---
_id: '5558'
abstract:
- lang: eng
text: PhD thesis LaTeX source code
article_processing_charge: No
author:
- first_name: Morten
full_name: Bojsen-Hansen, Morten
id: 439F0C8C-F248-11E8-B48F-1D18A9856A87
last_name: Bojsen-Hansen
orcid: 0000-0002-4417-3224
citation:
ama: Bojsen-Hansen M. Tracking, Correcting and Absorbing Water Surface Waves. 2016.
doi:10.15479/AT:ISTA:48
apa: Bojsen-Hansen, M. (2016). Tracking, Correcting and Absorbing Water Surface
Waves. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:48
chicago: Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface
Waves.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:48.
ieee: M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.”
Institute of Science and Technology Austria, 2016.
ista: Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:48.
mla: Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface
Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:48.
short: M. Bojsen-Hansen, (2016).
datarep_id: '48'
date_created: 2018-12-12T12:31:31Z
date_published: 2016-09-23T00:00:00Z
date_updated: 2026-04-08T14:24:05Z
day: '23'
ddc:
- '004'
department:
- _id: ChWo
doi: 10.15479/AT:ISTA:48
file:
- access_level: open_access
checksum: 5b1b256ad796fbddb4b7729f5e45e444
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month: '09'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
publist_id: '6238'
pubrep_id: '640'
related_material:
record:
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relation: other
status: public
status: public
title: Tracking, Correcting and Absorbing Water Surface Waves
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
OA_place: publisher
_id: '1126'
abstract:
- lang: eng
text: "Traditionally machine learning has been focusing on the problem of solving
a single\r\ntask in isolation. While being quite well understood, this approach
disregards an\r\nimportant aspect of human learning: when facing a new problem,
humans are able to\r\nexploit knowledge acquired from previously learned tasks.
Intuitively, access to several\r\nproblems simultaneously or sequentially could
also be advantageous for a machine\r\nlearning system, especially if these tasks
are closely related. Indeed, results of many\r\nempirical studies have provided
justification for this intuition. However, theoretical\r\njustifications of this
idea are rather limited.\r\nThe focus of this thesis is to expand the understanding
of potential benefits of information\r\ntransfer between several related learning
problems. We provide theoretical\r\nanalysis for three scenarios of multi-task
learning - multiple kernel learning, sequential\r\nlearning and active task selection.
We also provide a PAC-Bayesian perspective on\r\nlifelong learning and investigate
how the task generation process influences the generalization\r\nguarantees in
this scenario. In addition, we show how some of the obtained\r\ntheoretical results
can be used to derive principled multi-task and lifelong learning\r\nalgorithms
and illustrate their performance on various synthetic and real-world datasets."
acknowledgement: "First and foremost I would like to express my gratitude to my supervisor,
Christoph\r\nLampert. Thank you for your patience in teaching me all aspects of
doing research\r\n(including English grammar), for your trust in my capabilities
and endless support. Thank\r\nyou for granting me freedom in my research and, at
the same time, having time and\r\nhelping me cope with the consequences whenever
I needed it. Thank you for creating\r\nan excellent atmosphere in the group, it
was a great pleasure and honor to be a part of\r\nit. There could not have been
a better and more inspiring adviser and mentor.\r\nI thank Shai Ben-David for welcoming
me into his group at the University of Waterloo,\r\nfor inspiring discussions and
support. It was a great pleasure to work together. I am\r\nalso thankful to Ruth
Urner for hosting me at the Max-Planck Institute Tübingen, for the\r\nfruitful
collaboration and for taking care of me during that not-so-sunny month of May.\r\nI
thank Jan Maas for kindly joining my thesis committee despite the short notice and\r\nproviding
me with insightful comments.\r\nI would like to thank my colleagues for their support,
entertaining conversations and\r\nendless table soccer games we shared together:
Georg, Jan, Amelie and Emilie, Michal\r\nand Alex, Alex K. and Alex Z., Thomas,
Sameh, Vlad, Mayu, Nathaniel, Silvester, Neel,\r\nCsaba, Vladimir, Morten. Thank
you, Mabel and Ram, for the wonderful time we spent\r\ntogether. I am thankful to
Shrinu and Samira for taking care of me during my stay at the\r\nUniversity of Waterloo.
Special thanks to Viktoriia for her never-ending optimism and for\r\nbeing so inspiring
and supportive, especially at the beginning of my PhD journey.\r\nThanks to IST
administration, in particular, Vlad and Elisabeth for shielding me from\r\nmost
of the bureaucratic paperwork.\r\n\r\nThis dissertation would not have been possible
without funding from the European\r\nResearch Council under the European Union's
Seventh Framework Programme\r\n(FP7/2007-2013)/ERC grant agreement no 308036."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Anastasia
full_name: Pentina, Anastasia
id: 42E87FC6-F248-11E8-B48F-1D18A9856A87
last_name: Pentina
citation:
ama: Pentina A. Theoretical foundations of multi-task lifelong learning. 2016. doi:10.15479/AT:ISTA:TH_776
apa: Pentina, A. (2016). Theoretical foundations of multi-task lifelong learning.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_776
chicago: Pentina, Anastasia. “Theoretical Foundations of Multi-Task Lifelong Learning.”
Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:TH_776.
ieee: A. Pentina, “Theoretical foundations of multi-task lifelong learning,” Institute
of Science and Technology Austria, 2016.
ista: Pentina A. 2016. Theoretical foundations of multi-task lifelong learning.
Institute of Science and Technology Austria.
mla: Pentina, Anastasia. Theoretical Foundations of Multi-Task Lifelong Learning.
Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:TH_776.
short: A. Pentina, Theoretical Foundations of Multi-Task Lifelong Learning, Institute
of Science and Technology Austria, 2016.
corr_author: '1'
date_created: 2018-12-11T11:50:17Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2026-04-09T10:49:34Z
day: '01'
ddc:
- '006'
degree_awarded: PhD
department:
- _id: ChLa
doi: 10.15479/AT:ISTA:TH_776
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:07Z
date_updated: 2018-12-12T10:14:07Z
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file_date_updated: 2018-12-12T10:14:07Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '127'
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6234'
pubrep_id: '776'
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
title: Theoretical foundations of multi-task lifelong learning
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2016'
...
---
OA_place: publisher
_id: '1121'
abstract:
- lang: eng
text: "Horizontal gene transfer (HGT), the lateral acquisition of genes across existing
species\r\nboundaries, is a major evolutionary force shaping microbial genomes
that facilitates\r\nadaptation to new environments as well as resistance to antimicrobial
drugs. As such,\r\nunderstanding the mechanisms and constraints that determine
the outcomes of HGT\r\nevents is crucial to understand the dynamics of HGT and
to design better strategies to\r\novercome the challenges that originate from
it.\r\nFollowing the insertion and expression of a newly transferred gene, the
success of an\r\nHGT event will depend on the fitness effect it has on the recipient
(host) cell. Therefore,\r\npredicting the impact of HGT on the genetic composition
of a population critically\r\ndepends on the distribution of fitness effects (DFE)
of horizontally transferred genes.\r\nHowever, to date, we have little knowledge
of the DFE of newly transferred genes, and\r\nhence little is known about the
shape and scale of this distribution.\r\nIt is particularly important to better
understand the selective barriers that determine\r\nthe fitness effects of newly
transferred genes. In spite of substantial bioinformatics\r\nefforts to identify
horizontally transferred genes and selective barriers, a systematic\r\nexperimental
approach to elucidate the roles of different selective barriers in defining\r\nthe
fate of a transfer event has largely been absent. Similarly, although the fact
that\r\nenvironment might alter the fitness effect of a horizontally transferred
gene may seem\r\nobvious, little attention has been given to it in a systematic
experimental manner.\r\nIn this study, we developed a systematic experimental
approach that consists of\r\ntransferring 44 arbitrarily selected Salmonella typhimurium
orthologous genes into an\r\nEscherichia coli host, and estimating the fitness
effects of these transferred genes at a\r\nconstant expression level by performing
competition assays against the wild type.\r\nIn chapter 2, we performed one-to-one
competition assays between a mutant strain\r\ncarrying a transferred gene and
the wild type strain. By using flow cytometry we\r\nestimated selection coefficients
for the transferred genes with a precision level of 10-3,and obtained the DFE
of horizontally transferred genes. We then investigated if these\r\nfitness effects
could be predicted by any of the intrinsic properties of the genes, namely,\r\nfunctional
category, degree of complexity (protein-protein interactions), GC content,\r\ncodon
usage and length. Our analyses revealed that the functional category and length\r\nof
the genes act as potential selective barriers. Finally, using the same procedure
with\r\nthe endogenous E. coli orthologs of these 44 genes, we demonstrated that
gene dosage is\r\nthe most prominent selective barrier to HGT.\r\nIn chapter 3,
using the same set of genes we investigated the role of environment on the\r\nsuccess
of HGT events. Under six different environments with different levels of stress\r\nwe
performed more complex competition assays, where we mixed all 44 mutant strains\r\ncarrying
transferred genes with the wild type strain. To estimate the fitness effects of\r\ngenes
relative to wild type we used next generation sequencing. We found that the DFEs\r\nof
horizontally transferred genes are highly dependent on the environment, with\r\nabundant
gene–by-environment interactions. Furthermore, we demonstrated a\r\nrelationship
between average fitness effect of a gene across all environments and its\r\nenvironmental
variance, and thus its predictability. Finally, in spite of the fitness effects\r\nof
genes being highly environment-dependent, we still observed a common shape of\r\nDFEs
across all tested environments."
acknowledgement: "This study was supported by European Research Council ERC CoG 2014
– EVOLHGT,\r\nunder the grant number 648440.\r\n\r\nIt is a pleasure to thank the
many people who made this thesis possible.\r\nI would like to first thank my advisor,
Jonathan Paul Bollback for providing guidance in\r\nall aspects of my life, encouragement,
sound advice, and good teaching over the last six\r\nyears.\r\nI would also like
to thank the members of my dissertation committee – Călin C. Guet\r\nand John F.
Baines – not only for their time and guidance, but for their intellectual\r\ncontributions
to my development as a scientist.\r\nI would like to thank Flavia Gama and Rodrigo
Redondo who have taught me all the\r\nskills in the laboratory with their graciousness
and friendship. Also special thanks to\r\nBollback group for their support and for
providing a stimulating and fun environment:\r\nIsabella Tomanek, Fabienne Jesse,
Claudia Igler, and Pavel Payne.\r\nJerneja Beslagic is not only an amazing assistant,
she also has a smile brighter and\r\nwarmer than the sunshine, bringing happiness
to every moment. Always keep your light\r\nNeja, I will miss our invaluable chatters
a lot."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Hande
full_name: Acar, Hande
id: 2DDF136A-F248-11E8-B48F-1D18A9856A87
last_name: Acar
orcid: 0000-0003-1986-9753
citation:
ama: Acar H. Selective barriers to horizontal gene transfer. 2016.
apa: Acar, H. (2016). Selective barriers to horizontal gene transfer. Institute
of Science and Technology Austria.
chicago: Acar, Hande. “Selective Barriers to Horizontal Gene Transfer.” Institute
of Science and Technology Austria, 2016.
ieee: H. Acar, “Selective barriers to horizontal gene transfer,” Institute of Science
and Technology Austria, 2016.
ista: Acar H. 2016. Selective barriers to horizontal gene transfer. Institute of
Science and Technology Austria.
mla: Acar, Hande. Selective Barriers to Horizontal Gene Transfer. Institute
of Science and Technology Austria, 2016.
short: H. Acar, Selective Barriers to Horizontal Gene Transfer, Institute of Science
and Technology Austria, 2016.
corr_author: '1'
date_created: 2018-12-11T11:50:16Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2026-04-09T10:51:38Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: JoBo
ec_funded: 1
file:
- access_level: closed
checksum: 94bbbc754c36115bf37f8fc11fad43c4
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T11:17:50Z
date_updated: 2019-08-13T11:17:50Z
file_id: '6814'
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content_type: application/pdf
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date_created: 2021-02-22T11:51:13Z
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file_date_updated: 2021-02-22T11:51:13Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '75'
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: '6239'
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: Selective barriers to horizontal gene transfer
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2016'
...
---
OA_place: publisher
_id: '1398'
abstract:
- lang: eng
text: Hybrid zones represent evolutionary laboratories, where recombination brings
together alleles in combinations which have not previously been tested by selection.
This provides an excellent opportunity to test the effect of molecular variation
on fitness, and how this variation is able to spread through populations in a
natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for
two loci controlling the distribution of yellow and magenta floral pigments. Where
the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley
in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine
to give striking transgressive variation for flower colour. The sharp transition
in phenotype over ~1km implies strong selection maintaining the hybrid zone. An
indirect assay of pollinator visitation in the field found that pollinators forage
in a positive-frequency dependent manner on Antirrhinum, matching previous data
on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds
demonstrated assortative mating for pigmentation alleles, and that pollinator
behaviour alone is sufficient to explain this pattern. Selection by pollinators
should be sufficiently strong to maintain the hybrid zone, although other mechanisms
may be at work. At a broader scale I examined evolutionary transitions between
yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection
has acted strate that pollinators are a major determinant of reproductive success
and mating patterns in wild Antirrhinum.
acknowledgement: "I am indebted to many people for their support during my PhD, but
I particularly wish to thank Nick Barton for his guidance and intuition, and for
encouraging me to take the time to look beyond the immediate topic of my PhD to
understand the broader context. I am also especially grateful to David Field his
bottomless patience, invaluable advice on experimental design, analysis and scientific
writing, and for tireless work on the population surveys and genomic work without
most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work
with the combined strengths of the groups at The John Innes Centre, University of
Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in
Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank
David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections,
as well as Monique Burrus and Christophe Andalo and a large number of volunteers
for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski
for providing seeds and for her input into the design of the experimental arrays,
and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those
mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous
reviewers for their insightful comments on sections of this manuscript. I also thank
Jana Porsche for her e ff orts in tracking down the more obscure references for
chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted
to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer
and Magnus Nordborg for taking the time to read and evaluate the thesis given a
shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been
the supportive atmosphere of IST. In particular, I have come to appreciate the enormous
support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann
and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for
their enthusiasm and readiness to help where possible in setting up our greenhouse
and experiments. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Ellis T. The role of pollinator-mediated selection in the maintenance of a
flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:10.15479/AT:ISTA:TH_526
apa: Ellis, T. (2016). The role of pollinator-mediated selection in the maintenance
of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_526
chicago: Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance
of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute
of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:TH_526 .
ieee: T. Ellis, “The role of pollinator-mediated selection in the maintenance of
a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of
Science and Technology Austria, 2016.
ista: Ellis T. 2016. The role of pollinator-mediated selection in the maintenance
of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute
of Science and Technology Austria.
mla: Ellis, Thomas. The Role of Pollinator-Mediated Selection in the Maintenance
of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone. Institute
of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:TH_526 .
short: T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of
a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of
Science and Technology Austria, 2016.
corr_author: '1'
date_created: 2018-12-11T11:51:47Z
date_published: 2016-02-18T00:00:00Z
date_updated: 2026-04-09T10:52:07Z
day: '18'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
- _id: GradSch
doi: '10.15479/AT:ISTA:TH_526 '
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checksum: f0f7c260e19ec1416824b165afe2d5fd
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creator: system
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month: '02'
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page: '130'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5809'
pubrep_id: '526'
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relation: dissertation_contains
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relation: dissertation_contains
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relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: The role of pollinator-mediated selection in the maintenance of a flower color
polymorphism in an Antirrhinum majus hybrid zone
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2016'
...
---
_id: '1432'
abstract:
- lang: eng
text: CA3–CA3 recurrent excitatory synapses are thought to play a key role in memory
storage and pattern completion. Whether the plasticity properties of these synapses
are consistent with their proposed network functions remains unclear. Here, we
examine the properties of spike timing-dependent plasticity (STDP) at CA3–CA3
synapses. Low-frequency pairing of excitatory postsynaptic potentials (EPSPs)
and action potentials (APs) induces long-term potentiation (LTP), independent
of temporal order. The STDP curve is symmetric and broad (half-width ~150 ms).
Consistent with these STDP induction properties, AP–EPSP sequences lead to supralinear
summation of spine [Ca2+] transients. Furthermore, afterdepolarizations (ADPs)
following APs efficiently propagate into dendrites of CA3 pyramidal neurons, and
EPSPs summate with dendritic ADPs. In autoassociative network models, storage
and recall are more robust with symmetric than with asymmetric STDP rules. Thus,
a specialized STDP induction rule allows reliable storage and recall of information
in the hippocampal CA3 network.
acknowledgement: 'We thank Jozsef Csicsvari and Nelson Spruston for critically reading
the manuscript. We also thank A. Schlögl for programming, F. Marr for technical
assistance and E. Kramberger for manuscript editing. '
article_number: '11552'
article_processing_charge: No
author:
- first_name: Rajiv Kumar
full_name: Mishra, Rajiv Kumar
id: 46CB58F2-F248-11E8-B48F-1D18A9856A87
last_name: Mishra
- first_name: Sooyun
full_name: Kim, Sooyun
id: 394AB1C8-F248-11E8-B48F-1D18A9856A87
last_name: Kim
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Mishra RK, Kim S, Guzmán J, Jonas PM. Symmetric spike timing-dependent plasticity
at CA3–CA3 synapses optimizes storage and recall in autoassociative networks.
Nature Communications. 2016;7. doi:10.1038/ncomms11552
apa: Mishra, R. K., Kim, S., Guzmán, J., & Jonas, P. M. (2016). Symmetric spike
timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in
autoassociative networks. Nature Communications. Nature Publishing Group.
https://doi.org/10.1038/ncomms11552
chicago: Mishra, Rajiv Kumar, Sooyun Kim, José Guzmán, and Peter M Jonas. “Symmetric
Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall
in Autoassociative Networks.” Nature Communications. Nature Publishing
Group, 2016. https://doi.org/10.1038/ncomms11552.
ieee: R. K. Mishra, S. Kim, J. Guzmán, and P. M. Jonas, “Symmetric spike timing-dependent
plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative
networks,” Nature Communications, vol. 7. Nature Publishing Group, 2016.
ista: Mishra RK, Kim S, Guzmán J, Jonas PM. 2016. Symmetric spike timing-dependent
plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative
networks. Nature Communications. 7, 11552.
mla: Mishra, Rajiv Kumar, et al. “Symmetric Spike Timing-Dependent Plasticity at
CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” Nature
Communications, vol. 7, 11552, Nature Publishing Group, 2016, doi:10.1038/ncomms11552.
short: R.K. Mishra, S. Kim, J. Guzmán, P.M. Jonas, Nature Communications 7 (2016).
corr_author: '1'
date_created: 2018-12-11T11:51:59Z
date_published: 2016-05-13T00:00:00Z
date_updated: 2026-04-09T10:52:26Z
day: '13'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/ncomms11552
ec_funded: 1
external_id:
isi:
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checksum: 7e84d0392348c874d473b62f1042de22
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month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5766'
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related_material:
record:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage
and recall in autoassociative networks
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 7
year: '2016'
...
---
OA_place: publisher
_id: '1396'
abstract:
- lang: eng
text: CA3 pyramidal neurons are thought to pay a key role in memory storage and
pattern completion by activity-dependent synaptic plasticity between CA3-CA3 recurrent
excitatory synapses. To examine the induction rules of synaptic plasticity at
CA3-CA3 synapses, we performed whole-cell patch-clamp recordings in acute hippocampal
slices from rats (postnatal 21-24 days) at room temperature. Compound excitatory
postsynaptic potentials (ESPSs) were recorded by tract stimulation in stratum
oriens in the presence of 10 µM gabazine. High-frequency stimulation (HFS) induced
N-methyl-D-aspartate (NMDA) receptor-dependent long-term potentiation (LTP). Although
LTP by HFS did not requier postsynaptic spikes, it was blocked by Na+-channel
blockers suggesting that local active processes (e.g.) dendritic spikes) may contribute
to LTP induction without requirement of a somatic action potential (AP). We next
examined the properties of spike timing-dependent plasticity (STDP) at CA3-CA3
synapses. Unexpectedly, low-frequency pairing of EPSPs and backpropagated action
potentialy (bAPs) induced LTP, independent of temporal order. The STDP curve was
symmetric and broad, with a half-width of ~150 ms. Consistent with these specific
STDP induction properties, post-presynaptic sequences led to a supralinear summation
of spine [Ca2+] transients. Furthermore, in autoassociative network models, storage
and recall was substantially more robust with symmetric than with asymmetric STDP
rules. In conclusion, we found associative forms of LTP at CA3-CA3 recurrent collateral
synapses with distinct induction rules. LTP induced by HFS may be associated with
dendritic spikes. In contrast, low frequency pairing of pre- and postsynaptic
activity induced LTP only if EPSP-AP were temporally very close. Together, these
induction mechanisms of synaptiic plasticity may contribute to memory storage
in the CA3-CA3 microcircuit at different ranges of activity.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rajiv Kumar
full_name: Mishra, Rajiv Kumar
id: 46CB58F2-F248-11E8-B48F-1D18A9856A87
last_name: Mishra
citation:
ama: Mishra RK. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus.
2016.
apa: Mishra, R. K. (2016). Synaptic plasticity rules at CA3-CA3 recurrent synapses
in hippocampus. Institute of Science and Technology Austria.
chicago: Mishra, Rajiv Kumar. “Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses
in Hippocampus.” Institute of Science and Technology Austria, 2016.
ieee: R. K. Mishra, “Synaptic plasticity rules at CA3-CA3 recurrent synapses in
hippocampus,” Institute of Science and Technology Austria, 2016.
ista: Mishra RK. 2016. Synaptic plasticity rules at CA3-CA3 recurrent synapses in
hippocampus. Institute of Science and Technology Austria.
mla: Mishra, Rajiv Kumar. Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses
in Hippocampus. Institute of Science and Technology Austria, 2016.
short: R.K. Mishra, Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus,
Institute of Science and Technology Austria, 2016.
corr_author: '1'
date_created: 2018-12-11T11:51:46Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2026-04-09T10:52:26Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: PeJo
file:
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checksum: 5a010a838faf040f7064f3cfb802f743
content_type: application/pdf
creator: dernst
date_created: 2019-08-09T12:14:46Z
date_updated: 2020-07-14T12:44:48Z
file_id: '6782'
file_name: Thesis_Mishra_Rajiv (Final).pdf
file_size: 2407572
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checksum: 81b26d9ede92c99f1d8cc6fa1d04cbbb
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:48:44Z
date_updated: 2021-02-22T11:48:44Z
file_id: '9183'
file_name: 2016_RajivMishra_Thesis.pdf
file_size: 2407572
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success: 1
file_date_updated: 2021-02-22T11:48:44Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '83'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5811'
related_material:
record:
- id: '1432'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
title: Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2016'
...
---
_id: '5553'
abstract:
- lang: eng
text: "Genotypic, phenotypic and demographic data for 2128 wild snapdragons and
1127 open-pollinated progeny from a natural hybrid zone, collected as part of
Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent
to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers
by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been
removed from this dataset.\r\n\r\nOther data were retreived from an online database
of this population at www.antspec.org."
article_processing_charge: No
author:
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Field D, Ellis T. Inference of mating patterns among wild snapdragons in a
natural hybrid zone in 2012. 2016. doi:10.15479/AT:ISTA:37
apa: Field, D., & Ellis, T. (2016). Inference of mating patterns among wild
snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:37
chicago: Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild
Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology
Austria, 2016. https://doi.org/10.15479/AT:ISTA:37.
ieee: D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons
in a natural hybrid zone in 2012.” Institute of Science and Technology Austria,
2016.
ista: Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons
in a natural hybrid zone in 2012, Institute of Science and Technology Austria,
10.15479/AT:ISTA:37.
mla: Field, David, and Thomas Ellis. Inference of Mating Patterns among Wild
Snapdragons in a Natural Hybrid Zone in 2012. Institute of Science and Technology
Austria, 2016, doi:10.15479/AT:ISTA:37.
short: D. Field, T. Ellis, (2016).
contributor:
- contributor_type: project_manager
first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
datarep_id: '37'
date_created: 2018-12-12T12:31:30Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2026-04-09T10:52:06Z
day: '19'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:37
file:
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checksum: 4ae751b1fa4897fa216241f975a57313
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:02Z
date_updated: 2020-07-14T12:47:01Z
file_id: '5620'
file_name: IST-2016-37-v1+1_paternity_archive.zip
file_size: 132808
relation: main_file
file_date_updated: 2020-07-14T12:47:01Z
has_accepted_license: '1'
keyword:
- paternity assignment
- pedigree
- matting patterns
- assortative mating
- Antirrhinum majus
- frequency-dependent selection
- plant-pollinator interaction
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1398'
relation: part_of_dissertation
status: public
status: public
title: Inference of mating patterns among wild snapdragons in a natural hybrid zone
in 2012
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5551'
abstract:
- lang: eng
text: "Data from array experiments investigating pollinator behaviour on snapdragons
in controlled conditions, and their effect on plant mating. Data were collected
as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a
total of 36 plants in a grid inside a closed organza tent, with a single hive
of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered
Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus,
at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn
how to deal with snapdragons, I observed pollinators foraging on plants, and recorded
the transitions between plants. Thereafter seeds on plants were allowed to develops.
A sample of these were grown to maturity when their flower colour could be determined,
and they were scored as yellow, magenta, or hybrid."
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:10.15479/AT:ISTA:35
apa: Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:35
chicago: Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.”
Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:35.
ieee: T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute
of Science and Technology Austria, 2016.
ista: Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:35.
mla: Ellis, Thomas. Data on Pollinator Observations and Offpsring Phenotypes.
Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:35.
short: T. Ellis, (2016).
contributor:
- first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
- first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
datarep_id: '35'
date_created: 2018-12-12T12:31:29Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2026-04-09T10:52:07Z
day: '19'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:35
file:
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checksum: aa3eb85d52b110cd192aa23147c4d4f3
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creator: system
date_created: 2018-12-12T13:05:12Z
date_updated: 2020-07-14T12:47:01Z
file_id: '5640'
file_name: IST-2016-35-v1+1_array_data.zip
file_size: 32775
relation: main_file
file_date_updated: 2020-07-14T12:47:01Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1398'
relation: part_of_dissertation
status: public
status: public
title: Data on pollinator observations and offpsring phenotypes
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5552'
abstract:
- lang: eng
text: "Data on pollinator visitation to wild snapdragons in a natural hybrid zone,
collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon
flowers have a mouth-like structure which pollinators must open to access nectar.
We placed 5mm cellophane tags in these mouths, which are held in place by the
pressure of the flower until a pollinator visits. When she opens the flower, the
tag drops out, and one can infer a visit. We surveyed plants over multiple days
in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic
variables which may be explanatory variables for pollinator visitation."
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with
phenotypic and frequency data. 2016. doi:10.15479/AT:ISTA:36
apa: Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants,
with phenotypic and frequency data. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:36
chicago: Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants,
with Phenotypic and Frequency Data.” Institute of Science and Technology Austria,
2016. https://doi.org/10.15479/AT:ISTA:36.
ieee: T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with
phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.
ista: Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants,
with phenotypic and frequency data., Institute of Science and Technology Austria,
10.15479/AT:ISTA:36.
mla: Ellis, Thomas. Pollinator Visitation Data for Wild Antirrhinum Majus Plants,
with Phenotypic and Frequency Data. Institute of Science and Technology Austria,
2016, doi:10.15479/AT:ISTA:36.
short: T. Ellis, (2016).
contributor:
- first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
- first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
datarep_id: '36'
date_created: 2018-12-12T12:31:30Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2026-04-09T10:52:07Z
day: '19'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:36
file:
- access_level: open_access
checksum: cbc61b523d4d475a04a737d50dc470ef
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:07Z
date_updated: 2020-07-14T12:47:01Z
file_id: '5625'
file_name: IST-2016-36-v1+1_tag_assay_archive.zip
file_size: 44905
relation: main_file
file_date_updated: 2020-07-14T12:47:01Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1398'
relation: part_of_dissertation
status: public
status: public
title: Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic
and frequency data.
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
OA_place: publisher
_id: '1130'
abstract:
- lang: eng
text: "In this thesis we present a computer-aided programming approach to concurrency.
Our approach helps the programmer by automatically fixing concurrency-related
bugs, i.e. bugs that occur when the program is executed using an aggressive preemptive
scheduler, but not when using a non-preemptive (cooperative) scheduler. Bugs are
program behaviours that are incorrect w.r.t. a specification. We consider both
user-provided explicit specifications in the form of assertion\r\nstatements in
the code as well as an implicit specification. The implicit specification is inferred
from the non-preemptive behaviour. Let us consider sequences of calls that the
program makes to an external interface. The implicit specification requires that
any such sequence produced under a preemptive scheduler should be included in
the set of sequences produced under a non-preemptive scheduler. We consider several
semantics-preserving fixes that go beyond atomic sections typically explored in
the synchronisation synthesis literature. Our synthesis is able to place locks,
barriers and wait-signal statements and last, but not least reorder independent
statements. The latter may be useful if a thread is released to early, e.g., before
some initialisation is completed. We guarantee that our synthesis does not introduce
deadlocks and that the synchronisation inserted is optimal w.r.t. a given objective
function. We dub our solution trace-based synchronisation synthesis and it is
loosely based on counterexample-guided inductive synthesis (CEGIS). The synthesis
works by discovering a trace that is incorrect w.r.t. the specification and identifying
ordering constraints crucial to trigger the specification violation. Synchronisation
may be placed immediately (greedy approach) or delayed until all incorrect traces
are found (non-greedy approach). For the non-greedy approach we construct a set
of global constraints over synchronisation placements. Each model of the global
constraints set corresponds to a correctness-ensuring synchronisation placement.
The placement that is optimal w.r.t. the given objective function is chosen as
the synchronisation solution. We evaluate our approach on a number of realistic
(albeit simplified) Linux device-driver\r\nbenchmarks. The benchmarks are versions
of the drivers with known concurrency-related bugs. For the experiments with an
explicit specification we added assertions that would detect the bugs in the experiments.
Device drivers lend themselves to implicit specification, where the device and
the operating system are the external interfaces. Our experiments demonstrate
that our synthesis method is precise and efficient. We implemented objective functions
for coarse-grained and fine-grained locking and observed that different synchronisation
placements are produced for our experiments, favouring e.g. a minimal number of
synchronisation operations or maximum concurrency."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: Tarrach T. Automatic synthesis of synchronisation primitives for concurrent
programs. 2016. doi:10.15479/at:ista:1130
apa: Tarrach, T. (2016). Automatic synthesis of synchronisation primitives for
concurrent programs. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:1130
chicago: Tarrach, Thorsten. “Automatic Synthesis of Synchronisation Primitives for
Concurrent Programs.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/at:ista:1130.
ieee: T. Tarrach, “Automatic synthesis of synchronisation primitives for concurrent
programs,” Institute of Science and Technology Austria, 2016.
ista: Tarrach T. 2016. Automatic synthesis of synchronisation primitives for concurrent
programs. Institute of Science and Technology Austria.
mla: Tarrach, Thorsten. Automatic Synthesis of Synchronisation Primitives for
Concurrent Programs. Institute of Science and Technology Austria, 2016, doi:10.15479/at:ista:1130.
short: T. Tarrach, Automatic Synthesis of Synchronisation Primitives for Concurrent
Programs, Institute of Science and Technology Austria, 2016.
corr_author: '1'
date_created: 2018-12-11T11:50:19Z
date_published: 2016-07-07T00:00:00Z
date_updated: 2026-04-09T10:54:01Z
day: '07'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ToHe
- _id: GradSch
doi: 10.15479/at:ista:1130
ec_funded: 1
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language:
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url: http://thorstent.github.io/theses/phd_thorsten_tarrach.pdf
month: '07'
oa: 1
oa_version: Published Version
page: '151'
project:
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call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication_identifier:
issn:
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publisher: Institute of Science and Technology Austria
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status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
title: Automatic synthesis of synchronisation primitives for concurrent programs
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2016'
...
---
OA_place: publisher
_id: '1131'
abstract:
- lang: eng
text: "Evolution of gene regulation is important for phenotypic evolution and diversity.
Sequence-specific binding of regulatory proteins is one of the key regulatory
mechanisms determining gene expression. Although there has been intense interest
in evolution of regulatory binding sites in the last decades, a theoretical understanding
is far from being complete. In this thesis, I aim at a better understanding of
the evolution of transcriptional regulatory binding sequences by using biophysical
and population genetic models.\r\nIn the first part of the thesis, I discuss how
to formulate the evolutionary dynamics of binding se- quences in a single isolated
binding site and in promoter/enhancer regions. I develop a theoretical framework
bridging between a thermodynamical model for transcription and a mutation-selection-drift
model for monomorphic populations. I mainly address the typical evolutionary rates,
and how they de- pend on biophysical parameters (e.g. binding length and specificity)
and population genetic parameters (e.g. population size and selection strength).\r\nIn
the second part of the thesis, I analyse empirical data for a better evolutionary
and biophysical understanding of sequence-specific binding of bacterial RNA polymerase.
First, I infer selection on regulatory and non-regulatory binding sites of RNA
polymerase in the E. coli K12 genome. Second, I infer the chemical potential of
RNA polymerase, an important but unknown physical parameter defining the threshold
energy for strong binding. Furthermore, I try to understand the relation between
the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial
isolates by constructing a simple but biophysically motivated gene expression
model. Lastly, I lay out a statistical framework to predict adaptive point mutations
in de novo promoter evolution in a selection experiment."
acknowledgement: This PhD thesis may not have been completed without the help and
care I received from some peo- ple during my PhD life. I am especially grateful
to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices
but also for their patience and support. I thank Calin Guet and Jonathan Bollback
for allowing me to “play around” in their labs and get some experience on experimental
evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and
sharing their experimental data with me. I thank Johannes Jaeger for reviewing my
thesis. I thank all members of Barton group (aka bartonians) for their feedback,
and all workers of IST Austria for making the best working conditions. Lastly, I
thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous
support and encouragement. I truly had a great chance of having right people around
me.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
citation:
ama: Tugrul M. Evolution of transcriptional regulatory sequences. 2016.
apa: Tugrul, M. (2016). Evolution of transcriptional regulatory sequences.
Institute of Science and Technology Austria.
chicago: Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute
of Science and Technology Austria, 2016.
ieee: M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute
of Science and Technology Austria, 2016.
ista: Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute
of Science and Technology Austria.
mla: Tugrul, Murat. Evolution of Transcriptional Regulatory Sequences. Institute
of Science and Technology Austria, 2016.
short: M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of
Science and Technology Austria, 2016.
corr_author: '1'
date_created: 2018-12-11T11:50:19Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2026-04-09T10:52:40Z
day: '01'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
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language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '89'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6229'
related_material:
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status: public
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relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Evolution of transcriptional regulatory sequences
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2016'
...
---
_id: '5554'
abstract:
- lang: eng
text: "The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which
is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena
Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments
and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student
in Jon Bollback's group at IST Austria) performed the experiments and created
the data on lac promoter evolution."
article_processing_charge: No
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
citation:
ama: Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.
2016. doi:10.15479/AT:ISTA:43
apa: Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial
RNA Polymerase. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:43
chicago: Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial
RNA Polymerase.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:43.
ieee: M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA
Polymerase.” Institute of Science and Technology Austria, 2016.
ista: Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial
RNA Polymerase, Institute of Science and Technology Austria, 10.15479/AT:ISTA:43.
mla: Tugrul, Murat. Experimental Data for Binding Site Evolution of Bacterial
RNA Polymerase. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:43.
short: M. Tugrul, (2016).
contributor:
- contributor_type: researcher
first_name: Magdalena
id: 2C023F40-F248-11E8-B48F-1D18A9856A87
last_name: Steinrück
- contributor_type: researcher
first_name: Fabienne
id: 4C8C26A4-F248-11E8-B48F-1D18A9856A87
last_name: Jesse
datarep_id: '43'
date_created: 2018-12-12T12:31:30Z
date_published: 2016-05-12T00:00:00Z
date_updated: 2026-04-09T10:52:40Z
day: '12'
department:
- _id: NiBa
- _id: JoBo
doi: 10.15479/AT:ISTA:43
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checksum: 1fc0a10bb7ce110fcb5e1fbe3cf0c4e2
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creator: system
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file_date_updated: 2020-07-14T12:47:01Z
has_accepted_license: '1'
keyword:
- RNAP binding
- de novo promoter evolution
- lac promoter
month: '05'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
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status: public
title: Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase
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image: /images/cc_0.png
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short: CC0 (1.0)
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year: '2016'
...
---
OA_place: publisher
_id: '1125'
abstract:
- lang: eng
text: "Natural environments are never constant but subject to spatial and temporal
change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial
to understand the\r\nimpact of environmental variation on evolutionary processes.
In this thesis, I present\r\nthree topics that share the common theme of environmental
variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst,
I show how a temporally fluctuating environment gives rise to second-order\r\nselection
on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations
are adapted to their environment, mutation rates are minimized. I argue\r\nthat
a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly
subjected to diverse environmental challenges, and I outline implications of\r\nthe
presented results to antibiotic treatment strategies.\r\nSecond, I discuss my
work on the evolution of dispersal. Besides reproducing\r\nknown results about
the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes
in dispersal type frequencies as a source for selection for increased\r\npropensities
to disperse. This concept contains effects of relatedness that are known\r\nto
promote dispersal, and I explain how it identifies other forces selecting for
dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances
of phenotypic traits under multivariate stabilizing\r\nselection. For the case
of constant environments, I generalize known formulae of\r\nequilibrium variances
to multiple traits and discuss how the genetic variance of a focal\r\ntrait is
influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary
work aiming at including environmental fluctuations in the form of moving\r\ntrait
optima into the model."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
citation:
ama: Novak S. Evolutionary proccesses in variable emvironments. 2016.
apa: Novak, S. (2016). Evolutionary proccesses in variable emvironments.
Institute of Science and Technology Austria.
chicago: Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute
of Science and Technology Austria, 2016.
ieee: S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of
Science and Technology Austria, 2016.
ista: Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute
of Science and Technology Austria.
mla: Novak, Sebastian. Evolutionary Proccesses in Variable Emvironments.
Institute of Science and Technology Austria, 2016.
short: S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of
Science and Technology Austria, 2016.
corr_author: '1'
date_created: 2018-12-11T11:50:17Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2026-04-09T14:25:34Z
day: '01'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
file:
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checksum: 81dcc838dfcf7aa0b1a27ecf4fe2da4e
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T09:01:00Z
date_updated: 2019-08-13T09:01:00Z
file_id: '6811'
file_name: Novak_thesis.pdf
file_size: 3564901
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creator: dernst
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has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '124'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6235'
related_material:
record:
- id: '2023'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Evolutionary proccesses in variable emvironments
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2016'
...
---
_id: '1662'
abstract:
- lang: eng
text: We introduce a modification of the classic notion of intrinsic volume using
persistence moments of height functions. Evaluating the modified first intrinsic
volume on digital approximations of a compact body with smoothly embedded boundary
in Rn, we prove convergence to the first intrinsic volume of the body as the resolution
of the approximation improves. We have weaker results for the other modified intrinsic
volumes, proving they converge to the corresponding intrinsic volumes of the n-dimensional
unit ball.
acknowledgement: "This research is partially supported by the Toposys project FP7-ICT-318493-STREP,
and by ESF under the ACAT Research Network Programme.\r\nBoth authors thank Anne
Marie Svane for her comments on an early version of this paper. The second author
wishes to thank Eva B. Vedel Jensen and Markus Kiderlen from Aarhus University for
enlightening discussions and their kind hospitality during a visit of their department
in 2014."
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: Edelsbrunner H, Pausinger F. Approximation and convergence of the intrinsic
volume. Advances in Mathematics. 2016;287:674-703. doi:10.1016/j.aim.2015.10.004
apa: Edelsbrunner, H., & Pausinger, F. (2016). Approximation and convergence
of the intrinsic volume. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2015.10.004
chicago: Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence
of the Intrinsic Volume.” Advances in Mathematics. Academic Press, 2016.
https://doi.org/10.1016/j.aim.2015.10.004.
ieee: H. Edelsbrunner and F. Pausinger, “Approximation and convergence of the intrinsic
volume,” Advances in Mathematics, vol. 287. Academic Press, pp. 674–703,
2016.
ista: Edelsbrunner H, Pausinger F. 2016. Approximation and convergence of the intrinsic
volume. Advances in Mathematics. 287, 674–703.
mla: Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence
of the Intrinsic Volume.” Advances in Mathematics, vol. 287, Academic Press,
2016, pp. 674–703, doi:10.1016/j.aim.2015.10.004.
short: H. Edelsbrunner, F. Pausinger, Advances in Mathematics 287 (2016) 674–703.
corr_author: '1'
date_created: 2018-12-11T11:53:20Z
date_published: 2016-01-10T00:00:00Z
date_updated: 2026-04-09T14:26:05Z
day: '10'
ddc:
- '004'
department:
- _id: HeEd
doi: 10.1016/j.aim.2015.10.004
ec_funded: 1
external_id:
isi:
- '000375634100016'
file:
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checksum: f8869ec110c35c852ef6a37425374af7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:10Z
date_updated: 2020-07-14T12:45:10Z
file_id: '4928'
file_name: IST-2017-774-v1+1_2016-J-03-FirstIntVolume.pdf
file_size: 248985
relation: main_file
file_date_updated: 2020-07-14T12:45:10Z
has_accepted_license: '1'
intvolume: ' 287'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 674 - 703
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Advances in Mathematics
publication_status: published
publisher: Academic Press
publist_id: '5488'
pubrep_id: '774'
quality_controlled: '1'
related_material:
record:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Approximation and convergence of the intrinsic volume
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 287
year: '2016'
...
---
_id: '1093'
abstract:
- lang: eng
text: 'We introduce a general class of distances (metrics) between Markov chains,
which are based on linear behaviour. This class encompasses distances given topologically
(such as the total variation distance or trace distance) as well as by temporal
logics or automata. We investigate which of the distances can be approximated
by observing the systems, i.e. by black-box testing or simulation, and we provide
both negative and positive results. '
acknowledgement: "This research was funded in part by the European Research Council
(ERC) under grant agreement 267989\r\n(QUAREM), the Austrian Science Fund (FWF)
under grants project S11402-N23 (RiSE and SHiNE)\r\nand Z211-N23 (Wittgenstein Award),
by the Czech Science Foundation Grant No. P202/12/G061, and\r\nby the SNSF Advanced
Postdoc. Mobility Fellowship – grant number P300P2_161067."
alternative_title:
- LIPIcs
article_number: '20'
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- 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: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: 'Daca P, Henzinger TA, Kretinsky J, Petrov T. Linear distances between Markov
chains. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.20'
apa: 'Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2016). Linear
distances between Markov chains (Vol. 59). Presented at the CONCUR: Concurrency
Theory, Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.CONCUR.2016.20'
chicago: Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov.
“Linear Distances between Markov Chains,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.20.
ieee: 'P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Linear distances
between Markov chains,” presented at the CONCUR: Concurrency Theory, Quebec City;
Canada, 2016, vol. 59.'
ista: 'Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Linear distances between
Markov chains. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 20.'
mla: Daca, Przemyslaw, et al. Linear Distances between Markov Chains. Vol.
59, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.20.
short: P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Schloss Dagstuhl -
Leibniz-Zentrum für Informatik, 2016.
conference:
end_date: 2016-08-26
location: Quebec City; Canada
name: 'CONCUR: Concurrency Theory'
start_date: 2016-08-23
date_created: 2018-12-11T11:50:06Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2026-04-15T10:02:12Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
- _id: KrCh
- _id: CaGu
doi: 10.4230/LIPIcs.CONCUR.2016.20
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:39Z
date_updated: 2018-12-12T10:11:39Z
file_id: '4895'
file_name: IST-2017-794-v1+1_LIPIcs-CONCUR-2016-20.pdf
file_size: 501827
relation: main_file
file_date_updated: 2018-12-12T10:11:39Z
has_accepted_license: '1'
intvolume: ' 59'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6283'
pubrep_id: '794'
quality_controlled: '1'
related_material:
record:
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relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Linear distances between Markov chains
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 59
year: '2016'
...
---
_id: '1234'
abstract:
- lang: eng
text: We present a new algorithm for the statistical model checking of Markov chains
with respect to unbounded temporal properties, including full linear temporal
logic. The main idea is that we monitor each simulation run on the fly, in order
to detect quickly if a bottom strongly connected component is entered with high
probability, in which case the simulation run can be terminated early. As a result,
our simulation runs are often much shorter than required by termination bounds
that are computed a priori for a desired level of confidence on a large state
space. In comparison to previous algorithms for statistical model checking our
method is not only faster in many cases but also requires less information about
the system, namely, only the minimum transition probability that occurs in the
Markov chain. In addition, our method can be generalised to unbounded quantitative
properties such as mean-payoff bounds.
acknowledgement: "This research was funded in part by the European Research Council
(ERC) under\r\ngrant agreement 267989 (QUAREM), the Austrian Science Fund
\ (FWF) under\r\ngrants project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award),
the Peo-\r\nple Programme (Marie Curie Actions) of the European Union’s Seventh
Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734, the SNSF Advanced Postdoc.\r\nMobility
Fellowship – grant number P300P2\r\n161067, and the Czech Science Foun-\r\ndation
under grant agreement P202/12/G061."
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- 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: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: 'Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking
for unbounded temporal properties. In: Vol 9636. Springer; 2016:112-129. doi:10.1007/978-3-662-49674-9_7'
apa: 'Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2016). Faster
statistical model checking for unbounded temporal properties (Vol. 9636, pp. 112–129).
Presented at the TACAS: Tools and Algorithms for the Construction and Analysis
of Systems, Eindhoven, The Netherlands: Springer. https://doi.org/10.1007/978-3-662-49674-9_7'
chicago: Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov.
“Faster Statistical Model Checking for Unbounded Temporal Properties,” 9636:112–29.
Springer, 2016. https://doi.org/10.1007/978-3-662-49674-9_7.
ieee: 'P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical
model checking for unbounded temporal properties,” presented at the TACAS: Tools
and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands,
2016, vol. 9636, pp. 112–129.'
ista: 'Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Faster statistical model
checking for unbounded temporal properties. TACAS: Tools and Algorithms for the
Construction and Analysis of Systems, LNCS, vol. 9636, 112–129.'
mla: Daca, Przemyslaw, et al. Faster Statistical Model Checking for Unbounded
Temporal Properties. Vol. 9636, Springer, 2016, pp. 112–29, doi:10.1007/978-3-662-49674-9_7.
short: P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Springer, 2016, pp.
112–129.
conference:
end_date: 2016-04-08
location: Eindhoven, The Netherlands
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2016-04-02
date_created: 2018-12-11T11:50:51Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2026-04-15T10:02:12Z
day: '01'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1007/978-3-662-49674-9_7
ec_funded: 1
external_id:
arxiv:
- '1504.05739'
isi:
- '000406428000007'
intvolume: ' 9636'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.05739
month: '01'
oa: 1
oa_version: Preprint
page: 112 - 129
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '6099'
quality_controlled: '1'
related_material:
record:
- id: '471'
relation: later_version
status: public
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Faster statistical model checking for unbounded temporal properties
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9636
year: '2016'
...
---
_id: '1391'
abstract:
- lang: eng
text: "We present an extension to the quantifier-free theory of integer arrays which
allows us to express counting. The properties expressible in Array Folds Logic
(AFL) include statements such as "the first array cell contains the array
length," and "the array contains equally many minimal and maximal elements."
These properties cannot be expressed in quantified fragments of the theory of
arrays, nor in the theory of concatenation. Using reduction to counter machines,
we show that the satisfiability problem of AFL is PSPACE-complete, and with a
natural restriction the complexity decreases to NP. We also show that adding either
universal quantifiers or concatenation leads to undecidability.\r\nAFL contains
terms that fold a function over an array. We demonstrate that folding, a well-known
concept from functional languages, allows us to concisely summarize loops that
count over arrays, which occurs frequently in real-life programs. We provide a
tool that can discharge proof obligations in AFL, and we demonstrate on practical
examples that our decision procedure can solve a broad range of problems in symbolic
testing and program verification."
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- 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: Andrey
full_name: Kupriyanov, Andrey
id: 2C311BF8-F248-11E8-B48F-1D18A9856A87
last_name: Kupriyanov
citation:
ama: 'Daca P, Henzinger TA, Kupriyanov A. Array folds logic. In: Vol 9780. Springer;
2016:230-248. doi:10.1007/978-3-319-41540-6_13'
apa: 'Daca, P., Henzinger, T. A., & Kupriyanov, A. (2016). Array folds logic
(Vol. 9780, pp. 230–248). Presented at the CAV: Computer Aided Verification, Toronto,
Canada: Springer. https://doi.org/10.1007/978-3-319-41540-6_13'
chicago: Daca, Przemyslaw, Thomas A Henzinger, and Andrey Kupriyanov. “Array Folds
Logic,” 9780:230–48. Springer, 2016. https://doi.org/10.1007/978-3-319-41540-6_13.
ieee: 'P. Daca, T. A. Henzinger, and A. Kupriyanov, “Array folds logic,” presented
at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9780, pp.
230–248.'
ista: 'Daca P, Henzinger TA, Kupriyanov A. 2016. Array folds logic. CAV: Computer
Aided Verification, LNCS, vol. 9780, 230–248.'
mla: Daca, Przemyslaw, et al. Array Folds Logic. Vol. 9780, Springer, 2016,
pp. 230–48, doi:10.1007/978-3-319-41540-6_13.
short: P. Daca, T.A. Henzinger, A. Kupriyanov, in:, Springer, 2016, pp. 230–248.
conference:
end_date: 2016-07-23
location: Toronto, Canada
name: 'CAV: Computer Aided Verification'
start_date: 2016-07-17
corr_author: '1'
date_created: 2018-12-11T11:51:45Z
date_published: 2016-07-13T00:00:00Z
date_updated: 2026-04-15T10:02:12Z
day: '13'
department:
- _id: ToHe
doi: 10.1007/978-3-319-41540-6_13
ec_funded: 1
external_id:
arxiv:
- '1603.06850'
isi:
- '000387731400013'
intvolume: ' 9780'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1603.06850
month: '07'
oa: 1
oa_version: Preprint
page: 230 - 248
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication_status: published
publisher: Springer
publist_id: '5818'
quality_controlled: '1'
related_material:
record:
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Array folds logic
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9780
year: '2016'
...
---
_id: '1230'
abstract:
- lang: eng
text: Concolic testing is a promising method for generating test suites for large
programs. However, it suffers from the path-explosion problem and often fails
to find tests that cover difficult-to-reach parts of programs. In contrast, model
checkers based on counterexample-guided abstraction refinement explore programs
exhaustively, while failing to scale on large programs with precision. In this
paper, we present a novel method that iteratively combines concolic testing and
model checking to find a test suite for a given coverage criterion. If concolic
testing fails to cover some test goals, then the model checker refines its program
abstraction to prove more paths infeasible, which reduces the search space for
concolic testing. We have implemented our method on top of the concolictesting
tool Crest and the model checker CpaChecker. We evaluated our tool on a collection
of programs and a category of SvComp benchmarks. In our experiments, we observed
an improvement in branch coverage compared to Crest from 48% to 63% in the best
case, and from 66% to 71% on average.
acknowledgement: "We thank Andrey Kupriyanov for feedback on the manuscript,\r\nand
Michael Tautschnig for help with preparing the experiments. This research was supported
in part by the European Research Council (ERC) under grant 267989 (QUAREM) and by
the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein
Award)."
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- 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: 'Daca P, Gupta A, Henzinger TA. Abstraction-driven concolic testing. In: Vol
9583. Springer; 2016:328-347. doi:10.1007/978-3-662-49122-5_16'
apa: 'Daca, P., Gupta, A., & Henzinger, T. A. (2016). Abstraction-driven concolic
testing (Vol. 9583, pp. 328–347). Presented at the VMCAI: Verification, Model
Checking and Abstract Interpretation, St. Petersburg, FL, USA: Springer. https://doi.org/10.1007/978-3-662-49122-5_16'
chicago: Daca, Przemyslaw, Ashutosh Gupta, and Thomas A Henzinger. “Abstraction-Driven
Concolic Testing,” 9583:328–47. Springer, 2016. https://doi.org/10.1007/978-3-662-49122-5_16.
ieee: 'P. Daca, A. Gupta, and T. A. Henzinger, “Abstraction-driven concolic testing,”
presented at the VMCAI: Verification, Model Checking and Abstract Interpretation,
St. Petersburg, FL, USA, 2016, vol. 9583, pp. 328–347.'
ista: 'Daca P, Gupta A, Henzinger TA. 2016. Abstraction-driven concolic testing.
VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 9583,
328–347.'
mla: Daca, Przemyslaw, et al. Abstraction-Driven Concolic Testing. Vol. 9583,
Springer, 2016, pp. 328–47, doi:10.1007/978-3-662-49122-5_16.
short: P. Daca, A. Gupta, T.A. Henzinger, in:, Springer, 2016, pp. 328–347.
conference:
end_date: 2016-01-19
location: St. Petersburg, FL, USA
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2016-01-17
date_created: 2018-12-11T11:50:50Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2026-04-15T10:02:12Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-662-49122-5_16
ec_funded: 1
external_id:
arxiv:
- '1511.02615'
isi:
- '000375148800016'
intvolume: ' 9583'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.02615
month: '01'
oa: 1
oa_version: Preprint
page: 328 - 347
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '6104'
quality_controlled: '1'
related_material:
record:
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Abstraction-driven concolic testing
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9583
year: '2016'
...
---
OA_type: closed access
_id: '21522'
abstract:
- lang: eng
text: In this Letter, we demonstrate highly efficient, polarization-insensitive
planar lenses (metalenses) at red, green, and blue wavelengths (λ = 660, 532,
and 405 nm). Metalenses with numerical apertures (NA) of 0.85 and 0.6 and corresponding
efficiencies as high as 60% and 90% are achieved. These metalenses are less than
600 nm-thick and can focus incident light down to diffraction-limited spots as
small as ∼0.64λ and provide high-resolution imaging. In addition, the focal spots
are very symmetric with high Strehl ratios. The single step lithography and compatibility
with large-scale fabrication processes make metalenses highly promising for widespread
applications in imaging and spectroscopy.
article_processing_charge: No
article_type: original
author:
- first_name: M.
full_name: Khorasaninejad, M.
last_name: Khorasaninejad
- first_name: A. Y.
full_name: Zhu, A. Y.
last_name: Zhu
- first_name: Charles
full_name: Roques-Carmes, Charles
id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82
last_name: Roques-Carmes
- first_name: W. T.
full_name: Chen, W. T.
last_name: Chen
- first_name: J.
full_name: Oh, J.
last_name: Oh
- first_name: I.
full_name: Mishra, I.
last_name: Mishra
- first_name: R. C.
full_name: Devlin, R. C.
last_name: Devlin
- first_name: F.
full_name: Capasso, F.
last_name: Capasso
citation:
ama: Khorasaninejad M, Zhu AY, Roques-Carmes C, et al. Polarization-insensitive
metalenses at visible wavelengths. Nano Letters. 2016;16(11):7229-7234.
doi:10.1021/acs.nanolett.6b03626
apa: Khorasaninejad, M., Zhu, A. Y., Roques-Carmes, C., Chen, W. T., Oh, J., Mishra,
I., … Capasso, F. (2016). Polarization-insensitive metalenses at visible wavelengths.
Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.6b03626
chicago: Khorasaninejad, M., A. Y. Zhu, Charles Roques-Carmes, W. T. Chen, J. Oh,
I. Mishra, R. C. Devlin, and F. Capasso. “Polarization-Insensitive Metalenses
at Visible Wavelengths.” Nano Letters. American Chemical Society, 2016.
https://doi.org/10.1021/acs.nanolett.6b03626.
ieee: M. Khorasaninejad et al., “Polarization-insensitive metalenses at visible
wavelengths,” Nano Letters, vol. 16, no. 11. American Chemical Society,
pp. 7229–7234, 2016.
ista: Khorasaninejad M, Zhu AY, Roques-Carmes C, Chen WT, Oh J, Mishra I, Devlin
RC, Capasso F. 2016. Polarization-insensitive metalenses at visible wavelengths.
Nano Letters. 16(11), 7229–7234.
mla: Khorasaninejad, M., et al. “Polarization-Insensitive Metalenses at Visible
Wavelengths.” Nano Letters, vol. 16, no. 11, American Chemical Society,
2016, pp. 7229–34, doi:10.1021/acs.nanolett.6b03626.
short: M. Khorasaninejad, A.Y. Zhu, C. Roques-Carmes, W.T. Chen, J. Oh, I. Mishra,
R.C. Devlin, F. Capasso, Nano Letters 16 (2016) 7229–7234.
date_created: 2026-03-30T12:22:47Z
date_published: 2016-10-24T00:00:00Z
date_updated: 2026-04-15T11:53:17Z
day: '24'
ddc:
- '530'
doi: 10.1021/acs.nanolett.6b03626
extern: '1'
external_id:
pmid:
- '27791380'
intvolume: ' 16'
issue: '11'
keyword:
- Metasurface
- polarization-insensitive metalenses
- visible wavelength
- titanium dioxide
language:
- iso: eng
month: '10'
oa_version: None
page: 7229-7234
pmid: 1
publication: Nano Letters
publication_identifier:
eissn:
- 1530-6992
issn:
- 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Polarization-insensitive metalenses at visible wavelengths
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2016'
...
---
_id: '1341'
abstract:
- lang: eng
text: In resource allocation games, selfish players share resources that are needed
in order to fulfill their objectives. The cost of using a resource depends on
the load on it. In the traditional setting, the players make their choices concurrently
and in one-shot. That is, a strategy for a player is a subset of the resources.
We introduce and study dynamic resource allocation games. In this setting, the
game proceeds in phases. In each phase each player chooses one resource. A scheduler
dictates the order in which the players proceed in a phase, possibly scheduling
several players to proceed concurrently. The game ends when each player has collected
a set of resources that fulfills his objective. The cost for each player then
depends on this set as well as on the load on the resources in it – we consider
both congestion and cost-sharing games. We argue that the dynamic setting is the
suitable setting for many applications in practice. We study the stability of
dynamic resource allocation games, where the appropriate notion of stability is
that of subgame perfect equilibrium, study the inefficiency incurred due to selfish
behavior, and also study problems that are particular to the dynamic setting,
like constraints on the order in which resources can be chosen or the problem
of finding a scheduler that achieves stability.
acknowledgement: This research was supported in part by the European Research Council
(ERC) under grants 267989 (QUAREM) and 278410 (QUALITY), and by the Austrian Science
Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- 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: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: 'Avni G, Henzinger TA, Kupferman O. Dynamic resource allocation games. In:
Vol 9928. Springer; 2016:153-166. doi:10.1007/978-3-662-53354-3_13'
apa: 'Avni, G., Henzinger, T. A., & Kupferman, O. (2016). Dynamic resource allocation
games (Vol. 9928, pp. 153–166). Presented at the SAGT: Symposium on Algorithmic
Game Theory, Liverpool, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-53354-3_13'
chicago: Avni, Guy, Thomas A Henzinger, and Orna Kupferman. “Dynamic Resource Allocation
Games,” 9928:153–66. Springer, 2016. https://doi.org/10.1007/978-3-662-53354-3_13.
ieee: 'G. Avni, T. A. Henzinger, and O. Kupferman, “Dynamic resource allocation
games,” presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool,
United Kingdom, 2016, vol. 9928, pp. 153–166.'
ista: 'Avni G, Henzinger TA, Kupferman O. 2016. Dynamic resource allocation games.
SAGT: Symposium on Algorithmic Game Theory, LNCS, vol. 9928, 153–166.'
mla: Avni, Guy, et al. Dynamic Resource Allocation Games. Vol. 9928, Springer,
2016, pp. 153–66, doi:10.1007/978-3-662-53354-3_13.
short: G. Avni, T.A. Henzinger, O. Kupferman, in:, Springer, 2016, pp. 153–166.
conference:
end_date: 2016-09-21
location: Liverpool, United Kingdom
name: 'SAGT: Symposium on Algorithmic Game Theory'
start_date: 2016-09-19
corr_author: '1'
date_created: 2018-12-11T11:51:28Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2026-04-16T09:35:14Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-662-53354-3_13
ec_funded: 1
external_id:
isi:
- '000389020400013'
file:
- access_level: open_access
checksum: 0825eefd4e22774f6f62cb7d7389b05a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:22Z
date_updated: 2020-07-14T12:44:45Z
file_id: '5073'
file_name: IST-2016-645-v1+1_sagt-cr.pdf
file_size: 243458
relation: main_file
file_date_updated: 2020-07-14T12:44:45Z
has_accepted_license: '1'
intvolume: ' 9928'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Preprint
page: 153 - 166
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication_status: published
publisher: Springer
publist_id: '5926'
pubrep_id: '645'
quality_controlled: '1'
related_material:
record:
- id: '6761'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Dynamic resource allocation games
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9928
year: '2016'
...