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial
tasks,” Institute of Science and Technology Austria, 2017.
ista: Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed
spatial tasks. Institute of Science and Technology Austria.
mla: Xu, Haibing. Reactivation of the Hippocampal Cognitive Map in Goal-Directed
Spatial Tasks. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_858.
short: H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial
Tasks, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:46Z
date_published: 2017-08-23T00:00:00Z
date_updated: 2023-09-07T12:06:38Z
day: '23'
ddc:
- '571'
degree_awarded: PhD
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:th_858
file:
- access_level: closed
checksum: f11925fbbce31e495124b6bc4f10573c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T08:59:51Z
date_updated: 2020-07-14T12:48:12Z
file_id: '6213'
file_name: 2017_Xu_Haibing_Thesis_Source.docx
file_size: 3589490
relation: source_file
- access_level: open_access
checksum: ffb10749a537d615fab1ef0937ccb157
content_type: application/pdf
creator: dernst
date_created: 2019-04-05T08:59:51Z
date_updated: 2020-07-14T12:48:12Z
file_id: '6214'
file_name: 2017_Xu_Thesis_IST.pdf
file_size: 11668613
relation: main_file
file_date_updated: 2020-07-14T12:48:12Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '93'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6811'
pubrep_id: '858'
related_material:
record:
- id: '5828'
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: Reactivation of the hippocampal cognitive map in goal-directed spatial tasks
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '938'
abstract:
- lang: eng
text: The thesis encompasses several topics of plant cell biology which were studied
in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone
auxin and its polar transport through cells and tissues. The highly controlled,
directional transport of auxin is facilitated by plasma membrane-localized transporters.
Transporters from the PIN family direct auxin transport due to their polarized
localizations at cell membranes. Substantial effort has been put into research
on cellular trafficking of PIN proteins, which is thought to underlie their polar
distribution. I participated in a forward genetic screen aimed at identifying
novel regulators of PIN polarity. The screen yielded several genes which may be
involved in PIN polarity regulation or participate in polar auxin transport by
other means. Chapter 2 focuses on the endomembrane system, with particular attention
to clathrin-mediated endocytosis. The project started with identification of several
proteins that interact with clathrin light chains. Among them, I focused on two
putative homologues of auxilin, which in non-plant systems is an endocytotic factor
known for uncoating clathrin-coated vesicles in the final step of endocytosis.
The body of my work consisted of an in-depth characterization of transgenic A.
thaliana lines overexpressing these putative auxilins in an inducible manner.
Overexpression of these proteins leads to an inhibition of endocytosis, as documented
by imaging of cargoes and clathrin-related endocytic machinery. An extension of
this work is an investigation into a concept of homeostatic regulation acting
between distinct transport processes in the endomembrane system. With auxilin
overexpressing lines, where endocytosis is blocked specifically, I made observations
on the mutual relationship between two opposite trafficking processes of secretion
and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their
relationship to auxin signaling and polarized growth in elongating cells. In plants,
microtubules are organized into arrays just below the plasma membrane, and it
is thought that their function is to guide membrane-docked cellulose synthase
complexes. These, in turn, influence cell wall structure and cell shape by directed
deposition of cellulose fibres. In elongating cells, cortical microtubule arrays
are able to reorient in relation to long cell axis, and these reorientations have
been linked to cell growth and to signaling of growth-regulating factors such
as auxin or light. In this chapter, I am addressing the causal relationship between
microtubule array reorientation, growth, and auxin signaling. I arrive at a model
where array reorientation is not guided by auxin directly, but instead is only
controlled by growth, which, in turn, is regulated by auxin.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
citation:
ama: Adamowski M. Investigations into cell polarity and trafficking in the plant
model Arabidopsis thaliana . 2017. doi:10.15479/AT:ISTA:th_842
apa: Adamowski, M. (2017). Investigations into cell polarity and trafficking
in the plant model Arabidopsis thaliana . Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:th_842
chicago: Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in
the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria,
2017. https://doi.org/10.15479/AT:ISTA:th_842.
ieee: M. Adamowski, “Investigations into cell polarity and trafficking in the plant
model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017.
ista: Adamowski M. 2017. Investigations into cell polarity and trafficking in the
plant model Arabidopsis thaliana . Institute of Science and Technology Austria.
mla: Adamowski, Maciek. Investigations into Cell Polarity and Trafficking in
the Plant Model Arabidopsis Thaliana . Institute of Science and Technology
Austria, 2017, doi:10.15479/AT:ISTA:th_842.
short: M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant
Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:49:18Z
date_published: 2017-06-02T00:00:00Z
date_updated: 2023-09-07T12:06:09Z
day: '02'
ddc:
- '581'
- '583'
- '580'
degree_awarded: PhD
department:
- _id: JiFr
doi: 10.15479/AT:ISTA:th_842
file:
- access_level: closed
checksum: 193425764d9aaaed3ac57062a867b315
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T09:03:20Z
date_updated: 2020-07-14T12:48:15Z
file_id: '6215'
file_name: 2017_Adamowski-Thesis_Source.docx
file_size: 46903863
relation: source_file
- access_level: open_access
checksum: df5ab01be81f821e1b958596a1ec8d21
content_type: application/pdf
creator: dernst
date_created: 2019-04-05T09:03:19Z
date_updated: 2020-07-14T12:48:15Z
file_id: '6216'
file_name: 2017_Adamowski-Thesis.pdf
file_size: 8698888
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '117'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6483'
pubrep_id: '842'
related_material:
record:
- id: '1591'
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
title: 'Investigations into cell polarity and trafficking in the plant model Arabidopsis
thaliana '
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '992'
abstract:
- lang: eng
text: "An instance of the Constraint Satisfaction Problem (CSP) is given by a finite
set of\r\nvariables, a finite domain of labels, and a set of constraints, each
constraint acting on\r\na subset of the variables. The goal is to find an assignment
of labels to its variables\r\nthat satisfies all constraints (or decide whether
one exists). If we allow more general\r\n“soft” constraints, which come with (possibly
infinite) costs of particular assignments,\r\nwe obtain instances from a richer
class called Valued Constraint Satisfaction Problem\r\n(VCSP). There the goal
is to find an assignment with minimum total cost.\r\nIn this thesis, we focus
(assuming that P\r\n6\r\n=\r\nNP) on classifying computational com-\r\nplexity
of CSPs and VCSPs under certain restricting conditions. Two results are the core\r\ncontent
of the work. In one of them, we consider VCSPs parametrized by a constraint\r\nlanguage,
that is the set of “soft” constraints allowed to form the instances, and finish\r\nthe
complexity classification modulo (missing pieces of) complexity classification
for\r\nanalogously parametrized CSP. The other result is a generalization of Edmonds’
perfect\r\nmatching algorithm. This generalization contributes to complexity classfications
in two\r\nways. First, it gives a new (largest known) polynomial-time solvable
class of Boolean\r\nCSPs in which every variable may appear in at most two constraints
and second, it\r\nsettles full classification of Boolean CSPs with planar drawing
(again parametrized by a\r\nconstraint language)."
acknowledgement: FP7/2007-2013/ERC grant agreement no 616160
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: Rolinek M. Complexity of constraint satisfaction. 2017. doi:10.15479/AT:ISTA:th_815
apa: Rolinek, M. (2017). Complexity of constraint satisfaction. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_815
chicago: Rolinek, Michal. “Complexity of Constraint Satisfaction.” Institute of
Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_815.
ieee: M. Rolinek, “Complexity of constraint satisfaction,” Institute of Science
and Technology Austria, 2017.
ista: Rolinek M. 2017. Complexity of constraint satisfaction. Institute of Science
and Technology Austria.
mla: Rolinek, Michal. Complexity of Constraint Satisfaction. Institute of
Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_815.
short: M. Rolinek, Complexity of Constraint Satisfaction, Institute of Science and
Technology Austria, 2017.
date_created: 2018-12-11T11:49:35Z
date_published: 2017-05-01T00:00:00Z
date_updated: 2023-09-07T12:05:41Z
day: '01'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: VlKo
doi: 10.15479/AT:ISTA:th_815
ec_funded: 1
file:
- access_level: open_access
checksum: 81761fb939acb7585c36629f765b4373
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:55Z
date_updated: 2020-07-14T12:48:18Z
file_id: '4654'
file_name: IST-2017-815-v1+3_final_blank_signature_maybe_pdfa.pdf
file_size: 786145
relation: main_file
- access_level: closed
checksum: 2b2d7e1d6c1c79a9795a7aa0f860baf3
content_type: application/zip
creator: dernst
date_created: 2019-04-05T08:43:24Z
date_updated: 2020-07-14T12:48:18Z
file_id: '6208'
file_name: 2017_Thesis_Rolinek_source.zip
file_size: 5936337
relation: source_file
file_date_updated: 2020-07-14T12:48:18Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '97'
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6407'
pubrep_id: '815'
status: public
supervisor:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
title: Complexity of constraint satisfaction
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '718'
abstract:
- lang: eng
text: Mapping every simplex in the Delaunay mosaic of a discrete point set to the
radius of the smallest empty circumsphere gives a generalized discrete Morse function.
Choosing the points from a Poisson point process in ℝ n , we study the expected
number of simplices in the Delaunay mosaic as well as the expected number of critical
simplices and nonsingular intervals in the corresponding generalized discrete
gradient. Observing connections with other probabilistic models, we obtain precise
expressions for the expected numbers in low dimensions. In particular, we obtain
the expected numbers of simplices in the Poisson–Delaunay mosaic in dimensions
n ≤ 4.
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Anton
full_name: Nikitenko, Anton
id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87
last_name: Nikitenko
orcid: 0000-0002-0659-3201
- first_name: Matthias
full_name: Reitzner, Matthias
last_name: Reitzner
citation:
ama: Edelsbrunner H, Nikitenko A, Reitzner M. Expected sizes of poisson Delaunay
mosaics and their discrete Morse functions. Advances in Applied Probability.
2017;49(3):745-767. doi:10.1017/apr.2017.20
apa: Edelsbrunner, H., Nikitenko, A., & Reitzner, M. (2017). Expected sizes
of poisson Delaunay mosaics and their discrete Morse functions. Advances in
Applied Probability. Cambridge University Press. https://doi.org/10.1017/apr.2017.20
chicago: Edelsbrunner, Herbert, Anton Nikitenko, and Matthias Reitzner. “Expected
Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” Advances
in Applied Probability. Cambridge University Press, 2017. https://doi.org/10.1017/apr.2017.20.
ieee: H. Edelsbrunner, A. Nikitenko, and M. Reitzner, “Expected sizes of poisson
Delaunay mosaics and their discrete Morse functions,” Advances in Applied Probability,
vol. 49, no. 3. Cambridge University Press, pp. 745–767, 2017.
ista: Edelsbrunner H, Nikitenko A, Reitzner M. 2017. Expected sizes of poisson Delaunay
mosaics and their discrete Morse functions. Advances in Applied Probability. 49(3),
745–767.
mla: Edelsbrunner, Herbert, et al. “Expected Sizes of Poisson Delaunay Mosaics and
Their Discrete Morse Functions.” Advances in Applied Probability, vol.
49, no. 3, Cambridge University Press, 2017, pp. 745–67, doi:10.1017/apr.2017.20.
short: H. Edelsbrunner, A. Nikitenko, M. Reitzner, Advances in Applied Probability
49 (2017) 745–767.
date_created: 2018-12-11T11:48:07Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-09-07T12:07:12Z
day: '01'
department:
- _id: HeEd
doi: 10.1017/apr.2017.20
ec_funded: 1
external_id:
arxiv:
- '1607.05915'
intvolume: ' 49'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1607.05915
month: '09'
oa: 1
oa_version: Preprint
page: 745 - 767
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Advances in Applied Probability
publication_identifier:
issn:
- '00018678'
publication_status: published
publisher: Cambridge University Press
publist_id: '6962'
quality_controlled: '1'
related_material:
record:
- id: '6287'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Expected sizes of poisson Delaunay mosaics and their discrete Morse functions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 49
year: '2017'
...
---
_id: '559'
abstract:
- lang: eng
text: 'Proofs of space (PoS) were suggested as more ecological and economical alternative
to proofs of work, which are currently used in blockchain designs like Bitcoin.
The existing PoS are based on rather sophisticated graph pebbling lower bounds.
Much simpler and in several aspects more efficient schemes based on inverting
random functions have been suggested, but they don’t give meaningful security
guarantees due to existing time-memory trade-offs. In particular, Hellman showed
that any permutation over a domain of size N can be inverted in time T by an algorithm
that is given S bits of auxiliary information whenever (Formula presented). For
functions Hellman gives a weaker attack with S2· T≈ N2 (e.g., S= T≈ N2/3). To
prove lower bounds, one considers an adversary who has access to an oracle f:
[ N] → [N] and can make T oracle queries. The best known lower bound is S· T∈
Ω(N) and holds for random functions and permutations. We construct functions that
provably require more time and/or space to invert. Specifically, for any constant
k we construct a function [N] → [N] that cannot be inverted unless Sk· T∈ Ω(Nk)
(in particular, S= T≈ (Formula presented). Our construction does not contradict
Hellman’s time-memory trade-off, because it cannot be efficiently evaluated in
forward direction. However, its entire function table can be computed in time
quasilinear in N, which is sufficient for the PoS application. Our simplest construction
is built from a random function oracle g: [N] × [N] → [ N] and a random permutation
oracle f: [N] → N] and is defined as h(x) = g(x, x′) where f(x) = π(f(x′)) with
π being any involution without a fixed point, e.g. flipping all the bits. For
this function we prove that any adversary who gets S bits of auxiliary information,
makes at most T oracle queries, and inverts h on an ϵ fraction of outputs must
satisfy S2· T∈ Ω(ϵ2N2).'
alternative_title:
- LNCS
author:
- first_name: Hamza M
full_name: Abusalah, Hamza M
id: 40297222-F248-11E8-B48F-1D18A9856A87
last_name: Abusalah
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Bram
full_name: Cohen, Bram
last_name: Cohen
- first_name: Danylo
full_name: Khilko, Danylo
last_name: Khilko
- 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: Leonid
full_name: Reyzin, Leonid
last_name: Reyzin
citation:
ama: 'Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. Beyond Hellman’s
time-memory trade-offs with applications to proofs of space. In: Vol 10625. Springer;
2017:357-379. doi:10.1007/978-3-319-70697-9_13'
apa: 'Abusalah, H. M., Alwen, J. F., Cohen, B., Khilko, D., Pietrzak, K. Z., &
Reyzin, L. (2017). Beyond Hellman’s time-memory trade-offs with applications to
proofs of space (Vol. 10625, pp. 357–379). Presented at the ASIACRYPT: Theory
and Applications of Cryptology and Information Security, Hong Kong, China: Springer.
https://doi.org/10.1007/978-3-319-70697-9_13'
chicago: Abusalah, Hamza M, Joel F Alwen, Bram Cohen, Danylo Khilko, Krzysztof Z
Pietrzak, and Leonid Reyzin. “Beyond Hellman’s Time-Memory Trade-Offs with Applications
to Proofs of Space,” 10625:357–79. Springer, 2017. https://doi.org/10.1007/978-3-319-70697-9_13.
ieee: 'H. M. Abusalah, J. F. Alwen, B. Cohen, D. Khilko, K. Z. Pietrzak, and L.
Reyzin, “Beyond Hellman’s time-memory trade-offs with applications to proofs of
space,” presented at the ASIACRYPT: Theory and Applications of Cryptology and
Information Security, Hong Kong, China, 2017, vol. 10625, pp. 357–379.'
ista: 'Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. 2017. Beyond
Hellman’s time-memory trade-offs with applications to proofs of space. ASIACRYPT:
Theory and Applications of Cryptology and Information Security, LNCS, vol. 10625,
357–379.'
mla: Abusalah, Hamza M., et al. Beyond Hellman’s Time-Memory Trade-Offs with
Applications to Proofs of Space. Vol. 10625, Springer, 2017, pp. 357–79, doi:10.1007/978-3-319-70697-9_13.
short: H.M. Abusalah, J.F. Alwen, B. Cohen, D. Khilko, K.Z. Pietrzak, L. Reyzin,
in:, Springer, 2017, pp. 357–379.
conference:
end_date: 2017-12-07
location: Hong Kong, China
name: 'ASIACRYPT: Theory and Applications of Cryptology and Information Security'
start_date: 2017-12-03
date_created: 2018-12-11T11:47:10Z
date_published: 2017-11-18T00:00:00Z
date_updated: 2023-09-07T12:30:22Z
day: '18'
department:
- _id: KrPi
doi: 10.1007/978-3-319-70697-9_13
ec_funded: 1
intvolume: ' 10625'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/893.pdf
month: '11'
oa: 1
oa_version: Submitted Version
page: 357 - 379
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
isbn:
- 978-331970696-2
publication_status: published
publisher: Springer
publist_id: '7257'
quality_controlled: '1'
related_material:
record:
- id: '83'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Beyond Hellman’s time-memory trade-offs with applications to proofs of space
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10625
year: '2017'
...
---
_id: '550'
abstract:
- lang: eng
text: For large random matrices X with independent, centered entries but not necessarily
identical variances, the eigenvalue density of XX* is well-approximated by a deterministic
measure on ℝ. We show that the density of this measure has only square and cubic-root
singularities away from zero. We also extend the bulk local law in [5] to the
vicinity of these singularities.
article_number: '63'
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
citation:
ama: Alt J. Singularities of the density of states of random Gram matrices. Electronic
Communications in Probability. 2017;22. doi:10.1214/17-ECP97
apa: Alt, J. (2017). Singularities of the density of states of random Gram matrices.
Electronic Communications in Probability. Institute of Mathematical Statistics.
https://doi.org/10.1214/17-ECP97
chicago: Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.”
Electronic Communications in Probability. Institute of Mathematical Statistics,
2017. https://doi.org/10.1214/17-ECP97.
ieee: J. Alt, “Singularities of the density of states of random Gram matrices,”
Electronic Communications in Probability, vol. 22. Institute of Mathematical
Statistics, 2017.
ista: Alt J. 2017. Singularities of the density of states of random Gram matrices.
Electronic Communications in Probability. 22, 63.
mla: Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.”
Electronic Communications in Probability, vol. 22, 63, Institute of Mathematical
Statistics, 2017, doi:10.1214/17-ECP97.
short: J. Alt, Electronic Communications in Probability 22 (2017).
date_created: 2018-12-11T11:47:07Z
date_published: 2017-11-21T00:00:00Z
date_updated: 2023-09-07T12:38:08Z
day: '21'
ddc:
- '539'
department:
- _id: LaEr
doi: 10.1214/17-ECP97
ec_funded: 1
file:
- access_level: open_access
checksum: 0ec05303a0de190de145654237984c79
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:04Z
date_updated: 2020-07-14T12:47:00Z
file_id: '4663'
file_name: IST-2018-926-v1+1_euclid.ecp.1511233247.pdf
file_size: 470876
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
has_accepted_license: '1'
intvolume: ' 22'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Electronic Communications in Probability
publication_identifier:
issn:
- 1083589X
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '7265'
pubrep_id: '926'
quality_controlled: '1'
related_material:
record:
- id: '149'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Singularities of the density of states of random Gram matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2017'
...
---
_id: '647'
abstract:
- lang: eng
text: Despite researchers’ efforts in the last couple of decades, reachability analysis
is still a challenging problem even for linear hybrid systems. Among the existing
approaches, the most practical ones are mainly based on bounded-time reachable
set over-approximations. For the purpose of unbounded-time analysis, one important
strategy is to abstract the original system and find an invariant for the abstraction.
In this paper, we propose an approach to constructing a new kind of abstraction
called conic abstraction for affine hybrid systems, and to computing reachable
sets based on this abstraction. The essential feature of a conic abstraction is
that it partitions the state space of a system into a set of convex polyhedral
cones which is derived from a uniform conic partition of the derivative space.
Such a set of polyhedral cones is able to cut all trajectories of the system into
almost straight segments so that every segment of a reach pipe in a polyhedral
cone tends to be straight as well, and hence can be over-approximated tightly
by polyhedra using similar techniques as HyTech or PHAVer. In particular, for
diagonalizable affine systems, our approach can guarantee to find an invariant
for unbounded reachable sets, which is beyond the capability of bounded-time reachability
analysis tools. We implemented the approach in a tool and experiments on benchmarks
show that our approach is more powerful than SpaceEx and PHAVer in dealing with
diagonalizable systems.
alternative_title:
- LNCS
author:
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- 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: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
citation:
ama: 'Bogomolov S, Giacobbe M, Henzinger TA, Kong H. Conic abstractions for hybrid
systems. In: Vol 10419. Springer; 2017:116-132. doi:10.1007/978-3-319-65765-3_7'
apa: 'Bogomolov, S., Giacobbe, M., Henzinger, T. A., & Kong, H. (2017). Conic
abstractions for hybrid systems (Vol. 10419, pp. 116–132). Presented at the FORMATS:
Formal Modelling and Analysis of Timed Systems, Berlin, Germany: Springer. https://doi.org/10.1007/978-3-319-65765-3_7'
chicago: Bogomolov, Sergiy, Mirco Giacobbe, Thomas A Henzinger, and Hui Kong. “Conic
Abstractions for Hybrid Systems,” 10419:116–32. Springer, 2017. https://doi.org/10.1007/978-3-319-65765-3_7.
ieee: 'S. Bogomolov, M. Giacobbe, T. A. Henzinger, and H. Kong, “Conic abstractions
for hybrid systems,” presented at the FORMATS: Formal Modelling and Analysis of
Timed Systems, Berlin, Germany, 2017, vol. 10419, pp. 116–132.'
ista: 'Bogomolov S, Giacobbe M, Henzinger TA, Kong H. 2017. Conic abstractions for
hybrid systems. FORMATS: Formal Modelling and Analysis of Timed Systems, LNCS,
vol. 10419, 116–132.'
mla: Bogomolov, Sergiy, et al. Conic Abstractions for Hybrid Systems. Vol.
10419, Springer, 2017, pp. 116–32, doi:10.1007/978-3-319-65765-3_7.
short: S. Bogomolov, M. Giacobbe, T.A. Henzinger, H. Kong, in:, Springer, 2017,
pp. 116–132.
conference:
end_date: 2017-09-07
location: Berlin, Germany
name: 'FORMATS: Formal Modelling and Analysis of Timed Systems'
start_date: 2017-09-05
date_created: 2018-12-11T11:47:41Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-09-07T12:53:00Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-319-65765-3_7
file:
- access_level: open_access
checksum: faf546914ba29bcf9974ee36b6b16750
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:38Z
date_updated: 2020-07-14T12:47:31Z
file_id: '4956'
file_name: IST-2017-831-v1+1_main.pdf
file_size: 3806864
relation: main_file
file_date_updated: 2020-07-14T12:47:31Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 116 - 132
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
isbn:
- 978-331965764-6
publication_status: published
publisher: Springer
publist_id: '7129'
pubrep_id: '831'
quality_controlled: '1'
related_material:
record:
- id: '6894'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Conic abstractions for hybrid systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: '10419 '
year: '2017'
...
---
_id: '631'
abstract:
- lang: eng
text: Template polyhedra generalize intervals and octagons to polyhedra whose facets
are orthogonal to a given set of arbitrary directions. They have been employed
in the abstract interpretation of programs and, with particular success, in the
reachability analysis of hybrid automata. While previously, the choice of directions
has been left to the user or a heuristic, we present a method for the automatic
discovery of directions that generalize and eliminate spurious counterexamples.
We show that for the class of convex hybrid automata, i.e., hybrid automata with
(possibly nonlinear) convex constraints on derivatives, such directions always
exist and can be found using convex optimization. We embed our method inside a
CEGAR loop, thus enabling the time-unbounded reachability analysis of an important
and richer class of hybrid automata than was previously possible. We evaluate
our method on several benchmarks, demonstrating also its superior efficiency for
the special case of linear hybrid automata.
acknowledgement: This research was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), by
the European Commission under grant 643921 (UnCoVerCPS), and by the ARC project
DP140104219 (Robust AI Planning for Hybrid Systems).
alternative_title:
- LNCS
author:
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Bogomolov S, Frehse G, Giacobbe M, Henzinger TA. Counterexample guided refinement
of template polyhedra. In: Vol 10205. Springer; 2017:589-606. doi:10.1007/978-3-662-54577-5_34'
apa: 'Bogomolov, S., Frehse, G., Giacobbe, M., & Henzinger, T. A. (2017). Counterexample
guided refinement of template polyhedra (Vol. 10205, pp. 589–606). Presented at
the TACAS: Tools and Algorithms for the Construction and Analysis of Systems,
Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54577-5_34'
chicago: Bogomolov, Sergiy, Goran Frehse, Mirco Giacobbe, and Thomas A Henzinger.
“Counterexample Guided Refinement of Template Polyhedra,” 10205:589–606. Springer,
2017. https://doi.org/10.1007/978-3-662-54577-5_34.
ieee: 'S. Bogomolov, G. Frehse, M. Giacobbe, and T. A. Henzinger, “Counterexample
guided refinement of template polyhedra,” presented at the TACAS: Tools and Algorithms
for the Construction and Analysis of Systems, Uppsala, Sweden, 2017, vol. 10205,
pp. 589–606.'
ista: 'Bogomolov S, Frehse G, Giacobbe M, Henzinger TA. 2017. Counterexample guided
refinement of template polyhedra. TACAS: Tools and Algorithms for the Construction
and Analysis of Systems, LNCS, vol. 10205, 589–606.'
mla: Bogomolov, Sergiy, et al. Counterexample Guided Refinement of Template Polyhedra.
Vol. 10205, Springer, 2017, pp. 589–606, doi:10.1007/978-3-662-54577-5_34.
short: S. Bogomolov, G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2017,
pp. 589–606.
conference:
end_date: 2017-04-29
location: Uppsala, Sweden
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2017-04-22
date_created: 2018-12-11T11:47:36Z
date_published: 2017-03-31T00:00:00Z
date_updated: 2023-09-07T12:53:00Z
day: '31'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-662-54577-5_34
file:
- access_level: open_access
checksum: f395d0d20102b89aeaad8b4ef4f18f4f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:41Z
date_updated: 2020-07-14T12:47:27Z
file_id: '4897'
file_name: IST-2017-741-v1+1_main.pdf
file_size: 569863
relation: main_file
- access_level: open_access
checksum: f416ee1ae4497b23ecdf28b1f18bb8df
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:42Z
date_updated: 2020-07-14T12:47:27Z
file_id: '4898'
file_name: IST-2018-741-v2+2_main.pdf
file_size: 563276
relation: main_file
file_date_updated: 2020-07-14T12:47:27Z
has_accepted_license: '1'
intvolume: ' 10205'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 589 - 606
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
isbn:
- 978-366254576-8
publication_status: published
publisher: Springer
publist_id: '7162'
pubrep_id: '966'
quality_controlled: '1'
related_material:
record:
- id: '6894'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Counterexample guided refinement of template polyhedra
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10205
year: '2017'
...
---
_id: '1144'
abstract:
- lang: eng
text: We show that matrix elements of functions of N × N Wigner matrices fluctuate
on a scale of order N−1/2 and we identify the limiting fluctuation. Our result
holds for any function f of the matrix that has bounded variation thus considerably
relaxing the regularity requirement imposed in [7, 11].
acknowledgement: Partially supported by the IST Austria Excellence Scholarship.
article_number: '86'
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Erdös L, Schröder DJ. Fluctuations of functions of Wigner matrices. Electronic
Communications in Probability. 2017;21. doi:10.1214/16-ECP38
apa: Erdös, L., & Schröder, D. J. (2017). Fluctuations of functions of Wigner
matrices. Electronic Communications in Probability. Institute of Mathematical
Statistics. https://doi.org/10.1214/16-ECP38
chicago: Erdös, László, and Dominik J Schröder. “Fluctuations of Functions of Wigner
Matrices.” Electronic Communications in Probability. Institute of Mathematical
Statistics, 2017. https://doi.org/10.1214/16-ECP38.
ieee: L. Erdös and D. J. Schröder, “Fluctuations of functions of Wigner matrices,”
Electronic Communications in Probability, vol. 21. Institute of Mathematical
Statistics, 2017.
ista: Erdös L, Schröder DJ. 2017. Fluctuations of functions of Wigner matrices.
Electronic Communications in Probability. 21, 86.
mla: Erdös, László, and Dominik J. Schröder. “Fluctuations of Functions of Wigner
Matrices.” Electronic Communications in Probability, vol. 21, 86, Institute
of Mathematical Statistics, 2017, doi:10.1214/16-ECP38.
short: L. Erdös, D.J. Schröder, Electronic Communications in Probability 21 (2017).
date_created: 2018-12-11T11:50:23Z
date_published: 2017-01-02T00:00:00Z
date_updated: 2023-09-07T12:54:12Z
day: '02'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1214/16-ECP38
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:10Z
date_updated: 2018-12-12T10:18:10Z
file_id: '5329'
file_name: IST-2017-747-v1+1_euclid.ecp.1483347665.pdf
file_size: 440770
relation: main_file
file_date_updated: 2018-12-12T10:18:10Z
has_accepted_license: '1'
intvolume: ' 21'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Electronic Communications in Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '6214'
pubrep_id: '747'
quality_controlled: '1'
related_material:
record:
- id: '6179'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Fluctuations of functions of Wigner matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2017'
...
---
_id: '486'
abstract:
- lang: eng
text: Color texture reproduction in 3D printing commonly ignores volumetric light
transport (cross-talk) between surface points on a 3D print. Such light diffusion
leads to significant blur of details and color bleeding, and is particularly severe
for highly translucent resin-based print materials. Given their widely varying
scattering properties, this cross-talk between surface points strongly depends
on the internal structure of the volume surrounding each surface point. Existing
scattering-aware methods use simplified models for light diffusion, and often
accept the visual blur as an immutable property of the print medium. In contrast,
our work counteracts heterogeneous scattering to obtain the impression of a crisp
albedo texture on top of the 3D print, by optimizing for a fully volumetric material
distribution that preserves the target appearance. Our method employs an efficient
numerical optimizer on top of a general Monte-Carlo simulation of heterogeneous
scattering, supported by a practical calibration procedure to obtain scattering
parameters from a given set of printer materials. Despite the inherent translucency
of the medium, we reproduce detailed surface textures on 3D prints. We evaluate
our system using a commercial, five-tone 3D print process and compare against
the printer’s native color texturing mode, demonstrating that our method preserves
high-frequency features well without having to compromise on color gamut.
article_number: '241'
article_processing_charge: No
article_type: original
author:
- first_name: Oskar
full_name: Elek, Oskar
last_name: Elek
- first_name: Denis
full_name: Sumin, Denis
last_name: Sumin
- first_name: Ran
full_name: Zhang, Ran
id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0002-3808-281X
- first_name: Tim
full_name: Weyrich, Tim
last_name: Weyrich
- first_name: Karol
full_name: Myszkowski, Karol
last_name: Myszkowski
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Alexander
full_name: Wilkie, Alexander
last_name: Wilkie
- first_name: Jaroslav
full_name: Krivanek, Jaroslav
last_name: Krivanek
citation:
ama: Elek O, Sumin D, Zhang R, et al. Scattering-aware texture reproduction for
3D printing. ACM Transactions on Graphics. 2017;36(6). doi:10.1145/3130800.3130890
apa: Elek, O., Sumin, D., Zhang, R., Weyrich, T., Myszkowski, K., Bickel, B., …
Krivanek, J. (2017). Scattering-aware texture reproduction for 3D printing. ACM
Transactions on Graphics. ACM. https://doi.org/10.1145/3130800.3130890
chicago: Elek, Oskar, Denis Sumin, Ran Zhang, Tim Weyrich, Karol Myszkowski, Bernd
Bickel, Alexander Wilkie, and Jaroslav Krivanek. “Scattering-Aware Texture Reproduction
for 3D Printing.” ACM Transactions on Graphics. ACM, 2017. https://doi.org/10.1145/3130800.3130890.
ieee: O. Elek et al., “Scattering-aware texture reproduction for 3D printing,”
ACM Transactions on Graphics, vol. 36, no. 6. ACM, 2017.
ista: Elek O, Sumin D, Zhang R, Weyrich T, Myszkowski K, Bickel B, Wilkie A, Krivanek
J. 2017. Scattering-aware texture reproduction for 3D printing. ACM Transactions
on Graphics. 36(6), 241.
mla: Elek, Oskar, et al. “Scattering-Aware Texture Reproduction for 3D Printing.”
ACM Transactions on Graphics, vol. 36, no. 6, 241, ACM, 2017, doi:10.1145/3130800.3130890.
short: O. Elek, D. Sumin, R. Zhang, T. Weyrich, K. Myszkowski, B. Bickel, A. Wilkie,
J. Krivanek, ACM Transactions on Graphics 36 (2017).
date_created: 2018-12-11T11:46:44Z
date_published: 2017-11-20T00:00:00Z
date_updated: 2023-09-07T13:11:15Z
day: '20'
ddc:
- '003'
- '000'
- '005'
department:
- _id: BeBi
doi: 10.1145/3130800.3130890
ec_funded: 1
file:
- access_level: open_access
checksum: 48386fa6956c3645fc89594dc898b147
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:46Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4836'
file_name: IST-2018-1052-v1+1_ElekSumin2017SGA.pdf
file_size: 107349827
relation: main_file
- access_level: open_access
checksum: 21c89c28fb8d70f6602f752bf997aa0f
content_type: application/pdf
creator: bbickel
date_created: 2019-12-16T14:48:57Z
date_updated: 2020-07-14T12:46:35Z
file_id: '7189'
file_name: ElekSumin2017SGA_reduced_file_size.pdf
file_size: 4683145
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 36'
issue: '6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ACM Transactions on Graphics
publication_identifier:
issn:
- '07300301'
publication_status: published
publisher: ACM
publist_id: '7334'
pubrep_id: '1052'
quality_controlled: '1'
related_material:
record:
- id: '8386'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Scattering-aware texture reproduction for 3D printing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2017'
...
---
_id: '637'
abstract:
- lang: eng
text: For many cryptographic primitives, it is relatively easy to achieve selective
security (where the adversary commits a-priori to some of the choices to be made
later in the attack) but appears difficult to achieve the more natural notion
of adaptive security (where the adversary can make all choices on the go as the
attack progresses). A series of several recent works shows how to cleverly achieve
adaptive security in several such scenarios including generalized selective decryption
(Panjwani, TCC ’07 and Fuchsbauer et al., CRYPTO ’15), constrained PRFs (Fuchsbauer
et al., ASIACRYPT ’14), and Yao garbled circuits (Jafargholi and Wichs, TCC ’16b).
Although the above works expressed vague intuition that they share a common technique,
the connection was never made precise. In this work we present a new framework
that connects all of these works and allows us to present them in a unified and
simplified fashion. Moreover, we use the framework to derive a new result for
adaptively secure secret sharing over access structures defined via monotone circuits.
We envision that further applications will follow in the future. Underlying our
framework is the following simple idea. It is well known that selective security,
where the adversary commits to n-bits of information about his future choices,
automatically implies adaptive security at the cost of amplifying the adversary’s
advantage by a factor of up to 2n. However, in some cases the proof of selective
security proceeds via a sequence of hybrids, where each pair of adjacent hybrids
locally only requires some smaller partial information consisting of m ≪ n bits.
The partial information needed might be completely different between different
pairs of hybrids, and if we look across all the hybrids we might rely on the entire
n-bit commitment. Nevertheless, the above is sufficient to prove adaptive security,
at the cost of amplifying the adversary’s advantage by a factor of only 2m ≪ 2n.
In all of our examples using the above framework, the different hybrids are captured
by some sort of a graph pebbling game and the amount of information that the adversary
needs to commit to in each pair of hybrids is bounded by the maximum number of
pebbles in play at any point in time. Therefore, coming up with better strategies
for proving adaptive security translates to various pebbling strategies for different
types of graphs.
alternative_title:
- LNCS
author:
- first_name: Zahra
full_name: Jafargholi, Zahra
last_name: Jafargholi
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Karen
full_name: Klein, Karen
id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87
last_name: Klein
- first_name: Ilan
full_name: Komargodski, Ilan
last_name: Komargodski
- 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: Daniel
full_name: Wichs, Daniel
last_name: Wichs
citation:
ama: 'Jafargholi Z, Kamath Hosdurg C, Klein K, Komargodski I, Pietrzak KZ, Wichs
D. Be adaptive avoid overcommitting. In: Katz J, Shacham H, eds. Vol 10401. Springer;
2017:133-163. doi:10.1007/978-3-319-63688-7_5'
apa: 'Jafargholi, Z., Kamath Hosdurg, C., Klein, K., Komargodski, I., Pietrzak,
K. Z., & Wichs, D. (2017). Be adaptive avoid overcommitting. In J. Katz &
H. Shacham (Eds.) (Vol. 10401, pp. 133–163). Presented at the CRYPTO: Cryptology,
Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-319-63688-7_5'
chicago: Jafargholi, Zahra, Chethan Kamath Hosdurg, Karen Klein, Ilan Komargodski,
Krzysztof Z Pietrzak, and Daniel Wichs. “Be Adaptive Avoid Overcommitting.” edited
by Jonathan Katz and Hovav Shacham, 10401:133–63. Springer, 2017. https://doi.org/10.1007/978-3-319-63688-7_5.
ieee: 'Z. Jafargholi, C. Kamath Hosdurg, K. Klein, I. Komargodski, K. Z. Pietrzak,
and D. Wichs, “Be adaptive avoid overcommitting,” presented at the CRYPTO: Cryptology,
Santa Barbara, CA, United States, 2017, vol. 10401, pp. 133–163.'
ista: 'Jafargholi Z, Kamath Hosdurg C, Klein K, Komargodski I, Pietrzak KZ, Wichs
D. 2017. Be adaptive avoid overcommitting. CRYPTO: Cryptology, LNCS, vol. 10401,
133–163.'
mla: Jafargholi, Zahra, et al. Be Adaptive Avoid Overcommitting. Edited by
Jonathan Katz and Hovav Shacham, vol. 10401, Springer, 2017, pp. 133–63, doi:10.1007/978-3-319-63688-7_5.
short: Z. Jafargholi, C. Kamath Hosdurg, K. Klein, I. Komargodski, K.Z. Pietrzak,
D. Wichs, in:, J. Katz, H. Shacham (Eds.), Springer, 2017, pp. 133–163.
conference:
end_date: 2017-07-24
location: Santa Barbara, CA, United States
name: 'CRYPTO: Cryptology'
start_date: 2017-07-20
date_created: 2018-12-11T11:47:38Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-07T13:32:11Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-319-63688-7_5
ec_funded: 1
editor:
- first_name: Jonathan
full_name: Katz, Jonathan
last_name: Katz
- first_name: Hovav
full_name: Shacham, Hovav
last_name: Shacham
intvolume: ' 10401'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/515
month: '01'
oa: 1
oa_version: Submitted Version
page: 133 - 163
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
isbn:
- 978-331963687-0
publication_status: published
publisher: Springer
publist_id: '7151'
quality_controlled: '1'
related_material:
record:
- id: '10035'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Be adaptive avoid overcommitting
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10401
year: '2017'
...
---
_id: '9842'
abstract:
- lang: eng
text: Mathematica notebooks used to generate figures.
article_processing_charge: No
author:
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic
adaptation. 2017. doi:10.17632/nw68fxzjpm.1'
apa: 'Etheridge, A., & Barton, N. H. (2017). Data for: Establishment in a new
habitat by polygenic adaptation. Mendeley Data. https://doi.org/10.17632/nw68fxzjpm.1'
chicago: 'Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in
a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. https://doi.org/10.17632/nw68fxzjpm.1.'
ieee: 'A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat
by polygenic adaptation.” Mendeley Data, 2017.'
ista: 'Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by
polygenic adaptation, Mendeley Data, 10.17632/nw68fxzjpm.1.'
mla: 'Etheridge, Alison, and Nicholas H. Barton. Data for: Establishment in a
New Habitat by Polygenic Adaptation. Mendeley Data, 2017, doi:10.17632/nw68fxzjpm.1.'
short: A. Etheridge, N.H. Barton, (2017).
date_created: 2021-08-09T13:18:55Z
date_published: 2017-12-29T00:00:00Z
date_updated: 2023-09-11T13:41:21Z
day: '29'
department:
- _id: NiBa
doi: 10.17632/nw68fxzjpm.1
main_file_link:
- open_access: '1'
url: https://doi.org/10.17632/nw68fxzjpm.1
month: '12'
oa: 1
oa_version: Published Version
publisher: Mendeley Data
related_material:
record:
- id: '564'
relation: used_in_publication
status: public
status: public
title: 'Data for: Establishment in a new habitat by polygenic adaptation'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '14206'
abstract:
- lang: eng
text: Greedy optimization methods such as Matching Pursuit (MP) and Frank-Wolfe
(FW) algorithms regained popularity in recent years due to their simplicity, effectiveness
and theoretical guarantees. MP and FW address optimization over the linear span
and the convex hull of a set of atoms, respectively. In this paper, we consider
the intermediate case of optimization over the convex cone, parametrized as the
conic hull of a generic atom set, leading to the first principled definitions
of non-negative MP algorithms for which we give explicit convergence rates and
demonstrate excellent empirical performance. In particular, we derive sublinear
(O(1/t)) convergence on general smooth and convex objectives, and linear convergence
(O(e−t)) on strongly convex objectives, in both cases for general sets of atoms.
Furthermore, we establish a clear correspondence of our algorithms to known algorithms
from the MP and FW literature. Our novel algorithms and analyses target general
atom sets and general objective functions, and hence are directly applicable to
a large variety of learning settings.
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Michael
full_name: Tschannen, Michael
last_name: Tschannen
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
- first_name: Martin
full_name: Jaggi, Martin
last_name: Jaggi
citation:
ama: 'Locatello F, Tschannen M, Rätsch G, Jaggi M. Greedy algorithms for cone constrained
optimization with convergence guarantees. In: Advances in Neural Information
Processing Systems. ; 2017.'
apa: Locatello, F., Tschannen, M., Rätsch, G., & Jaggi, M. (2017). Greedy algorithms
for cone constrained optimization with convergence guarantees. In Advances
in Neural Information Processing Systems. Long Beach, CA, United States.
chicago: Locatello, Francesco, Michael Tschannen, Gunnar Rätsch, and Martin Jaggi.
“Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.”
In Advances in Neural Information Processing Systems, 2017.
ieee: F. Locatello, M. Tschannen, G. Rätsch, and M. Jaggi, “Greedy algorithms for
cone constrained optimization with convergence guarantees,” in Advances in
Neural Information Processing Systems, Long Beach, CA, United States, 2017.
ista: 'Locatello F, Tschannen M, Rätsch G, Jaggi M. 2017. Greedy algorithms for
cone constrained optimization with convergence guarantees. Advances in Neural
Information Processing Systems. NeurIPS: Neural Information Processing Systems.'
mla: Locatello, Francesco, et al. “Greedy Algorithms for Cone Constrained Optimization
with Convergence Guarantees.” Advances in Neural Information Processing Systems,
2017.
short: F. Locatello, M. Tschannen, G. Rätsch, M. Jaggi, in:, Advances in Neural
Information Processing Systems, 2017.
conference:
end_date: 2017-12-09
location: Long Beach, CA, United States
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2017-12-04
date_created: 2023-08-22T14:17:38Z
date_published: 2017-05-31T00:00:00Z
date_updated: 2023-09-13T08:32:23Z
day: '31'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1705.11041'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.11041
month: '05'
oa: 1
oa_version: Preprint
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781510860964'
publication_status: published
quality_controlled: '1'
status: public
title: Greedy algorithms for cone constrained optimization with convergence guarantees
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '14205'
abstract:
- lang: eng
text: Two of the most fundamental prototypes of greedy optimization are the matching
pursuit and Frank-Wolfe algorithms. In this paper, we take a unified view on both
classes of methods, leading to the first explicit convergence rates of matching
pursuit methods in an optimization sense, for general sets of atoms. We derive
sublinear (1/t) convergence for both classes on general smooth objectives, and
linear convergence on strongly convex objectives, as well as a clear correspondence
of algorithm variants. Our presented algorithms and rates are affine invariant,
and do not need any incoherence or sparsity assumptions.
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Rajiv
full_name: Khanna, Rajiv
last_name: Khanna
- first_name: Michael
full_name: Tschannen, Michael
last_name: Tschannen
- first_name: Martin
full_name: Jaggi, Martin
last_name: Jaggi
citation:
ama: 'Locatello F, Khanna R, Tschannen M, Jaggi M. A unified optimization view on
generalized matching pursuit and Frank-Wolfe. In: Proceedings of the 20th International
Conference on Artificial Intelligence and Statistics. Vol 54. ML Research
Press; 2017:860-868.'
apa: 'Locatello, F., Khanna, R., Tschannen, M., & Jaggi, M. (2017). A unified
optimization view on generalized matching pursuit and Frank-Wolfe. In Proceedings
of the 20th International Conference on Artificial Intelligence and Statistics
(Vol. 54, pp. 860–868). Fort Lauderdale, FL, United States: ML Research Press.'
chicago: Locatello, Francesco, Rajiv Khanna, Michael Tschannen, and Martin Jaggi.
“A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.”
In Proceedings of the 20th International Conference on Artificial Intelligence
and Statistics, 54:860–68. ML Research Press, 2017.
ieee: F. Locatello, R. Khanna, M. Tschannen, and M. Jaggi, “A unified optimization
view on generalized matching pursuit and Frank-Wolfe,” in Proceedings of the
20th International Conference on Artificial Intelligence and Statistics, Fort
Lauderdale, FL, United States, 2017, vol. 54, pp. 860–868.
ista: 'Locatello F, Khanna R, Tschannen M, Jaggi M. 2017. A unified optimization
view on generalized matching pursuit and Frank-Wolfe. Proceedings of the 20th
International Conference on Artificial Intelligence and Statistics. AISTATS: Conference
on Artificial Intelligence and Statistics vol. 54, 860–868.'
mla: Locatello, Francesco, et al. “A Unified Optimization View on Generalized Matching
Pursuit and Frank-Wolfe.” Proceedings of the 20th International Conference
on Artificial Intelligence and Statistics, vol. 54, ML Research Press, 2017,
pp. 860–68.
short: F. Locatello, R. Khanna, M. Tschannen, M. Jaggi, in:, Proceedings of the
20th International Conference on Artificial Intelligence and Statistics, ML Research
Press, 2017, pp. 860–868.
conference:
end_date: 2017-04-22
location: Fort Lauderdale, FL, United States
name: 'AISTATS: Conference on Artificial Intelligence and Statistics'
start_date: 2017-04-20
date_created: 2023-08-22T14:17:19Z
date_published: 2017-02-21T00:00:00Z
date_updated: 2023-09-13T09:49:10Z
day: '21'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1702.06457'
intvolume: ' 54'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1702.06457
month: '02'
oa: 1
oa_version: Preprint
page: 860-868
publication: Proceedings of the 20th International Conference on Artificial Intelligence
and Statistics
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
status: public
title: A unified optimization view on generalized matching pursuit and Frank-Wolfe
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 54
year: '2017'
...
---
_id: '202'
abstract:
- lang: eng
text: 'Restriction-modification (RM) represents the simplest and possibly the most
widespread mechanism of self/non-self discrimination in nature. In order to provide
bacteria with immunity against bacteriophages and other parasitic genetic elements,
RM systems rely on a balance between two enzymes: the restriction enzyme, which
cleaves non-self DNA at specific restriction sites, and the modification enzyme,
which tags the host’s DNA as self and thus protects it from cleavage. In this
thesis, I use population and single-cell level experiments in combination with
mathematical modeling to study different aspects of the interplay between RM systems,
bacteria and bacteriophages. First, I analyze how mutations in phage restriction
sites affect the probability of phage escape – an inherently stochastic process,
during which phages accidently get modified instead of restricted. Next, I use
single-cell experiments to show that RM systems can, with a low probability, attack
the genome of their bacterial host and that this primitive form of autoimmunity
leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally,
I investigate the nature of interactions between bacteria, RM systems and temperate
bacteriophages to find that, as a consequence of phage escape and its impact on
population dynamics, RM systems can promote acquisition of symbiotic bacteriophages,
rather than limit it. The results presented here uncover new fundamental biological
properties of RM systems and highlight their importance in the ecology and evolution
of bacteria, bacteriophages and their interactions.'
acknowledgement: "During my PhD studies, I received help from many people, all of
which unfortunately cannot be listed here. I thank them deeply and hope that I never
made them regret their kindness.\r\nI would like to express my deepest gratitude
to Călin Guet, who went far beyond his responsibilities as an advisor and was to
me also a great mentor and a friend. Călin never questioned my potential or lacked
compassion and I cannot thank him enough for cultivating in me an independent scientist.
I was amazed by his ability to recognize the most fascinating scientific problems
in objects of study that others would find mundane. I hope I adopted at least a
fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his
support and especially for giving me the best possible example of how one can practice
excellent science with humor and style. Working with Bruce was a true privilege.\r\nI
thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the
Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI
thank all our lab members: Tobias Bergmiller for his guidance, especially in the
first years of my research, and for being a good friend throughout; Remy Chait for
staying in the lab at unreasonable hours and for the good laughs at bad jokes we
shared; Anna Staron for supportively listening to my whines whenever I had to run
a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for
keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek
for always being nice to me, no matter how much bench space I took from her.\r\nI
thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing
the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics
analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical
modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally,
I would like to thank my family and especially my wife Edita, who sacrificed a lot
so that I can pursue my goals and dreams.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
citation:
ama: Pleska M. Biology of restriction-modification systems at the single-cell and
population level. 2017. doi:10.15479/AT:ISTA:th_916
apa: Pleska, M. (2017). Biology of restriction-modification systems at the single-cell
and population level. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_916
chicago: Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell
and Population Level.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_916.
ieee: M. Pleska, “Biology of restriction-modification systems at the single-cell
and population level,” Institute of Science and Technology Austria, 2017.
ista: Pleska M. 2017. Biology of restriction-modification systems at the single-cell
and population level. Institute of Science and Technology Austria.
mla: Pleska, Maros. Biology of Restriction-Modification Systems at the Single-Cell
and Population Level. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_916.
short: M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell
and Population Level, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:45:10Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2023-09-15T12:04:56Z
day: '01'
ddc:
- '576'
- '579'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:th_916
file:
- access_level: open_access
checksum: 33cfb59674e91f82e3738396d3fb3776
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:48Z
date_updated: 2020-07-14T12:45:24Z
file_id: '4710'
file_name: IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf
file_size: 18569590
relation: main_file
- access_level: closed
checksum: dcc239968decb233e7f98cf1083d8c26
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T08:33:14Z
date_updated: 2020-07-14T12:45:24Z
file_id: '6204'
file_name: 2017_Pleska_Maros_Thesis.docx
file_size: 2801649
relation: source_file
file_date_updated: 2020-07-14T12:45:24Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '126'
project:
- _id: 251D65D8-B435-11E9-9278-68D0E5697425
grant_number: '24210'
name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems
at the Single-Cell Level (DOC Fellowship)
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7711'
pubrep_id: '916'
related_material:
record:
- id: '1243'
relation: part_of_dissertation
status: public
- id: '561'
relation: part_of_dissertation
status: public
- id: '457'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: Biology of restriction-modification systems at the single-cell and population
level
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '6287'
abstract:
- lang: eng
text: The main objects considered in the present work are simplicial and CW-complexes
with vertices forming a random point cloud. In particular, we consider a Poisson
point process in R^n and study Delaunay and Voronoi complexes of the first and
higher orders and weighted Delaunay complexes obtained as sections of Delaunay
complexes, as well as the Čech complex. Further, we examine theDelaunay complex
of a Poisson point process on the sphere S^n, as well as of a uniform point cloud,
which is equivalent to the convex hull, providing a connection to the theory of
random polytopes. Each of the complexes in question can be endowed with a radius
function, which maps its cells to the radii of appropriately chosen circumspheres,
called the radius of the cell. Applying and developing discrete Morse theory for
these functions, joining it together with probabilistic and sometimes analytic
machinery, and developing several integral geometric tools, we aim at getting
the distributions of circumradii of typical cells. For all considered complexes,
we are able to generalize and obtain up to constants the distribution of radii
of typical intervals of all types. In low dimensions the constants can be computed
explicitly, thus providing the explicit expressions for the expected numbers of
cells. In particular, it allows to find the expected density of simplices of every
dimension for a Poisson point process in R^4, whereas the result for R^3 was known
already in 1970's.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Anton
full_name: Nikitenko, Anton
id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87
last_name: Nikitenko
orcid: 0000-0002-0659-3201
citation:
ama: Nikitenko A. Discrete Morse theory for random complexes . 2017. doi:10.15479/AT:ISTA:th_873
apa: Nikitenko, A. (2017). Discrete Morse theory for random complexes . Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_873
chicago: Nikitenko, Anton. “Discrete Morse Theory for Random Complexes .” Institute
of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_873.
ieee: A. Nikitenko, “Discrete Morse theory for random complexes ,” Institute of
Science and Technology Austria, 2017.
ista: Nikitenko A. 2017. Discrete Morse theory for random complexes . Institute
of Science and Technology Austria.
mla: Nikitenko, Anton. Discrete Morse Theory for Random Complexes . Institute
of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_873.
short: A. Nikitenko, Discrete Morse Theory for Random Complexes , Institute of Science
and Technology Austria, 2017.
date_created: 2019-04-09T15:04:32Z
date_published: 2017-10-27T00:00:00Z
date_updated: 2023-09-15T12:10:34Z
day: '27'
ddc:
- '514'
- '516'
- '519'
degree_awarded: PhD
department:
- _id: HeEd
doi: 10.15479/AT:ISTA:th_873
file:
- access_level: open_access
checksum: ece7e598a2f060b263c2febf7f3fe7f9
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T14:54:51Z
date_updated: 2020-07-14T12:47:26Z
file_id: '6289'
file_name: 2017_Thesis_Nikitenko.pdf
file_size: 2324870
relation: main_file
- access_level: closed
checksum: 99b7ad76e317efd447af60f91e29b49b
content_type: application/zip
creator: dernst
date_created: 2019-04-09T14:54:51Z
date_updated: 2020-07-14T12:47:26Z
file_id: '6290'
file_name: 2017_Thesis_Nikitenko_source.zip
file_size: 2863219
relation: source_file
file_date_updated: 2020-07-14T12:47:26Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '86'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
pubrep_id: '873'
related_material:
record:
- id: '718'
relation: part_of_dissertation
status: public
- id: '5678'
relation: part_of_dissertation
status: public
- id: '87'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: 'Discrete Morse theory for random complexes '
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '1127'
abstract:
- lang: eng
text: "Plant hormone auxin and its transport between cells belong to the most important\r\nmechanisms
controlling plant development. Auxin itself could change localization of PINs
and\r\nthereby control direction of its own flow. We performed an expression profiling
experiment\r\nin Arabidopsis roots to identify potential regulators of PIN polarity
which are transcriptionally\r\nregulated by auxin signalling. We identified several
novel regulators and performed a detailed\r\ncharacterization of the transcription
factor WRKY23 (At2g47260) and its role in auxin\r\nfeedback on PIN polarity. Gain-of-function
and dominant-negative mutants revealed that\r\nWRKY23 plays a crucial role in
mediating the auxin effect on PIN polarity. In concordance,\r\ntypical polar auxin
transport processes such as gravitropism and leaf vascular pattern\r\nformation
were disturbed by interfering with WRKY23 function.\r\nIn order to identify direct
targets of WRKY23, we performed consequential expression\r\nprofiling experiments
using a WRKY23 inducible gain-of-function line and dominant-negative\r\nWRKY23
line that is defunct in PIN re-arrangement. Among several genes mostly related
to\r\nthe groups of cell wall and defense process regulators, we identified LYSINE-HISTIDINE\r\nTRANSPORTER
1 (LHT1; At5g40780), a small amino acid permease gene from the amino\r\nacid/auxin
permease family (AAAP), we present its detailed characterisation in auxin feedback\r\non
PIN repolarization, identified its transcriptional regulation, we propose a potential\r\nmechanism
of its action. Moreover, we identified also a member of receptor-like protein\r\nkinase
LRR-RLK (LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN KINASE PROTEIN 1;\r\nLRRK1;
At1g05700), which also affects auxin-dependent PIN re-arrangement. We described\r\nits
transcriptional behaviour, subcellular localization. Based on global expression
data, we\r\ntried to identify ligand responsible for mechanism of signalling and
suggest signalling partner\r\nand interactors. Additionally, we described role
of novel phytohormone group, strigolactone,\r\nin auxin-dependent PIN re-arrangement,
that could be a fundament for future studies in this\r\nfield.\r\nOur results
provide first insights into an auxin transcriptional network targeting PIN\r\nlocalization
and thus regulating plant development. We highlighted WRKY23 transcriptional\r\nnetwork
and characterised its mediatory role in plant development. We identified direct\r\neffectors
of this network, LHT1 and LRRK1, and describe their roles in PIN re-arrangement
and\r\nPIN-dependent auxin transport processes."
acknowledgement: I would like to first acknowledge my supervisor Jiří Friml for support,
kind advice and patience. It was a pleasure to be a part of your lab, Jiří. I will
remember the atmosphere present in auxin lab at VIB in Ghent and at IST in Klosterneuburg
forever. I would like to thank all past and present lab members for the friendship
and friendly and scientific environment in the groups. It was so nice to cooperate
with you, guys. There was always someone who helped me with experiments, troubleshoot
issues coming from our work etc. At this place, I would like to thank especially
to Gergo Molnár. I’m happy (and lucky) that I have met him; he naturally became
my tutor and guide through my PhD. From no one else during my entire professional
career, I’ve learned that much.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Tomas
full_name: Prat, Tomas
id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87
last_name: Prat
citation:
ama: Prat T. Identification of novel regulators of PIN polarity and development
of novel auxin sensor. 2017.
apa: Prat, T. (2017). Identification of novel regulators of PIN polarity and
development of novel auxin sensor. Institute of Science and Technology Austria.
chicago: Prat, Tomas. “Identification of Novel Regulators of PIN Polarity and Development
of Novel Auxin Sensor.” Institute of Science and Technology Austria, 2017.
ieee: T. Prat, “Identification of novel regulators of PIN polarity and development
of novel auxin sensor,” Institute of Science and Technology Austria, 2017.
ista: Prat T. 2017. Identification of novel regulators of PIN polarity and development
of novel auxin sensor. Institute of Science and Technology Austria.
mla: Prat, Tomas. Identification of Novel Regulators of PIN Polarity and Development
of Novel Auxin Sensor. Institute of Science and Technology Austria, 2017.
short: T. Prat, Identification of Novel Regulators of PIN Polarity and Development
of Novel Auxin Sensor, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:50:17Z
date_published: 2017-01-12T00:00:00Z
date_updated: 2023-09-19T10:39:33Z
day: '12'
ddc:
- '580'
degree_awarded: PhD
department:
- _id: JiFr
file:
- access_level: closed
checksum: d192c7c6c5ea32c8432437286dc4909e
content_type: application/pdf
creator: dernst
date_created: 2019-04-05T08:45:14Z
date_updated: 2019-04-05T08:45:14Z
file_id: '6209'
file_name: IST_Austria_Thesis_Tomáš_Prát.pdf
file_size: 10285946
relation: main_file
- access_level: open_access
checksum: bab18b52cf98145926042d8ed99fdb3b
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:52:56Z
date_updated: 2021-02-22T11:52:56Z
file_id: '9185'
file_name: 2017_Thesis_Prat.pdf
file_size: 9802991
relation: main_file
success: 1
file_date_updated: 2021-02-22T11:52:56Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '131'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6233'
related_material:
record:
- id: '449'
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
title: Identification of novel regulators of PIN polarity and development of novel
auxin sensor
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...